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Steinbach A, Kun J, Urbán P, Palkovics T, Polgár B, Schneider G. Molecular Responses of the Eukaryotic Cell Line INT407 on the Internalized Campylobacter jejuni-The Other Side of the Coin. Pathogens 2024; 13:386. [PMID: 38787238 PMCID: PMC11124400 DOI: 10.3390/pathogens13050386] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2024] [Revised: 04/21/2024] [Accepted: 04/29/2024] [Indexed: 05/25/2024] Open
Abstract
Campylobacter jejuni is a zoonotic bacterium with the capacity to invade the epithelial cells during the pathogenic process. Several bacterial factors have been identified to contribute to this process, but our knowledge is still very limited about the response of the host. To reveal the major routes of this response, a whole-transcriptome analysis (WTA) was performed where gene expressions were compared between the 1st and the 3rd hours of internalization in INT407 epithelial cells. From the 41,769 human genes tested, altogether, 19,060 genes were shown through WTA to be influenced to different extents. The genes and regulation factors of transcription (296/1052; 28%), signal transduction (215/1052; 21%), apoptosis (153/1052; 15%), immune responses (97/1052; 9%), transmembrane transport (64/1052; 6%), cell-cell signaling (32/1052; 3%), cell-cell adhesions (29/1052; 3%), and carbohydrate metabolism (28/1052; 3%) were the most affected biological functions. A striking feature of the gene expression of this stage of the internalization process is the activation of both immune functions and apoptosis, which convincingly outlines that the invaded cell faces a choice between death and survival. The seemingly balanced status quo between the invader and the host is the result of a complex process that also affects genes known to be associated with postinfectious pathological conditions. The upregulation of TLR3 (3.79×) and CD36 (2.73×), two general tumor markers, and SERPINEB9 (11.37×), FNDC1 (7.58×), and TACR2 (8.84×), three factors of tumorigenesis, confirms the wider pathological significance of this bacterium.
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Affiliation(s)
- Anita Steinbach
- Department of Medical Microbiology and Immunology, Medical School, University of Pécs, 7624 Pécs, Hungary; (A.S.); (T.P.); (B.P.)
| | - József Kun
- Hungarian Centre for Genomics and Bioinformatics, Szentágothai Research Centre, University of Pécs, 7624 Pécs, Hungary; (J.K.); (P.U.)
- Department of Pharmacology and Pharmacotherapy, Medical School, University of Pécs, 7624 Pécs, Hungary
| | - Péter Urbán
- Hungarian Centre for Genomics and Bioinformatics, Szentágothai Research Centre, University of Pécs, 7624 Pécs, Hungary; (J.K.); (P.U.)
| | - Tamás Palkovics
- Department of Medical Microbiology and Immunology, Medical School, University of Pécs, 7624 Pécs, Hungary; (A.S.); (T.P.); (B.P.)
| | - Beáta Polgár
- Department of Medical Microbiology and Immunology, Medical School, University of Pécs, 7624 Pécs, Hungary; (A.S.); (T.P.); (B.P.)
| | - György Schneider
- Department of Medical Microbiology and Immunology, Medical School, University of Pécs, 7624 Pécs, Hungary; (A.S.); (T.P.); (B.P.)
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2
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Ghielmetti G, Seth-Smith HMB, Roloff T, Cernela N, Biggel M, Stephan R, Egli A. Whole-genome-based characterization of Campylobacter jejuni from human patients with gastroenteritis collected over an 18 year period reveals increasing prevalence of antimicrobial resistance. Microb Genom 2023; 9:mgen000941. [PMID: 36809179 PMCID: PMC9997746 DOI: 10.1099/mgen.0.000941] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/23/2023] Open
Abstract
Campylobacteriosis is the most common cause of acute gastrointestinal bacterial infection in Europe, with most infections linked to the consumption of contaminated food. While previous studies found an increasing rate of antimicrobial resistance (AMR) in Campylobacter spp. over the past decades, the investigation of additional clinical isolates is likely to provide novel insights into the population structure and mechanisms of virulence and drug resistance of this important human pathogen. Therefore, we combined whole-genome sequencing and antimicrobial-susceptibility testing of 340 randomly selected Campylobacter jejuni isolates from humans with gastroenteritis, collected in Switzerland over an 18 year period. In our collection, the most common multilocus sequence types (STs) were ST-257 (n=44), ST-21 (n=36) and ST-50 (n=35); the most common clonal complexes (CCs) were CC-21 (n=102), CC-257 (n=49) and CC-48 (n=33). High heterogeneity was observed among STs, with the most abundant STs recurring over the entire study period, while others were observed only sporadically. Source attribution based on ST assigned more than half of the strains to the 'generalist' category (n=188), 25 % as 'poultry specialist' (n=83), and only a few to 'ruminant specialist' (n=11) or 'wild bird' origin (n=9). The isolates displayed an increased frequency of AMR from 2003 to 2020, with the highest rates of resistance observed for ciprofloxacin and nalidixic acid (49.8 %), followed by tetracycline (36.9 %). Quinolone-resistant isolates carried chromosomal gyrA mutations T86I (99.4 %) and T86A (0.6 %), whereas tetracycline-resistant isolates carried tet(O) (79.8 %) or mosaic tetO/32/O (20.2 %) genes. A novel chromosomal cassette carrying several resistance genes, including aph(3')-III, satA and aad(6), and flanked by insertion sequence elements was detected in one isolate. Collectively, our data revealed an increasing prevalence of resistance to quinolones and tetracycline in C. jejuni isolates from Swiss patients over time, linked to clonal expansion of gyrA mutants and acquisition of the tet(O) gene. Investigation of source attribution suggests that infections are most likely related to isolates from poultry or generalist backgrounds. These findings are relevant to guide future infection prevention and control strategies.
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Affiliation(s)
- Giovanni Ghielmetti
- Institute for Food Safety and Hygiene, Section of Veterinary Bacteriology, University of Zurich, Zurich, Switzerland.,Applied Microbiology Research, Department of Biomedicine, University of Basel, Basel, Switzerland
| | - Helena M B Seth-Smith
- Applied Microbiology Research, Department of Biomedicine, University of Basel, Basel, Switzerland.,Clinical Bacteriology and Mycology, University Hospital Basel, Basel, Switzerland.,Swiss Institute for Bioinformatics, Basel, Switzerland
| | - Tim Roloff
- Applied Microbiology Research, Department of Biomedicine, University of Basel, Basel, Switzerland.,Clinical Bacteriology and Mycology, University Hospital Basel, Basel, Switzerland.,Swiss Institute for Bioinformatics, Basel, Switzerland
| | - Nicole Cernela
- Institute for Food Safety and Hygiene, University of Zurich, Zurich, Switzerland
| | - Michael Biggel
- Institute for Food Safety and Hygiene, University of Zurich, Zurich, Switzerland
| | - Roger Stephan
- Institute for Food Safety and Hygiene, University of Zurich, Zurich, Switzerland
| | - Adrian Egli
- Applied Microbiology Research, Department of Biomedicine, University of Basel, Basel, Switzerland.,Clinical Bacteriology and Mycology, University Hospital Basel, Basel, Switzerland
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3
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El-Adawy H, Hotzel H, García-Soto S, Tomaso H, Hafez HM, Schwarz S, Neubauer H, Linde J. Genomic insight into Campylobacter jejuni isolated from commercial turkey flocks in Germany using whole-genome sequencing analysis. Front Vet Sci 2023; 10:1092179. [PMID: 36875995 PMCID: PMC9978446 DOI: 10.3389/fvets.2023.1092179] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Accepted: 01/23/2023] [Indexed: 02/18/2023] Open
Abstract
Campylobacter (C.) jejuni is a zoonotic bacterium of public health significance. The present investigation was designed to assess the epidemiology and genetic heterogeneity of C. jejuni recovered from commercial turkey farms in Germany using whole-genome sequencing. The Illumina MiSeq® technology was used to sequence 66 C. jejuni isolates obtained between 2010 and 2011 from commercial meat turkey flocks located in ten German federal states. Phenotypic antimicrobial resistance was determined. Phylogeny, resistome, plasmidome and virulome profiles were analyzed using whole-genome sequencing data. Genetic resistance markers were identified with bioinformatics tools (AMRFinder, ResFinder, NCBI and ABRicate) and compared with the phenotypic antimicrobial resistance. The isolates were assigned to 28 different sequence types and 11 clonal complexes. The average pairwise single nucleotide-polymorphisms distance of 14,585 SNPs (range: 0-26,540 SNPs) revealed a high genetic distinction between the isolates. Thirteen virulence-associated genes were identified in C. jejuni isolates. Most of the isolates harbored the genes flaA (83.3%) and flaB (78.8%). The wlaN gene associated with the Guillain-Barré syndrome was detected in nine (13.6%) isolates. The genes for resistance to ampicillin (bla OXA), tetracycline [tet(O)], neomycin [aph(3')-IIIa], streptomycin (aadE) and streptothricin (sat4) were detected in isolated C. jejuni using WGS. A gene cluster comprising the genes sat4, aph(3')-IIIa and aadE was present in six isolates. The single point mutation T86I in the housekeeping gene gyrA conferring resistance to quinolones was retrieved in 93.6% of phenotypically fluoroquinolone-resistant isolates. Five phenotypically erythromycin-susceptible isolates carried the mutation A103V in the gene for the ribosomal protein L22 inferring macrolide resistance. An assortment of 13 β-lactam resistance genes (bla OXA variants) was detected in 58 C. jejuni isolates. Out of 66 sequenced isolates, 28 (42.4%) carried plasmid-borne contigs. Six isolates harbored a pTet-like plasmid-borne contig which carries the tet(O) gene. This study emphasized the potential of whole-genome sequencing to ameliorate the routine surveillance of C. jejuni. Whole-genome sequencing can predict antimicrobial resistance with a high degree of accuracy. However, resistance gene databases need curation and updates to revoke inaccuracy when using WGS-based analysis pipelines for AMR detection.
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Affiliation(s)
- Hosny El-Adawy
- Institute of Bacterial Infections and Zoonoses, Friedrich-Loeffler-Institut, Jena, Germany.,Faculty of Veterinary Medicine, Kafrelsheikh University, Kafr El-Sheikh, Egypt
| | - Helmut Hotzel
- Institute of Bacterial Infections and Zoonoses, Friedrich-Loeffler-Institut, Jena, Germany
| | - Silvia García-Soto
- Institute of Bacterial Infections and Zoonoses, Friedrich-Loeffler-Institut, Jena, Germany
| | - Herbert Tomaso
- Institute of Bacterial Infections and Zoonoses, Friedrich-Loeffler-Institut, Jena, Germany
| | - Hafez M Hafez
- Institute of Poultry Diseases, Free University Berlin, Berlin, Germany
| | - Stefan Schwarz
- Institute of Microbiology and Epizootics, Centre for Infection Medicine, Department of Veterinary Medicine, Freie Universität Berlin, Berlin, Germany.,Veterinary Centre of Resistance Research (TZR), Freie Universität Berlin, Berlin, Germany
| | - Heinrich Neubauer
- Institute of Bacterial Infections and Zoonoses, Friedrich-Loeffler-Institut, Jena, Germany
| | - Jörg Linde
- Institute of Bacterial Infections and Zoonoses, Friedrich-Loeffler-Institut, Jena, Germany
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Tanoeiro L, Oleastro M, Nunes A, Marques AT, Duarte SV, Gomes JP, Matos APA, Vítor JMB, Vale FF. Cryptic Prophages Contribution for Campylobacter jejuni and Campylobacter coli Introgression. Microorganisms 2022; 10:microorganisms10030516. [PMID: 35336092 PMCID: PMC8955182 DOI: 10.3390/microorganisms10030516] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Revised: 02/22/2022] [Accepted: 02/23/2022] [Indexed: 11/23/2022] Open
Abstract
Campylobacter coli and C. jejuni, the causing agents of campylobacteriosis, are described to be undergoing introgression events, i.e., the transference of genetic material between different species, with some isolates sharing almost a quarter of its genome. The participation of phages in introgression events and consequent impact on host ecology and evolution remain elusive. Three distinct prophages, named C. jejuni integrated elements 1, 2, and 4 (CJIE1, CJIE2, and CJIE4), are described in C. jejuni. Here, we identified two unreported prophages, Campylobacter coli integrated elements 1 and 2 (CCIE1 and CCIE2 prophages), which are C. coli homologues of CJIE1 and CJIE2, respectively. No induction was achieved for both prophages. Conversely, induction assays on CJIE1 and CJIE2 point towards the inducibility of these prophages. CCIE2-, CJIE1-, and CJIE4-like prophages were identified in a Campylobacter spp. population of 840 genomes, and phylogenetic analysis revealed clustering in three major groups: CJIE1-CCIE1, CJIE2-CCIE2, and CJIE4, clearly segregating prophages from C. jejuni and C. coli, but not from human- and nonhuman-derived isolates, corroborating the flowing between animals and humans in the agricultural context. Punctual bacteriophage host-jumps were observed in the context of C. jejuni and C. coli, and although random chance cannot be fully discarded, these observations seem to implicate prophages in evolutionary introgression events that are modulating the hybridization of C. jejuni and C. coli species.
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Affiliation(s)
- Luís Tanoeiro
- Pathogen Genome Bioinformatics and Computational Biology, Research Institute for Medicines (iMed-ULisboa), Faculty of Pharmacy, Universidade de Lisboa, 1649-003 Lisboa, Portugal; (L.T.); (A.T.M.); (J.M.B.V.)
| | - Mónica Oleastro
- National Reference Laboratory for Gastrointestinal Infections, Department of Infectious Diseases, National Institute of Health Dr. Ricardo Jorge, 1600-609 Lisboa, Portugal;
| | - Alexandra Nunes
- Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health Dr. Ricardo Jorge, 1600-609 Lisboa, Portugal; (A.N.); (J.P.G.)
| | - Andreia T. Marques
- Pathogen Genome Bioinformatics and Computational Biology, Research Institute for Medicines (iMed-ULisboa), Faculty of Pharmacy, Universidade de Lisboa, 1649-003 Lisboa, Portugal; (L.T.); (A.T.M.); (J.M.B.V.)
| | - Sílvia Vaz Duarte
- Innovation and Technology Unit, Department of Human Genetics, National Institute of Health Dr. Ricardo Jorge, 1600-609 Lisboa, Portugal;
| | - João Paulo Gomes
- Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health Dr. Ricardo Jorge, 1600-609 Lisboa, Portugal; (A.N.); (J.P.G.)
| | - António Pedro Alves Matos
- Centro de Investigação Interdisciplinar Egas Moniz (CiiEM), Cooperativa de Ensino Superior Egas Moniz, Quinta da Granja, 2829-511 Caparica, Portugal;
| | - Jorge M. B. Vítor
- Pathogen Genome Bioinformatics and Computational Biology, Research Institute for Medicines (iMed-ULisboa), Faculty of Pharmacy, Universidade de Lisboa, 1649-003 Lisboa, Portugal; (L.T.); (A.T.M.); (J.M.B.V.)
| | - Filipa F. Vale
- Pathogen Genome Bioinformatics and Computational Biology, Research Institute for Medicines (iMed-ULisboa), Faculty of Pharmacy, Universidade de Lisboa, 1649-003 Lisboa, Portugal; (L.T.); (A.T.M.); (J.M.B.V.)
- Correspondence: or
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Bloomfield SJ, Midwinter AC, Biggs PJ, French NP, Marshall JC, Hayman DTS, Carter PE, Mather AE, Fayaz A, Thornley C, Kelly DJ, Benschop J. Genomic adaptations of Campylobacter jejuni to long-term human colonization. Gut Pathog 2021; 13:72. [PMID: 34893079 PMCID: PMC8665580 DOI: 10.1186/s13099-021-00469-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Accepted: 12/01/2021] [Indexed: 01/23/2023] Open
Abstract
BACKGROUND Campylobacter is a genus of bacteria that has been isolated from the gastrointestinal tract of humans and animals, and the environments they inhabit around the world. Campylobacter adapt to new environments by changes in their gene content and expression, but little is known about how they adapt to long-term human colonization. In this study, the genomes of 31 isolates from a New Zealand patient and 22 isolates from a United Kingdom patient belonging to Campylobacter jejuni sequence type 45 (ST45) were compared with 209 ST45 genomes from other sources to identify the mechanisms by which Campylobacter adapts to long-term human colonization. In addition, the New Zealand patient had their microbiota investigated using 16S rRNA metabarcoding, and their level of inflammation and immunosuppression analyzed using biochemical tests, to determine how Campylobacter adapts to a changing gastrointestinal tract. RESULTS There was some evidence that long-term colonization led to genome degradation, but more evidence that Campylobacter adapted through the accumulation of non-synonymous single nucleotide polymorphisms (SNPs) and frameshifts in genes involved in cell motility, signal transduction and the major outer membrane protein (MOMP). The New Zealand patient also displayed considerable variation in their microbiome, inflammation and immunosuppression over five months, and the Campylobacter collected from this patient could be divided into two subpopulations, the proportion of which correlated with the amount of gastrointestinal inflammation. CONCLUSIONS This study demonstrates how genomics, phylogenetics, 16S rRNA metabarcoding and biochemical markers can provide insight into how Campylobacter adapts to changing environments within human hosts. This study also demonstrates that long-term human colonization selects for changes in Campylobacter genes involved in cell motility, signal transduction and the MOMP; and that genetically distinct subpopulations of Campylobacter evolve to adapt to the changing gastrointestinal environment.
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Affiliation(s)
| | - Anne C Midwinter
- mEpiLab, Hopkirk Research Institute, Massey University, Palmerston North, 4410, New Zealand
- Infectious Disease Research Centre, Hopkirk Research Institute, Massey University, Palmerston North, 4410, New Zealand
| | - Patrick J Biggs
- mEpiLab, Hopkirk Research Institute, Massey University, Palmerston North, 4410, New Zealand
- Infectious Disease Research Centre, Hopkirk Research Institute, Massey University, Palmerston North, 4410, New Zealand
- School of Fundamental Science, Massey University, Palmerston North, 4410, New Zealand
| | - Nigel P French
- Infectious Disease Research Centre, Hopkirk Research Institute, Massey University, Palmerston North, 4410, New Zealand
- New Zealand Food Safety Science and Research Centre, Hopkirk Research Institute, Massey University, Palmerston North, 4410, New Zealand
| | - Jonathan C Marshall
- mEpiLab, Hopkirk Research Institute, Massey University, Palmerston North, 4410, New Zealand
- Infectious Disease Research Centre, Hopkirk Research Institute, Massey University, Palmerston North, 4410, New Zealand
- School of Fundamental Science, Massey University, Palmerston North, 4410, New Zealand
| | - David T S Hayman
- mEpiLab, Hopkirk Research Institute, Massey University, Palmerston North, 4410, New Zealand
- Infectious Disease Research Centre, Hopkirk Research Institute, Massey University, Palmerston North, 4410, New Zealand
- Centre of Research Excellence for Complex Systems, Te Pūnaha Matatini, Auckland, New Zealand
| | - Philip E Carter
- Institute of Environmental Science of Research, 34 Kenepuru Drive, Kenepuru, Porirua, 5022, New Zealand
| | - Alison E Mather
- Quadram Institute Bioscience, Norwich Research Park, Norwich, Norfolk, UK
- University of East Anglia, Norwich, Norfolk, UK
| | - Ahmed Fayaz
- mEpiLab, Hopkirk Research Institute, Massey University, Palmerston North, 4410, New Zealand
- Infectious Disease Research Centre, Hopkirk Research Institute, Massey University, Palmerston North, 4410, New Zealand
| | - Craig Thornley
- Regional Public Health, Hutt Hospital, Lower Hutt, 5040, New Zealand
| | - David J Kelly
- School of Biosciences, The University of Sheffield, Sheffield, South Yorkshire, UK
| | - Jackie Benschop
- mEpiLab, Hopkirk Research Institute, Massey University, Palmerston North, 4410, New Zealand
- Infectious Disease Research Centre, Hopkirk Research Institute, Massey University, Palmerston North, 4410, New Zealand
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6
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Gomes CN, Barker DOR, Duque SDS, Che EV, Jayamanna V, Taboada EN, Falcão JP. Campylobacter coli isolated in Brazil typed by core genome Multilocus Sequence Typing shows high genomic diversity in a global context. INFECTION GENETICS AND EVOLUTION 2021; 95:105018. [PMID: 34332158 DOI: 10.1016/j.meegid.2021.105018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Revised: 07/21/2021] [Accepted: 07/25/2021] [Indexed: 11/29/2022]
Abstract
Campylobacter has been one of the most common causative agent of bacterial food-borne gastroenteritis in humans worldwide. However, in Brazil the campylobacteriosis has been a neglected disease and there is insufficient data to estimate the incidence of this pathogen in the country. AIMS The current study aimed to determine the phylogenetic relationships among Campylobacter coli strains isolated in Brazil and to compare them with international Campylobacter isolates available in some public databases. METHODS AND RESULTS A total of 63C. coli strains isolated in Brazil were studied. The MLST analysis showed 18 different STs including three STs not yet described in the PubMLST database. The cgMLST allocated the Brazilian strains studied into five main clusters and each cluster comprised groups of strains with nearly identical cgMLST profiles and with significant genetic distance observed among the distinct clusters. The comparison of the Brazilian strains with 3401 isolates from different countries showed a wide distribution of these strains isolated in this country. CONCLUSIONS The results showed a high similarity among some strains studied and a wide distribution of the Brazilian strains when compared to isolates from different countries, which is an interesting data set since it showed a high genetic diversity of these strains from Brazil in a global context. This study contributed for a better genomic characterization of C. coli strains isolated in Brazil and provided important information about the diversity of this clinically-relevant pathogen.
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Affiliation(s)
- Carolina Nogueira Gomes
- Departamento de Análises Clínicas, Toxicológicas e Bromatológicas, Faculdade de Ciências Farmacêuticas de Ribeirão Preto-Universidade de São Paulo, Ribeirão Preto, São Paulo, Brazil
| | | | | | - Emily Victoria Che
- National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Manitoba, Canada
| | - Vasena Jayamanna
- National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Manitoba, Canada
| | | | - Juliana Pfrimer Falcão
- Departamento de Análises Clínicas, Toxicológicas e Bromatológicas, Faculdade de Ciências Farmacêuticas de Ribeirão Preto-Universidade de São Paulo, Ribeirão Preto, São Paulo, Brazil.
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Joensen KG, Kiil K, Gantzhorn MR, Nauerby B, Engberg J, Holt HM, Nielsen HL, Petersen AM, Kuhn KG, Sandø G, Ethelberg S, Nielsen EM. Whole-Genome Sequencing to Detect Numerous Campylobacter jejuni Outbreaks and Match Patient Isolates to Sources, Denmark, 2015-2017. Emerg Infect Dis 2021; 26:523-532. [PMID: 32091364 PMCID: PMC7045838 DOI: 10.3201/eid2603.190947] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Abstract
In industrialized countries, the leading cause of bacterial gastroenteritis is Campylobacter jejuni. However, outbreaks are rarely reported, which may reflect limitations of surveillance, for which molecular typing is not routinely performed. To determine the frequency of genetic clusters among patients and to find links to concurrent isolates from poultry meat, broiler chickens, cattle, pigs, and dogs, we performed whole-genome sequencing on 1,509 C. jejuni isolates from 774 patients and 735 food or animal sources in Denmark during 2015–2017. We found numerous clusters; 366/774 (47.3%) clinical isolates formed 104 clusters of >2 isolates. A total of 41 patient clusters representing 199/366 (54%) patients matched a potential source, primarily domestic chickens/broilers. This study revealed serial outbreaks and numerous matches to concurrent food and animal isolates and highlighted the potential of whole-genome sequencing for improving routine surveillance of C. jejuni by enhancing outbreak detection, source tracing, and potentially prevention of human infections.
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8
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Analysis of Campylobacter jejuni Subtype Distribution in the Chicken Broiler Production Continuum: a Longitudinal Examination To Identify Primary Contamination Points. Appl Environ Microbiol 2021; 87:AEM.02001-20. [PMID: 33158900 DOI: 10.1128/aem.02001-20] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2020] [Accepted: 11/04/2020] [Indexed: 01/13/2023] Open
Abstract
Significant knowledge gaps exist in our understanding of Campylobacter jejuni contamination of the poultry production continuum. Microbiological surveillance and genotypic characterization were undertaken on C. jejuni isolates longitudinally recovered from three poultry farms (weekly samples), the abattoir at which birds were processed, and at retail over a 542-day period in southwestern Alberta, Canada, as a model location. Subtypes were compared to concurrent isolates from diarrheic humans living in the study region. Barn outbreaks in broiler chickens occurred infrequently. Subtypes from colonized birds, including clinically relevant subtypes of C. jejuni, were recovered within barns and from subsequent production stages. When C. jejuni was detected in barns, most birds rapidly became colonized by a limited number of subtypes late in the cycle. However, the diversity of subtypes recovered from birds in the abattoir increased substantially. Moreover, birds deemed free of C. jejuni upon exit from the barn became contaminated within the abattoir environment, and a high prevalence of meat at retail was contaminated with C. jejuni, including subtypes that had not been previously observed in the barns. The observed increase in prevalence of contamination and diversity of C. jejuni subtypes along the chicken production continuum indicates that birds from a relatively small number of barns contaminate transport trucks and the abattoir with C. jejuni strains, which are collectively transferred to poultry within the abattoir and conveyed to and persist on retail products. We conclude that the abattoir was the primary contamination point of poultry by C. jejuni but only a subset of subtypes were a high risk to human beings.IMPORTANCE The longitudinal examination of Campylobacter jejuni subtypes throughout the broiler production continuum is required to determine transmission mechanisms and to identify potential reservoirs and the foodborne risk posed. We showed that a limited number of C. jejuni subtypes are responsible for infrequent outbreaks in broilers within production barns and that colonized birds from a small number of farms are introduced into the abattoir where a high prevalence of carcasses are subsequently contaminated with a diversity of subtypes, which are transferred onto poultry in retail settings. However, only a subset of strains on poultry was determined to be clinically relevant. The study findings showed that resolving C. jejuni at the subtype level is important to ascertain health risks, and the knowledge obtained in the study provides information to mitigate clinically relevant subtypes to reduce the burden of campylobacteriosis.
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Nennig M, Llarena AK, Herold M, Mossong J, Penny C, Losch S, Tresse O, Ragimbeau C. Investigating Major Recurring Campylobacter jejuni Lineages in Luxembourg Using Four Core or Whole Genome Sequencing Typing Schemes. Front Cell Infect Microbiol 2021; 10:608020. [PMID: 33489938 PMCID: PMC7819963 DOI: 10.3389/fcimb.2020.608020] [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: 09/18/2020] [Accepted: 11/23/2020] [Indexed: 12/31/2022] Open
Abstract
Campylobacter jejuni is the leading cause of bacterial gastroenteritis, which has motivated the monitoring of genetic profiles circulating in Luxembourg since 13 years. From our integrated surveillance using a genotyping strategy based on an extended MLST scheme including gyrA and porA markers, an unexpected endemic pattern was discovered in the temporal distribution of genotypes. We aimed to test the hypothesis of stable lineages occurrence by implementing whole genome sequencing (WGS) associated with comprehensive and internationally validated schemes. This pilot study assessed four WGS-based typing schemes to classify a panel of 108 strains previously identified as recurrent or sporadic profiles using this in-house typing system. The strain collection included four common lineages in human infection (N = 67) initially identified from recurrent combination of ST-gyrA-porA alleles also detected in non-human samples: veterinary (N = 19), food (N = 20), and environmental (N = 2) sources. An additional set of 19 strains belonging to sporadic profiles completed the tested panel. All the strains were processed by WGS by using Illumina technologies and by applying stringent criteria for filtering sequencing data; we ensure robustness in our genomic comparison. Four typing schemes were applied to classify the strains: (i) the cgMLST SeqSphere+ scheme of 637 loci, (ii) the cgMLST Oxford scheme of 1,343 loci, (iii) the cgMLST INNUENDO scheme of 678 loci, and (iv) the wgMLST INNUENDO scheme of 2,795 loci. A high concordance between the typing schemes was determined by comparing the calculated adjusted Wallace coefficients. After quality control and analyses with these four typing schemes, 60 strains were confirmed as members of the four recurrent lineages regardless of the method used (N = 32, 12, 7, and 9, respectively). Our results indicate that, regardless of the typing scheme used, epidemic or endemic signals were detected as reflected by lineage B (ST2254-gyrA9-porA1) in 2014 or lineage A (ST19-gyrA8-porA7), respectively. These findings support the clonal expansion of stable genomes in Campylobacter population exhibiting a multi-host profile and accounting for the majority of clinical strains isolated over a decade. Such recurring genotypes suggest persistence in reservoirs, sources or environment, emphasizing the need to investigate their survival strategy in greater depth.
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Affiliation(s)
- Morgane Nennig
- Epidemiology and Microbial Genomics, Laboratoire National de Santé, Dudelange, Luxembourg.,INRAE, Oniris, SECALIM, Nantes, France
| | - Ann-Katrin Llarena
- Faculty of Veterinary Medicine, Norwegian University of Life Sciences, Oslo, Norway
| | - Malte Herold
- Epidemiology and Microbial Genomics, Laboratoire National de Santé, Dudelange, Luxembourg
| | - Joël Mossong
- Epidemiology and Microbial Genomics, Laboratoire National de Santé, Dudelange, Luxembourg
| | - Christian Penny
- Luxembourg Institute of Science and Technology, Environmental Research and Innovation Department, Belvaux, Luxembourg
| | - Serge Losch
- Laboratoire de Médecine Vétérinaire de l'Etat, Veterinary Services Administration, Dudelange, Luxembourg
| | | | - Catherine Ragimbeau
- Epidemiology and Microbial Genomics, Laboratoire National de Santé, Dudelange, Luxembourg
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10
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Davies E, Ebbesen M, Johansson C, Kaden R, Rautelin H. Genomic and Phenotypic Characterisation of Campylobacter jejuni Isolates From a Waterborne Outbreak. Front Cell Infect Microbiol 2020; 10:594856. [PMID: 33194843 PMCID: PMC7658296 DOI: 10.3389/fcimb.2020.594856] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2020] [Accepted: 10/06/2020] [Indexed: 01/15/2023] Open
Abstract
Campylobacter infections are the leading cause of bacterial gastroenteritis. In Europe, over 246,000 cases are confirmed annually. Infections are often transmitted via contaminated food, such as poultry products, but water may be the source of infection as well. The aim of this study was to characterise a selection of Campylobacter jejuni human isolates, together with a water isolate, from a waterborne outbreak in Norway in 2019, including human isolates from early, mid-, and late epidemic. The isolates were characterised with whole-genome sequencing, analysing the expression of putative virulence genes and demonstrating the pathogenic potential in an in vitro adhesion model using HT-29 cells. All isolates belonged to the multilocus sequence type 1701 and ST45 clonal complex. In the genomic analysis, the water isolate clustered somewhat separately from the human isolates. There was some variation between the human isolates, but the water isolate seemed to display the greatest pathogenic potential, demonstrated by the highest levels of virulence gene expression, adhesion to epithelial cells and IL-8 induction. These results suggest that the water isolate of the study has potential to cause human infections, and that some bacterial changes due to host or environmental adaptation, may occur during a waterborne Campylobacter epidemic. This is, to the best of our knowledge, the first study on C. jejuni isolates from a waterborne outbreak, including both human isolates and a water isolate, characterised with genomic and phenotypic approaches.
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Affiliation(s)
- Emma Davies
- Clinical Microbiology, Department of Medical Sciences, Uppsala University, Uppsala, Sweden
| | - Marit Ebbesen
- Department of Microbiology, Haukeland University Hospital, Bergen, Norway
| | - Cecilia Johansson
- Clinical Microbiology, Department of Medical Sciences, Uppsala University, Uppsala, Sweden
| | - René Kaden
- Clinical Microbiology, Department of Medical Sciences, Uppsala University, Uppsala, Sweden
| | - Hilpi Rautelin
- Clinical Microbiology, Department of Medical Sciences, Uppsala University, Uppsala, Sweden
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11
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Kelley BR, Ellis JC, Large A, Schneider LG, Jacobson D, Johnson JG. Whole-Genome Sequencing and Bioinformatic Analysis of Environmental, Agricultural, and Human Campylobacter jejuni Isolates From East Tennessee. Front Microbiol 2020; 11:571064. [PMID: 33224113 PMCID: PMC7674308 DOI: 10.3389/fmicb.2020.571064] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Accepted: 10/08/2020] [Indexed: 12/28/2022] Open
Abstract
As a leading cause of bacterial-derived gastroenteritis worldwide, Campylobacter jejuni has a significant impact on human health in both the developed and developing worlds. Despite its prevalence as a human pathogen, the source of these infections remains poorly understood due to the mutation frequency of the organism and past limitations of whole genome analysis. Recent advances in both whole genome sequencing and computational methods have allowed for the high-resolution analysis of intraspecies diversity, leading multiple groups to postulate that these approaches may be used to identify the sources of Campylobacter jejuni infection. To address this hypothesis, our group conducted a regionally and temporally restricted sampling of agricultural and environmental Campylobacter sources and compared isolated C. jejuni genomes to those that caused human infections in the same region during the same time period. Through a network analysis comparing genomes from various sources, we found that human C. jejuni isolates clustered with those isolated from cattle and chickens, indicating these as potential sources of human infection in the region.
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Affiliation(s)
- Brittni R Kelley
- Department of Microbiology, The University of Tennessee, Knoxville, Knoxville, TN, United States
| | | | - Annabel Large
- Biosciences, Oak Ridge National Laboratory, Oak Ridge, TN, United States
| | - Liesel G Schneider
- Department of Animal Science, The University of Tennessee, Knoxville, Knoxville, TN, United States
| | - Daniel Jacobson
- Biosciences, Oak Ridge National Laboratory, Oak Ridge, TN, United States
- Bredesen Center, The University of Tennessee, Knoxville, Knoxville, TN, United States
| | - Jeremiah G Johnson
- Department of Microbiology, The University of Tennessee, Knoxville, Knoxville, TN, United States
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12
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Prevalence and Genetic Diversity of C. Jejuni Isolated from Broilers and their Environment Using flaA-RFLP Typing and MLST Analysis. ANNALS OF ANIMAL SCIENCE 2020. [DOI: 10.2478/aoas-2020-0008] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Abstract
Campylobacter is highly diverse genetically and also undergoes frequent intraspecific recombination. A major source of campylobacteriosis, which is transmitted to humans is found in poultry. The assessment of the genetic diversity among Campylobacter population is critical to our understanding of the epidemiology. The genetic diversity of Campylobacter jejuni isolates in broilers and their environment were investigated by flaA-restriction fragment length polymorphism (RFLP) and multilocus sequence typing (MLST). The study revealed that 92.3% of the examined broiler flocks were contaminated with Campylobacter spp. A total number of 35 different flaA types defined by flaA-RFLP were found in 448 C. jejuni isolates originated from broilers, litter, puddles, zones, anteroom and wild birds. The most dominant flaA type was XXV. MLST defined 20 sequence types (STs) belonging to 10 clonal complexes (CCs). Among all the STs 9 isolates (15%) were consigned to 2 different STs (ST-7413 and ST-4800), which could not be assigned. The most common CCs were ST-21 and ST-179. The ST-21 CC was common in broilers and environment (puddle water and concentric zones) and the ST-179 CC was specific to wild birds, but also was found in puddle water and concentric zones.
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13
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Koutsoumanis K, Allende A, Alvarez-Ordóñez A, Bolton D, Bover-Cid S, Chemaly M, Davies R, De Cesare A, Hilbert F, Lindqvist R, Nauta M, Peixe L, Ru G, Simmons M, Skandamis P, Suffredini E, Jenkins C, Malorny B, Ribeiro Duarte AS, Torpdahl M, da Silva Felício MT, Guerra B, Rossi M, Herman L. Whole genome sequencing and metagenomics for outbreak investigation, source attribution and risk assessment of food-borne microorganisms. EFSA J 2019; 17:e05898. [PMID: 32626197 PMCID: PMC7008917 DOI: 10.2903/j.efsa.2019.5898] [Citation(s) in RCA: 64] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
This Opinion considers the application of whole genome sequencing (WGS) and metagenomics for outbreak investigation, source attribution and risk assessment of food‐borne pathogens. WGS offers the highest level of bacterial strain discrimination for food‐borne outbreak investigation and source‐attribution as well as potential for more precise hazard identification, thereby facilitating more targeted risk assessment and risk management. WGS improves linking of sporadic cases associated with different food products and geographical regions to a point source outbreak and can facilitate epidemiological investigations, allowing also the use of previously sequenced genomes. Source attribution may be favoured by improved identification of transmission pathways, through the integration of spatial‐temporal factors and the detection of multidirectional transmission and pathogen–host interactions. Metagenomics has potential, especially in relation to the detection and characterisation of non‐culturable, difficult‐to‐culture or slow‐growing microorganisms, for tracking of hazard‐related genetic determinants and the dynamic evaluation of the composition and functionality of complex microbial communities. A SWOT analysis is provided on the use of WGS and metagenomics for Salmonella and Shigatoxin‐producing Escherichia coli (STEC) serotyping and the identification of antimicrobial resistance determinants in bacteria. Close agreement between phenotypic and WGS‐based genotyping data has been observed. WGS provides additional information on the nature and localisation of antimicrobial resistance determinants and on their dissemination potential by horizontal gene transfer, as well as on genes relating to virulence and biological fitness. Interoperable data will play a major role in the future use of WGS and metagenomic data. Capacity building based on harmonised, quality controlled operational systems within European laboratories and worldwide is essential for the investigation of cross‐border outbreaks and for the development of international standardised risk assessments of food‐borne microorganisms.
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14
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Kovanen S, Rossi M, Pohja-Mykrä M, Nieminen T, Raunio-Saarnisto M, Sauvala M, Fredriksson-Ahomaa M, Hänninen ML, Kivistö R. Population Genetics and Characterization of Campylobacter jejuni Isolates from Western Jackdaws and Game Birds in Finland. Appl Environ Microbiol 2019; 85:e02365-18. [PMID: 30552190 PMCID: PMC6365822 DOI: 10.1128/aem.02365-18] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2018] [Accepted: 12/08/2018] [Indexed: 01/18/2023] Open
Abstract
Poultry are considered a major reservoir and source of human campylobacteriosis, but the roles of environmental reservoirs, including wild birds, have not been assessed in depth. In this study, we isolated and characterized Campylobacter jejuni from western jackdaws (n = 91, 43%), mallard ducks (n = 82, 76%), and pheasants (n = 9, 9%). Most of the western jackdaw and mallard duck C. jejuni isolates represented multilocus sequence typing (MLST) sequence types (STs) that diverged from those previously isolated from human patients and various animal species, whereas all pheasant isolates represented ST-19, a common ST among human patients and other hosts worldwide. Whole-genome MLST revealed that mallard duck ST-2314 and pheasant ST-19 isolates represented bacterial clones that were genetically highly similar to human isolates detected previously. Further analyses revealed that in addition to a divergent ClonalFrame genealogy, certain genomic characteristics of the western jackdaw C. jejuni isolates, e.g., a novel cdtABC gene cluster and the type VI secretion system (T6SS), may affect their host specificity and virulence. Game birds may thus pose a risk for acquiring campylobacteriosis; therefore, hygienic measures during slaughter and meat handling warrant special attention.IMPORTANCE The roles of environmental reservoirs, including wild birds, in the molecular epidemiology of Campylobacter jejuni have not been assessed in depth. Our results showed that game birds may pose a risk for acquiring campylobacteriosis, because they had C. jejuni genomotypes highly similar to human isolates detected previously. Therefore, hygienic measures during slaughter and meat handling warrant special attention. On the contrary, a unique phylogeny was revealed for the western jackdaw isolates, and certain genomic characteristics identified among these isolates are hypothesized to affect their host specificity and virulence. Comparative genomics within sequence types (STs), using whole-genome multilocus sequence typing (wgMLST), and phylogenomics are efficient methods to analyze the genomic relationships of C. jejuni isolates.
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Affiliation(s)
- Sara Kovanen
- Department of Food Hygiene and Environmental Health, Faculty of Veterinary Medicine, University of Helsinki, Helsinki, Finland
| | - Mirko Rossi
- Department of Food Hygiene and Environmental Health, Faculty of Veterinary Medicine, University of Helsinki, Helsinki, Finland
| | - Mari Pohja-Mykrä
- Ruralia Institute, Faculty of Agriculture and Forestry, University of Helsinki, Seinäjoki, Finland
| | - Timo Nieminen
- Ruralia Institute, Faculty of Agriculture and Forestry, University of Helsinki, Seinäjoki, Finland
| | | | - Mikaela Sauvala
- Department of Food Hygiene and Environmental Health, Faculty of Veterinary Medicine, University of Helsinki, Helsinki, Finland
| | - Maria Fredriksson-Ahomaa
- Department of Food Hygiene and Environmental Health, Faculty of Veterinary Medicine, University of Helsinki, Helsinki, Finland
| | - Marja-Liisa Hänninen
- Department of Food Hygiene and Environmental Health, Faculty of Veterinary Medicine, University of Helsinki, Helsinki, Finland
| | - Rauni Kivistö
- Department of Food Hygiene and Environmental Health, Faculty of Veterinary Medicine, University of Helsinki, Helsinki, Finland
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15
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Ricke SC, Feye KM, Chaney WE, Shi Z, Pavlidis H, Yang Y. Developments in Rapid Detection Methods for the Detection of Foodborne Campylobacter in the United States. Front Microbiol 2019; 9:3280. [PMID: 30728816 PMCID: PMC6351486 DOI: 10.3389/fmicb.2018.03280] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2018] [Accepted: 12/17/2018] [Indexed: 12/27/2022] Open
Abstract
The accurate and rapid detection of Campylobacter spp. is critical for optimal surveillance throughout poultry processing in the United States. The further development of highly specific and sensitive assays to detect Campylobacter in poultry matrices has tremendous utility and potential for aiding the reduction of foodborne illness. The introduction and development of molecular methods such as polymerase chain reaction (PCR) have enhanced the diagnostic capabilities of the food industry to identify the presence of foodborne pathogens throughout poultry production. Further innovations in various methodologies, such as immune-based typing and detection as well as high throughput analyses, will provide important epidemiological data such as the identification of unique or region-specific Campylobacter. Comparable to traditional microbiology and enrichment techniques, molecular techniques/methods have the potential to have improved sensitivity and specificity, as well as speed of data acquisition. This review will focus on the development and application of rapid molecular methods for identifying and quantifying Campylobacter in U.S. poultry and the emergence of novel methods that are faster and more precise than traditional microbiological techniques.
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Affiliation(s)
- Steven C. Ricke
- Department of Food Science, Center of Food Safety, University of Arkansas, Fayetteville, AR, United States
| | - Kristina M. Feye
- Department of Food Science, Center of Food Safety, University of Arkansas, Fayetteville, AR, United States
| | | | - Zhaohao Shi
- Department of Food Science, Center of Food Safety, University of Arkansas, Fayetteville, AR, United States
| | | | - Yichao Yang
- Department of Poultry Science, University of Arkansas, Fayetteville, AR, United States
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16
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García-Sánchez L, Melero B, Diez AM, Jaime I, Rovira J. Characterization of Campylobacter species in Spanish retail from different fresh chicken products and their antimicrobial resistance. Food Microbiol 2018; 76:457-465. [DOI: 10.1016/j.fm.2018.07.004] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2018] [Revised: 05/30/2018] [Accepted: 07/12/2018] [Indexed: 11/16/2022]
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17
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Rokney A, Valinsky L, Moran-Gilad J, Vranckx K, Agmon V, Weinberger M. Genomic Epidemiology of Campylobacter jejuni Transmission in Israel. Front Microbiol 2018; 9:2432. [PMID: 30386311 PMCID: PMC6198274 DOI: 10.3389/fmicb.2018.02432] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2018] [Accepted: 09/21/2018] [Indexed: 01/22/2023] Open
Abstract
Objectives: Campylobacter jejuni is responsible for 80% of Campylobacter infections in Israel, a country with a high incidence reaching 91/100,000 population. We studied the phylogeny, diversity and prevalence of virulence factors using whole genome sequencing (WGS) of a national sample of C. jejuni clinical, food, and animal isolates collected over a 10-year period (2003-2012). Methods: C. jejuni isolates (n = 263) were subject to WGS using Illumina sequencing (PE 250bpx2). Raw reads and de novo assemblies were analyzed with the BioNumerics whole genome MLST (wgMLST) pipeline. Reads were screened for 71 virulence genes by the SRST2 script. Allelic profiles were analyzed to create minimum spanning trees and allelic core distances were investigated to determine a reliable cutoff for strain determination. Results: wgMLST analysis of 263 C. jejuni isolates indicated significant diversity among the prevalent clonal complexes (CCs) with CC-21 and CC-353 being the most diverse, and CC-574 the most clonal. Within CC-21, sequence type (ST)-1359 created a separate clade. Human, poultry and bovine isolates clustered together across the different STs. Forty four percent of studied isolates were assigned to 29 genetic clusters. Temporal and geographical relatedness were found among the minority of clusters, while most phylogenetically associated cases appeared diffuse and unassociated epidemiologically. The majority of virulence factors were highly prevalent across the dataset and not associated with genotype, source of isolation or invasiveness. Conversely, all 13 genes associated with type VI secretion system (T6SS) were lineage-related and identified in only 18% of the isolates. T6SS was detected in 95.2% of ST-1359, a common type in Israel. Conclusions: wgMLST supported the assessment that poultry and cattle are likely food sources of infection in Israel. Substantial genetic clustering among C. jejuni isolates suggested multiple point source and diffuse outbreaks that were previously unreported in Israel. The high prevalence of T6SS among ST-1359 isolates is unique to Israel, and requires further investigation. This study exemplifies the importance of studying foodborne pathogens using advanced genomic approaches across the entire spectrum of One Health.
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Affiliation(s)
- Assaf Rokney
- Central Government Laboratories, Israel Ministry of Health, Jerusalem, Israel
| | - Lea Valinsky
- Central Government Laboratories, Israel Ministry of Health, Jerusalem, Israel
| | - Jacob Moran-Gilad
- Public Health Services, Israel Ministry of Health, Jerusalem, Israel.,Department of Health Policy and Management, Faculty of Health Sciences, School of Public Health, Ben-Gurion University of the Negev, Be'er-Sheva, Israel.,ESCMID Study Group for Genomic and Molecular Diagnostics, Basel, Switzerland
| | | | - Vered Agmon
- Central Government Laboratories, Israel Ministry of Health, Jerusalem, Israel
| | - Miriam Weinberger
- Infectious Diseases Unit, Assaf Harofeh Medical Center, Zerifin, Israel.,Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
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18
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Campylobacter jejuni survival in a poultry processing plant environment. Food Microbiol 2017; 65:185-192. [DOI: 10.1016/j.fm.2017.02.009] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2016] [Revised: 02/22/2017] [Accepted: 02/24/2017] [Indexed: 02/07/2023]
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19
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Taboada EN, Graham MR, Carriço JA, Van Domselaar G. Food Safety in the Age of Next Generation Sequencing, Bioinformatics, and Open Data Access. Front Microbiol 2017; 8:909. [PMID: 28588568 PMCID: PMC5440521 DOI: 10.3389/fmicb.2017.00909] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2017] [Accepted: 05/04/2017] [Indexed: 11/24/2022] Open
Abstract
Public health labs and food regulatory agencies globally are embracing whole genome sequencing (WGS) as a revolutionary new method that is positioned to replace numerous existing diagnostic and microbial typing technologies with a single new target: the microbial draft genome. The ability to cheaply generate large amounts of microbial genome sequence data, combined with emerging policies of food regulatory and public health institutions making their microbial sequences increasingly available and public, has served to open up the field to the general scientific community. This open data access policy shift has resulted in a proliferation of data being deposited into sequence repositories and of novel bioinformatics software designed to analyze these vast datasets. There also has been a more recent drive for improved data sharing to achieve more effective global surveillance, public health and food safety. Such developments have heightened the need for enhanced analytical systems in order to process and interpret this new type of data in a timely fashion. In this review we outline the emergence of genomics, bioinformatics and open data in the context of food safety. We also survey major efforts to translate genomics and bioinformatics technologies out of the research lab and into routine use in modern food safety labs. We conclude by discussing the challenges and opportunities that remain, including those expected to play a major role in the future of food safety science.
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Affiliation(s)
- Eduardo N Taboada
- National Microbiology Laboratory, Public Health Agency of Canada, WinnipegMB, Canada.,Department of Biological Sciences, University of Lethbridge, LethbridgeAB, Canada
| | - Morag R Graham
- National Microbiology Laboratory, Public Health Agency of Canada, WinnipegMB, Canada.,Department of Medical Microbiology and Infectious Diseases, Max Rady College of Medicine, University of Manitoba, WinnipegMB, Canada
| | - João A Carriço
- Instituto de Microbiologia, Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de LisboaLisbon, Portugal
| | - Gary Van Domselaar
- National Microbiology Laboratory, Public Health Agency of Canada, WinnipegMB, Canada.,Department of Medical Microbiology and Infectious Diseases, Max Rady College of Medicine, University of Manitoba, WinnipegMB, Canada
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20
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Abstract
This review describes the current state of knowledge regarding the application of whole-genome sequencing (WGS) in the epidemiology of Campylobacter jejuni, the leading cause of bacterial gastroenteritis worldwide. We describe how WGS has increased our understanding of the evolutionary and epidemiological dynamics of this pathogen and how WGS has the potential to improve surveillance and outbreak detection. We have identified hurdles to the full implementation of WGS in public health settings. Despite these challenges, we think that ample evidence is available to support the benefits of integrating WGS into the routine monitoring of C. jejuni infections and outbreak investigations.
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21
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Clark CG, Berry C, Walker M, Petkau A, Barker DOR, Guan C, Reimer A, Taboada EN. Genomic insights from whole genome sequencing of four clonal outbreak Campylobacter jejuni assessed within the global C. jejuni population. BMC Genomics 2016; 17:990. [PMID: 27912729 PMCID: PMC5135748 DOI: 10.1186/s12864-016-3340-8] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2016] [Accepted: 11/23/2016] [Indexed: 12/28/2022] Open
Abstract
BACKGROUND Whole genome sequencing (WGS) is useful for determining clusters of human cases, investigating outbreaks, and defining the population genetics of bacteria. It also provides information about other aspects of bacterial biology, including classical typing results, virulence, and adaptive strategies of the organism. Cell culture invasion and protein expression patterns of four related multilocus sequence type 21 (ST21) C. jejuni isolates from a significant Canadian water-borne outbreak were previously associated with the presence of a CJIE1 prophage. Whole genome sequencing was used to examine the genetic diversity among these isolates and confirm that previous observations could be attributed to differential prophage carriage. Moreover, we sought to determine the presence of genome sequences that could be used as surrogate markers to delineate outbreak-associated isolates. RESULTS Differential carriage of the CJIE1 prophage was identified as the major genetic difference among the four outbreak isolates. High quality single-nucleotide variant (hqSNV) and core genome multilocus sequence typing (cgMLST) clustered these isolates within expanded datasets consisting of additional C. jejuni strains. The number and location of homopolymeric tract regions was identical in all four outbreak isolates but differed from all other C. jejuni examined. Comparative genomics and PCR amplification enabled the identification of large chromosomal inversions of approximately 93 kb and 388 kb within the outbreak isolates associated with transducer-like proteins containing long nucleotide repeat sequences. The 93-kb inversion was characteristic of the outbreak-associated isolates, and the gene content of this inverted region displayed high synteny with the reference strain. CONCLUSIONS The four outbreak isolates were clonally derived and differed mainly in the presence of the CJIE1 prophage, validating earlier findings linking the prophage to phenotypic differences in virulence assays and protein expression. The identification of large, genetically syntenous chromosomal inversions in the genomes of outbreak-associated isolates provided a unique method for discriminating outbreak isolates from the background population. Transducer-like proteins appear to be associated with the chromosomal inversions. CgMLST and hqSNV analysis also effectively delineated the outbreak isolates within the larger C. jejuni population structure.
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Affiliation(s)
- Clifford G. Clark
- Division of Enteric Diseases, National Microbiology Laboratory, Public Health Agency of Canada, Canadian Science Centre for Human and Animal Health, 1015 Arlington Street, Winnipeg, MB R3E 3R2 Canada
| | - Chrystal Berry
- Division of Enteric Diseases, National Microbiology Laboratory, Public Health Agency of Canada, Canadian Science Centre for Human and Animal Health, 1015 Arlington Street, Winnipeg, MB R3E 3R2 Canada
| | - Matthew Walker
- Division of Enteric Diseases, National Microbiology Laboratory, Public Health Agency of Canada, Canadian Science Centre for Human and Animal Health, 1015 Arlington Street, Winnipeg, MB R3E 3R2 Canada
| | - Aaron Petkau
- Bioinformatics Core Facility, National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, MB R3E 3R2 Canada
| | - Dillon O. R. Barker
- Division of Enteric Diseases, National Microbiology Laboratory, Public Health Agency of Canada, Lethbridge, AB T1J 3Z4 Canada
- Department of Biological Sciences, University of Lethbridge, Lethbridge, AB Canada
| | - Cai Guan
- Division of Enteric Diseases, National Microbiology Laboratory, Public Health Agency of Canada, Canadian Science Centre for Human and Animal Health, 1015 Arlington Street, Winnipeg, MB R3E 3R2 Canada
| | - Aleisha Reimer
- Division of Enteric Diseases, National Microbiology Laboratory, Public Health Agency of Canada, Canadian Science Centre for Human and Animal Health, 1015 Arlington Street, Winnipeg, MB R3E 3R2 Canada
| | - Eduardo N. Taboada
- Division of Enteric Diseases, National Microbiology Laboratory, Public Health Agency of Canada, Lethbridge, AB T1J 3Z4 Canada
- Department of Biological Sciences, University of Lethbridge, Lethbridge, AB Canada
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22
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Comparative genomic fingerprinting of Campylobacter: application in routine public health surveillance and epidemiological investigations. Epidemiol Infect 2016; 145:299-309. [PMID: 27766988 DOI: 10.1017/s0950268816002351] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
A subtyping methodology for Campylobacter, Comparative Genomic Fingerprinting (CGF40), has been described recently. The objective of this study was to assess the utility of CGF40 as a tool to enhance routine public health surveillance of campylobacteriosis. Isolates of Campylobacter from across the province were requested and sent for CGF40 subtyping. Epidemiological data from cases reported to public health officials in Nova Scotia, Canada, from January 2012 to March 2015 were linked with blinded CGF40 subtyping results. CGF40 was epidemiologically valid; subtyping discerned known epidemiologically related isolates and augmented case-finding. Predominant sources and locations of subtype detection from the national reference database showed some study subtypes were rare and even novel to the database, while others were more commonly identified over multiple years and with exposures locally and internationally. A case-case study design was applied to examine risk factors for the most common CGF40 subtypes detected. Differences in the epidemiology of different CGF40 subtypes were observed. Statistically significant associations were noted for specific subtypes with rural residence, local exposure, contact with a pet dog or cat, contact with chickens, and drinking unpasteurized milk. With prospective use, CGF40 could potentially identify unrecognized outbreaks and contribute to epidemiological investigations of case clusters.
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23
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Llarena AK, Zhang J, Vehkala M, Välimäki N, Hakkinen M, Hänninen ML, Roasto M, Mäesaar M, Taboada E, Barker D, Garofolo G, Cammà C, Di Giannatale E, Corander J, Rossi M. Monomorphic genotypes within a generalist lineage of Campylobacter jejuni show signs of global dispersion. Microb Genom 2016; 2:e000088. [PMID: 28348829 PMCID: PMC5359405 DOI: 10.1099/mgen.0.000088] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2016] [Accepted: 09/12/2016] [Indexed: 01/05/2023] Open
Abstract
The decreased costs of genome sequencing have increased the capability to apply whole-genome sequencing to epidemiological surveillance of zoonotic Campylobacter jejuni. However, knowledge of the genetic diversity of this bacteria is vital for inferring relatedness between epidemiologically linked isolates and a necessary prerequisite for correct application of this methodology. To address this issue in C. jejuni we investigated the spatial and temporal signals in the genomes of a major clonal complex and generalist lineage, ST-45 CC, by analysing the population structure and genealogy as well as applying genome-wide association analysis of 340 isolates from across Europe collected over a wide time range. The occurrence and strength of the geographical signal varied between sublineages and followed the clonal frame when present, while no evidence of a temporal signal was found. Certain sublineages of ST-45 formed discrete and genetically isolated clades containing isolates with extremely similar genomes regardless of time and location of sampling. Based on a separate data set, these monomorphic genotypes represent successful C. jejuni clones, possibly spread around the globe by rapid animal (migrating birds), food or human movement. In addition, we observed an incongruence between the genealogy of the strains and multilocus sequence typing (MLST), challenging the existing clonal complex definition and the use of whole-genome gene-by-gene hierarchical nomenclature schemes for C. jejuni.
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Affiliation(s)
- Ann-Katrin Llarena
- Department of Food Hygiene and Environmental Health, Faculty of Veterinary Medicine, University of Helsinki, Helsinki, Finland
| | - Ji Zhang
- Institute of Veterinary, Animal & Biomedical Sciences, College of Sciences, Massey University, Palmerstone North, New Zealand
| | - Minna Vehkala
- Department of Mathematics and Statistics, Faculty of Science, University of Helsinki, Helsinki, Finland
| | - Niko Välimäki
- Department of Medical and Clinical Genetics, Genome-Scale Biology Research Program, University of Helsinki, Helsinki, Finland
| | - Marjaana Hakkinen
- Food and Feed Microbiology Research Unit, Research and Laboratory Department, Finnish Food Safety Authority Evira, Helsinki, Finland
| | - Marja-Liisa Hänninen
- Department of Food Hygiene and Environmental Health, Faculty of Veterinary Medicine, University of Helsinki, Helsinki, Finland
| | - Mati Roasto
- Department of Food Hygiene, Institute of Veterinary Medicine and Animal Sciences, Estonian University of Life Sciences, Tartu, Estonia
| | - Mihkel Mäesaar
- Department of Food Hygiene, Institute of Veterinary Medicine and Animal Sciences, Estonian University of Life Sciences, Tartu, Estonia
- Veterinary and Food Laboratory, VFL, Tartu, Estonia
| | - Eduardo Taboada
- National Microbiology Laboratory, Public Health Agency of Canada, c/o Animal Diseases Research Institute, Lethbridge, Canada
| | - Dillon Barker
- National Microbiology Laboratory, Public Health Agency of Canada, c/o Animal Diseases Research Institute, Lethbridge, Canada
| | - Giuliano Garofolo
- National Reference Laboratory for Campylobacter, Istituto Zooprofilattico Sperimentale dell'Abruzzo e del Molise ‘G. Caporale’, Teramo, Italy
| | - Cesare Cammà
- National Reference Laboratory for Campylobacter, Istituto Zooprofilattico Sperimentale dell'Abruzzo e del Molise ‘G. Caporale’, Teramo, Italy
| | - Elisabetta Di Giannatale
- National Reference Laboratory for Campylobacter, Istituto Zooprofilattico Sperimentale dell'Abruzzo e del Molise ‘G. Caporale’, Teramo, Italy
| | - Jukka Corander
- Institute of Basic Medical Sciences, Department of Biostatistics, Faculty of Medicine, University of Oslo, Oslo, Norway
| | - Mirko Rossi
- Department of Food Hygiene and Environmental Health, Faculty of Veterinary Medicine, University of Helsinki, Helsinki, Finland
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Ronholm J, Nasheri N, Petronella N, Pagotto F. Navigating Microbiological Food Safety in the Era of Whole-Genome Sequencing. Clin Microbiol Rev 2016; 29:837-57. [PMID: 27559074 PMCID: PMC5010751 DOI: 10.1128/cmr.00056-16] [Citation(s) in RCA: 103] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
The epidemiological investigation of a foodborne outbreak, including identification of related cases, source attribution, and development of intervention strategies, relies heavily on the ability to subtype the etiological agent at a high enough resolution to differentiate related from nonrelated cases. Historically, several different molecular subtyping methods have been used for this purpose; however, emerging techniques, such as single nucleotide polymorphism (SNP)-based techniques, that use whole-genome sequencing (WGS) offer a resolution that was previously not possible. With WGS, unlike traditional subtyping methods that lack complete information, data can be used to elucidate phylogenetic relationships and disease-causing lineages can be tracked and monitored over time. The subtyping resolution and evolutionary context provided by WGS data allow investigators to connect related illnesses that would be missed by traditional techniques. The added advantage of data generated by WGS is that these data can also be used for secondary analyses, such as virulence gene detection, antibiotic resistance gene profiling, synteny comparisons, mobile genetic element identification, and geographic attribution. In addition, several software packages are now available to generate in silico results for traditional molecular subtyping methods from the whole-genome sequence, allowing for efficient comparison with historical databases. Metagenomic approaches using next-generation sequencing have also been successful in the detection of nonculturable foodborne pathogens. This review addresses state-of-the-art techniques in microbial WGS and analysis and then discusses how this technology can be used to help support food safety investigations. Retrospective outbreak investigations using WGS are presented to provide organism-specific examples of the benefits, and challenges, associated with WGS in comparison to traditional molecular subtyping techniques.
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Affiliation(s)
- J Ronholm
- Bureau of Microbial Hazards, Food Directorate, Health Canada, Ottawa, ON, Canada
| | - Neda Nasheri
- Bureau of Microbial Hazards, Food Directorate, Health Canada, Ottawa, ON, Canada
| | - Nicholas Petronella
- Biostatistics and Modelling Division, Bureau of Food Surveillance and Science Integration, Food Directorate, Health Canada, Ottawa, ON, Canada
| | - Franco Pagotto
- Bureau of Microbial Hazards, Food Directorate, Health Canada, Ottawa, ON, Canada Listeriosis Reference Centre, Bureau of Microbial Hazards, Food Directorate, Health Canada, Ottawa, ON, Canada
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Manfreda G, Parisi A, De Cesare A, Mion D, Piva S, Zanoni RG. Typing of Campylobacter jejuni Isolated from Turkey by Genotypic Methods, Antimicrobial Susceptibility, and Virulence Gene Patterns: A Retrospective Study. Foodborne Pathog Dis 2015; 13:93-100. [PMID: 26693797 DOI: 10.1089/fpd.2015.2048] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
In this retrospective study, typing ability, discriminatory power, and concordance between typing results obtained on 123 Campylobacter jejuni turkey isolates, collected in 1998, within 14 different farms, applying multilocus sequence typing (MLST), pulsed-field gel electrophoresis (PFGE), antibiotic resistance profile, and virulence gene pattern, were assessed and compared. Overall, 33 sequence types, 28 pulsotypes, 10 resistotypes, and 5 pathotypes were identified. MLST and PFGE showed the better discriminatory ability (i.e., Simpson's diversity index >0.90) as well as unidirectional (i.e., Wallace and adjusted Wallace coefficients >0.86) and bidirectional (i.e., adjusted Rand coefficient >0.60) concordance. Moreover, both methods showed a good unidirectional and bidirectional concordance with the resistotype. On the contrary, the congruence of both genotyping methods and resistotype with the pathotype seemed due to chance alone. A clonal relationship was identified among 66.7% of the isolates. Furthermore, 59.7% of the investigated isolates were resistant to two or more antimicrobials and 92% to tetracycline. All the isolates harbored cadF and pldA genes, whereas a flaA gene product and a cdtB gene product were amplified from 85.4% and 79.7% of the isolates, respectively, using the primers designed by Bang et al. (2003). The results of this study clarify the level of genetic diversity among the C. jejuni originating from turkeys. MLST level of correlation with PFGE, resistotype, and pathotype is assessed. This result supports the selection of type and number of typing methods to use in epidemiological studies. Finally, the identification of clonal complexes (i.e., groups of profiles differing by no more than one gene from at least one other profile of the group using the entire Campylobacter MLST database) shared between turkey and human isolates suggests that turkeys could be a possible source of Campylobacter infection.
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Affiliation(s)
- Gerardo Manfreda
- 1 Department of Agricultural and Food Sciences, University of Bologna , Ozzano dell'Emilia, Italy
| | - Antonio Parisi
- 2 Experimental Zooprophylactic Institute of Apulia and Basilicata , Foggia, Italy
| | - Alessandra De Cesare
- 1 Department of Agricultural and Food Sciences, University of Bologna , Ozzano dell'Emilia, Italy
| | - Domenico Mion
- 3 Department of Veterinary Medical Sciences, University of Bologna , Ozzano dell'Emilia, Italy
| | - Silvia Piva
- 3 Department of Veterinary Medical Sciences, University of Bologna , Ozzano dell'Emilia, Italy
| | - Renato G Zanoni
- 3 Department of Veterinary Medical Sciences, University of Bologna , Ozzano dell'Emilia, Italy
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Olkkola S, Kovanen S, Roine J, Hänninen ML, Hielm-Björkman A, Kivistö R. Population Genetics and Antimicrobial Susceptibility of Canine Campylobacter Isolates Collected before and after a Raw Feeding Experiment. PLoS One 2015; 10:e0132660. [PMID: 26172151 PMCID: PMC4501809 DOI: 10.1371/journal.pone.0132660] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2015] [Accepted: 06/17/2015] [Indexed: 11/26/2022] Open
Abstract
In recent years, increasing numbers of consumers have become interested in feeding raw food for their pet dogs as opposed to commercial dry food, in the belief of health advantages. However, raw meat and internal organs, possibly contaminated by pathogens such as Campylobacter spp., may pose a risk of transmission of zoonoses to the pet owners. Campylobacter jejuni is the leading cause of bacterial gastroenteritis in humans but C. upsaliensis has also been associated with human disease. In this study we investigated the effect of different feeding strategies on the prevalence of Campylobacter spp. in Finnish dogs. We further characterized the isolates using multilocus sequence typing (MLST), whole-genome (wg) MLST and antimicrobial susceptibility testing. Dogs were sampled before and after a feeding period consisting of commercial raw feed or dry pellet feed. Altogether 56% (20/36) of the dogs yielded at least one Campylobacter-positive fecal sample. C. upsaliensis was the major species detected from 39% of the dogs before and 30% after the feeding period. Two C. jejuni isolates were recovered, both from raw-fed dogs after the dietary regimen. The isolates represented the same genotype (ST-1326), suggesting a common infection source. However, no statistically significant correlation was found between the feeding strategies and Campylobacter spp. carriage. The global genealogy of MLST types of dog and human C. upsaliensis isolates revealed weakly clonal population structure as most STs were widely dispersed. Major antimicrobial resistance among C. upsaliensis isolates was against streptomycin (STR MIC > 4 mg/l). Apart from that, all isolates were highly susceptible against the antimicrobials tested. Mutations were found in the genes rpsL or rpsL and rsmG in streptomycin resistant isolates. In conclusion, increasing trend to feed dogs with raw meat warrants more studies to evaluate the risk associated with raw feeding of pets in transmission of zoonoses to humans.
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Affiliation(s)
- Satu Olkkola
- Department of Food Hygiene and Environmental Health, Faculty of Veterinary Medicine, University of Helsinki, Helsinki, Finland
| | - Sara Kovanen
- Department of Food Hygiene and Environmental Health, Faculty of Veterinary Medicine, University of Helsinki, Helsinki, Finland
| | - Johanna Roine
- Department of Equine and Small Animal Medicine, Faculty of Veterinary Medicine, University of Helsinki, Helsinki, Finland
| | - Marja-Liisa Hänninen
- Department of Food Hygiene and Environmental Health, Faculty of Veterinary Medicine, University of Helsinki, Helsinki, Finland
| | - Anna Hielm-Björkman
- Department of Equine and Small Animal Medicine, Faculty of Veterinary Medicine, University of Helsinki, Helsinki, Finland
| | - Rauni Kivistö
- Department of Food Hygiene and Environmental Health, Faculty of Veterinary Medicine, University of Helsinki, Helsinki, Finland
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Refinement of whole-genome multilocus sequence typing analysis by addressing gene paralogy. J Clin Microbiol 2015; 53:1765-7. [PMID: 25788543 DOI: 10.1128/jcm.00051-15] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2015] [Accepted: 03/10/2015] [Indexed: 11/20/2022] Open
Abstract
We developed a user-friendly program, Genome Profiler (GeP), to refine whole-genome multilocus sequence typing analysis by addressing gene paralogy with conserved gene neighborhoods. In comparison to similar programs, GeP produced overall the best results in terms of accuracy and is thus a useful alternative to resolve relationships of bacterial isolates.
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28
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Llarena AK, Huneau A, Hakkinen M, Hänninen ML. Predominant Campylobacter jejuni sequence types persist in Finnish chicken production. PLoS One 2015; 10:e0116585. [PMID: 25700264 PMCID: PMC4336332 DOI: 10.1371/journal.pone.0116585] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2014] [Accepted: 12/11/2014] [Indexed: 12/04/2022] Open
Abstract
Consumption and handling of chicken meat are well-known risk factors for acquiring campylobacteriosis. This study aimed to describe the Campylobacter jejuni population in Finnish chickens and to investigate the distribution of C. jejuni genotypes on Finnish chicken farms over a period of several years. We included 89.8% of the total C. jejuni population recovered in Finnish poultry during 2004, 2006, 2007, 2008, and 2012 and used multilocus sequence typing (MLST) and pulsed-field gel electrophoresis (PFGE) to characterize the 380 isolates. The typing data was combined with isolate information on collection-time and farm of origin. The C. jejuni prevalence in chicken slaughter batches was low (mean 3.0%, CI95% [1.8%, 4.2%]), and approximately a quarter of Finnish chicken farms delivered at least one positive chicken batch yearly. In general, the C. jejuni population was diverse as represented by a total of 63 sequence types (ST), but certain predominant MLST lineages were identified. ST-45 clonal complex (CC) accounted for 53% of the isolates while ST-21 CC and ST-677 CC covered 11% and 9% of the isolates, respectively. Less than half of the Campylobacter positive farms (40.3%) delivered C. jejuni-contaminated batches in multiple years, but the genotypes (ST and PFGE types) generally varied from year to year. Therefore, no evidence for a persistent C. jejuni source for the colonization of Finnish chickens emerged. Finnish chicken farms are infrequently contaminated with C. jejuni compared to other European Union (EU) countries, making Finland a valuable model for further epidemiological studies of the C. jejuni in poultry flocks.
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Affiliation(s)
- Ann-Katrin Llarena
- Department of Food Hygiene and Environmental Health, Faculty of Veterinary Medicine, University of Helsinki, Helsinki, Finland
| | - Adeline Huneau
- Anses, Ploufragan-Plouzané laboratory, BP 53, 22440, Ploufragan, France
| | - Marjaana Hakkinen
- Food and Feed Microbiology Research Unit, Research and Laboratory Department, Finnish Food Safety Authority, Evira, Helsinki, Finland
| | - Marja-Liisa Hänninen
- Department of Food Hygiene and Environmental Health, Faculty of Veterinary Medicine, University of Helsinki, Helsinki, Finland
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