Chromosomal Integration of the Klebsiella pneumoniaeCarbapenemase Gene, blaKPC, in KlebsiellaSpecies Is Elusive but Not Rare

ABSTRACTCarbapenemase genes in Enterobacteriaceaeare mostly described as being plasmid associated. However, the genetic context of carbapenemase genes is not always confirmed in epidemiological surveys, and the frequency of their chromosomal integration therefore is unknown. A previously sequenced collection of blaKPC-positive Enterobacteriaceaefrom a single U.S. institution (2007 to 2012; n= 281 isolates from 182 patients) was analyzed to identify chromosomal insertions of Tn4401, the transposon most frequently harboring blaKPC. Using a combination of short- and long-read sequencing, we confirmed five independent chromosomal integration events from 6/182 (3%) patients, corresponding to 15/281 (5%) isolates. Three patients had isolates identified by perirectal screening, and three had infections which were all successfully treated. When a single copy of blaKPCwas in the chromosome, one or both of the phenotypic carbapenemase tests were negative. All chromosomally integrated blaKPCgenes were from Klebsiellaspp., predominantly K. pneumoniaeclonal group 258 (CG258), even though these represented only a small proportion of the isolates. Integration occurred via IS15-ΔI-mediated transposition of a larger, composite region encompassing Tn4401at one locus of chromosomal integration, seen in the same strain (K. pneumoniaeST340) in two patients. In summary, we identified five independent chromosomal integrations of blaKPCin a large outbreak, demonstrating that this is not a rare event. blaKPCwas more frequently integrated into the chromosome of epidemic CG258 K. pneumoniaelineages (ST11, ST258, and ST340) and was more difficult to detect by routine phenotypic methods in this context. The presence of chromosomally integrated blaKPCwithin successful, globally disseminated K. pneumoniaestrains therefore is likely underestimated.