Genomic insight of extremely drug-resistant Klebsiella pneumoniae ST5378 from a paediatric bloodstream infection

Rajesh Kumar Sahoo; Mahendra Gaur; Suchanda Dey; Saubhagini Sahoo; Aradhana Das; Enketeswara Subudhi

doi:10.1016/j.jgar.2023.04.002

Genomic insight of extremely drug-resistant Klebsiella pneumoniae ST5378 from a paediatric bloodstream infection

J Glob Antimicrob Resist. 2023 Jun:33:227-230. doi: 10.1016/j.jgar.2023.04.002. Epub 2023 Apr 21.

Authors

Rajesh Kumar Sahoo¹, Mahendra Gaur², Suchanda Dey³, Saubhagini Sahoo³, Aradhana Das³, Enketeswara Subudhi⁴

Affiliations

¹ Centre for Biotechnology, Siksha 'O' Anusandhan (Deemed to be University), Bhubaneswar, Odisha, India. Electronic address: rajeshkumarsahoo@soa.ac.in.
² Drug Development and Analysis Laboratory, School of Pharmaceutical Sciences, Siksha 'O' Anusandhan (Deemed to be University), Bhubaneswar, India; Department of Biotechnology and Food Technology, Punjabi University, Patiala, India.
³ Centre for Biotechnology, Siksha 'O' Anusandhan (Deemed to be University), Bhubaneswar, Odisha, India.
⁴ Centre for Biotechnology, Siksha 'O' Anusandhan (Deemed to be University), Bhubaneswar, Odisha, India. Electronic address: enketeswarasubudhi@soa.ac.in.

PMID: 37086894
DOI: 10.1016/j.jgar.2023.04.002

Abstract

Objectives: This study investigated the draft genome and phylogeny of an extremely drug-resistant and novel sequence type Klebsiella pneumoniae isolated from a paediatric bloodstream infection.

Methods: An isolate from a 7-year-old child with severe respiratory infection was identified, and the whole genome was sequenced using the Illumina MiSeq platform. High-quality reads were de novo assembled via Unicycler and annotated via PROKKA. Antimicrobial resistance genes, virulence factors, and plasmid and phage sequences were identified using the resistance gene identifier, VFanalyzer, Plasmidfinder, and PHASTER, respectively. Phylogenetics of closely related strains were inferred using core-genome multi-locus sequence typing and single nucleotide polymorphism.

Results: The draft genome of carbapenem-resistant K. pneumoniae RKS87 was 5 580 330 bp in size, with a GC content of 57.73%. The final assembly resulted in 38 contigs comprising 5075 CDS, 124 pseudo genes, 83 tRNA, 25 rRNA, and 10 ncRNA. The strain was assigned to a novel sequence type, ST5378, and harboured bla_SHV-11, bla_CTX-M-15, bla_TEM-1, bla_NDM-1, APH(3')-VI, OqxA, QnrS1, and fosA. We also identified the mutations in outer membrane porin (OmpK36 and OmpK37) and two-component system genes (PmrB and EptB). Three biomarkers (iroE, iroN, and iutA) associated with hypervirulent phenotype were also present in the genome. Phylogenetics of closely related strains revealed the clonal lineage of ST2938.

Conclusions: The genome sequence and phylogenetics of the strain offer valuable insight into the clonal lineage, resistance genes, and pathogenicity of the novel sequence type ST5378.

Keywords: Carbapenem-resistant; Colistin; Extremely drug resistant; Klebsiella pneumoniae; Novel sequence type; Pediatric bloodstream infection.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Anti-Bacterial Agents / pharmacology
Anti-Bacterial Agents / therapeutic use
Genomics
Humans
Klebsiella Infections* / drug therapy
Klebsiella pneumoniae
Multilocus Sequence Typing
Sepsis* / drug therapy
Whole Genome Sequencing
beta-Lactamases / genetics

Substances

Anti-Bacterial Agents
beta-Lactamases