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Rahman MK, Rodriguez-Mori H, Loneragan GH, Awosile B. Beta-lactamase genes in bacteria from food animals, retail meat, and human surveillance programs in the United States from 2002 to 2021. Comp Immunol Microbiol Infect Dis 2024; 106:102139. [PMID: 38325128 DOI: 10.1016/j.cimid.2024.102139] [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: 12/04/2023] [Revised: 01/24/2024] [Accepted: 01/30/2024] [Indexed: 02/09/2024]
Abstract
The spread of beta-lactamase-producing bacteria is a global public-health concern. This study aimed to explore the distribution of beta-lactamases reported in three sampling sources (cecal, retail meat, and human) collected as part of integrated surveillance in the United States. We retrieved and analyzed data from the United States National Antimicrobial Resistance Monitoring Systems (NARMS) from 2002 to 2021. A total of 115 beta-lactamase genes were detected in E. coli, Salmonella enterica, Campylobacter, Shigella and Vibrio: including 35 genes from cecal isolates, 32 genes from the retail meat isolates, and 104 genes from the human isolates. Three genes in E. coli (blaCMY-2,blaTEM-1A, and blaTEM-1B), 6 genes in Salmonella enterica (blaCARB-2, blaCMY-2, blaCTXM-65, blaTEM-1A, blaTEM-1B, and blaHERA-3), and 2 genes in Campylobacter spp. (blaOXA-61 and blaOXA-449) have been detected across food animals (cattle, chicken, swine, and turkey) and humans over the study period. blaCTXM-55 has been detected in E. coli isolates from the four food animal sources while blaCTXM-15 and blaCTXM-27 were found only in cattle and swine. In Salmonella enterica, blaCTXM-2, blaCTXM-9, blaCTXM-14, blaCTXM-15, blaCTXM-27, blaCTXM-55, and blaNDM-1 were only detected among human isolates. blaOXAs and blaCARB were bacteria-specific and the only beta-lactamase genes detected in Campylobacter spp. and Vibrio spp respectively. The proportions of beta-lactamase genes detected varies from bacteria to bacteria. This study provided insights on the beta-lactamase genes detected in bacteria in food animals and humans in the United States. This is necessary for better understanding the molecular epidemiology of clinically important beta-lactamases in one health interface.
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Affiliation(s)
- Md Kaisar Rahman
- Texas Tech University School of Veterinary Medicine, Amarillo, TX 79106, USA
| | | | - Guy H Loneragan
- Texas Tech University School of Veterinary Medicine, Amarillo, TX 79106, USA
| | - Babafela Awosile
- Texas Tech University School of Veterinary Medicine, Amarillo, TX 79106, USA.
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Gelalcha BD, Gelgie AE, Kerro Dego O. Prevalence and antimicrobial resistance profiles of extended-spectrum beta-lactamase-producing Escherichia coli in East Tennessee dairy farms. Front Vet Sci 2023; 10:1260433. [PMID: 38239744 PMCID: PMC10795760 DOI: 10.3389/fvets.2023.1260433] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Accepted: 11/16/2023] [Indexed: 01/22/2024] Open
Abstract
Introduction The extended-spectrum beta-lactamase (ESBL)-producing Enterobacteriaceae, such as Escherichia coli, are emerging as a serious threat to global health due to their rapid spread and their multidrug-resistant (MDR) phenotypes. However, limited information is available regarding the prevalence and antimicrobial resistance (AMR) profile of ESBL-E. coli in the United States dairy farms. This study aimed to determine the prevalence and AMR pattern of ESBL-E. coli in East Tennessee dairy cattle farms. Methods Rectal fecal samples from dairy cattle (n = 508) and manure (n = 30), water (n = 19), and feed samples (n = 15) were collected from 14 farms. The presumptive E. coli was isolated on CHROMagar™ ESBL and confirmed by matrix-assisted laser desorption/ionization-time of flight mass spectrometry (MALDI-TOF MS). Antimicrobial susceptibility testing was performed on the ESBL-E. coli isolates. Results and discussion From 572 fecal and farm environmental samples, a total of 233 (41%, n = 572) ESBL-E. coli were identified. The prevalence of fecal ESBL-E. coli was 47.5% (95% CI: 46.2-49.2). The within-farm prevalence of ESBL-E. coli ranged from 8 to 100%. Recent treatment history with third-generation cephalosporins (3GC), cow parity ≥3, and calves were the independent risk factors associated (P < 0.05) with fecal carriage of ESBL-E. coli. Overall, 99.6% (n = 231) ESBL-E. coli tested were phenotypically resistant to at least one of the 14 antimicrobial agents tested. The most common AMR phenotypes were against beta-lactam antibiotics, ampicillin (99.1%; n = 231 isolates), and ceftriaxone (98.7%, n = 231). Most ESBL-E. coli isolates (94.4%) were MDR (resistance to ≥3 antimicrobial classes), of which 42.6% showed co-resistance to at least six classes of antimicrobials. ESBL-E. coli isolates with concurrent resistance to ceftriaxone, ampicillin, streptomycin, tetracycline, sulfisoxazole, and chloramphenicol are widespread and detected in all the farms. The detection of MDR ESBL-E. coli suggests that dairy cattle can be a reservoir for these bacteria, highlighting the associated public health risk.
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Affiliation(s)
| | | | - Oudessa Kerro Dego
- Department of Animal Science, The University of Tennessee, Knoxville, TN, United States
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Gelalcha BD, Mohammed RI, Gelgie AE, Kerro Dego O. Molecular epidemiology and pathogenomics of extended-spectrum beta-lactamase producing- Escherichia coli and - Klebsiella pneumoniae isolates from bulk tank milk in Tennessee, USA. Front Microbiol 2023; 14:1283165. [PMID: 38029210 PMCID: PMC10658008 DOI: 10.3389/fmicb.2023.1283165] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2023] [Accepted: 10/09/2023] [Indexed: 12/01/2023] Open
Abstract
Introduction The rise in extended-spectrum beta-lactamase (ESBL)-producing Enterobacteriaceae in dairy cattle farms poses a risk to human health as they can spread to humans through the food chain, including raw milk. This study was designed to determine the status, antimicrobial resistance, and pathogenic potential of ESBL-producing -E. coli and -Klebsiella spp. isolates from bulk tank milk (BTM). Methods Thirty-three BTM samples were collected from 17 dairy farms and screened for ESBL-E. coli and -Klebsiella spp. on CHROMagar ESBL plates. All isolates were confirmed by matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS) and subjected to antimicrobial susceptibility testing and whole genome sequencing (WGS). Results Ten presumptive ESBL-producing bacteria, eight E. coli, and two K. pneumoniae were isolated. The prevalence of ESBL-E. coli and -K. pneumoniae in BTM was 21.2% and 6.1%, respectively. ESBL-E. coli were detected in 41.2% of the study farms. Seven of the ESBL-E. coli isolates were multidrug resistant (MDR). The two ESBL-producing K. pneumoniae isolates were resistant to ceftriaxone. Seven ESBL-E. coli strains carry the blaCTX-M gene, and five of them co-harbored blaTEM-1. ESBL-E. coli co-harbored blaCTX-M with other resistance genes, including qnrB19, tet(A), aadA1, aph(3'')-Ib, aph(6)-Id), floR, sul2, and chromosomal mutations (gyrA, gyrB, parC, parE, and pmrB). Most E. coli resistance genes were associated with mobile genetic elements, mainly plasmids. Six sequence types (STs) of E. coli were detected. All ESBL-E. coli were predicted to be pathogenic to humans. Four STs (three ST10 and ST69) were high-risk clones of E. coli. Up to 40 virulence markers were detected in all E. coli isolates. One of the K. pneumoniae was ST867; the other was novel strain. K. pneumoniae isolates carried three types of beta-lactamase genes (blaCTX-M, blaTEM-1 and blaSHV). The novel K. pneumoniae ST also carried a novel IncFII(K) plasmid ST. Conclusion Detection of high-risk clones of MDR ESBL-E. coli and ESBL-K. pneumoniae in BTM indicates that raw milk could be a reservoir of potentially zoonotic ESBL-E. coli and -K. pneumoniae.
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Affiliation(s)
- Benti D. Gelalcha
- Department of Animal Science, The University of Tennessee, Knoxville, TN, United States
| | - Ruwaa I. Mohammed
- Department of Genome Science and Technology, The University of Tennessee, Knoxville, TN, United States
| | - Aga E. Gelgie
- Department of Animal Science, The University of Tennessee, Knoxville, TN, United States
| | - Oudessa Kerro Dego
- Department of Animal Science, The University of Tennessee, Knoxville, TN, United States
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Gu G, Pei H, Zhou A, Fan B, Zhou H, Choi A, Huang Z. A Comprehensive Study of Historical Detection Data for Pathogen Isolates from U.S. Cattle. Antibiotics (Basel) 2023; 12:1509. [PMID: 37887210 PMCID: PMC10604524 DOI: 10.3390/antibiotics12101509] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2023] [Revised: 09/27/2023] [Accepted: 09/28/2023] [Indexed: 10/28/2023] Open
Abstract
Foodborne pathogens pose substantial health hazards and result in considerable economic losses in the U.S. Fortunately, the National Center for Biotechnology Information Pathogen Detection Isolates Browser (NPDIB) provides valuable access to antimicrobial resistance (AMR) genes and antimicrobial assay data. This study aimed to conduct the first comprehensive investigation of AMR genes in pathogens isolated from U.S. cattle over the past decade, driven by the urgent need to address the dangers of AMR specifically originating in pathogens isolated from U.S. cattle. In this study, around 28,000 pathogen isolate samples were extracted from the NPDIB and then analyzed using multivariate statistical methods, mainly principal component analysis (PCA) and hierarchical clustering (H-clustering). These approaches were necessary due to the high dimensions of the raw data. Specifically, PCA was utilized to reduce the dimensions of the data, converting it to a two-dimensional space, and H-clustering was used to better identify the differences among data points. The findings from this work highlighted Salmonella enterica and Escherichia coli as the predominant pathogens among the isolates, with E. coli being the more concerning pathogen due to its increasing prevalence in recent years. Moreover, tetracycline was observed as the most commonly resistant antimicrobial, with the resistance genes mdsA, mdsB, mdtM, blaEC, and acrF being the most prevalent in pathogen isolates from U.S. cattle. The occurrence of mdtM, blaEC, acrF, and glpT_E448k showed an increase in pathogens isolated from U.S. cattle in recent years. Furthermore, based on the data collected for the locations of AMR cases, Texas, California, and Nebraska were the major areas carrying major AMR genes or antimicrobials with detected resistance. The results from this study provide potential directions for targeted interventions to mitigate pathogens' antimicrobial resistance in U.S. cattle.
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Affiliation(s)
| | | | | | | | | | | | - Zuyi Huang
- Department of Chemical and Biological Engineering, Villanova University, Villanova, PA 19085, USA; (G.G.); (H.P.); (A.Z.); (B.F.); (H.Z.); (A.C.)
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Fonseca M, Heider LC, Stryhn H, McClure JT, Léger D, Rizzo D, Warder L, Dufour S, Roy JP, Kelton DF, Renaud D, Barkema HW, Sanchez J. Intramammary and systemic use of antimicrobials and their association with resistance in generic Escherichia coli recovered from fecal samples from Canadian dairy herds: A cross-sectional study. Prev Vet Med 2023; 216:105948. [PMID: 37263090 DOI: 10.1016/j.prevetmed.2023.105948] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Revised: 05/10/2023] [Accepted: 05/21/2023] [Indexed: 06/03/2023]
Abstract
Antimicrobial resistance (AMR) in animals, including dairy cattle, is a significant concern for animal and public health worldwide. In this study, we used data collected through the Canadian Dairy Network for Antimicrobial Stewardship and Resistance (CaDNetASR) to: (1) describe the proportions of AMR in fecal E. coli, and (2) investigate the relationship between antimicrobial use (AMU) (intramammary and systemic routes, while accounting for confounding by other variables) and AMR/multidrug resistance (MDR - resistance to ≥ 3 antimicrobial classes) in fecal E. coli from Canadian dairy farms. We hypothesized that an increase of the AMU was associated with an increase in AMR in E. coli isolates. A total of 140 dairy farms across five provinces in Canada were included in the study. Fecal samples from pre-weaned calves, post-weaned heifers, lactating cows, and farm manure storage were cultured, and E. coli isolates were identified using MALDI-TOF MS. The minimum inhibitory concentrations (MIC) to 14 antimicrobials were evaluated using a microbroth dilution methodology. AMU was quantified in Defined Course Dose (DCD - the dose for a standardized complete treatment course on a standard size animal) and converted to a rate indicator - DCD/100 animal-years. Of 1134 fecal samples collected, the proportion of samples positive for E. coli in 2019 and 2020 was 97.1% (544/560) and 94.4% (542/574), respectively. Overall, 24.5% (266/1086) of the E. coli isolates were resistant to at least one antimicrobial. Resistance towards tetracycline was commonly observed (20.7%), whereas resistance to third-generation cephalosporins, fluoroquinolones, and carbapenems was found in 2.2%, 1.4%, and 0.1% of E. coli isolates, respectively. E. coli isolates resistant to two or ≥ 3 antimicrobial classes (MDR) was 2.7% and 15%, respectively. Two multilevel models were built to explore risk factors associated with AMR with AMU being the main exposure. Systemic AMU was associated with increased E. coli resistance. For an increase in systemic AMU equivalent to its IQR, the odds of resistance to any antimicrobial in the model increased by 18%. Fecal samples from calves had higher odds of being resistant to any antimicrobial when compared to other production ages and farm manure storage. The samples collected in 2020 were less likely to be resistant when compared to samples collected in 2019. Compared to previous studies in dairy cattle in North America, AMR in E. coli was lower.
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Affiliation(s)
- Mariana Fonseca
- Department of Health Management, University of Prince Edward Island, Charlottetown, PE, Canada.
| | - Luke C Heider
- Department of Health Management, University of Prince Edward Island, Charlottetown, PE, Canada
| | - Henrik Stryhn
- Department of Health Management, University of Prince Edward Island, Charlottetown, PE, Canada
| | - J Trenton McClure
- Department of Health Management, University of Prince Edward Island, Charlottetown, PE, Canada
| | - David Léger
- Public Health Agency of Canada, Center for Foodborne, Environmental and Zoonotic Infectious Diseases, Guelph, ON, Canada
| | - Daniella Rizzo
- Public Health Agency of Canada, Center for Foodborne, Environmental and Zoonotic Infectious Diseases, Guelph, ON, Canada
| | - Landon Warder
- Department of Health Management, University of Prince Edward Island, Charlottetown, PE, Canada
| | - Simon Dufour
- Department of Pathology and Microbiology, Faculty of Veterinary Medicine, Université de Montréal, Saint-Hyacinthe, QC, Canada
| | - Jean-Philippe Roy
- Department of Clinical Sciences, Faculty of Veterinary Medicine, Université de Montréal, Saint-Hyacinthe, QC, Canada
| | - David F Kelton
- Department of Population Medicine, Ontario Veterinary College, University of Guelph, Guelph, ON, Canada
| | - David Renaud
- Department of Population Medicine, Ontario Veterinary College, University of Guelph, Guelph, ON, Canada
| | | | - Javier Sanchez
- Department of Health Management, University of Prince Edward Island, Charlottetown, PE, Canada
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Tseng CH, Liu CW, Liu PY. Extended-Spectrum β-Lactamases (ESBL) Producing Bacteria in Animals. Antibiotics (Basel) 2023; 12:antibiotics12040661. [PMID: 37107023 PMCID: PMC10135299 DOI: 10.3390/antibiotics12040661] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2023] [Revised: 03/22/2023] [Accepted: 03/26/2023] [Indexed: 03/30/2023] Open
Abstract
Animals have been identified as potential reservoirs and vectors of resistance genes, with studies showing that Gram-negative bacteria can acquire resistance through the horizontal transmission of resistance genes on plasmids. It is important to understand the distribution of antimicrobial-resistant bacteria and their drug-resistant genes in animals. Previous review articles mostly focused on a single bacterium or a single animal. Our objective is to compile all ESBL-producing bacteria isolated from various animals in recent years and provide a comprehensive viewpoint. Using a thorough PubMed literature search spanning from 1 January 2020 to 30 June 2022, studies exploring extended-spectrum beta-lactamase (ESBL) producing bacteria in animals were included. ESBL-producing bacteria are present in animals from various countries around the world. The most common sources of these bacteria were farm animals, and the most frequently isolated bacteria were Escherichia coli and Klebsiella pneumoniae. The most detected ESBL genes were blaTEM, blaSHV, and blaCTX-M. The presence of ESBL-producing bacteria in animals highlights the importance of the One Health approach to address the issue of antibiotic resistance. Further research is needed to better understand the epidemiology and mechanisms of the spread of ESBL-producing bacteria in animal populations and their potential impact on human and animal health.
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Gelalcha BD, Kerro Dego O. Extended-Spectrum Beta-Lactamases Producing Enterobacteriaceae in the USA Dairy Cattle Farms and Implications for Public Health. Antibiotics (Basel) 2022; 11:antibiotics11101313. [PMID: 36289970 PMCID: PMC9598938 DOI: 10.3390/antibiotics11101313] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2022] [Revised: 09/21/2022] [Accepted: 09/22/2022] [Indexed: 11/29/2022] Open
Abstract
Antimicrobial resistance (AMR) is one of the top global health threats of the 21th century. Recent studies are increasingly reporting the rise in extended-spectrum beta-lactamases producing Enterobacteriaceae (ESBLs-Ent) in dairy cattle and humans in the USA. The causes of the increased prevalence of ESBLs-Ent infections in humans and commensal ESBLs-Ent in dairy cattle farms are mostly unknown. However, the extensive use of beta-lactam antibiotics, especially third-generation cephalosporins (3GCs) in dairy farms and human health, can be implicated as a major driver for the rise in ESBLs-Ent. The rise in ESBLs-Ent, particularly ESBLs-Escherichia coli and ESBLs-Klebsiella species in the USA dairy cattle is not only an animal health issue but also a serious public health concern. The ESBLs-E. coli and -Klebsiella spp. can be transmitted to humans through direct contact with carrier animals or indirectly through the food chain or via the environment. The USA Centers for Disease Control and Prevention reports also showed continuous increase in community-associated human infections caused by ESBLs-Ent. Some studies attributed the elevated prevalence of ESBLs-Ent infections in humans to the frequent use of 3GCs in dairy farms. However, the status of ESBLs-Ent in dairy cattle and their contribution to human infections caused by ESBLs-producing enteric bacteria in the USA is the subject of further study. The aims of this review are to give in-depth insights into the status of ESBL-Ent in the USA dairy farms and its implication for public health and to highlight some critical research gaps that need to be addressed.
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Collis RM, Biggs PJ, Burgess SA, Midwinter AC, Brightwell G, Cookson AL. Prevalence and distribution of extended-spectrum β-lactamase and AmpC-producing Escherichia coli in two New Zealand dairy farm environments. Front Microbiol 2022; 13:960748. [PMID: 36033848 PMCID: PMC9403332 DOI: 10.3389/fmicb.2022.960748] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2022] [Accepted: 07/25/2022] [Indexed: 11/13/2022] Open
Abstract
Antimicrobial resistance (AMR) is a global threat to human and animal health, with the misuse and overuse of antimicrobials being suggested as the main driver of resistance. In a global context, New Zealand (NZ) is a relatively low user of antimicrobials in animal production. However, the role antimicrobial usage on pasture-based dairy farms, such as those in NZ, plays in driving the spread of AMR within the dairy farm environment remains equivocal. Culture-based methods were used to determine the prevalence and distribution of extended-spectrum β-lactamase (ESBL)- and AmpC-producing Escherichia coli from farm environmental samples collected over a 15-month period from two NZ dairy farms with contrasting management practices. Whole genome sequencing was utilised to understand the genomic epidemiology and antimicrobial resistance gene repertoire of a subset of third-generation cephalosporin resistant E. coli isolated in this study. There was a low sample level prevalence of ESBL-producing E. coli (faeces 1.7%; farm dairy effluent, 6.7% from Dairy 4 and none from Dairy 1) but AmpC-producing E. coli were more frequently isolated across both farms (faeces 3.3% and 8.3%; farm dairy effluent 38.4%, 6.7% from Dairy 1 and Dairy 4, respectively). ESBL- and AmpC-producing E. coli were isolated from faeces and farm dairy effluent in spring and summer, during months with varying levels of antimicrobial use, but no ESBL- or AmpC-producing E. coli were isolated from bulk tank milk or soil from recently grazed paddocks. Hybrid assemblies using short- and long-read sequence data from a subset of ESBL- and AmpC-producing E. coli enabled the assembly and annotation of nine plasmids from six E. coli, including one plasmid co-harbouring 12 antimicrobial resistance genes. ESBL-producing E. coli were infrequently identified from faeces and farm dairy effluent on the two NZ dairy farms, suggesting they are present at a low prevalence on these farms. Plasmids harbouring several antimicrobial resistance genes were identified, and bacteria carrying such plasmids are a concern for both animal and public health. AMR is a burden for human, animal and environmental health and requires a holistic “One Health” approach to address.
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Affiliation(s)
- Rose M. Collis
- The Hopkirk Research Institute, AgResearch Ltd., Massey University, Palmerston North, New Zealand
- EpiLab, School of Veterinary Science, Massey University, Palmerston North, New Zealand
- Rose M. Collis,
| | - Patrick J. Biggs
- EpiLab, School of Veterinary Science, Massey University, Palmerston North, New Zealand
- School of Natural Sciences, Massey University, Palmerston North, New Zealand
- New Zealand Food Safety Science and Research Centre, Massey University, Palmerston North, New Zealand
| | - Sara A. Burgess
- EpiLab, School of Veterinary Science, Massey University, Palmerston North, New Zealand
| | - Anne C. Midwinter
- EpiLab, School of Veterinary Science, Massey University, Palmerston North, New Zealand
| | - Gale Brightwell
- The Hopkirk Research Institute, AgResearch Ltd., Massey University, Palmerston North, New Zealand
- New Zealand Food Safety Science and Research Centre, Massey University, Palmerston North, New Zealand
| | - Adrian L. Cookson
- The Hopkirk Research Institute, AgResearch Ltd., Massey University, Palmerston North, New Zealand
- EpiLab, School of Veterinary Science, Massey University, Palmerston North, New Zealand
- *Correspondence: Adrian L. Cookson,
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