WHOLE GENOME SEQUENCING REVEALS DIVERSE MODES OF CARBAPENEMASE GENE DISSEMINATION IN INDIAN KLEBSIELLA PNEUMONIAE CLINICAL ISOLATES

Abstract

Intro: Mobile genetic elements and plasmids harboring multiple drug resistance genes are a significant concern in Klebsiella pneumoniae causing nosocomial infections. The dynamics underlying the dissemination of these genes remain poorly resolved in the Indian context. Hence, using whole-genome sequencing (WGS), we described the mobile genetic elements (MGE) harboring carbapenemases genes and studied the evolutionary dynamics of horizontal gene transfer (HGT) of these genes within the population. Methods: A total of 1072 K. pneumoniae clinical isolates collected from 21 centers across India during 2013-2021 were sequenced on the Illumina platform. Antimicrobial resistance (AMR) determinants, mobile genetic elements (MGEs), and plasmids were identified using AMR finder, Mobile Element Finder, and Plasmid finder respectively. The sequence type analysis was performed using pub MLST. Additionally, subsets of isolates were sequenced using Nanopore to determine carbapenemase-encoding plasmids' complete structure. Findings: The 1072 isolates, belonged to 105 different STs and ST231 (n=225), ST147(n=170) & ST395 (n=83) were the major lineages. The AMR analysis showed 791 strains (74%) as carbapenemase-producing K. pneumoniae (CP-Kp) with 54% (n=427) producing OXA48-like carbapenemases; 17% (n= 138) NDM producers and the remaining 29% (n= 226) are co-producers of NDM and OXA. The plasmid analysis revealed carbapenemase gene dissemination through 104 different plasmids. blaOXA-48-like genes such as OXA-181 and OXA-232 have spread primarily via the ColKP3 plasmid transmitted predominantly by stable association with clonal lineage ST147 and ST231 respectively. Whereas, blaNDM genes have spread via IncF type of plasmids across numerous lineages. Further, the complete structure of plasmids carrying the NDM and OXA genes was deduced through the hybrid assembly. Discussion: Our study shows that CRKP-genes located on hybridplasmids are transmitted vertically & horizontally between strains and species. Conclusion: Mobile genetic element analysis in genomic surveillance systems provides a more comprehensive understanding of AMR spread. Identifying the key molecular markers of resistance and plasmids harboring them improves strategies to control AMR dissemination.