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Nagaraj G, Shamanna V, Govindan V, Rose S, Sravani D, Akshata KP, Shincy MR, Venkatesha VT, Abrudan M, Argimón S, Kekre M, Underwood A, Aanensen DM, Ravikumar KL. High-Resolution Genomic Profiling of Carbapenem-Resistant Klebsiella pneumoniae Isolates: A Multicentric Retrospective Indian Study. Clin Infect Dis 2021; 73:S300-S307. [PMID: 34850832 PMCID: PMC8634558 DOI: 10.1093/cid/ciab767] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
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.
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Affiliation(s)
- Geetha Nagaraj
- Central Research Laboratory, Kempegowda Institute of Medical Sciences, Bengaluru, India
| | - Varun Shamanna
- Central Research Laboratory, Kempegowda Institute of Medical Sciences, Bengaluru, India
| | - Vandana Govindan
- Central Research Laboratory, Kempegowda Institute of Medical Sciences, Bengaluru, India
| | - Steffimole Rose
- Central Research Laboratory, Kempegowda Institute of Medical Sciences, Bengaluru, India
| | - D Sravani
- Central Research Laboratory, Kempegowda Institute of Medical Sciences, Bengaluru, India
| | - K P Akshata
- Central Research Laboratory, Kempegowda Institute of Medical Sciences, Bengaluru, India
| | - M R Shincy
- Central Research Laboratory, Kempegowda Institute of Medical Sciences, Bengaluru, India
| | - V T Venkatesha
- Central Research Laboratory, Kempegowda Institute of Medical Sciences, Bengaluru, India
| | - Monica Abrudan
- Centre for Genomic Pathogen Surveillance, Big Data Institute, University of Oxford, Oxford, UK
- Wellcome Genome Campus, Hinxton, UK
| | - Silvia Argimón
- Centre for Genomic Pathogen Surveillance, Big Data Institute, University of Oxford, Oxford, UK
- Wellcome Genome Campus, Hinxton, UK
| | - Mihir Kekre
- Centre for Genomic Pathogen Surveillance, Big Data Institute, University of Oxford, Oxford, UK
- Wellcome Genome Campus, Hinxton, UK
| | - Anthony Underwood
- Centre for Genomic Pathogen Surveillance, Big Data Institute, University of Oxford, Oxford, UK
- Wellcome Genome Campus, Hinxton, UK
| | - David M Aanensen
- Centre for Genomic Pathogen Surveillance, Big Data Institute, University of Oxford, Oxford, UK
- Wellcome Genome Campus, Hinxton, UK
| | - K L Ravikumar
- Central Research Laboratory, Kempegowda Institute of Medical Sciences, Bengaluru, India
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