Resistance Determinants and Mobile Genetic Elements of an NDM-1-Encoding Klebsiella pneumoniae Strain

Abstract

Multidrug-resistant Enterobacteriaceae are emerging as a serious infectious disease challenge. These strains can accumulate many antibiotic resistance genes though horizontal transfer of genetic elements, those for β-lactamases being of particular concern. Some β-lactamases are active on a broad spectrum of β-lactams including the last-resort carbapenems. The gene for the broad-spectrum and carbapenem-active metallo-β-lactamase NDM-1 is rapidly spreading. We present the complete genome of Klebsiella pneumoniae ATCC BAA-2146, the first U.S. isolate found to encode NDM-1, and describe its repertoire of antibiotic-resistance genes and mutations, including genes for eight β-lactamases and 15 additional antibiotic-resistance enzymes. To elucidate the evolution of this rich repertoire, the mobile elements of the genome were characterized, including four plasmids with varying degrees of conservation and mosaicism and eleven chromosomal genomic islands. One island was identified by a novel phylogenomic approach, that further indicated the cps-lps polysaccharide synthesis locus, where operon translocation and fusion was noted. Unique plasmid segments and mosaic junctions were identified. Plasmid-borne bla CTX-M-15 was transposed recently to the chromosome by ISEcp1. None of the eleven full copies of IS26, the most frequent IS element in the genome, had the expected 8-bp direct repeat of the integration target sequence, suggesting that each copy underwent homologous recombination subsequent to its last transposition event. Comparative analysis likewise indicates IS26 as a frequent recombinational junction between plasmid ancestors, and also indicates a resolvase site. In one novel use of high-throughput sequencing, homologously recombinant subpopulations of the bacterial culture were detected. In a second novel use, circular transposition intermediates were detected for the novel insertion sequence ISKpn21 of the ISNCY family, suggesting that it uses the two-step transposition mechanism of IS3. Robust genome-based phylogeny showed that a unified Klebsiella cluster contains Enterobacter aerogenes and Raoultella, suggesting the latter genus should be abandoned.

Outbreak of NDM-1-Producing Klebsiella pneumoniae in a Dutch Hospital, with Interspecies Transfer of the Resistance Plasmid and Unexpected Occurrence in Unrelated Health Care Centers

“…The bla NDM-1 gene was located on a variant of the pNDM-US plasmid (CP006661), a 140-kb plasmid belonging to the IncA/C2 group (13). Compared to the pNDM-US reference genome, the plasmid in the 33 ST873 K. pneumoniae isolates lacked a 740-bp segment that carried the aac(6=)-1B-cr (fluoroquinolone and aminoglycoside resistance) gene.…”

Genetic Contexts of bla NDM-1 in Patients Carrying Multiple NDM-Producing Strains

“…In addition, the genetic structure or context in which bla NDM resides varies between different plasmid types and even within the same plasmid type (14). The bla NDM-1 genetic contexts observed with Enterobacteriaceae plasmids frequently involve various mechanisms of gene acquisition, including different ISCR elements (15), class one integrons (16), flanking insertion (IS) elements (15), and singleton IS elements present in close proximity (8,10). In contrast, bla NDM genetic contexts within Acinetobacter spp.…”

Risk Factors for Carbapenem Resistant Klebsiella pneumoniae Hospital Infection in the Intensive Care Unit

“…The most important mechanism of resistance of carbapenems is the production of a carbapenemase enzyme, blaKPC. The gene for this enzyme is carried on a mobile piece of genetic material, which increases the risk for dissemination, even to other Enterobacteriaceae (23,24). The emergence and spread of CR-Kp underlines the need for immediate aggressive detection and control strategies to preserve their efficacy in the future (25).…”