Decentralized nanopore genomics reveals diverse Klebsiella pneumoniae and no evidence of patient-patient transmission in a New Zealand hospital.

Klebsiella pneumoniae is a leading cause of healthcare-associated infections worldwide, yet its population structure and transmission dynamics remain largely uncharacterized in New Zealand hospitals. We conducted a 15-month prospective genomic surveillance pilot at Wellington Regional Hospital, embedding Oxford Nanopore MinION sequencing directly within the diagnostic laboratory. Clinical and screening isolates (n=157) underwent on-site sequencing and genotyping. Following quality control, 121 (77%) high-quality genomes (118 complete assemblies) were analysed for diversity, antimicrobial resistance (AMR), virulence loci and plasmid content and assessed for evidence of in-hospital transmission. The cohort covered many ages (0 to 95 years), with nearly half of the patients aged ≥65 years. The local K. pneumoniae population was highly diverse, comprising 75 distinct sequence types (STs), of which 68% were single-isolate STs. Although a few lineages recurred intermittently (e.g. ST253 and ST17), no clone showed evidence of patient-patient transmission. Plasmid reconstructions showed backbones dominated by F-type, Col, and mosaic multi-replicon elements. Acquired AMR genes were plasmid-borne in 35/118 complete genomes. Chromosomes mostly carried intrinsic determinants typical of K. pneumoniae: bla SHV (intrinsic ampicillin resistance) and fosA and oqxAB (which may raise minimum inhibitory concentrations but, in their intrinsic forms, do not exceed clinical breakpoints). Few isolates carried markers of K. pneumoniae virulence plasmids (iuc/iro siderophores and rmpA/rmpA2; Kleborate virulence score ≥3), and none showed convergence of virulence and acquired AMR. This study shows that prospective, hospital-based nanopore sequencing is feasible in routine diagnostic settings and can deliver high-resolution genomic intelligence for infection prevention and control. In this setting, K. pneumoniae isolates arose from a genotypically heterogeneous background without evidence of patient-patient transmission. This pilot establishes a genomic baseline for K. pneumoniae in a major New Zealand hospital and supports a trigger-based framework for early detection of high-risk clones before they become established.