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United States Department of Agriculture

Agricultural Research Service

Research Project: Efficient Management and Use of Animal Manure to Protect Human Health and Environmental Quality

Location: Food Animal Environmental Systems Research Unit

Title: Escherichia coli diversity in livestock manures and agriculturally impacted stream waters

Authors
item Cook, Kimberly
item Bolster, Carl
item Ayers, Kati -
item Reynolds, Dale -

Submitted to: Current Microbiology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: August 7, 2011
Publication Date: August 29, 2011
Repository URL: http://handle.nal.usda.gov/10113/54519
Citation: Cook, K.L., Bolster, C.H., Ayers, K.A., Reynolds, D.N. 2011. Escherichia coli diversity in livestock manures and agriculturally impacted stream waters. Current Microbiology. 63(5):439–449.

Interpretive Summary: Escherichia coli (E. coli) is a dominant intestinal commensal organism, an important fecal indicator bacterium (FIB), a pathogen and a target for microbial source tracking (MST). Strain level differences (genotypic and phenotypic) influence E. coli fate and transport and therefore have important implications for its validity as an FIB and for MST. The goals of this study were to (1) determine the diversity of E. coli in manures from livestock and stream-water samples taken following dry and wet weather events; (2) determine the profile of virulence-associated genes and; (3) evaluate the effect of strain level differences on the attachment and transport of E. coli. To evaluate diversity, 1346 E. coli isolates were obtained from three livestock species and seventeen stream-water samples. We found that many E. coli strains isolated from water sources had DNA fingerprints that were significantly different than those from stream-water in a predominantly agricultural area. Furthemore, significant differences were also seen between E. coli isolates from stream-water samples taken following wet and dry weather events. Wide diversity in the attachment efficiency of E. coli isolates from different sources occurred and those differences corresponded with the occurrence of virulence factors often correlated with adhesion. These findings underscore the genetic variation inherent to this important indicator organism. The influence of diversity on genetic exchange and the concomitant effect on the organisms’ fitness and adaptation to in situ environmental conditions require further investigation. The resultant issues for purposes of modeling, source tracking and risk assessment require careful consideration in future research studies.

Technical Abstract: Escherichia coli (E. coli) is a dominant intestinal commensal organism, an important fecal indicator bacterium (FIB), a pathogen and a target for microbial source tracking (MST). Strain level differences (genotypic and phenotypic) influence E. coli fate and transport and therefore have important implications for its validity as an FIB and for MST. The goals of this study were to (1) determine the diversity of E. coli in manures from livestock and stream-water samples taken following dry and wet weather events; (2) determine the profile of virulence-associated genes and; (3) evaluate the effect of strain level differences on the attachment and transport of E. coli. To evaluate diversity, 1346 E. coli isolates were obtained from three livestock species and seventeen stream-water samples. Strain diversity was evaluated by using repetitive extragenic palindromic PCR, phylotyping and virulence gene profiling. Attachment efficiencies to quartz sand were calculated for seventeen E. coli isolates following transport through saturated porous media. Richness of genotype profiles for livestock samples was relatively low (25, 12 and 11 for swine, poultry and dairy, respectively) compared to that of E. coli isolates from stream-water following dry or wet weather events (115 and 126, respectively). Genotype profiles for E. coli isolates from stream-water clustered with isolates from livestock species; however, over 34% of E. coli isolates from stream-water had genotype profiles that were distinct from those of the tested livestock species. Furthermore, only 18% of the 84 E. coli isolates from the wet and dry events clustered together, suggesting a high degree of temporal diversity. Genes associated with virulence (adhesions, toxins and siderophores) were present in E. coli isolates from all sources. The most commonly detected genes were the adhesions fimH (present in 80% to 95% of isolates) and agn43 (present in 40% to 100% of isolates). Bacterial attachment efficiencies among the seventeen E. coli isolates varied by an order of magnitude (0.039 to 0.44). The isolate with the highest attachment efficiency possessed the largest suite of targeted genes including those for adherence (iha, agn43, fimH), surface exclusion (traT) and the siderophore iroNE.coli. The five E. coli isolates with the highest attachments efficiencies were all positive for agn43and fimH. Data from this study underscore 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 require further investigation. These factors also require careful consideration for purposes of modeling, source tracking and risk assessment.

Last Modified: 7/24/2014
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