Whole-genome sequencing of two multidrug-resistant carbapenemase-producing Serratia marcescens strains.

Abstract

To understand the resistance phenotype and the carriage of resistance genes in carbapenem-resistant Serratia marcescens in our hospital. Two S. marcescens clinical isolates were analyzed retrospectively to determine their sensitivity to 27 antimicrobial agents using the BD Phoenix™ M50 System (Becton, Dickinson and Company, Franklin Lakes, NJ, USA) and Kirby-Bauer disk diffusion method (Oxoid, Hampshire, UK). Whole-genome sequencing of both strains was performed using the Illumina platform. ABRicate software was used to predict the resistance genes and plasmid replicon types carried by the strains. Sequence type (ST) analysis was performed using multilocus sequence typing. A phylogenetic tree was constructed, and homology analysis was conducted by comparing the two strains with 106 blaKPC-2-carrying carbapenem-resistant S. marcescens isolates downloaded from the NCBI database. Two S. marcescens strains were isolated from the sputum samples of patients with lower respiratory tract infections after ICU surgery. Antimicrobial sensitivity testing revealed that both strains were resistant to antimicrobial agents, including β-lactams, sulfonamides, and carbapenems, whereas they were susceptible to tigecycline and ceftazidime/avibactam. In total, 12 resistance genes were predicted, with both WF0070 and WF0071 carrying the carbapenem resistance gene blaKPC-2. Among the remaining resistance genes, the aminoglycoside resistance genes were most commonly predicted, with five types identified. The two strains in this study and the 106 blaKPC-2-carrying carbapenem-resistant S. marcescens isolates downloaded from NCBI were divided into five evolutionary groups, and both strains in this experiment were categorized into clade E. Meanwhile, 18 STs were predicted, and both strains in this study belonged to ST366. In terms of phylogenetic relationships, these strains exhibited high homology with a strain isolated in France in 2018. The two S. marcescens strains in this study displayed high resistance to multiple antimicrobial agents, and both carried the carbapenem resistance gene blaKPC-2 along with several other resistance genes. The two strains displayed close phylogenetic relationships, and the possibility of nosocomial transmission cannot be dismissed.