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Bennett C, Coughlan S, Hunt K, Butler F, Fanning S, Ryan E, De Gascun C, O'Gorman J. Detection of hepatitis E RNA in pork products at point of retail in Ireland - Are consumers at risk? Int J Food Microbiol 2024; 410:110492. [PMID: 37988969 DOI: 10.1016/j.ijfoodmicro.2023.110492] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Revised: 11/09/2023] [Accepted: 11/12/2023] [Indexed: 11/23/2023]
Abstract
Hepatitis E (HEV), a zoonotic virus, is the leading cause of acute viral hepatitis in Europe. The presence of HEV in domestic pigs can result in infections in humans through consumption of pork products which are undercooked or where processing methods are insufficient to inactivate the virus. In Ireland, pork accounts for 34 % of all meat consumption (CSO, 2022) and the prevalence of HEV in products at point of retail has not previously been characterised. A sampling strategy was designed in which high pork content sausages, fresh pork liver and raw fermented sausages were systematically purchased from three types of retailers between May 2018 and March 2019. In total, 200 pork products were tested using a lysing agent to release the HEV from the product for detection. RT-PCR for HEV was performed on samples with an extraction efficiency >1 % (n = 188/200) (94 %). Low level HEV RNA was detected in 9/188 (4.8 %) pork products tested. The highest incidence of HEV RNA was in pork liver where 6/25 (24 %) samples were positive. The concentration of HEV ranged from 0.02 - to 9.4 genome copies/g of pork. Based on these data an exposure assessment was performed which found that if consumers followed advice from the Food Safety Authority of Ireland to achieve core temperatures of 70 °C or higher when cooking, the risk was likely to be negligible.
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Affiliation(s)
- Charlene Bennett
- UCD-National Virus Reference Laboratory, University College Dublin, Belfield, Dublin 4, Ireland.
| | - Suzie Coughlan
- UCD-National Virus Reference Laboratory, University College Dublin, Belfield, Dublin 4, Ireland
| | - Kevin Hunt
- UCD-School of Biosystems and Food Engineering, University College Dublin, Belfield, Dublin 4, Ireland
| | - Francis Butler
- UCD-School of Biosystems and Food Engineering, University College Dublin, Belfield, Dublin 4, Ireland
| | - Séamus Fanning
- UCD-Centre for Food Safety, School of Public Health, Physiotherapy & Sports Science, Belfield, Dublin 4, Ireland
| | - Eoin Ryan
- Central Veterinary Research Laboratory, Department Agriculture Food and the Marine (DAFM), Backweston, Kildare, Ireland
| | - Cillian De Gascun
- UCD-National Virus Reference Laboratory, University College Dublin, Belfield, Dublin 4, Ireland
| | - Joanne O'Gorman
- UCD-National Virus Reference Laboratory, University College Dublin, Belfield, Dublin 4, Ireland
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2
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Cheng Y, Mousavi ZE, Pennone V, Hurley D, Butler F. Association between the Presence of Resistance Genes and Sanitiser Resistance of Listeria monocytogenes Isolates Recovered from Different Food-Processing Facilities. Microorganisms 2023; 11:2989. [PMID: 38138133 PMCID: PMC10746039 DOI: 10.3390/microorganisms11122989] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2023] [Revised: 12/11/2023] [Accepted: 12/12/2023] [Indexed: 12/24/2023] Open
Abstract
Sanitisers are widely used in cleaning food-processing facilities, but their continued use may cause an increased resistance of pathogenic bacteria. Several genes have been attributed to the increased sanitiser resistance ability of L. monocytogenes. This study determined the presence of sanitiser resistance genes in Irish-sourced L. monocytogenes isolates and explored the association with phenotypic sanitiser resistance. The presence of three genes associated with sanitiser resistance and a three-gene cassette (mdrL, qacH, emrE, bcrABC) were determined in 150 L. monocytogenes isolates collected from Irish food-processing facilities. A total of 23 isolates contained bcrABC, 42 isolates contained qacH, one isolate contained emrE, and all isolates contained mdrL. Additionally, 47 isolates were selected and grouped according to the number and type of resistance genes, and the minimal inhibitory concentration (MIC) of these isolates for benzalkonium chloride (BAC) was determined experimentally using the broth microdilution method. The BAC resistance of the strain carrying the bcrABC gene cassette was significantly higher than that of strains lacking the gene cassette, and the BAC resistance of the strain carrying the qacH gene was significantly higher than that of strains lacking the qacH gene (p < 0.05). Isolates harbouring both the qacH and bcrABC genes did not show higher BAC resistance. With respect to environmental factors, there was no significant difference in MIC values for isolates recovered from different processing facilities. In summary, this investigation highlights the prevalence of specific sanitiser resistance genes in L. monocytogenes isolates from Irish food-processing settings. While certain genes correlated with increased resistance to benzalkonium chloride, the combination of multiple genes did not necessarily amplify this resistance.
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Affiliation(s)
- Yue Cheng
- UCD School of Biosystems and Food Engineering, University College Dublin, D04 C1P1 Dublin, Ireland; (Y.C.); (Z.E.M.)
| | - Zeinabossadat Ebrahimzadeh Mousavi
- UCD School of Biosystems and Food Engineering, University College Dublin, D04 C1P1 Dublin, Ireland; (Y.C.); (Z.E.M.)
- Department of Food Science and Engineering, Faculty of Agriculture and Natural Resources, University of Tehran, Karaj 77871-31587, Iran
| | - Vincenzo Pennone
- Teagasc Food Research Centre Moorepark, Fermoy, P61 C996 Cork, Ireland;
| | - Daniel Hurley
- UCD School of Agriculture and Food Science, University College Dublin, D04 C1P1 Dublin, Ireland;
| | - Francis Butler
- UCD School of Biosystems and Food Engineering, University College Dublin, D04 C1P1 Dublin, Ireland; (Y.C.); (Z.E.M.)
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3
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Mousavi ZE, Koolman L, Macori G, Fanning S, Butler F. Comprehensive Genomic Characterization of Cronobacter sakazakii Isolates from Infant Formula Processing Facilities Using Whole-Genome Sequencing. Microorganisms 2023; 11:2749. [PMID: 38004760 PMCID: PMC10673598 DOI: 10.3390/microorganisms11112749] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2023] [Revised: 11/07/2023] [Accepted: 11/09/2023] [Indexed: 11/26/2023] Open
Abstract
Cronobacter sakazakii is an opportunistic pathogen linked to outbreaks in powdered infant formula (PIF), primarily causing meningitis and necrotizing enterocolitis. Whole-genome sequencing (WGS) was used to characterize 18 C. sakazakii strains isolated from PIF (powdered infant formula) manufacturing plants (2011-2015). Sequence Type (ST) 1 was identified as the dominant sequence type, and all isolates carried virulence genes for chemotaxis, flagellar motion, and heat shock proteins. Multiple antibiotic resistance genes were detected, with all isolates exhibiting resistance to Cephalosporins and Tetracycline. A significant correlation existed between genotypic and phenotypic antibiotic resistance. The plasmid Col(pHAD28) was identified in the isolates recovered from the same PIF environment. All isolates harbored at least one intact phage. All the study isolates were compared with a collection of 96 publicly available C. sakazakii genomes to place these isolates within a global context. This comprehensive study, integrating phylogenetic, genomic, and epidemiological data, contributes to a deeper understanding of Cronobacter outbreaks. It provides valuable insights to enhance surveillance, prevention, and control strategies in food processing and public health contexts.
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Affiliation(s)
- Zeinab Ebrahimzadeh Mousavi
- UCD-Centre for Food Safety, School of Public Health, Physiotherapy and Sports Science, University College Dublin, D04 V1W8 Dublin, Ireland; (L.K.); (G.M.); (S.F.)
- School of Biosystems and Food Engineering, University College Dublin, D04 V1W8 Dublin, Ireland;
- Department of Food Science and Engineering, Faculties of Agriculture and Natural Resources, University of Tehran, Karaj 6719418314, Iran
| | - Leonard Koolman
- UCD-Centre for Food Safety, School of Public Health, Physiotherapy and Sports Science, University College Dublin, D04 V1W8 Dublin, Ireland; (L.K.); (G.M.); (S.F.)
| | - Guerrino Macori
- UCD-Centre for Food Safety, School of Public Health, Physiotherapy and Sports Science, University College Dublin, D04 V1W8 Dublin, Ireland; (L.K.); (G.M.); (S.F.)
| | - Séamus Fanning
- UCD-Centre for Food Safety, School of Public Health, Physiotherapy and Sports Science, University College Dublin, D04 V1W8 Dublin, Ireland; (L.K.); (G.M.); (S.F.)
| | - Francis Butler
- School of Biosystems and Food Engineering, University College Dublin, D04 V1W8 Dublin, Ireland;
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4
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Bennett C, Hunt K, Butler F, Keaveney S, Fanning S, De Gascun C, Coughlan S, O'Gorman J. Detection of Hepatitis A RNA, Hepatitis E RNA, Human Adenovirus F DNA, and Norovirus RNA in Fresh and Frozen Berry Products at Point of Retail in Ireland. Food Environ Virol 2023; 15:246-254. [PMID: 37528267 PMCID: PMC10499670 DOI: 10.1007/s12560-023-09561-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/02/2023] [Accepted: 07/22/2023] [Indexed: 08/03/2023]
Abstract
Soft fruits are at particular risk of contamination with enteric viruses such as Hepatitis A virus (HAV), Hepatitis E Virus (HEV), Norovirus (NoV), Human Adenovirus (HAdV) and Sapovirus (SaV). The aim of this study was to investigate, for the first time, the presence of these biological agents in ready to eat (RTE) berries at point of retail in Ireland. A sampling strategy was designed in which RTE fresh and frozen strawberries and raspberries were purchased from five retailers between May and October 2018. Reverse Transcriptase Polymerase Chain Reaction (RT-qPCR) assays for HEV RNA, Nov RNA, SaV RNA, and human Adenovirus species F DNA (HAdV-F) were performed on 239 samples (25g portions). Viral nucleic acid was present in 6.7% (n = 16) of samples tested as follows: HAV RNA (n = 5), HAdV-F DNA (n = 5), HEV RNA (n = 3) and NoV GII RNA (n = 3). Sapovirus RNA was not detected in any product. No significant differences were found between berry type, fresh/frozen status, or supermarket source. This study suggests a risk that exists across all retail outlets however only low levels of nucleic acid ranging from 0 to 16 genome copies/g were present. Although these findings may reflect non-viable/non-infectious virus the continued provision of risk mitigation advice to consumers is warranted and further work is required to ensure control measures to reduce contamination are implemented and enforced.
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Affiliation(s)
- Charlene Bennett
- UCD-National Virus Reference Laboratory, University College Dublin, Belfield, Dublin, 4, Ireland.
| | - Kevin Hunt
- UCD-School of Biosystems and Food Engineering, University College Dublin, Belfield, Dublin, 4, Ireland
| | - Francis Butler
- UCD-School of Biosystems and Food Engineering, University College Dublin, Belfield, Dublin, 4, Ireland
| | | | - Séamus Fanning
- UCD-Centre for Food Safety, School of Public Health, Physiotherapy & Sports Science, Belfield, Dublin, 4, Ireland
| | - Cillian De Gascun
- UCD-National Virus Reference Laboratory, University College Dublin, Belfield, Dublin, 4, Ireland
| | - Suzie Coughlan
- UCD-National Virus Reference Laboratory, University College Dublin, Belfield, Dublin, 4, Ireland
| | - Joanne O'Gorman
- UCD-National Virus Reference Laboratory, University College Dublin, Belfield, Dublin, 4, Ireland
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5
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Lourenco A, Li F, Quijada NM, Duffy G, Tobin JT, Butler F, Jordan K, O'Brien T. Draft Genome Sequences of Bacillus licheniformis and Bacillus paralicheniformis Strains Isolated from Irish Skim Milk Powder. Microbiol Resour Announc 2023:e0013723. [PMID: 37278649 DOI: 10.1128/mra.00137-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2023] Open
Abstract
Nineteen Bacillus licheniformis strains and four strains of the closely related species Bacillus paralicheniformis were isolated from a variety of Irish medium-heat skim milk powders. The draft genome sequences of these 23 isolates provide valuable genetic data for research work relevant to dairy products and process development. The isolates are available at Teagasc.
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Affiliation(s)
- Antonio Lourenco
- Food Bioscience Department, Teagasc Food Research Centre, Moorepark, Fermoy, County Cork, Ireland
| | - Fang Li
- Food Safety Department, Teagasc Food Research Centre, Moorepark, Fermoy, County Cork, Ireland
- Food Chemistry and Technology Department, Teagasc Food Research Centre, Moorepark, Fermoy, County Cork, Ireland
- School of Biosystems and Food Engineering, Agriculture and Food Science Centre, University College Dublin, Belfield, Dublin, Ireland
| | - Narciso M Quijada
- Department of Microbiology and Genetics, Institute for Agribiotechnology Research (CIALE), University of Salamanca (USAL), Salamanca, Spain
| | - Geraldine Duffy
- Food Safety Department, Teagasc Food Research Centre, Moorepark, Fermoy, County Cork, Ireland
| | - John T Tobin
- Food Chemistry and Technology Department, Teagasc Food Research Centre, Moorepark, Fermoy, County Cork, Ireland
| | - Francis Butler
- School of Biosystems and Food Engineering, Agriculture and Food Science Centre, University College Dublin, Belfield, Dublin, Ireland
| | - Kieran Jordan
- Food Safety Department, Teagasc Food Research Centre, Moorepark, Fermoy, County Cork, Ireland
| | - Triona O'Brien
- Food Safety Department, Teagasc Food Research Centre, Moorepark, Fermoy, County Cork, Ireland
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6
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Mousavi ZE, Hunt K, Koolman L, Butler F, Fanning S. Cronobacter Species in the Built Food Production Environment: A Review on Persistence, Pathogenicity, Regulation and Detection Methods. Microorganisms 2023; 11:1379. [PMID: 37374881 DOI: 10.3390/microorganisms11061379] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Revised: 05/17/2023] [Accepted: 05/22/2023] [Indexed: 06/29/2023] Open
Abstract
The powdered formula market is large and growing, with sales and manufacturing increasing by 120% between 2012 and 2021. With this growing market, there must come an increasing emphasis on maintaining a high standard of hygiene to ensure a safe product. In particular, Cronobacter species pose a risk to public health through their potential to cause severe illness in susceptible infants who consume contaminated powdered infant formula (PIF). Assessment of this risk is dependent on determining prevalence in PIF-producing factories, which can be challenging to measure with the heterogeneity observed in the design of built process facilities. There is also a potential risk of bacterial growth occurring during rehydration, given the observed persistence of Cronobacter in desiccated conditions. In addition, novel detection methods are emerging to effectively track and monitor Cronobacter species across the food chain. This review will explore the different vehicles that lead to Cronobacter species' environmental persistence in the food production environment, as well as their pathogenicity, detection methods and the regulatory framework surrounding PIF manufacturing that ensures a safe product for the global consumer.
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Affiliation(s)
- Zeinab Ebrahimzadeh Mousavi
- UCD-Centre for Food Safety, School of Public Health, Physiotherapy and Sports Science, University College Dublin, D04 V1W8 Dublin, Ireland
- School of Biosystems and Food Engineering, University College Dublin, Belfield, Dublin 4, D04 V1W8 Dublin, Ireland
- Department of Food Science and Engineering, Faculties of Agriculture and Natural Resources, University of Tehran, Karaj 6719418314, Iran
| | - Kevin Hunt
- School of Biosystems and Food Engineering, University College Dublin, Belfield, Dublin 4, D04 V1W8 Dublin, Ireland
| | - Leonard Koolman
- UCD-Centre for Food Safety, School of Public Health, Physiotherapy and Sports Science, University College Dublin, D04 V1W8 Dublin, Ireland
| | - Francis Butler
- School of Biosystems and Food Engineering, University College Dublin, Belfield, Dublin 4, D04 V1W8 Dublin, Ireland
| | - Séamus Fanning
- UCD-Centre for Food Safety, School of Public Health, Physiotherapy and Sports Science, University College Dublin, D04 V1W8 Dublin, Ireland
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7
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Wang X, Bouzembrak Y, Marvin HJP, Clarke D, Butler F. Bayesian Networks modeling of diarrhetic shellfish poisoning in Mytilus edulis harvested in Bantry Bay, Ireland. Harmful Algae 2022; 112:102171. [PMID: 35144818 DOI: 10.1016/j.hal.2021.102171] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/07/2021] [Revised: 12/20/2021] [Accepted: 12/21/2021] [Indexed: 06/14/2023]
Abstract
Diarrhetic Shellfish Poisoning (DSP) results from the human consumption of contaminated shellfish with marine biotoxins, which are produced by some species of marine dinoflagellates, mainly belonging to the genus Dinophysis. Shellfish contamination with marine biotoxins not only pose a threat to human health, but also lead to financial loss to aquaculture operations from the temporary closure of production areas when toxin concentrations exceed regulatory levels. In this study, we developed a Bayesian Network (BN) model for forecasting the short-term variations of DSP toxins in blue mussels (Mytilus edulis) from Bantry Bay, Southwest Ireland. Data inputs to a BN model from 10 production sites in Bantry Bay included plankton cell densities in sea water, DSP toxin concentration in mussels and sea surface temperature. The model was trained with data from 2014 to 2018, and validated with data of 2019. Validation consisted of predicting the DSP toxin concentration at one production site using the model parameters from the other locations as input values. Model validation showed that the prediction accuracy was higher than 86%. Sensitivity analysis indicated that in general, DSP toxin concentration was more relevant than plankton abundance. This initial work has demonstrated the usefulness of BN modeling as an approach to short term forecasting. Further work is ongoing to use the model for scenario testing and to increase the number of environmental parameters used as inputs to the model.
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Affiliation(s)
- Xiyao Wang
- UCD School of Biosystems and Food Engineering, University College Dublin, Belfield, Dublin 4, Ireland.
| | - Yamine Bouzembrak
- Wageningen Food Safety Research, P.O. Box 230, 6700 AE Wageningen, The Netherlands
| | - Hans J P Marvin
- Wageningen Food Safety Research, P.O. Box 230, 6700 AE Wageningen, The Netherlands
| | - Dave Clarke
- Marine Institute, Rinville, Oranmore, Co. Galway, H91 R673, Ireland
| | - Francis Butler
- UCD School of Biosystems and Food Engineering, University College Dublin, Belfield, Dublin 4, Ireland
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8
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McAloon CG, Wall P, Butler F, Codd M, Gormley E, Walsh C, Duggan J, Murphy TB, Nolan P, Smyth B, O'Brien K, Teljeur C, Green MJ, O'Grady L, Culhane K, Buckley C, Carroll C, Doyle S, Martin J, More SJ. Numbers of close contacts of individuals infected with SARS-CoV-2 and their association with government intervention strategies. BMC Public Health 2021; 21:2238. [PMID: 34886842 PMCID: PMC8655330 DOI: 10.1186/s12889-021-12318-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Accepted: 11/22/2021] [Indexed: 12/23/2022] Open
Abstract
Background Contact tracing is conducted with the primary purpose of interrupting transmission from individuals who are likely to be infectious to others. Secondary analyses of data on the numbers of close contacts of confirmed cases could also: provide an early signal of increases in contact patterns that might precede larger than expected case numbers; evaluate the impact of government interventions on the number of contacts of confirmed cases; or provide data information on contact rates between age cohorts for the purpose of epidemiological modelling. We analysed data from 140,204 close contacts of 39,861 cases in Ireland from 1st May to 1st December 2020. Results Negative binomial regression models highlighted greater numbers of contacts within specific population demographics, after correcting for temporal associations. Separate segmented regression models of the number of cases over time and the average number of contacts per case indicated that a breakpoint indicating a rapid decrease in the number of contacts per case in October 2020 preceded a breakpoint indicating a reduction in the number of cases by 11 days. Conclusions We found that the number of contacts per infected case was overdispersed, the mean varied considerable over time and was temporally associated with government interventions. Analysis of the reported number of contacts per individual in contact tracing data may be a useful early indicator of changes in behaviour in response to, or indeed despite, government restrictions. This study provides useful information for triangulating assumptions regarding the contact mixing rates between different age cohorts for epidemiological modelling. Supplementary Information The online version contains supplementary material available at 10.1186/s12889-021-12318-y.
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Affiliation(s)
- Conor G McAloon
- School of Veterinary Medicine, University College Dublin, Belfield, Dublin 4, Ireland.
| | - Patrick Wall
- School of Public Health, Physiotherapy and Sports Science, University College Dublin, Belfield, Dublin 4, Ireland
| | - Francis Butler
- School of Biosystems and Food Engineering, University College Dublin, Belfield, Dublin 4, Ireland
| | - Mary Codd
- School of Public Health, Physiotherapy and Sports Science, University College Dublin, Belfield, Dublin 4, Ireland
| | - Eamonn Gormley
- School of Veterinary Medicine, University College Dublin, Belfield, Dublin 4, Ireland
| | - Cathal Walsh
- Department of Mathematics and Statistics, University of Limerick, Limerick, Ireland
| | - Jim Duggan
- School of Computer Science, National University of Ireland Galway, Galway, Ireland
| | - T Brendan Murphy
- School of Mathematics and Statistics, University College Dublin, Belfield, Dublin 4, Ireland
| | - Philip Nolan
- National University of Ireland Maynooth, Kildare, Ireland
| | - Breda Smyth
- Department of Public Health, Health Service Executive West, Galway, Ireland
| | | | - Conor Teljeur
- Health Information and Quality Authority, George's Court, Dublin 7, Ireland
| | - Martin J Green
- School of Veterinary Medicine and Science, University of Nottingham, Nottingham, UK
| | - Luke O'Grady
- School of Veterinary Medicine, University College Dublin, Belfield, Dublin 4, Ireland.,School of Veterinary Medicine and Science, University of Nottingham, Nottingham, UK
| | - Kieran Culhane
- Central Statistics Office, Ardee road, Rathmines, Dublin, Ireland
| | - Claire Buckley
- COVID-19 Contact Management Programme, Health Service Executive, Dublin, Ireland
| | - Ciara Carroll
- COVID-19 Contact Management Programme, Health Service Executive, Dublin, Ireland
| | - Sarah Doyle
- COVID-19 Contact Management Programme, Health Service Executive, Dublin, Ireland
| | - Jennifer Martin
- COVID-19 Contact Management Programme, Health Service Executive, Dublin, Ireland
| | - Simon J More
- School of Veterinary Medicine, University College Dublin, Belfield, Dublin 4, Ireland.,Centre for Veterinary Epidemiology and Risk Analysis, School of Veterinary Medicine, University College Dublin, Belfield, Dublin, Ireland
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9
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Casey-Bryars M, Griffin J, McAloon C, Byrne A, Madden J, Mc Evoy D, Collins Á, Hunt K, Barber A, Butler F, Lane EA, O'Brien K, Wall P, Walsh K, More SJ. Presymptomatic transmission of SARS-CoV-2 infection: a secondary analysis using published data. BMJ Open 2021; 11:e041240. [PMID: 34183334 PMCID: PMC8245290 DOI: 10.1136/bmjopen-2020-041240] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/11/2020] [Accepted: 05/16/2021] [Indexed: 12/13/2022] Open
Abstract
OBJECTIVE To estimate the proportion of presymptomatic transmission of SARS-CoV-2 infection that can occur, and the timing of transmission relative to symptom onset. SETTING/DESIGN Secondary analysis of international published data. DATA SOURCES Meta-analysis of COVID-19 incubation period and a rapid review of serial interval and generation time, which are published separately. PARTICIPANTS Data from China, the Islamic Republic of Iran, Italy, Republic of Korea, Singapore and Vietnam from December 2019 to May 2020. METHODS Simulations were generated of incubation period and of serial interval or generation time. From these, transmission times relative to symptom onset, and the proportion of presymptomatic transmission, were estimated. OUTCOME MEASURES Transmission time of SARS-CoV-2 relative to symptom onset and proportion of presymptomatic transmission. RESULTS Based on 18 serial interval/generation time estimates from 15 papers, mean transmission time relative to symptom onset ranged from -2.6 (95% CI -3.0 to -2.1) days before infector symptom onset to 1.4 (95% CI 1.0 to 1.8) days after symptom onset. The proportion of presymptomatic transmission ranged from 45.9% (95% CI 42.9% to 49.0%) to 69.1% (95% CI 66.2% to 71.9%). CONCLUSIONS There is substantial potential for presymptomatic transmission of SARS-CoV-2 across a range of different contexts. This highlights the need for rapid case detection, contact tracing and quarantine. The transmission patterns that we report reflect the combination of biological infectiousness and transmission opportunities which vary according to context.
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Affiliation(s)
- Miriam Casey-Bryars
- Centre for Veterinary Epidemiology and Risk Analysis, University College Dublin, Dublin, Ireland
| | - John Griffin
- Centre for Veterinary Epidemiology and Risk Analysis, University College Dublin, Dublin, Ireland
| | - Conor McAloon
- School of Veterinary Medicine, UCD School of Agriculture Food Science and Veterinary Medicine, Dublin, Ireland
| | - Andrew Byrne
- One Health Scientific Support Unit, Government of Ireland Department of Agriculture Food and the Marine, Dublin, Ireland
| | - Jamie Madden
- Centre for Veterinary Epidemiology and Risk Analysis, University College Dublin, Dublin, Ireland
| | - David Mc Evoy
- School of Public Health, Physiotherapy and Sports Science, University College Dublin, Dublin, Ireland
| | - Áine Collins
- Centre for Veterinary Epidemiology and Risk Analysis, University College Dublin, Dublin, Ireland
| | - Kevin Hunt
- Centre for Food Safety, University College Dublin, Dublin, Ireland
| | - Ann Barber
- Centre for Veterinary Epidemiology and Risk Analysis, University College Dublin, Dublin, Ireland
| | - Francis Butler
- Centre for Food Safety, University College Dublin, Dublin, Ireland
| | - Elizabeth Ann Lane
- Centre for Veterinary Epidemiology and Risk Analysis, University College Dublin, Belfield, Ireland
| | | | - Patrick Wall
- Public Health, University College Dublin, Dublin, Ireland
| | - Kieran Walsh
- Health Information and Quality Authority, Cork, Ireland
| | - Simon John More
- Centre for Veterinary Epidemiology and Risk Analysis, University College Dublin, Dublin, Ireland
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10
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Rupnik A, Doré W, Devilly L, Fahy J, Fitzpatrick A, Schmidt W, Hunt K, Butler F, Keaveney S. Evaluation of Norovirus Reduction in Environmentally Contaminated Pacific Oysters During Laboratory Controlled and Commercial Depuration. Food Environ Virol 2021; 13:229-240. [PMID: 33649884 PMCID: PMC8116253 DOI: 10.1007/s12560-021-09464-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Accepted: 01/23/2021] [Indexed: 06/12/2023]
Abstract
Norovirus contamination of oysters is the lead cause of non-bacterial gastroenteritis and a significant food safety concern for the oyster industry. Here, norovirus reduction from Pacific oysters (Crassostrea gigas), contaminated in the marine environment, was studied in laboratory depuration trials and in two commercial settings. Norovirus concentrations were measured in oyster digestive tissue before, during and post-depuration using the ISO 15216-1 quantitative real-time RT-PCR method. Results of the laboratory-based studies demonstrate that statistically significant reductions of up to 74% of the initial norovirus GII concentration was achieved after 3 days at 17-21 °C and after 4 days at 11-15 °C, compared to 44% reduction at 7-9 °C. In many trials norovirus GII concentrations were reduced to levels below 100 genome copies per gram (gcg-1; limit of quantitation; LOQ). Virus reduction was also assessed in commercial depuration systems, routinely used by two Irish oyster producers. Up to 68% reduction was recorded for norovirus GI and up to 90% for norovirus GII reducing the geometric mean virus concentration close to or below the LOQ. In both commercial settings there was a significant difference between the levels of reduction of norovirus GI compared to GII (p < 0.05). Additionally, the ability to reduce the norovirus concentration in oysters to < LOQ differed when contaminated with concentrations below and above 1000 gcg-1. These results indicate that depuration, carried out at elevated (> 11 °C) water temperatures for at least 3 days, can reduce the concentration of norovirus in oysters and therefore consumer exposure providing a practical risk management tool for the shellfish industry.
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Affiliation(s)
| | | | | | - James Fahy
- Marine Institute, Rinville, Oranmore, Ireland
| | | | | | - Kevin Hunt
- Centre for Food Safety, University College Dublin, Dublin, Ireland
| | - Francis Butler
- Centre for Food Safety, University College Dublin, Dublin, Ireland
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11
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Butler F, Luijckx NL, Marvin HJP, Bouzembrak Y, Mojtahed V. Role of analytical testing for food fraud risk mitigation - A commentary on implementation of analytical fraud testing: Role of analytical testing for food fraud mitigation. Curr Res Food Sci 2021; 4:301-307. [PMID: 33997797 PMCID: PMC8105182 DOI: 10.1016/j.crfs.2021.03.013] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Revised: 03/30/2021] [Accepted: 03/30/2021] [Indexed: 11/05/2022] Open
Abstract
Food fraud is of high concern to the food industry. A multitude of analytical technologies exist to detect fraud. However, this testing is often expensive. Available databases detailing fraud occurrences were systematically examined to determine how frequently analytical testing triggered fraud detection. A conceptual framework was developed for deciding when to implement analytical testing programmes for fraud and a framework to consider the economic costs of fraud and the benefits of its early detection. Factors associated with statistical sampling for fraud detection were considered. Choice of sampling location on the overall food-chain may influence the likelihood of fraud detection. A conceptual framework was developed for deciding when to implement analytical testing programmes for fraud. A conceptual framework for the economic impact damage of food fraud is presented. Sampling for fraudulent activity poses several unique challenges compared to other food safety related sampling activities.
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Affiliation(s)
- Francis Butler
- UCD School of Biosystems and Food Engineering, University College Dublin, Belfield, Dublin 4, Ireland
| | | | - Hans J P Marvin
- Wageningen Food Safety Research, P.O. Box 230, 6700, AE, Wageningen, the Netherlands
| | - Yamine Bouzembrak
- Wageningen Food Safety Research, P.O. Box 230, 6700, AE, Wageningen, the Netherlands
| | - Vahid Mojtahed
- Institute for Global Food Security, Queen's University Belfast, University Road, Belfast, BT7 1NN, UK
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12
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Pennone V, Barron UG, Hunt K, Cadavez V, McAuliffe O, Butler F. Omnibus Modeling of Listeria monocytogenes Growth Rates at Low Temperatures. Foods 2021; 10:foods10051099. [PMID: 34063480 PMCID: PMC8156314 DOI: 10.3390/foods10051099] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Revised: 04/13/2021] [Accepted: 05/12/2021] [Indexed: 11/23/2022] Open
Abstract
Listeria monocytogenes is a pathogen of considerable public health importance with a high case fatality. L. monocytogenes can grow at refrigeration temperatures and is of particular concern for ready-to-eat foods that require refrigeration. There is substantial interest in conducting and modeling shelf-life studies on L. monocytogenes, especially relating to storage temperature. Growth model parameters are generally estimated from constant-temperature growth experiments. Traditionally, first-order and second-order modeling (or primary and secondary) of growth data has been done sequentially. However, omnibus modeling, using a mixed-effects nonlinear regression approach, can model a full dataset covering all experimental conditions in one step. This study compared omnibus modeling to conventional sequential first-order/second-order modeling of growth data for five strains of L. monocytogenes. The omnibus model coupled a Huang primary model for growth with secondary models for growth rate and lag phase duration. First-order modeling indicated there were small significant differences in growth rate depending on the strain at all temperatures. Omnibus modeling indicated smaller differences. Overall, there was broad agreement between the estimates of growth rate obtained by the first-order and omnibus modeling. Through an appropriate choice of fixed and random effects incorporated in the omnibus model, potential errors in a dataset from one environmental condition can be identified and explored.
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Affiliation(s)
- Vincenzo Pennone
- Teagasc Food Research Centre, Moorepark, Fermoy, P61 C996 Co Cork, Ireland; (V.P.); (O.M.)
| | - Ursula-Gonzales Barron
- Centro de Investigação de Montanha (CIMO), Instituto Politécnico de Bragança, Campus de Santa Apolónia, 5300-253 Bragança, Portugal; (U.G.-B.); (V.C.)
| | - Kevin Hunt
- UCD School of Biosystems and Food Engineering, University College Dublin, Belfield, Dublin 4, Ireland;
| | - Vasco Cadavez
- Centro de Investigação de Montanha (CIMO), Instituto Politécnico de Bragança, Campus de Santa Apolónia, 5300-253 Bragança, Portugal; (U.G.-B.); (V.C.)
| | - Olivia McAuliffe
- Teagasc Food Research Centre, Moorepark, Fermoy, P61 C996 Co Cork, Ireland; (V.P.); (O.M.)
| | - Francis Butler
- UCD School of Biosystems and Food Engineering, University College Dublin, Belfield, Dublin 4, Ireland;
- Correspondence:
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13
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McEvoy D, McAloon C, Collins A, Hunt K, Butler F, Byrne A, Casey-Bryars M, Barber A, Griffin J, Lane EA, Wall P, More SJ. Relative infectiousness of asymptomatic SARS-CoV-2 infected persons compared with symptomatic individuals: a rapid scoping review. BMJ Open 2021; 11:e042354. [PMID: 33947725 PMCID: PMC8098293 DOI: 10.1136/bmjopen-2020-042354] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Revised: 04/01/2021] [Accepted: 04/21/2021] [Indexed: 11/17/2022] Open
Abstract
OBJECTIVES The aim of this study was to determine the relative infectiousness of asymptomatic SARS-CoV-2 infected persons compared with symptomatic individuals based on a scoping review of available literature. DESIGN Rapid scoping review of peer-reviewed literature from 1 January to 5 December 2020 using the LitCovid database and the Cochrane library. SETTING International studies on the infectiousness of individuals infected with SARS-CoV-2. PARTICIPANTS Studies were selected for inclusion if they defined asymptomatics as a separate cohort distinct from presymptomatics and if they provided a quantitative measure of the infectiousness of asymptomatics relative to symptomatics. PRIMARY OUTCOME MEASURES PCR result (PCR studies), the rate of infection (mathematical modelling studies) and secondary attack rate (contact tracing studies) - in each case from asymptomatic in comparison with symptomatic individuals. RESULTS There are only a limited number of published studies that report estimates of relative infectiousness of asymptomatic compared with symptomatic individuals. 12 studies were included after the screening process. Significant differences exist in the definition of infectiousness. PCR studies in general show no difference in shedding levels between symptomatic and asymptomatic individuals; however, the number of study subjects is generally limited. Two modelling studies estimate relative infectiousness to be 0.43 and 0.57, but both of these were more reflective of the infectiousness of undocumented rather than asymptomatic cases. The results from contact tracing studies include estimates of relative infectiousness of 0, but with insufficient evidence to conclude that it is significantly different from 1. CONCLUSIONS There is considerable heterogeneity in estimates of relative infectiousness highlighting the need for further investigation of this important parameter. It is not possible to provide any conclusive estimate of relative infectiousness, as the estimates from the reviewed studies varied between 0 and 1.
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Affiliation(s)
- David McEvoy
- Department of Population Health and Health Services, Royal College of Surgeons in Ireland Division of Population Health Sciences, Dublin, Ireland
| | - Conor McAloon
- School of Veterinary Medicine, UCD School of Agriculture Food Science and Veterinary Medicine, Dublin, Ireland
| | - Aine Collins
- Centre for Veterinary Epidemiology and Risk Analysis, University College Dublin, Dublin, Ireland
| | - Kevin Hunt
- Centre for Food Safety, University College Dublin, Dublin, Ireland
| | - Francis Butler
- Centre for Food Safety, University College Dublin, Dublin, Ireland
| | - Andrew Byrne
- One Health Scientific Support Unit, Government of Ireland Department of Agriculture Food and the Marine, Dublin, Ireland
| | - Miriam Casey-Bryars
- Centre for Veterinary Epidemiology and Risk Analysis, University College Dublin, Dublin, Ireland
| | - Ann Barber
- Centre for Veterinary Epidemiology and Risk Analysis, University College Dublin, Dublin, Ireland
| | - John Griffin
- Centre for Veterinary Epidemiology and Risk Analysis, University College Dublin, Dublin, Ireland
| | - Elizabeth Ann Lane
- Centre for Veterinary Epidemiology and Risk Analysis, University College Dublin, Dublin, Ireland
- Department of Agriculture Food and the Marine, Government of Ireland, Dublin, Ireland
| | - Patrick Wall
- School of Public Health, Physiotherapy and Sports Science, University College Dublin, Dublin, Ireland
| | - Simon John More
- Centre for Veterinary Epidemiology and Risk Analysis, University College Dublin, Dublin, Ireland
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14
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McAloon CG, Wall P, Griffin J, Casey M, Barber A, Codd M, Gormley E, Butler F, McV Messam LL, Walsh C, Teljeur C, Smyth B, Nolan P, Green MJ, O'Grady L, Culhane K, Buckley C, Carroll C, Doyle S, Martin J, More SJ. Estimation of the serial interval and proportion of pre-symptomatic transmission events of COVID- 19 in Ireland using contact tracing data. BMC Public Health 2021; 21:805. [PMID: 33906635 PMCID: PMC8076671 DOI: 10.1186/s12889-021-10868-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Accepted: 04/16/2021] [Indexed: 12/02/2022] Open
Abstract
BACKGROUND The serial interval is the period of time between the onset of symptoms in an infector and an infectee and is an important parameter which can impact on the estimation of the reproduction number. Whilst several parameters influencing infection transmission are expected to be consistent across populations, the serial interval can vary across and within populations over time. Therefore, local estimates are preferable for use in epidemiological models developed at a regional level. We used data collected as part of the national contact tracing process in Ireland to estimate the serial interval of SARS-CoV-2 infection in the Irish population, and to estimate the proportion of transmission events that occurred prior to the onset of symptoms. RESULTS After data cleaning, the final dataset consisted of 471 infected close contacts from 471 primary cases. The median serial interval was 4 days, mean serial interval was 4.0 (95% confidence intervals 3.7, 4.3) days, whilst the 25th and 75th percentiles were 2 and 6 days respectively. We found that intervals were lower when the primary or secondary case were in the older age cohort (greater than 64 years). Simulating from an incubation period distribution from international literature, we estimated that 67% of transmission events had greater than 50% probability of occurring prior to the onset of symptoms in the infector. CONCLUSIONS Whilst our analysis was based on a large sample size, data were collected for the primary purpose of interrupting transmission chains. Similar to other studies estimating the serial interval, our analysis is restricted to transmission pairs where the infector is known with some degree of certainty. Such pairs may represent more intense contacts with infected individuals than might occur in the overall population. It is therefore possible that our analysis is biased towards shorter serial intervals than the overall population.
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Affiliation(s)
- Conor G McAloon
- School of Veterinary Medicine, University College Dublin, Belfield, Dublin 4, Ireland.
| | - Patrick Wall
- School of Public Health, Physiotherapy and Sports Science, University College Dublin, Belfield, Dublin 4, Ireland
| | - John Griffin
- Centre for Veterinary Epidemiology and Risk Analysis, School of Veterinary Medicine, University College Dublin, Belfield, Dublin, Ireland
| | - Miriam Casey
- Centre for Veterinary Epidemiology and Risk Analysis, School of Veterinary Medicine, University College Dublin, Belfield, Dublin, Ireland
| | - Ann Barber
- Centre for Veterinary Epidemiology and Risk Analysis, School of Veterinary Medicine, University College Dublin, Belfield, Dublin, Ireland
| | - Mary Codd
- School of Public Health, Physiotherapy and Sports Science, University College Dublin, Belfield, Dublin 4, Ireland
| | - Eamonn Gormley
- School of Veterinary Medicine, University College Dublin, Belfield, Dublin 4, Ireland
| | - Francis Butler
- School of Biosystems and Food Engineering, University College Dublin, Belfield, Dublin 4, Ireland
| | - Locksley L McV Messam
- School of Veterinary Medicine, University College Dublin, Belfield, Dublin 4, Ireland
| | - Cathal Walsh
- Department of Mathematics and Statistics, University of Limerick, Limerick, Ireland
| | - Conor Teljeur
- Health Information and Quality Authority, George's Court, Dublin 7, Ireland
| | - Breda Smyth
- Department of Public Health, Health Service Executive West, Galway, Ireland
| | - Philip Nolan
- National University of Ireland Maynooth, Kildare, Ireland
| | - Martin J Green
- School of Veterinary Medicine and Science, University of Nottingham, Nottingham, UK
| | - Luke O'Grady
- School of Veterinary Medicine, University College Dublin, Belfield, Dublin 4, Ireland
- School of Veterinary Medicine and Science, University of Nottingham, Nottingham, UK
| | - Kieran Culhane
- Central Statistics Office, Ardee Road, Rathmines, Dublin, Ireland
| | - Claire Buckley
- COVID-19 Contact Management Programme, Health Service Executive, Dublin, Ireland
- School of Public Health, University College Cork, Cork, Ireland
| | - Ciara Carroll
- COVID-19 Contact Management Programme, Health Service Executive, Dublin, Ireland
| | - Sarah Doyle
- COVID-19 Contact Management Programme, Health Service Executive, Dublin, Ireland
| | - Jennifer Martin
- COVID-19 Contact Management Programme, Health Service Executive, Dublin, Ireland
| | - Simon J More
- School of Veterinary Medicine, University College Dublin, Belfield, Dublin 4, Ireland
- Centre for Veterinary Epidemiology and Risk Analysis, School of Veterinary Medicine, University College Dublin, Belfield, Dublin, Ireland
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15
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Hunt K, Doré B, Keaveney S, Rupnik A, Butler F. Estimating the distribution of norovirus in individual oysters. Int J Food Microbiol 2020; 333:108785. [DOI: 10.1016/j.ijfoodmicro.2020.108785] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2020] [Revised: 07/01/2020] [Accepted: 07/02/2020] [Indexed: 12/18/2022]
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16
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McAloon C, Collins Á, Hunt K, Barber A, Byrne AW, Butler F, Casey M, Griffin J, Lane E, McEvoy D, Wall P, Green M, O'Grady L, More SJ. Incubation period of COVID-19: a rapid systematic review and meta-analysis of observational research. BMJ Open 2020; 10:e039652. [PMID: 32801208 PMCID: PMC7430485 DOI: 10.1136/bmjopen-2020-039652] [Citation(s) in RCA: 280] [Impact Index Per Article: 70.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/22/2020] [Revised: 07/06/2020] [Accepted: 07/23/2020] [Indexed: 12/25/2022] Open
Abstract
OBJECTIVES The aim of this study was to conduct a rapid systematic review and meta-analysis of estimates of the incubation period of COVID-19. DESIGN Rapid systematic review and meta-analysis of observational research. SETTING International studies on incubation period of COVID-19. PARTICIPANTS Searches were carried out in PubMed, Google Scholar, Embase, Cochrane Library as well as the preprint servers MedRxiv and BioRxiv. Studies were selected for meta-analysis if they reported either the parameters and CIs of the distributions fit to the data, or sufficient information to facilitate calculation of those values. After initial eligibility screening, 24 studies were selected for initial review, nine of these were shortlisted for meta-analysis. Final estimates are from meta-analysis of eight studies. PRIMARY OUTCOME MEASURES Parameters of a lognormal distribution of incubation periods. RESULTS The incubation period distribution may be modelled with a lognormal distribution with pooled mu and sigma parameters (95% CIs) of 1.63 (95% CI 1.51 to 1.75) and 0.50 (95% CI 0.46 to 0.55), respectively. The corresponding mean (95% CIs) was 5.8 (95% CI 5.0 to 6.7) days. It should be noted that uncertainty increases towards the tail of the distribution: the pooled parameter estimates (95% CIs) resulted in a median incubation period of 5.1 (95% CI 4.5 to 5.8) days, whereas the 95th percentile was 11.7 (95% CI 9.7 to 14.2) days. CONCLUSIONS The choice of which parameter values are adopted will depend on how the information is used, the associated risks and the perceived consequences of decisions to be taken. These recommendations will need to be revisited once further relevant information becomes available. Accordingly, we present an R Shiny app that facilitates updating these estimates as new data become available.
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Affiliation(s)
- Conor McAloon
- Section of Herd Health and Animal Husbandry, School of Veterinary Medicine, University College Dublin, Dublin, Ireland
| | - Áine Collins
- Centre for Veterinary Epidemiology and Risk Analysis, School of Veterinary Medicine, University College Dublin, Dublin, Ireland
| | - Kevin Hunt
- Centre for Food Safety, School of Biosystems and Food Engineering, University College Dublin, Dublin, Ireland
| | - Ann Barber
- Centre for Veterinary Epidemiology and Risk Analysis, School of Veterinary Medicine, University College Dublin, Dublin, Ireland
| | - Andrew W Byrne
- One Health Scientific Support Unit, Department of Agriculture, Food and the Marine, Dublin, Ireland
| | - Francis Butler
- Centre for Food Safety, School of Biosystems and Food Engineering, University College Dublin, Dublin, Ireland
| | - Miriam Casey
- Centre for Veterinary Epidemiology and Risk Analysis, School of Veterinary Medicine, University College Dublin, Dublin, Ireland
| | | | - Elizabeth Lane
- Backweston Campus, Department of Agriculture, Food and the Marine, Celbridge, Ireland
| | - David McEvoy
- School of Public Health, Physiotherapy and Sports Science, University College Dublin, Dublin, Ireland
| | - Patrick Wall
- School of Public Health, Physiotherapy and Sports Science, University College Dublin, Dublin, Ireland
| | - Martin Green
- School of Veterinary Medicine and Science, University of Nottingham, Nottingham, UK
| | - Luke O'Grady
- Section of Herd Health and Animal Husbandry, School of Veterinary Medicine, University College Dublin, Dublin, Ireland
- School of Veterinary Medicine and Science, University of Nottingham, Nottingham, UK
| | - Simon J More
- Centre for Veterinary Epidemiology and Risk Analysis, School of Veterinary Medicine, University College Dublin, Dublin, Ireland
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17
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Byrne AW, McEvoy D, Collins AB, Hunt K, Casey M, Barber A, Butler F, Griffin J, Lane EA, McAloon C, O'Brien K, Wall P, Walsh KA, More SJ. Inferred duration of infectious period of SARS-CoV-2: rapid scoping review and analysis of available evidence for asymptomatic and symptomatic COVID-19 cases. BMJ Open 2020; 10:e039856. [PMID: 32759252 DOI: 10.1101/2020.04.25.20079889] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 05/26/2023] Open
Abstract
OBJECTIVES Our objective was to review the literature on the inferred duration of the infectious period of COVID-19, caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) virus, and provide an overview of the variation depending on the methodological approach. DESIGN Rapid scoping review. Literature review with fixed search terms, up to 1 April 2020. Central tendency and variation of the parameter estimates for infectious period in (A) asymptomatic and (B) symptomatic cases from (1) virological studies (repeated testing), (2) tracing studies and (3) modelling studies were gathered. Narrative review of viral dynamics. INFORMATION SOURCES Search strategies developed and the following searched: PubMed, Google Scholar, MedRxiv and BioRxiv. Additionally, the Health Information Quality Authority (Ireland) viral load synthesis was used, which screened literature from PubMed, Embase, ScienceDirect, NHS evidence, Cochrane, medRxiv and bioRxiv, and HRB open databases. RESULTS There was substantial variation in the estimates, and how infectious period was inferred. One study provided approximate median infectious period for asymptomatic cases of 6.5-9.5 days. Median presymptomatic infectious period across studies varied over <1-4 days. Estimated mean time from symptom onset to two negative RT-PCR tests was 13.4 days (95% CI 10.9 to 15.8) but was shorter when studies included children or less severe cases. Estimated mean duration from symptom onset to hospital discharge or death (potential maximal infectious period) was 18.1 days (95% CI 15.1 to 21.0); time to discharge was on average 4 days shorter than time to death. Viral dynamic data and model infectious parameters were often shorter than repeated diagnostic data. CONCLUSIONS There are limitations of inferring infectiousness from repeated diagnosis, viral loads and viral replication data alone and also potential patient recall bias relevant to estimating exposure and symptom onset times. Despite this, available data provide a preliminary evidence base to inform models of central tendency for key parameters and variation for exploring parameter space and sensitivity analysis.
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Affiliation(s)
- Andrew William Byrne
- One-Health Scientific Support Unit, Government of Ireland Department of Agriculture Food and the Marine, Dublin, Ireland
| | - David McEvoy
- School of Public Health, Physiotherapy and Sports Science, University College Dublin, Dublin, Ireland
| | - Aine B Collins
- Centre for Veterinary Epidemiology and Risk Analysis, School of Veterinary Medicine, University College Dublin, Dublin, Ireland
- Government of Ireland Department of Agriculture Food and the Marine, Dublin, Ireland
| | - Kevin Hunt
- Centre for Food Safety, School of Biosystems and Food Engineering, University College Dublin, Dublin, Ireland
| | - Miriam Casey
- Centre for Veterinary Epidemiology and Risk Analysis, School of Veterinary Medicine, University College Dublin, Dublin, Ireland
| | - Ann Barber
- Centre for Veterinary Epidemiology and Risk Analysis, School of Veterinary Medicine, University College Dublin, Dublin, Ireland
| | - Francis Butler
- Centre for Food Safety, School of Biosystems and Food Engineering, University College Dublin, Dublin, Ireland
| | - John Griffin
- Government of Ireland Department of Agriculture Food and the Marine, Dublin, Ireland
| | - Elizabeth A Lane
- Centre for Veterinary Epidemiology and Risk Analysis, School of Veterinary Medicine, University College Dublin, Dublin, Ireland
- Government of Ireland Department of Agriculture Food and the Marine, Dublin, Ireland
| | - Conor McAloon
- School of Veterinary Medicine, University College Dublin, Dublin, Ireland
| | - Kirsty O'Brien
- Health Information and Quality Authority, Cork, Munster, Ireland
| | - Patrick Wall
- Department of Public Health, School of Public Health, Physiotherapy and Sports Science, University College Dublin, Dublin, Ireland
| | - Kieran A Walsh
- Health Information and Quality Authority, Cork, Munster, Ireland
| | - Simon J More
- Centre for Veterinary Epidemiology and Risk Analysis, School of Veterinary Medicine, University College Dublin, Dublin, Ireland
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18
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Byrne AW, McEvoy D, Collins AB, Hunt K, Casey M, Barber A, Butler F, Griffin J, Lane EA, McAloon C, O'Brien K, Wall P, Walsh KA, More SJ. Inferred duration of infectious period of SARS-CoV-2: rapid scoping review and analysis of available evidence for asymptomatic and symptomatic COVID-19 cases. BMJ Open 2020; 10:e039856. [PMID: 32759252 PMCID: PMC7409948 DOI: 10.1136/bmjopen-2020-039856] [Citation(s) in RCA: 199] [Impact Index Per Article: 49.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Revised: 07/06/2020] [Accepted: 07/10/2020] [Indexed: 12/13/2022] Open
Abstract
OBJECTIVES Our objective was to review the literature on the inferred duration of the infectious period of COVID-19, caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) virus, and provide an overview of the variation depending on the methodological approach. DESIGN Rapid scoping review. Literature review with fixed search terms, up to 1 April 2020. Central tendency and variation of the parameter estimates for infectious period in (A) asymptomatic and (B) symptomatic cases from (1) virological studies (repeated testing), (2) tracing studies and (3) modelling studies were gathered. Narrative review of viral dynamics. INFORMATION SOURCES Search strategies developed and the following searched: PubMed, Google Scholar, MedRxiv and BioRxiv. Additionally, the Health Information Quality Authority (Ireland) viral load synthesis was used, which screened literature from PubMed, Embase, ScienceDirect, NHS evidence, Cochrane, medRxiv and bioRxiv, and HRB open databases. RESULTS There was substantial variation in the estimates, and how infectious period was inferred. One study provided approximate median infectious period for asymptomatic cases of 6.5-9.5 days. Median presymptomatic infectious period across studies varied over <1-4 days. Estimated mean time from symptom onset to two negative RT-PCR tests was 13.4 days (95% CI 10.9 to 15.8) but was shorter when studies included children or less severe cases. Estimated mean duration from symptom onset to hospital discharge or death (potential maximal infectious period) was 18.1 days (95% CI 15.1 to 21.0); time to discharge was on average 4 days shorter than time to death. Viral dynamic data and model infectious parameters were often shorter than repeated diagnostic data. CONCLUSIONS There are limitations of inferring infectiousness from repeated diagnosis, viral loads and viral replication data alone and also potential patient recall bias relevant to estimating exposure and symptom onset times. Despite this, available data provide a preliminary evidence base to inform models of central tendency for key parameters and variation for exploring parameter space and sensitivity analysis.
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Affiliation(s)
- Andrew William Byrne
- One-Health Scientific Support Unit, Government of Ireland Department of Agriculture Food and the Marine, Dublin, Ireland
| | - David McEvoy
- School of Public Health, Physiotherapy and Sports Science, University College Dublin, Dublin, Ireland
| | - Aine B Collins
- Centre for Veterinary Epidemiology and Risk Analysis, School of Veterinary Medicine, University College Dublin, Dublin, Ireland
- Government of Ireland Department of Agriculture Food and the Marine, Dublin, Ireland
| | - Kevin Hunt
- Centre for Food Safety, School of Biosystems and Food Engineering, University College Dublin, Dublin, Ireland
| | - Miriam Casey
- Centre for Veterinary Epidemiology and Risk Analysis, School of Veterinary Medicine, University College Dublin, Dublin, Ireland
| | - Ann Barber
- Centre for Veterinary Epidemiology and Risk Analysis, School of Veterinary Medicine, University College Dublin, Dublin, Ireland
| | - Francis Butler
- Centre for Food Safety, School of Biosystems and Food Engineering, University College Dublin, Dublin, Ireland
| | - John Griffin
- Government of Ireland Department of Agriculture Food and the Marine, Dublin, Ireland
| | - Elizabeth A Lane
- Centre for Veterinary Epidemiology and Risk Analysis, School of Veterinary Medicine, University College Dublin, Dublin, Ireland
- Government of Ireland Department of Agriculture Food and the Marine, Dublin, Ireland
| | - Conor McAloon
- School of Veterinary Medicine, University College Dublin, Dublin, Ireland
| | - Kirsty O'Brien
- Health Information and Quality Authority, Cork, Munster, Ireland
| | - Patrick Wall
- Department of Public Health, School of Public Health, Physiotherapy and Sports Science, University College Dublin, Dublin, Ireland
| | - Kieran A Walsh
- Health Information and Quality Authority, Cork, Munster, Ireland
| | - Simon J More
- Centre for Veterinary Epidemiology and Risk Analysis, School of Veterinary Medicine, University College Dublin, Dublin, Ireland
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Li F, Hunt K, Buggy AK, Murphy KM, Ho QT, O'Callaghan TF, Butler F, Jordan K, Tobin JT. The effects of sequential heat treatment on microbial reduction and spore inactivation during milk processing. Int Dairy J 2020. [DOI: 10.1016/j.idairyj.2020.104648] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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21
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Alvarez‐Ordóñez A, Leong D, Hunt K, Scollard J, Butler F, Jordan K. Production of safer food by understanding risk factors for
L. monocytogenes
occurrence and persistence in food processing environments. J Food Saf 2018. [DOI: 10.1111/jfs.12516] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Affiliation(s)
| | - Dara Leong
- Moorepark Teagasc Food Research Centre Fermoy Ireland
| | - Karen Hunt
- Moorepark Teagasc Food Research Centre Fermoy Ireland
| | | | - Francis Butler
- UCD Centre for Food SafetySchool of Biosystems and Food Engineering, University College Dublin Ireland
| | - Kieran Jordan
- Moorepark Teagasc Food Research Centre Fermoy Ireland
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22
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Rupnik A, Keaveney S, Devilly L, Butler F, Doré W. The Impact of Winter Relocation and Depuration on Norovirus Concentrations in Pacific Oysters Harvested from a Commercial Production Site. Food Environ Virol 2018; 10:288-296. [PMID: 29725931 PMCID: PMC6096948 DOI: 10.1007/s12560-018-9345-5] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2018] [Accepted: 04/19/2018] [Indexed: 05/15/2023]
Abstract
Oysters contaminated with norovirus present a significant public health risk when consumed raw. In this study, norovirus genome copy concentrations were determined in Pacific oysters (Magallana gigas) harvested from a sewage-impacted production site and then subjected to site-specific management procedures. These procedures consisted of relocation of oysters to an alternative production area during the norovirus high-risk winter periods (November to March) followed by an extended depuration (self-purification) under controlled temperature conditions. Significant differences in norovirus RNA concentrations were demonstrated at each point in the management process. Thirty-one percent of oyster samples from the main harvest area (Site 1) contained norovirus concentrations > 500 genome copies/g and 29% contained norovirus concentrations < 100 genome copies/g. By contrast, no oyster sample from the alternative harvest area (Site 2) or following depuration contained norovirus concentrations > 500 genome copies/g. In addition, 60 and 88% of oysters samples contained norovirus concentrations < 100 genome copies/g in oysters sampled from Site 2 and following depuration, respectively. These data demonstrate that site-specific management processes, supported by norovirus monitoring, can be an effective strategy to reduce, but not eliminate, consumer exposure to norovirus genome copies.
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Affiliation(s)
| | | | | | - Francis Butler
- Centre for Food Safety, University College Dublin, Dublin, Ireland
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Abstract
Despite the ever increase in rigorous control and monitoring measures to assure safe food along the entire farm‐to‐fork chain, the past decade has also witnessed an increase in microbial food alerts. Hence, research on food safety and quality remain of utmost importance. Complementary, and at least as important, is the necessity to be able to assess the potential microbial risks along the food chain. Risk assessment relies on sound scientific data. Unfortunately, often, quality data are limited if not lacking. High‐throughput tools such as next‐generation sequencing (NGS) could fill this gap. NGS approaches can be used to generate ample qualitative and quantitative data to be used in the risk assessment process. NGS applications are not new in food microbiology with applications ranging from pathogen detection along the food chain, food epidemiology studies, whole genome analysis of food‐associated microorganisms up to describing complete food microbiomes. Yet, its application in the area of microbial risk assessment is still at an early stage and faces important challenges. The possibilities of NGS for risk assessment are ample, but so are the questions on the subject. One of the major strengths of NGS lies in its capacity to generate a lot of data, but to what extend can this wealth be of use in hazard identification, hazard characterisation and exposure assessment to perform a sound risk characterisation, which in turn will make it possible to take substantiated risk management decisions.
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Peters G, Cleveland B, Higgins J, Butler F, Meghen C. A Genetic Method To Evaluate the Prevalence of Unique DNA Profiles between Sequential Ground Beef Batches. J Food Prot 2017; 80:425-430. [PMID: 28199149 DOI: 10.4315/0362-028x.jfp-16-221] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
The delineation of ground beef batches has implications for the management of product disposition policies in the event of Shiga toxin-producing Escherichia coli contamination. Analysis of individual contributor animal-specific DNA profiles can provide valuable empirical data for understanding the dynamics of ground meat production processes and can act as a surrogate for cross-contamination. A genetic method was developed for characterizing the source raw material flow and carryover between discrete batches of ground beef in a large-scale commercial beef grinding operation. The application developed involves the introduction of a genetically distinct source raw material batch into the grinding system and comprehensive sampling of that index batch and subsequent batches followed by single nucleotide polymorphism genotyping of random subsamples. Capture-mark-recapture statistical techniques were used to estimate (i) the number of carcass contributors and (ii) the associated level of carryover between batches. Carryover, expressed as a percentage of the total weight of the batch material (in pounds), was observed between the genetically distinct index batch and the next sequential batch at approximately 1%. The nondetection of additional carryover to subsequent batches, with a detection level of approximately 0.2%, supports a serial dilution model of same source raw material carryover, consistent with the recorded weight of beef trimmings used in each batch. For ground beef manufacturers, this method is a simple approach for validating the independence of finished batches of beef in their grind systems in support of product disposition policies.
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Affiliation(s)
- G Peters
- IdentiGEN North America Inc., 2029 Becker Drive, Lawrence, Kansas 66047, USA (ORCID: http://orcid.org/0000-0003-3640-9898 [B.C.])
| | - B Cleveland
- IdentiGEN North America Inc., 2029 Becker Drive, Lawrence, Kansas 66047, USA (ORCID: http://orcid.org/0000-0003-3640-9898 [B.C.])
| | - J Higgins
- IdentiGEN Ltd., Blackrock Office Park, Carysfort Avenue, Blackrock, County Dublin, Ireland
| | - F Butler
- School of Biosystems and Food Engineering, University College Dublin, Dublin, Ireland
| | - C Meghen
- IdentiGEN Ltd., Blackrock Office Park, Carysfort Avenue, Blackrock, County Dublin, Ireland
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Cadavez V, Gonzales-Barron U, Pires P, Fernandes E, Pereira A, Gomes A, Araújo J, Lopes-da-Silva F, Rodrigues P, Fernandes C, Saavedra M, Butler F, Dias T. An assessment of the processing and physicochemical factors contributing to the microbial contamination of salpicão, a naturally-fermented Portuguese sausage. Lebensm Wiss Technol 2016. [DOI: 10.1016/j.lwt.2016.04.038] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
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26
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Danaher M, Shanahan C, Butler F, Evans R, O’Sullivan D, Glynn D, Camon T, Lawlor P, O’Keeffe M. Risk-based approach to developing a national residue sampling plan for testing under European Union regulation for veterinary medicinal products and coccidiostat feed additives in domestic animal production. Food Addit Contam Part A Chem Anal Control Expo Risk Assess 2016; 33:1155-65. [DOI: 10.1080/19440049.2016.1190236] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Affiliation(s)
- Martin Danaher
- Food Safety Department, Teagasc Food Research Centre, Dublin, Ireland
| | - Conor Shanahan
- UCD School of Biosystems and Food Engineering, University College Dublin, Dublin, Ireland
| | - Francis Butler
- UCD School of Biosystems and Food Engineering, University College Dublin, Dublin, Ireland
| | - Rhodri Evans
- Food Science and Standards Division, Food Safety Authority of Ireland, Dublin, Ireland
| | - Dan O’Sullivan
- Department of Agriculture, Food and the Marine, Celbridge, Ireland
| | - Denise Glynn
- Marine Environment and Food Safety Services, Marine Institute, Oranmore, Ireland
| | - Tim Camon
- Food Science and Standards Division, Food Safety Authority of Ireland, Dublin, Ireland
| | - Peadar Lawlor
- Teagasc, Pig Development Department, Animal and Grassland Research and Innovation Centre, Fermoy, Ireland
| | - Michael O’Keeffe
- Food Science and Standards Division, Food Safety Authority of Ireland, Dublin, Ireland
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Mousavi ZE, Condell O, Fanning S, Butler F. Quaternary Ammonium Compounds (QACs) induced inactivation of Pseudomonas spp.: Effect of material surface. Food and Bioproducts Processing 2016. [DOI: 10.1016/j.fbp.2015.12.009] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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Gonzales-Barron U, Cadavez V, Pereira A, Gomes A, Araújo J, Saavedra M, Estevinho L, Butler F, Pires P, Dias T. Relating physicochemical and microbiological safety indicators during processing of linguiça , a Portuguese traditional dry-fermented sausage. Food Res Int 2015; 78:50-61. [DOI: 10.1016/j.foodres.2015.11.007] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2015] [Revised: 11/03/2015] [Accepted: 11/04/2015] [Indexed: 12/28/2022]
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Mousavi ZE, Kennedy E, Fanning S, Rice JH, Butler F. The effect of Quaternary Ammonium Compounds on the attachment of wild and adapted Pseudomonas putida strains to different contact materials used in the food sector. Food Control 2014. [DOI: 10.1016/j.foodcont.2014.02.018] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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31
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Schvartzman MS, Gonzalez-Barron U, Butler F, Jordan K. Modeling the growth of Listeria monocytogenes on the surface of smear- or mold-ripened cheese. Front Cell Infect Microbiol 2014; 4:90. [PMID: 25072033 PMCID: PMC4079949 DOI: 10.3389/fcimb.2014.00090] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2013] [Accepted: 06/12/2014] [Indexed: 11/13/2022] Open
Abstract
Surface-ripened cheeses are matured by means of manual or mechanical technologies posing a risk of cross-contamination, if any cheeses are contaminated with Listeria monocytogenes. In predictive microbiology, primary models are used to describe microbial responses, such as growth rate over time and secondary models explain how those responses change with environmental factors. In this way, primary models were used to assess the growth rate of L. monocytogenes during ripening of the cheeses and the secondary models to test how much the growth rate was affected by either the pH and/or the water activity (aw) of the cheeses. The two models combined can be used to predict outcomes. The purpose of these experiments was to test three primary (the modified Gompertz equation, the Baranyi and Roberts model, and the Logistic model) and three secondary (the Cardinal model, the Ratowski model, and the Presser model) mathematical models in order to define which combination of models would best predict the growth of L. monocytogenes on the surface of artificially contaminated surface-ripened cheeses. Growth on the surface of the cheese was assessed and modeled. The primary models were firstly fitted to the data and the effects of pH and aw on the growth rate (μmax) were incorporated and assessed one by one with the secondary models. The Logistic primary model by itself did not show a better fit of the data among the other primary models tested, but the inclusion of the Cardinal secondary model improved the final fit. The aw was not related to the growth of Listeria. This study suggests that surface-ripened cheese should be separately regulated within EU microbiological food legislation and results expressed as counts per surface area rather than per gram.
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Affiliation(s)
- M. Sol Schvartzman
- Food Safety Department, Teagasc Food Research CentreMoorepark, Fermoy, Ireland
- Biosystems Engineering, School of Agriculture, Food Science and Veterinary Medicine, University College DublinDublin, Ireland
| | - Ursula Gonzalez-Barron
- Biosystems Engineering, School of Agriculture, Food Science and Veterinary Medicine, University College DublinDublin, Ireland
| | - Francis Butler
- Biosystems Engineering, School of Agriculture, Food Science and Veterinary Medicine, University College DublinDublin, Ireland
| | - Kieran Jordan
- Food Safety Department, Teagasc Food Research CentreMoorepark, Fermoy, Ireland
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Gonzales-Barron U, Cadavez V, Butler F. Conducting inferential statistics for low microbial counts in foods using the Poisson-gamma regression. Food Control 2014. [DOI: 10.1016/j.foodcont.2013.09.032] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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Gibbons JF, Boland F, Buckley JF, Butler F, Egan J, Fanning S, Markey BK, Leonard FC. Patterns of antimicrobial resistance in pathogenic Escherichia coli isolates from cases of calf enteritis during the spring-calving season. Vet Microbiol 2014; 170:73-80. [PMID: 24556339 DOI: 10.1016/j.vetmic.2014.01.010] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2013] [Revised: 12/04/2013] [Accepted: 01/15/2014] [Indexed: 11/27/2022]
Abstract
Neonatal enteritis is a common condition of young calves and can be caused by pathogenic strains of Escherichia coli. We hypothesised that on-farm antimicrobial use would result in an increased frequency of resistance in these strains during the calving season. We also sought to determine if the frequency of resistance reflected on-farm antimicrobial use. Faecal samples were collected from cases of calf enteritis on 14 spring-calving dairy farms during two 3 week periods: Period 1 - February 11th through March 2nd 2008 and Period 2 - April 14th through May 5th 2008. E. coli were cultured from these samples, pathogenic strains were identified and antimicrobial susceptibility testing was carried out on these pathogenic isolates. Antimicrobial prescribing data were collected from each farm for the previous 12 months as an indicator of antimicrobial use. The correlation between antimicrobial use and resistance was assessed using Spearman's correlation coefficient. Logistic regression analysis was used to investigate the relationship between resistance, sampling period and pathotype. Penicillins and aminopenicillins, streptomycin, and tetracyclines were the most frequently prescribed antimicrobials and the greatest frequencies of resistance were detected to these 3 antimicrobial classes. A strong correlation (ρ=0.879) was observed between overall antimicrobial use and frequencies of antimicrobial resistance on farms. Sampling period was significant in the regression model for ampicillin resistance while pathotype was significant in the models for streptomycin, tetracycline and trimethoprim/sulphamethoxazole resistance. The frequencies of resistance observed have implications for veterinary therapeutics and prudent antimicrobial use. Resistance did not increase during the calving season and factors other than antimicrobial use, such as calf age and bacterial pathotype, may influence the occurrence of resistance in pathogenic E. coli.
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Affiliation(s)
- James F Gibbons
- School of Veterinary Medicine, University College Dublin, Belfield, Dublin 4, Ireland.
| | - Fiona Boland
- School of Mathematical Sciences, University College Dublin, Belfield, Dublin 4, Ireland
| | - James F Buckley
- Veterinary Department, Cork County Council, County Hall, Cork, Ireland
| | - Francis Butler
- UCD Institute of Food and Health University College Dublin, Belfield, Dublin 4, Ireland
| | - John Egan
- Central Veterinary Research Laboratory, DAFF Laboratories, Backweston, Co. Kildare, Ireland
| | - Séamus Fanning
- UCD Institute of Food and Health University College Dublin, Belfield, Dublin 4, Ireland
| | - Bryan K Markey
- School of Veterinary Medicine, University College Dublin, Belfield, Dublin 4, Ireland
| | - Finola C Leonard
- School of Veterinary Medicine, University College Dublin, Belfield, Dublin 4, Ireland
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Mussida A, Gonzales-Barron U, Butler F. Effectiveness of sampling plans by attributes based on mixture distributions characterising microbial clustering in food. Food Control 2013. [DOI: 10.1016/j.foodcont.2013.04.001] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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35
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Mussida A, Vose D, Butler F. Efficiency of the sampling plan for Cronobacter spp. assuming a Poisson lognormal distribution of the bacteria in powder infant formula and the implications of assuming a fixed within and between-lot variability. Food Control 2013. [DOI: 10.1016/j.foodcont.2013.02.021] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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36
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Mousavi ZE, Fanning S, Butler F. Effect of surface properties of different food contact materials on the efficiency of quaternary ammonium compounds residue recovery and persistence. Int J Food Sci Technol 2013. [DOI: 10.1111/ijfs.12152] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Zeinab E. Mousavi
- School of Biosystems Engineering; Agriculture and Food Science Centre; University College Dublin; Belfield Dublin 4; Ireland
| | - Seamus Fanning
- School of Public Health, Physiotherapy & Population Science; University College Dublin; Belfield Dublin 4; Ireland
| | - Francis Butler
- School of Biosystems Engineering; Agriculture and Food Science Centre; University College Dublin; Belfield Dublin 4; Ireland
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37
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Juneja VK, Gonzales-Barron U, Butler F, Yadav AS, Friedman M. Predictive thermal inactivation model for the combined effect of temperature, cinnamaldehyde and carvacrol on starvation-stressed multiple Salmonella serotypes in ground chicken. Int J Food Microbiol 2013; 165:184-99. [PMID: 23756235 DOI: 10.1016/j.ijfoodmicro.2013.04.025] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2012] [Revised: 04/01/2013] [Accepted: 04/21/2013] [Indexed: 11/19/2022]
Abstract
We investigated the combined effect of three internal temperatures (60, 65 and 71.1 °C) and four concentrations (0.0, 0.1, 0.5 and 1% vol/wt) of two natural antimicrobials on the heat resistance of an eight-strain cocktail of Salmonella serovars in chicken meat. A complete factorial design (3×4×4) was used to assess the effects and interactions of heating temperature and the two antimicrobials, carvacrol and cinnamaldehyde. The 48 variable combinations were replicated to provide a total of 96 survivor curves from the experimental data. Mathematical models were then developed to quantify the combined effect of these parameters on heat resistance of starved Salmonella cells. The theoretical analysis shows that the addition of plant-derived antimicrobials overcomes the heat resistance of starvation-stressed Salmonella in ground chicken meat. The influence of the antimicrobials allows reduced heat treatments, thus reducing heat-induced damage to the nutritional quality of ground-chicken products. Although the reported omnibus log-linear model with tail and the omnibus sigmoid model could represent the experimental survivor curves, their discrepancy only became apparent in the present study when lethality times (D-values and t7.0) from each of the models were calculated. Given the concave nature of the inactivation curves, the log-linear model with tail greatly underestimates the times needed to obtain 7.0 log lethality. Thus, a polynomial secondary model, based on the sigmoid model, was developed to accurately predict the 7.0-log reduction times. The three-factor predictive model can be used to estimate the processing times and temperatures required to achieve specific log reductions, including the regulatory recommendation of 7.0-log reduction of Salmonella in ground chicken.
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Affiliation(s)
- Vijay K Juneja
- U.S. Department of Agriculture, Agricultural Research Service, Eastern Regional Research Center, 600 E. Mermaid Lane, Wyndmoor, PA 19038, USA.
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Gonzales-Barron U, Cadavez V, Sheridan JJ, Butler F. Modelling the effect of chilling on the occurrence of Salmonella on pig carcasses at study, abattoir and batch levels by meta-analysis. Int J Food Microbiol 2013; 163:101-13. [DOI: 10.1016/j.ijfoodmicro.2013.03.006] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2012] [Revised: 01/23/2013] [Accepted: 03/02/2013] [Indexed: 11/24/2022]
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39
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Gonzales-Barron U, Zwietering MH, Butler F. A novel derivation of a within-batch sampling plan based on a Poisson-gamma model characterising low microbial counts in foods. Int J Food Microbiol 2013; 161:84-96. [PMID: 23279817 DOI: 10.1016/j.ijfoodmicro.2012.11.026] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2012] [Revised: 11/19/2012] [Accepted: 11/21/2012] [Indexed: 10/27/2022]
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Gibbons JF, Boland F, Buckley JF, Butler F, Egan J, Fanning S, Markey BK, Leonard FC. Influences on antimicrobial prescribing behaviour of veterinary practitioners in cattle practice in Ireland. Vet Rec 2012; 172:14. [PMID: 23293148 DOI: 10.1136/vr.100782] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
Guidelines on prudent antimicrobial use in veterinary medicine have been developed to reduce inappropriate prescribing of antimicrobials. Such guidelines focus mainly on the clinical and pharmacological indications for prescribing. A questionnaire study of veterinary surgeons engaged in cattle practice was completed to determine if non-clinical issues influence the decision to prescribe antimicrobials, and to assess if pharmacological and non-pharmacological issues influence the choice of antimicrobial prescribed. Non-clinical issues, including issues related to professional stress, influenced the prescribing decision of the majority of respondents. However, the nature of the veterinarian-client relationship did not influence the prescribing behaviour of the majority of respondents. Pharmacological and non-pharmacological issues influenced the choice of antimicrobial prescribed. The veterinary surgeon's prior experience of a drug was considered 'often' or 'always' by 95.7 per cent of respondents when making this decision. The findings of this study have implications for the recognition and management of stress within the profession, and for the development of intervention strategies to reduce inappropriate antimicrobial prescribing.
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Affiliation(s)
- J F Gibbons
- Pathobiology Section, School of Veterinary Medicine, University College Dublin, Belfield, Dublin 4, Ireland.
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Murphy-Lavoie H, Butler F, Hagan C. Central retinal artery occlusion treated with oxygen: a literature review and treatment algorithm. Undersea Hyperb Med 2012; 39:943-953. [PMID: 23045923] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
Central retinal artery occlusion (CRAO) is an uncommon eye disorder, but one that typically produces severe and irreversible vision loss in the affected eye. The retina has a dual blood supply, with the retinal circulation supplying the inner layers and the choroidal circulation supplying the outer layers. In CRAO, vision loss results from cell death in the inner retinal layers despite relative sparing of the outer layers. If supplemental oxygen is provided, however, oxygen from the choroidal circulation may diffuse in adequate quantity to the inner layers of the retina to maintain retinal function and restore vision. In some patients this can be achieved with normobaric hyperoxia; in others, hyperbaric oxygen (HBO2) may be required. The challenge is to provide the supplemental oxygen early enough after the onset of vision loss to prevent irreversible damage to the retina. In experimental models of complete CRAO, the ischemic time window before permanent retinal damage occurs is just over 90 minutes; in the clinical setting where occlusion may be incomplete, return of vision may be achieved even after delays of eight to 24 hours. In patients with a clinical picture of CRAO who present within 24 hours of vision loss, supplemental oxygen should be started immediately at the highest possible fraction of inspired oxygen (FiO2). If vision is not quickly restored, emergent HBO2 should be undertaken if feasible. If the patient responds to HBO2, follow-up treatment with supplemental oxygen should be customized to maintain retinal viability until the obstructed retinal artery recanalizes, which typically occurs within the first 72 hours. This paper reviews the pertinent literature on CRAO and HBO2 and provides a treatment algorithm.
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Affiliation(s)
- H Murphy-Lavoie
- Section of Emergency Medicine, Louisiana State University Undersea Hyperbaric Medicine Fellowship, Louisiana State University Medical Center, New Orleans, Louisiana, USA.
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Hunt K, Drummond N, Murphy M, Butler F, Buckley J, Jordan K. A case of bovine raw milk contamination with Listeria monocytogenes. Ir Vet J 2012; 65:13. [PMID: 22769601 PMCID: PMC3526472 DOI: 10.1186/2046-0481-65-13] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2012] [Accepted: 06/22/2012] [Indexed: 11/11/2022] Open
Abstract
During routine sampling of bulk raw milk on a dairy farm, the pathogenic bacteria Listeria monocytogenes was found to be a contaminant, at numbers < 100 cfu/ml. A strain with an indistinguishable pulsed-field gel electrophoresis pattern was isolated from the bulk milk two months later. Environmental swabs taken at the dairy environment were negative for the presence of L. monocytogenes, indicating a possible case of excretion of the L. monocytogenes directly into the milk. Milk samples were collected from the individual cows and analysed, resulting in the identification of L. monocytogenes excretion (at 280 cfu/ml) from one of the 4 mammary quarters of one dairy cow out of 180. When the infected cow was isolated from the herd, no L. monocytogenes was detected from the remaining herd. The pulsed-field gel electrophoresis pattern of the strain from the individual cow was indistinguishable from that originally isolated from the bulk milk. The infected cow did not show any clinical signs of disease, nor did the appearance of the milk have any physical abnormalities. Antibiotic treatment of the infected mammary quarter was found to be ineffective. This study shows that there can be risks associated with direct contamination of raw milk with L. monocytogenes.
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Affiliation(s)
- Karen Hunt
- Teagasc Food Research Centre, Moorepark, Fermoy, Co, Cork, Ireland.
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Yan QQ, Condell O, Power K, Butler F, Tall BD, Fanning S. Cronobacter species (formerly known as Enterobacter sakazakii) in powdered infant formula: a review of our current understanding of the biology of this bacterium. J Appl Microbiol 2012; 113:1-15. [PMID: 22420458 DOI: 10.1111/j.1365-2672.2012.05281.x] [Citation(s) in RCA: 98] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Cronobacter species (formerly known as Enterobacter sakazakii) are opportunistic pathogens that can cause necrotizing enterocolitis, bacteraemia and meningitis, predominantly in neonates. Infection in these vulnerable infants has been linked to the consumption of contaminated powdered infant formula (PIF). Considerable research has been undertaken on this organism in the past number of years which has enhanced our understanding of this neonatal pathogen leading to improvements in its control within the PIF production environment. The taxonomy of the organism resulted in the recognition of a new genus, Cronobacter, which consists of seven species. This paper presents an up-to-date review of our current knowledge of Cronobacter species. Taxonomy, genome sequencing, current detection protocols and epidemiology are all discussed. In addition, consideration is given to the control of this organism in the manufacturing environment, as a first step towards reducing the occurrence of this pathogen in PIF.
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Affiliation(s)
- Q Q Yan
- UCD Centre for Food Safety, WHO Collaborating Centre for Research, Reference & Training on Cronobacter, School of Public Health, Physiotherapy & Population Science, University College Dublin, Dublin, Ireland
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Keenan DF, Brunton NP, Gormley TR, Butler F. Quality and sensory acceptability of a chilled functional apple ready-dessert. FOOD SCI TECHNOL INT 2012; 18:167-77. [PMID: 22407955 DOI: 10.1177/1082013211415087] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
An apple and dairy based ready-dessert with an added prebiotic was stored and chill temperatures and number of quality attributes were monitored during chill (4 °C) storage for 30 days. All ready-desserts were thermally processed by sous vide (P (90) > 10 min). The stability of the dairy component in ready-desserts was monitored by measuring volatile free fatty acids. Changes in these components were more evident in prebiotic-enriched samples compared to controls. However, no significant differences were observed over storage in control and prebiotic-enriched ready-desserts. This was supported by sensory analysis that showed no significant changes over storage in control or prebiotic-enriched samples. Of the other quality parameters, the addition of prebiotic inclusions resulted in lower L and b values and dry matter (p < 0.05), while increasing (p < 0.05) soluble solids content compared to control samples. Fluctuations in some of the quality parameters were also observed over storage. Rheological characteristics, i.e. flow behaviour (n), consistency index (K), storage (G'), loss (G″) and complex (G*) moduli were unaffected by prebiotic inclusion. However, storage affected the rheological characteristics of ready-desserts. A decrease (p < 0.05) in flow behaviour (n) led to concomitant increases in consistency index (K) and complex modulus (G*) values in control samples.
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Affiliation(s)
- D F Keenan
- Teagasc, Food Research Centre, Ashtown, Dublin 15, Ireland.
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Stojceska V, Butler F. Investigation of reported correlation coefficients between rheological properties of the wheat bread doughs and baking performance of the corresponding wheat flours. Trends Food Sci Technol 2012. [DOI: 10.1016/j.tifs.2011.09.005] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
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Keenan DF, Tiwari BK, Patras A, Gormley R, Butler F, Brunton NP. Effect of sonication on the bioactive, quality and rheological characteristics of fruit smoothies. Int J Food Sci Technol 2012. [DOI: 10.1111/j.1365-2621.2011.02915.x] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
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Abbott IM, Harrison S, Butler F. Clutter‐adaptation of bat species predicts their use of under‐motorway passageways of contrasting sizes – a natural experiment. J Zool (1987) 2012. [DOI: 10.1111/j.1469-7998.2011.00894.x] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- I. M. Abbott
- Department of Biological Earth and Environmental Sciences University College Cork Cork Ireland
| | - S. Harrison
- Department of Biological Earth and Environmental Sciences University College Cork Cork Ireland
| | - F. Butler
- Department of Biological Earth and Environmental Sciences University College Cork Cork Ireland
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Keenan DF, Brunton NP, Mitchell M, Gormley R, Butler F. Flavour profiling of fresh and processed fruit smoothies by instrumental and sensory analysis. Food Res Int 2012. [DOI: 10.1016/j.foodres.2011.10.002] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/16/2022]
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Schvartzman MS, Belessi C, Butler F, Skandamis PN, Jordan KN. Effect of pH and water activity on the growth limits of Listeria monocytogenes in a cheese matrix at two contamination levels. J Food Prot 2011; 74:1805-13. [PMID: 22054180 DOI: 10.4315/0362-028x.jfp-11-102] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Listeria monocytogenes can proliferate at the beginning of cheesemaking as the conditions favor growth. The objective of this study was to establish the growth limits of L. monocytogenes in a cheese matrix, in case of potential contamination of the milk prior to cheese manufacture. A semisoft laboratory scale model cheese system was made at different initial pH and water activity (a(w)) levels with a mix of two strains of L. monocytogenes. A factorial design of five pH values (5.6 to 6.5), four a(w) values (0.938 to 0.96), and two L. monocytogenes inoculation levels (1 to 20 CFU/ml and 500 to 1,000 CFU/ml) was carried out. Each combination was evaluated in six independent replicates. In order to determine if there was a dominant strain, isolated colonies from the cheeses were analyzed by pulsed-field gel electrophoresis. The data relating to growth initiation were fitted to a logistic regression model. The a(w) of milk influenced the probability of growth initiation of L. monocytogenes at both low and high contamination levels. The pH, at the concentrations tested, had a lower effect on the probability of growth initiation. At pH 6.5 and a(w) of 0.99 for low contamination levels and pH 6.5 and a(w) of 0.97 for high contamination levels, increases in population of up to 4 and 2 log were observed at low and high contamination levels, respectively. This shows that if conditions are favorable for growth initiation at the early stages of the cheesemaking process, contamination of milk, even with low numbers, could lead to L. monocytogenes populations that exceed the European Union's microbiological limit of 100 CFU/g of cheese.
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Affiliation(s)
- M S Schvartzman
- Teagasc Moorepark Food Research Centre, Fermoy, Co. Cork, Ireland
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