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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

Circular map of the KP617 chromosome. Circular map of the KP617 genome, generated using cgview (version 2.2.2); from outside to inside, the tracks display the following information: CDSs of KP617 on the + strand (1); CDSs of KP617 on the − strand (2); tblastx result against PittNDM01 (3), tblastx result against NUHL24835 (4), tblastx result against ATCC BAA-2146 (5), GC content (6), GC skew with + value (green) and − value (purple) (7)
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Fig2: Circular map of the KP617 chromosome. Circular map of the KP617 genome, generated using cgview (version 2.2.2); from outside to inside, the tracks display the following information: CDSs of KP617 on the + strand (1); CDSs of KP617 on the − strand (2); tblastx result against PittNDM01 (3), tblastx result against NUHL24835 (4), tblastx result against ATCC BAA-2146 (5), GC content (6), GC skew with + value (green) and − value (purple) (7)

Mentions: A total of 316,881,346 (32,005,015,946 bp) paired-end reads were generated using Illumina-HiSeq 2500. Using the PacBio RS II platform, 46,134 (421,257,386 bp) raw reads were produced. The complete genome of KP617 consists of a 5,416,282-bp circular chromosome and two plasmids of 273,628 bp and 6141 bp in size. The genomic features of KP617 and the reference strains are summarized in Table 1. Based on a RAST analysis, 5024 putative open reading frames (ORFs) and 110 RNA genes on the circular chromosome (Figs. 1, 2; Additional file 1: Table S1), 342 putative ORFs on plasmid 1, and 9 putative ORFs on plasmid 2 were identified.Table 1


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)

Circular map of the KP617 chromosome. Circular map of the KP617 genome, generated using cgview (version 2.2.2); from outside to inside, the tracks display the following information: CDSs of KP617 on the + strand (1); CDSs of KP617 on the − strand (2); tblastx result against PittNDM01 (3), tblastx result against NUHL24835 (4), tblastx result against ATCC BAA-2146 (5), GC content (6), GC skew with + value (green) and − value (purple) (7)
© Copyright Policy - OpenAccess
Related In: Results  -  Collection

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

Fig2: Circular map of the KP617 chromosome. Circular map of the KP617 genome, generated using cgview (version 2.2.2); from outside to inside, the tracks display the following information: CDSs of KP617 on the + strand (1); CDSs of KP617 on the − strand (2); tblastx result against PittNDM01 (3), tblastx result against NUHL24835 (4), tblastx result against ATCC BAA-2146 (5), GC content (6), GC skew with + value (green) and − value (purple) (7)
Mentions: A total of 316,881,346 (32,005,015,946 bp) paired-end reads were generated using Illumina-HiSeq 2500. Using the PacBio RS II platform, 46,134 (421,257,386 bp) raw reads were produced. The complete genome of KP617 consists of a 5,416,282-bp circular chromosome and two plasmids of 273,628 bp and 6141 bp in size. The genomic features of KP617 and the reference strains are summarized in Table 1. Based on a RAST analysis, 5024 putative open reading frames (ORFs) and 110 RNA genes on the circular chromosome (Figs. 1, 2; Additional file 1: Table S1), 342 putative ORFs on plasmid 1, and 9 putative ORFs on plasmid 2 were identified.Table 1

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