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Comparative genomic analysis of Klebsiella pneumoniae subsp. pneumoniae KP617 and PittNDM01, NUHL24835, and ATCC BAA-2146 reveals unique evolutionary history of this strain.

Kwon T, Jung YH, Lee S, Yun MR, Kim W, Kim DW - Gut Pathog (2016)

Bottom Line: Nineteen antibiotic resistance genes were identified in the KP617 genome: bla OXA-1 and bla SHV-28 in the chromosome, bla NDM-1 in plasmid 1, and bla OXA-232 in plasmid 2 conferred resistance to beta-lactams; however, colistin- and tetracycline-resistance genes were not found.A comparative analysis of phage-associated regions indicated that two phage regions are specific to the KP617 genome and that prophages did not act as a vehicle for transfer of antimicrobial resistance genes in this strain.In order to elucidate the precise role of these factors in the pathogenicity of KP617, further studies are required.

View Article: PubMed Central - PubMed

Affiliation: School of Biological Sciences, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul, 151-742 Republic of Korea.

ABSTRACT

Background: Klebsiella pneumoniae subsp. pneumoniae KP617 is a pathogenic strain that coproduces OXA-232 and NDM-1 carbapenemases. We sequenced the genome of KP617, which was isolated from the wound of a Korean burn patient, and performed a comparative genomic analysis with three additional strains: PittNDM01, NUHL24835 and ATCC BAA-2146.

Results: The complete genome of KP617 was obtained via multi-platform whole-genome sequencing. Phylogenetic analysis along with whole genome and multi-locus sequence typing of genes of the Klebsiella pneumoniae species showed that KP617 belongs to the WGLW2 group, which includes PittNDM01 and NUHL24835. Comparison of annotated genes showed that KP617 shares 98.3 % of its genes with PittNDM01. Nineteen antibiotic resistance genes were identified in the KP617 genome: bla OXA-1 and bla SHV-28 in the chromosome, bla NDM-1 in plasmid 1, and bla OXA-232 in plasmid 2 conferred resistance to beta-lactams; however, colistin- and tetracycline-resistance genes were not found. We identified 117 virulence factors in the KP617 genome, and discovered that the genes encoding these factors were also harbored by the reference strains; eight genes were lipopolysaccharide-related and four were capsular polysaccharide-related. A comparative analysis of phage-associated regions indicated that two phage regions are specific to the KP617 genome and that prophages did not act as a vehicle for transfer of antimicrobial resistance genes in this strain.

Conclusions: Whole-genome sequencing and bioinformatics analysis revealed similarity in the genome sequences and content, and differences in phage-related genes, plasmids and antimicrobial resistance genes between KP617 and the references. In order to elucidate the precise role of these factors in the pathogenicity of KP617, further studies are required.

No MeSH data available.


Related in: MedlinePlus

Comparative analysis of genome structures between KP617 and the reference strains PittNDM01, NUHL24835, and ATCC BAA-2146. a Comparison of chromosome structure between KP617 and the reference strains. An inversion spanning 233,805 bp to 1,517,597 bp (1 Mb in size) in the KP617 chromosome is shown. b Comparison between the structure of plasmid 1 of KP617 and plasmid 4 of PittNDM01. There was a 71 kb inversion, from 18,633 bp to 90,686 bp, in plasmid 1 of the KP617 strain
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Fig4: Comparative analysis of genome structures between KP617 and the reference strains PittNDM01, NUHL24835, and ATCC BAA-2146. a Comparison of chromosome structure between KP617 and the reference strains. An inversion spanning 233,805 bp to 1,517,597 bp (1 Mb in size) in the KP617 chromosome is shown. b Comparison between the structure of plasmid 1 of KP617 and plasmid 4 of PittNDM01. There was a 71 kb inversion, from 18,633 bp to 90,686 bp, in plasmid 1 of the KP617 strain

Mentions: The comparison of genomic structures of the chromosome indicated the presence of highly conserved structures in the KP617, NUHL24835, and PittNDM01 strains (Fig. 4a). Interestingly, a 1-Mb region (233,805–1,517,597) of the KP617 chromosome was inverted relative to its arrangement in the chromosome of PittNDM01 (1,500,972–225,619). Despite this inversion, KP617 and PittNDM01 exhibited a lower substitution rate (score 20) than NUHL24835 (score 30) (Fig. 3). However, the chromosomal structure of the ATCC BAA-2146 strain, which consisted of two large inverted regions, was significantly different from that of the other strains. In addition, a 71 Kb inversion was found in the sequence of plasmid 1 of KP617 (18,633–90,686) relative to plasmid 1 of PittNDM01 (91,507–19,453); however, the two plasmids were highly homologous to each other (Fig. 4b).Fig. 4


Comparative genomic analysis of Klebsiella pneumoniae subsp. pneumoniae KP617 and PittNDM01, NUHL24835, and ATCC BAA-2146 reveals unique evolutionary history of this strain.

Kwon T, Jung YH, Lee S, Yun MR, Kim W, Kim DW - Gut Pathog (2016)

Comparative analysis of genome structures between KP617 and the reference strains PittNDM01, NUHL24835, and ATCC BAA-2146. a Comparison of chromosome structure between KP617 and the reference strains. An inversion spanning 233,805 bp to 1,517,597 bp (1 Mb in size) in the KP617 chromosome is shown. b Comparison between the structure of plasmid 1 of KP617 and plasmid 4 of PittNDM01. There was a 71 kb inversion, from 18,633 bp to 90,686 bp, in plasmid 1 of the KP617 strain
© Copyright Policy - OpenAccess
Related In: Results  -  Collection

License 1 - License 2
Show All Figures
getmorefigures.php?uid=PMC4940875&req=5

Fig4: Comparative analysis of genome structures between KP617 and the reference strains PittNDM01, NUHL24835, and ATCC BAA-2146. a Comparison of chromosome structure between KP617 and the reference strains. An inversion spanning 233,805 bp to 1,517,597 bp (1 Mb in size) in the KP617 chromosome is shown. b Comparison between the structure of plasmid 1 of KP617 and plasmid 4 of PittNDM01. There was a 71 kb inversion, from 18,633 bp to 90,686 bp, in plasmid 1 of the KP617 strain
Mentions: The comparison of genomic structures of the chromosome indicated the presence of highly conserved structures in the KP617, NUHL24835, and PittNDM01 strains (Fig. 4a). Interestingly, a 1-Mb region (233,805–1,517,597) of the KP617 chromosome was inverted relative to its arrangement in the chromosome of PittNDM01 (1,500,972–225,619). Despite this inversion, KP617 and PittNDM01 exhibited a lower substitution rate (score 20) than NUHL24835 (score 30) (Fig. 3). However, the chromosomal structure of the ATCC BAA-2146 strain, which consisted of two large inverted regions, was significantly different from that of the other strains. In addition, a 71 Kb inversion was found in the sequence of plasmid 1 of KP617 (18,633–90,686) relative to plasmid 1 of PittNDM01 (91,507–19,453); however, the two plasmids were highly homologous to each other (Fig. 4b).Fig. 4

Bottom Line: Nineteen antibiotic resistance genes were identified in the KP617 genome: bla OXA-1 and bla SHV-28 in the chromosome, bla NDM-1 in plasmid 1, and bla OXA-232 in plasmid 2 conferred resistance to beta-lactams; however, colistin- and tetracycline-resistance genes were not found.A comparative analysis of phage-associated regions indicated that two phage regions are specific to the KP617 genome and that prophages did not act as a vehicle for transfer of antimicrobial resistance genes in this strain.In order to elucidate the precise role of these factors in the pathogenicity of KP617, further studies are required.

View Article: PubMed Central - PubMed

Affiliation: School of Biological Sciences, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul, 151-742 Republic of Korea.

ABSTRACT

Background: Klebsiella pneumoniae subsp. pneumoniae KP617 is a pathogenic strain that coproduces OXA-232 and NDM-1 carbapenemases. We sequenced the genome of KP617, which was isolated from the wound of a Korean burn patient, and performed a comparative genomic analysis with three additional strains: PittNDM01, NUHL24835 and ATCC BAA-2146.

Results: The complete genome of KP617 was obtained via multi-platform whole-genome sequencing. Phylogenetic analysis along with whole genome and multi-locus sequence typing of genes of the Klebsiella pneumoniae species showed that KP617 belongs to the WGLW2 group, which includes PittNDM01 and NUHL24835. Comparison of annotated genes showed that KP617 shares 98.3 % of its genes with PittNDM01. Nineteen antibiotic resistance genes were identified in the KP617 genome: bla OXA-1 and bla SHV-28 in the chromosome, bla NDM-1 in plasmid 1, and bla OXA-232 in plasmid 2 conferred resistance to beta-lactams; however, colistin- and tetracycline-resistance genes were not found. We identified 117 virulence factors in the KP617 genome, and discovered that the genes encoding these factors were also harbored by the reference strains; eight genes were lipopolysaccharide-related and four were capsular polysaccharide-related. A comparative analysis of phage-associated regions indicated that two phage regions are specific to the KP617 genome and that prophages did not act as a vehicle for transfer of antimicrobial resistance genes in this strain.

Conclusions: Whole-genome sequencing and bioinformatics analysis revealed similarity in the genome sequences and content, and differences in phage-related genes, plasmids and antimicrobial resistance genes between KP617 and the references. In order to elucidate the precise role of these factors in the pathogenicity of KP617, further studies are required.

No MeSH data available.


Related in: MedlinePlus