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Jehanne Q, Bénéjat L, Azzi Martin L, Korolik V, Ducournau A, Aptel J, Ménard A, Jauvain M, Aguilera C, Doreille A, Mesnard L, Eckert C, Lehours P. First isolation of Campylobacter vicugnae sp. nov. in humans suffering from gastroenteritis. Microbiol Spectr 2024:e0152324. [PMID: 39365090 DOI: 10.1128/spectrum.01523-24] [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: 06/26/2024] [Accepted: 08/01/2024] [Indexed: 10/05/2024] Open
Abstract
The present study describes the first isolation of a recently described Campylobacter species, Campylobacter vicugnae, in humans. The isolates were recovered by two independent French laboratories in 2020 and 2022 from a man and a woman suffering from gastroenteritis. Biochemical and growth characteristics, and electron microscopy for these two strains indicated that they belong to Campylobacter genus. 16S rDNA and GyrA-based phylogeny, as well as average nucleotide identity and in silico DNA-DNA Hybridization analyses revealed that both strains belong to the Campylobacter vicugnae species. Both isolates possess a complete cytolethal distending toxin (CDT) locus with cdtA, cdtB, and cdtC, and features of CDT activity were demonstrated in vitro with Caco-2 intestinal epithelial cells. Our data suggest that these two isolates of C. vicugnae were associated with gastroenteritis in humans and induced major cytopathogenic effects in vitro. C. vicugnae is likely to be a novel human pathogen, with a source of foodborne infection that needs to be determined.IMPORTANCECampylobacter species that display toxicity features are a worldwide public health issue. In clinical contexts, it is crucial to identify which isolate could be an urgent threat to a patient. Actual and widely used laboratory methods such as mass spectrometry or PCR may be flawed in the field of species identification. In contrast, the present study shows that next-generation sequencing allows to precisely identify isolates to species level that may have been omitted otherwise. Moreover, it helps to identify emerging species before they become a threat to human health. Recovery of a new Campylobacter species in human sample, such as the new species "Campylobacter vicugnae," is an important step for the identification of emerging pathogens posing threat to global health.
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Affiliation(s)
- Quentin Jehanne
- National Reference Centre for Campylobacters and Helicobacters, Bordeaux, France
| | - Lucie Bénéjat
- National Reference Centre for Campylobacters and Helicobacters, Bordeaux, France
| | - Lamia Azzi Martin
- University of Bordeaux, Inserm, UMR 1312, Bordeaux Institute of Oncology (BRIC), Bordeaux, France
| | - Victoria Korolik
- Institute for Glycomics, Griffith University, Gold Coast, Australia
| | - Astrid Ducournau
- National Reference Centre for Campylobacters and Helicobacters, Bordeaux, France
| | - Johanna Aptel
- National Reference Centre for Campylobacters and Helicobacters, Bordeaux, France
| | - Armelle Ménard
- University of Bordeaux, Inserm, UMR 1312, Bordeaux Institute of Oncology (BRIC), Bordeaux, France
| | - Marine Jauvain
- National Reference Centre for Campylobacters and Helicobacters, Bordeaux, France
- University of Bordeaux, Inserm, UMR 1312, Bordeaux Institute of Oncology (BRIC), Bordeaux, France
| | | | - Alice Doreille
- Sorbonne Université, Inserm, U1135, Centre d'Immunologie et des Maladies Infectieuses, Paris, France
- AP-HP, Soins Intensifs Néphrologique et Rein Aigu, Hôpital Tenon, Paris, France
| | - Laurent Mesnard
- Sorbonne Université, Inserm, U1135, Centre d'Immunologie et des Maladies Infectieuses, Paris, France
- AP-HP, Soins Intensifs Néphrologique et Rein Aigu, Hôpital Tenon, Paris, France
| | - Catherine Eckert
- Sorbonne Université, Inserm, U1135, Centre d'Immunologie et des Maladies Infectieuses, Paris, France
- Département de Bactériologie, AP-HP, Sorbonne-Université, Hôpital Saint-Antoine, Paris, France
| | - Philippe Lehours
- National Reference Centre for Campylobacters and Helicobacters, Bordeaux, France
- University of Bordeaux, Inserm, UMR 1312, Bordeaux Institute of Oncology (BRIC), Bordeaux, France
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Wei HL, Liao YS, Chen BH, Teng RH, Wang YW, Chang JH, Chiou CS. Antimicrobial resistance and genetic relatedness among Campylobacter coli and Campylobacter jejuni from humans and retail chicken meat in Taiwan. J Glob Antimicrob Resist 2024; 38:27-34. [PMID: 38821444 DOI: 10.1016/j.jgar.2024.05.013] [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: 10/22/2023] [Revised: 04/19/2024] [Accepted: 05/17/2024] [Indexed: 06/02/2024] Open
Abstract
OBJECTIVES Campylobacter is a significant zoonotic pathogen primarily transmitted through poultry. Our study aimed to assess antimicrobial resistance and genetic relationships among Campylobacter isolates from retail chicken meat and humans in Taiwan. METHODS Campylobacter isolates were analysed using whole-genome sequencing to investigate their antimicrobial resistance, genetic determinants of resistance, and genotypes. RESULTS Campylobacter coli and Campylobacter jejuni accounted for 44.9% and 55.1% of chicken meat isolates, and 11.4% and 88.6% of human isolates, respectively. C. coli displayed significantly higher resistance levels. Furthermore, isolates from chicken meat exhibited higher levels of resistance to most tested antimicrobials compared to isolates from humans. Multidrug resistance was observed in 96.3% of C. coli and 43.3% of C. jejuni isolates from chicken meat and 80.6% of C. coli and 15.8% of C. jejuni isolates from humans. Macrolide resistance was observed in 85.5% of C. coli isolates, primarily attributed to the erm(B) rather than the A2075G mutation in 23S rRNA. Among the 511 genomes, we identified 133 conventional MLST sequence types, indicating significant diversity among Campylobacter strains. Notably, hierarchical Core-genome multilocus sequence typing clustering, including HC0, HC5, and HC10, revealed a significant proportion of closely related isolates from chicken meat and humans. CONCLUSIONS Our research highlights significant associations in antimicrobial resistance and genetic relatedness between Campylobacter isolates from chicken meat and humans in Taiwan. The genetic analysis data suggest that campylobacteriosis outbreaks may occur more frequently in Taiwan than previously assumed. Our study emphasizes the need for strategies to control multidrug-resistant strains and enhance outbreak prevention.
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Affiliation(s)
- Hsiao-Lun Wei
- Center for Diagnostics and Vaccine Development, Centers for Disease Control, Taipei, Taiwan
| | - Ying-Shu Liao
- Center for Diagnostics and Vaccine Development, Centers for Disease Control, Taipei, Taiwan
| | - Bo-Han Chen
- Center for Diagnostics and Vaccine Development, Centers for Disease Control, Taipei, Taiwan
| | - Ru-Hsiou Teng
- Center for Diagnostics and Vaccine Development, Centers for Disease Control, Taipei, Taiwan
| | - You-Wun Wang
- Center for Diagnostics and Vaccine Development, Centers for Disease Control, Taipei, Taiwan
| | - Jui-Hsien Chang
- Center for Diagnostics and Vaccine Development, Centers for Disease Control, Taipei, Taiwan
| | - Chien-Shun Chiou
- Center for Diagnostics and Vaccine Development, Centers for Disease Control, Taipei, Taiwan.
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Nobi MA, Haque AKMZ, Islam MR, Islam SS, Arif M, Sikder MH, Kabir SML. Detection of Campylobacter spp. in farmed sheep in Mymensingh division of Bangladesh: Prevalence, risk factors, and antimicrobial susceptibility status. Vet World 2024; 17:245-254. [PMID: 38595663 PMCID: PMC11000463 DOI: 10.14202/vetworld.2024.245-254] [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: 09/18/2023] [Accepted: 12/30/2023] [Indexed: 04/11/2024] Open
Abstract
Background and Aim Campylobacter infections in sheep may be asymptomatic or cause enteritis, ileitis, infertility, and abortion. Thus, this study aimed to estimate the prevalence of Campylobacter spp. in farming sheep and to detect risk factors, molecular patterns, and antimicrobial susceptibility status of these pathogens. Materials and Methods Four hundred and eight fecal samples were collected from 12 flocks in the Mymensingh and Sherpur districts. Samples were tested by both basic (culture and biochemical tests) and molecular (initially 16S rRNA and later hipO gene-based polymerase chain reaction). Furthermore, the antimicrobial susceptibility status of Campylobacter jejuni was confirmed using disk diffusion. Flock- and animal-level data were captured using semi-structured interviews with farm owners under bivariate and multivariate logistic regression analyses to confirm the risk factors for Campylobacter-positive status. Results The prevalence of C. jejuni staining at the animal and flock levels was 8.82% (36/408) and 66.70% (8/12), respectively. The age of sheep was identified as an important risk factor. Up to 1 year of age, sheep were 3.78 times more likely to be infected with C. jejuni (95% confidence interval: 1.0736-13.3146, p = 0.038). Of the 36 isolates of C. jejuni, all were found to be fully susceptible (100%) to gentamicin and ciprofloxacin. In this study, three antimicrobial agents, oxytetracycline, azithromycin, and ceftriaxone, were fully resistant (100%). The majority of isolates were resistant to a combination of 4-6 antimicrobial agents. Conclusion The present study highlights the predominant maintenance of zoonotic Campylobacter species in sheep, and their burden on human health is enormous. Therefore, environmental, animal, and human health needs to be focused under a One Health lens to mitigate the occurrence of Campylobacter in farm settings and to prevent further introduction to animals and humans.
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Affiliation(s)
- Md. Ashiquen Nobi
- Department of Microbiology and Hygiene, Bangladesh Agricultural University, Mymensingh-2202, Bangladesh
| | - A. K. M. Ziaul Haque
- Kazi Farms Poultry Laboratory, Holding no-8/1, Floor no-A3 and A4, Padma Plaza (Opposite of Gazipur Commerce College), Chandana - Chowrasta, Gazipur-1704, Bangladesh
| | - M. Rafiqul Islam
- Department of Microbiology and Hygiene, Bangladesh Agricultural University, Mymensingh-2202, Bangladesh
| | - Sk Shaheenur Islam
- Department of Livestock Services, Ministry of Fisheries and Livestock, Dhaka-1215, Bangladesh
| | - Mohammad Arif
- Department of Microbiology and Hygiene, Bangladesh Agricultural University, Mymensingh-2202, Bangladesh
| | - Mahmudul Hasan Sikder
- Department of Pharmacology, Bangladesh Agricultural University, Mymensingh-2202, Bangladesh
| | - S. M. Lutful Kabir
- Department of Microbiology and Hygiene, Bangladesh Agricultural University, Mymensingh-2202, Bangladesh
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Zang X, Pascoe B, Mourkas E, Kong K, Jiao X, Sheppard SK, Huang J. Evidence of potential Campylobacter jejuni zooanthroponosis in captive macaque populations. Microb Genom 2023; 9:001121. [PMID: 37877958 PMCID: PMC10634442 DOI: 10.1099/mgen.0.001121] [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: 08/16/2023] [Accepted: 10/09/2023] [Indexed: 10/26/2023] Open
Abstract
Non-human primates share recent common ancestry with humans and exhibit comparable disease symptoms. Here, we explored the transmission potential of enteric bacterial pathogens in monkeys exhibiting symptoms of recurrent diarrhoea in a biomedical research facility in China. The common zoonotic bacterium Campylobacter jejuni was isolated from macaques (Macaca mulatta and Macaca fascicularis) and compared to isolates from humans and agricultural animals in Asia. Among the monkeys sampled, 5 % (44/973) tested positive for C. jejuni, 11 % (5/44) of which displayed diarrhoeal symptoms. Genomic analysis of monkey isolates, and 1254 genomes from various sources in Asia, were used to identify the most likely source of human infection. Monkey and human isolates shared high average nucleotide identity, common MLST clonal complexes and clustered together on a phylogeny. Furthermore, the profiles of putative antimicrobial resistance genes were similar between monkeys and humans. Taken together these findings suggest that housed macaques became infected with C. jejuni either directly from humans or via a common contamination source.
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Affiliation(s)
- Xiaoqi Zang
- Jiangsu Key Laboratory of Zoonosis, Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, PR China
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, Ministry of Education of China, Yangzhou University, Yangzhou, PR China
- Ineos Oxford Institute for Antimicrobial Research, Department of Biology, University of Oxford, Oxford, UK
| | - Ben Pascoe
- Ineos Oxford Institute for Antimicrobial Research, Department of Biology, University of Oxford, Oxford, UK
- Centre for Genomic Pathogen Surveillance, Big Data Institute, University of Oxford, Oxford, UK
| | - Evangelos Mourkas
- Ineos Oxford Institute for Antimicrobial Research, Department of Biology, University of Oxford, Oxford, UK
| | - Ke Kong
- Jiangsu Key Laboratory of Zoonosis, Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, PR China
| | - Xinan Jiao
- Jiangsu Key Laboratory of Zoonosis, Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, PR China
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, Ministry of Education of China, Yangzhou University, Yangzhou, PR China
| | - Samuel K. Sheppard
- Ineos Oxford Institute for Antimicrobial Research, Department of Biology, University of Oxford, Oxford, UK
| | - Jinlin Huang
- Jiangsu Key Laboratory of Zoonosis, Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, PR China
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, Ministry of Education of China, Yangzhou University, Yangzhou, PR China
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Nouws S, Verhaegen B, Denayer S, Crombé F, Piérard D, Bogaerts B, Vanneste K, Marchal K, Roosens NHC, De Keersmaecker SCJ. Transforming Shiga toxin-producing Escherichia coli surveillance through whole genome sequencing in food safety practices. Front Microbiol 2023; 14:1204630. [PMID: 37520372 PMCID: PMC10381951 DOI: 10.3389/fmicb.2023.1204630] [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: 04/12/2023] [Accepted: 06/22/2023] [Indexed: 08/01/2023] Open
Abstract
Introduction Shiga toxin-producing Escherichia coli (STEC) is a gastrointestinal pathogen causing foodborne outbreaks. Whole Genome Sequencing (WGS) in STEC surveillance holds promise in outbreak prevention and confinement, in broadening STEC epidemiology and in contributing to risk assessment and source attribution. However, despite international recommendations, WGS is often restricted to assist outbreak investigation and is not yet fully implemented in food safety surveillance across all European countries, in contrast to for example in the United States. Methods In this study, WGS was retrospectively applied to isolates collected within the context of Belgian food safety surveillance and combined with data from clinical isolates to evaluate its benefits. A cross-sector WGS-based collection of 754 strains from 1998 to 2020 was analyzed. Results We confirmed that WGS in food safety surveillance allows accurate detection of genomic relationships between human cases and strains isolated from food samples, including those dispersed over time and geographical locations. Identifying these links can reveal new insights into outbreaks and direct epidemiological investigations to facilitate outbreak management. Complete WGS-based isolate characterization enabled expanding epidemiological insights related to circulating serotypes, virulence genes and antimicrobial resistance across different reservoirs. Moreover, associations between virulence genes and severe disease were determined by incorporating human metadata into the data analysis. Gaps in the surveillance system were identified and suggestions for optimization related to sample centralization, harmonizing isolation methods, and expanding sampling strategies were formulated. Discussion This study contributes to developing a representative WGS-based collection of circulating STEC strains and by illustrating its benefits, it aims to incite policymakers to support WGS uptake in food safety surveillance.
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Affiliation(s)
- Stéphanie Nouws
- Transversal Activities in Applied Genomics, Sciensano, Brussels, Belgium
- IDlab, Department of Information Technology, Ghent University—IMEC, Ghent, Belgium
| | - Bavo Verhaegen
- National Reference Laboratory for Shiga Toxin-Producing Escherichia coli (NRL STEC) and for Foodborne Outbreaks (NRL FBO), Foodborne Pathogens, Sciensano, Brussels, Belgium
| | - Sarah Denayer
- National Reference Laboratory for Shiga Toxin-Producing Escherichia coli (NRL STEC) and for Foodborne Outbreaks (NRL FBO), Foodborne Pathogens, Sciensano, Brussels, Belgium
| | - Florence Crombé
- National Reference Centre for Shiga Toxin-Producing Escherichia coli (NRC STEC), Universitair Ziekenhuis Brussel, Vrije Universiteit Brussel, Brussels, Belgium
| | - Denis Piérard
- National Reference Centre for Shiga Toxin-Producing Escherichia coli (NRC STEC), Universitair Ziekenhuis Brussel, Vrije Universiteit Brussel, Brussels, Belgium
| | - Bert Bogaerts
- Transversal Activities in Applied Genomics, Sciensano, Brussels, Belgium
| | - Kevin Vanneste
- Transversal Activities in Applied Genomics, Sciensano, Brussels, Belgium
| | - Kathleen Marchal
- IDlab, Department of Information Technology, Ghent University—IMEC, Ghent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
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Teixeira JS, Boras VF, Hetman BM, Taboada EN, Inglis GD. Molecular Epidemiological Evidence Implicates Cattle as a Primary Reservoir of Campylobacter jejuni Infecting People via Contaminated Chickens. Pathogens 2022; 11:1366. [PMID: 36422616 PMCID: PMC9698452 DOI: 10.3390/pathogens11111366] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Revised: 11/07/2022] [Accepted: 11/08/2022] [Indexed: 09/10/2024] Open
Abstract
The study aimed to determine the relative contribution of cattle to the burden of illness in a model agroecosystem with high rates of human campylobacteriosis (≥ 115 cases/100 K), and high densities of cattle, including large numbers of cattle housed in confined feeding operations (i.e., in southwestern Alberta, Canada). To accomplish this, a large-scale molecular epidemiological analysis of Campylobacter jejuni circulating within the study location was completed. In excess of 8000 isolates of C. jejuni from people (n = 2548 isolates), chickens (n = 1849 isolates), cattle (n = 2921 isolates), and water (n = 771 isolates) were subtyped. In contrast to previous studies, the source attribution estimates of clinical cases attributable to cattle vastly exceeded those attributed to chicken (i.e., three- to six-fold). Moreover, cattle were often colonized by C. jejuni (51%) and shed the bacterium in their feces. A large proportion of study isolates were found in subtypes primarily associated with cattle (46%), including subtypes infecting people and those associated with chickens (19%). The implication of cattle as a primary amplifying reservoir of C. jejuni subtypes in circulation in the study location is supported by the strong cattle association with subtypes that were found in chickens and in people, a lack of evidence indicating the foodborne transmission of C. jejuni from beef and dairy, and the large number of cattle and the substantial quantities of untreated manure containing C. jejuni cells. Importantly, the evidence implicated cattle as a source of C. jejuni infecting people through a transmission pathway from cattle to people via the consumption of chicken. This has implications for reducing the burden of campylobacteriosis in the study location and elsewhere.
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Affiliation(s)
- Januana S. Teixeira
- Lethbridge Research and Development Centre, Agriculture and Agri-Food Canada, Lethbridge, AB T1J 4B1, Canada
| | - Valerie F. Boras
- Chinook Regional Hospital, Alberta Health Services, Lethbridge, AB T1J 1W5, Canada
| | - Benjamin M. Hetman
- Office of Public Health Field Services and Training, Public Health Agency of Canada, Winnipeg, MB R3C 0P4, Canada
| | - Eduardo N. Taboada
- National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, MB R3E 3R2, Canada
| | - G. Douglas Inglis
- Lethbridge Research and Development Centre, Agriculture and Agri-Food Canada, Lethbridge, AB T1J 4B1, Canada
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Asakura H, Yamamoto S, Yamada K, Kawase J, Nakamura H, Abe KI, Sasaki Y, Ikeda T, Nomoto R. Quantitative detection and genetic characterization of thermotolerant Campylobacter spp. in fresh chicken meats at retail in Japan. Front Microbiol 2022; 13:1014212. [PMID: 36299715 PMCID: PMC9589359 DOI: 10.3389/fmicb.2022.1014212] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Accepted: 09/23/2022] [Indexed: 11/17/2022] Open
Abstract
Campylobacter jejuni and C. coli are one of the leading causes of gastrointestinal illnesses, and which are considered to be transmitted to humans mainly from chicken meats. Considering the less availability of quantitative contamination data in the retail chicken meats in Japan, 510 fresh chicken meats retailed at five distinct regions in Japan between June 2019 and March 2021 were examined. The quantitative testing resulted that 45.7% of the samples (254/510) were positive at mean ± standard deviation of 1.15 ± 1.03 logCFU/g, whereas 43 samples (8.4%) exceeded 3.0 logCFU/g. Seasonal comparison revealed increased bacterial counts in fall compared with spring and summer. As for the chicken slaughter age, those slaughtered at >75 days old were less contaminated than those at <75 days old. Genome sequencing analyses of 111 representative C. jejuni isolates resulted in the detection of three antimicrobial resistance genes (gyrA substitution T86I, tetO and blaOXA-61) at 25.2, 27.9 and 42.3%, respectively. In silico MLST analysis revealed the predominance of sequence types (ST)-21 clonal complex (CC), followed by ST-45CC and ST-464CC. The single nucleotide polymorphism (SNP)-based phylogenetic tree largely classified the sequenced C. jejuni isolates into two clusters (I and II), where all C. jejuni from highly contaminated samples (STs-21CC, -22CC and -45CC) belonged to cluster I, independent of both season and slaughter age. To our knowledge, this is the first example to study the current status of Campylobacter contamination levels in fresh chicken meats retailed in Japan. Our data would be contributable to future quantitative microbial risk assessment, to establish effective control measures for campylobacteriosis.
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Affiliation(s)
- Hiroshi Asakura
- Division of Biomedical Food Research, National Institute of Health Sciences, Kawasaki, Kanagawa, Japan
- *Correspondence: Hiroshi Asakura,
| | - Shiori Yamamoto
- Division of Biomedical Food Research, National Institute of Health Sciences, Kawasaki, Kanagawa, Japan
| | - Kazuhiro Yamada
- Department of Microbiology and Medical Zoology, Aichi Prefectural Institute of Public Health, Nagoya, Aichi, Japan
| | - Jun Kawase
- Department of Bacteriology, Shimane Prefectural Institute of Public Health and Environmental Science, Matsue, Shimane, Japan
| | - Hiromi Nakamura
- Department of Microbiology, Osaka Institute of Public Health, Osaka, Japan
| | - Kou-ichiro Abe
- Kawasaki City Institute of Public Health, Kawasaki, Kanagawa, Japan
| | - Yoshimasa Sasaki
- Division of Biomedical Food Research, National Institute of Health Sciences, Kawasaki, Kanagawa, Japan
| | - Tetsuya Ikeda
- Department of Infectious Diseases, Hokkaido Institute of Public Health, Sapporo, Hokkaido, Japan
| | - Ryohei Nomoto
- Department of Infectious Diseases, Kobe Institute of Health, Kobe, Hyogo, Japan
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Mughini‐Gras L, Benincà E, McDonald SA, de Jong A, Chardon J, Evers E, Bonačić Marinović AA. A statistical modelling approach for source attribution meta-analysis of sporadic infection with foodborne pathogens. Zoonoses Public Health 2022; 69:475-486. [PMID: 35267243 PMCID: PMC9545847 DOI: 10.1111/zph.12937] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2021] [Revised: 02/15/2022] [Accepted: 02/26/2022] [Indexed: 11/30/2022]
Abstract
Numerous source attribution studies for foodborne pathogens based on epidemiological and microbiological methods are available. These studies provide empirical data for modelling frameworks that synthetize the quantitative evidence at our disposal and reduce reliance on expert elicitations. Here, we develop a statistical model within a Bayesian estimation framework to integrate attribution estimates from expert elicitations with estimates from microbial subtyping and case-control studies for sporadic infections with four major bacterial zoonotic pathogens in the Netherlands (Campylobacter, Salmonella, Shiga toxin-producing E. coli [STEC] O157 and Listeria). For each pathogen, we pooled the published fractions of human cases attributable to each animal reservoir from the microbial subtyping studies, accounting for the uncertainty arising from the different typing methods, attribution models, and year(s) of data collection. We then combined the population attributable fractions (PAFs) from the case-control studies according to five transmission pathways (domestic food, environment, direct animal contact, human-human transmission and travel) and 11 groups within the foodborne pathway (beef/lamb, pork, poultry meat, eggs, dairy, fish/shellfish, fruit/vegetables, beverages, grains, composite foods and food handlers/vermin). The attribution estimates were biologically plausible, allowing the human cases to be attributed in several ways according to reservoirs, transmission pathways and food groups. All pathogens were predominantly foodborne, with Campylobacter being mostly attributable to the chicken reservoir, Salmonella to pigs (albeit closely followed by layers), and Listeria and STEC O157 to cattle. Food-wise, the attributions reflected those at the reservoir level in terms of ranking. We provided a modelling solution to reach consensus attribution estimates reflecting the empirical evidence in the literature that is particularly useful for policy-making and is extensible to other pathogens and domains.
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Affiliation(s)
- Lapo Mughini‐Gras
- Centre for Infectious Disease Control (CIb)National Institute for Public Health and the Environment (RIVM)BilthovenThe Netherlands
- Institute for Risk Assessment Sciences (IRAS), Faculty of Veterinary MedicineUtrecht UniversityUtrechtThe Netherlands
| | - Elisa Benincà
- Centre for Infectious Disease Control (CIb)National Institute for Public Health and the Environment (RIVM)BilthovenThe Netherlands
| | - Scott A. McDonald
- Centre for Infectious Disease Control (CIb)National Institute for Public Health and the Environment (RIVM)BilthovenThe Netherlands
| | - Aarieke de Jong
- Office for Risk Assessment & Research (BuRO)Netherlands Food and Consumer Product Safety AuthorityUtrechtThe Netherlands
| | - Jurgen Chardon
- Centre for Infectious Disease Control (CIb)National Institute for Public Health and the Environment (RIVM)BilthovenThe Netherlands
| | - Eric Evers
- Centre for Infectious Disease Control (CIb)National Institute for Public Health and the Environment (RIVM)BilthovenThe Netherlands
| | - Axel A. Bonačić Marinović
- Centre for Infectious Disease Control (CIb)National Institute for Public Health and the Environment (RIVM)BilthovenThe Netherlands
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Draft genome sequence of a multidrug-resistant Campylobacter coli ST825 carrying several acquired antibiotic resistance genes isolated from poultry in China. J Glob Antimicrob Resist 2022; 30:265-268. [PMID: 35817262 DOI: 10.1016/j.jgar.2022.07.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Revised: 06/19/2022] [Accepted: 07/03/2022] [Indexed: 11/22/2022] Open
Abstract
OBJECTIVES Campylobacter coli is a typical food-borne pathogen worldwide known to cause bacterial gastroenteritis in humans. This study reported a draft whole genome sequence of C. coli isolate obtained from the caecal contents of poultry in Jinhua, China. METHODS Whole genomic DNA was sequenced using an Illumina Novaseq 6000 platform in 150 bp paired-end mode. The generated reads were de novo assembled by SPAdes v.3.12.0. All probable coding sequences were annotated using the RAST (Rapid Annotation using Subsystem Technology), and antibiotic resistance-related genes were also further identified by ResFinder 4.1 and rgi 5.1.1. RESULTS The draft genome contained 1 794 608 bp, a total of 69 contigs, belonging to sequence type (ST) ST825, comprising 1972 coding genes, 42 transfer RNAs, 2 ribosomal RNA, and with a GC content of 31.2%. The RAST analysis revealed a total of 698 subsystems in the genome of C. coli WL32 strain, with most of the genes associated with amino acids and derivatives (21.35%) and protein metabolism (17.05%). The genes related to antibiotic resistance, including erm(B) gene associated with macrolide resistance, blaOXA-61 gene associated with resistance to β-lactams, aac (6')-aph(2'), ant(6)-Ia, aph(2')-If, aph(3')-III gene associated with resistance to aminoglycosides, tetO gene associated with resistance to tetracycline, cat gene associated with amphenicol, and gyrA with fluoroquinolone Thr-86-Ile substitution, were identified. Also, the virulence genes, including motA, motB, flaG, fliE, fliF, fliG, flhB, and flhF genes, were identified by WGS analysis. CONCLUSION We report the draft genome sequence of C. coli ST825 isolate obtained from a poultry in China, which could provide potential information for tracking the potential spread of such a multidrug-resistant clone from poultry product processing to human beings.
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10
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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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11
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Clinquart A, Ellies-Oury MP, Hocquette JF, Guillier L, Santé-Lhoutellier V, Prache S. Review: On-farm and processing factors affecting bovine carcass and meat quality. Animal 2022; 16 Suppl 1:100426. [PMID: 35031228 DOI: 10.1016/j.animal.2021.100426] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Revised: 11/10/2021] [Accepted: 11/18/2021] [Indexed: 11/30/2022] Open
Abstract
This paper reviews the current state of knowledge on beef carcass and meat quality, with particular emphasis on on-farm and processing factors associated with its high and inconsistent variability. The diversity of livestock systems comes from the diversity of breeds (dairy or beef), ages and gender (bulls, steers, heifers, cull cows) used to produce either mainly beef or beef and milk. In addition, there are factors linked to farming practices (including diet, especially grazing) which significantly influence the sensory, nutritional, technological and extrinsic (such as image) quality attributes of meat. These can become factors of positive differentiation when controlled by the application and certification of technical specifications. Finally, preslaughter (such as stress), slaughter (such as the chilling and hanging method of carcasses) and postslaughter (such as ageing, packaging and cooking) conditions have a strong influence on the microbiological, sensory, technological and image quality attributes of beef. In this review, potential synergisms or antagonisms between the different quality attributes are highlighted. For example, finishing cattle on grass, compared to indoor fattening on a high concentrate diet, has the advantage of producing leaner meat with a higher proportion of omega-3 fatty acids while exhibiting superior oxidative stability, but with the consequence of a darker meat colour and lower productivity, as well as higher seasonality and land surface requirements. Moreover, the control of on-farm factors is often guided by productivity (growth rate, feed conversion ratio) and carcass quality attributes (weight, conformation and fatness). Genetic selection has often been oriented in this direction, without taking other quality attributes into account. Finally, the interactions between all these factors (and especially between on-farm and slaughter or processing factors) are not considered in the quality grading schemes in European countries. This means that positive efforts at farm level may be mitigated or even eliminated by poor slaughtering or processing conditions. All these considerations explain why between-animal variability in quality can be high, even when animals come from the same farming system. The ability to predict the sensory and nutritional properties of meat according to production factors has become a major objective of the supply chain.
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Affiliation(s)
- A Clinquart
- FARAH, Faculté de Médecine vétérinaire, Université de Liège, 4000 Liège, Belgium.
| | - M P Ellies-Oury
- Bordeaux Science Agro, 33175 Gradignan, France; Université d'Auvergne, INRAE, Vetagro Sup, UMR Herbivores, 63122 Saint Genès-Champanelle, France
| | - J F Hocquette
- Université d'Auvergne, INRAE, Vetagro Sup, UMR Herbivores, 63122 Saint Genès-Champanelle, France
| | - L Guillier
- Agence nationale de sécurité de l'alimentation, de l'environnement et du travail (ANSES), Direction de l'évaluation des risques, F-94700 Maisons-Alfort, France
| | | | - S Prache
- Université d'Auvergne, INRAE, Vetagro Sup, UMR Herbivores, 63122 Saint Genès-Champanelle, France
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12
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Hudson LK, Andershock WE, Yan R, Golwalkar M, M’ikanatha NM, Nachamkin I, Thomas LS, Moore C, Qian X, Steece R, Garman KN, Dunn JR, Kovac J, Denes TG. Phylogenetic Analysis Reveals Source Attribution Patterns for Campylobacter spp. in Tennessee and Pennsylvania. Microorganisms 2021; 9:microorganisms9112300. [PMID: 34835426 PMCID: PMC8625337 DOI: 10.3390/microorganisms9112300] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2021] [Revised: 10/27/2021] [Accepted: 10/29/2021] [Indexed: 11/22/2022] Open
Abstract
Campylobacteriosis is the most common bacterial foodborne illness in the United States and is frequently associated with foods of animal origin. The goals of this study were to compare clinical and non-clinical Campylobacter populations from Tennessee (TN) and Pennsylvania (PA), use phylogenetic relatedness to assess source attribution patterns, and identify potential outbreak clusters. Campylobacter isolates studied (n = 3080) included TN clinical isolates collected and sequenced for routine surveillance, PA clinical isolates collected from patients at the University of Pennsylvania Health System facilities, and non-clinical isolates from both states for which sequencing reads were available on NCBI. Phylogenetic analyses were conducted to categorize isolates into species groups and determine the population structure of each species. Most isolates were C. jejuni (n = 2132, 69.2%) and C. coli (n = 921, 29.9%), while the remaining were C. lari (0.4%), C. upsaliensis (0.3%), and C. fetus (0.1%). The C. jejuni group consisted of three clades; most non-clinical isolates were of poultry (62.7%) or cattle (35.8%) origin, and 59.7 and 16.5% of clinical isolates were in subclades associated with poultry or cattle, respectively. The C. coli isolates grouped into two clades; most non-clinical isolates were from poultry (61.2%) or swine (29.0%) sources, and 74.5, 9.2, and 6.1% of clinical isolates were in subclades associated with poultry, cattle, or swine, respectively. Based on genomic similarity, we identified 42 C. jejuni and one C. coli potential outbreak clusters. The C. jejuni clusters contained 188 clinical isolates, 19.6% of the total C. jejuni clinical isolates, suggesting that a larger proportion of campylobacteriosis may be associated with outbreaks than previously determined.
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Affiliation(s)
- Lauren K. Hudson
- Department of Food Science, University of Tennessee, Knoxville, TN 37996, USA;
| | | | - Runan Yan
- Department of Food Science, The Pennsylvania State University, University Park, PA 16802, USA; (R.Y.); (J.K.)
| | - Mugdha Golwalkar
- Tennessee Department of Health, Nashville, TN 37243, USA; (M.G.); (K.N.G.); (J.R.D.)
| | | | - Irving Nachamkin
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, The University of Pennsylvania, Philadelphia, PA 19104, USA;
| | - Linda S. Thomas
- Division of Laboratory Services, Tennessee Department of Health, Nashville, TN 37216, USA; (L.S.T.); (C.M.); (X.Q.); (R.S.)
| | - Christina Moore
- Division of Laboratory Services, Tennessee Department of Health, Nashville, TN 37216, USA; (L.S.T.); (C.M.); (X.Q.); (R.S.)
| | - Xiaorong Qian
- Division of Laboratory Services, Tennessee Department of Health, Nashville, TN 37216, USA; (L.S.T.); (C.M.); (X.Q.); (R.S.)
| | - Richard Steece
- Division of Laboratory Services, Tennessee Department of Health, Nashville, TN 37216, USA; (L.S.T.); (C.M.); (X.Q.); (R.S.)
| | - Katie N. Garman
- Tennessee Department of Health, Nashville, TN 37243, USA; (M.G.); (K.N.G.); (J.R.D.)
| | - John R. Dunn
- Tennessee Department of Health, Nashville, TN 37243, USA; (M.G.); (K.N.G.); (J.R.D.)
| | - Jasna Kovac
- Department of Food Science, The Pennsylvania State University, University Park, PA 16802, USA; (R.Y.); (J.K.)
| | - Thomas G. Denes
- Department of Food Science, University of Tennessee, Knoxville, TN 37996, USA;
- Correspondence:
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13
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Campylobacter jejuni in Different Canine Populations: Characteristics and Zoonotic Potential. Microorganisms 2021; 9:microorganisms9112231. [PMID: 34835357 PMCID: PMC8618475 DOI: 10.3390/microorganisms9112231] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2021] [Revised: 10/18/2021] [Accepted: 10/25/2021] [Indexed: 01/18/2023] Open
Abstract
With most epidemiological studies focused on poultry, dogs are often overlooked as a reservoir of Campylobacter, even though these animals maintain close daily contact with humans. The present study aimed to obtain a first insight into the presence and characteristics of Campylobacter spp. in different canine populations in Portugal, and to evaluate its zoonotic potential through genomic analysis. From a total of 125 rectal swabs collected from companion (n = 71) and hunting dogs (n = 54) living in two different settings, rural (n = 75) and urban (n = 50), 32 Campylobacter spp. isolates were obtained. Four different Campylobacter species were identified by Multiplex PCR and MALDI-TOF mass spectrometry, of which Campylobacter jejuni (n = 14, 44%) was overall the most frequently found species. Relevant resistance phenotypes were detected in C. jejuni, with 93% of the isolates being resistant to ciprofloxacin, 64% to tetracycline, and 57% to ampicillin, and three isolates being multi-drug-resistant. Comparison of the phenotypic and genotypic traits with human isolates from Portuguese patients revealed great similarity between both groups. Particularly relevant, the wgMLST analysis allowed the identification of isolates from human and dogs without any apparent epidemiological relationship, sharing high genetic proximity. Notwithstanding the limited sample size, considering the high genomic diversity of C. jejuni, the genetic overlap between human and dog strains observed in this study confirmed that the occurrence of this species in dogs is of public health concern, reinforcing the call for a One Health approach.
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14
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Arning N, Sheppard SK, Bayliss S, Clifton DA, Wilson DJ. Machine learning to predict the source of campylobacteriosis using whole genome data. PLoS Genet 2021; 17:e1009436. [PMID: 34662334 PMCID: PMC8553134 DOI: 10.1371/journal.pgen.1009436] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2021] [Revised: 10/28/2021] [Accepted: 08/26/2021] [Indexed: 11/18/2022] Open
Abstract
Campylobacteriosis is among the world's most common foodborne illnesses, caused predominantly by the bacterium Campylobacter jejuni. Effective interventions require determination of the infection source which is challenging as transmission occurs via multiple sources such as contaminated meat, poultry, and drinking water. Strain variation has allowed source tracking based upon allelic variation in multi-locus sequence typing (MLST) genes allowing isolates from infected individuals to be attributed to specific animal or environmental reservoirs. However, the accuracy of probabilistic attribution models has been limited by the ability to differentiate isolates based upon just 7 MLST genes. Here, we broaden the input data spectrum to include core genome MLST (cgMLST) and whole genome sequences (WGS), and implement multiple machine learning algorithms, allowing more accurate source attribution. We increase attribution accuracy from 64% using the standard iSource population genetic approach to 71% for MLST, 85% for cgMLST and 78% for kmerized WGS data using the classifier we named aiSource. To gain insight beyond the source model prediction, we use Bayesian inference to analyse the relative affinity of C. jejuni strains to infect humans and identified potential differences, in source-human transmission ability among clonally related isolates in the most common disease causing lineage (ST-21 clonal complex). Providing generalizable computationally efficient methods, based upon machine learning and population genetics, we provide a scalable approach to global disease surveillance that can continuously incorporate novel samples for source attribution and identify fine-scale variation in transmission potential.
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Affiliation(s)
- Nicolas Arning
- Big Data institute, Nuffield Department of Population Health, University of Oxford, Li Ka Shing Centre for Health Information and Discovery, Old Road Campus, Oxford, United Kingdom
- * E-mail:
| | - Samuel K. Sheppard
- The Milner Centre of Evolution, Department of Biology & Biochemistry, University of Bath, Claverton Down, Bath, United Kingdom
| | - Sion Bayliss
- The Milner Centre of Evolution, Department of Biology & Biochemistry, University of Bath, Claverton Down, Bath, United Kingdom
| | - David A. Clifton
- Department of Engineering Science, University of Oxford, Oxford, UK; Oxford-Suzhou Centre for Advanced Research, Suzhou, China
| | - Daniel J. Wilson
- Big Data institute, Nuffield Department of Population Health, University of Oxford, Li Ka Shing Centre for Health Information and Discovery, Old Road Campus, Oxford, United Kingdom
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15
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Kürekci C, Sakin F, Epping L, Knüver MT, Semmler T, Stingl K. Characterization of Campylobacter spp. Strains Isolated From Wild Birds in Turkey. Front Microbiol 2021; 12:712106. [PMID: 34489902 PMCID: PMC8416542 DOI: 10.3389/fmicb.2021.712106] [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: 05/19/2021] [Accepted: 07/12/2021] [Indexed: 11/13/2022] Open
Abstract
Turkey is an important stopover site for many migrating birds between Europe, Asia and Africa. Campylobacter spp. are frequently found in wildlife, in particular waterfowl, and distinct strains are disseminated within this reservoir. In this study, 183 wild birds of hunting areas in Turkey were collected and thermophilic Campylobacter spp. from cloacal swabs were isolated at a prevalence of 5.2% from song thrushes (6/116) and 93% from Eurasian coots (41/44). After PCR species differentiation and flaA restriction profiles determination, C. jejuni and C. coli strains were further investigated by whole genome sequencing. PCR target amplification of the ceuE gene, commonly used for C. coli species-identification was inefficient and even hampered in one isolate. A close look on the ceuE sequence revealed that various mismatches in the ceuE oligo annealing sites caused less efficient diagnostic detection. All C. coli isolates belonged to the environmental clade II and clade III, for which thirty-six novel MLST types were identified. Further single nucleotide polymorphism (SNP) analysis showed a high genomic divergence between the C. coli isolates. High variability was also implicated for putative plasmid-located genes detected in 51% of the C. coli isolates. Distinct gene variants in clades II and III C. coli were identified by a k-mer analysis. After substracting k-mers in common with C. coli clade I database, 11 and 35 distinct genes were identified in clades II and III isolates, mainly involved in surface structures and modifications as well as signal transduction, suggesting niche adaptation of C. coli strains in wild birds. All strains were susceptible against (fluoro-)quinolones, erythromycin, tetracycline, gentamicin and only one isolate was resistant against streptomycin, suggesting that the sensitive phenotype was due to absence of selective pressure and niche separation in wild birds in Turkey. We conclude that Campylobacter spp. isolates from wildlife and environmental sources are still scarce in the databases and that there is a need for more studies on thermophilic Campylobacter spp. from different places all over the world in order to complement our understanding on dissemination and adaptation to distinct niches of this global food-borne pathogen.
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Affiliation(s)
- Cemil Kürekci
- Department of Food Hygiene and Technology, Faculty of Veterinary Medicine, Hatay Mustafa Kemal University, Hatay, Turkey
| | - Fatih Sakin
- Department of Pharmacology and Toxicology, Faculty of Veterinary Medicine, Hatay Mustafa Kemal University, Hatay, Turkey
| | - Lennard Epping
- Robert Koch Institute, Genome Sequencing and Genomic Epidemiology, Berlin, Germany
| | - Marie-Theres Knüver
- German Federal Institute for Risk Assessment, Department of Biological Safety, National Reference Laboratory for Campylobacter, Berlin, Germany
| | - Torsten Semmler
- Robert Koch Institute, Genome Sequencing and Genomic Epidemiology, Berlin, Germany
| | - Kerstin Stingl
- German Federal Institute for Risk Assessment, Department of Biological Safety, National Reference Laboratory for Campylobacter, Berlin, Germany
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16
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Emergence of erythromycin resistance methyltransferases in Campylobacter coli strains in France. Antimicrob Agents Chemother 2021; 65:e0112421. [PMID: 34370579 DOI: 10.1128/aac.01124-21] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Antimicrobial resistance in Campylobacters is described worldwide. The emergence of multiresistant isolates, particularly among C. coli, is concerning. New resistance mechanisms appear frequently, and DNA-sequence-based methods such as whole genome sequencing (WGS) have become useful tools to monitor their emergence. The genomes of 51 multiresistant French Campylobacter sp. clinical strains from 2018 to 2019 were analyzed to identify associated resistance mechanisms. Analyses of erythromycin-resistant strains revealed 23S ribosomal RNA mutations among most of them and two different methyltransferases in 4 strains: Erm(B) and a novel methyltransferase, here named Erm(N). The erm(B) gene was found in multidrug-resistant genomic islands, whereas erm(N) was inserted within CRISPR arrays of the CRISPR-cas9 operon. Moreover, using PCR screening in erythromycin-resistant strains from our collection, we showed that erm(N) was already present in 3 French clinical strains 2 years before its first report in 2018 in Quebec. Bacterial transformations confirmed that insertion of erm(N) into a CRISPR-cas9 operon can confer macrolide resistance. Campylobacter species are easily able to adapt to their environment and acquire new resistance mechanisms, and the emergence of methyltransferases in Campylobacters in France is a matter of concern in the coming years.
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17
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Lopez-Chavarrias V, Ugarte-Ruiz M, Barcena C, Olarra A, Garcia M, Saez JL, de Frutos C, Serrano T, Perez I, Moreno MA, Dominguez L, Alvarez J. Monitoring of Antimicrobial Resistance to Aminoglycosides and Macrolides in Campylobacter coli and Campylobacter jejuni From Healthy Livestock in Spain (2002-2018). Front Microbiol 2021; 12:689262. [PMID: 34276619 PMCID: PMC8283307 DOI: 10.3389/fmicb.2021.689262] [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: 03/31/2021] [Accepted: 06/08/2021] [Indexed: 11/13/2022] Open
Abstract
Antimicrobial resistance (AMR) in Campylobacter spp. (Campylobacter coli and Campylobacter jejuni) is a concern due to its importance in public health, particularly when it involves aminoglycosides and macrolides, drugs of choice for treatment of human cases. Co-resistance to these two antimicrobial classes involves transfer of genetic elements and/or acquisition of mutations in different genetic loci, which can in turn spread through vertical or horizontal gene transfer (HGT) phenomena, with each route having different potential implications. This study aimed at evaluating the association between the presence of phenotypic resistance to these two antimicrobial classes in C. coli and C. jejuni recovered from livestock at slaughterhouses in Spain (as part of the AMR surveillance program), and at assessing the genetic heterogeneity between resistant and susceptible isolates by analysing the "short variable region" (SVR) of the flaA gene. Over the 2002-2018 period, antimicrobial susceptibility test results from 10,965 Campylobacter isolates retrieved from fecal samples of broilers, turkeys, pigs and cattle were collected to compare the proportion of resistant isolates and the Minimum Inhibitory Concentrations (MICs) against six antimicrobials including gentamicin (GEN), streptomycin (STR), and erythromycin (ERY). AMR-associated genes were determined for a group of 51 isolates subjected to whole genome sequencing, and the flaA SVR of a subset of 168 isolates from all hosts with different resistotypes was used to build a Neighbor-Joining-based phylogenetic tree and assess the existence of groups by means of "relative synonymous codon usage" (RSCU) analysis. The proportion of antimicrobial resistant isolates to both, aminoglycosides and macrolides, varied widely for C. coli (7-91%) and less for C. jejuni (all hosts 0-11%). Across hosts, these proportions were 7-56% in poultry, 12-82% in cattle, and 22-91% in pigs for C. coli and 0-8% in poultry and 1-11% in cattle for C. jejuni. Comparison of the MIC distributions revealed significant host-specific differences only for ERY in C. jejuni (p = 0.032). A significant association in the simultaneous presentation of AMR to both antimicrobial classes was observed across hosts/bacterial species. The flaA gene analysis showed clustering of isolates sharing resistotype and to a lesser degree bacterial species and host. Several resistance markers associated with resistance to aminoglycosides and macrolides were found among the sequenced isolates. The consistent association between the simultaneous presentation of AMR to aminoglycosides and macrolides in all hosts could be due to the persistence of strains and/or resistance mechanisms in Campylobacter populations in livestock over time. Further studies based on whole genome sequencing are needed to assess the epidemiological links between hosts and bacterial strains.
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Affiliation(s)
| | - Maria Ugarte-Ruiz
- VISAVET Health Surveillance Centre, Universidad Complutense de Madrid, Madrid, Spain
| | - Carmen Barcena
- VISAVET Health Surveillance Centre, Universidad Complutense de Madrid, Madrid, Spain
| | - Adolfo Olarra
- Facultad de Medicina Veterinaria y Zootecnia, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Maria Garcia
- VISAVET Health Surveillance Centre, Universidad Complutense de Madrid, Madrid, Spain
| | - Jose Luis Saez
- Subdirección General de Sanidad e Higiene Animal y Trazabilidad, Dirección General de la Producción Agraria, Ministerio de Agricultura, Pesca y Alimentación, Madrid, Spain
| | - Cristina de Frutos
- Laboratorio Central de Veterinaria (LCV Algete), Ministerio de Agricultura, Pesca y Alimentación, Madrid, Spain
| | - Tania Serrano
- TRAGSATEC, Tecnologías y Servicios Agrarios S.A., Madrid, Spain
| | - Iratxe Perez
- Laboratorio Central de Veterinaria (LCV Algete), Ministerio de Agricultura, Pesca y Alimentación, Madrid, Spain
| | - Miguel Angel Moreno
- Departamento de Sanidad Animal, Facultad de Veterinaria, Universidad Complutense de Madrid, Madrid, Spain
| | - Lucas Dominguez
- VISAVET Health Surveillance Centre, Universidad Complutense de Madrid, Madrid, Spain.,Departamento de Sanidad Animal, Facultad de Veterinaria, Universidad Complutense de Madrid, Madrid, Spain
| | - Julio Alvarez
- VISAVET Health Surveillance Centre, Universidad Complutense de Madrid, Madrid, Spain.,Departamento de Sanidad Animal, Facultad de Veterinaria, Universidad Complutense de Madrid, Madrid, Spain
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18
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Duarte ASR, Röder T, Van Gompel L, Petersen TN, Hansen RB, Hansen IM, Bossers A, Aarestrup FM, Wagenaar JA, Hald T. Metagenomics-Based Approach to Source-Attribution of Antimicrobial Resistance Determinants - Identification of Reservoir Resistome Signatures. Front Microbiol 2021; 11:601407. [PMID: 33519742 PMCID: PMC7843941 DOI: 10.3389/fmicb.2020.601407] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Accepted: 12/14/2020] [Indexed: 12/11/2022] Open
Abstract
Metagenomics can unveil the genetic content of the total microbiota in different environments, such as food products and the guts of humans and livestock. It is therefore considered of great potential to investigate the transmission of foodborne hazards as part of source-attribution studies. Source-attribution of antimicrobial resistance (AMR) has traditionally relied on pathogen isolation, while metagenomics allows investigating the full span of AMR determinants. In this study, we hypothesized that the relative abundance of fecal resistome components can be associated with specific reservoirs, and that resistomes can be used for AMR source-attribution. We used shotgun-sequences from fecal samples of pigs, broilers, turkeys- and veal calves collected across Europe, and fecal samples from humans occupationally exposed to livestock in one country (pig slaughterhouse workers, pig and broiler farmers). We applied both hierarchical and flat forms of the supervised classification ensemble algorithm Random Forests to classify resistomes into corresponding reservoir classes. We identified country-specific and -independent AMR determinants, and assessed the impact of country-specific determinants when attributing AMR resistance in humans. Additionally, we performed a similarity percentage analysis with the full spectrum of AMR determinants to identify resistome signatures for the different reservoirs. We showed that the number of AMR determinants necessary to attribute a resistome into the correct reservoir increases with a larger reservoir heterogeneity, and that the impact of country-specific resistome signatures on prediction varies between countries. We predicted a higher occupational exposure to AMR determinants among workers exposed to pigs than among those exposed to broilers. Additionally, results suggested that AMR exposure on pig farms was higher than in pig slaughterhouses. Human resistomes were more similar to pig and veal calves’ resistomes than to those of broilers and turkeys, and the majority of these resistome dissimilarities can be explained by a small set of AMR determinants. We identified resistome signatures for each individual reservoir, which include AMR determinants significantly associated with on-farm antimicrobial use. We attributed human resistomes to different livestock reservoirs using Random Forests, which allowed identifying pigs as a potential source of AMR in humans. This study thus demonstrates that it is possible to apply metagenomics in AMR source-attribution.
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Affiliation(s)
- Ana Sofia Ribeiro Duarte
- Division of Genomic Epidemiology, National Food Institute, Technical University of Denmark, Kgs Lyngby, Denmark
| | - Timo Röder
- Division of Genomic Epidemiology, National Food Institute, Technical University of Denmark, Kgs Lyngby, Denmark
| | - Liese Van Gompel
- Institute for Risk Assessment Sciences, Faculty of Veterinary Medicine, Utrecht University, Utrecht, Netherlands
| | - Thomas Nordahl Petersen
- Division of Genomic Epidemiology, National Food Institute, Technical University of Denmark, Kgs Lyngby, Denmark
| | | | - Inge Marianne Hansen
- Division of Genomic Epidemiology, National Food Institute, Technical University of Denmark, Kgs Lyngby, Denmark
| | - Alex Bossers
- Institute for Risk Assessment Sciences, Faculty of Veterinary Medicine, Utrecht University, Utrecht, Netherlands.,Wageningen Bioveterinary Research, Lelystad, Netherlands
| | - Frank M Aarestrup
- Division of Genomic Epidemiology, National Food Institute, Technical University of Denmark, Kgs Lyngby, Denmark
| | - Jaap A Wagenaar
- Wageningen Bioveterinary Research, Lelystad, Netherlands.,Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, Utrecht, Netherlands
| | - Tine Hald
- Division of Genomic Epidemiology, National Food Institute, Technical University of Denmark, Kgs Lyngby, Denmark
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Kumagai Y, Pires SM, Kubota K, Asakura H. Attributing Human Foodborne Diseases to Food Sources and Water in Japan Using Analysis of Outbreak Surveillance Data. J Food Prot 2020; 83:2087-2094. [PMID: 32649749 DOI: 10.4315/jfp-20-151] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2020] [Accepted: 07/10/2020] [Indexed: 11/11/2022]
Abstract
ABSTRACT In Japan, strategies for ensuring food safety have been developed without reliable scientific evidence on the relationship between foodborne diseases and food sources. This study aimed to provide information on the proportions of foodborne diseases caused by seven major causative pathogens (Campylobacter spp., Salmonella, enterohemorrhagic Escherichia coli [EHEC], Vibrio parahaemolyticus, Clostridium perfringens, Staphylococcus aureus, and norovirus) attributed to foods and to explore factors affecting changes in these source attribution proportions over time using analysis of outbreak surveillance data. For the calculation of the number of outbreaks attributed to each source, simple-food outbreaks were assigned to the single-food category in question, and complex-food outbreaks were classified under each category proportional to the estimated probability. During 2007 to 2018, 8,730 outbreaks of foodborne diseases caused by seven pathogens were reported, of which 6,690 (76.6%) were of unknown source. We estimated the following source attribution proportions of foodborne diseases: chicken products (80.3%, 95% uncertainty interval [UI] 80.1 to 80.4) for Campylobacter spp.; beef products (50.1%, UI 47.0 to 51.5) and vegetables (42.3%, UI 40.9 to 45.5) for EHEC; eggs (34.6%, UI 27.8 to 41.4) and vegetables (34.4%, UI 27.8 to 40.8) for Salmonella; finfish (50.3%, UI 33.3 to 66.7) and shellfish (49.7%, UI 33.3 to 66.7) for V. parahaemolyticus; grains and beans (57.8%, UI 49.7 to 64.9) for S. aureus; vegetables (63.6%, UI 48.5 to 74.6), chicken products (12.7%, UI 4.6 to 21.5), and beef products (11.1%, UI 8.5 to 13.1) for C. perfringens; and shellfish (75.5%, UI 74.7 to 76.2) for norovirus. In this study, we provide the best available evidence-based information to evaluate the link between foodborne diseases and foods. Our results on source attribution for Campylobacter spp. and EHEC suggest that the strict health regulations for raw beef were reflected in the proportions of these diseases attributed to this food. HIGHLIGHTS
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Affiliation(s)
- Yuko Kumagai
- Laboratory of Foodborne Diseases, Department of Human Ecology, The Wayo Women's University, 2-3-1, Kohnodai, Ichicawa City, Chiba 272-8533, Japan (ORCID: https://orcid.org/0000-0001-6205-2736 [Y.K.])
| | - Sara Monteiro Pires
- National Food Institute, Technical University of Denmark, Kemitorvet, Building 201, Room 116, 2800 Kgs. Lyngby, Denmark
| | - Kunihiro Kubota
- National Institute of Health Sciences, 3-25-26, Tonomachi, Kawasaki-ku, Kawasaki City, Kanagawa 210-9501, Japan
| | - Hiroshi Asakura
- National Institute of Health Sciences, 3-25-26, Tonomachi, Kawasaki-ku, Kawasaki City, Kanagawa 210-9501, Japan
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Mughini-Gras L, Pijnacker R, Coipan C, Mulder AC, Fernandes Veludo A, de Rijk S, van Hoek AHAM, Buij R, Muskens G, Koene M, Veldman K, Duim B, van der Graaf-van Bloois L, van der Weijden C, Kuiling S, Verbruggen A, van der Giessen J, Opsteegh M, van der Voort M, Castelijn GAA, Schets FM, Blaak H, Wagenaar JA, Zomer AL, Franz E. Sources and transmission routes of campylobacteriosis: A combined analysis of genome and exposure data. J Infect 2020; 82:216-226. [PMID: 33275955 DOI: 10.1016/j.jinf.2020.09.039] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2020] [Revised: 09/13/2020] [Accepted: 09/26/2020] [Indexed: 01/24/2023]
Abstract
OBJECTIVES To determine the contributions of several animal and environmental sources of human campylobacteriosis and identify source-specific risk factors. METHODS 1417 Campylobacter jejuni/coli isolates from the Netherlands in 2017-2019 were whole-genome sequenced, including isolates from human cases (n = 280), chickens/turkeys (n = 238), laying hens (n = 56), cattle (n = 158), veal calves (n = 49), sheep/goats (n = 111), pigs (n = 110), dogs/cats (n = 100), wild birds (n = 62), and surface water (n = 253). Questionnaire-based exposure data was collected. Source attribution was performed using core-genome multilocus sequence typing. Risk factors were determined on the attribution estimates. RESULTS Cases were mostly attributed to chickens/turkeys (48.2%), dogs/cats (18.0%), cattle (12.1%), and surface water (8.5%). Of the associations identified, never consuming chicken, as well as frequent chicken consumption, and rarely washing hands after touching raw meat, were risk factors for chicken/turkey-attributable infections. Consuming unpasteurized milk or barbecued beef increased the risk for cattle-attributable infections. Risk factors for infections attributable to environmental sources were open water swimming, contact with dog faeces, and consuming non-chicken/turkey avian meat like game birds. CONCLUSIONS Poultry and cattle are the main livestock sources of campylobacteriosis, while pets and surface water are important non-livestock sources. Foodborne transmission is only partially consistent with the attributions, as frequency and alternative pathways of exposure are significant.
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Affiliation(s)
- Lapo Mughini-Gras
- Centre for Infectious Disease Control (CIb), National Institute for Public Health and the Environment (RIVM), Bilthoven, the Netherlands; Institute for Risk Assessment Sciences (IRAS), Utrecht University, Utrecht, the Netherlands.
| | - Roan Pijnacker
- Centre for Infectious Disease Control (CIb), National Institute for Public Health and the Environment (RIVM), Bilthoven, the Netherlands
| | - Claudia Coipan
- Centre for Infectious Disease Control (CIb), National Institute for Public Health and the Environment (RIVM), Bilthoven, the Netherlands
| | - Annemieke C Mulder
- Centre for Infectious Disease Control (CIb), National Institute for Public Health and the Environment (RIVM), Bilthoven, the Netherlands
| | | | - Sharona de Rijk
- Centre for Infectious Disease Control (CIb), National Institute for Public Health and the Environment (RIVM), Bilthoven, the Netherlands
| | - Angela H A M van Hoek
- Centre for Infectious Disease Control (CIb), National Institute for Public Health and the Environment (RIVM), Bilthoven, the Netherlands
| | - Ralph Buij
- Wageningen Environmental Research (WER), Wageningen University & Research (WUR), Wageningen, the Netherlands
| | - Gerard Muskens
- Wageningen Environmental Research (WER), Wageningen University & Research (WUR), Wageningen, the Netherlands
| | - Miriam Koene
- Wageningen Bioveterinary Research (WBVR), Wageningen University & Research (WUR), Lelystad, the Netherlands
| | - Kees Veldman
- Wageningen Bioveterinary Research (WBVR), Wageningen University & Research (WUR), Lelystad, the Netherlands
| | - Birgitta Duim
- Department of Infectious Diseases and Immunology (I&I), Utrecht University & WHO Collaborating Center for Campylobacter/OIE Reference Laboratory for Campylobacteriosis, Utrecht, the Netherlands
| | - Linda van der Graaf-van Bloois
- Department of Infectious Diseases and Immunology (I&I), Utrecht University & WHO Collaborating Center for Campylobacter/OIE Reference Laboratory for Campylobacteriosis, Utrecht, the Netherlands
| | - Coen van der Weijden
- Netherlands Food and Consumer Product Safety Authority (NVWA), Utrecht, the Netherlands
| | - Sjoerd Kuiling
- Centre for Infectious Disease Control (CIb), National Institute for Public Health and the Environment (RIVM), Bilthoven, the Netherlands
| | - Anjo Verbruggen
- Centre for Infectious Disease Control (CIb), National Institute for Public Health and the Environment (RIVM), Bilthoven, the Netherlands
| | - Joke van der Giessen
- Centre for Infectious Disease Control (CIb), National Institute for Public Health and the Environment (RIVM), Bilthoven, the Netherlands
| | - Marieke Opsteegh
- Centre for Infectious Disease Control (CIb), National Institute for Public Health and the Environment (RIVM), Bilthoven, the Netherlands
| | - Menno van der Voort
- Wageningen Food Safety Research (WFSR), Wageningen University & Research (WUR), Wageningen, the Netherlands
| | - Greetje A A Castelijn
- Wageningen Food Safety Research (WFSR), Wageningen University & Research (WUR), Wageningen, the Netherlands
| | - Franciska M Schets
- Centre for Infectious Disease Control (CIb), National Institute for Public Health and the Environment (RIVM), Bilthoven, the Netherlands
| | - Hetty Blaak
- Centre for Infectious Disease Control (CIb), National Institute for Public Health and the Environment (RIVM), Bilthoven, the Netherlands
| | - Jaap A Wagenaar
- Department of Infectious Diseases and Immunology (I&I), Utrecht University & WHO Collaborating Center for Campylobacter/OIE Reference Laboratory for Campylobacteriosis, Utrecht, the Netherlands
| | - Aldert L Zomer
- Department of Infectious Diseases and Immunology (I&I), Utrecht University & WHO Collaborating Center for Campylobacter/OIE Reference Laboratory for Campylobacteriosis, Utrecht, the Netherlands
| | - Eelco Franz
- Centre for Infectious Disease Control (CIb), National Institute for Public Health and the Environment (RIVM), Bilthoven, the Netherlands
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Genome-Wide Identification of Host-Segregating Single-Nucleotide Polymorphisms for Source Attribution of Clinical Campylobacter coli Isolates. Appl Environ Microbiol 2020; 86:AEM.01787-20. [PMID: 33036986 DOI: 10.1128/aem.01787-20] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2020] [Accepted: 09/30/2020] [Indexed: 12/27/2022] Open
Abstract
Campylobacter is among the most common causes of gastroenteritis worldwide. Campylobacter jejuni and Campylobacter coli are the most common species causing human disease. DNA sequence-based methods for strain characterization have focused largely on C. jejuni, responsible for 80 to 90% of infections, meaning that C. coli epidemiology has lagged behind. Here, we have analyzed the genome of 450 C. coli isolates to determine genetic markers that can discriminate isolates sampled from 3 major reservoir hosts (chickens, cattle, and pigs). These markers then were applied to identify the source of infection of 147 C. coli strains from French clinical cases. Using STRUCTURE software, 259 potential host-segregating markers were revealed by probabilistic characterization of single-nucleotide polymorphism (SNP) frequency variation in strain collections from three different hosts. These SNPs were found in 41 genes or intergenic regions, mostly coding for proteins involved in motility and membrane functions. Source attribution of clinical isolates based on the differential presence of these markers confirmed chickens as the most common source of C. coli infection in France.IMPORTANCE Genome-wide and source attribution studies based on Campylobacter species have shown their importance for the understanding of foodborne infections. Although the use of multilocus sequence typing based on 7 genes from C. jejuni is a powerful method to structure populations, when applied to C. coli, results have not clearly demonstrated its robustness. Therefore, we aim to provide more accurate data based on the identification of single-nucleotide polymorphisms. Results from this study reveal an important number of host-segregating SNPs, found in proteins involved in motility, membrane functions, or DNA repair systems. These findings offer new, interesting opportunities for further study of C. coli adaptation to its environment. Additionally, the results demonstrate that poultry is potentially the main reservoir of C. coli in France.
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22
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Hansson I, Tamminen LM, Frosth S, Fernström LL, Emanuelson U, Boqvist S. Occurrence of Campylobacter spp. in Swedish calves, common sequence types and antibiotic resistance patterns. J Appl Microbiol 2020; 130:2111-2122. [PMID: 33119192 PMCID: PMC8246890 DOI: 10.1111/jam.14914] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Revised: 10/22/2020] [Accepted: 10/25/2020] [Indexed: 12/14/2022]
Abstract
Aims Cattle are the second most important cause of human campylobacteriosis, after poultry, but there are knowledge gaps regarding Campylobacter in cattle. This study examined the occurrence of Campylobacter, the species present, sequence types and antibiotic resistance in Swedish cattle. Methods and Results Faeces samples collected from 154 calves on seven Swedish farms, and 69 follow‐up samples from a second collection occasion, were analysed. Campylobacter were isolated from 77% of calves at the first sampling, with Campylobacter jejuni as the most frequently isolated species. Animals kept on deep straw bedding were less likely to be colonized with Campylobacter. Whole‐genome sequencing of 90 C. jejuni samples resulted in 11 sequence types, among which ST‐19 and ST‐21 were most frequent. Antimicrobial resistance analyses showed that 46% of 142 isolates analysed were resistant to quinolones, while all isolates belonging to ST‐19, ST‐22 and ST‐441 were resistant to ciprofloxacin and nalidixic acid. Conclusions Campylobacter jejuni was the species most frequently isolated in calves and a strong association was found between sequence type and antimicrobial resistance pattern. Significance and Impact of the Study The high proportion of calves with quinolone‐resistant Campylobacter jejuni should be considered in a One Health perspective.
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Affiliation(s)
- I Hansson
- Department of Biomedical Sciences and Veterinary Public Health, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - L-M Tamminen
- Department of Clinical Sciences, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - S Frosth
- Department of Biomedical Sciences and Veterinary Public Health, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - L-L Fernström
- Department of Biomedical Sciences and Veterinary Public Health, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - U Emanuelson
- Department of Clinical Sciences, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - S Boqvist
- Department of Biomedical Sciences and Veterinary Public Health, Swedish University of Agricultural Sciences, Uppsala, Sweden
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23
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Contribution of Foods and Poor Food-Handling Practices to the Burden of Foodborne Infectious Diseases in France. Foods 2020; 9:foods9111644. [PMID: 33187291 PMCID: PMC7697675 DOI: 10.3390/foods9111644] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Revised: 11/03/2020] [Accepted: 11/06/2020] [Indexed: 01/25/2023] Open
Abstract
The foodborne disease burden (FBDB) related to 26 major biological hazards in France was attributed to foods and poor food-handling practices at the final food preparation step, in order to develop effective intervention strategies, especially food safety campaigns. Campylobacter spp. and non-typhoidal Salmonella accounted for more than 60% of the FBDB. Approximately 30% of the FBDB were attributed to 11 other hazards including bacteria, viruses and parasites. Meats were estimated as the main contributing food category causing (50-69%) (CI90) of the FBDB with (33-44%), (9-21%), (4-20%) (CI90) of the FBDB for poultry, pork and beef, respectively. Dairy products, eggs, raw produce and complex foods caused each approximately (5-20%) (CI90) of the FBDB. When foods are contaminated before the final preparation step, we estimated that inadequate cooking, cross-contamination and inadequate storage contribute for (19-49%), (7-34%) and (9-23%) (CI90) of the FBDB, respectively; (15-33%) (CI90) of the FBDB were attributed to the initial contamination of ready-to-eat foods-without any contribution from final food handlers. The thorough implementation of good hygienic practices (GHPs) at the final food preparation step could potentially reduce the FBDB by (67-85%) (CI90) (mainly with the prevention of cross-contamination and adequate cooking and storage).
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24
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Kelley BR, Ellis JC, Large A, Schneider LG, Jacobson D, Johnson JG. Whole-Genome Sequencing and Bioinformatic Analysis of Environmental, Agricultural, and Human Campylobacter jejuni Isolates From East Tennessee. Front Microbiol 2020; 11:571064. [PMID: 33224113 PMCID: PMC7674308 DOI: 10.3389/fmicb.2020.571064] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Accepted: 10/08/2020] [Indexed: 12/28/2022] Open
Abstract
As a leading cause of bacterial-derived gastroenteritis worldwide, Campylobacter jejuni has a significant impact on human health in both the developed and developing worlds. Despite its prevalence as a human pathogen, the source of these infections remains poorly understood due to the mutation frequency of the organism and past limitations of whole genome analysis. Recent advances in both whole genome sequencing and computational methods have allowed for the high-resolution analysis of intraspecies diversity, leading multiple groups to postulate that these approaches may be used to identify the sources of Campylobacter jejuni infection. To address this hypothesis, our group conducted a regionally and temporally restricted sampling of agricultural and environmental Campylobacter sources and compared isolated C. jejuni genomes to those that caused human infections in the same region during the same time period. Through a network analysis comparing genomes from various sources, we found that human C. jejuni isolates clustered with those isolated from cattle and chickens, indicating these as potential sources of human infection in the region.
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Affiliation(s)
- Brittni R Kelley
- Department of Microbiology, The University of Tennessee, Knoxville, Knoxville, TN, United States
| | | | - Annabel Large
- Biosciences, Oak Ridge National Laboratory, Oak Ridge, TN, United States
| | - Liesel G Schneider
- Department of Animal Science, The University of Tennessee, Knoxville, Knoxville, TN, United States
| | - Daniel Jacobson
- Biosciences, Oak Ridge National Laboratory, Oak Ridge, TN, United States
- Bredesen Center, The University of Tennessee, Knoxville, Knoxville, TN, United States
| | - Jeremiah G Johnson
- Department of Microbiology, The University of Tennessee, Knoxville, Knoxville, TN, United States
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25
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Šimunović K, Zajkoska S, Bezek K, Klančnik A, Barlič Maganja D, Smole Možina S. Comparison of Campylobacter jejuni Slaughterhouse and Surface-Water Isolates Indicates Better Adaptation of Slaughterhouse Isolates to the Chicken Host Environment. Microorganisms 2020; 8:microorganisms8111693. [PMID: 33143223 PMCID: PMC7693524 DOI: 10.3390/microorganisms8111693] [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: 10/13/2020] [Revised: 10/29/2020] [Accepted: 10/30/2020] [Indexed: 01/10/2023] Open
Abstract
Campylobacter jejuni is an emerging food-borne pathogen that poses a high risk to human health. Knowledge of the strain source can contribute significantly to an understanding of this pathogen, and can lead to improved control measures in the food-processing industry. In this study, slaughterhouse and surface-water isolates of C. jejuni were characterized and compared in terms of their antimicrobial resistance profiles and adhesion to stainless steel and chicken skin. Resistance of C. jejuni biofilm cells to benzalkonium chloride and Satureja montana ethanolic extract was also tested. The data show that the slaughterhouse isolates are more resistant to ciprofloxacin, and adhere better to stainless steel at 42 °C, and at 37 °C in 50% chicken juice. Additionally, biofilm cells of the isolate with the greatest adhesion potential (C. jejuni S6) were harvested and tested for resistance to S. montana ethanolic extract, benzalkonium chloride, and erythromycin; and for efflux-pump activity, as compared to their planktonic cells. The biofilm cells showed increased resistance to both S. montana ethanolic extract and erythromycin, and increased efflux-pump activity. These data indicate adaptation of C. jejuni slaughterhouse isolates to the chicken host, as well as increased biofilm cell resistance due to increased efflux-pump activity.
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Affiliation(s)
- Katarina Šimunović
- Department of Food Science and Technology, Biotechnical Faculty, University of Ljubljana, Jamnikarjeva 101, 1000 Ljubljana, Slovenia; (K.Š.); (S.Z.); (A.K.)
| | - Sandra Zajkoska
- Department of Food Science and Technology, Biotechnical Faculty, University of Ljubljana, Jamnikarjeva 101, 1000 Ljubljana, Slovenia; (K.Š.); (S.Z.); (A.K.)
| | - Katja Bezek
- Faculty of Health Sciences, University of Primorska, Polje 42, 6310 Izola, Slovenia; (K.B.); (D.B.M.)
| | - Anja Klančnik
- Department of Food Science and Technology, Biotechnical Faculty, University of Ljubljana, Jamnikarjeva 101, 1000 Ljubljana, Slovenia; (K.Š.); (S.Z.); (A.K.)
| | - Darja Barlič Maganja
- Faculty of Health Sciences, University of Primorska, Polje 42, 6310 Izola, Slovenia; (K.B.); (D.B.M.)
| | - Sonja Smole Možina
- Department of Food Science and Technology, Biotechnical Faculty, University of Ljubljana, Jamnikarjeva 101, 1000 Ljubljana, Slovenia; (K.Š.); (S.Z.); (A.K.)
- Correspondence: ; Tel.: +386-1-3203751; Fax: +386-1-2565782
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Pascoe B, Schiaffino F, Murray S, Méric G, Bayliss SC, Hitchings MD, Mourkas E, Calland JK, Burga R, Yori PP, Jolley KA, Cooper KK, Parker CT, Olortegui MP, Kosek MN, Sheppard SK. Genomic epidemiology of Campylobacter jejuni associated with asymptomatic pediatric infection in the Peruvian Amazon. PLoS Negl Trop Dis 2020; 14:e0008533. [PMID: 32776937 PMCID: PMC7440661 DOI: 10.1371/journal.pntd.0008533] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2020] [Revised: 08/20/2020] [Accepted: 06/29/2020] [Indexed: 12/20/2022] Open
Abstract
Campylobacter is the leading bacterial cause of gastroenteritis worldwide and its incidence is especially high in low- and middle-income countries (LMIC). Disease epidemiology in LMICs is different compared to high income countries like the USA or in Europe. Children in LMICs commonly have repeated and chronic infections even in the absence of symptoms, which can lead to deficits in early childhood development. In this study, we sequenced and characterized C. jejuni (n = 62) from a longitudinal cohort study of children under the age of 5 with and without diarrheal symptoms, and contextualized them within a global C. jejuni genome collection. Epidemiological differences in disease presentation were reflected in the genomes, specifically by the absence of some of the most common global disease-causing lineages. As in many other countries, poultry-associated strains were likely a major source of human infection but almost half of local disease cases (15 of 31) were attributable to genotypes that are rare outside of Peru. Asymptomatic infection was not limited to a single (or few) human adapted lineages but resulted from phylogenetically divergent strains suggesting an important role for host factors in the cryptic epidemiology of campylobacteriosis in LMICs.
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Affiliation(s)
- Ben Pascoe
- The Milner Centre for Evolution, Department of Biology and Biochemistry, University of Bath, Bath, United Kingdom
- Faculty of Associated Medical Sciences, Chiang Mai University, Chiang Mai, Thailand
| | - Francesca Schiaffino
- Department of International Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, United States of America
- Faculty of Veterinary Medicine, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Susan Murray
- Swansea University Medical School, Swansea University, Singleton Park, Swansea, United Kingdom
- Department of Medical Biochemistry and Microbiology, Science for Life Laboratories, Uppsala University, Uppsala, Sweden
| | - Guillaume Méric
- The Milner Centre for Evolution, Department of Biology and Biochemistry, University of Bath, Bath, United Kingdom
| | - Sion C. Bayliss
- The Milner Centre for Evolution, Department of Biology and Biochemistry, University of Bath, Bath, United Kingdom
| | - Matthew D. Hitchings
- Swansea University Medical School, Swansea University, Singleton Park, Swansea, United Kingdom
| | - Evangelos Mourkas
- The Milner Centre for Evolution, Department of Biology and Biochemistry, University of Bath, Bath, United Kingdom
| | - Jessica K. Calland
- The Milner Centre for Evolution, Department of Biology and Biochemistry, University of Bath, Bath, United Kingdom
| | - Rosa Burga
- Bacteriology Department, Naval Medical Research Unit-6 (NAMRU-6), Iquitos, Peru
| | - Pablo Peñataro Yori
- The Division of Infectious Diseases and International Health, University of Virginia, Charlottesville, Virginia, United States of America
- Asociacion Benefica Prisma, Loreto, Peru
| | - Keith A. Jolley
- Department of Zoology, University of Oxford, South Parks Road, Oxford, United Kingdom
| | - Kerry K. Cooper
- School of Animal and Comparative Biomedical Sciences, University of Arizona, Tucson, Arizona, United States of America
| | - Craig T. Parker
- Produce Safety and Microbiology Research Unit, Agricultural Research Service, US Department of Agriculture, Albany, California, United States of America
| | | | - Margaret N. Kosek
- The Division of Infectious Diseases and International Health, University of Virginia, Charlottesville, Virginia, United States of America
- Asociacion Benefica Prisma, Loreto, Peru
| | - Samuel K. Sheppard
- The Milner Centre for Evolution, Department of Biology and Biochemistry, University of Bath, Bath, United Kingdom
- Faculty of Associated Medical Sciences, Chiang Mai University, Chiang Mai, Thailand
- Department of Zoology, University of Oxford, South Parks Road, Oxford, United Kingdom
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Thépault A, Rose V, Queguiner M, Chemaly M, Rivoal K. Dogs and Cats: Reservoirs for Highly Diverse Campylobacter jejuni and a Potential Source of Human Exposure. Animals (Basel) 2020; 10:E838. [PMID: 32408633 PMCID: PMC7278488 DOI: 10.3390/ani10050838] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2020] [Revised: 04/23/2020] [Accepted: 04/30/2020] [Indexed: 12/11/2022] Open
Abstract
Assessing the carriage of Campylobacter in animal reservoirs is essential to better understand Campylobacter epidemiology. Here, we evaluated the prevalence of thermophilic Campylobacter spp. in dogs and cats, hereafter defined as pets, and characterized Campylobacter jejuni (C. jejuni) isolates to assess their genetic diversity and their potential link with isolates from other animals or human cases. During a 6-month period, 304 feces samples were collected from pets. A significantly higher prevalence of thermophilic Campylobacter spp. was found in dogs compared with cats, as well as in dogs ≤ 1-year-old compared with older dogs. C. jejuni was the predominant species found in pets, and its genomic characterization revealed a high genetic diversity. Genotypes comparison with previously characterized isolates revealed a partial overlap between C. jejuni isolates from pets, chicken, cattle, and clinical cases. This overlap suggests the potential role of livestock and humans in pets' exposure to Campylobacter, or vice versa. The isolation of pets' specific profiles may suggest the existence of other sources of pet contamination or imply that pets may constitute a reservoir for Campylobacter. Because of the proximity between humans and pets, along with their frequent carriage of C. jejuni, human exposure to Campylobacter from pets can be more important than previously thought.
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Affiliation(s)
- Amandine Thépault
- ANSES, Ploufragan-Plouzané-Niort Laboratory, Hygiene and Quality of Poultry and Pig Products Unit, BP53, 22440 Ploufragan, France; (A.T.); (V.R.); (M.Q.); (M.C.)
- French Agency for Food, Environmental and Occupational Health & Safety, Rennes 1 University, rue du Thabor, 35000 Rennes, France
| | - Valérie Rose
- ANSES, Ploufragan-Plouzané-Niort Laboratory, Hygiene and Quality of Poultry and Pig Products Unit, BP53, 22440 Ploufragan, France; (A.T.); (V.R.); (M.Q.); (M.C.)
| | - Marilyne Queguiner
- ANSES, Ploufragan-Plouzané-Niort Laboratory, Hygiene and Quality of Poultry and Pig Products Unit, BP53, 22440 Ploufragan, France; (A.T.); (V.R.); (M.Q.); (M.C.)
| | - Marianne Chemaly
- ANSES, Ploufragan-Plouzané-Niort Laboratory, Hygiene and Quality of Poultry and Pig Products Unit, BP53, 22440 Ploufragan, France; (A.T.); (V.R.); (M.Q.); (M.C.)
| | - Katell Rivoal
- ANSES, Ploufragan-Plouzané-Niort Laboratory, Hygiene and Quality of Poultry and Pig Products Unit, BP53, 22440 Ploufragan, France; (A.T.); (V.R.); (M.Q.); (M.C.)
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Thépault A, Roulleau X, Loiseau P, Cauquil L, Poezevara T, Hyronimus B, Quesne S, Souchaud F, Keita A, Chemaly M, Guyard-Nicodème M. Effect of Litter Treatment on Campylobacter jejuni in Broilers and on Cecal Microbiota. Pathogens 2020; 9:E333. [PMID: 32365731 PMCID: PMC7281257 DOI: 10.3390/pathogens9050333] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Revised: 04/27/2020] [Accepted: 04/27/2020] [Indexed: 01/23/2023] Open
Abstract
Since 2018, when a process hygiene criterion for Campylobacter in broilers at the slaughterhouse was implemented across Europe, efforts to reduce Campylobacter at farm level have increased. Despite numerous studies aiming to reduce Campylobacter colonization in broilers, no efficient control strategy has been identified so far. The present work assessed first the efficacy of a commercial litter treatment to reduce Campylobacter colonization in broilers during two in-vivo trials and second, its impact on cecal microbiota. The treatment does not affect broiler growth and no effect on Campylobacter counts was observed during the in-vivo trials. Nevertheless, cecal microbiota were affected by the treatment. Alpha and beta diversity were significantly different for the control and litter-treated groups on day 35. In addition, several taxa were identified as significantly associated with the different experimental groups. Further work is needed to find a suitable control measure combining different strategies in order to reduce Campylobacter.
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Affiliation(s)
- Amandine Thépault
- ANSES, Ploufragan-Plouzané-Niort Laboratory, Hygiene and Quality of Poultry and Pork Products Unit, BP53, 22440 Ploufragan, France; (A.T.); (T.P.); (S.Q.); (F.S.); (M.C.)
| | - Xavier Roulleau
- Laboratoire COBIOTEX/TERAXION, 44430 Le Loroux Bottereau, France; (X.R.); (B.H.)
| | | | - Laurent Cauquil
- GenPhySE, Université de Toulouse, INRAE, ENVT, F-31326 Castanet Tolosan, France;
| | - Typhaine Poezevara
- ANSES, Ploufragan-Plouzané-Niort Laboratory, Hygiene and Quality of Poultry and Pork Products Unit, BP53, 22440 Ploufragan, France; (A.T.); (T.P.); (S.Q.); (F.S.); (M.C.)
| | - Bertrand Hyronimus
- Laboratoire COBIOTEX/TERAXION, 44430 Le Loroux Bottereau, France; (X.R.); (B.H.)
| | - Ségolène Quesne
- ANSES, Ploufragan-Plouzané-Niort Laboratory, Hygiene and Quality of Poultry and Pork Products Unit, BP53, 22440 Ploufragan, France; (A.T.); (T.P.); (S.Q.); (F.S.); (M.C.)
| | - Florent Souchaud
- ANSES, Ploufragan-Plouzané-Niort Laboratory, Hygiene and Quality of Poultry and Pork Products Unit, BP53, 22440 Ploufragan, France; (A.T.); (T.P.); (S.Q.); (F.S.); (M.C.)
| | - Alassane Keita
- ANSES, Ploufragan-Plouzané-Niort Laboratory, Epidemiology, Health and Welfare Unit, BP53, 22440 Ploufragan, France;
| | - Marianne Chemaly
- ANSES, Ploufragan-Plouzané-Niort Laboratory, Hygiene and Quality of Poultry and Pork Products Unit, BP53, 22440 Ploufragan, France; (A.T.); (T.P.); (S.Q.); (F.S.); (M.C.)
| | - Muriel Guyard-Nicodème
- ANSES, Ploufragan-Plouzané-Niort Laboratory, Hygiene and Quality of Poultry and Pork Products Unit, BP53, 22440 Ploufragan, France; (A.T.); (T.P.); (S.Q.); (F.S.); (M.C.)
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Hlashwayo DF, Sigaúque B, Bila CG. Epidemiology and antimicrobial resistance of Campylobacter spp. in animals in Sub-Saharan Africa: A systematic review. Heliyon 2020; 6:e03537. [PMID: 32181402 PMCID: PMC7063338 DOI: 10.1016/j.heliyon.2020.e03537] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2019] [Revised: 11/20/2019] [Accepted: 03/02/2020] [Indexed: 01/05/2023] Open
Abstract
INTRODUCTION Low sanitary conditions characterize the rural and urban households in Sub-Saharan African region. Those environmental conditions propitiate the transmission of bacterial infections between animals and humans. Campylobacter spp. is a zoonotic bacterium and cause of human gastroenteritis worldwide, whose main symptom is diarrhea. It is normally found in the digestive tract of many farm animals as a commensal but some species cause diseases in animals. It is important to understand the occurrence of these bacteria in animals, as they may also play a role in transmission to humans. The main objective of this review was to describe the prevalence of Campylobacter in animals in Sub-Saharan Africa. We also report findings on antibiotic resistance. METHODS We followed PRISMA guidelines to find studies about occurrence of Campylobacter spp. in animals in all countries from Sub-Saharan Africa. PubMed, Cochrane Library, CINAHL, African Index Medicus, African Journals Online, Google Scholar and Science Direct were searched for studies published between 2000 and 2019. RESULTS We found 70 studies that described occurrence of Campylobacter spp. in animals in 18 out of 53 countries of Sub-Saharan Africa. Campylobacter jejuni and C. coli were the predominant species isolated. The majority of studies were found in Western Africa. Middle Africa had the lowest amount of data. Most records presented data from Nigeria (n = 25), South Africa (n = 14) and Tanzania (n = 11). Cattle and chickens appear to be important hosts and may be playing an important role in transmitting to humans. Most Campylobacter isolates were resistant to erythromycin (44%), ampicillin (39%), tetracycline (33%), nalidixic acid (31%) and ciprofloxacin (30%). CONCLUSION Several studies about Campylobacter spp. in animals have been published in the last 19 years but information on the epidemiology of campylobacteriosis is scarce in most Sub-Saharan African countries. Antibiotic resistance is an increasing concern in many countries. Measures should be taken to prevent infection by this pathogen in the region and to control antibiotic resistance.
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Affiliation(s)
- Delfina Fernandes Hlashwayo
- Department of Biological Sciences, Faculty of Sciences, Eduardo Mondlane University, Maputo, Mozambique
- Faculty of Veterinary Science, Eduardo Mondlane University, Maputo, Mozambique
| | - Betuel Sigaúque
- Centro de Investigação em Saúde de Manhiça, Maputo, Mozambique
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Greige S, Rivoal K, Osman M, Safadi DE, Dabboussi F, Hage RE, Viscogliosi E, Hamze M, Chemaly M. Prevalence and genetic diversity of Campylobacter spp. in the production chain of broiler chickens in Lebanon and its association with the intestinal protozoan Blastocystis sp. Poult Sci 2020; 98:5883-5891. [PMID: 31134283 DOI: 10.3382/ps/pez286] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2018] [Accepted: 05/06/2019] [Indexed: 01/09/2023] Open
Abstract
Campylobacter jejuni is recognized as the most common foodborne pathogen associated with human gastroenteritis worldwide. Broilers are frequently infected by the bacteria and are considered the main source of exposure to humans. However, despite its public health impact, no recent data are currently available in Lebanon about Campylobacter spp. in poultry and human population. Therefore, this study aimed to determine the prevalence and genetic diversity of Campylobacter spp. in 227 ceca and on 227 carcasses of broiler chickens collected in Lebanese slaughterhouses. Overall, the prevalence of Campylobacter was shown to reach 67.0% in ceca and 17.2% on carcasses of Lebanese poultry. The only 2 Campylobacter species identified were C. jejuni and C. coli, with a slightly higher prevalence of C. coli in ceca and of C. jejuni on carcasses. A high level of genetic diversity was reported among the 51 C. jejuni isolates selected, since 25 distinct profiles were identified according to the comparative genomic fingerprinting typing method based on a subset of 40 genes using the 90% similarity threshold. Predominant clusters observed in Lebanese poultry isolates were also frequently found among French human clinical cases, highlighting that broiler chickens represent a potential reservoir for human campylobacteriosis. In addition, a significantly higher prevalence of Campylobacter spp. was found in slaughterhouse workers than in a cohort of hospitalized patients with no contact with poultry, confirming that contaminated broiler chickens in slaughterhouse appeared to be a non-negligible source of Campylobacter spp. transmission. Interestingly, a significant association between Campylobacter spp. and Blastocystis sp. has been observed. This correlation suggested that the presence of Campylobacter spp. would be favored when Blastocystis sp. is present and, similarly, the absence of one would favor the absence of the other. This is the first large-scale investigation focusing on the impact of Campylobacter spp. in broiler chickens in Lebanon and confirmed the need to implement prevention and control measures in the poultry production to reduce the burden of campylobacteriosis in the human population.
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Affiliation(s)
- S Greige
- Université de Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, U1019 - UMR 8204 - CIIL - Centre d'Infection et d'Immunité de Lille, 59000 Lille, France.,Laboratoire Microbiologie Santé Environnement (LMSE), Ecole Doctorale des Sciences et de Technologie, Faculté de Santé Publique, Université Libanaise, Tripoli, Liban.,ANSES, Ploufragan-Plouzané Laboratory, Hygiene and Quality of Poultry and Pig Products Unit, Bretagne-Loire University, 22440 Ploufragan, France
| | - K Rivoal
- ANSES, Ploufragan-Plouzané Laboratory, Hygiene and Quality of Poultry and Pig Products Unit, Bretagne-Loire University, 22440 Ploufragan, France
| | - M Osman
- Laboratoire Microbiologie Santé Environnement (LMSE), Ecole Doctorale des Sciences et de Technologie, Faculté de Santé Publique, Université Libanaise, Tripoli, Liban
| | - D El Safadi
- Laboratoire Microbiologie Santé Environnement (LMSE), Ecole Doctorale des Sciences et de Technologie, Faculté de Santé Publique, Université Libanaise, Tripoli, Liban
| | - F Dabboussi
- Laboratoire Microbiologie Santé Environnement (LMSE), Ecole Doctorale des Sciences et de Technologie, Faculté de Santé Publique, Université Libanaise, Tripoli, Liban
| | - R El Hage
- Institut de Recherche Agronomique Libanais (IRAL), Laboratoire de Microbiologie Alimentaire, Station de Fanar, Jdeideh El-Metn, Lebanon
| | - E Viscogliosi
- Université de Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, U1019 - UMR 8204 - CIIL - Centre d'Infection et d'Immunité de Lille, 59000 Lille, France
| | - M Hamze
- Laboratoire Microbiologie Santé Environnement (LMSE), Ecole Doctorale des Sciences et de Technologie, Faculté de Santé Publique, Université Libanaise, Tripoli, Liban
| | - M Chemaly
- ANSES, Ploufragan-Plouzané Laboratory, Hygiene and Quality of Poultry and Pig Products Unit, Bretagne-Loire University, 22440 Ploufragan, France
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31
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Koutsoumanis K, Allende A, Alvarez-Ordóñez A, Bolton D, Bover-Cid S, Chemaly M, Davies R, De Cesare A, Hilbert F, Lindqvist R, Nauta M, Peixe L, Ru G, Simmons M, Skandamis P, Suffredini E, Jenkins C, Malorny B, Ribeiro Duarte AS, Torpdahl M, da Silva Felício MT, Guerra B, Rossi M, Herman L. Whole genome sequencing and metagenomics for outbreak investigation, source attribution and risk assessment of food-borne microorganisms. EFSA J 2019; 17:e05898. [PMID: 32626197 PMCID: PMC7008917 DOI: 10.2903/j.efsa.2019.5898] [Citation(s) in RCA: 64] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
This Opinion considers the application of whole genome sequencing (WGS) and metagenomics for outbreak investigation, source attribution and risk assessment of food‐borne pathogens. WGS offers the highest level of bacterial strain discrimination for food‐borne outbreak investigation and source‐attribution as well as potential for more precise hazard identification, thereby facilitating more targeted risk assessment and risk management. WGS improves linking of sporadic cases associated with different food products and geographical regions to a point source outbreak and can facilitate epidemiological investigations, allowing also the use of previously sequenced genomes. Source attribution may be favoured by improved identification of transmission pathways, through the integration of spatial‐temporal factors and the detection of multidirectional transmission and pathogen–host interactions. Metagenomics has potential, especially in relation to the detection and characterisation of non‐culturable, difficult‐to‐culture or slow‐growing microorganisms, for tracking of hazard‐related genetic determinants and the dynamic evaluation of the composition and functionality of complex microbial communities. A SWOT analysis is provided on the use of WGS and metagenomics for Salmonella and Shigatoxin‐producing Escherichia coli (STEC) serotyping and the identification of antimicrobial resistance determinants in bacteria. Close agreement between phenotypic and WGS‐based genotyping data has been observed. WGS provides additional information on the nature and localisation of antimicrobial resistance determinants and on their dissemination potential by horizontal gene transfer, as well as on genes relating to virulence and biological fitness. Interoperable data will play a major role in the future use of WGS and metagenomic data. Capacity building based on harmonised, quality controlled operational systems within European laboratories and worldwide is essential for the investigation of cross‐border outbreaks and for the development of international standardised risk assessments of food‐borne microorganisms.
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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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Kempf I, Adam C, Chauvin C. Commentary to the paper entitled "Increased incidence of Campylobacter enteritis and their quinolone resistance between 2010 and 2015: Results of a French national observatory conducted in 21 general hospitals (CHG)". Clin Res Hepatol Gastroenterol 2019; 43:e37-e38. [PMID: 30878339 DOI: 10.1016/j.clinre.2019.02.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/01/2019] [Revised: 02/11/2019] [Accepted: 02/21/2019] [Indexed: 02/04/2023]
Affiliation(s)
- Isabelle Kempf
- ANSES, laboratoire de Ploufragan-Plouzané-Niort, 22440 Ploufragan, France; Université Bretagne Loire, 35065 Rennes cedex, France.
| | - Cécile Adam
- Bureau des intrants et de la santé publique en Élevage, direction générale de l'alimentation, Ministère de l'Agriculture et de l'Alimentation, 251, rue de Vaugirard, 75732 Paris Cedex 15, France
| | - Claire Chauvin
- ANSES, laboratoire de Ploufragan-Plouzané-Niort, 22440 Ploufragan, France; Université Bretagne Loire, 35065 Rennes cedex, France
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Xia J, Pang J, Tang Y, Wu Z, Dai L, Singh K, Xu C, Ruddell B, Kreuder A, Xia L, Ma X, Brooks KS, Ocal MM, Sahin O, Plummer PJ, Griffith RW, Zhang Q. High Prevalence of Fluoroquinolone-Resistant Campylobacter Bacteria in Sheep and Increased Campylobacter Counts in the Bile and Gallbladders of Sheep Medicated with Tetracycline in Feed. Appl Environ Microbiol 2019; 85:e00008-19. [PMID: 30926726 PMCID: PMC6532027 DOI: 10.1128/aem.00008-19] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2019] [Accepted: 03/22/2019] [Indexed: 02/03/2023] Open
Abstract
Campylobacter is a major foodborne pathogen in humans and a significant cause of abortion in sheep. Although ruminants are increasingly recognized as important reservoirs for Campylobacter species, limited information is available about the molecular epidemiology and antimicrobial resistance (AMR) profiles of sheep Campylobacter Here, we describe a two-trial study that examined Campylobacter profiles in sheep and determined whether in-feed tetracycline (TET) influenced the distribution and AMR profiles of Campylobacter Each trial involved 80 commercial sheep naturally infected with Campylobacter: 40 of these sheep were medicated with tetracycline in feed, while the other 40 received feed without antibiotics. Fecal and bile samples were collected for the isolation of Campylobacter The bacterial isolates were analyzed for antimicrobial susceptibility and genotypes. The results revealed that 87.0% and 61.3% of the fecal and bile samples were positive for Campylobacter (Campylobacter jejuni and Campylobacter coli), with no significant differences between the medicated and nonmedicated groups. All but one of the tested Campylobacter isolates were resistant to tetracycline. Although fluoroquinolone (FQ) resistance remained low in C. jejuni (1.7%), 95.0% of the C. coli isolates were resistant to FQ. Genotyping revealed that C. jejuni sequence type 2862 (ST2862) and C. coli ST902 were the predominant genotypes in the sheep. Feed medication with tetracycline did not affect the overall prevalence, species distribution, and AMR profiles of Campylobacter, but it did increase the total Campylobacter counts in bile and gallbladder. These findings identify predominant Campylobacter clones, reveal the high prevalence of FQ-resistant C. coli, and provide new insights into the epidemiology of Campylobacter in sheep.IMPORTANCECampylobacter is a major cause of foodborne illness in humans, and antibiotic-resistant Campylobacter is considered a serious threat to public health in the United States and worldwide. As a foodborne pathogen, Campylobacter commonly exists in the intestinal tract of ruminant animals, such as sheep and cattle. Results from this study reveal the predominant genotypes and high prevalence of tetracycline (TET) and fluoroquinolone (FQ) resistance in sheep Campylobacter The finding on fluoroquinolone resistance in sheep Campylobacter is unexpected, as this class of antibiotics is not used for sheep in the United States, and it may suggest the transmission of fluoroquinolone-resistant Campylobacter from cattle to sheep. Additionally, the results demonstrate that in-feed medication with tetracycline increases Campylobacter counts in gallbladders, suggesting that the antibiotic promotes Campylobacter colonization of the gallbladder. These findings provide new information on Campylobacter epidemiology in sheep, which may be useful for curbing the spread of antibiotic-resistant Campylobacter in animal reservoirs.
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Affiliation(s)
- Jing Xia
- Department of Veterinary Microbiology and Preventive Medicine, College of Veterinary Medicine, Iowa State University, Ames, Iowa, USA
- National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
| | - Jinji Pang
- Department of Veterinary Microbiology and Preventive Medicine, College of Veterinary Medicine, Iowa State University, Ames, Iowa, USA
| | - Yizhi Tang
- Department of Veterinary Microbiology and Preventive Medicine, College of Veterinary Medicine, Iowa State University, Ames, Iowa, USA
| | - Zuowei Wu
- Department of Veterinary Microbiology and Preventive Medicine, College of Veterinary Medicine, Iowa State University, Ames, Iowa, USA
| | - Lei Dai
- Department of Veterinary Microbiology and Preventive Medicine, College of Veterinary Medicine, Iowa State University, Ames, Iowa, USA
| | - Kritika Singh
- Department of Veterinary Microbiology and Preventive Medicine, College of Veterinary Medicine, Iowa State University, Ames, Iowa, USA
| | - Changyun Xu
- Department of Veterinary Microbiology and Preventive Medicine, College of Veterinary Medicine, Iowa State University, Ames, Iowa, USA
| | - Brandon Ruddell
- Department of Veterinary Microbiology and Preventive Medicine, College of Veterinary Medicine, Iowa State University, Ames, Iowa, USA
| | - Amanda Kreuder
- Department of Veterinary Diagnostic and Production Animal Medicine, College of Veterinary Medicine, Iowa State University, Ames, Iowa, USA
| | - Lining Xia
- Department of Veterinary Microbiology and Preventive Medicine, College of Veterinary Medicine, Iowa State University, Ames, Iowa, USA
| | - Xiaoping Ma
- Department of Veterinary Microbiology and Preventive Medicine, College of Veterinary Medicine, Iowa State University, Ames, Iowa, USA
| | - Kelly S Brooks
- Department of Veterinary Diagnostic and Production Animal Medicine, College of Veterinary Medicine, Iowa State University, Ames, Iowa, USA
| | - Melda M Ocal
- Department of Veterinary Microbiology and Preventive Medicine, College of Veterinary Medicine, Iowa State University, Ames, Iowa, USA
| | - Orhan Sahin
- Department of Veterinary Diagnostic and Production Animal Medicine, College of Veterinary Medicine, Iowa State University, Ames, Iowa, USA
| | - Paul J Plummer
- Department of Veterinary Microbiology and Preventive Medicine, College of Veterinary Medicine, Iowa State University, Ames, Iowa, USA
- Department of Veterinary Diagnostic and Production Animal Medicine, College of Veterinary Medicine, Iowa State University, Ames, Iowa, USA
| | - Ronald W Griffith
- Department of Veterinary Microbiology and Preventive Medicine, College of Veterinary Medicine, Iowa State University, Ames, Iowa, USA
| | - Qijing Zhang
- Department of Veterinary Microbiology and Preventive Medicine, College of Veterinary Medicine, Iowa State University, Ames, Iowa, USA
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Berthenet E, Thépault A, Chemaly M, Rivoal K, Ducournau A, Buissonnière A, Bénéjat L, Bessède E, Mégraud F, Sheppard SK, Lehours P. Source attribution of Campylobacter jejuni shows variable importance of chicken and ruminants reservoirs in non-invasive and invasive French clinical isolates. Sci Rep 2019; 9:8098. [PMID: 31147581 PMCID: PMC6542803 DOI: 10.1038/s41598-019-44454-2] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2018] [Accepted: 05/17/2019] [Indexed: 01/07/2023] Open
Abstract
Campylobacter jejuni is the most common cause of bacterial gastroenteritis worldwide. Mainly isolated from stool samples, C. jejuni can also become invasive. C. jejuni belongs to the commensal microbiota of a number of hosts, and infection by this bacterium can sometimes be traced back to exposure to a specific source. Here we genome sequenced 200 clinical isolates (2010–2016) and analyzed them with 701 isolate genomes from human infection, chicken, ruminants and the environment to examine the relative contribution of different reservoirs to non-invasive and invasive infection in France. Host-segregating genetic markers that can discriminate C. jejuni source were used with STRUCTURE software to probabilistically attribute the source of clinical strains. A self-attribution correction step, based upon the accuracy of source apportionment within each potential reservoir, improved attribution accuracy of clinical strains and suggested an important role for ruminant reservoirs in non-invasive infection and a potentially increased contribution of chicken as a source of invasive isolates. Structured sampling of Campylobacter in the clinic and from potential reservoirs provided evidence for variation in the contribution of different infection sources over time and an important role for non-poultry reservoirs in France. This provides a basis for ongoing genomic epidemiology surveillance and targeted interventions.
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Affiliation(s)
- Elvire Berthenet
- French National Reference Center for Campylobacters & Helicobacters, Bordeaux, France
| | - Amandine Thépault
- Unit of Hygiene and Quality of Poultry & Pork Products, Laboratory of Ploufragan-Plouzané-Niort, 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-Niort, French Agency for Food Environmental and Occupational Health & Safety (ANSES), Ploufragan, France
| | - Katell Rivoal
- Unit of Hygiene and Quality of Poultry & Pork Products, Laboratory of Ploufragan-Plouzané-Niort, French Agency for Food Environmental and Occupational Health & Safety (ANSES), Ploufragan, France
| | - Astrid Ducournau
- French National Reference Center for Campylobacters & Helicobacters, Bordeaux, France
| | - Alice Buissonnière
- French National Reference Center for Campylobacters & Helicobacters, Bordeaux, France
| | - Lucie Bénéjat
- French National Reference Center for Campylobacters & Helicobacters, Bordeaux, France
| | - Emilie Bessède
- French National Reference Center for Campylobacters & Helicobacters, Bordeaux, France.,Univ. Bordeaux, INSERM, UMR1053 Bordeaux Research in Translational Oncology, BaRITOn, 33076, Bordeaux, France
| | - Francis Mégraud
- French National Reference Center for Campylobacters & Helicobacters, Bordeaux, France.,Univ. Bordeaux, INSERM, UMR1053 Bordeaux Research in Translational Oncology, BaRITOn, 33076, Bordeaux, France
| | - Samuel K Sheppard
- The Milner Centre for Evolution, Department of Biology and Biochemistry, University of Bath, Claverton Down, Bath, United Kingdom
| | - Philippe Lehours
- French National Reference Center for Campylobacters & Helicobacters, Bordeaux, France. .,Univ. Bordeaux, INSERM, UMR1053 Bordeaux Research in Translational Oncology, BaRITOn, 33076, Bordeaux, France.
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36
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Ricke SC, Feye KM, Chaney WE, Shi Z, Pavlidis H, Yang Y. Developments in Rapid Detection Methods for the Detection of Foodborne Campylobacter in the United States. Front Microbiol 2019; 9:3280. [PMID: 30728816 PMCID: PMC6351486 DOI: 10.3389/fmicb.2018.03280] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2018] [Accepted: 12/17/2018] [Indexed: 12/27/2022] Open
Abstract
The accurate and rapid detection of Campylobacter spp. is critical for optimal surveillance throughout poultry processing in the United States. The further development of highly specific and sensitive assays to detect Campylobacter in poultry matrices has tremendous utility and potential for aiding the reduction of foodborne illness. The introduction and development of molecular methods such as polymerase chain reaction (PCR) have enhanced the diagnostic capabilities of the food industry to identify the presence of foodborne pathogens throughout poultry production. Further innovations in various methodologies, such as immune-based typing and detection as well as high throughput analyses, will provide important epidemiological data such as the identification of unique or region-specific Campylobacter. Comparable to traditional microbiology and enrichment techniques, molecular techniques/methods have the potential to have improved sensitivity and specificity, as well as speed of data acquisition. This review will focus on the development and application of rapid molecular methods for identifying and quantifying Campylobacter in U.S. poultry and the emergence of novel methods that are faster and more precise than traditional microbiological techniques.
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Affiliation(s)
- Steven C. Ricke
- Department of Food Science, Center of Food Safety, University of Arkansas, Fayetteville, AR, United States
| | - Kristina M. Feye
- Department of Food Science, Center of Food Safety, University of Arkansas, Fayetteville, AR, United States
| | | | - Zhaohao Shi
- Department of Food Science, Center of Food Safety, University of Arkansas, Fayetteville, AR, United States
| | | | - Yichao Yang
- Department of Poultry Science, University of Arkansas, Fayetteville, AR, United States
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