Genetic Characterization of Escherichia coli Populations from Host Sources of Fecal Pollution by Using DNA Fingerprinting

Abstract

Escherichia coli isolates were obtained from common host sources of fecal pollution and characterized by using repetitive extragenic palindromic (REP) PCR fingerprinting. The genetic relationship of strains within each host group was assessed as was the relationship of strains among different host groups. Multiple isolates from a single host animal (gull, human, or dog) were found to be identical; however, in some of the animals, additional strains occurred at a lower frequency. REP PCR fingerprint patterns of isolates from sewage (n ‫؍‬ 180), gulls (n ‫؍‬ 133), and dairy cattle (n ‫؍‬ 121) were diverse; within a host group, pairwise comparison similarity indices ranged from 98% to as low as 15%. A composite dendrogram of E. coli fingerprint patterns did not cluster the isolates into distinct host groups but rather produced numerous subclusters (approximately >80% similarity scores calculated with the cosine coefficient) that were nearly exclusive for a host group. Approximately 65% of the isolates analyzed were arranged into host-specific groups. Comparable results were obtained by using enterobacterial repetitive intergenic consensus PCR and pulsed-field gel electrophoresis (PFGE), where PFGE gave a higher differentiation of closely related strains than both PCR techniques. These results demonstrate that environmental studies with genetic comparisons to detect sources of E. coli contamination will require extensive isolation of strains to encompass E. coli strain diversity found in host sources of contamination. These findings will assist in the development of approaches to determine sources of fecal pollution, an effort important for protecting water resources and public health.

Population dynamics and genetic variability of Escherichia coli in a mixed land-use watershed

“…Thus, the diversity of E. coli populations present in fecal materials from humans and animals has been the subject of numerous studies (e.g. Carson et al 2001;Gordon & Cowling 2003;McLellan et al 2003;Johnson et al 2004). …”

Faecal contamination of a municipal drinking water distribution system in association with Campylobacter jejuni infections

“…However, our work outlined the use of rep-PCR within one contamination incident and consequently our dataset consisted of only 56 coliform isolates all originating from the same system. In previously reported analyses using rep-PCR, a large pattern library is used, as the goal of studies has been to discriminate between different possible host sources (Dombek et al 2000;Carson et al 2003;McLellan et al 2003;Leung et al 2004). In our work, we did not aim to distinguish between possible hosts, since direct faecal samples from the suspected wild birds were not available.…”

“…There are three groups of repetitive elements that are used in the applications of rep-PCR: repetitive extragenic palindromic (REP) sequence, enterobacterial repetitive intergenic consensus (ERIC) sequence, and BOX element (Rademaker et al 1998). In the microbial source tracking studies conducted, the use of the rep-PCR method with Escherichia coli isolates has been library dependent with the goal of differentiation between human and non-human sources when the analysis of a large collection of micro-organisms from different sources is required (Simpson et al 2002;McLellan et al 2003). In addition to the PFGE and rep-PCR techniques, other molecular methods, such as amplified fragment length polymorphism (AFLP), and phenotypic methods including antibiotic resistance analysis are applied in microbial source tracking (Simpson et al 2002;Leung et al 2004).…”

Analysis of major band of Enterobacter sakazakii by ERIC-PCR and development of a species-specific PCR for detection of Ent. sakazakii in dry food samples

“…Recently, ERIC-PCR was used for the evaluation of genetic analysis and epidemiology investigation of some pathogens such as Vibrio parahaemolyticus, Campylobacter, Escherichia coli, Salmonella enterica and Aeromonas sp. strains (Versalovic et al, 1991;Wong and Lin, 2001;Da Silverra et al, 2002;Mclellan et al, 2003;Szczuka and Kaznowski, 2004;Houf et al, 2005;Mouwen et al, 2005). However, little attempt has been focused on the typing of Ent.…”