Background: Pandemic COVID-19 caused by the coronavirus SARS-CoV-2 has a high incidence of patients with severe acute respiratory syndrome (SARS). Many of these patients require admission to an intensive care unit (ICU) for invasive ventilation and are at significant risk of developing a secondary, ventilator-associated pneumonia (VAP). Objectives: To study the incidence of VAP and bacterial lung microbiome composition of ventilated COVID-19 and non-COVID-19 patients. Methods: In this retrospective observational study, we compared the incidence of VAP and secondary infections using a combination of microbial culture and a TaqMan multi-pathogen array. In addition, we determined the lung microbiome composition using 16S RNA analysis in a subset of samples. The study involved 81 COVID-19 and 144 non-COVID-19 patients receiving invasive ventilation in a single University teaching hospital between March 15th 2020 and August 30th 2020. Results: COVID-19 patients were significantly more likely to develop VAP than patients without COVID (Cox proportional hazard ratio 2.01 95% CI 1.14–3.54, p = 0.0015) with an incidence density of 28/1000 ventilator days versus 13/1000 for patients without COVID (p = 0.009). Although the distribution of organisms causing VAP was similar between the two groups, and the pulmonary microbiome was similar, we identified 3 cases of invasive aspergillosis amongst the patients with COVID-19 but none in the non-COVID-19 cohort. Herpesvirade activation was also numerically more frequent amongst patients with COVID-19. Conclusion: COVID-19 is associated with an increased risk of VAP, which is not fully explained by the prolonged duration of ventilation. The pulmonary dysbiosis caused by COVID-19, and the causative organisms of secondary pneumonia observed are similar to that seen in critically ill patients ventilated for other reasons.
Bibliographical noteFunding Information:
This study was funded by the National Institute for Health Research [Cambridge Biomedical Research Centre at the Cambridge University Hospitals NHS Foundation Trust, AMR theme]. The views expressed are those of the authors and not necessarily those of the NHS, the NIHR or the Department of Health and Social Care. Dr Conway Morris is supported by a Clinical Research Career Development Fellowship from the Wellcome Trust (WT 2055214/Z/16/Z).
Our thanks go out to all the ICU clinicians, nurses and physiotherapists who have ensured proper patient care and sample management even in these hard times, as well as to PHE microbiologists for running standard microbiology tests. Furthermore, the authors wish to thank Mark Wills for his help as Biological Safety Officer to ensure we work in a safe environment. We also thank M Est?e T?r?k and Ian Goodfellow for access to consumables and the GridION for Nanopore sequencing, and Satpal Ubhi for help with clinical data collection. Finally, we wish to acknowledge our funders the NIHR BRC. In addition we would like to acknowledge the grant awarded by Addenbrooke?s Charitable Trust for the initial study of the clinical utility of the TaqMan microarray .
© 2021, The Author(s).
- Critical care
- Molecular diagnostics
- Nosocomial infections
- Ventilator-associated pneumonia