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Bumunang EW, Castro VS, Alexander T, Zaheer R, McAllister TA, Guan LL, Stanford K. In Silico Analysis of Shiga Toxin-Producing Escherichia coli O157:H7 Strains from Presumptive Super- and Low-Shedder Cattle. Toxins (Basel) 2024; 16:86. [PMID: 38393164 PMCID: PMC10893428 DOI: 10.3390/toxins16020086] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Revised: 01/19/2024] [Accepted: 02/03/2024] [Indexed: 02/25/2024] Open
Abstract
Cattle are the primary reservoir for STEC O157, with some shedding >104 CFU/g in feces, a phenomenon known as super-shedding (SS). The mechanism(s) responsible for SS are not understood but have been attributed to the environment, host, and pathogen. This study aimed to compare genetic characteristics of STEC O157 strains from cattle in the same commercial feedlot pens with SS or low-shedding (LS) status. Strains from SS (n = 35) and LS (n = 28) collected from 11 pens in three feedlots were analyzed for virulence genes, Shiga toxin-carrying bacteriophage insertion sites, and phylogenetic relationships. In silico analysis showed limited variation regarding virulence gene profiles. Stx-encoding prophage insertion sites mrlA and wrbA for stx1a and stx2a, respectively, were all occupied, but two isolates had fragments of the stx-carrying phage in mrlA and wrbA loci without stx1a and stx2a. All strains screened for lineage-specific polymorphism assay (LSPA-6) were 111111, lineage I. Of the isolates, 61 and 2 were clades 1 and 8, respectively. Phylogenetic analysis revealed that pens with more than one SS had multiple distantly related clusters of SS and LS isolates. Although virulence genes and lineage were largely similar within and across feedlots, multiple genetic origins of strains within a single feedlot pen illustrate challenges for on-farm control of STEC.
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Affiliation(s)
- Emmanuel W. Bumunang
- Agriculture and Agri-Food Canada, Lethbridge Research and Development Centre, Lethbridge, AB T1J 4B1, Canada; (E.W.B.); (T.A.); (R.Z.); (T.A.M.)
| | - Vinicius S. Castro
- Faculty of Agronomy and Zootechnics, Federal University of Mato Grosso (UFMT), Cuiabá 78010-715, Brazil;
- Department of Biological Sciences, University of Lethbridge, Lethbridge, AB T1K 1M4, Canada
| | - Trevor Alexander
- Agriculture and Agri-Food Canada, Lethbridge Research and Development Centre, Lethbridge, AB T1J 4B1, Canada; (E.W.B.); (T.A.); (R.Z.); (T.A.M.)
| | - Rahat Zaheer
- Agriculture and Agri-Food Canada, Lethbridge Research and Development Centre, Lethbridge, AB T1J 4B1, Canada; (E.W.B.); (T.A.); (R.Z.); (T.A.M.)
| | - Tim A. McAllister
- Agriculture and Agri-Food Canada, Lethbridge Research and Development Centre, Lethbridge, AB T1J 4B1, Canada; (E.W.B.); (T.A.); (R.Z.); (T.A.M.)
| | - Le Luo Guan
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB T6G 2P9, Canada;
| | - Kim Stanford
- Department of Biological Sciences, University of Lethbridge, Lethbridge, AB T1K 1M4, Canada
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Fang Y, Tran F, Stanford K, Yang X. Stress Resistance and Virulence Gene Profiles Associated with Phylogeny and Phenotypes of Escherichia coli from Cattle. J Food Prot 2023; 86:100122. [PMID: 37355007 DOI: 10.1016/j.jfp.2023.100122] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Revised: 06/15/2023] [Accepted: 06/19/2023] [Indexed: 06/26/2023]
Abstract
Seven serogroups of E. coli (Top seven E. coli) are frequently implicated in foodborne outbreaks in North America, largely due to their carriage of Shiga toxin genes (stx). This study aimed to profile resistance genes and virulence factors (VF), and their potential association with phylogeny and phenotypes of Top seven E. coli originating from cattle in Canada. 155 Top seven E. coli isolates previously characterized for heat and acid resistance and biofilm-forming ability were whole-genome sequenced and analyzed for phylogeny, VF, and stress resistance genes. The 155 E. coli strains belonged to six phylogroups: A (n = 32), B1 (n = 93), C (n = 3), D (n = 11), E (n = 15), and G (n = 1). Different phylogroups were clearly separated on the core genome tree, with strains of the same serotype closely clustered. The carriage of stx and the transmissible locus of stress tolerance (tLST), the extreme heat resistance marker, was mutually exclusive, in 33 and 15 genomes, respectively. A novel O84:H2 strain carrying stx1a was also identified. In total, 70, 41, and 32 VF, stress resistance genes and antibiotic resistance genes were identified. The stress resistance genes included those for metal (n = 29), biocides/acid (n = 4), and heat (n = 8) resistance. All heat resistance genes and most metal-resistance genes that were differentially distributed among the phylogroups were exclusively in phylogroup A. VF were least and most present in phylogroups A and D, respectively. No specific genes associated with acid resistance or biofilm formation phenotypes were identified. VF were more abundant (P < 0.05) in the non-biofilm-forming population and acid-resistant population.
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Affiliation(s)
- Yuan Fang
- Agriculture and Agri-Food Canada Lacombe Research and Development Centre, 6000 C & E Trail, Lacombe, AB T4L 1W1, Canada
| | - Frances Tran
- Agriculture and Agri-Food Canada Lacombe Research and Development Centre, 6000 C & E Trail, Lacombe, AB T4L 1W1, Canada
| | - Kim Stanford
- University of Lethbridge, Lethbridge, AB T1K 3M4, Canada
| | - Xianqin Yang
- Agriculture and Agri-Food Canada Lacombe Research and Development Centre, 6000 C & E Trail, Lacombe, AB T4L 1W1, Canada.
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Xu ZS, Ju T, Yang X, Gänzle M. A Meta-Analysis of Bacterial Communities in Food Processing Facilities: Driving Forces for Assembly of Core and Accessory Microbiomes across Different Food Commodities. Microorganisms 2023; 11:1575. [PMID: 37375077 DOI: 10.3390/microorganisms11061575] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2023] [Revised: 05/31/2023] [Accepted: 06/04/2023] [Indexed: 06/29/2023] Open
Abstract
Microbial spoilage is a major cause of food waste. Microbial spoilage is dependent on the contamination of food from the raw materials or from microbial communities residing in food processing facilities, often as bacterial biofilms. However, limited research has been conducted on the persistence of non-pathogenic spoilage communities in food processing facilities, or whether the bacterial communities differ among food commodities and vary with nutrient availability. To address these gaps, this review re-analyzed data from 39 studies from various food facilities processing cheese (n = 8), fresh meat (n = 16), seafood (n = 7), fresh produce (n = 5) and ready-to-eat products (RTE; n = 3). A core surface-associated microbiome was identified across all food commodities, including Pseudomonas, Acinetobacter, Staphylococcus, Psychrobacter, Stenotrophomonas, Serratia and Microbacterium. Commodity-specific communities were additionally present in all food commodities except RTE foods. The nutrient level on food environment surfaces overall tended to impact the composition of the bacterial community, especially when comparing high-nutrient food contact surfaces to floors with an unknown nutrient level. In addition, the compositions of bacterial communities in biofilms residing in high-nutrient surfaces were significantly different from those of low-nutrient surfaces. Collectively, these findings contribute to a better understanding of the microbial ecology of food processing environments, the development of targeted antimicrobial interventions and ultimately the reduction of food waste and food insecurity and the promotion of food sustainability.
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Affiliation(s)
- Zhaohui S Xu
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB T6G 2P5, Canada
| | - Tingting Ju
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB T6G 2P5, Canada
| | - Xianqin Yang
- Lacombe Research and Development Centre, Agriculture and Agri-Food Canada, Lacombe, AB T4L 1W1, Canada
| | - Michael Gänzle
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB T6G 2P5, Canada
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Development and validation of high-resolution melting assays for the detection of potentially virulent strains of Escherichia coli O103 and O121. Food Control 2022. [DOI: 10.1016/j.foodcont.2022.109095] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Bumunang EW, Zaheer R, Stanford K, Laing C, Niu D, Guan LL, Chui L, Tarr GAM, McAllister TA. Genomic Analysis of Shiga Toxin-Producing E. coli O157 Cattle and Clinical Isolates from Alberta, Canada. Toxins (Basel) 2022; 14:toxins14090603. [PMID: 36136541 PMCID: PMC9505746 DOI: 10.3390/toxins14090603] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Revised: 08/24/2022] [Accepted: 08/24/2022] [Indexed: 12/02/2022] Open
Abstract
Shiga toxin (stx) is the principal virulence factor of the foodborne pathogen, Shiga toxin-producing Escherichia coli (STEC) O157:H7 and is associated with various lambdoid bacterio (phages). A comparative genomic analysis was performed on STEC O157 isolates from cattle (n = 125) and clinical (n = 127) samples to characterize virulence genes, stx-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 stx1a and stx2a. Most cattle (76.0%) and clinical (76.4%) isolates carried the virulence gene combination of stx1, stx2, eae and hlyA. Characterization of stx1 and stx2-carrying phages in assembled contigs revealed that they were associated with mlrA and wrbA insertion sites, respectively. In cattle isolates, mlrA and wrbA 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, n = 8 and clinical, n = 6) with streptomycin (aadA1, aadA2, ant(3’’)-Ia and aph(3’’)-Ib) being the most prevalent gene in ARCs. The profound disparity between the cattle and clinical strains in occupancy of the wrbA locus suggests that this trait may serve to differentiate cattle from human clinical STEC O157:H7. These findings are important for stx screening and stx-phage insertion site genotyping as well as monitoring ARGs in isolates from cattle and clinical samples.
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Affiliation(s)
- Emmanuel W. Bumunang
- Faculty of Veterinary Medicine, University of Calgary, Calgary, AB T2N 1N4, Canada
| | - Rahat Zaheer
- Agriculture and Agri-Food Canada, Lethbridge Research and Development Centre, Lethbridge, AB T1J 4B1, Canada
| | - Kim Stanford
- Department of Biological Sciences, University of Lethbridge, Lethbridge, AB T1K 1M4, Canada
| | - Chad Laing
- National Centre for Animal Disease Canadian Food Inspection Agency, Lethbridge, AB T1J 0P3, Canada
| | - Dongyan Niu
- Faculty of Veterinary Medicine, University of Calgary, Calgary, AB T2N 1N4, Canada
| | - Le Luo Guan
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB T6G 2P9, Canada
| | - Linda Chui
- Alberta Precisions Laboratory, Alberta Public Health, Edmonton, AB T6G 2J2, Canada
- Department of Laboratory Medicine and Pathology, University of Alberta, Edmonton, AB T6G 2B7, Canada
| | - Gillian A. M. Tarr
- Division of Environmental Health Sciences, School of Public Health, University of Minnesota, Minneapolis, MN 55455, USA
| | - Tim A. McAllister
- Agriculture and Agri-Food Canada, Lethbridge Research and Development Centre, Lethbridge, AB T1J 4B1, Canada
- Correspondence:
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