Genome evolution in major Escherichia coli O157:H7 lineages

Zhang, Yongxiang; Laing, Chad R.; Steele, M. William; Ziebell, Kim; Johnson, Roger P.; Benson, Andrew K.; Taboada, Eduardo N.; Gannon, Victor P. J.

doi:10.1186/1471-2164-8-121

Cited by 140 publications

(171 citation statements)

References 54 publications

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“…Figure S2) lends credence to the view that the observed phenomenon is more widespread and likely not limited to the specific set of mutants analysed here. In line with this interpretation is an analysis of 32 E. coli strains, in which genomic differences between strains have been identified (Zhang et al, 2007). About 20% of those strains lacked ppc as well as essential biosynthetic genes of one or more (p6) amino acids (Supplementary Table 1), suggesting that these strains potentially show an amino-acid cross-feeding phenotype (Figure 1).…”

Section: Distribution Of Obligate Cross-feeding Interactionsmentioning

confidence: 86%

Fitness and stability of obligate cross-feeding interactions that emerge upon gene loss in bacteria

et al. 2013

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Cross-feeding interactions, in which bacterial cells exchange costly metabolites to the benefit of both interacting partners, are very common in the microbial world. However, it generally remains unclear what maintains this type of interaction in the presence of non-cooperating types. We investigate this problem using synthetic cross-feeding interactions: by simply deleting two metabolic genes from the genome of Escherichia coli, we generated genotypes that require amino acids to grow and release other amino acids into the environment. Surprisingly, in a vast majority of cases, cocultures of two cross-feeding strains showed an increased Darwinian fitness (that is, rate of growth) relative to prototrophic wild type cells-even in direct competition. This unexpected growth advantage was due to a division of metabolic labour: the fitness cost of overproducing amino acids was less than the benefit of not having to produce others when they were provided by their partner. Moreover, frequency-dependent selection maintained cross-feeding consortia and limited exploitation by non-cooperating competitors. Together, our synthetic study approach reveals ecological principles that can help explain the widespread occurrence of obligate metabolic cross-feeding interactions in nature.

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Section: Distribution Of Obligate Cross-feeding Interactionsmentioning

confidence: 86%

Fitness and stability of obligate cross-feeding interactions that emerge upon gene loss in bacteria

et al. 2013

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“…human and bovine) and phylogenetic lineage (i.e. I, II and I/II) (Zhang et al, 2007;Laing et al, 2009). A higher level of Stx2 is typically produced by isolates from humans (lineage I and I/II strains) than by isolates from cattle (lineage II strains) (Zhang et al, 2010).…”

Section: Discussionmentioning

confidence: 99%

“…Multiple subtyping methods have been developed, including high-resolution genotyping based on single nucleotide polymorphisms (SNPs) (Manning et al, 2008;Eppinger et al, 2011b), octamer-based genome scanning (Kim et al, 1999) and comparative genome hybridization (Zhang et al, 2007). However, these methods are labour intensive and not feasible for high throughput.…”

Section: Introductionmentioning

confidence: 99%

“…Shringi et al, 2012;Boerlin et al, 1999). Genome analysis by octamer-based genomic scanning and microarraybased comparative genomic hybridization (Kim et al, 1999;Zhang et al, 2007) has shown that E. coli O157 : H7 can be assigned to three main phylogenetic lineages: termed lineages I, II and I/II. Typically, lineage I isolates originate from human clinical and bovine sources; whereas, lineage II strains predominantly have a bovine origin, while I/II strains are associated with human infection and include a hyper-virulent group consisting of the multistate 'spinach' outbreak strains Kulasekara et al, 2009;Laing et al, 2009).…”

Section: Introductionmentioning

confidence: 99%

“…However, these methods are labour intensive and not feasible for high throughput. Comparative genomic fingerprinting using 23 of the most variable loci and the lineage-specific polymorphism assay (LSPA-6) (Zhang et al, 2007) are available for rapid genotyping/lineage typing but a majority of the markers are based on genetic variation in the chromosomal backbone, not in the hypervariable regions of the E. coli O157 : H7 chromosome. The chromosomal distribution pattern of IS629 has been shown to be highly discriminatory and segregated by lineages defined by LSPA-6 (Yokoyama et al, 2011).…”

Section: Introductionmentioning

confidence: 99%

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Phylogenetic characterization of Escherichia coli O157 : H7 based on IS629 distribution and Shiga toxin genotype

et al. 2014

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Shiga toxin (stx)-producing Escherichia coli O157 : H7 is a prominent food-borne pathogen. Symptoms in human infections range from asymptomatic to haemorrhagic colitis and haemolytic uraemic syndrome, and there is a need for methods that yield information that can be used to better predict clinical and epidemiological outcomes. IS629 is an insertion sequence notable for its prevalence and variable distribution in the chromosome of E. coli O157 : H7, which has been exploited for subtyping and strain characterization. In particular, IS629 distribution is closely aligned with the major phylogenetic lineages that are known to be distinctive in their genome structure and virulence potential. In the present study, a comprehensive subtyping method in which IS629-typing was combined with stx genotyping was developed using a conventional PCR approach. This method consisted of a set of 32 markers based on the unique distribution of IS629 in the three major phylogenetic lineages of E. coli O157 : H7 and six additional markers to determine the stx genotype, a key virulence signature associated with each lineage. The analysis of IS629 loci variation with the 32 markers allowed us to determine the IS629 distribution profile (IDP), phylogenetic lineage and genetic relatedness of the 31 E. coli O157 : H7 strains examined. An association between IDP typing and stx genotype was observed. The use of both IDP and the stx genotype for strain characterization provided confirmative and complementary data in support of lineage placement of closely related strains. In addition, IS629/stx profiles were in agreement with strain segregation based on LSPA-6 (lineage-specific polymorphism assay) and PFGE subtyping, demonstrating its potential as a subtyping and strain tracking method.

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