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Draft genome sequence of non-shiga toxin-producing Escherichia coli O157 NCCP15738.

Kwon T, Kim JB, Bak YS, Yu YB, Kwon KS, Kim W, Cho SH - Gut Pathog (2016)

Bottom Line: MG1655 and EHEC O157:H7 EDL933 by bioinformatics analyses revealed unique genes in NCCP15738 associated with lysis protein S, two-component signal transduction system, conjugation, the flagellum, nucleotide-binding proteins, and metal-ion binding proteins.Notably, NCCP15738 has a dual flagella system like that in Vibrio parahaemolyticus, Aeromonas spp., and Rhodospirillum centenum.The draft genome sequence and the results of bioinformatics analysis of NCCP15738 provide the basis for understanding the genomic evolution of this strain.

View Article: PubMed Central - PubMed

Affiliation: School of Biological Sciences, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul, 151-742 Republic of Korea ; Division of Biosafety Evaluation and Control, Korea National Institute of Health, Cheongju, 363-951 Republic of Korea.

ABSTRACT

Background: The non-shiga toxin-producing Escherichia coli (non-STEC) O157 is a pathogenic strain that cause diarrhea but does not cause hemolytic-uremic syndrome, or hemorrhagic colitis. Here, we present the 5-Mb draft genome sequence of non-STEC O157 NCCP15738, which was isolated from the feces of a Korean patient with diarrhea, and describe its features and the structural basis for its genome evolution.

Results: A total of 565-Mbp paired-end reads were generated using the Illumina-HiSeq 2000 platform. The reads were assembled into 135 scaffolds throughout the de novo assembly. The assembled genome size of NCCP15738 was 5,005,278 bp with an N50 value of 142,450 bp and 50.65 % G+C content. Using Rapid Annotation using Subsystem Technology analysis, we predicted 4780 ORFs and 31 RNA genes. The evolutionary tree was inferred from multiple sequence alignment of 45 E. coli species. The most closely related neighbor of NCCP15738 indicated by whole-genome phylogeny was E. coli UMNK88, but that indicated by multilocus sequence analysis was E. coli DH1(ME8569).

Conclusions: A comparison between the NCCP15738 genome and those of reference strains, E. coli K-12 substr. MG1655 and EHEC O157:H7 EDL933 by bioinformatics analyses revealed unique genes in NCCP15738 associated with lysis protein S, two-component signal transduction system, conjugation, the flagellum, nucleotide-binding proteins, and metal-ion binding proteins. Notably, NCCP15738 has a dual flagella system like that in Vibrio parahaemolyticus, Aeromonas spp., and Rhodospirillum centenum. The draft genome sequence and the results of bioinformatics analysis of NCCP15738 provide the basis for understanding the genomic evolution of this strain.

No MeSH data available.


Related in: MedlinePlus

Phylogenetic tree of NCCP15738. a Whole-genome phylogeny, b MLSA phylogeny. Evolutionary time is scaled by 100; lower values imply relatively recent branching. The scale indicates the number of substitutions per site. NCCP15738 (red) was not placed in a single clade with E. coli K-12 substr. MG1655 (blue) in either the whole-genome phylogeny or the MLSA phylogeny. In addition, NCCP15738 did not belong to the E. coli O157:H7 serotype and was evolutionarily far from E. coli O157:H7 str. EDL933 (green). The most closely related neighbor indicated by whole-genome phylogeny was E. coli UMNK88, but that indicated by MLSA phylogeny was E. coli DH1 (ME8569)
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Fig2: Phylogenetic tree of NCCP15738. a Whole-genome phylogeny, b MLSA phylogeny. Evolutionary time is scaled by 100; lower values imply relatively recent branching. The scale indicates the number of substitutions per site. NCCP15738 (red) was not placed in a single clade with E. coli K-12 substr. MG1655 (blue) in either the whole-genome phylogeny or the MLSA phylogeny. In addition, NCCP15738 did not belong to the E. coli O157:H7 serotype and was evolutionarily far from E. coli O157:H7 str. EDL933 (green). The most closely related neighbor indicated by whole-genome phylogeny was E. coli UMNK88, but that indicated by MLSA phylogeny was E. coli DH1 (ME8569)

Mentions: The phylogenetic comparison of gene candidates predicted by SEED [31] revealed E. coli O104:H4 GOS1 [32] as the closest neighbor of NCCP15738 (score 513). To investigate the detailed evolutionary history of NCCP15738, we performed a multiple sequence alignment of 45 E. coli species including NCCP15738 (Fig. 2, Additional file 1: Table S1). Whole-genome phylogenetic analysis revealed that NCCP15738 did not cluster with E. coli strain K-12 substr. MG1655 into a single clade. Moreover, NCCP15738 was not grouped with E. coli O157:H7 str. EDL933. The most closely related neighbor of NCCP15738 was the pathogenic E. coli UMNK88 [33]. In MLSA, NCCP15738 clustered with E. coli DH1 (ME8569) into a single clade. The E. coli UMNK88 strain and K-12 substr. MG1655 were farther from NCCP15738 in the MLSA tree than in the whole-genome phylogenetic tree. However, this difference between the whole-genome phylogenetic tree and the MLST phylogenetic tree was not significant, as there was consensus in the topology among trees. It is concordant with previous research with Phylomark [34].Fig. 2


Draft genome sequence of non-shiga toxin-producing Escherichia coli O157 NCCP15738.

Kwon T, Kim JB, Bak YS, Yu YB, Kwon KS, Kim W, Cho SH - Gut Pathog (2016)

Phylogenetic tree of NCCP15738. a Whole-genome phylogeny, b MLSA phylogeny. Evolutionary time is scaled by 100; lower values imply relatively recent branching. The scale indicates the number of substitutions per site. NCCP15738 (red) was not placed in a single clade with E. coli K-12 substr. MG1655 (blue) in either the whole-genome phylogeny or the MLSA phylogeny. In addition, NCCP15738 did not belong to the E. coli O157:H7 serotype and was evolutionarily far from E. coli O157:H7 str. EDL933 (green). The most closely related neighbor indicated by whole-genome phylogeny was E. coli UMNK88, but that indicated by MLSA phylogeny was E. coli DH1 (ME8569)
© Copyright Policy - OpenAccess
Related In: Results  -  Collection

License 1 - License 2
Show All Figures
getmorefigures.php?uid=PMC4835932&req=5

Fig2: Phylogenetic tree of NCCP15738. a Whole-genome phylogeny, b MLSA phylogeny. Evolutionary time is scaled by 100; lower values imply relatively recent branching. The scale indicates the number of substitutions per site. NCCP15738 (red) was not placed in a single clade with E. coli K-12 substr. MG1655 (blue) in either the whole-genome phylogeny or the MLSA phylogeny. In addition, NCCP15738 did not belong to the E. coli O157:H7 serotype and was evolutionarily far from E. coli O157:H7 str. EDL933 (green). The most closely related neighbor indicated by whole-genome phylogeny was E. coli UMNK88, but that indicated by MLSA phylogeny was E. coli DH1 (ME8569)
Mentions: The phylogenetic comparison of gene candidates predicted by SEED [31] revealed E. coli O104:H4 GOS1 [32] as the closest neighbor of NCCP15738 (score 513). To investigate the detailed evolutionary history of NCCP15738, we performed a multiple sequence alignment of 45 E. coli species including NCCP15738 (Fig. 2, Additional file 1: Table S1). Whole-genome phylogenetic analysis revealed that NCCP15738 did not cluster with E. coli strain K-12 substr. MG1655 into a single clade. Moreover, NCCP15738 was not grouped with E. coli O157:H7 str. EDL933. The most closely related neighbor of NCCP15738 was the pathogenic E. coli UMNK88 [33]. In MLSA, NCCP15738 clustered with E. coli DH1 (ME8569) into a single clade. The E. coli UMNK88 strain and K-12 substr. MG1655 were farther from NCCP15738 in the MLSA tree than in the whole-genome phylogenetic tree. However, this difference between the whole-genome phylogenetic tree and the MLST phylogenetic tree was not significant, as there was consensus in the topology among trees. It is concordant with previous research with Phylomark [34].Fig. 2

Bottom Line: MG1655 and EHEC O157:H7 EDL933 by bioinformatics analyses revealed unique genes in NCCP15738 associated with lysis protein S, two-component signal transduction system, conjugation, the flagellum, nucleotide-binding proteins, and metal-ion binding proteins.Notably, NCCP15738 has a dual flagella system like that in Vibrio parahaemolyticus, Aeromonas spp., and Rhodospirillum centenum.The draft genome sequence and the results of bioinformatics analysis of NCCP15738 provide the basis for understanding the genomic evolution of this strain.

View Article: PubMed Central - PubMed

Affiliation: School of Biological Sciences, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul, 151-742 Republic of Korea ; Division of Biosafety Evaluation and Control, Korea National Institute of Health, Cheongju, 363-951 Republic of Korea.

ABSTRACT

Background: The non-shiga toxin-producing Escherichia coli (non-STEC) O157 is a pathogenic strain that cause diarrhea but does not cause hemolytic-uremic syndrome, or hemorrhagic colitis. Here, we present the 5-Mb draft genome sequence of non-STEC O157 NCCP15738, which was isolated from the feces of a Korean patient with diarrhea, and describe its features and the structural basis for its genome evolution.

Results: A total of 565-Mbp paired-end reads were generated using the Illumina-HiSeq 2000 platform. The reads were assembled into 135 scaffolds throughout the de novo assembly. The assembled genome size of NCCP15738 was 5,005,278 bp with an N50 value of 142,450 bp and 50.65 % G+C content. Using Rapid Annotation using Subsystem Technology analysis, we predicted 4780 ORFs and 31 RNA genes. The evolutionary tree was inferred from multiple sequence alignment of 45 E. coli species. The most closely related neighbor of NCCP15738 indicated by whole-genome phylogeny was E. coli UMNK88, but that indicated by multilocus sequence analysis was E. coli DH1(ME8569).

Conclusions: A comparison between the NCCP15738 genome and those of reference strains, E. coli K-12 substr. MG1655 and EHEC O157:H7 EDL933 by bioinformatics analyses revealed unique genes in NCCP15738 associated with lysis protein S, two-component signal transduction system, conjugation, the flagellum, nucleotide-binding proteins, and metal-ion binding proteins. Notably, NCCP15738 has a dual flagella system like that in Vibrio parahaemolyticus, Aeromonas spp., and Rhodospirillum centenum. The draft genome sequence and the results of bioinformatics analysis of NCCP15738 provide the basis for understanding the genomic evolution of this strain.

No MeSH data available.


Related in: MedlinePlus