Open Access

Comparative genomic analysis of Shiga toxin-producing and non-Shiga toxin-producing Escherichia coli O157 isolated from outbreaks in Korea

Contributed equally
Gut Pathogens20179:7

https://doi.org/10.1186/s13099-017-0156-2

Received: 14 June 2016

Accepted: 24 January 2017

Published: 6 February 2017

Abstract

Background

The Shiga toxin-producing Escherichia coli (STEC) O157 strain NCCP15739 and non-STEC O157 strain NCCP15738 were isolated from outbreaks in Korea. We characterized NCCP15739 and NCCP15738 by genome sequencing and a comparative genomic analysis using two additional strains, E. coli K-12 substr. MG1655 and O157:H7 EDL933.

Results

Using the Illumina HiSeq 2000 platform and the RAST server, the whole genomes of NCCP15739 and NCCP15738 were obtained and annotated. NCCP15739 and NCCP15738 clustered with different E. coli strains based on a whole-genome phylogeny and multi-locus sequence typing analysis. Functional annotation clustering indicated enrichment for virulence plasmid and hemolysis-related genes in NCCP15739 and conjugation- and flagellum-related genes in NCCP15738. Defense mechanism- and pathogenicity-related pathways were enriched in NCCP15739 and pathways related to the assimilation of energy sources were enriched in NCCP15738. We identified 66 and 18 virulence factors from the NCCP15739 and NCCP15738 genome, respectively. Five and eight antibiotic resistance genes were identified in the NCCP15739 and NCCP15738 genomes, respectively. Based on a comparative analysis of phage-associated regions, NCCP15739 and NCCP15738 had specific prophages. The prophages in NCCP15739 carried virulence factors, but those in NCCP15738 did not, and no antibiotic resistance genes were found in the phage-associated regions.

Conclusions

Our whole-genome sequencing and comparative genomic analysis revealed that NCCP15739 and NCCP15738 have specific genes and pathways. NCCP15739 had more genes (410), virulence factors (48), and phage-related regions (11) than NCCP15738. However, NCCP15738 had three more antibiotic resistance genes than NCCP15739. These differences may explain differences in pathogenicity and biological characteristics.

Keywords

Shiga-like toxin-producing Escherichia coli O157 Non-Shiga-like toxin-producing Escherichia coli O157 Draft genome Comparative genomics Alpha-hemolysin

Background

In 1983, outbreaks of EHEC O157:H7 in humans were first reported [13]. Since then, EHEC has been recognized as an important food-borne pathogen that causes hemorrhagic colitis and hemolytic uremic syndrome [4, 5]. Shiga toxin (Stx) is the major virulence factor and a defining characteristic of EHEC. Shiga toxin-producing Escherichia coli (STEC) strains produce one or two major Shiga toxins, designated Stx1 and Stx2 [4]. Typical STEC strains possess a 35-kb locus of enterocyte effacement (LEE) pathogenicity island containing eae [6], which encodes an outer membrane protein (intimin) required for intimate attachment to epithelial cells; this pathogenicity island is also found in EPEC strains. LEE encodes a type III secretion system (TTSS) through which E. coli secretes proteins, resulting in the delivery of effector molecules to the host cell and disrupting the host cytoskeleton [710]. STEC strains cause hemolytic-uremic syndrome and hemorrhagic colitis.

Numerous comparative genomics studies of STEC O157 and non-O157 STEC have been performed, but non-STEC O157 has not been a focus of past research. Few cases of non-STEC O157 have been reported in human patients with diarrhea [11]. Moreover, there are no whole-genome sequencing data or comparative genomics studies of non-STEC O157 strains. However, there was a recent outbreak of non-STEC O157 in human hosts in Korea [12]. Even though non-STEC O157 does not produce Shiga-like toxins, it could be a public health problem because it is pathogenic and causes diarrhea in humans. STEC NCCP15739 [13] and non-STEC NCCP15738 [12] were isolated from the feces of two Korean patients with diarrhea. To characterize NCCP15739 and NCCP15738 as well as the origin of pathogenicity, whole-genome sequencing and comparative genomic analyses using two additional strains, E. coli K-12 substr. MG1655 and O157:H7 EDL933 (as non-STEC and STEC reference strains, respectively), were performed.

Methods

Strain, isolation, and serotyping

Escherichia coli were isolated from patients with diarrhea using MacConkey agar and Trypticase Soy Broth containing vancomycin (Sigma Co., St. Louis, MO, USA). Candidate colonies were identified based on phenotypes and biochemical properties using the API20E system (Biomerieux, Marcy l’Etoile, France). The O antigen of the isolates was determined using the methods of Guinee et al. [14] with all available O (O1 to O181) antisera (Lugo, Spain, http://www.lugo.usc.es/ecoli). The isolated strains have been deposited in the National Culture Collection for Pathogens (NCCP) at the Korea National Institute of Health under accession numbers NCCP15739 [13] and NCCP15738 [12]. E. coli K-12 substr. MG1655 and NCCP15738 were used as reference strains for non-STEC and EHEC O157:H7 str. EDL933 was used as the reference strain for STEC.

Library preparation and whole genome sequencing

The Illumina HiSeq 2000 platform was used for the whole genome sequencing of NCCP15739 and NCCP15738 (Theragen Etex Bio Institute, Suwon, Republic of Korea).

Genome assembly and annotation

A de novo assembly was performed using SOAPdenovo (version 1.05) [15]. Only scaffolds longer than 500 bp were used for further analysis. Annotated open reading frames of the NCCP15739 and NCCP15738 genomes were identified using the RAST (Rapid Annotation using Subsystem Technology, version 4.0) [16] server. The genomes of two reference strains, K-12 substr. MG1655 and O157:H7 str. EDL933, were re-annotated using the RAST server. For the comparison of the coding sequences (CDSs) of the four strains, OrthoMCL (version 2.0.9) was used [17]. The sequence similarity and coverage [18] were considered simultaneously to assess the orthologous proteins of all four E. coli strains.

Functional annotation enrichment in the set of genes in NCCP15739 and NCCP15738 was performed using the Database for Annotation, Visualization and Integrated Discovery (DAVID) (http://david.abcc.ncifcrf.gov). To identify lineage-specific genes in the NCCP15739 and NCCP15738 genomes, the BLAST Score Ratio (BSR) was calculated. Unique genes with a BSR score of ≤0.4 were selected. A comparative KEGG metabolic pathway analysis was conducted for the total CDSs of NCCP15739 and NCCP15738 using Model SEED (version 1.0). To investigate the virulence factor genes in the four E. coli strains, a BLAST search of the total ORFs of the four E. coli strains against the virulence factor genes of E. coli listed in VFDB [19] was performed with an e-value threshold of 1e-5. We determined the antibiotic resistance genes in the genome sequences of the four E. coli strains using ResFinder 2.1 (https://cge.cbs.dtu.dk/services/ResFinder/) [20]. To compare the genomic structures among the four strains, the genomic scaffolds of NCCP15739, NCCP15738, E. coli K-12 substr. MG1655, and O157:H7 EDL933 were aligned using the progressive alignment algorithm of Mauve (version 2.3.1) [21]. After the alignment, the scaffolds of NCCP15739 were reordered against the complete genome of E. coli O157:H7 EDL933 using the Move Contig tool of Mauve. The scaffolds of NCCP15738 were reordered against the genome sequence of E. coli K-12 substr. MG1655. The BLAST algorithm was used to identify syntenic genes and to analyze the genes of interest. The resulting reordered scaffolds and syntenic genes were visualized using Circos (version 0.64) [22].

Phylogenetic analysis

To calculate the evolutionary distances among 44 E. coli, including NCCP15739 and NCCP15738, concatenated whole genomes and multi-locus sequence typing (MLST) genes [23, 24] were used. Three Shigella genome sequences were included in the phylogenetic analysis as an outgroup. The seven MLST genes were adk, fumC, gyrB, icd, mdh, purA, and recA from 44 E. coli strains according to the protocol described in the E. coli MLST database (http://mlst.warwick.ac.uk/mlst/dbs/Ecoli/documents/primersColi_html) [25]. Any locus with a gap or indel was excluded from the analysis [26]. Multiple sequence alignments of the whole genomes and MLST genes were obtained using Mugsy (version 1.2.3) [27]. The generalized time-reversible [28] + CAT model [29] was employed to infer the approximately maximum-likelihood phylogenetic trees with 1000 iterations using FastTree (version 2.1.7) [30]. FigTree (version 1.3.1) (http://tree.bio.ed.ac.uk/software/figtree/) was used for tree visualization.

Analysis of mobile genetic elements

To identify insertion sequences (ISs), all ISs were downloaded from the IS Finder DB (http://www-is.biotoul.fr), and the genome sequences of four E. coli strains, NCCP15739, NCCP15738, K-12 substr. MG1655, and EDL933, were mapped to the sequence database using RepeatMasker (version 4.0.1) (http://www.repeatmasker.org). Phage-associated regions in the genome sequences of the four E. coli strains were predicted using the PHAST server [31]. Genomic scaffolds, including prophages, were confirmed based on the RAST annotation results.

Quality assurance

The genomic DNAs were purified from a pure culture of a single bacterial isolate of NCCP15739 and NCCP15738. Potential contamination of the genomic libraries by other microorganisms was evaluated using a BLAST search against the non-redundant database.

Results and discussion

General features

The draft genome size of NCCP15739 was 5,373,767 bp and NCCP15738 was 5,005,278 bp. The G+C contents of NCCP15739 and NCCP15738 were 50.25 and 50.65%, respectively. The genomic features of E. coli strains used in the analysis, including NCCP15739 and NCCP15738, are summarized in Table 1. Based on a RAST analysis, 5190 putative CDSs from NCCP15739 and 4780 putative CDSs from NCCP15738 (Fig. 1; Additional file 1: Table S1) were identified. The syntenic regions between NCCP15739 and three other E. coli strains based on a BLAST search are depicted on the reordered contigs of NCCP15739 in Fig. 1.
Table 1

Genomic features of Escherichia coli strains used in this study

Strain

NCCP15739

NCCP15738

E. coli str. K-12 substr. MG1655

E. coli O157:H7 str. EDL933

Genome (Mb)

5.37

5.0

4.64

5.62

%GC

50.25

50.65

50.8

50.4

Total open reading frames

5226

4811

4527

5411

tRNAs

30

27

88

98

rRNAs

6

4

22

87

Fig. 1

Circular map of the NCCP15739 and NCCP15738 draft genomes. Circular map of genes and genome statistics were visualized for NCCP15739 and NCCP15738 using Circos (version 0.64). All CDSs are syntenic regions of NCCP15739 that were determined using BLAST searches

Phylogenetic analysis

A whole-genome phylogenetic analysis of 44 E. coli strains revealed that NCCP15739 is closely related to the pathogenic E. coli Xuzhou21 and TW14588 (Fig. 2a). However, a multilocus sequence analysis showed that NCCP15739 is closely related to O157:H7 serotypes, such as E. coli O157:H7 Sakai, EDL933, TW14588, and E. coli Xuzhou21 (Fig. 2b). The serotype O157:H7 clustered into a recently diverged group according to the MLST-based phylogeny. Based on the whole-genome phylogenetic analysis, NCCP15738 was grouped with UMNK88 (Fig. 2a), but it grouped with DH1 (ME8569) based on MLST analyses (Fig. 2b). The clusters in the whole-genome phylogenetic tree and the MLST phylogenetic tree were different; we think the difference comes from how many genotypes were considered in the phylogenetic analysis. The whole-genome phylogenetic tree considered all of variation throughout the whole-genome, but MLST phylogenetic tree only considered the genotypes of the seven MLST genes. Based on the phylogenetic analysis, we concluded that NCCP15739 and NCCP15738 are different strains belonging to their own groups.
Fig. 2

Phylogenetic tree of NCCP15739 and NCCP15738. a Whole-genome phylogeny, b multi-locus sequence typing phylogeny. Evolutionary time was scaled by 100; lower values imply a relatively recent branching event. The scale indicates the number of substitutions per site. NCCP15739, NCCP15738, and the reference strains are highlighted in different colors: NCCP15739 (red), NCCP15738 (orange), Escherichia coli K-12 substr. MG1655 (blue), and E. coli O157:H7 str. EDL933 (green)

Functional annotation clustering

Based on BSR scores, we selected 534 genes from NCCP15739 and 651 genes from NCCP15738 for functional annotation clustering (Additional file 1: Table S1). According to this analysis, 534 genes of NCCP5739 were classified into 7 groups and 651 genes of NCCP15738 were classified into 8 groups. In NCCP15739, the virulence plasmid and hemolysis-related genes were enriched, while the NCCP15738 genome exhibited enrichment for conjugation- and flagellum-related genes (Table 2). In particular, the flagellum is an important characteristic of NCCP15738 because the strain has a dual flagellar system [12], like those found in Vibrio parahaemolyticus, Aeromonas spp., and Rhodospirillum centenum [32]. NCCP15738 had 65 genes encoding flagellar biosynthesis or structural proteins.
Table 2

Functional annotation clustering using the DAVID (http://david.abcc.ncifcrf.gov)

Cluster

Strain

Term

Count

Enrichment score

P value

Benjamini

1

NCCP15738

Conjugation

6

4.03

0.000

0.000

 

NCCP15739

Virulence plasmid of Escherichia coli O157:H7

40

50.4

0.000

0.000

2

NCCP15738

Flagellum

5

2.76

0.000

0.005

 

NCCP15739

Hemolysis

4

5.9

0.000

0.000

3

NCCP15738

Viral capsid assembly

3

1.941

0.004

0.180

 

NCCP15739

Bacterial secretion system

6

4.36

0.000

0.000

4

NCCP15738

Ribonucleotide binding

9

1.043

0.033

0.674

 

NCCP15739

Methylation

4

2.77

0.003

0.021

5

NCCP15738

Copper ion binding

3

0.521

0.010

0.505

 

NCCP15739

Transfer region of pO113 from enterohemorrhagic Escherichia coli

5

1.76

0.000

0.004

6

NCCP15738

DNA recombination

3

0.496

0.029

0.336

 

NCCP15739

Metal ion binding

4

0.314

0.471

1.000

7

NCCP15738

Two-component signal transduction system (phosphorelay)

4

0.423

0.070

0.687

 

NCCP15739

Transmembrane protein

4

0.198

0.280

0.927

Metabolic pathway comparison

Based on a metabolic pathway comparison, we found that seven pathways were more developed in NCCP15739 than in NCCP15738. Genes in the pathways that determine folate biosynthesis, purine metabolism, amino sugar metabolism, atrazine degradation [33], urea cycle, amino acid metabolism, and the biosynthesis of siderophores [3436] were more highly enriched in NCCP15739. For example, the folate biosynthesis pathway had more genes in NCCP15739 than in NCCP15738 (Additional file 2: Table S2). Folate is important for frequent divisions and rapid cell growth because it is required for methylation reactions and nucleic acid synthesis [37]. The pathways enriched in NCCP15739 were closely related to defense mechanisms and the pathogenicity of bacteria. NCCP15739 is pathogenic and causes hemolytic-uremic syndrome in the host [13].

By contrast, sixteen pathways were more developed in NCCP15738. The enriched pathways in NCCP15738 were responsible for the assimilation of various energy sources (Additional file 2: Table S2). Genes in the pathways that determine tyrosine metabolism, pentose and glucuronate interconversion [38], phenylalanine metabolism [39], galactose metabolism [40], glycerolipid metabolism, and ascorbate and aldarate metabolism were more highly enriched in NCCP15738. A comparative genomic analysis with the reference strains E. coli K-12 substr. MG1655 and O157:H7 EDL933 showed that NCCP15738 has a dual flagellar system [12]. However, we did not observe its locomotion and did not test its function in the strain; the structure and function should be investigated in further studies.

Virulence factors

We detected 66 and 18 [12] virulence factors from NCCP15739 and NCCP15738, respectively (Additional file 3: Table S3). All 18 virulence genes of NCCP15738 were shared with NCCP15739; NCCP15738 did not contain any unique virulence factors. The 66 virulence genes of NCCP15739 were grouped into 7 categories: adherence, autotransporter, iron uptake, LEE-encoded TTSS effectors, non-LEE-encoded TTSS effectors, secretion system, and toxins. Some virulence factors were found in NCCP15739, but not in NCCP1738, i.e., genes in the adherence category (eae, paa, and toxB), autotransporter category [the aida (adhesion involved in diffuse adherence)-related genes espP and sat), iron uptake category (hemin uptake-related genes (chuA, S, T, U, W, X, and Y), salmochelin and siderophore-related genes (iroB, D, and N)], toxins [alpha-hemolysin-related genes (hlyA, B, C, and D), and Shiga toxin-related genes (stx1A, 1B, 2A, and 2B)]. Notably, in the non-LEE and LEE-encoded TTSS effector category, espG, map, tir, espJ, nleA/espI, and nleC were found in NCCP15739. Many LEE TTSS-related genes (cesD2, F, T, escC, D, F, J, N, R, S, T, U, V, espA, B, D, glrR, ler, sepL, and Q) belonged to the secretion systems category. NCCP15739 possessed all of the TTSS effectors and secretion system-related genes. However, NCCP15738 did not have all LEE TTSS-related genes, and it harbored only one secretion gene, escR [41], which might be lineage-specific (percent sequence identity = 46.85%). In the toxin category, alpha-hemolysin was a main virulence gene in STEC strains. The alpha-hemolysin–related genes (hlyA, B, C, and D) were only present in NCCP15739. It is thought to be acquired by horizontal gene transfer via conjugative plasmids [42]. The 92-kb virulence plasmid pO157 carried 3.4 kb of hemolysin genes [43]. In the NCCP15739 genome, pO157 was on scaffolds 35 and 38. Shiga toxin-related genes (stx1A, 1B, 2A, and 2B) [44] were present in NCCP15739, but no toxin genes were found in NCCP15738. In brief, the NCCP15738 strain had fewer virulence factors than NCCP15739. However, NCCP15738 is pathogenic and causes diarrhea in human hosts. We propose that the strain NCCP15738 is a model organism for studies of pathogenicity in non-STEC O157 strains because its genome does not contain toxin-related genes. To identify the virulence genes related to diarrhea in humans, additional studies are needed.

Phage-associated regions

Prophages are mobile genetic elements that deliver antimicrobial-resistance genes [45] or virulence factors [46] to bacterial hosts and contribute to the diversity of host genomes [47]. We identified sixteen phage-associated regions (S1–S16) from the NCCP15739 genome and five phage-associated regions (N1–N5) from the NCCP15738 genome using the PHAST algorithm (Additional file 4: Table S4). Only five of the sixteen phages in NCCP15739 were intact, whereas all five phages in NCCP15738 were intact. Based on a BLAST search, only one phage-associated region, i.e., the N3 region from NCCP15738, was identical to the S2 region from the NCCP15739 genome, whereas the four remaining phages (N1, N2, N4, and N5) were specific to NCCP15738. In terms of virulence, the S2, S4, S11, S12, and S13 regions in NCCP15739 had the virulence factors nleC, stx2A and stx2B, paa, nleA/espI, espJ and stx1A, and stx1B, respectively. Meanwhile, NCCP15738 had no virulence factors in the phage-associated regions. Therefore, we hypothesized that prophages are not causal factors of virulence in NCCP15738. In addition, we examined antibiotic resistance-related genes in prophage regions of NCCP15739 and NCCP15738, but no antibiotic resistance genes were found in either genome (Additional file 5: Table S5). According to these results, we concluded that prophages are not vehicles of antibiotic resistance genes in NCCP15739 and NCCP15738.

Future directions

STEC O157 NCCP15739 and non-STEC NCCP15738 belong to the O157 serotype, which has strong pathogenicity and can cause foodborne disease. In this study, we performed a comparative genomic analysis of NCCP15739, NCCP15738, E. coli K-12 substr. MG1655, and O157:H7 EDL933. We found that NCCP15739 and NCCP15738 have specific functional genes and pathways related to pathogenicity and motility, and their genomes contained specific prophages. NCCP15739 had more genes (410), virulence factors (48), and phage-related regions (11) than NCCP15738. However, NCCP15738 had three more antibiotic resistance genes than NCCP15739. To investigate the effect of these differences on pathogenicity and biological properties, further studies are needed.

Notes

Abbreviations

CDS: 

coding DNA sequences

EHEC: 

enterohemorrhagic Escherichia coli

IS: 

insertion sequences

MLST: 

multi locus sequence typing

NCCP: 

National Culture Collection for Pathogens

RAST: 

Rapid Annotation using Subsystem Technology

STEC: 

Shiga toxin-producing Escherichia coli

str.: 

strain

substr.: 

substrain

TTSS: 

type III secretion system

Declarations

Authors’ contributions

SHC and WK planned and directed the project and interpreted the results. SHC drafted the manuscript. TK performed the gene annotation and comparative genomic analysis and wrote the manuscript. All authors read and approved the final manuscript.

Acknowledgements

Not applicable.

Competing interests

The authors declare that they have no competing interests.

Availability of data and materials

Nucleotide sequence accession numbers The whole-genome shotgun sequencing data have been deposited in DDBJ/EMBL/GenBank under the accession numbers ASHA00000000 [13] and ASHB00000000 [12] for NCCP15739 and NCCP15738, respectively.

Ethics approval and consent to participate

This research has been reviewed and approved by the Institutional Review Board of the Korea Centers for Disease Control and Prevention (Reference No.: 2013-12-04-P). Written informed consent was obtained from all patients with diarrhea to participate the research.

Funding

This work was supported by a grant from the Marine Biotechnology Program (Genome Analysis of Marine Organisms and Development of Functional Applications) funded by the Ministry of Oceans and Fisheries).

Open AccessThis article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.

Authors’ Affiliations

(1)
Interdisciplinary Program in Bioinformatics, Seoul National University
(2)
Division of Biosafety Evaluation and Control, Korea National Institute of Health
(3)
Division of Enteric Diseases, Center for Infectious Diseases, Korea National Institute of Health

References

  1. Karmali MA, Steele BT, Petric M, Lim C. Sporadic cases of haemolytic-uraemic syndrome associated with faecal cytotoxin and cytotoxin-producing Escherichia coli in stools. Lancet. 1983;1(8325):619–20.View ArticlePubMedGoogle Scholar
  2. Riley LW, Remis RS, Helgerson SD, McGee HB, Wells JG, Davis BR, Hebert RJ, Olcott ES, Johnson LM, Hargrett NT, et al. Hemorrhagic colitis associated with a rare Escherichia coli serotype. N Engl J Med. 1983;308(12):681–5.View ArticlePubMedGoogle Scholar
  3. Wells JG, Davis BR, Wachsmuth IK, Riley LW, Remis RS, Sokolow R, Morris GK. Laboratory investigation of hemorrhagic colitis outbreaks associated with a rare Escherichia coli serotype. J Clin Microbiol. 1983;18(3):512–20.PubMedPubMed CentralGoogle Scholar
  4. Nataro JP, Kaper JB. Diarrheagenic Escherichia coli. Clin Microbiol Rev. 1998;11(1):142–201.PubMedPubMed CentralGoogle Scholar
  5. Caprioli A, Morabito S, Brugere H, Oswald E. Enterohaemorrhagic Escherichia coli: emerging issues on virulence and modes of transmission. Vet Res. 2005;36(3):289–311.View ArticlePubMedGoogle Scholar
  6. Zhang WL, Kohler B, Oswald E, Beutin L, Karch H, Morabito S, Caprioli A, Suerbaum S, Schmidt H. Genetic diversity of intimin genes of attaching and effacing Escherichia coli strains. J Clin Microbiol. 2002;40(12):4486–92.View ArticlePubMedPubMed CentralGoogle Scholar
  7. Clarke SC, Haigh RD, Freestone PP, Williams PH. Virulence of enteropathogenic Escherichia coli, a global pathogen. Clin Microbiol Rev. 2003;16(3):365–78.View ArticlePubMedPubMed CentralGoogle Scholar
  8. Garmendia J, Frankel G, Crepin VF. Enteropathogenic and enterohemorrhagic Escherichia coli infections: translocation, translocation, translocation. Infect Immun. 2005;73(5):2573–85.View ArticlePubMedPubMed CentralGoogle Scholar
  9. Makino S, Tobe T, Asakura H, Watarai M, Ikeda T, Takeshi K, Sasakawa C. Distribution of the secondary type III secretion system locus found in enterohemorrhagic Escherichia coli O157:H7 isolates among Shiga toxin-producing E. coli strains. J Clin Microbiol. 2003;41(6):2341–7.View ArticlePubMedPubMed CentralGoogle Scholar
  10. Taylor KA, O’Connell CB, Luther PW, Donnenberg MS. The EspB protein of enteropathogenic Escherichia coli is targeted to the cytoplasm of infected HeLa cells. Infect Immun. 1998;66(11):5501–7.PubMedPubMed CentralGoogle Scholar
  11. Blank TE, Lacher DW, Scaletsky IC, Zhong H, Whittam TS, Donnenberg MS. Enteropathogenic Escherichia coli O157 strains from Brazil. Emerg Infect Dis. 2003;9(1):113–5.View ArticlePubMedPubMed CentralGoogle Scholar
  12. Kwon T, Kim JB, Bak YS, Yu YB, Kwon KS, Kim W, Cho SH. Draft genome sequence of non-shiga toxin-producing Escherichia coli O157 NCCP15738. Gut Pathog. 2016;8:13.View ArticlePubMedPubMed CentralGoogle Scholar
  13. Kwon T, Cho SH. Draft Genome Sequence of Enterohemorrhagic Escherichia coli O157 NCCP15739, Isolated in the Republic of Korea. Genome Announc. 2015;3(3):e00522–15.View ArticlePubMedPubMed CentralGoogle Scholar
  14. Guinee PA, Agterberg CM, Jansen WH. Escherichia coli O antigen typing by means of a mechanized microtechnique. Appl Microbiol. 1972;24(1):127–31.PubMedPubMed CentralGoogle Scholar
  15. Li R, Zhu H, Ruan J, Qian W, Fang X, Shi Z, Li Y, Li S, Shan G, Kristiansen K, et al. De novo assembly of human genomes with massively parallel short read sequencing. Genome Res. 2010;20(2):265–72.View ArticlePubMedPubMed CentralGoogle Scholar
  16. Aziz RK, Bartels D, Best AA, DeJongh M, Disz T, Edwards RA, Formsma K, Gerdes S, Glass EM, Kubal M, et al. The RAST Server: rapid annotations using subsystems technology. BMC Genom. 2008;9:75.View ArticleGoogle Scholar
  17. Li L, Stoeckert CJ Jr, Roos DS. OrthoMCL: identification of ortholog groups for eukaryotic genomes. Genome Res. 2003;13(9):2178–89.View ArticlePubMedPubMed CentralGoogle Scholar
  18. Fischer S, Brunk BP, Chen F, Gao X, Harb OS, Iodice JB, Shanmugam D, Roos DS, Stoeckert CJ, Jr.: Using OrthoMCL to assign proteins to OrthoMCL-DB groups or to cluster proteomes into new ortholog groups. Current Protocols Bioinformatics, Chapter 6:Unit 6.12.1–19; 2011. doi:https://doi.org/10.1002/0471250953.bi0612s35.
  19. Chen L, Yang J, Yu J, Yao Z, Sun L, Shen Y, Jin Q. VFDB: a reference database for bacterial virulence factors. Nucleic Acids Res. 2005;33(Database issue):D325–8.View ArticlePubMedGoogle Scholar
  20. Zankari E, Hasman H, Cosentino S, Vestergaard M, Rasmussen S, Lund O, Aarestrup FM, Larsen MV. Identification of acquired antimicrobial resistance genes. J Antimicrob Chemother. 2012;67(11):2640–4.View ArticlePubMedPubMed CentralGoogle Scholar
  21. Darling AC, Mau B, Blattner FR, Perna NT. Mauve: multiple alignment of conserved genomic sequence with rearrangements. Genome Res. 2004;14(7):1394–403.View ArticlePubMedPubMed CentralGoogle Scholar
  22. Krzywinski M, Schein J, Birol I, Connors J, Gascoyne R, Horsman D, Jones SJ, Marra MA. Circos: an information aesthetic for comparative genomics. Genome Res. 2009;19(9):1639–45.View ArticlePubMedPubMed CentralGoogle Scholar
  23. Khan NH, Ahsan M, Yoshizawa S, Hosoya S, Yokota A, Kogure K. Multilocus sequence typing and phylogenetic analyses of Pseudomonas aeruginosa Isolates from the ocean. Appl Environ Microbiol. 2008;74(20):6194–205.View ArticlePubMedPubMed CentralGoogle Scholar
  24. Glaeser SP, Kampfer P. Multilocus sequence analysis (MLSA) in prokaryotic taxonomy. Syst Appl Microbiol. 2015;38(4):237–45.View ArticlePubMedGoogle Scholar
  25. Wirth T, Falush D, Lan R, Colles F, Mensa P, Wieler LH, Karch H, Reeves PR, Maiden MC, Ochman H, et al. Sex and virulence in Escherichia coli: an evolutionary perspective. Mol Microbiol. 2006;60(5):1136–51.View ArticlePubMedPubMed CentralGoogle Scholar
  26. Sahl JW, Matalka MN, Rasko DA. Phylomark, a tool to identify conserved phylogenetic markers from whole-genome alignments. Appl Environ Microbiol. 2012;78(14):4884–92.View ArticlePubMedPubMed CentralGoogle Scholar
  27. Angiuoli SV, Salzberg SL. Mugsy: fast multiple alignment of closely related whole genomes. Bioinformatics. 2011;27(3):334–42.View ArticlePubMedGoogle Scholar
  28. Tavaré S. Some probabilistic and statistical problems in the analysis of DNA sequences. Lect Math Life Sci. 1986;17:57–86.Google Scholar
  29. Stamatakis A: Phylogenetic models of rate heterogeneity: a high performance computing perspective. In: Parallel and distributed processing symposium, 2006 IPDPS 2006 20th international 2006.Google Scholar
  30. Price MN, Dehal PS, Arkin AP. FastTree: computing large minimum evolution trees with profiles instead of a distance matrix. Mol Biol Evol. 2009;26(7):1641–50.View ArticlePubMedPubMed CentralGoogle Scholar
  31. Zhou Y, Liang Y, Lynch KH, Dennis JJ, Wishart DS. PHAST: a fast phage search tool. Nucleic Acids Res. 2011;39(Web Server issue):W347–52.View ArticlePubMedPubMed CentralGoogle Scholar
  32. McCarter LL. Dual flagellar systems enable motility under different circumstances. J Mol Microbiol Biotechnol. 2004;7(1–2):18–29.View ArticlePubMedGoogle Scholar
  33. Wackett LP, Sadowsky MJ, Martinez B, Shapir N. Biodegradation of atrazine and related s-triazine compounds: from enzymes to field studies. Appl Microbiol Biotechnol. 2002;58(1):39–45.View ArticlePubMedGoogle Scholar
  34. Neilands JB. Siderophores: structure and function of microbial iron transport compounds. J Biol Chem. 1995;270(45):26723–6.View ArticlePubMedGoogle Scholar
  35. Franke J, Ishida K, Hertweck C. Evolution of siderophore pathways in human pathogenic bacteria. J Am Chem Soc. 2014;136(15):5599–602.View ArticlePubMedGoogle Scholar
  36. Skaar EP. The battle for iron between bacterial pathogens and their vertebrate hosts. PLoS Pathog. 2010;6(8):e1000949.View ArticlePubMedPubMed CentralGoogle Scholar
  37. Figueiredo JC, Grau MV, Haile RW, Sandler RS, Summers RW, Bresalier RS, Burke CA, McKeown-Eyssen GE, Baron JA. Folic acid and risk of prostate cancer: results from a randomized clinical trial. J Natl Cancer Inst. 2009;101(6):432–5.View ArticlePubMedPubMed CentralGoogle Scholar
  38. Ley RE, Hamady M, Lozupone C, Turnbaugh PJ, Ramey RR, Bircher JS, Schlegel ML, Tucker TA, Schrenzel MD, Knight R, et al. Evolution of mammals and their gut microbes. Science. 2008;320(5883):1647–51.View ArticlePubMedPubMed CentralGoogle Scholar
  39. Teufel R, Mascaraque V, Ismail W, Voss M, Perera J, Eisenreich W, Haehnel W, Fuchs G. Bacterial phenylalanine and phenylacetate catabolic pathway revealed. Proc Natl Acad Sci USA. 2010;107(32):14390–5.View ArticlePubMedPubMed CentralGoogle Scholar
  40. Chai Y, Beauregard PB, Vlamakis H, Losick R, Kolter R. Galactose metabolism plays a crucial role in biofilm formation by Bacillus subtilis. MBio. 2012;3(4):e00184–12.View ArticlePubMedPubMed CentralGoogle Scholar
  41. Pallen MJ, Beatson SA, Bailey CM. Bioinformatics analysis of the locus for enterocyte effacement provides novel insights into type-III secretion. BMC Microbiol. 2005;5:9.View ArticlePubMedPubMed CentralGoogle Scholar
  42. Burgos Y, Beutin L. Common origin of plasmid encoded alpha-hemolysin genes in Escherichia coli. BMC Microbiol. 2010;10:193.View ArticlePubMedPubMed CentralGoogle Scholar
  43. Lim JY, Yoon J, Hovde CJ. A brief overview of Escherichia coli O157:H7 and its plasmid O157. J Microbiol Biotechnol. 2010;20(1):5–14.PubMedPubMed CentralGoogle Scholar
  44. Lee JE, Reed J, Shields MS, Spiegel KM, Farrell LD, Sheridan PP. Phylogenetic analysis of Shiga toxin 1 and Shiga toxin 2 genes associated with disease outbreaks. BMC Microbiol. 2007;7:109.View ArticlePubMedPubMed CentralGoogle Scholar
  45. Colomer-Lluch M, Imamovic L, Jofre J, Muniesa M. Bacteriophages carrying antibiotic resistance genes in fecal waste from cattle, pigs, and poultry. Antimicrob Agents Chemother. 2011;55(10):4908–11.View ArticlePubMedPubMed CentralGoogle Scholar
  46. O’Brien AD, Newland JW, Miller SF, Holmes RK, Smith HW, Formal SB. Shiga-like toxin-converting phages from Escherichia coli strains that cause hemorrhagic colitis or infantile diarrhea. Science. 1984;226(4675):694–6.View ArticlePubMedGoogle Scholar
  47. Ventura M, Canchaya C, Bernini V, Altermann E, Barrangou R, McGrath S, Claesson MJ, Li Y, Leahy S, Walker CD, et al. Comparative genomics and transcriptional analysis of prophages identified in the genomes of Lactobacillus gasseri, Lactobacillus salivarius, and Lactobacillus casei. Appl Environ Microbiol. 2006;72(5):3130–46.View ArticlePubMedPubMed CentralGoogle Scholar

Copyright

© The Author(s) 2017

Advertisement