Respiratory coinfections in COVID-19 patients evaluated by BioFire Pneumonia Panel

Abstract

Abstract Background Routine administration of antibacterials in patients with Covid-19 has been a subject of debate, with no solid data about the true prevalence of respiratory coinfections in Covid-19 patients in different geographic areas. The aim of the current study was to identify respiratory coinfections in Covid-19 patients admitted to the hospital and to identify its genetic resistance pattern using the respiratory multiplex polymerase chain reaction (PCR). Results The study included 40 patients, 32 males (80%) and 8 (20%) females with a mean age of 59.3 ± 12.6. Half of the patients had respiratory bacterial coinfections documented by pneumonia (PN) panel. The most common isolate was Klebsiella pneumoniae (10/20, 50%), followed by Acinetobacter calcoaceticus baumanni complex (7/20, 35%). Regarding genetic resistance, thirteen (13/20, 65%) isolates were proven extended spectrum beta lactamase (ESBL)-producing Enterobacteriaceae. Thirteen (13/20, 65%) isolates were proven carbapenemase-producing organisms testing positive for New Delhi metallo-β-lactamase (NDM), oxacillinase β-lactamases (OXA-48), and Verona Integron-Encoded Metallo-β-Lactamase (VIM) (7/20, 35%; 5/20, 25%; 1/20, 5%, respectively). The four isolated Staphylococcus aureus were methicillin-resistant (4/20, 20%). Conclusion In our cohort, there was 50% rate of bacterial respiratory coinfection in patients with severe Covid-19 admitted to the ICU with high rates of carbapenemase-producing gram-negative bacteria that required escalation of antibacterials and represented a challenge to clinicians.

Keywords

• COVID-19
• SARS-CoV-2
• Klebsiella pneumoniae
• Acinetobacter calcoaceticus baumanni complex
• BioFire FilmArray Pneumonia Panel