Microbial Genomics

Microbial Genomics Quantitative assessment of insertion sequence impact on bacterial genome architecture --Manuscript Draft-Manuscript Number:

MGEN-D-16-00010R1

Full Title:

Quantitative assessment of insertion sequence impact on bacterial genome architecture

Article Type:

Research Paper

Section/Category:

Microbial evolution and epidemiology: Mechanisms of evolution

Corresponding Author:

Mark D. Adams, Ph.D. J Craig Venter Institute La Jolla, CA UNITED STATES

First Author:

Mark D. Adams, Ph.D.

Order of Authors:

Mark D. Adams, Ph.D. Brian Bishop Meredith S Wright, PhD

Abstract:

Insertion sequence (IS) elements are important mediators of genome plasticity and can lead to phenotypic changes with evolutionary significance. In multidrug-resistant Acinetobacter baumannii and Klebsiella pneumoniae, IS elements have contributed significantly to the mobilization of genes that encode resistance to antimicrobial drugs. A systematic analysis of IS elements is needed for a more comprehensive understanding of their evolutionary impact. We developed a computational approach (ISseeker) to annotate IS elements in draft genome assemblies and applied the method to analysis of IS elements in all publicly available A. baumannii (>1000) and K. pneumoniae (>800) genome sequences, in a phylogenetic context. Most IS elements in A. baumannii genomes are species-specific ISAba elements, whereas K. pneumoniae genomes contain significant numbers of both ISKpn elements and elements that are found throughout the Enterobacteriaceae. A. baumannii genomes have a higher density of IS elements than K. pneumoniae, averaging ~33 vs ~27 copies per genome. In K. pneumoniae, several insertion sites are shared by most genomes in the ST258 clade, whereas in A. baumannii, different IS elements are abundant in different phylogenetic groups, even among closely related Global Clone 2 strains. IS elements differ in the distribution of insertion locations relative to genes, with some more likely to disrupt genes and others predominantly in intergenic regions. Several genes and intergenic regions had multiple independent insertion events, suggesting that those events may confer a selective advantage. Genome- and taxonwide characterization of insertion locations revealed that IS elements have been active contributors to genome diversity in both species.

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Quantitative assessment of insertion sequence impact on bacterial genome architecture

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ABSTRACT Insertion sequence (IS) elements are important mediators of genome plasticity and

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can lead to phenotypic changes with evolutionary significance. In multidrug-resistant

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Acinetobacter baumannii and Klebsiella pneumoniae, IS elements have contributed

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significantly to the mobilization of genes that encode resistance to antimicrobial drugs. A

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systematic analysis of IS elements is needed for a more comprehensive understanding of

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their evolutionary impact. We developed a computational approach (ISseeker) to annotate

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IS elements in draft genome assemblies and applied the method to analysis of IS elements in

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all publicly available A. baumannii (>1000) and K. pneumoniae (>800) genome sequences, in

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a phylogenetic context. Most IS elements in A. baumannii genomes are species-specific

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ISAba elements, whereas K. pneumoniae genomes contain significant numbers of both

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ISKpn elements and elements that are found throughout the Enterobacteriaceae. A.

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baumannii genomes have a higher density of IS elements than K. pneumoniae, averaging

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~33 vs ~27 copies per genome. In K. pneumoniae, several insertion sites are shared by most

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genomes in the ST258 clade, whereas in A. baumannii, different IS elements are abundant in

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different phylogenetic groups, even among closely related Global Clone 2 strains. IS

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elements differ in the distribution of insertion locations relative to genes, with some more

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likely to disrupt genes and others predominantly in intergenic regions. Several genes and

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intergenic regions had multiple independent insertion events, suggesting that those events

Downloaded from www.microbiologyresearch.org by IP: 172.245.146.248 On: Mon, 16 May 2016 03:09:54

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may confer a selective advantage. Genome- and taxon-wide characterization of insertion

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locations revealed that IS elements have been active contributors to genome diversity in

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both species.


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DATA SUMMARY

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1. The ISseeker software has been deposited in Github at http://github.com/JCVIVIRIFX/ISseeker

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I/We confirm all supporting data, code and protocols have been provided within the article or through supplementary data files. ☒

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IMPACT STATEMENT

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Mobile genetic elements are well recognized for the role they have played in the

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dissemination of antimicrobial resistance genes in Gram-negative bacteria and in the rise of

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multi-drug resistance in several human pathogens. With large collections of genome

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sequences available for many bacterial species, it is now possible to quantify the abundance

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and distribution of these elements and assess the role they have played in genome

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evolution. Genome-wide surveys of the locations of insertions sequence (IS) elements in A.

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baumannii and K. pneumoniae showed that several different IS elements are common

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within each species, and that IS elements have made significant contributions to the

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evolution of genome structure and variation in both species.

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INTRODUCTION

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Insertion sequences (IS) are mobile genetic elements smaller than ~2 kbp that

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encode only a transposase. Once acquired, IS elements can spread in a genome by

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transposition, creating genetic variation and playing important roles in adaptation (Bennett,

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2004, Siguier et al., 2014). The density of coding content in bacterial genomes means that

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most random insertions occur in functional genome regions. Intragenic insertions can cause

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loss-of-function mutations, while intergenic insertions may disrupt promoter function or can

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result in up-regulation of adjacent genes, in cases where the IS element encodes an

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outward-facing promoter. Most insertions are presumed to be deleterious, but some may

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confer a selective advantage. For example, in A. baumannii an ISAba1 insertion upstream of

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the chromosomal ampC gene results in over-expression of the Acinetobacter-derived

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cephalosporinase (ADC) beta-lactamase and resistance to extended-spectrum

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cephalosporins (Corvec et al., 2003, Heritier et al., 2006, Turton et al., 2006). In addition to

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disrupting a gene and modifying gene expression, pairs of IS elements can act as a

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transposon mobilizing new genetic material via lateral gene transfer such as the ISAba1-

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flanked blaOXA-23 termed Tn2006 that confers carbapenem resistance (Mugnier et al., 2009).

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The blaKPC carbapenemase is bracketed by ISKpn7 and ISKpn6 in Tn4401a (Naas et al., 2008)

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and the ISAba125 element was involved in the emergence of blaNDM-1 (Poirel et al., 2012,

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Poirel et al., 2011). Several IS elements have been reported that drive mobilization and

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expression of blaOXA-58 (Poirel and Nordmann, 2006) and blaRTG (Potron et al., 2009, Bonnin

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et al., 2012).


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Despite the importance of these elements in the evolution of antimicrobial

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resistance, few studies have addressed their genome-wide distribution across a diverse set

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of strains. Gaffé, et al. found that IS elements contributed significantly to adaptive evolution

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of Escherichia coli under controlled growth conditions in continuous culture (Gaffe et al.,

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2011). They examined the distribution of eight IS elements in 120 Escherichia coli genomes

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following long-term growth in chemostats and identified new IS locations that altered the

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global regulatory program. A study of eight clinical isolates of E. coli O157 found that IS629

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and ISEc8 caused frequent small-size structural polymorphisms and suggested that IS

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elements may play a role in the inactivation of incoming phage and plasmids (Ooka et al.,

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2009). Open questions remain regarding the genome-wide impact of IS elements, the

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relative abundance and diversity across evolutionary lineages, and the extent to which IS

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elements may be reshaping the genomes of clinically important pathogens.

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In draft genome assemblies, multi-copy IS elements are typically collapsed into a

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single contig that represents the full-length IS element sequence. Each IS copy cannot be

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placed in its correct genome location during assembly unless long reads, mate pairs, or

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some other long-range linking strategy is employed. Typically, contigs are broken at IS

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locations, and sequence reads that span the junction from chromosomal sequence to IS

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element sequence extend several bases into the IS sequence (Fig. 1(a)). This extension or

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“stub” is often approximately half the read length when using the velvet (Zerbino and

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Birney, 2008) or SPAdes (Bankevich et al., 2012) assemblers. Three software programs have

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been described for mapping transposable element locations: ISmapper (Hawkey et al.,

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2015), TIF (Nakagome et al., 2014), and breseq (Barrick et al., 2014). Each of these programs

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relies on primary read data rather than sequence assemblies, making them effective at

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defining junctions, but difficult to apply to large surveys involving hundreds of genomes


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given the very large input datasets. We developed the ISseeker software to identify flanks of

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IS elements in genome assemblies – both full length copies in long contiguous sequences

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and stubs at contig edges – extract the flanking sequences, and align those flanks to a

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common reference to enable comparison of IS locations across many strains.

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Thirty-six Acinetobacter baumannii species-specific ISAba elements have been

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registered with the ISfinder database https://www-is.biotoul.fr/ (Siguier et al., 2006).

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Twenty-five ISKpn elements are in the ISfinder database. Several of these elements were

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initially described in genome sequencing projects, while others were identified based on

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their participation in antibiotic resistance gene mobilization (Table 1). K. pneumoniae strains

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also have elements that are commonly found throughout the Enterobacteriaceae. Other IS

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elements that have been described in both genomes were included in the analysis as well.

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ISseeker was used to define the location of IS elements in over 1000 A. baumannii genome

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sequences and in over 800 K. pneumoniae genomes. The resulting patterns of IS distribution

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show that several elements are abundant in both species and that IS elements have played a

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significant role in genome evolution.

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METHODS

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ISseeker was written in perl to annotate the locations of a range of IS elements in

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complete and draft genome sequences. Search results are stored in a MySQL database to

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facilitate complex queries. The outline of the program is illustrated in Fig. 1. ISseeker

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identifies complete and partial IS matches in a query genome using blastn, with a user-

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specifiable percent identity threshold (default 97%). Using contig length information,

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matches are classified as embedded in a contig (and either full-length or partial), consisting


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of an entire contig (this is common in draft assemblies), or representing the edge of the IS

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element matching the edge of a contig. Full-length embedded matches and valid edge

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matches are selected for annotation. A 500 bp sequence region adjacent to the IS element is

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extracted from the contig and searched against the reference genome using blastn. Matches

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are evaluated using user-defined thresholds for percent identity (default 97%) and length

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and those passing the threshold are reported. The location relative to adjacent genes in the

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reference is reported. The program attempts to link matches into pairs representing the

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start and end of the IS element that map to equivalent sites in the reference and thus

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correspond to a single insertion event. In practice, this is incomplete because it appears that

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deletions are common near IS elements and it is not obvious whether a single event is

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represented. Flanks that do not match the reference are also included in the output as

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“unannotated” flanks. Output is saved in a log file and as SQL statements for bulk import

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into a MySQL database, which facilitates complex queries. When evaluating the IS locations,

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we found many instances of IS sites clustered within a few bases of one another. These

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could represent independent insertion events or alignment artifacts. Manual review

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suggested that the latter was common, so for the purpose of reporting the number of

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distinct insertion sites, we bundled annotated locations within 10 bases of each other as a

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single event. Locations relative to genes were inferred based on the GenBank annotation for

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the reference genome, with location outside of annotated coding regions designated as

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intergenic and those inside coding regions designated intragenic. The ISseeker software and

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the MySQL schema are available at https://github.com/JCVI-VIRIFX/ISseeker.

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A user-specified reference genome is required for ISseeker analysis. The TYTH-1

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genome sequence (GenBank accession CP003856.1 (Liou et al., 2012)) was selected as the

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reference A. baumannii genome after consideration of several completed genome


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sequences. TYTH-1 was isolated in Taiwan in 2008 and is a GC2 strain (Nemec et al., 2004),

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as are a majority of strains with genome sequences in GenBank. NJST258_1 (GenBank

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accession CP006923.1 (Deleo et al., 2014)) was selected as the K. pneumoniae reference

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genome. NJST258_1 is a KPC-positive ST258 strain isolated in New Jersey, USA, in 2010. All

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completed and draft A. baumannii and K. pneumoniae genomes available in GenBank as of

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August 1, 2015 were downloaded. Genome assemblies that were highly fragmented (>300

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contigs), were assembled with newbler, or represented non-baumannii Acinetobacter

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strains or non-pneumoniae Klebsiella strains were excluded. 1035 complete and draft A.

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baumannii genomes and 807 complete and draft K. pneumoniae genomes were analyzed.

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All species-specific IS elements cataloged in the ISfinder database (Siguier et al.,

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2006) were downloaded and compared against the full genome set for each species. In

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addition, several complete genome sequences for each species were searched against the

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ISfinder database by BLAST to identify species non-specific elements. Eighteen additional

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(non-ISKpn) IS elements found in K. pneumoniae genomes were analyzed and seven

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additional (non-ISAba) were analyzed in A. baumannii genomes. Results are included in

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Table 1 for those elements that were present in more than five genomes.

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ISseeker was compared with ISmapper using a set of genomes for which both a

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finished genome sequence (e.g. a “gold standard”) and Illumina short reads were available.

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Illumina read sets were downloaded from NCBI’s Sequence Read Archive (SRA) using the

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SRA Toolkit utility fastq-dump. ISmapper was run on each read set using default parameters.

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Each Illumina read set was assembled using SPAdes (Bankevich et al., 2012). ISseeker was

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run on the finished genome sequence and on the Illumina assembly. The performance of

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ISseeker was evaluated by performing runs against the full set of sequences for each species


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using varying values for percent identify of matches to the IS element and of IS-flanking

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sequences to the reference, and using an alternative reference genome. It should be noted

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that the newbler assembler (Miller et al., 2010) suppresses these stubs so newbler

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assemblies cannot be used by ISseeker.

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A core phylogeny based on single-nucleotide variants (SNVs; 278,322 SNVs for A.

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baumannii, 332,571 SNVs for K. pneumoniae) was inferred using SNVs identified by NASP

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(Sahl et al., 2016) and constructed using FastTree 2 (Price et al., 2010). Genome positions

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with allele calls in at least 80% of strains were included in the analysis. Figure 2 was

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prepared using the graphics tools available through the interactive Tree of Life (iTOL) web

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service (Letunic and Bork, 2011).

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The statistical significance of comparisons of IS element composition between strain sets was assessed using Student’s t-test.

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RESULTS

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Description and evaluation of the ISseeker program Four classes of IS alignment are considered by the ISseeker program (Fig. 1(a)):

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contigs that are comprised entirely of IS sequence, IS element matches that are full-length

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and embedded in a long genomic contig, matches to the beginning or end of an IS element

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at the start of end of a contig, and partial matches internal to a contig. Contig sequences

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flanking each IS element are extracted and compared to a reference genome (Fig. 1(b)). By

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mapping all IS/genome junctions to a single reference, it is possible to compare IS locations

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across strains.


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The performance of ISseeker was evaluated from two perspectives: 1) comparison

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with ISmapper, using IS locations in completely sequenced reference genomes as a gold

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standard, and 2) to determine the impact of alternative run parameters on the detection of

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IS element locations. Two other programs that can identify IS elements in short read data

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were not included in the evaluation because they are not strictly comparable. Breseq was

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designed for mutation-finding in long-term culture experiments and is best suited to

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comparing very closely related genomes to a sequenced reference. TIF uses the unix grep

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command to identify IS-matching reads and is thus unable to identify non-exact matches.

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Results from ISseeker and ISmapper were compared on four K. pneumoniae

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genomes and four A. baumannii genome for which Illumina reads, Illumina assemblies, and

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finished genome sequences were available (Supplemental Table 1). Across these eight

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genomes, there were 74 insertion sites for the test IS elements ISAba1 or ISKpn26. ISseeker

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found all 74 sites when run using both the finished sequences and the draft genome

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assemblies, while ISmapper missed 20 sites for a sensitivity of 73%. This is lower than the

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value reported by Hawkey, et al. (Hawkey et al., 2015). Further analysis showed that most

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missed sites were in genomes with low read coverage (10 copies per genome in some A. baumannii

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strains. IS26 and ISKpn1 have 2 and 6 copies in shared locations per genome, respectively, in

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300 strains, corresponding to ST258 strains.

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There are more distinct IS element insertions in the examined A. baumannii

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genomes compared to K. pneumoniae. With respect to distinct sites mapped to each

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reference genome (TYTH-1 for A. baumannii and NJST258_1 for K. pneumoniae), there were

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1,843 distinct K. pneumoniae genome locations with IS insertions and 5,341 distinct A.

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baumannii locations. These distinct insertion sites represent the minimum number of

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insertion events that occurred over time because some insertion sites could not be mapped

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to the selected reference genomes and because multiple independent insertions could have

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occurred at a given site. Twelve different IS elements have over 100 distinct insertion sites

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across the A. baumannii strain set, but only five IS elements have that many distinct

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insertion sites in K. pneumoniae genomes. There are many more IS insertion sites shared by

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up to 100 A. baumannii genomes than there are shared sites across similar numbers of K.

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pneumoniae genomes (Table 2). In contrast, K. pneumoniae genomes have more sites

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shared in >250 genomes reflecting the relatively homogenous IS patterns in the dominant

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ST258 clade in the dataset. In addition, there are many more strain-specific insertion events

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in A. baumannii (3,194 vs 1,234). Another view of the extent of shared insertion sites is

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given in Supplemental Figure 2 that depicts the number of genomes that share sites along


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on the A. baumannii or K. pneumoniae reference chromosome. There are many more

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moderately abundant shared sites among A. baumannii strains than K. pneumoniae strains. A majority of genomes in the datasets for both species belong to multidrug-resistant

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clonal groups that have recently expanded: 62% of A. baumannii genomes belong to GC2

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(i.e., multi-locus sequence type (MLST) ST2) and 53% of K. pneumoniae genomes belong to

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MLST ST258. In these subsets of strains, IS elements are also much more frequent and their

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locations are more diverse in A. baumannii compared to K. pneumoniae (see Figure 2). In K.

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pneumoniae, the common location of IS insertion sites shared by large numbers of ST258

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strains regardless of geographic origin supports a model of recent expansion with limited

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strain- or clade-specific IS gain or loss. Variability in IS element composition and abundance

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is higher in the A. baumannii GC2 set, with more clustering of IS patterns by geographic

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location and phylogenetic position. It has been hypothesized that the ST258 lineage of K.

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pneumoniae arose around 1995 (Bowers et al., 2015), whereas the oldest known MDR GC2

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strain of A. baumannii was isolated in 1982 (Diancourt et al., 2010, Blackwell et al., 2015).

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A. baumannii IS elements ISAba1 has had the largest impact on A. baumannii genomes, with copies detected in

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815 of the A. baumannii genome assemblies and over 14,500 total insertions mapped in

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those strains. An ISAba1 insertion site is present upstream of the blaADC (ampC) gene in most

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of the genomes that have copies of this element – 736 genomes. The second most common

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insertion site for ISAba1 is upstream of the other chromosomal -lactamase gene, blaOXA-51-

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like,

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carbapenemase and resistance to imipenem and meropenem (Nemec et al., 2008). The

in 369 genomes. This insertion results in over-expression of the OXA-51-like


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median number of ISAba1 sites per genome was 19 and the maximum number in a single

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genome was 34.

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Four other elements were present in over 350 strains each – ISAba125, ISAba13,

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ISAba26, and IS26 and five additional elements were present in more than 100 strains (Table

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1(a)). In a few cases, it seems that an IS element has run amok in a genome, such as the

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ISAba6 and ISAba7 elements in A. baumannii strain SDF (Vallenet et al., 2008). Most ST79

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strains have 50-100 copies of ISAba27. Seven genomes have copies of 10 or more different

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IS elements and five genomes have more than 100 total IS copies.

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ISAba4, ISAba15, ISAba23, ISAba30, and ISAba32 were not found in any of the

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sequenced genomes. ISAba6 and ISAba7 were found only in the SDF genome (Vallenet et al.,

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2008). ISAba8 and ISAba28 were also only found in one genome each. ISAba2, ISAba18,

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ISAba19, and ISAba29 are IS3-family elements and are 85-95% identical to one another,

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making inference of their abundance and correct locations difficult in draft genomes.

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Likewise, ISAba16 and ISAba25 are 97% identical to one another and many of their

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annotated sites overlap with one another and are thus ambiguous as to the specific element

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that is present at each location. ISAba12 and ISAba13 are 84.8% identical, including regions

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of 100% identity in the first 23 bases and last 21 bases and are also difficult to discriminate

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in draft genomes. Of the non-ISAba elements examined, only IS26 was abundant enough to

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be included.

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Genomes that are closely related to each other on the phylogenetic tree tended to

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have similar patterns of IS element composition (Fig. 2). There are a few large strain

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collections representing restricted geographic regions among the 1035 genomes, including

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442 isolates from Maryland [NCBI BioProject PRJNA224116] and 174 from Ohio (Wright et


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al., 2014). Many of these genomes are very similar, potentially representing clonal series,

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but differences in IS content are apparent within each group. Among the GC2 genomes

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there are several interesting phylogenetic clusters, some of which correspond to

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geographically restricted strain collections. For example, some clusters of strains isolated in

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Maryland have copies of ISAba16/ISAba25 that are largely absent from other strains. Strains

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previously identified as Clade D (Wright et al., 2014) are clearly distinct from other GC2

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strains by having 7-31 copies of ISAba12. Most Ohio strains have one or two copies of

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ISAba22, ISAba24, and ISAba26 that are found in relatively few other strains. Most Maryland

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strains have 7-10 copies of ISAba13 and of ISAba17, elements that are not as abundant in

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other branches of the tree.

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K. pneumoniae IS elements

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Overall, there are fewer IS element copies in K. pneumoniae genomes than in A.

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baumannii. This difference is reflected across both the number of distinct insertion sites

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(reflecting historical independent insertion events) and in the total number of copies across

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the genome set (reflecting the success of strains carrying those elements) (Figure 2, Table

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1). In K. pneumoniae, about 350 ST258 genomes share IS insertion locations for ISKpn1,

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ISKpn26, and IS1F. This suggests that ST258 genomes have spread rapidly worldwide with a

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reasonably stable repertoire of IS elements and only limited new IS mobilization activity.

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Thirteen IS elements were present in >100 K. pneumoniae genomes (Table 1(b), Fig.

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2). ISKpn6 and ISKpn7 are present on Tn4401 that carries the blaKPC gene; the presence of

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those two elements corresponded closely with the presence of the blaKPC gene. Both of

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those elements were only observed in the Tn4401 context and so appear not to have

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mobilized to other sites in the K. pneumoniae genomes. ISKpn24 is also present on the


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pNJST258N2 plasmid that carries Tn4401 and copies in most ST258 genomes map to that

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plasmid. Unlike ISKpn6 and ISKpn7, ISKpn24 was observed at several other sites in a subset

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of genomes.

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Eight additional IS elements were found in more than 200 genomes (ISKpn1,

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ISKpn18, ISKpn26, ISKpn28, IS26, IS903B, IS1F, and IS6100). Of these, ISKpn18 is almost

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entirely restricted to ST258 strains, but the other IS elements are found throughout the

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phylogenetic tree. ISKpn1 was the most broadly distributed, appearing in 583 genomes.

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Most ST258 genomes share five common ISKpn1 insertion sites. The number of copies of

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ISKpn26 is more variable across genomes, indicating more active mobilization than other

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elements. NJST258_1 has seven chromosomal copies of ISKpn26 and one on pNJST258N1.

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Copies at equivalent positions are present in other ST258 strains. ISKpn28 mapped to

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another large plasmid (pNJST258N1) in the reference genome, and one copy was present in

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the chromosome in most ST258 strains.

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ST258 genomes have more than three times as many IS copies than non-ST258

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genomes (average 34.5 vs 10; p100 genomes) are shown in the context of the A. baumannii (a) and K.

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pneumoniae (b) phylogeny based on SNP markers. Isolation locations for the strains from

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the largest collections have a color code in the inner circle. The height of each bar

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represents the number of copies of each element in each genome. Scale rings illustrate the

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height of the histograms on each tree diagram. In (a), strain groups are denoted with

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colored branches: Global Clone 1 (pink), GC2 (green), and ST79 (orange). In (b), the two

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major sub-groups of ST258 are denoted as ST258A (orange) and ST258B (blue).


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Figure 3. Distribution of conserved IS clusters for the most common IS elements. The

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number of strains sharing a set of IS element locations is plotted for the five IS elements

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with the largest number of copies (>1500 total copies for each element) in A. baumannii and

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ISAba27 that is greatly expanded in certain genomes (a) and six K. pneumoniae (>1000 total

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copies) (b).

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Table 1(a). IS Elements Surveyed in A. baumannii genomes

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Table 1(b). IS Elements Surveyed in K. pneumoniae genomes

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Table 2. Shared IS element sites

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List of Supplemental Files

619

Supplemental Figure 1. Example of a complex transposition event. The creation and

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mobilization of a complex transposon is illustrated. A single copy of ISAba1 is present in this

621

region in the reference strain TYTH-1, shown at the top. In strain ORAB01, a second copy, in

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an inverted orientation, is inserted 1580 bases downstream (middle diagram). The resulting

623

complex transposon then apparently mobilized and is present in a second location in the

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genome starting at base 2036206 based on reference coordinates (bottom diagram). Blue

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letters above each IS/genomic junction indicate which junctions were called by ISseeker

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analysis of the PacBio assembly (S-PB) or the Illumina assembly (S-Ill) and by ISmapper

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(ISM). Note that ISmapper also calls a spurious location upstream of the original ISAba1 site.

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Supplemental Figure 2. Shared sites across the chromosome. The number of genomes

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sharing IS insertion sites for the most abundant IS elements are shown, mapped by


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chromosome coordinates for A. baumannii (a) and K. pneumoniae (b).Supplemental Table 1.

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Comparison of ISseeker and ISmapper

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Supplemental Table 2. Results from ISseeker analysis using alternative run parameters

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Supplemental Table 3. IS copies in A. baumannii genomes

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Supplemental Table 4. IS copies in K. pneumoniae genomes

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Supplemental Table 5. A. baumannii genes with multiple different IS elements inserted

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Supplemental Table 6 A. baumannii intergenic regions with multiple different IS elements

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inserted.

638 639 640 641


Table 1

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Table 1(a). IS Elements Surveyed in A. baumannii genomes # of Genomes with Distinct Sites† Annotated Un# of In Between % In % Sites annotated Sites Genes Genes Genes Between Sites Genes IS26 776 30 265 208 57 78.5 21.5 ISAba1 815 20 1229 735 497 59.8 40.4 ISAba2 46 31 57 43 14 75.4 24.6 ISAba3 4 12 14 9 5 64.3 35.7 ISAba4 0 ISAba5 19 31 41 25 16 61.0 39.0 ISAba6 1 ISAba7 1 ISAba8 1 4 4 3 1 75.0 25.0 ISAba9 2 2 2 0.0 100.0 ISAba10 38 12 97 59 38 60.8 39.2 ISAba11 12 19 69 39 30 56.5 43.5 ISAba12 142 122 357 209 148 58.5 41.5 ISAba13 393 80 572 309 263 54.0 46.0 ISAba14 13 15 13 9 4 69.2 30.8 ISAba15 0 ISAba16 140 15 258 172 86 66.7 33.3 ISAba17 276 12 98 60 38 61.2 38.8 ISAba18 46 25 60 46 14 76.7 23.3 ISAba19 62 25 163 132 31 81.0 19.0 ISAba20 3 1 5 4 1 80.0 20.0 ISAba21 3 20 12 10 2 83.3 16.7 ISAba22 63 301 71 49 22 69.0 31.0 ISAba23 0 ISAba24 200 1 9 7 2 77.8 22.2 ISAba25 157 19 340 219 121 64.4 35.6 ISAba26 381 39 190 136 54 71.6 28.4 ISAba27 46 20 343 116 227 33.8 66.2 ISAba28 1 1 ISAba29 56 25 128 102 26 79.7 20.3 ISAba30 0 ISAba31 29 51 93 34 60 36.6 64.5 ISAba32 0 16 ISAba33 29 20 64 33 31 51.6 48.4 ISAba36 42 1 253 172 81 68.0 32.0 ISAba125 402 160 528 338 190 64.0 36.0 ISAba825 3 2 6 3 3 50.0 50.0 †Distinct sites is the number of unique annotated locations on the reference genome. *(Number of distinct insertion sites)/(Total insertions in all genomes) IS Element

# of Sites

In Genes

Total Sites‡ Between % In Genes Genes

3087 14510 185 20

1612 7383 160 13

1475 7127 25 7

52.2 50.9 86.5 65.0

% Between Genes 47.8 49.1 13.5 35.0

Diversity Ratio*

59

36

23

61.0

39.0

0.695

4 2 241 85 990 3639 25

3 143 48 592 1865 20

1 2 98 37 398 1774 5

75.0 0.0 59.3 56.5 59.8 51.3 80.0

25.0 100.0 40.7 43.5 40.2 48.7 20.0

1.000 1.000 0.402 0.812 0.361 0.157 0.520

1032 2007 199 387 5 12 112

661 1119 172 328 4 10 89

371 888 27 59 1 2 23

64.1 55.8 86.4 84.8 80.0 83.3 79.5

35.9 44.2 13.6 15.2 20.0 16.7 20.5

0.250 0.049 0.302 0.421 1.000 1.000 0.634

240 1391 652 818

49 884 255 258

191 507 397 560

20.4 63.6 39.1 31.5

79.6 36.4 60.9 68.5

0.038 0.244 0.291 0.419

308

263

45

85.4

14.6

0.416

122

39

83

32.0

68.0

0.762

0.086 0.085 0.308 0.700

Linked Genes

OXA-58

RTG-4 OXA-23 LpxA /C

RTG-6 LpxD OXA-51

RTG-5 AadB

94 41 53 43.6 56.4 0.681 712 446 266 62.6 37.4 0.355 1595 1054 541 66.1 33.9 0.331 OXA-58 6 3 3 50.0 50.0 1.000 OXA-58 ‡Total sites in the number of annotated and unannotated sites summed for all genomes.


Table 1(b). IS Elements Surveyed in K. pneumoniae genomes # of Genomes with Distinct Sites† Total Sites‡ Annotated Un# of In Between % In % # of In Between % In % Diversity Linked Sites annotated Sites Genes Genes Genes Between Sites Genes Genes Genes Between Ratio* Genes Sites Genes Genes IS1294 40 16 127 97 30 76.4 23.6 325 227 98 69.8 30.2 0.391 IS1F 452 49 87 52 35 59.8 40.2 1030 75 955 7.3 92.7 0.084 IS26 494 69 211 160 51 75.9 24.2 2064 1577 487 76.4 23.6 0.102 IS4321R 159 33 21 13 8 61.9 38.1 376 141 235 37.5 62.5 0.056 IS5 19 23 44 22 22 50.0 50.0 53 26 27 49.1 50.9 0.830 IS5075 318 26 36 22 14 61.1 38.9 883 292 591 33.1 66.9 0.041 IS6100 430 30 15 11 4 73.3 26.7 937 140 797 14.9 85.1 0.016 IS903B 491 73 194 119 75 61.3 38.7 1403 467 936 33.3 66.7 0.138 ISEcp1B 90 16 51 35 16 68.6 31.4 136 99 37 72.8 27.2 0.375 ISKpn1 583 4 146 27 119 18.5 81.5 2967 57 2910 1.9 98.1 0.049 ISKpn2 0 35 ISKpn3 0 ISKpn4 0 ISKpn6 413 1 3 3 0.0 100.0 823 823 0.0 100.0 0.004 KPC ISKpn7 414 1 3 3 0.0 100.0 824 824 0.0 100.0 0.004 KPC ISKpn8 24 5 8 1 7 12.5 87.5 32 3 29 9.4 90.6 0.250 ISKpn9 0 ISKpn10 0 ISKpn11 0 6 ISKpn12 0 12 ISKpn13 0 ISKpn14 64 142 58 33 25 56.9 43.1 98 51 47 52.0 48.0 0.592 ISKpn15 0 ISKpn18 387 1 85 76 9 89.4 10.6 1188 1153 35 97.1 2.9 0.072 ISKpn19 12 16 11 9 2 81.8 18.2 12 10 2 83.3 16.7 0.917 ISKpn20 3 3 ISKpn21 47 36 19 9 10 47.4 52.6 80 43 37 53.8 46.3 0.238 ISKpn23 0 ISKpn24 235 19 29 20 9 69.0 31.0 458 37 421 8.1 91.9 0.063 ISKpn25 71 76 13 6 7 46.2 53.8 76 6 70 7.9 92.1 0.171 ISKpn26 486 33 621 379 242 61.0 39.0 4238 1627 2611 38.4 61.6 0.147 ISKpn27 0 ISKpn28 452 25 49 20 29 40.8 59.2 855 166 689 19.4 80.6 0.057 ISKpn31 0 10 †Distinct sites is the number of unique annotated locations on the reference genome. ‡Total sites in the number of annotated and unannotated sites summed for all genomes. *(Number of distinct insertion sites)/(Total insertions in all genomes) IS Element


Table 2

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Table 2. Shared IS element sites Total copies Number of genomes sharing a site

A. baumannii

Distinct sites

K. pneumoniae

A. baumannii

K. pneumoniae

>500

736

0

1

0

250-499

6975

12789

25

36

150-249

3794

3385

18

18

100-149

2561

1136

21

9

50-99

1559

911

21

14

20-49

4985

950

172

32

10-19

2642

612

195

42

2-9

5590

1634

1694

471

1

3194

1234

3194

1234


Figure 1

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(a)

Entire length of contig is IS element Full length IS element is present in a contig IS element edge sequence is present at a contig edge

Partial match internal to contig (b) IS Element

Full-length Match

BLAST

Query Genome

Partial Match

Full-contig Match Embedded Match

BLAST

IS edge at contig edge

Interpret Matches

Internal to contig Discard

Reference Genome Sequence

Extract 500bp Flank

Reference Genome Annotation

No Match to Reference

Match to Reference

Note IS as unmapped

Annotate as mapped


100

Figure 2

Click here to download Figure ab_kp_tree_figs_v6b.eps

50

50

A.baumannii 25

IS26

25

ISAba1

ABUH504238 UH225 472 UH225 492 UH225 493 UH81 389 UH81 452

57 C

96

2590 6112 52

8881

6

2168 BIDM 72

84 69476

2 13969 WC-4 70 87

11301 45

15715

25977 25977 10 79638 9 25977 0-137 25977 3 5 25977 2 25977 1 25977 8 25977 7 25977 4 6

12819 907131

3-2b

269

07 ABUHUH29 07 UH10 UH23 408 308 UH12 364 UH12 2 UH81 908-1 2-7 AB -04-0 C 56 111 2009 BIDMAb11 202 182 AB UH17 151 5 UH17 UH17 909-0 AB

UH18 MAYT CS01 ORAB CR17 8 1582- 89 AB OIFC153264 4805596 0 128 UH41 0 108 UH41 0 103 UH41 0 808 UH41 UH12 108 4 UH16 52435373 3

15788 12452 04 WC-137243115642 49 32 26390 6 26390 3-2

15661

09

UH225 433 UH5307 UH293 UH293 377 UH134 412 UH134 167 UH134 168 UH129 192 UH129 408 UH129 404 UH129 409 UH71 415 UH71 278 UH71 277 UH71 279 296

UH243 56 UH243 57 UH243 66 UH280 81 UH370 270 UH475 197 UH484 95 UH487 41 UH487 63 UH487 64 UH507 247 UH507 263 UH5707

UH299 338 ABUH304350 ABUH304352

UH243 43 UH243 73 UH280 93 UH280 92 UH280 99 UH9907

UH487 78 UH7807

UH367 548 UH367 565 UH532 387 UH532 392 UH532 386 ABUH518307 UH81 366 ABUH504227

UH19908

ABUH80286 ABUH42783 ABUH319118 UH8107 UH507 300 342 UH299 UH9007

UH16008 UH15208

UH243 55 UH243 54 UH243 33 UH243 14

UH10107 UH315 100 UH10007 UH6107 UH243 68 UH299 341

UH14508 UH475 239 UH455 61 UH315 101

45002 5 45002 1552389 4 45002 5 148868 0-132 127647323408 11126 5

MDR-ZJ0B1 2011ZJA B2 2011ZJA 6 45002 3 45002 7 45002 10

TG27335 AB TG27331 AB TG27323 AB TG26316 AB

TG27407

AB TG2026 TG27411 TG27383 TG27379 TG27319 TG27315 TG2014

155286 145660 730795 8 45002 339786 1 45057 825610 9 45002 6 153902 70136

20 12918 11 12774 50 14407 76 10511 03 11461 68 14283 113 Naval- CI77 4 295

ISAba26

ORABSC ORAB6B ORAB21 ORAB18 ORAB17 ORAB16 ORAB13 ORAB09 ORAB08 ORAB03 ORAB02 ORAB01 ORAB23 ORAB14 ORAB19 ORAB15 TG22202 01-7 8 AB 2008-23-07AB 1766 AB TG27327 TG27371 TG2013

ISAba13

WC-14

1

ISAba125

1064 9720 293 UMB 82 45 1043 002 2321 794 2686 84 80 1267 AB03 820 1

WM9 2004 AB1H 9c 2003 BJAB 2004 BJAB 8 2004 BJAB 14 12 BJAB 10 2011 13 NIPH BJAB BJ8 UH45 2061 4 UH45 5 UH45 62 ABUH 5 6 5 38 UH02 4837 UH62 07 UH38 07 UH89 07

ISAba17

7

320

1293198 339 5-017-01 -16-2 1 TG22 TG27 -16-2 U-2 AB 2007 TJAB AB 2007 BZIC 2011 AB

LY1 601 LY2 NIPH BJ4

ISAba10

8 -mff 1797 17978

ATCC ATCC

410 70

NIPH NIPH

4749 5E4 -92

UH88 07 UH11 07 UH34 608 UH12 8 UH20 6 13725 UH18 UH18 4 108 UH53 4 310 UH53 5 309 419 UH19 5 UH19 5 418 UH19 5 568 573 UH66 5 560 UH514 268 UH514 ABUH 288 49714287 UH66 UH66 276 4 ABUH 241 UH12660486 UH126 106 UH186 102 UH139 08 UH381 08 ABUH4 482 63346

AB40 WC-A

21072 22

1440480

0-01-7

NIPH 09-11 2007-391 TG27 T229-82 190 Naval NIPH 79 1106583444

AB

4 615 62597 NIPH 17 8 TG020 12173

6 2338430 14191

4190 CI79 CI86 18 Naval- 43 OIFC1 107m 5256 5-69 984213 2008-1 3 AB

LY3 AC29 T173 T122

UMB00 4 1297 1391439 25569 8 25569 3 25569 2 120225 3 105828 562700 942194 1 25569 3 25493 8 25493 1039621 1040094 52 1032241 2008-15- 71 AB 2008-15AB 43926 5 45052 3 45052 4 45052 1 45052 6 45075 1 45075 8 45075 9 45075 2 45052 5 45075 10 45075 2 45075 3 45075 1075025 42887 10 25569 2 25569 4 25569 7 25569 5 25569

T25

T7 BJAB07AB07 MRY10 104 -0558 TYTH-5 TYTH-4 2011HN AB1 UH8407 UH236 UH236 85 UH870784 UH236 2005JSA 87

B1 TG27299 AB 515-8 AB 1595-8 XH386 MRY09-0 642 LY9 LY5 LY4 ZWS1219 ZWS1122

ISAba12

BJ7 MRY12-02BJ6 77 2011BJAB6 2011BJAB5 2011BJAB2 2011ZJAB3 2011SHAB1 BJ2 2011BJAB8 2011SDAB3

MDR-TJ 2011LNAB3 2011BJAB7 2011SDAB2 2011SDAB1 2011LNAB2 2011BJAB3 2011BJAB1 2005LNAB4 2004ZJAB5 BJAB0868

AB 2009-04-01-7 -7 AB 909-01-7 AB 2008-23-01-01

TG27395 TG27399 AB TG2018 AB 1594-8 6 25493 4 25493 5 25493 10 25493 9 25493 2 25493 25493 1

BJ3 W7282 W6976 AB210 TCDC-AB0715

ISAba16

444 UH384 UH384 450 UH106 447 UH367 558

TYTH-6

BJ5 BJ1 2011LNAB1

TG07725 TG22332 TG22336 AB TG2030

T258 2011GDAB4

UH41 491 UH41 490 UH41 489 UH41 488 UH41 486 UH326 495 UH17 465 UH41 487 UH326 461 UH326 445 UH381 467 UH175 677 UH355 569 UH355 545 UH189 348 UH189 349 UH189 355 UH430 466 UH430 459 UH10707 UH315 58 UH315 39

ISAba19

TG27295 AB TG2031 AB TG2028 AB TG2032 NIPH 1669

Naval-13 OIFC109 OIFC137 Naval-81 IS-123 4857 WC-A-694 940793 1406589 1237893 480175 45075 4 1188188 42057 3 29280 42057 5 472237-120

Clade D

UH2907 UH0707 UH348 27 UH2707 UH0807 UH7707 UH348 13 UH370 301 UH370 269

42057 4 42057 6 1271213 1276470-86 6013150 6013113 D36 Naval-21 OIFC074 Pulsotype 27 TG19582

OIFC338 NIPH 528

1999BJAB11 NIPH 24

NIPH 290 Naval-83 AYE VEB NIPH 527 ABNIH19

AB5711 5711 16553 9 16553 6 16553 8 16553 10 16553 3 2 16553 4 16553

ISAba24

MRSN 58 ABNIH11 ABNIH6 ABNIH7 A144

GC1

929679-598 AB 2008-15-70 AB 2008-15-45 ABNIH3 DU202 1656-2

AB 908-14-7 1362 NIPH ACICU 237 NCGM LY8 LY7 LY6

ANC 4097 R1B IS-235 IS-58 IS-251 5075 AB5075-UW 6870155 1605 TG20277 Canada Canada BC-5 AB0057 BC1

AB 908-13 AB 909-02-7 TG22196 TG22194 TG22190 TG22148 TG22112 TG22214

2011GDAB3 T87

2011GDAB1 T188 T185 TYTH-3 TYTH-2 TYTH-1 Naval-17 6014059 OIFC180 341

ISAba25

SDF TG22142 TG22146 TG22150 144107

ABNIH24 ABNIH23 ABNIH20 ABNIH22 ABNIH2

1062314 OIFC016 2

UH392 WC-348 OIFC047 659 TG27387 1297549 6200 IOMTU 1525283 433 OIFC08 OIFC03 7 OIFC09 2 129574 9 AB4A3 3 IS-116 OIFC06

ABNIH17 ABNIH16 ABNIH26 ABNIH14 ABNIH13 5 ABNIH1 273929 23671

1207552 1526966 532413 2 124718 58452 1 104605 8 103693 6935

5 D12797 2011BJ 79 2004ZJAB9 BJAB0 AB6 715

9

TG1523 38 TG152 33 TG152 36 TG152 37 TG152 663 UH588 656

4 UH588 TG506 3 AB TG202 2 AB TG202 2 AB TG201 12 TG222 10

ISAba27

ST79

92

TG221TG221IS-1432

Naval- 4 ABNIH MMC411 MDR TG273 307 18 TG27 ABNIH -78 0 Naval 65302242 5 TG15 ABNIH 25 1 ABNIH ABNIH 444 Ab44 2 684 1

T214 Ab04-m LAC-4 ff OIFC0 NIPH 98 466760 335 UH392

MSP4-1

UH39 40457 c ColiS ABUH c ColiR679 ABIsa 5

2568 2601 1 2601 6 5 2601 6 7 1032 6 3 359 2 AB 1284 2303 2008 4432 800 7 -15-3 7 1043 6 4-7 5640 903 9935 12 2569 20 2569 1 25750 1 7 8 25750 8 25691 6 10466 5

34654

34001 662545-1347

24845 9 472237-1196

44437 9 44437 5 44437 8 44298 8 44298 7 44298 5 44298 4 44298 6 44298 3 44298 1 44437 4 44298 9 44298 10 44437 3 44437 7 44298 2 24845 7 24845 4 24845 1 24845 5 24845 3 24845 10

25878 2 25878 1 26016 3 25681 1 8361902

25569 6 737393 466215

10519 1575710

2887 25681 26016 9 25681 9 25766 6 25766 9 25766 3 10 25766 25766 5 26016 7 10450926 25766 6 25766 929679-209 4 796380-210 5 2

400834 1294217 1159076

942133 25935 6 25561 2 25691 2 959073 947299

25750 74 17534 1 4446710314 25935 10 33 44467 4 44467 7 44467 5 25935 4 25691 5 25935 9 44467 8 44467 6 44467 1 44467 2 44467 8 44327 9 44327 1 44327 4 44467 2 655555 3 44362 44327 6 44362 7 44327 3 26016 5 44362 8 44327 2 44362 8 44362 7 43557 1 44362 1 44362 9 44362 8 44362 5 44362 4 142699310 26016 26016 4 26016 5 25878 10

61-97 11178 12627 09 12325 09 13925 13 46 13975 93 10642 36 12649 51 12716 44 11780 73736 2 42057 9 64760 64

2 21369 2 30300 02 45828 12372 12 14710 19

GC2

10954 82 0 14061 105183 554515 3 159327 4 146223 7 UH700 15827 40 TG152 41 TG152 6 TG2054 9-1265 104296 4 25307 6 24812 8 24812 7 24860 2 25307 2 24860 5 -1197 24860 10429694 24812 7 24812 9 24860 923118 1494580 7893 98826 9 44839 10 44857 10 44839 8 44839 4 45057 9 44857 3 44895 2 44895 6 44895 1 44895 10 44895 4 44895 7 24975 2 24812 1 16553 9 25442 1 25442 10 25561 10 25935 2 25935 7 25750 1 25691 4 24975 5 25442 6 24860 9 24975 1 24860 10 24975 7 25442 1 25561 6 25691 1 25935 25935 9 25935 7 25691 10 25561 7 24860 3 24860 8 25253 4 25307 6 25253 10 25253 3 25307 3 25253 6 25253 1 25307 1 25307 8 25253 8 24845 6 44895 8 44895 5 44895 9 25307 5 24845 8 24812 10 25253 5 25253 7

ISAba36

820 2 818 1482 9651 22 1552 4709 234 546 TG15 220 1289 18 1266 6284 76 222 9811 1294 959 1022 29 7558 084 1397 750 85 1406 52 14654 129627 9 6 13586 72490756477

10 5 ABIsa UH17ORAB 5 10 2497 0 1 5 2486 67 2497 9165 21 9874 06 9 1367 1868 001 2 UMB 6 3 1 1 2576 6 8 2568 1 2576 2568

ISAba29

2011Z 536 50595 JAB4 12627 10072 61-105 3390 14

ZW85

60780NIPH -16 60 A3340 5 AB 5 AB 1583AbH1 TG27 8 AB03 2O-A2 343 TG02 0 ORAB 011 ORAB ASHR UH79 RICT UH53 07 UH10 5 UH10 6 423 429 UH76 6 440 UH69 07 UH22 07 UH19 908 UH12 608 UH16 208 NIPH 208 T271 1734 AB-H AB10 KU3AB-H I9 AB18 08 KU31505 G7 1287 10 311 1457 985 1475 504 764

Location Maryland

K.pneumoniae

50

Ohio

ISKpn1 25

IS903B

40

CHS107 WGLW5

JH1 MGH 66BO 17

501 KPNE 500 887 KPNE KPNE KPNE

813

743 KPNE '755.rep

MGH841 KPNE'

741 2 KPNE KPNE' '755.rep

BIDMC MGH 23 MGH 32 MGH11 21 BIDMCMRSN 6 3852

27 648 KPNE

BIDMC 24 UCI 11227- 56 31

ST323

JT4 436

14

1239

BIDMC

KPNE 95

16

BIDMC

21PV

60 MGH 48 89 P1 BWH LAU-K BIDMC 7 E 35 7699 UCICR BIDMC 64 UCI

1041 KPNE

3

18

98SG MGH JS86C 70 MGH 69

R

94153 37AVR CCBH 0379 13327 KPNE

3

UCICRE

MGH96 MGH11

C91 8 R BWH5 100SG 41AVR R

47AV

MGH12

BIDM

25955

UCI

62

BIDMC 1

65

19PV

BIDMC 33B MGH111

MGH115

1158

MGH117

T2-1-1

MGH81

MGH 63

T2-1-2

MGH

2242

2026

43

48

T69

KCTC

BWH62

DSM

Ecl8

CHS

MGH 75 845 KPNE 1263 KPNE CHS206

CHS

ATCC G5-2

91SG

R CHS1 MGH CHS1 46 MGH9 XDR 61 66 0

CHS1

UCI94 69BO 30 BWH 14PV 13883 4640 ATCC 30104 1662 DSM JCM 36

96SGR 53BG 52 63BG MGH 92SGR 7 MGH9

98 KPNE BWH UCI 46 KPNIH 34

9-C

UCI 1010 26 KPNE 1012 MGH98 KPNE

BIDMC MGH11852

325

B5055

Kp52.145 EGD-HP1

84RE

PittNDM01

BIDMC 11

SB2390

JHCK1

MGH124

WGLW2

303K

CHS112

PMK1

MGH101

UCI96

BAMC 07-18

ST15 NDM-1 101712

99SGR

2

NB60

9451658 BWH

yzusk-4UCI76 MGH 48 51BG PR04

79RE

CHS174 BWH 28

26BO

55BG

RYC492 25BO MGH 64

93SGR

32AVR

MGH 36

CH1034

221 KPNE

CHS159

MGH 46

CHS140

BIDMC 47 187 KPNE

UCICRE 4

CHS 66

KP617

CHS175

ST101

ST101

93999682 5 95708916 6 ST101 95708389 20 ST101 9570833 38

ST101

ST101

KPNE 25

ST2017 95014239 U44822 9 ST2017 ST101 94516965 3 ST101 94515423 4

15PV B199

BIDMC

ST101 950118422 ST2017 950117510 8

1183

BJ1-GA

CHS201 570 KPNE KPPR1 UCI70

912 KPNE 930 KPNE

951362657 ST2016 951373950 ST101 951363981 ST101 960186733 ST101 951384356 ST101 950173000 ST101 950171785

11296

13884

K2044 NTUH- 22PV

ATCC

ATCC

BIDMC 85 BIDMC MGH94 1084

CHS16 86

76RE 65BO 2

909957 82RE

80

6

76

MGH

700603

KPNE MGH12 CHS121 34AVR

KPNE

KPNE KPNE

KPNE KPNE

KPNE

90 KPNE

MGH

KPNE

1162281 913 KPNE

194

KPNE 863 UCI92 234-1220PV

837

836 835

834 833

780

223 14 UCI 18 BIDMC MGH1 14 88

BIDMC 1335

1294

1kgm

IS26

18PV

25

IS1F

ST14 944535499

IS1294

865 KPNE

LZ

45AVR

15

78RE

29

BWH KPNIH GOS FDAAR74 MGH GN8

84

1319 MRSN 55

BIDMC 1 IA565 CDPE0 #1721' 'Top52

17PV 9PV 43 MGH 10PV 40AVR 77RE SA1 CG43 42 UCI

IS4321R

hvKP1 6 HK787 UCICRE

349 52BG 20 UCI

KPNE 51 BIDMC 4541-2 KP-11

1035

KP-7

CHS145 2404

MRSN CHS 70 CHS 05 CHS230

HE12

IS5075

3562

MRSN

WGLW1

CHS228

WGLW3

CHS225

LCT-KP182

CHS217

LCT-KP214

CHS213

LCT-KP289

CHS212

95SGR 39 MGH MGH112 KPNE 1331

CHS209

CHS181

CHS108

KpN01

CHS117

KpN06

CHS238

BIDMC96 46b BIDMC 67BO UCI 25

CHS133 CHS124

CHS147 CHS135

ST485

CHS 33

60BG

CHS 45 CHS 02

MGH102

94SGR CHS 21

CHS 74 CHS148

27BO

CHS 14 CHS138

UCI82

4006

CHS 07

1098 KPNE BIDMC 22 MGH 78578

CHS 18 CHS 80 CHS 52 CHS 54

49BG 81RE

CHS83

83RE

CHS 11 CHS173

KPNIH31 MGH89

MGH 35

CHS168

CHS167

IS6100

MGH93

CHS155

62BG

ST147

CHS 13

CDPH3823

CHS142

CDPH3020

CHS 16

CDPH5262

CHS 29

CDPH3707

CHS109

731 KPNE

CHS 63

BIDMC 36

CHS 61

UCICRE 8

CHS 60

36AVR

CHS 50

MGH 30

CHS196

MGH83

CHS149 5422

CHS122

UCI 68 BIDMC 48

CHS189 CHS 20

MGH 47 BIDMC 21

CHS223

CHS 44 CHS 17

BIDMC 18D BIDMC 41

CHS235

BIDMC 46a BIDMC 53

CHS226

CHS152

KpQ3

CHS84

KpQ15

CHS116 CHS 59

ISKpn6

KpQ24 MGH82

CHS 65

MGH 72 UCICRE 2

CHS88 CHS187

16BO

CHS95

28BO

CHS186

70BO

CHS185

85RE

CHS165

68BO

CHS154

Kp13

CHS100

KPLM21

CHS85

CAV1193

CHS160

CAV1344

CHS101

blaNDM-1

CHS129

101488

CHS99

1191100241

CHS102 56 CHS

CHS

39AVR 46AVR HS11286

57

CHS163 B86 KP ST11 OXA48 MGH 69

CHS139 76 CHS

CHS89

ATCC

CHS200

IS33

CHS220

CAV1392

CHS197

ISKpn7

CHS86

CHS178 67 CHS

CHS208

CHS211

CHS234

CHS93

CHS131

CHS229

CHS12346 CHS 51 CHS 47 CHS 19 CHS

CHS 24 ST-437 UCI 17 34618 UCI 61 UCI 22 MGH VA360 51

CHS134 75

CHS

72 CHS 64 CHS 62 CHS

CHS151 Kb140 CHS144 CHS KPNIH349

41

CHS

39

CHS

38 37 36 CHS 32 CHS 28 CHS CHS90

CHS

CHS

ST258A

CHS240 9 CHS23 1 CHS22 5 CHS19 3 CHS11 7

CHS15 0 9 CHS15 CHS21 8 CHS21 6 CHS21 5 4 CHS21 2 CHS21 9 CHS18 CHS16 73 CHS 27 CHS CHS82 37

MGH91

UCI69

UCI95

UCI 67

Kb677

ST258 FL

UCI 44

BIDMC 54

MGH125

CAV1596

UCICRE 1

NJST258 2

BIDMC 12B

BIDMC 12C

BIDMC 12A

UCI75

UCI93

UCI91

16

4

13

32

UCI 33 BIDMC 5 2A

10 42b

CHS2

CHS9 07 CHS1 CHS1 05 4 CHS1 76

BIDMC

BIDMC

BIDMC

BIDMC

BIDMC

BIDMC

BWH 36

BIDMC

42a BIDMC 7A BIDMC 7B

BIDMC

CHS104

KPNIH32

BWH53

MGH 73 BIDMC 14 BWH 47 BWH 45 UCI81

CHS91 8 CHS11 CHS10 9

CHS 3 CHS 53 CHS19 12

CHS 8 CHS20503 CHS141

CHS98 CHS166

CHS CHS 23 CHS 22 CHS23634

CHS232

CHS CHS21009

CHS184

CHS CHS132 42

CHS156

CHS CHS12758

CHS125

CHS231

35 CHS106

CHS171

CHS 06 CHS202

KPNIH 2 KPNIH KPNIH5

KKBO- 10

CHS130

705

BAA-1 MGH ATCC 60 MP14 68 BIDMC 7 BIDMC KpVA- 6 KpVAKpVA-5 -K28BO ST258 -K26BO ST258 1 KKBO- 4

4 KpVA KpVA12PV 11PV 13PV 23PV 67

97SGR

74RE

O

29BO

102BO

103BO

101BO

87SGR

48AVR

43AVR

KPB-2

KPB-1

30BO

104BO

ST512-K30B

KpVA-16

KpVA-1

KpVA-15

44AVR

42AVR

31AVR

58BG

88SGR

KPNIH9 0

ST258-49 86SGR 89SGR 90SGR

KPNIH8

KPNIH4

KPNIH22

UCI 43

UCI 38

UCI 37

UCI 55

UCI 41

SY-B2

SY-B

CHS 08

SY-A

NJST258 1 CHS 55

KPNIH33

MGH 31

MGH 79 733 KPNE

Downloaded from www.microbiologyresearch.org by Tree scale: 0.1 IP: 172.245.146.248 On: Mon, 16 May 2016 03:09:54

KpVA-9

Washington

KpVA-8

North Carolina

BIDMC 1 MGH 59

Maryland

KpVA-14

Massachusetts

KpVA-13

Italy

BWH 41

California

KpVA-12

Location

KpVA-11

ISKpn28

KpVA-10

ISKpn26

KPNIH6 1 KPNIH1 KPNIH1 KPNIH7 0 3 KPNIH2 KPNIH2 6 KPNIH1 7 KPNIH1 2 KPNIH1 4 KPNIH1 8 KPNIH1 KPNIH19 KPNIH21

ISKpn24

CHS9 11 CHS CHS1 30 7 CHS1 70

37

56BG 54BG 57BG 50BG -3

26 CHS1 83 CHS CHS1 79

CHS

40 CHS1 24 CHS 71 CHS2 2 CHS CHS9 91

CHS1 CHS1

MGH 22 32192 45 MRSN6 MRSN 920 MRSN 8157 KPNIH 6902

MGH9 24 MGH 5

BIDMC 29 BIDMC 18B BIDMC 18C BIDMC 18A BIDMC UKKV 34 CHS1 90166 45 75RE 94 4 72RE 73RE 71RE KK207 KpMD 1 ST258 U1 CHS 24PV 31 KpVA

ST258B

1 CHS2 CHS8 6 CHS9 72

CHS 14 CHS1 25 CHS1 CHS17 64 92 CHS12 7 CHS15 0 CHS12 8 CHS12 8 CHS11 6 CHS11 0 CHS87 5 CHS11

ISKpn18

KPR092 0 UCI 8 UCI 19

UCI 63 59 UCICRE UCI 13 MGH 21 BWH 71

-2

KPM

BAA-2146 nasey

Figure 3

Click here to download Figure Figure 3.pptx

(a)

# of Genomes

200

IS26

180

ISAba1

160

ISAba13

140

ISAba17

120

ISAba27 ISAba125

100 80 60 40 20 0

(b)

0

10

20

30

350

40 IS1F IS26

300

IS903B

# of Genomes

250

ISKpn1 ISKpn18

200

ISKpn26

150 100 50 0 0

5

10 15 # of Shared Sites per Genome

20


Supplementary Material Files

Click here to download Supplementary Material Files Supplemental Files.pdf

Supplemental Figure 1. Example of a complex transposition event

ISAba1

1634916

1625106

ISM ISM

1625621 S-Ill S-PB ISM

S-Ill S-PB ISM

ISAba1

1625621

M3Q_1540

M3Q_1541

crp

osmC

TYTH-1 1628380

1626800 S-PB ISM

crp

osmC

1626800

S-Ill S-PB ISM

ISAba1

1628380 S-Ill S-PB S-PB

ORAB01

ISAba1

S-PB

crp

osmC

2036206


S-Ill S-PB

ISAba1

2036214

SupplementalSFigureS2a 800 700

ISAba1

600 500 400 300 200 100

35 30

ISAba12

25 20 15 10 5

300

NumberSofSGenomes

250

ISAba13

200 150 100 50

300

ISAba17

250 200 150 100 50

350

ISAba26

300 250 200 150 100 50

160 140

ISAba125

120 100 80 60 40 20

0.5

1.0

1.5

2.0

2.5

3.0

A. baumannii TYTH-1S(Mbp) Downloaded from www.microbiologyresearch.org by IP: 172.245.146.248 On: Mon, 16 May 2016 03:09:54

3.5

4.0

SupplementaltFiguret2b 450

ISKpn1

400 350 300 250 200 150 100 50 400 350

ISKpn18

300 250 200 150 100

NumbertoftGenomes

50

400 350

ISKpn26

300 250 200 150 100 50

350

ISKpn28

300 250 200 150 100 50

400 350

IS903B

300 250 200 150 100 50

1.0

2.0

3.0

4.0

K. pneumoniaetNJST258_1t(Mbp)


5.0

Supplemental Table 1. Comparison of ISseeker and ISmapper Genome ORAB01 AB5075‐UW D36 IOMTU 433 UHKPC05 KPR9028 KPNIH10 NJST258_1

IS element Read lengthMb in Reads ISAba1 100 2754 ISAba1 250 7750 ISAba1 100 1028 ISAba1 300 348 ISKpn26 100 1187 ISKpn26 200 513 ISKpn26 200 439 ISKpn26 100 2829

ORAB01

ISAba1

AB5075‐UW

ISAba1

D36

BLAST in Finished Genome Y Y Y Y Y Y N Y Y Y Y Y Y Y Y Y Y Y Y Y

ISseeker ‐ Finished Genome Y Y Y Y Y Y N Y Y Y Y Y Y Y Y Y Y Y Y Y

ISseeker‐ Illumina Assembly Y Y Y Y Y Y N Y Y Y Y Y Y Y Y Y Y Y Y Y

Non‐ ISMapper ‐ Present in standard orien‐ Reads reference structure tation Novel N R Novel N R Novel N R Known Y R Novel N F Novel N R Novel? N F Known Y R Novel N F Novel N R None N Y F/R Known Y R Known Y F Novel N R Novel N F Novel N R Known Y R Novel N F Known Y R Novel N R

Y Y

Y Y

Y Y

Novel Novel

N N

R F

1794598 3535712

Y Y Y Y Y Y Y Y Y Y Y



Novel Novel Novel? Novel Novel Novel Novel Novel Novel Novel Novel

N N N N N N N N N N N

R R F/R R F F F R R F R

226592 469972 482182 642099 766046 791110 1759986 1785142 1938677 2310208 2766531

Reference Location 34724 67290 110761 494100 796459 958283 1625106 1625620 1628371 1788677 2036214 2247274 2291073 2384827 2595616 2600380 2675906 2837695 3007459 3543523

ISAba1


Y

IOMTU 433

UHKPC05

KPR9028

KPNIH10

NJST258_1

Partial Y Y Y Y

N Y Y Y Y

N Y Y Y Y

Novel? Known Novel Novel Novel

N Y N N N

F R F F R

2811080 3007457 3102099 3283542 3318119

Y Y Y Y

Y Y Y Y

Y Y Y Y

None None None None

N N N N

F R F R

482460 1447695 3479865 3723168

Y Y Y Y Y Y Y

Y Y Y Y Y Y Y

Y Y Y Y Y Y Y

Novel Known None None Novel None None

N Y N N N Y Y

R F R R F R R

775416 2102340 2312687 2530495 4597790 4861007 5085043




Novel Novel None Novel* Known None None Novel None Known None

N N N Y Y N N N N Y Y

R R R F F R F R F R R

909160 1004339 1227769 1898102 2102333 2530495 2752178 3335424 4218305 4861020 5085043

Y Y Y Y Y Y Y Y Y

Y Y Y Y Y Y Y Y Y

Y Y Y Y Y Y Y Y Y

Novel* Novel* Novel* None None None None None None

Y

F R F F F R R R R

126251 787890 1004411 1825488 2102327 2312684 2537299 4861007 5085043

Y Y Y Y Y Y Y

Y Y Y Y Y Y Y

Y Y Y Y Y Y Y

Known Known Known Known Known Known Known

Y Y Y Y Y Y Y

F F R F R R R

921273 2102345 2537321 2751005 4690392 4861029 5085064

ISAba1 Y

ISKpn26

Y Y Y Y

ISKpn26

Y

Y Y Y Y

ISKpn26

Y

Y Y Y

Y

ISKpn26

Total "Y"

74

74

56 Total Known + Novel


TP FP FN Sensitivity

ISseeker ISmapper 74 54 0 2 0 20 1 0.730

20 None 2 False positive 54 True positive


Supplemental Table 2. Results from ISseeker analysis using alternative run parameters A. baumannii Reference

TYTH-1 TYTH-1 TYTH-1 AB5075-UW TYTH-1 TYTH-1 K. pneumoniae Reference

NJST258-1 NJST258-1 NJST258-1 NJST258-1 NJST258-1

Parameters

Results

is_pct flank_pct flank_len Location bundle 97 97 100 1 95 95 100 1 97 97 500 1 97 97 100 1 97 97 100 5 97 97 100 10

#distinct sites 1363 1409 1209 1206 1070 1038

#total

#genomes %sites %total

14526 14765 12606 13441 14526 14526

823 825 819 820 823 823

Parameters

103% 89% 88% 79% 76%

102% 87% 93% 100% 100%

Results

is_pct flank_pct flank_len Location bundle 97 97 100 1 95 95 100 1 97 97 500 1 97 97 100 5 97 97 100 10

#distinct sites 687 713 599 649 622

#total

#genomes %sites %total

4294 4373 3940 4294 4294

494 497 480 494 494


104% 87%

102% 92%

7 2

6

1

8

7 5 1

2 2

1

2

2

2

2

8

1

2

4

1 1

1 1 1 1

1 12 11 2

1

1 9 2

1

6

1

2

1

1 4 5 2 3 4 6 2 4 1 3 4 4 2 5 5 4 3

19 23 28 20 29 22 19 1

1

1 18 15

1 11 14 5 1

1 1 16 9 1 8 3 13 1 11 5

1

21 26 13 21 23 20 20 23

1

1 4 1

1

3 3

4 1

6

15 6

1

1 10 2

4 1

22

7 10 2 1 5 1

4 1

4 27 6 19

1 2

1

10 21 31 16 2 2 13 10

8

2 2 2

2 4 2

5 6

1

17 1 15 2 10

10 6 7 7

5 3 23 4 22 3 22 1 4 26 4

5

1 17

4

1

1 4 1 1 1

1

1

2

7 12

2 5

1 19 10 10

10 2

2 1

6

1

6

1

22

1 1

2 1 2 1

3 2 3 2 6 1 7 2 1 23 1 2 6

3 7 3 23 5 23

13 11

3 20

3 1

9 7

4 11 1 2 1 1

1

1

3

1

9

2 1 3 1

1

5 26 4 3

3 2

5 5 4

9

1

3 10

5

1

2 1 2

1 1

4

3

21 6 4

1

1 4

1 3

4 18

4 26

1

1 1

14

1

1 45

8

2

1 3 21 3 20

3 3

1 1 3 1

2 24

1

2 1 15

3

1 1

2 16

5


13 12 2

18

2

12

10 2

ISAba825

ISAba125

ISAba32

ISAba36

ISAba31

4

ISAba33

ISAba3

ISAba29

ISAba28

1

1

1 5

1 1

2

1

1 2

1

1

3 2 8 3 14

ISAba27

1

ISAba26

1 1

1

ISAba25

ISAba21

ISAba20

ISAba19

ISAba18

ISAba17

ISAba16

ISAba24

1 1 2 1 2 2 18

ISAba22

1 2

ISAba14

ISAba13

ISAba12

ISAba11

ISAba10

ISAba9

ISAba8

ISAba7

ISAba6

1 2

1 5 18 4 2 2 6 21 1 1

ISAba5

ISAba2

ISAba1

Accession* Total 3 JSAO00000000 22 JQNV00000000 30 JQSD00000000 13 JEZJ00000000 13 AUWL00000000 67 JFEP00000000 11 JFER00000000 4 AEOZ00000000 3 AEOY00000000 4 AEPA00000000 28 JEXC00000000 17 AHAG00000000 7 AHAH00000000 10 AHAI00000000 27 AHAJ00000000 12 JMNY00000000 CP010397.1,CP0104 18 31 JMHM00000000 74 JFDK00000000 83 JFFF00000000 39 JFWS00000000 15 JFXN00000000 JMNX01 61 45 JEYQ00000000 49 JMNI00000000 54 JMOD00000000 13 JEWV00000000 50 JMOC00000000 59 JFEN00000000 19 JEZI00000000 36 JEZK00000000 44 JEZL00000000 25 JEYG00000000 29 JEXW00000000 30 AOSP00000000 18 JEXP00000000 30 ALPW00000000 38 JEZV00000000 34 JFYK00000000 11 JMNZ00000000 48 JFFE00000000 144 JEYC00000000 13 JFYG00000000 99 JMNK00000000 51 JFYJ00000000 JEWB00000000 3 13 JFDB00000000 58 JMNP00000000 52 JEZH00000000 3 JEYE00000000 38 JFXU00000000 JEWS00000000 55 JFYE00000000 15 JFXR00000000 14 JFEM00000000 24 JFXV00000000 9 JEWW00000000 7 JEYI00000000 7 JMOG00000000 9 JEYJ00000000 4 JEYN00000000 4 JEWX00000000 72 JFEO00000000 JFXS00000000 JEWY00000000 54 JFXW00000000 1 JFEQ00000000 42 JFCZ00000000 40 JFXO00000000 JEWZ00000000 36 JEVW00000000 1 JEYD00000000 84 JEXA00000000 JFYF00000000

IS26

Genome 1 269 341 1297 1605 2887 3390 3909 3990 4190 4749 4857 5075 5256 5711 6112 6200 6935 7893 10519 11126 14216 15827 17534 18689 21072 21871 23037 23671 29280 34001 34654 42887 43926 48055 50595 53264 58452 70136 72431 73736 83444 88816 96512 98826 118362 121738 135867 136706 144107 145660 146457 213697 214216 216872 225588 230853 232184 233846 259052 268680 272263 273929 277047 299505 303002 318814 323408 339786 342950 348935 397971 400834 426863

IS1396

Supplemental Table 3. IS copies in A. baumannii genomes

457946 458282 466215 466760 470922 478810 479375 480175 496487 532279 532413 541915 554515 562700 564012 573719 607805 625974 628418 647609 653020 655555 694762 722310 723929 724909 730795 737393 742879 754286 755829 756476 766875 781407 809848 825610 826659 831240 836190 846928 855125 869535 883425 907131 916567 923118 940793 942133 942194 947299 951631 959073 972082 981176 983759 984213 987421 993520 1007214 1022959 1031433 1032241 1032359 1035119 1036938 1039621 1040094 1043794 1043903 1045092 1046051 1046674 1051176 1051830 1058283 1062314 1075025 1095464

JFET00000000 JFCY00000000 JFXP00000000 JEXB00000000 JFCX00000000 JFFH00000000 JEZN00000000 JFEU00000000 JMNR00000000 JEYH00000000 JEZO00000000 JFXQ00000000 JEXT00000000 JEZP00000000 JEZQ00000000 JFYA00000000 JFES00000000 JEXD00000000 JFXX00000000 JEXE00000000 JEZU00000000 JFEW00000000 JFEV00000000 JFCV00000000 JFEX00000000 JEXF00000000 JFYB00000000 JFEY00000000 JFYC00000000 JMNU00000000 JFXY00000000 JMOR00000000 JEXX00000000 JEZS00000000 JEXG00000000 JFEZ00000000 JFYD00000000 JEYO00000000 JFFA00000000 JFFD00000000 JMNT00000000 JEXH00000000 JFXZ00000000 JEXS00000000 JMNJ00000000 JFFB00000000 JMNW00000000 JEZX00000000 JFAC00000000 JEZY00000000 JEXI00000000 JEZZ00000000 JFAA00000000 JFYH00000000 JEXO00000000 JEVX00000000 JMNL00000000 JFAB00000000 JFWQ00000000 JFDQ00000000 JEYR00000000 JEYS00000000 MHK01 JEVY00000000 JEYT00000000 JEYU00000000 JEYV00000000 JEYX00000000 JEYY00000000 JFFC00000000 JEYZ00000000 JEZA00000000 JEZB00000000 JEZC00000000 JFWR00000000 JFDR00000000 JEZD00000000 JFDT00000000

34 54 69 2 90 33 27 26 18

10 13 2

38

4 19

5

49 19 50 14 24 16 74 51 36 79 39 17 26 49 41 52

1 17 3 16 5 22

1 17

15 88 57 5 1

2 6 24 4 24

27

4 20

2 59

6 20

2 10 2 3 61 75 26 57 20 53 16 47 6 114 9 24 48 51 18 102 54 19 61 34 23 23 3 54 64 32 49 27 38 43 5 25 47

3 5 25 4 28

3 12 13

5 28

11 1 2 1

28 1 5

8 5

1 10

12

9

24

2 4 2

1 1

17

3

2

1 26

1

2

1 3

1

11 1 1 2 12 14 3 3 14 1 1 1 1 12

3 3 26 21 24 23 2

1

3 1 3 24 3 20 4 23

15 1

4

4 3 2 3

2

10 2 1

1

7 6

1

2 1

3

13

1

8 8 7 8

1

2

5

1 5

13 4

4

1

3

13

1

6

5

8 9

22 1

12 13 1

1 2 1

1

3

1 1

1

1

1 1

7

1 1

5 4 9 6 3 5 3 6 1 2

20 1 26 1

1 2

2 25 5 22 7 6 3 6

26 21 15 25

1

8 1

3 7 4 11

4 4

9

6

8

6

10 1 10 1 13

4

7

4

8

1

30

6

36

7 7

13 8

1 2 4 20 3

8 7

2 4 7 27 7

1 15

2

7

4

1 9 9

1 15 3 1 2 12

1

1 8 1 1

1

1

4

3

3 4 4 4 1 5 2

1 10 13 1 11

1

1 1

1 6

8 6

2 7

1

7

3

1 1

1 6 11

7

6

5

9


3 1 1 1 1 2 1

6

7

1

1

7 2

5 20 3 22

1 3 1 6 13 1 1 2 1 2

1

4 18 3 20 3 20 27 27 19 22 24 18 18

1 7

1

1 1 1 14 19

26 18 14 21 17 21

23 2 13 1

8 1

1

2 16

3

1

13

17

1

2

20

3

1 2

19 1

3

1 14 1 15

8

3 6

1096934 1106579 1117819 1130196 1146103 1159076 1170863 1178044 1179249 1188188 1202252 1207552 1232509 1237202 1237893 1239920 1245249 1245593 1247182 1264765 1264936 1266220 1267820 1271213 1271651 1277411 1281984 1284800 1287985 1289546 1289694 1291820 1293320 1294217 1294222 1294243 1294596 1295259 1295549 1295743 1296252 1297549 1391434 1392509 1396970 1397084 1397513 1406182 1406589 1406750 1412924 1413735 1417041 1419130 1424608 1426993 1428368 1429530 1437282 1440422 1440750 1457504 1461402 1461963 1462234 1465485 1471012 1475718 1475764 1482820 1488685 1494580 1499986 1505311 1525283 1526966 1533268 1539026

JEXM00000000 JEXN00000000 JFWW00000000 JFWX00000000 JMNS00000000 JEWA00000000 JFWT00000000 JFDU00000000 JFXC00000000 JFDV00000000 JEWC00000000 JFEC00000000 JFWY00000000 JFWU00000000 JFEA00000000 JEXZ00000000 JFDY00000000 JFDW00000000 JEZF00000000 JMNG00000000 JFED00000000 JFXA00000000 JEWD00000000 JFDX00000000 JFDZ00000000 JEXL00000000 JFXD00000000 JMOB00000000 JFFG00000000 JEZG00000000 JEWE00000000 JEXK00000000 JFEE00000000 JEWF00000000 JFXF00000000 JFXG00000000 JFCC00000000 JEWG00000000 JFXB00000000 JEWH00000000 JFFU00000000 JEVV00000000 JFXH00000000 JFXJ00000000 JEWI00000000 JEWJ00000000 JFXI00000000 JFXK00000000 JFYI00000000 JEWK00000000 JFEF00000000 JFWZ00000000 JEYP00000000 JEWL00000000 JFXL00000000 JFCU00000000 JFXM00000000 JEWM00000000 JEWN00000000 JEWO00000000 JEXQ00000000 JFEG00000000 JEWP00000000 JEWQ00000000 JEWR00000000 JEWT00000000 JFEH00000000 JEWU00000000 JFEJ00000000 JFEK00000000 JFCT00000000 JFXT00000000 JMOA00000000 JMOL00000000 JEXR00000000 JEXV00000000 JFEI00000000 JMNH00000000

117 46 6 35 96 17 45 21 25 36 51 46 50 26 1 8 8 37 15 47 70 6 24 49 30 2 86 51 88 31 28 1 83 104 1 14 39

1 3 22

39 96 28 14 47 25 94 45 45 32 107

1 6 22

13

3

10 14 67 37 3 113 31 47 11 6 59 116 53 27 50 50 38 75 19 61 3 40 28

1

27 17 9 1

2 5 23 5 25 4 2 26 6 4 3 6 6 9

1 10

1 2 19 1 9 1

15 18 23 21 24 14

9

2

1 1

1

2

6

9

6

3

4

34 6 1 4 1 1 1 12 1

6

16

8

19

7 5

8

4 3

1

11 1 8

20

5 9

4 2 1 3 2 3

1 2 2

4 21 4 24 6 24 5 5 16 4 27 4 22

1 1

2

10 1 11

7

9

1 2

6 8 1

2 2 1 14

1 15 9 13 2

7 26 6 24

16 14 1

1 1 8

3 1 3 2

7

13 17

1

1

12

1

4 27 6 23 6 23 6 5 20

1

7 7 8

2 1

1 1

16

3 6 1 18

20 1

3 1

1 2

1 13 23

6 8

14 28

1 1 1

7

6 23 1 4 24 6 21 2 22 8 17 6 24

2

1

1

1

1

16 13 1 14 10 1 1 14 9 6 2 2 14

4

3

1

15 20

7

19

5 4 7 5 8

23

8

7

27

1 27 3

1

3

2

1

6

2

24

1 4 7 5 1

29

1 3

9

2 1 16

1 25 10 22

3 2

1 6

2

5

3

1

1

1 23

1 28 10 21

3 18

9

3

1 2

15 1

2

13 21

1

3 3

1

6 1

14 15 1

17

7

5

6

1 10

1 1

1

1 7 15 13 1 1 1 9 9

5 33 6 23 4 26 1 10 10 3 5 2 5

1

23 24 20 22

29

1

1

7 2 2 21 1 1 10 15

1

1

6 6 1

18 1 14 1

1 33

3

21

4 20

1 6 8 8

1

11

4

5

1

1 2

4 22

2 1


3 1

1

16 9

3

11

1

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3 20 2 25 3 21

3

1 13

29

1 2 2

2 26

14 1 1 15

8 2 24 1 1 2 1 2 2

12 12 15 3 17 17 1 7 21 18 3

1 1

1 1

1

1 1

1 1

16

2

2 3 4

8

1 2 2 11

1 1

2 5 5 6 5 5 6 6 5 8

3 3

1 1 2 8 7

10

7

1

3 1 8

11 1 11 14

5

1 1

2 2 3 2

8

2

1

19 20 15 18 16 17 19 16 17 16 19 15 9 12 12 15 12 13 10 8 13 13 17 13 10 17 17 16 20

14

9

1 7 1 1 1 1 1 1 1

4 5 4 4 4 4 4 21

1

4 3 11 2 2

1

10

2 4

1

5

5

4

1 1 1 1 1

1 1 1 1 1 1

1 1 1 1

1

3 1

1 1 1

1 1 1 1 1 1 2 6

18 10 13 10 13 12 13 13 17 21

1 1 1 1 1

1

3

4

4 2 2

8 9 9 9 9 8 9 9

1 1 1

1 1 2 1 2 1 1

1 1 1

5

6 3 13 4 12 4 21 5 2 16 2 18 2 16 2 19 2 17 1 19 4 22 4 17

2

7

2

6 18 6 1 3 4 5 5 5 5 6 8

5

14

1 6 3 5 5 5 6 2 7 6 7 5 7 2 7 8 5 6 5

1 2 4

19

5 1

1 1

5

2 9 8

11 1 10 1

32

3 4

1

7

3 8

6

1

1 1 10 15 2 1 1 1

8 8 9 8 8 7 9 9


1 1 1

1 2 1 1

1 1 1 1 1 1 2 2

1

1

3 7

1 1 3 1 1 1 5

4

1 8 1 1 2 1

2 2

24845_3 24845_4 24845_5 24845_6 24845_7 24845_8 24845_9 24860_1 24860_10 24860_2 24860_3 24860_5 24860_6 24860_7 24860_8 24860_9 24975_1 24975_10 24975_4 24975_5 24975_7 24975_9 25253_1 25253_10 25253_3 25253_4 25253_5 25253_6 25253_7 25253_8 25307_1 25307_2 25307_3 25307_4 25307_5 25307_6 25307_8 25442_1 25442_5 25442_7 25442_9 25493_1 25493_10 25493_2 25493_3 25493_4 25493_5 25493_6 25493_8 25493_9 25561_1 25561_10 25561_2 25561_7 25569_1 25569_10 25569_2 25569_3 25569_4 25569_5 25569_6 25569_7 25569_8 25569_9 25681_2 25681_3 25681_5 25681_6 25681_8 25681_9 25691_1 25691_10 25691_2 25691_5 25691_6 25691_7 25691_8 25691_9

JFWL00000000 JFWK00000000 JFWJ00000000 JFWI00000000 JFWH00000000 JFWG00000000 JFWF00000000 JIDG00000000 JFDG00000000 JFDF00000000 JMOO00000000 JMOP00000000 JIDF00000000 JFDD00000000 JFDC00000000 JMOQ00000000 JGAI00000000 JIDE00000000 JGAH00000000 JGAG00000000 JGAF00000000 JGAE00000000 JFWD00000000 JFWE00000000 JFWC00000000 JFWB00000000 JFWA00000000 JFVZ00000000 JFVY00000000 JFVX00000000 JFWO00000000 JFVW00000000 JFVV00000000 JFVU00000000 JFVT00000000 JFVS00000000 JFVR00000000 JMHI00000000 JICS00000000 JICR00000000 JICQ00000000 JHDD00000000 JHDE00000000 JHDC00000000 JHDB00000000 JHDA00000000 JHCZ00000000 JHCY00000000 JHCX00000000 JHCW00000000 JGAD00000000 JGBG00000000 JGAC00000000 JGAB00000000 JHPE00000000 JMNO00000000 JHPD00000000 JHOW00000000 JHPC00000000 JHOR00000000 JHOT00000000 JHOV00000000 JICU00000000 JICT00000000 JGCI00000000 JGCH00000000 JGCG00000000 JGCF00000000 JGCE00000000 JGCD00000000 JGAW00000000 JGAS00000000 JGAV00000000 JMOV00000000 JGAU00000000 JMPH00000000 JMOW01 JGAT00000000

47 44 43 42 44 43 50 36 40 37 34 36 36 36 38 35 39 36 39 37 33 35 36 36 34 36 34 35 37 36 35 33 35 34 36 35 33 50 42 43 50 18 17 18 21 18 18 22 20 19 52 52 56 55 19 20 24 22 23 21 56 21 19 20 57 59 59 60 56 57 51 50 44 48 49 51 54 51

4 4 4 2 4 4 3 2 1 2 2 2 2 2 2 2 1 2 2 1 2 2 2 2 2 2 1 2 2 2 2 1 2 2 2 2 2 5 4 5 5 5 4 5 3 5 5 4 3 5 5 5 5 5 3 4 6 4 6 5 5 6 3 4 5 4 4 5 4 5 6 5 4 2 5 5 6 5

23 21 19 20 20 19 20 17 17 18 15 17 17 16 20 16 18 17 20 16 15 17 18 18 16 18 17 18 16 18 17 14 17 16 18 17 15 23 18 22 23 13 13 13 18 13 13 17 17 14 25 23 25 25 16 16 18 18 17 16 23 15 16 16 22 22 22 24 22 21 22 22 18 23 25 22 25 22

1

2 4

1

1

1

9 9 9 9 9 9 12 9 10 9 9 9 9 9 8 9 10 9 9 11 8 8 8 8 8 8 8 8 8 8 8 9 8 8 8 8 8 8 9 8 8

3

2

9 8 9 9 9 9 9 8 8 8 8 8 8 9 8 8 8 8 8 7 8 8 8 8 8 8 8 7 8 8 8 8 8 8 8 8 8 7 9 7 7

1

2 2 2 2 2 2 2

1

1

1

2

3

4

1 2 1 1

1

8 8 8 8

2 3 5 4

7 7 7 7

4 5 5 5

1 1 1 1

12

3

6

6

1

12 12 12 12 12 12 8 8 8 9 8 2 8 8 8

5 7 7 6 5 5 3 2 3 3

5 6 6 6 6 6 7 7 6 6 7 6 5 7

7 7 7 6 6 7 4 5 4 4 3 3 4 5

1 1 1 1 1 1 1 1 1 1 1 1 1 1

3 4 3


1 1

25750_1 25750_6 25750_7 25750_8 25766_1 25766_10 25766_2 25766_3 25766_4 25766_5 25766_6 25766_7 25766_9 25878_1 25878_2 25878_3 25935_1 25935_10 25935_2 25935_4 25935_5 25935_6 25935_7 25935_8 25935_9 25977_1 25977_10 25977_2 25977_3 25977_4 25977_6 25977_7 25977_8 25977_9 26016_1 26016_10 26016_2 26016_3 26016_4 26016_5 26016_6 26016_7 26016_8 26016_9 263903‐1 263903‐2 42057_2 42057_3 42057_4 42057_5 42057_6 43557_1 44298_1 44298_10 44298_2 44298_3 44298_4 44298_5 44298_6 44298_7 44298_8 44298_9 44327_1 44327_2 44327_4 44327_5 44327_6 44327_7 44327_8 44362_1 44362_10 44362_2 44362_3 44362_4 44362_5 44362_6 44362_7 44362_8

JMOX00000000 JGCC00000000 JGCB00000000 JGCA00000000 JGBF00000000 JGAX00000000 JGBE00000000 JGBD00000000 JGBC00000000 JGBB00000000 JGBA00000000 JGAZ00000000 JGAY00000000 JHCV00000000 JHCU00000000 JHCT00000000 JGAR00000000 JGAJ00000000 JGAQ00000000 JGAP00000000 JGAO00000000 JGAN00000000 JGAM00000000 JGAL00000000 JGAK00000000 JFVP00000000 JFVQ00000000 JFVO00000000 JFVN00000000 JFVM00000000 JFVL00000000 JFVK00000000 JFVJ00000000 JMPF00000000 JHOY00000000 JHOU00000000 JMOY00000000 JMOZ00000000 JHPB00000000 JHOS00000000 JHOX00000000 JMPA00000000 JHOO00000000 JIDC00000000 JMNM00000000 JFDA00000000 JICP00000000 JMPB00000000 JMHJ00000000 JMPC00000000 JICO00000000 JHCS00000000 JIDB00000000 JICV00000000 JIDA00000000 JMHA00000000 JICZ00000000 JMHB00000000 JICY00000000 JICX00000000 JMHC00000000 JICW00000000 JGBZ00000000 JGBY00000000 JGBX00000000 JGBW00000000 JGBH00000000 JGBV00000000 JGBU00000000 JHCQ00000000 JHCR00000000 JHCP00000000 JHCO00000000 JHCN00000000 JHCM00000000 JHCL00000000 JHCK00000000 JHCJ00000000

52 48 52 51 56 56 61 49 61 58 61 60 55 48 45 47 50 54 52 47 49 48 51 45 50 23 27 26 30 25 26 27 26 27 56 56 58 49 53 52 52 61 54 55 23 11 48 24 23 23 23 66 53 54 56 53 54 55 52 50 53 55 70 79 73 74 73 75 75 81 56 79 72 77 78 84 76 50

4 4 5 4 3 5 5 5 5 4 5 5 5 5 5 5 5 5 5 5 4 5 5 5 4

23 23 24 23 22 22 24 21 24 22 24 21 22 22 21 21 22 23 23 22 22 23 23 21 23

1

2 2 2 2 2 2 2 2 2

2 1 1 1 4 5 5 3 3 5 5 5 3 5 5

23 24 26 21 24 23 22 26 21 25

8 8 8 9 14 12 12 12 12 12 12 12 12 12 11 12 8 9 8 8 8 8 8 8 8 1 2 2 3 1 2 1 1 1 14 12 2 14 12 12 12 12 1 13 12 12

4 2 3 3 4 3 6 5 6 5 7 3

3 4 3 2 3 2 3 2 3

6 7 7 7 5 6 6 4 6 6 6 6 5 6 6 6 7 7 7 6 7 5 7 6 7 1 1

1 1 1 3 1 4 1 1

1 4 1

3 3 5 3 5 4 6 6 6 6 5 6 6 4 5 6 3 3 3 4 4 3 4 4 4 4 3 4 4 3 4 4

21 19 16 17 16 25 19 20 22 20 21 21 18 18 19 21 23 26 22 23 28 23 23 26 27 24 23 26 26 30 24 24

1 10

1 14 10 10 10 10 10 10 10 10 10 10 12 12 1 12 14 1 13 13 13 1 15 13 13 13 13 13 13 14 14

1 1 1 3 1 1 1 1 1

6 5 7 6 6 6 6 7 6 6

2 1

1 2 2 2 1 2 2 2 2

1

5 3 4 4 7 7 6 5 7 7 7 7 7 2 1 2 4 5 5 3 4 4 4 2 4 2 2 1 1 2 2

6 5 6 6 6 6 6 6 6

5 6 5 5 6 5 5 5 3

1 2 2 2 1 2 2 2 1

1 1 1 1 1 1 1 1 1

6 5 3 5 5 5 5 6 8 6 2

1 1 1 1 1 3 1 1 1

1

1 6

1

8

11

12 14 13 12 9 14 12 12 1 14 11 12 13 13 12

6 10 10 10 9 10 10 10 10 10 10 5 7 5 5 4 5 6 5 5 5 6 5 5 6 5 5


2

12 14 14 13 12 15 13 14 2 15 12 13 14 15 13

1

1 1 1 1 1 1 2 2 2 1 2 2 1 1 1 1 1 1 1 1 1 1 1 1 1 2 2 2 2 2 2 2 2 2 1 1 1 1 1 1 1 1 1 1 17 2 6 2 2 3 2 3 8 8 8 8 8 8 8 8 9 8 3 3 3 3 2 2 4 4 4 4 3 4 3 4 4 3

44362_9 77 JHCI00000000 44437_3 52 JHCH00000000 44437_4 53 JHCG00000000 44437_5 55 JHCF00000000 44437_7 54 JHCE00000000 44437_8 53 JHCD00000000 44437_9 53 JHCC00000000 44467_1 80 JGBS00000000 44467_10 JGBT00000000 81 44467_2 80 JGBR00000000 44467_3 79 JGBQ00000000 44467_4 80 JGBP00000000 44467_5 75 JGBO00000000 44467_6 78 JGBN00000000 44467_7 77 JGBM00000000 44467_8 76 JGBL00000000 44467_9 82 JGBK00000000 44839_10 JIDD00000000 49 44839_8 49 JMHD00000000 44839_9 53 JMHE00000000 44857_10 JGBJ00000000 50 44857_9 49 JGBI00000000 44895_1 47 JFVH00000000 44895_10 JFVI00000000 49 44895_2 52 JFVG00000000 44895_3 50 JFVF00000000 44895_4 48 JFVE00000000 44895_5 50 JFVD00000000 44895_6 50 JFVC00000000 44895_8 49 JFVB00000000 44895_9 52 JFVA00000000 45002_10 JFUZ00000000 39 45002_3 40 JFUY00000000 40 45002_4 JFUX00000000 45002_5 40 JFUW00000000 45002_6 40 JFUV00000000 45002_7 40 JFUU00000000 45002_8 42 JFUT00000000 45002_9 48 JMPG00000000 45052_1 20 JHOQ00000000 45052_2 20 JMPD00000000 45052_3 20 JHPA00000000 45052_4 20 JICN00000000 45052_5 20 JHOZ00000000 45057_1 38 JMPE00000000 45057_4 49 JHOP00000000 45075_1 21 JMHF00000000 45075_10 JMNV00000000 19 45075_2 20 JMHG00000000 45075_3 19 JMHH00000000 45075_4 24 JMND00000000 45075_5 21 JMHN00000000 45075_6 20 JMHO00000000 45075_8 22 JMNE00000000 45075_9 21 JMNF00000000 43 472237‐1196JEZM00000000 472237‐120 JFCW00000000 25 43 662545‐1347JEZR00000000 20 796380‐1375JMOS00000000 61 796380‐2102JEZT00000000 929679‐2095EZW00000000 58 929679‐598 JMOT01 54 A1 CP010781.1,CP0107 1 A144 9 JQSF00000000 A33405 18 JPXZ00000000 AA‐014 AMGA00000000 AB_1536‐8 AMHA00000000 AB_1582‐8 AMHB00000000 25 AB_1583‐8 AMHC00000000 21 AB_1594‐8 AMHD00000000 29 AB_1595‐8 AMHE00000000 34 AB_1649‐8 AMHF00000000 AB_1650‐8 AMHG00000000 AB_1766_8 AMJO00000000 24 221 AB_2007‐09‐AMHH00000000 20 AB_2007‐16‐AMHI00000000 20 AB_2007‐16‐AMHJ00000000 48 AB_2008‐15‐AMHK00000000

4 6 6 6 6 6 6 4 4 4 3 4 4 4 4 3 4 5 5 5 6 5 4 6 6 5 2 6 6 6 6 1 3 3 3 3 3 3 3 5 5 5 5 4 1 5 5 4 4 4 5 5 5 5 5 3 6 5

24 18 19 21 20 19 17 26 27 25 28 27 26 24 25 25 26 19 18 23 19 19 18 18 20 20 20 18 18 19 19 20 20 20 20 20 20 22 24 15 15 15 15 16 20 17 16 15 16 15 16 16 15 17 16 19 16 18

13 10 10 10 10 10 11 13 13 13 12 13 1 13 13 13 13 13 10 10 9 9 9 9 9 9 9 10 9 10 10 9 5 5 5 5 5 5 5 5

13

13 13 14 13 13 10 13 12 12 14

5 10 10 10 10 10 10 6 6 5 6 5 5 6 6 6 5 9 10 10 10 10 10 10 10 10 10 10 10 8 10

1

3

9

10

5

14

4 8 8 8 8 8 9 4 4 4 4 4 4 4 4 4 4 6 6 6 6 6 6 6 7 6 6 7 6 6 8 11 10 10 10 10 10 10 10

14 14 15 13 14 12 14 13 13 16

1 1 1 1 1 1 1 1

1 1 1 1 1 1 1 1

1

1

10 8

3

10

9

7

12

2 5 21 6 21 9 23 1 3 1 8

5

1 1 12 12 1 5

7 4

2 8 8

6 6 8

6

5

1

2

3 15 3 2 3 16 4 26

1

3

1 1

3

26 31 28

7

7

1

6 6

1

1

3

1 19 19 5 5 5 5 5


1 1

1

4 1

1

3 18 5 19 20 5 5 4 18

2 3 1 2 1 1 3

6 10 1

2

1

1 3 12

3

3

19 5 5

7

2

5

1

1

1

43 AB_2008‐15‐AMHL00000000 AB_2008‐15‐AMHM00000000 19 17 AB_2008‐15‐AMHN00000000 43 AB_2008‐15‐AMHO00000000 21 AB_2008‐15‐AMHP00000000 29 AB_2008‐23‐AMHQ00000000 25 AB_2008‐23‐AMHR00000000 28 AB_2009‐04‐AMHS00000000 22 AB_2009‐04‐AMHT00000000 AB_515‐8 AMHU00000000 35 AB_908‐12 AMHV00000000 23 AB_908‐13 AMHW00000000 15 34 AB_908‐14‐7AMHX00000000 33 AB_909‐01‐7AMHY00000000 17 AB_909‐02‐7AMHZ00000000 AB_909‐05 AMIA00000000 27 AB_TG19617AMID00000000 AB_TG2018 AMIE00000000 28 AB_TG2022 AMIF00000000 24 AB_TG2023 AMIG00000000 24 AB_TG2026 AMIH01 23 AB_TG2028 AMII00000000 3 AB_TG2030 AMIJ00000000 4 AB_TG2031 AMIK00000000 4 AB_TG2032 AMIL00000000 4 AB_TG2631 AMIM00000000 22 23 AB_TG27323AMIN00000000 31 AB_TG27327AMIO00000000 25 AB_TG27331AMIP00000000 23 AB_TG27335AMIQ00000000 9 AB_TG27339AMIR00000000 21 AB_TG27343AMIS00000000 AB_TG5064 AMIU00000000 22 AB0057 CP001182,CP00118312 AB030 CP009257.1 73 AB031 CP009256.1 10 Ab04‐mff CP012006.1 27 AB07 CP006963.1,CP0069 10 AB10I9 50 ATHY00000000 Ab11111 28 AKAQ00000000 AB18G7 57 ATHZ00000000 AB1H8 15 ANNC00000000 AB210 26 AEOX00000000 AB307‐0294 CP001172 Ab33333 AKAS00000000 AB405E4 36 ANND00000000 Ab44444 40 AKAT00000000 AB4A3 16 AOLU00000000 AB5075‐UW CP008706.1 5 AB5711 AHAJ01 27 AB900 ABXK00000000 AbH12O‐A2 CP009534.1 13 AB‐HKU3‐08 ATHY01 50 AB‐HKU3‐10 THZ01 57 ABIsac_ColiRCAKB00000000 ABIsac_ColiS CAKA00000000 ABNIH1 AFSZ00000000 1 ABNIH11 15 APBA00000000 ABNIH13 46 APBB00000000 ABNIH14 45 APBC00000000 ABNIH15 43 APBD00000000 ABNIH16 54 APBE00000000 ABNIH17 44 APBF00000000 ABNIH18 30 APBG00000000 ABNIH19 16 APBH00000000 ABNIH2 2 AFTA00000000 ABNIH20 46 APBI00000000 ABNIH22 53 APBJ00000000 ABNIH23 49 APBK00000000 ABNIH24 44 APBL00000000 ABNIH25 2 APBM00000000 ABNIH26 3 AOGD00000000 ABNIH3 2 AFTB00000000 ABNIH4 39 AFTC00000000 ABNIH5 31 APAW00000000 ABNIH6 15 APAX00000000 ABNIH7 17 APAY00000000 29 ABUH304350JWSF00000000

6 2 3 6 2 3 4 3 2 5 3

15 17

20

1

1

15 19 16 19 15 16 26 16 9 5 13 3 19 10 17

20

1

14 1

3 2 2 1 1 2 1 2 2 3 5 3 2

10 1 4 1 1 1 2

1 1 2

4

1

1

1 1 1 2 1

4

20 18 12 11 19

10

1

1 1 1 1 1

1 1 1 1 1

3

6

3

2 2

1

52 1 4

2 1

1

1

1 16

1 1

1 1

3 17

1 1

1

8 12 1 2

1

1 7 4 3 1 3 1

1 1

8

13 5 14

1

1

11

8

4

6 1 9

1 3

1 1

1

1 16 3 17

1 1

3 3

3 13 14 4 2

1

2 1 1 1 1 1 6

1 1 1 1 1

1 1 1 1 1

1 1 1 1

1 1 1 1 1

1

1

25 23 23 28 25

5 2

1 1 1 1 1

27 32 28 25

1 1 10 4

1

1 1

1 1 2 4 1 4 4

1

1 1 1

2

3

13 15 14 13 1

1

1 1 1 1 1

1 21 15 2 3 14

3 3 4 3

1

1 2

10

2

1 6 5 9 5 13 2 3 1 1 12 3 15 4 15 3 14 4 19 3 13 2 17 2 12

6 2 1 2

1 2 1 1

3

15

15 21 21 20 1 1 2 1 17 18 23 19 18

3 2 2 19 3 6 2 18 8 5 4 5 9 3 18 5 13 2 12 7 17

1

7 5

1


1

1

2 2 3

29 ABUH304352JWSH00000000 29 ABUH319118JWRW00000000 40 ABUH404571JWSJ00000000 ABUH42783 JWRU00000000 28 21 ABUH463346JWSE00000000 ABUH4837 JWRT00000000 23 23 ABUH497144JWRY00000000 29 ABUH504227JWRZ00000000 28 ABUH504238JWSA00000000 28 ABUH518307JWSC00000000 21 ABUH524354JWSI00000000 ABUH60486 JWRV00000000 26 ABUH80286 JWSB00000000 27 AC29 CP007535.2 8 ACICU CP000863,CP00086512 ANC_4097 APRF00000000 14 ATCC_17978 CP000521,CP0005236 4 ATCC_17978 CP012004.1 ATCC_19606 ACQB00000000 AYE NC_010410.1 BIDMC_56 JMUH00000000 38 BIDMC_57 JMUI00000000 28 BJ1 19 JPLF00000000 BJ2 21 JPLG00000000 BJ3 15 JPLH00000000 BJ4 14 JPLI00000000 BJ5 18 JPLJ00000000 BJ6 26 JPLK00000000 BJ7 26 JPLL00000000 BJ8 21 JPLM00000000 BJAB07104 CP003846.1,CP0039 22 BJAB0715 CP003847.1,CP0038 22 BJAB0868 CP003849.1,CP0038 18 BZICU‐2 21 ALOH00000000 Canada_BC1 AMSZ00000000 18 18 Canada_BC‐5AFDN00000000 CI77 24 AVOC00000000 CI78 AVOE00000000 CI79 30 AVOD00000000 CI86 29 AVOB00000000 CIP_70 2 CR17 CCCV000000000 CS01 CCCU000000000 D1279779 AERZ00000000 15 D36 CP012952.1 20 DU202 39 AVGF00000000 EGD‐HP18 AVST00000000 4 GTC_03324 BBNH01 GTC_03329 BBNJ01 IOMTU_433 AP014649.1,AP014650.1 IS‐116 4 AMGF00000000 IS‐123 14 ALII00000000 IS‐143 16 AMGE00000000 IS‐235 7 AMEI00000000 IS‐251 7 AMEJ00000000 IS‐58 7 AMGH00000000 JCM_6841 BALA00000000 LAC‐4 64 JICJ00000000 LY1 2 JDSV00000000 LY2 1 JDSW00000000 LY3 27 JDSX00000000 LY4 24 JDSY00000000 LY5 24 JDSZ00000000 LY6 JDTA01 35 LY7 JDTB01 36 LY8 DTC01 34 LY9 26 JDTD00000000 MAR002 JRHB00000000 40 MDR_MMC4AZNQ00000000 MDR‐TJ NC_017847.1 19 MDR‐ZJ06 CP001937,CP00193823 MRSN_3405 JNOU00000000 2 MRSN_57 JABT00000000 2 MRY09‐0642BASA00000000 MRY10‐0558BASB00000000 MRY12‐0277BASC00000000 MSP4‐16 2 AODW00000000 Naval‐113 AMZU00000000 25

5 3 3 4 4 5 2 5 5 4 1 5 4 2 1 3

18 21 21 18 13 13 15 18 17 18 17 17 18 1

3

7

1 1

1 1

1 1 1 1 1 1 1 1 1 1 1

1 1 3 2 1 1 1

1 1 1 1 1 1 1 1 1 1 2

3 2 1 3 1

5

2 1 2

2 3 3 3 1 2

1

2

1 1

2

4 2 2 1

3 21 6 21 9 4 13 5 14 3 11 11 18 18 14 15 13 5 12 1 1 12 1 12 3 19

1

1

2 1

1

8 1

1 1

4

4

2

4

1 9 1 1

1

1 1 1 1

8 1

1 1

4

1 1 1 1

4 6 6 5 4

2 2

1 1

1 1

2 1 1 1 1 1

1

1 1

2

1

5

1 2

2

3

1 4 4

2

2

1

3 1 1 1

1

5 5

8 8

1

2

1

1

12 12

2 2

2 4 13 5 13

1 1

1 1

15 1 15 3 14

1

3 1

21 1

2 5

6 4 1 1 2 2 2

1

2 10

2 2 2 11 1

18 18 18 20 20 20 19

7

6 6 6

1

11

1 1 1 1 1 1 1

1

2

1

1 1 1

1 1 1

2 2 2

6 1 1 2 1 1 1 1 1 2

10

6 2

1 1

1 3 4 4

1

1

4 14 4 12 5 11 1

1

10

19

5 4 4 6 6 5 4

3

6 8 6

12 1 1 1

1 2

1 1

1 1 1

1 1 1

1 1 1

2 4 19

1


1

1

Naval‐13 16 2 3 AMDR00000000 Naval‐17 24 3 17 AFDO00000000 Naval‐18 12 2 7 AFDA00000000 Naval‐2 36 3 15 AMSX00000000 Naval‐21 26 4 21 AMSY00000000 Naval‐57 3 AMFP00000000 Naval‐72 AMFI00000000 Naval‐78 33 2 17 AMFZ00000000 Naval‐81 15 2 2 AFDB00000000 Naval‐82 85 1 AMSW00000000 Naval‐83 32 2 14 AMFK00000000 NCGM_237 AP013357.1 3 19 NIPH_1362 APOR00000000 7 1 3 NIPH_146 APOU00000000 NIPH_1669 APOQ00000000 7 2 NIPH_1734 APOX00000000 8 1 NIPH_190 APPL00000000 68 NIPH_201 APQV00000000 1 NIPH_2061 APOW00000000 13 8 NIPH_24 7 4 3 APOF00000000 NIPH_290 APRD00000000 12 2 1 NIPH_329 APQY00000000 NIPH_335 APQX00000000 21 1 7 1 NIPH_410 ATGJ00000000 33 NIPH_527 APQW00000000 4 3 1 NIPH_528 APRB00000000 4 3 1 NIPH_60 11 APPM00000000 NIPH_601 APQZ00000000 9 NIPH_615 APOV00000000 33 1 NIPH_67 APRA00000000 NIPH_70 15 1 APRC00000000 NIPH_80 59 APRE00000000 OIFC0162 AMFH00000000 10 2 1 OIFC021 6 AMFR00000000 OIFC032 6 AFCZ00000000 OIFC035 1 AMTB00000000 OIFC047 3 AMFW00000000 OIFC065 1 1 AMFV00000000 OIFC074 19 1 17 AMDE00000000 OIFC087 18 AMFS00000000 OIFC098 12 3 AMDF00000000 OIFC099 13 1 AMFT00000000 OIFC109 14 2 2 ALAL00000000 OIFC110 AMFL00000000 OIFC111 1 AMFY00000000 OIFC137 14 2 2 AFDK00000000 OIFC143 8 2 3 AFDL00000000 OIFC180 22 2 16 AMDQ00000000 OIFC189 25 6 17 AFDM00000000 OIFC338 27 4 21 AMFX00000000 JZCP00000000 30 6 21 ORAB01 ORAB02 JZCO00000000 29 4 22 ORAB03 JZCN00000000 28 3 22 ORAB08 JZCM00000000 29 4 22 ORAB09 JZCL00000000 30 4 23 ORAB10 JZCK00000000 58 1 25 ORAB13 JZCJ00000000 31 5 23 ORAB14 JZCI00000000 29 3 23 ORAB15 JZCH00000000 29 4 23 ORAB16 JZCG00000000 30 5 22 ORAB17 JZCF00000000 30 5 22 ORAB18 JZCE00000000 31 5 23 ORAB19 JZCD00000000 31 5 23 ORAB21 LRME00000000 31 4 25 ORAB23 LRMF00000000 28 4 22 ORAB6B LRMJ00000000 34 4 28 ORABASHR LRMG00000000 30 1 6 ORABMAYT LRMI00000000 37 7 28 ORABRICT LRMH00000000 31 1 5 ORABSC LRMK00000000 30 4 23 Pulsotype_27CBXD00000000 R1B 11 2 2 JICK00000000 SDF CU468230,CU468231,CU468232,CU468233 T122 2 1 JRTX00000000 T173 13 5 3 JRTY00000000 T185 12 1 JRQU00000000 T188 9 1 JRQV00000000

2

11 1 2

1 1

9

9 1

1 1

1 7

1

6 1

1 1

15 17 8

1

2 11

8 1

1

7 1

2

10 17 5 26 3

1

1

1 17 20

3 1

5 5 13

1 8

4 1 2

1

1

1

1

1

2

2 1

7

1 1

4 2

4

6 10

1

1 4 2

1 6

5 3 13

1 2

8 18

1 1

2 4 23

1

3

1

1

1

1

2

1 1

3

16

4 3

3

1 1 4 4

3

8

1 1

1 2

3 3 2

1

1 5 6 4

1 6

9

10 1 10 1

1 1

1 1

1 1 1

1

1

10 11

1 1 1 1 1 1

1 1 1 1 1

1 1 1 1 1

1 1 1 1 1 1 1 1 1 1

1 1

1 1 1 1 1 1 1 1 1 1

1

1

1 1

1

5

6

1 1 1 1

23 25 1 2

3

1 1

1

179 180

1 1

3 3


1 1 1

1 1

2 3

1 1

1 1 1

1 1

T214 1 JRTZ00000000 T229 7 JRQW00000000 T25 18 JPKX00000000 T258 7 JRQX00000000 T271 10 JRQY00000000 T7 11 JRQT00000000 T87 22 JRQS00000000 TCDC‐AB071 CP002522,CP0025233 TG00314 ASER00000000 4 TG02011 23 ASES00000000 TG02017 42 ASET00000000 TG07725 14 ASEU00000000 TG15233 58 ASEV00000000 TG15234 65 ASEW00000000 TG15236 54 ASEX00000000 TG15237 48 ASEY00000000 TG15238 54 ASEZ00000000 TG15239 55 ASFA00000000 TG15240 36 ASFB00000000 TG15241 50 ASFC00000000 TG15242 38 ASFD00000000 TG19582 2 AMIV00000000 TG2012 24 ASFE00000000 TG2013 30 ASFF00000000 TG2014 25 ASFG00000000 TG20277 16 ASFH00000000 TG20546 38 ASFI00000000 TG22110 24 ASFJ00000000 TG22112 24 ASFK00000000 TG22142 27 ASFL00000000 TG22146 41 ASFM00000000 TG22148 24 ASFN00000000 TG22150 41 ASFO00000000 TG22190 21 ASFP00000000 TG22192 25 ASFQ00000000 TG22194 21 ASFR00000000 TG22196 20 ASFS00000000 TG22198 4 ASFT00000000 TG22202 30 ASFU00000000 TG22204 ASFV00000000 TG22212 30 ASFW00000000 TG22214 23 ASFX00000000 TG22332 8 ASFY00000000 TG22336 7 ASFZ00000000 TG27295 9 ASGA00000000 TG27299 37 ASGB00000000 TG27307 34 ASGC00000000 TG27311 31 ASGD00000000 TG27315 24 ASGE00000000 TG27319 25 ASGF00000000 TG27371 25 ASGG00000000 TG27379 31 ASGH00000000 TG27383 28 ASGI00000000 TG27387 3 ASGJ00000000 TG27391 166 ASGK00000000 TG27395 34 ASGL00000000 TG27399 30 ASGM00000000 TG27407 32 ASGN00000000 TG27411 31 ASGO00000000 TYTH‐1 11 CP003856.1 TYTH‐2 21 AGSQ00000000 TYTH‐3 20 AGSR00000000 TYTH‐4 24 AGSS00000000 TYTH‐5 22 AGST00000000 TYTH‐6 17 AGSU00000000 TYTH‐7 4 AGSV00000000 UH0207 23 AYGS00000000 UH0707 77 AYGR00000000 76 UH0807 AYGQ00000000 UH10007 23 AYGO00000000 UH1007 25 AYGP00000000 UH10107 28 AYGN00000000 UH106_429 JWVB00000000 84 UH106_440 JWUZ00000000 86 UH106_447 JWUW00000000 32 UH10707 46 AYOI00000000 UH11608 30 AYGL00000000 UH12208 46 AYGK00000000

1 5

5 2 2

5 1 1 2 4

1

2

3 1 1

2 2

2 1

5

1

1 1

1 1 1

5

1 1

1 1 2 1 1 1 1

4 1 1 1 2 1

4 1 1 3 5 3 4 4 4 5 7 4 2 5 5 3 5 1 2 2 3 5 2 2 1 4 5

9 4 12 16 20 18 15 15 16 16 19 21 1 21 21 17 10 18 22 15 7 8 11 8 15 23 10 10

13 1

1

3 4 6 2 1 2 5

1

6 3

6

5

9

4

4 1 1

12

7

5

1

33

1 1 1

28 25 29 29

11 2 1 1 1

1 1 5 6 3

3

1

6 8 7

4 4

1 1 1 2 6 1 1 1

1

5

4

4

1 1

1 1 1 12

1

1 11

1

15 16

6 1

1 1 1 1

1 1

1

1 17

3 4 3

1 1

1 1 1 1

3

1

1

1 1

1

4 2 23 1 3 3 3 1 6 3 4 3 3 2 5 5

22 12 4 3 6 26 18 18 18 19 19 23 20

2 1 5 5 3 4 4 5 5 1

9 19 19 23 23 6 15 14 15 13 13

4 3 3 2 3 5 1 1 3 4 5 4

16 28 29 16 18 18 7 7 22 31 18 5

1 6 2

4

3 1

1 22 24 24

9 16

1 1 2 1 1 1 1 1 1 1 1

6 2

12 13

1 1 1 1 1 1

1

1 1

9

2 2 1

1 1 1 1 1 1 1 1

1

1

1 3 3

20 15 19 14

2 2

2 1 2 1 1 1 1 1

2 1 3

1

3

7

1 1 1 1 1 1 1 1 3 1 2 2

1

1 1 1

1 1

2

2 3

3 13 10

1

2 2 1 1 1

9

2 2 3 2 2

75 77 1

6

11 1

3

1

2 37


UH12308 UH12408 UH126_102 UH126_106 UH126_137 UH12808 UH129_404 UH129_408 UH129_409 UH129_415 UH134_167 UH134_168 UH134_192 UH13908 UH14508 UH15208 UH16008 UH16108 UH16208 UH17_151 UH17_182 UH17_202 UH17_465 UH17_52 UH175_677 UH175_679 UH184_295 UH184_309 UH184_310 UH18608 UH189_348 UH189_349 UH189_355 UH195_560 UH195_568 UH195_573 UH19608 UH19908 UH20108 UH225_433 UH225_472 UH225_492 UH225_493 UH22908 UH2307 UH236_84 UH236_85 UH236_87 UH243_14 UH243_33 UH243_43 UH243_54 UH243_55 UH243_56 UH243_57 UH243_66 UH243_68 UH243_73 UH2707 UH280_81 UH280_92 UH280_93 UH280_99 UH2907 UH293_373 UH293_377 UH293_412 UH299_338 UH299_341 UH299_342 UH315_100 UH315_101 UH315_39 UH315_58 UH326_445 UH326_461 UH326_495 UH348_13

AYGJ00000000 AYGI00000000 JWXL00000000 JWXJ00000000 JWXF00000000 AYGH00000000 JWVJ00000000 JWVI00000000 JWVH00000000 JWVF00000000 JWXA00000000 JWWZ00000000 JWWW00000000 AYGG00000000 AYGF00000000 AYGE00000000 AYGD00000000 AYGC00000000 AYGB00000000 JWXB00000000 JWWY00000000 JWWT00000000 JWUR00000000 JWYK00000000 JWTP00000000 JWTO00000000 JWWE00000000 JWWA00000000 JWVZ00000000 AYGA00000000 JWVU00000000 JWVT00000000 JWVS00000000 JWTX00000000 JWTV00000000 JWTT00000000 AYFZ00000000 AYFY00000000 AYFX00000000 JWVA00000000 JWUO00000000 JWUF00000000 JWUE00000000 AYFV00000000 AYFU00000000 JWXV00000000 JWXU00000000 JWXT00000000 JWYS00000000 JWYP00000000 JWYL00000000 JWYJ00000000 JWYI00000000 JWYH00000000 JWYG00000000 JWYA00000000 JWXZ00000000 JWXY00000000 AYFT00000000 JWXW00000000 JWXS00000000 JWXR00000000 JWXO03000000 AYFS00000000 JWVP00000000 JWVO00000000 JWVG00000000 JWVX00000000 JWVW00000000 JWVV00000000 JWXN00000000 JWXM00000000 JWYN00000000 JWYF00000000 JWUX00000000 JWUS00000000 JWUD00000000 JWYT00000000

26 26 17 21 24 28 29 27 29 30 26 26 29 25 31 32 32 28 47 27 26 29 61 1 123 56 19 27 27 27 96 84 99 29 28 32 47 31 28 29 29 28 30 40 25 24 25 22 29 29 30 27 30 28 30 27 31 30 77 29 32 31 29 76 22 28 26 29 31 31 26 27 76 79 56 61 65 78

3 3 3 3 5 2 5 5 6 6 4 3 5 4 5 5 5 2 4 2 2 3 3 4 1 7 8 5 3 3 3 7 6 7 4 5 5 3 5 5 6 5 3 6 6 5 4 4 5 5 4 4 4 4 5 4 3 4 6 4 4 3 2 4 3 4 2 2 4 4 3 4 3 3 4 4

20 20 12 16 13 21 18 17 18 19 16 17 18 18 20 21 21 21 5 18 18 19 29 1 28 20 16 14 13 17 30 28 28 17 15 15 5 19 19 20 20 19 20 5 17 16 17 15 19 19 19 18 21 18 20 18 20 20 29 19 20 21 20 29 17 18 18 18 17 18 18 17 29 29 28 27 28 28

1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1

1

3 1 1 1 1 1 1 1 1 1 1 1

1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1

1 1

1 3 2 2 2 2 3 3 3 3 3 3 3 38

1 1 1 3

12

6

5

46 27 11 11

2

2

2

4

4

4

6 1 2 2 1

4 1 4

29 21 31 17 32 22

1

2 2 2

3 1 3

1

2 2 3

1 1 1 1

3 1 3

1

1 1 1 1

2 3 3

1 1 1

3 1 3

1 1

4 3 4 2 1 7 1 1 1

1 1 1 1

38 1 1 1 1 1 1

1

1 2 1 1 1 1

1 1 1 1 1 1

1 1 1 1 1 1 1 1 1 1 1 1 1 1

1 1 1 1 1 1 1 1 1 1

1 1 1 1 1 1 1 1 1 1 1 1 1 1

1 1 1 1

1 1 1 1

1 1 1 1

4 1

1 1 1 1

30

3

20 14

3

1 1

3 4 2 2 3 3

19 14

1

1 1

2

2

3

2

2

2

1

1 1

1 1

20 14 18 14 11 5 14 7 15 7 20 14

2 3 2 2 2 2

2 3 2 2 2 2


2 1 1 1 1 1 1 1 1

1 1 1 1 1 1

1 1 1 1 1 1 1 1

1 1 1

2 3 2 2 2 2

3 3 3 1 2 3 3 2 3 3 2 3 3 3 2 2 1 3 2 3 2 3 2 3 1 1 1 2 2 3

UH348_25 UH348_27 UH355_545 UH355_569 UH367_548 UH367_558 UH367_565 UH370_269 UH370_270 UH370_301 UH3807 UH381_467 UH381_482 UH384_444 UH384_450 UH392_536 UH392_659 UH392_684 UH41_486 UH41_487 UH41_488 UH41_489 UH41_490 UH41_491 UH410_103 UH410_108 UH410_128 UH410_96 UH430_459 UH430_466 UH455_38 UH455_6 UH455_61 UH455_62 UH475_197 UH475_239 UH484_95 UH487_41 UH487_63 UH487_64 UH487_78 UH507_247 UH507_263 UH507_300 UH5107 UH514_287 UH514_288 UH5207 UH5307 UH532_386 UH532_387 UH532_392 UH535_418 UH535_419 UH535_423 UH5707 UH588_656 UH588_663 UH6107 UH6207 UH6507 UH66_241 UH66_268 UH66_276 UH6907 UH7007 UH71_277 UH71_278 UH71_279 UH71_296 UH7607 UH7707 UH7807 UH7907 UH81_364 UH81_366 UH81_389 UH81_452

JWYR00000000 JWYQ00000000 JWUB00000000 JWTU00000000 JWTZ00000000 JWTY00000000 JWTW00000000 JWWM00000000 JWYA00000000 JWWB00000000 AYFR00000000 JWUP00000000 JWUM00000000 JWUY00000000 JWUV00000000 JWUC00000000 JWTR00000000 JWTN00000000 JWUL00000000 JWUK00000000 JWUJ00000000 JWUI00000000 JWUH00000000 JWUG00000000 JWXK00000000 JWXI00000000 JWXH00000000 JWXP00000000 JWUT00000000 JWUT00000000 JWYO00000000 JWUT00000000 JWYE00000000 JWYD00000000 JWUT00000000 JWUT00000000 JWUT00000000 JWUT00000000 JWUT00000000 JWUT00000000 JWXX00000000 JWUT00000000 JWUT00000000 JWUT00000000 AYFQ00000000 JWUT00000000 JWUT00000000 JWUT00000000 JWUT00000000 JWUT00000000 JWUT00000000 JWUT00000000 JWUT00000000 JWUT00000000 JWVC00000000 AYFN00000000 JWTS00000000 JWTQ00000000 AYFM00000000 AYFL00000000 AYFK00000000 JWWQ00000000 JWWN00000000 JWWK00000000 AYFJ00000000 AYFI00000000 JWWJ00000000 JWWI00000000 JWWH00000000 JWWD00000000 AYFH00000000 AYFG00000000 AYFF00000000 AYFE00000000 JWVR00000000 JWVQ00000000 JWVL00000000 JWUU00000000

26 76 100 102 46 25 45 65 27 60 21 72 36 24 27 10 19 64 61 60 68 62 63 68 29 27 28 24 63 69 25 26 27 27 30 32 27 30 29 31 29 30 30 31 3 5 27

4 3 3 3 10 1 9 3 4 3 4 3 7 1 1

18 29 34 34 24 18 24 32 18 30 14 26 17 18 19 3 7 21 27 27 29 28 29 27 20 18 21 17 27 29 16 16 17 16 20 21 18 20 20 20 19 19 19 18

30 35 34 34 28 29 98 32 49 63 28 25

5 6 6 6 8 9 1 4 4 5 4 4

19 22 21 22 14 14 7 22 21 23 18 16

28 28 30 48 34 28 27 26 29 50 86 29 59 27 27 31 26

5 5 5 4 4 5 6 4 4 3 3 4 1 1 4 6 4

16 16 18 5 15 17 16 17 18 6 29 21 6 21 18 19 16

3 3 3 4 4 4 3 4 2 2 2 2 3 4 4 5 4 4 6 6 4 4 4 5 6 5 5 6 2 1 1 4 16

1 3 5 2

19 14 27 15 35 21

3

12

1

13

3 1

2 5 2

7

2

8

1

20 12 3 1

2 1

2

1

2 5 2

2 5 2 1 1 1

1

1

1

1

1

1

1

1

1

1

1 1 1

1

1

2

2

1 2 1

1 2 1

4 14 14 13 7 12 6 13 7 13 7 13 7 14 8

3 3 4 3 3 4

2 2 3 2 2 3

2 2 3 2 2 3 1 1 1 1

1 3

16 17

9 8

1 2

1 1 1 1

1 2

2 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1

1

2 2 2

1 1

1 2

2 1 4 6 2 9 7 2 2 2 1 2 2 5 5 3 3 2 2

3 3 1 3 1 1 1 1 1 1 1 1 1 1

1 1 1 1 1 1 1 1 1 1 1 1 1 1

3 2 1 2 2 3 2 3 1 3 3 3

1 3

1 1

2

1 1 2 1 2 2

1

1 1 1 1 1 1

1

1

1 1 1 1 1

1 1

88 1 1 19 1 27 1 1

3 2 1 2 1 1 1 3 3 3 3 2

3 3 2

1 1 1

2 2 3

2 2

1 1 2

1

5 2 2 3 2 2 3

2 1 1 9 5 9 2 2 2

2

39 7

7 1 1 1 1

1

1 1 1 1

1 3 2 2 3

1 1 1 1 41

3

4

22 17

2

2

2 1

1

1

1 1 1

1 1 1 1

1

51 1 1 1 1


2 1 3 2 3 3

UH8107 33 5 22 AYFD00000000 UH8407 25 6 17 AYFC00000000 UH8707 25 6 17 AYFB00000000 UH8807 27 4 18 AYFA00000000 UH8907 26 4 17 AYEZ00000000 UH9007 29 4 19 AYEY00000000 UH9907 34 6 21 AYOH00000000 UMB001 51 5 21 AEPK00000000 UMB002 3 AEPL00000000 UMB003 17 3 AEPM00000000 1 VEB CU459141.1,CU459139.1,CU459 3 21 W6976 AIEG01 19 4 14 W7282 23 7 15 AIEH00000000 WC‐136 23 3 1 AMST00000000 WC‐141 13 3 AMSS00000000 WC‐323 17 1 AMZS00000000 WC‐348 9 2 1 AMZT00000000 WC‐487 34 2 1 AMZR00000000 WC‐692 AMGG00000000 WC‐A‐694 AMTA00000000 15 2 2 WC‐A‐92 101 1 3 2 AMFU00000000 WM99c 4 1 AERY00000000 XH386 CP010779.1 24 6 15 ZW85‐1 1 1 CP006768.1,CP0067 ZWS1122 AMGR00000000 27 4 20 ZWS1219 AMGS00000000 29 5 21 *GenBank records are available at http://www.ncbi.nlm.nih.gov/nuccore/[Accession]

1 1 1 1 1 1 2 9

4

1

1 1 1 1 1 1 1

1 1 1 1

7

3

2 2 3 3 1 3 14

4

1 1 1 6

1

3

1 1 2

1 3

3

1 1

4 5 1

1 1

6

1

1 5

10 2

7

3 1 1

1

10 1 1

1 1

1 1

1 1

1

1 1

1 1

2

8 11

3 19

1 32


27 1

1

2

2 1

3 2

2

3 1 3 2

1 1 1 2 3 3 3 4 1 2

2 2 2 2 2 1 1 3

1

2 1

2 2 2

1 1

3

1

1 2 1 2

5 2 3

1

1 1 2

2

1

2 1 1

5

1

5 5 11 6 5 4

1 2 1

2 1

1

6 7 5

1 1

1 1

1

2 2 1

1

2 1

1

1

1 7 1 11 1 1 1 3

1 1

4 2

2 1

3 1

4 2 3 4

1 3

1 2 7 3 9 2

1

2 1

2

2

3

4

2

1

1 1

6

1 6 2

1 4

4 1

2 2

5

1 4 1 2

2

6 6 3 6 1 6 7 8 3

2 2

2 2

2

1

2

2

2

2

5

2 2

2 2

1 2

2

3 2

4 2

3

5

9

2

2

6 1

3 1

1

2

3

4 2 5

1

2 2 1 2 1 7

2 2

2 3

2

1

3

5

1

10 2 1

1 5 1 1

2 5 1

2 1 2

1 4

2

2

1

4 4 1

5 4

2

5

2 2

10 1 6 5 8

1 1

2

1

1

2

3 1 2

2

2

2

3 2

2

1 11 2 1 11 1 1 1 1 10 2 3 2 1 10 2

2 1

1 1 1 1 14 2 1 11 3 3

3

14

1 2 2

1

2 1

1

2

7

2

1 16

2

1

2 2

2

2 1

3 15

3

2 1

1 1

1 1

1

1

1 1

1

1

1

2

2

2 Downloaded from www.microbiologyresearch.org by IP: 172.245.146.248 On: Mon, 16 May 2016 03:09:54

1 2

1 2

3 5 1

1

1

1 2

4

3 2

1

2

1 1 2

1

1 2

1

1

2 3

2 1 1

3 1

1 1 1

11 2 14 1 4

ISKpn31

ISKpn28

ISKpn26

ISKpn25

ISKpn24

ISKpn21

ISKpn20

ISKpn2

ISKpn19

ISKpn18

ISKpn14

ISKpn8

ISKpn7

ISKpn6

ISKpn1

ISHe3

ISEcp1B

ISEc21

IS903B

IS6100

IS5075

IS5

IS4321R

Total 6 0 9 5 13 11 10 13 16 18 28 14 12 15 2 14 2 28 12 0 0 36 37 25 36 28 37 12 26 22 3 40 7 46 8 0 39 17 14 41 8 32 1 37 12 21 2 13 1 19 1 31 35 12 10 4

IS26

Accession* JQGN01 NC_011283.1 JQSE01 NC_018522.1 NZ_CP006722.1 JDWP01 JSZL01 JGYH01 JDWM01 NZ_CP010361.1 NZ_CP010392.1 JSZK01 JSZJ01 AQOC01 AOGO01 AXUL01 AFQL01 AFXH01 CCEX01 JWGK01 JWGI01 CCEY01 CCFM01 JWFI01 CCFN01 JWFB01 CCFO01 JWDA01 CCFP01 JDWN01 JVZX01 CCFQ01 ARSO01 JVXM01 JVWL01 JVVC01 CCFR01 JVTI01 JVTE01 CCFT01 ARSP01 CCFS01 CCFV01 JMMY01 CCFU01 CCFW01 JVQU01 CCFX01 JVQM01 CCGA01 JXBI01 CCFZ01 CCGB01 JVPK01 JRTV01 CCFY01

IS1F

Genome 325 342 349 1084 1158 4006 4640 5422 7699 32192 34618 101488 101712 12‐3578 700603 909957 1162281 1191100241 100SGR 1010_KPNE 1012_KPNE 101BO 102BO 1035_KPNE 103BO 1041_KPNE 104BO 1098_KPNE 10PV 11227‐1 1183_KPNE 11PV 120_1020 1239_KPNE 1263_KPNE 1294_KPNE 12PV 1331_KPNE 1335_KPNE 13PV 140_1040 14PV 15PV 160_1080 16BO 17PV 187_KPNE 18PV 194_KPNE 19PV 1kgm 20PV 21PV 221_KPNE 223_14 22PV

IS1294

Supplemental Table 4. IS copies in K. pneumoniae genomes

234‐12 23PV 24PV 25BO 26BO 27BO 280_1220 28BO 29BO 303K 30BO 31AVR 32AVR 34AVR 361_1301 36AVR 37AVR 39AVR 40AVR 41AVR 42AVR 436_KPNE 43AVR 440_1540 44AVR 4541‐2 45AVR 45T1‐2A 46AVR 47AVR 48AVR 49BG 500_1420 500_KPNE 501_KPNE 50BG 51BG 52BG 53BG 540_1460 54BG 55BG 56BG 570_KPNE 57BG 58BG 60BG 62BG 63BG 646_1568 648_KPNE 65BO 66BO 67BO 68BO 69BO 70BO 71RE 72RE

NZ_CP011313.1 CCGC01 CCGH01 CCGD01 CCGE01 CCJA01 ARSQ01 CCGG01 CCGF01 AVAN01 CCGK01 CCGI01 CCGJ01 CCGL01 APWF01 CCGM01 CCGN01 CCGP01 CCGO01 CCGQ01 CCGR01 JVHD01 CCGS01 APWG01 CCGY01 JDWO01 CCGT01 CDMU01 CCGV01 CCGU01 CCGW01 CCGX01 NZ_CP011980.1 JVER01 JVEQ01 CCHA01 CCGZ01 CCHC01 CCHB01 APWI01 CCHD01 CCHG01 CCHE01 JVBQ01 CCHF01 CCHI01 CCHH01 CCHJ01 CCHK01 APWJ01 JUYR01 CCHM01 CCHL01 CCHN01 CCHO01 CCHQ01 CCHP01 CCHS01 CCHU01

11 36 32 10 8 8 5 16 36 16 41 41 11 2 6 12 16 18 23 13 40 4 43 9 34 22 5 0 21 13 34 4 24 4 4 34 14 14 8 6 39 13 35 25 41 41 15 10 12 5 28 18 18 4 22 8 24 35 39

1 2 3

4 3

2 2

2

1

1

2 2 3 3 2

3 4 4 2 3 1 2 2 2

3

3

2 3 4 7 5 2

2 5 1 4 4 4 2 4 1 3 3

2 4 6

2 3 1

1

1

1

1

1

3

1

3

2

1

1

3

1

2 2 2 3 2

2 2 2 1 2 2 1 2 1

2 2 1

2

5 6

2 1 2 3

2 1 1

6 6 7 2

1 1 1

2 3 1

2 3

1 1

2 2 2 4

3 1 3 5 5

3

2

2 1 3

1 3 2

1

2

2 1 1 1 2 1 1

1 2

1

2

1 1

2 3 1

10 1 2

3

2

3

2 1 1

3 4

2

2

1

2 2

2 2

2

2

1 1

2 3

1 12 2 1 2 1 9 3 1 11 2

2

6

2 2

2 2 1

1

1 1

1 1 1 1 2

2

1

3

4 1 11

2

3

1 14

3

3

1 11 1

3 1

6

2

1

2

2

9

1

13

1

12 1 1 1

2

1

1

6 1

3

1

2

2

2

3 1 1

1 3

2

1 2 2

2 2

2

2

1

3

2 2

2 2

2

2

2 2

2 2


2 10

3 1

6 1 2 2 3 3

1 2

9 2 1 1 2 9 3 1 13 2 1 1

2

3 2

1 1

3 5 7 4 5 4 5 6 6

2 3

1

3 4

1 1 1

1 1

5

2

6 7 5 7 6 6 4 3

1

1

1

6

6 4 6 3 3 6

3 1 3 2 3 3 1 3

2

3 2 12 2 9 2

3 3

5 7

1 2 2 3 1 3 4 1 1 1

2

6 5 5

2 1 3 3

2 2

3

2 1 1 2 2 5

3

1 2 2

2

3 1 3 1 2 3

1

4 5 6 10 8 2

1 1 4

1 2 1

1

3

1

2 1 1

2

1 1 1

3 3

2

3

1 2

1 2 7 9

1 1 2 1

1

731_KPNE 733_KPNE 73RE 741_KPNE 743_KPNE 74RE 75RE 76RE 77RE 780_KPNE 78RE 79RE 813_KPNE 81RE 82RE 833_KPNE 834_KPNE 835_KPNE 836_KPNE 837_KPNE 83RE 845_KPNE 84RE 85RE 863_KPNE 865_KPNE 86SGR 87SGR 887_KPNE 88SGR 89SGR 90SGR 912_KPNE 913_KPNE 91SGR 92SGR 930_KPNE 93SGR 94SGR 95SGR 96SGR 97SGR 98_KPNE 98SGR 99SGR 9PV ATCC_11296 ATCC_13883 ATCC_13884 ATCC_25955 ATCC_BAA‐1705 ATCC_BAA‐2146 B1 B199 B5055 B86 BAMC_07‐18 BIDMC_1 BIDMC_10

JUVI01 JUVG01 CCHT01 JUUX01 JUUV01 CCHR01 CCHW01 CCHX01 CCHV01 JUTF01 CCHY01 CCHZ01 JURV01 CCIA01 CCIC01 JURI01 JURH01 JURG01 JURF01 JURE01 CCID01 JUQV01 CCIB01 CCIE01 JUQD01 JUQB01 CCIF01 CCIH01 JUPH01 CCIG01 CCII01 CCIJ01 JUOG01 JUOE01 CCJB01 CCIK01 JUND01 CCJC01 CCIL01 CCIM01 CCIN01 CCJD01 JULE01 CCIO01 CCIQ01 CCIP01 CDJH01 JSZI01 CDOT01 AQQH01 AOGQ01 NZ_CP006659.1 JSWX01 LJCB01 AQCG01 LJCD01 JRQE01 JCNK01 JNVG01

3 40 38 2 2 38 40 6 7 1 2 8 0 4 22 1 1 1 1 1 8 1 8 8 9 20 38 44 7 38 41 42 1 1 12 10 1 9 15 9 4 34 4 8 14 23 11 7 1 24 23 13 0 12 6 4 3 33 34

4

3 4 2

1 4 1 1 2 5

2 10

2 1

3 2

2 1

2 2

1 4 6

6 6 2 7

1

1

2

2

1

1 3

2 2

2 2

1 1

3 3

12 1 10 1 1 13 1 11 1

5 2

2 2 1

1 2 5

1 1 4

1 4

3

3

2

2

2 4

1

1

1 1 1 1 1 1

2

1

1 1 2

1 1 1 2 2

4 7

2 3

2 3 3

4 5 5

2 2 3

1

2

1

2 12 2 2 4 2 2 2

2 1 6 5 3

1 1 1 1

1 6 6 3 6 6 5

2 2

1 2

2 1 1

2 2 2

2 2 2

1 1 1

1 3 4

1 12 2 1 12 2

3 3 3

1 11 2 1 12 2 1 12 3 1 1

3 2

2

2

1 1

1

1

2 1

5 1

1 2 3 1

4 2 1 3

2 2 4 7 2

2 1 4

3 3

1 3 2

3

4

1 1

2 3

2 2

2 4 1 1

4

9 2 4 1 6

3 1

2 1

1 8 1 4

2

2

2 9

2

1 1

1 1

3 1

1

1

4

6 1 2

2 5 2

2

2

2 2

2 1

4

9 3 2

1

1 1

2 2

2

6 6

1 2

1

5 3 1

4

2

2

1 3 1 1

2

1

1

2 2

2 2


2

2 3

1

10 1 8 1

BIDMC_11 BIDMC_12A BIDMC_12B BIDMC_12C BIDMC_13 BIDMC_14 BIDMC_16 BIDMC_18A BIDMC_18B BIDMC_18C BIDMC_18D BIDMC_21 BIDMC_22 BIDMC_23 BIDMC_24 BIDMC_25 BIDMC_2A BIDMC_31 BIDMC_32 BIDMC_33B BIDMC_34 BIDMC_35 BIDMC_36 BIDMC_4 BIDMC_40 BIDMC_41 BIDMC_42a BIDMC_42b BIDMC_45 BIDMC_46a BIDMC_46b BIDMC_47 BIDMC_48 BIDMC_5 BIDMC_51 BIDMC_52 BIDMC_53 BIDMC_54 BIDMC_55 BIDMC_60 BIDMC_61 BIDMC_68 BIDMC_69 BIDMC_7A BIDMC_7B BIDMC85 BIDMC86 BIDMC88 BIDMC89 BIDMC90 BIDMC91 BIDMC95 BIDMC96 BJ1‐GA blaNDM‐1 BWH_15 BWH_2 BWH_22 BWH_28

JCNF01 JCNE01 JCND01 AXLG01 JCNC01 JCNB01 AXLF01 JCNA01 JMVX01 AXLE01 JCMZ01 AYIB01 AYIA01 AYHZ01 AYHY01 AYHX01 JCNJ01 JAPW01 JCMY01 JNVK01 JCMX01 JCMW01 AYHW01 JCNI01 AYHS01 AYHR01 JCMV01 JCMU01 JCMM01 JCMT01 JCMS01 JCMR01 JCMQ01 JCNH01 JCMP01 JCMO01 JCMN01 JMVY01 JMVZ01 JMWA01 JMWB01 JMWC01 JMWD01 JAPO01 JCNG01 LFAY01 LFAZ01 LFBA01 LFBB01 LFBC01 LFBD01 LFBE01 LFBF01 CBTU01 NZ_CP009114.1 JCNP01 JCNQ01 JCNO01 AYIS01

16 44 47 46 35 32 53 43 39 43 18 14 14 5 15 18 33 12 50 20 42 27 3 30 31 17 35 36 45 21 4 12 9 36 13 3 22 46 7 39 0 41 7 31 30 7 8 5 33 17 10 9 15 1 14 20 12 34 10

2 4 4 5 2 7

2 2 2 2 2 2 2 2 2 2 2 2 2

4 6 2 7 4 7 2 3 2 2 8 7 4 4 5 1

2 2 2

2 2 2 2 2 2 2 1 2 1 3 1 3 3 2 1 3 3 3

1

3 1 5

2 1 2 3 8

2 2 2 2

5

3 6 4 3

6

2 14 1 2 1 10 1 11 2 2 5 2 3

3

3

2

15

1 2

2 2 2 2

1 3 4

4 2 1 6 5 2 1 1

2 1 3

8

1

2 2 1

2 2 5 1

2

1

1 2

1 1 1 2

3 3

1 4 4 5

1 1 2

2

2

2 4 4

1

2

1

2 1 2 2 1 1

1

2 1

5 1 2

3 6 1 1 6 6 6 1 4 4 2 6 9 2 1 6 2 6

2 1

1

2

1 1 2

6

1 1

2

3 4 2 2

1

2 1

1

1

2 2

2

1

3

3

2 2 2

9 1 13 2 17 8

1 2

7 8 1 1 10 1 9 8 19 3 1 12 1

1 2 2 3

1

1 2

2

1 7 1

2 1

1 1 1

2

2

2

2

1

3

2

2

1

3

6 6 6 7

2 2

1

1 12 1 10 1 1 11 2

2

7

2

2 2

1 14

3 3

2 1

2

2 2 1

10 10

1 1

1

1

1 1

3 1 1

1 2

2 2 2 1 1 1 2 2 2 1 1

1 2

1 1 2 2 2

2 8 9 8 10 11 11 17 14 15 1 11 9

2 1

8

2 2 1

2 2 2

2

1 1

2 1 2 2 2 3 3 3 3

1

2 4

1 1

2 2 3 2 2 2

2 2 6 2 2 6 2 2 6 2 2 6 2 2 5 2 2 6 2 2 6 2 2 6 2 2 6 2 2 1 1 7 1 9 15 6 2 2 6 6 2 2 2 2 6 2 2

6 7 3 6 8

1 2

2

2

2


2 1

1 2

2 1

3 3 1 1 1

2 2 1

4 1

1

10

2

BWH_30 BWH_36 BWH_41 BWH_45 BWH_46 BWH_47 BWH_48 BWH53 BWH58 BWH62 CAV1193 CAV1344 CAV1392 CAV1596 CCBH13327 CDPE01 CDPH3020 CDPH3707 CDPH3823 CDPH5262 CG43 CH1034 CH4 CHS_02 CHS_03 CHS_05 CHS_06 CHS_07 CHS_08 CHS_09 CHS_11 CHS_12 CHS_13 CHS_14 CHS_16 CHS_17 CHS_18 CHS_19 CHS_20 CHS_21 CHS_22 CHS_23 CHS_24 CHS_25 CHS_26 CHS_27 CHS_28 CHS_29 CHS_30 CHS_31 CHS_32 CHS_33 CHS_34 CHS_35 CHS_36 CHS_37 CHS_38 CHS_39 CHS_40

AYIQ01 JCNN01 JCNM01 JMWE01 JMWF01 JMWG01 JMWH01 LEZU01 LEZV01 LEZW01 CP013322.1 NZ_CP011624.1 NZ_CP011578.1 NZ_CP011647.1 JSER01 CDPE01 LAFV01 LAFX01 LAFW01 LAFU01 NC_022566.1 CXPD01 JSXA01 JMWI01 JMWJ01 JMWK01 JMWL01 JMWM01 JJNH01 JMWN01 JMWO01 JMWP01 JMWQ01 JMWR01 JJNG01 JMWS01 JMWT01 JMWU01 JMWV01 JJNF01 JMWW01 JMWX01 JMWY01 JMWZ01 JMXA01 JMXB01 JMXC01 JMXD01 JMXE01 JMXF01 JMXG01 JMXH01 JMXI01 JMXJ01 JMXK01 JMXL01 JMXM01 JMXN01 JMXO01

15 48 35 36 3 36 10 29 14 7 16 18 19 30 15 24 10 10 8 10 3 8 0 42 47 46 41 41 32 42 30 46 42 37 40 31 34 32 23 18 42 43 17 36 39 41 35 45 39 36 37 43 36 40 50 45 39 45 38

2 18 2 2 2 2 2

3 2 1 3

4 1 1

4 3

2 2 2 3

1 1 1

2 1 3 1 3 3 3

1

1

1

3 1

2 6

2 4 3 4 3 4

2 1 3

2 1 2

3

2 2 2 3

2 3 3 4 1 2 2 2 2 2 3 3 2 2 3 2 2 2 2 2

6 8 7 5 1 5 6 8 6 4 3 4 5 4

3 4 3 3 3

1

4 6 6

1

3 2 4 3 2 4 1 2 3 2

4 2 2 1 2

2

2 2 2 2 4 1 3 2 1 2 2 2 2 2

1 3

1 2

2 2 2 3 3 2

2 3 1 1 2 3 1 2 2 2 1 4 2 2 2

4 2 4 4 4 3 4 3 4 4 4 7 2 3 4 3 5 4 2 1

1 5 6 7 1 1 5 8 7 8 8 5 6 4

1

3 3 2 2 3 4 1 3 2

1

5

2

2

2 1

2 2 2

10 15 1 11 1 2 14 1 1 9 2

4

5 7 3 3 4 6

2 2

2 2

3 1 2 2

2

2

4 4 4 3 5 4 4 4 3 2 4 5 2 2 4 4

3 2 2 2 2 1 6 6 6 6 6 6 5 6 6 3 6 6 4 5 6 6 3 2 6 6 4 6 6 6 6 6 4 6 6 6 6 6 6 6 6 6 5

8 2 9 2 3 15

4 4 3

2

2 2 3 2 2 2 1 2

2

2

2

1 2 2

10 6 6 6

1 1 1 1

4 1 1

1 1 1 1

2

2 2 2 2 2 1 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2

2 2 2 2 2 2 2 2 2 2 2 2 2 2 2

4 4 4 3 3 2 3 4 4 3 3 3 3 4 3 2

2 2 2 2 2 1 2 2 2 2 2 2 2 2 2 2

2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2

4 4 5 3 4 4 6 3 4 2 3 4 4 3 4 4 4 4 4

2 2


2 2 2 2 2 2 2 2 2 2 2 2 2 2 2

8 10 11 9 11 13 7

1 2 1 1 2 1 3 1 11 3 8 2 7 1 7 1 7 1 5 1 1 1 6 1 2 2 9 2 7 3 2 8 3 9 2 8 3 2 9 2 10 3 13 2 8 2 11 1 3 8 1 9 3 7 3 9 2 9 3 10 3

CHS_41 CHS_42 CHS_43 CHS_44 CHS_45 CHS_46 CHS_47 CHS_48 CHS_49 CHS_50 CHS_51 CHS_52 CHS_53 CHS_54 CHS_55 CHS_56 CHS_57 CHS_58 CHS_59 CHS_60 CHS_61 CHS_62 CHS_63 CHS_64 CHS_65 CHS_66 CHS_67 CHS_70 CHS_71 CHS_72 CHS_73 CHS_74 CHS_75 CHS_76 CHS_80 CHS100 CHS101 CHS102 CHS103 CHS104 CHS105 CHS106 CHS107 CHS108 CHS109 CHS110 CHS111 CHS112 CHS113 CHS114 CHS115 CHS116 CHS117 CHS118 CHS119 CHS120 CHS121 CHS122 CHS123

JMXP01 JJNE01 JMXQ01 JMXR01 JMXS01 JMXT01 JJND01 JMXU01 JMXV01 JMXW01 JMXX01 JMXY01 JMXZ01 JMYA01 JMYB01 JMYC01 JMYD01 JMYE01 JMYF01 JJNC01 JMYG01 JMYH01 JMYI01 JMYJ01 JMYK01 JMYL01 JMYM01 JMYN01 JMYO01 JMYP01 JMYQ01 JMYR01 JMYS01 JMYT01 JMYU01 LEVL01 LEVM01 LEVN01 LGKA01 LEVO01 LEVP01 LEVQ01 LEVR01 LGJZ01 LEVS01 LEVT01 LEVU01 LEVV01 LEVW01 LEVX01 LEVY01 LEVZ01 LEWA01 LEWB01 LGJY01 LGJX01 LEWC01 LEWD01 LEWE01

42 40 13 40 33 45 42 14 32 38 48 48 46 47 59 46 48 42 41 32 36 37 37 39 47 8 47 44 43 36 47 47 31 30 40 46 47 48 28 44 45 36 12 48 45 43 47 9 49 55 50 43 42 50 52 45 18 45 39

2 4 1 2 3 3 2 2 2 2 2 14 2 2 2 2 2

5 2 1

1 1

6 6 3 1 3 6 7 7 6 7 5 6 7 6

2 1

1 1 2 1 1 1 1

3 4 2 2 2 2

5 6 7 3 7 7

1

2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 3 2

4 7 8 3

6 7 7 3 4 2 5 7 4 5 4 7 9 8 4 4 7 8 5 2 7 1

1

1

2 2 1 3 3 4 3 1 2 4 3 4 3 4 3 3 3 3 2 2 2 2 2 3 1 7 3 2 2 3 2 1 4 3 3 5 4 2 2 2 4 3 4 4 2 3 2 2 3 2 3 5 4 4 2 4 2 7

2 1 2 2 2 2 1 2 1 2 2 2 2 4 2 2 2 2 2 1 2 2 2 1 2 2 1 2 3 2 2 3 1 3 2 4 4 4 2 2 2 1 2 2 2 2 5 2 5 4 4 1 4 4 2 2 4 1

4 7 1 4 4 5 6 1 3 4 6 4 5 4 2 6 6 1 4 4 4 4 4 1 4 1 4 4 4 4 4 4 6 4 4 2 2 2 4 4 4 4

6 4 3 6 6 6 4 3 6 6 5 7 6 6 6 6 6 6 6 5 6 6 6 6 6

2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2

2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2

4 3

2 1

9 9

2 2 2 1

9

3 3 4 3 2 3 1 4 4 4 6 2 3 4 3 4 4

2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2

2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2

3 4 4 4 4 3 4 3 3 5 4 4 4 4 5 2

4 4 4 4

6 6 6 6 6 6 6 6 6 6 6 6 2 6 6 6 1 6 6 5 6

2 2 2 2

2 2 2 2

4 3 4 4

2 2 2 2

4 4 4 4 4 4 4 4 1 4 3

6 6 6 6 5 6 6 6 4 6 5

2 2 2 2 2 2 2 2

2 2 2 2 2 2 2 2

4 3 4 5 4 4 4 4

2 2

2 2

3 3

2 2

1 5 3 3 4

3 1 8 2 10 1

1 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2

7 8 11 11 9 9 12 8 8 8 1 8 8 8 9 8 8 10

3 1 1 2 3 3 3 2 3 3 2 1 1 2 1 3 3

9 11 13 7 10 12

1 1 3 1 3 1 2 2 1 3 3 3 1 3 3 2

1

1

1

2 2 2 2 2 2 2 2 2 2 2 2 2 3 2 2

13 9 8 10 5 11 11 9

1 2 2 3 2

2 2 2 2 2 2 2 2

13 9 11 10 1 10 15 11 9 11 9 12 11

2 2

12 9

1 1

3 3 3 3 1 3 2 3

1


CHS124 CHS125 CHS126 CHS127 CHS128 CHS129 CHS130 CHS131 CHS132 CHS133 CHS134 CHS135 CHS136 CHS137 CHS138 CHS139 CHS140 CHS141 CHS142 CHS144 CHS145 CHS146 CHS147 CHS148 CHS149 CHS150 CHS151 CHS152 CHS154 CHS155 CHS156 CHS157 CHS158 CHS159 CHS160 CHS161 CHS162 CHS163 CHS164 CHS165 CHS166 CHS167 CHS168 CHS169 CHS170 CHS171 CHS172 CHS173 CHS174 CHS175 CHS176 CHS177 CHS178 CHS179 CHS181 CHS182 CHS183 CHS184 CHS185

LGJW01 LEWF01 LEWG01 LEWH01 LEWI01 LEWJ01 LGJV01 LEWK01 LEWL01 LEWM01 LEWN01 LEWO01 LGJU01 LEWP01 LEWQ01 LEWR01 LEWS01 LEWT01 LEWU01 LEWV01 LEWW01 LEWX01 LEWY01 LEWZ01 LEXA01 LEXB01 LEXC01 LEXD01 LEXE01 LEXF01 LEXG01 LEXH01 LEXI01 LEXJ01 LEXK01 LEXL01 LEXM01 LEXN01 LEXO01 LEXP01 LEXQ01 LEXR01 LEXS01 LEXT01 LEXU01 LGJT01 LEXV01 LEXW01 LEXX01 LGJS01 LEXY01 LEXZ01 LGJR01 LEYA01 LEYB01 LEYC01 LEYD01 LEYE01 LEYF01

46 43 40 38 50 51 42 48 38 48 51 36 11 42 38 44 9 47 50 44 13 6 40 40 43 47 34 50 49 38 25 41 48 3 38 15 10 33 47 41 49 47 43 47 46 42 47 44 1 26 38 49 43 39 51 51 42 50 45

2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 3 2 2

2 2 2 2 2 2 2 2 2

3 6 3 3 8 7 4 6 3 5 8 1 2 2 8 3 6 8 3 1 2 3 4 6 5 3 7 6 2 2 4 7

5 4 3 4 2 5 2 4 3 5 5 5 2 3 3 3

1

4 4 4 4 4 4 4 2 4 4 2 2 2 4

1 5

3 3

1 5 2 4 2

2 1 2 4 4 2 4 4 4 1

5 5 4 3 2 2

4

4 1 5 1 4 2 4 4 1 4 4 4

2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2

2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2

4 4 4 5 4 4 3 3 4 4 3 4

3 2 4

6 6 6 6 6 6 6 6 6 6 6 6 1 5 6 6

2 2 2 2 2 2 2 2 2 2 2 2

11 8 4 8 11 12 9 11 8 11 11 6

1 2 3 3 3 3 2 2 3 1 2 1

3 2 3

2 2 2

2 2 2

4 4 2

2 2

13 9 10 2 11 10 22

3 2 2 2 3 2 2

4 5 3 3

6 5 6 9

2 2 2

4 4 2 4 4 4 1 3 4

3 6 6 6 6 5 4 6 3 5 5

2 2 2 2 2 2 2 2 2 2 2

2 2 2 2 2 2 2 2 2 2 2

3 4 3 4 2 4 4 3 4 3 4

2 2 2 2 2 2 2 2 2 2

12 12 9 11 1 12 10 11 5 1 12 11

1 2 1 3 1 3 3 2 2 3 3

2

6

2

2

2

9

3

2 2 2 2 2 2 2 2 2 2 2

9 11 13 8 11 9 12 9 11 10 11

1 3 2 2 2 2 2 3 3 2 1

3 2 2 3 2 2 2 2 2 2

7 11 12 12 12 11 13 11 11 8

4 2 3 1 2 2 3 3 3 3

1

1 4

1

3 3 2 2 2 2 3 2 2 2 1 2 2 3 2 2 2 2 2 2 2 2 2 2

1 4 1 1 6 2 7 6 4 6 7 3 6 3 5 3 6 3 3 8 8 5 6

1

1

1

3 1

1

3 3 4 1 1 4 3 4 2 3 4 3 4 1 2 2 3 2 5 1 2 4 4

1 2

4 4 4 4 2 4 2 4 4

2

3 2

2

1 3 4 4 4 4 3 4 3 1 4 3

2 4 6 6 5 6 6 6 6 6 6 6 1

2 2 2 2 2 2 2 2 2 2 2 2

2 2 2 2 2 2 2 2 2 2 2 2

3 4 4 6 3 3 4 4 4 4 3

4 4 4 4 4 4 4 5 2

3 6 6 5 6 6 6 6 6

2 2 2 2 2 2 2 2 2

2 2 2 2 2 2 2 2 2

2 4 3 3 5 4 4 4 4

1 2 4 2 2 3 4 4 4


CHS186 CHS187 CHS189 CHS191 CHS192 CHS194 CHS195 CHS196 CHS197 CHS198 CHS200 CHS201 CHS202 CHS205 CHS206 CHS207 CHS208 CHS209 CHS210 CHS211 CHS212 CHS213 CHS214 CHS215 CHS216 CHS217 CHS218 CHS219 CHS220 CHS221 CHS223 CHS224 CHS225 CHS226 CHS228 CHS229 CHS230 CHS231 CHS232 CHS234 CHS235 CHS236 CHS237 CHS238 CHS239 CHS240 CHS81 CHS82 CHS83 CHS84 CHS85 CHS86 CHS87 CHS88 CHS89 CHS90 CHS91 CHS92 CHS93

LEYG01 LGJQ01 LEYH01 LEYI01 LEYJ01 LEYK01 LEYL01 LGJP01 LEYM01 LGJO01 LEYO01 LEYP01 LEYQ01 LEYR01 LEYS01 LEYT01 LEYU01 LEYV01 LEYW01 LEYX01 LGJN01 LEYY01 LEYZ01 LEZA01 LEZB01 LEZC01 LEZD01 LEZE01 LEZF01 LEZG01 LEZH01 LEZI01 LEZJ01 LEZK01 LEZL01 LEZM01 LEZN01 LEZO01 LEZP01 LEZQ01 LEZR01 LEZS01 LEZT01 LGJM01 LGJL01 LGJK01 LEUU01 LEUV01 LEUW01 LEUX01 LEUY01 LGKC01 LGKB01 LEUZ01 LEVA01 LEVB01 LEVC01 LEVD01 LEVE01

36 47 39 35 48 24 52 42 40 56 40 12 40 35 17 46 25 51 49 21 46 46 53 43 40 50 41 37 48 38 34 44 46 35 53 22 48 44 48 50 44 44 46 50 44 49 48 51 38 45 40 29 51 54 40 49 33 48 24

2 2 2 2 2 2 2 2

2

1 5 6 4 6

4 5 2 1 3

6 6 2 9 5

5 2 2 5 3

1

3 4 2 7 4 7 6

1 2 3 2 1 2 3 2 3 2 5 2 11 2 5 1 3 4 2 7 2 3 2 3 2 4 4 6 2 7 2 6 2 3 2 2 2 2 2 2 2 2 2 2 2 2 2 2 3 2 2 2 3 2 2 1

8 6 6 6 6 7 5 6 7 3 7 6 8 4 1 4 4 6 8 10 4 7 1 3 7 5

3 2

1 4 2 2 1 4 4 1 4 2 2 2 2

3 5 4 5 4 3 2 2 5 1 3 3 2 2 1 3 2 6 1 5 4 3 7 2 2 2 5 3 2 3 4 3 5 5 1 3 4 3 2 1 1

3 2 4 4 2 2 4 4 4 4 4 1 4 1 4

2 4 4 2 2 2 2 1 4 1 1 4 3 2 3 2 3 4 1 2 4 4 4 4 4 4 3 4 4 4 4 1 2 2 1 4 4 2 3 2 4 1

2 4 4 2 4 4 4 4 4 3 3 3 4 4 3 4 3 4 4 1 4 1 4 4 4 4 4 4 3 4 4 4 4 4 2 1 4 4 4 4 5 4

1

2

2 6 6 3 6 3 7 6 5 6 6 1 6 4 5 6 4 6 6 4 6 6 5 4 2 6 5 1 6 6 2 6 6 6 6 4 6 6 6 6 6 6 6 6 6 6 6 6 4 6 4 4 6 6 6 6 5 6 4

2 2 2 2 2

2 2 2 2 2

2 2 2 2 2 2 2 2 2 2

2 2 2 2 2 2 2 2 2 2

2 2

2 2

2 2 2 2 2 2 2 2 2 2 2 2 2 2 2

2 2 2 2 2 2 2 2 2 2 2 2 2 2 2

2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2

2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2

2

2


4 4 3 3 7 2 4 3 5 4 3

2 2 2 2 2 3 2 2 2 2

3 3

2 2

3

2 4 5 4 4 5 4 4 4 4 4 4 5 3 5 4 4 4 4 3 4 5 4 4 5 2 3 3 3 4 4 4 4 4 2 3 4 4 4 4 3 4 4 4 5

2 2 2 2 2 2 2 2 2 2 2 2 2 2 3 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2

10 10 9 11 11 12 10 10 10 12 9 1 9 12 3 11 4 11 11 4 12 11 13 12 12 11 12 12 11 7 8 7 12 9 11 6 11 8 9 11 11 9 10 11 10 11 10 10 9 12 8 3 11 11 9 11 9 12 4

3 3 1 1 3 2 3 1 2 4 2 2 1 3 1 1 2 1 2 2 3 3 2 2 3 3 3 2 1 3 2 2 2 1 2 3 3 2 1 3 3 2 3 3 3 3 2 1 3 1 3 3 1 2 3 2 1

CHS94 CHS95 CHS96 CHS97 CHS98 CHS99 CICC10011 DMC0526 DMC0799 DMC1097 DMC1316 DSM_2026 DSM_30104 Ecl8 EGD‐HP19‐C FDAARGOS_84 G5‐2 GN8 HE12 HK787 HKUOPLC HS11286 HSL4 hvKP1 IA565 IS33 JCM_1662 JCM_20051 JH1 JHCK1 JS86C16 JT4 Kb140 Kb677 KCTC_2242 KK207_1 KKBO‐1 KKBO‐4 KP‐11 Kp13 KP1‐I KP2‐R KP3‐S KP4‐R KP5‐1 Kp52 KP5‐R KP617 KP‐7 KPB‐1 KPB‐2 KPLM21 KPM_nasey KpMDU1 KpN01 KpN06 KPNIH1 KPNIH10 KPNIH11

LEVF01 LEVG01 LEVH01 LEVI01 LEVJ01 LEVK01 LBCM01 ARPO01 ARRZ01 NZ_CP011976.1 ARSB01 JYBC01 AJJI01 CANH01 AUTW02 JTAX01 AQQI01 JWPY01 LBLV01 NZ_CP006738.1 NZ_CP012300.1 NC_016845.1 APFG01 AOIZ01 JPIQ01 CBWI01 BAKZ01 BBEV01 AFQK01 ANGH02 LDZO01 JAPZ01 AQRD01 AQPG01 NC_017540.1 LJOO01 AVFC01 AVFD01 APWE01 NZ_CP003999.1 AQCJ01 AQCI01 AOSJ01 APMF01 CP008700.1 NZ_FO834906.1 APMG01 CP012753.1 AQQD01 AYOV01 AYOW01 CCVM01 CDNA01 AMWO01 CP012987.1 CP012992.1 NZ_CP008827.1 NZ_CP007727.1 AKAD01

48 47 47 31 45 35 0 12 7 23 3 3 3 7 3 11 23 3 12 10 0 13 0 2 8 26 3 0 4 11 12 13 38 36 16 35 38 43 8 13 7 7 10 6 0 5 7 10 8 39 39 10 23 32 5 6 25 26 43

2 2 2 2 2 2

8 6 7 5 4

3 1

2 4 2 2 3 3 2

4 4 3 2 2 3

4 2 4

1

1

1

6 6 6 3 4 4

4 2

2

2 2 2 2 2 2

2 2 2 2 2 2

2 2

2 2

1

2

4 4 4 3 4 4

1

1

1 11

3

2 1 5

1

1 1

1 3 1

2 1

9 3 10 3 10 3 5 3 14 2 9 2

1

6

1

2 2 2 2 2 2

2 4

1 1 1 1

6

2

2

2 9

2 1

2

2

1

3

6 1

1 1

3

3 1

5

3

2

2

2 4 1

2 2 2 3 1

1 2

1 1 1

1

1

4

5

1

2 5

4 1

1

1 1

1

2 3

3

1

1

1

1 1 2 1 2

4 4 4 3

1 1 2

1 2 9 3 2 3

1 2 2

3 4 3

1

2 1 1

1 1 1 1 1

3

1 2 1

6 2 6 2 10 6 2 5 2 6 2 2 6 2 2 2 2

2 2

1

2 5

2 2 2 2

1 1 1 1

3 2 2

1

1 1 15 9

2 1 6 1 8 2 1 11 2 1 15 2 1 1 1 1 1 1

1 2 2 2 2

1 1 1

5 1 1 3 4

3 3

2 2

2 4

2

2 2 7

3 1

1

2

2

1

2 2 2

1

2 2

2 2 2

1 1

1

2 1

1 3

2 1

1 2 2 3

4 3 8

6 6 3

3 1 1 2 2 2

5 5 4 4 6 6 5

2 2 1

2

2

2

1 2

2

2 2 2


1

2

13 2 13 2 2

1 1

1 1

7

1 2

10 1 11 1 1 14 2

KPNIH12 KPNIH14 KPNIH16 KPNIH17 KPNIH18 KPNIH19 KPNIH2 KPNIH20 KPNIH21 KPNIH22 KPNIH23 KPNIH24 KPNIH27 KPNIH29 KPNIH30 KPNIH31 KPNIH32 KPNIH33 KPNIH4 KPNIH5 KPNIH6 KPNIH7 KPNIH8 KPNIH9 KPPR1 KpQ15 KpQ24 KpQ3 KPR0928 KpVA‐1 KpVA‐10 KpVA‐11 KpVA‐12 KpVA‐13 KpVA‐14 KpVA‐15 KpVA‐16 KpVA‐2 KpVA‐3 KpVA‐4 KpVA‐5 KpVA‐6 KpVA‐7 KpVA‐8 KpVA‐9 LAU‐KP1 LCT‐KP182 LCT‐KP214 LCT‐KP289 LZ MGH_17 MGH_18 MGH_19 MGH_20 MGH_21 MGH_29 MGH_30 MGH_31 MGH_32

AKAE01 AKAF01 AKAG01 AKAH01 AKAI01 AKAJ01 AJZV01 AKAK01 AKAL01 AKAM01 AKAN01 NZ_CP008797.1 NZ_CP007731.1 NZ_CP009863.1 NZ_CP009872.1 NZ_CP009876.1 NZ_CP009775.1 NZ_CP009771.1 AJZW01 AJZX01 AJZY01 AJZZ01 AKAA01 AKAB01 NZ_CP009208.1 AWOM01 AWON01 AMSU01 NZ_CP008831.1 CDFM01 CDFT01 CDFU01 CDFV01 CDFY01 CDFW01 CDFZ01 CDFX01 CDFP01 CDFR01 CDFQ01 CDFO01 CDGA01 CDGB01 CDGC01 CDGD01 AYQE01 ATRN01 AJHE02 ATRO01 AJVY01 AYJN01 AYJM01 AYJL01 AYJK01 AYJJ01 JCNY01 AYJC01 JCNX01 AYJB01

46 44 45 46 45 47 44 45 46 47 47 29 7 10 23 12 24 26 44 44 45 45 43 45 7 5 6 4 25 46 45 45 37 43 43 43 39 34 41 32 47 49 47 44 44 10 7 7 6 33 10 6 0 0 5 29 11 38 3

3 3 2 3 3 3 2 2 2 2 3

7 7 8 8 7 8 6 7 8 8 6 4

3 3 3 3 3 3 3 3 3 3 3 2

1

1

2 2 2 2 2 2

3 2 3 3 3 2 2 2 4 2 3 3 3 2 3 3 2 2 1

2 2

3 2 1 7 7 7 7 8 7

3 3 3 3 3 3

2 2 2

1 1 1

8 5 5 4 4 5 7 6 4 5 3 7 7 6 5 4 4 2 2 2 2

3 4 3 2 3 3 2 2

1 1 1 1

4

1

1 2 1 6

1

2 2 2 2 2 3 2 2 2 2 3 2 2 1 2

6 6 6 6 6 5 6 6 6 6 6 6

1

1

2

2 3 3 3 3 3 2 2 2 2

1

1

1 1 1 2 2 2 3 2 2 2 2 2 2 3 3 3 3 4 2 2

1

6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6

2 2 2 2 2 2 2 2 2 2 2

1 1 1 1 1 1 1 1 1 1 1

2 2 2 2 2 2 2 2 2 2 2 3

1 1 1 1 1 1 1 1 1 1 1

1 2

1

2

2 2 2 2 2 2 2

2 2 2 2 2 2 2

2 2 2 2 2

2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2

2 2 2 1 2 2 2 2 2 2

2 2 2 2 2 2 2 2 2 2 2 2 1

12

1

10 9 14 14 15 15 13 15

2 2 2 2 2 2

14 13 14 13 11 13 14 13 11 11 10 8 15 17 15 15 14

1 3 2 2 2 2 2 3 2 2 2 2 2 2 2 2 2

1

1

1 2

2

15 13 14 14 14 14 15 15 15 16 16 10 1

1

1 1 1 1 1 1

1 1 1 1 1 1 1 1

1 1 1 1 1

3 4 2 2 2 2 2 2

2 2 4 4 4 4 4 2 2 3 2 2 2 2 2 4 4

1 1 1 1 1 1

1 1 1 1 1 1 1 1 1 2 1 1 1 1

1

12

5 10

5

4

1

2 3

3 2 2 2 2 2 2 2

6 6 3 6 6 6 6 6 6 5 6 7 1 1

2 2 2 2 2 2 2 2 2 2 2

3

1 1 3 2

1 6 6 6 3

2

2


3 2

1 7 1 9

2 5

MGH_35 MGH_36 MGH_39 MGH_40 MGH_43 MGH_44 MGH_45 MGH_46 MGH_47 MGH_48 MGH_51 MGH_52 MGH_59 MGH_60 MGH_63 MGH_64 MGH_65 MGH_66 MGH_67 MGH_68 MGH_69 MGH_70 MGH_71 MGH_72 MGH_73 MGH_74 MGH_75 MGH_76 MGH_78578 MGH_79 MGH_80 MGH101 MGH102 MGH111 MGH112 MGH113 MGH114 MGH115 MGH116 MGH117 MGH118 MGH123 MGH124 MGH125 MGH126 MGH81 MGH82 MGH83 MGH84 MGH89 MGH90 MGH91 MGH92 MGH93 MGH94 MGH95 MGH96 MGH97 MGH98

JCNW01 AYIZ01 JCNV01 AYIX01 JCNT01 AYIV01 JCNS01 AYIU01 JCNR01 AYIT01 JMYV01 JMYW01 JMYX01 JMYY01 JJNB01 JMYZ01 JMZA01 JMZB01 JMZC01 JMZD01 JMZE01 JMZF01 JMZG01 JMZH01 JMZI01 JMZJ01 JJNK01 JMZK01 NC_009648.1 JMZL01 JMZM01 LFAK01 LFAL01 LFAM01 LFAN01 LFAO01 LFAP01 LFAQ01 LFAR01 LFAS01 LFAT01 LFAU01 LFAV01 LFAW01 LFAX01 LEZX01 LEZY01 LGJJ01 LEZZ01 LFAA01 LFAB01 LFAC01 LFAD01 LFAE01 LFAF01 LFAG01 LFAH01 LFAI01 LFAJ01

12 11 16 0 19 0 31 10 22 10 37 5 23 7 26 7 15 11 36 0 16 15 29 10 24 8 24 1 10 38 7 10 14 19 3 16 13 15 4 16 11 14 5 34 2 15 7 16 3 12 11 41 0 9 6 37 4 18 5

4 2 1

2

2 2 2

5

2

2 2 2 2 2 1

3 2 3 1 6

3 1

1 1 6 1

2

3 1

2 1

1

1

1

1 3

1

1

8

1

1 1 2

2 3

2

2

2

2

2

2

1

1

1

6

1

2 1

8 3 16

2 1

1 1 6 1 2

2

2

1 1 1 1

6

3

1

1

1

1

1

1

2 2

1 1 10 2 1 5 1 1 2

2

5

5 3 3 2 3 5

2 7 4 8

1 2 1 2

1 1 2

2

2 1

2 1 2

2

6 1 4

2 6 2

2

1 5 2

1

2 1

1

1

3 1 1 10

6 4 5

2

2

2

2

2

2

1 5 8

1

2

6

1 1 1

1

8 3 1

4 1

3

1

1

1 3 1

1

1 2

1

1 1

1 2

3

2 1 3 1 2

3 1

1 2

2

5 6

2

2 2

2

1

1 1

1 1 1 13

2 2

1 1

1 6 1

1

3 1

1 1 1

1

1

1

2 2

2

1

7

3 2

2

3 2 6 2 6

2

1

2 1 2

3 1

2

1 1 1 1 1 1

2 2

2 1

2 1 2 2 2

3

1 1 2

5

3

4 1 2

1

1

1 1 2

5

1 1 1 2

4

2 1 1 2 1

2

2 4

2 1

3 1 1

1

4

3 3

2

2

3 5

1 1 2

1

2

1 5 7 2 1 2 6 2 5 6

1 2 2

1 1 15 1

2

1

2

1 3

1

1

1 4

2

1

1 1

2

2

2 1 3

2

2

4 2

2

2

1

9

2 1

16

3

2 4 1

3

1 5


2

2

MP14 MRSN_1319 MRSN_2404 MRSN_3562 MRSN_3852 MRSN_6902 MRSN6920 MRSN8157 MS6671 NB60 NJST258_1 NJST258_2 NTUH‐K2044 PittNDM01 PMK1 PR04 RYC492 SA1 SB2390 SB3193 SB3432 ST147 ST15_NDM‐1 ST258 ST258_FL ST258‐490 ST258‐K26BO ST258‐K28BO ST‐437 ST485 ST512‐K30BO SY‐A SY‐B SY‐B2 T2‐1‐1 T2‐1‐2 T69 Top52_#1721 UCI_17 UCI_18 UCI_19 UCI_20 UCI_21 UCI_22 UCI_25 UCI_26 UCI_33 UCI_34 UCI_37 UCI_38 UCI_41 UCI_42 UCI_43 UCI_44 UCI_55 UCI_56 UCI_59 UCI_60 UCI_61

ATAK01 14 JSVB01 15 LBIK01 14 LBIE01 11 LBID01 5 LBLU01 36 JPGS01 9 JPGT01 10 LN824133.1 0 AZAP01 24 NZ_CP006923.1 20 NZ_CP006918.1 21 NC_012731.1 5 NZ_CP006798.1 10 NZ_CP008929.1 6 AOPN02 11 APGM01000001.1 9 CBTW01 5 CCBO01 3 CCCQ02 0 NC_021232.1 0 JXBF01 12 CDQG01 21 LGAB01 17 LAKK01 44 ALIS01 16 CANR01 35 CANS01 32 LART01 33 JXCH01 6 CAJM02 22 LIPM01 49 LIPL01 52 LIPK01 50 JAQL01 8 JAQM01 8 CBTV01 2 JNFE01 9 JNVF01 43 JCML01 6 JCMK01 34 JCMJ01 17 JCMI01 28 JCMH01 27 JCMG01 11 JCMF01 8 JCME01 39 JCMD01 20 JCMC01 45 JCMB01 45 JCMA01 33 JCLZ01 7 JCLY01 49 JCLX01 38 JMZN01 40 JMZO01 13 JMZP01 25 JJNJ01 0 JMZQ01 32

2 3 2 1 1 3 3

1 3 5 2 2 5

1

1 2

1 2

1 1 1

6

1

3 2

1 1

1

3

2 4 2 1 1 2

2

1

2 2 2

2 2 2

1 4 5 5

1 1 1 2

2

2

1

2

12 12 11

3

2

3 14 9

14 6

1 2

3 1 2 1 2 3 2 2 4 3 3 2 1 2 5 2 5 3 5 3

2 8 1 4 1 4 3 4 2 3 7 5 8 6 4 1 4 6

1 1 2

1

1 1 2 2 2

2 2 2 1 1 1 3 1 3 1 3 1 2 2 3 1 2 2 2

1 1

1 4 1

4 2 4 1 2

2 2 2 2 1 1

1

2 2 2 3 1

2

2 2 3

2 2 3

2 2 2

1

13

2

3

2 7 10

2 1

2

3 1

2 2

1 2 2

2 2 2 2 1 1

2

3 3

1

3 9 2

1 1

1 1

1

2 2

1

3 2 2 2 3 2 2 1

1

1

2

1 1 3

1 2 6

1

1 1

1 1 1 2 2

2

2 1 2

1 1 2 2 2 2 2

2

1 1

2 2 6 2 2 2 2 3 2 2 3 2 2 5 1 4 2 6 2 2 6 2 2 5 2 2 5 5 1 1 4 2 2 6 7 5 5 1 7 6

2 1 2 2 2 1 2 2 2 1 2

6 6 6 5 6 6 6 7 5

3

3

2

2

2

2

1

3 2

2

2 5 1 1 1 1 1 1 1

2

1

1

1 3 1 1 1

1 1 1

2

7 1 12 1 14 1 14 1 2 2 1 2 1 14 1 1 13 1 1 9 2 10 2

3

2 2 2 2 1

2

2 2

2

1

2 1

2

2

2

2 2 1

2 2 2

2

2

1 1 1

2 2

2

2

2

2

2


3 2 13 1 1 2 2 11 1 2 11 2 1 2 1

1

1

2

9 2 7 3 8 10 8 1 12 15 8 2 1 7 1 1 11

UCI_62 UCI_63 UCI_64 UCI_67 UCI_68 UCI69 UCI70 UCI75 UCI76 UCI81 UCI82 UCI91 UCI92 UCI93 UCI94 UCI95 UCI96 UCICRE_1 UCICRE_10 UCICRE_13 UCICRE_14 UCICRE_2 UCICRE_4 UCICRE_6 UCICRE_7 UCICRE_8 UHKPC_52 UHKPC01 UHKPC02 UHKPC04 UHKPC05 UHKPC06 UHKPC07 UHKPC09 UHKPC17 UHKPC179 UHKPC18 UHKPC22 UHKPC23 UHKPC24 UHKPC26 UHKPC27 UHKPC28 UHKPC29 UHKPC31 UHKPC32 UHKPC33 UHKPC40 UHKPC45 UHKPC47 UHKPC48 UHKPC57 UHKPC59 UHKPC61 UHKPC67 UHKPC69 UHKPC77 UHKPC81 UHKPC96

JMZR01 JMZS01 JJNI01 JMZT01 JMZU01 LGJI01 LFBG01 LFBH01 LFBI01 LFBJ01 LFBK01 LFBL01 LFBM01 LFBN01 LFBO01 LFBP01 LFBQ01 JCNL01 JCOA01 AYIC01 AYIN01 AYIL01 AYIJ01 AYII01 AYIH01 JMSY01 ARVN01 APVP01 ARSK01 APVV01 JNBM01 ARSJ01 NZ_CP011985.1 APVO01 ARSG01 ARSM01 ARSH01 APVU01 AQQA01 APVS01 APVT01 APVR01 ARRU01 ARVQ01 ARSI01 ARPQ01 NZ_CP011989.1 AQOT01 JMSX01 ARRV01 ARPP01 ARPR01 ARSE01 ARSC01 ARSL01 ARRW01 ARRX01 APVQ01 ARRY01

11 30 20 40 12 39 4 36 13 44 14 52 5 34 9 33 2 38 0 29 9 14 9 9 11 6 3 8 12 9 35 7 23 7 11 14 10 11 9 7 7 7 6 8 7 11 21 5 42 8 8 11 9 8 4 11 10 7 10

1 10 5

4 3

2 2 2 2 2 2 2 2 2 2

3

1 5

2

2 1 3 2 3 3

1 2

2 1 2

1

4 2 4 2 8

2 6

2

4

3

3

1

2

2

2

2

1 2

6

2

1 1 2

3

4 4 1 2

3

2 6 4 2 2 2 2

4

3

5 4

3

4

1 2 2 2

1

2

2

1 2

16

1

10 2 11

1 2 1

3

9 1 7

1 1

9

1

11

1

2 1 2 2 2

2

2

5

2

2

2

2

1 7 1

6

2 1

2

1 1 1 1 1 1

1 1 2

6

2

6

1

1 3

1 1 1 1 1

2 2 2 2 2

2 2 2 2 2

2 2

2 2

2 2 2 2 2 2 2 2 2 2

2 2 2 2 2 2 2 2 2 2

2 2 2 2 2 2 2 2 2 2 2 2

2 2 2 2 2 2 2 2 2 2 2 2

1 1

1 1

2 3

1

1 1 1

2 1 3 1

2 1

1

1 1

1

1

1

1 1 1 1 1 1 1

6 6

1

1 3 1 1 1

2 2

2

1

5

2

1

1 1

6

1

1

11

2

1 1

1

2

2

6 2 2 5 6 2 2

2

1 1 1 1 1

4

6

1 1 1 1

2

1

1

3

3 7 4 7

2

1

2

3 8 1 1

2

6 7 6 2 2 5 6 2 2 3 6 2 2 2 6 2 2

2 2 2

6

2

2 1 2

1 1 2

1

5 1 1 1 1 1 1 12 2 1 1 11 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1

2


3 1

1

1 2

1 1 1 10 1 11

1 1 1 1 1

1 1 1

1 1 1 1 1 1 1 1 1

1

UKKV901664 ATEZ01 19 2 4 1 1 3 VA360 ANGI02 35 3 1 3 VAKPC252 APVW01 4 VAKPC254 APVX01 4 VAKPC269 APVY01 6 1 VAKPC270 APWA01 6 1 1 VAKPC276 APWB01 7 1 1 VAKPC278 ARVP01 36 2 1 2 VAKPC280 APVZ01 7 1 1 VAKPC297 APWC01 9 3 1 1 VAKPC309 APWD01 7 1 1 WGLW1 AMLL01 5 2 1 WGLW2 AMLM01 9 3 3 1 WGLW3 AMLN01 4 2 WGLW5 AMLO01 21 2 7 1 1 1 XDR JRGE01 16 3 2 1 2 2 2 3 XH209 NZ_CP009461.1 0 755.rep1_KPNE JUUI01000000 2 1 KP_ST11_OXA48 JNHB01 5 2 1 1 1 ST101_939996824LJEU00000000 22 5 5 1 1 1 1 ST101_945154233LJEM00000000 23 5 6 3 1 1 ST101_945165838LJEC00000000 25 4 6 1 3 1 1 1 ST101_945169659LJEE01000001 24 3 7 1 2 1 1 1 ST101_950171785LJDK01000001 22 2 4 2 2 2 ST101_950173000LJDN01000001 23 2 4 1 2 3 2 ST101_951363981LJFE01000001 32 4 8 3 2 1 2 ST101_951373950LJEA01000001 30 3 7 1 3 2 3 ST101_951384356LJEJ01000001 25 3 5 1 3 2 1 2 ST101_957083320LJEL01000001 22 4 7 1 1 1 ST101_957083896LJEI01000001 4 1 ST101_957089165LJEK01000001 22 3 6 1 1 1 1 ST101_960186733LJDT01000001 19 2 2 1 2 2 1 2 ST101_U44822 LJEN01000001 23 3 8 2 1 1 ST14_944535499 LJDW01000001 32 3 6 3 2 1 2 ST1478_93999710LJEQ01000001 8 4 2 2 ST2016_95136265LJDZ01000001 33 4 9 3 3 1 2 ST2017_95011751LJEF01000001 33 3 7 5 3 1 2 1 1 ST2017_95011842LJEH01000001 25 2 7 3 1 1 2 2 ST2017_95014239LJEG01000001 29 2 7 4 3 2 2 1 ST323_941530379LJDR0000000 8 1 2 1 2 1 1 UHKPC52 ARVN00000000 27 2 1 2 Yangling_I2 CP013338.1 5 1 2 yzusk‐4 CP011421.1 2 *GenBank records are available at http://www.ncbi.nlm.nih.gov/nuccore/[Accession]

5

6

2 2 2 2 2 2 2 2 2 2 2

2 2 2 2 2 2 2 2 2 2 2

1

2 2

1 13

2 2

1 1 2

1 16 1

2

1 1

7

1

2 1 2 1

1 1 3 3 3 3 2 1 3 3 3 3 3 3 3

1 1

1 2 1 1 2 2 2 2 1 1

1 4 1 2

6

1

1 1 2 2 2 2 2 2

1 1

1 1

1 2 1 1

3 3 3 3


1

1

1 2 2 2 2

2

1

2 1 2 2 2 2 4 3 3 3

1 1

3 3 2 8

3

4 2 2 2

1 1 1 1

11

2

2 2

Supplemental Table 5. A. baumannii genes with multiple different IS elements inserted In Gene M3Q_1781 M3Q_926 M3Q_1891 M3Q_2805 M3Q_2954 M3Q_3077 M3Q_3141 M3Q_1390 M3Q_1901 M3Q_1975 M3Q_2182 M3Q_2832 M3Q_3266 M3Q_41 M3Q_798

#IS elemen # GenomesDescription 11 30 competence/damage‐inducible protein CinA 10 75 ATPase 9 297 integrase 9 48 protein MorA 9 59 subtilisin‐like serine protease 9 28 OmpA protein 9 50 surface adhesion protein 8 295 tape measure domain‐containing protein 8 14 P pilus assembly protein, porin PapC 8 30 hypothetical protein 8 18 Signal transduction histidine kinase AdeS 8 8 hypothetical protein 8 73 hypothetical protein 8 15 mutator family transposase 8 23 diguanylate cyclase

M3Q_947 M3Q_1692 M3Q_2158 M3Q_2379 M3Q_2529 M3Q_2685 M3Q_2688 M3Q_2895 M3Q_3078 M3Q_3420 M3Q_531

8 7 7 7 7 7 7 7 7 7 7

31 6 32 9 13 36 63 13 53 338 59

M3Q_589 M3Q_946 M3Q_1185 M3Q_1365 M3Q_1869

7 7 6 6 6

4 48 3 40 49

M3Q_1895 M3Q_1976 M3Q_1987 M3Q_2005 M3Q_2071 M3Q_2156 M3Q_2242 M3Q_2358 M3Q_2448 M3Q_2527 M3Q_2560 M3Q_2694 M3Q_2787 M3Q_2993 M3Q_3167 M3Q_3476 M3Q_352 M3Q_463 M3Q_730

6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6

9 18 3 9 17 42 13 2 186 15 5 4 9 80 11 7 17 219 18

Signal transduction histidine kinase regulating C4‐dicarboxylate transport system shikimate transporter hypothetical protein ferrichrome‐iron receptor hypothetical protein type 1 pili subunit CsuA/B protein TetR family transcriptional regulator hypothetical protein hypothetical protein hypothetical protein thioesterase Type II secretory pathway, ATPase PulE/Tfp pilus assembly pathway, ATPase PilB hypothetical protein hypothetical protein hypothetical protein hypothetical protein inner membrane protein, putative permease for cytosine/purines, uracil, thiamine, allantoin flavoprotein dipeptide ABC transporter substrate‐binding protein adenylate/guanylate cyclase ribonuclease D phosphatidylserine/phosphatidylglycerophosphate/cardiolipin synthase RTX toxin metal‐dependent hydrolase transcriptional regulator hypothetical protein hypothetical protein AraC‐type DNA‐binding domain‐containing protein branched‐chain amino acid permease (azaleucine resistance) D‐alanyl‐D‐alanine carboxypeptidase poly‐gamma‐glutamate biosynthesis protein TRAP‐type C4‐dicarboxylate transport system, large permease component hypothetical protein IS4 family transposase ORF 1 Outer membrane receptor for monomeric catechols Downloaded from www.microbiologyresearch.org by IP: 172.245.146.248 On: Mon, 16 May 2016 03:09:54

M3Q_927 M3Q_935 M3Q_940 M3Q_101 M3Q_111 M3Q_1329

6 6 6 5 5 5

12 25 8 279 17 13

hypothetical protein hypothetical protein transposase PGAP1‐like protein hypothetical protein hemagglutinin‐like protein

M3Q_1399 M3Q_1495 M3Q_1591 M3Q_1620 M3Q_1671 M3Q_1682 M3Q_1711 M3Q_1774 M3Q_1896 M3Q_1933 M3Q_2018 M3Q_203 M3Q_2048 M3Q_2082 M3Q_2112 M3Q_2118 M3Q_214 M3Q_2160 M3Q_2241 M3Q_2291 M3Q_2396 M3Q_2419 M3Q_2488 M3Q_2612 M3Q_2680 M3Q_2695 M3Q_2697 M3Q_2820 M3Q_2885 M3Q_2998 M3Q_3047 M3Q_3235 M3Q_3251 M3Q_3271 M3Q_3288 M3Q_334 M3Q_3343 M3Q_3471 M3Q_435 M3Q_627 M3Q_9 M3Q_954 M3Q_1042 M3Q_1073 M3Q_1164 M3Q_1187 M3Q_1200 M3Q_1202

5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 4 4 4 4 4 4

11 278 24 23 25 4 20 3 6 10 8 9 54 56 99 33 9 6 37 36 2 8 6 50 5 7 13 34 120 6 9 11 2 4 34 5 38 7 12 17 266 17 5 4 1 4 27 15

Lipid A phosphoethanolamine transferase, associated with polymyxin resistance Rhs family protein pyrroline‐5‐carboxylate reductase drug/metabolite transporter permease hypothetical protein transcriptional regulator SecC motif‐containing protein hypothetical protein hypothetical protein hypothetical protein terminal alkane‐1‐monooxygenase transcriptional regulator TonB‐dependent siderophore receptor diguanylate cyclase TonB‐dependent siderophore receptor acetyl‐CoA acetyltransferase low temperature requirement A protein (LtrA) family protein hypothetical protein multidrug resistance efflux pump transcriptional regulator hypothetical protein sulfate permease iron‐regulated membrane protein hemin‐binding outer membrane transmembrane protein major facilitator superfamily permease threonine efflux protein hypothetical protein aminopeptidase N regulator of polyketide synthase expression hypothetical protein porin protein associated with imipenem resistance DcaP‐like protein DNA‐binding domain‐containing protein long‐chain fatty acid ABC transporter permease/ATPase chemotaxis protein histidine kinase hypothetical protein SAM‐dependent methyltransferase phosphoserine phosphatase outer membrane porin, OprD family hypothetical protein NAD/FAD‐binding protein diguanylate cyclase multimeric flavodoxin WrbA Tyrosine‐‐tRNA ligase, putative hypothetical protein type III restriction enzyme, res subunit family ABC oligo/dipeptide transport, ATP‐binding protein hypothetical protein Downloaded from www.microbiologyresearch.org by IP: 172.245.146.248 On: Mon, 16 May 2016 03:09:54

M3Q_1279 M3Q_1285 M3Q_1325 M3Q_1330 M3Q_1405 M3Q_1490 M3Q_1494 M3Q_1520 M3Q_1523 M3Q_1540 M3Q_1578 M3Q_1593 M3Q_1594 M3Q_1610 M3Q_1632 M3Q_1633 M3Q_1686 M3Q_1691 M3Q_1712 M3Q_1773 M3Q_1777 M3Q_1785 M3Q_1890 M3Q_1897 M3Q_1900 M3Q_1921 M3Q_2051 M3Q_2054 M3Q_2061 M3Q_2068 M3Q_2193

4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4

15 2 1 4 1 67 148 9 6 281 238 16 9 13 19 3 3 2 25 3 3 8 6 2 1 115 2 5 3 6 11

M3Q_2206 M3Q_2288 M3Q_2357 M3Q_2395 M3Q_2418 M3Q_2421 M3Q_2422 M3Q_2487 M3Q_2520 M3Q_2523 M3Q_2526 M3Q_2576 M3Q_2670 M3Q_2683 M3Q_2686 M3Q_2687 M3Q_2702 M3Q_2774 M3Q_2830 M3Q_2879 M3Q_2880 M3Q_2881 M3Q_2997

4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4

7 24 1 1 11 7 6 19 23 6 5 5 9 21 26 21 6 1 246 25 3 6 6

TonB‐dependent siderophore receptor ABC transporter heat shock protein outer membrane protein/peptidoglycan‐associated (lipo)protein hypothetical protein hypothetical protein Rhs element Vgr protein metal‐dependent hydrolase hypothetical protein cAMP‐binding protein hypothetical protein hypothetical protein hypothetical protein HlyD family type I secretion membrane fusion protein beta‐lactamase class A Rhs element Vgr protein hypothetical protein hypothetical protein retron‐type reverse transcriptase transcriptional regulator hypothetical protein hypothetical protein hypothetical protein DMT family permease P pilus assembly protein, pilin FimA hypothetical protein membrane‐fusion protein multidrug ABC transporter permease hypothetical protein hypothetical protein hypothetical protein response regulator containing a CheY‐like receiver domain and an HTH DNA‐binding domain symporter hypothetical protein hypothetical protein hypothetical protein esterase/lipase gamma‐aminobutyrate permease transcriptional regulator hypothetical protein TonB‐dependent siderophore receptor acetyltransferase hypothetical protein hypothetical protein P pilus assembly protein, porin PapC protein CsuA protein CsuA/B, secreted protein related to type I pili acyl‐CoA dehydrogenase hypothetical protein IS4 family transposase ORF 1 choline‐glycine betaine transporter transcriptional regulator gamma‐aminobutyrate permease hypothetical protein Downloaded from www.microbiologyresearch.org by IP: 172.245.146.248 On: Mon, 16 May 2016 03:09:54

M3Q_3000 M3Q_3125 M3Q_3128 M3Q_3151 M3Q_32 M3Q_3234 M3Q_3394 M3Q_3419 M3Q_3421 M3Q_3470 M3Q_3608 M3Q_3609 M3Q_3687 M3Q_385 M3Q_387 M3Q_532 M3Q_660 M3Q_690 M3Q_790 M3Q_809 M3Q_818 M3Q_925 M3Q_100 M3Q_1007 M3Q_1026 M3Q_1056 M3Q_1083 M3Q_112 M3Q_1142 M3Q_1169 M3Q_119 M3Q_1229 M3Q_1234 M3Q_1271 M3Q_1281 M3Q_1334 M3Q_1361 M3Q_140 M3Q_1475 M3Q_1486 M3Q_1488 M3Q_150 M3Q_1503 M3Q_1504 M3Q_1507 M3Q_1518 M3Q_1519 M3Q_1527 M3Q_1539 M3Q_1543 M3Q_1588 M3Q_1608 M3Q_1609 M3Q_161 M3Q_1619

4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3

5 106 1 5 40 3 31 9 13 8 5 8 7 3 1 9 10 3 25 5 1 7 127 3 2 2 17 9 9 2 2 2 6 3 7 4 4 2 3 27 5 5 28 3 3 11 9 15 148 6 6 6 7 5 20

hypothetical protein hypothetical protein transcription elongation factor and transcript cleavage phosphodiesterase/alkaline phosphatase D choline‐glycine betaine transporter Lipid A phosphoethanolamine transferase Signal transduction histidine kinase hypothetical protein outer membrane protein hypothetical protein O‐antigen ligase prepilin‐type N‐terminal cleavage/methylation domain‐containing protein hypothetical protein glutathione peroxidase MFS family transporter DNA binding protein transcriptional regulator zinc‐binding alcohol dehydrogenase family protein membrane‐fusion protein transcriptional regulator Dehydrogenase/reductase transcriptional regulator esterase trehalose‐6‐phosphate synthase phosphatase hypothetical protein phosphomannomutase hypothetical protein hypothetical protein hypothetical protein hypothetical protein BCCT family high‐affinity choline transporter Na+/H+ dicarboxylate symporter phosphate transporter lipase signal peptide‐containing protein Lipoprotein, putative hypothetical protein hypothetical protein diguanylate cyclase NADH:flavin oxidoreductase acyltransferase gamma‐aminobutyrate permease glycine/D‐amino acid oxidase, deaminating transcriptional regulator transcriptional regulator pirin‐like protein signal peptide protein IS4 family transposase ORF 1 metalloendopeptidase‐like membrane protein threonine efflux protein RND efflux transporter type I secretion system ATPase, LssB family transporter, sodium/bile acid transporter family protein transcriptional regulator Downloaded from www.microbiologyresearch.org by IP: 172.245.146.248 On: Mon, 16 May 2016 03:09:54

M3Q_1630 M3Q_1648 M3Q_1654 M3Q_1669 M3Q_1672 M3Q_1673 M3Q_1688 M3Q_1716 M3Q_1772 M3Q_1830 M3Q_1834 M3Q_1859 M3Q_1872 M3Q_1889 M3Q_1912 M3Q_1998 M3Q_2017 M3Q_2057 M3Q_2066 M3Q_2078 M3Q_2085 M3Q_2107 M3Q_2129 M3Q_2145 M3Q_2157 M3Q_2162 M3Q_2169 M3Q_2181 M3Q_2204 M3Q_2236 M3Q_2260 M3Q_2264 M3Q_2277 M3Q_2311 M3Q_2359 M3Q_2371 M3Q_2388 M3Q_2406 M3Q_2412 M3Q_2416 M3Q_2417 M3Q_2420 M3Q_2428 M3Q_2433 M3Q_2455 M3Q_2513 M3Q_2516 M3Q_2519 M3Q_2528 M3Q_2534 M3Q_2558 M3Q_2595 M3Q_2599 M3Q_2603 M3Q_2611

3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3

2 4 4 3 19 2 2 9 15 22 256 29 4 13 362 2 7 6 3 36 4 1 4 3 3 3 5 5 6 2 16 3 4 3 4 3 2 7 2 8 3 2 4 4 4 15 3 134 20 5 2 2 3 6 4

acetyltransferase transcriptional regulator NADPH‐quinone reductase hypothetical protein hypothetical protein hypothetical protein hypothetical protein catalase lysophospholipase L1 hypothetical protein signal peptide protein amino acid efflux protein, threonine efflux protein D‐and L‐methionine ABC transporter ATP‐binding protein transcriptional regulator Beta‐lactamase class D nucleoside‐diphosphate‐sugar epimerase AraC‐type DNA‐binding domain‐containing protein hypothetical protein Poly(3‐hydroxyalkanoate) synthetase hypothetical protein lipoyl synthase nitrate/sulfonate/bicarbonate ABC transporter permease major facilitator superfamily permease Fe2+/Zn2+ uptake regulation protein hypothetical protein hypothetical protein hypothetical protein response regulator AdeR RND family drug transporter fumarylacetoacetate (FAA) hydrolase family protein hemagglutinin protein hypothetical protein hypothetical protein Penicillin G amidase alpha/beta hydrolase hypothetical protein histone acetyltransferase HPA2 alpha/beta hydrolase hypothetical protein stress protein glucose/sorbosone dehydrogenase subtilisin‐like serine protease Fels‐1 Prophage Protein hypothetical protein hypothetical protein magnesium‐translocating P‐type ATPase signal peptide protein ABC transporter ATPase hypothetical protein hypothetical protein hypothetical protein acetyl‐CoA synthetase/AMP‐(fatty) acid ligase nitrate/sulfonate/bicarbonate ABC transporter substrate‐binding protein chaperone xylanase/chitin deacetylase Downloaded from www.microbiologyresearch.org by IP: 172.245.146.248 On: Mon, 16 May 2016 03:09:54

M3Q_2615 M3Q_2634 M3Q_2667 M3Q_2678 M3Q_2684 M3Q_2690 M3Q_2803 M3Q_2817 M3Q_2831 M3Q_2836 M3Q_2890 M3Q_2978 M3Q_3011 M3Q_3012 M3Q_3086 M3Q_3099 M3Q_3126 M3Q_3143 M3Q_3169 M3Q_3226 M3Q_3231 M3Q_3245 M3Q_333 M3Q_3378 M3Q_3386 M3Q_3417 M3Q_3447 M3Q_351 M3Q_3545 M3Q_3556 M3Q_3595 M3Q_3619 M3Q_3626 M3Q_3691 M3Q_395 M3Q_4 M3Q_444 M3Q_462 M3Q_470 M3Q_484 M3Q_500 M3Q_501 M3Q_562 M3Q_576 M3Q_60 M3Q_799 M3Q_800 M3Q_85 M3Q_883 M3Q_885 M3Q_891 M3Q_991

3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3

18 4 164 15 7 3 5 9 3 4 5 4 4 7 4 3 6 3 5 2 16 8 4 2 21 3 5 43 140 2 28 5 2 2 2 5 5 8 7 7 3 3 3 4 141 6 4 3 20 4 21 12

hypothetical protein hypothetical protein histone acetyltransferase HPA2 DMT family permease P pilus assembly protein, chaperone PapD transcriptional regulator methylenetetrahydrofolate reductase amino acid/peptide transporter (peptide:H symporter) Class C Beta‐lactamase AmpC hypothetical protein hypothetical protein hypothetical protein hypothetical protein hypothetical protein DNA internalization‐related competence protein ComEC/Rec2 glycosyltransferase non‐ribosomal peptide synthetase module sphingosine kinase hemolysin‐type calcium‐binding domain‐containing protein SAM‐dependent methyltransferase Pap2 chaperone protein HchA amino acid APC transporter phospholipase D hypothetical protein Ig‐like, group 1 precursor hypothetical protein hypothetical protein DNA metabolism protein subtilisin‐like serine protease DNA binding and uptake competence factor ComC Type II secretory pathway, component HofQ hypothetical protein hypothetical protein hypothetical protein transcriptional regulator TniB protein IS4 family transposase ORF 2 transposition helper ATPase Type 4 fimbriae expression regulatory protein signal transduction histidine kinase alpha/beta hydrolase hypothetical protein hypothetical protein transcriptional regulator transcriptional regulator hypothetical protein long‐chain fatty acid ABC transporter protein FilF Peptidase C13 family hypothetical protein


Supplemental Table 46 A. baumannii intergenic regions with multiple different IS elements inserted. #IS Elemen #Genomes After Gene Description 12 389 hypothetical protein

After Gene M3Q_2382

Before Gene M3Q_2383

M3Q_2687 M3Q_313 M3Q_1363 M3Q_1834 M3Q_190 M3Q_1903

M3Q_2688 M3Q_314 M3Q_1364 M3Q_1835 M3Q_191 M3Q_1904

11 9 8 8 8 8

M3Q_3168

M3Q_3169

8

M3Q_1490 M3Q_1689 M3Q_2212 M3Q_2487 M3Q_2679 M3Q_880 M3Q_1328 M3Q_1632 M3Q_1663 M3Q_2067 M3Q_2153 M3Q_2282 M3Q_2420 M3Q_2527

M3Q_1491 M3Q_1690 M3Q_2214 M3Q_2488 M3Q_2680 M3Q_881 M3Q_1329 M3Q_1633 M3Q_1664 M3Q_2068 M3Q_2154 M3Q_2283 M3Q_2421 M3Q_2528

7 7 7 7 7 7 6 6 6 6 6 6 6 6

11 222 7 21 22 272 26 10 156 10 74 44 32 7

hypothetical protein hypothetical protein hypothetical protein transcriptional regulator TetR family transcriptional regulator pilus subunit (FilA) DNA‐binding ATP‐dependent protease La beta‐lactamase class A hypothetical protein O‐succinylhomoserine sulfhydrylase hypothetical protein hypothetical protein subtilisin‐like serine protease hypothetical protein

M3Q_2576 M3Q_2695 M3Q_312 M3Q_3141 M3Q_41 M3Q_1073 M3Q_1359 M3Q_1620 M3Q_2057


6 6 6 6 6 5 5 5 5

16 94 10 151 300 263 153 6 10

hypothetical protein threonine efflux protein hypothetical protein surface adhesion protein mutator family transposase Tyrosine‐‐tRNA ligase, putative hypothetical protein drug/metabolite transporter permease hypothetical protein

M3Q_209

M3Q_210

5

184 27 15 48 11 31

protein CsuA/B, secreted protein related to type I pili hypothetical protein hypothetical protein signal peptide protein membrane‐fusion protein fimbrial protein (pilin)

7 hypothetical protein

5 membrane‐bound lytic murein transglycosylase B Downloaded from www.microbiologyresearch.org by IP: 172.245.146.248 On: Mon, 16 May 2016 03:09:54

Before Gene Description hypothetical protein TetR family transcriptional regulator hypothetical protein hypothetical protein hypothetical protein transcriptional regulator hypothetical protein hemolysin‐type calcium‐binding domain‐containing protein metal ion ABC transporter substrate‐binding protein/surface antigen hemolysin hypothetical protein iron‐regulated membrane protein major facilitator superfamily permease double‐glycine peptidase hemagglutinin‐like protein Rhs element Vgr protein signal peptide protein hypothetical protein hypothetical protein catalase esterase/lipase hypothetical protein bifunctional aconitate hydratase 2/2‐methylisocitrate dehydratase hypothetical protein hypothetical protein phosphohydrolase Lrp family transcriptional regulator hypothetical protein hypothetical protein EAL domain‐containing protein outer membrane protein (porin) phosphoribosylaminoimidazole carboxylase

M3Q_2123 M3Q_2159 M3Q_2378 M3Q_2449 M3Q_2454 M3Q_2529 M3Q_2531 M3Q_2533 M3Q_2669 M3Q_2680


5 5 5 5 5 5 5 5 5 5

11 9 13 5 9 6 12 11 33 33

M3Q_2686 M3Q_2828 M3Q_2881 M3Q_3126 M3Q_3179 M3Q_3469 M3Q_5 M3Q_531


5 5 5 5 5 5 5 5

17 737 22 31 36 12 13 27

M3Q_566 M3Q_660 M3Q_101 M3Q_1331

M3Q_567 M3Q_661 M3Q_102 M3Q_1332

5 5 4 4

8 10 8 13



4 4 4 4 4 4 4 4 4 4

12 11 27 14 7 8 4 9 7 14

M3Q_1832 M3Q_1853 M3Q_1854

M3Q_1833 M3Q_1854 M3Q_1855

4 4 4

hypothetical protein catalase Zn‐dependent peptidase ornithine carbamoyltransferase hypothetical protein hypothetical protein small‐conductance mechanosensitive channel TetR family transcriptional regulator glucose/sorbosone dehydrogenase major facilitator superfamily permease

H+/gluconate symporter family protein hypothetical protein ferrichrome‐iron receptor hypothetical protein hypothetical protein hypothetical protein TonB‐dependent siderophore receptor hypothetical protein hypothetical protein hypothetical protein

protein CsuA GTP cyclohydrolase I gamma‐aminobutyrate permease non‐ribosomal peptide synthetase module hypothetical protein nitroreductase‐like oxidoreductase arabinose efflux permease family protein thioesterase multifunctional fatty acid oxidation complex subunit alpha transcriptional regulator PGAP1‐like protein 5,10‐methenyltetrahydrofolate synthetase

protein CsuA/B, secreted protein related to type I pili IS4 family transposase methylmalonic acid semialdehyde dehydrogenase hypothetical protein NhaP‐type Na+/H+ and K+/H+ antiporter hypothetical protein hypothetical protein DNA binding protein

outer membrane receptor protein TetR family transcriptional regulator K+ transport protein hypothetical protein hypothetical protein hypothetical protein cyanate permease acyl‐CoA dehydrogenase response regulator major membrane protein I (MMP‐I) coenzyme F420‐dependent N5,N10‐methylene 8 tetrahydromethanopterin reductase 11 L‐asparaginase type II family protein 8 Na+/H+ dicarboxylate symporter Downloaded from www.microbiologyresearch.org by IP: 172.245.146.248 On: Mon, 16 May 2016 03:09:54

beta‐hydroxylase Zn‐dependent hydrolase methionine aminopeptidase signal peptide‐containing protein Lipid A phosphoethanolamine transferase, associated with polymyxin resistance Rhs element Vgr protein hypothetical protein pyrroline‐5‐carboxylate reductase surface antigen transcriptional regulator hypothetical protein hypothetical protein acetyltransferase serine acetyltransferase transporter Na+/H+ dicarboxylate symporter aspartate/tyrosine/aromatic aminotransferase



4 4 4 4 4 4 4 4

17 10 4 11 21 20 10 5

DcaP‐like protein 1‐acyl‐sn‐glycerol‐3‐phosphate acyltransferase hypothetical protein hypothetical protein ribonuclease D hypothetical protein P pilus assembly protein, pilin FimA hypothetical protein

transcriptional regulator transcriptional regulator flavoprotein hypothetical protein hypothetical protein hypothetical protein hypothetical protein long‐chain fatty acid transport protein

M3Q_2184 M3Q_2217 M3Q_2447 M3Q_2465 M3Q_2520 M3Q_2522 M3Q_2534 M3Q_2675 M3Q_314 M3Q_3183 M3Q_3219 M3Q_343 M3Q_344

M3Q_2185 M3Q_2218 M3Q_2448 M3Q_2466 M3Q_2521 M3Q_2523 M3Q_2535 M3Q_2676 M3Q_315 M3Q_3184 M3Q_3220 M3Q_344 M3Q_345

4 4 4 4 4 4 4 4 4 4 4 4 4

1 3 9 5 14 16 13 33 6 86 6 21 13

AraC‐type DNA‐binding domain‐containing protein hypothetical protein response regulator transcriptional regulator hypothetical protein outer membrane protein W hypothetical protein paraquat‐inducible protein A hypothetical protein tryptophanyl‐tRNA synthetase II outer membrane protein hypothetical protein transcriptional regulator



4 4 4 4 4 4 4 4 4

3 10 41 23 5 2 69 12 1

hypothetical protein transcriptional regulator YdzF outer membrane porin, OprD family IS4 family transposase ORF 2 phaAB exodeoxyribonuclease V subunit alpha diguanylate cyclase transcriptional regulator acyl‐CoA synthetase

alpha/beta fold family hydrolase methylenetetrahydrofolate reductase transcriptional regulator molybdopterin biosynthesis protein hypothetical protein TonB‐dependent siderophore receptor transcriptional regulator permease hypothetical protein succinyl‐CoA synthetase subunit alpha hypothetical protein transcriptional regulator acyl‐CoA synthetase TRAP‐type C4‐dicarboxylate transport system, large permease component hypothetical protein hypothetical protein IS4 family transposase ORF 1 ATP‐binding protein penicillin‐binding protein, beta‐lactamase class C transcriptional regulator hypothetical protein threonyl‐tRNA synthetase

M3Q_871 M3Q_987 M3Q_1008 M3Q_1139

M3Q_872 M3Q_988 M3Q_1009 M3Q_1140

4 4 3 3

16 6 38 13

M3Q_1175

M3Q_1176

3

lipoprotein precursor (VacJ) transmembrane hypothetical protein trehalose‐6‐phosphatase hypothetical protein cytotoxic translational repressor of toxin‐antitoxin 2 stability system Downloaded from www.microbiologyresearch.org by IP: 172.245.146.248 On: Mon, 16 May 2016 03:09:54

DNA‐directed RNA polymerase specialized sigma subunit threonine efflux protein alpha/beta superfamily hydrolase/acyltransferase hypothetical protein hypothetical protein

M3Q_1201 M3Q_1234 M3Q_1293 M3Q_1303

M3Q_1202 M3Q_1235 M3Q_1294 M3Q_1304

3 3 3 3

7 7 3 13

site‐specific DNA methylase Na+/H+ dicarboxylate symporter rubredoxin citrate transporter, CitMHS family

hypothetical protein YaeQ protein hypothetical protein hemolysin‐like protein

M3Q_1324 M3Q_1345 M3Q_1364 M3Q_149

M3Q_1325 M3Q_1346 M3Q_1365 M3Q_150

3 3 3 3

2 2 12 3

heat shock protein hypothetical protein hypothetical protein acyltransferase

M3Q_1491 M3Q_1492 M3Q_1496 M3Q_1502 M3Q_1529 M3Q_1537 M3Q_1553 M3Q_1566 M3Q_1592 M3Q_1593 M3Q_1599 M3Q_1601 M3Q_1643 M3Q_1688 M3Q_1780 M3Q_1785 M3Q_1804 M3Q_1829 M3Q_1879 M3Q_1891 M3Q_1899 M3Q_1912 M3Q_1920 M3Q_1986 M3Q_200 M3Q_2022 M3Q_2060 M3Q_2062 M3Q_2063

M3Q_1492 M3Q_1493 M3Q_1497 M3Q_1503 M3Q_1530 M3Q_1538 M3Q_1554 M3Q_1567 M3Q_1593 M3Q_1594 M3Q_1600 M3Q_1602 M3Q_1644 M3Q_1689 M3Q_1781 M3Q_1786 M3Q_1805 M3Q_1830 M3Q_1880 M3Q_1892 M3Q_1900 M3Q_1913 M3Q_1921 M3Q_1987 M3Q_201 M3Q_2023 M3Q_2061 M3Q_2063 M3Q_2064

3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3

3 4 3 3 7 284 4 4 19 2 15 12 2 4 6 19 98 107 7 31 7 305 124 53 3 5 12 8 6

glutamate dehydrogenase/leucine dehydrogenase hypothetical protein hypothetical protein histidine utilization repressor metal ion ABC transporter substrate‐binding protein/surface antigen hypothetical protein TPR repeat‐containing SEL1 subfamily protein hypothetical protein carbon storage regulator CsrA oxidoreductase glutathione S‐transferase Benzoate transport protein hypothetical protein hypothetical protein hypothetical protein surface antigen chloride channel protein EriC hypothetical protein hypothetical protein hypothetical protein rhodanese‐related sulfurtransferase cytochrome bd ubiquinol oxidase, subunit I acyl‐CoA dehydrogenase integrase hypothetical protein Beta‐lactamase class D hypothetical protein hypothetical protein lipoprotein hypothetical protein hypothetical protein hypothetical protein hypothetical protein Downloaded from www.microbiologyresearch.org by IP: 172.245.146.248 On: Mon, 16 May 2016 03:09:54

hypothetical protein TetR family transcriptional regulator TPR repeat‐containing SEL1 subfamily protein gamma‐aminobutyrate permease aspartate kinase IS4 family transposase ORF 2 trmB benzoate transporter hypothetical protein hypothetical protein hypothetical protein cysteinyl‐tRNA synthetase TPR repeat‐containing SEL1 subfamily protein hypothetical protein competence/damage‐inducible protein CinA hypothetical protein dehydrogenase hypothetical protein glutathione S‐transferase hypothetical protein P pilus assembly protein, pilin FimA suppressor of F exclusion of phage T7 (FxsA) hypothetical protein dipeptide ABC transporter substrate‐binding protein lipoprotein ybaK/ebsC protein hypothetical protein hypothetical protein hypothetical protein

20 lipoyl synthase 12 transcriptional regulator

M3Q_2085 M3Q_2122

M3Q_2086 M3Q_2123

3 3

M3Q_2152

M3Q_2153

3

M3Q_2156 M3Q_2181 M3Q_2204 M3Q_2257 M3Q_2269 M3Q_2278

M3Q_2157 M3Q_2182 M3Q_2205 M3Q_2258 M3Q_2270 M3Q_2279

3 3 3 3 3 3

272 Zn‐dependent dipeptidase, microsomal dipeptidase phosphatidylserine/phosphatidylglycerophosphate/c 7 ardiolipin synthase 4 response regulator AdeR 7 RND family drug transporter 44 major facilitator superfamily permease 268 antibiotic biosynthesis monooxygenase 18 NADH:flavin oxidoreductase



3 3 3 3 3 3 3 3 3

10 1 27 4 4 10 10 274 2

M3Q_2612 M3Q_2641 M3Q_2702 M3Q_2792 M3Q_2793 M3Q_280 M3Q_2869 M3Q_2880 M3Q_2954 M3Q_30 M3Q_3063 M3Q_3093 M3Q_3097 M3Q_3125 M3Q_321 M3Q_3235

M3Q_2613 M3Q_2643 M3Q_2703 M3Q_2793 M3Q_2794 M3Q_281 M3Q_2870 M3Q_2881 M3Q_2955 M3Q_31 M3Q_3064 M3Q_3094 M3Q_3098 M3Q_3126 M3Q_322 M3Q_3236

3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3

5 36 4 5 6 6 114 5 6 15 7 7 2 4 6 15

catI ABC transporter ATPase hypothetical protein glucose/sorbosone dehydrogenase hypothetical protein hypothetical protein hypothetical protein hypothetical protein hypothetical protein hemin‐binding outer membrane transmembrane protein Zn‐dependent hydrolase acyl‐CoA dehydrogenase methionine aminopeptidase outer membrane protein W FKBP‐type peptidyl‐prolyl cis‐trans isomerase drug/metabolite transporter permease transcriptional regulator subtilisin‐like serine protease diguanylate cyclase Holliday junction DNA helicase subunit RuvB phosphoserine aminotransferase multidrug ABC transporter permease hypothetical protein hypothetical protein DcaP‐like protein Downloaded from www.microbiologyresearch.org by IP: 172.245.146.248 On: Mon, 16 May 2016 03:09:54

pyruvate/2‐oxoglutarate dehydrogenase complex, dehydrogenase component subunit alpha hypothetical protein hypothetical protein hypothetical protein Signal transduction histidine kinase AdeS amidase hypothetical protein TetR family transcriptional regulator marR family transcriptional regulator 2‐C‐methyl‐D‐erythritol 4‐phosphate cytidylyltransferase RND type efflux pump diguanylate cyclase hypothetical protein sulfate permease Fels‐1 Prophage Protein transcriptional regulator small‐conductance mechanosensitive channel hypothetical protein hypothetical protein Na+/H+‐dicarboxylate symporter hypothetical protein outer membrane protein W nitrate transporter transmembrane protein tyrosine‐protein kinase hypothetical protein gamma‐aminobutyrate permease periplasmic protease 34 kDa Outer Membrane Protein amidohydrolase outer membrane protein hypothetical protein non‐ribosomal peptide synthetase module hypothetical protein major facilitator superfamily permease

M3Q_3244

M3Q_3245

3

2 gamma‐aminobutyrate permease

M3Q_3248 M3Q_3266

M3Q_3249 M3Q_3267

3 3

5 undecaprenyl‐diphosphatase UppP 39 hypothetical protein



3 3 3 3 3 3 3 3 3

17 3 18 7 62 166 3 9 2

response regulator with CheY‐like receiver domain and winged‐helix DNA‐binding domain Signal transduction histidine kinase sulfate/thiosulfate‐binding protein HopJ type III effector protein acetate kinase hypothetical protein transcriptional regulator p‐aminobenzoate synthetase hypothetical protein


chaperone protein HchA phenylacetic acid degradation operon negative regulatory protein intracellular protease/amidase

hypothetical protein queA hypothetical protein 50S ribosomal protein L31 phosphogluconate dehydratase TonB‐dependent receptor protein transcriptional regulator pilus subunit (FilA) transcriptional regulator