Supplemental Digital Content to:
Respiratory Viruses in Invasively Ventilated Critically ill Patients – a Prospective Multicenter Observational Study Frank van Someren Gréve, MD1,2, Nicole P. Juffermans, MD, PhD1, Lieuwe D.J. Bos, PhD1, Jan M. Binnekade, PhD1, Annemarije Braber, MD, PhD3, Olaf L. Cremer, MD, PhD4, Evert de Jonge, MD, PhD6, Richard Molenkamp, PhD2, David S.Y. Ong, MD, PhD, PharmD4,5, Sjoerd P.H. Rebers, BASc2, Angelique M.E. Spoelstra–de Man, MD, PhD7, Koenraad F. van der Sluijs, PhD1, Peter E. Spronk, MD, PhD3, Kirsten D. Verheul, BASc2, Monique C. de Waard, PhD7, Rob B.P. de Wilde, PhD6, Tineke Winters, CCRN1, Menno D. de Jong, MD, PhD2, Marcus J. Schultz, MD, PhD1 Academic Medical Center, Amsterdam, The Netherlands 1 Department of Intensive Care 2 Department of Medical Microbiology Gelre Hospitals, Apeldoorn, The Netherlands 3 Department of Intensive Care University Medical Center Utrecht, Utrecht, The Netherlands 4 Department of Intensive Care Medicine 5 Department of Medical Microbiology Leiden University Medical Center, Leiden, The Netherlands 6 Department of Intensive Care VU University Medical Center, Amsterdam, The Netherlands 7 Department of Intensive Care
Corresponding author: Frank van Someren Gréve, MD Department of Intensive Care Academic Medical Center Meibergdreef 9, 1105 AZ Amsterdam, The Netherlands Tel: +31 20 566 6345, Email:
[email protected];
[email protected] 1
MATERIALS AND METHODS Data collection For each patient at ICU admission, the attending ICU physician ticked one or more diagnoses from a list of APACHE II diagnostic categories, using medical history, clinical findings and the results of diagnostic procedures. The APACHE II diagnoses consisted of the following categories: 'Medical - Cardiovascular - Multiple trauma', 'Medical - Cardiovascular - Coronary artery disease', 'Medical - Cardiovascular Thoracic or abdominal aneurysm', 'Medical - Cardiovascular - Congestive heart failure', 'Medical - Cardiovascular - Hypertension', 'Medical - Cardiovascular - Rhythm disturbance', 'Medical - Cardiovascular - Cardiogenic shock' - 'Medical - Neurological - Intracerebral subdural or subarachnoid hemorrhage', 'Medical - Neurological Seizure disorder', 'Medical - Neurological - Not further specified', 'Medical Respiratory - Infection', 'Medical - Respiratory - Neoplasm', 'Medical - Respiratory Pulmonary embolus', 'Medical - Respiratory - Non-cardiogenic lung edema', 'Medical - Respiratory - Asthma or allergy', 'Medical - Respiratory - Acute exacerbation of chronic obstructive lung disease ', 'Medical - Respiratory - Aspiration poisoning or toxic', 'Medical - Respiratory - Not further specified', 'Surgical - Cardiovascular Multiple trauma', 'Surgical - Cardiovascular - Heart valve surgery', 'Surgical Cardiovascular - Peripheral vascular surgery', 'Surgical - Cardiovascular Hemorrhagic shock', 'Surgical - Cardiovascular - Chronic cardiovascular disease', 'Surgical - Cardiovascular - Not further specified', 'Surgical - Gastrointestinal Neoplasm', 'Surgical - Gastrointestinal - Bleeding ', 'Surgical - Gastrointestinal Perforation or obstruction', 'Surgical - Gastrointestinal - Not further specified', 'Surgical - Hematological', 'Surgical - Renal - Neoplasm', 'Surgical - Renal Transplant ', 'Surgical - Renal - Not further specified', 'Surgical - Metabolic', 'Surgical 2
Neurological - Craniotomy for neoplasm ', 'Surgical - Neurological - Head trauma', 'Surgical - Neurological - Craniotomy for intracerebral subdural or subarachnoid hemorrhage', 'Surgical - Neurological - Not further specified', 'Surgical - Respiratory Thoracic surgery for neoplasm', 'Surgical - Respiratory - Not further specified', 'Sepsis', 'After cardiac arrest', 'After respiratory arrest', and 'Unknown diagnosis'. Sampling and microbiological testing A transnasal nasopharyngeal (NP) flocked swab was obtained in virus transport medium (Copan Diagnostics, Brescia, Italy), and a tracheobronchial aspirate (TA) was collected using a suction catheter into a sterile container (Medisize BV, Hillegom, the Netherlands) within 48 hours following intubation. Samples were locally stored at –20ºC, until batch wise transport to the Department of Medical Microbiology at the AMC, where they were stored at –80ºC until further processing. TA samples were diluted 1:1 with 1.54 mg/ml Dithiothreitol (DTT) prior to processing. Nucleic acids were extracted using the MagNA Pure Total Nucleic Acid Kit on a MagNA Pure 96 (Roche Diagnostics, Penzberg, Germany), followed by a semi-quantitative multiplex RT-PCR on the LightCycler 480 (Roche Diagnostics, Penzberg, Germany), using a validated protocol for influenza A and B virus, parainfluenza virus 1–4, respiratory syncytial virus (RSV), human metapneumovirus (hMPV), human bocavirus, human coronavirus, human rhinovirus, enterovirus, parechovirus and adenovirus (1). Analysis Clinical outcomes of patients with the presence of a virus were compared to those without, and included ventilator-free days and alive at day 28 (VFD28), ICU-free days and alive at day 28 (ICUFD28), ICU mortality, and hospital mortality. The number of VFD28 and ICUFD28 was defined as 28 minus the duration of ventilation or minus the duration of stay in the ICU in days, respectively. Patients who died before day 28 3
were scored as 0. Furthermore, survival was compared between patients with and without detection of a virus, as well as the association between the presence of a virus and time to successful weaning and death while on invasive ventilation.
Statistical analysis To identify associations between the presence of a respiratory virus and duration of invasive ventilation and mortality, a multivariate competing risk survival model was used (2). In this model we considered death while on invasive ventilation as a competing endpoint to time to successful weaning of invasive ventilation. It provides 2 measures of association: cause-specific hazard ratios (CSHR), which estimate the direct effect on the clinical outcome; and subdistribution hazard ratios (SDHR), which describe the effect on the outcome while accounting for the competing events (i.e., death and successful weaning). The model included adjustment for the following predefined covariates: APACHE II score, gender, history of COPD and history of asthma. In the posthoc model, age was added as a separate numerical covariate, and an adjusted APACHE II score without age score was used instead of the APACHE II score. The adjusted APACHE II score was calculated by subtracting the points attributed by age from the APACHE II score. Missing data for these covariates was imputed using multivariate imputation by chained equations in 5 datasets (3). Model assumptions were tested with Schoenfeld residuals; colinearity was tested using variance inflation factors.
4
REFERENCES 1.
Jansen RR, Schinkel J, Koekkoek S, et al.: Development and evaluation of a four-tube real time multiplex PCR assay covering fourteen respiratory viruses, and comparison to its corresponding single target counterparts. J Clin Virol Off Publ Pan Am Soc Clin Virol 2011; 51:179–85
2.
Scrucca L, Santucci A, Aversa F: Regression modeling of competing risk using R: an in depth guide for clinicians. Bone Marrow Transplant 2010; 45:1388– 1395
3.
Buuren S van, Groothuis-Oudshoorn K: mice : Multivariate Imputation by Chained Equations in R. J Stat Softw 2011; 45:1–67
5
Figure S1. CONSORT diagram. Abbreviations: ICU = intensive care unit; NP = nasopharyngeal swab; SARI = severe acute respiratory infection (at ICU admission); TA = tracheobronchial aspirate
6
Table S1. Antimicrobial treatment in SARI patients SARI Antimicrobial 3rd gen. Cephalosporine
n = 156 99 (63%)
Penicillin
44 (28%)
Fluoroquinolone
40 (26%)
Macrolide
37 (24%)
2nd gen. Cephalosporine
27 (17%)
Aminoglycoside
24 (15%)
Oseltamivir
24 (15%)
Metronidazole
22 (14%)
Carbapenem
19 (12%)
Glycopeptide
18 (12%)
Sulfonamide
18 (12%)
Antifungal
18 (12%)
Other antiviral
12 (8%)
Lincosamide
3 (2%)
1st gen. Cephalosporine
3 (2%)
Tetracycline
3 (2%)
Polypeptide
1 (1%)
Nitrofurans
1 (1%)
Rifampicin 1 (1%) Data are number of patients (%) receiving antimicrobial treatment within 48 hours of inclusion
7
Table S2. Distribution of viral pathogens and site of virus detection All patients SARI n = 1,407
n = 156
non–SARI n = 1,251
p
Virus type Adenovirus
3
(0.2%)
1
(0.6%)
2
(0.2%)
0.22
Bocavirus
21
(1.5%)
2
(1.3%)
19
(1.5%)
0.82
Coronavirus
41
(2.9%)
8
(5.1%)
33
(2.6%)
0.08
Enterovirus
4
(0.3%)
0
4
(0.3%)
0.48
Human metapneumovirus
7
(0.5%)
4
(2.6%)
3
(0.2%)
