Klebsiella pneumoniae Carbapenemase (KPC)-Producing K. pneumoniae at a Single Institution: Insights into Endemicity from Whole-Genome Sequencing

Abstract

The global emergence of Klebsiella pneumoniae carbapenemase-producing K. pneumoniae (KPC-Kp) multilocus sequence type ST258 is widely recognized. Less is known about the molecular and epidemiological details of non-ST258 K. pneumoniae in the setting of an outbreak mediated by an endemic plasmid. We describe the interplay of blaKPC plasmids and K. pneumoniae strains and their relationship to the location of acquisition in a U.S. health care institution. Whole-genome sequencing (WGS) analysis was applied to KPC-Kp clinical isolates collected from a single institution over 5 years following the introduction of blaKPC in August 2007, as well as two plasmid transformants. KPC-Kp from 37 patients yielded 16 distinct sequence types (STs). Two novel conjugative blaKPC plasmids (pKPC_UVA01 and pKPC_UVA02), carried by the hospital index case, accounted for the presence of blaKPC in 21/37 (57%) subsequent cases. Thirteen (35%) isolates represented an emergent lineage, ST941, which contained pKPC_UVA01 in 5/13 (38%) and pKPC_UVA02 in 6/13 (46%) cases. Seven (19%) isolates were the epidemic KPC-Kp strain, ST258, mostly imported from elsewhere and not carrying pKPC_UVA01 or pKPC_UVA02. Using WGS-based analysis of clinical isolates and plasmid transformants, we demonstrate the unexpected dispersal of blaKPC to many non-ST258 lineages in a hospital through spread of at least two novel blaKPC plasmids. In contrast, ST258 KPC-Kp was imported into the institution on numerous occasions, with other blaKPC plasmid vectors and without sustained transmission. Instead, a newly recognized KPC-Kp strain, ST941, became associated with both novel blaKPC plasmids and spread locally, making it a future candidate for clinical persistence and dissemination.

Whole-Genome Multilocus Sequence Typing of Extended-Spectrum-Beta-Lactamase-Producing Enterobacteriaceae

“…These high thresholds for E. coli may reflect higher mutation and recombination rates or may be related to within-patient microevolution of coexisting isolates with common ancestry. Estimates of the mutation and recombination rates of Enterobacteriaceae are limited and range from 0 to 10 mutations per genome per year (38,39). These rates reflect fixed substitution rates; short-term mutation (polymorphism) rates may be higher and are known to increase under antibiotic pressure or other environmental stress (40).…”

The Problem of Carbapenemase-Producing-Carbapenem-Resistant-Enterobacteriaceae Detection

“…This technology can query the entire bacterial genome for all known resistance mechanisms and thus can provide resistance information for numerous antimicrobial classes, rather than targeting only carbapenemases, and can identify other contributors to resistance, such as porin mutations. WGS also provides information on the type of plasmid carrying resistance genes, the evolutionary lineage of the bacterium, and the relatedness of isolates, all of which can help to elucidate the source of the isolate or inform outbreak investigations (45). Furthermore, data generated with WGS can be stored for future inquiry as new resistance determinants or virulence factors of interest are identified.…”

Genomic analysis of diversity, population structure, virulence, and antimicrobial resistance in Klebsiella pneumoniae , an urgent threat to public health

“…Several recent genomic analyses indicate that sequence type (ST) 258 is a recombinant strain that has undergone capsular exchange since its emergence as a cause of KPC outbreaks (28)(29)(30). However, little attention has been paid to other MDR clones, which also are common and can spread carbapenem resistance (31). Relatively little is known about this broader population of K. pneumoniae, and there remains a lack of data regarding transmission, pathogenicity, and the evolution and spread of MDR clones globally.…”