Here we describe the case of a COVID-19 patient who developed recurring ventilator-associated pneumonia caused by Pseudomonas aeruginosa that acquired increasing levels of antimicrobial resistance (AMR) in response to treatment. Metagenomic analysis revealed the AMR genotype, while immunological analysis revealed massive and escalating levels of T-cell activation. These were both SARS-CoV-2 and P. aeruginosa specific, and bystander activated, which may have contributed to this patient's persistent symptoms and radiological changes.
Human-filtered sequencing data for this study have been deposited in the European Nucleotide Archive (ENA) at EMBL-EBI under accession PRJEB40239.
Metagenomic analysis of respiratory samples from a COVID-19 ICU patientEuropean Nucleotide Archive, PRJEB40239.
- Fergus Hamilton
- Ruth C Massey
- Laura Rivino
- Rosemary J Boyton
- Daniel M Altmann
- David K Butler
The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.
Human subjects: The patient was enrolled onto the DISCOVER study (Diagnostic and Severity markers of COVID-19 to Enable Rapid triage study), a single centre prospective study recruiting consecutive patients admitted with COVID-19, from 30.03.2020 until present (Ethics approval via South Yorkshire REC: 20/YH/0121, CRN approval no: 45469). Blood/serum samples from pre-pandemic healthy controls and asymptomatic healthy controls were obtained under the Bristol Biobank (NHS Research Ethics Committee approval ref 14/WA/1253).
- Anurag Agrawal, CSIR Institute of Genomics and Integrative Biology, India
© 2020, Gregorova et al.
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