{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,11]],"date-time":"2026-04-11T21:40:01Z","timestamp":1775943601320,"version":"3.50.1"},"reference-count":52,"publisher":"Elsevier BV","license":[{"start":{"date-parts":[[2021,9,1]],"date-time":"2021-09-01T00:00:00Z","timestamp":1630454400000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.elsevier.com\/tdm\/userlicense\/1.0\/"},{"start":{"date-parts":[[2021,9,1]],"date-time":"2021-09-01T00:00:00Z","timestamp":1630454400000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.elsevier.com\/legal\/tdmrep-license"},{"start":{"date-parts":[[2021,4,29]],"date-time":"2021-04-29T00:00:00Z","timestamp":1619654400000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100001584","name":"Department of Agriculture, Food and the Marine, Ireland","doi-asserted-by":"publisher","award":["14\/SF\/847"],"award-info":[{"award-number":["14\/SF\/847"]}],"id":[{"id":"10.13039\/501100001584","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["elsevier.com","sciencedirect.com"],"crossmark-restriction":true},"short-container-title":["Science of The Total Environment"],"published-print":{"date-parts":[[2021,9]]},"DOI":"10.1016\/j.scitotenv.2021.147474","type":"journal-article","created":{"date-parts":[[2021,4,30]],"date-time":"2021-04-30T11:33:50Z","timestamp":1619782430000},"page":"147474","update-policy":"https:\/\/doi.org\/10.1016\/elsevier_cm_policy","source":"Crossref","is-referenced-by-count":7,"special_numbering":"C","title":["A Bayesian inference approach to quantify average pathogen loads in farmyard manure and slurry using open-source Irish datasets"],"prefix":"10.1016","volume":"786","author":[{"given":"Rajat","family":"Nag","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Bryan K.","family":"Markey","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Paul","family":"Whyte","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Vincent","family":"O'Flaherty","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Declan","family":"Bolton","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Owen","family":"Fenton","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Karl G.","family":"Richards","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Enda","family":"Cummins","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"78","reference":[{"key":"10.1016\/j.scitotenv.2021.147474_bb0005","series-title":"All-Island animal disease surveillance report","first-page":"1","author":"AFBI and DAFM","year":"2011"},{"key":"10.1016\/j.scitotenv.2021.147474_bb0010","series-title":"All-Island animal disease surveillance report","first-page":"1","author":"AFBI and DAFM","year":"2015"},{"key":"10.1016\/j.scitotenv.2021.147474_bb0015","series-title":"All-Island animal disease surveillance report","first-page":"1","author":"AFBI and DAFM","year":"2016"},{"key":"10.1016\/j.scitotenv.2021.147474_bb0020","series-title":"All-Island animal disease surveillance report","first-page":"1","author":"AFBI and DAFM","year":"2017"},{"key":"10.1016\/j.scitotenv.2021.147474_bb0025","series-title":"All-Island animal disease surveillance report","first-page":"1","author":"AFBI and DAFM","year":"2018"},{"issue":"6","key":"10.1016\/j.scitotenv.2021.147474_bb0030","first-page":"127","article-title":"Bacteriological studies of poultry litter fed to livestock","volume":"9","author":"Alexander","year":"1968","journal-title":"Can. Vet. J."},{"key":"10.1016\/j.scitotenv.2021.147474_bb0035","doi-asserted-by":"crossref","first-page":"302","DOI":"10.1016\/j.vetmic.2009.01.015","article-title":"Prevalence of Clostridium difficile in diarrhoeic and non-diarrhoeic piglets","volume":"137","author":"Alvarez-Perez","year":"2009","journal-title":"Vet. Microbiol."},{"issue":"2","key":"10.1016\/j.scitotenv.2021.147474_bb0040","doi-asserted-by":"crossref","first-page":"e416","DOI":"10.1111\/tbed.12776","article-title":"Molecular epidemiology of Mycobacterium tuberculosis complex strains isolated from livestock and wild animals in Italy suggests the need for a different eradication strategy for bovine tuberculosis","volume":"65","author":"Amato","year":"2018","journal-title":"Transbound. Emerg. Dis."},{"key":"10.1016\/j.scitotenv.2021.147474_bb0045","doi-asserted-by":"crossref","first-page":"4879","DOI":"10.1016\/j.watres.2005.03.016","article-title":"The effect of hygienic treatment on the microbial flora of biowaste at biogas plants","volume":"39","author":"Bagge","year":"2005","journal-title":"Water Res."},{"issue":"1","key":"10.1016\/j.scitotenv.2021.147474_bb0050","doi-asserted-by":"crossref","first-page":"95","DOI":"10.56808\/2985-1130.2556","article-title":"Quantitative microbial risk assessment of Salmonella in surface water as a source of tap water","volume":"44","author":"Banmairuroy","year":"2014","journal-title":"Thai J. Vet. Med."},{"issue":"1","key":"10.1016\/j.scitotenv.2021.147474_bb0055","first-page":"5","article-title":"How Mycobacterium avium paratuberculosis is affected by the composting process","volume":"2","author":"Bonhotal","year":"2011","journal-title":"Trends Anim. Vet. Sci. J."},{"key":"10.1016\/j.scitotenv.2021.147474_bb0060","doi-asserted-by":"crossref","first-page":"24135","DOI":"10.1007\/s11356-017-0011-5","article-title":"The effect of anaerobic digestion and storage on indicator microorganisms in swine and dairy manure","volume":"24","author":"Costa","year":"2017","journal-title":"Environ. Sci. Pollut. Res."},{"key":"10.1016\/j.scitotenv.2021.147474_bb0065","doi-asserted-by":"crossref","first-page":"545","DOI":"10.1016\/S0962-8479(96)90053-2","article-title":"Tuberculosis due to Mycobacterium bovis in humans in the south-west region of Ireland: is there a relationship with infection prevalence in cattle?","volume":"77","author":"Cotter","year":"1996","journal-title":"Tuber. Lung Dis."},{"issue":"10","key":"10.1016\/j.scitotenv.2021.147474_bb0070","doi-asserted-by":"crossref","first-page":"5929","DOI":"10.1128\/AEM.71.10.5929-5934.2005","article-title":"Concentrations of pathogens and indicators in animal feces in the Sydney watershed","volume":"71","author":"Cox","year":"2005","journal-title":"Appl. Environ. Microbiol."},{"key":"10.1016\/j.scitotenv.2021.147474_bb0075","doi-asserted-by":"crossref","first-page":"1036","DOI":"10.1016\/j.scitotenv.2014.06.053","article-title":"Estimating environmental conditions affecting protozoal pathogen removal in surface water wetland systems using a multi-scale, model-based approach","volume":"493","author":"Daniels","year":"2014","journal-title":"Sci. Total Environ."},{"issue":"8","key":"10.1016\/j.scitotenv.2021.147474_bb0080","doi-asserted-by":"crossref","first-page":"2534","DOI":"10.1128\/AEM.03613-12","article-title":"Panmictic structure of the cryptosporidium parvum population in irish calves: influence of prevalence and host movement","volume":"79","author":"de Waele","year":"2013","journal-title":"Appl. Environ. Microbiol."},{"key":"10.1016\/j.scitotenv.2021.147474_bb0085","doi-asserted-by":"crossref","first-page":"51","DOI":"10.1016\/j.prevetmed.2007.05.007","article-title":"Risk factors for ovine Johne\u2019s disease in infected sheep flocks in Australia","volume":"82","author":"Dhand","year":"2007","journal-title":"Prev. Vet. Med."},{"issue":"3","key":"10.1016\/j.scitotenv.2021.147474_bb0090","doi-asserted-by":"crossref","first-page":"257","DOI":"10.14202\/vetworld.2015.257-272","article-title":"The commercial impact of pig salmonella spp. Infections in border-free markets during an economic recession","volume":"8","author":"Evangelopoulou","year":"2015","journal-title":"Vet. World"},{"key":"10.1016\/j.scitotenv.2021.147474_bb0095","series-title":"Exposure Assessment of Microbiological Hazards in Food: Guidelines","author":"FAO\/WHO","year":"2008"},{"issue":"11","key":"10.1016\/j.scitotenv.2021.147474_bb0100","doi-asserted-by":"crossref","first-page":"1890","DOI":"10.1002\/jsfa.3669","article-title":"Quantification of uncertainty using Bayesian and bootstrap models to simulate the impact of nitrogen fertilisation on \u03b2-glucan levels in barley","volume":"89","author":"Fontana","year":"2009","journal-title":"J. Sci. Food Agric."},{"issue":"5","key":"10.1016\/j.scitotenv.2021.147474_bb0105","doi-asserted-by":"crossref","first-page":"1409","DOI":"10.1111\/j.1365-2672.2008.04036.x","article-title":"The effect of climate change on the occurrence and prevalence of livestock diseases in Great Britain","volume":"106","author":"Gale","year":"2009","journal-title":"J. Appl. Microbiol."},{"key":"10.1016\/j.scitotenv.2021.147474_bb0110","doi-asserted-by":"crossref","first-page":"149","DOI":"10.1016\/j.ifset.2017.07.001","article-title":"Kinetic desorption models for the release of nanosilver from an experimental nanosilver coating on polystyrene food packaging","volume":"44(May","author":"Hannon","year":"2017","journal-title":"Innov. Food Sci. Emerg. Technol."},{"issue":"2","key":"10.1016\/j.scitotenv.2021.147474_bb0115","doi-asserted-by":"crossref","first-page":"207","DOI":"10.1111\/j.1472-765X.2004.01564.x","article-title":"Levels of zoonotic agents in British livestock manures","volume":"39","author":"Hutchison","year":"2004","journal-title":"Lett. Appl. Microbiol."},{"issue":"3","key":"10.1016\/j.scitotenv.2021.147474_bb0120","doi-asserted-by":"crossref","first-page":"959","DOI":"10.2134\/jeq2010.0355","article-title":"Microbial and chemical markers: runoff transfer in animal manure\u2013amended soils","volume":"40","author":"Jaffrezic","year":"2011","journal-title":"J. Environ. Qual."},{"key":"10.1016\/j.scitotenv.2021.147474_bb0125","doi-asserted-by":"crossref","DOI":"10.1016\/j.scitotenv.2020.140021","article-title":"Informing water distribution line rehabilitation through quantitative microbial risk assessment","volume":"739","author":"Jamal","year":"2020","journal-title":"Sci. Total Environ."},{"key":"10.1016\/j.scitotenv.2021.147474_bb0130","doi-asserted-by":"crossref","unstructured":"Kr\u00fcger, M., Gro\u00dfe-Herrenthey, A., Schr\u00f6dl, W., Gerlach, A., Rodloff, A. (2012) \u2018Pathogenesis and toxins Visceral botulism at dairy farms in Schleswig Holstein, Germany - prevalence of Clostridium botulinum in feces of cows, in animal feeds, in feces of the farmers, and in house dust\u2019, Anaerobe, 18, 221\u2013223.","DOI":"10.1016\/j.anaerobe.2011.12.013"},{"key":"10.1016\/j.scitotenv.2021.147474_bb0135","unstructured":"Longhurst, P., Tyrrel, S., Pollard, S., Sakrabani, R., Chambers, B., Taylor, M., Litterick, A., Gale, P., Goddard, A., Snary, E. (2013) Risk-Based Guidance for the Use of Source-Segregated Anaerobic Digestates in GB Agriculture, Oxon, UK."},{"key":"10.1016\/j.scitotenv.2021.147474_bb0140","doi-asserted-by":"crossref","first-page":"253","DOI":"10.1016\/j.envint.2019.03.044","article-title":"Risk assessments for quality-assured, source-segregated composts and anaerobic digestates for a circular bioeconomy in the UK","volume":"127","author":"Longhurst","year":"2019","journal-title":"Environ. Int."},{"issue":"2","key":"10.1016\/j.scitotenv.2021.147474_bb0145","doi-asserted-by":"crossref","first-page":"115","DOI":"10.1111\/j.1472-765X.2006.02064.x","article-title":"Carriage of four bacterial pathogens by beef cattle in Northern Ireland at time of slaughter","volume":"44","author":"Madden","year":"2007","journal-title":"Lett. Appl. Microbiol."},{"issue":"1","key":"10.1016\/j.scitotenv.2021.147474_bb0150","doi-asserted-by":"crossref","first-page":"133","DOI":"10.20506\/rst.20.1.1275","article-title":"Mycobacterium avium subsp. paratuberculosis: pathogen, pathogenesis and diagnosis","volume":"20","author":"Manning","year":"2001","journal-title":"Scientific and Technical Review of the Office International des Epizooties (Paris)"},{"key":"10.1016\/j.scitotenv.2021.147474_bb0155","doi-asserted-by":"crossref","DOI":"10.1016\/j.scitotenv.2019.134915","article-title":"Water and sediment act as reservoirs for microbial taxa associated with invasive dreissenid mussels","volume":"703","author":"Mathai","year":"2020","journal-title":"Sci. Total Environ."},{"key":"10.1016\/j.scitotenv.2021.147474_bb0160","doi-asserted-by":"crossref","first-page":"95","DOI":"10.1016\/j.prevetmed.2016.04.014","article-title":"Bayesian estimation of prevalence of paratuberculosis in dairy herds enrolled in a voluntary Johne\u2019s Disease Control Programme in Ireland","volume":"128","author":"McAloon","year":"2016","journal-title":"Prev. Vet. Med."},{"key":"10.1016\/j.scitotenv.2021.147474_bb0165","doi-asserted-by":"crossref","first-page":"712","DOI":"10.1016\/j.scitotenv.2013.06.069","article-title":"Assessing the biosafety risks of pig manure for use as a feedstock for composting","volume":"463\u2013464","author":"Mccarthy","year":"2013","journal-title":"Sci. Total Environ."},{"issue":"4","key":"10.1016\/j.scitotenv.2021.147474_bb0170","doi-asserted-by":"crossref","first-page":"693","DOI":"10.1046\/j.1365-2672.2003.01898.x","article-title":"The prevalence of Salmonella spp. in bovine faecal, rumen and carcass samples at a commercial abattoir","volume":"94","author":"McEvoy","year":"2003","journal-title":"J. Appl. Microbiol."},{"key":"10.1016\/j.scitotenv.2021.147474_bb0175","doi-asserted-by":"crossref","first-page":"18","DOI":"10.1016\/j.vetpar.2015.12.002","article-title":"Molecular epidemiology of Cryptosporidium species in livestock in Ireland","volume":"216","author":"Mirhashemi","year":"2016","journal-title":"Vet. Parasitol."},{"issue":"2","key":"10.1016\/j.scitotenv.2021.147474_bb0180","doi-asserted-by":"crossref","first-page":"616","DOI":"10.1111\/j.1365-2672.2009.04229.x","article-title":"Isolation and sources of blown pack spoilage clostridia in beef abattoirs","volume":"107","author":"Moschonas","year":"2009","journal-title":"J. Appl. Microbiol."},{"key":"10.1016\/j.scitotenv.2021.147474_bb0185","doi-asserted-by":"crossref","first-page":"460","DOI":"10.1016\/j.scitotenv.2019.06.512","article-title":"Anaerobic digestion of agricultural manure and biomass \u2013 critical indicators of risk and knowledge gaps","volume":"690","author":"Nag","year":"2019","journal-title":"Sci. Total Environ."},{"key":"10.1016\/j.scitotenv.2021.147474_bb0190","series-title":"11th International Conference on Simulation and Modelling in the Food and Bio-Industry 2020 (FOODSIM\u20192020)","first-page":"141","article-title":"A quantitative risk assessment of E. coli O157:H7 on ready to eat foods following the application of biomaterials on land","author":"Nag","year":"2020"},{"issue":"136297","key":"10.1016\/j.scitotenv.2021.147474_bb0195","first-page":"1","article-title":"Ranking hazards pertaining to human health concerns from land application of anaerobic digestate","volume":"710","author":"Nag","year":"2020","journal-title":"Sci. Total Environ."},{"issue":"8","key":"10.1016\/j.scitotenv.2021.147474_bb0200","doi-asserted-by":"crossref","first-page":"4458","DOI":"10.1128\/AEM.70.8.4458-4467.2004","article-title":"Ecology and transmission of listeria monocytogenes infecting ruminants and in the farm environment","volume":"70","author":"Nightingale","year":"2004","journal-title":"Appl. Environ. Microbiol."},{"key":"10.1016\/j.scitotenv.2021.147474_bb0205","first-page":"1","article-title":"Toward assessing farm-based anaerobic digestate public health risks: comparative investigation with slurry, effect of pasteurization treatments, and use of miniature bioreactors as proxies for pathogen spiking trials","volume":"2(July","author":"Nolan","year":"2018","journal-title":"Front. Sustain. Food Syst."},{"issue":"4","key":"10.1016\/j.scitotenv.2021.147474_bb0210","doi-asserted-by":"crossref","first-page":"660","DOI":"10.4315\/0362-028X-68.4.660","article-title":"Prevalence and numbers of Escherichia coli O157 on bovine hides at a beef slaughter plant","volume":"68","author":"O\u2019Brien","year":"2005","journal-title":"J. Food Prot."},{"key":"10.1016\/j.scitotenv.2021.147474_bb0215","doi-asserted-by":"crossref","first-page":"2643","DOI":"10.1098\/rstb.2009.0097","article-title":"The impacts of livestock diseases and their control on growth and development processes that are pro-poor","volume":"364","author":"Perry","year":"2009","journal-title":"Philos. Trans. R. Soc. B"},{"issue":"4","key":"10.1016\/j.scitotenv.2021.147474_bb0220","doi-asserted-by":"crossref","first-page":"458","DOI":"10.5455\/javar.2015.b118","article-title":"Prevalence and antibiogram profile of Mycobacterium spp. in poultry and its environments","volume":"2","author":"Reza","year":"2015","journal-title":"J. Adv. Vet. Anim. Res."},{"key":"10.1016\/j.scitotenv.2021.147474_bb0225","doi-asserted-by":"crossref","first-page":"133","DOI":"10.1099\/00222615-45-2-133","article-title":"The distribution of Clostridium difficile in the environment of South Wales","volume":"45","author":"Salf","year":"1996","journal-title":"J. Med. Microbiol."},{"issue":"8","key":"10.1016\/j.scitotenv.2021.147474_bb0230","first-page":"412","article-title":"The survival of Mycobacterium bovis in sterilized cattle slurry and its relevance to the persistence of this pathogen in the environment","volume":"53","author":"Scanlon","year":"2000","journal-title":"Ir. Vet. J."},{"key":"10.1016\/j.scitotenv.2021.147474_bb0235","doi-asserted-by":"crossref","first-page":"2637","DOI":"10.1098\/rstb.2009.0133","article-title":"Livestock infectious diseases and zoonoses","volume":"364","author":"Tomley","year":"2009","journal-title":"Philos. Trans. R. Soc. B"},{"issue":"1","key":"10.1016\/j.scitotenv.2021.147474_bb0240","first-page":"84","article-title":"Field test for estimating dry matter and fertiliser value of slurry: preliminary report","volume":"14","author":"Tunney","year":"1975","journal-title":"Ir. J. Agric. Res."},{"key":"10.1016\/j.scitotenv.2021.147474_bb0245","doi-asserted-by":"crossref","first-page":"1330","DOI":"10.1016\/j.scitotenv.2017.10.267","article-title":"Estimating virus occurrence using Bayesian modeling in multiple drinking water systems of the United States","volume":"619\u2013620","author":"Varughese","year":"2018","journal-title":"Sci. Total Environ."},{"issue":"100083","key":"10.1016\/j.scitotenv.2021.147474_bb0250","first-page":"1","article-title":"A Bayesian estimation of the concentration of microbial organisms in powdered foods arising from repeat testing for microbial contamination","volume":"14","author":"von Westerholt","year":"2020","journal-title":"Microb. Risk Anal."},{"key":"10.1016\/j.scitotenv.2021.147474_bb0255","unstructured":"Vose, D. (2009) Risk Analysis: A Quantitative Guide, third. ed, John Wiley & Sons, Ltd."},{"key":"10.1016\/j.scitotenv.2021.147474_bb0260","doi-asserted-by":"crossref","first-page":"1149","DOI":"10.1016\/j.scitotenv.2018.09.087","article-title":"Linking landscape patterns to sources of water contamination: implications for tracking fecal contaminants with geospatial and Bayesian approaches","volume":"650","author":"Wu","year":"2019","journal-title":"Sci. Total Environ."}],"container-title":["Science of The Total Environment"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/api.elsevier.com\/content\/article\/PII:S0048969721025456?httpAccept=text\/xml","content-type":"text\/xml","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/api.elsevier.com\/content\/article\/PII:S0048969721025456?httpAccept=text\/plain","content-type":"text\/plain","content-version":"vor","intended-application":"text-mining"}],"deposited":{"date-parts":[[2025,9,24]],"date-time":"2025-09-24T12:26:36Z","timestamp":1758716796000},"score":1,"resource":{"primary":{"URL":"https:\/\/linkinghub.elsevier.com\/retrieve\/pii\/S0048969721025456"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2021,9]]},"references-count":52,"alternative-id":["S0048969721025456"],"URL":"https:\/\/doi.org\/10.1016\/j.scitotenv.2021.147474","relation":{},"ISSN":["0048-9697"],"issn-type":[{"value":"0048-9697","type":"print"}],"subject":[],"published":{"date-parts":[[2021,9]]},"assertion":[{"value":"Elsevier","name":"publisher","label":"This article is maintained by"},{"value":"A Bayesian inference approach to quantify average pathogen loads in farmyard manure and slurry using open-source Irish datasets","name":"articletitle","label":"Article Title"},{"value":"Science of The Total Environment","name":"journaltitle","label":"Journal Title"},{"value":"https:\/\/doi.org\/10.1016\/j.scitotenv.2021.147474","name":"articlelink","label":"CrossRef DOI link to publisher maintained version"},{"value":"article","name":"content_type","label":"Content Type"},{"value":"\u00a9 2021 The Author(s). Published by Elsevier B.V.","name":"copyright","label":"Copyright"}],"article-number":"147474"}}