1
|
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: 0] [Impact Index Per Article: 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.
Collapse
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.
| |
Collapse
|
2
|
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.
Collapse
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:
| |
Collapse
|
3
|
Zhang P, Essendoubi S, Keenliside J, Reuter T, Stanford K, King R, Lu P, Yang X. Genomic analysis of Shiga toxin-producing Escherichia coli O157:H7 from cattle and pork-production related environments. NPJ Sci Food 2021; 5:15. [PMID: 34210979 PMCID: PMC8249597 DOI: 10.1038/s41538-021-00097-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2020] [Accepted: 04/06/2021] [Indexed: 02/04/2023] Open
Abstract
Three E. coli O157:H7 outbreaks have been attributed to contaminated pork in Alberta, Canada, recently. This study investigates the phylogenetic relatedness of E. coli O157:H7 from pigs, cattle, and pork-production environments for source attribution. Limited strain diversity was observed using five conventional subtyping methods, with most or all strains being in one subgroup. Whole-genome single nucleotide polymorphism analysis confirmed the recent ancestry of the isolates from all three sources. Most environmental isolates clustered closer with pig isolates than cattle isolates. Also, a direct link was observed between 2018-outbreak environmental isolates and isolates collected from a pig farm in 2018. The majority of pig isolates harbor only one Shiga toxin gene, stx2a, while 70% (35/50) of the cattle isolates have both stx1a and stx2a. The results show some E. coli O157:H7 strains could establish persistence on pig farms and as such, pigs can be a significant source of the organism.
Collapse
Affiliation(s)
- Peipei Zhang
- grid.55614.330000 0001 1302 4958Agriculture and Agri-Food Canada, Lacombe, Alberta Canada
| | | | | | - Tim Reuter
- Alberta Agriculture and Forestry, Lethbridge, Alberta Canada ,grid.47609.3c0000 0000 9471 0214University of Lethbridge, Lethbridge, Alberta Canada
| | - Kim Stanford
- Alberta Agriculture and Forestry, Lethbridge, Alberta Canada ,grid.47609.3c0000 0000 9471 0214University of Lethbridge, Lethbridge, Alberta Canada
| | - Robin King
- Alberta Agriculture and Forestry, Edmonton, Alberta Canada
| | - Patricia Lu
- Alberta Agriculture and Forestry, Edmonton, Alberta Canada
| | - Xianqin Yang
- grid.55614.330000 0001 1302 4958Agriculture and Agri-Food Canada, Lacombe, Alberta Canada
| |
Collapse
|
4
|
Genome Sequences of 104 Escherichia coli O157:H7 Isolates from Pigs, Cattle, and Pork Production Environments in Alberta, Canada. Microbiol Resour Announc 2021; 10:10/4/e01320-20. [PMID: 33509991 PMCID: PMC7844076 DOI: 10.1128/mra.01320-20] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Genome sequences of Escherichia coli O157:H7 originating from pigs are limited in the public databases. We sequenced 104 E. coli O157:H7 isolates from pig and cattle feces and pork production environments in Alberta, Canada. The information will aid studies investigating sources of E. coli O157:H7 contaminating pork and the associated environments. Genome sequences of Escherichia coli O157:H7 originating from pigs are limited in the public databases. We sequenced 104 E. coli O157:H7 isolates from pig and cattle feces and pork production environments in Alberta, Canada. The information will aid studies investigating sources of E. coli O157:H7 contaminating pork and the associated environments.
Collapse
|
5
|
Are Antimicrobial Interventions Associated with Heat-Resistant Escherichia coli on Meat? Appl Environ Microbiol 2020; 86:AEM.00512-20. [PMID: 32303544 DOI: 10.1128/aem.00512-20] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2020] [Accepted: 04/14/2020] [Indexed: 01/01/2023] Open
Abstract
Decontamination practices, which often involve thermal treatments, are routinely performed in beef packing plants and have generally improved the safety of meat in North America. We investigated whether Escherichia coli in the beef production chain is becoming more heat resistant due to those treatments. Cattle isolates (n = 750) included seven serogroups (O157, O103, O111, O121, O145, O26, and O45) which were collected between 2002 and 2017. Beef plant isolates (n = 700) from carcasses, fabrication equipment, and beef products were included. Heat resistance was determined in Luria-Bertani broth at 60°C and by PCR screening for the locus of heat resistance (LHR). The decimal reduction for E. coli at 60°C (D 60ºC values) ranged from 0 to 7.54 min, with 97.2% of the values being <2 min. The prevalence of E. coli with D 60ºC values of >2 min was not significantly different (P > 0.05) among cattle and meat plant isolates. E. coli from equipment before sanitation (median, 1.03 min) was more heat resistant than that after sanitation (median, 0.9 min). No significant difference in D 60ºC values was observed among E. coli isolates from different years, from carcasses before and after antimicrobial interventions, or from before and during carcass chilling. Of all isolates, 1.97% harbored LHR, and the LHR-positive isolates had greater median D 60ºC values than the LHR-negative isolates (3.25 versus 0.96 min). No increase in heat resistance in E. coli was observed along the beef production chain or with time.IMPORTANCE The implementation of multiple hurdles in the beef production chain has resulted in substantial improvement in the microbial safety of beef in Canada. In this study, we characterized a large number of Escherichia coli isolates (n = 1,450) from various sources/stages of beef processing to determine whether the commonly used antimicrobial interventions would give rise to heat-resistant E. coli on meat, which in turn may require alternatives to the current control of pathogens and/or modifications to the current cooking recommendations for meat. The findings show that the degree and rate of heat resistance in E. coli did not increase along the production chain or with time. This furthers our understanding of man-made ecological niches that are required for the development of heat resistance in E. coli.
Collapse
|
6
|
Jancewicz LJ, Penner GB, Swift ML, Waldner CL, Koenig KM, Beauchemin KA, McAllister TA. Predicting fecal nutrient concentrations and digestibilities and growth performance in feedlot cattle by near-infrared spectroscopy. J Anim Sci 2017; 95:455-474. [PMID: 28177389 DOI: 10.2527/jas.2016.0876] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Fecal nutrients and apparent total tract digestibility (ATTD) were predicted using near-infrared spectroscopy (NIRS) of feces collected from the pen floor or the rectum of feedlot cattle in 2 studies, and pen floor samples were assessed for their ability to predict NE, ADG, and G:F. In study 1, 160 crossbred beef steers in 16 pens (4 pens per treatment) were fed dry-rolled barley or wheat (89% of diet DM) processed at 2 levels. Study 2 utilized 160 crossbred beef steers in 20 pens (5 pens per treatment) that were fed dryrolled barley with 4 levels of barley silage (0%, 4%, 8%, and 12% of diet DM). Both studies fed steers to a target weight of 650 kg. Differences in composition of feces collected from the rectum and the pen floor of a subset of steers (3 to 7) were examined. Fecal pats from the pen floor of each pen were collected throughout the feeding period and composited by pen. Except for DM, which was higher ( 0.01) in pen floor than rectal fecal samples, there were minimal differences in fecal constituents between collection methods. In study 1, interactions between grain type and processing index ( ≤ 0.05) were observed, with a reduction in DM, OM, and starch and an increase in NDF and ADL concentrations being associated with more extensively processed wheat than barley. As grain was more extensively processed, ATTD of all nutrients increased ( 0.01). In study 2, fecal ADF and ADL linearly increased ( 0.01) with increasing silage in the diet, whereas fecal DM and N linearly decreased ( 0.01). Digestibility of all nutrients except starch linearly decreased ( 0.01) with increasing silage. Apparent total tract digestibility of GE predicted using NIRS was related to NEg of the diets as estimated by performance for the wheat-fed steers in study 1 ( = 0.58, = 0.03) and those fed increasing silage in study 2 ( = 0.43, < 0.01). Similarly, observed ADG could be predicted using NIRS for steers fed wheat in study 1 ( = 0.48, = 0.05) and silage in study 2 ( = 0.40, < 0.01), but G:F could not. Using NIRS of feces collected from multiple cattle off the feedlot pen floor demonstrated potential for predicting growth performance of finishing cattle. However, grain type and stage of maturity of the cattle impacted the predictability of equations. Increasing the sample size and sampling frequency may be necessary to improve predictions.
Collapse
|
7
|
Stanford K, Bach S, Baah J, McAllister T. A mixture of Lactobacillus casei, Lactobacillus lactis, and Paenibacillus polymyxa reduces Escherichia coli O157:H7 in finishing feedlot cattle. J Food Prot 2014; 77:738-44. [PMID: 24780327 DOI: 10.4315/0362-028x.jfp-13-433] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
A direct-fed microbial (DFM) containing Paenibacillus polymyxa, Lactobacillus casei, and Lactobacillus lactis was fed to cattle (n = 120) to determine impacts on shedding and survival of Escherichia coli O157:H7 in feces. Cattle were individually penned and fed diets containing 0 (control), 4 × 10(7) CFU (DFM-4), 8 × 10(7) CFU (DFM-8), or 1.2 × 10(8) CFU (DFM-12) lactobacilli per kg of dietary dry matter over 84-day fall-winter growing and 140-day spring-summer finishing periods. Fecal grab samples were collected from cattle at 28-day intervals, E. coli O157:H7 was detected by immunomagnetic separation, and isolates were compared by pulsed-field gel electrophoresis. During the growing period, feces negative for E. coli O157 from each dietary treatment were inoculated with 10(5) CFU/g nalidixic acid-resistant E. coli O157:H7 and were incubated at 4 and 22(u) C for 11 weeks. Fecal pH and fecal dry matter were measured on days 0, 1, 3, and 7 and weekly thereafter, with E. coli O157:H7 enumerated through dilution plating. Treatment with DFMs did not affect survival of E. coli O157:H7 in feces or fecal pH (P > 0.05). Only one steer was positive for E. coli O157:H7 during the growing period, but during the finishing period, DFM-8 and DFM-12 reduced the prevalence of E. coli O157:H7 in feces (P < 0.05). Feeding DFMs also reduced the frequency of individual steers shedding E. coli O157:H7 during finishing (P < 0.05), with control steers shedding E. coli O157:H7 up to four times, whereas DFM-12 steers shed E. coli O157:H7 a maximum of twice. Treatment with DFMs influenced pulsed-field gel electrophoresis profiles; steers that were fed DFM-8 and DFM-12 shed more diverse subtypes of E. coli O157:H7 than did control or DFM-4 steers. Because a companion study found linear improvement in performance with increasing dosage of DFMs in the first 28 days of the growing period, targeted use of DFM-12 during this time and for the final 1 or 2 weeks prior to slaughter may optimize performance and reduce E. coli O157:H7 while minimizing feed costs.
Collapse
Affiliation(s)
- Kim Stanford
- Alberta Agriculture and Rural Development, Lethbridge, Alberta, Canada T1J 4V6
| | - Susan Bach
- Agriculture and Agri-Food Canada, Summerland, British Columbia, Canada VOH 1ZO
| | - John Baah
- Agriculture and Agri-Food Canada, Lethbridge, Alberta, Canada T1J 4V6
| | - Tim McAllister
- Agriculture and Agri-Food Canada, Lethbridge, Alberta, Canada T1J 4V6.
| |
Collapse
|