Genomic Analysis of Shiga Toxin-Producing <i>E. coli</i> O157 Cattle and Clinical Isolates from Alberta, Canada
Shiga toxin (<i>stx</i>) is the principal virulence factor of the foodborne pathogen, Shiga toxin-producing <i>Escherichia coli</i> (STEC) O157:H7 and is associated with various lambdoid bacterio (phages). A comparative genomic analysis was performed on STEC O157 isolates fro...
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| Format: | Article |
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MDPI AG
2022-08-01
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| Series: | Toxins |
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| Online Access: | https://www.mdpi.com/2072-6651/14/9/603 |
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| author | Emmanuel W. Bumunang Rahat Zaheer Kim Stanford Chad Laing Dongyan Niu Le Luo Guan Linda Chui Gillian A. M. Tarr Tim A. McAllister |
| author_facet | Emmanuel W. Bumunang Rahat Zaheer Kim Stanford Chad Laing Dongyan Niu Le Luo Guan Linda Chui Gillian A. M. Tarr Tim A. McAllister |
| author_sort | Emmanuel W. Bumunang |
| collection | DOAJ |
| description | Shiga toxin (<i>stx</i>) is the principal virulence factor of the foodborne pathogen, Shiga toxin-producing <i>Escherichia coli</i> (STEC) O157:H7 and is associated with various lambdoid bacterio (phages). A comparative genomic analysis was performed on STEC O157 isolates from cattle (<i>n</i> = 125) and clinical (<i>n</i> = 127) samples to characterize virulence genes, <i>stx</i>-phage insertion sites and antimicrobial resistance genes that may segregate strains circulating in the same geographic region. In silico analyses revealed that O157 isolates harboured the toxin subtypes <i>stx1a</i> and <i>stx2a.</i> Most cattle (76.0%) and clinical (76.4%) isolates carried the virulence gene combination of <i>stx1</i>, <i>stx2</i>, <i>eae</i> and <i>hlyA</i>. Characterization of <i>stx1</i> and <i>stx2</i>-carrying phages in assembled contigs revealed that they were associated with <i>mlrA</i> and <i>wrbA</i> insertion sites, respectively. In cattle isolates, <i>mlrA</i> and <i>wrbA</i> insertion sites were occupied more often (77% and 79% isolates respectively) than in clinical isolates (38% and 1.6% isolates, respectively). Profiling of antimicrobial resistance genes (ARGs) in the assembled contigs revealed that 8.8% of cattle (11/125) and 8.7% of clinical (11/127) isolates harboured ARGs. Eight antimicrobial resistance genes cassettes (ARCs) were identified in 14 isolates (cattle, <i>n</i> = 8 and clinical, <i>n</i> = 6) with streptomycin (<i>aadA1</i>, <i>aadA2</i>, <i>ant(3’’)-Ia</i> and <i>aph(3’’)</i>-<i>Ib</i>) being the most prevalent gene in ARCs. The profound disparity between the cattle and clinical strains in occupancy of the <i>wrbA</i> locus suggests that this trait may serve to differentiate cattle from human clinical STEC O157:H7. These findings are important for <i>stx</i> screening and <i>stx</i>-phage insertion site genotyping as well as monitoring ARGs in isolates from cattle and clinical samples. |
| first_indexed | 2024-03-09T22:20:21Z |
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| id | doaj.art-9229bd8ba9c34db9916d240727479357 |
| institution | Directory Open Access Journal |
| issn | 2072-6651 |
| language | English |
| last_indexed | 2024-03-09T22:20:21Z |
| publishDate | 2022-08-01 |
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| series | Toxins |
| spelling | doaj.art-9229bd8ba9c34db9916d2407274793572023-11-23T19:16:33ZengMDPI AGToxins2072-66512022-08-0114960310.3390/toxins14090603Genomic Analysis of Shiga Toxin-Producing <i>E. coli</i> O157 Cattle and Clinical Isolates from Alberta, CanadaEmmanuel W. Bumunang0Rahat Zaheer1Kim Stanford2Chad Laing3Dongyan Niu4Le Luo Guan5Linda Chui6Gillian A. M. Tarr7Tim A. McAllister8Faculty of Veterinary Medicine, University of Calgary, Calgary, AB T2N 1N4, CanadaAgriculture and Agri-Food Canada, Lethbridge Research and Development Centre, Lethbridge, AB T1J 4B1, CanadaDepartment of Biological Sciences, University of Lethbridge, Lethbridge, AB T1K 1M4, CanadaNational Centre for Animal Disease Canadian Food Inspection Agency, Lethbridge, AB T1J 0P3, CanadaFaculty of Veterinary Medicine, University of Calgary, Calgary, AB T2N 1N4, CanadaDepartment of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB T6G 2P9, CanadaAlberta Precisions Laboratory, Alberta Public Health, Edmonton, AB T6G 2J2, CanadaDivision of Environmental Health Sciences, School of Public Health, University of Minnesota, Minneapolis, MN 55455, USAAgriculture and Agri-Food Canada, Lethbridge Research and Development Centre, Lethbridge, AB T1J 4B1, CanadaShiga toxin (<i>stx</i>) is the principal virulence factor of the foodborne pathogen, Shiga toxin-producing <i>Escherichia coli</i> (STEC) O157:H7 and is associated with various lambdoid bacterio (phages). A comparative genomic analysis was performed on STEC O157 isolates from cattle (<i>n</i> = 125) and clinical (<i>n</i> = 127) samples to characterize virulence genes, <i>stx</i>-phage insertion sites and antimicrobial resistance genes that may segregate strains circulating in the same geographic region. In silico analyses revealed that O157 isolates harboured the toxin subtypes <i>stx1a</i> and <i>stx2a.</i> Most cattle (76.0%) and clinical (76.4%) isolates carried the virulence gene combination of <i>stx1</i>, <i>stx2</i>, <i>eae</i> and <i>hlyA</i>. Characterization of <i>stx1</i> and <i>stx2</i>-carrying phages in assembled contigs revealed that they were associated with <i>mlrA</i> and <i>wrbA</i> insertion sites, respectively. In cattle isolates, <i>mlrA</i> and <i>wrbA</i> insertion sites were occupied more often (77% and 79% isolates respectively) than in clinical isolates (38% and 1.6% isolates, respectively). Profiling of antimicrobial resistance genes (ARGs) in the assembled contigs revealed that 8.8% of cattle (11/125) and 8.7% of clinical (11/127) isolates harboured ARGs. Eight antimicrobial resistance genes cassettes (ARCs) were identified in 14 isolates (cattle, <i>n</i> = 8 and clinical, <i>n</i> = 6) with streptomycin (<i>aadA1</i>, <i>aadA2</i>, <i>ant(3’’)-Ia</i> and <i>aph(3’’)</i>-<i>Ib</i>) being the most prevalent gene in ARCs. The profound disparity between the cattle and clinical strains in occupancy of the <i>wrbA</i> locus suggests that this trait may serve to differentiate cattle from human clinical STEC O157:H7. These findings are important for <i>stx</i> screening and <i>stx</i>-phage insertion site genotyping as well as monitoring ARGs in isolates from cattle and clinical samples.https://www.mdpi.com/2072-6651/14/9/603<i>Escherichia coli</i> O157Shiga toxins<i>stx</i>-carrying phagesinsertion sitesantimicrobial resistance |
| spellingShingle | Emmanuel W. Bumunang Rahat Zaheer Kim Stanford Chad Laing Dongyan Niu Le Luo Guan Linda Chui Gillian A. M. Tarr Tim A. McAllister Genomic Analysis of Shiga Toxin-Producing <i>E. coli</i> O157 Cattle and Clinical Isolates from Alberta, Canada Toxins <i>Escherichia coli</i> O157 Shiga toxins <i>stx</i>-carrying phages insertion sites antimicrobial resistance |
| title | Genomic Analysis of Shiga Toxin-Producing <i>E. coli</i> O157 Cattle and Clinical Isolates from Alberta, Canada |
| title_full | Genomic Analysis of Shiga Toxin-Producing <i>E. coli</i> O157 Cattle and Clinical Isolates from Alberta, Canada |
| title_fullStr | Genomic Analysis of Shiga Toxin-Producing <i>E. coli</i> O157 Cattle and Clinical Isolates from Alberta, Canada |
| title_full_unstemmed | Genomic Analysis of Shiga Toxin-Producing <i>E. coli</i> O157 Cattle and Clinical Isolates from Alberta, Canada |
| title_short | Genomic Analysis of Shiga Toxin-Producing <i>E. coli</i> O157 Cattle and Clinical Isolates from Alberta, Canada |
| title_sort | genomic analysis of shiga toxin producing i e coli i o157 cattle and clinical isolates from alberta canada |
| topic | <i>Escherichia coli</i> O157 Shiga toxins <i>stx</i>-carrying phages insertion sites antimicrobial resistance |
| url | https://www.mdpi.com/2072-6651/14/9/603 |
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