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Resistance determinants and mobile genetic elements of an NDM-1-encoding Klebsiella pneumoniae strain.

Hudson CM, Bent ZW, Meagher RJ, Williams KP - PLoS ONE (2014)

Bottom Line: 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.In one novel use of high-throughput sequencing, homologously recombinant subpopulations of the bacterial culture were detected.Robust genome-based phylogeny showed that a unified Klebsiella cluster contains Enterobacter aerogenes and Raoultella, suggesting the latter genus should be abandoned.

View Article: PubMed Central - PubMed

Affiliation: Department of Systems Biology, Sandia National Laboratories, Livermore, California, United States of America.

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 blaCTX-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.

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Klebsiella phylogeny.Tree for 108 genomes based on a 2.93-Mbp alignment, rooted at the midpoint of the outgroup (Ecl/Yre) branch. Nodes with <30% bootstrap support were combined forming the multifurcated dashed line; otherwise support values are shown only when <100%. Brackets: Kpn multilocus sequence type (ST). Inset: enlargement of the “core Kpn” phylogeny. Kpn2146 falls in a clade containing fellow ST11 strains Kpn JM45 and Kpn HS11286 and a tight clade (circled) of ST258 and ST512 strains. The ST258/ST512 clade is heavily sequenced, and represented here with only five of its most diverse members. Bold: complete genomes used for phyloblocks analysis. Species name abbreviations: Kpn, K. pneumoniae; Ksp, K. sp.; Kpl, K. cf. planticola; Kox, K. oxytoca; Kva, K. variicola; Eae, Enterobacter aerogenes; Ecl, E. cloacae; Ror, Raoultella ornithinolytica; Yre, Yokanella regensburgei.
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pone-0099209-g001: Klebsiella phylogeny.Tree for 108 genomes based on a 2.93-Mbp alignment, rooted at the midpoint of the outgroup (Ecl/Yre) branch. Nodes with <30% bootstrap support were combined forming the multifurcated dashed line; otherwise support values are shown only when <100%. Brackets: Kpn multilocus sequence type (ST). Inset: enlargement of the “core Kpn” phylogeny. Kpn2146 falls in a clade containing fellow ST11 strains Kpn JM45 and Kpn HS11286 and a tight clade (circled) of ST258 and ST512 strains. The ST258/ST512 clade is heavily sequenced, and represented here with only five of its most diverse members. Bold: complete genomes used for phyloblocks analysis. Species name abbreviations: Kpn, K. pneumoniae; Ksp, K. sp.; Kpl, K. cf. planticola; Kox, K. oxytoca; Kva, K. variicola; Eae, Enterobacter aerogenes; Ecl, E. cloacae; Ror, Raoultella ornithinolytica; Yre, Yokanella regensburgei.

Mentions: Phylotypes were analyzed with Mowgli [34], parsimoniously counting gain/loss events required to reconcile our robust genome tree (Fig. 1) with its subtree of only the phylotype taxa. This allowed us to classify nonubiquitous phylotypes as either simple (explainable by a single gain/loss event), or complex (requiring multiple gains/losses). The complex class was significantly overrepresented among the learned phylotypes (36 of 38) relative to the remaining phylotypes (183 of 246) (one-sided χ2 test of proportions: P<0.005). Only two learned phylotypes were simple: Kpn2146-only and Kpn2146/KpnHS11286-only.


Resistance determinants and mobile genetic elements of an NDM-1-encoding Klebsiella pneumoniae strain.

Hudson CM, Bent ZW, Meagher RJ, Williams KP - PLoS ONE (2014)

Klebsiella phylogeny.Tree for 108 genomes based on a 2.93-Mbp alignment, rooted at the midpoint of the outgroup (Ecl/Yre) branch. Nodes with <30% bootstrap support were combined forming the multifurcated dashed line; otherwise support values are shown only when <100%. Brackets: Kpn multilocus sequence type (ST). Inset: enlargement of the “core Kpn” phylogeny. Kpn2146 falls in a clade containing fellow ST11 strains Kpn JM45 and Kpn HS11286 and a tight clade (circled) of ST258 and ST512 strains. The ST258/ST512 clade is heavily sequenced, and represented here with only five of its most diverse members. Bold: complete genomes used for phyloblocks analysis. Species name abbreviations: Kpn, K. pneumoniae; Ksp, K. sp.; Kpl, K. cf. planticola; Kox, K. oxytoca; Kva, K. variicola; Eae, Enterobacter aerogenes; Ecl, E. cloacae; Ror, Raoultella ornithinolytica; Yre, Yokanella regensburgei.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4048246&req=5

pone-0099209-g001: Klebsiella phylogeny.Tree for 108 genomes based on a 2.93-Mbp alignment, rooted at the midpoint of the outgroup (Ecl/Yre) branch. Nodes with <30% bootstrap support were combined forming the multifurcated dashed line; otherwise support values are shown only when <100%. Brackets: Kpn multilocus sequence type (ST). Inset: enlargement of the “core Kpn” phylogeny. Kpn2146 falls in a clade containing fellow ST11 strains Kpn JM45 and Kpn HS11286 and a tight clade (circled) of ST258 and ST512 strains. The ST258/ST512 clade is heavily sequenced, and represented here with only five of its most diverse members. Bold: complete genomes used for phyloblocks analysis. Species name abbreviations: Kpn, K. pneumoniae; Ksp, K. sp.; Kpl, K. cf. planticola; Kox, K. oxytoca; Kva, K. variicola; Eae, Enterobacter aerogenes; Ecl, E. cloacae; Ror, Raoultella ornithinolytica; Yre, Yokanella regensburgei.
Mentions: Phylotypes were analyzed with Mowgli [34], parsimoniously counting gain/loss events required to reconcile our robust genome tree (Fig. 1) with its subtree of only the phylotype taxa. This allowed us to classify nonubiquitous phylotypes as either simple (explainable by a single gain/loss event), or complex (requiring multiple gains/losses). The complex class was significantly overrepresented among the learned phylotypes (36 of 38) relative to the remaining phylotypes (183 of 246) (one-sided χ2 test of proportions: P<0.005). Only two learned phylotypes were simple: Kpn2146-only and Kpn2146/KpnHS11286-only.

Bottom Line: 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.In one novel use of high-throughput sequencing, homologously recombinant subpopulations of the bacterial culture were detected.Robust genome-based phylogeny showed that a unified Klebsiella cluster contains Enterobacter aerogenes and Raoultella, suggesting the latter genus should be abandoned.

View Article: PubMed Central - PubMed

Affiliation: Department of Systems Biology, Sandia National Laboratories, Livermore, California, United States of America.

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 blaCTX-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.

Show MeSH
Related in: MedlinePlus