Co-colonization of different species harboring KPC or NDM carbapenemase in the same host gut: insight of resistance evolution by horizontal gene transfer

Abstract

Introduction: The dissemination of carbapenem-resistant Enterobacteriales (CRE) in nosocomial settings is primarily associated with the horizontal transfer of plasmids. However, limited research has focused on the in-host transferability of carbapenem resistance. In this study, ten isolates were collected from gut specimens of five individuals, each hosting two different species, including Escherichia coli, Klebsiella pneumoniae, Klebsiella aerogenes, Enterobacter cloacae, or Citrobacter koseri.

Methods: Species identification and antimicrobial susceptibility were determined by MALDI-TOF MS and broth microdilution method. Carbapenemase genes were detected and localized using PCR, S1-PFGE and southern blot. The transferability of carbapenemase genes between species was investigated through filter mating experiments, and the genetic contexts of the plasmids were analyzed using whole genome sequencing.

Results and discussion: Our results revealed that each of the ten isolates harbored a carbapenemase gene, including bla _NDM-5, bla _NDM-1, or bla _KPC-2, on a plasmid. Five different plasmids were successfully transferred to recipient cells of E. coli, K. pneumoniae or A. baumannii by transconjugation. The genetic contexts of the carbapenemase gene were remarkably similar between the two CRE isolates from each individual. This study highlights the potential for interspecies plasmid transmission in human gut, emphasizing the colonization of CRE as a significant risk factor for the dissemination of carbapenemase genes within the host. These findings underscore the need for appropriate intestinal CRE screening and colonization prevention.

Keywords: KPC; NDM; carbapenem-resistant Enterobacteriales; horizontal gene transfer; host gut; interspecies.

Figure 1

S1 PFGE and Southern blot hybridization of 10 CRE isolates. (A) S1 PFGE of the 10 CRE isolates. (B) Southern blot hybridization of probe bla_NDM and bla_KPC. The white arrows showed the positive bands of plasmid hybridized with bla_NDM probe or bla_KPC probe. M, the Salmonella serotype Braenderup strain H9812 was used as a molecular marker.

Figure 2

Plasmid comparison based on WGS. (A) WGS of Kpn40 plasmid versus reference sequence CP084538.1, Eco13188, Cko20222, and Eco41. (B) WGS of Kpn20795 plasmid versus reference sequence MH917283.1, and Ecl20823. (C) WGS of Eco20155 plasmid versus reference sequence CP047692.1. (D) WGS of Kpn20156 plasmid versus reference sequence MT269826.1. (E) WGS of Eco20779 plasmid versus reference sequence KF914891.1, and Eae20780 contig22,23,26,31,33,34. Different colors represent various genetic types. , antibiotic resistance; , hypothetical protein; , IS; , CDS; , reference sequence; , GC Skew+; , GC Skew−; , GC content; , Eae20780 contig22, 23, 26, 31, 33, 34; , Ecl20823; , Eco13188; , Cko20222; , Eco41.