combination of PhP typing and β-d-glucuronidase gene sequence variation analysis for differentiation of Escherichia coli from humans and animals

• Published in: Canadian journal of microbiology Vol. 61; no. 6; pp. 409 - 416
• Main Authors: Masters, N, Christie, M, Katouli, M, Stratton, H
• Format: Journal Article
• Language: English
• Published: Canada NRC Research Press 01.06.2015
• Subjects: algorithms; analyse numérique; Animals; Animals, Domestic - microbiology; Animals, Wild - microbiology; Bacterial Typing Techniques - methods; beta-glucuronidase; Cattle; Chickens; Dogs; E. coli; Escherichia coli; Escherichia coli - classification; Escherichia coli - enzymology; Escherichia coli - genetics; Escherichia coli - isolation & purification; Escherichia coli Infections - microbiology; Escherichia coli Infections - veterinary; Escherichia coli Proteins - genetics; Escherichia coli Proteins - metabolism; Feces - microbiology; genes; genetic markers; Genetic Variation; glucuronidase; Glucuronidase - genetics; Glucuronidase - metabolism; glucuronidase gene; gène de la β; Horses; host specificity; hosts; Humans; loci; Molecular Sequence Data; nucleotide sequences; numerical analysis; phenotype; PhP typing; Phylogeny; pollution; Sequence Analysis, DNA; Swine; typage PhP; variance; wild animals; β-d-glucuronidase gene; gène de la β-d-glucuronidase; analyse numérique; numerical analysis; PhP typing; E. coli; typage PhP
• ISSN: 1480-3275; 0008-4166; 1480-3275
• DOI: 10.1139/cjm-2015-0048

We investigated the usefulness of the β-d-glucuronidase gene variance in Escherichia coli as a microbial source tracking tool using a novel algorithm for comparison of sequences from a prescreened set of host-specific isolates using a high-resolution PhP typing method. A total of 65 common biochemical phenotypes belonging to 318 E. coli strains isolated from humans and domestic and wild animals were analysed for nucleotide variations at 10 loci along a 518 bp fragment of the 1812 bp β-d-glucuronidase gene. Neighbour-joining analysis of loci variations revealed 86 (76.8%) human isolates and 91.2% of animal isolates were correctly identified. Pairwise hierarchical clustering improved assignment; where 92 (82.1%) human and 204 (99%) animal strains were assigned to their respective cluster. Our data show that initial typing of isolates and selection of common types from different hosts prior to analysis of the β-d-glucuronidase gene sequence improves source identification. We also concluded that numerical profiling of the nucleotide variations can be used as a valuable approach to differentiate human from animal E. coli. This study signifies the usefulness of the β-d-glucuronidase gene as a marker for differentiating human faecal pollution from animal sources.