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Miller WG, Lopes BS, Ramjee M, Jay-Russell MT, Chapman MH, Williams TG, Wood DF, Gruntar I, Papić B, Forbes KJ. Campylobacter devanensis sp. nov., Campylobacter porcelli sp. nov., and Campylobacter vicugnae sp. nov., three novel Campylobacter lanienae-like species recovered from swine, small ruminants, and camelids. Int J Syst Evol Microbiol 2024; 74:006405. [PMID: 38842428 PMCID: PMC11261738 DOI: 10.1099/ijsem.0.006405] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2024] [Accepted: 05/20/2024] [Indexed: 06/07/2024] Open
Abstract
In a previous study characterizing Campylobacter strains deficient in selenium metabolism, 50 strains were found to be similar to, but distinct from, the selenonegative species Campylobacter lanienae. Initial characterization based on multilocus sequence typing and the phylogeny of a set of 20 core genes determined that these strains form three putative taxa within the selenonegative cluster. A polyphasic study was undertaken here to further clarify their taxonomic position within the genus. The 50 selenonegative strains underwent phylogenetic analyses based on the sequences of the 16S rRNA gene and an expanded set of 330 core genes. Standard phenotypic testing was also performed. All strains were microaerobic and anaerobic, Gram-negative, spiral or curved cells with some displaying coccoid morphologies. Strains were motile, oxidase, catalase, and alkaline phosphatase positive, urease negative, and reduced nitrate. Strains within each clade had unique phenotypic profiles that distinguished them from other members of the genus. Core genome phylogeny clearly placed the 50 strains into three clades. Pairwise average nucleotide identity and digital DNA-DNA hybridization values were all below the recommended cut-offs for species delineation with respect to C. lanienae and other related Campylobacter species. The data presented here clearly show that these strains represent three novel species within the genus, for which the names Campylobacter devanensis sp. nov. (type strain RM3662T=LMG 33097T=NCTC 15074T), Campylobacter porcelli sp. nov. (type strain RM6137T=LMG 33098T=CCUG 77054T=NCTC 15075T) and Campylobacter vicugnae sp. nov. (type strain RM12175T=LMG 33099T=CCUG 77055T=NCTC 15076T) are proposed.
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Affiliation(s)
- William G. Miller
- Produce Safety and Microbiology Research Unit, Agricultural Research Service, U.S. Department of Agriculture, Albany, CA, USA
| | - Bruno S. Lopes
- School of Health and Life Sciences, Teesside University, Middlesbrough, UK
- National Horizons Centre, Teesside University, Darlington, UK
| | - Meenakshi Ramjee
- Wolfson Wohl Cancer Research Centre, Glasgow. The University of Glasgow, Glasgow, UK
| | | | - Mary H. Chapman
- Produce Safety and Microbiology Research Unit, Agricultural Research Service, U.S. Department of Agriculture, Albany, CA, USA
| | - Tina G. Williams
- Bioproducts Research Unit, Agricultural Research Service, U.S. Department of Agriculture, Albany, CA, USA
| | - Delilah F. Wood
- Bioproducts Research Unit, Agricultural Research Service, U.S. Department of Agriculture, Albany, CA, USA
| | - Igor Gruntar
- University of Ljubljana, Veterinary Faculty, Institute of Microbiology and Parasitology, Ljubljana, Slovenia
| | - Bojan Papić
- University of Ljubljana, Veterinary Faculty, Institute of Microbiology and Parasitology, Ljubljana, Slovenia
| | - Ken J. Forbes
- School of Medicine, Medical Sciences and Nutrition, University of Aberdeen, Aberdeen, UK
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2
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Luk CYM, Lee SA, Naidovski N, Liu F, Tay ACY, Wang L, Riordan S, Zhang L. Investigation of Campylobacter concisus gastric epithelial pathogenicity using AGS cells. Front Microbiol 2024; 14:1289549. [PMID: 38274743 PMCID: PMC10808343 DOI: 10.3389/fmicb.2023.1289549] [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: 09/06/2023] [Accepted: 12/19/2023] [Indexed: 01/27/2024] Open
Abstract
Campylobacter concisus is an oral bacterium. Recent studies suggest that C. concisus may be involved in human gastric diseases. The mechanisms, however, by which C. concisus causes human gastric diseases have not been investigated. Here we examined the gastric epithelial pathogenicity of C. concisus using a cell culture model. Six C. concisus strains and the human gastric epithelial cell line AGS cells were used. IL-8 produced by AGS cells after incubation with C. concisus was measured using enzyme-linked immunosorbent assay (ELISA), and AGS cell apoptosis was determined by caspase 3/7 activities. The effects of C. concisus on actin arrangement in AGS cells was determined using fluorescence staining. The effects of C. concisus on global gene expression in AGS cells was determined by transcriptomic analysis and quantitative real-time PCR (qRT-PCR). The role of the upregulated CYP1A1 gene in gastric cancer survival was assessed using the Kaplan-Meier method. C. concisus induced production of IL-8 by AGS cells with strain variation. Significantly increased caspase 3/7 activities were observed in AGS cells incubated with C. concisus strains when compared to AGS cells without bacteria. C. concisus induced actin re-arrangement in AGS cells. C. concisus upregulated 30 genes in AGS cells and the upregulation of CYP1A1 gene was confirmed by qRT-PCR. The Kaplan-Meier analysis showed that upregulation of CYP1A1 gene is associated with worse survival in gastric cancer patients. Our findings suggest that C. concisus may play a role in gastric inflammation and the progression of gastric cancer. Further investigation in clinical studies is warranted.
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Affiliation(s)
- Christopher Yau Man Luk
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, Australia
| | - Seul A. Lee
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, Australia
| | - Nicholas Naidovski
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, Australia
| | - Fang Liu
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, Australia
| | - Alfred Chin Yen Tay
- Helicobacter Research Laboratory, School of Pathology and Laboratory Medicine, Marshall Centre for Infectious Diseases Research and Training, University of Western Australia, Perth, WA, Australia
| | - Liang Wang
- Laboratory Medicine, Guangdong Provincial People’s Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, Guangdong, China
- The Center for Precision Health, School of Medical and Health Sciences, Edith Cowan University, Perth, WA, Australia
- Department of Medical Informatics, School of Medical Informatics and Engineering, Xuzhou Medical University, Xuzhou, Jiangsu, China
| | - Stephen Riordan
- Gastrointestinal and Liver Unit, Prince of Wales Hospital, University of New South Wales, Sydney, NSW, Australia
| | - Li Zhang
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, Australia
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Castillo-Contreras R, Marín M, López-Olvera JR, Ayats T, Fernandez Aguilar X, Lavín S, Mentaberre G, Cerdà-Cuéllar M. Zoonotic Campylobacter spp. and Salmonella spp. carried by wild boars in a metropolitan area: occurrence, antimicrobial susceptibility and public health relevance. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 822:153444. [PMID: 35092769 DOI: 10.1016/j.scitotenv.2022.153444] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Revised: 01/18/2022] [Accepted: 01/22/2022] [Indexed: 06/14/2023]
Abstract
Campylobacter spp. and Salmonella spp. are the most reported zoonotic agents in Europe. They can be transmitted from wildlife to humans, and wild boars (Sus scrofa) can harbour them. In the Metropolitan Area of Barcelona (MAB, NE Spain) wild boars are found in urbanized areas. To assess the potential public health risk of this increasing wild boar population, we collected stool samples from 130 wild boars from the MAB (June 2015 - February 2016), to determine the Campylobacter and Salmonella occurrence and the antimicrobial susceptibility of the isolates. We also investigated the genetic diversity and virulence potential of Campylobacter. Campylobacter prevalence in wild boars was 61%. Forty six percent of wild boars carried Campylobacter lanienae, 16% carried Campylobacter coli, and 1% carried Campylobacter hyointestinalis; 4% carried both C. lanienae and C. coli, and 1% carried both C. lanienae and C. hyointestinalis. This is the first report of C. hyointestinalis in wildlife in Spain. Using pulse-field gel electrophoresis and multilocus sequence typing, we observed a high genetic diversity of Campylobacter and identified new sequence types. Thirty-three percent of C. coli and 14% of C. lanienae isolates showed a high virulence potential. All of the Campylobacter isolates analysed were resistant to at least one antimicrobial agent. Multidrug resistance was only detected in C. coli (67%). Salmonella enterica subsp. enterica was detected in four wild boars (3%) and included a S. Enteritidis serovar (1/4 wild boars) and a multidrug-resistant (ASSuT) monophasic S. Typhimurium serovar (1/4 wild boars) which is associated with human infections and pig meat in Europe. The characteristics of some of the Campylobacter and Salmonella isolates recovered suggest an anthropogenic origin. Wild boars are a reservoir of Campylobacter and have the potential to spread antimicrobial resistant Campylobacter and Salmonella in urbanized areas in the MAB.
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Affiliation(s)
- Raquel Castillo-Contreras
- Wildlife Ecology and Health group (WE&H) and Servei d'Ecopatologia de Fauna Salvatge (SEFaS), Universitat Autònoma de Barcelona, 08193, Bellaterra, Barcelona, Spain
| | - Marta Marín
- IRTA, Centre de Recerca en Sanitat Animal (CReSA, IRTA-UAB), Campus de la Universitat Autònoma de Barcelona, 08193, Bellaterra, Barcelona, Spain
| | - Jorge Ramón López-Olvera
- Wildlife Ecology and Health group (WE&H) and Servei d'Ecopatologia de Fauna Salvatge (SEFaS), Universitat Autònoma de Barcelona, 08193, Bellaterra, Barcelona, Spain
| | - Teresa Ayats
- IRTA, Centre de Recerca en Sanitat Animal (CReSA, IRTA-UAB), Campus de la Universitat Autònoma de Barcelona, 08193, Bellaterra, Barcelona, Spain
| | - Xavier Fernandez Aguilar
- Wildlife Ecology and Health group (WE&H) and Servei d'Ecopatologia de Fauna Salvatge (SEFaS), Universitat Autònoma de Barcelona, 08193, Bellaterra, Barcelona, Spain
| | - Santiago Lavín
- Wildlife Ecology and Health group (WE&H) and Servei d'Ecopatologia de Fauna Salvatge (SEFaS), Universitat Autònoma de Barcelona, 08193, Bellaterra, Barcelona, Spain
| | - Gregorio Mentaberre
- Wildlife Ecology and Health group (WE&H) and Servei d'Ecopatologia de Fauna Salvatge (SEFaS), Universitat Autònoma de Barcelona, 08193, Bellaterra, Barcelona, Spain; Serra Húnter fellow; Wildlife Ecology & Health group (WE&H) and Departament de Ciència Animal, Escola Tècnica Superior d'Enginyeria Agrària (ETSEA), Universitat de Lleida (UdL), Av. Rovira Roure 191, E-25098 Lleida, Spain
| | - Marta Cerdà-Cuéllar
- IRTA, Centre de Recerca en Sanitat Animal (CReSA, IRTA-UAB), Campus de la Universitat Autònoma de Barcelona, 08193, Bellaterra, Barcelona, Spain; OIE Collaborating Centre for the Research and Control of Emerging and Re-Emerging Swine Diseases in Europe (IRTA-CReSA), 08193, Bellaterra, Barcelona, Spain.
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4
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Markers for discriminating Campylobacter concisus genomospecies using MALDI-TOF analysis. CURRENT RESEARCH IN MICROBIAL SCIENCES 2021; 2:100019. [PMID: 34841311 PMCID: PMC8610327 DOI: 10.1016/j.crmicr.2020.100019] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2020] [Revised: 12/06/2020] [Accepted: 12/10/2020] [Indexed: 02/08/2023] Open
Abstract
Strains identified as Campylobacter concisus may belong to one of at least two biochemically indistinguishable, but genomically distinct, groups referred to as "genomospecies" that may differ in their pathogenic and zoonotic potential. Reliable, affordable and available identification methods are required to improve understanding of their significance in human illness. We examined the potential for MALDI-TOF MS, increasingly used in routine laboratories, for this task. Nineteen well-characterised strains were examined using a widely used MALDI-TOF MS commercial system, however only one strain confidently identified using their database. Data mining of the spectra obtained revealed a number of markers that could be used to help discriminate these genomospecies. We conclude that careful application of MALDI-TOF analysis could be useful to determine the role and significance of diverse C. concisus genomospecies in human disease.
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5
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Fornefett J, Busch A, Döpping S, Hotzel H, Rimek D. Bacterial gastroenteritis caused by the putative zoonotic pathogen Campylobacter lanienae: First reported case in Germany. Access Microbiol 2021; 3:000199. [PMID: 34151154 PMCID: PMC8209712 DOI: 10.1099/acmi.0.000199] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2020] [Accepted: 12/22/2020] [Indexed: 11/23/2022] Open
Abstract
Foodborne campylobacteriosis is the most common cause of human bacterial enteritis in Germany. Campylobacter jejuni and Campylobacter coli are the main causative agents for enteric disease, but a number of other species are involved, including rare ones. These rare Campylobacter spp. are emerging zoonotic pathogens in humans due to increasing international movement of supplies, livestock and people. Campylobacter lanienae was first isolated from healthy abattoir workers in Switzerland and at first its pathogenic potential for humans was considered to be low. Recently, the first case of Campylobacter lanienae -associated human enteritis was reported in Canada. Here, we describe a case of mild Campylobacter lanienae -associated enteritis with subsequent asymptomatic excretion in a butcher. The isolate is available at the TLV strain collection (no. TP00333/18). This first reported case of human Campylobacter lanienae campylobacteriosis in Germany demonstrates the agent's likely zoonotic pathogenicity.
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Affiliation(s)
- Juliane Fornefett
- Thuringian State Authority for Consumer Protection, Tennstedter Str. 8/9, 99947 Bad Langensalza, Thuringia, Germany
| | - Anne Busch
- Friedrich-Loeffler-Institut, Institute of Bacterial Infections and Zoonoses, Naumburger Str. 96a, 07743 Jena, Thuringia, Germany
| | - Sandra Döpping
- Thuringian State Authority for Consumer Protection, Tennstedter Str. 8/9, 99947 Bad Langensalza, Thuringia, Germany
| | - Helmut Hotzel
- Friedrich-Loeffler-Institut, Institute of Bacterial Infections and Zoonoses, Naumburger Str. 96a, 07743 Jena, Thuringia, Germany
| | - Dagmar Rimek
- Thuringian State Authority for Consumer Protection, Tennstedter Str. 8/9, 99947 Bad Langensalza, Thuringia, Germany
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6
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Cornelius AJ, Huq M, On SLW, French NP, Vandenberg O, Miller WG, Lastovica AJ, Istivan T, Biggs PJ. Genetic characterisation of Campylobacter concisus: Strategies for improved genomospecies discrimination. Syst Appl Microbiol 2021; 44:126187. [PMID: 33677170 DOI: 10.1016/j.syapm.2021.126187] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2020] [Revised: 02/03/2021] [Accepted: 02/08/2021] [Indexed: 02/08/2023]
Abstract
Although at least two genetically distinct groups, or genomospecies, have been well documented for Campylobacter concisus, no phenotype has yet been identified for their differentiation and thus formal description as separate species. C. concisus has been isolated from a variety of sites in the human body, including saliva and stool samples from both healthy and diarrhoeic individuals. We evaluated the ability of a range of whole genome-based tools to distinguish between the two C. concisus genomospecies (GS) using a collection of 190 C. concisus genomes. Nine genomes from related Campylobacter species were included in some analyses to provide context. Analyses incorporating sequence analysis of multiple ribosomal genes generated similar levels of C. concisus GS discrimination as genome-wide comparisons. The C. concisus genomes formed two groups; GS1 represented by ATCC 33237T and GS2 by CCUG 19995. The two C. concisus GS were separated from the nine genomes of related species. GS1 and GS2 also differed in G+C content with medians of 37.56% and 39.51%, respectively. The groups are consistent with previously established GS and are supported by DNA reassociation results. Average Nucleotide Identity using MUMmer (ANIm) and Genome BLAST Distance Phylogeny generated in silico DNA-DNA hybridisation (isDDH) (against ATCC 33237T and CCUG 19995), plus G+C content provides cluster-independent GS discrimination suitable for routine use. Pan-genomic analysis identified genes specific to GS1 and GS2. WGS data and genomic species identification methods support the existence of two GS within C. concisus. These data provide genome-level metrics for strain identification to genomospecies level.
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Affiliation(s)
- Angela J Cornelius
- Institute of Environmental Science and Research Ltd, P.O. Box 29181, Christchurch 8540, New Zealand.
| | - Mohsina Huq
- School of Science, RMIT University, G.P.O. Box 2476, Bundoora, Victoria 3001, Australia
| | - Stephen L W On
- Lincoln University, P.O. Box 85084, Lincoln 7647, New Zealand
| | - Nigel P French
- Massey University, Private Bag 11 222, Palmerston North 4442, New Zealand
| | - Olivier Vandenberg
- National Reference Centre for Campylobacter, Laboratoire Hospitalier Universitaire de Bruxelles, 322 rue Haute, 1000 Brussels, Belgium; School of Public Health, Campus Erasme - Bâtiment A, Route de Lennik 808 - CP591, Université Libre de Bruxelles, 1070 Bruxelles, Belgium
| | - William G Miller
- Produce Safety and Microbiology Research Unit, Agricultural Research Service, United States Department of Agriculture, 800 Buchanan Street, Albany, CA 94710, USA
| | - Albert J Lastovica
- University of Western Cape, Private Bag X17, Bellville 7535, South Africa
| | - Taghrid Istivan
- School of Science, RMIT University, G.P.O. Box 2476, Bundoora, Victoria 3001, Australia
| | - Patrick J Biggs
- Massey University, Private Bag 11 222, Palmerston North 4442, New Zealand
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Costa D, Lévesque S, Kumar N, Fresia P, Ferrés I, Lawley TD, Iraola G. Pangenome analysis reveals genetic isolation in Campylobacter hyointestinalis subspecies adapted to different mammalian hosts. Sci Rep 2021; 11:3431. [PMID: 33564053 PMCID: PMC7873201 DOI: 10.1038/s41598-021-82993-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2018] [Accepted: 01/24/2021] [Indexed: 11/10/2022] Open
Abstract
Campylobacter hyointestinalis is an emerging pathogen currently divided in two subspecies: C. hyointestinalis subsp. lawsonii which is predominantly recovered from pigs, and C. hyointestinalis subsp. hyointestinalis which can be found in a much wider range of mammalian hosts. Despite C. hyointestinalis being reported as an emerging pathogen, its evolutionary and host-associated diversification patterns are still vastly unexplored. For this reason, we generated whole-genome sequences of 13 C. hyointestinalis subsp. hyointestinalis strains and performed a comprehensive comparative analysis including publicly available C. hyointestinalis subsp. hyointestinalis and C. hyointestinalis subsp. lawsonii genomes, to gain insight into the genomic variation of these differentially-adapted subspecies. Both subspecies are distinct phylogenetic lineages which present an apparent barrier to homologous recombination, suggesting genetic isolation. This is further supported by accessory gene patterns that recapitulate the core genome phylogeny. Additionally, C. hyointestinalis subsp. hyointestinalis presents a bigger and more diverse accessory genome, which probably reflects its capacity to colonize different mammalian hosts unlike C. hyointestinalis subsp. lawsonii that is presumably host-restricted. This greater plasticity in the accessory genome of C. hyointestinalis subsp. hyointestinalis correlates to a higher incidence of genome-wide recombination events, that may be the underlying mechanism driving its diversification. Concordantly, both subspecies present distinct patterns of gene families involved in genome plasticity and DNA repair like CRISPR-associated proteins and restriction-modification systems. Together, our results provide an overview of the genetic mechanisms shaping the genomes of C. hyointestinalis subspecies, contributing to understand the biology of Campylobacter species that are increasingly recognized as emerging pathogens.
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Affiliation(s)
- Daniela Costa
- Microbial Genomics Laboratory, Institut Pasteur Montevideo, 11400, Montevideo, Uruguay.,Sección Genética Evolutiva, Facultad de Ciencias, Universidad de la República, Montevideo, Uruguay
| | - Simon Lévesque
- Laboratoire de Santé Publique du Québec, Quebec City, Canada
| | - Nitin Kumar
- Wellcome Sanger Institute, Hinxton, Cambridgeshire, UK
| | - Pablo Fresia
- Microbial Genomics Laboratory, Institut Pasteur Montevideo, 11400, Montevideo, Uruguay.,Unidad Mixta UMPI, Institut Pasteur de Montevideo + Instituto Nacional de Investigación Agropecuaria INIA, Montevideo, Uruguay
| | - Ignacio Ferrés
- Microbial Genomics Laboratory, Institut Pasteur Montevideo, 11400, Montevideo, Uruguay
| | | | - Gregorio Iraola
- Microbial Genomics Laboratory, Institut Pasteur Montevideo, 11400, Montevideo, Uruguay. .,Wellcome Sanger Institute, Hinxton, Cambridgeshire, UK. .,Center for Integrative Biology, Universidad Mayor, Santiago de Chile, Chile.
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8
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Fan S, Foster D, Miller WG, Osborne J, Kathariou S. Impact of Ceftiofur Administration in Steers on the Prevalence and Antimicrobial Resistance of Campylobacter spp. Microorganisms 2021; 9:microorganisms9020318. [PMID: 33557120 PMCID: PMC7913856 DOI: 10.3390/microorganisms9020318] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Revised: 01/22/2021] [Accepted: 02/01/2021] [Indexed: 01/07/2023] Open
Abstract
Bacterial resistance to ceftiofur raises health concerns due to ceftiofur’s extensive veterinary usage and structural similarity with the human antibiotic ceftriaxone. Ceftiofur crystalline-free acid (CCFA) and ceftiofur hydrochloride (CHCL) are ceftiofur types used therapeutically in cattle, but their potential impacts on Campylobacter prevalence and antimicrobial resistance remain unclear. In this study two groups of steers were each treated with CCFA or CHCL. In vivo active drug concentrations were measured and fecal samples were analyzed for Campylobacter for up to 42 days post-treatment. Following administration, the colonic concentration of ceftiofur initially increased then dropped to pre-treatment levels by day 8. The estimated prevalence of Campylobacter spp. was significantly (p = 0.0009) higher during the first week after CCFA treatment than after CHCL treatment (81.3% vs. 45.2%). Campylobacter jejuni predominated overall, with other Campylobacter spp. mainly identified in the first week after CCFA treatment. No treatment impacts were noted on ceftiofur minimum inhibitory concentration (MIC) for C. jejuni (10–20 μg/mL). More C. jejuni genotypes were detected in CCFA-treated than CHCL-treated steers. These findings suggest that ceftiofur did not significantly impact Campylobacter prevalence or ceftiofur MIC. However, CHCL may be preferable due to the lower likelihood of temporary increases in Campylobacter prevalence.
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Affiliation(s)
- Sicun Fan
- Department of Food, Bioprocessing and Nutrition Sciences, North Carolina State University, Raleigh, NC 27695, USA;
| | - Derek Foster
- Department of Population Health and Pathobiology, College of Veterinary Medicine, North Carolina State University, Raleigh, NC 27695, USA;
| | - William G. Miller
- Produce Safety and Microbiology Research Unit, Agricultural Research Service, U.S. Department of Agriculture, Albany, CA 94710, USA;
| | - Jason Osborne
- Department of Statistics, College of Sciences, North Carolina State University, Raleigh, NC 27695, USA;
| | - Sophia Kathariou
- Department of Food, Bioprocessing and Nutrition Sciences, North Carolina State University, Raleigh, NC 27695, USA;
- Correspondence: ; Tel.: +1-919-513-2075
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9
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Aagaard MEY, Kirk KF, Nielsen H, Nielsen HL. High genetic diversity in Campylobacter concisus isolates from patients with microscopic colitis. Gut Pathog 2021; 13:3. [PMID: 33436056 PMCID: PMC7805038 DOI: 10.1186/s13099-020-00397-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Accepted: 12/22/2020] [Indexed: 02/07/2023] Open
Abstract
The emerging intestinal pathogen Campylobacter concisus has been associated with prolonged diarrhoea and classic inflammatory bowel diseases (IBD) and was recently also linked with microscopic colitis (MC). Previous reports have observed a high genetic diversity within isolates from diarrhoeic and IBD patients and from healthy controls (HC), and division of isolates into two major genomospecies (GS1 and GS2). The aim of this study was to describe genetic diversity in 80 recently cultivated MC biopsy and faecal isolates of C. concisus by multi-locus sequence typing (MLST); and to compare the phylogenetic relatedness to 102 isolates from diarrhoeic and IBD patients and HCs by k-mer-based distance estimation. MLST revealed high genetic diversity in MC isolates with 72 novel sequence types. K-mer divided MC isolates into two distinct clusters (cluster 1 n = 21, cluster 2 n = 49), with a significantly higher prevalence of cluster 2 isolates in biopsies than in faeces, p = 0.009. K-mer divided the 182 isolates into two major phylogenetic clusters: cluster 1 (GS1 isolates) and cluster 2 (GS2 isolates), which further differentiated into three subgroups. Cluster 1 and the three cluster 2 subgroups were each distinctive in mean genome size and GC count. Isolates from all disease phenotypes were present in cluster 1 and cluster 2 subgroup 2 and 3, whereas cluster 2 subgroup 1 only contained isolates restricted to patients with ulcerative colitis (n = 10) and HC (n = 4).
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Affiliation(s)
- Marta Emilie Yde Aagaard
- Department of Infectious Diseases, Aalborg University Hospital, Hobrovej 18-22, 9000, Aalborg, Denmark. .,Department of Clinical Medicine, Aalborg University, Søndre Skovvej 15, 9000, Aalborg, Denmark.
| | - Karina Frahm Kirk
- Department of Infectious Diseases, Aalborg University Hospital, Hobrovej 18-22, 9000, Aalborg, Denmark
| | - Henrik Nielsen
- Department of Infectious Diseases, Aalborg University Hospital, Hobrovej 18-22, 9000, Aalborg, Denmark.,Department of Clinical Medicine, Aalborg University, Søndre Skovvej 15, 9000, Aalborg, Denmark
| | - Hans Linde Nielsen
- Department of Clinical Medicine, Aalborg University, Søndre Skovvej 15, 9000, Aalborg, Denmark.,Department of Clinical Microbiology, Aalborg University Hospital, Hobrovej 18-22, 9000, Aalborg, Denmark
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10
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Liu F, Chen S, Luu LDW, Lee SA, Tay ACY, Wu R, Riordan SM, Lan R, Liu L, Zhang L. Analysis of complete Campylobacter concisus genomes identifies genomospecies features, secretion systems and novel plasmids and their association with severe ulcerative colitis. Microb Genom 2020; 6:mgen000457. [PMID: 33111662 PMCID: PMC7725323 DOI: 10.1099/mgen.0.000457] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Accepted: 10/01/2020] [Indexed: 12/12/2022] Open
Abstract
Campylobacter concisus is an emerging enteric pathogen that is associated with several gastrointestinal diseases, such as inflammatory bowel disease (IBD), which includes Crohn's disease (CD) and ulcerative colitis (UC). Currently, only three complete C. concisus genomes are available and more complete C. concisus genomes are needed in order to better understand the genomic features and pathogenicity of this emerging pathogen. DNA extracted from 22 C. concisus strains were subjected to Oxford Nanopore genome sequencing. Complete genome assembly was performed using Nanopore genome data in combination with previously reported short-read Illumina data. Genome features of complete C. concisus genomes were analysed using bioinformatic tools. The enteric disease associations of C. concisus plasmids were examined using 239 C. concisus strains and confirmed using PCRs. Proteomic analysis was used to examine T6SS secreted proteins. We successfully obtained 13 complete C. concisus genomes in this study. Analysis of 16 complete C. concisus genomes (3 from public databases) identified multiple novel plasmids. pSma1 plasmid was found to be associated with severe UC. Sec-SRP, Tat and T6SS were found to be the main secretion systems in C. concisus and proteomic data showed a functional T6SS despite the lack of ClpV. T4SS was found in 25% of complete C. concisus genomes. This study also found that GS2 strains had larger genomes and higher GC content than GS1 strains and more often had plasmids. In conclusion, this study provides fundamental genomic data for understanding C. concisus plasmids, genomospecies features, evolution, secretion systems and pathogenicity.
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Affiliation(s)
- Fang Liu
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, Australia
| | - Siying Chen
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, Australia
| | - Laurence Don Wai Luu
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, Australia
| | - Seul A. Lee
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, Australia
| | - Alfred Chin Yen Tay
- Helicobacter Research Laboratory, Marshall Centre for Infectious Diseases Research and Training, School of Pathology and Laboratory Medicine, University of Western Australia, Perth, Australia
| | - Ruochen Wu
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, Australia
| | - Stephen M. Riordan
- Gastrointestinal and Liver Unit, Prince of Wales Hospital, University of New South Wales, Sydney, Australia
| | - Ruiting Lan
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, Australia
| | - Lu Liu
- School of Medical Sciences, University of New South Wales, Sydney, NSW, Australia
| | - Li Zhang
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, Australia
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11
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A One Health approach to prevention, treatment, and control of campylobacteriosis. Curr Opin Infect Dis 2020; 32:453-460. [PMID: 31305492 DOI: 10.1097/qco.0000000000000570] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
PURPOSE OF REVIEW To review recent findings regarding the control and treatment of campylobacteriosis. RECENT FINDINGS The application of improved diagnostics has led to an upward shift in the attributable burden of Campylobacter infections, in both the United States and Europe as well as in resource-poor settings. Increased focus has brought a fundamental feature of campylobacteriosis -- the ability to cause relapsing disease back into focus, and expanding data on antimicrobial resistance has lead from a switch in first-line therapy for severe diarrhea from quinolones to azithromycin in most contexts, even as evidence of expanding macrolide resistance emerges. SUMMARY Campylobacter spp. infection is a common infection worldwide. Antibiotic-resistant Campylobacter spp. has become an emerging threat with the increase in industrial poultry production, as well as the broad use of antibiotics in both animals and humans.
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12
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Terefe Y, Deblais L, Ghanem M, Helmy YA, Mummed B, Chen D, Singh N, Ahyong V, Kalantar K, Yimer G, Yousuf Hassen J, Mohammed A, McKune SL, Manary MJ, Ordiz MI, Gebreyes W, Havelaar AH, Rajashekara G. Co-occurrence of Campylobacter Species in Children From Eastern Ethiopia, and Their Association With Environmental Enteric Dysfunction, Diarrhea, and Host Microbiome. Front Public Health 2020; 8:99. [PMID: 32351922 PMCID: PMC7174729 DOI: 10.3389/fpubh.2020.00099] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2019] [Accepted: 03/12/2020] [Indexed: 12/20/2022] Open
Abstract
High Campylobacter prevalence during early childhood has been associated with stunting and environmental enteric dysfunction (EED), especially in low resource settings. This study assessed the prevalence, diversity, abundance, and co-occurrence of Campylobacter spp. in stools from children in a rural area of eastern Ethiopia and their association with microbiome, diarrhea, and EED in children. Stool samples (n = 100) were collected from randomly selected children (age range: 360-498 days) in five kebeles in Haramaya District, Ethiopia. Diarrhea, compromised gut permeability, and gut inflammation were observed in 48, 45, and 57% of children, respectively. Campylobacter prevalence and species diversity were assessed using PCR and meta-total RNA sequencing (MeTRS). The prevalence of Campylobacter spp. in the children's stools was 50% (41-60%) by PCR and 88% (80-93.6%) by MeTRS (P < 0.01). Further, seven Campylobacter species (Campylobacter jejuni, Campylobacter upsaliensis, Campylobacter hyointestinalis, Campylobacter coli, Campylobacter sp. RM6137, uncultured Campylobacter sp., and Campylobacter sp. RM12175) were detected by MeTRS in at least 40% of children stools in high abundance (>1.76-log read per million per positive stool sample). Four clusters of Campylobacter species (5-12 species per cluster) co-occurred in the stool samples, suggesting that Campylobacter colonization of children may have occurred through multiple reservoirs or from a reservoir in which several Campylobacter species may co-inhabit. No associations between Campylobacter spp., EED, and diarrhea were detected in this cross-sectional study; however, characteristic microbiome profiles were identified based on the prevalence of Campylobacter spp., EED severity, and diarrhea. Forty-seven bacterial species were correlated with Campylobacter, and 13 of them also correlated with gut permeability, gut inflammation and/or EED severity. Forty-nine species not correlated with Campylobacter were correlated with gut permeability, gut inflammation, EED severity and/or diarrhea. This study demonstrated that (1) in addition to C. jejuni and C. coli, multiple non-thermophilic Campylobacter spp. (i.e., Campylobacter hyointestinalis, Campylobacter fetus, and Campylobacter concisus) were frequently detected in the children's stools and (2) the Campylobacter, gut permeability, gut inflammation, EED severity, and diarrhea were associated with characteristic microbiome composition. Additional spatial and longitudinal studies are needed to identify environmental reservoirs and sources of infection of children with disparate Campylobacter species and to better define their associations with EED in low-income countries.
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Affiliation(s)
- Yitagele Terefe
- The Ohio State University, Columbus, OH, United States
- Veterinary Medicine, Haramaya University, Dire Dawa, Ethiopia
- Global One Health Initiative, The Ohio State University, Addis Ababa, Ethiopia
| | - Loïc Deblais
- The Ohio State University, Columbus, OH, United States
- Global One Health Initiative, The Ohio State University, Addis Ababa, Ethiopia
| | - Mostafa Ghanem
- The Ohio State University, Columbus, OH, United States
- Global One Health Initiative, The Ohio State University, Addis Ababa, Ethiopia
| | | | - Bahar Mummed
- Veterinary Medicine, Haramaya University, Dire Dawa, Ethiopia
| | - Dehao Chen
- Department of Environmental and Global Health, University of Florida, Gainesville, FL, United States
| | - Nitya Singh
- Emerging Pathogens Institute, University of Florida, Gainesville, FL, United States
| | - Vida Ahyong
- Chan Zuckerberg Biohub, San Francisco, CA, United States
| | | | - Getnet Yimer
- The Ohio State University, Columbus, OH, United States
- Global One Health Initiative, The Ohio State University, Addis Ababa, Ethiopia
| | - Jemal Yousuf Hassen
- Department of Rural Development and Agricultural Extension, Haramaya University, Dire Dawa, Ethiopia
| | | | - Sarah L. McKune
- Department of Environmental and Global Health, University of Florida, Gainesville, FL, United States
| | - Mark J. Manary
- Department of Pediatrics, Washington University, St. Louis, MI, United States
| | - Maria Isabel Ordiz
- Department of Pediatrics, Washington University, St. Louis, MI, United States
| | - Wondwossen Gebreyes
- The Ohio State University, Columbus, OH, United States
- Global One Health Initiative, The Ohio State University, Addis Ababa, Ethiopia
| | - Arie H. Havelaar
- Emerging Pathogens Institute, University of Florida, Gainesville, FL, United States
| | - Gireesh Rajashekara
- The Ohio State University, Columbus, OH, United States
- Global One Health Initiative, The Ohio State University, Addis Ababa, Ethiopia
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13
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Abstract
Campylobacter is among the four main causes of gastroenteritis worldwide and has increased in both developed and developing countries over the last 10 years. The vast majority of reported Campylobacter infections are caused by Campylobacter jejuni and, to a lesser extent, C. coli; however, the increasing recognition of other emerging Campylobacter pathogens is urgently demanding a better understanding of how these underestimated species cause disease, transmit, and evolve. In parallel to the enhanced clinical awareness of campylobacteriosis due to improved diagnostic protocols, the application of high-throughput sequencing has increased the number of whole-genome sequences available to dozens of strains of many emerging campylobacters. This has allowed for comprehensive comparative pathogenomic analyses for several species, such as C. fetus and C. concisus These studies have started to reveal the evolutionary forces shaping their genomes and have brought to light many genomic features related to pathogenicity in these neglected species, promoting the development of new tools and approaches relevant for clinical microbiology. Despite the need for additional characterization of genomic diversity in emerging campylobacters, the increasing body of literature describing pathogenomic studies on these species deserves to be discussed from an integrative perspective. This review compiles the current knowledge and highlights future work toward deepening our understanding about genome dynamics and the mechanisms governing the evolution of pathogenicity in emerging Campylobacter species, which is urgently needed to develop strategies to prevent or control the spread of these pathogens.
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Affiliation(s)
- Daniela Costa
- Microbial Genomics Laboratory, Institut Pasteur de Montevideo, Montevideo, Uruguay
- Sección Genética Evolutiva, Facultad de Ciencias, Universidad de la República, Montevideo, Uruguay
| | - Gregorio Iraola
- Microbial Genomics Laboratory, Institut Pasteur de Montevideo, Montevideo, Uruguay
- Center for Integrative Biology, Universidad Mayor, Santiago de Chile, Chile
- Wellcome Sanger Institute, Hinxton, United Kingdom
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14
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Nielsen HL, Dalager-Pedersen M, Nielsen H. Risk of inflammatory bowel disease after Campylobacter jejuni and Campylobacter concisus infection: a population-based cohort study. Scand J Gastroenterol 2019; 54:265-272. [PMID: 30905214 DOI: 10.1080/00365521.2019.1578406] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Objectives: In this population-based cohort study, we aimed to examine the risk of IBD following a positive stool culture with Campylobacter jejuni or Campylobacter concisus, as well as following culture-negative stool testing. Materials and methods: Patients with a first-time positive stool culture with C. jejuni or C. concisus, as well as negative stool testing, from 2009 through 2013 in North Denmark Region, Denmark, were identified. Patients diagnosed with IBD during follow-up (to 1 March 2018) were identified using national registries. For each case, we selected ten population comparisons matched by age, gender, and calendar-time. Results: We identified 1693 patients with C. jejuni, 910 C. concisus-positive patients, and 11,383 patients with culture-negative stools. During the first year of follow-up C. jejuni-positive patients had higher risk of IBD (HR 2.2, 95% CI 1.3-3.7) compared to population comparisons, but not after exclusion of the first year (HR 1.1, 95% CI 0.5-2.3). Campylobacter concisus-positive patients and culture-negative patients had similar risk of IBD (HR 12.9, 95% CI 7.2-22.9 and HR 8.7, 95% CI 7.5-10.2), during the first year, which decreased to (HR 3.3, 95% CI 1.3-8.5 and HR 3.2, 95% CI 2.6-4.0) after exclusion of the first year. Conclusions: This study does not support exposure of C. jejuni or C. concisus infection as a causal trigger in subsequent development of IBD, since culture-negative patients had similar risk for IBD on long term follow-up. Additional studies including C. concisus exposures for an evaluation of the specific risk of IBD are needed.
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Affiliation(s)
- Hans Linde Nielsen
- a Department of Clinical Microbiology , Aalborg University Hospital , Aalborg , Denmark.,b Department of Clinical Medicine , Aalborg University , Aalborg , Denmark
| | - Michael Dalager-Pedersen
- b Department of Clinical Medicine , Aalborg University , Aalborg , Denmark.,c Department of Infectious Diseases , Aalborg University Hospital , Aalborg , Denmark
| | - Henrik Nielsen
- b Department of Clinical Medicine , Aalborg University , Aalborg , Denmark.,c Department of Infectious Diseases , Aalborg University Hospital , Aalborg , Denmark
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15
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Benoit SL, Maier RJ. Site-directed mutagenesis of Campylobacter concisus respiratory genes provides insight into the pathogen's growth requirements. Sci Rep 2018; 8:14203. [PMID: 30242194 PMCID: PMC6155014 DOI: 10.1038/s41598-018-32509-9] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2018] [Accepted: 09/10/2018] [Indexed: 12/30/2022] Open
Abstract
Campylobacter concisus is an emerging human pathogen found throughout the entire human oral-gastrointestinal tract. The ability of C. concisus to colonize diverse niches of the human body indicates the pathogen is metabolically versatile. C. concisus is able to grow under both anaerobic conditions and microaerophilic conditions. Hydrogen (H2) has been shown to enhance growth and may even be required. Analysis of several C. concisus genome sequences reveals the presence of two sets of genes encoding for distinct hydrogenases: a H2-uptake-type ("Hyd") complex and a H2-evolving hydrogenase ("Hyf"). Whole cells hydrogenase assays indicate that the former (H2-uptake) activity is predominant in C. concisus, with activity among the highest we have found for pathogenic bacteria. Attempts to generate site-directed chromosomal mutants were partially successful, as we could disrupt hyfB, but not hydB, suggesting that H2-uptake, but not H2-evolving activity, is an essential respiratory pathway in C. concisus. Furthermore, the tetrathionate reductase ttrA gene was inactivated in various C. concisus genomospecies. Addition of tetrathionate to the medium resulted in a ten-fold increase in cell yield for the WT, while it had no effect on the ttrA mutant growth. To our knowledge, this is the first report of mutants in C. concisus.
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Affiliation(s)
- Stéphane L Benoit
- Department of Microbiology, University of Georgia, Athens, 30602, Georgia.
- Center for Metalloenzyme Studies, University of Georgia, Athens, 30602, Georgia.
| | - Robert J Maier
- Department of Microbiology, University of Georgia, Athens, 30602, Georgia
- Center for Metalloenzyme Studies, University of Georgia, Athens, 30602, Georgia
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16
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Draft Genome Sequences of Nine Campylobacter hyointestinalis subsp. lawsonii Strains. Microbiol Resour Announc 2018; 7:MRA01016-18. [PMID: 30533618 PMCID: PMC6256594 DOI: 10.1128/mra.01016-18] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2018] [Accepted: 08/05/2018] [Indexed: 01/07/2023] Open
Abstract
With increasing reports of Campylobacter hyointestinalis species associated with human diseases, more genome sequences are required to understand the virulence mechanisms of this emerging pathogen. Here, we describe the genome sequences of nine C. hyointestinalis subsp. lawsonii strains. With increasing reports of Campylobacter hyointestinalis species associated with human diseases, more genome sequences are required to understand the virulence mechanisms of this emerging pathogen. Here, we describe the genome sequences of nine C. hyointestinalis subsp. lawsonii strains.
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17
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Liu F, Ma R, Wang Y, Zhang L. The Clinical Importance of Campylobacter concisus and Other Human Hosted Campylobacter Species. Front Cell Infect Microbiol 2018; 8:243. [PMID: 30087857 PMCID: PMC6066527 DOI: 10.3389/fcimb.2018.00243] [Citation(s) in RCA: 68] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2018] [Accepted: 06/25/2018] [Indexed: 12/14/2022] Open
Abstract
Historically, Campylobacteriosis has been considered to be zoonotic; the Campylobacter species that cause human acute intestinal disease such as Campylobacter jejuni and Campylobacter coli originate from animals. Over the past decade, studies on human hosted Campylobacter species strongly suggest that Campylobacter concisus plays a role in the development of inflammatory bowel disease (IBD). C. concisus primarily colonizes the human oral cavity and some strains can be translocated to the intestinal tract. Genome analysis of C. concisus strains isolated from saliva samples has identified a bacterial marker that is associated with active Crohn's disease (one major form of IBD). In addition to C. concisus, humans are also colonized by a number of other Campylobacter species, most of which are in the oral cavity. Here we review the most recent advancements on C. concisus and other human hosted Campylobacter species including their clinical relevance, transmission, virulence factors, disease associated genes, interactions with the human immune system and pathogenic mechanisms.
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Affiliation(s)
- Fang Liu
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, Australia
| | - Rena Ma
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, Australia
| | - Yiming Wang
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, Australia
| | - Li Zhang
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, Australia
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18
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Ma R, Liu F, Yap SF, Lee H, Leong RW, Riordan SM, Grimm MC, Zhang L. The Growth and Protein Expression of Inflammatory Bowel Disease-Associated Campylobacter concisus Is Affected by the Derivatives of the Food Additive Fumaric Acid. Front Microbiol 2018; 9:896. [PMID: 29867807 PMCID: PMC5966568 DOI: 10.3389/fmicb.2018.00896] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2017] [Accepted: 04/18/2018] [Indexed: 12/22/2022] Open
Abstract
Inflammatory bowel diseases (IBD) are chronic inflammatory conditions of the gastrointestinal tract with multifactorial etiology. Both dietary factors and the microbe Campylobacter concisus have been found to be associated with the condition. The current study examined the effects of sodium fumarate, a neutralized product of the food additives fumaric acid and monosodium fumarate when in the intestinal environment, on the growth of C. concisus to determine the effects of these food additives on IBD-associated bacterial species. Through culture methods and quantification, it was found that neutralized fumaric acid, neutralized monosodium fumarate, and sodium fumarate increased the growth of C. concisus, with the greatest increase in growth at a concentration of 0.4%. Further examination of 50 C. concisus strains on media with added sodium fumarate showed that greatest growth was also achieved at a concentration of 0.4%. At a concentration of 2% sodium fumarate, all strains examined displayed less growth in comparison with those cultured on media without sodium fumarate. Using mass spectrometry, multiple C. concisus proteins showed significant differential expression when cultured on media with and without 0.4% sodium fumarate. The findings presented suggest that patients with IBD should consider avoiding excessive consumption of foods with fumaric acid or its sodium salts, and that the addition of 0.4% sodium fumarate alone to media may assist in the isolation of C. concisus from clinical samples.
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Affiliation(s)
- Rena Ma
- The School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, Australia
| | - Fang Liu
- The School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, Australia
| | - Soe F Yap
- The School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, Australia
| | - Hoyul Lee
- The School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, Australia
| | - Rupert W Leong
- Concord Hospital, University of New South Wales, Sydney, NSW, Australia
| | - Stephen M Riordan
- Gastrointestinal and Liver Unit, The Prince of Wales Hospital, Sydney, NSW, Australia
| | - Michael C Grimm
- St George and Sutherland Clinical School, University of New South Wales, Sydney, NSW, Australia
| | - Li Zhang
- The School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, Australia
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19
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Miller WG, Yee E, Chapman MH, Bono JL. Comparative Genomics of All Three Campylobacter sputorum Biovars and a Novel Cattle-Associated C. sputorum Clade. Genome Biol Evol 2018. [PMID: 28633450 PMCID: PMC5499875 DOI: 10.1093/gbe/evx112] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
Campylobacter sputorum is a nonthermotolerant campylobacter that is primarily isolated from food animals such as cattle and sheep. C. sputorum is also infrequently associated with human illness. Based on catalase and urease activity, three biovars are currently recognized within C. sputorum: bv. sputorum (catalase negative, urease negative), bv. fecalis (catalase positive, urease negative), and bv. paraureolyticus (catalase negative, urease positive). A multi-locus sequence typing (MLST) method was recently constructed for C. sputorum. MLST typing of several cattle-associated C. sputorum isolates suggested that they are members of a divergent C. sputorum clade. Although catalase positive, and thus technically bv. fecalis, the taxonomic position of these strains could not be determined solely by MLST. To further characterize C. sputorum, the genomes of four strains, representing all three biovars and the divergent clade, were sequenced to completion. Here we present a comparative genomic analysis of the four C. sputorum genomes. This analysis indicates that the three biovars and the cattle-associated strains are highly related at the genome level with similarities in gene content. Furthermore, the four genomes are strongly syntenic with one or two minor inversions. However, substantial differences in gene content were observed among the three biovars. Finally, although the strain representing the cattle-associated isolates was shown to be C. sputorum, it is possible that this strain is a member of a novel C. sputorum subspecies; thus, these cattle-associated strains may form a second taxon within C. sputorum.
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Affiliation(s)
- William G Miller
- Produce Safety and Microbiology Research Unit, Agricultural Research Service, U.S. Department of Agriculture, Albany, California
| | - Emma Yee
- Produce Safety and Microbiology Research Unit, Agricultural Research Service, U.S. Department of Agriculture, Albany, California
| | - Mary H Chapman
- Produce Safety and Microbiology Research Unit, Agricultural Research Service, U.S. Department of Agriculture, Albany, California
| | - James L Bono
- Meat Safety and Quality Research Unit, Agricultural Research Service, U.S. Department of Agriculture, Clay Center, Nebraska
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20
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Liu F, Ma R, Tay CYA, Octavia S, Lan R, Chung HKL, Riordan SM, Grimm MC, Leong RW, Tanaka MM, Connor S, Zhang L. Genomic analysis of oral Campylobacter concisus strains identified a potential bacterial molecular marker associated with active Crohn's disease. Emerg Microbes Infect 2018; 7:64. [PMID: 29636463 PMCID: PMC5893538 DOI: 10.1038/s41426-018-0065-6] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2018] [Revised: 03/14/2018] [Accepted: 03/20/2018] [Indexed: 02/08/2023]
Abstract
Campylobacter concisus is an oral bacterium that is associated with inflammatory bowel disease (IBD) including Crohn’s disease (CD) and ulcerative colitis (UC). C. concisus consists of two genomospecies (GS) and diverse strains. This study aimed to identify molecular markers to differentiate commensal and IBD-associated C. concisus strains. The genomes of 63 oral C. concisus strains isolated from patients with IBD and healthy controls were examined, of which 38 genomes were sequenced in this study. We identified a novel secreted enterotoxin B homologue, Csep1. The csep1 gene was found in 56% of GS2 C. concisus strains, presented in the plasmid pICON or the chromosome. A six-nucleotide insertion at the position 654–659 bp in csep1 (csep1-6bpi) was found. The presence of csep1-6bpi in oral C. concisus strains isolated from patients with active CD (47%, 7/15) was significantly higher than that in strains from healthy controls (0/29, P = 0.0002), and the prevalence of csep1-6bpi positive C. concisus strains was significantly higher in patients with active CD (67%, 4/6) as compared to healthy controls (0/23, P = 0.0006). Proteomics analysis detected the Csep1 protein. A csep1 gene hot spot in the chromosome of different C. concisus strains was found. The pICON plasmid was only found in GS2 strains isolated from the two relapsed CD patients with small bowel complications. This study reports a C. concisus molecular marker (csep1-6bpi) that is associated with active CD.
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Affiliation(s)
- Fang Liu
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, Australia
| | - Rena Ma
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, Australia
| | - Chin Yen Alfred Tay
- Helicobacter Research Laboratory, Marshall Centre for Infectious Diseases Research and Training, School of Pathology and Laboratory Medicine, University of Western Australia, Perth, WA, Australia
| | - Sophie Octavia
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, Australia
| | - Ruiting Lan
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, Australia
| | - Heung Kit Leslie Chung
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, Australia
| | - Stephen M Riordan
- Gastrointestinal and Liver Unit, Prince of Wales Hospital, University of New South Wales, Sydney, NSW, Australia
| | - Michael C Grimm
- St George and Sutherland Clinical School, University of New South Wales, Sydney, NSW, Australia
| | - Rupert W Leong
- Concord Hospital, University of New South Wales, Sydney, NSW, Australia
| | - Mark M Tanaka
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, Australia
| | - Susan Connor
- Liverpool Hospital, University of New South Wales, Sydney, NSW, Australia
| | - Li Zhang
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, Australia.
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21
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Updating the genomic taxonomy and epidemiology of Campylobacter hyointestinalis. Sci Rep 2018; 8:2393. [PMID: 29403020 PMCID: PMC5799301 DOI: 10.1038/s41598-018-20889-x] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2017] [Accepted: 01/25/2018] [Indexed: 12/24/2022] Open
Abstract
Campylobacter hyointestinalis is a member of an emerging group of zoonotic Campylobacter spp. that are increasingly identified in both gastric and non-gastric disease in humans. Here, we discovered C. hyointestinalis in three separate classes of New Zealand ruminant livestock; cattle, sheep and deer. To investigate the relevance of these findings we performed a systematic literature review on global C. hyointestinalis epidemiology and used comparative genomics to better understand and classify members of the species. We found that C. hyointestinalis subspecies hyointestinalis has an open pangenome, with accessory gene contents involved in many essential processes such as metabolism, virulence and defence. We observed that horizontal gene transfer is likely to have played an overwhelming role in species diversification, favouring a public-goods-like mechanism of gene ‘acquisition and resampling’ over a tree-of-life-like vertical inheritance model of evolution. As a result, simplistic gene-based inferences of taxonomy by similarity are likely to be misleading. Such genomic plasticity will also mean that local evolutionary histories likely influence key species characteristics, such as host-association and virulence. This may help explain geographical differences in reported C. hyointestinalis epidemiology and limits what characteristics may be generalised, requiring further genomic studies of C. hyointestinalis in areas where it causes disease.
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Molecular epidemiology and comparative genomics of Campylobacter concisus strains from saliva, faeces and gut mucosal biopsies in inflammatory bowel disease. Sci Rep 2018; 8:1902. [PMID: 29382867 PMCID: PMC5790007 DOI: 10.1038/s41598-018-20135-4] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2017] [Accepted: 01/12/2018] [Indexed: 12/17/2022] Open
Abstract
Campylobacter concisus is an emerging pathogen associated with inflammatory bowel disease (IBD), yet little is known about the genetic diversity of C. concisus in relation to host niches and disease. We isolated 104 C. concisus isolates from saliva, mucosal biopsies and faecal samples from 41 individuals (26 IBD, 3 Gastroenteritis (GE), 12 Healthy controls (HC)). Whole genomes were sequenced and the dataset pan-genome examined, and genomic information was used for typing using multi-locus-sequence typing (MLST). C. concisus isolates clustered into two main groups/genomospecies (GS) with 71 distinct sequence types (STs) represented. Sampling site (p < 0.001), rather than disease phenotype (p = 1.00) was associated with particular GS. We identified 97 candidate genes associated with increase or decrease in prevalence during the anatomical descent from the oral cavity to mucosal biopsies to faeces. Genes related to cell wall/membrane biogenesis were more common in oral isolates, whereas genes involved in cell transport, metabolism and secretory pathways were more prevalent in enteric isolates. Furthermore, there was no correlation between individual genetic diversity and clinical phenotype. This study confirms the genetic heterogeneity of C. concisus and provides evidence that genomic variation is related to the source of isolation, but not clinical phenotype.
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Miller WG, Yee E, Lopes BS, Chapman MH, Huynh S, Bono JL, Parker CT, Strachan NJC, Forbes KJ. Comparative Genomic Analysis Identifies a Campylobacter Clade Deficient in Selenium Metabolism. Genome Biol Evol 2017; 9:1843-1858. [PMID: 28854596 PMCID: PMC5570042 DOI: 10.1093/gbe/evx093] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/09/2017] [Indexed: 12/19/2022] Open
Abstract
The nonthermotolerant Campylobacter species C. fetus, C. hyointestinalis, C. iguaniorum, and C. lanienae form a distinct phylogenetic cluster within the genus. These species are primarily isolated from foraging (swine) or grazing (e.g., cattle, sheep) animals and cause sporadic and infrequent human illness. Previous typing studies identified three putative novel C. lanienae-related taxa, based on either MLST or atpA sequence data. To further characterize these putative novel taxa and the C. fetus group as a whole, 76 genomes were sequenced, either to completion or to draft level. These genomes represent 26 C. lanienae strains and 50 strains of the three novel taxa. C. fetus, C. hyointestinalis and C. iguaniorum genomes were previously sequenced to completion; therefore, a comparative genomic analysis across the entire C. fetus group was conducted (including average nucleotide identity analysis) that supports the initial identification of these three novel Campylobacter species. Furthermore, C. lanienae and the three putative novel species form a discrete clade within the C. fetus group, which we have termed the C. lanienae clade. This clade is distinguished from other members of the C. fetus group by a reduced genome size and distinct CRISPR/Cas systems. Moreover, there are two signature characteristics of the C. lanienae clade. C. lanienae clade genomes carry four to ten unlinked and similar, but nonidentical, flagellin genes. Additionally, all 76 C. lanienae clade genomes sequenced demonstrate a complete absence of genes related to selenium metabolism, including genes encoding the selenocysteine insertion machinery, selenoproteins, and the selenocysteinyl tRNA.
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Affiliation(s)
- William G Miller
- Produce Safety and Microbiology Research Unit, Agricultural Research Service, U.S. Department of Agriculture, Albany, CA
| | - Emma Yee
- Produce Safety and Microbiology Research Unit, Agricultural Research Service, U.S. Department of Agriculture, Albany, CA
| | - Bruno S Lopes
- School of Medicine, Medical Sciences and Nutrition, University of Aberdeen, United Kingdom
| | - Mary H Chapman
- Produce Safety and Microbiology Research Unit, Agricultural Research Service, U.S. Department of Agriculture, Albany, CA
| | - Steven Huynh
- Produce Safety and Microbiology Research Unit, Agricultural Research Service, U.S. Department of Agriculture, Albany, CA
| | - James L Bono
- Meat Safety and Quality Research Unit, Agricultural Research Service, U.S. Department of Agriculture, Clay Center, NE
| | - Craig T Parker
- Produce Safety and Microbiology Research Unit, Agricultural Research Service, U.S. Department of Agriculture, Albany, CA
| | - Norval J C Strachan
- School of Medicine, Medical Sciences and Nutrition, University of Aberdeen, United Kingdom
| | - Ken J Forbes
- School of Medicine, Medical Sciences and Nutrition, University of Aberdeen, United Kingdom
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On SLW, Miller WG, Houf K, Fox JG, Vandamme P. Minimal standards for describing new species belonging to the families Campylobacteraceae and Helicobacteraceae: Campylobacter, Arcobacter, Helicobacter and Wolinella spp. Int J Syst Evol Microbiol 2017; 67:5296-5311. [PMID: 29034857 PMCID: PMC5845751 DOI: 10.1099/ijsem.0.002255] [Citation(s) in RCA: 72] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2017] [Accepted: 07/24/2017] [Indexed: 01/25/2023] Open
Abstract
Ongoing changes in taxonomic methods, and in the rapid development of the taxonomic structure of species assigned to the Epsilonproteobacteria have lead the International Committee of Systematic Bacteriology Subcommittee on the Taxonomy of Campylobacter and Related Bacteria to discuss significant updates to previous minimal standards for describing new species of Campylobacteraceae and Helicobacteraceae. This paper is the result of these discussions and proposes minimum requirements for the description of new species belonging to the families Campylobacteraceae and Helicobacteraceae, thus including species in Campylobacter, Arcobacter, Helicobacter, and Wolinella. The core underlying principle remains the use of appropriate phenotypic and genotypic methods to characterise strains sufficiently so as to effectively and unambiguously determine their taxonomic position in these families, and provide adequate means by which the new taxon can be distinguished from extant species and subspecies. This polyphasic taxonomic approach demands the use of appropriate reference data for comparison to ensure the novelty of proposed new taxa, and the recommended study of at least five strains to enable species diversity to be assessed. Methodological approaches for phenotypic and genotypic (including whole-genome sequence comparisons) characterisation are recommended.
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Affiliation(s)
- Stephen L. W. On
- Department of Wine, Food and Molecular Biosciences, Lincoln University, PO Box 85084, Lincoln, New Zealand
| | - William G. Miller
- U.S. Department of Agriculture, Produce Safety and Microbiology Research Unit, Agricultural Research Service, Albany, CA, USA
| | - Kurt Houf
- Department of Veterinary Public Health, Faculty of Sciences, Ghent University, K. L. Ledeganckstraat 35, B-9000 Ghent, Belgium
- Department of Biochemistry and Microbiology, Laboratory of Microbiology, Faculty of Sciences, Ghent University, K. L. Ledeganckstraat 35, B-9000 Ghent, Belgium
| | - James G. Fox
- Department of Comparative Medicine, Massachusetts Institute of Technology, 77, Massachusetts Avenue, Cambiridge, MA 02139, USA
| | - Peter Vandamme
- Department of Biochemistry and Microbiology, Laboratory of Microbiology, Faculty of Sciences, Ghent University, K. L. Ledeganckstraat 35, B-9000 Ghent, Belgium
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Petrovska L, Tang Y, Jansen van Rensburg MJ, Cawthraw S, Nunez J, Sheppard SK, Ellis RJ, Whatmore AM, Crawshaw TR, Irvine RM. Genome Reduction for Niche Association in Campylobacter Hepaticus, A Cause of Spotty Liver Disease in Poultry. Front Cell Infect Microbiol 2017; 7:354. [PMID: 28848714 PMCID: PMC5554493 DOI: 10.3389/fcimb.2017.00354] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2017] [Accepted: 07/21/2017] [Indexed: 01/31/2023] Open
Abstract
The term “spotty liver disease” (SLD) has been used since the late 1990s for a condition seen in the UK and Australia that primarily affects free range laying hens around peak lay, causing acute mortality and a fall in egg production. A novel thermophilic SLD-associated Campylobacter was reported in the United Kingdom (UK) in 2015. Subsequently, similar isolates occurring in Australia were formally described as a new species, Campylobacter hepaticus. We describe the comparative genomics of 10 C. hepaticus isolates recovered from 5 geographically distinct poultry holdings in the UK between 2010 and 2012. Hierarchical gene-by-gene analyses of the study isolates and representatives of 24 known Campylobacter species indicated that C. hepaticus is most closely related to the major pathogens Campylobacter jejuni and Campylobacter coli. We observed low levels of within-farm variation, even between isolates collected over almost 3 years. With respect to C. hepaticus genome features, we noted that the study isolates had a ~140 Kb reduction in genome size, ~144 fewer genes, and a lower GC content compared to C. jejuni. The most notable reduction was in the subsystem containing genes for iron acquisition and metabolism, supported by reduced growth of C. hepaticus in an iron depletion assay. Genome reduction is common among many pathogens and in C. hepaticus has likely been driven at least in part by specialization following the occupation of a new niche, the chicken liver.
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Affiliation(s)
- Liljana Petrovska
- Bacteriology, Animal and Plant Health Agency WeybridgeAddlestone, United Kingdom
| | - Yue Tang
- Bacteriology, Animal and Plant Health Agency WeybridgeAddlestone, United Kingdom
| | - Melissa J Jansen van Rensburg
- Department of Zoology, University of OxfordOxford, United Kingdom.,NIHR Health Protection Research Unit in Gastrointestinal Infections, University of OxfordOxford, United Kingdom
| | - Shaun Cawthraw
- Bacteriology, Animal and Plant Health Agency WeybridgeAddlestone, United Kingdom
| | - Javier Nunez
- Veterinary Surveillance, Animal and Plant Health Agency WeybridgeAddlestone, United Kingdom
| | - Samuel K Sheppard
- Department of Biology and Biotechnology, The Milner Centre for Evolution, University of BathBath, United Kingdom
| | - Richard J Ellis
- Bacteriology, Animal and Plant Health Agency WeybridgeAddlestone, United Kingdom
| | - Adrian M Whatmore
- Bacteriology, Animal and Plant Health Agency WeybridgeAddlestone, United Kingdom
| | - Tim R Crawshaw
- Bacteriology, Animal and Plant Health Agency WeybridgeAddlestone, United Kingdom
| | - Richard M Irvine
- Bacteriology, Animal and Plant Health Agency WeybridgeAddlestone, United Kingdom
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26
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Wang Y, Liu F, Zhang X, Chung HKL, Riordan SM, Grimm MC, Zhang S, Ma R, Lee SA, Zhang L. Campylobacter concisus Genomospecies 2 Is Better Adapted to the Human Gastrointestinal Tract as Compared with Campylobacter concisus Genomospecies 1. Front Physiol 2017; 8:543. [PMID: 28824443 PMCID: PMC5541300 DOI: 10.3389/fphys.2017.00543] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2017] [Accepted: 07/12/2017] [Indexed: 01/26/2023] Open
Abstract
Campylobacter concisus was previously shown to be associated with inflammatory bowel disease including Crohn's disease (CD) and ulcerative colitis (UC). C. concisus has two genomospecies (GS). This study systematically examined the colonization of GS1 and GS2 C. concisus in the human gastrointestinal tract. GS1 and GS2 specific polymorphisms in 23S rRNA gene were identified by comparison of the 23S rRNA genes of 49 C. concisus strains. Two newly designed PCR methods, based on the polymorphisms of 23S rRNA gene, were developed and validated. These PCR methods were used to detect and quantify GS1 and GS2 C. concisus in 56 oral and enteric samples collected from the gastrointestinal tract of patients with IBD and healthy controls. Meta-analysis of the composition of the isolated GS1 and GS2 C. concisus strains in previous studies was also conducted. The quantitative PCR methods revealed that there was more GS2 than GS1 C. concisus in samples collected from the upper and lower gastrointestinal tract of both patients with IBD and healthy controls, showing that GS2 C. concisus is better adapted to the human gastrointestinal tract. Analysis of GS1 and GS2 composition of isolated C. concisus strains in previous studies showed similar findings except that in healthy individuals a significantly lower GS2 than GS1 C. concisus strains were isolated from fecal samples, suggesting a potential difference in the C. concisus strains or the enteric environment between patients with gastrointestinal diseases and healthy controls. This study provides novel information regarding the adaptation of different genomospecies of C. concisus in the human gastrointestinal tract.
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Affiliation(s)
- Yiming Wang
- School of Biotechnology and Biomolecular Sciences, University of New South WalesSydney, NSW, Australia
| | - Fang Liu
- School of Biotechnology and Biomolecular Sciences, University of New South WalesSydney, NSW, Australia
| | - Xiang Zhang
- Clinical Research Center, The First Affiliated Hospital of Nanjing Medical UniversityNanjing, China
| | - Heung Kit Leslie Chung
- School of Biotechnology and Biomolecular Sciences, University of New South WalesSydney, NSW, Australia
| | - Stephen M Riordan
- Gastrointestinal and Liver Unit, Prince of Wales Hospital, University of New South WalesSydney, NSW, Australia
| | - Michael C Grimm
- St George and Sutherland Clinical School, University of New South WalesSydney, NSW, Australia
| | - Shu Zhang
- Clinical Research Center, The First Affiliated Hospital of Nanjing Medical UniversityNanjing, China
| | - Rena Ma
- School of Biotechnology and Biomolecular Sciences, University of New South WalesSydney, NSW, Australia
| | - Seul A Lee
- School of Biotechnology and Biomolecular Sciences, University of New South WalesSydney, NSW, Australia
| | - Li Zhang
- School of Biotechnology and Biomolecular Sciences, University of New South WalesSydney, NSW, Australia
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27
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Genome analysis of Campylobacter concisus strains from patients with inflammatory bowel disease and gastroenteritis provides new insights into pathogenicity. Sci Rep 2016; 6:38442. [PMID: 27910936 PMCID: PMC5133609 DOI: 10.1038/srep38442] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2016] [Accepted: 11/09/2016] [Indexed: 12/14/2022] Open
Abstract
Campylobacter concisus is an oral bacterium that is associated with inflammatory bowel disease. C. concisus has two major genomospecies, which appear to have different enteric pathogenic potential. Currently, no studies have compared the genomes of C. concisus strains from different genomospecies. In this study, a comparative genome analysis of 36 C. concisus strains was conducted including 27 C. concisus strains sequenced in this study and nine publically available C. concisus genomes. The C. concisus core-genome was defined and genomospecies-specific genes were identified. The C. concisus core-genome, housekeeping genes and 23S rRNA gene consistently divided the 36 strains into two genomospecies. Two novel genomic islands, CON_PiiA and CON_PiiB, were identified. CON_PiiA and CON_PiiB islands contained proteins homologous to the type IV secretion system, LepB-like and CagA-like effector proteins. CON_PiiA islands were found in 37.5% of enteric C. concisus strains (3/8) isolated from patients with enteric diseases and none of the oral strains (0/27), which was statistically significant. This study reports the findings of C. concisus genomospecies-specific genes, novel genomic islands that contain type IV secretion system and putative effector proteins, and other new genomic features. These data provide novel insights into understanding of the pathogenicity of this emerging opportunistic pathogen.
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Gilbert MJ, Miller WG, Yee E, Kik M, Zomer AL, Wagenaar JA, Duim B. Comparative Genomics of Campylobacter iguaniorum to Unravel Genetic Regions Associated with Reptilian Hosts. Genome Biol Evol 2016; 8:3022-3029. [PMID: 27604878 PMCID: PMC5630845 DOI: 10.1093/gbe/evw218] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Campylobacter iguaniorum is most closely related to the species C. fetus, C. hyointestinalis, and C. lanienae. Reptiles, chelonians and lizards in particular, appear to be a primary reservoir of this Campylobacter species. Here we report the genome comparison of C. iguaniorum strain 1485E, isolated from a bearded dragon (Pogona vitticeps), and strain 2463D, isolated from a green iguana (Iguana iguana), with the genomes of closely related taxa, in particular with reptile-associated C. fetus subsp. testudinum. In contrast to C. fetus, C. iguaniorum is lacking an S-layer encoding region. Furthermore, a defined lipooligosaccharide biosynthesis locus, encoding multiple glycosyltransferases and bounded by waa genes, is absent from C. iguaniorum. Instead, multiple predicted glycosylation regions were identified in C. iguaniorum. One of these regions is > 50 kb with deviant G + C content, suggesting acquisition via lateral transfer. These similar, but non-homologous glycosylation regions were located at the same position on the genome in both strains. Multiple genes encoding respiratory enzymes not identified to date within the C. fetus clade were present. C. iguaniorum shared highest homology with C. hyointestinalis and C. fetus. As in reptile-associated C. fetus subsp. testudinum, a putative tricarballylate catabolism locus was identified. However, despite colonizing a shared host, no recent recombination between both taxa was detected. This genomic study provides a better understanding of host adaptation, virulence, phylogeny, and evolution of C. iguaniorum and related Campylobacter taxa.
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Affiliation(s)
- Maarten J Gilbert
- Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands
| | - William G Miller
- Produce Safety and Microbiology Research Unit, Agricultural Research Service, U.S. Department of Agriculture, Albany, California, USA
| | - Emma Yee
- Produce Safety and Microbiology Research Unit, Agricultural Research Service, U.S. Department of Agriculture, Albany, California, USA
| | - Marja Kik
- Department of Pathobiology, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands
| | - Aldert L Zomer
- Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands WHO Collaborating Center for Campylobacter/OIE Reference Laboratory for Campylobacteriosis, Utrecht, The Netherlands
| | - Jaap A Wagenaar
- Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands WHO Collaborating Center for Campylobacter/OIE Reference Laboratory for Campylobacteriosis, Utrecht, The Netherlands Central Veterinary Institute of Wageningen UR, Lelystad, The Netherlands
| | - Birgitta Duim
- Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands WHO Collaborating Center for Campylobacter/OIE Reference Laboratory for Campylobacteriosis, Utrecht, The Netherlands
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29
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Nielsen HL, Nielsen H, Torpdahl M. Multilocus sequence typing of Campylobacter concisus from Danish diarrheic patients. Gut Pathog 2016; 8:44. [PMID: 27688814 PMCID: PMC5034547 DOI: 10.1186/s13099-016-0126-0] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/15/2016] [Accepted: 09/13/2016] [Indexed: 12/11/2022] Open
Abstract
The emerging enteric pathogen Campylobacter concisus is associated with prolonged diarrhea and inflammatory bowel disease. Previous studies have shown that C. concisus strains are very genetically diverse. Nevertheless, C. concisus strains have been divided into two genomospecies, where GS1 strains have been isolated predominantly from healthy individuals, while the GS2 cluster consists of isolates primarily from diarrheic individuals. The aim of the present study was to determine the genetic diversity of C. concisus isolates from Danish diarrheic patients. Multilocus sequence typing using the loci aspA, atpA, glnA, gltA, glyA, ilvD and pgm, as well as genomospecies based on specific differences in the 23S rRNA, was used to characterize 67 isolates (63 fecal and 4 oral), from 49 patients with different clinical presentations (29 with diarrhea, eight with bloody diarrhea, seven with collagenous colitis and five with Crohn’s disease). MLST revealed a high diversity of C. concisus with 53 sequence types (STs), of which 52 were identified as ‘new’ STs. Allele sequences showed more than 90 % similarity between isolates, with only four outliers. Dendrogram profiles of each allele showed a division into two groups, which more or less correlated with genomospecies A and genomospecies B. However, in contrary to previous results, this subgrouping had no association to the clinical severity of disease.
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Affiliation(s)
- Hans Linde Nielsen
- Department of Clinical Microbiology, Aalborg University Hospital, Aalborg, Denmark
| | - Henrik Nielsen
- Department of Infectious Diseases, Aalborg University Hospital, Aalborg, Denmark ; Department of Clinical Medicine, Aalborg University, Aalborg, Denmark
| | - Mia Torpdahl
- Department of Microbiology and Infection Control, Statens Serum Institut (SSI), Copenhagen, Denmark
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Complete Genome Sequences of Campylobacter hyointestinalis subsp. hyointestinalis Strain LMG 9260 and C. hyointestinalis subsp. lawsonii Strain LMG 15993. GENOME ANNOUNCEMENTS 2016; 4:4/4/e00665-16. [PMID: 27417840 PMCID: PMC4945800 DOI: 10.1128/genomea.00665-16] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Campylobacter hyointestinalis is isolated primarily from ruminants and swine, but is also occasionally isolated from humans. C. hyointestinalis is currently divided into two subspecies, C. hyointestinalis subsp. hyointestinalis and C. hyointestinalis subsp. lawsonii This study describes the first closed whole-genome sequences of C. hyointestinalis subsp. hyointestinalis isolate LMG 9260 and C. hyointestinalis subsp. lawsonii isolate LMG 15993.
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Mahendran V, Octavia S, Demirbas OF, Sabrina S, Ma R, Lan R, Riordan SM, Grimm MC, Zhang L. Delineation of genetic relatedness and population structure of oral and enteric Campylobacter concisus strains by analysis of housekeeping genes. MICROBIOLOGY-SGM 2015; 161:1600-1612. [PMID: 26002953 DOI: 10.1099/mic.0.000112] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Campylobacter concisus is an oral bacterium that has been shown to be associated with inflammatory bowel disease (IBD). In this study we examined clusters of oral C. concisus strains isolated from patients with IBD and healthy controls by analysing six housekeeping genes. In addition, we investigated the population structure of C. concisus strains. Whether oral and enteric strains form distinct clusters based on the sequences of these housekeeping genes was also investigated. The oral C. concisus strains were found to contain two genomospecies, which belong to the two genomospecies previously found in enteric C. concisus strains. C. concisus clusters formed based on the sequences of a single aspA gene were the same as that formed by using previously reported MLST schemes. The analysis of combined oral and enteric C. concisus strains found that enteric C. concisus strains did not form distinct clusters. Genetic structure analysis identified five subpopulations of C. concisus and showed that genetic recombination between C. concisus strains was common. However, genetic recombination was significantly less in oral strains isolated from patients with IBD than from healthy individuals. Previously reported oral and enteric intestinal epithelial invasive C. concisus strains were in cluster II and subpopulation III. Furthermore, this study shows that there are no distinct enteric C. concisus strain clusters or subpopulations.
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Affiliation(s)
- Vikneswari Mahendran
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, Australia
| | - Sophie Octavia
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, Australia
| | - Omer Faruk Demirbas
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, Australia
| | - Sheryl Sabrina
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, Australia
| | - Rena Ma
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, Australia
| | - Ruiting Lan
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, Australia
| | - Stephen M Riordan
- Gastrointestinal and Liver Unit, Prince of Wales Hospital, Sydney, Australia
| | - Michael C Grimm
- St George and Sutherland Clinical School, University of New South Wales, Sydney, Australia
| | - Li Zhang
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, Australia
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Alonso R, Girbau C, Martinez-Malaxetxebarria I, Fernández-Astorga A. Multilocus sequence typing reveals genetic diversity of foodborne Arcobacter butzleri isolates in the North of Spain. Int J Food Microbiol 2014; 191:125-8. [PMID: 25261830 DOI: 10.1016/j.ijfoodmicro.2014.09.012] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2014] [Revised: 09/07/2014] [Accepted: 09/14/2014] [Indexed: 10/24/2022]
Abstract
The emerging pathogen Arcobacter butzleri is being increasingly isolated from different animal food products but the routes of its transmission to human are not well established yet. Typing methods would be useful in gaining such knowledge. Here we report the great genetic diversity observed among A. butzleri isolates from different food products. Forty-five isolates were analyzed by Multilocus Sequence Typing (MLST). A total of 157 alleles were identified across all seven loci, ranging from 16 alleles at glnA to 31 at glyA. MLST differentiated the isolates into 34 sequence types (STs), with the majority of isolates containing a unique sequence type. Seventy-four new alleles were identified, which resulted in the assignment of 33 new STs. No association of alleles or STs with food source was observed. For the first time, lateral gene transfer from Arcobacter skirrowii to A. butzleri at the glyA locus is also reported.
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Affiliation(s)
- Rodrigo Alonso
- Department of Immunology, Microbiology and Parasitology, University of the Basque Country (UPV/EHU), Paseo de la Universidad 7, Vitoria-Gasteiz 01006, Spain
| | - Cecilia Girbau
- Department of Immunology, Microbiology and Parasitology, University of the Basque Country (UPV/EHU), Paseo de la Universidad 7, Vitoria-Gasteiz 01006, Spain
| | - Irati Martinez-Malaxetxebarria
- Department of Immunology, Microbiology and Parasitology, University of the Basque Country (UPV/EHU), Paseo de la Universidad 7, Vitoria-Gasteiz 01006, Spain
| | - Aurora Fernández-Astorga
- Department of Immunology, Microbiology and Parasitology, University of the Basque Country (UPV/EHU), Paseo de la Universidad 7, Vitoria-Gasteiz 01006, Spain.
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Navarro-Gonzalez N, Ugarte-Ruiz M, Porrero MC, Zamora L, Mentaberre G, Serrano E, Mateos A, Lavín S, Domínguez L. Campylobacter shared between free-ranging cattle and sympatric wild ungulates in a natural environment (NE Spain). ECOHEALTH 2014; 11:333-342. [PMID: 24595731 DOI: 10.1007/s10393-014-0921-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/08/2013] [Accepted: 02/10/2014] [Indexed: 06/03/2023]
Abstract
Campylobacter infections are a public health concern and an increasingly common cause of food-borne zoonoses in the European Union. However, little is known about their spill-over from free-ranging livestock to sympatric wild ungulates, especially in regards to uncommon Campylobacter species. In this study, we aim to determine the prevalence of C. coli, C. jejuni and other C. spp. in game ungulates (wild boar Sus scrofa and Iberian ibex Capra pyrenaica) and free-ranging sympatric cattle in a National Game Reserve in NE Spain. Furthermore, we explore the extent to which Campylobacter species are shared among these co-habiting hosts. Faecal samples from Iberian ibex (n = 181) were negative for C. spp. By direct plating, two wild boars out of 150 were positive for C. coli (1.3%, 95% CI 0.16-4.73), and one was positive for C. jejuni (0.67%, 95% CI 0.02-3.66). The latter was predominant in cattle: 5.45% (n = 55, 95% CI 1.14-5.12), while C. coli was not isolated from this host. C. lanienae was the most frequent species in wild boar at 10% (95% CI 5.7-15.96), and one cow cohabiting with positive wild boars in the same canyon also carried C. lanienae. Four enrichment protocols (using Bolton or Preston broth combined with either mCCDA or CFA) were added for 172 samples (57 from wild boars, 55 cattle and 60 Iberian ibexes) to increase the number of isolates obtained allowing the detection of statistically significant differences. The prevalence of C. lanienae was statistically significantly higher in wild boar than in cattle (P < 0.01), but the prevalence of C. jejuni was higher in the latter (P = 0.045). These results suggest that wild boar and cattle carry their own predominant Campylobacter species, while Iberian ibex do not seem to play an important role in the epidemiology of Campylobacter. However, there is a potential spill-over of C. spp., and thus, further research is needed to elucidate the factors determining inter-species transmission.
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Affiliation(s)
- N Navarro-Gonzalez
- Servei d' Ecopatologia de Fauna Salvatge (SEFaS), Departament de Medicina i Cirurgia Animals, UniversitatAutònoma de Barcelona (UAB), Bellaterra, Barcelona, Spain
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Gilbert MJ, Kik M, Timmerman AJ, Severs TT, Kusters JG, Duim B, Wagenaar JA. Occurrence, diversity, and host association of intestinal Campylobacter, Arcobacter, and Helicobacter in reptiles. PLoS One 2014; 9:e101599. [PMID: 24988130 PMCID: PMC4079654 DOI: 10.1371/journal.pone.0101599] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2013] [Accepted: 06/09/2014] [Indexed: 11/19/2022] Open
Abstract
Campylobacter, Arcobacter, and Helicobacter species have been isolated from many vertebrate hosts, including birds, mammals, and reptiles. Multiple studies have focused on the prevalence of these Epsilonproteobacteria genera in avian and mammalian species. However, little focus has been given to the presence within reptiles, and their potential zoonotic and pathogenic roles. In this study, occurrence, diversity, and host association of intestinal Epsilonproteobacteria were determined for a large variety of reptiles. From 2011 to 2013, 444 cloacal swabs and fecal samples originating from 417 predominantly captive-held reptiles were screened for Epsilonproteobacteria. Campylobacter, Arcobacter, and Helicobacter genus specific PCRs were performed directly on all samples. All samples were also cultured on selective media and screened for the presence of Epsilonproteobacteria. Using a tiered approach of AFLP, atpA, and 16S rRNA sequencing, 432 Epsilonproteobacteria isolates were characterized at the species level. Based on PCR, Campylobacter, Arcobacter, and Helicobacter were detected in 69.3% of the reptiles; 82.5% of the chelonians, 63.8% of the lizards, and 58.0% of the snakes were positive for one or more of these genera. Epsilonproteobacteria were isolated from 22.1% of the reptiles and were isolated most frequently from chelonians (37.0%), followed by lizards (19.6%) and snakes (3.0%). The most commonly isolated taxa were Arcobacter butzleri, Arcobacter skirrowii, reptile-associated Campylobacter fetus subsp. testudinum, and a putative novel Campylobacter taxon. Furthermore, a clade of seven related putative novel Helicobacter taxa was isolated from lizards and chelonians. This study shows that reptiles carry various intestinal Epsilonproteobacteria taxa, including several putative novel taxa.
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Affiliation(s)
- Maarten J. Gilbert
- Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands
- * E-mail:
| | - Marja Kik
- Department of Pathobiology, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands
| | - Arjen J. Timmerman
- Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands
| | - Tim T. Severs
- Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Johannes G. Kusters
- Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Birgitta Duim
- Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands
- WHO Collaborating Center for Campylobacter/OIE Reference Laboratory for Campylobacteriosis, Utrecht, The Netherlands
| | - Jaap A. Wagenaar
- Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands
- WHO Collaborating Center for Campylobacter/OIE Reference Laboratory for Campylobacteriosis, Utrecht, The Netherlands
- Central Veterinary Institute of Wageningen UR, Lelystad, The Netherlands
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Miller W, Yee E, Jolley K, Chapman M. Use of an improved atpA
amplification and sequencing method to identify members of the Campylobacteraceae and Helicobacteraceae. Lett Appl Microbiol 2014; 58:582-90. [DOI: 10.1111/lam.12228] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2013] [Revised: 01/15/2014] [Accepted: 02/05/2014] [Indexed: 11/30/2022]
Affiliation(s)
- W.G. Miller
- USDA; ARS; WRRC; Produce Safety and Microbiology; Albany CA USA
| | - E. Yee
- USDA; ARS; WRRC; Produce Safety and Microbiology; Albany CA USA
| | - K.A. Jolley
- Department of Zoology; University of Oxford; Oxford UK
| | - M.H. Chapman
- USDA; ARS; WRRC; Produce Safety and Microbiology; Albany CA USA
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Abstract
BACKGROUND There is only sparse information about the clinical impact of Campylobacter concisus infections in children. METHODS A study was performed during a 2-year period to determine the clinical manifestations in C. concisus-positive children with gastroenteritis. A case patient was defined as a child or teenager (<18 years) with a C. concisus-positive stool sample during the study period. Clinical data were obtained with use of a questionnaire study supplemented with the patients' medical records. The clinical manifestations in these patients were compared with those of patients with Campylobacter jejuni/coli infection. RESULTS Two thousand three hundred seventy-two diarrheic stool samples from 1867 children were cultured for pathogenic enteric bacteria during the study period, and 85 and 109 children with C. concisus and C. jejuni/coli, respectively, were identified. Comparison of the acute clinical manifestations in 44 C. concisus patients with those in 64 C. jejuni/coli patients showed a significantly lower prevalence of fever, chills and blood in stools in the former. However, half of C. concisus patients compared with one-fourth of C. jejuni/coli patients had prolonged diarrhea for more than 2 weeks and two-thirds of all children with C. concisus reported loose stools after 6-month follow-up. CONCLUSIONS C. concisus infection in children seems to have a milder course of acute gastroenteritis compared with C. jejuni/coli infection but is associated with more prolonged diarrhea. Children with C. concisus have the same degree of late gastrointestinal complaints as children diagnosed with C. jejuni/coli infection.
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Isolation, identification and subtyping of Campylobacter: Where to from here? J Microbiol Methods 2013; 95:3-7. [DOI: 10.1016/j.mimet.2013.06.011] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2013] [Revised: 05/01/2013] [Accepted: 06/05/2013] [Indexed: 12/14/2022]
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New concepts in diagnostics for infectious diarrhea. Mucosal Immunol 2013; 6:876-85. [PMID: 23881355 DOI: 10.1038/mi.2013.50] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2013] [Accepted: 06/11/2013] [Indexed: 02/04/2023]
Abstract
Conventional approaches to the diagnosis of infectious diarrhea must include several modalities to detect an array of potential viruses, bacteria, and parasites. We will provide a general overview of the wide range of diagnostic modalities available for enteropathogens, briefly discuss some of the limitations of conventional methods, and then focus on new molecular methods, including real-time PCR and next-generation sequencing. In particular, we will discuss quantitation of pathogen load with these techniques. We will then describe examples whereby novel diagnostics may help illuminate the etiology of infectious diarrhea, where they may not, and how they may benefit studies of immunity to enteric infections.
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Taboada EN, Clark CG, Sproston EL, Carrillo CD. Current methods for molecular typing of Campylobacter species. J Microbiol Methods 2013; 95:24-31. [PMID: 23871858 DOI: 10.1016/j.mimet.2013.07.007] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2013] [Revised: 07/01/2013] [Accepted: 07/02/2013] [Indexed: 12/11/2022]
Abstract
Campylobacter remains one of the most common bacterial causes of gastroenteritis worldwide. Tracking sources of this organism is challenging due to the large numbers of human cases, and the prevalence of this organism throughout the environment due to growth in a wide range of animal species. Many molecular subtyping methods have been developed to characterize Campylobacter species, but only a few are commonly used in molecular epidemiology studies. This review examines the applicability of these methods, as well as the role that emerging whole genome sequencing technologies will play in tracking sources of Campylobacter spp. infection.
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Affiliation(s)
- Eduardo N Taboada
- Laboratory for Foodborne Zoonoses, Public Health Agency of Canada, PO Box 640, Township Rd. 9-1, Lethbridge, AB T1J 3Z4, Canada.
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Serraino A, Florio D, Giacometti F, Piva S, Mion D, Zanoni RG. Presence of Campylobacter and Arcobacter species in in-line milk filters of farms authorized to produce and sell raw milk and of a water buffalo dairy farm in Italy. J Dairy Sci 2013; 96:2801-7. [PMID: 23453517 DOI: 10.3168/jds.2012-6249] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2012] [Accepted: 01/07/2013] [Indexed: 01/28/2023]
Abstract
The objectives of this study were to investigate the presence of Campylobacter spp. and Arcobacter spp. in dairy herds authorized for the production and sale of raw milk and in a water buffalo dairy farm, and to test the antimicrobial susceptibility of the isolates. A total of 196 in-line milk filters were collected from 14 dairy farms (13 bovine and 1 water buffalo) for detection of Campylobacter spp. and Arcobacter spp. by microbiological culture. For each farm investigated, 1 isolate for each Campylobacter and Arcobacter species isolated was tested using the Etest method (AB Biodisk, Solna, Sweden) to evaluate the susceptibility to ciprofloxacin, tetracycline, chloramphenicol, ampicillin, erythromycin, and gentamicin. A total of 52 isolates were detected in 49 milk filters in 12 farms (85.7%) out of 14 and the isolates were identified as Campylobacter jejuni (6), Campylobacter hyointestinalis ssp. hyointestinalis (8), Campylobacter concisus (1), Campylobacter fetus ssp. fetus (1), Arcobacter butzleri (22), and Arcobacter cryaerophilus (14). The small number of isolates tested for antimicrobial susceptibility precludes any epidemiological consideration but highlights that all Campylobacter isolates were susceptible to macrolides, which are the first-choice drugs for the treatment of campylobacteriosis, and that resistance to fluoroquinolones and tetracycline was detected; for Arcobacter isolates, resistance to ampicillin and chloramphenicol was detected. The sale of raw milk for human consumption by self-service automatic vending machines has been allowed in Italy since 2004 and the presence of C. jejuni in in-line milk filters confirms that raw milk consumption is a significant risk factor for human infection. The high occurrence of emerging Campylobacter spp. and Arcobacter spp. discovered in dairy farms authorized for production and sale of raw milk represents an emerging hazard for human health.
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Affiliation(s)
- A Serraino
- Department of Veterinary Medical Sciences, via Tolara di Sopra 50, 40064 Ozzano Emilia, Bologna, Italy.
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Merrell DS, Stintzi A. Research advances in the study of Campylobacter, Helicobacter, and related organisms. Front Cell Infect Microbiol 2012; 2:159. [PMID: 23267439 PMCID: PMC3525878 DOI: 10.3389/fcimb.2012.00159] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2012] [Accepted: 11/28/2012] [Indexed: 01/22/2023] Open
Affiliation(s)
- D. Scott Merrell
- Department of Microbiology and Immunology, Uniformed Services UniversityBethesda, MD, USA
- *Correspondence: ;
| | - Alain Stintzi
- Department of Biochemistry, Microbiology and Immunology, University of OttawaOttawa, ON, Canada
- *Correspondence: ;
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Comprehensive detection and discrimination of Campylobacter species by use of confocal micro-Raman spectroscopy and multilocus sequence typing. J Clin Microbiol 2012; 50:2932-46. [PMID: 22740711 DOI: 10.1128/jcm.01144-12] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
A novel strategy for the rapid detection and identification of traditional and emerging Campylobacter strains based upon Raman spectroscopy (532 nm) is presented here. A total of 200 reference strains and clinical isolates of 11 different Campylobacter species recovered from infected animals and humans from China and North America were used to establish a global Raman spectroscopy-based dendrogram model for Campylobacter identification to the species level and cross validated for its feasibility to predict Campylobacter-associated food-borne outbreaks. Bayesian probability coupled with Monte Carlo estimation was employed to validate the established Raman classification model on the basis of the selected principal components, mainly protein secondary structures, on the Campylobacter cell membrane. This Raman spectroscopy-based typing technique correlates well with multilocus sequence typing and has an average recognition rate of 97.21%. Discriminatory power for the Raman classification model had a Simpson index of diversity of 0.968. Intra- and interlaboratory reproducibility with different instrumentation yielded differentiation index values of 4.79 to 6.03 for wave numbers between 1,800 and 650 cm(-1) and demonstrated the feasibility of using this spectroscopic method at different laboratories. Our Raman spectroscopy-based partial least-squares regression model could precisely discriminate and quantify the actual concentration of a specific Campylobacter strain in a bacterial mixture (regression coefficient, >0.98; residual prediction deviation, >7.88). A standard protocol for sample preparation, spectral collection, model validation, and data analyses was established for the Raman spectroscopic technique. Raman spectroscopy may have advantages over traditional genotyping methods for bacterial epidemiology, such as detection speed and accuracy of identification to the species level.
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