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Narimisa N, Razavi S, Masjedian Jazi F. Prevalence of antibiotic resistance in Salmonella Typhimurium isolates originating from Iran: a systematic review and meta-analysis. Front Vet Sci 2024; 11:1388790. [PMID: 38860007 PMCID: PMC11163077 DOI: 10.3389/fvets.2024.1388790] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2024] [Accepted: 05/13/2024] [Indexed: 06/12/2024] Open
Abstract
Objective Antibiotic resistance in Salmonella represents a significant global public health concern. Among various serovars, Salmonella enterica serovar Typhimurium is prevalent in multiple countries. This study aims to conduct a systematic review and meta-analysis to evaluate the pattern of antibiotic resistance in S. Typhimurium isolates from diverse sources in Iran. Methods We conducted a comprehensive and systematic search for relevant articles until December 2023 in the following databases: PubMed, Scopus, Web of Science, and SID. The collected data were analyzed using Stata software version 17. Results Eighteen studies examined the pattern of antibiotic resistance in S. Typhimurium for various antibiotics in Iran. Piperacillin and tetracycline exhibited the highest resistance rates, at 79 and 60% respectively, while cefixime and ceftriaxone had the lowest resistance rates at 0%. Conclusion Our findings indicate a high level of antibiotic resistance among the studied antibiotics. This high level of antibiotic resistance raises concerns and underscores the necessity for monitoring the use of antibiotics. Moreover, resistance to these antibiotics was more prevalent in samples isolated from animals compared to other sources. This highlights the importance of animal screening to detect the presence of drug-resistant isolates, with the ultimate goal of reducing antibiotic resistance and preventing the transmission of resistant strains to humans.
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Affiliation(s)
| | | | - Faramarz Masjedian Jazi
- Department of Microbiology, School of Medicine, Iran University of Medical Sciences, Tehran, Iran
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2
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Cardim Falcao R, Edwards MR, Hurst M, Fraser E, Otterstatter M. A Review on Microbiological Source Attribution Methods of Human Salmonellosis: From Subtyping to Whole-Genome Sequencing. Foodborne Pathog Dis 2024; 21:137-146. [PMID: 38032610 PMCID: PMC10924193 DOI: 10.1089/fpd.2023.0075] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2023] Open
Abstract
Salmonella is one of the main causes of human foodborne illness. It is endemic worldwide, with different animals and animal-based food products as reservoirs and vehicles of infection. Identifying animal reservoirs and potential transmission pathways of Salmonella is essential for prevention and control. There are many approaches for source attribution, each using different statistical models and data streams. Some aim to identify the animal reservoir, while others aim to determine the point at which exposure occurred. With the advance of whole-genome sequencing (WGS) technologies, new source attribution models will greatly benefit from the discriminating power gained with WGS. This review discusses some key source attribution methods and their mathematical and statistical tools. We also highlight recent studies utilizing WGS for source attribution and discuss open questions and challenges in developing new WGS methods. We aim to provide a better understanding of the current state of these methodologies with application to Salmonella and other foodborne pathogens that are common sources of illness in the poultry and human sectors.
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Affiliation(s)
- Rebeca Cardim Falcao
- British Columbia Centre for Disease Control, Vancouver, Canada
- School of Population and Public Health, The University of British Columbia, Vancouver, Canada
| | - Megan R Edwards
- British Columbia Centre for Disease Control, Vancouver, Canada
- School of Population and Public Health, The University of British Columbia, Vancouver, Canada
| | - Matt Hurst
- Public Health Agency of Canada, Guelph, Canada
| | - Erin Fraser
- British Columbia Centre for Disease Control, Vancouver, Canada
- School of Population and Public Health, The University of British Columbia, Vancouver, Canada
| | - Michael Otterstatter
- British Columbia Centre for Disease Control, Vancouver, Canada
- School of Population and Public Health, The University of British Columbia, Vancouver, Canada
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3
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Fastl C, De Carvalho Ferreira HC, Babo Martins S, Sucena Afonso J, di Bari C, Venkateswaran N, Pires SM, Mughini-Gras L, Huntington B, Rushton J, Pigott D, Devleesschauwer B. Animal sources of antimicrobial-resistant bacterial infections in humans: a systematic review. Epidemiol Infect 2023; 151:e143. [PMID: 37577944 PMCID: PMC10540179 DOI: 10.1017/s0950268823001309] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Revised: 08/02/2023] [Accepted: 08/05/2023] [Indexed: 08/15/2023] Open
Abstract
Bacterial antimicrobial resistance (AMR) is among the leading global health challenges of the century. Animals and their products are known contributors to the human AMR burden, but the extent of this contribution is not clear. This systematic literature review aimed to identify studies investigating the direct impact of animal sources, defined as livestock, aquaculture, pets, and animal-based food, on human AMR. We searched four scientific databases and identified 31 relevant publications, including 12 risk assessments, 16 source attribution studies, and three other studies. Most studies were published between 2012 and 2022, and most came from Europe and North America, but we also identified five articles from South and South-East Asia. The studies differed in their methodologies, conceptual approaches (bottom-up, top-down, and complex), definitions of the AMR hazard and outcome, the number and type of sources they addressed, and the outcome measures they reported. The most frequently addressed animal source was chicken, followed by cattle and pigs. Most studies investigated bacteria-resistance combinations. Overall, studies on the direct contribution of animal sources of AMR are rare but increasing. More recent publications tailor their methodologies increasingly towards the AMR hazard as a whole, providing grounds for future research to build on.
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Affiliation(s)
- Christina Fastl
- Global Burden of Animal Diseases Programme, University of Liverpool, Liverpool, UK
- Department of Epidemiology and Public Health, Sciensano, Brussels, Belgium
| | | | - Sara Babo Martins
- Global Burden of Animal Diseases Programme, University of Liverpool, Liverpool, UK
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Neston, UK
| | - João Sucena Afonso
- Global Burden of Animal Diseases Programme, University of Liverpool, Liverpool, UK
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Neston, UK
| | - Carlotta di Bari
- Global Burden of Animal Diseases Programme, University of Liverpool, Liverpool, UK
- Department of Epidemiology and Public Health, Sciensano, Brussels, Belgium
- Department of Translational Physiology, Infectiology and Public Health, Ghent University, Merelbeke, Belgium
| | - Narmada Venkateswaran
- Global Burden of Animal Diseases Programme, University of Liverpool, Liverpool, UK
- Institute for Health Metrics and Evaluation, Department of Health Metrics Sciences, University of Washington, Seattle, WA, USA
| | | | - Lapo Mughini-Gras
- Centre for Infectious Disease Control (CIb), National Institute for Public Health and the Environment (RIVM), Bilthoven, The Netherlands
- Faculty of Veterinary Medicine, Utrecht University, Institute for Risk Assessment Sciences (IRAS), Utrecht, The Netherlands
| | - Ben Huntington
- Global Burden of Animal Diseases Programme, University of Liverpool, Liverpool, UK
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Neston, UK
- Pengwern Animal Health Ltd, Wallasey, UK
| | - Jonathan Rushton
- Global Burden of Animal Diseases Programme, University of Liverpool, Liverpool, UK
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Neston, UK
| | - David Pigott
- Global Burden of Animal Diseases Programme, University of Liverpool, Liverpool, UK
- Institute for Health Metrics and Evaluation, Department of Health Metrics Sciences, University of Washington, Seattle, WA, USA
| | - Brecht Devleesschauwer
- Global Burden of Animal Diseases Programme, University of Liverpool, Liverpool, UK
- Department of Epidemiology and Public Health, Sciensano, Brussels, Belgium
- Department of Translational Physiology, Infectiology and Public Health, Ghent University, Merelbeke, Belgium
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4
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Chao E, Chato C, Vender R, Olabode AS, Ferreira RC, Poon AFY. Molecular source attribution. PLoS Comput Biol 2022; 18:e1010649. [PMID: 36395093 PMCID: PMC9671344 DOI: 10.1371/journal.pcbi.1010649] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Affiliation(s)
- Elisa Chao
- Department of Pathology and Laboratory Medicine, Western University, London, Ontario, Canada
| | - Connor Chato
- Department of Pathology and Laboratory Medicine, Western University, London, Ontario, Canada
| | - Reid Vender
- Department of Pathology and Laboratory Medicine, Western University, London, Ontario, Canada
- School of Medicine, Queen’s University, Kingston, Ontario, Canada
| | - Abayomi S. Olabode
- Department of Pathology and Laboratory Medicine, Western University, London, Ontario, Canada
| | - Roux-Cil Ferreira
- Department of Pathology and Laboratory Medicine, Western University, London, Ontario, Canada
| | - Art F. Y. Poon
- Department of Pathology and Laboratory Medicine, Western University, London, Ontario, Canada
- * E-mail:
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Quantitative Risk Assessment of Susceptible and Ciprofloxacin-Resistant Salmonella from Retail Pork in Chiang Mai Province in Northern Thailand. Foods 2022; 11:foods11192942. [PMID: 36230018 PMCID: PMC9562186 DOI: 10.3390/foods11192942] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Revised: 08/26/2022] [Accepted: 09/16/2022] [Indexed: 11/16/2022] Open
Abstract
The adverse human health effects as a result of antimicrobial resistance have been recognized worldwide. Salmonella is a leading cause of foodborne illnesses while antimicrobial resistant (AMR) Salmonella has been isolated from foods of animal origin. The quantitative risk assessment (RA) as part of the guidelines for the risk analysis of foodborne antimicrobial resistance was issued by the Codex Alimentarius Commission more than a decade ago. However, only two risk assessments reported the human health effects of AMR Salmonella in dry-cured pork sausage and pork mince. Therefore, the objective of this study was to quantitatively evaluate the adverse health effects attributable to consuming retail pork contaminated with Salmonella using risk assessment models. The sampling frame covered pork at the fresh market (n = 100) and modern trade where pork is refrigerated (n = 50) in Chiang Mai province in northern Thailand. The predictive microbiology models were used in the steps where data were lacking. Susceptible and quinolone-resistant (QR) Salmonella were determined by antimicrobial susceptibility testing and the presence of AMR genes. The probability of mortality conditional to foodborne illness by susceptible Salmonella was modeled as the hazard characterization of susceptible and QR Salmonella. For QR Salmonella, the probabilistic prevalences from the fresh market and modern trade were 28.4 and 1.9%, respectively; the mean concentrations from the fresh market and modern trade were 346 and 0.02 colony forming units/g, respectively. The probability of illness (PI) and probability of mortality given illness (PMI) from QR Salmonella-contaminated pork at retails in Chiang Mai province were in the range of 2.2 × 10−8–3.1 × 10−4 and 3.9 × 10−10–5.4 × 10−6, respectively, while those from susceptible Salmonella contaminated-pork at retails were in the range 1.8 × 10−4–3.2 × 10−4 and 2.3 × 10−7–4.2 × 10−7, respectively. After 1000 iterations of Monte Carlo simulations of the risk assessment models, the annual mortality rates for QR salmonellosis simulated by the risk assessment models were in the range of 0–32, which is in line with the AMR adverse health effects previously reported. Therefore, the risk assessment models used in both exposure assessment and hazard characterization were applicable to evaluate the adverse health effects of AMR Salmonella spp. in Thailand.
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Perestrelo S, Correia Carreira G, Valentin L, Fischer J, Pfeifer Y, Werner G, Schmiedel J, Falgenhauer L, Imirzalioglu C, Chakraborty T, Käsbohrer A. Comparison of approaches for source attribution of ESBL-producing Escherichia coli in Germany. PLoS One 2022; 17:e0271317. [PMID: 35839265 PMCID: PMC9286285 DOI: 10.1371/journal.pone.0271317] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Accepted: 06/28/2022] [Indexed: 11/19/2022] Open
Abstract
Extended-spectrum beta-lactamase (ESBL)-producing Escherichia (E.) coli have been widely described as the cause of treatment failures in humans around the world. The origin of human infections with these microorganisms is discussed controversially and in most cases hard to identify. Since they pose a relevant risk to human health, it becomes crucial to understand their sources and the transmission pathways. In this study, we analyzed data from different studies in Germany and grouped ESBL-producing E. coli from different sources and human cases into subtypes based on their phenotypic and genotypic characteristics (ESBL-genotype, E. coli phylogenetic group and phenotypic antimicrobial resistance pattern). Then, a source attribution model was developed in order to attribute the human cases to the considered sources. The sources were from different animal species (cattle, pig, chicken, dog and horse) and also from patients with nosocomial infections. The human isolates were gathered from community cases which showed to be colonized with ESBL-producing E. coli. We used the attribution model first with only the animal sources (Approach A) and then additionally with the nosocomial infections (Approach B). We observed that all sources contributed to the human cases, nevertheless, isolates from nosocomial infections were more related to those from human cases than any of the other sources. We identified subtypes that were only detected in the considered animal species and others that were observed only in the human population. Some subtypes from the human cases could not be allocated to any of the sources from this study and were attributed to an unknown source. Our study emphasizes the importance of human-to-human transmission of ESBL-producing E. coli and the different role that pets, livestock and healthcare facilities may play in the transmission of these resistant bacteria. The developed source attribution model can be further used to monitor future trends. A One Health approach is necessary to develop source attribution models further to integrate also wildlife, environmental as well as food sources in addition to human and animal data.
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Affiliation(s)
- Sara Perestrelo
- Biological Safety, German Federal Institute for Risk Assessment, Berlin, Germany
- * E-mail:
| | | | - Lars Valentin
- Biological Safety, German Federal Institute for Risk Assessment, Berlin, Germany
| | - Jennie Fischer
- Biological Safety, German Federal Institute for Risk Assessment, Berlin, Germany
| | - Yvonne Pfeifer
- Nosocomial Pathogens and Antibiotic Resistance, Robert Koch Institute, Wernigerode, Germany
| | - Guido Werner
- Nosocomial Pathogens and Antibiotic Resistance, Robert Koch Institute, Wernigerode, Germany
| | - Judith Schmiedel
- Institute of Medical Microbiology, Justus Liebig University, Giessen, Germany
| | - Linda Falgenhauer
- Institute of Hygiene and Environmental Medicine, Justus Liebig University, Giessen, Germany
- German Center for Infection Research (DZIF), Partner Site Giessen-Marburg-Langen, Campus Giessen, Giessen, Germany
- Hessisches universitäres Kompetenzzentrum Krankenhaushygiene (HuKKH), Giessen, Germany
| | - Can Imirzalioglu
- Institute of Medical Microbiology, Justus Liebig University, Giessen, Germany
- German Center for Infection Research (DZIF), Partner Site Giessen-Marburg-Langen, Campus Giessen, Giessen, Germany
| | - Trinad Chakraborty
- Institute of Medical Microbiology, Justus Liebig University, Giessen, Germany
- German Center for Infection Research (DZIF), Partner Site Giessen-Marburg-Langen, Campus Giessen, Giessen, Germany
| | - Annemarie Käsbohrer
- Biological Safety, German Federal Institute for Risk Assessment, Berlin, Germany
- Veterinary Public Health and Epidemiology, University of Veterinary Medicine, Vienna, Austria
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7
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Temporal changes in the proportion of Salmonella outbreaks associated with twelve food commodity groups in the United States. Epidemiol Infect 2022; 150:e126. [PMID: 35703081 PMCID: PMC9274825 DOI: 10.1017/s0950268822001042] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Using data from 20 years of Salmonella foodborne outbreaks, this study investigates significant trends in the proportion of outbreaks associated with 12 broad commodity groups. Outbreak counts are demonstrated to have a stronger trend signal than outbreak illness counts. The number of outbreaks with an identified food vehicle increased significantly between 1998 and 2000. This was followed by a 10-year period when the number of outbreaks decreased. The number of outbreaks increased significantly between 2010 and 2014 and then remained unchanged for the remainder of the study period. During the period of 1998 through 2017, the proportion of outbreaks for three commodities groups, consisting of eggs, pork and seeded vegetables, changed significantly. No significant changes were observed in the remaining nine commodity groups. Simple approximations are derived to highlight the effect of dependencies between outbreak proportions and a consumption analysis for meat and poultry is used to enhance the limited interpretability of the changes in these proportions. Given commodity-specific approaches to verifying food safety and promoting pathogen reduction, regulatory agencies benefit from analyses that elucidate illness trends attributable to the products under their jurisdiction. Results from this trend analysis can be used to inform the development and assessment of new pathogen reduction programmes in the United States.
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8
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Dorph K, Haughan J, Robinson M, Redding LE. Critically important antimicrobials are frequently used on equine racetracks. J Am Vet Med Assoc 2022; 260:774-779. [PMID: 35239509 DOI: 10.2460/javma.22.01.0022] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
OBJECTIVE To characterize antimicrobial use on four racetracks in the eastern US during the peak racing 2017-2018 seasons. PROCEDURES Handwritten daily treatment sheets provided by attending veterinarians who listed treatments administered to horses stabled at the racetrack were obtained. Information contained in the treatment sheets included the date, name of the horse and its trainer, type of treatment, and a brief (usually 1-word) indication for treatment. The handwritten data listed on the racetrack treatment sheets were manually transcribed and analyzed. RESULTS A total of 2,684 antimicrobial prescriptions were recorded, representing 6.8% of all drug treatments. The most frequently prescribed antimicrobials were enrofloxacin, with 854 prescriptions (31.8% of antimicrobial treatments), followed by gentamicin (570 [21.2%] prescriptions), ceftiofur (388 [14.5%] prescriptions,), and penicillin (220 [8.2%] prescriptions). The relative frequencies of antimicrobial class and indication for treatment varied significantly by racetrack and by prescribing veterinarian. Limitations associated with the data precluded ascertainment of the proportion of horses treated or exact indications for treatment. CLINICAL RELEVANCE Antimicrobials appeared to be prescribed relatively infrequently at racetracks relative to other drugs, but highly or critically important antimicrobials were most often used. The appropriateness of use of these drugs remains unknown.
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9
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Arnold M, Smith RP, Tang Y, Guzinski J, Petrovska L. Bayesian Source Attribution of Salmonella Typhimurium Isolates From Human Patients and Farm Animals in England and Wales. Front Microbiol 2021; 12:579888. [PMID: 33584605 PMCID: PMC7876086 DOI: 10.3389/fmicb.2021.579888] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2020] [Accepted: 01/07/2021] [Indexed: 12/13/2022] Open
Abstract
The purpose of the study was to apply a Bayesian source attribution model to England and Wales based data on Salmonella Typhimurium (ST) and monophasic variants (MST), using different subtyping approaches based on sequence data. The data consisted of laboratory confirmed human cases and mainly livestock samples collected from surveillance or monitoring schemes. Three different subtyping methods were used, 7-loci Multi-Locus Sequence Typing (MLST), Core-genome MLST, and Single Nucleotide Polymorphism distance, with the impact of varying the genetic distance over which isolates would be grouped together being varied for the latter two approaches. A Bayesian frequency matching method, known as the modified Hald method, was applied to the data from each of the subtyping approaches. Pigs were found to be the main contributor to human infection for ST/MST, with approximately 60% of human cases attributed to them, followed by other mammals (mostly horses) and cattle. It was found that the use of different clustering methods based on sequence data had minimal impact on the estimates of source attribution. However, there was an impact of genetic distance over which isolates were grouped: grouping isolates which were relatively closely related increased uncertainty but tended to have a better model fit.
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Affiliation(s)
- Mark Arnold
- Department of Epidemiological Sciences, Animal and Plant Health Agency (APHA), Addlestone, United Kingdom
| | - Richard Piers Smith
- Department of Epidemiological Sciences, Animal and Plant Health Agency (APHA), Addlestone, United Kingdom
| | - Yue Tang
- Department of Bacteriology, Animal and Plant Health Agency (APHA), Addlestone, United Kingdom
| | - Jaromir Guzinski
- Department of Bacteriology, Animal and Plant Health Agency (APHA), Addlestone, United Kingdom
| | - Liljana Petrovska
- Department of Bacteriology, Animal and Plant Health Agency (APHA), Addlestone, United Kingdom
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10
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Williams MS, Ebel ED, Nyirabahizi E. Comparative history of Campylobacter contamination on chicken meat and campylobacteriosis cases in the United States: 1994-2018. Int J Food Microbiol 2021; 342:109075. [PMID: 33550153 DOI: 10.1016/j.ijfoodmicro.2021.109075] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2020] [Revised: 10/20/2020] [Accepted: 01/17/2021] [Indexed: 01/28/2023]
Abstract
In many countries campylobacteriosis ranks as one of the most frequently reported foodborne illnesses and poultry is the commodity that is most often associated with these illnesses. Nevertheless, efforts to reduce the occurrence of pathogen contamination on poultry are often more focused on Salmonella. While some control measures are pathogen specific, such as pre-harvest vaccination for Salmonella, improvements in sanitary dressing and interventions applied during the slaughter process can be effective against all forms of microbial contamination. To investigate the potential effectiveness of these non-specific pathogen reduction strategies in the United States, it is helpful to assess if, and by how much, Campylobacter contamination of chicken meat has changed across time. This study assesses change considering data collected in both slaughter and retail establishments and comparing observed trends in contamination with trends in human surveillance data. The results support the assertion that substantial reductions in Campylobacter contamination of chicken meat in the late 1990s and early 2000s contributed to a reduction in the human case rate of campylobacteriosis. Further reductions in chicken meat contamination between 2013 and 2018 are more difficult to associate with trends in human illnesses, with one contributing factor being the inclusion of culture independent diagnostic test results in the official case counts during that time. Other contributing factors are discussed.
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Affiliation(s)
- Michael S Williams
- Risk Assessment and Analytics Staff, Office of Public Health Science, Food Safety Inspection Service, USDA, 2150 Centre Avenue, Building D, Fort Collins, CO 80526, USA.
| | - Eric D Ebel
- Risk Assessment and Analytics Staff, Office of Public Health Science, Food Safety Inspection Service, USDA, 2150 Centre Avenue, Building D, Fort Collins, CO 80526, USA
| | - Epiphanie Nyirabahizi
- National Antimicrobial Resistance Monitoring System, Center for Veterinary Medicine, U.S. Food & Drug Administration, 8401 Muirkirk Road, Laurel, MD 20708, USA
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11
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Duarte ASR, Röder T, Van Gompel L, Petersen TN, Hansen RB, Hansen IM, Bossers A, Aarestrup FM, Wagenaar JA, Hald T. Metagenomics-Based Approach to Source-Attribution of Antimicrobial Resistance Determinants - Identification of Reservoir Resistome Signatures. Front Microbiol 2021; 11:601407. [PMID: 33519742 PMCID: PMC7843941 DOI: 10.3389/fmicb.2020.601407] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Accepted: 12/14/2020] [Indexed: 12/11/2022] Open
Abstract
Metagenomics can unveil the genetic content of the total microbiota in different environments, such as food products and the guts of humans and livestock. It is therefore considered of great potential to investigate the transmission of foodborne hazards as part of source-attribution studies. Source-attribution of antimicrobial resistance (AMR) has traditionally relied on pathogen isolation, while metagenomics allows investigating the full span of AMR determinants. In this study, we hypothesized that the relative abundance of fecal resistome components can be associated with specific reservoirs, and that resistomes can be used for AMR source-attribution. We used shotgun-sequences from fecal samples of pigs, broilers, turkeys- and veal calves collected across Europe, and fecal samples from humans occupationally exposed to livestock in one country (pig slaughterhouse workers, pig and broiler farmers). We applied both hierarchical and flat forms of the supervised classification ensemble algorithm Random Forests to classify resistomes into corresponding reservoir classes. We identified country-specific and -independent AMR determinants, and assessed the impact of country-specific determinants when attributing AMR resistance in humans. Additionally, we performed a similarity percentage analysis with the full spectrum of AMR determinants to identify resistome signatures for the different reservoirs. We showed that the number of AMR determinants necessary to attribute a resistome into the correct reservoir increases with a larger reservoir heterogeneity, and that the impact of country-specific resistome signatures on prediction varies between countries. We predicted a higher occupational exposure to AMR determinants among workers exposed to pigs than among those exposed to broilers. Additionally, results suggested that AMR exposure on pig farms was higher than in pig slaughterhouses. Human resistomes were more similar to pig and veal calves’ resistomes than to those of broilers and turkeys, and the majority of these resistome dissimilarities can be explained by a small set of AMR determinants. We identified resistome signatures for each individual reservoir, which include AMR determinants significantly associated with on-farm antimicrobial use. We attributed human resistomes to different livestock reservoirs using Random Forests, which allowed identifying pigs as a potential source of AMR in humans. This study thus demonstrates that it is possible to apply metagenomics in AMR source-attribution.
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Affiliation(s)
- Ana Sofia Ribeiro Duarte
- Division of Genomic Epidemiology, National Food Institute, Technical University of Denmark, Kgs Lyngby, Denmark
| | - Timo Röder
- Division of Genomic Epidemiology, National Food Institute, Technical University of Denmark, Kgs Lyngby, Denmark
| | - Liese Van Gompel
- Institute for Risk Assessment Sciences, Faculty of Veterinary Medicine, Utrecht University, Utrecht, Netherlands
| | - Thomas Nordahl Petersen
- Division of Genomic Epidemiology, National Food Institute, Technical University of Denmark, Kgs Lyngby, Denmark
| | | | - Inge Marianne Hansen
- Division of Genomic Epidemiology, National Food Institute, Technical University of Denmark, Kgs Lyngby, Denmark
| | - Alex Bossers
- Institute for Risk Assessment Sciences, Faculty of Veterinary Medicine, Utrecht University, Utrecht, Netherlands.,Wageningen Bioveterinary Research, Lelystad, Netherlands
| | - Frank M Aarestrup
- Division of Genomic Epidemiology, National Food Institute, Technical University of Denmark, Kgs Lyngby, Denmark
| | - Jaap A Wagenaar
- Wageningen Bioveterinary Research, Lelystad, Netherlands.,Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, Utrecht, Netherlands
| | - Tine Hald
- Division of Genomic Epidemiology, National Food Institute, Technical University of Denmark, Kgs Lyngby, Denmark
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12
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Costard S, Pouzou JG, Belk KE, Morley PS, Schmidt JW, Wheeler TL, Arthur TM, Zagmutt FJ. No Change in Risk for Antibiotic-Resistant Salmonellosis from Beef, United States, 2002-2010. Emerg Infect Dis 2020; 26:2108-2117. [PMID: 32818395 PMCID: PMC7454111 DOI: 10.3201/eid2609.190922] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Restricting antibiotic use in food production animals is a target for reducing antimicrobial drug–resistant infections in humans. To estimate the probability of antibiotic-resistant nontyphoidal salmonellosis per meal made with beef during 2002–2010, we used US surveillance data. Applying data for nontyphoidal Salmonella in raised-without-antibiotics cattle, we tested the effect of removing antibiotic use from all beef cattle production. We found an average of 1.2 antibiotic-resistant nontyphoidal salmonellosis cases per 1 million beef meals made with beef initially contaminated with antibiotic-resistant nontyphoidal Salmonella at slaughter or retail and 0.031 cases per 1 million meals irrespective of beef contamination status. Neither outcome showed sustained change except for increases in 2003 and 2009 (>98% confidence) when larger or more outbreaks occurred. Switching all beef production to a raised-without-antibiotics system may not have a significant effect on antibiotic-resistant nontyphoidal salmonellosis (94.3% confidence).
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13
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Bennani H, Mateus A, Mays N, Eastmure E, Stärk KDC, Häsler B. Overview of Evidence of Antimicrobial Use and Antimicrobial Resistance in the Food Chain. Antibiotics (Basel) 2020; 9:E49. [PMID: 32013023 PMCID: PMC7168130 DOI: 10.3390/antibiotics9020049] [Citation(s) in RCA: 81] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2019] [Revised: 01/25/2020] [Accepted: 01/27/2020] [Indexed: 01/06/2023] Open
Abstract
Antimicrobial resistance (AMR) is a global health problem. Bacteria carrying resistance genes can be transmitted between humans, animals and the environment. There are concerns that the widespread use of antimicrobials in the food chain constitutes an important source of AMR in humans, but the extent of this transmission is not well understood. The aim of this review is to examine published evidence on the links between antimicrobial use (AMU) in the food chain and AMR in people and animals. The evidence showed a link between AMU in animals and the occurrence of resistance in these animals. However, evidence of the benefits of a reduction in AMU in animals on the prevalence of resistant bacteria in humans is scarce. The presence of resistant bacteria is documented in the human food supply chain, which presents a potential exposure route and risk to public health. Microbial genome sequencing has enabled the establishment of some links between the presence of resistant bacteria in humans and animals but, for some antimicrobials, no link could be established. Research and monitoring of AMU and AMR in an integrated manner is essential for a better understanding of the biology and the dynamics of antimicrobial resistance.
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Affiliation(s)
- Houda Bennani
- Veterinary Epidemiology, Economics and Public Health Group, Department of Pathobiology and Population Sciences, Royal Veterinary College, Hawkshead Lane, North Mymms, Hatfield, Hertfordshire AL9 7TA, UK; (A.M.); (K.D.C.S.); (B.H.)
| | - Ana Mateus
- Veterinary Epidemiology, Economics and Public Health Group, Department of Pathobiology and Population Sciences, Royal Veterinary College, Hawkshead Lane, North Mymms, Hatfield, Hertfordshire AL9 7TA, UK; (A.M.); (K.D.C.S.); (B.H.)
| | - Nicholas Mays
- Policy Innovation Research Unit, Department of Health Services Research & Policy, London School of Hygiene and Tropical Medicine, London WC1H 9SH, UK; (N.M.); (E.E.)
| | - Elizabeth Eastmure
- Policy Innovation Research Unit, Department of Health Services Research & Policy, London School of Hygiene and Tropical Medicine, London WC1H 9SH, UK; (N.M.); (E.E.)
| | - Katharina D. C. Stärk
- Veterinary Epidemiology, Economics and Public Health Group, Department of Pathobiology and Population Sciences, Royal Veterinary College, Hawkshead Lane, North Mymms, Hatfield, Hertfordshire AL9 7TA, UK; (A.M.); (K.D.C.S.); (B.H.)
- SAFOSO AG, Waldeggstrasse 1, CH 3097 Liebefeld, Switzerland
| | - Barbara Häsler
- Veterinary Epidemiology, Economics and Public Health Group, Department of Pathobiology and Population Sciences, Royal Veterinary College, Hawkshead Lane, North Mymms, Hatfield, Hertfordshire AL9 7TA, UK; (A.M.); (K.D.C.S.); (B.H.)
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14
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Mughini-Gras L, Kooh P, Fravalo P, Augustin JC, Guillier L, David J, Thébault A, Carlin F, Leclercq A, Jourdan-Da-Silva N, Pavio N, Villena I, Sanaa M, Watier L. Critical Orientation in the Jungle of Currently Available Methods and Types of Data for Source Attribution of Foodborne Diseases. Front Microbiol 2019; 10:2578. [PMID: 31798549 PMCID: PMC6861836 DOI: 10.3389/fmicb.2019.02578] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2019] [Accepted: 10/24/2019] [Indexed: 12/29/2022] Open
Abstract
With increased interest in source attribution of foodborne pathogens, there is a need to sort and assess the applicability of currently available methods. Herewith we reviewed the most frequently applied methods for source attribution of foodborne diseases, discussing their main strengths and weaknesses to be considered when choosing the most appropriate methods based on the type, quality, and quantity of data available, the research questions to be addressed, and the (epidemiological and microbiological) characteristics of the pathogens in question. A variety of source attribution approaches have been applied in recent years. These methods can be defined as top–down, bottom–up, or combined. Top–down approaches assign the human cases back to their sources of infection based on epidemiological (e.g., outbreak data analysis, case-control/cohort studies, etc.), microbiological (i.e., microbial subtyping), or combined (e.g., the so-called ‘source-assigned case-control study’ design) methods. Methods based on microbial subtyping are further differentiable according to the modeling framework adopted as frequency-matching (e.g., the Dutch and Danish models) or population genetics (e.g., Asymmetric Island Models and STRUCTURE) models, relying on the modeling of either phenotyping or genotyping data of pathogen strains from human cases and putative sources. Conversely, bottom–up approaches like comparative exposure assessment start from the level of contamination (prevalence and concentration) of a given pathogen in each source, and then go upwards in the transmission chain incorporating factors related to human exposure to these sources and dose-response relationships. Other approaches are intervention studies, including ‘natural experiments,’ and expert elicitations. A number of methodological challenges concerning all these approaches are discussed. In absence of an universally agreed upon ‘gold’ standard, i.e., a single method that satisfies all situations and needs for all pathogens, combining different approaches or applying them in a comparative fashion seems to be a promising way forward.
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Affiliation(s)
- Lapo Mughini-Gras
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven, Netherlands.,Faculty of Veterinary Medicine, Institute for Risk Assessment Sciences, Utrecht University, Utrecht, Netherlands
| | - Pauline Kooh
- Department of Risk Assessment, French Agency for Food, Environmental and Occupational Health and Safety, Maisons-Alfort, France
| | - Philippe Fravalo
- Research Chair in Meat-Safety, Faculty of Veterinary Medicine, University of Montreal, Saint-Hyacinthe, QC, Canada
| | | | - Laurent Guillier
- Laboratory for Food Safety, French Agency for Food, Environmental and Occupational Health and Safety, Maisons-Alfort, France
| | - Julie David
- Ploufragan-Plouzané Laboratory, French Agency for Food, Environmental and Occupational Health and Safety, Ploufragan, France
| | - Anne Thébault
- Department of Risk Assessment, French Agency for Food, Environmental and Occupational Health and Safety, Maisons-Alfort, France
| | - Frederic Carlin
- UMR 408 SQPOV "Sécurité et Qualité des Produits d'Origine Végétale" INRA, Avignon Université, Avignon, France
| | - Alexandre Leclercq
- Institut Pasteur, Biology of Infection Unit, National Reference Centre and WHO Collaborating Centre for Listeria, Paris, France
| | | | - Nicole Pavio
- Laboratory for Animal Health, French Agency for Food, Environmental and Occupational Health and Safety, Maisons-Alfort, France
| | - Isabelle Villena
- Laboratory of Parasitology-Mycology, EA ESCAPE, University of Reims Champagne-Ardenne, Reims, France
| | - Moez Sanaa
- Department of Risk Assessment, French Agency for Food, Environmental and Occupational Health and Safety, Maisons-Alfort, France
| | - Laurence Watier
- Department of Biostatistics, Biomathematics, Pharmacoepidemiology and Infectious Diseases (B2PHI), Institut National de la Santé et de la Recherche Médicale (INSERM), UVSQ, Institut Pasteur, Université Paris-Saclay, Paris, France
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15
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Jabin H, Correia Carreira G, Valentin L, Käsbohrer A. The role of parameterization in comparing source attribution models based on microbial subtyping for salmonellosis. Zoonoses Public Health 2019; 66:943-960. [PMID: 31478354 DOI: 10.1111/zph.12645] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2018] [Revised: 06/07/2019] [Accepted: 07/19/2019] [Indexed: 11/29/2022]
Abstract
Source attribution methods attribute human cases of a zoonotic disease to a certain source putatively responsible for this disease. Identifying and quantifying the contribution of different sources to human infections is important for taking appropriate actions for reducing the exposure of the consumer to zoonotic pathogens. One widely used method is the microbial subtyping approach, whose principle is to compare the frequency of pathogen subtypes from different sources (e.g. animals or food) with the frequency of these subtypes in human cases. This paper studies the relationship between a Bayesian microbial subtyping approach described by Hald and coworkers subsequently modified by David and coworkers, here called the Hald model, and a frequentist approach known as the "Dutch model." The comparison between the Bayesian and frequentist model is done for two data sets on salmonellosis in Germany from different time periods (year 2004-2007 and 2010-2011). The results of both approaches are in good agreement with each other for the used data. It is shown here mathematically that a certain parameterization can be used to transform the probabilistic Hald model into a deterministic form, which is equivalent to the Dutch model. That certain parameterization secures independence of the model outcomes from the choice of so-called unique subtypes (which are unique in the sense that they are found exclusively in one of the sources). It is shown that deviating from that certain parameterization leads variations in the model outcome dependent on which unique subtypes are chosen in the process of modelling.
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Affiliation(s)
- Hannah Jabin
- German Federal Institute for Risk Assessment, Berlin, Germany
| | | | - Lars Valentin
- German Federal Institute for Risk Assessment, Berlin, Germany
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16
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Niewiadomska AM, Jayabalasingham B, Seidman JC, Willem L, Grenfell B, Spiro D, Viboud C. Population-level mathematical modeling of antimicrobial resistance: a systematic review. BMC Med 2019; 17:81. [PMID: 31014341 PMCID: PMC6480522 DOI: 10.1186/s12916-019-1314-9] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/17/2018] [Accepted: 03/25/2019] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Mathematical transmission models are increasingly used to guide public health interventions for infectious diseases, particularly in the context of emerging pathogens; however, the contribution of modeling to the growing issue of antimicrobial resistance (AMR) remains unclear. Here, we systematically evaluate publications on population-level transmission models of AMR over a recent period (2006-2016) to gauge the state of research and identify gaps warranting further work. METHODS We performed a systematic literature search of relevant databases to identify transmission studies of AMR in viral, bacterial, and parasitic disease systems. We analyzed the temporal, geographic, and subject matter trends, described the predominant medical and behavioral interventions studied, and identified central findings relating to key pathogens. RESULTS We identified 273 modeling studies; the majority of which (> 70%) focused on 5 infectious diseases (human immunodeficiency virus (HIV), influenza virus, Plasmodium falciparum (malaria), Mycobacterium tuberculosis (TB), and methicillin-resistant Staphylococcus aureus (MRSA)). AMR studies of influenza and nosocomial pathogens were mainly set in industrialized nations, while HIV, TB, and malaria studies were heavily skewed towards developing countries. The majority of articles focused on AMR exclusively in humans (89%), either in community (58%) or healthcare (27%) settings. Model systems were largely compartmental (76%) and deterministic (66%). Only 43% of models were calibrated against epidemiological data, and few were validated against out-of-sample datasets (14%). The interventions considered were primarily the impact of different drug regimens, hygiene and infection control measures, screening, and diagnostics, while few studies addressed de novo resistance, vaccination strategies, economic, or behavioral changes to reduce antibiotic use in humans and animals. CONCLUSIONS The AMR modeling literature concentrates on disease systems where resistance has been long-established, while few studies pro-actively address recent rise in resistance in new pathogens or explore upstream strategies to reduce overall antibiotic consumption. Notable gaps include research on emerging resistance in Enterobacteriaceae and Neisseria gonorrhoeae; AMR transmission at the animal-human interface, particularly in agricultural and veterinary settings; transmission between hospitals and the community; the role of environmental factors in AMR transmission; and the potential of vaccines to combat AMR.
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Affiliation(s)
- Anna Maria Niewiadomska
- Division of International Epidemiology and Population Studies, Fogarty International Center, National Institutes of Health, Bethesda, USA
| | - Bamini Jayabalasingham
- Division of International Epidemiology and Population Studies, Fogarty International Center, National Institutes of Health, Bethesda, USA.,Present Address: Elsevier Inc., 230 Park Ave, Suite B00, New York, NY, 10169, USA
| | - Jessica C Seidman
- Division of International Epidemiology and Population Studies, Fogarty International Center, National Institutes of Health, Bethesda, USA
| | | | - Bryan Grenfell
- Division of International Epidemiology and Population Studies, Fogarty International Center, National Institutes of Health, Bethesda, USA.,Princeton University, Princeton, NJ, USA
| | - David Spiro
- Division of International Epidemiology and Population Studies, Fogarty International Center, National Institutes of Health, Bethesda, USA
| | - Cecile Viboud
- Division of International Epidemiology and Population Studies, Fogarty International Center, National Institutes of Health, Bethesda, USA.
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17
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Lu X, Zeng M, Xu J, Zhou H, Gu B, Li Z, Jin H, Wang X, Zhang W, Hu Y, Xiao W, Zhu B, Xu X, Kan B. Epidemiologic and genomic insights on mcr-1-harbouring Salmonella from diarrhoeal outpatients in Shanghai, China, 2006-2016. EBioMedicine 2019; 42:133-144. [PMID: 30905850 PMCID: PMC6491383 DOI: 10.1016/j.ebiom.2019.03.006] [Citation(s) in RCA: 69] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2019] [Revised: 02/27/2019] [Accepted: 03/04/2019] [Indexed: 01/21/2023] Open
Abstract
BACKGROUND Colistin resistance mediated by mcr-1-harbouring plasmids is an emerging threat in Enterobacteriaceae, like Salmonella. Based on its major contribution to the diarrhoea burden, the epidemic state and threat of mcr-1-harbouring Salmonella in community-acquired infections should be estimated. METHODS This retrospective study analysed the mcr-1 gene incidence in Salmonella strains collected from a surveillance on diarrhoeal outpatients in Shanghai Municipality, China, 2006-2016. Molecular characteristics of the mcr-1-positive strains and their plasmids were determined by genome sequencing. The transfer abilities of these plasmids were measured with various conjugation strains, species, and serotypes. FINDINGS Among the 12,053 Salmonella isolates, 37 mcr-1-harbouring strains, in which 35 were serovar Typhimurium, were detected first in 2012 and with increasing frequency after 2015. Most patients infected with mcr-1-harbouring strains were aged <5 years. All strains, including fluoroquinolone-resistant and/or extended-spectrum β-lactamase-producing strains, were multi-drug resistant. S. Typhimurium had higher mcr-1 plasmid acquisition ability compared with other common serovars. Phylogeny based on the genomes combined with complete plasmid sequences revealed some clusters, suggesting the presence of mcr-1-harbouring Salmonella outbreaks in the community. Most mcr-1-positive strains were clustered together with the pork strains, strongly suggesting pork consumption as a main infection source. INTERPRETATION The mcr-1-harbouring Salmonella prevalence in community-acquired diarrhoea displays a rapid increase trend, and the ESBL-mcr-1-harbouring Salmonella poses a threat for children. These findings highlight the necessary and significance of prohibiting colistin use in animals and continuous monitoring of mcr-1-harbouring Salmonella.
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Affiliation(s)
- Xin Lu
- State Key Laboratory of Infectious Disease Prevention and Control, Beijing, China; National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China; Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Hangzhou, China; Beijing Advanced Innovation Center for Food Nutrition and Human Health, Beijing Technology and Business University, Beijing, China
| | - Mei Zeng
- Children's Hospital of Fudan University, Shanghai, China
| | - Jialiang Xu
- Beijing Technology and Business University, Beijing, China
| | - Haijian Zhou
- State Key Laboratory of Infectious Disease Prevention and Control, Beijing, China; National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China; Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Hangzhou, China; Beijing Advanced Innovation Center for Food Nutrition and Human Health, Beijing Technology and Business University, Beijing, China
| | - Baoke Gu
- Shanghai Municipal Center for Disease Control and Prevention, Shanghai, China
| | - Zhenpeng Li
- State Key Laboratory of Infectious Disease Prevention and Control, Beijing, China; National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China; Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Hangzhou, China; Beijing Advanced Innovation Center for Food Nutrition and Human Health, Beijing Technology and Business University, Beijing, China
| | - Huiming Jin
- Shanghai Municipal Center for Disease Control and Prevention, Shanghai, China
| | - Xiaoxun Wang
- State Key Laboratory of Infectious Disease Prevention and Control, Beijing, China; National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China; Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Hangzhou, China; Beijing Advanced Innovation Center for Food Nutrition and Human Health, Beijing Technology and Business University, Beijing, China; Beijing Technology and Business University, Beijing, China
| | - Wen Zhang
- State Key Laboratory of Infectious Disease Prevention and Control, Beijing, China; National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China; Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Hangzhou, China; Beijing Advanced Innovation Center for Food Nutrition and Human Health, Beijing Technology and Business University, Beijing, China
| | - Yongfei Hu
- Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Wenjia Xiao
- Shanghai Municipal Center for Disease Control and Prevention, Shanghai, China
| | - Baoli Zhu
- Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Xuebin Xu
- Shanghai Municipal Center for Disease Control and Prevention, Shanghai, China.
| | - Biao Kan
- State Key Laboratory of Infectious Disease Prevention and Control, Beijing, China; National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China; Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Hangzhou, China; Beijing Advanced Innovation Center for Food Nutrition and Human Health, Beijing Technology and Business University, Beijing, China.
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18
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Koutsoumanis K, Allende A, Alvarez-Ordóñez A, Bolton D, Bover-Cid S, Chemaly M, De Cesare A, Herman L, Hilbert F, Lindqvist R, Nauta M, Peixe L, Ru G, Simmons M, Skandamis P, Suffredini E, Dewulf J, Hald T, Michel V, Niskanen T, Ricci A, Snary E, Boelaert F, Messens W, Davies R. Salmonella control in poultry flocks and its public health impact. EFSA J 2019; 17:e05596. [PMID: 32626222 PMCID: PMC7009056 DOI: 10.2903/j.efsa.2019.5596] [Citation(s) in RCA: 65] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
An increase in confirmed human salmonellosis cases in the EU after 2014 triggered investigation of contributory factors and control options in poultry production. Reconsideration of the five current target serovars for breeding hens showed that there is justification for retaining Salmonella Enteritidis, Salmonella Typhimurium (including monophasic variants) and Salmonella Infantis, while Salmonella Virchow and Salmonella Hadar could be replaced by Salmonella Kentucky and either Salmonella Heidelberg, Salmonella Thompson or a variable serovar in national prevalence targets. However, a target that incorporates all serovars is expected to be more effective as the most relevant serovars in breeding flocks vary between Member State (MS) and over time. Achievement of a 1% target for the current target serovars in laying hen flocks is estimated to be reduced by 254,400 CrI95[98,540; 602,700] compared to the situation in 2016. This translates to a reduction of 53.4% CrI95[39.1; 65.7] considering the layer-associated human salmonellosis true cases and 6.2% considering the overall human salmonellosis true cases in the 23 MSs included in attribution modelling. A review of risk factors for Salmonella in laying hens revealed that overall evidence points to a lower occurrence in non-cage compared to cage systems. A conclusion on the effect of outdoor access or impact of the shift from conventional to enriched cages could not be reached. A similar review for broiler chickens concluded that the evidence that outdoor access affects the occurrence of Salmonella is inconclusive. There is conclusive evidence that an increased stocking density, larger farms and stress result in increased occurrence, persistence and spread of Salmonella in laying hen flocks. Based on scientific evidence, an impact of Salmonella control programmes, apart from general hygiene procedures, on the prevalence of Campylobacter in broiler flocks at the holding and on broiler meat at the end of the slaughter process is not expected.
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Abstract
Source attribution and microbial risk assessment methods have been widely applied for the control of several foodborne pathogens worldwide by identifying (i) the most important pathogen sources and (ii) the risk represented by specific foods and the critical points in these foods' production chains for microbial control. Such evidence has proved crucial for risk managers to identify and prioritize effective food safety and public health strategies. In the context of antimicrobial resistance (AMR) from livestock and pets, the utility of these methods is recognized, but a number of challenges have largely prevented their application and routine use. One key challenge has been to define the hazard in question: Is it the antimicrobial drug use in animals, the antimicrobial-resistant bacteria in animals and foods, or the antimicrobial resistance genes that can be transferred between commensal and pathogenic bacteria in the animal or human gut or in the environment? Other important limitations include the lack of occurrence and transmission data and the lack of evidence to inform dose-response relationships. We present the main principles, available methods, strengths, and weaknesses of source attribution and risk assessment methods, discuss their utility to identify sources and estimate risks of AMR from livestock and pets, and provide an overview of conducted studies. In addition, we discuss remaining challenges and current and future opportunities to improve methods and knowledge of the sources and transmission routes of AMR from animals through food, direct contact, or the environment, including improvements in surveillance and developments in genotypic typing methods.
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Mughini-Gras L, Kooh P, Augustin JC, David J, Fravalo P, Guillier L, Jourdan-Da-Silva N, Thébault A, Sanaa M, Watier L. Source Attribution of Foodborne Diseases: Potentialities, Hurdles, and Future Expectations. Front Microbiol 2018; 9:1983. [PMID: 30233509 PMCID: PMC6129602 DOI: 10.3389/fmicb.2018.01983] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2018] [Accepted: 08/06/2018] [Indexed: 11/21/2022] Open
Affiliation(s)
- Lapo Mughini-Gras
- Centre for Infectious Disease Control (CIb), National Institute for Public Health and the Environment (RIVM), Bilthoven, Netherlands.,Faculty of Veterinary Medicine, Utrecht University, Utrecht, Netherlands
| | - Pauline Kooh
- Risk Assessment Department, French Agency for Food, Environmental and Occupational Health & Safety (Anses), Maisons-Alfort, France
| | | | - Julie David
- Ploufragan-Plouzané Laboratory, French Agency for Food, Environmental and Occupational Health & Safety (Anses), Ploufragan, France
| | - Philippe Fravalo
- NSERC Industrial Research Chair in Meat-Safety (CRSV), Faculty of Veterinary Medicine, University of Montreal, Saint-Hyacinthe, QC, Canada
| | - Laurent Guillier
- Laboratory for Food Safety, French Agency for Food, Environmental and Occupational Health & Safety (Anses), Maisons-Alfort, France
| | | | - Anne Thébault
- Risk Assessment Department, French Agency for Food, Environmental and Occupational Health & Safety (Anses), Maisons-Alfort, France
| | - Moez Sanaa
- Risk Assessment Department, French Agency for Food, Environmental and Occupational Health & Safety (Anses), Maisons-Alfort, France
| | - Laurence Watier
- Biostatistics, Biomathematics, Pharmacoepidemiology and Infectious Diseases (B2PHI), Inserm, UVSQ, Institut Pasteur, Université Paris-Saclay, Paris, France
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Antimicrobial Resistance in the Food Chain in the European Union. ADVANCES IN FOOD AND NUTRITION RESEARCH 2018; 86:115-136. [PMID: 30077219 DOI: 10.1016/bs.afnr.2018.04.004] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Consumers require safety foods but without losing enough supply and low prices. Food concerns about antimicrobial residues and antimicrobial-resistant (AMR) bacteria are not usually appropriately separated and could be perceived as the same problem. The monitoring of residues of antimicrobials in animal food is well established at different levels (farm, slaughterhouse, and industry), and it is preceded by the legislation of veterinary medicines where maximum residues limits are required for medicines to be used in food animal. Following the strategy of the World Health Organization, one of the proposed measures consists in controlling the use of critical antibiotics. The European Union surveillance program currently includes the animal species with the highest meat production (pigs, chickens, turkeys, and cattle) and the food derived from them, investigating antimicrobial resistance of zoonotic (Salmonella and Campylobacter) and indicator (Escherichia coli and enterococci) bacteria. AMR mechanisms encoded by genes have a greater impact on transfer than mutations. Sometimes these genes are found in mobile genetic elements such as plasmids, transposons, or integrons, capable of passing from one bacterium to another by horizontal transfer. It is important to know that depending on how the resistance mechanism is transferred, the power of dissemination is different. By vertical transfer of the resistance gene, whatever its origin, will be transmitted to the following generations. In the case of horizontal transfer, the resistance gene moves to neighboring bacteria and therefore the range of resistance can be much greater.
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22
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Salmonella Typhimurium in livestock in Great Britain - trends observed over a 32-year period. Epidemiol Infect 2018; 146:409-422. [PMID: 29415790 DOI: 10.1017/s095026881800002x] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
Abstract
In this retrospective study, we describe and analyse Salmonella data from four livestock species in Great Britain between 1983 and 2014, focusing on Salmonella Typhimurium. A total of 96 044 Salmonella isolates were obtained during the study period. S. Typhimurium was the predominant serovar isolated from cattle and pigs and represented 40.7% (18 455/45 336) and 58.3% (4495/7709) of isolates from these species respectively, while it only accounted for 6.7% (2114/31 492) of chicken isolates and 8.1% (926/11 507) of turkey isolates. Over the study period, DT104 was the most common phage type in all four species; however, DT104 peaked in occurrence between 1995 and 1999, but is currently rare. Monophasic strains of S. Typhimurium represented less than 3% of all Salmonella isolates in cattle and chickens in 2014, but accounted for 10.4% of all turkey isolates and 39.0% of all pig isolates in the same year. Salmonella isolates were tested for their in vitro susceptibility to 16 antimicrobials. Antimicrobial resistance of S. Typhimurium isolates is largely influenced by the dominance of specific phage types at a certain time, which are commonly associated with particular resistance patterns. Changes in resistance patterns over time were analysed and compared between species.
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Ferri M, Ranucci E, Romagnoli P, Giaccone V. Antimicrobial resistance: A global emerging threat to public health systems. Crit Rev Food Sci Nutr 2018; 57:2857-2876. [PMID: 26464037 DOI: 10.1080/10408398.2015.1077192] [Citation(s) in RCA: 460] [Impact Index Per Article: 76.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
Antimicrobial resistance (AMR) became in the last two decades a global threat to public health systems in the world. Since the antibiotic era, with the discovery of the first antibiotics that provided consistent health benefits to human medicine, the misuse and abuse of antimicrobials in veterinary and human medicine have accelerated the growing worldwide phenomenon of AMR. This article presents an extensive overview of the epidemiology of AMR, with a focus on the link between food producing-animals and humans and on the legal framework and policies currently implemented at the EU level and globally. The ways of responding to the AMR challenges foresee an array of measures that include: designing more effective preventive measures at farm level to reduce the use of antimicrobials; development of novel antimicrobials; strengthening of AMR surveillance system in animal and human populations; better knowledge of the ecology of resistant bacteria and resistant genes; increased awareness of stakeholders on the prudent use of antibiotics in animal productions and clinical arena; and the public health and environmental consequences of AMR. Based on the global nature of AMR and considering that bacterial resistance does not recognize barriers and can spread to people and the environment, the article ends with specific recommendations structured around a holistic approach and targeted to different stakeholders.
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Affiliation(s)
| | | | | | - Valerio Giaccone
- d Department of Animal Medicine , Veterinary School, Padua University , Padua , Italy
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Egorova PA, Bezprozvanny IB. Inositol 1,4,5-trisphosphate receptors and neurodegenerative disorders. FEBS J 2018; 285:3547-3565. [PMID: 29253316 DOI: 10.1111/febs.14366] [Citation(s) in RCA: 52] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2017] [Revised: 11/27/2017] [Accepted: 12/12/2017] [Indexed: 12/15/2022]
Abstract
The inositol 1,4,5-trisphosphate receptor (IP3 R) is an intracellular ion channel that mediates the release of calcium ions from the endoplasmic reticulum. It plays a role in basic biological functions, such as cell division, differentiation, fertilization and cell death, and is involved in developmental processes including learning, memory and behavior. Deregulation of neuronal calcium signaling results in disturbance of cell homeostasis, synaptic loss and dysfunction, eventually leading to cell death. Three IP3 R subtypes have been identified in mammalian cells and the predominant isoform in neurons is IP3 R type 1. Dysfunction of IP3 R type 1 may play a role in the pathogenesis of certain neurodegenerative diseases as enhanced activity of the IP3 R was observed in models of Huntington's disease, spinocerebellar ataxias and Alzheimer's disease. These results suggest that IP3 R-mediated signaling is a potential target for treatment of these disorders. In this review we discuss the structure, functions and regulation of the IP3 R in healthy neurons and in conditions of neurodegeneration.
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Affiliation(s)
- Polina A Egorova
- Laboratory of Molecular Neurodegeneration, Peter the Great St. Petersburg Polytechnic University, St Petersburg, Russia
| | - Ilya B Bezprozvanny
- Laboratory of Molecular Neurodegeneration, Peter the Great St. Petersburg Polytechnic University, St Petersburg, Russia.,Department of Physiology, University of Texas Southwestern Medical Center, Dallas, TX, USA
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Mughini-Gras L, Franz E, van Pelt W. New paradigms for Salmonella source attribution based on microbial subtyping. Food Microbiol 2017; 71:60-67. [PMID: 29366470 DOI: 10.1016/j.fm.2017.03.002] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2016] [Revised: 02/24/2017] [Accepted: 03/03/2017] [Indexed: 10/19/2022]
Abstract
Microbial subtyping is the most common approach for Salmonella source attribution. Typically, attributions are computed using frequency-matching models like the Dutch and Danish models based on phenotyping data (serotyping, phage-typing, and antimicrobial resistance profiling). Herewith, we critically review three major paradigms facing Salmonella source attribution today: (i) the use of genotyping data, particularly Multi-Locus Variable Number of Tandem Repeats Analysis (MLVA), which is replacing traditional Salmonella phenotyping beyond serotyping; (ii) the integration of case-control data into source attribution to improve risk factor identification/characterization; (iii) the investigation of non-food sources, as attributions tend to focus on foods of animal origin only. Population genetics models or simplified MLVA schemes may provide feasible options for source attribution, although there is a strong need to explore novel modelling options as we move towards whole-genome sequencing as the standard. Classical case-control studies are enhanced by incorporating source attribution results, as individuals acquiring salmonellosis from different sources have different associated risk factors. Thus, the more such analyses are performed the better Salmonella epidemiology will be understood. Reparametrizing current models allows for inclusion of sources like reptiles, the study of which improves our understanding of Salmonella epidemiology beyond food to tackle the pathogen in a more holistic way.
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Affiliation(s)
- Lapo Mughini-Gras
- National Institute for Public Health and the Environment (RIVM), Centre for Infectious Disease Control (CIb), Bilthoven, The Netherlands; Utrecht University, Department of Infectious Diseases and Immunology, Utrecht, The Netherlands.
| | - Eelco Franz
- National Institute for Public Health and the Environment (RIVM), Centre for Infectious Disease Control (CIb), Bilthoven, The Netherlands
| | - Wilfrid van Pelt
- National Institute for Public Health and the Environment (RIVM), Centre for Infectious Disease Control (CIb), Bilthoven, The Netherlands
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26
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Nieuwenhuijse DF, Koopmans MPG. Metagenomic Sequencing for Surveillance of Food- and Waterborne Viral Diseases. Front Microbiol 2017; 8:230. [PMID: 28261185 PMCID: PMC5309255 DOI: 10.3389/fmicb.2017.00230] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2016] [Accepted: 02/01/2017] [Indexed: 12/25/2022] Open
Abstract
A plethora of viruses can be transmitted by the food- and waterborne route. However, their recognition is challenging because of the variety of viruses, heterogeneity of symptoms, the lack of awareness of clinicians, and limited surveillance efforts. Classical food- and waterborne viral disease outbreaks are mainly caused by caliciviruses, but the source of the virus is often not known and the foodborne mode of transmission is difficult to discriminate from human-to-human transmission. Atypical food- and waterborne viral disease can be caused by viruses such as hepatitis A and hepatitis E. In addition, a source of novel emerging viruses with a potential to spread via the food- and waterborne route is the repeated interaction of humans with wildlife. Wildlife-to-human adaptation may give rise to self- limiting outbreaks in some cases, but when fully adjusted to the human host can be devastating. Metagenomic sequencing has been investigated as a promising solution for surveillance purposes as it detects all viruses in a single protocol, delivers additional genomic information for outbreak tracing, and detects novel unknown viruses. Nevertheless, several issues must be addressed to apply metagenomic sequencing in surveillance. First, sample preparation is difficult since the genomic material of viruses is generally overshadowed by host- and bacterial genomes. Second, several data analysis issues hamper the efficient, robust, and automated processing of metagenomic data. Third, interpretation of metagenomic data is hard, because of the lack of general knowledge of the virome in the food chain and the environment. Further developments in virus-specific nucleic acid extraction methods, bioinformatic data processing applications, and unifying data visualization tools are needed to gain insightful surveillance knowledge from suspect food samples.
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de Knegt LV, Pires SM, Löfström C, Sørensen G, Pedersen K, Torpdahl M, Nielsen EM, Hald T. Application of Molecular Typing Results in Source Attribution Models: The Case of Multiple Locus Variable Number Tandem Repeat Analysis (MLVA) of Salmonella Isolates Obtained from Integrated Surveillance in Denmark. RISK ANALYSIS : AN OFFICIAL PUBLICATION OF THE SOCIETY FOR RISK ANALYSIS 2016; 36:571-88. [PMID: 27002674 DOI: 10.1111/risa.12483] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
Salmonella is an important cause of bacterial foodborne infections in Denmark. To identify the main animal-food sources of human salmonellosis, risk managers have relied on a routine application of a microbial subtyping-based source attribution model since 1995. In 2013, multiple locus variable number tandem repeat analysis (MLVA) substituted phage typing as the subtyping method for surveillance of S. Enteritidis and S. Typhimurium isolated from animals, food, and humans in Denmark. The purpose of this study was to develop a modeling approach applying a combination of serovars, MLVA types, and antibiotic resistance profiles for the Salmonella source attribution, and assess the utility of the results for the food safety decisionmakers. Full and simplified MLVA schemes from surveillance data were tested, and model fit and consistency of results were assessed using statistical measures. We conclude that loci schemes STTR5/STTR10/STTR3 for S. Typhimurium and SE9/SE5/SE2/SE1/SE3 for S. Enteritidis can be used in microbial subtyping-based source attribution models. Based on the results, we discuss that an adjustment of the discriminatory level of the subtyping method applied often will be required to fit the purpose of the study and the available data. The issues discussed are also considered highly relevant when applying, e.g., extended multi-locus sequence typing or next-generation sequencing techniques.
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Affiliation(s)
- Leonardo V de Knegt
- Research Group for Genomic Epidemiology, National Food Institute, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Sara M Pires
- Research Group for Risk-Benefit, National Food Institute, Technical University of Denmark, Søborg, Denmark
| | - Charlotta Löfström
- Research Group for Diagnostic Engineering, National Food Institute, Technical University of Denmark, Søborg, Denmark
| | - Gitte Sørensen
- Research Group for Diagnostic Engineering, National Food Institute, Technical University of Denmark, Søborg, Denmark
| | - Karl Pedersen
- Section for Bacteriology, Pathology and Parasitology, National Veterinary Institute, Technical University of Denmark, Frederiksberg, Denmark
| | - Mia Torpdahl
- Microbiology and Infection Control, Statens Serum Institut, Copenhagen, Denmark
| | - Eva M Nielsen
- Microbiology and Infection Control, Statens Serum Institut, Copenhagen, Denmark
| | - Tine Hald
- Research Group for Genomic Epidemiology, National Food Institute, Technical University of Denmark, Kongens Lyngby, Denmark
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Attribution of Salmonella enterica serotype Hadar infections using antimicrobial resistance data from two points in the food supply system. Epidemiol Infect 2016; 144:1983-90. [PMID: 26838291 DOI: 10.1017/s0950268816000066] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
Abstract
A challenge to the development of foodborne illness prevention measures is determining the sources of enteric illness. Microbial subtyping source-attribution models attribute illnesses to various sources, requiring data characterizing bacterial isolate subtypes collected from human and food sources. We evaluated the use of antimicrobial resistance data on isolates of Salmonella enterica serotype Hadar, collected from ill humans, food animals, and from retail meats, in two microbial subtyping attribution models. We also compared model results when either antimicrobial resistance or pulsed-field gel electrophoresis (PFGE) patterns were used to subtype isolates. Depending on the subtyping model used, 68-96% of the human infections were attributed to meat and poultry food products. All models yielded similar outcomes, with 86% [95% confidence interval (CI) 80-91] to 91% (95% CI 88-96) of the attributable infections attributed to turkey, and 6% (95% CI 2-10) to 14% (95% CI 8-20) to chicken. Few illnesses (<3%) were attributed to cattle or swine. Results were similar whether the isolates were obtained from food animals during processing or from retail meat products. Our results support the view that microbial subtyping models are a flexible and robust approach for attributing Salmonella Hadar.
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Starting from the bench--prevention and control of foodborne and zoonotic diseases. Prev Vet Med 2014; 118:189-95. [PMID: 25481625 DOI: 10.1016/j.prevetmed.2014.11.004] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2014] [Revised: 10/30/2014] [Accepted: 11/02/2014] [Indexed: 01/18/2023]
Abstract
Foodborne diseases are estimated to cause around 50 million disease cases and 3000 deaths a year in the US. Worldwide, food and waterborne diseases are estimated to cause more than 2 million deaths per year. Lab-based research is a key component of efforts to prevent and control foodborne diseases. Over the last two decades, molecular characterization of pathogen isolates has emerged as a key component of foodborne and zoonotic disease prevention and control. Characterization methods have evolved from banding pattern-based subtyping methods to sequenced-based approaches, including full genome sequencing. Molecular subtyping methods not only play a key role for characterizing pathogen transmission and detection of disease outbreaks, but also allow for identification of clonal pathogen groups that show distinct transmission characteristics. Importantly, the data generated from molecular characterization of foodborne pathogens also represent critical inputs for epidemiological and modeling studies. Continued and enhanced collaborations between infectious disease related laboratory sciences and epidemiologists, modelers, and other quantitative scientists will be critical to a One-Health approach that delivers societal benefits, including improved surveillance systems and prevention approaches for zoonotic and foodborne pathogens.
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30
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Mughini-Gras L, Smid J, Enserink R, Franz E, Schouls L, Heck M, van Pelt W. Tracing the sources of human salmonellosis: a multi-model comparison of phenotyping and genotyping methods. INFECTION GENETICS AND EVOLUTION 2014; 28:251-60. [PMID: 25315490 DOI: 10.1016/j.meegid.2014.10.003] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/04/2014] [Revised: 09/29/2014] [Accepted: 10/05/2014] [Indexed: 10/24/2022]
Abstract
Salmonella source attribution is usually performed using frequency-matched models, such as the (modified) Dutch and Hald models, based on phenotyping data, i.e. serotyping, phage typing, and antimicrobial resistance profiling. However, for practical and economic reasons, genotyping methods such as Multi-locus Variable Number of Tandem Repeats Analysis (MLVA) are gradually replacing traditional phenotyping of salmonellas beyond the serovar level. As MLVA-based source attribution of human salmonellosis using frequency-matched models is problematic due to the high variability of the genetic targets investigated, other models need to be explored. Using a comprehensive data set from the Netherlands in 2005-2013, this study aimed at attributing sporadic and domestic cases of Salmonella Typhimurium/4,[5],12:i:- and Salmonella Enteritidis to four putative food-producing animal sources (pigs, cattle, broilers, and layers/eggs) using the modified Dutch and Hald models (based on sero/phage typing data) in comparison with a widely applied population genetics model - the asymmetric island model (AIM) - supplied with MLVA data. This allowed us to compare model outcomes and to corroborate whether MLVA-based Salmonella source attribution using the AIM is able to provide sound, comparable results. All three models provided very similar results, confirming once more that most S. Typhimurium/4,[5],12:i:- and S. Enteritidis cases are attributable to pigs and layers/eggs, respectively. We concluded that MLVA-based source attribution using the AIM is a feasible option, at least for S. Typhimurium/4,[5],12:i:- and S. Enteritidis. Enough information seems to be contained in the MLVA profiles to trace the sources of human salmonellosis even in presence of imperfect temporal overlap between human and source isolates. Besides Salmonella, the AIM might also be applicable to other pathogens that do not always comply to clonal models. This would add further value to current surveillance activities by performing source attribution using genotyping data that are being collected in a standardized fashion internationally.
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Affiliation(s)
- Lapo Mughini-Gras
- National Institute for Public Health and the Environment (RIVM), Centre for Infectious Disease Control (CIb), Bilthoven, The Netherlands; Utrecht University, Faculty of Veterinary Medicine, Department of Infectious Diseases and Immunology, Utrecht, The Netherlands.
| | - Joost Smid
- Utrecht University, Institute for Risk Assessment Sciences, Utrecht, The Netherlands
| | - Remko Enserink
- National Institute for Public Health and the Environment (RIVM), Centre for Infectious Disease Control (CIb), Bilthoven, The Netherlands
| | - Eelco Franz
- National Institute for Public Health and the Environment (RIVM), Centre for Infectious Disease Control (CIb), Bilthoven, The Netherlands
| | - Leo Schouls
- National Institute for Public Health and the Environment (RIVM), Centre for Infectious Disease Control (CIb), Bilthoven, The Netherlands
| | - Max Heck
- National Institute for Public Health and the Environment (RIVM), Centre for Infectious Disease Control (CIb), Bilthoven, The Netherlands
| | - Wilfrid van Pelt
- National Institute for Public Health and the Environment (RIVM), Centre for Infectious Disease Control (CIb), Bilthoven, The Netherlands
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Salmonella source attribution based on microbial subtyping: does including data on food consumption matter? Int J Food Microbiol 2014; 191:109-15. [PMID: 25261828 DOI: 10.1016/j.ijfoodmicro.2014.09.010] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2013] [Revised: 06/10/2014] [Accepted: 09/14/2014] [Indexed: 11/23/2022]
Abstract
Source attribution based on microbial subtyping is being performed in many countries to ascertain the main reservoirs of human salmonellosis and to assess the impact of food safety interventions. To account for differences in exposure, the amount of food available for consumption within a country is often included in Salmonella source attribution models along with the level of contamination. However, not all foods have an equal probability of serving as vehicles for salmonellas, as some foods are more likely to be consumed raw/undercooked than others, posing a relatively higher risk. Using Salmonella data from the Netherlands in 2001-2004, this study aims at elucidating whether and how the incorporation of food consumption data in two source attribution models - the (modified) Dutch and Hald models - affects their attributions. We also propose the incorporation of an additional parameter to weight the amount of food consumed by its likelihood to be consumed raw/undercooked by the population. Incorporating the amount of food consumed caused a drastic change in the ranking of the top reservoirs in the Dutch model, but not in the Hald model, which proved to be insensitive to additional weightings given that its source-dependent factor can account for both food consumption and the ability for foods to serve as vehicles for salmonellas. Compared to attributions without food consumption, the Dutch model including the amount of food consumed showed an increase in the percentage of cases attributable to pigs and a decrease in that of layers/eggs, which became the second reservoir, after pigs. This was not consistent with established knowledge indicating that layers/eggs, rather than pigs, were the main reservoir of human salmonellosis in that period. By incorporating the additional weight reflecting the likelihood for different foods to be consumed raw/undercooked, the attributions of the Dutch model were effectively adjusted, both in terms of ranking and percent contributions of the different reservoirs. We concluded that incorporating food consumption data in the Dutch model can significantly affect the results. Therefore, such data should be either excluded from this model or used together with an additional weight able to adjust the amount of food consumed by its likelihood to be consumed insufficiently cooked. This may help identifying the correct reservoirs, allowing attributions to more closely reflect the real chance for a given food to serve as a vehicle for salmonellas. Conversely, the Hald model works properly irrespective of inclusion of food consumption data.
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Valentin L, Sharp H, Hille K, Seibt U, Fischer J, Pfeifer Y, Michael GB, Nickel S, Schmiedel J, Falgenhauer L, Friese A, Bauerfeind R, Roesler U, Imirzalioglu C, Chakraborty T, Helmuth R, Valenza G, Werner G, Schwarz S, Guerra B, Appel B, Kreienbrock L, Käsbohrer A. Subgrouping of ESBL-producing Escherichia coli from animal and human sources: an approach to quantify the distribution of ESBL types between different reservoirs. Int J Med Microbiol 2014; 304:805-16. [PMID: 25213631 DOI: 10.1016/j.ijmm.2014.07.015] [Citation(s) in RCA: 105] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
Escherichia (E.) coli producing extended-spectrum beta-lactamases (ESBLs) are an increasing problem for public health. The success of ESBLs may be due to spread of ESBL-producing bacterial clones, transfer of ESBL gene-carrying plasmids or exchange of ESBL encoding genes on mobile elements. This makes it difficult to identify transmission routes and sources for ESBL-producing bacteria. The objectives of this study were to compare the distribution of genotypic and phenotypic properties of E. coli isolates from different animal and human sources collected in studies in the scope of the national research project RESET. ESBL-producing E. coli from two longitudinal and four cross-sectional studies in broiler, swine and cattle farms, a cross-sectional and a case-control study in humans and diagnostic isolates from humans and animals were used. In the RESET consortium, all laboratories followed harmonized methodologies for antimicrobial susceptibility testing, confirmation of the ESBL phenotype, specific PCR assays for the detection of bla(TEM), bla(CTX), and bla(SHV) genes and sequence analysis of the complete ESBL gene as well as a multiplex PCR for the detection of the four major phylogenetic groups of E. coli. Most ESBL genes were found in both, human and non-human populations but quantitative differences for distinct ESBL-types were detectable. The enzymes CTX-M-1 (63.3% of all animal isolates, 29.3% of all human isolates), CTX-M-15 (17.7% vs. 48.0%) and CTX-M-14 (5.3% vs. 8.7%) were the most common ones. More than 70% of the animal isolates and more than 50% of the human isolates contained the broadly distributed ESBL genes bla(CTX-M-1), bla(CTX-M-15), or the combinations bla(SHV-12)+bla(TEM) or bla(CTX-M-1)+bla(TEM). While the majority of animal isolates carried bla(CTX-M-1) (37.5%) or the combination bla(CTX-M-1)+bla(TEM) (25.8%), this was the case for only 16.7% and 12.6%, respectively, of the human isolates. In contrast, 28.2% of the human isolates carried bla(CTX-M-15) compared to 10.8% of the animal isolates. When grouping data by ESBL types and phylogroups bla(CTX-M-1) genes, mostly combined with phylogroup A or B1, were detected frequently in all settings. In contrast, bla(CTX-M-15) genes common in human and animal populations were mainly combined with phylogroup A, but not with the more virulent phylogroup B2 with the exception of companion animals, where a few isolates were detectable. When E. coli subtype definition included ESBL types, phylogenetic grouping and antimicrobial susceptibility data, the proportion of isolates allocated to common clusters was markedly reduced. Nevertheless, relevant proportions of same subtypes were detected in isolates from the human and livestock and companion animal populations included in this study, suggesting exchange of bacteria or bacterial genes between these populations or a common reservoir. In addition, these results clearly showed that there is some similarity between ESBL genes, and bacterial properties in isolates from the different populations. Finally, our current approach provides good insight into common and population-specific clusters, which can be used as a basis for the selection of ESBL-producing isolates from interesting clusters for further detailed characterizations, e.g. by whole genome sequencing.
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Affiliation(s)
- Lars Valentin
- Federal Institute for Risk Assessment, Department Biological Safety, Berlin, Germany
| | - Hannah Sharp
- Federal Institute for Risk Assessment, Department Biological Safety, Berlin, Germany
| | - Katja Hille
- Department of Biometry, Epidemiology and Information Processing, WHO-Collaborating Centre for Research and Training in Veterinary Public Health, University of Veterinary Medicine, Hannover, Germany
| | - Uwe Seibt
- Institute of Pharmacology, Pharmacy and Toxicology, Faculty of Veterinary Medicine, University of Leipzig, Leipzig, Germany
| | - Jennie Fischer
- Federal Institute for Risk Assessment, Department Biological Safety, Berlin, Germany
| | - Yvonne Pfeifer
- Robert Koch Institute, FG13 Nosocomial Pathogens and Antibiotic Resistance, Wernigerode, Germany
| | | | - Silke Nickel
- Bavarian Health and Food Safety Authority, Erlangen, Germany
| | - Judith Schmiedel
- Institute for Medical Microbiology, Justus Liebig University Giessen, Giessen, Germany; German Center for Infection Research (DZIF), Partnersite Giessen-Marburg-Langen, Campus Giessen, Germany
| | - Linda Falgenhauer
- Institute for Medical Microbiology, Justus Liebig University Giessen, Giessen, Germany; German Center for Infection Research (DZIF), Partnersite Giessen-Marburg-Langen, Campus Giessen, Germany
| | - Anika Friese
- Institute for Animal Hygiene and Environmental Health, Free University Berlin, Berlin, Germany
| | - Rolf Bauerfeind
- Institute of Hygiene and Infectious Diseases of Animals, Justus Liebig University Giessen, Giessen, Germany
| | - Uwe Roesler
- Institute for Animal Hygiene and Environmental Health, Free University Berlin, Berlin, Germany
| | - Can Imirzalioglu
- Institute for Medical Microbiology, Justus Liebig University Giessen, Giessen, Germany; German Center for Infection Research (DZIF), Partnersite Giessen-Marburg-Langen, Campus Giessen, Germany
| | - Trinad Chakraborty
- Institute for Medical Microbiology, Justus Liebig University Giessen, Giessen, Germany; German Center for Infection Research (DZIF), Partnersite Giessen-Marburg-Langen, Campus Giessen, Germany
| | - Reiner Helmuth
- Federal Institute for Risk Assessment, Department Biological Safety, Berlin, Germany
| | | | - Guido Werner
- Robert Koch Institute, FG13 Nosocomial Pathogens and Antibiotic Resistance, Wernigerode, Germany
| | - Stefan Schwarz
- Institute of Farm Animal Genetics, Friedrich-Loeffler-Institut, Neustadt-Mariensee, Germany
| | - Beatriz Guerra
- Federal Institute for Risk Assessment, Department Biological Safety, Berlin, Germany
| | - Bernd Appel
- Federal Institute for Risk Assessment, Department Biological Safety, Berlin, Germany
| | - Lothar Kreienbrock
- Department of Biometry, Epidemiology and Information Processing, WHO-Collaborating Centre for Research and Training in Veterinary Public Health, University of Veterinary Medicine, Hannover, Germany
| | - Annemarie Käsbohrer
- Federal Institute for Risk Assessment, Department Biological Safety, Berlin, Germany.
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Jensen HH, Hayes DJ. Impact of Denmark's ban on antimicrobials for growth promotion. Curr Opin Microbiol 2014; 19:30-36. [PMID: 24997397 DOI: 10.1016/j.mib.2014.05.020] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2014] [Revised: 05/27/2014] [Accepted: 05/28/2014] [Indexed: 11/19/2022]
Abstract
Denmark was among the first countries to ban the use of antimicrobials for growth promotion (AGPs) in animal production through an on-going series of actions and regulations since 1995. In 2010 the Yellow Card scheme was adopted to decrease total antimicrobial consumption in pig production through additional restrictions on pig farmers. The withdrawal of AGPs and other restrictions have reduced total antimicrobial use, but at the same time therapeutic drug use has increased and resistance in key zoonotic bacteria has not decreased. Improved use of vaccines and management practices can help reduce losses especially for weaner pigs, but come with additional costs to producers.
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Affiliation(s)
- Helen H Jensen
- Department of Economics and Center for Agricultural and Rural Development, Iowa State University, 578 Heady Hall, Ames, IA 50011-1070, USA.
| | - Dermot J Hayes
- Department of Economics and Center for Agricultural and Rural Development, Iowa State University, 568 Heady Hall, Ames, IA 50011-1070, USA.
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34
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Ranjbar R, Naghoni A, Farshad S, Lashini H, Najafi A, Sadeghifard N, Mammina C. Use of TaqMan® real-time PCR for rapid detection of Salmonella enterica serovar Typhi. Acta Microbiol Immunol Hung 2014; 61:121-30. [PMID: 24939681 DOI: 10.1556/amicr.61.2014.2.3] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
We evaluated the performances of a newly designed real-time polymerase chain reaction (PCR) assay using TaqMan® probes to detect Salmonella Typhi. TaqMan® real-time PCR assays were performed by designed primers and probe based on the staG gene for detecting S. Typhi. The specificity of the assay was evaluated on 15 Salmonella serovars. The analytical specificity was evaluated on 20 non-Salmonella microorganisms. The analytical sensitivity was assessed using decreasing DNA quantities of S. Typhi ATCC 19430. Finally the detection capability of the TaqMan® real-time PCR assay on isolates recovered from patients with Salmonella infections was compared to the conventional PCR assay. Only S. Typhi strain had positive results when subjected to the assay using Typhi-specific real-time PCR. No amplification products were observed in real-time PCR with any of the non-Salmonella microorganisms tested. The TaqMan® real-time PCR was more sensitive than the conventional PCR. In conclusion, we found that the easy-to-use real-time PCR assays were faster than conventional PCR systems. The staG-based TaqMan® real-time PCR assay showed to be specific and sensitive method for the safe and rapid detection of the S. Typhi.
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Affiliation(s)
- Reza Ranjbar
- 1 Baqiyatallah University of Medical Sciences Molecular Biology Research Center Tehran Iran
| | - Ali Naghoni
- 1 Baqiyatallah University of Medical Sciences Molecular Biology Research Center Tehran Iran
| | - Shohreh Farshad
- 2 Shiraz University of Medical Sciences Prof. Alborzi Clinical Microbiology Research Center Shiraz Iran
| | - Hadi Lashini
- 3 Baqiyatallah University of Medical Sciences Applied Virology Research Center Tehran Iran
| | - Ali Najafi
- 1 Baqiyatallah University of Medical Sciences Molecular Biology Research Center Tehran Iran
| | - Nourkhoda Sadeghifard
- 4 Ilam University of Medical Sciences Clinical Microbiology Research Center Ilam Iran
| | - Caterina Mammina
- 5 Department of Sciences for Health Promotion and Mother-Child Care ‘G. D’Alessandro’, University Palermo Italy
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35
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Scientific Opinion on the evaluation of molecular typing methods for major food‐borne microbiological hazards and their use for attribution modelling, outbreak investigation and scanning surveillance: Part 1 (evaluation of methods and applications). EFSA J 2013. [DOI: 10.2903/j.efsa.2013.3502] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
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36
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Laxminarayan R, Duse A, Wattal C, Zaidi AKM, Wertheim HFL, Sumpradit N, Vlieghe E, Hara GL, Gould IM, Goossens H, Greko C, So AD, Bigdeli M, Tomson G, Woodhouse W, Ombaka E, Peralta AQ, Qamar FN, Mir F, Kariuki S, Bhutta ZA, Coates A, Bergstrom R, Wright GD, Brown ED, Cars O. Antibiotic resistance-the need for global solutions. THE LANCET. INFECTIOUS DISEASES 2013; 13:1057-98. [PMID: 24252483 DOI: 10.1016/s1473-3099(13)70318-9] [Citation(s) in RCA: 2490] [Impact Index Per Article: 226.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The causes of antibiotic resistance are complex and include human behaviour at many levels of society; the consequences affect everybody in the world. Similarities with climate change are evident. Many efforts have been made to describe the many different facets of antibiotic resistance and the interventions needed to meet the challenge. However, coordinated action is largely absent, especially at the political level, both nationally and internationally. Antibiotics paved the way for unprecedented medical and societal developments, and are today indispensible in all health systems. Achievements in modern medicine, such as major surgery, organ transplantation, treatment of preterm babies, and cancer chemotherapy, which we today take for granted, would not be possible without access to effective treatment for bacterial infections. Within just a few years, we might be faced with dire setbacks, medically, socially, and economically, unless real and unprecedented global coordinated actions are immediately taken. Here, we describe the global situation of antibiotic resistance, its major causes and consequences, and identify key areas in which action is urgently needed.
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Affiliation(s)
- Ramanan Laxminarayan
- Center for Disease Dynamics, Economics and Policy, Washington, DC, USA; Princeton University, Princeton NJ, USA; Public Health Foundation of India, New Delhi, India
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Abstract
A risk ranking process identified Toxoplasma gondii and pathogenic verocytotoxin-producing Escherichia coli (VTEC) as the most relevant biological hazards for meat inspection of sheep and goats. As these are not detected by traditional meat inspection, a meat safety assurance system using risk-based interventions was proposed. Further studies are required on T. gondii and pathogenic VTEC. If new information confirms these hazards as a high risk to public health from meat from sheep or goats, setting targets at carcass level should be considered. Other elements of the system are risk-categorisation of flocks/herds based on improved Food Chain Information (FCI), classification of abattoirs according to their capability to reduce faecal contamination, and use of improved process hygiene criteria. It is proposed to omit palpation and incision from post-mortem inspection in animals subjected to routine slaughter. For chemical hazards, dioxins and dioxin-like polychlorinated biphenyls were ranked as being of high potential concern. Monitoring programmes for chemical hazards should be more flexible and based on the risk of occurrence, taking into account FCI, which should be expanded to reflect the extensive production systems used, and the ranking of chemical substances, which should be regularly updated and include new hazards. Control programmes across the food chain, national residue control plans, feed control and monitoring of environmental contaminants should be better integrated. Meat inspection is a valuable tool for surveillance and monitoring of animal health and welfare conditions. Omission of palpation and incision would reduce detection effectiveness for tuberculosis and fasciolosis at animal level. Surveillance of tuberculosis at the slaughterhouse in small ruminants should be improved and encouraged, as this is in practice the only surveillance system available. Extended use of FCI could compensate for some, but not all, the information on animal health and welfare lost if only visual post-mortem inspection is applied.
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Barco L, Barrucci F, Olsen JE, Ricci A. Salmonella source attribution based on microbial subtyping. Int J Food Microbiol 2013; 163:193-203. [PMID: 23562696 DOI: 10.1016/j.ijfoodmicro.2013.03.005] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2012] [Revised: 01/20/2013] [Accepted: 03/02/2013] [Indexed: 10/27/2022]
Abstract
Source attribution of cases of food-borne disease represents a valuable tool for identifying and prioritizing effective food-safety interventions. Microbial subtyping is one of the most common methods to infer potential sources of human food-borne infections. So far, Salmonella microbial subtyping source attribution models have been implemented by using serotyping and phage-typing data. Molecular-based methods may prove to be similarly valuable in the future, as already demonstrated for other food-borne pathogens like Campylobacter. This review assesses the state of the art concerning Salmonella source attribution through microbial subtyping approach. It summarizes the available microbial subtyping attribution models and discusses the use of conventional phenotypic typing methods, as well as of the most commonly applied molecular typing methods in the European Union (EU) laboratories in the context of their potential applicability for Salmonella source attribution studies.
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Affiliation(s)
- Lisa Barco
- OIE, National Reference Laboratory for Salmonella, Istituto Zooprofilattico Sperimentale delle Venezie, Viale dell'Università 10, Padova, 35020 Legnaro, Italy
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Venkitanarayanan K, Kollanoor-Johny A, Darre MJ, Donoghue AM, Donoghue DJ. Use of plant-derived antimicrobials for improving the safety of poultry products. Poult Sci 2013; 92:493-501. [PMID: 23300319 DOI: 10.3382/ps.2012-02764] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Salmonella Enteritidis and Campylobacter jejuni are the 2 major foodborne pathogens transmitted through poultry products. Chickens are the reservoir hosts of these pathogens, with their intestinal colonization being the most significant factor causing contamination of meat and eggs. Effective preslaughter strategies for reducing the colonization of birds with these pathogens are critical to improve the microbiological safety of poultry products. An antimicrobial treatment that can be applied through feed represents the most practical and economically viable method for adoption on farms. Additionally, a natural and safe antimicrobial will be better accepted by producers without concerns for toxicity. This symposium talk discussed the potential use of plant-derived, GRAS (generally recognized as safe)-status molecules, caprylic acid, trans-cinnamaldehyde, eugenol, carvacrol, and thymol as feed supplements for reducing cecal populations of Salmonella Enteritidis and C. jejuni in chickens. Additionally, the effect of plant molecules on Salmonella virulence genes critical for cecal colonization in chickens was also discussed.
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Affiliation(s)
- K Venkitanarayanan
- Department of Animal Science, University of Connecticut, Storrs 06269, USA.
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40
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Capita R, Alonso-Calleja C. Antibiotic-resistant bacteria: a challenge for the food industry. Crit Rev Food Sci Nutr 2013; 53:11-48. [PMID: 23035919 DOI: 10.1080/10408398.2010.519837] [Citation(s) in RCA: 229] [Impact Index Per Article: 20.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
Antibiotic-resistant bacteria were first described in the 1940s, but whereas new antibiotics were being discovered at a steady rate, the consequences of this phenomenon were slow to be appreciated. At present, the paucity of new antimicrobials coming into the market has led to the problem of antibiotic resistance fast escalating into a global health crisis. Although the selective pressure exerted by the use of antibiotics (particularly overuse or misuse) has been deemed the major factor in the emergence of bacterial resistance to these antimicrobials, concerns about the role of the food industry have been growing in recent years and have been raised at both national and international levels. The selective pressure exerted by the use of antibiotics (primary production) and biocides (e.g., disinfectants, food and feed preservatives, or decontaminants) is the main driving force behind the selection and spread of antimicrobial resistance throughout the food chain. Genetically modified (GM) crops with antibiotic resistance marker genes, microorganisms added intentionally to the food chain (probiotic or technological) with potentially transferable antimicrobial resistance genes, and food processing technologies used at sub-lethal doses (e.g., alternative non-thermal treatments) are also issues for concern. This paper presents the main trends in antibiotic resistance and antibiotic development in recent decades, as well as their economic and health consequences, current knowledge concerning the generation, dissemination, and mechanisms of antibacterial resistance, progress to date on the possible routes for emergence of resistance throughout the food chain and the role of foods as a vehicle for antibiotic-resistant bacteria. The main approaches to prevention and control of the development, selection, and spread of antibacterial resistance in the food industry are also addressed.
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Affiliation(s)
- Rosa Capita
- Department of Food Hygiene and Food Technology, Veterinary Faculty, University of León, Spain.
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Collignon P. Antibiotic resistance in human Salmonella isolates are related to animal strains. Proc Biol Sci 2012; 279:2922-3; author reply 2924-5. [PMID: 22572205 DOI: 10.1098/rspb.2012.0349] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
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Müller K, Aabo S, Birk T, Mordhorst H, Bjarnadóttir B, Agersø Y. Survival and growth of epidemically successful and nonsuccessful Salmonella enterica clones after freezing and dehydration. J Food Prot 2012; 75:456-64. [PMID: 22410218 DOI: 10.4315/0362-028x.jfp-11-167] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
The spread of epidemically successful nontyphoidal Salmonella clones has been suggested as the most important cause of salmonellosis in industrialized countries. Factors leading to the emergence of success clones are largely unknown, but their ability to survive and grow after physical stress may contribute. During epidemiological studies, a mathematical model was developed that allowed estimation of a factor (q) accounting for the relative ability of Salmonella serovars with different antimicrobial resistances to survive in the food chain and cause human disease. Based on this q-factor, 26 Salmonella isolates were characterized as successful or nonsuccessful. We studied the survival and growth of stationary- and exponential-phase cells of these isolates after freezing for up to 336 days in minced meat. We also investigated survival and growth after dehydration at 10°C and 82% relative humidity (RH) and 25°C and 49% RH for 112 days. Stationary-phase cells were reduced by less than 1 log unit during 1 year of freezing, and growth was initiated with an average lag phase of 1.7 h. Survival was lower in exponentialphase cells, but lag phases tended to be shorter. High humidity and low temperature were less harmful to Salmonella than were low humidity and high temperature. Tolerance to adverse conditions was highest for Salmonella Infantis and one Salmonella Typhimurium U292 isolate and lowest for Salmonella Derby and one Salmonella Typhimurium DT170 isolate. Dehydration, in contrast to freezing, was differently tolerated by the Salmonella strains in this study, but tolerance to freezing and dehydration does not appear to contribute to the emergence of successful Salmonella clones.
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Affiliation(s)
- Karoline Müller
- National Food Institute, Technical University of Denmark, Kemitorvet 204, 2800 Kgs. Lyngby, Denmark.
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Source attribution of human campylobacteriosis using a meta-analysis of case-control studies of sporadic infections. Epidemiol Infect 2012; 140:970-81. [PMID: 22214729 DOI: 10.1017/s0950268811002676] [Citation(s) in RCA: 131] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Campylobacter spp. is a widespread and important cause of human illness worldwide. Disease is frequently associated with foodborne transmission, but other routes of exposure, such as direct contact with live animals and person-to-person transmission, are also recognized. Identifying the most important sources of human disease is essential for prioritizing food safety interventions and setting public health goals. Numerous case-control studies of sporadic infections of campylobacteriosis have been published. These studies investigated a variety of potential risk factors for disease, often using different methodologies and settings. Systematic reviews (SRs) consist of a formal process for literature review focused on a specific research question, and include the identification of relevant literature, quality assessment of relevant studies, summarization or statistical analysis of data, and conclusions. With the objective of identifying the most important risk factors for human sporadic campylobacteriosis, we performed a SR of case-control studies of human sporadic cases and a meta-analysis of the obtained results. A combined SR focusing on Salmonella and Campylobacter studies was performed and the results analysed separately. From 1295 identified references, 131 passed the relevance screening, 73 passed the quality assessment stage, and data was extracted from 72 studies. Of these, 38 focused on campylobacteriosis. Information on exposures of cases and controls, and estimated odds ratios for investigated risk factors were collected and analysed. In the meta-analysis, heterogeneity between the studies and possible sources of bias were investigated, and pooled odds ratios for identified risk factors were estimated. Results suggest that travelling abroad, eating undercooked chicken, environmental sources, and direct contact with farm animals were significant risk factors for campylobacteriosis. Sub-analyses by geographical region, age group, and study period were performed, and differences were discussed.
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Ran L, Wu S, Gao Y, Zhang X, Feng Z, Wang Z, Kan B, Klena JD, Lo Fo Wong DM, Angulo FJ, Varma JK. Laboratory-Based Surveillance of NontyphoidalSalmonellaInfections in China. Foodborne Pathog Dis 2011; 8:921-7. [PMID: 21492026 DOI: 10.1089/fpd.2010.0827] [Citation(s) in RCA: 74] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
Affiliation(s)
- Lu Ran
- Chinese Center for Disease Control and Prevention, Beijing, People's Republic of China
| | - Shuyu Wu
- United States Centers for Disease Control and Prevention China Office, Beijing, People's Republic of China
| | - Yongjun Gao
- Chinese Center for Disease Control and Prevention, Beijing, People's Republic of China
| | - Xin Zhang
- Chinese Center for Disease Control and Prevention, Beijing, People's Republic of China
| | - Zijian Feng
- Chinese Center for Disease Control and Prevention, Beijing, People's Republic of China
| | - Zijun Wang
- Chinese Center for Disease Control and Prevention, Beijing, People's Republic of China
| | - Biao Kan
- Chinese Center for Disease Control and Prevention, Beijing, People's Republic of China
| | - John D. Klena
- United States Centers for Disease Control and Prevention China Office, Beijing, People's Republic of China
| | | | | | - Jay K. Varma
- United States Centers for Disease Control and Prevention China Office, Beijing, People's Republic of China
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Hendriksen RS, Vieira AR, Karlsmose S, Lo Fo Wong DM, Jensen AB, Wegener HC, Aarestrup FM. Global Monitoring of Salmonella Serovar Distribution from the World Health Organization Global Foodborne Infections Network Country Data Bank: Results of Quality Assured Laboratories from 2001 to 2007. Foodborne Pathog Dis 2011; 8:887-900. [DOI: 10.1089/fpd.2010.0787] [Citation(s) in RCA: 434] [Impact Index Per Article: 33.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Affiliation(s)
- Rene S. Hendriksen
- National Food Institute, WHO Collaborating Centre for Antimicrobial Resistance in Foodborne Pathogens and Community Reference Laboratory for Antimicrobial Resistance, Technical University of Denmark, Copenhagen, Denmark
| | - Antonio R. Vieira
- National Food Institute, WHO Collaborating Centre for Antimicrobial Resistance in Foodborne Pathogens and Community Reference Laboratory for Antimicrobial Resistance, Technical University of Denmark, Copenhagen, Denmark
| | - Susanne Karlsmose
- National Food Institute, WHO Collaborating Centre for Antimicrobial Resistance in Foodborne Pathogens and Community Reference Laboratory for Antimicrobial Resistance, Technical University of Denmark, Copenhagen, Denmark
| | | | - Arne B. Jensen
- National Food Institute, WHO Collaborating Centre for Antimicrobial Resistance in Foodborne Pathogens and Community Reference Laboratory for Antimicrobial Resistance, Technical University of Denmark, Copenhagen, Denmark
| | - Henrik C. Wegener
- National Food Institute, WHO Collaborating Centre for Antimicrobial Resistance in Foodborne Pathogens and Community Reference Laboratory for Antimicrobial Resistance, Technical University of Denmark, Copenhagen, Denmark
| | - Frank M. Aarestrup
- National Food Institute, WHO Collaborating Centre for Antimicrobial Resistance in Foodborne Pathogens and Community Reference Laboratory for Antimicrobial Resistance, Technical University of Denmark, Copenhagen, Denmark
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Majtanova L, Majtan J, Majtan V. Trends in phage types of Salmonella enterica serovars Enteritidis and Typhimurium isolated in Slovakia from 1995 to 2009. Diagn Microbiol Infect Dis 2011; 69:454-6. [PMID: 21396545 DOI: 10.1016/j.diagmicrobio.2010.10.017] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2010] [Revised: 10/04/2010] [Accepted: 10/19/2010] [Indexed: 11/25/2022]
Abstract
The phage typing of 3900 isolates of Salmonella Enteritidis and 1741 isolates of Salmonella Typhimurium has been carried out in the period 1995-2009. Among Salmonella Enteritidis in individual years, the most prevalent phage type (PT) was 8. The most predominant PTs of Salmonella Typhimurium were DT104 and U302.
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Affiliation(s)
- Lubica Majtanova
- National Reference Centre for Phage Typing of Salmonellae, Slovak Medical University, Limbova 14, 833 03, Bratislava, Slovakia.
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Vose D, Koupeev T, Mintiens K. A Quantitative Microbiological Risk Assessment of Salmonella spp. in broiler (Gallus gallus) meat production. ACTA ACUST UNITED AC 2011. [DOI: 10.2903/sp.efsa.2011.en-183] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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50
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JENSEN VF, EMBORG HD, AARESTRUP FM. Indications and patterns of therapeutic use of antimicrobial agents in the Danish pig production from 2002 to 2008. J Vet Pharmacol Ther 2011; 35:33-46. [DOI: 10.1111/j.1365-2885.2011.01291.x] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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