L D Tymensen1, F Pyrdok2, D Coles1, W Koning3, T A McAllister4, C C Jokinen1, S E Dowd5, N F Neumann6. 1. Alberta Agriculture and Rural Development, Lethbridge, AB, Canada. 2. Umwelt-und Ingenieurtechnik GmbH, Dresden, Germany. 3. Alberta Environment and Sustainable Resource Development, Calgary, AB, Canada. 4. Agriculture and Agri-Food Canada, Lethbridge, AB, Canada. 5. Molecular Research LP, Shallowater, TX, USA. 6. Department of Public Health Sciences, University of Alberta, Edmonton, AB, Canada.
Abstract
AIMS: To utilize comparative accessory gene fingerprinting to discriminate between naturalized and faecal Escherichia coli, with particular emphasis on strains from phylogroup B1. METHODS AND RESULTS: Fourteen accessory genes that were potentially ecotype-specific were selected on the basis of comparative genomic DNA sequence analysis between faecal and environmental strains and also using a literature-based strategy. PCR assays were designed for each gene, and used to screen 107 faecal strains from various hosts and 106 environmental strains from surface water and sediment. While none of the 14 accessory genes were ecotype-specific, six of the genes were ecotype-enriched. Specifically, toxin-antitoxin system genes were more abundant among faecal strains, whereas genes involved in iron acquisition, complement resistance/surface exclusion, and biofilm formation were more abundant among environmental strains. These six genes were used to form composite fingerprints which revealed the presence of several ecotype-specific and -enriched fingerprints. Notably, some of the environmental strain-specific or -enriched fingerprints consisted of strains putatively belonging to clade ET-1, which has been previously recognized as a naturalized subpopulation. CONCLUSIONS: Unlike single genes which did not reliably distinguish between faecal and naturalized phylogroup B1 E. coli strains, composite fingerprints of ecotype-enriched accessory genes may offer a novel method for distinguishing between these two populations. SIGNIFICANCE AND IMPACT OF THE STUDY: Accessory gene fingerprinting may have important practical implications for improving the specificity of methods that are widely used for quantifying and identifying the sources of faecal contamination in surface water.
AIMS: To utilize comparative accessory gene fingerprinting to discriminate between naturalized and faecal Escherichia coli, with particular emphasis on strains from phylogroup B1. METHODS AND RESULTS: Fourteen accessory genes that were potentially ecotype-specific were selected on the basis of comparative genomic DNA sequence analysis between faecal and environmental strains and also using a literature-based strategy. PCR assays were designed for each gene, and used to screen 107 faecal strains from various hosts and 106 environmental strains from surface water and sediment. While none of the 14 accessory genes were ecotype-specific, six of the genes were ecotype-enriched. Specifically, toxin-antitoxin system genes were more abundant among faecal strains, whereas genes involved in iron acquisition, complement resistance/surface exclusion, and biofilm formation were more abundant among environmental strains. These six genes were used to form composite fingerprints which revealed the presence of several ecotype-specific and -enriched fingerprints. Notably, some of the environmental strain-specific or -enriched fingerprints consisted of strains putatively belonging to clade ET-1, which has been previously recognized as a naturalized subpopulation. CONCLUSIONS: Unlike single genes which did not reliably distinguish between faecal and naturalized phylogroup B1 E. coli strains, composite fingerprints of ecotype-enriched accessory genes may offer a novel method for distinguishing between these two populations. SIGNIFICANCE AND IMPACT OF THE STUDY: Accessory gene fingerprinting may have important practical implications for improving the specificity of methods that are widely used for quantifying and identifying the sources of faecal contamination in surface water.
Authors: Shuai Zhi; Graham Banting; Qiaozhi Li; Thomas A Edge; Edward Topp; Mykola Sokurenko; Candis Scott; Shannon Braithwaite; Norma J Ruecker; Yutaka Yasui; Tim McAllister; Linda Chui; Norman F Neumann Journal: Appl Environ Microbiol Date: 2016-08-30 Impact factor: 4.792
Authors: José Antonio Magaña-Lizárraga; Bruno Gómez-Gil; José Guadalupe Rendón-Maldonado; Francisco Delgado-Vargas; Inés Fernando Vega-López; María Elena Báez-Flores Journal: Microorganisms Date: 2022-03-20