Molecular epidemiology of a carbapenem-resistant outbreak during the COVID-19 pandemic.

INTRODUCTION

is a significant causative agent of hospital-acquired infections (HAIs), particularly in intensive care units (ICUs). Carbapenem resistance represents a major concern in HAI management, as carbapenem-resistant bacteria can trigger outbreaks in hospital settings. While molecular evaluation of outbreaks typically relies on pulse field gel electrophoresis (PFGE) or core genome multilocus sequence typing (cgMLST) methods, alternative rapid, reliable, and cost-effective methods for assessing clonal relatedness are needed.

METHODS

This study aimed to characterize a carbapenem-resistant outbreak that occurred during the COVID-19 pandemic in a tertiary care hospital, using the flagellin gene as a single-locus sequence typing (SLST) method. In addition, we evaluated the genetic context of carbapenemase genes through whole-genome sequencing (WGS).

RESULTS

Among the 170 carbapenem-resistant isolates recovered, high resistance to gentamicin, ciprofloxacin, and cefepime was observed. The predominant carbapenemase gene detected by qPCR-HRM was blaKPC (92.2%). Phylogenetic analysis of the flagellin gene grouped the sequences into two distinct clades, with all outbreak-related -positive isolates clustering within clade B. The gene was carried on an IncP6 plasmid.

DISCUSSION

Our findings indicate that the flagellin gene serves as an effective marker for characterizing carbapenem-resistant carrying , confirming that the outbreak was caused by the clonal expansion of isolates harboring on an IncP6 plasmid.