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

Geetha Nagaraj | Zendy; Varun Shamanna | Zendy; Vandana Govindan | Zendy; Steffimole Rose | Zendy; D Sravani | Zendy; K. P. Akshata | Zendy; M R Shincy | Zendy; VT Venkatesha | Zendy; Monica Abrudan | Zendy; Silvia Argimón | Zendy; Mihir Kekre | Zendy; Anthony Underwood | Zendy; David M. Aanensen | Zendy; K L Ravikumar | Zendy; Khalil Abudahab | Zendy; Harry Harste | Zendy; Dawn Muddyman | Zendy; Ben Taylor | Zendy; Nicole E. Wheeler | Zendy; Sophia David | Zendy; Pilar Donado-Godoy | Zendy; Johan Fabian Bernal | Zendy; Alejandra Arévalo | Zendy; María Fernanda Valencia | Zendy; Erik C D Osma Castro | Zendy; K N Ravishankar | Zendy; Iruka N. Okeke | Zendy; Anderson O. Oaikhena | Zendy; Ayorinde O. Afolayan | Zendy; Jolaade J Ajiboye | Zendy; Erkison Ewomazino Odih | Zendy; Celia Carlos | Zendy; Marietta L Lagrada | Zendy; Polle Krystle V Macaranas | Zendy; Agnettah M Olorosa | Zendy; June M Gayeta | Zendy; Elmer M Herrera | Zendy

Open Access

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

Author(s) -

Geetha Nagaraj,

Varun Shamanna,

Vandana Govindan,

Steffimole Rose,

D Sravani,

K. P. Akshata,

M R Shincy,

VT Venkatesha,

Monica Abrudan,

Silvia Argimón,

Mihir Kekre,

Anthony Underwood,

David M. Aanensen,

K L Ravikumar,

Khalil Abudahab,

Harry Harste,

Dawn Muddyman,

Ben Taylor,

Nicole E. Wheeler,

Sophia David,

Pilar Donado-Godoy,

Johan Fabian Bernal,

Alejandra Arévalo,

María Fernanda Valencia,

Erik C D Osma Castro,

K N Ravishankar,

Iruka N. Okeke,

Anderson O. Oaikhena,

Ayorinde O. Afolayan,

Jolaade J Ajiboye,

Erkison Ewomazino Odih,

Celia Carlos,

Marietta L Lagrada,

Polle Krystle V Macaranas,

Agnettah M Olorosa,

June M Gayeta,

Elmer M Herrera

Publication year - 2021

Publication title -

clinical infectious diseases

Language(s) - English

Resource type - Journals

SCImago Journal Rank - 3.44

H-Index - 336

eISSN - 1537-6591

pISSN - 1058-4838

DOI - 10.1093/cid/ciab767

Subject(s) - klebsiella pneumoniae , multilocus sequence typing , biology , locus (genetics) , virulence , genetics , plasmid , antibiotic resistance , microbiology and biotechnology , typing , population , genetic diversity , phylogenetic tree , genotype , gene , medicine , antibiotics , environmental health , escherichia coli

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. bla OXA-48-like and bla NDM-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.

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