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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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Learned phyloblocks identify a new island and the highly variable capsular polysaccharide and lipopolysaccharide synthesis gene cluster (cps-lps).Nonubiquity phyloblocks: those missing in at least one of the 11 reference chromosomes. Complex phyloblocks: those requiring more than one gain/loss event to reconcile the phylotype with the genome tree of Fig. 1. As a percentage of their combined 411 kbp, the learned phyloblocks mapped either to the training islands (81.9%), the two newly indicated regions (12.0%), insertion sequences (2.1%), or to small scattered regions that did not show hallmarks of islands (4.0%). Red segments: the 11 final islands (including a tandem array of Kpn21L and Kpn11L). Circles, the two newly indicated regions.
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pone-0099209-g005: Learned phyloblocks identify a new island and the highly variable capsular polysaccharide and lipopolysaccharide synthesis gene cluster (cps-lps).Nonubiquity phyloblocks: those missing in at least one of the 11 reference chromosomes. Complex phyloblocks: those requiring more than one gain/loss event to reconcile the phylotype with the genome tree of Fig. 1. As a percentage of their combined 411 kbp, the learned phyloblocks mapped either to the training islands (81.9%), the two newly indicated regions (12.0%), insertion sequences (2.1%), or to small scattered regions that did not show hallmarks of islands (4.0%). Red segments: the 11 final islands (including a tandem array of Kpn21L and Kpn11L). Circles, the two newly indicated regions.

Mentions: Plasmids frequently disseminate antibiotic resistance genes in Klebsiella, but genomic islands are also potential vehicles. Our program Islander [31] found six islands in tRNA/tmRNA genes, including a tandem island pair at a tRNALeu gene. PHAST [32] confirmed three of these and identified four additional prophage-like islands, one precisely within the gene for the short regulatory RNA RybB. The 10 resulting islands accounted for 6.3% of the Kpn2146 chromosome. We used these 10 Islander/PHAST islands (Table 3) as a training set for a phylogenomic approach to find additional islands, based on the principle that islands tend to occur sporadically among closely related strains. The Kpn2146 chromosome was partitioned into “phyloblocks”, which we define as DNA intervals where all positions share the same phylotype, i.e., the same presence/absence profile among a given set of closely related genomes. We selected phyloblocks that were enriched in (i.e., “learned” from) the training islands. These learned phyloblocks pointed to the island Kpn23SapB, with an integrase gene and att site pair, that was missed by Islander and Phast. Learned phyloblocks also pointed to the non-island genomic locus cps-lps, described further below. An overview of learned phyloblocks across the chromosome (Fig. 5) shows the tight mapping to cps-lps, mobile islands and ISs.


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)

Learned phyloblocks identify a new island and the highly variable capsular polysaccharide and lipopolysaccharide synthesis gene cluster (cps-lps).Nonubiquity phyloblocks: those missing in at least one of the 11 reference chromosomes. Complex phyloblocks: those requiring more than one gain/loss event to reconcile the phylotype with the genome tree of Fig. 1. As a percentage of their combined 411 kbp, the learned phyloblocks mapped either to the training islands (81.9%), the two newly indicated regions (12.0%), insertion sequences (2.1%), or to small scattered regions that did not show hallmarks of islands (4.0%). Red segments: the 11 final islands (including a tandem array of Kpn21L and Kpn11L). Circles, the two newly indicated regions.
© Copyright Policy
Related In: Results  -  Collection

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

pone-0099209-g005: Learned phyloblocks identify a new island and the highly variable capsular polysaccharide and lipopolysaccharide synthesis gene cluster (cps-lps).Nonubiquity phyloblocks: those missing in at least one of the 11 reference chromosomes. Complex phyloblocks: those requiring more than one gain/loss event to reconcile the phylotype with the genome tree of Fig. 1. As a percentage of their combined 411 kbp, the learned phyloblocks mapped either to the training islands (81.9%), the two newly indicated regions (12.0%), insertion sequences (2.1%), or to small scattered regions that did not show hallmarks of islands (4.0%). Red segments: the 11 final islands (including a tandem array of Kpn21L and Kpn11L). Circles, the two newly indicated regions.
Mentions: Plasmids frequently disseminate antibiotic resistance genes in Klebsiella, but genomic islands are also potential vehicles. Our program Islander [31] found six islands in tRNA/tmRNA genes, including a tandem island pair at a tRNALeu gene. PHAST [32] confirmed three of these and identified four additional prophage-like islands, one precisely within the gene for the short regulatory RNA RybB. The 10 resulting islands accounted for 6.3% of the Kpn2146 chromosome. We used these 10 Islander/PHAST islands (Table 3) as a training set for a phylogenomic approach to find additional islands, based on the principle that islands tend to occur sporadically among closely related strains. The Kpn2146 chromosome was partitioned into “phyloblocks”, which we define as DNA intervals where all positions share the same phylotype, i.e., the same presence/absence profile among a given set of closely related genomes. We selected phyloblocks that were enriched in (i.e., “learned” from) the training islands. These learned phyloblocks pointed to the island Kpn23SapB, with an integrase gene and att site pair, that was missed by Islander and Phast. Learned phyloblocks also pointed to the non-island genomic locus cps-lps, described further below. An overview of learned phyloblocks across the chromosome (Fig. 5) shows the tight mapping to cps-lps, mobile islands and ISs.

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