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Edache DO, Beyene TJ, Baruch J, Shi X, Sanderson MW, Nagaraja TG, Smolensky D, Cernicchiaro N. Sample Type and Processing Plant Differences in the Proportion of Enterohemorrhagic Escherichia coli O157 and Non-O157 Serogroups in Feces and on Hides of Cull Dairy Cattle at Slaughter. Foodborne Pathog Dis 2024. [PMID: 39093865 DOI: 10.1089/fpd.2024.0017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/04/2024] Open
Abstract
The study was conducted to determine the proportion and concentration of enterohemorrhagic Escherichia coli (EHEC) O157 and six non-O157 (O26, O45, O103, O111, O121, and O145) serogroups and identify seasonal and processing plant differences in feces and on hides of cull dairy cattle processed in commercial slaughterhouses in the United States. Approximately 60 rectal and 60 hide-on samples from matched carcasses were collected in each of three processing plants, in two periods; summer of 2017 and spring of 2018. Samples before enrichment were spiral plated to quantify EHEC, and postenriched samples underwent culture methods that included immuno-magnetic separation, plating on selective media, and PCR assays for identification and serogroup confirmation of putative isolates. An isolate was considered EHEC O157 positive if it harbored serogroup-specific (rfbE), Shiga toxin (stx1 and/or stx2), and intimin (eae) genes and EHEC non-O157 positive if at least one of the non-O157 serogroup-specific, stx1 and/or stx2, and eae genes was identified. Generalized linear mixed models were fitted to estimate overall proportion of positives for EHEC O157 and non-O157 EHEC serogroups, as well as seasonal and processing plant differences in fecal and hide-on proportion of positives. The fecal EHEC proportion at the sample level was 1.8% (95% CI = 0.0-92.2%) and 4.2% (95% CI = 0.0-100.0%) for EHEC O157 and EHEC non-O157, respectively. Hide sample level proportion of positives was 3.0% (95% CI = 0.0-99.9%) for EHEC O157 and 1.6% (95% CI = 0.0-100.0%) for EHEC non-O157. The proportion of EHEC O157 and non-O157 significantly differed by processing plant and sample type (hide vs. feces), but not by season. The association between proportion of EHEC serogroups in feces with the proportion on hides collected from matched cattle was 7.8% (95% CI = 0.6-53.3%) and 3.8% (95% CI = 0.3-30.8%) for EHEC O157 and non-O157, respectively. Taken together, our findings provide evidence of a low proportion of EHEC serogroups in the feces and on hides of cull dairy cattle and that their proportion varies across processing plants.
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Affiliation(s)
- David O Edache
- Center for Outcomes Research and Epidemiology, College of Veterinary MediciMine, Kansas State University, Manhattan, Kansas, USA
- Department of Diagnostic Medicine/Pathobiology, College of Veterinary Medicine, Kansas State University, Manhattan, Kansas, USA
| | - Tariku J Beyene
- Center for Outcomes Research and Epidemiology, College of Veterinary MediciMine, Kansas State University, Manhattan, Kansas, USA
- Carelon Research, Wilmington, Delaware, USA
| | - Joaquin Baruch
- Center for Outcomes Research and Epidemiology, College of Veterinary MediciMine, Kansas State University, Manhattan, Kansas, USA
| | - Xiaorong Shi
- Department of Diagnostic Medicine/Pathobiology, College of Veterinary Medicine, Kansas State University, Manhattan, Kansas, USA
| | - Michael W Sanderson
- Center for Outcomes Research and Epidemiology, College of Veterinary MediciMine, Kansas State University, Manhattan, Kansas, USA
- Department of Diagnostic Medicine/Pathobiology, College of Veterinary Medicine, Kansas State University, Manhattan, Kansas, USA
| | - T G Nagaraja
- Department of Diagnostic Medicine/Pathobiology, College of Veterinary Medicine, Kansas State University, Manhattan, Kansas, USA
| | - Dmitriy Smolensky
- Grain Quality and Structure Research, Center for Grain and Animal health Research, United States Department of Agriculture, Agricultural Research Service, Manhattan, Kansas, USA
| | - Natalia Cernicchiaro
- Center for Outcomes Research and Epidemiology, College of Veterinary MediciMine, Kansas State University, Manhattan, Kansas, USA
- Department of Diagnostic Medicine/Pathobiology, College of Veterinary Medicine, Kansas State University, Manhattan, Kansas, USA
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2
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Agga GE, Galloway HO. Dynamics of Extended-spectrum Beta-lactamase-producing, Third-generation Cephalosporin-resistant and Tetracycline-resistant Escherichia coli in Feedlot Cattle With or Without Tylosin Administration. J Food Prot 2023; 86:100144. [PMID: 37597606 DOI: 10.1016/j.jfp.2023.100144] [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: 06/08/2023] [Revised: 08/04/2023] [Accepted: 08/12/2023] [Indexed: 08/21/2023]
Abstract
The impact of in-feed use of tylosin in feedlot cattle on Gram-negative foodborne bacteria is unknown. We evaluated the effect of continuous in-feed tylosin use on the concentration and prevalence of tetracycline-resistant (TETr)-, third-generation cephalosporin-resistant (3GCr)-, and extended-spectrum β-lactamase-producing (ESBLs) E. coli in feedlot cattle. A cohort of weaned calves (10 animals/group) were randomized to receive a feed ration with or without tylosin. Fecal samples, regularly collected over the entire feeding period, and pen surface and feed samples, collected at the end of the feeding period, were cultured on selective media. Enumeration and binary outcomes were analyzed by mixed effects linear regression or logistic regression, respectively, using treatment and days on feed as fixed factors, and animal ID as a random variable. Tylosin supplementation did not affect the fecal concentrations of TETrE. coli or fecal prevalence of 3GCrE. coli. However, cattle in the tylosin group were 1.5 times more likely (Odds ratio = 1.5: 95% confidence interval: 1.1-2.0) to harbor ESBLs E. coli than the control cattle. Regardless of tylosin treatment, fecal concentrations of TETrE. coli and the prevalence of 3GCr- and ESBLs-E. coli increased over time. Tylosin-supplemented feed did not affect the prevalence of TETrE. coli; 3GCr and ESBLs-E. coli were not detected from the feed samples. Most of the 3GCr- and ESBLs-E. coli isolates carried the blaCTX-M-15 gene, widely detected among ESBLs-E. coli human isolates. In summary, although in-feed tylosin use in feedlot cattle did not select for TETr- and 3GCr-E. coli, it increased the likelihood of detecting ESBL-producing E. coli. Furthermore, the study indicated that the feedlot production setting gradually increases the levels of E. coli resistant to the critically and/or important antibiotics for public health, indicating an increased risk of their dissemination beyond the feedlot environment.
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Affiliation(s)
- Getahun E Agga
- Food Animal Environmental Systems Research Unit, Agricultural Research Service, U.S. Department of Agriculture, 2413 Nashville Road, B-5, Bowling Green, KY 42101, USA.
| | - Hunter O Galloway
- Department of Agriculture and Food Science, Western Kentucky University, Bowling Green, KY 42101, USA
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3
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Pomeroy LW, Magsi S, McGill S, Wheeler CE. Mumps epidemic dynamics in the United States before vaccination (1923-1932). Epidemics 2023; 44:100700. [PMID: 37379775 PMCID: PMC11057333 DOI: 10.1016/j.epidem.2023.100700] [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: 09/06/2022] [Revised: 04/25/2023] [Accepted: 06/12/2023] [Indexed: 06/30/2023] Open
Abstract
Mumps is a vaccine-preventable, reemerging, and highly transmissible infectious disease. Widespread vaccination dramatically reduced cases; however, case counts have been increasing over the past 20 years. To provide a quantitative overview of historical mumps dynamics that can act as baseline information to help identify causes of mumps reemergence, we analyzed timeseries of cases reported from 1923 to 1932 in the United States. During that time, 239,230 mumps cases were reported in 70 cities. Larger cities reported annual epidemics and smaller cities reported intermittent, sporadic outbreaks. The critical community size above which transmission continuously occurred was likely between 365,583 and 781,188 individuals but could range as high as 3,376,438 individuals. Mumps cases increased as city size increased, suggesting density-dependent transmission. Using a density-dependent SEIR model, we calculated a mean effective reproductive number (Re) of 1.2. Re varied by city and over time, with periodic high values that could characterize short periods of very high transmission known as superspreading events. Case counts most often peaked in March, with higher-than-average transmission from December through April and showed a correlation with weekly births. While certain city pairs in Midwestern states had synchronous outbreaks, most outbreaks were less synchronous and not driven by distance between cities. This work demonstrates the importance of long-term infectious disease surveillance data and will inform future studies on mumps reemergence and control.
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Affiliation(s)
- Laura W Pomeroy
- Division of Environmental Health Sciences, College of Public Health, Ohio State University, Columbus, OH 43210, USA; Translational Data Analytics Institute, Ohio State University, Columbus, OH 43210, USA.
| | - Senya Magsi
- College of Public Health, Ohio State University, Columbus, OH 43210, USA
| | - Shannon McGill
- College of Public Health, Ohio State University, Columbus, OH 43210, USA
| | - Caroline E Wheeler
- Computer & Information Science, College of Arts and Sciences, Ohio State University, Columbus, OH 43210, USA
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4
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Baker M, Zhang X, Maciel-Guerra A, Dong Y, Wang W, Hu Y, Renney D, Hu Y, Liu L, Li H, Tong Z, Zhang M, Geng Y, Zhao L, Hao Z, Senin N, Chen J, Peng Z, Li F, Dottorini T. Machine learning and metagenomics reveal shared antimicrobial resistance profiles across multiple chicken farms and abattoirs in China. NATURE FOOD 2023; 4:707-720. [PMID: 37563495 PMCID: PMC10444626 DOI: 10.1038/s43016-023-00814-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Accepted: 07/07/2023] [Indexed: 08/12/2023]
Abstract
China is the largest global consumer of antimicrobials and improving surveillance methods could help to reduce antimicrobial resistance (AMR) spread. Here we report the surveillance of ten large-scale chicken farms and four connected abattoirs in three Chinese provinces over 2.5 years. Using a data mining approach based on machine learning, we analysed 461 microbiomes from birds, carcasses and environments, identifying 145 potentially mobile antibiotic resistance genes (ARGs) shared between chickens and environments across all farms. A core set of 233 ARGs and 186 microbial species extracted from the chicken gut microbiome correlated with the AMR profiles of Escherichia coli colonizing the same gut, including Arcobacter, Acinetobacter and Sphingobacterium, clinically relevant for humans, and 38 clinically relevant ARGs. Temperature and humidity in the barns were also correlated with ARG presence. We reveal an intricate network of correlations between environments, microbial communities and AMR, suggesting multiple routes to improving AMR surveillance in livestock production.
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Affiliation(s)
- Michelle Baker
- School of Veterinary Medicine and Science, University of Nottingham, Sutton Bonington, UK
| | - Xibin Zhang
- Shandong New Hope Liuhe Group Co. Ltd and Qingdao Key Laboratory of Animal Feed Safety, Qingdao, People's Republic of China
| | | | - Yinping Dong
- NHC Key Laboratory of Food Safety Risk Assessment, China National Center for Food Safety Risk Assessment, Beijing, People's Republic of China
| | - Wei Wang
- NHC Key Laboratory of Food Safety Risk Assessment, China National Center for Food Safety Risk Assessment, Beijing, People's Republic of China
| | - Yujie Hu
- NHC Key Laboratory of Food Safety Risk Assessment, China National Center for Food Safety Risk Assessment, Beijing, People's Republic of China
| | - David Renney
- Nimrod Veterinary Products Ltd., Moreton-in-Marsh, UK
| | - Yue Hu
- School of Veterinary Medicine and Science, University of Nottingham, Sutton Bonington, UK
| | - Longhai Liu
- Shandong Kaijia Food Co., Weifang, People's Republic of China
| | - Hui Li
- Luoyang Center for Disease Control and Prevention, Luoyang City, People's Republic of China
| | - Zhiqin Tong
- Luoyang Center for Disease Control and Prevention, Luoyang City, People's Republic of China
| | - Meimei Zhang
- Liaoning Provincial Center for Disease Control and Prevention, Shenyang City, People's Republic of China
| | - Yingzhi Geng
- Liaoning Provincial Center for Disease Control and Prevention, Shenyang City, People's Republic of China
| | - Li Zhao
- Agricultural Biopharmaceutical Laboratory, College of Chemistry and Pharmaceutical Sciences, Qingdao Agricultural University, Qingdao City, People's Republic of China
| | - Zhihui Hao
- Chinese Veterinary Medicine Innovation Center, College of Veterinary Medicine, China Agricultural University, Beijing City, People's Republic of China
| | - Nicola Senin
- Department of Engineering, University of Perugia, Perugia, Italy
| | - Junshi Chen
- NHC Key Laboratory of Food Safety Risk Assessment, China National Center for Food Safety Risk Assessment, Beijing, People's Republic of China
| | - Zixin Peng
- NHC Key Laboratory of Food Safety Risk Assessment, China National Center for Food Safety Risk Assessment, Beijing, People's Republic of China.
| | - Fengqin Li
- NHC Key Laboratory of Food Safety Risk Assessment, China National Center for Food Safety Risk Assessment, Beijing, People's Republic of China.
| | - Tania Dottorini
- School of Veterinary Medicine and Science, University of Nottingham, Sutton Bonington, UK.
- Centre for Smart Food Research, Nottingham Ningbo China Beacons of Excellence Research and Innovation Institute, University of Nottingham Ningbo China, Ningbo, People's Republic of China.
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5
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Maciel-Guerra A, Baker M, Hu Y, Wang W, Zhang X, Rong J, Zhang Y, Zhang J, Kaler J, Renney D, Loose M, Emes RD, Liu L, Chen J, Peng Z, Li F, Dottorini T. Dissecting microbial communities and resistomes for interconnected humans, soil, and livestock. THE ISME JOURNAL 2023; 17:21-35. [PMID: 36151458 PMCID: PMC9751072 DOI: 10.1038/s41396-022-01315-7] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Revised: 08/26/2022] [Accepted: 09/01/2022] [Indexed: 12/24/2022]
Abstract
A debate is currently ongoing as to whether intensive livestock farms may constitute reservoirs of clinically relevant antimicrobial resistance (AMR), thus posing a threat to surrounding communities. Here, combining shotgun metagenome sequencing, machine learning (ML), and culture-based methods, we focused on a poultry farm and connected slaughterhouse in China, investigating the gut microbiome of livestock, workers and their households, and microbial communities in carcasses and soil. For both the microbiome and resistomes in this study, differences are observed across environments and hosts. However, at a finer scale, several similar clinically relevant antimicrobial resistance genes (ARGs) and similar associated mobile genetic elements were found in both human and broiler chicken samples. Next, we focused on Escherichia coli, an important indicator for the surveillance of AMR on the farm. Strains of E. coli were found intermixed between humans and chickens. We observed that several ARGs present in the chicken faecal resistome showed correlation to resistance/susceptibility profiles of E. coli isolates cultured from the same samples. Finally, by using environmental sensing these ARGs were found to be correlated to variations in environmental temperature and humidity. Our results show the importance of adopting a multi-domain and multi-scale approach when studying microbial communities and AMR in complex, interconnected environments.
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Affiliation(s)
- Alexandre Maciel-Guerra
- grid.4563.40000 0004 1936 8868School of Veterinary Medicine and Science, University of Nottingham, College Road, Sutton Bonington, Leicestershire, LE12 5RD UK
| | - Michelle Baker
- grid.4563.40000 0004 1936 8868School of Veterinary Medicine and Science, University of Nottingham, College Road, Sutton Bonington, Leicestershire, LE12 5RD UK
| | - Yue Hu
- grid.4563.40000 0004 1936 8868School of Veterinary Medicine and Science, University of Nottingham, College Road, Sutton Bonington, Leicestershire, LE12 5RD UK
| | - Wei Wang
- grid.464207.30000 0004 4914 5614NHC Key Laboratory of Food Safety Risk Assessment, China National Center for Food Safety Risk Assessment, Beijing, 100021 People’s Republic of China
| | - Xibin Zhang
- grid.508175.eNew Hope Liuhe Co., Ltd., Laboratory of Feed and Livestock and Poultry Products Quality & Safety Control, Ministry of Agriculture, Beijing 100102 and Weifang Heshengyuan Food Co. Ltd., Weifang, 262167 People’s Republic of China
| | - Jia Rong
- grid.508175.eNew Hope Liuhe Co., Ltd., Laboratory of Feed and Livestock and Poultry Products Quality & Safety Control, Ministry of Agriculture, Beijing 100102 and Weifang Heshengyuan Food Co. Ltd., Weifang, 262167 People’s Republic of China
| | - Yimin Zhang
- grid.440622.60000 0000 9482 4676College of Food Science and Engineering, Shandong Agricultural University, Tai’an, Shandong 271018 People’s Republic of China
| | - Jing Zhang
- grid.464207.30000 0004 4914 5614NHC Key Laboratory of Food Safety Risk Assessment, China National Center for Food Safety Risk Assessment, Beijing, 100021 People’s Republic of China
| | - Jasmeet Kaler
- grid.4563.40000 0004 1936 8868School of Veterinary Medicine and Science, University of Nottingham, College Road, Sutton Bonington, Leicestershire, LE12 5RD UK
| | - David Renney
- Nimrod Veterinary Products Limited, 2, Wychwood Court, Cotswold Business Village, Moreton-in-Marsh, GL56 0JQ UK
| | - Matthew Loose
- grid.4563.40000 0004 1936 8868DeepSeq, School of Life Sciences, Queens Medical Centre, University of Nottingham, Nottingham, NG7 2UH UK
| | - Richard D. Emes
- grid.4563.40000 0004 1936 8868School of Veterinary Medicine and Science, University of Nottingham, College Road, Sutton Bonington, Leicestershire, LE12 5RD UK
| | - Longhai Liu
- grid.508175.eNew Hope Liuhe Co., Ltd., Laboratory of Feed and Livestock and Poultry Products Quality & Safety Control, Ministry of Agriculture, Beijing 100102 and Weifang Heshengyuan Food Co. Ltd., Weifang, 262167 People’s Republic of China
| | - Junshi Chen
- grid.464207.30000 0004 4914 5614NHC Key Laboratory of Food Safety Risk Assessment, China National Center for Food Safety Risk Assessment, Beijing, 100021 People’s Republic of China
| | - Zixin Peng
- NHC Key Laboratory of Food Safety Risk Assessment, China National Center for Food Safety Risk Assessment, Beijing, 100021, People's Republic of China.
| | - Fengqin Li
- NHC Key Laboratory of Food Safety Risk Assessment, China National Center for Food Safety Risk Assessment, Beijing, 100021, People's Republic of China.
| | - Tania Dottorini
- School of Veterinary Medicine and Science, University of Nottingham, College Road, Sutton Bonington, Leicestershire, LE12 5RD, UK.
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6
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Incorporating global dynamics to improve the accuracy of disease models: Example of a COVID-19 SIR model. PLoS One 2022; 17:e0265815. [PMID: 35395018 PMCID: PMC8993010 DOI: 10.1371/journal.pone.0265815] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2021] [Accepted: 03/08/2022] [Indexed: 01/03/2023] Open
Abstract
Mathematical models of infectious diseases exhibit robust dynamics, such as stable endemic, disease-free equilibriums or convergence of the solutions to periodic epidemic waves. The present work shows that the accuracy of such dynamics can be significantly improved by including global effects of host movements in disease models. To demonstrate improved accuracy, we extended a standard Susceptible-Infected-Recovered (SIR) model by incorporating the global dynamics of the COVID-19 pandemic. The extended SIR model assumes three possibilities for susceptible individuals traveling outside of their community: • They can return to the community without any exposure to the infection. • They can be exposed and develop symptoms after returning to the community. • They can be tested positively during the trip and remain quarantined until fully recovered. To examine the predictive accuracy of the extended SIR model, we studied the prevalence of the COVID-19 infection in six randomly selected cities and states in the United States: Kansas City, Saint Louis, San Francisco, Missouri, Illinois, and Arizona. The extended SIR model was parameterized using a two-step model-fitting algorithm. The extended SIR model significantly outperformed the standard SIR model and revealed oscillatory behaviors with an increasing trend of infected individuals. In conclusion, the analytics and predictive accuracy of disease models can be significantly improved by incorporating the global dynamics of the infection.
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Abstract
Temperature variation-through time and across climatic gradients-affects individuals, populations, and communities. Yet how the thermal response of biological systems is altered by environmental stressors is poorly understood. Here, we quantify two key features-optimal temperature and temperature breadth-to investigate how temperature responses vary in the presence of antibiotics. We use high-throughput screening to measure growth of Escherichia coli under single and pairwise combinations of 12 antibiotics across seven temperatures that range from 22°C to 46°C. We find that antibiotic stress often results in considerable changes in the optimal temperature for growth and a narrower temperature breadth. The direction of the optimal temperature shifts can be explained by the similarities between antibiotic-induced and temperature-induced damage to the physiology of the bacterium. We also find that the effects of pairs of stressors in the temperature response can often be explained by just one antibiotic out of the pair. Our study has implications for a general understanding of how ecological systems adapt and evolve to environmental changes. IMPORTANCE The growth of living organisms varies with temperature. This dependence is described by a temperature response curve that is described by an optimal temperature where growth is maximized and a temperature range (termed breadth) across which the organism can grow. Because an organism's temperature response evolves or acclimates to its environment, it is often assumed to change over only evolutionary or developmental timescales. Counter to this, we show here that antibiotics can quickly (over hours) change the optimal growth temperature and temperature breadth for the bacterium Escherichia coli. Moreover, our results suggest a shared-damage hypothesis: when an antibiotic damages similar cellular components as hot (or cold) temperatures do, this shared damage will combine and compound to more greatly reduce growth when that antibiotic is administered at hot (or cold) temperatures. This hypothesis could potentially also explain how temperature responses are modified by stressors other than antibiotics.
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Al-Ajmi D, Rahman S, Banu S. Occurrence, virulence genes, and antimicrobial profiles of Escherichia coli O157 isolated from ruminants slaughtered in Al Ain, United Arab Emirates. BMC Microbiol 2020; 20:210. [PMID: 32677884 PMCID: PMC7364618 DOI: 10.1186/s12866-020-01899-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2020] [Accepted: 07/12/2020] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Shiga toxin-producing Escherichia coli (STEC) is a major source of food-borne illness around the world. E. coli O157 has been widely reported as the most common STEC serogroup and has emerged as an important enteric pathogen. Cattle, in particular have been identified as a major E. coli O157:H7 reservoir of human infections; however, the prevalence of this organism in camels, sheep, and goats is less understood. The aim of this study was to evaluate the occurrence and concentration of E. coli serotype O157 in the feces of healthy camels (n = 140), cattle (n = 137), sheep (n = 141) and goats (n = 150) slaughtered in United Arab Emirates (UAE) for meat consumption between September 2017 and August 2018. We used immunomagnetic separation coupled with a culture-plating method to detect E. coli O157. Non-sorbitol fermenting colonies were assessed via latex-agglutination testing, and positive cultures were analyzed by performing polymerase chain reactions to detect genes encoding attaching and effacing protein (eaeA), hemolysin A (hlyA, also known as ehxA) and Shiga toxin (stx1 and stx2), and E. coli O157:H7 specific genes (rfb O157, uidA, and fliC). All E. coli O157 isolates were analyzed for their susceptibility to 20 selected antimicrobials. RESULTS E. coli O157 was observed in camels, goats, and cattle fecal samples at abundances of 4.3, 2, and 1.46%, respectively, but it was undetectable in sheep feces. The most prevalent E. coli O157 gene in all STEC isolates was stx2;, whereas, stx1 was not detected in any of the samples. The fecal samples from camels, goats, and cattle harbored E. coli O157 isolates that were 100% susceptible to cefotaxime, chloramphenicol, ciprofloxacin, norfloxacin, and polymyxin B. CONCLUSION To our knowledge, this is the first report on the occurrence of E. coli O157 in slaughter animals in the UAE. Our results clearly demonstrate the presence of E. coli O157 in slaughtered animals, which could possibly contaminate meat products intended for human consumption.
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Affiliation(s)
- Dawood Al-Ajmi
- Department of Integrative Agriculture, College of Food and Agriculture, United Arab Emirates University (UAEU), Al Ain, United Arab Emirates.
| | - Shafeeq Rahman
- Department of Integrative Agriculture, College of Food and Agriculture, United Arab Emirates University (UAEU), Al Ain, United Arab Emirates
| | - Sharmila Banu
- Department of Integrative Agriculture, College of Food and Agriculture, United Arab Emirates University (UAEU), Al Ain, United Arab Emirates
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9
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10
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Widgren S, Engblom S, Emanuelson U, Lindberg A. Spatio-temporal modelling of verotoxigenic Escherichia coli O157 in cattle in Sweden: exploring options for control. Vet Res 2018; 49:78. [PMID: 30068384 PMCID: PMC6071428 DOI: 10.1186/s13567-018-0574-2] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2018] [Accepted: 07/20/2018] [Indexed: 01/21/2023] Open
Abstract
A spatial data-driven stochastic model was developed to explore the spread of verotoxigenic Escherichia coli O157 (VTEC O157) by livestock movements and local transmission among neighbouring holdings in the complete Swedish cattle population. Livestock data were incorporated to model the time-varying contact network between holdings and population demographics. Furthermore, meteorological data with the average temperature at the geographical location of each holding was used to incorporate season. The model was fitted against observed data and extensive numerical experiments were conducted to investigate the model’s response to control strategies aimed at reducing shedding and susceptibility, as well as interventions informed by network measures. The results showed that including local spread and season improved agreement with prevalence studies. Also, control strategies aimed at reducing the average shedding rate were more efficient in reducing the VTEC O157 prevalence than strategies based on network measures. The methodology presented in this study could provide a basis for developing disease surveillance on regional and national scales, where observed data are combined with readily available high-resolution data in simulations to get an overview of potential disease spread in unobserved regions.
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Affiliation(s)
- Stefan Widgren
- Department of Disease Control and Epidemiology, National Veterinary Institute, 751 89, Uppsala, Sweden. .,Division of Scientific Computing, Department of Information Technology, Uppsala University, 751 05, Uppsala, Sweden.
| | - Stefan Engblom
- Division of Scientific Computing, Department of Information Technology, Uppsala University, 751 05, Uppsala, Sweden
| | - Ulf Emanuelson
- Department of Clinical Sciences, Swedish University of Agricultural Sciences, 750 07, Uppsala, Sweden
| | - Ann Lindberg
- Department of Disease Control and Epidemiology, National Veterinary Institute, 751 89, Uppsala, Sweden
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11
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MacFadden DR, McGough SF, Fisman D, Santillana M, Brownstein JS. Antibiotic Resistance Increases with Local Temperature. NATURE CLIMATE CHANGE 2018; 8:510-514. [PMID: 30369964 PMCID: PMC6201249 DOI: 10.1038/s41558-018-0161-6] [Citation(s) in RCA: 201] [Impact Index Per Article: 33.5] [Reference Citation Analysis] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/02/2017] [Accepted: 04/11/2018] [Indexed: 05/19/2023]
Affiliation(s)
- Derek R. MacFadden
- Division of Infectious Diseases, Department of Medicine, University of Toronto, Canada
- Harvard Chan School of Public Health, Harvard University, Boston, United States
- Computational Epidemiology Group, Boston Children’s Hospital, Boston, United States
| | - Sarah F. McGough
- Harvard Chan School of Public Health, Harvard University, Boston, United States
- Computational Health Informatics Program, Boston Children’s Hospital, Boston, United States
| | - David Fisman
- Division of Infectious Diseases, Department of Medicine, University of Toronto, Canada
| | - Mauricio Santillana
- Computational Epidemiology Group, Boston Children’s Hospital, Boston, United States
- Computational Health Informatics Program, Boston Children’s Hospital, Boston, United States
- Department of Pediatrics, Harvard Medical School, Harvard University, Boston, United States
| | - John S. Brownstein
- Computational Epidemiology Group, Boston Children’s Hospital, Boston, United States
- Computational Health Informatics Program, Boston Children’s Hospital, Boston, United States
- Department of Pediatrics, Harvard Medical School, Harvard University, Boston, United States
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12
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Beauvais W, Gart EV, Bean M, Blanco A, Wilsey J, McWhinney K, Bryan L, Krath M, Yang CY, Manriquez Alvarez D, Paudyal S, Bryan K, Stewart S, Cook PW, Lahodny G, Baumgarten K, Gautam R, Nightingale K, Lawhon SD, Pinedo P, Ivanek R. The prevalence of Escherichia coli O157:H7 fecal shedding in feedlot pens is affected by the water-to-cattle ratio: A randomized controlled trial. PLoS One 2018; 13:e0192149. [PMID: 29414986 PMCID: PMC5802916 DOI: 10.1371/journal.pone.0192149] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2017] [Accepted: 01/17/2018] [Indexed: 11/28/2022] Open
Abstract
Escherichia coli O157:H7 fecal shedding in feedlot cattle is common and is a public health concern due to the risk of foodborne transmission that can result in severe, or even fatal, disease in people. Despite a large body of research, few practical and cost-effective farm-level interventions have been identified. In this study, a randomized controlled trial was conducted to assess the effect of reducing the level of water in automatically refilling water-troughs on fecal shedding of E. coli O157:H7 in feedlot cattle. Pens in a feedlot in the Texas Panhandle were randomly allocated as control (total number: 17) or intervention (total number: 18) pens. Fecal samples (2,759 in total) were collected both at baseline and three weeks after the intervention, and tested for the presence of E. coli O157:H7 using immunomagnetic bead separation and selective culture. There was a strong statistical association between sampling date and the likelihood of a fecal sample testing positive for E. coli O157:H7. Pen was also a strong predictor of fecal prevalence. Despite accounting for this high level of clustering, a statistically significant association between reduced water levels in the trough and increased prevalence of E. coli O157:H7 in the feces was observed (Odds Ratio = 1.6; 95% Confidence Interval: 1.2–2.0; Likelihood Ratio Test: p = 0.02). This is the first time that such an association has been reported, and suggests that increasing water-trough levels may be effective in reducing shedding of E. coli O157:H7 in cattle feces, although further work would be needed to test this hypothesis. Controlling E. coli O157:H7 fecal shedding at the pre-harvest level may lead to a reduced burden of human foodborne illness attributed to this pathogen in beef.
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Affiliation(s)
- Wendy Beauvais
- College of Veterinary Medicine, Cornell University, Ithaca, New York, United States of America
- * E-mail:
| | - Elena V. Gart
- College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, Texas, United States of America
| | - Melissa Bean
- College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, Texas, United States of America
| | - Anthony Blanco
- College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, Texas, United States of America
| | - Jennifer Wilsey
- College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, Texas, United States of America
| | - Kallie McWhinney
- College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, Texas, United States of America
| | - Laura Bryan
- College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, Texas, United States of America
| | - Mary Krath
- College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, Texas, United States of America
| | - Ching-Yuan Yang
- College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, Texas, United States of America
| | - Diego Manriquez Alvarez
- College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, Texas, United States of America
| | - Sushil Paudyal
- West Texas A&M University, Canyon, Texas, United States of America
| | - Kelsey Bryan
- Texas A&M Agrilife Research, Amarillo, Texas, United States of America
| | - Samantha Stewart
- Animal and Food Sciences, Texas Tech University, Lubbock, Texas, United States of America
| | - Peter W. Cook
- Animal and Food Sciences, Texas Tech University, Lubbock, Texas, United States of America
| | - Glenn Lahodny
- College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, Texas, United States of America
| | - Karina Baumgarten
- College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, Texas, United States of America
| | - Raju Gautam
- College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, Texas, United States of America
| | - Kendra Nightingale
- Animal and Food Sciences, Texas Tech University, Lubbock, Texas, United States of America
| | - Sara D. Lawhon
- College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, Texas, United States of America
| | - Pablo Pinedo
- Texas A&M Agrilife Research, Amarillo, Texas, United States of America
| | - Renata Ivanek
- College of Veterinary Medicine, Cornell University, Ithaca, New York, United States of America
- College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, Texas, United States of America
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Testa F, Marano G, Ambrogi F, Boracchi P, Casula A, Biganzoli E, Moroni P. Study of the association of atmospheric temperature and relative humidity with bulk tank milk somatic cell count in dairy herds using Generalized additive mixed models. Res Vet Sci 2017; 114:511-517. [DOI: 10.1016/j.rvsc.2017.09.027] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2016] [Revised: 06/29/2017] [Accepted: 09/27/2017] [Indexed: 10/18/2022]
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Abstract
This article provides an overview of the emerging field of mathematical modeling in preharvest food safety. We describe the steps involved in developing mathematical models, different types of models, and their multiple applications. The introduction to modeling is followed by several sections that introduce the most common modeling approaches used in preharvest systems. We finish the chapter by outlining potential future directions for the field.
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Venegas-Vargas C, Henderson S, Khare A, Mosci RE, Lehnert JD, Singh P, Ouellette LM, Norby B, Funk JA, Rust S, Bartlett PC, Grooms D, Manning SD. Factors Associated with Shiga Toxin-Producing Escherichia coli Shedding by Dairy and Beef Cattle. Appl Environ Microbiol 2016; 82:5049-56. [PMID: 27342555 PMCID: PMC4968536 DOI: 10.1128/aem.00829-16] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2016] [Accepted: 06/01/2016] [Indexed: 11/20/2022] Open
Abstract
UNLABELLED Shiga toxin-producing Escherichia coli (STEC) is an important foodborne pathogen that can cause hemorrhagic colitis and hemolytic-uremic syndrome. Cattle are the primary reservoir for STEC, and food or water contaminated with cattle feces is the most common source of infections in humans. Consequently, we conducted a cross-sectional study of 1,096 cattle in six dairy herds (n = 718 animals) and five beef herds (n = 378 animals) in the summers of 2011 and 2012 to identify epidemiological factors associated with shedding. Fecal samples were obtained from each animal and cultured for STEC. Multivariate analyses were performed to identify risk factors associated with STEC positivity. The prevalence of STEC was higher in beef cattle (21%) than dairy cattle (13%) (odds ratio [OR], 1.76; 95% confidence interval [CI], 1.25, 2.47), with considerable variation occurring across herds (range, 6% to 54%). Dairy cattle were significantly more likely to shed STEC when the average temperature was >28.9°C 1 to 5 days prior to sampling (OR, 2.5; 95% CI, 1.25, 4.91), during their first lactation (OR, 1.8; 95% CI, 1.1, 2.8), and when they were <30 days in milk (OR, 3.9; 95% CI, 2.1, 7.2). These data suggest that the stress or the negative energy balance associated with lactation may result in increased STEC shedding frequencies in Michigan during the warm summer months. Future prevention strategies aimed at reducing stress during lactation or isolating high-risk animals could be implemented to reduce herd-level shedding levels and avoid transmission of STEC to susceptible animals and people. IMPORTANCE STEC shedding frequencies vary considerably across cattle herds in Michigan, and the shedding frequency of strains belonging to non-O157 serotypes far exceeds the shedding frequency of O157 strains, which is congruent with human infections in the state. Dairy cattle sampled at higher temperatures, in their first lactation, and early in the milk production stage were significantly more likely to shed STEC, which could be due to stress or a negative energy balance. Future studies should focus on the isolation of high-risk animals to decrease herd shedding levels and the potential for contamination of the food supply.
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Affiliation(s)
- Cristina Venegas-Vargas
- Department of Large Animal Clinical Sciences, College of Veterinary Medicine, Michigan State University, East Lansing, Michigan, USA
| | - Scott Henderson
- Department of Large Animal Clinical Sciences, College of Veterinary Medicine, Michigan State University, East Lansing, Michigan, USA Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, Michigan, USA
| | - Akanksha Khare
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, Michigan, USA
| | - Rebekah E Mosci
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, Michigan, USA
| | - Jonathan D Lehnert
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, Michigan, USA
| | - Pallavi Singh
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, Michigan, USA
| | - Lindsey M Ouellette
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, Michigan, USA
| | - Bo Norby
- Department of Large Animal Clinical Sciences, College of Veterinary Medicine, Michigan State University, East Lansing, Michigan, USA
| | - Julie A Funk
- Department of Large Animal Clinical Sciences, College of Veterinary Medicine, Michigan State University, East Lansing, Michigan, USA
| | - Steven Rust
- Department of Animal Science, Michigan State University, East Lansing, Michigan, USA
| | - Paul C Bartlett
- Department of Large Animal Clinical Sciences, College of Veterinary Medicine, Michigan State University, East Lansing, Michigan, USA
| | - Daniel Grooms
- Department of Large Animal Clinical Sciences, College of Veterinary Medicine, Michigan State University, East Lansing, Michigan, USA
| | - Shannon D Manning
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, Michigan, USA
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Widgren S, Engblom S, Bauer P, Frössling J, Emanuelson U, Lindberg A. Data-driven network modelling of disease transmission using complete population movement data: spread of VTEC O157 in Swedish cattle. Vet Res 2016; 47:81. [PMID: 27515697 PMCID: PMC4982012 DOI: 10.1186/s13567-016-0366-5] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2016] [Accepted: 07/18/2016] [Indexed: 11/10/2022] Open
Abstract
European Union legislation requires member states to keep national databases of all bovine animals. This allows for disease spread models that includes the time-varying contact network and population demographic. However, performing data-driven simulations with a high degree of detail are computationally challenging. We have developed an efficient and flexible discrete-event simulator SimInf for stochastic disease spread modelling that divides work among multiple processors to accelerate the computations. The model integrates disease dynamics as continuous-time Markov chains and livestock data as events. In this study, all Swedish livestock data (births, movements and slaughter) from July 1st 2005 to December 31st 2013 were included in the simulations. Verotoxigenic Escherichia coli O157:H7 (VTEC O157) are capable of causing serious illness in humans. Cattle are considered to be the main reservoir of the bacteria. A better understanding of the epidemiology in the cattle population is necessary to be able to design and deploy targeted measures to reduce the VTEC O157 prevalence and, subsequently, human exposure. To explore the spread of VTEC O157 in the entire Swedish cattle population during the period under study, a within- and between-herd disease spread model was used. Real livestock data was incorporated to model demographics of the population. Cattle were moved between herds according to real movement data. The results showed that the spatial pattern in prevalence may be due to regional differences in livestock movements. However, the movements, births and slaughter of cattle could not explain the temporal pattern of VTEC O157 prevalence in cattle, despite their inherently distinct seasonality.
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Affiliation(s)
- Stefan Widgren
- Department of Clinical Sciences, Swedish University of Agricultural Sciences, 750 07 Uppsala, Sweden
- Department of Disease Control and Epidemiology, National Veterinary Institute, 751 89 Uppsala, Sweden
| | - Stefan Engblom
- Division of Scientific Computing, Department of Information Technology, Uppsala University, 751 05 Uppsala, Sweden
| | - Pavol Bauer
- Division of Scientific Computing, Department of Information Technology, Uppsala University, 751 05 Uppsala, Sweden
| | - Jenny Frössling
- Department of Disease Control and Epidemiology, National Veterinary Institute, 751 89 Uppsala, Sweden
- Department of Animal Environment and Health, Swedish University of Agricultural Sciences, Box 234, 532 23 Skara, Sweden
| | - Ulf Emanuelson
- Department of Clinical Sciences, Swedish University of Agricultural Sciences, 750 07 Uppsala, Sweden
| | - Ann Lindberg
- Department of Disease Control and Epidemiology, National Veterinary Institute, 751 89 Uppsala, Sweden
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"Preharvest" Food Safety for Escherichia coli O157 and Other Pathogenic Shiga Toxin-Producing Strains. Microbiol Spectr 2016; 2. [PMID: 26104364 DOI: 10.1128/microbiolspec.ehec-0021-2013] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
Preharvest food safety refers to the concept of reducing the rates of contamination of unprocessed foods with food-borne disease pathogens in order to reduce human exposure and disease. This article addresses the search for effective preharvest food safety practices for application to live cattle to reduce both contamination of foods of bovine origin and environmental contamination resulting from cattle. Although this research has resulted in several practices that significantly decrease contamination by Escherichia coli O157, the effects are limited in magnitude and unlikely to affect the incidence of human disease without much wider application and considerably higher efficacy than is presently apparent. Infection of cattle with E. coli O157 is transient and seasonally variable, likely resulting from a complex web of exposures. It is likely that better identification of the true maintenance reservoir of this agent and related Shiga toxin-producing E. coli is required to develop more effective control measures for these important food- and waterborne disease agents.
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Brookes VJ, Jordan D, Davis S, Ward MP, Heller J. Saltelli Global Sensitivity Analysis and Simulation Modelling to Identify Intervention Strategies to Reduce the Prevalence of Escherichia coli O157 Contaminated Beef Carcasses. PLoS One 2015; 10:e0146016. [PMID: 26713610 PMCID: PMC4694618 DOI: 10.1371/journal.pone.0146016] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2015] [Accepted: 12/12/2015] [Indexed: 01/28/2023] Open
Abstract
Introduction Strains of Shiga-toxin producing Escherichia coli O157 (STEC O157) are important foodborne pathogens in humans, and outbreaks of illness have been associated with consumption of undercooked beef. Here, we determine the most effective intervention strategies to reduce the prevalence of STEC O157 contaminated beef carcasses using a modelling approach. Method A computational model simulated events and processes in the beef harvest chain. Information from empirical studies was used to parameterise the model. Variance-based global sensitivity analysis (GSA) using the Saltelli method identified variables with the greatest influence on the prevalence of STEC O157 contaminated carcasses. Following a baseline scenario (no interventions), a series of simulations systematically introduced and tested interventions based on influential variables identified by repeated Saltelli GSA, to determine the most effective intervention strategy. Results Transfer of STEC O157 from hide or gastro-intestinal tract to carcass (improved abattoir hygiene) had the greatest influence on the prevalence of contaminated carcases. Due to interactions between inputs (identified by Saltelli GSA), combinations of interventions based on improved abattoir hygiene achieved a greater reduction in maximum prevalence than would be expected from an additive effect of single interventions. The most effective combination was improved abattoir hygiene with vaccination, which achieved a greater than ten-fold decrease in maximum prevalence compared to the baseline scenario. Conclusion Study results suggest that effective interventions to reduce the prevalence of STEC O157 contaminated carcasses should initially be based on improved abattoir hygiene. However, the effect of improved abattoir hygiene on the distribution of STEC O157 concentration on carcasses is an important information gap—further empirical research is required to determine whether reduced prevalence of contaminated carcasses is likely to result in reduced incidence of STEC O157 associated illness in humans. This is the first use of variance-based GSA to assess the drivers of STEC O157 contamination of beef carcasses.
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Affiliation(s)
- Victoria J. Brookes
- Graham Centre for Agricultural Innovation, NSW Department of Primary Industries and Charles Sturt University, Pugsley Place, Wagga Wagga, NSW 2650, Australia
- School of Animal and Veterinary Sciences, Faculty of Science, Charles Sturt University, Wagga Wagga, NSW 2678, Australia
- * E-mail:
| | - David Jordan
- NSW Department of Primary Industries, Wollongbar, NSW, Australia
| | - Stephen Davis
- School of Mathematical and Geospatial Sciences, RMIT University, Melbourne, Victoria 3001, Australia
| | - Michael P. Ward
- Faculty of Veterinary Science, The University of Sydney, Camden, NSW 2570, Australia
| | - Jane Heller
- Graham Centre for Agricultural Innovation, NSW Department of Primary Industries and Charles Sturt University, Pugsley Place, Wagga Wagga, NSW 2650, Australia
- School of Animal and Veterinary Sciences, Faculty of Science, Charles Sturt University, Wagga Wagga, NSW 2678, Australia
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Ivanek R, Lahodny G. From the bench to modeling--R0 at the interface between empirical and theoretical approaches in epidemiology of environmentally transmitted infectious diseases. Prev Vet Med 2014; 118:196-206. [PMID: 25441048 DOI: 10.1016/j.prevetmed.2014.11.003] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2014] [Revised: 10/15/2014] [Accepted: 11/02/2014] [Indexed: 11/19/2022]
Abstract
For environmentally transmitted infectious diseases (ETIDs), which spread through the contaminated environment (such as foods, surfaces and fomites), there is a lack of consensus about the mathematical approach to derive R0, leading to inconsistent predictions about the spread and control of these infections in their host populations. The objective of this study was to explain three current, though conflicting, approaches to derive a theoretical expression for R0 for ETIDs and assess their validity through comparison with available empirical data. Salmonella Typhimurium in laboratory mice was used as a theoretical and empirical model system. The three conflicting theoretical expressions for R0 were derived using the next generation matrix approach according to three unverified hypotheses about the role of the environmental phase in the transmission of ETIDs. The hypotheses assume that the environment contaminated with a pathogen is: (H1) an extension of the host's infectious period, (H2) a reservoir for the infectious agent, or (H3) has both of these characteristics. For the parameter values describing the empirical model system, the theoretical values of R0 corresponding to the hypotheses H2 and H3 were very similar (1.38 and 1.62, respectively) and their values were approximately half of the value of R0 for hypothesis H1 (2.94). The theoretical R0 values were compared with an empirical R0 (1.58, 95% confidence interval: 1.14, 2.02) estimated using a Martingale method from published experimental data on Salmonella Typhimurium transmission in mice. The results of the comparison suggested that hypothesis H1 is unlikely to hold true but it could not be rejected with confidence because of uncertainty in the value of the pathogen growth rate in the environment. The hypotheses H2 and H3 were both equally strongly supported with the empirical data suggesting that either of them could be valid. A sensitivity analysis identified critical information gaps about the indirect transmission rate of infection and the pathogen growth rate in the environment. Moreover, we identified experimental conditions for which the theoretical R0 predictions based on the hypotheses H2 and H3 differ greatly, which would assist their discrimination and conclusive validation against future empirical studies. Once a valid theoretical R0 is identified for Salmonella Typhimurium in mice, its generalizability to other host-pathogen-environment systems should be tested. The present study may serve as a template for integrated empirical and theoretical research of R0 in the epidemiology of ETIDs.
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Affiliation(s)
- Renata Ivanek
- Department of Veterinary Integrative Biosciences, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX 77843, USA.
| | - Glenn Lahodny
- Department of Veterinary Integrative Biosciences, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX 77843, USA
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Lahodny GE, Gautam R, Ivanek R. Estimating the probability of an extinction or major outbreak for an environmentally transmitted infectious disease. JOURNAL OF BIOLOGICAL DYNAMICS 2014; 9 Suppl 1:128-155. [PMID: 25198247 DOI: 10.1080/17513758.2014.954763] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Indirect transmission through the environment, pathogen shedding by infectious hosts, replication of free-living pathogens within the environment, and environmental decontamination are suspected to play important roles in the spread and control of environmentally transmitted infectious diseases. To account for these factors, the classic Susceptible-Infectious-Recovered-Susceptible epidemic model is modified to include a compartment representing the amount of free-living pathogen within the environment. The model accounts for host demography, direct and indirect transmission, replication of free-living pathogens in the environment, and removal of free-living pathogens by natural death or environmental decontamination. Based on the assumptions of the deterministic model, a continuous-time Markov chain model is developed. An estimate for the probability of disease extinction or a major outbreak is obtained by approximating the Markov chain with a multitype branching process. Numerical simulations illustrate important differences between the deterministic and stochastic counterparts, relevant for outbreak prevention, that depend on indirect transmission, pathogen shedding by infectious hosts, replication of free-living pathogens, and environmental decontamination. The probability of a major outbreak is computed for salmonellosis in a herd of dairy cattle as well as cholera in a human population. An explicit expression for the probability of disease extinction or a major outbreak in terms of the model parameters is obtained for systems with no direct transmission or replication of free-living pathogens.
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Affiliation(s)
- G E Lahodny
- a Veterinary Integrative Biosciences , Texas A&M University , College Station , TX , USA
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Risk factors for Escherichia coli O157 shedding and super-shedding by dairy heifers at pasture. Epidemiol Infect 2014; 143:1004-15. [PMID: 24977432 DOI: 10.1017/s0950268814001630] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
We undertook a longitudinal study within a cohort of 52 dairy heifers maintained under constant management systems and sampled weekly to investigate a comprehensive range of risk factors which may influence shedding or super-shedding of E. coli O157 (detected by direct faecal culture and immunomagnetic separation). E. coli O157 was detected from 416/933 (44.6%) samples (faeces and recto-anal mucosal swabs) and 32 (3.4%) samples enumerated at >10000 c.f.u./g. Weekly point prevalence ranged from 9.4% to 94.3%. Higher temperature (P < 0.001), rainfall (P = 0.02), relative humidity (P < 0.001), pasture growth (P = 0.013) and body score (P = 0.029) were positively associated with increased shedding. Higher rainfall (P < 0.001), hide contamination (P = 0.002) and increased faecal consistency (P = 0.023) were positively associated with super-shedding. Increased solar exposure had a negative effect on both shedding and super-shedding within bivariate analyses but in the final multivariate model for shedding demonstrated a positive effect (P = 0.017). Results suggest that environmental factors are important in E. coli O157 shedding in cattle.
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Rajkhowa S, Sarma DK. Prevalence and antimicrobial resistance of porcine O157 and non-O157 Shiga toxin-producing Escherichia coli from India. Trop Anim Health Prod 2014; 46:931-7. [PMID: 24743858 DOI: 10.1007/s11250-014-0587-4] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/27/2014] [Indexed: 01/25/2023]
Abstract
The aims of this study were to determine the prevalence of Shiga toxin-producing Escherichia coli (STEC) strains in pigs as a possible STEC reservoir in India as well as to characterize the STEC strains and to determine the antimicrobial resistance pattern of the strains. A total of 782 E. coli isolates from clinically healthy (n = 473) and diarrhoeic piglets (309) belonging to major pig-producing states of India were screened by the polymerase chain reaction (PCR) assay for the presence of virulence genes characteristic for STEC, that is, Shiga toxin-producing gene(s) (stx1, stx2), intimin (eae), enterohemolysin (hlyA) and STEC autoagglutinating adhesin (Saa). Overall STEC were detected in 113 (14.4%) piglets, and the prevalence of E. coli O157 and non-O157 STEC were 4 (0.5%) and 109 (13.9%), respectively. None of the O157 STEC isolates carried gene encoding for H7 antigen (fliCh7). The various combinations of virulence genes present in the strains studied were stx1 in 4.6%, stx1 in combination with stx2 gene in 5.1%, stx1 in combination with stx2 and ehxA in 0.6%, stx1 in combination with stx2 and eae in 0.2% and stx2 alone in 3.7%. All STEC isolates were found negative for STEC autoagglutinating adhesin (Saa). The number of STEC isolates which showed resistance to antimicrobials such as ampicillin, tetracycline, streptomycin, lincomycin, nalidixic acid, sulfadiazine, penicillin, gentamicin, kanamycin and ceftriaxone were 100, 99, 98, 97, 95, 94, 92, 88, 85 and 85, respectively. Ninety-seven isolates showed resistance to more than 2 antimicrobials, and 8 resistance groups (R1 to R8) were observed. This study demonstrates that pigs in India harbour both O157 and non-O157 STEC, and this may pose serious public health problems in future.
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Affiliation(s)
- Swaraj Rajkhowa
- National Research Centre on Pig, Indian Council of Agricultural Research (ICAR), Rani Guwahati, 781 131, Assam, India,
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Transmission of Escherichia coli O157:H7 in cattle is influenced by the level of environmental contamination. Epidemiol Infect 2014; 143:274-87. [PMID: 24731271 PMCID: PMC4301210 DOI: 10.1017/s0950268814000867] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
A pen infection-transmission experiment was conducted to elucidate the role of pathogen strain and environmental contamination in transmission of Escherichia coli O157:H7 (ECO157) in cattle. Five steers were inoculated with a three-strain mixture of ECO157 and joined with five susceptible steers in each of two experimental replicates. Faecal and environmental samples were monitored for ECO157 presence over 30 days. One ECO157 strain did not spread. Transmission rates for the other two strains were estimated using a generalized linear model developed based on a modified ‘Susceptible–Infectious–Susceptible’ mathematical model. Transmission rates estimated for the two strains (0·11 and 0·14) were similar. However, the rates significantly (P = 0·0006) increased 1·5 times for every 1-unit increase in the level of environmental contamination measured as log10 c.f.u. Depending on the level of environmental contamination, the estimated basic reproduction numbers varied from <1 to 8. The findings indicate the importance of on-farm measures to reduce environmental contamination for ECO157 control in cattle that should be validated under field conditions.
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A stochastic model for transmission, extinction and outbreak of Escherichia coli O157:H7 in cattle as affected by ambient temperature and cleaning practices. J Math Biol 2013; 69:501-32. [PMID: 23864122 DOI: 10.1007/s00285-013-0707-1] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2012] [Revised: 06/26/2013] [Indexed: 10/26/2022]
Abstract
Many infectious agents transmitting through a contaminated environment are able to persist in the environment depending on the temperature and sanitation determined rates of their replication and clearance, respectively. There is a need to elucidate the effect of these factors on the infection transmission dynamics in terms of infection outbreaks and extinction while accounting for the random nature of the process. Also, it is important to distinguish between the true and apparent extinction, where the former means pathogen extinction in both the host and the environment while the latter means extinction only in the host population. This study proposes a stochastic-differential equation model as an approximation to a Markov jump process model, using Escherichia coli O157:H7 in cattle as a model system. In the model, the host population infection dynamics are described using the standard susceptible-infected-susceptible framework, and the E. coli O157:H7 population in the environment is represented by an additional variable. The backward Kolmogorov equations that determine the probability distribution and the expectation of the first passage time are provided in a general setting. The outbreak and apparent extinction of infection are investigated by numerically solving the Kolmogorov equations for the probability density function of the associated process and the expectation of the associated stopping time. The results provide insight into E. coli O157:H7 transmission and apparent extinction, and suggest ways for controlling the spread of infection in a cattle herd. Specifically, this study highlights the importance of ambient temperature and sanitation, especially during summer.
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Identification of virulence factors by multiplex PCR in Escherichia coli isolated from calves in Minas Gerais, Brazil. Trop Anim Health Prod 2012; 44:1783-90. [DOI: 10.1007/s11250-012-0139-8] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/21/2012] [Indexed: 12/11/2022]
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Bani-Yaghoub M, Gautam R, Shuai Z, van den Driessche P, Ivanek R. Reproduction numbers for infections with free-living pathogens growing in the environment. JOURNAL OF BIOLOGICAL DYNAMICS 2012; 6:923-40. [PMID: 22881277 DOI: 10.1080/17513758.2012.693206] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
The basic reproduction number ℛ(0) for a compartmental disease model is often calculated by the next generation matrix (NGM) approach. When the interactions within and between disease compartments are interpreted differently, the NGM approach may lead to different ℛ(0) expressions. This is demonstrated by considering a susceptible-infectious-recovered-susceptible model with free-living pathogen (FLP) growing in the environment. Although the environment could play different roles in the disease transmission process, leading to different ℛ(0) expressions, there is a unique type reproduction number when control strategies are applied to the host population. All ℛ(0) expressions agree on the threshold value 1 and preserve their order of magnitude. However, using data for salmonellosis and cholera, it is shown that the estimated ℛ(0) values are substantially different. This study highlights the utility and limitations of reproduction numbers to accurately quantify the effects of control strategies for infections with FLPs growing in the environment.
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Affiliation(s)
- Majid Bani-Yaghoub
- Department of Veterinary Integrative Biosciences, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX 77843, USA.
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Gautam R, Kulow M, Döpfer D, Kaspar C, Gonzales T, Pertzborn K, Carroll R, Grant W, Ivanek R. The strain-specific dynamics of Escherichia coli O157:H7 faecal shedding in cattle post inoculation. JOURNAL OF BIOLOGICAL DYNAMICS 2012; 6:1052-1066. [PMID: 22988977 PMCID: PMC3983691 DOI: 10.1080/17513758.2012.722232] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
This study reports analysis of faecal shedding dynamics in cattle for three Escherichia coli O157:H7 (ECO157) strains (S1, S2 and S3) of different genotype and ecological history, using experimental inoculation data. The three strains were compared for their shedding frequency and level of ECO157 in faeces. A multistate Markov chain model was used to compare shedding patterns of S1 and S2. Strains S1 and S2 were detected seven to eight times more often and at 10(4) larger levels than strain S3. Strains S1 and S2 had similar frequencies and levels of shedding. However, the total time spent in the shedding state during colonization was on average four times longer for S1 (15 days) compared to S2 (4 days). These results indicate that an ECO157 strain effect on the frequency, level, pattern and the duration of faecal shedding may need to be considered in control of ECO157 in the cattle reservoir.
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Affiliation(s)
- R. Gautam
- Department of Veterinary Integrative Biosciences, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX 77843, USA
| | - M. Kulow
- School of Veterinary Medicine, University of Wisconsin, Madison, WI 53706, USA
| | - D. Döpfer
- School of Veterinary Medicine, University of Wisconsin, Madison, WI 53706, USA
| | - C. Kaspar
- Department of Bacteriology, University of Wisconsin, Madison, WI 53706, USA
| | - T. Gonzales
- School of Veterinary Medicine, University of Wisconsin, Madison, WI 53706, USA
| | - K.M. Pertzborn
- School of Veterinary Medicine, University of Wisconsin, Madison, WI 53706, USA
| | - R.J. Carroll
- Department of Statistics, Texas A&M University, College Station, TX 77843, USA
| | - W. Grant
- Department of Wildlife and Fisheries Sciences, College of Agriculture and Life Sciences, Texas A&M University, College Station, TX 77843, USA
| | - R. Ivanek
- Department of Veterinary Integrative Biosciences, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX 77843, USA
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Jalava K, Ollgren J, Eklund M, Siitonen A, Kuusi M. Agricultural, socioeconomic and environmental variables as risks for human verotoxigenic Escherichia coli (VTEC) infection in Finland. BMC Infect Dis 2011; 11:275. [PMID: 22008456 PMCID: PMC3226588 DOI: 10.1186/1471-2334-11-275] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2010] [Accepted: 10/18/2011] [Indexed: 11/28/2022] Open
Abstract
Background Verotoxigenic E. coli (VTEC) is the cause of severe gastrointestinal infection especially among infants. Between 10 and 20 cases are reported annually to the National Infectious Disease Register (NIDR) in Finland. The aim of this study was to identify explanatory variables for VTEC infections reported to the NIDR in Finland between 1997 and 2006. We applied a hurdle model, applicable for a dataset with an excess of zeros. Methods We enrolled 131 domestically acquired primary cases of VTEC between 1997 and 2006 from routine surveillance data. The isolated strains were characterized by virulence type, serogroup, phage type and pulsed-field gel electrophoresis. By applying a two-part Bayesian hurdle model to infectious disease surveillance data, we were able to create a model in which the covariates were associated with the probability for occurrence of the cases in the logistic regression part and the magnitude of covariate changes in the Poisson regression part if cases do occur. The model also included spatial correlations between neighbouring municipalities. Results The average annual incidence rate was 4.8 cases per million inhabitants based on the cases as reported to the NIDR. Of the 131 cases, 74 VTEC O157 and 58 non-O157 strains were isolated (one person had dual infections). The number of bulls per human population and the proportion of the population with a higher education were associated with an increased occurrence and incidence of human VTEC infections in 70 (17%) of 416 of Finnish municipalities. In addition, the proportion of fresh water per area, the proportion of cultivated land per area and the proportion of low income households with children were associated with increased incidence of VTEC infections. Conclusions With hurdle models we were able to distinguish between risk factors for the occurrence of the disease and the incidence of the disease for data characterised by an excess of zeros. The density of bulls and the proportion of the population with higher education were significant both for occurrence and incidence, while the proportion of fresh water, cultivated land, and the proportion of low income households with children were significant for the incidence of the disease.
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Affiliation(s)
- Katri Jalava
- Department of Infectious Disease Surveillance and Control, National Institute for Health and Welfare, Helsinki, Finland.
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