Chromosomal Integration of the Klebsiella pneumoniae Carbapenemase Gene, blaKPC, in Klebsiella Species Is Elusive but Not Rare

Abstract

Carbapenemase genes in Enterobacteriaceae are 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 bla_KPC-positive Enterobacteriaceae from 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 bla_KPC 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 bla_KPC was in the chromosome, one or both of the phenotypic carbapenemase tests were negative. All chromosomally integrated bla_KPC genes were from Klebsiella spp., predominantly K. pneumoniae clonal 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 Tn4401 at one locus of chromosomal integration, seen in the same strain (K. pneumoniae ST340) in two patients. In summary, we identified five independent chromosomal integrations of bla_KPC in a large outbreak, demonstrating that this is not a rare event. bla_KPC was more frequently integrated into the chromosome of epidemic CG258 K. pneumoniae lineages (ST11, ST258, and ST340) and was more difficult to detect by routine phenotypic methods in this context. The presence of chromosomally integrated bla_KPC within successful, globally disseminated K. pneumoniae strains therefore is likely underestimated.

Keywords: KPC; Klebsiella; Klebsiella pneumoniae carbapenemase; antibiotic resistance; carbapenemase; chromosomal; plasmid analysis; plasmids; transposons; whole-genome sequencing.

FIG 1

Chromosomal integration of Tn4401 in Klebsiella pneumoniae ST340 isolates. (A) Alignment of ∼50-kb region of the CAV1417 chromosome with the homologous region of the NJST258_2 reference genome. Pink and blue shading indicate high sequence similarity (>99.8%) in the same or opposite orientations, respectively. Flanking sequences for mobile elements present in the complete (PacBio) CAV1417 genome are indicated (an asterisk indicates that the sequence shown has been reverse complemented). (B) Coverage of Illumina reads for CAV1417, CAV1217, or CAV1518 mapped to the complete CAV1417 genome across the region shown in panel A. Flanking sequences for Tn4401 and the right side of the 16-kb region were determined from the mapped Illumina reads.

FIG 2

Schematic showing the presumed sequence of events affecting bla_KPC in Klebsiella pneumoniae ST340 isolates.