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. 2021 Dec 1;73(Suppl_4):S300-S307.
doi: 10.1093/cid/ciab767.

High-Resolution Genomic Profiling of Carbapenem-Resistant Klebsiella pneumoniae Isolates: A Multicentric Retrospective Indian Study

Geetha Nagaraj  1 , Varun Shamanna  1 , Vandana Govindan  1 , Steffimole Rose  1 , D Sravani  1 , K P Akshata  1 , M R Shincy  1 , V T Venkatesha  1 , Monica Abrudan  2   3 , Silvia Argimón  2   3 , Mihir Kekre  2   3 , Anthony Underwood  2   3 , David M Aanensen  2   3 , K L Ravikumar  1 ; NIHR Global Health Research Unit on Genomic Surveillance of Antimicrobial Resistance
Collaborators, Affiliations

High-Resolution Genomic Profiling of Carbapenem-Resistant Klebsiella pneumoniae Isolates: A Multicentric Retrospective Indian Study

Geetha Nagaraj et al. Clin Infect Dis. .

Abstract

Background: Carbapenem-resistant Klebsiella pneumoniae (CRKP) is a threat to public health in India because of its high dissemination, mortality, and limited treatment options. Its genomic variability is reflected in the diversity of sequence types, virulence factors, and antimicrobial resistance (AMR) mechanisms. This study aims to characterize the clonal relationships and genetic mechanisms of resistance and virulence in CRKP isolates in India.

Materials and methods: We characterized 344 retrospective K. pneumoniae clinical isolates collected from 8 centers across India collected in 2013-2019. Susceptibility to antibiotics was tested with VITEK 2. Capsular types, multilocus sequence type, virulence genes, AMR determinants, plasmid replicon types, and a single-nucleotide polymorphism phylogeny were inferred from their whole genome sequences.

Results: Phylogenetic analysis of the 325 Klebsiella isolates that passed quality control revealed 3 groups: K. pneumoniae sensu stricto (n = 307), K. quasipneumoniae (n = 17), and K. variicola (n = 1). Sequencing and capsular diversity analysis of the 307 K. pneumoniae sensu stricto isolates revealed 28 sequence types, 26 K-locus types, and 11 O-locus types, with ST231, KL51, and O1V2 being predominant. blaOXA-48-like and blaNDM-1/5 were present in 73.2% and 24.4% of isolates, respectively. The major plasmid replicon types associated with carbapenase genes were IncF (51.0%) and Col group (35.0%).

Conclusion: Our study documents for the first time the genetic diversity of K and O antigens circulating in India. The results demonstrate the practical applicability of genomic surveillance and its utility in tracking the population dynamics of CRKP. It alerts us to the urgency for longitudinal surveillance of these transmissible lineages.

Keywords: K. pneumoniae; ColKP3; KL51; ST231; blaOXA232; carbapenem resistance.

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Figures

Figure 1.
Figure 1.
Carbapenem resistance mechanisms by ST. (A) Mechanisms of resistance to carbapenems identified in the genomes of 280 isolates grouped by their phenotypic carbapenem resistance profile. Genes responsible for carbapenems are indicated. (B) The determinants present in each ST and responsible for carbapenem resistance. Note, where more than 1 determinant is present, the single determinant or combination likely to result in the highest increased in susceptibility to carbapenems is recorded. ST, sequence type.
Figure 2.
Figure 2.
Phylogenetic analysis of ST231 lineage. A phylogenetic tree of 107 ST231 genomes from India. The lineage highlighted in the box is shown in detail, with metadata blocks showing ST, K locus, AMR determinants, and virulence factors. The full data are available at https://microreact.org/project/5GDXCkZsvajcXTmW89LRED/746bb511. AMR, antimicrobial resistance; ST, sequence type.
See this image and copyright information in PMC

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