Unraveling the Genetic Diversity of Enterobacter and Klebsiella spp.

Abstract

Enterobacter and Klebsiella spp. are widespread gram-negative opportunistic pathogens linked to nosocomial infections and posing public health concerns. E. hormaechei, K. aerogenes, and K pneumoniae are among the most common in hospital settings, exhibiting intrinsic but also acquired resistance against many antimicrobial agents through the acquisition of mobile elements. This study aimed at determining resistance trends and virulence patterns in 19 Enterobacter spp. and seven Klebsiella spp. clinical isolates. Short- and long-read whole-genome sequencing platforms were used for in-depth molecular characterization to reveal resistance patterns, virulence determinants, and mobile elements mediating dissemination. Our genome-based identification showed diversity at the species level, but detecting E. mori, E. bugandensis, and E. kobei was noteworthy. All the isolates, except for two K. pneumoniae, were resistant to cefoxitin. At the same time, all were susceptible to carbapenems except for two E. hormaechei exhibiting resistance against imipenem and ertapenem while being susceptible to meropenem. The two isolates had the blaNDM-1 gene. We also identified plasmids having 32 different Inc groups, with IncFIB, IncFII, and Col(pHAD28) being the most common, and many insertion sequences (IS) belonging to different families were detected. IS are essential elements in introducing genetic variability, adaptability, and mediating the mobilization of resistance determinants. Multi-locus sequence typing revealed many novel genotypes and high genetic diversity. The isolates clustered within 18 known and nine unknown sequence types; ST93 and ST50 were the most common. The results of this study demonstrated the presence of many mobile elements, including plasmids, IS, and transposons, facilitating the spread of resistance determinants within bacterial populations in healthcare settings and contributing to their evolution and adaptability, highlighting their impact on public health.