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

Abstract

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 blaSHV-11, blaCTX-M-15, blaTEM-1, blaNDM-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

• Colistin
• Carbapenem-resistant
• Extremely drug resistant
• Novel sequence type
• Pediatric bloodstream infection
• Klebsiella pneumoniae