Resistance Determinants and Mobile Genetic Elements of an NDM-1-Encoding <i>Klebsiella pneumoniae</i> Strain

<div><p>Multidrug-resistant <i>Enterobacteriaceae</i> 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 <i>Klebsiella pneumoniae</i> 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 <i>cps-lps</i> polysaccharide synthesis locus, where operon translocation and fusion was noted. Unique plasmid segments and mosaic junctions were identified. Plasmid-borne <i>bla</i>_CTX-M-15 was transposed recently to the chromosome by IS<i>Ecp1</i>. None of the eleven full copies of IS<i>26</i>, 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 IS<i>26</i> 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 IS<i>Kpn21</i> of the IS<i>NCY</i> family, suggesting that it uses the two-step transposition mechanism of IS<i>3</i>. Robust genome-based phylogeny showed that a unified <i>Klebsiella</i> cluster contains <i>Enterobacter aerogenes</i> and <i>Raoultella</i>, suggesting the latter genus should be abandoned.</p>