Epidemiology and genomic analysis of Klebsiella oxytoca from a single hospital network in Australia

Abstract

AbstractInfections caused by Klebsiella oxytoca are the second most common cause of Klebsiella infections in humans. Most studies to date have focused on K. oxytoca outbreaks and few have examined the broader clinical context of K. oxytoca. Here, we collected all clinical isolates identified as K. oxytoca in a hospital microbiological diagnostic lab across a 15-month period (n=239). The majority of isolates were sensitive to antimicrobials, however 22 isolates were resistant to third-generation cephalosporins (3GCR), of which five were also carbapenem resistant. Whole genome sequencing of a subset of 92 isolates (all invasive, 3GCR and non-urinary isolates collected >48h after admission) showed those identified as K. oxytoca by the clinical laboratory actually encompassed four distinct species (K. oxytoca, Klebsiella michiganensis, Klebsiella grimontii and Klebsiella pasteurii), referred to as the K. oxytoca species complex (KoSC). There was significant diversity within the population, with only 10/67 multi-locus sequence types (STs) represented by more than one isolate. Strain transmission was rare, with only a single likely event identified. Six isolates had either extended spectrum beta-lactamase (blaSHV-12 and/or blaCTX-M-9) or carbapenemase (blaIMP-4) genes. One pair of K. michiganensis and K. pasteurii genomes carried an identical blaIMP-4 IncL/M plasmid, indicative of plasmid transmission. Whilst antimicrobial resistance was rare, the resistance plasmids were similar to those found in other Enterobacterales, demonstrating that KoSC has access to the same plasmid reservoir and thus there is potential for multi-drug resistance. Further genomic studies are required to improve our understanding of the KoSC population and facilitate investigation into the attributes of successful nosocomial isolates.