Abstract
Carbapenem-resistant Klebsiella pneumoniae (CRKP) strains belonging to sequence type 258 (ST258) are frequent causes of hospital-associated outbreaks and are a major contributor to the spread of carbapenemases. This genetic lineage emerged several decades ago and remains a major global health care challenge. In this study, genomic epidemiology was used to investigate the emergence, evolution, and persistence of ST258 carbapenem-resistant K. pneumoniae outbreak-causing lineages at a large tertiary care hospital over 8 years. A time-based phylogenetic analysis of 136 ST258 isolates demonstrated the succession of multiple genetically distinct ST258 sublineages over the 8-year period. Ongoing genomic surveillance identified the emergence and persistence of several distinct clonal ST258 populations. Patterns of multidrug resistance determinants and plasmid replicons were consistent with continued evolution and persistence of these populations. Five ST258 outbreaks were documented, including three that were caused by the same clonal lineage. Mutations in genes encoding effectors of biofilm production and iron acquisition were identified among persistent clones. Two emergent lineages bearing K. pneumoniae integrative conjugative element 10 (ICEKp10) and harboring yersiniabactin and colibactin virulence factors were identified. The results show how distinct ST258 subpopulations have evolved and persisted within the same hospital over nearly a decade.IMPORTANCE The carbapenem class of antibiotics is invaluable for the treatment of selected multidrug-resistant Gram-negative pathogens. The continued transmission of carbapenem-resistant bacteria such as ST258 K. pneumoniae is of serious global public health concern, as treatment options for these infections are limited. This genomic epidemiologic investigation traced the natural history of ST258 K. pneumoniae in a single health care setting over nearly a decade. We found that distinct ST258 subpopulations have caused both device-associated and ward-associated outbreaks, and some of these populations remain endemic within our hospital to the present day. The finding of virulence determinants among emergent ST258 clones supports the idea of convergent evolution of drug-resistant and virulent CRKP strains and highlights the need for continued surveillance, prevention, and control efforts to address emergent and evolving ST258 populations in the health care setting.
Highlights
Carbapenem-resistant Klebsiella pneumoniae (CRKP) strains belonging to sequence type 258 (ST258) are frequent causes of hospital-associated outbreaks and are a major contributor to the spread of carbapenemases
Whole-genome sequencing (WGS) performed on clinical K. pneumoniae isolates collected for outbreak investigations (n ϭ 53), routine infection prevention (IP) (n ϭ 17), studies of antimicrobial resistance (AMR) (n ϭ 37), and a prospective genomic epidemiology surveillance project, Enhanced Detection System for Hospital-Associated Transmission (EDS-HAT) (n ϭ 29), identified 136 isolates belonging to ST258
A maximum likelihood phylogenetic tree constructed on the basis of 1,130 core genome single nucleotide polymorphisms from these genomes was consistent with the ST258 population structure originally described by DeLeo et al [10] (Fig. 1)
Summary
Carbapenem-resistant Klebsiella pneumoniae (CRKP) strains belonging to sequence type 258 (ST258) are frequent causes of hospital-associated outbreaks and are a major contributor to the spread of carbapenemases. This genetic lineage emerged several decades ago and remains a major global health care challenge. Carbapenem-resistant Klebsiella pneumoniae (CRKP) strains belonging to sequence type 258 (ST258) have spread globally in the past several decades This genetic lineage has caused numerous hospital-associated outbreaks and is of public health concern due to the presence of plasmid-encoded K. pneumoniae carbapenemases (KPCs) [1,2,3,4,5,6]. The aim of this study was to investigate the emergence, evolution, and persistence of ST258 lineages and their propensity for causing outbreaks in our hospital by studying the genomic epidemiology of a collection of 136 ST258 CRKP isolates collected over an 8-year period
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