Comparison of microbiological and molecular diagnosis for identification of respiratory secondary infections in COVID-19 patients and their antimicrobial resistance patterns

• DOI: 10.1016/j.diagmicrobio.2024.116479
• Publication Date: 2024-08-03T22:34:21Z
• Authors: Valentina Margarita; Maria Carmina Pau; Gavino Carboni; Franca Mannu; Francesco Turrini; Paola Rappelli; Antonella Pantaleo; Daniele Dessì; Elisabetta Zinellu; Barbara Piras; Alessandro G. Fois; Salvatore Rubino; Pietro Pirina; Pier Luigi Fiori
• Keywords: Male; Adult; Bacteria; SARS-CoV-2; Coinfection; COVID-19; Microbial Sensitivity Tests; Bacterial Infections; Middle Aged; Real-Time Polymerase Chain Reaction; Anti-Bacterial Agents; Molecular Diagnostic Techniques; antimicrobial-resistance; culture-based diagnosis; molecular-based syndromic test; Real-Time PCR; SARS-CoV-2; secondary infection; Drug Resistance, Bacterial; Humans; Female; Respiratory Tract Infections; Multiplex Polymerase Chain Reaction; Aged

We report the use of a new multiplex Real-Time PCR platform to simultaneously identify 24 pathogens and 3 antimicrobial-resistance genes directly from respiratory samples of COVID-19 patients. Results were compared to culture-based diagnosis. Secondary infections were detected in 60% of COVID-19 patients by molecular analysis and 73% by microbiological assays, with no significant differences in accuracy, indicating Gram-negative bacteria as the predominant species. Among fungal superinfections, Aspergillus spp. were detected by both methods in more than 7% of COVID-19 patients. Oxacillin-resistant S. aureus and carbapenem-resistant K. pneumoniae were highlighted by both methods. Secondary microbial infections in SARS-CoV-2 patients are associated with poor outcomes and an increased risk of death. Since PCR-based tests significantly reduce the turnaround time to 4 hours and 30 minutes (compared to 48 hours for microbial culture), we strongly support the routine use of molecular techniques, in conjunction with microbiological analysis, to identify co/secondary infections.