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First genomic insights into carbapenem-resistant Klebsiella pneumoniae from Malaysia

journal contribution
posted on 2020-03-01, 00:00 authored by Han Ming Gan, Wilhelm Wei Han Eng, Amreeta Dhanoa
OBJECTIVES: Despite the increasing report of carbapenem-resistant Enterobacteriaceae in Malaysia, genomic resource for carbapenem-resistant clinical strains of Klebsiella pneumoniae remains unavailable. In this study, we aim to fill in this gap by sequencing the genomes of multiple carbapenem-resistant K. pneumoniae strains from Malaysia in addition to identifying the genetic basis for their resistance. METHODS: Illumina whole-genome sequencing was performed on eight carbapenem-resistant Klebsiella pneumoniae isolated from a Malaysian hospital. Genetic diversity was inferred from the assembled genomes based on in-silico multi locus sequence typing (MLST). In addition, plasmid- and chromosome-derived contigs were predicted using machine learning approach. After genome annotation, genes associated with carbapenem resistance were identified based on similarity search against the ResFinder database. RESULTS: The eight K. pneumoniae isolates were grouped into six different sequence types, some of which were only represented by a single isolate in the MLST database. Genomic potential for carbapenem-resistance was attributed to the presence of plasmid-localized blaNDM (blaNDM-1/blaNDM-5) or blaKPC (blaKPC-2/blaKPC-6) in these sequenced strains. A majority of these carbapenem resistance genes were flanked by repetitive (transposase or integrase) sequences, suggesting their potential mobility. We also report the first blaKPC-6-harboring plasmid contig to be assembled for K. pneumoniae, the second for the genus Klebsiella. CONCLUSION: We report the first genomic resources for carbapenem-resistant K. pneumoniae from Malaysia. The high diversity of carbapenem resistance genes and sequence types uncovered from only 8 isolates from the same hospital is worrying and indicates an urgent need to improve the genomic surveillance of clinical K. pneumoniae in Malaysia.

History

Journal

Journal of global antimicrobial resistance

Volume

20

Pagination

153 - 159

Publisher

Elsevier

Location

Amsterdam, The Netherlands

ISSN

2213-7165

eISSN

2213-7173

Language

eng

Publication classification

C1 Refereed article in a scholarly journal

Copyright notice

2019, Published by Elsevier Ltd on behalf of International Society for Antimicrobial Chemotherapy