Horizontal Gene Transfer in Multidrug-Resistant Klebsiella pneumoniae Clinical Isolates
DOI:
https://doi.org/10.5281/zenodo.22688045Keywords:
Klebsiella pneumoniae, horizontal gene transfer, plasmid, carbapenem resistance, whole-genome sequencing, nosocomial outbreakAbstract
Carbapenem-resistant Klebsiella pneumoniae (CRKP) is among the pathogens the World Health Organization has
designated a critical priority for new antibiotic development, and outbreaks driven by plasmid-mediated spread of
resistance genes between otherwise unrelated bacterial lineages complicate infection control because standard
strain-typing methods can miss transmission events that occur through plasmid transfer rather than clonal
expansion. We report a case study of a seven-month intensive care unit outbreak involving 14 multidrug-resistant
K. pneumoniae isolates from 11 patients, investigated by whole-genome sequencing and comparative plasmid
analysis after initial multi-locus sequence typing suggested the isolates belonged to three apparently unrelated
sequence types (ST258, ST15 and ST307). Long-read and short-read hybrid assembly resolved a 113 kb
IncFIB/IncHI1B plasmid carrying blaKPC-3 embedded within a Tn4401b transposon that was present, at greater
than 99.9% nucleotide identity, in isolates from all three sequence types, indicating that horizontal plasmid
transfer, rather than clonal spread of a single strain, was responsible for at least part of the outbreak. Phylogenetic
and plasmid-network analysis placed the likely origin of the plasmid in an ST258 index isolate and identified two
probable inter-strain transfer events, the second coinciding with a period of prolonged co-colonisation of a single
patient by two sequence types. The plasmid additionally carried a class 1 integron with three further resistance
determinants and a toxin-antitoxin maintenance system consistent with its stable persistence across the outbreak
period without antibiotic selection data suggesting continuous carbapenem pressure. These findings illustrate why
genomic surveillance of nosocomial CRKP outbreaks should routinely include plasmid-resolved sequencing rather
than sequence typing alone, since strain-level typing can substantially understate the true extent of a
resistance-transfer event.
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