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Schadron T, van den Beld M, Mughini-Gras L, Franz E. Use of whole genome sequencing for surveillance and control of foodborne diseases: status quo and quo vadis. Front Microbiol 2024; 15:1460335. [PMID: 39345263 PMCID: PMC11427404 DOI: 10.3389/fmicb.2024.1460335] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2024] [Accepted: 08/27/2024] [Indexed: 10/01/2024] Open
Abstract
Improvements in sequencing quality, availability, speed and costs results in an increased presence of genomics in infectious disease applications. Nevertheless, there are still hurdles in regard to the optimal use of WGS for public health purposes. Here, we discuss the current state ("status quo") and future directions ("quo vadis") based on literature regarding the use of genomics in surveillance, hazard characterization and source attribution of foodborne pathogens. The future directions include the application of new techniques, such as machine learning and network approaches that may overcome the current shortcomings. These include the use of fixed genomic distances in cluster delineation, disentangling similarity or lack thereof in source attribution, and difficulties ascertaining function in hazard characterization. Although, the aforementioned methods can relatively easily be applied technically, an overarching challenge is the inference and biological/epidemiological interpretation of these large amounts of high-resolution data. Understanding the context in terms of bacterial isolate and host diversity allows to assess the level of representativeness in regard to sources and isolates in the dataset, which in turn defines the level of certainty associated with defining clusters, sources and risks. This also marks the importance of metadata (clinical, epidemiological, and biological) when using genomics for public health purposes.
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Affiliation(s)
- Tristan Schadron
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), Bilthoven, Netherlands
| | - Maaike van den Beld
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), Bilthoven, Netherlands
| | - Lapo Mughini-Gras
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), Bilthoven, Netherlands
- Institute for Risk Assessment Sciences, Utrecht University, Utrecht, Netherlands
| | - Eelco Franz
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), Bilthoven, Netherlands
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2
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Mourkas E, Valdebenito JO, Marsh H, Hitchings MD, Cooper KK, Parker CT, Székely T, Johansson H, Ellström P, Pascoe B, Waldenström J, Sheppard SK. Proximity to humans is associated with antimicrobial-resistant enteric pathogens in wild bird microbiomes. Curr Biol 2024; 34:3955-3965.e4. [PMID: 39142288 DOI: 10.1016/j.cub.2024.07.059] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2024] [Revised: 05/21/2024] [Accepted: 07/16/2024] [Indexed: 08/16/2024]
Abstract
Humans are radically altering global ecology, and one of the most apparent human-induced effects is urbanization, where high-density human habitats disrupt long-established ecotones. Changes to these transitional areas between organisms, especially enhanced contact among humans and wild animals, provide new opportunities for the spread of zoonotic pathogens. This poses a serious threat to global public health, but little is known about how habitat disruption impacts cross-species pathogen spread. Here, we investigated variation in the zoonotic enteric pathogen Campylobacter jejuni. The ubiquity of C. jejuni in wild bird gut microbiomes makes it an ideal organism for understanding how host behavior and ecology influence pathogen transition and spread. We analyzed 700 C. jejuni isolate genomes from 30 bird species in eight countries using a scalable generalized linear model approach. Comparing multiple behavioral and ecological traits showed that proximity to human habitation promotes lineage diversity and is associated with antimicrobial-resistant (AMR) strains in natural populations. Specifically, wild birds from urban areas harbored up to three times more C. jejuni genotypes and AMR genes. This study provides novel methodology and much-needed quantitative evidence linking urbanization to gene pool spread and zoonoses.
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Affiliation(s)
- Evangelos Mourkas
- Ineos Oxford Institute, Department of Biology, University of Oxford, 11a Mansfield Road, Oxford OX1 3SZ, UK; Zoonosis Science Centre, Department of Medical Sciences, Uppsala University, Husargatan 3, 751 23 Uppsala, Sweden
| | - José O Valdebenito
- Bird Ecology Lab, Instituto de Ciencias Marinas y Limnológicas, Universidad Austral de Chile, Independencia 631, 5110566 Valdivia, Chile; Centro de Humedales Río Cruces (CEHUM), Universidad Austral de Chile, Camino Cabo Blanco Alto s/n, 5090000 Valdivia, Chile; HUN-REN-DE Reproductive Strategies Research Group, Department of Evolutionary Zoology and Human Biology, University of Debrecen, Egyetem tér 1, 4032 Debrecen, Hungary; Instituto Milenio Biodiversidad de Ecosistemas Antárticos y Subantárticos (BASE), Las Palmeras 3425, 8320000 Santiago, Chile
| | - Hannah Marsh
- Milner Centre for Evolution, Department of Life Sciences, University of Bath, Claverton Down, Bath BA2 7AY, UK
| | - Matthew D Hitchings
- Institute of Life Science, Swansea University Medical School, Swansea University, Singleton Park, SA2 8PP Swansea, Wales
| | - Kerry K Cooper
- School of Animal and Comparative Biomedical Sciences, University of Arizona, 1117 E. Lowell St., Tucson, AZ 85721, USA
| | - Craig T Parker
- Produce Safety and Microbiology Unit, Western Region Research Center, USDA, Agricultural Research Service, Albany, CA 94710, USA
| | - Tamás Székely
- HUN-REN-DE Reproductive Strategies Research Group, Department of Evolutionary Zoology and Human Biology, University of Debrecen, Egyetem tér 1, 4032 Debrecen, Hungary; Milner Centre for Evolution, Department of Life Sciences, University of Bath, Claverton Down, Bath BA2 7AY, UK
| | - Håkan Johansson
- Centre for Ecology and Evolution in Microbial Model Systems, Linnaeus University, Stuvaregatan 2, 392 31 Kalmar, Sweden
| | - Patrik Ellström
- Zoonosis Science Centre, Department of Medical Sciences, Uppsala University, Husargatan 3, 751 23 Uppsala, Sweden
| | - Ben Pascoe
- Ineos Oxford Institute, Department of Biology, University of Oxford, 11a Mansfield Road, Oxford OX1 3SZ, UK
| | - Jonas Waldenström
- Centre for Ecology and Evolution in Microbial Model Systems, Linnaeus University, Stuvaregatan 2, 392 31 Kalmar, Sweden
| | - Samuel K Sheppard
- Ineos Oxford Institute, Department of Biology, University of Oxford, 11a Mansfield Road, Oxford OX1 3SZ, UK.
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3
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Pascoe B, Futcher G, Pensar J, Bayliss SC, Mourkas E, Calland JK, Hitchings MD, Joseph LA, Lane CG, Greenlee T, Arning N, Wilson DJ, Jolley KA, Corander J, Maiden MCJ, Parker CT, Cooper KK, Rose EB, Hiett K, Bruce BB, Sheppard SK. Machine learning to attribute the source of Campylobacter infections in the United States: A retrospective analysis of national surveillance data. J Infect 2024; 89:106265. [PMID: 39245152 DOI: 10.1016/j.jinf.2024.106265] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2024] [Revised: 08/27/2024] [Accepted: 08/30/2024] [Indexed: 09/10/2024]
Abstract
OBJECTIVES Integrating pathogen genomic surveillance with bioinformatics can enhance public health responses by identifying risk and guiding interventions. This study focusses on the two predominant Campylobacter species, which are commonly found in the gut of birds and mammals and often infect humans via contaminated food. Rising incidence and antimicrobial resistance (AMR) are a global concern, and there is an urgent need to quantify the main routes to human infection. METHODS During routine US national surveillance (2009-2019), 8856 Campylobacter genomes from human infections and 16,703 from possible sources were sequenced. Using machine learning and probabilistic models, we target genetic variation associated with host adaptation to attribute the source of human infections and estimate the importance of different disease reservoirs. RESULTS Poultry was identified as the primary source of human infections, responsible for an estimated 68% of cases, followed by cattle (28%), and only a small contribution from wild birds (3%) and pork sources (1%). There was also evidence of an increase in multidrug resistance, particularly among isolates attributed to chickens. CONCLUSIONS National surveillance and source attribution can guide policy, and our study suggests that interventions targeting poultry will yield the greatest reductions in campylobacteriosis and spread of AMR in the US. DATA AVAILABILITY All sequence reads were uploaded and shared on NCBI's Sequence Read Archive (SRA) associated with BioProjects; PRJNA239251 (CDC / PulseNet surveillance), PRJNA287430 (FSIS surveillance), PRJNA292668 & PRJNA292664 (NARMS) and PRJNA258022 (FDA surveillance). Publicly available genomes, including reference genomes and isolates sampled worldwide from wild birds are associated with BioProject accessions: PRJNA176480, PRJNA177352, PRJNA342755, PRJNA345429, PRJNA312235, PRJNA415188, PRJNA524300, PRJNA528879, PRJNA529798, PRJNA575343, PRJNA524315 and PRJNA689604. Contiguous assemblies of all genome sequences compared are available at Mendeley data (assembled C. coli genomes doi: 10.17632/gxswjvxyh3.1; assembled C. jejuni genomes doi: 10.17632/6ngsz3dtbd.1) and individual project and accession numbers can be found in Supplementary tables S1 and S2, which also includes pubMLST identifiers for assembled genomes. Figshare (10.6084/m9.figshare.20279928). Interactive phylogenies are hosted on microreact separately for C. jejuni (https://microreact.org/project/pascoe-us-cjejuni) and C. coli (https://microreact.org/project/pascoe-us-ccoli).
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Affiliation(s)
- Ben Pascoe
- Ineos Oxford Institute for Antimicrobial Research, Department of Biology, University of Oxford, Oxford, United Kingdom
| | - Georgina Futcher
- The Milner Centre for Evolution, Department of Biology and Biochemistry, University of Bath, Claverton Down, Bath, United Kingdom
| | - Johan Pensar
- Department of Mathematics, University of Oslo, Oslo, Norway
| | - Sion C Bayliss
- Bristol Veterinary School, University of Bristol, Langford, Bristol, United Kingdom
| | - Evangelos Mourkas
- Ineos Oxford Institute for Antimicrobial Research, Department of Biology, University of Oxford, Oxford, United Kingdom; Zoonosis Science Centre, Department of Medical Sciences, Uppsala University, Uppsala, Sweden
| | - Jessica K Calland
- Oslo University Hospital, Oslo Centre for Biostatistics and Epidemiology, Oslo, Norway
| | - Matthew D Hitchings
- Swansea University Medical School, Swansea University, Swansea, United Kingdom
| | - Lavin A Joseph
- Division of Foodborne, Waterborne, and Environmental Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Charlotte G Lane
- Division of Foodborne, Waterborne, and Environmental Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Tiffany Greenlee
- Center for Food Safety and Applied Nutrition, Food and Drug Administration, College Park, MD, USA
| | - Nicolas Arning
- Big Data Institute, Oxford Population Health, University of Oxford, Li Ka Shing Centre for Health Information and Discovery, Old Road Campus, Oxford, United Kingdom
| | - Daniel J Wilson
- Big Data Institute, Oxford Population Health, University of Oxford, Li Ka Shing Centre for Health Information and Discovery, Old Road Campus, Oxford, United Kingdom; Department for Continuing Education, University of Oxford, United Kingdom
| | - Keith A Jolley
- Department of Biology, University of Oxford, Oxford, United Kingdom
| | - Jukka Corander
- Oslo University Hospital, Oslo Centre for Biostatistics and Epidemiology, Oslo, Norway; Department of Mathematics and Statistics, University of Helsinki, Helsinki, Finland; Parasites and Microbes, Wellcome Sanger Institute, Cambridge, United Kingdom
| | | | - Craig T Parker
- Produce Safety and Microbiology Research Unit, Agricultural Research Service, US Department of Agriculture, Albany, CA, USA
| | - Kerry K Cooper
- School of Animal and Comparative Biomedical Sciences, University of Arizona, Tucson, AZ, USA
| | - Erica B Rose
- Division of Foodborne, Waterborne, and Environmental Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Kelli Hiett
- Center for Food Safety and Applied Nutrition, Food and Drug Administration, Laurel, MD, USA
| | - Beau B Bruce
- Division of Foodborne, Waterborne, and Environmental Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Samuel K Sheppard
- Ineos Oxford Institute for Antimicrobial Research, Department of Biology, University of Oxford, Oxford, United Kingdom.
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Eliasson E, Sun L, Cervin G, Pavia H, Tällberg G, Ellström P, Ivarsson E. No colonization resistance to Campylobacter jejuni in broilers fed brown algal extract-supplemented diets. Front Microbiol 2024; 15:1396949. [PMID: 38993493 PMCID: PMC11236747 DOI: 10.3389/fmicb.2024.1396949] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2024] [Accepted: 06/06/2024] [Indexed: 07/13/2024] Open
Abstract
Introduction Campylobacter jejuni gastroenteritis is the most commonly reported zoonosis within the EU, with poultry products regarded as the primary source of transmission to humans. Therefore, finding strategies to reduce Campylobacter colonization in broilers holds importance for public health. Recent studies suggest that supplementation of broiler feed with brown algal extracts, particularly laminarin, can provide beneficial effects on broiler gut health, growth performance, and gut microbiota. However, its effect on gut microbiota development and subsequent reduction of Campylobacter loads in broiler caeca during the later stages of the birds' lives remains unclear. Methods Experimental colonization of Ross 308 broilers with two different strains of C. jejuni was conducted, with groups fed either a basal diet or the same basal diet supplemented with 725 ppm algal extract from Saccharina latissima to provide 290 ppm laminarin. Fecal samples were collected for bacterial enumeration, and caecal samples were obtained before and after the C. jejuni challenge for the determination of microbiota development. Results and discussion No significant differences in fecal C. jejuni concentrations between the groups fed different diets or exposed to different C. jejuni strains were observed. This suggests that both strains colonized the birds equally well and that the laminarin rich algal extract did not have any inhibitory effect on C. jejuni colonization. Notably, 16S rRNA amplicon sequencing revealed detailed data on the caecal microbiota development, likely influenced by both bird age and C. jejuni colonization, which can be valuable for further development of broiler feed formulations aimed at promoting gut health.
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Affiliation(s)
- Eliška Eliasson
- Department of Applied Animal Science and Welfare, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Li Sun
- Department of Applied Animal Science and Welfare, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Gunnar Cervin
- Department of Marine Sciences, Tjärnö, University of Gothenburg, Strömstad, Sweden
| | - Henrik Pavia
- Department of Marine Sciences, Tjärnö, University of Gothenburg, Strömstad, Sweden
| | - Gustav Tällberg
- Zoonosis Science Center, Uppsala University, Uppsala, Sweden
| | - Patrik Ellström
- Zoonosis Science Center, Department of Medical Sciences, Uppsala University, Uppsala, Sweden
| | - Emma Ivarsson
- Department of Applied Animal Science and Welfare, Swedish University of Agricultural Sciences, Uppsala, Sweden
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5
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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: 5] [Impact Index Per Article: 2.5] [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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6
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Mouftah SF, Pascoe B, Calland JK, Mourkas E, Tonkin N, Lefevre C, Deuker D, Smith S, Wickenden H, Hitchings MD, Sheppard SK, Elhadidy M. Local accessory gene sharing among Egyptian Campylobacter potentially promotes the spread of antimicrobial resistance. Microb Genom 2022; 8. [PMID: 35675117 PMCID: PMC9455717 DOI: 10.1099/mgen.0.000834] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
Campylobacter is the most common cause of bacterial gastroenteritis worldwide, and diarrhoeal disease is a major cause of child morbidity, growth faltering and mortality in low- and middle-income countries. Despite evidence of high incidence and differences in disease epidemiology, there is limited genomic data from studies in developing countries. In this study, we aimed to quantify the extent of gene sharing in local and global populations. We characterized the genetic diversity and accessory-genome content of a collection of Campylobacter isolates from the Cairo metropolitan area, Egypt. In total, 112 Campylobacter isolates were collected from broiler carcasses (n=31), milk and dairy products (n=24), and patients suffering from gastroenteritis (n=57). Among the most common sequence types (STs), we identified the globally disseminated host generalist ST-21 clonal complex (CC21) and the poultry specialists CC206, CC464 and CC48. Notably, CC45 and the cattle-specialist CC42 were under-represented, with a total absence of CC61. Core- and accessory-genome sharing was compared among isolates from Egypt and a comparable collection from the UK (Oxford). Lineage-specific accessory-genome sharing was significantly higher among isolates from the same country, particularly CC21, which demonstrated greater local geographical clustering. In contrast, no geographical clustering was noted in either the core or accessory genome of CC828, suggesting a highly admixed population. A greater proportion of Campylobacter coli isolates were multidrug resistant compared to Campylobacter jejuni. Our results suggest that there is more horizontal transfer of accessory genes between strains in Egypt. This has strong implications for controlling the spread of antimicrobial resistance among this important pathogen.
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Affiliation(s)
- Shaimaa F Mouftah
- Biomedical Sciences Program, University of Science and Technology, Zewail City of Science and Technology, Giza, Egypt
| | - Ben Pascoe
- Milner Centre of Evolution, University of Bath, Claverton Down, Bath, UK.,Chiang Mai University, Chiang Mai, Thailand
| | - Jessica K Calland
- Milner Centre of Evolution, University of Bath, Claverton Down, Bath, UK
| | - Evangelos Mourkas
- Milner Centre of Evolution, University of Bath, Claverton Down, Bath, UK
| | - Naomi Tonkin
- Milner Centre of Evolution, University of Bath, Claverton Down, Bath, UK
| | - Charlotte Lefevre
- Milner Centre of Evolution, University of Bath, Claverton Down, Bath, UK.,Present address: Division of Virology, Department of Pathology, University of Cambridge, Tennis Court Road, Cambridge, UK
| | - Danielle Deuker
- Milner Centre of Evolution, University of Bath, Claverton Down, Bath, UK.,Present address: Nuffield Department of Medicine, Jenner Institute, University of Oxford, Oxford, UK
| | - Sunny Smith
- Milner Centre of Evolution, University of Bath, Claverton Down, Bath, UK
| | - Harry Wickenden
- Milner Centre of Evolution, University of Bath, Claverton Down, Bath, UK
| | | | - Samuel K Sheppard
- Milner Centre of Evolution, University of Bath, Claverton Down, Bath, UK.,Department of Zoology, University of Oxford, Oxford, UK
| | - 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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7
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Ahmed NA, Gulhan T. Campylobacter in Wild Birds: Is It an Animal and Public Health Concern? Front Microbiol 2022; 12:812591. [PMID: 35222311 PMCID: PMC8867025 DOI: 10.3389/fmicb.2021.812591] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Accepted: 12/14/2021] [Indexed: 11/17/2022] Open
Abstract
Campylobacteriosis continues to be one of the leading causes of foodborne bacterial zoonotic infections worldwide. Despite its public health importance, the status of this disease in wild birds and the possibility of transmission from wild birds to domestic animals and humans have not been clearly elucidated yet. This article reviews the available literature with the aim of making a comprehensive manuscript on this disease status in wild birds and the possibility of interspecies transmission. Campylobacter has been isolated from various species of wild birds worldwide, with C. jejuni being the most commonly isolated species. The prevalence of Campylobacter in wild birds may vary depending on several factors like geographical location, season, the bird’s health status, bird species, sample type, the method used, and ecological factors. Molecular studies over the past two to three decades have characterized Campylobacter strains isolated from wild birds and have come up with results that fall into two categories. The first are those that report overlapping strains among human, domestic animal, and wild bird isolates. The results of the studies under this category emphasize that wild birds carry strains of Campylobacter, which are indistinguishable from domestic animals and humans and are therefore an important public and animal health concern. In contrast, the studies under the second category highlight significant differences in Campylobacter population structure among these hosts. Despite the controversiality and the inadequacy of current research to draw a full conclusion, the role of wild birds in the epidemiology of Campylobacter should not be undermined as drug-resistant strains, especially resistance to tetracycline and fluoroquinolones, are increasingly documented. In addition, source attribution studies have linked human cases of Campylobacter infections to wild birds. Therefore, the role of wild birds in the epidemiology of Campylobacter infection should not be neglected. However, in order to determine disease status in wild birds and the precise role of wild birds in domestic animals and human health, detail-oriented epidemiological investigations characterizing the genetic relatedness of isolates from the respective species and environment through one health approach are warranted.
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8
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Mourkas E, Yahara K, Bayliss SC, Calland JK, Johansson H, Mageiros L, Muñoz-Ramirez ZY, Futcher G, Méric G, Hitchings MD, Sandoval-Motta S, Torres J, Jolley KA, Maiden MCJ, Ellström P, Waldenström J, Pascoe B, Sheppard SK. Host ecology regulates interspecies recombination in bacteria of the genus Campylobacter. eLife 2022; 11:73552. [PMID: 35191377 PMCID: PMC8912921 DOI: 10.7554/elife.73552] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Accepted: 02/20/2022] [Indexed: 01/16/2023] Open
Abstract
Horizontal gene transfer (HGT) can allow traits that have evolved in one bacterial species to transfer to another. This has potential to rapidly promote new adaptive trajectories such as zoonotic transfer or antimicrobial resistance. However, for this to occur requires gaps to align in barriers to recombination within a given time frame. Chief among these barriers is the physical separation of species with distinct ecologies in separate niches. Within the genus Campylobacter, there are species with divergent ecologies, from rarely isolated single-host specialists to multihost generalist species that are among the most common global causes of human bacterial gastroenteritis. Here, by characterizing these contrasting ecologies, we can quantify HGT among sympatric and allopatric species in natural populations. Analyzing recipient and donor population ancestry among genomes from 30 Campylobacter species, we show that cohabitation in the same host can lead to a six-fold increase in HGT between species. This accounts for up to 30% of all SNPs within a given species and identifies highly recombinogenic genes with functions including host adaptation and antimicrobial resistance. As described in some animal and plant species, ecological factors are a major evolutionary force for speciation in bacteria and changes to the host landscape can promote partial convergence of distinct species through HGT.
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Affiliation(s)
- Evangelos Mourkas
- The Milner Centre for Evolution, Department of Biology and Biochemistry, University of BathBathUnited Kingdom
| | - Koji Yahara
- Antimicrobial Resistance Research Center, National Institute of Infectious DiseasesTokyoJapan
| | - Sion C Bayliss
- The Milner Centre for Evolution, Department of Biology and Biochemistry, University of BathBathUnited Kingdom
| | - Jessica K Calland
- The Milner Centre for Evolution, Department of Biology and Biochemistry, University of BathBathUnited Kingdom
| | - Håkan Johansson
- Centre for Ecology and Evolution in Microbial Model Systems, Linnaeus UniversityKalmarSweden
| | - Leonardos Mageiros
- The Milner Centre for Evolution, Department of Biology and Biochemistry, University of BathBathUnited Kingdom
| | - Zilia Y Muñoz-Ramirez
- Unidad de Investigacion en Enfermedades Infecciosas, UMAE Pediatria, Instituto Mexicano del Seguro SocialMexico CityMexico
| | - Grant Futcher
- The Milner Centre for Evolution, Department of Biology and Biochemistry, University of BathBathUnited Kingdom
| | - Guillaume Méric
- The Milner Centre for Evolution, Department of Biology and Biochemistry, University of BathBathUnited Kingdom
| | | | - Santiago Sandoval-Motta
- Unidad de Investigacion en Enfermedades Infecciosas, UMAE Pediatria, Instituto Mexicano del Seguro SocialMexico CityMexico
| | - Javier Torres
- Unidad de Investigacion en Enfermedades Infecciosas, UMAE Pediatria, Instituto Mexicano del Seguro SocialMexico CityMexico
| | - Keith A Jolley
- Department of Zoology, University of OxfordOxfordUnited Kingdom
| | | | - Patrik Ellström
- Department of Medical Sciences, Zoonosis Science Centre, Uppsala UniversityUppsalaSweden
| | - Jonas Waldenström
- Centre for Ecology and Evolution in Microbial Model Systems, Linnaeus UniversityKalmarSweden
| | - Ben Pascoe
- The Milner Centre for Evolution, Department of Biology and Biochemistry, University of BathBathUnited Kingdom,Faculty of Veterinary Medicine, Chiang Mai UniversityChiang MaiThailand
| | - Samuel K Sheppard
- The Milner Centre for Evolution, Department of Biology and Biochemistry, University of BathBathUnited Kingdom,Department of Zoology, University of OxfordOxfordUnited Kingdom
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9
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van Vliet AHM, Charity OJ, Reuter M. A Campylobacter integrative and conjugative element with a CRISPR-Cas9 system targeting competing plasmids: a history of plasmid warfare? Microb Genom 2021; 7. [PMID: 34766904 PMCID: PMC8743540 DOI: 10.1099/mgen.0.000729] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Microbial genomes are highly adaptable, with mobile genetic elements (MGEs) such as integrative conjugative elements (ICEs) mediating the dissemination of new genetic information throughout bacterial populations. This is countered by defence mechanisms such as CRISPR-Cas systems, which limit invading MGEs by sequence-specific targeting. Here we report the distribution of the pVir, pTet and PCC42 plasmids and a new 70–129 kb ICE (CampyICE1) in the foodborne bacterial pathogens Campylobacter jejuni and Campylobacter coli. CampyICE1 contains a degenerated Type II-C CRISPR system consisting of a sole Cas9 protein, which is distinct from the previously described Cas9 proteins from C. jejuni and C. coli. CampyICE1 is conserved in structure and gene order, containing blocks of genes predicted to be involved in recombination, regulation and conjugation. CampyICE1 was detected in 134/5829 (2.3 %) C. jejuni genomes and 92/1347 (6.8 %) C. coli genomes. Similar ICEs were detected in a number of non-jejuni/coli Campylobacter species, although these lacked a CRISPR-Cas system. CampyICE1 carries three separate short CRISPR spacer arrays containing a combination of 108 unique spacers and 16 spacer-variant families. A total of 69 spacers and 10 spacer-variant families (63.7 %) were predicted to target Campylobacter plasmids. The presence of a functional CampyICE1 Cas9 protein and matching anti-plasmid spacers was associated with the absence of the pVir, pTet and pCC42 plasmids (188/214 genomes, 87.9 %), suggesting that the CampyICE1-encoded CRISPR-Cas has contributed to the exclusion of competing plasmids. In conclusion, the characteristics of the CRISPR-Cas9 system on CampyICE1 suggests a history of plasmid warfare in Campylobacter.
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Affiliation(s)
- Arnoud H M van Vliet
- Department of Pathology and Infectious Diseases, School of Veterinary Medicine, University of Surrey, Guildford, UK
| | - Oliver J Charity
- Quadram Institute Bioscience, Microbes in the Food Chain programme, Norwich, UK
| | - Mark Reuter
- Quadram Institute Bioscience, Microbes in the Food Chain programme, Norwich, UK
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10
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Mencía-Gutiérrez A, Martín-Maldonado B, Pastor-Tiburón N, Moraleda V, González F, García-Peña FJ, Pérez-Cobo I, Revuelta L, Marín M. Prevalence and antimicrobial resistance of Campylobacter from wild birds of prey in Spain. Comp Immunol Microbiol Infect Dis 2021; 79:101712. [PMID: 34688167 DOI: 10.1016/j.cimid.2021.101712] [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: 04/27/2021] [Revised: 09/18/2021] [Accepted: 09/22/2021] [Indexed: 10/20/2022]
Abstract
Wild birds have been identified as a relevant reservoir of Campylobacter spp., therefore, a potential source of infection in humans and domestic animals. The objective of this study was to determine the occurrence of Campylobacter spp. on birds of prey in Spain. In addition, antibiotic resistance profiles of the isolates were evaluated. A total of 689 specimens of 28 raptor species were analyzed, with a resulting individual prevalence of 7.5%. C. jejuni was the most frequently isolated species (88.5%), followed by C. coli and C. lari (3.8% each). The occurrence of Campylobacter was significantly higher (p < 0.05) in nocturnal birds of prey (15.3%), in spring season (12.2%) and in carnivorous species (9.4%). Isolates displayed a remarkable resistance to nalidixic acid (69.9%), ciprofloxacin (69.9%), and tetracycline (55.6%), and a low resistance to streptomycin (6.7%). Our findings highlight the importance of birds of prey as reservoirs of Campylobacter strains and their significant role as carriers of antimicrobial resistance.
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Affiliation(s)
- Aida Mencía-Gutiérrez
- Department of Animal Physiology, Faculty of Veterinary Sciences, Complutense University of Madrid, Madrid, Spain; Grupo de Estudio de la Medicina y Conservación de la Fauna Silvestre (GEMAS), Spain.
| | - Bárbara Martín-Maldonado
- Grupo de Rehabilitación de la Fauna Autóctona y su Hábitat (GREFA), Monte del Pilar, Majadahonda, Madrid, Spain; Grupo de Estudio de la Medicina y Conservación de la Fauna Silvestre (GEMAS), Spain
| | - Natalia Pastor-Tiburón
- Grupo de Rehabilitación de la Fauna Autóctona y su Hábitat (GREFA), Monte del Pilar, Majadahonda, Madrid, Spain; Grupo de Estudio de la Medicina y Conservación de la Fauna Silvestre (GEMAS), Spain
| | - Virginia Moraleda
- Grupo de Rehabilitación de la Fauna Autóctona y su Hábitat (GREFA), Monte del Pilar, Majadahonda, Madrid, Spain; Grupo de Estudio de la Medicina y Conservación de la Fauna Silvestre (GEMAS), Spain
| | - Fernando González
- Grupo de Rehabilitación de la Fauna Autóctona y su Hábitat (GREFA), Monte del Pilar, Majadahonda, Madrid, Spain; Grupo de Estudio de la Medicina y Conservación de la Fauna Silvestre (GEMAS), Spain
| | | | - Iratxe Pérez-Cobo
- Laboratorio Central de Veterinaria (Ministerio de Agricultura, Pesca y Alimentación), Algete, Spain
| | - Luis Revuelta
- Department of Animal Physiology, Faculty of Veterinary Sciences, Complutense University of Madrid, Madrid, Spain; Grupo de Estudio de la Medicina y Conservación de la Fauna Silvestre (GEMAS), Spain
| | - María Marín
- Grupo de Estudio de la Medicina y Conservación de la Fauna Silvestre (GEMAS), Spain; Department of Nutrition and Food Science, Faculty of Veterinary Sciences, Complutense University of Madrid, Madrid, Spain
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11
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Dieckmann AL, Riedel T, Bunk B, Spröer C, Overmann J, Groß U, Bader O, Bohne W, Morgenstern B, Hosseini M, Zautner AE. Genome and Methylome analysis of a phylogenetic novel Campylobacter coli cluster with C. jejuni introgression. Microb Genom 2021; 7. [PMID: 34661518 PMCID: PMC8627207 DOI: 10.1099/mgen.0.000679] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The intriguing recent discovery of Campylobacter coli strains, especially of clade 1, that (i) possess mosaic C. coli/C. jejuni alleles, (ii) demonstrate mixed multilocus sequence types (MLSTs) and (iii) have undergone genome-wide introgression has led to the speculation that these two species may be involved in an accelerated rate of horizontal gene transfer that is progressively leading to the merging of both species in a process coined ‘despeciation’. In an MLST-based neighbour-joining tree of a number of C. coli and C. jejuni isolates of different clades, three prominent Campylobacter isolates formed a seemingly separate cluster besides the previously described C. coli and C. jejuni clades. In the light of the suspected, ongoing genetic introgression between the C. coli and C. jejuni species, this cluster of Campylobacter isolates is proposed to present one of the hybrid clonal complexes in the despeciation process of the genus. Specific DNA methylation as well as restriction modification systems are known to be involved in selective uptake of external DNA and their role in such genetic introgression remains to be further investigated. In this study, the phylogeny and DNA methylation of these putative C. coli/C. jejuni hybrid strains were explored, their genomic mosaic structure caused by C. jejuni introgression was demonstrated and basic phenotypic assays were used to characterize these isolates. The genomes of the three hybrid Campylobacter strains were sequenced using PacBio SMRT sequencing, followed by methylome analysis by Restriction-Modification Finder and genome analysis by Parsnp, Smash++ and blast. Additionally, the strains were phenotypically characterized with respect to growth behaviour, motility, eukaryotic cell invasion and adhesion, autoagglutination, biofilm formation, and water survival ability. Our analyses show that the three hybrid Campylobacter strains are clade 1 C. coli strains, which have acquired between 8.1 and 9.1 % of their genome from C. jejuni. The C. jejuni genomic segments acquired are distributed over the entire genome and do not form a coherent cluster. Most of the genes originating from C. jejuni are involved in chemotaxis and motility, membrane transport, cell signalling, or the resistance to toxic compounds such as bile acids. Interspecies gene transfer from C. jejuni has contributed 8.1–9.1% to the genome of three C. coli isolates and initiated the despeciation between C. jejuni and C. coli. Based on their functional annotation, the genes originating from C. jejuni enable the adaptation of the three strains to an intra-intestinal habitat. The transfer of a fused type II restriction-modification system that recognizes the CAYNNNNNCTC/GAGNNNNNRTG motif seems to be the key for the recombination of the C. jejuni genetic material with C. coli genomes.
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Affiliation(s)
- Anastasia-Lisa Dieckmann
- Institut für Medizinische Mikrobiologie und Virologie, Universitätsmedizin Göttingen, Göttingen, Germany
| | - Thomas Riedel
- Leibniz-Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH, Braunschweig, Germany.,Deutsches Zentrum für Infektionsforschung (DZIF) Hannover-Braunschweig, Braunschweig, Germany
| | - Boyke Bunk
- Leibniz-Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH, Braunschweig, Germany
| | - Cathrin Spröer
- Leibniz-Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH, Braunschweig, Germany
| | - Jörg Overmann
- Leibniz-Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH, Braunschweig, Germany.,Deutsches Zentrum für Infektionsforschung (DZIF) Hannover-Braunschweig, Braunschweig, Germany
| | - Uwe Groß
- Institut für Medizinische Mikrobiologie und Virologie, Universitätsmedizin Göttingen, Göttingen, Germany
| | - Oliver Bader
- Institut für Medizinische Mikrobiologie und Virologie, Universitätsmedizin Göttingen, Göttingen, Germany
| | - Wolfgang Bohne
- Institut für Medizinische Mikrobiologie und Virologie, Universitätsmedizin Göttingen, Göttingen, Germany
| | - Burkhard Morgenstern
- Institut für Mikrobiologie und Genetik, Abteilung Bioinformatik, Universität Göttingen, Göttingen, Germany
| | - Morteza Hosseini
- Institut für Mikrobiologie und Genetik, Abteilung Bioinformatik, Universität Göttingen, Göttingen, Germany.,IEETA/DETI, University of Aveiro, Aveiro, Portugal
| | - Andreas E Zautner
- Institut für Medizinische Mikrobiologie und Virologie, Universitätsmedizin Göttingen, Göttingen, Germany
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12
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Sen K, Berglund T, Patel N, Chhabra N, Ricci DM, Dutta S, Mukhopadhyay AK. Genotypic analyses and antimicrobial resistance profiles of Campylobacter jejuni from crows (Corvidae) of United States and India reflect their respective local antibiotic burdens. J Appl Microbiol 2021; 132:696-706. [PMID: 34260789 DOI: 10.1111/jam.15220] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2021] [Revised: 07/05/2021] [Accepted: 07/06/2021] [Indexed: 11/29/2022]
Abstract
AIM The study examined the hypothesis that crow-borne Campylobacter can function as environmental reservoirs and indicators of antibiotic resistance (AR) determinants circulating in a human population. METHODS AND RESULTS Two species of crows from Washington (WA), United States, and Kolkata, India, respectively, were examined for their ability to carry antibiotic resistant Campylobacter. Campylobacter jejuni was the only species isolated by selective agar plating from crow faecal samples. Disk diffusion method used to compare the AR profile of the isolates showed tetracycline (TET) resistance to be the most prevalent (27%) among WA isolates, followed by ciprofloxacin (CIP; 24%). Among Kolkata isolates, nalidixic acid resistance was most common (36%), followed by CIP (27%). The AR profile demonstrated by crow isolates of WA reflects those reported by the US National Antimicrobial Resistance Monitoring System for human isolates (2007-2011), where resistance to TET was most prevalent (≈45%), followed by quinolones (≈24%). The Kolkata crow isolates reflected the AR profile of human clinical isolates from India, where 97% resistance was shown to quinolones, followed by TET (18%). Multilocus sequence typing of 37 isolates, including 11 water isolates from the crow roost area, showed 24 different sequence types (STs). Seventeen of these were previously found in wild birds, 2 in human diarrhoea, 4 in poultry and 8 in environmental water. One isolate was found in both water and faeces, though from different sites within WA. CONCLUSIONS The results indicate that crows most likely acquire the AR from anthropogenic sources. Although they are colonized by specific STs, rarely isolated from humans, they can facilitate the spread of AR. SIGNIFICANCE AND IMPACT OF THE STUDY By studying two areas in different continents, this research demonstrates that Campylobacter borne by crows can function as environmental reservoirs and indicators of AR determinants that circulate in a human population. This information will be of importance to scientists from the medical and poultry industries.
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Affiliation(s)
- Keya Sen
- Division of Biological Sciences, STEM, University of Washington, Bothell, Washington, USA
| | - Tanner Berglund
- Division of Biological Sciences, STEM, University of Washington, Bothell, Washington, USA
| | - Nidhi Patel
- Division of Biological Sciences, STEM, University of Washington, Bothell, Washington, USA
| | - Neha Chhabra
- Division of Biological Sciences, STEM, University of Washington, Bothell, Washington, USA
| | - David M Ricci
- Division of Biological Sciences, STEM, University of Washington, Bothell, Washington, USA
| | - Shanta Dutta
- Division of Bacteriology, National Institute of Cholera and Enteric disease, Kolkata, India
| | - Asish K Mukhopadhyay
- Division of Bacteriology, National Institute of Cholera and Enteric disease, Kolkata, India
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13
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Espinosa-Gongora C, Hansen MJ, Bertelsen MF, Bojesen AM. Polar bear-adapted Ursidibacter maritimus are remarkably conserved after generations in captivity. Mol Ecol 2021; 30:4497-4504. [PMID: 34250662 DOI: 10.1111/mec.16075] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2020] [Revised: 06/15/2021] [Accepted: 07/07/2021] [Indexed: 10/20/2022]
Abstract
Most species in the bacterial family of Pasteurellaceae colonize one specific host species. Vertebrates of very different evolutionary descent including fish, turtles, marsupials, eutherians and birds are colonized by different members of Pasteurellaceae. This one-to-one microbial-host species partnership makes Pasteurellaceae species valuable candidates to study biodiversity, bacterial-host co-evolution and host adaptation, and their widespread distribution across vertebrates provide the possibility to collect a wide array of data, where wildlife species are essential. However, obtaining samples from wild animals comes with logistic, technical and ethical challenges, and previous microbiota studies have led to the presumption that captive animals are poor models for microbial studies in wildlife. Here, we show that colonization of polar bears by Ursidibacter maritimus is unaffected by factors related to captivity, reflecting a deep symbiotic bond to the host. We argue that the study of ecological and evolutionary principles in captive wildlife is possible for host-adapted taxa such as those in the Pasteurellaceae family. Moreover, studying captive, often trained animals protects wild populations from the stress associated with obtaining samples.
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Affiliation(s)
- Carmen Espinosa-Gongora
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Frederiksberg C, Denmark
| | - Mie Johanne Hansen
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Frederiksberg C, Denmark.,Center for Zoo and Wild Animal Health, Copenhagen Zoo, Frederiksberg, Denmark
| | - Mads Frost Bertelsen
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Frederiksberg C, Denmark.,Center for Zoo and Wild Animal Health, Copenhagen Zoo, Frederiksberg, Denmark
| | - Anders Miki Bojesen
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Frederiksberg C, Denmark
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14
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Pavlovikj N, Gomes-Neto JC, Deogun JS, Benson AK. ProkEvo: an automated, reproducible, and scalable framework for high-throughput bacterial population genomics analyses. PeerJ 2021; 9:e11376. [PMID: 34055480 PMCID: PMC8142932 DOI: 10.7717/peerj.11376] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2020] [Accepted: 04/08/2021] [Indexed: 12/28/2022] Open
Abstract
Whole Genome Sequence (WGS) data from bacterial species is used for a variety of applications ranging from basic microbiological research, diagnostics, and epidemiological surveillance. The availability of WGS data from hundreds of thousands of individual isolates of individual microbial species poses a tremendous opportunity for discovery and hypothesis-generating research into ecology and evolution of these microorganisms. Flexibility, scalability, and user-friendliness of existing pipelines for population-scale inquiry, however, limit applications of systematic, population-scale approaches. Here, we present ProkEvo, an automated, scalable, reproducible, and open-source framework for bacterial population genomics analyses using WGS data. ProkEvo was specifically developed to achieve the following goals: (1) Automation and scaling of complex combinations of computational analyses for many thousands of bacterial genomes from inputs of raw Illumina paired-end sequence reads; (2) Use of workflow management systems (WMS) such as Pegasus WMS to ensure reproducibility, scalability, modularity, fault-tolerance, and robust file management throughout the process; (3) Use of high-performance and high-throughput computational platforms; (4) Generation of hierarchical-based population structure analysis based on combinations of multi-locus and Bayesian statistical approaches for classification for ecological and epidemiological inquiries; (5) Association of antimicrobial resistance (AMR) genes, putative virulence factors, and plasmids from curated databases with the hierarchically-related genotypic classifications; and (6) Production of pan-genome annotations and data compilation that can be utilized for downstream analysis such as identification of population-specific genomic signatures. The scalability of ProkEvo was measured with two datasets comprising significantly different numbers of input genomes (one with ~2,400 genomes, and the second with ~23,000 genomes). Depending on the dataset and the computational platform used, the running time of ProkEvo varied from ~3-26 days. ProkEvo can be used with virtually any bacterial species, and the Pegasus WMS uniquely facilitates addition or removal of programs from the workflow or modification of options within them. To demonstrate versatility of the ProkEvo platform, we performed a hierarchical-based population structure analyses from available genomes of three distinct pathogenic bacterial species as individual case studies. The specific case studies illustrate how hierarchical analyses of population structures, genotype frequencies, and distribution of specific gene functions can be integrated into an analysis. Collectively, our study shows that ProkEvo presents a practical viable option for scalable, automated analyses of bacterial populations with direct applications for basic microbiology research, clinical microbiological diagnostics, and epidemiological surveillance.
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Affiliation(s)
- Natasha Pavlovikj
- Department of Computer Science and Engineering, University of Nebraska-Lincoln, Lincoln, Nebraska, United States of America
| | - Joao Carlos Gomes-Neto
- Department of Food Science and Technology, University of Nebraska-Lincoln, Lincoln, Nebraska, United States of America.,Nebraska Food for Health Center, University of Nebraska-Lincoln, Lincoln, Nebraska, United States of America
| | - Jitender S Deogun
- Department of Computer Science and Engineering, University of Nebraska-Lincoln, Lincoln, Nebraska, United States of America
| | - Andrew K Benson
- Department of Food Science and Technology, University of Nebraska-Lincoln, Lincoln, Nebraska, United States of America.,Nebraska Food for Health Center, University of Nebraska-Lincoln, Lincoln, Nebraska, United States of America
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15
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Genome-wide insights into population structure and host specificity of Campylobacter jejuni. Sci Rep 2021; 11:10358. [PMID: 33990625 PMCID: PMC8121833 DOI: 10.1038/s41598-021-89683-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Accepted: 04/26/2021] [Indexed: 11/15/2022] Open
Abstract
The zoonotic pathogen Campylobacter jejuni is among the leading causes of foodborne diseases worldwide. While C. jejuni colonises many wild animals and livestock, persistence mechanisms enabling the bacterium to adapt to host species' guts are not fully understood. In order to identify putative determinants influencing host preferences of distinct lineages, bootstrapping based on stratified random sampling combined with a k-mer-based genome-wide association was conducted on 490 genomes from diverse origins in Germany and Canada. We show a strong association of both the core and the accessory genome characteristics with distinct host animal species, indicating multiple adaptive trajectories defining the evolution of C. jejuni lifestyle preferences in different ecosystems. Here, we demonstrate that adaptation towards a specific host niche ecology is most likely a long evolutionary and multifactorial process, expressed by gene absence or presence and allele variations of core genes. Several host-specific allelic variants from different phylogenetic backgrounds, including dnaE, rpoB, ftsX or pycB play important roles for genome maintenance and metabolic pathways. Thus, variants of genes important for C. jejuni to cope with specific ecological niches or hosts may be useful markers for both surveillance and future pathogen intervention strategies.
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16
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Antilles N, García-Bocanegra I, Alba-Casals A, López-Soria S, Pérez-Méndez N, Saco M, González-Solís J, Cerdà-Cuéllar M. Occurrence and antimicrobial resistance of zoonotic enteropathogens in gulls from southern Europe. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 763:143018. [PMID: 33158539 DOI: 10.1016/j.scitotenv.2020.143018] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/11/2020] [Revised: 10/07/2020] [Accepted: 10/08/2020] [Indexed: 06/11/2023]
Abstract
Campylobacter spp. and Salmonella spp. are the two most frequent zoonotic bacteria involved in human enteric infections in the European Union. Both enteropathogens have been isolated from a diversity of wild birds in Northern Europe, but there is limited information about gulls as potential reservoirs in Southern Europe. A broad sampling of fledglings from nine colonies of yellow-legged gull (Larus michahellis, N = 1222) and Audouin's gull (Larus audouinii, N = 563) has been conducted in Spain and Tunisia during the late chick-rearing period. Overall, the occurrence of Campylobacter spp. and Salmonella spp. was 5.2% (93/1785, CI95%: 4.2-6.2%) and 20.8% (371/1785, CI95%: 18.9-22.7%), respectively. The most predominant Campylobacter species was C. jejuni (94.6%). A high diversity of Salmonella serovars was isolated and the most frequent were those also reported in human outbreaks, such as Salmonella Typhimurium. A high proportion of Campylobacter and Salmonella isolates showed resistance to at least one antimicrobial agent (20.2% and 51.5%, respectively), while 19.2% of Salmonella isolates were multidrug-resistant. These results show the relevance of gulls as reservoirs of Campylobacter and Salmonella by maintaining and spreading these bacteria, including resistant and multidrug resistant strains, in the environment. Our results suggest that gulls can serve as sentinel species for antibiotic pressure in the environment.
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Affiliation(s)
- Noelia Antilles
- IRTA, Centre de Recerca en Sanitat Animal (CReSA, IRTA-UAB), Campus de la Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain
| | - Ignacio García-Bocanegra
- Departamento de Sanidad Animal, Facultad de Veterinaria, Universidad de Córdoba-Agrifood Excellence International Campus (ceiA3), 14071 Córdoba, Spain
| | - Ana Alba-Casals
- IRTA, Centre de Recerca en Sanitat Animal (CReSA, IRTA-UAB), Campus de la Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain
| | - Sergio López-Soria
- IRTA, Centre de Recerca en Sanitat Animal (CReSA, IRTA-UAB), Campus de la Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain
| | - Néstor Pérez-Méndez
- Institut de Recerca de la Biodiversitat (IRBio) and Departament de Biologia Evolutiva, Ecologia i Ciències Ambientals, Universitat de Barcelona, 08028 Barcelona, Spain
| | - Montse Saco
- Departament de Microbiologia, Laboratori Agroalimentari de Cabrils, Departament d'Agricultura, Ramaderia, Pesca i Alimentació, Generalitat de Catalunya, Barcelona, Spain
| | - Jacob González-Solís
- Institut de Recerca de la Biodiversitat (IRBio) and Departament de Biologia Evolutiva, Ecologia i Ciències Ambientals, Universitat de Barcelona, 08028 Barcelona, Spain
| | - Marta Cerdà-Cuéllar
- IRTA, Centre de Recerca en Sanitat Animal (CReSA, IRTA-UAB), Campus de la Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain.
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17
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Parker CT, Cooper KK, Schiaffino F, Miller WG, Huynh S, Gray HK, Olortegui MP, Bardales PG, Trigoso DR, Penataro-Yori P, Kosek MN. Genomic Characterization of Campylobacter jejuni Adapted to the Guinea Pig ( Cavia porcellus) Host. Front Cell Infect Microbiol 2021; 11:607747. [PMID: 33816330 PMCID: PMC8012767 DOI: 10.3389/fcimb.2021.607747] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2020] [Accepted: 02/22/2021] [Indexed: 11/13/2022] Open
Abstract
Campylobacter jejuni is the leading bacterial cause of gastroenteritis worldwide with excessive incidence in low-and middle-income countries (LMIC). During a survey for C. jejuni from putative animal hosts in a town in the Peruvian Amazon, we were able to isolate and whole genome sequence two C. jejuni strains from domesticated guinea pigs (Cavia porcellus). The C. jejuni isolated from guinea pigs had a novel multilocus sequence type that shared some alleles with other C. jejuni collected from guinea pigs. Average nucleotide identity and phylogenetic analysis with a collection of C. jejuni subsp. jejuni and C. jejuni subsp. doylei suggest that the guinea pig isolates are distinct. Genomic comparisons demonstrated gene gain and loss that could be associated with guinea pig host specialization related to guinea pig diet, anatomy, and physiology including the deletion of genes involved with selenium metabolism, including genes encoding the selenocysteine insertion machinery and selenocysteine-containing proteins.
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Affiliation(s)
- Craig T Parker
- Produce Safety and Microbiology Research Unit, Agricultural Research Service, US Department of Agriculture, Albany, CA, United States
| | - Kerry K Cooper
- School of Animal and Comparative Biomedical Sciences, University of Arizona, Tucson, AZ, United States
| | - Francesca Schiaffino
- Faculty of Veterinary Medicine, Universidad Peruana Cayetano Heredia, Lima, Peru.,The Division of Infectious Diseases and International Health and Public Health Sciences, University of Virginia, Charlottesville, VA, United States
| | - William G Miller
- Produce Safety and Microbiology Research Unit, Agricultural Research Service, US Department of Agriculture, Albany, CA, United States
| | - Steven Huynh
- Produce Safety and Microbiology Research Unit, Agricultural Research Service, US Department of Agriculture, Albany, CA, United States
| | - Hannah K Gray
- Whiting School of Engineering, Johns Hopkins University, Baltimore, MD, United States
| | | | | | | | - Pablo Penataro-Yori
- The Division of Infectious Diseases and International Health and Public Health Sciences, University of Virginia, Charlottesville, VA, United States.,Biomedical Research, Asociación Benéfica PRISMA, Iquitos, Peru
| | - Margaret N Kosek
- The Division of Infectious Diseases and International Health and Public Health Sciences, University of Virginia, Charlottesville, VA, United States.,Biomedical Research, Asociación Benéfica PRISMA, Iquitos, Peru
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18
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Espunyes J, Cabezón O, Dias-Alves A, Miralles P, Ayats T, Cerdà-Cuéllar M. Assessing the role of livestock and sympatric wild ruminants in spreading antimicrobial resistant Campylobacter and Salmonella in alpine ecosystems. BMC Vet Res 2021; 17:79. [PMID: 33588859 PMCID: PMC7885356 DOI: 10.1186/s12917-021-02784-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2020] [Accepted: 02/02/2021] [Indexed: 11/10/2022] Open
Abstract
Background Livestock play an important role as reservoir of enteric pathogens and antimicrobial resistance (AMR), a health and economic concern worldwide. However, little is known regarding the transmission and maintenance of these pathogens at the wildlife-livestock interface. In this study, we assessed the occurrence, genetic diversity and AMR of Campylobacter spp. and Salmonella spp. shed by sympatric free-ranging livestock and a wild herbivore in an alpine ecosystem. Results Campylobacter spp. was isolated from 23.3 % of cattle and 7.7 % of sheep but was not isolated from horses nor Pyrenean chamois (Rupicapra pyrenaica). Campylobacter jejuni was the most frequent species. A high genetic diversity and certain host specificity of C. jejuni isolates was observed. The main AMR detected in Campylobacter isolates was to nalidixic acid (88.2 %), ciprofloxacin (82.4 %) and tetracycline (82.4 %); only 11.7 % of the isolates were pan-susceptible and 17.6 % were multi-resistant. Salmonella ser. Newport was isolated only from one Pyrenean chamois and was pan-susceptible. Conclusions Results show that free-ranging cattle and sheep are spreaders of Campylobacter as well as their AMR strains in the alpine environment. Therefore, contaminated alpine pastures or streams may constitute a source for the dissemination of AMR enteropathogens. However, apparently, alpine wild ungulates such as Pyrenean chamois play a negligible role in the epidemiology of zoonotic enteropathogens and AMR, and are not potential bioindicators of the burden of alpine environments.
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Affiliation(s)
- Johan Espunyes
- Wildlife Conservation Medicine Research Group (WildCoM), Departament de Medicina i Cirurgia Animals, Universitat Autònoma de Barcelona, Bellaterra, Spain. .,Research and Conservation Department, Zoo de Barcelona, Barcelona, Spain.
| | - Oscar Cabezón
- Wildlife Conservation Medicine Research Group (WildCoM), Departament de Medicina i Cirurgia Animals, Universitat Autònoma de Barcelona, Bellaterra, Spain.,UAB, Centre de Recerca en Sanitat Animal (CReSA, IRTA-UAB), Campus de la Universitat Autònoma de Barcelona, Bellaterra, Barcelona, Spain
| | - Andrea Dias-Alves
- Wildlife Conservation Medicine Research Group (WildCoM), Departament de Medicina i Cirurgia Animals, Universitat Autònoma de Barcelona, Bellaterra, Spain
| | - Pol Miralles
- UAB, Centre de Recerca en Sanitat Animal (CReSA, IRTA-UAB), Campus de la Universitat Autònoma de Barcelona, Bellaterra, Barcelona, Spain
| | - Teresa Ayats
- IRTA, Centre de Recerca en Sanitat Animal (CReSA, IRTA-UAB), Campus de la Universitat Autònoma de Barcelona, Bellaterra, Barcelona, Spain
| | - Marta Cerdà-Cuéllar
- IRTA, Centre de Recerca en Sanitat Animal (CReSA, IRTA-UAB), Campus de la Universitat Autònoma de Barcelona, Bellaterra, Barcelona, Spain
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Kreling V, Falcone FH, Kehrenberg C, Hensel A. Campylobacter sp.: Pathogenicity factors and prevention methods-new molecular targets for innovative antivirulence drugs? Appl Microbiol Biotechnol 2020; 104:10409-10436. [PMID: 33185702 PMCID: PMC7662028 DOI: 10.1007/s00253-020-10974-5] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2020] [Revised: 08/24/2020] [Accepted: 10/21/2020] [Indexed: 02/08/2023]
Abstract
Infections caused by bacterial species from the genus Campylobacter are one of the four main causes of strong diarrheal enteritis worldwide. Campylobacteriosis, a typical food-borne disease, can range from mild symptoms to fatal illness. About 550 million people worldwide suffer from campylobacteriosis and lethality is about 33 million p.a. This review summarizes the state of the current knowledge on Campylobacter with focus on its specific virulence factors. Using this knowledge, multifactorial prevention strategies can be implemented to reduce the prevalence of Campylobacter in the food chain. In particular, antiadhesive strategies with specific adhesion inhibitors seem to be a promising concept for reducing Campylobacter bacterial load in poultry production. Antivirulence compounds against bacterial adhesion to and/or invasion into the host cells can open new fields for innovative antibacterial agents. Influencing chemotaxis, biofilm formation, quorum sensing, secretion systems, or toxins by specific inhibitors can help to reduce virulence of the bacterium. In addition, the unusual glycosylation of the bacterium, being a prerequisite for effective phase variation and adaption to different hosts, is yet an unexplored target for combating Campylobacter sp. Plant extracts are widely used remedies in developing countries to combat infections with Campylobacter. Therefore, the present review summarizes the use of natural products against the bacterium in an attempt to stimulate innovative research concepts on the manifold still open questions behind Campylobacter towards improved treatment and sanitation of animal vectors, treatment of infected patients, and new strategies for prevention. KEY POINTS: • Campylobacter sp. is a main cause of strong enteritis worldwide. • Main virulence factors: cytolethal distending toxin, adhesion proteins, invasion machinery. • Strong need for development of antivirulence compounds.
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Affiliation(s)
- Vanessa Kreling
- Institute of Pharmaceutical Biology and Phytochemistry, University of Münster, Corrensstraße 48, 48149, Münster, Germany
| | - Franco H Falcone
- Institute of Parasitology, University of Gießen, Schubertstraße 81, 35392, Gießen, Germany
| | - Corinna Kehrenberg
- Institute of Veterinary Food Science, University of Gießen, Frankfurterstraße 81, 35392, Gießen, Germany
| | - Andreas Hensel
- Institute of Pharmaceutical Biology and Phytochemistry, University of Münster, Corrensstraße 48, 48149, Münster, Germany.
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20
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Marotta F, Di Marcantonio L, Janowicz A, Pedonese F, Di Donato G, Ardelean A, Nuvoloni R, Di Giannatale E, Garofolo G. Genotyping and Antibiotic Resistance Traits in Campylobacter jejuni and coli From Pigs and Wild Boars in Italy. Front Cell Infect Microbiol 2020; 10:592512. [PMID: 33178635 PMCID: PMC7593542 DOI: 10.3389/fcimb.2020.592512] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2020] [Accepted: 09/25/2020] [Indexed: 11/16/2022] Open
Abstract
The present study investigated the genomic constitution and antimicrobial resistance (AMR) of 238 Campylobacter from pigs and wild boars in Italy between 2012 and 2019. Campylobacter strains were genotyped using multilocus sequence typing (MLST) and whole genome MLST (wgMLST), screened for antimicrobial resistance genes, and tested for phenotypic susceptibility to six different antibiotics. C. coli was detected in 98.31% and 91.66% of pigs and wild boars, while C. jejuni was isolated in the remaining cases. MLST assigned 73 STs and 13 STs in pigs and wild boars, respectively, including 44 novel STs. The predominant ST in pigs was ST-854 (12.36%), followed by ST-9264 (6.18%). ST-1055 and ST-1417 were predominant in wild boars (30% and 13.33%, respectively). The minimum spanning tree using 1,121 global MLST profiles showed specific Italian clusters and a clear separation between pig and wild boar profiles. The wgMLST confirmed the MLST clustering and revealed a high genetic diversity within C. coli population in Italy. Minimum inhibitory concentrations (MIC) of six antibiotics revealed higher resistance in pigs to ciprofloxacin, nalidixic acid, streptomycin and tetracycline, compared to wild boar. In contrast, most strains were susceptible to gentamicin. Worrying levels of multidrug resistance (MDR) were observed mostly in pig isolates. Molecular screening of AMR mechanisms revealed the predominance of gyrA T86I substitution among fluoroquinolone- and quinolone-resistant isolates, and the 23S rRNA A2075G mutation among macrolide-resistant isolates. Other resistance determinants were observed: (i) tet(O) gene was present among tetracycline-resistant isolates; (ii) rpsL and aph(3')-III genes conferring resistance to aminoglycosides, were identified only in streptomycin or gentamicin-resistant pig isolates; (iii) cmeA, cmeB, cmeC, cmeR genes responsible of pump efflux mechanisms, were observed in almost all the strains; (iv) OXA-61, encoding β-lactamase, was found in the half of the strains. Genotypic and phenotypic AMR profiling was fairly correlated for quinolones/fluoroquinolones. Campylobacter infection is common also in wild boar populations in Italy, suggesting that wild boars could be a reservoir of resistant and multi-resistant Campylobacter species, which may be of public health concern. The present study adds to our knowledge on the epidemiological and ecological traits of this pathogen in domesticated and wild swine.
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Affiliation(s)
- Francesca Marotta
- National Reference Laboratory for Campylobacter, Istituto Zooprofilattico Sperimentale dell’Abruzzo e del Molise “G. Caporale”, Teramo, Italy
| | - Lisa Di Marcantonio
- National Reference Laboratory for Campylobacter, Istituto Zooprofilattico Sperimentale dell’Abruzzo e del Molise “G. Caporale”, Teramo, Italy
| | - Anna Janowicz
- National Reference Laboratory for Campylobacter, Istituto Zooprofilattico Sperimentale dell’Abruzzo e del Molise “G. Caporale”, Teramo, Italy
| | | | - Guido Di Donato
- National Reference Laboratory for Campylobacter, Istituto Zooprofilattico Sperimentale dell’Abruzzo e del Molise “G. Caporale”, Teramo, Italy
| | - Adrian Ardelean
- Institute for Diagnosis and Animal Health, National Reference for TSEs and Anatomic Pathology Laboratory, Bucharest, Romania
| | - Roberta Nuvoloni
- Department of Veterinary Sciences, University of Pisa, Pisa, Italy
| | - Elisabetta Di Giannatale
- National Reference Laboratory for Campylobacter, Istituto Zooprofilattico Sperimentale dell’Abruzzo e del Molise “G. Caporale”, Teramo, Italy
| | - Giuliano Garofolo
- National Reference Laboratory for Campylobacter, Istituto Zooprofilattico Sperimentale dell’Abruzzo e del Molise “G. Caporale”, Teramo, Italy
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21
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Molecular epidemiology of Campylobacter jejuni isolates from the broiler production chain: first report of MLST profiles in Argentina. Rev Argent Microbiol 2020; 53:59-63. [PMID: 32736818 DOI: 10.1016/j.ram.2020.06.005] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2019] [Revised: 02/26/2020] [Accepted: 06/16/2020] [Indexed: 11/24/2022] Open
Abstract
Campylobacter jejuni is an important foodborne pathogen with global distribution. We describe a genotyping study of a collection of C. jejuni (n=137) isolated from different broiler farms and from multiple sites along the processing line in a slaughterhouse in Argentina during 2011, 2012 and 2015. The isolates were genotyped using pulsed-field gel electrophoresis (PFGE) and multilocus sequence typing (MLST). Based on the PFGE results, the isolates were grouped into 26 pulsotypes. Subsequently, the isolates representing these 26 pulsotypes were chosen for MLST genotyping, which identified 16 different sequence types (STs) and 6 clonal complexes (CCs) (21, 45, 48, 353, 354, 446). Several of the STs (n=7) have not been previously reported in the PubMLST.org database. The most prevalent CCs were 21, 45 (both associated with human campylobacteriosis worldwide) and 353. This study showed high genetic diversity among C. jejuni in the broiler production environment in Argentina with novel MLST genotypes.
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22
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Marotta F, Janowicz A, Di Marcantonio L, Ercole C, Di Donato G, Garofolo G, Di Giannatale E. Molecular Characterization and Antimicrobial Susceptibility of C. jejuni Isolates from Italian Wild Bird Populations. Pathogens 2020; 9:E304. [PMID: 32326051 PMCID: PMC7238051 DOI: 10.3390/pathogens9040304] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2020] [Revised: 04/17/2020] [Accepted: 04/17/2020] [Indexed: 12/11/2022] Open
Abstract
Poultry is considered a major reservoir of human campylobacteriosis. It also been reported that not only poultry, but also wild birds, are capable of carrying C. jejuni, thus demonstrating to be a risk of spreading the bacteria in the environment. To gain insight into the population structure and investigate the antimicrobial resistance genotypes and phenotypes, we analyzed a collection of 135 C. jejuni from 15 species of wild birds in Italy. MLST revealed the presence of 41 sequence types (STs) and 13 clonal complexes (CCs). ST-179 complex and the generalist ST-45 complex were the most prevalent. Core genome MLST revealed that C. jejuni from ST-45 complex clustered according to the bird species, unlike the ST-179 complex which featured 3 different species in the same cluster. Overall we found a moderate prevalence of resistance to tetracycline (12.5%), ciprofloxacin and nalidixic acid (10%). The novel ST isolated from one pigeon showed resistance to all the antibiotics tested. The ST-179 complex (33.3%) was identified with significantly higher nalidixic acid resistance relative to other tested STs. Nine AMR genes (tet(O), cmeA, cmeB, cmeC, cmeR, aad, blaOXA-61, blaOXA-184 and erm(B)) and 23S rRNA and gyrA-associated point mutations were also described, indicating a concordance level between genotypic and phenotypic resistance of 23.3%, 23.4% and of 37.5% for streptomycin, tetracycline and quinolones/fluoroquinolones, respectively. We recommend that particular attention should be given to wild birds as key sentinel animals for the ecosystem contamination surveillance.
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Affiliation(s)
- Francesca Marotta
- Istituto Zooprofilattico Sperimentale dell’Abruzzo e del Molise “G. Caporale”, National Reference Laboratory for Campylobacter, 64100 Teramo, Italy; (A.J.); (L.D.M.); (G.D.D.); (G.G.); (E.D.G.)
| | - Anna Janowicz
- Istituto Zooprofilattico Sperimentale dell’Abruzzo e del Molise “G. Caporale”, National Reference Laboratory for Campylobacter, 64100 Teramo, Italy; (A.J.); (L.D.M.); (G.D.D.); (G.G.); (E.D.G.)
| | - Lisa Di Marcantonio
- Istituto Zooprofilattico Sperimentale dell’Abruzzo e del Molise “G. Caporale”, National Reference Laboratory for Campylobacter, 64100 Teramo, Italy; (A.J.); (L.D.M.); (G.D.D.); (G.G.); (E.D.G.)
| | - Claudia Ercole
- Department of Life, Health and Environmental Sciences, University of L’Aquila, 67100 L’Aquila, Italy;
| | - Guido Di Donato
- Istituto Zooprofilattico Sperimentale dell’Abruzzo e del Molise “G. Caporale”, National Reference Laboratory for Campylobacter, 64100 Teramo, Italy; (A.J.); (L.D.M.); (G.D.D.); (G.G.); (E.D.G.)
| | - Giuliano Garofolo
- Istituto Zooprofilattico Sperimentale dell’Abruzzo e del Molise “G. Caporale”, National Reference Laboratory for Campylobacter, 64100 Teramo, Italy; (A.J.); (L.D.M.); (G.D.D.); (G.G.); (E.D.G.)
| | - Elisabetta Di Giannatale
- Istituto Zooprofilattico Sperimentale dell’Abruzzo e del Molise “G. Caporale”, National Reference Laboratory for Campylobacter, 64100 Teramo, Italy; (A.J.); (L.D.M.); (G.D.D.); (G.G.); (E.D.G.)
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23
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Mutschall SK, Hetman BM, Bondo KJ, Gannon VPJ, Jardine CM, Taboada EN. Campylobacter jejuni Strain Dynamics in a Raccoon ( Procyon lotor) Population in Southern Ontario, Canada: High Prevalence and Rapid Subtype Turnover. Front Vet Sci 2020; 7:27. [PMID: 32118057 PMCID: PMC7026257 DOI: 10.3389/fvets.2020.00027] [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: 01/14/2020] [Indexed: 12/04/2022] Open
Abstract
Free-ranging wildlife are increasingly recognized as potential reservoirs of disease-causing Campylobacter species such as C. jejuni and C. coli. Raccoons (Procyon lotor), which live at the interface of rural, urban, and more natural environments, are ideal subjects for exploring the potential role that wildlife play in the epidemiology of campylobacteriosis. We studied the prevalence and genetic diversity of Campylobacter from live-captured raccoons on five swine farms and five conservation areas in southwest Ontario. From 2011 to 2013, we collected fecal swabs (n = 1,096) from raccoons, and (n = 50) manure pit samples from the swine farm environment. We subtyped the resulting Campylobacter isolates (n = 581) using Comparative Genomic Fingerprinting (CGF) and 114 distinct subtypes were observed, including 96 and 18 subtypes among raccoon and manure pit isolates, respectively. Campylobacter prevalence in raccoons was 46.3%, with 98.7% of isolates recovered identified as C. jejuni. Novel raccoon-specific CGF subtypes (n = 40/96) accounted for 24.6% (n = 143/581) of Campylobacter isolates collected in this study. Our results also show that C. jejuni is readily acquired and lost in this wild raccoon population and that a high Campylobacter prevalence is observed despite transient carriage typically lasting 30 days or fewer. Moreover, although raccoons appeared to be colonized by species-adapted subtypes, they also harbored agriculture-associated genotypes that accounted for the majority of isolates observed (66.4%) and that are strongly associated with human infections. This suggests that raccoons may act as vectors in the transmission of clinically-relevant C. jejuni subtypes at the interface of rural, urban, and more natural environments.
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Affiliation(s)
- Steven K Mutschall
- National Centre for Animal Diseases, Canadian Food Inspection Agency, Lethbridge, AB, Canada
| | - Benjamin M Hetman
- Department of Population Medicine, Ontario Veterinary College, University of Guelph, Guelph, ON, Canada
| | - Kristin J Bondo
- Department of Pathobiology, Ontario Veterinary College, University of Guelph, Guelph, ON, Canada
| | - Victor P J Gannon
- National Microbiology Laboratory at Lethbridge, Public Health Agency of Canada, Lethbridge, AB, Canada
| | - Claire M Jardine
- Department of Pathobiology, Ontario Veterinary College, University of Guelph, Guelph, ON, Canada.,Canadian Wildlife Health Cooperative, Ontario Veterinary College, University of Guelph, Guelph, ON, Canada
| | - Eduardo N Taboada
- National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, MB, Canada
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24
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Smith OM, Snyder WE, Owen JP. Are we overestimating risk of enteric pathogen spillover from wild birds to humans? Biol Rev Camb Philos Soc 2020; 95:652-679. [PMID: 32003106 PMCID: PMC7317827 DOI: 10.1111/brv.12581] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2019] [Revised: 01/08/2020] [Accepted: 01/13/2020] [Indexed: 01/07/2023]
Abstract
Enteric illnesses remain the second largest source of communicable diseases worldwide, and wild birds are suspected sources for human infection. This has led to efforts to reduce pathogen spillover through deterrence of wildlife and removal of wildlife habitat, particularly within farming systems, which can compromise conservation efforts and the ecosystem services wild birds provide. Further, Salmonella spp. are a significant cause of avian mortality, leading to additional conservation concerns. Despite numerous studies of enteric bacteria in wild birds and policies to discourage birds from food systems, we lack a comprehensive understanding of wild bird involvement in transmission of enteric bacteria to humans. Here, we propose a framework for understanding spillover of enteric pathogens from wild birds to humans, which includes pathogen acquisition, reservoir competence and bacterial shedding, contact with people and food, and pathogen survival in the environment. We place the literature into this framework to identify important knowledge gaps. Second, we conduct a meta‐analysis of prevalence data for three human enteric pathogens, Campylobacter spp., E. coli, and Salmonella spp., in 431 North American breeding bird species. Our literature review revealed that only 3% of studies addressed the complete system of pathogen transmission. In our meta‐analysis, we found a Campylobacter spp. prevalence of 27% across wild birds, while prevalence estimates of pathogenic E. coli (20%) and Salmonella spp. (6.4%) were lower. There was significant bias in which bird species have been tested, with most studies focusing on a small number of taxa that are common near people (e.g. European starlings Sturnus vulgaris and rock pigeons Columba livia) or commonly in contact with human waste (e.g. gulls). No pathogen prevalence data were available for 65% of North American breeding bird species, including many commonly in contact with humans (e.g. black‐billed magpie Pica hudsonia and great blue heron Ardea herodias), and our metadata suggest that some under‐studied species, taxonomic groups, and guilds may represent equivalent or greater risk to human infection than heavily studied species. We conclude that current data do not provide sufficient information to determine the likelihood of enteric pathogen spillover from wild birds to humans and thus preclude management solutions. The primary focus in the literature on pathogen prevalence likely overestimates the probability of enteric pathogen spillover from wild birds to humans because a pathogen must survive long enough at an infectious dose and be a strain that is able to colonize humans to cause infection. We propose that future research should focus on the large number of under‐studied species commonly in contact with people and food production and demonstrate shedding of bacterial strains pathogenic to humans into the environment where people may contact them. Finally, studies assessing the duration and intensity of bacterial shedding and survival of bacteria in the environment in bird faeces will help provide crucial missing information necessary to calculate spillover probability. Addressing these essential knowledge gaps will support policy to reduce enteric pathogen spillover to humans and enhance bird conservation efforts that are currently undermined by unsupported fears of pathogen spillover from wild birds.
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Affiliation(s)
- Olivia M Smith
- School of Biological Sciences, Washington State University, P.O. Box 644236, Pullman, WA, 99164, U.S.A
| | - William E Snyder
- Department of Entomology, Washington State University, 100 Dairy Road, P.O. Box 646382, Pullman, WA, 99164, U.S.A
| | - Jeb P Owen
- Department of Entomology, Washington State University, 100 Dairy Road, P.O. Box 646382, Pullman, WA, 99164, U.S.A
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25
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Mourkas E, Florez‐Cuadrado D, Pascoe B, Calland JK, Bayliss SC, Mageiros L, Méric G, Hitchings MD, Quesada A, Porrero C, Ugarte‐Ruiz M, Gutiérrez‐Fernández J, Domínguez L, Sheppard SK. Gene pool transmission of multidrug resistance among Campylobacter from livestock, sewage and human disease. Environ Microbiol 2019; 21:4597-4613. [PMID: 31385413 PMCID: PMC6916351 DOI: 10.1111/1462-2920.14760] [Citation(s) in RCA: 54] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2019] [Revised: 07/22/2019] [Accepted: 07/22/2019] [Indexed: 11/30/2022]
Abstract
The use of antimicrobials in human and veterinary medicine has coincided with a rise in antimicrobial resistance (AMR) in the food-borne pathogens Campylobacter jejuni and Campylobacter coli. Faecal contamination from the main reservoir hosts (livestock, especially poultry) is the principal route of human infection but little is known about the spread of AMR among source and sink populations. In particular, questions remain about how Campylobacter resistomes interact between species and hosts, and the potential role of sewage as a conduit for the spread of AMR. Here, we investigate the genomic variation associated with AMR in 168 C. jejuni and 92 C. coli strains isolated from humans, livestock and urban effluents in Spain. AMR was tested in vitro and isolate genomes were sequenced and screened for putative AMR genes and alleles. Genes associated with resistance to multiple drug classes were observed in both species and were commonly present in multidrug-resistant genomic islands (GIs), often located on plasmids or mobile elements. In many cases, these loci had alleles that were shared among C. jejuni and C. coli consistent with horizontal transfer. Our results suggest that specific antibiotic resistance genes have spread among Campylobacter isolated from humans, animals and the environment.
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Affiliation(s)
- Evangelos Mourkas
- The Milner Centre for Evolution, Department of Biology and BiochemistryUniversity of BathBA27AYBathUK
| | | | - Ben Pascoe
- The Milner Centre for Evolution, Department of Biology and BiochemistryUniversity of BathBA27AYBathUK
- MRC CLIMB ConsortiumUniversity of BathBathUK
| | - Jessica K. Calland
- The Milner Centre for Evolution, Department of Biology and BiochemistryUniversity of BathBA27AYBathUK
| | - Sion C. Bayliss
- The Milner Centre for Evolution, Department of Biology and BiochemistryUniversity of BathBA27AYBathUK
- MRC CLIMB ConsortiumUniversity of BathBathUK
| | - Leonardos Mageiros
- The Milner Centre for Evolution, Department of Biology and BiochemistryUniversity of BathBA27AYBathUK
| | - Guillaume Méric
- The Milner Centre for Evolution, Department of Biology and BiochemistryUniversity of BathBA27AYBathUK
- Cambridge Baker Systems Genomics InitiativeBaker Heart and Diabetes Institute, 75 Commercial RdMelbourne3004VictoriaAustralia
- Department of Infectious Diseases, Central Clinical SchoolMonash UniversityMelbourneVictoria3004Australia
| | | | - Alberto Quesada
- Department of Biochemistry, Molecular Biology and Genetics, Faculty of Veterinary MedicineUniversity of ExtremaduraCáceresSpain
| | - Concepción Porrero
- VISAVET Health Surveillance CentreUniversidad Complutense MadridMadridSpain
| | - María Ugarte‐Ruiz
- VISAVET Health Surveillance CentreUniversidad Complutense MadridMadridSpain
| | | | - Lucas Domínguez
- VISAVET Health Surveillance CentreUniversidad Complutense MadridMadridSpain
- Department of Animal Health, Faculty of Veterinary MedicineUniversidad Complutense MadridMadridSpain
| | - Samuel K. Sheppard
- The Milner Centre for Evolution, Department of Biology and BiochemistryUniversity of BathBA27AYBathUK
- MRC CLIMB ConsortiumUniversity of BathBathUK
- Department of ZoologyUniversity of OxfordOxfordUK
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26
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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: 42] [Impact Index Per Article: 8.4] [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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27
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Rukambile E, Sintchenko V, Muscatello G, Kock R, Alders R. Infection, colonization and shedding of Campylobacter and Salmonella in animals and their contribution to human disease: A review. Zoonoses Public Health 2019; 66:562-578. [PMID: 31179637 DOI: 10.1111/zph.12611] [Citation(s) in RCA: 50] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2018] [Revised: 04/17/2019] [Accepted: 05/20/2019] [Indexed: 12/15/2022]
Abstract
Livestock meat and offal contribute significantly to human nutrition as sources of high-quality protein and micronutrients. Livestock products are increasingly in demand, particularly in low- and middle-income settings where economies are growing and meat is increasingly seen as an affordable and desirable food item. Demand is also driving intensification of livestock keeping and processing. An unintended consequence of intensification is increased exposure to zoonotic agents, and a contemporary emerging problem is infection with Campylobacter and Salmonella spp. from livestock (avian and mammalian), which can lead to disease, malabsorption and undernutrition through acute and chronic diarrhoea. This can occur at the farm, in households or through the food chain. Direct infection occurs when handling livestock and through bacteria shed into the environment, on food preparation surfaces or around the house and surroundings. This manuscript critically reviews Campylobacter and Salmonella infections in animals, examines the factors affecting colonization and faecal shedding of bacteria of these two genera as well as risk factors for human acquisition of the infection from infected animals or environment and analyses priority areas for preventive actions with a focus on resource-poor settings.
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Affiliation(s)
- Elpidius Rukambile
- School of Life and Environmental Sciences, Faculty of Science, The University of Sydney, Sydney, New South Wales, Australia.,Charles Perkins Centre, The University of Sydney, Sydney, New South Wales, Australia.,Marie Bashir Institute for Infectious Diseases and Biosecurity, The University of Sydney, Sydney, New South Wales, Australia.,Tanzania Veterinary Laboratory Agency, Dar es Salaam, Tanzania
| | - Vitali Sintchenko
- Marie Bashir Institute for Infectious Diseases and Biosecurity, The University of Sydney, Sydney, New South Wales, Australia.,Centre for Infectious Diseases and Microbiology-Public Health, Westmead Hospital and New South Wales Health Pathology, Sydney, New South Wales, Australia
| | - Gary Muscatello
- School of Life and Environmental Sciences, Faculty of Science, The University of Sydney, Sydney, New South Wales, Australia
| | - Richard Kock
- The Royal Veterinary College, University of London, London, UK
| | - Robyn Alders
- Marie Bashir Institute for Infectious Diseases and Biosecurity, The University of Sydney, Sydney, New South Wales, Australia.,Kyeema Foundation, Brisbane, Queensland, Australia.,Centre on Global Health Security, Chatham House, London, UK
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28
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Gilbert MJ, Duim B, Zomer AL, Wagenaar JA. Living in Cold Blood: Arcobacter, Campylobacter, and Helicobacter in Reptiles. Front Microbiol 2019; 10:1086. [PMID: 31191467 PMCID: PMC6530492 DOI: 10.3389/fmicb.2019.01086] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2019] [Accepted: 04/30/2019] [Indexed: 01/10/2023] Open
Abstract
Species of the Epsilonproteobacteria genera Arcobacter, Campylobacter, and Helicobacter are commonly associated with vertebrate hosts and some are considered significant pathogens. Vertebrate-associated Epsilonproteobacteria are often considered to be largely confined to endothermic mammals and birds. Recent studies have shown that ectothermic reptiles display a distinct and largely unique Epsilonproteobacteria community, including taxa which can cause disease in humans. Several Arcobacter taxa are widespread amongst reptiles and often show a broad host range. Reptiles carry a large diversity of unique and novel Helicobacter taxa, which apparently evolved in an ectothermic host. Some species, such as Campylobacter fetus, display a distinct intraspecies host dichotomy, with genetically divergent lineages occurring either in mammals or reptiles. These taxa can provide valuable insights in host adaptation and co-evolution between symbiont and host. Here, we present an overview of the biodiversity, ecology, epidemiology, and evolution of reptile-associated Epsilonproteobacteria from a broader vertebrate host perspective.
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Affiliation(s)
- Maarten J Gilbert
- Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, Utrecht, Netherlands.,Reptile, Amphibian and Fish Conservation Netherlands, Nijmegen, Netherlands
| | - Birgitta Duim
- Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, Utrecht, Netherlands.,WHO Collaborating Center for Campylobacter/OIE Reference Laboratory for Campylobacteriosis, Utrecht, Netherlands
| | - Aldert L Zomer
- Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, Utrecht, Netherlands.,WHO Collaborating Center for Campylobacter/OIE Reference Laboratory for Campylobacteriosis, Utrecht, Netherlands
| | - Jaap A Wagenaar
- Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, Utrecht, Netherlands.,WHO Collaborating Center for Campylobacter/OIE Reference Laboratory for Campylobacteriosis, Utrecht, Netherlands.,Wageningen Bioveterinary Research, Lelystad, Netherlands
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29
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Kovanen S, Rossi M, Pohja-Mykrä M, Nieminen T, Raunio-Saarnisto M, Sauvala M, Fredriksson-Ahomaa M, Hänninen ML, Kivistö R. Population Genetics and Characterization of Campylobacter jejuni Isolates from Western Jackdaws and Game Birds in Finland. Appl Environ Microbiol 2019; 85:e02365-18. [PMID: 30552190 PMCID: PMC6365822 DOI: 10.1128/aem.02365-18] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2018] [Accepted: 12/08/2018] [Indexed: 01/18/2023] Open
Abstract
Poultry are considered a major reservoir and source of human campylobacteriosis, but the roles of environmental reservoirs, including wild birds, have not been assessed in depth. In this study, we isolated and characterized Campylobacter jejuni from western jackdaws (n = 91, 43%), mallard ducks (n = 82, 76%), and pheasants (n = 9, 9%). Most of the western jackdaw and mallard duck C. jejuni isolates represented multilocus sequence typing (MLST) sequence types (STs) that diverged from those previously isolated from human patients and various animal species, whereas all pheasant isolates represented ST-19, a common ST among human patients and other hosts worldwide. Whole-genome MLST revealed that mallard duck ST-2314 and pheasant ST-19 isolates represented bacterial clones that were genetically highly similar to human isolates detected previously. Further analyses revealed that in addition to a divergent ClonalFrame genealogy, certain genomic characteristics of the western jackdaw C. jejuni isolates, e.g., a novel cdtABC gene cluster and the type VI secretion system (T6SS), may affect their host specificity and virulence. Game birds may thus pose a risk for acquiring campylobacteriosis; therefore, hygienic measures during slaughter and meat handling warrant special attention.IMPORTANCE The roles of environmental reservoirs, including wild birds, in the molecular epidemiology of Campylobacter jejuni have not been assessed in depth. Our results showed that game birds may pose a risk for acquiring campylobacteriosis, because they had C. jejuni genomotypes highly similar to human isolates detected previously. Therefore, hygienic measures during slaughter and meat handling warrant special attention. On the contrary, a unique phylogeny was revealed for the western jackdaw isolates, and certain genomic characteristics identified among these isolates are hypothesized to affect their host specificity and virulence. Comparative genomics within sequence types (STs), using whole-genome multilocus sequence typing (wgMLST), and phylogenomics are efficient methods to analyze the genomic relationships of C. jejuni isolates.
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Affiliation(s)
- Sara Kovanen
- Department of Food Hygiene and Environmental Health, Faculty of Veterinary Medicine, University of Helsinki, Helsinki, Finland
| | - Mirko Rossi
- Department of Food Hygiene and Environmental Health, Faculty of Veterinary Medicine, University of Helsinki, Helsinki, Finland
| | - Mari Pohja-Mykrä
- Ruralia Institute, Faculty of Agriculture and Forestry, University of Helsinki, Seinäjoki, Finland
| | - Timo Nieminen
- Ruralia Institute, Faculty of Agriculture and Forestry, University of Helsinki, Seinäjoki, Finland
| | | | - Mikaela Sauvala
- Department of Food Hygiene and Environmental Health, Faculty of Veterinary Medicine, University of Helsinki, Helsinki, Finland
| | - Maria Fredriksson-Ahomaa
- Department of Food Hygiene and Environmental Health, Faculty of Veterinary Medicine, University of Helsinki, Helsinki, Finland
| | - Marja-Liisa Hänninen
- Department of Food Hygiene and Environmental Health, Faculty of Veterinary Medicine, University of Helsinki, Helsinki, Finland
| | - Rauni Kivistö
- Department of Food Hygiene and Environmental Health, Faculty of Veterinary Medicine, University of Helsinki, Helsinki, Finland
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30
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Johansson H, Ellström P, Artursson K, Berg C, Bonnedahl J, Hansson I, Hernandez J, Lopez-Martín J, Medina-Vogel G, Moreno L, Olsen B, Olsson Engvall E, Skarin H, Troell K, Waldenström J, Ågren J, González-Acuña D. Characterization of Campylobacter spp. isolated from wild birds in the Antarctic and Sub-Antarctic. PLoS One 2018; 13:e0206502. [PMID: 30412585 PMCID: PMC6226163 DOI: 10.1371/journal.pone.0206502] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2018] [Accepted: 10/15/2018] [Indexed: 01/06/2023] Open
Abstract
A lack of knowledge of naturally occurring pathogens is limiting our ability to use the Antarctic to study the impact human-mediated introduction of infectious microorganisms have on this relatively uncontaminated environment. As no large-scale coordinated effort to remedy this lack of knowledge has taken place, we rely on smaller targeted efforts to both study present microorganisms and monitor the environment for introductions. In one such effort, we isolated Campylobacter species from fecal samples collected from wild birds in the Antarctic Peninsula and the sub-Antarctic island of South Georgia. Indeed, in South Georgia, we found Campylobacter lari and the closely related Campylobacter peloridis, but also distantly related human-associated multilocus sequence types of Campylobacter jejuni. In contrast, in the Antarctic Peninsula, we found C. lari and two closely related species, Campylobacter subantarcticus and Campylobacter volucris, but no signs of human introduction. In fact, our finding of human-associated sequence types of C. jejuni in South Georgia, but not in the Antarctic Peninsula, suggests that efforts to limit the spread of infectious microorganisms to the Antarctic have so far been successful in preventing the introduction of C. jejuni. However, we do not know how it came to South Georgia and whether the same mode of introduction could spread it from there to the Antarctic Peninsula.
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Affiliation(s)
- Håkan Johansson
- Centre for Ecology and Evolution in Microbial Model Systems, Linnaeus University, Kalmar, Sweden
| | - Patrik Ellström
- Zoonosis Science Center, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
- Department of Medical Sciences, Uppsala University, Uppsala, Sweden
| | | | - Charlotte Berg
- Department of Animal Environment and Health, Swedish University of Agricultural Sciences, Skara, Sweden
| | - Jonas Bonnedahl
- Centre for Ecology and Evolution in Microbial Model Systems, Linnaeus University, Kalmar, Sweden
- Department of Infectious Diseases, Kalmar County Hospital, Kalmar, Sweden
| | - Ingrid Hansson
- Department of Biomedical Sciences and Veterinary Public Health, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Jorge Hernandez
- Zoonosis Science Center, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
- Laboratory of Microbiology, Kalmar County Hospital, Kalmar, Sweden
| | - Juana Lopez-Martín
- Departamento de Patología y Medicina Preventiva, Facultad de Ciencias Veterinarias, Universidad de Concepción, Chillán, Chile
| | - Gonzalo Medina-Vogel
- Centro de Investigación para la Sustentabilidad, Universidad Andrés Bello, Santiago, Chile
| | - Lucila Moreno
- Facultad de Ciencias Naturales y Oceanográficas, Universidad de Concepción, Concepción, Chile
| | - Björn Olsen
- Zoonosis Science Center, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
- Department of Medical Sciences, Uppsala University, Uppsala, Sweden
| | | | | | | | - Jonas Waldenström
- Centre for Ecology and Evolution in Microbial Model Systems, Linnaeus University, Kalmar, Sweden
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Abstract
Some bacteria can transfer to new host species, and this poses a risk to human health. Indeed, an estimated 60% of all human pathogens have originated from other animal species. Similarly, human-to-animal transitions are recognized as a major threat to sustainable livestock production, and emerging pathogens impose an increasing burden on crop yield and global food security. Recent advances in high-throughput sequencing technologies have enabled comparative genomic analyses of bacterial populations from multiple hosts. Such studies are providing new insights into the evolutionary processes that underpin the establishment of bacteria in new host niches. A better understanding of the genetic and mechanistic basis for bacterial host adaptation may reveal novel targets for controlling infection or inform the design of approaches to limit the emergence of new pathogens.
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Affiliation(s)
- Samuel K Sheppard
- Milner Centre for Evolution, Department of Biology & Biotechnology, University of Bath, Claverton Down, Bath, UK
| | - David S Guttman
- Department of Cell & Systems Biology, University of Toronto, Toronto, Ontario, Canada
- Centre for the Analysis of Genome Evolution & Function, University of Toronto, Toronto, Ontario, Canada
| | - J Ross Fitzgerald
- The Roslin Institute, University of Edinburgh, Easter Bush Campus, Edinburgh, UK.
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32
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Iglesias-Torrens Y, Miró E, Guirado P, Llovet T, Muñoz C, Cerdà-Cuéllar M, Madrid C, Balsalobre C, Navarro F. Population Structure, Antimicrobial Resistance, and Virulence-Associated Genes in Campylobacter jejuni Isolated From Three Ecological Niches: Gastroenteritis Patients, Broilers, and Wild Birds. Front Microbiol 2018; 9:1676. [PMID: 30116225 PMCID: PMC6083060 DOI: 10.3389/fmicb.2018.01676] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2018] [Accepted: 07/04/2018] [Indexed: 11/13/2022] Open
Abstract
Campylobacter jejuni is the causal agent of the food-borne infection with the highest incidence in Europe. Both poultry and wild birds are a major reservoir. To gain insight into the population structure, virulence potential, and antimicrobial resistance (AMR), a collection of 150 isolates from three different ecological niches (broilers, wild birds, and human patients) was studied. Despite the high genetic diversity found, the population structure defined two distinct clusters, one formed mostly by broiler and human isolates and another one by most wild bird isolates. The ST-21 complex exhibits highest prevalence (in humans and broilers), followed by ST-1275 complex (only in wild birds). The ST-48, -45, and -354 complexes were found in all three niches, but represent only 22 out of 150 studied strains. A higher occurrence of AMR and multidrug resistance was detected among broiler and human isolates. Moreover, significant differences were found in the distribution of certain putative virulence genes. Remarkably, many wild bird strains were negative for either cdtA, cdtB, or cdtC from the canonical strain 81-176, whereas all broiler and human strains were positive. These data suggest that the different variants of the cdt genes might be relevant for the efficient colonization of certain hosts by C. jejuni. Our study contributes to the understanding of the role of the diverse Campylobacter reservoirs in the transmission of campylobacteriosis to humans.
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Affiliation(s)
- Yaidelys Iglesias-Torrens
- Hospital de la Santa Creu i Sant Pau, Institut d’Investigació Biomèdica Sant Pau (IIB Sant Pau), Barcelona, Spain
- Departament de Genètica i Microbiologia, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Elisenda Miró
- Hospital de la Santa Creu i Sant Pau, Institut d’Investigació Biomèdica Sant Pau (IIB Sant Pau), Barcelona, Spain
| | - Pedro Guirado
- Departament de Genètica, Microbiologia i Estadística, Universitat de Barcelona, Barcelona, Spain
| | - Teresa Llovet
- Hospital de la Santa Creu i Sant Pau, Institut d’Investigació Biomèdica Sant Pau (IIB Sant Pau), Barcelona, Spain
- Departament de Genètica i Microbiologia, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Carmen Muñoz
- Hospital de la Santa Creu i Sant Pau, Institut d’Investigació Biomèdica Sant Pau (IIB Sant Pau), Barcelona, Spain
- Departament de Genètica i Microbiologia, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Marta Cerdà-Cuéllar
- Centre de Recerca en Sanitat Animal (CReSA)-IRTA, Campus de la Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Cristina Madrid
- Departament de Genètica, Microbiologia i Estadística, Universitat de Barcelona, Barcelona, Spain
| | - Carlos Balsalobre
- Departament de Genètica, Microbiologia i Estadística, Universitat de Barcelona, Barcelona, Spain
| | - Ferran Navarro
- Hospital de la Santa Creu i Sant Pau, Institut d’Investigació Biomèdica Sant Pau (IIB Sant Pau), Barcelona, Spain
- Departament de Genètica i Microbiologia, Universitat Autònoma de Barcelona, Barcelona, Spain
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Bulbow H, Wu J, Turner D, McEntire M, Tizard I. Campylobacter colonization is not associated with proventricular dilatation disease in psittacines. VETERINARY MEDICINE-RESEARCH AND REPORTS 2018; 8:37-40. [PMID: 30050854 PMCID: PMC6042502 DOI: 10.2147/vmrr.s137213] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Psittacine proventricular dilatation disease (PDD) is a neurological disease caused by parrot bornaviruses. A competing theory suggests that intestinal colonization by Campylobacter species may also be a potential cause of PDD or that their presence may be required for disease development. This theory proposes that PDD results from the activities of antiganglioside antibodies on enteric neurons in a manner similar to the pathogenesis of Guillain–Barré syndrome in humans. We therefore cultured feces from domestic chickens as well as from multiple parrot species to determine whether Campylobacter spp. could be detected in the latter. We failed to detect Campylobacter in a flock of cockatiels known to be highly susceptible to experimental parrot bornavirus-induced PDD. Even in naturally infected psittacines suffering from clinical PDD, no Campylobacter species were detected. Conversely, Campylobacter was readily cultured from domestic poultry samples and confirmed by using matrix-associated laser desorption ionization mass spectroscopy/real-time polymerase chain reaction. We conclude that not only are Campylobacter infections of psittacines uncommon, but also that infection by Campylobacter species is not related to the etiology of PDD.
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Affiliation(s)
- Holden Bulbow
- Schubot Exotic Bird Health Center, Department of Veterinary Pathobiology, College of Veterinary Medicine, Texas A&M University, College Station, TX, USA,
| | - Jing Wu
- Schubot Exotic Bird Health Center, Department of Veterinary Pathobiology, College of Veterinary Medicine, Texas A&M University, College Station, TX, USA,
| | - Debra Turner
- Schubot Exotic Bird Health Center, Department of Veterinary Pathobiology, College of Veterinary Medicine, Texas A&M University, College Station, TX, USA,
| | - Michael McEntire
- Schubot Exotic Bird Health Center, Department of Veterinary Pathobiology, College of Veterinary Medicine, Texas A&M University, College Station, TX, USA,
| | - Ian Tizard
- Schubot Exotic Bird Health Center, Department of Veterinary Pathobiology, College of Veterinary Medicine, Texas A&M University, College Station, TX, USA,
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34
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Elhadidy M, Arguello H, Álvarez-Ordóñez A, Miller WG, Duarte A, Martiny D, Hallin M, Vandenberg O, Dierick K, Botteldoorn N. Orthogonal typing methods identify genetic diversity among Belgian Campylobacter jejuni strains isolated over a decade from poultry and cases of sporadic human illness. Int J Food Microbiol 2018; 275:66-75. [PMID: 29649751 DOI: 10.1016/j.ijfoodmicro.2018.04.004] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2017] [Revised: 02/08/2018] [Accepted: 04/02/2018] [Indexed: 11/30/2022]
Abstract
Campylobacter jejuni is a zoonotic pathogen commonly associated with human gastroenteritis. Retail poultry meat is a major food-related transmission source of C. jejuni to humans. The present study investigated the genetic diversity, clonal relationship, and strain risk-analysis of 403 representative C. jejuni isolates from chicken broilers (n = 204) and sporadic cases of human diarrhea (n = 199) over a decade (2006-2015) in Belgium, using multilocus sequence typing (MLST), PCR binary typing (P-BIT), and identification of lipooligosaccharide (LOS) biosynthesis locus classes. A total of 123 distinct sequence types (STs), clustered in 28 clonal complexes (CCs) were assigned, including ten novel sequence types that were not previously documented in the international database. Sequence types ST-48, ST-21, ST-50, ST-45, ST-464, ST-2274, ST-572, ST-19, ST-257 and ST-42 were the most prevalent. Clonal complex 21 was the main clonal complex in isolates from humans and chickens. Among observed STs, a total of 35 STs that represent 72.2% (291/403) of the isolates were identified in both chicken and human isolates confirming considerable epidemiological relatedness; these 35 STs also clustered together in the most prevalent CCs. A majority of the isolates harbored sialylated LOS loci associated with potential neuropathic outcomes in humans. Although the concordance between MLST and P-BIT, determined by the adjusted Rand and Wallace coefficients, showed low congruence between both typing methods. The discriminatory power of P-BIT and MLST was similar, with Simpson's diversity indexes of 0.978 and 0.975, respectively. Furthermore, P-BIT could provide additional epidemiological information that would provide further insights regarding the potential association to human health from each strain. In addition, certain clones could be linked to specific clinical symptoms. Indeed, LOS class E was associated with less severe infections. Moreover, ST-572 was significantly associated with clinical infections occurring after travelling abroad. Ultimately, the data generated from this study will help to better understand the molecular epidemiology of C. jejuni infection.
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Affiliation(s)
- Mohamed Elhadidy
- Department of Bacteriology, Mycology and Immunology, Faculty of Veterinary Medicine, Mansoura University, Mansoura, Egypt; University of Science and Technology, Zewail City of Science and Technology, Giza, Egypt.
| | - Hector Arguello
- Genomic and Animal Biotechnology, Department of Genetics, Veterinary Faculty, Universidad de Córdoba, 14047, Córdoba, Spain
| | - Avelino Álvarez-Ordóñez
- Department of Food Hygiene and Technology and Institute of Food Science and Technology, University of León, Spain
| | - William G Miller
- Produce Safety and Microbiology Research Unit, Agricultural Research Service, U.S. Department of Agriculture, Albany, CA, USA
| | - Alexandra Duarte
- Laboratory of Food Microbiology and Food Preservation, Department of Food Safety and Food Quality, Faculty of Bioscience Engineering, Ghent University, Coupure Links 653, B-9000 Gent, Belgium; National Reference Laboratory for Campylobacter, Scientific Institute of Public Health (WIV-ISP), Scientific Service: Foodborne Pathogens, Juliette Wytsman Street 14, 1050 Brussels, Belgium
| | - Delphine Martiny
- National Reference Center for Campylobacter, Saint Pierre University Hospital, Brussels, Belgium; Department of Microbiology, LHUB-ULB, Pôle Hospitalier Universitaire de Bruxelles, Brussels, Belgium
| | - Marie Hallin
- National Reference Center for Campylobacter, Saint Pierre University Hospital, Brussels, Belgium; Department of Microbiology, LHUB-ULB, Pôle Hospitalier Universitaire de Bruxelles, Brussels, Belgium; Department of Molecular Diagnosis, LHUB-ULB, Pôle Hospitalier Universitaire de Bruxelles, Brussels, Belgium
| | - Olivier Vandenberg
- National Reference Center for Campylobacter, Saint Pierre University Hospital, Brussels, Belgium; Department of Microbiology, LHUB-ULB, Pôle Hospitalier Universitaire de Bruxelles, Brussels, Belgium; Center for Environmental Health and Occupational Health, School of Public Health, Université Libre de Bruxelles, Brussels, Belgium
| | - Katelijne Dierick
- National Reference Laboratory for Campylobacter, Scientific Institute of Public Health (WIV-ISP), Scientific Service: Foodborne Pathogens, Juliette Wytsman Street 14, 1050 Brussels, Belgium
| | - Nadine Botteldoorn
- National Reference Laboratory for Campylobacter, Scientific Institute of Public Health (WIV-ISP), Scientific Service: Foodborne Pathogens, Juliette Wytsman Street 14, 1050 Brussels, Belgium
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35
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Atterby C, Mourkas E, Méric G, Pascoe B, Wang H, Waldenström J, Sheppard SK, Olsen B, Järhult JD, Ellström P. The Potential of Isolation Source to Predict Colonization in Avian Hosts: A Case Study in Campylobacter jejuni Strains From Three Bird Species. Front Microbiol 2018; 9:591. [PMID: 29651281 PMCID: PMC5884941 DOI: 10.3389/fmicb.2018.00591] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2017] [Accepted: 03/14/2018] [Indexed: 12/28/2022] Open
Abstract
Campylobacter jejuni is the primary cause of bacterial gastroenteritis worldwide, infecting humans mostly through consumption of contaminated poultry. C. jejuni is common in the gut of wild birds, and shows distinct strain-specific association to particular bird species. This contrasts with farm animals, in which several genotypes co-exist. It is unclear if the barriers restricting transmission between host species of such specialist strains are related to environmental factors such as contact between host species, bacterial survival in the environment, etc., or rather to strain specific adaptation to the intestinal environment of specific hosts. We compared colonization dynamics in vivo between two host-specific C. jejuni from a song thrush (ST-1304 complex) and a mallard (ST-995), and a generalist strain from chicken (ST-21 complex) in a wild host, the mallard (Anas platyrhynchos). In 18-days infection experiments, the song thrush strain showed only weak colonization and was cleared from all birds after 10 days, whereas both mallard and chicken strains remained stable. When the chicken strain was given 4 days prior to co-infection of the same birds with a mallard strain, it was rapidly outcompeted by the latter. In contrast, when the mallard strain was given 4 days prior to co-infection with the chicken strain, the mallard strain remained and expansion of the chicken strain was delayed. Our results suggest strain-specific differences in the ability of C. jejuni to colonize mallards, likely associated with host origin. This difference might explain observed host association patterns in C. jejuni from wild birds.
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Affiliation(s)
- Clara Atterby
- Department of Medical Sciences, Zoonosis Science Center, Uppsala University, Uppsala, Sweden
| | - Evangelos Mourkas
- Department of Medical Biochemistry and Microbiology, Zoonosis Science Center, Uppsala University, Uppsala, Sweden.,Department of Biology and Biochemistry, The Milner Centre for Evolution, University of Bath, Bath, United Kingdom
| | - Guillaume Méric
- Department of Biology and Biochemistry, The Milner Centre for Evolution, University of Bath, Bath, United Kingdom
| | - Ben Pascoe
- Department of Biology and Biochemistry, The Milner Centre for Evolution, University of Bath, Bath, United Kingdom.,MRC CLIMB Consortium, Bath, United Kingdom
| | - Helen Wang
- Department of Medical Biochemistry and Microbiology, Zoonosis Science Center, Uppsala University, Uppsala, Sweden
| | - Jonas Waldenström
- Centre for Ecology and Evolution in Microbial Model Systems, Linnaeus University, Kalmar, Sweden
| | - Samuel K Sheppard
- Department of Biology and Biochemistry, The Milner Centre for Evolution, University of Bath, Bath, United Kingdom.,MRC CLIMB Consortium, Bath, United Kingdom
| | - Björn Olsen
- Department of Medical Sciences, Zoonosis Science Center, Uppsala University, Uppsala, Sweden
| | - Josef D Järhult
- Department of Medical Sciences, Zoonosis Science Center, Uppsala University, Uppsala, Sweden
| | - Patrik Ellström
- Department of Medical Sciences, Zoonosis Science Center, Uppsala University, Uppsala, Sweden
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36
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Scott AB, Phalen D, Hernandez-Jover M, Singh M, Groves P, Toribio JALML. Wildlife Presence and Interactions with Chickens on Australian Commercial Chicken Farms Assessed by Camera Traps. Avian Dis 2018; 62:65-72. [DOI: 10.1637/11761-101917-reg.1] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
- Angela Bullanday Scott
- School of Veterinary Science, University of Sydney, Camden, New South Wales, 2570, Australia
| | - David Phalen
- School of Veterinary Science, University of Sydney, Camden, New South Wales, 2570, Australia
| | - Marta Hernandez-Jover
- Graham Centre for Agricultural Innovation, Charles Sturt University, School of Animal and Veterinary Sciences, Locked Bag 588, Wagga Wagga, New South Wales, 2678, Australia
| | - Mini Singh
- School of Veterinary Science, University of Sydney, Camden, New South Wales, 2570, Australia
| | - Peter Groves
- School of Veterinary Science, University of Sydney, Camden, New South Wales, 2570, Australia
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Campylobacter jejuni Colonization in the Crow Gut Involves Many Deletions within the Cytolethal Distending Toxin Gene Cluster. Appl Environ Microbiol 2018; 84:AEM.01893-17. [PMID: 29330183 DOI: 10.1128/aem.01893-17] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2017] [Accepted: 12/13/2017] [Indexed: 01/13/2023] Open
Abstract
Campylobacter spp. are major causes of gastroenteritis worldwide. The virulence potential of Campylobacter shed in crow feces obtained from a roost area in Bothell, Washington, was studied and compared with that from isolates from other parts of Washington and from a different crow species 7,000 miles away in Kolkata, India. Campylobacter organisms were isolated from 61% and 69% of the fecal samples obtained from Washington and Kolkata, respectively, and were confirmed to be C. jejuni The cytolethal distending toxin (CDT) gene cluster from these isolates revealed a truncated sequence of approximately 1,350 bp. Sequencing of the gene cluster revealed two types of mutations: a 668-bp deletion across cdtA and cdtB and a 51-bp deletion within cdtB Some strains had additional 20-bp deletions in cdtB In either case, a functional toxin is not expected; a functional toxin is produced by the expression of three tandem genes, cdtA, cdtB, and cdtC Reverse transcriptase PCR with total RNA extracted from the isolates showed no expression of cdtB A toxin assay performed with these isolates on HeLa cells failed to show cytotoxic effects on the cells. However, the isolates were able to colonize the chicken ceca for a period of at least 4 weeks, similar to that of a clinical isolate. Other virulence gene markers, flagellin A and CadF, were present in 100% of the isolates. Our study suggests that crows carry the bacterium C. jejuni but with a dysfunctional toxin protein that is expected to drastically reduce its potential to cause diarrhea.IMPORTANCE Campylobacters are a major cause of gastroenteritis in humans. Since outbreaks have most often been correlated with poultry or unpasteurized dairy products, contact with farm animals, or contaminated water, historically, the majority of the studies have been with campylobacter isolates from poultry, domestic animals, and human patients. However, the bacterium has a broad host range that includes birds. These reservoirs need to be investigated, because the identification of the source and a determination of the transmission routes for a pathogen are important for the development of evidence-based disease control programs. In this study, two species of the human-commensal crow, from two different geographical regions separated by 7,000 miles of land and water, have been examined for their ability to cause disease by shedding campylobacters. Our results show that the crow may not play a significant role in campylobacteriosis, because the campylobacter organisms they shed produce a nonfunctional toxin.
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Moré E, Ayats T, Ryan PG, Naicker PR, Keddy KH, Gaglio D, Witteveen M, Cerdà-Cuéllar M. Seabirds (Laridae) as a source of Campylobacter spp., Salmonella spp. and antimicrobial resistance in South Africa. Environ Microbiol 2017; 19:4164-4176. [PMID: 28752962 DOI: 10.1111/1462-2920.13874] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2017] [Accepted: 07/24/2017] [Indexed: 11/28/2022]
Abstract
Zoonotic thermophilic Campylobacter and nontyphoidal Salmonella enterica are a major cause of foodborne human gastroenteritis worldwide. There is little information about reservoirs of these zoonotic agents in Africa. Thus, chicks of kelp gulls (Larus dominicanus, n = 129) and greater crested terns (Thalasseus bergii, n = 100) were studied at five colonies on the Western Cape coast (South Africa) during summer 2013/2014. Campylobacter spp. occurrence was 14.0% (CI95% : 9.9-19.3), with C. jejuni the most frequently isolated species, whilst that of Salmonella was 27.5% (CI95% : 21.9-33.9) overall, with a higher prevalence in gulls (43.0%, CI95% : 34.8-52.4) than terns (7.0%, CI95% : 3.1-14.4). Among the 16 different S. enterica serovars found, Anatum, Enteritidis and Hadar were the most frequent. The same or highly similar pulsed-field gel electrophoresis genotype was found in some Salmonella isolates from seabirds and humans presenting with salmonellosis in Cape Town hospitals. Both Campylobacter and Salmonella isolates exhibited antimicrobial resistance to several agents, including critically important antimicrobials (quinolones, tetracyclines and β-lactams) and multidrug resistance in Salmonella serovars from kelp gulls. Our results highlight the importance of seabirds as reservoirs of Campylobacter and Salmonella resistant strains and their role in the maintenance and transmission of these bacteria in the environment, with implications for public health.
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Affiliation(s)
- Elisabet Moré
- Centre de Recerca en Sanitat Animal (CReSA), IRTA, Campus Universitat Autònoma de Barcelona, Bellaterra 08193, Barcelona, Spain
| | - Teresa Ayats
- Centre de Recerca en Sanitat Animal (CReSA), IRTA, Campus Universitat Autònoma de Barcelona, Bellaterra 08193, Barcelona, Spain
| | - Peter G Ryan
- FitzPatrick Institute of African Ornithology, DST-NRF Centre of Excellence, University of Cape Town, Rondebosch 7701, South Africa
| | - Preneshni R Naicker
- Division of Medical Microbiology, University of Cape Town, National Health Laboratory Service (NHLS) Groote Schuur Hospital, Cape Town 7925, South Africa
| | - Karen H Keddy
- National Institute for Communicable Diseases and Faculty of Health Sciences, University of the Witwatersrand, Centre for Enteric Diseases (CED), Johannesburg 2131, South Africa
| | - Davide Gaglio
- FitzPatrick Institute of African Ornithology, DST-NRF Centre of Excellence, University of Cape Town, Rondebosch 7701, South Africa
| | - Minke Witteveen
- FitzPatrick Institute of African Ornithology, DST-NRF Centre of Excellence, University of Cape Town, Rondebosch 7701, South Africa
| | - Marta Cerdà-Cuéllar
- Centre de Recerca en Sanitat Animal (CReSA), IRTA, Campus Universitat Autònoma de Barcelona, Bellaterra 08193, Barcelona, Spain
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Pascoe B, Méric G, Yahara K, Wimalarathna H, Murray S, Hitchings MD, Sproston EL, Carrillo CD, Taboada EN, Cooper KK, Huynh S, Cody AJ, Jolley KA, Maiden MCJ, McCarthy ND, Didelot X, Parker CT, Sheppard SK. Local genes for local bacteria: Evidence of allopatry in the genomes of transatlantic Campylobacter populations. Mol Ecol 2017; 26:4497-4508. [PMID: 28493321 PMCID: PMC5600125 DOI: 10.1111/mec.14176] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2016] [Revised: 04/25/2017] [Accepted: 05/01/2017] [Indexed: 12/14/2022]
Abstract
The genetic structure of bacterial populations can be related to geographical locations of isolation. In some species, there is a strong correlation between geographical distance and genetic distance, which can be caused by different evolutionary mechanisms. Patterns of ancient admixture in Helicobacter pylori can be reconstructed in concordance with past human migration, whereas in Mycobacterium tuberculosis it is the lack of recombination that causes allopatric clusters. In Campylobacter, analyses of genomic data and molecular typing have been successful in determining the reservoir host species, but not geographical origin. We investigated biogeographical variation in highly recombining genes to determine the extent of clustering between genomes from geographically distinct Campylobacter populations. Whole‐genome sequences from 294 Campylobacter isolates from North America and the UK were analysed. Isolates from within the same country shared more recently recombined DNA than isolates from different countries. Using 15 UK/American closely matched pairs of isolates that shared ancestors, we identify regions that have frequently and recently recombined to test their correlation with geographical origin. The seven genes that demonstrated the greatest clustering by geography were used in an attribution model to infer geographical origin which was tested using a further 383 UK clinical isolates to detect signatures of recent foreign travel. Patient records indicated that in 46 cases, travel abroad had occurred <2 weeks prior to sampling, and genomic analysis identified that 34 (74%) of these isolates were of a non‐UK origin. Identification of biogeographical markers in Campylobacter genomes will contribute to improved source attribution of clinical Campylobacter infection and inform intervention strategies to reduce campylobacteriosis.
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Affiliation(s)
- Ben Pascoe
- The Milner Centre for Evolution, Department of Biology and Biochemistry, Bath University, Claverton Down, Bath, UK.,MRC CLIMB Consortium, Bath, UK
| | - Guillaume Méric
- The Milner Centre for Evolution, Department of Biology and Biochemistry, Bath University, Claverton Down, Bath, UK
| | - Koji Yahara
- Department of Bacteriology II, National Institute of Infectious Diseases, Tokyo, Japan.,Swansea University Medical School, Swansea University, Swansea, UK
| | | | - Susan Murray
- Swansea University Medical School, Swansea University, Swansea, UK
| | | | - Emma L Sproston
- Bureau of Microbial Hazards, Health Canada, Ottawa, ON, Canada
| | | | - Eduardo N Taboada
- National Microbiology Laboratory at Lethbridge, Public Health Agency of Canada, Lethbridge, AB, Canada
| | - Kerry K Cooper
- Department of Biology, California State University Northridge, Northridge, CA, USA
| | - Steven Huynh
- Produce Safety and Microbiology Research Unit, Agricultural Research Service, US Department of Agriculture, Albany, CA, USA
| | - Alison J Cody
- Department of Zoology, University of Oxford, Oxford, UK
| | | | - Martin C J Maiden
- Department of Zoology, University of Oxford, Oxford, UK.,NIHR Health Protection Research Unit in Gastrointestinal Infections, Oxford, UK
| | - Noel D McCarthy
- Department of Zoology, University of Oxford, Oxford, UK.,NIHR Health Protection Research Unit in Gastrointestinal Infections, Oxford, UK.,University of Warwick, Coventry, UK
| | - Xavier Didelot
- Department of Infectious Disease Epidemiology, Imperial College London, London, UK
| | - Craig T Parker
- Produce Safety and Microbiology Research Unit, Agricultural Research Service, US Department of Agriculture, Albany, CA, USA
| | - Samuel K Sheppard
- The Milner Centre for Evolution, Department of Biology and Biochemistry, Bath University, Claverton Down, Bath, UK.,MRC CLIMB Consortium, Bath, UK.,Department of Zoology, University of Oxford, Oxford, UK
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Elmberg J, Berg C, Lerner H, Waldenström J, Hessel R. Potential disease transmission from wild geese and swans to livestock, poultry and humans: a review of the scientific literature from a One Health perspective. Infect Ecol Epidemiol 2017; 7:1300450. [PMID: 28567210 PMCID: PMC5443079 DOI: 10.1080/20008686.2017.1300450] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2016] [Accepted: 12/23/2016] [Indexed: 12/16/2022] Open
Abstract
There are more herbivorous waterfowl (swans and geese) close to humans, livestock and poultry than ever before. This creates widespread conflict with agriculture and other human interests, but also debate about the role of swans and geese as potential vectors of disease of relevance for human and animal health. Using a One Health perspective, we provide the first comprehensive review of the scientific literature about the most relevant viral, bacterial, and unicellular pathogens occurring in wild geese and swans. Research thus far suggests that these birds may play a role in transmission of avian influenza virus, Salmonella, Campylobacter, and antibiotic resistance. On the other hand, at present there is no evidence that geese and swans play a role in transmission of Newcastle disease, duck plague, West Nile virus, Vibrio, Yersinia, Clostridium, Chlamydophila, and Borrelia. Finally, based on present knowledge it is not possible to say if geese and swans play a role in transmission of Escherichia coli, Pasteurella, Helicobacter, Brachyspira, Cryptosporidium, Giardia, and Microsporidia. This is largely due to changes in classification and taxonomy, rapid development of identification methods and lack of knowledge about host specificity. Previous research tends to overrate the role of geese and swans as disease vectors; we do not find any evidence that they are significant transmitters to humans or livestock of any of the pathogens considered in this review. Nevertheless, it is wise to keep poultry and livestock separated from small volume waters used by many wild waterfowl, but there is no need to discourage livestock grazing in nature reserves or pastures where geese and swans are present. Under some circumstances it is warranted to discourage swans and geese from using wastewater ponds, drinking water reservoirs, and public beaches. Intensified screening of swans and geese for AIV, West Nile virus and anatid herpesvirus is warranted.
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Affiliation(s)
- Johan Elmberg
- Division of Natural Sciences, Kristianstad University, Kristianstad, Sweden
| | - Charlotte Berg
- Department of Animal Environment and Health, SLU Swedish University of Agricultural Sciences, Skara, Sweden
| | - Henrik Lerner
- Department of Health Care Sciences, Ersta Sköndal Bräcke University College, Stockholm, Sweden
| | - Jonas Waldenström
- Centre for Ecology and Evolution in Microbial Model Systems, Linneaus University, Kalmar, Sweden
| | - Rebecca Hessel
- Division of Natural Sciences, Kristianstad University, Kristianstad, Sweden
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41
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Clark NJ, Clegg SM. Integrating phylogenetic and ecological distances reveals new insights into parasite host specificity. Mol Ecol 2017; 26:3074-3086. [PMID: 28295937 DOI: 10.1111/mec.14101] [Citation(s) in RCA: 56] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2017] [Revised: 02/28/2017] [Accepted: 03/07/2017] [Indexed: 01/01/2023]
Abstract
The range of hosts a pathogen infects (host specificity) is a key element of disease risk that may be influenced by both shared phylogenetic history and shared ecological attributes of prospective hosts. Phylospecificity indices quantify host specificity in terms of host relatedness, but can fail to capture ecological attributes that increase susceptibility. For instance, similarity in habitat niche may expose phylogenetically unrelated host species to similar pathogen assemblages. Using a recently proposed method that integrates multiple distances, we assess the relative contributions of host phylogenetic and functional distances to pathogen host specificity (functional-phylogenetic host specificity). We apply this index to a data set of avian malaria parasite (Plasmodium and Haemoproteus spp.) infections from Melanesian birds to show that multihost parasites generally use hosts that are closely related, not hosts with similar habitat niches. We also show that host community phylogenetic ß-diversity (Pßd) predicts parasite Pßd and that individual host species carry phylogenetically clustered Haemoproteus parasite assemblages. Our findings were robust to phylogenetic uncertainty, and suggest that phylogenetic ancestry of both hosts and parasites plays important roles in driving avian malaria host specificity and community assembly. However, restricting host specificity analyses to either recent or historical timescales identified notable exceptions, including a 'habitat specialist' parasite that infects a diversity of unrelated host species with similar habitat niches. This work highlights that integrating ecological and phylogenetic distances provides a powerful approach to better understand drivers of pathogen host specificity and community assembly.
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Affiliation(s)
- Nicholas J Clark
- School of Veterinary Science, The University of Queensland, Gatton, Qld, 4343, Australia.,Environmental Futures Research Institute, Griffith University, Gold Coast, Qld, 4111, Australia
| | - Sonya M Clegg
- Department of Zoology, Edward Grey Institute of Field Ornithology, University of Oxford, Oxford, OX1 3PS, UK
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Webb AL, Taboada EN, Selinger LB, Boras VF, Inglis GD. Prevalence and diversity of waterborne Arcobacter butzleri in southwestern Alberta, Canada. Can J Microbiol 2017; 63:330-340. [DOI: 10.1139/cjm-2016-0745] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Arcobacter butzleri is a potential enteric pathogen to human beings, but its reservoirs and modes of transmission are largely unverified. Microbiological and molecular detection and subtyping techniques can facilitate surveillance of A. butzleri in hosts and environmental reservoirs. We isolated A. butzleri from 173 surface water samples (25.6%) and 81 treated wastewater samples (77.9%) collected in southwestern Alberta over a 1-year period. Arcobacter butzleri isolates (n = 500) were genotyped and compared to determine diversity of A. butzleri in southwestern Alberta. Culture methods affected the frequency of detection and genotype diversity of A. butzleri, and isolation comprehensiveness was different for surface waters and treated wastewaters. Detection of A. butzleri in the Oldman River Watershed corresponded with season, river flow rates, and fecal coliform densities. Arcobacter butzleri was detected most frequently in treated wastewater, in the Oldman River downstream from treated wastewater outfalls, and in tributaries near areas of intensive confined feeding operations. All sample sources possessed high genotype diversity, and A. butzleri isolates from treated wastewaters were genetically similar to isolates from the Oldman River downriver from treated wastewater outfall sites. In southwestern Alberta, municipal and agricultural activities contribute to the density and genotype diversity of A. butzleri in surface waters.
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Affiliation(s)
- Andrew L. Webb
- Agriculture and Agri-Food Canada, Lethbridge, Alberta, Canada
- Department of Biological Sciences, University of Lethbridge, Lethbridge, Alberta, Canada
| | | | - L. Brent Selinger
- Department of Biological Sciences, University of Lethbridge, Lethbridge, Alberta, Canada
| | - Valerie F. Boras
- Department of Laboratory Medicine, Chinook Regional Hospital, Lethbridge, Alberta, Canada
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43
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Thépault A, Méric G, Rivoal K, Pascoe B, Mageiros L, Touzain F, Rose V, Béven V, Chemaly M, Sheppard SK. Genome-Wide Identification of Host-Segregating Epidemiological Markers for Source Attribution in Campylobacter jejuni. Appl Environ Microbiol 2017; 83:e03085-16. [PMID: 28115376 PMCID: PMC5359498 DOI: 10.1128/aem.03085-16] [Citation(s) in RCA: 70] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2016] [Accepted: 01/03/2017] [Indexed: 11/20/2022] Open
Abstract
Campylobacter is among the most common worldwide causes of bacterial gastroenteritis. This organism is part of the commensal microbiota of numerous host species, including livestock, and these animals constitute potential sources of human infection. Molecular typing approaches, especially multilocus sequence typing (MLST), have been used to attribute the source of human campylobacteriosis by quantifying the relative abundance of alleles at seven MLST loci among isolates from animal reservoirs and human infection, implicating chicken as a major infection source. The increasing availability of bacterial genomes provides data on allelic variation at loci across the genome, providing the potential to improve the discriminatory power of data for source attribution. Here we present a source attribution approach based on the identification of novel epidemiological markers among a reference pan-genome list of 1,810 genes identified by gene-by-gene comparison of 884 genomes of Campylobacter jejuni isolates from animal reservoirs, the environment, and clinical cases. Fifteen loci involved in metabolic activities, protein modification, signal transduction, and stress response or coding for hypothetical proteins were selected as host-segregating markers and used to attribute the source of 42 French and 281 United Kingdom clinical C. jejuni isolates. Consistent with previous studies of British campylobacteriosis, analyses performed using STRUCTURE software attributed 56.8% of British clinical cases to chicken, emphasizing the importance of this host reservoir as an infection source in the United Kingdom. However, among French clinical isolates, approximately equal proportions of isolates were attributed to chicken and ruminant reservoirs, suggesting possible differences in the relative importance of animal host reservoirs and indicating a benefit for further national-scale attribution modeling to account for differences in production, behavior, and food consumption.IMPORTANCE Accurately quantifying the relative contribution of different host reservoirs to human Campylobacter infection is an ongoing challenge. This study, based on the development of a novel source attribution approach, provides the first results of source attribution in Campylobacter jejuni in France. A systematic analysis using gene-by-gene comparison of 884 genomes of C. jejuni isolates, with a pan-genome list of genes, identified 15 novel epidemiological markers for source attribution. The different proportions of French and United Kingdom clinical isolates attributed to each host reservoir illustrate a potential role for local/national variations in C. jejuni transmission dynamics.
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Affiliation(s)
- Amandine Thépault
- Unit of Hygiene and Quality of Poultry & Pork Products, Laboratory of Ploufragan-Plouzané, French Agency for Food Environmental and Occupational Health & Safety (ANSES), Ploufragan, France
- University of Rennes 1, Rennes, France
| | - Guillaume Méric
- The Milner Centre for Evolution, Department of Biology and Biochemistry, University of Bath, Claverton Down, Bath, United Kingdom
| | - Katell Rivoal
- Unit of Hygiene and Quality of Poultry & Pork Products, Laboratory of Ploufragan-Plouzané, French Agency for Food Environmental and Occupational Health & Safety (ANSES), Ploufragan, France
| | - Ben Pascoe
- 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
| | - Fabrice Touzain
- Viral Genetics & Biosafety Unit, Laboratory of Ploufragan-Plouzané, French Agency for Food Environmental and Occupational Health & Safety (ANSES), Ploufragan, France
| | - Valérie Rose
- Unit of Hygiene and Quality of Poultry & Pork Products, 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
| | - Marianne Chemaly
- Unit of Hygiene and Quality of Poultry & Pork Products, Laboratory of Ploufragan-Plouzané, French Agency for Food Environmental and Occupational Health & Safety (ANSES), Ploufragan, France
| | - 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, Oxford, United Kingdom
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Garcia-Mazcorro JF, Castillo-Carranza SA, Guard B, Gomez-Vazquez JP, Dowd SE, Brigthsmith DJ. Comprehensive Molecular Characterization of Bacterial Communities in Feces of Pet Birds Using 16S Marker Sequencing. MICROBIAL ECOLOGY 2017; 73:224-235. [PMID: 27568186 DOI: 10.1007/s00248-016-0840-7] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2016] [Accepted: 08/16/2016] [Indexed: 06/06/2023]
Abstract
Birds and other animals live and evolve in close contact with millions of microorganisms (microbiota). While the avian microbiota has been well characterized in domestic poultry, the microbiota of other bird species has been less investigated. The aim of this study was to describe the fecal bacterial communities of pet birds. Pooled fecal samples from 22 flocks representing over 150 individual birds of three different species (Melopsittacus undulatus or budgerigars, Nymphicus hollandicus or cockatiels, and Serinus canaria or domestic canaries) were used for analysis using the 16S rRNA gene sequencing in the MiSeq platform (Illumina). Firmicutes was the most abundant phylum (median 88.4 %; range 12.9-98.4 %) followed by other low-abundant phyla such as Proteobacteria (median 2.3 %; 0.1-85.3 %) and Actinobacteria (median 1.7 %; 0-18.3 %). Lactobacillaceae (mostly Lactobacillus spp.) was the most abundant family (median 78.1 %; 1.4-97.5 %), especially in budgerigars and canaries, and it deserves attention because of the ascribed beneficial properties of lactic acid bacteria. Importantly, feces from birds contain intestinal, urinary, and reproductive-associated microbiota thus posing a serious problem to study one anatomical region at a time. Other groups of interest include the family Clostridiaceae that showed very low abundance (overall median <0.1 %) with the exception of two samples from cockatiels (14 and 45.9 %) and one sample from budgerigars (19.9 %). Analysis of UniFrac metrics showed that overall, the microbial communities from the 22 flocks tended to cluster together for each bird species, meaning each species shed distinctive bacterial communities in feces. This descriptive analysis provides insight into the fecal microbiota of pet birds.
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Affiliation(s)
- Jose F Garcia-Mazcorro
- Faculty of Veterinary Medicine, Universidad Autónoma de Nuevo León (UANL), General Escobedo, NL, 66050, Mexico.
- Research Group Medical Eco-Biology, Faculty of Veterinary Medicine, UANL, General Escobedo, NL, 66050, Mexico.
| | | | - Blake Guard
- Gastrointestinal Laboratory, Department of Small Animal Clinical Sciences, Texas A&M University, College Station, TX, 77843-4474, USA
| | - Jose P Gomez-Vazquez
- Faculty of Veterinary Medicine, Universidad Autónoma de Nuevo León (UANL), General Escobedo, NL, 66050, Mexico
| | - Scot E Dowd
- Molecular Research LP, Shallowater, TX, 79363, USA
| | - Donald J Brigthsmith
- Schubot Exotic Bird Health Center, Texas A&M University, College Station, TX, 77843-4467, USA
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Mughini-Gras L, Penny C, Ragimbeau C, Schets FM, Blaak H, Duim B, Wagenaar JA, de Boer A, Cauchie HM, Mossong J, van Pelt W. Quantifying potential sources of surface water contamination with Campylobacter jejuni and Campylobacter coli. WATER RESEARCH 2016; 101:36-45. [PMID: 27244295 DOI: 10.1016/j.watres.2016.05.069] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2015] [Revised: 05/20/2016] [Accepted: 05/22/2016] [Indexed: 06/05/2023]
Abstract
Campylobacter is the most common causative agent of human bacterial gastroenteritis and is frequently found in surface water, where it indicates recent contamination with animal faeces, sewage effluent, and agricultural run-off. The contribution of different animal reservoirs to surface water contamination with Campylobacter is largely unknown. In the Netherlands, the massive poultry culling to control the 2003 avian influenza epidemic coincided with a 44-50% reduction in human campylobacteriosis cases in the culling areas, suggesting substantial environment-mediated spread of poultry-borne Campylobacter. We inferred the origin of surface water Campylobacter jejuni and Campylobacter coli strains in Luxembourg and the Netherlands, as defined by multilocus sequence typing, by comparison to strains from poultry, pigs, ruminants, and wild birds, using the asymmetric island model for source attribution. Most Luxembourgish water strains were attributed to wild birds (61.0%), followed by poultry (18.8%), ruminants (15.9%), and pigs (4.3%); whereas the Dutch water strains were mainly attributed to poultry (51.7%), wild birds (37.3%), ruminants (9.8%), and pigs (1.2%). Attributions varied over seasons and surface water types, and geographical variation in the relative contribution of poultry correlated with the magnitude of poultry production at either the national or provincial level, suggesting that environmental dissemination of Campylobacter from poultry farms and slaughterhouses can be substantial in poultry-rich regions.
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Affiliation(s)
- Lapo Mughini-Gras
- National Institute for Public Health and the Environment (RIVM), Centre for Infectious Disease Control (CIb), PO Box 1, 3720 BA Bilthoven, The Netherlands; Utrecht University, Faculty of Veterinary Medicine, Department of Infectious Diseases and Immunology, Yalelaan 1, De Uithof, 3584 CL Utrecht, The Netherlands.
| | - Christian Penny
- Luxembourg Institute of Science and Technology, Environmental Research and Innovation, 41 rue du Brill, L-4422 Belvaux, Luxembourg
| | - Catherine Ragimbeau
- National Health Laboratory (LNS), Surveillance and Epidemiology of Infectious Diseases, 1 rue Louis Rech, Dudelange L-3555, Luxembourg
| | - Franciska M Schets
- National Institute for Public Health and the Environment (RIVM), Centre for Infectious Disease Control (CIb), PO Box 1, 3720 BA Bilthoven, The Netherlands
| | - Hetty Blaak
- National Institute for Public Health and the Environment (RIVM), Centre for Infectious Disease Control (CIb), PO Box 1, 3720 BA Bilthoven, The Netherlands
| | - Birgitta Duim
- Utrecht University, Faculty of Veterinary Medicine, Department of Infectious Diseases and Immunology, Yalelaan 1, De Uithof, 3584 CL Utrecht, The Netherlands; WHO-Collaborating Center for Campylobacter and OIE Reference Laboratory for Campylobacteriosis, Yalelaan 1, De Uithof, 3584 CL Utrecht, The Netherlands
| | - Jaap A Wagenaar
- Utrecht University, Faculty of Veterinary Medicine, Department of Infectious Diseases and Immunology, Yalelaan 1, De Uithof, 3584 CL Utrecht, The Netherlands; Central Veterinary Institute of Wageningen UR, Houtribweg 39, 8221 RA Lelystad, The Netherlands; WHO-Collaborating Center for Campylobacter and OIE Reference Laboratory for Campylobacteriosis, Yalelaan 1, De Uithof, 3584 CL Utrecht, The Netherlands
| | - Albert de Boer
- Central Veterinary Institute of Wageningen UR, Houtribweg 39, 8221 RA Lelystad, The Netherlands
| | - Henry-Michel Cauchie
- Luxembourg Institute of Science and Technology, Environmental Research and Innovation, 41 rue du Brill, L-4422 Belvaux, Luxembourg
| | - Joel Mossong
- National Health Laboratory (LNS), Surveillance and Epidemiology of Infectious Diseases, 1 rue Louis Rech, Dudelange L-3555, Luxembourg
| | - Wilfrid van Pelt
- National Institute for Public Health and the Environment (RIVM), Centre for Infectious Disease Control (CIb), PO Box 1, 3720 BA Bilthoven, The Netherlands
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Whole-Genome Sequences of Agricultural, Host-Associated Campylobacter coli and Campylobacter jejuni Strains. GENOME ANNOUNCEMENTS 2016; 4:4/4/e00833-16. [PMID: 27540063 PMCID: PMC4991708 DOI: 10.1128/genomea.00833-16] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
We report here the genome sequences of four agricultural, multidrug-resistant Campylobacter spp.: C. coli 11601 and C. jejuni 11601MD, isolated from turkey cecum and jejunum, respectively, and C. coli 6067 and C. coli 6461, isolated from turkey-house water and swine feces, respectively. The genomes provide insights on Campylobacter antimicrobial resistance and host adaptations.
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Genetic Diversity of Campylobacter jejuni and Campylobacter coli Isolates from Conventional Broiler Flocks and the Impacts of Sampling Strategy and Laboratory Method. Appl Environ Microbiol 2016; 82:2347-2355. [PMID: 26873321 PMCID: PMC4959481 DOI: 10.1128/aem.03693-15] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2015] [Accepted: 01/30/2016] [Indexed: 01/10/2023] Open
Abstract
The genetic diversity of Campylobacter jejuni and Campylobacter coli isolates from commercial broiler farms was examined by multilocus sequence typing (MLST), with an assessment of the impact of the sample type and laboratory method on the genotypes of Campylobacter isolated. A total of 645 C. jejuni and 106 C. coli isolates were obtained from 32 flocks and 17 farms, with 47 sequence types (STs) identified. The Campylobacter jejuni isolates obtained by different sampling approaches and laboratory methods were very similar, with the same STs identified at similar frequencies, and had no major effect on the genetic profile of Campylobacter population in broiler flocks at the farm level. For C. coli, the results were more equivocal. While some STs were widely distributed within and among farms and flocks, analysis of molecular variance (AMOVA) revealed a high degree of genetic diversity among farms for C. jejuni, where farm effects accounted for 70.5% of variance, and among flocks from the same farm (9.9% of variance for C. jejuni and 64.1% for C. coli). These results show the complexity of the population structure of Campylobacter in broiler production and that commercial broiler farms provide an ecological niche for a wide diversity of genotypes. The genetic diversity of C. jejuni isolates among broiler farms should be taken into account when designing studies to understand Campylobacter populations in broiler production and the impact of interventions. We provide evidence that supports synthesis of studies on C. jejuni populations even when laboratory and sampling methods are not identical.
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Mossong J, Mughini-Gras L, Penny C, Devaux A, Olinger C, Losch S, Cauchie HM, van Pelt W, Ragimbeau C. Human Campylobacteriosis in Luxembourg, 2010-2013: A Case-Control Study Combined with Multilocus Sequence Typing for Source Attribution and Risk Factor Analysis. Sci Rep 2016; 6:20939. [PMID: 26860258 PMCID: PMC4748240 DOI: 10.1038/srep20939] [Citation(s) in RCA: 59] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2015] [Accepted: 01/14/2016] [Indexed: 02/06/2023] Open
Abstract
Campylobacteriosis has increased markedly in Luxembourg during recent years. We sought to determine which Campylobacter genotypes infect humans, where they may originate from, and how they may infect humans. Multilocus sequence typing was performed on 1153 Campylobacter jejuni and 136 C. coli human strains to be attributed to three putative animal reservoirs (poultry, ruminants, pigs) and to environmental water using the asymmetric island model. A nationwide case-control study (2010-2013) for domestic campylobacteriosis was also conducted, including 367 C. jejuni and 48 C. coli cases, and 624 controls. Risk factors were investigated by Campylobacter species, and for strains attributed to different sources using a combined case-control and source attribution analysis. 282 sequence types (STs) were identified: ST-21, ST-48, ST-572, ST-50 and ST-257 were prevailing. Most cases were attributed to poultry (61.2%) and ruminants (33.3%). Consuming chicken outside the home was the dominant risk factor for both Campylobacter species. Newly identified risk factors included contact with garden soil for either species, and consuming beef specifically for C. coli. Poultry-associated campylobacteriosis was linked to poultry consumption in wintertime, and ruminant-associated campylobacteriosis to tap-water provider type. Besides confirming chicken as campylobacteriosis primary source, additional evidence was found for other reservoirs and transmission routes.
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Affiliation(s)
- Joël Mossong
- National Health Laboratory (LNS), Surveillance and Epidemiology of Infectious Diseases, 1 rue Louis Rech, Dudelange L-3555, Luxembourg
| | - Lapo Mughini-Gras
- National Institute for Public Health and the Environment (RIVM), Centre for Infectious Disease Control (CIb). PO Box 1 - 3720 BA Bilthoven, The Netherlands
- Utrecht University, Faculty of Veterinary Medicine, Department of Infectious Diseases and Immunology, Yalelaan 1, De Uithof - 3584 CL Utrecht, The Netherlands
| | - Christian Penny
- Luxembourg Institute of Science and Technology, Environmental Research and Innovation, 41 rue du Brill, L-4422 Belvaux, Luxembourg
| | - Anthony Devaux
- National Health Laboratory (LNS), Surveillance and Epidemiology of Infectious Diseases, 1 rue Louis Rech, Dudelange L-3555, Luxembourg
| | - Christophe Olinger
- National Health Laboratory (LNS), Surveillance and Epidemiology of Infectious Diseases, 1 rue Louis Rech, Dudelange L-3555, Luxembourg
| | - Serge Losch
- Veterinary Services Administration, Laboratory of Veterinary Medicine, 54 av. Gaston Diderich, L-1420 Luxembourg
| | - Henry-Michel Cauchie
- Luxembourg Institute of Science and Technology, Environmental Research and Innovation, 41 rue du Brill, L-4422 Belvaux, Luxembourg
| | - Wilfrid van Pelt
- National Institute for Public Health and the Environment (RIVM), Centre for Infectious Disease Control (CIb). PO Box 1 - 3720 BA Bilthoven, The Netherlands
| | - Catherine Ragimbeau
- National Health Laboratory (LNS), Surveillance and Epidemiology of Infectious Diseases, 1 rue Louis Rech, Dudelange L-3555, Luxembourg
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Hald B, Skov MN, Nielsen EM, Rahbek C, Madsen JJ, Wainø M, Chriél M, Nordentoft S, Baggesen DL, Madsen M. Campylobacter jejuni and Campylobacter coli in wild birds on Danish livestock farms. Acta Vet Scand 2016; 58:11. [PMID: 26842400 PMCID: PMC4739333 DOI: 10.1186/s13028-016-0192-9] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2015] [Accepted: 01/21/2016] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Reducing the occurrence of campylobacteriosis is a food safety issue of high priority, as in recent years it has been the most commonly reported zoonosis in the EU. Livestock farms are of particular interest, since cattle, swine and poultry are common reservoirs of Campylobacter spp. The farm environment provides attractive foraging and breeding habitats for some bird species reported to carry thermophilic Campylobacter spp. We investigated the Campylobacter spp. carriage rates in 52 wild bird species present on 12 Danish farms, sampled during a winter and a summer season, in order to study the factors influencing the prevalence in wild birds according to their ecological guild. In total, 1607 individual wild bird cloacal swab samples and 386 livestock manure samples were cultured for Campylobacter spp. according to the Nordic Committee on Food Analysis method NMKL 119. RESULTS The highest Campylobacter spp. prevalence was seen in 110 out of 178 thrushes (61.8 %), of which the majority were Common Blackbird (Turdus merula), and in 131 out of 616 sparrows (21.3 %), a guild made up of House Sparrow (Passer domesticus) and Eurasian Tree Sparrow (Passer montanus). In general, birds feeding on a diet of animal or mixed animal and vegetable origin, foraging on the ground and vegetation in close proximity to livestock stables were more likely to carry Campylobacter spp. in both summer (P < 0.001) and winter (P < 0.001) than birds foraging further away from the farm or in the air. Age, fat score, gender, and migration range were not found to be associated with Campylobacter spp. carriage. A correlation was found between the prevalence (%) of C. jejuni in wild birds and the proportions (%) of C. jejuni in both manure on cattle farms (R(2) = 0.92) and poultry farms (R(2) = 0.54), and between the prevalence (%) of C. coli in wild birds and the proportions (%) of C. coli in manure on pig farms (R(2) = 0.62). CONCLUSIONS The ecological guild of wild birds influences the prevalence of Campylobacter spp. through the behavioural patterns of the birds. More specifically, wild birds eating food of animal or mixed animal and vegetable origin and foraging on the ground close to livestock were more likely to carry Campylobacter spp. than those foraging further away or hunting in the air. These findings suggest that wild birds may play a role in sustaining the epidemiology of Campylobacter spp. on farms.
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Affiliation(s)
- Birthe Hald
- Danish Veterinary Laboratory, Department of Poultry, Fish and Fur Animals, 8200, Aarhus N, Denmark.
- National Food Institute, Technical University of Denmark, 2860, Søborg, Denmark.
| | - Marianne Nielsine Skov
- Department of Microbiology, Danish Veterinary Laboratory, 1870, Frederiksberg C, Denmark.
- Research Unit for Clinical Microbiology, University of Southern Denmark, 5000, Odense C, Denmark.
| | - Eva Møller Nielsen
- Department of Microbiology, Danish Veterinary Laboratory, 1870, Frederiksberg C, Denmark.
- Department of Microbiology and Infection Control, Statens Serum Institut, 2300, Copenhagen S, Denmark.
| | - Carsten Rahbek
- Natural History Museum of Denmark, University of Copenhagen, 1350, Copenhagen K, Denmark.
- Center for Macroecology, Evolution, and Climate, Natural History Museum of Denmark, University of Copenhagen, 2100, Copenhagen Ø, Denmark.
- Imperial College London, Silwood Park Campus, Ascot, Berkshire, SL5 7PY, UK.
| | - Jesper Johannes Madsen
- Natural History Museum of Denmark, University of Copenhagen, 1350, Copenhagen K, Denmark.
| | - Michael Wainø
- Danish Veterinary Laboratory, Department of Poultry, Fish and Fur Animals, 8200, Aarhus N, Denmark.
- Chr. Hansen, 2970, Hørsholm, Denmark.
| | - Mariann Chriél
- The Danish Meatboard, 1609, Copenhagen V, Denmark.
- National Veterinary Institute, Technical University of Denmark, 1870, Frederiksberg C, Denmark.
| | - Steen Nordentoft
- Danish Veterinary Laboratory, Department of Poultry, Fish and Fur Animals, 8200, Aarhus N, Denmark.
- Novo Nordisk, 4400, Kalundborg, Denmark.
| | - Dorte Lau Baggesen
- Department of Microbiology, Danish Veterinary Laboratory, 1870, Frederiksberg C, Denmark.
- National Food Institute, Technical University of Denmark, 2860, Søborg, Denmark.
| | - Mogens Madsen
- Danish Veterinary Laboratory, Department of Poultry, Fish and Fur Animals, 8200, Aarhus N, Denmark.
- Dianova Ltd., 8200, Aarhus N, Denmark.
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Griekspoor P, Hansbro PM, Waldenström J, Olsen B. Campylobacter jejuni sequence types show remarkable spatial and temporal stability in Blackbirds. Infect Ecol Epidemiol 2015; 5:28383. [PMID: 26634844 PMCID: PMC4669312 DOI: 10.3402/iee.v5.28383] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2015] [Revised: 10/12/2015] [Accepted: 10/23/2015] [Indexed: 11/29/2022] Open
Abstract
Background The zoonotic bacterium Campylobacter jejuni has a broad host range but is especially associated with birds, both domestic and wild. Earlier studies have indicated thrushes of the genus Turdus in Europe to be frequently colonized with C. jejuni, and predominately with host-associated specific genotypes. The European Blackbird Turdus merula has a large distribution in Europe, including some oceanic islands, and was also introduced to Australia by European immigrants in the 1850s. Methods The host specificity and temporal stability of European Blackbird C. jejuni was investigated with multilocus sequence typing in a set of isolates collected from Sweden, Australia, and The Azores. Results Remarkably, we found that the Swedish, Australian, and Azorean isolates were genetically highly similar, despite extensive spatial and temporal isolation. This indicates adaptation, exquisite specificity, and stability in time for European Blackbirds, which is in sharp contrast with the high levels of recombination and mutation found in poultry-related C. jejuni genotypes. Conclusion The maintenance of host-specific signals in spatially and temporally separated C. jejuni populations suggests the existence of strong purifying selection for this bacterium in European Blackbirds.
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Affiliation(s)
- Petra Griekspoor
- Section for Zoonotic Ecology and Epidemiology, Centre for Ecology and Evolution in Microbial Model Systems (EEMiS), School of Natural Sciences, Linnaeus University, Kalmar, Sweden;
| | - Philip M Hansbro
- Centre for Asthma and Respiratory Disease, Hunter Medical Research Institute, University of Newcastle, Newcastle, Australia
| | - Jonas Waldenström
- Section for Zoonotic Ecology and Epidemiology, Centre for Ecology and Evolution in Microbial Model Systems (EEMiS), School of Natural Sciences, Linnaeus University, Kalmar, Sweden.,Section of Infectious Diseases, Department of Medical Sciences, Uppsala University, Uppsala, Sweden
| | - Björn Olsen
- Section of Infectious Diseases, Department of Medical Sciences, Uppsala University, Uppsala, Sweden.,Zoonosis Science Center, IMBIM, Uppsala University, Uppsala, Sweden
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