Genotyping of Escherichia coli from environmental and animal samples

Higgins, James; Hohn, Christina; Hornor, Sally; Frana, Mark F.; Denver, Mary C.; Joerger, Rolf D.

doi:10.1016/j.mimet.2007.04.009

Cited by 75 publications

(63 citation statements)

References 38 publications

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“…The virulent strains, groups D and B2, were less abundant. The predominance of groups A and B1 is similar to other studies (Higgins et al 2007;Orsi et al 2008;Unno et al 2009). Even though the distribution of E. coli phylogenetic groups is attributed to environmental factors such as dietary, climatic conditions and geographic (Duriez et al 2001;Unno et al 2009), no apparent difference between an eutrophic estuary and an oligotrophic coastal water system was found.…”

Section: Phylogenetic Grouping Of E Coli Environmental Isolatessupporting

confidence: 91%

“…However, in this study, about 20 % of the isolates placed in group A did not show any amplicon. This percentage was relatively higher than earlier reports (7-9 %) (Higgins et al 2007;Walk et al 2007;Gordon et al 2008). As Clermont typing is not suitable for group A E. coli that does not show any amplicons (Gordon et al 2008;Li et al 2010), further studies, e.g.…”

Section: Phylogenetic Grouping Of E Coli Environmental Isolatescontrasting

confidence: 66%

“…A simple and rapid triplex PCR method was used to detect the different phylogenetic groups of E. coli (Clermont et al 2000). This method is suitable for large-scale strain screening that can quickly detect virulent strains, and its utility is well documented (Higgins et al 2007;Gordon et al 2008;Li et al 2010). In this study, E. coli concentration reflected the trophic status of the seawater, but the population structure remains essentially similar.…”

Section: Introductionmentioning

confidence: 90%

“…In contrast, groups D and B2 were least abundant and rarely detected. Others have also reported a small percentage of groups D and B2 in aquatic systems albeit for rivers and streams (Higgins et al 2007;Walk et al 2007;Orsi et al 2008; Unno ). In this study, there was no apparent variation of E. coli groups.…”

Section: Phylogenetic Grouping Of E Coli Environmental Isolatesmentioning

confidence: 96%

“…Although such bacteria should be characterised further using a multi-locus sequence typing method (Gordon et al 2008), it was not carried out. Moreover, such strains are relatively rare (Higgins et al 2007;Walk et al 2007;Gordon et al 2008). …”

Section: Isolation and Enumeration Of Coliform And E Colimentioning

confidence: 99%

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Long-term and short-term variations of Escherichia coli population structure in tropical coastal waters

Tan

Lee

2013

Int. J. Environ. Sci. Technol.

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In this study, monthly and daily samplings were carried out at Klang, an eutrophic estuary, and at Port Dickson, an oligotrophic coastal water system. Escherichia coli concentration was measured via culture method, and the phylogenetic structure of E. coli population was via Clermont typing. Average E. coli concentration at Klang was higher than Port Dickson (t = 2.97, df = 10, p \ 0.05), and daily sampling did not show any apparent temporal variation at both sites. At Klang, salinity was inversely correlated with coliform (R 2 = 0.216, df = 25, p \ 0.05), suggesting that river flow was a mode of transport for coliform. Although E. coli concentration was higher at the eutrophic site, E. coli population structure at both Klang and Port Dickson were similar and showed neither long-term nor short-term variations. This study showed the predominance of commensal groups A and B1 in tropical coastal waters of Peninsular Malaysia.

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Section: Phylogenetic Grouping Of E Coli Environmental Isolatessupporting

confidence: 91%

Section: Phylogenetic Grouping Of E Coli Environmental Isolatescontrasting

confidence: 66%

Section: Introductionmentioning

confidence: 90%

Section: Phylogenetic Grouping Of E Coli Environmental Isolatesmentioning

confidence: 96%

Section: Isolation and Enumeration Of Coliform And E Colimentioning

confidence: 99%

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Long-term and short-term variations of Escherichia coli population structure in tropical coastal waters

Tan

Lee

2013

Int. J. Environ. Sci. Technol.

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CRISPR1 analysis of naturalized surface water and fecal Escherichia coli suggests common origin

Tymensen¹

2016

MicrobiologyOpen

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Clustered regularly interspaced short palindromic repeats (CRISPRs) are part of an acquired bacterial immune system that functions as a barrier to exogenous genetic elements. Since naturalized Escherichia coli are likely to encounter different genetic elements in aquatic environments compared to enteric strains, we hypothesized that such differences would be reflected within the hypervariable CRISPR alleles of these two populations. Comparison of CRISPR1 alleles from naturalized and fecal phylogroup B1 E. coli strains revealed that the alleles could be categorized into four major distinct groups (designated G6–G9), and all four allele groups were found among naturalized strains and fecal strains. The distribution of CRIPSR G6 and G8 alleles was similar among strains of both ecotypes, while naturalized strains tended to have CRISPR G7 alleles rather than G9 alleles. Since CRISPR G7 alleles were not specific to naturalized strains, they, however, would not be useful as a marker for identifying naturalized strains. Notably, CRISPR alleles from naturalized and fecal strains also had similar spacer repertoires. This indicates a shared history of encounter with mobile genetic elements and suggests that the two populations were derived from common ancestors.

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Escherichia coli Diversity in Livestock Manures and Agriculturally Impacted Stream Waters

et al. 2011

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Escherichia coli (E. coli) isolate diversity enhances the likelihood of survival, spread, and/or transmission of the organism among environments. Understanding the ecology of this important organism is requisite for development of more accurate protocols for monitoring and regulatory purposes. In this study, E. coli diversity, gene profiles and transport properties of isolates from different livestock and water sources were evaluated. Strain diversity was evaluated by BOX-PCR, phylotyping, and profiling for 15 genes associated with adhesion, toxin production, iron acquisition or capsular synthesis. Attachment efficiencies were calculated for 17 isolates following transport through saturated porous media. Richness of genotype profiles for livestock isolates was relatively low (25, 12, and 11 for swine, poultry and dairy, respectively) compared to those from stream-water (115 and 126 from dry or wet weather events, respectively). Attachment efficiencies varied by an order of magnitude (0.039-0.44) and the isolate with the highest attachment efficiency possessed the largest suite of targeted genes including those for adherence (iha, agn43, and fimH), surface exclusion (traT) and the siderophore iroN ( E.coli ). Variation in E. coli isolates based on temporal and ecological source was found to translate to equally broad ranges in transport efficiency underscoring the large degree of genotypic and phenotypic variation that exists among E. coli isolates. The impact of this diversity on genetic exchange and the concomitant effect on the organisms' fate and transport under in situ environmental conditions warrant further investigation. These factors also require careful consideration for purposes of modeling, source tracking, and risk assessment.

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Genotyping of Escherichia coli from environmental and animal samples

Cited by 75 publications

References 38 publications

Long-term and short-term variations of Escherichia coli population structure in tropical coastal waters

Long-term and short-term variations of Escherichia coli population structure in tropical coastal waters

CRISPR1 analysis of naturalized surface water and fecal Escherichia coli suggests common origin

Escherichia coli Diversity in Livestock Manures and Agriculturally Impacted Stream Waters

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