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Mather AE, Gilmour MW, Reid SWJ, French NP. Foodborne bacterial pathogens: genome-based approaches for enduring and emerging threats in a complex and changing world. Nat Rev Microbiol 2024:10.1038/s41579-024-01051-z. [PMID: 38789668 DOI: 10.1038/s41579-024-01051-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/16/2024] [Indexed: 05/26/2024]
Abstract
Foodborne illnesses pose a substantial health and economic burden, presenting challenges in prevention due to the diverse microbial hazards that can enter and spread within food systems. Various factors, including natural, political and commercial drivers, influence food production and distribution. The risks of foodborne illness will continue to evolve in step with these drivers and with changes to food systems. For example, climate impacts on water availability for agriculture, changes in food sustainability targets and evolving customer preferences can all have an impact on the ecology of foodborne pathogens and the agrifood niches that can carry microorganisms. Whole-genome and metagenome sequencing, combined with microbial surveillance schemes and insights from the food system, can provide authorities and businesses with transformative information to address risks and implement new food safety interventions across the food chain. In this Review, we describe how genome-based approaches have advanced our understanding of the evolution and spread of enduring bacterial foodborne hazards as well as their role in identifying emerging foodborne hazards. Furthermore, foodborne hazards exist in complex microbial communities across the entire food chain, and consideration of these co-existing organisms is essential to understanding the entire ecology supporting pathogen persistence and transmission in an evolving food system.
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Affiliation(s)
- Alison E Mather
- Quadram Institute Bioscience, Norwich, UK.
- University of East Anglia, Norwich, UK.
| | - Matthew W Gilmour
- Quadram Institute Bioscience, Norwich, UK
- University of East Anglia, Norwich, UK
| | | | - Nigel P French
- Tāuwharau Ora, School of Veterinary Science, Te Kunenga Ki Pūrehuroa, Massey University, Papaioea, Palmerston North, Aotearoa New Zealand
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2
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McLure A, Smith JJ, Firestone SM, Kirk MD, French N, Fearnley E, Wallace R, Valcanis M, Bulach D, Moffatt CRM, Selvey LA, Jennison A, Cribb DM, Glass K. Source attribution of campylobacteriosis in Australia, 2017-2019. RISK ANALYSIS : AN OFFICIAL PUBLICATION OF THE SOCIETY FOR RISK ANALYSIS 2023; 43:2527-2548. [PMID: 37032319 PMCID: PMC10947381 DOI: 10.1111/risa.14138] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Revised: 02/02/2023] [Accepted: 02/09/2023] [Indexed: 06/19/2023]
Abstract
Campylobacter jejuni and Campylobacter coli infections are the leading cause of foodborne gastroenteritis in high-income countries. Campylobacter colonizes a variety of warm-blooded hosts that are reservoirs for human campylobacteriosis. The proportions of Australian cases attributable to different animal reservoirs are unknown but can be estimated by comparing the frequency of different sequence types in cases and reservoirs. Campylobacter isolates were obtained from notified human cases and raw meat and offal from the major livestock in Australia between 2017 and 2019. Isolates were typed using multi-locus sequence genotyping. We used Bayesian source attribution models including the asymmetric island model, the modified Hald model, and their generalizations. Some models included an "unsampled" source to estimate the proportion of cases attributable to wild, feral, or domestic animal reservoirs not sampled in our study. Model fits were compared using the Watanabe-Akaike information criterion. We included 612 food and 710 human case isolates. The best fitting models attributed >80% of Campylobacter cases to chickens, with a greater proportion of C. coli (>84%) than C. jejuni (>77%). The best fitting model that included an unsampled source attributed 14% (95% credible interval [CrI]: 0.3%-32%) to the unsampled source and only 2% to ruminants (95% CrI: 0.3%-12%) and 2% to pigs (95% CrI: 0.2%-11%) The best fitting model that did not include an unsampled source attributed 12% to ruminants (95% CrI: 1.3%-33%) and 6% to pigs (95% CrI: 1.1%-19%). Chickens were the leading source of human Campylobacter infections in Australia in 2017-2019 and should remain the focus of interventions to reduce burden.
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Affiliation(s)
- Angus McLure
- National Centre for Epidemiology and Population HealthThe Australian National UniversityCanberraAustralia
| | - James J. Smith
- Food Safety Standards and Regulation, Health Protection BranchQueensland HealthBrisbaneAustralia
- School of Biology and Environmental Science, Faculty of ScienceQueensland University of TechnologyBrisbaneAustralia
| | - Simon Matthew Firestone
- Melbourne Veterinary School, Faculty of ScienceThe University of MelbourneMelbourneAustralia
| | - Martyn D. Kirk
- National Centre for Epidemiology and Population HealthThe Australian National UniversityCanberraAustralia
| | - Nigel French
- Infectious Disease Research Centre, Hopkirk Research InstituteMassey UniversityPalmerston NorthNew Zealand
- New Zealand Food Safety Science and Research Centre, Hopkirk Research InstituteMassey UniversityPalmerston NorthNew Zealand
| | - Emily Fearnley
- Department for Health and WellbeingGovernment of South AustraliaAdelaideAustralia
| | - Rhiannon Wallace
- Agassiz Research and Development Centre, Agriculture and Agri‐Food CanadaAgassizCanada
| | - Mary Valcanis
- The Doherty Institute for Infection and ImmunityMelbourneAustralia
- Microbiological Diagnostic Unit Public Health LaboratoryThe University of MelbourneMelbourneAustralia
| | - Dieter Bulach
- The Doherty Institute for Infection and ImmunityMelbourneAustralia
- Melbourne BioinformaticsThe University of MelbourneMelbourneAustralia
| | - Cameron R. M. Moffatt
- National Centre for Epidemiology and Population HealthThe Australian National UniversityCanberraAustralia
| | - Linda A. Selvey
- School of Public Health, Faculty of MedicineThe University of QueenslandBrisbaneAustralia
| | - Amy Jennison
- Public Health Microbiology, Forensic and Scientific Services, Queensland HealthBrisbaneAustralia
| | - Danielle M. Cribb
- National Centre for Epidemiology and Population HealthThe Australian National UniversityCanberraAustralia
| | - Kathryn Glass
- National Centre for Epidemiology and Population HealthThe Australian National UniversityCanberraAustralia
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Risk Communication: Epidemiology. REFERENCE MODULE IN FOOD SCIENCE 2023. [PMCID: PMC9423731 DOI: 10.1016/b978-0-12-822521-9.00022-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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dessouky YE, Elsayed SW, Abdelsalam NA, Saif NA, Álvarez-Ordóñez A, Elhadidy M. Genomic insights into zoonotic transmission and antimicrobial resistance in Campylobacter jejuni from farm to fork: a one health perspective. Gut Pathog 2022; 14:44. [PMID: 36471447 PMCID: PMC9721040 DOI: 10.1186/s13099-022-00517-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/19/2022] [Accepted: 11/08/2022] [Indexed: 12/09/2022] Open
Abstract
BACKGROUND Campylobacteriosis represents a global public health threat with various socio-economic impacts. Among different Campylobacter species, Campylobacter jejuni (C. jejuni) is considered to be the foremost Campylobacter species responsible for most of gastrointestinal-related infections. Although these species are reported to primarily inhabit birds, its high genetic and phenotypic diversity allowed their adaptation to other animal reservoirs and to the environment that may impact on human infection. MAIN BODY A stringent and consistent surveillance program based on high resolution subtyping is crucial. Recently, different epidemiological investigations have implemented high-throughput sequencing technologies and analytical pipelines for higher resolution subtyping, accurate source attribution, and detection of antimicrobial resistance determinants among these species. In this review, we aim to present a comprehensive overview on the epidemiology, clinical presentation, antibiotic resistance, and transmission dynamics of Campylobacter, with specific focus on C. jejuni. This review also summarizes recent attempts of applying whole-genome sequencing (WGS) coupled with bioinformatic algorithms to identify and provide deeper insights into evolutionary and epidemiological dynamics of C. jejuni precisely along the farm-to-fork continuum. CONCLUSION WGS is a valuable addition to traditional surveillance methods for Campylobacter. It enables accurate typing of this pathogen and allows tracking of its transmission sources. It is also advantageous for in silico characterization of antibiotic resistance and virulence determinants, and hence implementation of control measures for containment of infection.
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Affiliation(s)
- Yara El dessouky
- grid.440881.10000 0004 0576 5483Biomedical Sciences Program, University of Science and Technology, Zewail City of Science and Technology, Giza, Egypt ,grid.440881.10000 0004 0576 5483Center for Genomics, Helmy Institute for Medical Sciences, Zewail City of Science and Technology, Giza, Egypt
| | - Salma W. Elsayed
- grid.440881.10000 0004 0576 5483Biomedical Sciences Program, University of Science and Technology, Zewail City of Science and Technology, Giza, Egypt ,grid.440881.10000 0004 0576 5483Center for Genomics, Helmy Institute for Medical Sciences, Zewail City of Science and Technology, Giza, Egypt ,grid.7269.a0000 0004 0621 1570Department of Microbiology and Immunology, Faculty of Pharmacy, Ain Shams University, Cairo, Egypt
| | - Nehal Adel Abdelsalam
- grid.440881.10000 0004 0576 5483Biomedical Sciences Program, University of Science and Technology, Zewail City of Science and Technology, Giza, Egypt ,grid.440881.10000 0004 0576 5483Center for Genomics, Helmy Institute for Medical Sciences, Zewail City of Science and Technology, Giza, Egypt ,grid.7776.10000 0004 0639 9286Department of Microbiology and Immunology, Faculty of Pharmacy, Cairo University, Cairo, Egypt
| | - Nehal A. Saif
- grid.440881.10000 0004 0576 5483Biomedical Sciences Program, University of Science and Technology, Zewail City of Science and Technology, Giza, Egypt ,grid.440881.10000 0004 0576 5483Center for Genomics, Helmy Institute for Medical Sciences, Zewail City of Science and Technology, Giza, Egypt
| | - Avelino Álvarez-Ordóñez
- grid.4807.b0000 0001 2187 3167Department of Food Hygiene and Technology and Institute of Food Science and Technology, Universidad de León, León, Spain
| | - Mohamed Elhadidy
- grid.440881.10000 0004 0576 5483Biomedical Sciences Program, University of Science and Technology, Zewail City of Science and Technology, Giza, Egypt ,grid.440881.10000 0004 0576 5483Center for Genomics, Helmy Institute for Medical Sciences, Zewail City of Science and Technology, Giza, Egypt ,grid.10251.370000000103426662Department of Bacteriology, Mycology and Immunology, Faculty of Veterinary Medicine, Mansoura University, Mansoura, Egypt
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Molecular Epidemiological Evidence Implicates Cattle as a Primary Reservoir of Campylobacter jejuni Infecting People via Contaminated Chickens. Pathogens 2022; 11:pathogens11111366. [DOI: 10.3390/pathogens11111366] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Revised: 11/07/2022] [Accepted: 11/08/2022] [Indexed: 11/18/2022] Open
Abstract
The study aimed to determine the relative contribution of cattle to the burden of illness in a model agroecosystem with high rates of human campylobacteriosis (≥ 115 cases/100 K), and high densities of cattle, including large numbers of cattle housed in confined feeding operations (i.e., in southwestern Alberta, Canada). To accomplish this, a large-scale molecular epidemiological analysis of Campylobacter jejuni circulating within the study location was completed. In excess of 8000 isolates of C. jejuni from people (n = 2548 isolates), chickens (n = 1849 isolates), cattle (n = 2921 isolates), and water (n = 771 isolates) were subtyped. In contrast to previous studies, the source attribution estimates of clinical cases attributable to cattle vastly exceeded those attributed to chicken (i.e., three- to six-fold). Moreover, cattle were often colonized by C. jejuni (51%) and shed the bacterium in their feces. A large proportion of study isolates were found in subtypes primarily associated with cattle (46%), including subtypes infecting people and those associated with chickens (19%). The implication of cattle as a primary amplifying reservoir of C. jejuni subtypes in circulation in the study location is supported by the strong cattle association with subtypes that were found in chickens and in people, a lack of evidence indicating the foodborne transmission of C. jejuni from beef and dairy, and the large number of cattle and the substantial quantities of untreated manure containing C. jejuni cells. Importantly, the evidence implicated cattle as a source of C. jejuni which was infecting people through a transmission pathway from cattle to people via the consumption of chicken. This has implications for reducing the burden of campylobacteriosis in the study location and elsewhere.
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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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Resistome Analysis of Campylobacter jejuni Strains Isolated from Human Stool and Primary Sterile Samples in Croatia. Microorganisms 2022; 10:microorganisms10071410. [PMID: 35889129 PMCID: PMC9322926 DOI: 10.3390/microorganisms10071410] [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: 05/31/2022] [Revised: 07/08/2022] [Accepted: 07/11/2022] [Indexed: 11/16/2022] Open
Abstract
Campylobacteriosis represents a global health challenge due to continuously increasing trends of antimicrobial resistance in Campylobacter jejuni. C. jejuni can sometimes cause life-threatening and severe systematic infections (bacteremia, meningitis, and other extraintestinal infections) with very few antibiotics left as treatment options. Bearing in mind that C. jejuni is the predominant species in humans, in this paper, we present a study of the C. jejuni differences in antimicrobial resistance and genotype distribution between strains isolated from stool and primary sterile sites. We compared the genomic data obtained through whole genome sequencing (WGS) and phenotypic susceptibility data of C. jejuni strains. Once antimicrobial susceptibility testing of C. jejuni strains was carried out by the broth microdilution method for six of interest, results were compared to the identified genotypic determinants derived from WGS. The high rate of resistance to fluoroquinolones presented in this study is in accordance with national surveillance data. The proportion of strains with acquired resistance was 71% for ciprofloxacin and 20% for tetracycline. When invasive isolates were analysed separately, 40% exhibited MIC values of ciprofloxacin higher than the ECOFFs, suggesting a lower flouroquinolone resistance rate in invasive isolates. All isolates demonstrated wilde-type phenotype for chloramphenicol, erythromycin, gentamicin, and ertapenem. A special focus and review in this study was performed on a group of C.jejuni strains found in primary sterile samples. Apart from demonstrating a lower resistance rate, these isolates seem genetically more uniform, showing epidemiologically more homogenous patterns, which cluster to several clonal complexes, with CC49 being the most represented clonal complex.
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Tanui CK, Benefo EO, Karanth S, Pradhan AK. A Machine Learning Model for Food Source Attribution of Listeria monocytogenes. Pathogens 2022; 11:pathogens11060691. [PMID: 35745545 PMCID: PMC9230378 DOI: 10.3390/pathogens11060691] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2022] [Revised: 06/06/2022] [Accepted: 06/10/2022] [Indexed: 12/07/2022] Open
Abstract
Despite its low morbidity, listeriosis has a high mortality rate due to the severity of its clinical manifestations. The source of human listeriosis is often unclear. In this study, we investigate the ability of machine learning to predict the food source from which clinical Listeria monocytogenes isolates originated. Four machine learning classification algorithms were trained on core genome multilocus sequence typing data of 1212 L. monocytogenes isolates from various food sources. The average accuracies of random forest, support vector machine radial kernel, stochastic gradient boosting, and logit boost were found to be 0.72, 0.61, 0.7, and 0.73, respectively. Logit boost showed the best performance and was used in model testing on 154 L. monocytogenes clinical isolates. The model attributed 17.5 % of human clinical cases to dairy, 32.5% to fruits, 14.3% to leafy greens, 9.7% to meat, 4.6% to poultry, and 18.8% to vegetables. The final model also provided us with genetic features that were predictive of specific sources. Thus, this combination of genomic data and machine learning-based models can greatly enhance our ability to track L. monocytogenes from different food sources.
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Affiliation(s)
- Collins K. Tanui
- Department of Nutrition and Food Science, University of Maryland, College Park, MD 20742, USA; (C.K.T.); (E.O.B.); (S.K.)
- Center for Food Safety and Security Systems, University of Maryland, College Park, MD 20742, USA
| | - Edmund O. Benefo
- Department of Nutrition and Food Science, University of Maryland, College Park, MD 20742, USA; (C.K.T.); (E.O.B.); (S.K.)
| | - Shraddha Karanth
- Department of Nutrition and Food Science, University of Maryland, College Park, MD 20742, USA; (C.K.T.); (E.O.B.); (S.K.)
| | - Abani K. Pradhan
- Department of Nutrition and Food Science, University of Maryland, College Park, MD 20742, USA; (C.K.T.); (E.O.B.); (S.K.)
- Center for Food Safety and Security Systems, University of Maryland, College Park, MD 20742, USA
- Correspondence:
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Quino W, Caro-Castro J, Hurtado V, Flores-León D, Gonzalez-Escalona N, Gavilan RG. Genomic Analysis and Antimicrobial Resistance of Campylobacter jejuni and Campylobacter coli in Peru. Front Microbiol 2022; 12:802404. [PMID: 35087501 PMCID: PMC8787162 DOI: 10.3389/fmicb.2021.802404] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Accepted: 12/14/2021] [Indexed: 01/22/2023] Open
Abstract
Campylobacter is the leading cause of human bacterial gastroenteritis worldwide and has a major impact on global public health. Whole Genome Sequencing (WGS) is a powerful tool applied in the study of foodborne pathogens. The objective of the present study was to apply WGS to determine the genetic diversity, virulence factors and determinants of antimicrobial resistance of the populations of C. jejuni and C. coli in Peru. A total of 129 Campylobacter strains (108 C. jejuni and 21 C. coli) were sequenced using Illumina Miseq platform. In silico MLST analysis identified a high genetic diversity among those strains with 30 sequence types (STs), several of them within 11 clonal complexes (CC) for C. jejuni, while the strains of C. coli belonged to a single CC with 8 different STs. Phylogeny analysis showed that Peruvian C. jejuni strains were divided into 2 clades with 5 populations, while C. coli formed a single clade with 4 populations. Furthermore, in silico analyses showed the presence of several genes associated with adherence, colonization and invasion among both species: cadF (83.7%), jlpA (81.4%), racR (100%), dnaJ (83.7%), pebA (83.7%), pldA (82.1%), porA (84.5%), ceuE (82.9%), ciaB (78.3%), iamB (86.8%), and flaC (100%). The majority (82.9%) of the Campylobacter strains carried the cdtABC operon which code for cytolethal distending toxin (CDT). Half of them (50.4%) carried genes associated with the presence of T6SS, while the frequency of genes associated with T4SS were relatively low (11.6%). Genetic markers associated with resistance to quinolones, tetracycline (tetO, tetW/N/W), beta-lactamases (blaoxa–61), macrolides (A2075G in 23S rRNA) were found in 94.5, 21.7, 66.7, 6.2, 69.8, and 18.6% of strains, respectively. The cmeABC multidrug efflux operon was present in 78.3% of strains. This study highlights the importance of using WGS in the surveillance of emerging pathogens associated with foodborne diseases, providing genomic information on genetic diversity, virulence mechanisms and determinants of antimicrobial resistance. The description of several Campylobacter genotypes having many virulence factors and resistance to quinolones and tetracyclines circulating in Peru provides important information which helps in the monitoring, control and prevention strategies of this emerging pathogen in our country.
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Affiliation(s)
- Willi Quino
- Laboratorio de Referencia Nacional de Enteropatógenos, Instituto Nacional de Salud, Lima, Peru
| | - Junior Caro-Castro
- Laboratorio de Referencia Nacional de Enteropatógenos, Instituto Nacional de Salud, Lima, Peru
| | - Verónica Hurtado
- Laboratorio de Referencia Nacional de Enteropatógenos, Instituto Nacional de Salud, Lima, Peru
| | - Diana Flores-León
- Laboratorio de Referencia Nacional de Enteropatógenos, Instituto Nacional de Salud, Lima, Peru.,Escuela Profesional de Medicina Humana, Universidad Privada San Juan Bautista, Lima, Peru
| | - Narjol Gonzalez-Escalona
- Center for Food Safety and Applied Nutrition, Food and Drug Administration, College Park, MD, United States
| | - Ronnie G Gavilan
- Laboratorio de Referencia Nacional de Enteropatógenos, Instituto Nacional de Salud, Lima, Peru.,Escuela Profesional de Medicina Humana, Universidad Privada San Juan Bautista, Lima, Peru
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10
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Pasquali F, Remondini D, Snary EL, Hald T, Guillier L. Editorial: Integrating Whole Genome Sequencing Into Source Attribution and Risk Assessment of Foodborne Bacterial Pathogens. Front Microbiol 2021; 12:795098. [PMID: 34899675 PMCID: PMC8661528 DOI: 10.3389/fmicb.2021.795098] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Accepted: 11/01/2021] [Indexed: 11/20/2022] Open
Affiliation(s)
- Frederique Pasquali
- Department of Agricultural and Food Sciences, Alma Mater Studiorum - University of Bologna, Bologna, Italy
| | - Daniel Remondini
- Department of Physics and Astronomy, Alma Mater Studiorum - University of Bologna, Bologna, Italy
| | - Emma Louise Snary
- Department of Epidemiological Sciences, Animal and Plant Health Agency (APHA), Addlestone, United Kingdom
| | - Tine Hald
- National Food Institute, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Laurent Guillier
- Department of Risk Assessment, Agence Nationale de Sécurité Sanitaire de l'Alimentation, de l'Environnement et du Travail (ANSES), Maisons-Alfort, France
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11
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Greening SS, Zhang J, Midwinter AC, Wilkinson DA, Fayaz A, Williamson DA, Anderson MJ, Gates MC, French NP. Transmission dynamics of an antimicrobial resistant Campylobacter jejuni lineage in New Zealand's commercial poultry network. Epidemics 2021; 37:100521. [PMID: 34775297 DOI: 10.1016/j.epidem.2021.100521] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2020] [Revised: 08/05/2021] [Accepted: 11/07/2021] [Indexed: 11/26/2022] Open
Abstract
Understanding the relative contribution of different between-farm transmission pathways is essential in guiding recommendations for mitigating disease spread. This study investigated the association between contact pathways linking poultry farms in New Zealand and the genetic relatedness of antimicrobial resistant Campylobacter jejuni Sequence Type 6964 (ST-6964), with the aim of identifying the most likely contact pathways that contributed to its rapid spread across the industry. Whole-genome sequencing was performed on 167C. jejuni ST-6964 isolates sampled from across 30 New Zealand commercial poultry enterprises. The genetic relatedness between isolates was determined using whole genome multilocus sequence typing (wgMLST). Permutational multivariate analysis of variance and distance-based linear models were used to explore the strength of the relationship between pairwise genetic associations among the C. jejuni isolates and each of several pairwise distance matrices, indicating either the geographical distance between farms or the network distance of transportation vehicles. Overall, a significant association was found between the pairwise genetic relatedness of the C. jejuni isolates and the parent company, the road distance and the network distance of transporting feed vehicles. This result suggests that the transportation of feed within the commercial poultry industry as well as other local contacts between flocks, such as the movements of personnel, may have played a significant role in the spread of C. jejuni. However, further information on the historical contact patterns between farms is needed to fully characterise the risk of these pathways and to understand how they could be targeted to reduce the spread of C. jejuni.
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Affiliation(s)
- Sabrina S Greening
- Epicentre, School of Veterinary Science, Massey University, Palmerston North, New Zealand.
| | - Ji Zhang
- mEpiLab, Infectious Disease Research Centre, School of Veterinary Science, Massey University, Palmerston North, New Zealand; New Zealand Food Safety Science and Research Centre, Hopkirk Research Institute, Massey University, Palmerston North, New Zealand
| | - Anne C Midwinter
- mEpiLab, Infectious Disease Research Centre, School of Veterinary Science, Massey University, Palmerston North, New Zealand
| | - David A Wilkinson
- mEpiLab, Infectious Disease Research Centre, School of Veterinary Science, Massey University, Palmerston North, New Zealand; New Zealand Food Safety Science and Research Centre, Hopkirk Research Institute, Massey University, Palmerston North, New Zealand
| | - Ahmed Fayaz
- mEpiLab, Infectious Disease Research Centre, School of Veterinary Science, Massey University, Palmerston North, New Zealand
| | - Deborah A Williamson
- Microbiological Diagnostic Unit and Public Health Laboratory, University of Melbourne, Parkville, Victoria, Australia
| | - Marti J Anderson
- New Zealand Institute for Advanced Study, Massey University, Auckland, New Zealand
| | - M Carolyn Gates
- Epicentre, School of Veterinary Science, Massey University, Palmerston North, New Zealand
| | - Nigel P French
- mEpiLab, Infectious Disease Research Centre, School of Veterinary Science, Massey University, Palmerston North, New Zealand; New Zealand Food Safety Science and Research Centre, Hopkirk Research Institute, Massey University, Palmerston North, New Zealand
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12
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Campylobacter jejuni in Different Canine Populations: Characteristics and Zoonotic Potential. Microorganisms 2021; 9:microorganisms9112231. [PMID: 34835357 PMCID: PMC8618475 DOI: 10.3390/microorganisms9112231] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2021] [Revised: 10/18/2021] [Accepted: 10/25/2021] [Indexed: 01/18/2023] Open
Abstract
With most epidemiological studies focused on poultry, dogs are often overlooked as a reservoir of Campylobacter, even though these animals maintain close daily contact with humans. The present study aimed to obtain a first insight into the presence and characteristics of Campylobacter spp. in different canine populations in Portugal, and to evaluate its zoonotic potential through genomic analysis. From a total of 125 rectal swabs collected from companion (n = 71) and hunting dogs (n = 54) living in two different settings, rural (n = 75) and urban (n = 50), 32 Campylobacter spp. isolates were obtained. Four different Campylobacter species were identified by Multiplex PCR and MALDI-TOF mass spectrometry, of which Campylobacter jejuni (n = 14, 44%) was overall the most frequently found species. Relevant resistance phenotypes were detected in C. jejuni, with 93% of the isolates being resistant to ciprofloxacin, 64% to tetracycline, and 57% to ampicillin, and three isolates being multi-drug-resistant. Comparison of the phenotypic and genotypic traits with human isolates from Portuguese patients revealed great similarity between both groups. Particularly relevant, the wgMLST analysis allowed the identification of isolates from human and dogs without any apparent epidemiological relationship, sharing high genetic proximity. Notwithstanding the limited sample size, considering the high genomic diversity of C. jejuni, the genetic overlap between human and dog strains observed in this study confirmed that the occurrence of this species in dogs is of public health concern, reinforcing the call for a One Health approach.
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13
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Arning N, Sheppard SK, Bayliss S, Clifton DA, Wilson DJ. Machine learning to predict the source of campylobacteriosis using whole genome data. PLoS Genet 2021; 17:e1009436. [PMID: 34662334 PMCID: PMC8553134 DOI: 10.1371/journal.pgen.1009436] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2021] [Revised: 10/28/2021] [Accepted: 08/26/2021] [Indexed: 11/18/2022] Open
Abstract
Campylobacteriosis is among the world's most common foodborne illnesses, caused predominantly by the bacterium Campylobacter jejuni. Effective interventions require determination of the infection source which is challenging as transmission occurs via multiple sources such as contaminated meat, poultry, and drinking water. Strain variation has allowed source tracking based upon allelic variation in multi-locus sequence typing (MLST) genes allowing isolates from infected individuals to be attributed to specific animal or environmental reservoirs. However, the accuracy of probabilistic attribution models has been limited by the ability to differentiate isolates based upon just 7 MLST genes. Here, we broaden the input data spectrum to include core genome MLST (cgMLST) and whole genome sequences (WGS), and implement multiple machine learning algorithms, allowing more accurate source attribution. We increase attribution accuracy from 64% using the standard iSource population genetic approach to 71% for MLST, 85% for cgMLST and 78% for kmerized WGS data using the classifier we named aiSource. To gain insight beyond the source model prediction, we use Bayesian inference to analyse the relative affinity of C. jejuni strains to infect humans and identified potential differences, in source-human transmission ability among clonally related isolates in the most common disease causing lineage (ST-21 clonal complex). Providing generalizable computationally efficient methods, based upon machine learning and population genetics, we provide a scalable approach to global disease surveillance that can continuously incorporate novel samples for source attribution and identify fine-scale variation in transmission potential.
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Affiliation(s)
- Nicolas Arning
- Big Data institute, Nuffield Department of Population Health, University of Oxford, Li Ka Shing Centre for Health Information and Discovery, Old Road Campus, Oxford, United Kingdom
- * E-mail:
| | - Samuel K. Sheppard
- The Milner Centre of Evolution, Department of Biology & Biochemistry, University of Bath, Claverton Down, Bath, United Kingdom
| | - Sion Bayliss
- The Milner Centre of Evolution, Department of Biology & Biochemistry, University of Bath, Claverton Down, Bath, United Kingdom
| | - David A. Clifton
- Department of Engineering Science, University of Oxford, Oxford, UK; Oxford-Suzhou Centre for Advanced Research, Suzhou, China
| | - Daniel J. Wilson
- Big Data institute, Nuffield Department of Population Health, University of Oxford, Li Ka Shing Centre for Health Information and Discovery, Old Road Campus, Oxford, United Kingdom
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14
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Gomes CN, Barker DOR, Duque SDS, Che EV, Jayamanna V, Taboada EN, Falcão JP. Campylobacter coli isolated in Brazil typed by core genome Multilocus Sequence Typing shows high genomic diversity in a global context. INFECTION GENETICS AND EVOLUTION 2021; 95:105018. [PMID: 34332158 DOI: 10.1016/j.meegid.2021.105018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Revised: 07/21/2021] [Accepted: 07/25/2021] [Indexed: 11/29/2022]
Abstract
Campylobacter has been one of the most common causative agent of bacterial food-borne gastroenteritis in humans worldwide. However, in Brazil the campylobacteriosis has been a neglected disease and there is insufficient data to estimate the incidence of this pathogen in the country. AIMS The current study aimed to determine the phylogenetic relationships among Campylobacter coli strains isolated in Brazil and to compare them with international Campylobacter isolates available in some public databases. METHODS AND RESULTS A total of 63C. coli strains isolated in Brazil were studied. The MLST analysis showed 18 different STs including three STs not yet described in the PubMLST database. The cgMLST allocated the Brazilian strains studied into five main clusters and each cluster comprised groups of strains with nearly identical cgMLST profiles and with significant genetic distance observed among the distinct clusters. The comparison of the Brazilian strains with 3401 isolates from different countries showed a wide distribution of these strains isolated in this country. CONCLUSIONS The results showed a high similarity among some strains studied and a wide distribution of the Brazilian strains when compared to isolates from different countries, which is an interesting data set since it showed a high genetic diversity of these strains from Brazil in a global context. This study contributed for a better genomic characterization of C. coli strains isolated in Brazil and provided important information about the diversity of this clinically-relevant pathogen.
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Affiliation(s)
- Carolina Nogueira Gomes
- Departamento de Análises Clínicas, Toxicológicas e Bromatológicas, Faculdade de Ciências Farmacêuticas de Ribeirão Preto-Universidade de São Paulo, Ribeirão Preto, São Paulo, Brazil
| | | | | | - Emily Victoria Che
- National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Manitoba, Canada
| | - Vasena Jayamanna
- National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Manitoba, Canada
| | | | - Juliana Pfrimer Falcão
- Departamento de Análises Clínicas, Toxicológicas e Bromatológicas, Faculdade de Ciências Farmacêuticas de Ribeirão Preto-Universidade de São Paulo, Ribeirão Preto, São Paulo, Brazil.
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15
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Saif NA, Cobo-Díaz JF, Elserafy M, El-Shiekh I, Álvarez-Ordóñez A, Mouftah SF, Elhadidy M. A pilot study revealing host-associated genetic signatures for source attribution of sporadic Campylobacter jejuni infection in Egypt. Transbound Emerg Dis 2021; 69:1847-1861. [PMID: 34033263 DOI: 10.1111/tbed.14165] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Accepted: 05/22/2021] [Indexed: 11/30/2022]
Abstract
Campylobacter jejuni (C. jejuni), is considered among the most common bacterial causes of human bacterial gastroenteritis worldwide. The epidemiology and the transmission dynamics of campylobacteriosis in Egypt remain poorly defined due to the limited use of high-resolution typing methods. In this pilot study, we evaluated the discriminatory power of multiple typing 'gene-by-gene based' techniques to characterize C. jejuni obtained from different sources and estimate the relative contribution of different potential sources of C. jejuni infection in Egypt. Whole genome sequencing (WGS) was performed on 90 C. jejuni isolates recovered from clinical samples, retail chicken, and dairy products in Egypt from 2017 to 2018. Comparative genomic analysis was performed using conventional seven-locus multilocus sequence typing (MLST), ribosomal MLST (rMLST), core genome MLST (cgMLST), allelic variation in 15 host-segregating (HS) markers, and comparative genomic fingerprinting (CGF40). The probabilistic source attribution was performed via STRUCTURE software using MLST, CGF40, cgMLST and allelic variation in HS markers. Comparison of the discriminatory power of the aforementioned genotyping methods revealed cgMLST to be the most discriminative method, followed by HS markers. The source attribution analysis showed the role of retail chicken as a source of infection among clinical cases in Egypt when HS and cgMLST were used (64.2% and 52.3% of clinical isolates were assigned to this source, respectively). Interestingly, the cattle reservoir was also identified as a contributor to C. jejuni infection in Egypt; 35.8% and 47.7% of clinical isolates were assigned to this source by HS and cgMLST, respectively. Here, we provided evidence of the importance of using WGS typing methods to facilitate source tracking of C. jejuni. Our findings suggest the importance of non-poultry sources, together with the previously reported role of retail chicken in human campylobacteriosis in Egypt that can provide insights to inform national control measures.
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Affiliation(s)
- Nehal A Saif
- Biomedical Sciences Program, University of Science and Technology, Zewail City of Science and Technology, Giza, Egypt
| | - José F Cobo-Díaz
- Department of Food Hygiene and Technology, Universidad de León, León, Spain.,Institute of Food Science and Technology, Universidad de León, León, Spain
| | - Menattallah Elserafy
- Biomedical Sciences Program, University of Science and Technology, Zewail City of Science and Technology, Giza, Egypt.,Center for Genomics, Helmy Institute for Medical Sciences, Zewail City of Science and Technology, Giza, Egypt
| | - Iman El-Shiekh
- Biomedical Sciences Program, University of Science and Technology, Zewail City of Science and Technology, Giza, Egypt.,Center for Genomics, Helmy Institute for Medical Sciences, Zewail City of Science and Technology, Giza, Egypt
| | - Avelino Álvarez-Ordóñez
- Department of Food Hygiene and Technology, Universidad de León, León, Spain.,Institute of Food Science and Technology, Universidad de León, León, Spain
| | - Shaimaa F Mouftah
- Biomedical Sciences Program, University of Science and Technology, Zewail City of Science and Technology, Giza, Egypt
| | - Mohamed Elhadidy
- Biomedical Sciences Program, University of Science and Technology, Zewail City of Science and Technology, Giza, Egypt.,Department of Bacteriology, Mycology, and Immunology, Faculty of Veterinary Medicine, Mansoura University, Mansoura, Egypt
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16
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Mughini-Gras L, Pijnacker R, Coipan C, Mulder AC, Fernandes Veludo A, de Rijk S, van Hoek AHAM, Buij R, Muskens G, Koene M, Veldman K, Duim B, van der Graaf-van Bloois L, van der Weijden C, Kuiling S, Verbruggen A, van der Giessen J, Opsteegh M, van der Voort M, Castelijn GAA, Schets FM, Blaak H, Wagenaar JA, Zomer AL, Franz E. Sources and transmission routes of campylobacteriosis: A combined analysis of genome and exposure data. J Infect 2020; 82:216-226. [PMID: 33275955 DOI: 10.1016/j.jinf.2020.09.039] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2020] [Revised: 09/13/2020] [Accepted: 09/26/2020] [Indexed: 01/24/2023]
Abstract
OBJECTIVES To determine the contributions of several animal and environmental sources of human campylobacteriosis and identify source-specific risk factors. METHODS 1417 Campylobacter jejuni/coli isolates from the Netherlands in 2017-2019 were whole-genome sequenced, including isolates from human cases (n = 280), chickens/turkeys (n = 238), laying hens (n = 56), cattle (n = 158), veal calves (n = 49), sheep/goats (n = 111), pigs (n = 110), dogs/cats (n = 100), wild birds (n = 62), and surface water (n = 253). Questionnaire-based exposure data was collected. Source attribution was performed using core-genome multilocus sequence typing. Risk factors were determined on the attribution estimates. RESULTS Cases were mostly attributed to chickens/turkeys (48.2%), dogs/cats (18.0%), cattle (12.1%), and surface water (8.5%). Of the associations identified, never consuming chicken, as well as frequent chicken consumption, and rarely washing hands after touching raw meat, were risk factors for chicken/turkey-attributable infections. Consuming unpasteurized milk or barbecued beef increased the risk for cattle-attributable infections. Risk factors for infections attributable to environmental sources were open water swimming, contact with dog faeces, and consuming non-chicken/turkey avian meat like game birds. CONCLUSIONS Poultry and cattle are the main livestock sources of campylobacteriosis, while pets and surface water are important non-livestock sources. Foodborne transmission is only partially consistent with the attributions, as frequency and alternative pathways of exposure are significant.
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Affiliation(s)
- Lapo Mughini-Gras
- Centre for Infectious Disease Control (CIb), National Institute for Public Health and the Environment (RIVM), Bilthoven, the Netherlands; Institute for Risk Assessment Sciences (IRAS), Utrecht University, Utrecht, the Netherlands.
| | - Roan Pijnacker
- Centre for Infectious Disease Control (CIb), National Institute for Public Health and the Environment (RIVM), Bilthoven, the Netherlands
| | - Claudia Coipan
- Centre for Infectious Disease Control (CIb), National Institute for Public Health and the Environment (RIVM), Bilthoven, the Netherlands
| | - Annemieke C Mulder
- Centre for Infectious Disease Control (CIb), National Institute for Public Health and the Environment (RIVM), Bilthoven, the Netherlands
| | | | - Sharona de Rijk
- Centre for Infectious Disease Control (CIb), National Institute for Public Health and the Environment (RIVM), Bilthoven, the Netherlands
| | - Angela H A M van Hoek
- Centre for Infectious Disease Control (CIb), National Institute for Public Health and the Environment (RIVM), Bilthoven, the Netherlands
| | - Ralph Buij
- Wageningen Environmental Research (WER), Wageningen University & Research (WUR), Wageningen, the Netherlands
| | - Gerard Muskens
- Wageningen Environmental Research (WER), Wageningen University & Research (WUR), Wageningen, the Netherlands
| | - Miriam Koene
- Wageningen Bioveterinary Research (WBVR), Wageningen University & Research (WUR), Lelystad, the Netherlands
| | - Kees Veldman
- Wageningen Bioveterinary Research (WBVR), Wageningen University & Research (WUR), Lelystad, the Netherlands
| | - Birgitta Duim
- Department of Infectious Diseases and Immunology (I&I), Utrecht University & WHO Collaborating Center for Campylobacter/OIE Reference Laboratory for Campylobacteriosis, Utrecht, the Netherlands
| | - Linda van der Graaf-van Bloois
- Department of Infectious Diseases and Immunology (I&I), Utrecht University & WHO Collaborating Center for Campylobacter/OIE Reference Laboratory for Campylobacteriosis, Utrecht, the Netherlands
| | - Coen van der Weijden
- Netherlands Food and Consumer Product Safety Authority (NVWA), Utrecht, the Netherlands
| | - Sjoerd Kuiling
- Centre for Infectious Disease Control (CIb), National Institute for Public Health and the Environment (RIVM), Bilthoven, the Netherlands
| | - Anjo Verbruggen
- Centre for Infectious Disease Control (CIb), National Institute for Public Health and the Environment (RIVM), Bilthoven, the Netherlands
| | - Joke van der Giessen
- Centre for Infectious Disease Control (CIb), National Institute for Public Health and the Environment (RIVM), Bilthoven, the Netherlands
| | - Marieke Opsteegh
- Centre for Infectious Disease Control (CIb), National Institute for Public Health and the Environment (RIVM), Bilthoven, the Netherlands
| | - Menno van der Voort
- Wageningen Food Safety Research (WFSR), Wageningen University & Research (WUR), Wageningen, the Netherlands
| | - Greetje A A Castelijn
- Wageningen Food Safety Research (WFSR), Wageningen University & Research (WUR), Wageningen, the Netherlands
| | - Franciska M Schets
- Centre for Infectious Disease Control (CIb), National Institute for Public Health and the Environment (RIVM), Bilthoven, the Netherlands
| | - Hetty Blaak
- Centre for Infectious Disease Control (CIb), National Institute for Public Health and the Environment (RIVM), Bilthoven, the Netherlands
| | - Jaap A Wagenaar
- Department of Infectious Diseases and Immunology (I&I), Utrecht University & WHO Collaborating Center for Campylobacter/OIE Reference Laboratory for Campylobacteriosis, Utrecht, the Netherlands
| | - Aldert L Zomer
- Department of Infectious Diseases and Immunology (I&I), Utrecht University & WHO Collaborating Center for Campylobacter/OIE Reference Laboratory for Campylobacteriosis, Utrecht, the Netherlands
| | - Eelco Franz
- Centre for Infectious Disease Control (CIb), National Institute for Public Health and the Environment (RIVM), Bilthoven, the Netherlands
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17
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Lake RJ, Campbell DM, Hathaway SC, Ashmore E, Cressey PJ, Horn BJ, Pirikahu S, Sherwood JM, Baker MG, Shoemack P, Benschop J, Marshall JC, Midwinter AC, Wilkinson DA, French NP. Source attributed case-control study of campylobacteriosis in New Zealand. Int J Infect Dis 2020; 103:268-277. [PMID: 33221520 DOI: 10.1016/j.ijid.2020.11.167] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Revised: 11/11/2020] [Accepted: 11/15/2020] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND Following an initial reduction in human campylobacteriosis in New Zealand after the implementation of poultry food chain-focused interventions during 2006-2008, further decline has been relatively small. We report a year-long study of notified campylobacteriosis cases, incorporating a case control study combined with a source attribution study. The purpose was to generate up-to-date evidence on the relative contributions of different sources of campylobacteriosis in New Zealand. METHODS The study approach included: • A case-control study of notified cases (aged six months or more) sampled in a major urban centre (Auckland, every second case) and a mixed urban/rural area (Manawatū/Whanganui, every case), between 12 March 2018 and 11 March 2019. • Source attribution of human campylobacteriosis cases sampled from these two regions over the study period by modelling of multilocus sequence typing data of Campylobacter jejuni and C. coli isolates from faecal samples of notified human cases and relevant sources (poultry, cattle, sheep). RESULTS Most cases (84%) were infected with strains attributed to a poultry source, while 14% were attributed to a cattle source. Approximately 90% of urban campylobacteriosis cases were attributed to poultry sources, compared to almost 75% of rural cases. Poultry consumption per se was not identified as a significant risk factor. However specific risk factors related to poultry meat preparation and consumption did result in statistically significantly elevated odds ratios. CONCLUSIONS The overall findings combining source attribution and analysis of specific risk factors indicate that poultry meat remains a dominant pathway for exposure and infection.
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Affiliation(s)
- R J Lake
- Risk Assessment and Social Systems Group, Institute of Environmental Science and Research, Christchurch Science Centre, 27 Creyke Road, Ilam, Christchurch 8041, New Zealand; New Zealand Food Safety Science and Research Centre, School of Veterinary Science, Massey University, New Zealand.
| | - D M Campbell
- New Zealand Food Safety, Ministry of Primary Industries, PO Box 2526, Wellington 6140, New Zealand
| | - S C Hathaway
- New Zealand Food Safety, Ministry of Primary Industries, PO Box 2526, Wellington 6140, New Zealand
| | - E Ashmore
- Risk Assessment and Social Systems Group, Institute of Environmental Science and Research, Christchurch Science Centre, 27 Creyke Road, Ilam, Christchurch 8041, New Zealand
| | - P J Cressey
- Risk Assessment and Social Systems Group, Institute of Environmental Science and Research, Christchurch Science Centre, 27 Creyke Road, Ilam, Christchurch 8041, New Zealand
| | - B J Horn
- Risk Assessment and Social Systems Group, Institute of Environmental Science and Research, Christchurch Science Centre, 27 Creyke Road, Ilam, Christchurch 8041, New Zealand
| | - S Pirikahu
- School of Population and Global Health, The University of Western Australia, 35 Stirling Hwy, Crawley WA, Perth, Australia
| | - J M Sherwood
- Institute of Environmental Science and Research, Kenepuru Science Centre, PO Box 50348, Porirua 5240, New Zealand
| | - M G Baker
- University of Otago, Wellington, Box 7343, Wellington, 6242, New Zealand
| | - P Shoemack
- Bay of Plenty District Health Board, PO Box 2120, Tauranga, 3140, New Zealand
| | - J Benschop
- Tāwharau Ora, School of Veterinary Science, Massey University, Private Bag 11-222, Palmerston North, 4442, New Zealand
| | - J C Marshall
- School of Fundamental Sciences, Massey University, Tennent Drive, Palmerston North, 4474, New Zealand
| | - A C Midwinter
- Tāwharau Ora, School of Veterinary Science, Massey University, Private Bag 11-222, Palmerston North, 4442, New Zealand
| | - D A Wilkinson
- Tāwharau Ora, School of Veterinary Science, Massey University, Private Bag 11-222, Palmerston North, 4442, New Zealand
| | - N P French
- New Zealand Food Safety Science and Research Centre, School of Veterinary Science, Massey University, New Zealand; Tāwharau Ora, School of Veterinary Science, Massey University, Private Bag 11-222, Palmerston North, 4442, New Zealand
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18
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Contribution of Foods and Poor Food-Handling Practices to the Burden of Foodborne Infectious Diseases in France. Foods 2020; 9:foods9111644. [PMID: 33187291 PMCID: PMC7697675 DOI: 10.3390/foods9111644] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Revised: 11/03/2020] [Accepted: 11/06/2020] [Indexed: 01/25/2023] Open
Abstract
The foodborne disease burden (FBDB) related to 26 major biological hazards in France was attributed to foods and poor food-handling practices at the final food preparation step, in order to develop effective intervention strategies, especially food safety campaigns. Campylobacter spp. and non-typhoidal Salmonella accounted for more than 60% of the FBDB. Approximately 30% of the FBDB were attributed to 11 other hazards including bacteria, viruses and parasites. Meats were estimated as the main contributing food category causing (50-69%) (CI90) of the FBDB with (33-44%), (9-21%), (4-20%) (CI90) of the FBDB for poultry, pork and beef, respectively. Dairy products, eggs, raw produce and complex foods caused each approximately (5-20%) (CI90) of the FBDB. When foods are contaminated before the final preparation step, we estimated that inadequate cooking, cross-contamination and inadequate storage contribute for (19-49%), (7-34%) and (9-23%) (CI90) of the FBDB, respectively; (15-33%) (CI90) of the FBDB were attributed to the initial contamination of ready-to-eat foods-without any contribution from final food handlers. The thorough implementation of good hygienic practices (GHPs) at the final food preparation step could potentially reduce the FBDB by (67-85%) (CI90) (mainly with the prevention of cross-contamination and adequate cooking and storage).
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19
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Inglis GD, Taboada EN, Boras VF. Rates of fluoroquinolone resistance in domestically acquired Campylobacter jejuni are increasing in people living within a model study location in Canada. Can J Microbiol 2020; 67:37-52. [PMID: 32805182 DOI: 10.1139/cjm-2020-0146] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Antimicrobial resistance was evaluated in Campylobacter jejuni isolated from 1291 diarrheic people over a 15-year period (2004-2018) in southwestern Alberta, a model location in Canada with a high rate of campylobacteriosis. The prevalence of resistance to chloramphenicol, clindamycin, erythromycin, and gentamicin was low during the examination period (≤4.8%). Resistance to tetracycline remained consistently high (41.6%-65.1%), and resistance was primarily conferred by plasmid-borne tetO (96.2%). Resistance rates to ciprofloxacin and nalidixic acid increased substantially over the examination period, with a maximal fluoroquinolone resistance (FQR) prevalence of 28.9% in 2016. The majority of C. jejuni isolates resistant to ciprofloxacin (93.9%) contained a C257T single nucleotide polymorphism within the gyrA chromosomal gene. Follow up with infected people indicated that the observed increase in FQR was primarily due to domestically acquired infections. Moreover, the majority of FQ-resistant C. jejuni subtypes (82.6%) were endemic in Canada, primarily linked to cattle and chicken reservoirs; 18.4% of FQ-resistant isolates were assigned to three subtypes, predominantly associated with cattle. Study findings indicate the need to prioritize FQR monitoring in C. jejuni infections in Canada and to elucidate the dynamics of the emergence and transmission of resistant C. jejuni strains within and from cattle and chicken reservoirs.
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Affiliation(s)
- G Douglas Inglis
- Agriculture and Agri-Food Canada, 5403-1st Avenue South, Lethbridge, AB T1J 4B1, Canada
| | - Eduardo N Taboada
- National Microbiology Laboratory, Public Health Agency of Canada, 1015 Arlington Street, Winnipeg, MB R3E 3M4, Canada
| | - Valerie F Boras
- Department of Laboratory Medicine, Chinook Regional Hospital, 960-19th Street South, Lethbridge, AB T1J 1W5, Canada
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20
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Wallace RL, Bulach DM, Jennison AV, Valcanis M, McLure A, Smith JJ, Graham T, Saputra T, Firestone S, Symes S, Waters N, Stylianopoulos A, Kirk MD, Glass K. Molecular characterization of Campylobacter spp. recovered from beef, chicken, lamb and pork products at retail in Australia. PLoS One 2020; 15:e0236889. [PMID: 32730330 PMCID: PMC7392323 DOI: 10.1371/journal.pone.0236889] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2020] [Accepted: 07/15/2020] [Indexed: 02/02/2023] Open
Abstract
Australian rates of campylobacteriosis are among the highest in developed countries, yet only limited work has been done to characterize Campylobacter spp. in Australian retail products. We performed whole genome sequencing (WGS) on 331 C. coli and 285 C. jejuni from retail chicken meat, as well as beef, chicken, lamb and pork offal (organs). Campylobacter isolates were highly diverse, with 113 sequence types (STs) including 38 novel STs, identified from 616 isolates. Genomic analysis suggests very low levels (2.3-15.3%) of resistance to aminoglycoside, beta-lactam, fluoroquinolone, macrolide and tetracycline antibiotics. A majority (>90%) of isolates (52/56) possessing the fluoroquinolone resistance-associated T86I mutation in the gyrA gene belonged to ST860, ST2083 or ST7323. The 44 pork offal isolates were highly diverse, representing 33 STs (11 novel STs) and harboured genes associated with resistance to aminoglycosides, lincosamides and macrolides not generally found in isolates from other sources. Prevalence of multidrug resistant genotypes was very low (<5%), but ten-fold higher in C. coli than C. jejuni. This study highlights that Campylobacter spp. from retail products in Australia are highly genotypically diverse and important differences in antimicrobial resistance exist between Campylobacter species and animal sources.
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Affiliation(s)
- Rhiannon L. Wallace
- National Centre for Epidemiology and Population Health, The Australian National University, Canberra, Australian Capital Territory, Australia
| | - Dieter M. Bulach
- Melbourne Bioinformatics, The University of Melbourne, Melbourne, Victoria, Australia
- Microbiological Diagnostic Unit Public Health Laboratory, The Peter Doherty Institute, Melbourne, Victoria, Australia
| | - Amy V. Jennison
- Public Health Microbiology, Forensic and Scientific Services, Queensland Health, Brisbane, Queensland, Australia
| | - Mary Valcanis
- Microbiological Diagnostic Unit Public Health Laboratory, The Peter Doherty Institute, Melbourne, Victoria, Australia
| | - Angus McLure
- National Centre for Epidemiology and Population Health, The Australian National University, Canberra, Australian Capital Territory, Australia
| | - James J. Smith
- Food Safety Standards and Regulation, Health Protection Branch, Queensland Health, Brisbane, Queensland, Australia
| | - Trudy Graham
- Public Health Microbiology, Forensic and Scientific Services, Queensland Health, Brisbane, Queensland, Australia
| | - Themy Saputra
- New South Wales Food Authority, NSW Government, Sydney, New South Wales, Australia
| | - Simon Firestone
- Melbourne Veterinary School, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, Victoria, Australia
| | - Sally Symes
- Department of Health and Human Services, Victoria State Government, Melbourne, Victoria, Australia
| | - Natasha Waters
- ACT Government Analytical Laboratory, Australian Capital Territory Health Directorate, Canberra, Australian Capital Territory, Australia
| | - Anastasia Stylianopoulos
- Department of Health and Human Services, Victoria State Government, Melbourne, Victoria, Australia
| | - Martyn D. Kirk
- National Centre for Epidemiology and Population Health, The Australian National University, Canberra, Australian Capital Territory, Australia
| | - Kathryn Glass
- National Centre for Epidemiology and Population Health, The Australian National University, Canberra, Australian Capital Territory, Australia
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21
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A One Health approach to prevention, treatment, and control of campylobacteriosis. Curr Opin Infect Dis 2020; 32:453-460. [PMID: 31305492 DOI: 10.1097/qco.0000000000000570] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
PURPOSE OF REVIEW To review recent findings regarding the control and treatment of campylobacteriosis. RECENT FINDINGS The application of improved diagnostics has led to an upward shift in the attributable burden of Campylobacter infections, in both the United States and Europe as well as in resource-poor settings. Increased focus has brought a fundamental feature of campylobacteriosis -- the ability to cause relapsing disease back into focus, and expanding data on antimicrobial resistance has lead from a switch in first-line therapy for severe diarrhea from quinolones to azithromycin in most contexts, even as evidence of expanding macrolide resistance emerges. SUMMARY Campylobacter spp. infection is a common infection worldwide. Antibiotic-resistant Campylobacter spp. has become an emerging threat with the increase in industrial poultry production, as well as the broad use of antibiotics in both animals and humans.
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22
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French NP, Zhang J, Carter GP, Midwinter AC, Biggs PJ, Dyet K, Gilpin BJ, Ingle DJ, Mulqueen K, Rogers LE, Wilkinson DA, Greening SS, Muellner P, Fayaz A, Williamson DA. Genomic Analysis of Fluoroquinolone- and Tetracycline-Resistant Campylobacter jejuni Sequence Type 6964 in Humans and Poultry, New Zealand, 2014-2016. Emerg Infect Dis 2020; 25:2226-2234. [PMID: 31742539 PMCID: PMC6874264 DOI: 10.3201/eid2512.190267] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
In 2014, antimicrobial drug–resistant Campylobacter jejuni sequence type 6964 emerged contemporaneously in poultry from 3 supply companies in the North Island of New Zealand and as a major cause of campylobacteriosis in humans in New Zealand. This lineage, not previously identified in New Zealand, was resistant to tetracycline and fluoroquinolones. Genomic analysis revealed divergence into 2 major clades; both clades were associated with human infection, 1 with poultry companies A and B and the other with company C. Accessory genome evolution was associated with a plasmid, phage insertions, and natural transformation. We hypothesize that the tetO gene and a phage were inserted into the chromosome after conjugation, leaving a remnant plasmid that was lost from isolates from company C. The emergence and rapid spread of a resistant clone of C. jejuni in New Zealand, coupled with evolutionary change in the accessory genome, demonstrate the need for ongoing Campylobacter surveillance among poultry and humans.
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23
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Hetman BM, Mutschall SK, Carrillo CD, Thomas JE, Gannon VPJ, Inglis GD, Taboada EN. "These Aren't the Strains You're Looking for": Recovery Bias of Common Campylobacter jejuni Subtypes in Mixed Cultures. Front Microbiol 2020; 11:541. [PMID: 32328044 PMCID: PMC7160300 DOI: 10.3389/fmicb.2020.00541] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2019] [Accepted: 03/12/2020] [Indexed: 12/20/2022] Open
Abstract
Microbiological surveillance of the food chain plays a critical role in improving our understanding of the distribution and circulation of food-borne pathogens along the farm to fork continuum toward the development of interventions to reduce the burden of illness. The application of molecular subtyping to bacterial isolates collected through surveillance has led to the identification of strains posing the greatest risk to public health. Past evidence suggests that enrichment methods for Campylobacter jejuni, a leading bacterial foodborne pathogen worldwide, may lead to the differential recovery of subtypes, obscuring our ability to infer the composition of a mixed-strain sample and potentially biasing prevalence estimates in surveillance data. To assess the extent of potential selection bias resulting from enrichment-based isolation methods, we compared enrichment and non-enrichment isolation of mixed subtype cultures of C. jejuni, followed by subtype-specific enumeration using both colony plate-counts and digital droplet PCR. Results differed from the null hypothesis that similar proportions of C. jejuni subtypes are recovered from both methods. Our results also indicated a significant effect of subtype prevalence on isolation frequency post-recovery, with the recovery of more common subtypes being consistently favored. This bias was exacerbated when an enrichment step was included in the isolation procedure. Taken together, our results emphasize the importance of selecting multiple colonies per sample, and where possible, the use of both enrichment and non-enrichment isolation procedures to maximize the likelihood of recovering multiple subtypes present in a sample. Moreover, the effects of subtype-specific recovery bias should be considered in the interpretation of strain prevalence data toward improved risk assessment from microbiological surveillance data.
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Affiliation(s)
- Benjamin M Hetman
- Department of Biological Sciences, University of Lethbridge, Lethbridge, AB, Canada.,National Microbiology Laboratory at Lethbridge, Public Health Agency of Canada, Lethbridge, AB, Canada
| | - Steven K Mutschall
- National Centre for Animal Diseases, Canadian Food Inspection Agency, Lethbridge, AB, Canada
| | - Catherine D Carrillo
- Canadian Food Inspection Agency, Ottawa Laboratory (Carling), Ottawa, ON, Canada
| | - James E Thomas
- Department of Biological Sciences, University of Lethbridge, Lethbridge, AB, Canada
| | - Victor P J Gannon
- National Microbiology Laboratory at Lethbridge, Public Health Agency of Canada, Lethbridge, AB, Canada
| | - G Douglas Inglis
- Lethbridge Research and Development Centre, Agriculture and Agri-Food Canada, Lethbridge, AB, Canada
| | - Eduardo N Taboada
- National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, MB, Canada
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24
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Shifts in the Molecular Epidemiology of Campylobacter jejuni Infections in a Sentinel Region of New Zealand following Implementation of Food Safety Interventions by the Poultry Industry. Appl Environ Microbiol 2020; 86:AEM.01753-19. [PMID: 31862724 DOI: 10.1128/aem.01753-19] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2019] [Accepted: 12/12/2019] [Indexed: 01/19/2023] Open
Abstract
In 2006, New Zealand had the highest notification rate of campylobacteriosis in the world, and poultry was considered the leading source of campylobacteriosis. Implementation of food safety interventions by the poultry industry led to a decrease in the campylobacteriosis notification rate. The aim is to examine the impact of targeted food safety interventions implemented by the New Zealand poultry industry on the source attribution of Campylobacter jejuni infections in a sentinel region. Campylobacter jejuni isolates collected from the Manawatu region of New Zealand between 2005 and 2007 ("before intervention") and 2008 and 2015 ("after intervention") from human clinical cases, chicken meat, ruminant feces, environmental water, and wild bird sources were subtyped by multilocus sequence typing. Viable counts of Campylobacter spp. from carcasses were analyzed using a zero-inflated Poisson regression model. In the period before intervention, sequence type 474 (ST-474) was the most common sequence type (ST) recovered from human cases, accounting for 28.2% of the isolates. After intervention, the proportion of human cases positive for ST-474 reduced to 9.3%. Modeling indicated that chicken meat, primarily from one supplier, was the main source of C. jejuni infection in the Manawatu region before intervention. However, after intervention poultry collectively had a similar attribution to ruminants, but more human cases were attributed to ruminants than any single chicken supplier. Viable counts on carcasses were lower in all poultry suppliers after intervention. This study provides evidence of changes in the source attribution of campylobacteriosis following targeted food safety interventions in one sector of the food supply chain.IMPORTANCE This study provides a unique insight into the effects of food safety interventions implemented in one sector of the food industry on the transmission routes of a major foodborne agent. Following the implementation of food safety interventions by the poultry industry, shifts in the molecular epidemiology of Campylobacter jejuni infections in a sentinel region of New Zealand were observed. Targeted interventions to reduce disease incidence are effective but require continued surveillance and analysis to indicate where further interventions may be beneficial.
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25
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Thomas KM, de Glanville WA, Barker GC, Benschop J, Buza JJ, Cleaveland S, Davis MA, French NP, Mmbaga BT, Prinsen G, Swai ES, Zadoks RN, Crump JA. Prevalence of Campylobacter and Salmonella in African food animals and meat: A systematic review and meta-analysis. Int J Food Microbiol 2020; 315:108382. [PMID: 31710971 PMCID: PMC6985902 DOI: 10.1016/j.ijfoodmicro.2019.108382] [Citation(s) in RCA: 65] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2019] [Revised: 08/20/2019] [Accepted: 10/02/2019] [Indexed: 02/07/2023]
Abstract
BACKGROUND Campylobacter and Salmonella, particularly non-typhoidal Salmonella, are important bacterial enteric pathogens of humans which are often carried asymptomatically in animal reservoirs. Bacterial foodborne infections, including those derived from meat, are associated with illness and death globally but the burden is disproportionately high in Africa. Commercial meat production is increasing and intensifying in many African countries, creating opportunities and threats for food safety. METHODS Following Preferred Reporting Items for Systematic Reviews and Meta-analyses (PRISMA) guidelines, we searched six databases for English language studies published through June 2016, that reported Campylobacter or Salmonella carriage or infection prevalence in food animals and contamination prevalence in food animal products from African countries. A random effects meta-analysis and multivariable logistic regression were used to estimate the species-specific prevalence of Salmonella and Campylobacter and assess relationships between sample type and region and the detection or isolation of either pathogen. RESULTS Seventy-three studies reporting Campylobacter and 187 studies reporting Salmonella across 27 African countries were represented. Adjusted prevalence calculations estimate Campylobacter detection in 37.7% (95% CI 31.6-44.3) of 11,828 poultry samples; 24.6% (95% CI 18.0-32.7) of 1975 pig samples; 17.8% (95% CI 12.6-24.5) of 2907 goat samples; 12.6% (95% CI 8.4-18.5) of 2382 sheep samples; and 12.3% (95% CI 9.5-15.8) of 6545 cattle samples. Salmonella were detected in 13.9% (95% CI 11.7-16.4) of 25,430 poultry samples; 13.1% (95% CI 9.3-18.3) of 5467 pig samples; 9.3% (95% CI 7.2-12.1) of 2988 camel samples; 5.3% (95% CI 4.0-6.8) of 72,292 cattle samples; 4.8% (95% CI 3.6-6.3) of 11,335 sheep samples; and 3.4% (95% CI 2.2-5.2) of 4904 goat samples. 'External' samples (e.g. hide, feathers) were significantly more likely to be contaminated by both pathogens than 'gut' (e.g. faeces, cloaca) while meat and organs were significantly less likely to be contaminated than gut samples. CONCLUSIONS This study demonstrated widespread prevalence of Campylobacter species and Salmonella serovars in African food animals and meat, particularly in samples of poultry and pig origin. Source attribution studies could help ascertain which food animals are contributing to human campylobacteriosis and salmonellosis and direct potential food safety interventions.
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Affiliation(s)
- Kate M Thomas
- Centre for International Health, Dunedin School of Medicine, University of Otago, Dunedin, New Zealand; Kilimanjaro Clinical Research Institute, Good Samaritan Foundation, Moshi, United Republic of Tanzania.
| | - William A de Glanville
- Institute of Biodiversity Animal Health and Comparative Medicine, College of Medical Veterinary & Life Sciences, University of Glasgow, Glasgow, United Kingdom
| | | | | | - Joram J Buza
- School of Life Sciences and Bio-Engineering, Nelson Mandela African Institution of Science and Technology, Arusha, United Republic of Tanzania
| | - Sarah Cleaveland
- Institute of Biodiversity Animal Health and Comparative Medicine, College of Medical Veterinary & Life Sciences, University of Glasgow, Glasgow, United Kingdom
| | - Margaret A Davis
- Paul G. Allen School for Global Animal Health, Washington State University, Pullman, WA, United States of America
| | - Nigel P French
- mEpiLab, Massey University, Palmerston North, New Zealand; New Zealand Food Safety Science and Research Centre, New Zealand
| | - Blandina T Mmbaga
- Kilimanjaro Clinical Research Institute, Good Samaritan Foundation, Moshi, United Republic of Tanzania
| | - Gerard Prinsen
- School of People, Environment and Planning, Massey University, Palmerston North, New Zealand
| | - Emmanuel S Swai
- State Department of Veterinary Services, Ministry of Livestock and Fisheries, Dodoma, United Republic of Tanzania
| | - Ruth N Zadoks
- Institute of Biodiversity Animal Health and Comparative Medicine, College of Medical Veterinary & Life Sciences, University of Glasgow, Glasgow, United Kingdom
| | - John A Crump
- Centre for International Health, Dunedin School of Medicine, University of Otago, Dunedin, New Zealand
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26
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Wieczorek K, Wołkowicz T, Osek J. MLST-based genetic relatedness of Campylobacter jejuni isolated from chickens and humans in Poland. PLoS One 2020; 15:e0226238. [PMID: 31978059 PMCID: PMC6980552 DOI: 10.1371/journal.pone.0226238] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2018] [Accepted: 11/24/2019] [Indexed: 11/25/2022] Open
Abstract
Campylobacter jejuni infection is one of the most frequently reported foodborne bacterial diseases worldwide. The main transmission route of these microorganisms to humans is consumption of contaminated food, especially of chicken origin. The aim of this study was to analyze the genetic relatedness of C. jejuni from chicken sources (feces, carcasses, and meat) and from humans with diarrhea as well as to subtype the isolates to gain better insight into their population structure present in Poland. C. jejuni were genotyped using multilocus sequence typing (MLST) and sequence types (STs) were assigned in the MLST database. Among 602 isolates tested, a total of 121 different STs, including 70 (57.9%) unique to the isolates' origin, and 32 STs that were not present in the MLST database were identified. The most prevalent STs were ST464 and ST257, with 58 (9.6%) and 52 (8.6%) C. jejuni isolates, respectively. Isolates with some STs (464, 6411, 257, 50) were shown to be common in chickens, whereas others (e.g. ST21 and ST572) were more often identified among human C. jejuni. It was shown that of 47 human sequence types, 26 STs (106 isolates), 23 STs (102 isolates), and 29 STs (100 isolates) were also identified in chicken feces, meat, and carcasses, respectively. These results, together with the high and similar proportional similarity indexes (PSI) calculated for C. jejuni isolated from patients and chickens, may suggest that human campylobacteriosis was associated with contaminated chicken meat or meat products or other kinds of food cross-contaminated with campylobacters of chicken origin. The frequency of various sequence types identified in the present study generally reflects of the prevalence of STs in other countries which may suggest that C. jejuni with some STs have a global distribution, while other genotypes may be more restricted to certain countries.
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Affiliation(s)
- Kinga Wieczorek
- Department of Hygiene of Food of Animal Origin, National Veterinary Research Institute, Pulawy, Poland
| | - Tomasz Wołkowicz
- Department of Bacteriology and Biocontamination Control, National Institute of Public Health—National Institute of Hygiene, Warsaw, Poland
| | - Jacek Osek
- Department of Hygiene of Food of Animal Origin, National Veterinary Research Institute, Pulawy, Poland
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27
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Walker LJ, Wallace RL, Smith JJ, Graham T, Saputra T, Symes S, Stylianopoulos A, Polkinghorne BG, Kirk MD, Glass K. Prevalence of Campylobacter coli and Campylobacter jejuni in Retail Chicken, Beef, Lamb, and Pork Products in Three Australian States. J Food Prot 2019; 82:2126-2134. [PMID: 31729918 DOI: 10.4315/0362-028x.jfp-19-146] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
The aim of this study was to investigate the prevalence and distribution of Campylobacter species in a variety of fresh and frozen meat and offal products collected from retail outlets in New South Wales (NSW), Queensland (Qld), and Victoria (Vic). A total of 1,490 chicken, beef, lamb, and pork samples were collected from Australian supermarkets and butcher shops over a 2-year sampling period (October 2016 to October 2018). Campylobacter spp. were detected in 90% of chicken meat and 73% of chicken offal products (giblet and liver), with significantly lower prevalence in lamb (38%), pork (31%), and beef (14%) offal (kidney and liver). Although retail chicken meat was frequently contaminated with Campylobacter, the level of contamination was generally low. Where quantitative analysis was conducted, 98% of chicken meat samples, on average, had <10,000 CFU Campylobacter per carcass, with 10% <21 CFU per carcass. Campylobacter coli was the most frequently recovered species in chicken meat collected in NSW (53%) and Vic (56%) and in chicken offal collected in NSW (77%), Qld (59%), and Vic (58%). In beef, lamb, and pork offal, C. jejuni was generally the most common species (50 to 86%), with the exception of pork offal collected in NSW, where C. coli was more prevalent (69%). Campylobacter prevalence was significantly higher in fresh lamb (46%) and pork (31%) offal than in frozen offal (17 and 11%, respectively). For chicken, beef, and pork offal, the prevalence of Campylobacter spp. was significantly higher on delicatessen products compared with prepackaged products. This study demonstrated that meat and offal products are frequently contaminated with Campylobacter. However, the prevalence is markedly different in different meats, and the level of chicken meat portion contamination is generally low. By identifying the types of meat and offal products types that pose the greatest risk of Campylobacter infection to consumers, targeted control strategies can be developed.
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Affiliation(s)
- Liz J Walker
- National Centre for Epidemiology and Population Health, The Australian National University, Canberra, Australian Capital Territory 2601, Australia (ORCID: https://orcid.org/0000-0001-6978-7604 [R.L.W.]; https://orcid.org/0000-0001-5905-1310 [K.G.])
| | - Rhiannon L Wallace
- National Centre for Epidemiology and Population Health, The Australian National University, Canberra, Australian Capital Territory 2601, Australia (ORCID: https://orcid.org/0000-0001-6978-7604 [R.L.W.]; https://orcid.org/0000-0001-5905-1310 [K.G.])
| | - James J Smith
- Queensland Health, Food Safety Standards and Regulation, Health Protection Branch, Brisbane, Queensland 4006, Australia
| | - Trudy Graham
- Queensland Health Forensic and Scientific Services, Brisbane, Queensland 4108, Australia
| | - Themy Saputra
- New South Wales Food Authority, Sydney, New South Wales 2127, Australia
| | - Sally Symes
- Department of Health and Human Services, Melbourne, Victoria 3000, Australia
| | | | - Benjamin G Polkinghorne
- National Centre for Epidemiology and Population Health, The Australian National University, Canberra, Australian Capital Territory 2601, Australia (ORCID: https://orcid.org/0000-0001-6978-7604 [R.L.W.]; https://orcid.org/0000-0001-5905-1310 [K.G.])
| | - Martyn D Kirk
- National Centre for Epidemiology and Population Health, The Australian National University, Canberra, Australian Capital Territory 2601, Australia (ORCID: https://orcid.org/0000-0001-6978-7604 [R.L.W.]; https://orcid.org/0000-0001-5905-1310 [K.G.])
| | - Kathryn Glass
- National Centre for Epidemiology and Population Health, The Australian National University, Canberra, Australian Capital Territory 2601, Australia (ORCID: https://orcid.org/0000-0001-6978-7604 [R.L.W.]; https://orcid.org/0000-0001-5905-1310 [K.G.])
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28
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Campylobacter jejuni Strains Associated with Wild Birds and Those Causing Human Disease in Six High-Use Recreational Waterways in New Zealand. Appl Environ Microbiol 2019; 85:AEM.01228-19. [PMID: 31562175 DOI: 10.1128/aem.01228-19] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2019] [Accepted: 09/24/2019] [Indexed: 01/17/2023] Open
Abstract
Campylobacter jejuni, a leading cause of gastroenteritis worldwide, has been frequently isolated from recreational rivers and streams in New Zealand, yet the public health significance of this is unknown. This study uses molecular tools to improve our understanding of the epidemiology and sources of Campylobacter in recreational waterways, with a view to preventing human infection. Epidemiological and microbiological data were collected between 2005 and 2009 from six high-use recreational waterways in the Manawatu-Wanganui region of the North Island. Campylobacter spp. and C. jejuni were isolated from 33.2% and 20.4% of 509 samples, respectively. Isolation of Campylobacter was observed in both low and high river flows. After adjusting for the confounding effects of river flow, there was a significantly higher likelihood of isolating Campylobacter in the winter month of June compared to January. A high diversity of C. jejuni multilocus sequence types was seen, with the most commonly isolated being the water rail-associated ST-2381 (19/91 isolates [20.9%]), ST-1225 (8/91 isolates [8.8%]), and ST-45 (6/91 isolates [6.6%]). The ST-2381 was found in all rivers, while the most commonly isolated ST from human cases in New Zealand, the poultry-associated strain ST-474, was isolated only in one river. Although the majority of Campylobacter sequence types identified in river water were strains associated with wild birds that are rarely associated with human disease, poultry and ruminant-associated Campylobacter strains that are found in human infection were also identified and could present a public health risk.IMPORTANCE In 2016, there was a large-scale waterborne outbreak of campylobacteriosis in New Zealand, which was estimated to have affected over 5,000 people. This highlighted the need for a greater understanding of the sources of contamination of both surface and groundwater and risks associated with exposure to both drinking and recreational water. This study reports the prevalence and population structure of Campylobacter jejuni in six recreational waters of the Manawatu-Wanganui region of New Zealand and models the relationship between Campylobacter spp. and ruminant-associated Campylobacter and the parameters "sites," "months," and "river flow." Here, we demonstrate that both low and high river flows, month of the year, and recreational sites could influence the Campylobacter isolation from recreational waters. The presence of genotypes associated with human infection allowed us to describe potential risks associated with recreational waters.
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29
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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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30
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Jaksons R, Horn B, Moriarty E, Moltchanova E. Spatio-temporal analysis of differences in campylobacteriosis incidence between urban and rural areas in the Southern District Health Board, New Zealand. Spat Spatiotemporal Epidemiol 2019; 31:100304. [PMID: 31677762 DOI: 10.1016/j.sste.2019.100304] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/22/2018] [Revised: 08/07/2019] [Accepted: 08/08/2019] [Indexed: 10/26/2022]
Abstract
The objective of this paper is to investigate differences in campylobacteriosis incidence between urban and rural areas in the Southern District Health Board of New Zealand between 2000 and 2015. The data were analysed using a Bayesian change-point model to evaluate how campylobacteriosis incidence changed over time and to see whether the dynamics differed between rural and urban areas. A conditional auto regressive error term was introduced to account for any spatial effects. The results of our analysis showed that campylobacteriosis incidence increased between 2000 and 2005, decreased between 2006 and 2008 then stabilised from 2009 onward. In addition we found that the changes in incidence were greater in urban areas than in rural ones.
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Affiliation(s)
- Rodelyn Jaksons
- School of Mathematics and Statistics, University of Canterbury, Private Bag 4800, Christchurch 8140, New Zealand; Institute of Environmental Science and Research, ESR, 27 Creyke Road, Ilam, Christchurch 8041, PO Box 29181, Christchurch 8540, New Zealand.
| | - Beverley Horn
- Institute of Environmental Science and Research, ESR, 27 Creyke Road, Ilam, Christchurch 8041, PO Box 29181, Christchurch 8540, New Zealand
| | - Elaine Moriarty
- Institute of Environmental Science and Research, ESR, 27 Creyke Road, Ilam, Christchurch 8041, PO Box 29181, Christchurch 8540, New Zealand
| | - Elena Moltchanova
- School of Mathematics and Statistics, University of Canterbury, Private Bag 4800, Christchurch 8140, New Zealand
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31
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Cody AJ, Maiden MC, Strachan NJ, McCarthy ND. A systematic review of source attribution of human campylobacteriosis using multilocus sequence typing. Euro Surveill 2019; 24:1800696. [PMID: 31662159 PMCID: PMC6820127 DOI: 10.2807/1560-7917.es.2019.24.43.1800696] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2018] [Accepted: 06/07/2019] [Indexed: 12/31/2022] Open
Abstract
BackgroundCampylobacter is a leading global cause of bacterial gastroenteritis, motivating research to identify sources of human infection. Population genetic studies have been increasingly applied to this end, mainly using multilocus sequence typing (MLST) data.ObjectivesThis review aimed to summarise approaches and findings of these studies and identify best practice lessons for this form of genomic epidemiology.MethodsWe systematically reviewed publications using MLST data to attribute human disease isolates to source. Publications were from January 2001, when this type of approach began. Searched databases included Scopus, Web of Science and PubMed. Information on samples and isolate datasets used, as well as MLST schemes and attribution algorithms employed, was obtained. Main findings were extracted, as well as any results' validation with subsequent correction for identified biases. Meta-analysis is not reported given high levels of heterogeneity.ResultsOf 2,109 studies retrieved worldwide, 25 were included, and poultry, specifically chickens, were identified as principal source of human infection. Ruminants (cattle or sheep) were consistently implicated in a substantial proportion of cases. Data sampling and analytical approaches varied, with five different attribution algorithms used. Validation such as self-attribution of isolates from known sources was reported in five publications. No publication reported adjustment for biases identified by validation.ConclusionsCommon gaps in validation and adjustment highlight opportunities to generate improved estimates in future genomic attribution studies. The consistency of chicken as the main source of human infection, across high income countries, and despite methodological variations, highlights the public health importance of this source.
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Affiliation(s)
- Alison J Cody
- Department of Zoology, University of Oxford, Oxford, United Kingdom
- NIHR Health Protection Research Unit in Gastrointestinal Infections, University of Oxford, Oxford, United Kingdom
| | - Martin Cj Maiden
- Department of Zoology, University of Oxford, Oxford, United Kingdom
- NIHR Health Protection Research Unit in Gastrointestinal Infections, University of Oxford, Oxford, United Kingdom
| | - Norval Jc Strachan
- School of Biological Sciences, University of Aberdeen, St. Machar Drive, Aberdeen, United Kingdom
| | - Noel D McCarthy
- Department of Zoology, University of Oxford, Oxford, United Kingdom
- NIHR Health Protection Research Unit in Gastrointestinal Infections, University of Oxford, Oxford, United Kingdom
- Warwick Medical School, University of Warwick, Coventry, United Kingdom
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Egli A, Koch D, Danuser J, Hendriksen RS, Driesen S, Schmid DC, Neher R, Mäusezahl M, Seth-Smith HMB, Bloemberg G, Tschudin-Sutter S, Endimiani A, Perreten V, Greub G, Schrenzel J, Stephan R. Symposium report: One Health meets sequencing. Microbes Infect 2019; 22:1-7. [PMID: 31401354 DOI: 10.1016/j.micinf.2019.07.004] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2019] [Revised: 07/20/2019] [Accepted: 07/21/2019] [Indexed: 12/19/2022]
Affiliation(s)
- Adrian Egli
- Clinical Bacteriology and Mycology, University Hospital Basel, Basel, Switzerland; Applied Microbiology Research, University of Basel, Basel, Switzerland.
| | - Daniel Koch
- Federal Office of Public Health, Liebefeld, Switzerland
| | - Jürg Danuser
- Federal Food Safety and Veterinary Office, Bern, Switzerland
| | | | | | | | - Richard Neher
- Swiss Institute of Bioinformatics (SIB), Basel, Switzerland; Biozentrum, University of Basel, Basel, Switzerland
| | | | - Helena M B Seth-Smith
- Clinical Bacteriology and Mycology, University Hospital Basel, Basel, Switzerland; Applied Microbiology Research, University of Basel, Basel, Switzerland; Swiss Institute of Bioinformatics (SIB), Basel, Switzerland
| | - Guido Bloemberg
- National Center for Enteropathogenic Bacteria and Listeria (NENT), Institute for Food Safety and Hygiene, University of Zurich, Zurich, Switzerland
| | - Sarah Tschudin-Sutter
- Infectious Diseases and Hospital Epidemiology, University Hospital Basel and University of Basel, Basel, Switzerland
| | - Andrea Endimiani
- Institute for Infectious Diseases, University of Bern, Bern, Switzerland
| | - Vincent Perreten
- Institute of Veterinary Bacteriology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Gilbert Greub
- Institute of Microbiology, University Hospital Lausanne, Lausanne, Switzerland
| | - Jacques Schrenzel
- Bacteriology and Genomics Research Laboratories, University Hospital Geneva, Geneva, Switzerland
| | - Roger Stephan
- Institute for Food Safety and -hygiene, Vetsuisse Faculty, University of Zurich, Zurich, Switzerland
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Ocejo M, Oporto B, Hurtado A. Occurrence of Campylobacter jejuni and Campylobacter coli in Cattle and Sheep in Northern Spain and Changes in Antimicrobial Resistance in Two Studies 10-years Apart. Pathogens 2019; 8:E98. [PMID: 31288484 PMCID: PMC6789816 DOI: 10.3390/pathogens8030098] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2019] [Revised: 07/01/2019] [Accepted: 07/04/2019] [Indexed: 12/22/2022] Open
Abstract
A cross-sectional survey was conducted in 2014-2016 in 301 ruminant herds to estimate C. jejuni and C. coli prevalence, and investigate their susceptibility to antimicrobials. Risk of shedding C. jejuni was higher in cattle than sheep (81.2% vs. 45.2%; ORadj = 5.22, p < 0.001), whereas risk of shedding C. coli was higher in sheep than in cattle (19.1% vs. 11.3%; ORadj = 1.71, p = 0.128). Susceptibility to six antimicrobials was determined by broth microdilution using European Committee for Antimicrobial Susceptibility Testing (EUCAST) epidemiological cut-off values. C. coli exhibited higher resistance (94.1%, 32/34) than C. jejuni (65.1%, 71/109), and resistance was more widespread in isolates from dairy cattle than beef cattle or sheep. Compared to results obtained 10-years earlier (2003-2005) in a similar survey, an increase in fluoroquinolone-resistance was observed in C. jejuni from beef cattle (32.0% to 61.9%; OR = 3.45, p = 0.020), and a decrease in tetracycline-resistance in C. jejuni from dairy cattle (75.0% to 43.2%; OR = 0.25, p = 0.026). Resistance to macrolides remained stable at low rates and restricted to C. coli from dairy cattle, with all macrolide-resistant C. coli showing a pattern of pan-resistance. Presence of the single nucleotide polymorphisms (SNPs) associated to quinolone and macrolide resistance was confirmed in all phenotypically resistant isolates. The increase in fluoroquinolone resistance is worrisome but susceptibility to macrolides is reassuring.
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Affiliation(s)
- Medelin Ocejo
- NEIKER - Instituto Vasco de Investigación y Desarrollo Agrario, Animal Health Department, Bizkaia Science and Technology Park 812L, 48160 Derio, Bizkaia, Spain
| | - Beatriz Oporto
- NEIKER - Instituto Vasco de Investigación y Desarrollo Agrario, Animal Health Department, Bizkaia Science and Technology Park 812L, 48160 Derio, Bizkaia, Spain
| | - Ana Hurtado
- NEIKER - Instituto Vasco de Investigación y Desarrollo Agrario, Animal Health Department, Bizkaia Science and Technology Park 812L, 48160 Derio, Bizkaia, Spain.
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Epidemiology of Campylobacter Gastroenteritis in New Zealand Children and the Effect of The Campylobacter Strategy: A 20-year Observational Study. Pediatr Infect Dis J 2019; 38:569-576. [PMID: 31117116 DOI: 10.1097/inf.0000000000002228] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
BACKGROUND Campylobacter species are a common cause of gastroenteritis in New Zealand (NZ) as well as worldwide. This study aimed to describe epidemiologic trends in disease notifications and hospital admissions because of Campylobacter gastroenteritis in NZ children from 1997 to 2016. METHODS In this population-based descriptive study, age-specific and age-standardized notification and hospitalization rates were analyzed for Campylobacter infections in children <15 years of age. Variations in disease by time, sex, age, ethnicity and geography were described. RESULTS During the 20-year period considered, there were 39,970 notifications (59.1% male) and 1458 hospitalizations (61.8% male) because of Campylobacter gastroenteritis in NZ children. Before 2006, notification rates increased by 3.4% annually [95% confidence interval (CI): 0.7%-6.2%], with a peak of 340 notifications per 100,000 children in 2003. The average percentage change (APC) in hospitalizations was 7.4% (95% CI: 4.0%-10.9%) in the same period. From 2006 to 2008, notification and hospitalization rates fell by 25% and 30%, respectively. Since 2008, age-standardized incidence rates have been stable at 161 notifications (APC: -3.1; 95% CI: 0.82 to -6.9) and 6.73 hospitalizations (APC: 2.2; 95% CI: -2.0 to 6.5) per 100,000 children per year. Notification rates were highest in children 1-4 years of age. Hospitalizations rates were highest in children <1 year of age. CONCLUSIONS NZ has previously had high rates of Campylobacter gastroenteritis in children. Implementation of a national strategy to reduce foodborne Campylobacter infection appears to have contributed to an observed reduction in rates between 2006 and 2008. The burden of Campylobacter disease is highest in the community health setting, with only a small proportion of cases needing hospitalization.
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Ahlstrom CA, Bonnedahl J, Woksepp H, Hernandez J, Reed JA, Tibbitts L, Olsen B, Douglas DC, Ramey AM. Satellite tracking of gulls and genomic characterization of faecal bacteria reveals environmentally mediated acquisition and dispersal of antimicrobial-resistant Escherichia coli on the Kenai Peninsula, Alaska. Mol Ecol 2019; 28:2531-2545. [PMID: 30980689 DOI: 10.1111/mec.15101] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2018] [Revised: 04/05/2019] [Accepted: 04/08/2019] [Indexed: 12/20/2022]
Abstract
Gulls (Larus spp.) have frequently been reported to carry Escherichia coli exhibiting antimicrobial resistance (AMR E. coli); however, the pathways governing the acquisition and dispersal of such bacteria are not well described. We equipped 17 landfill-foraging gulls with satellite transmitters and collected gull faecal samples longitudinally from four locations on the Kenai Peninsula, Alaska to assess: (a) gull attendance and transitions between sites, (b) spatiotemporal prevalence of faecally shed AMR E. coli, and (c) genomic relatedness of AMR E. coli isolates among sites. We also sampled Pacific salmon (Oncorhynchus spp.) harvested as part of personal-use dipnet fisheries at two sites to assess potential contamination with AMR E. coli. Among our study sites, marked gulls most commonly occupied the lower Kenai River (61% of site locations) followed by the Soldotna landfill (11%), lower Kasilof River (5%) and upper Kenai River (<1%). Gulls primarily moved between the Soldotna landfill and the lower Kenai River (94% of transitions among sites), which were also the two locations with the highest prevalence of AMR E. coli. There was relatively high spatial and temporal variability in AMR E. coli prevalence in gull faeces and there was no evidence of contamination on salmon harvested in personal-use fisheries. We identified E. coli sequence types and AMR genes of clinical importance, with some isolates possessing genes associated with resistance to as many as eight antibiotic classes. Our findings suggest that gulls acquire AMR E. coli at habitats with anthropogenic inputs and subsequent movements may represent pathways through which AMR is dispersed.
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Affiliation(s)
| | - Jonas Bonnedahl
- Department of Clinical and Experimental Medicine, Linköping University, Linköping, Sweden.,Department of Infectious Diseases, Kalmar County Council, Kalmar, Sweden
| | - Hanna Woksepp
- Research Section, Department of Development and Public Health, Kalmar County Hospital, Kalmar, Sweden
| | - Jorge Hernandez
- Department of Clinical Microbiology, Kalmar County Hospital, Kalmar, Sweden
| | - John A Reed
- U.S. Geological Survey, Alaska Science Center, Anchorage, Alaska
| | - Lee Tibbitts
- U.S. Geological Survey, Alaska Science Center, Anchorage, Alaska
| | - Björn Olsen
- Zoonosis Science Center, Department of Medical Sciences, Uppsala University, Uppsala, Sweden
| | - David C Douglas
- U.S. Geological Survey, Alaska Science Center, Juneau, Alaska
| | - Andrew M Ramey
- U.S. Geological Survey, Alaska Science Center, Anchorage, Alaska
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Draft Whole-Genome Sequences of Three Isolates of a Novel Strain of a Campylobacter sp. Isolated from New Zealand Birds and Water. Microbiol Resour Announc 2019; 8:8/18/e00258-19. [PMID: 31048398 PMCID: PMC6498231 DOI: 10.1128/mra.00258-19] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Campylobacter spp. are frequently found associated with the avian intestinal tract. Most are commensals, but some can cause human campylobacteriosis. Campylobacter spp. are frequently found associated with the avian intestinal tract. Most are commensals, but some can cause human campylobacteriosis. Here, we report the draft genome sequences of three strains of a novel Campylobacter sp. isolated from urban birds and a rural river in New Zealand.
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Wieczorek K, Osek J. Genetic Diversity of Campylobacter Jejuni Isolated from the Poultry Food Chain. J Vet Res 2019; 63:35-40. [PMID: 30989133 PMCID: PMC6458563 DOI: 10.2478/jvetres-2019-0012] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2018] [Accepted: 02/20/2019] [Indexed: 11/20/2022] Open
Abstract
INTRODUCTION Campylobacter jejuni is one of the most frequently reported causes of foodborne bacterial enteric disease worldwide. The main source of these microorganisms is contaminated food, especially of poultry origin. There are several molecular methods for differentiation of Campylobacter isolates at the subgenus level, and one of these is porA-typing based on the sequencing of the major outer-membrane protein (MOMP) encoding gene. The aim of the study was to test the molecular relationship of C. jejuni strains isolated at different points along the poultry food chain and assess the population structure of the isolates. MATERIAL AND METHODS A total of 451 C. jejuni were used in the study, and a DNA fragment of 630 bp of the MOMP encoding gene was amplified and sequenced. RESULTS One hundred and ten sequence types were identified, with 69 (62.7%) unique to the isolates' origin and 30 not present in the database. The most prevalent nucleotide variant 1 was detected in 37 (8.2%) strains. These isolates were identified in all poultry sources tested, especially in faeces (15 isolates) but also in poultry carcasses and meat (11 isolates in each). CONCLUSION The porA typing method was highly discriminative for C. jejuni of poultry origin since the Simpson's diversity index (D) achieved a value of 0.876, indicating considerable diversity in the bacterial population tested. The method may be further used for epidemiological investigation purposes.
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Affiliation(s)
- Kinga Wieczorek
- Department of Hygiene of Food of Animal Origin, National Veterinary Research Institute, 24-100Puławy, Poland
| | - Jacek Osek
- Department of Hygiene of Food of Animal Origin, National Veterinary Research Institute, 24-100Puławy, Poland
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Liao SJ, Marshall J, Hazelton ML, French NP. Extending statistical models for source attribution of zoonotic diseases: a study of campylobacteriosis. J R Soc Interface 2019; 16:20180534. [PMID: 30958154 PMCID: PMC6364659 DOI: 10.1098/rsif.2018.0534] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2018] [Accepted: 01/09/2019] [Indexed: 11/12/2022] Open
Abstract
Preventing and controlling zoonoses through the design and implementation of public health policies requires a thorough understanding of transmission pathways. Modelling jointly the epidemiological data and genetic information of microbial isolates derived from cases provides a methodology for tracing back the source of infection. In this paper, the attribution probability for human cases of campylobacteriosis for each source, conditional on the extent to which each case resides in a rural compared to urban environment, is estimated. A model that incorporates genetic data and evolutionary processes is applied alongside a newly developed genetic-free model. We show that inference from each model is comparable except for rare microbial genotypes. Further, the effect of 'rurality' may be modelled linearly on the logit scale, with increasing rurality leading to the increasing likelihood of ruminant-sourced campylobacteriosis.
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Affiliation(s)
- Sih-Jing Liao
- School of Fundamental Sciences, Massey University, Palmerston North 4442, New Zealand
| | - Jonathan Marshall
- School of Fundamental Sciences, Massey University, Palmerston North 4442, New Zealand
| | - Martin L. Hazelton
- School of Fundamental Sciences, Massey University, Palmerston North 4442, New Zealand
| | - Nigel P. French
- mEpiLab, Infectious Disease Research Centre, School of Veterinary Science, Massey University, Palmerston North 4442, New Zealand
- New Zealand Food Safety Science & Research Centre, Massey University, Palmerston North 4442, New Zealand
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40
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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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Varrone L, Stafford RJ, Lilly K, Selvey L, Glass K, Ford L, Bulach D, Kirk MD. Investigating locally relevant risk factors for Campylobacter infection in Australia: protocol for a case-control study and genomic analysis. BMJ Open 2018; 8:e026630. [PMID: 30580279 PMCID: PMC6318611 DOI: 10.1136/bmjopen-2018-026630] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/17/2018] [Revised: 10/03/2018] [Accepted: 10/03/2018] [Indexed: 11/28/2022] Open
Abstract
INTRODUCTION The CampySource project aims to identify risk factors for human Campylobacter infection in Australia. We will investigate locally relevant risk factors and those significant in international studies in a case-control study. Case isolates and contemporaneous isolates from food and animal sources will be sequenced to conduct source attribution modelling, and findings will be combined with the case-control study in a source-assigned analysis. METHODS AND ANALYSIS The case-control study will include 1200 participants (600 cases and 600 controls) across three regions in Australia. Cases will be recruited from campylobacteriosis notifications to health departments. Only those with a pure and viable Campylobacter isolate will be eligible for selection to allow for whole genome sequencing of isolates. Controls will be recruited from notified cases of influenza, frequency matched by sex, age group and geographical area of residence. All participants will be interviewed by trained telephone interviewers using a piloted questionnaire.We will collect Campylobacter isolates from retail meats and companion animals (specifically dogs), and all food, animal and human isolates will undergo whole genome sequencing. We will use sequence data to estimate the proportion of human infections that can be attributed to animal and food reservoirs (source attribution modelling), and to identify spatial clusters and temporal trends. Source-assigned analysis of the case-control study data will also be conducted where cases are grouped according to attributed sources. ETHICS AND DISSEMINATION Human and animal ethics have been approved. Genomic data will be published in online archives accompanied by basic metadata. We anticipate several publications to come from this study.
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Affiliation(s)
- Liana Varrone
- Faculty of Medicine, University of Queensland, Herston, Queensland, Australia
| | - Russell J Stafford
- Communicable Diseases Branch, Queensland Health, Brisbane, Queensland, Australia
| | - Kim Lilly
- Hunter New England Population Health, Newcastle, New South Wales, Australia
| | - Linda Selvey
- Faculty of Medicine, University of Queensland, Herston, Queensland, Australia
| | - Kathryn Glass
- National Centre for Epidemiology and Population Health, The Australian National University, Canberra, Australian Capital Territory, Australia
| | - Laura Ford
- National Centre for Epidemiology and Population Health, The Australian National University, Canberra, Australian Capital Territory, Australia
| | - Dieter Bulach
- College of Health and Medicine, Melbourne Bioinformatics, Melbourne, Victoria, Australia
- Microbiological Diagnostic Unit Public Health Laboratory, The Peter Doherty Institute, Melbourne, Victoria, Australia
| | - Martyn D Kirk
- National Centre for Epidemiology and Population Health, The Australian National University, Canberra, Australian Capital Territory, Australia
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Bojanić K, Midwinter AC, Marshall JC, Biggs PJ, Acke E. Isolation of emerging Campylobacter species in working farm dogs and their frozen home-killed raw meat diets. J Vet Diagn Invest 2018; 31:23-32. [PMID: 30574836 DOI: 10.1177/1040638718820082] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
We applied 7 culture methods to 50 working farm dog fecal samples and 6 methods to 50 frozen home-killed raw meat diet samples to optimize recovery of a wide range of Campylobacter spp. Culture methods combined filtration, enrichment broths, and agars at 37°C and 42°C in conventional and hydrogen-enriched microaerobic atmospheres. Overall, a prevalence of 62% (31 of 50) and 6% (3 of 50) was detected in dog and meat samples, respectively, based on Campylobacter genus PCR. A total of 356 Campylobacter spp. isolates were recovered from dogs, with successful isolation by individual methods ranging from 2 to 25 dogs. The species detected most commonly were C. upsaliensis and C. jejuni, and less commonly C. coli and C. lari. Species isolated that are rarely reported from dogs included C. rectus, C. lari subsp. concheus, C. volucris, and Helicobacter winghamensis. Six isolates from dogs positive by Campylobacter genus PCR were confirmed, using 16S rRNA sequencing, as Arcobacter cryaerophilus (1) and Arcobacter butzleri (5). C. jejuni multi-locus sequence typing results revealed a diversity of sequence types in working dogs, with several uncommonly reported from other C. jejuni sources in New Zealand. Overall, 20 isolates from 3 meat samples were positive by Campylobacter genus PCR; 1 meat sample was positive for C. jejuni, 1 for C. rectus, and 1 isolate was subsequently identified as A. butzleri. The method using Campylobacter enrichment broth in a hydrogen-enriched environment on nonselective agar resulted in significantly reduced recovery of Campylobacter spp. from both sample types.
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Affiliation(s)
- Krunoslav Bojanić
- mEpiLab, School of Veterinary Science, Massey University, Palmerston North, New Zealand (Bojanić, Midwinter, Marshall, Biggs).,IDEXX VetMedLabor, Ludwigsburg, Germany (Acke)
| | - Anne C Midwinter
- mEpiLab, School of Veterinary Science, Massey University, Palmerston North, New Zealand (Bojanić, Midwinter, Marshall, Biggs).,IDEXX VetMedLabor, Ludwigsburg, Germany (Acke)
| | - Jonathan C Marshall
- mEpiLab, School of Veterinary Science, Massey University, Palmerston North, New Zealand (Bojanić, Midwinter, Marshall, Biggs).,IDEXX VetMedLabor, Ludwigsburg, Germany (Acke)
| | - Patrick J Biggs
- mEpiLab, School of Veterinary Science, Massey University, Palmerston North, New Zealand (Bojanić, Midwinter, Marshall, Biggs).,IDEXX VetMedLabor, Ludwigsburg, Germany (Acke)
| | - Els Acke
- mEpiLab, School of Veterinary Science, Massey University, Palmerston North, New Zealand (Bojanić, Midwinter, Marshall, Biggs).,IDEXX VetMedLabor, Ludwigsburg, Germany (Acke)
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Bailey RA, Kranis A, Psifidi A, Watson KA, Rothwell L, Hocking PM, Kaiser P, Stevens MP, Avendano S. Colonization of a commercial broiler line by Campylobacter is under limited genetic control and does not significantly impair performance or intestinal health. Poult Sci 2018; 97:4167-4176. [PMID: 29982748 PMCID: PMC6305830 DOI: 10.3382/ps/pey295] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2018] [Accepted: 06/14/2018] [Indexed: 12/22/2022] Open
Abstract
Campylobacter is the leading bacterial cause of foodborne diarrheal illness in humans and source attribution studies unequivocally identify handling or consumption of poultry meat as a key risk factor. Campylobacter colonizes the avian intestines in high numbers and rapidly spreads within flocks. A need therefore exists to devise strategies to reduce Campylobacter populations in poultry flocks. There has been a great deal of research aiming to understand the epidemiology and transmission characteristics of Campylobacter in poultry as a means to reduce carriage rates in poultry and reduce infection in humans. One potential strategy for control is the genetic selection of poultry for increased resistance to colonization by Campylobacter. The potential for genetic control of colonization has been demonstrated in inbred populations following experimental challenge with Campylobacter where quantitative trait loci associated with resistance have been identified. Currently in the literature there is no information of the genetic basis of Campylobacter colonization in commercial broiler lines and it is unknown whether these QTL are found in commercial broiler lines. The aim of this study was to estimate genetic parameters associated with Campylobacter load and genetic correlations with gut health and production traits following natural exposure of broiler chickens to Campylobacter.The results from the analysis show a low but significant heritability estimate (0.095 ± 0.037) for Campylobacter load which indicates a limited genetic basis and that non-genetic factors have a greater influence on the level of Campylobacter found in the broiler chicken.Furthermore, through examination of macroscopic intestinal health and absorptive capacity, our study indicated that Campylobacter has no detrimental effects on intestinal health and bird growth following natural exposure in the broiler line under study. These data indicate that whilst there is a genetic component to Campylobacter colonization worthy of further investigation, there is a large proportion of phenotypic variance under the influence of non-genetic effects. As such the control of Campylobacter will require understanding and manipulation of non-genetic host and environmental factors.
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Affiliation(s)
| | | | - Androniki Psifidi
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush, Midlothian, EH25 9RG, UK
- Royal Veterinary College, University of London, Hatfield AL9 7TA, UK
| | - Kellie A Watson
- Aviagen, Newbridge, Midlothian EH28 8SZ, UK
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush, Midlothian, EH25 9RG, UK
| | - Lisa Rothwell
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush, Midlothian, EH25 9RG, UK
| | - Paul M Hocking
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush, Midlothian, EH25 9RG, UK
| | - Pete Kaiser
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush, Midlothian, EH25 9RG, UK
| | - Mark P Stevens
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush, Midlothian, EH25 9RG, UK
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Ijaz UZ, Sivaloganathan L, McKenna A, Richmond A, Kelly C, Linton M, Stratakos AC, Lavery U, Elmi A, Wren BW, Dorrell N, Corcionivoschi N, Gundogdu O. Comprehensive Longitudinal Microbiome Analysis of the Chicken Cecum Reveals a Shift From Competitive to Environmental Drivers and a Window of Opportunity for Campylobacter. Front Microbiol 2018; 9:2452. [PMID: 30374341 PMCID: PMC6196313 DOI: 10.3389/fmicb.2018.02452] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2018] [Accepted: 09/25/2018] [Indexed: 02/02/2023] Open
Abstract
Chickens are a key food source for humans yet their microbiome contains bacteria that can be pathogenic to humans, and indeed potentially to chickens themselves. Campylobacter is present within the chicken gut and is the leading cause of bacterial foodborne gastroenteritis within humans worldwide. Infection can lead to secondary sequelae such as Guillain-Barré syndrome and stunted growth in children from low-resource areas. Despite the global health impact and economic burden of Campylobacter, how and when Campylobacter appears within chickens remains unclear. The lack of day to day microbiome data with replicates, relevant metadata, and a lack of natural infection studies have delayed our understanding of the chicken gut microbiome and Campylobacter. Here, we performed a comprehensive day to day microbiome analysis of the chicken cecum from day 3 to 35 (12 replicates each day; final n = 379). We combined metadata such as chicken weight and feed conversion rates to investigate what the driving forces are for the microbial changes within the chicken gut over time, and how this relates to Campylobacter appearance within a natural habitat setting. We found a rapidly increasing microbial diversity up to day 12 with variation observed both in terms of genera and abundance, before a stabilization of the microbial diversity after day 20. In particular, we identified a shift from competitive to environmental drivers of microbial community from days 12 to 20 creating a window of opportunity whereby Campylobacter can appear. Campylobacter was identified at day 16 which was 1 day after the most substantial changes in metabolic profiles observed. In addition, microbial variation over time is most likely influenced by the diet of the chickens whereby significant shifts in OTU abundances and beta dispersion of samples often corresponded with changes in feed. This study is unique in comparison to the most recent studies as neither sampling was sporadic nor Campylobacter was artificially introduced, thus the experiments were performed in a natural setting. We believe that our findings can be useful for future intervention strategies and help reduce the burden of Campylobacter within the food chain.
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Affiliation(s)
- Umer Zeeshan Ijaz
- School of Engineering, University of Glasgow, Glasgow, United Kingdom
| | - Lojika Sivaloganathan
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | | | | | - Carmel Kelly
- Agri-Food and Biosciences Institute, Food Microbiology, Newforge Lane, Belfast, United Kingdom
| | - Mark Linton
- Agri-Food and Biosciences Institute, Food Microbiology, Newforge Lane, Belfast, United Kingdom
| | | | | | - Abdi Elmi
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Brendan W. Wren
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Nick Dorrell
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Nicolae Corcionivoschi
- Agri-Food and Biosciences Institute, Food Microbiology, Newforge Lane, Belfast, United Kingdom
| | - Ozan Gundogdu
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, United Kingdom
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45
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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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46
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Nohra A, Grinberg A, Midwinter AC, Marshall JC, Collins-Emerson JM, French NP. Exposure to whole chicken carcasses may present a greater risk of campylobacteriosis compared to exposure to chicken drumsticks. Zoonoses Public Health 2018; 65:822-830. [PMID: 29998484 DOI: 10.1111/zph.12505] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2018] [Revised: 05/29/2018] [Accepted: 06/20/2018] [Indexed: 11/29/2022]
Abstract
In New Zealand, the major risk factor for campylobacteriosis has been identified as poultry consumption. New Zealanders consume different types of chicken meat which undergo different processing before entering the retail chain. The manipulations and jointing of chicken carcasses into pieces and the subsequent processing and packaging have the potential to cross-contaminate and reshuffle bacterial pathogens among the different products sold. The aim of this study was to analyse: (a) the differences in the viable count and population genetic structure between Campylobacter isolated from chicken drumsticks and whole carcass meat for retail sale over a 1-year period; and (b) the genetic relatedness of human and chicken isolates collected concurrently. Enumeration of Campylobacter was performed using a spiral plater combined with manual spread plating. Campylobacter isolates were identified by polymerase chain reaction and typed by multilocus sequence typing (MLST). C. jejuni was the dominant species among both whole carcasses (63.5%) and drumsticks samples (73.8%), followed by C. coli (27% and 23.1%, respectively). After sample weight adjustment, whole carcasses showed significantly higher Campylobacter counts than drumsticks, with a significant difference in the counts between the commercial suppliers in both types of retail meat. MLST revealed 28 different sequence types among the two types of meat. Using permutational multivariate analysis of variance, statistically significant differences in the population genetic structures were observed between different suppliers but were not observed between the two types of chicken retail meat. In conclusion, we found differences in Campylobacter viable counts, suggesting consumption of whole carcasses may determine an exposure to a higher number of Campylobacter bacteria than consumption of chicken drumsticks. The Campylobacter population genetic structure did not differ between the two types of chicken retail meat. Therefore, source attribution studies based on MLST are unlikely to be biased by the selection of these types of retail meat during sampling.
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Affiliation(s)
- Antoine Nohra
- Molecular Epidemiology and Veterinary Public Health Laboratory (mEpiLab), Infectious Disease Research Centre, Hopkirk Institute, Massey University, Palmerston North, New Zealand
| | - Alex Grinberg
- Infectious Diseases Group, School of Veterinary Science, Massey University, Palmerston North, New Zealand
| | - Anne C Midwinter
- Molecular Epidemiology and Veterinary Public Health Laboratory (mEpiLab), Infectious Disease Research Centre, Hopkirk Institute, Massey University, Palmerston North, New Zealand
| | - Jonathan C Marshall
- Institute of Fundamental Sciences, Massey University, Palmerston North, New Zealand
| | - Julie M Collins-Emerson
- Molecular Epidemiology and Veterinary Public Health Laboratory (mEpiLab), Infectious Disease Research Centre, Hopkirk Institute, Massey University, Palmerston North, New Zealand
| | - Nigel P French
- Molecular Epidemiology and Veterinary Public Health Laboratory (mEpiLab), Infectious Disease Research Centre, Hopkirk Institute, Massey University, Palmerston North, New Zealand.,New Zealand Food Safety Science and Research Centre, Palmerston North, New Zealand
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47
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Ugarte-Ruiz M, Domínguez L, Corcionivoschi N, Wren BW, Dorrell N, Gundogdu O. Exploring the oxidative, antimicrobial and genomic properties of Campylobacter jejuni strains isolated from poultry. Res Vet Sci 2018; 119:170-175. [PMID: 29957495 DOI: 10.1016/j.rvsc.2018.06.016] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2017] [Revised: 04/25/2018] [Accepted: 06/13/2018] [Indexed: 11/19/2022]
Abstract
Campylobacter jejuni is the leading cause of food-borne bacterial enteritis in humans, with contaminated poultry products considered the main source of infection. To survive the food chain, C. jejuni utilizes multiple defense mechanisms that counter oxidative and aerobic stresses. In this study, we phenotypically characterised 63 C. jejuni strains with oxidative stress survival and antimicrobial susceptibility testing to investigate correlations between these two phenotypes against the source of the strains and the presence of the MarR regulators RrpA and RrpB which have a role in regulating the response to oxidative and aerobic stress. C. jejuni strains isolated from meat and neck skin displayed the highest resistance to oxidative stress. In addition, C. jejuni strains that have an rrpA+rrpB- profile exhibit increased resistance to oxidative stress and to antimicrobials. Here we establish a preliminary link between the distribution of RrpA and RrpB and the increased resistance to antimicrobials. This study provides insight into how the genotypic make up of C. jejuni can influence the ability of the bacterium to survive within areas of high oxygen stress, such as the food chain, and subsequently can have a potential negative impact on human health.
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Affiliation(s)
- Maria Ugarte-Ruiz
- VISAVET Health Surveillance Centre, Universidad Complutense Madrid, Madrid, Spain.
| | - Lucas Domínguez
- VISAVET Health Surveillance Centre, Universidad Complutense Madrid, Madrid, Spain; Facultad de Veterinaria, Universidad Complutense Madrid, Madrid, Spain.
| | | | - Brendan W Wren
- Faculty of Infectious & Tropical Diseases, London School of Hygiene & Tropical Medicine, Keppel Street, London WC1E 7HT, UK.
| | - Nick Dorrell
- Faculty of Infectious & Tropical Diseases, London School of Hygiene & Tropical Medicine, Keppel Street, London WC1E 7HT, UK.
| | - Ozan Gundogdu
- Faculty of Infectious & Tropical Diseases, London School of Hygiene & Tropical Medicine, Keppel Street, London WC1E 7HT, UK.
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48
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Thépault A, Rose V, Quesne S, Poezevara T, Béven V, Hirchaud E, Touzain F, Lucas P, Méric G, Mageiros L, Sheppard SK, Chemaly M, Rivoal K. Ruminant and chicken: important sources of campylobacteriosis in France despite a variation of source attribution in 2009 and 2015. Sci Rep 2018; 8:9305. [PMID: 29915208 PMCID: PMC6006168 DOI: 10.1038/s41598-018-27558-z] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2018] [Accepted: 05/30/2018] [Indexed: 11/17/2022] Open
Abstract
Pathogen source attribution studies are a useful tool for identifying reservoirs of human infection. Based on Multilocus Sequence Typing (MLST) data, such studies have identified chicken as a major source of C. jejuni human infection. The use of whole genome sequence-based typing methods offers potential to improve the precision of attribution beyond that which is possible from 7 MLST loci. Using published data and 156 novel C. jejuni genomes sequenced in this study, we performed probabilistic host source attribution of clinical C. jejuni isolates from France using three types of genotype data: comparative genomic fingerprints; MLST genes; 15 host segregating genes previously identified by whole genome sequencing. Consistent with previous studies, chicken was an important source of campylobacteriosis in France (31-63% of clinical isolates assigned). There was also evidence that ruminants are a source (22-55% of clinical isolates assigned), suggesting that further investigation of potential transmission routes from ruminants to human would be useful. Additionally, we found evidence of environmental and pet sources. However, the relative importance as sources varied according to the year of isolation and the genotyping technique used. Annual variations in attribution emphasize the dynamic nature of zoonotic transmission and the need to perform source attribution regularly.
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Affiliation(s)
- Amandine Thépault
- Hygiene and Quality of Poultry & Pork Products Unit, Laboratory of Ploufragan-Plouzané, French Agency for Food Environmental and Occupational Health & Safety (Anses), Ploufragan, France
- University of Rennes 1, Rennes, France
| | - Valérie Rose
- Hygiene and Quality of Poultry & Pork Products Unit, Laboratory of Ploufragan-Plouzané, French Agency for Food Environmental and Occupational Health & Safety (Anses), Ploufragan, France
| | - Ségolène Quesne
- Hygiene and Quality of Poultry & Pork Products Unit, Laboratory of Ploufragan-Plouzané, French Agency for Food Environmental and Occupational Health & Safety (Anses), Ploufragan, France
| | - Typhaine Poezevara
- Hygiene and Quality of Poultry & Pork Products Unit, Laboratory of Ploufragan-Plouzané, French Agency for Food Environmental and Occupational Health & Safety (Anses), Ploufragan, France
| | - Véronique Béven
- Viral Genetics & Biosafety Unit, Laboratory of Ploufragan-Plouzané, French Agency for Food Environmental and Occupational Health & Safety (Anses), Ploufragan, France
| | - Edouard Hirchaud
- Viral Genetics & Biosafety Unit, Laboratory of Ploufragan-Plouzané, French Agency for Food Environmental and Occupational Health & Safety (Anses), Ploufragan, France
| | - Fabrice Touzain
- Viral Genetics & Biosafety Unit, Laboratory of Ploufragan-Plouzané, French Agency for Food Environmental and Occupational Health & Safety (Anses), Ploufragan, France
| | - Pierrick Lucas
- Viral Genetics & Biosafety Unit, Laboratory of Ploufragan-Plouzané, French Agency for Food Environmental and Occupational Health & Safety (Anses), Ploufragan, France
| | - Guillaume Méric
- The Milner Centre for Evolution, Department of Biology and Biochemistry, University of Bath, Claverton Down, Bath, United Kingdom
| | - Leonardos Mageiros
- Swansea University, Medical School, Institute of Life Science, Singleton Campus, Swansea, United Kingdom
| | - Samuel K Sheppard
- The Milner Centre for Evolution, Department of Biology and Biochemistry, University of Bath, Claverton Down, Bath, United Kingdom
- Department of Zoology, University of Oxford, South Parks Road, Oxford, OX1 3PS, United Kingdom
| | - Marianne Chemaly
- Hygiene and Quality of Poultry & Pork Products Unit, Laboratory of Ploufragan-Plouzané, French Agency for Food Environmental and Occupational Health & Safety (Anses), Ploufragan, France
| | - Katell Rivoal
- Hygiene and Quality of Poultry & Pork Products Unit, Laboratory of Ploufragan-Plouzané, French Agency for Food Environmental and Occupational Health & Safety (Anses), Ploufragan, France.
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49
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Hansson I, Sandberg M, Habib I, Lowman R, Engvall EO. Knowledge gaps in control of Campylobacter for prevention of campylobacteriosis. Transbound Emerg Dis 2018; 65 Suppl 1:30-48. [PMID: 29663680 DOI: 10.1111/tbed.12870] [Citation(s) in RCA: 86] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2016] [Indexed: 01/08/2023]
Abstract
Campylobacteriosis is an important, worldwide public health problem with numerous socio-economic impacts. Since 2015, approximately 230,000 cases have been reported annually in Europe. In the United States, Australia and New Zealand, campylobacteriosis is the most commonly reported disease. Poultry and poultry products are considered important sources of human infections. Poultry meat can become contaminated with Campylobacter during slaughter if live chickens are intestinal carriers. Campylobacter spp. can be transferred from animals to humans through consumption and handling of contaminated food products, with fresh chicken meat being the most commonly implicated food type. Regarding food-borne disease, the most important Campylobacter species are Campylobacter jejuni and Campylobacter coli. In humans, clinical signs of campylobacteriosis include diarrhoea, abdominal pain, fever, headache, nausea and vomiting. Most cases of campylobacteriosis are sporadic and self-limiting, but there are post-infection complications, for example, Guillain-Barrés syndrome. This review summarizes an analysis undertaken by the DISCONTOOLS group of experts on campylobacteriosis. Gaps were identified in: (i) knowledge of true number of infected humans; (ii) mechanisms of pathogenicity to induce infection in humans; (iii) training to prevent transfer of Campylobacter from raw to ready-to-eat food; (iv) development of effective vaccines; (v) understanding transmission routes to broiler flocks; (vi) knowledge of bacteriocins, bacteriophages and antimicrobial peptides as preventive therapies; (vii) ration formulation as an effective preventive measure at a farm level; (viii) development of kits for rapid detection and quantification of Campylobacter in animals and food products; and (ix) development of more effective antimicrobials for treatment of humans infected with Campylobacter. Some of these gaps are relevant worldwide, whereas others are more related to problems encountered with Campylobacter in industrialized countries.
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Affiliation(s)
- I Hansson
- Department of Biomedical Sciences, Veterinary Public Health, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - M Sandberg
- Food Safety, Veterinary Issues & Risk Analysis Danish Agriculture & Food Council, Copenhagen, Denmark
| | - I Habib
- School of Veterinary and Life Sciences, Murdoch University, Perth, WA, Australia
| | - R Lowman
- Independent Veterinary Public Health Research Specialist, Ottawa, ON, Canada
| | - E O Engvall
- Department of Biomedical Sciences, Veterinary Public Health, Swedish University of Agricultural Sciences, Uppsala, Sweden
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50
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Gölz G, Kittler S, Malakauskas M, Alter T. Survival of Campylobacter in the Food Chain and the Environment. CURRENT CLINICAL MICROBIOLOGY REPORTS 2018. [DOI: 10.1007/s40588-018-0092-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
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