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Admasie A, Wei X, Johnson B, Burns L, Pawar P, Aurand-Cravens A, Voloshchuk O, Dudley EG, Sisay Tessema T, Zewdu A, Kovac J. Genomic diversity of Campylobacter jejuni and Campylobacter coli isolated from the Ethiopian dairy supply chain. PLoS One 2024; 19:e0305581. [PMID: 39159178 PMCID: PMC11332940 DOI: 10.1371/journal.pone.0305581] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2023] [Accepted: 05/31/2024] [Indexed: 08/21/2024] Open
Abstract
Campylobacteriosis outbreaks have previously been linked to dairy foods. While the genetic diversity of Campylobacter is well understood in high-income countries, it is largely unknown in low-income countries, such as Ethiopia. This study therefore aimed to conduct the first genomic characterization of Campylobacter isolates from the Ethiopian dairy supply chain to aid in future epidemiological studies. Fourteen C. jejuni and four C. coli isolates were whole genome sequenced using an Illumina platform. Sequences were analyzed using the bioinformatics tools in the GalaxyTrakr platform to identify MLST types, and single nucleotide polymorphisms, and infer phylogenetic relationships among the studied isolates. Assembled genomes were further screened to detect antimicrobial resistance and virulence gene sequences. Among 14 C. jejuni, ST 2084 and ST 51, which belong to the clonal complexes ST-353 and ST-443, respectively, were identified. Among the 4 sequenced C. coli isolates, two isolates belonged to ST 1628 and two to ST 830 from the clonal complex ST-828. The isolates of C. jejuni ST 2084 and ST 51 carried β-lactam resistance gene blaOXA-605, a fluoroquinolone resistance-associated mutation T86I in the gryA gene, and a macrolide resistance-associated mutation A103V in 50S L22. Only ST 2084 isolates carried the tetracycline resistance gene tetO. Conversely, all four C. coli ST 830 and ST 1628 isolates carried tetO, but only ST 1628 isolates also carried blaOXA-605. Lastly, C. jejuni ST 2084 isolates carried a total of 89 virulence genes, and ST 51 isolates carried up to 88 virulence genes. Among C. coli, ST 830 isolates carried 71 genes involved in virulence, whereas two ST 1628 isolates carried up to 82 genes involved in virulence. Isolates from all identified STs have previously been isolated from human clinical cases, demonstrating a potential food safety concern. This finding warrants further monitoring of Campylobacter in dairy foods in Ethiopia to better understand and manage the risks associated with Campylobacter contamination and transmission.
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Affiliation(s)
- Abera Admasie
- Institute of Biotechnology, Addis Ababa University, Addis Ababa, Ethiopia
- Department of Biology, College of Natural and Computational Sciences, Arba Minch University, Arba Minch, Ethiopia
| | - Xiaoyuan Wei
- Department of Food Science, The Pennsylvania State University, University Park, PA, United States of America
| | - Beth Johnson
- Division of Laboratory Services, Kentucky Department of Public Health, Frankfort, KY, United States of America
| | - Logan Burns
- Division of Laboratory Services, Kentucky Department of Public Health, Frankfort, KY, United States of America
| | - Preeti Pawar
- Division of Laboratory Services, Kentucky Department of Public Health, Frankfort, KY, United States of America
| | - Ashley Aurand-Cravens
- Division of Laboratory Services, Kentucky Department of Public Health, Frankfort, KY, United States of America
| | - Olena Voloshchuk
- Department of Food Science, The Pennsylvania State University, University Park, PA, United States of America
| | - Edward G. Dudley
- Department of Food Science, The Pennsylvania State University, University Park, PA, United States of America
| | | | - Ashagrie Zewdu
- Center for Food Science and Nutrition, Addis Ababa University, Addis Ababa, Ethiopia
| | - Jasna Kovac
- Department of Food Science, The Pennsylvania State University, University Park, PA, United States of America
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Poorrashidi M, Hitchcock M, Xu J. Meta-analyses of the global multilocus genotypes of the human pathogen Campylobacter jejuni. Genome 2024; 67:189-203. [PMID: 38427983 DOI: 10.1139/gen-2023-0041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/03/2024]
Abstract
Campylobacter infections are a leading cause of bacterial diarrheal illness worldwide, with increasing reports of outbreaks in both developing and developed countries. Most studies investigating strain genotypes and epidemiology of Campylobacter jejuni examined on a local scale. Using the archived multilocus sequence typing data at seven loci, and associated strain metadata from the PubMLST database, here we investigated the spatial and temporal genetic structure of the global population of C. jejuni. Our analyses revealed evidence for clonal dispersals of multiple sequence types (STs) among countries and continents. However, despite the observed clonal dispersal and that most genetic variations were found within individual geographic subpopulations, both the non-clone-corrected and clone-corrected samples showed evidence of significant genetic differentiation among national and continental subpopulations, with non-clone-corrected samples showing greater differentiation than clone-corrected samples. Phylogenetic incompatibility analyses provided evidence for recombination within each continental subpopulation. However, linkage disequilibrium analyses rejected the hypothesis of random recombination across the samples. Temporally, multiple STs were found to persist across four decades and the five globally most common STs showed relatively stable frequencies over the last two decades. We discussed the implications of our results to food security, disease transmission, and public health management.
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Affiliation(s)
- Monir Poorrashidi
- Department of Biology, McMaster University, Hamilton, ON L8S 4K1, Canada
| | - Megan Hitchcock
- Department of Biology, McMaster University, Hamilton, ON L8S 4K1, Canada
| | - Jianping Xu
- Department of Biology, McMaster University, Hamilton, ON L8S 4K1, Canada
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Kong N, Luo Y, Liu J, Yao G, Hu Y, Shu S, Li C, Bi S. Subtyping of Campylobacter coli isolated from raw poultry meat in retail markets using amplified intergenic locus polymorphism - A novel rapid subtyping method. J Microbiol Methods 2023; 204:106662. [PMID: 36572193 DOI: 10.1016/j.mimet.2022.106662] [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: 11/02/2022] [Revised: 12/22/2022] [Accepted: 12/22/2022] [Indexed: 12/25/2022]
Abstract
In order to provide more phylogenetic information of Campylobacter coli in large-scale epidemiological investigation, this work was undertaken to develop a novel genotyping method based on amplified intergenic locus polymorphism (AILP), by using pulsed-field gel electrophoresis (PFGE; using SmaI enzymes) as control. Eleven pairs of primers were selected to type C. coli strains for this purpose. A total of 68 C. coli isolates recovered from 51 retail raw chicken and 37 retail raw duck were subtyped. The Simpson's index of diversity (SID) of AILP and PFGE, as well as the adjusted Rand index (AR) and the adjusted Wallace coefficient (AW) between AILP and PFGE, were calculated. The new AILP method differentiated 68 C. coli isolates into 55 different subtypes (SID = 0.993), compared with 46 different profiles obtained from PFGE (SID = 0.980). The SID value of the AILP method was improved with the increasing number of primers, and a combination of 7 loci was selected as the optimal combination. The congruent analysis of the AILP method and PFGE showed moderate congruence between the two methods (AR = 0.462). The AW indicated that if AILP data is the available one can confidently predict the PFGE cluster. The results of this study showed that the AILP method had higher discrimination than PFGE and also allowed for significant reduction in time and cost.
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Affiliation(s)
- Nianqing Kong
- College of Food Science, Guangdong Pharmaceutical University, Zhongshan 528458, Guangdong, China; College of Public Health, Guangdong Pharmaceutical University, Guangzhou 510220, Guangdong, China
| | - Yongwen Luo
- College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, Guangdong, China
| | - Jinhong Liu
- College of Food Science, Guangdong Pharmaceutical University, Zhongshan 528458, Guangdong, China; College of Public Health, Guangdong Pharmaceutical University, Guangzhou 510220, Guangdong, China
| | - Gefeng Yao
- College of Food Science, Guangdong Pharmaceutical University, Zhongshan 528458, Guangdong, China; College of Public Health, Guangdong Pharmaceutical University, Guangzhou 510220, Guangdong, China
| | - Yilin Hu
- College of Food Science, Guangdong Pharmaceutical University, Zhongshan 528458, Guangdong, China; College of Public Health, Guangdong Pharmaceutical University, Guangzhou 510220, Guangdong, China
| | - Shenghuang Shu
- College of Food Science, Guangdong Pharmaceutical University, Zhongshan 528458, Guangdong, China; College of Public Health, Guangdong Pharmaceutical University, Guangzhou 510220, Guangdong, China
| | - Chuyi Li
- College of Food Science, Guangdong Pharmaceutical University, Zhongshan 528458, Guangdong, China
| | - Shuilian Bi
- College of Food Science, Guangdong Pharmaceutical University, Zhongshan 528458, Guangdong, China.
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Liang KYH, Orata FD, Islam MT, Nasreen T, Alam M, Tarr CL, Boucher YF. A Vibrio cholerae Core Genome Multilocus Sequence Typing Scheme To Facilitate the Epidemiological Study of Cholera. J Bacteriol 2020; 202:e00086-20. [PMID: 32540931 PMCID: PMC7685551 DOI: 10.1128/jb.00086-20] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2020] [Accepted: 06/07/2020] [Indexed: 12/11/2022] Open
Abstract
Core genome multilocus sequence typing (cgMLST) has gained popularity in recent years in epidemiological research and subspecies-level classification. cgMLST retains the intuitive nature of traditional MLST but offers much greater resolution by utilizing significantly larger portions of the genome. Here, we introduce a cgMLST scheme for Vibrio cholerae, a bacterium abundant in marine and freshwater environments and the etiologic agent of cholera. A set of 2,443 core genes ubiquitous in V. cholerae were used to analyze a comprehensive data set of 1,262 clinical and environmental strains collected from 52 countries, including 65 newly sequenced genomes in this study. We established a sublineage threshold based on 133 allelic differences that creates clusters nearly identical to traditional MLST types, providing backwards compatibility to new cgMLST classifications. We also defined an outbreak threshold based on seven allelic differences that is capable of identifying strains from the same outbreak and closely related isolates that could give clues on outbreak origin. Using cgMLST, we confirmed the South Asian origin of modern epidemics and identified clustering affinity among sublineages of environmental isolates from the same geographic origin. Advantages of this method are highlighted by direct comparison with existing classification methods, such as MLST and single-nucleotide polymorphism-based methods. cgMLST outperforms all existing methods in terms of resolution, standardization, and ease of use. We anticipate this scheme will serve as a basis for a universally applicable and standardized classification system for V. cholerae research and epidemiological surveillance in the future. This cgMLST scheme is publicly available on PubMLST (https://pubmlst.org/vcholerae/).IMPORTANCE Toxigenic Vibrio cholerae isolates of the O1 and O139 serogroups are the causative agents of cholera, an acute diarrheal disease that plagued the world for centuries, if not millennia. Here, we introduce a core genome multilocus sequence typing scheme for V. cholerae Using this scheme, we have standardized the definition for subspecies-level classification, facilitating global collaboration in the surveillance of V. cholerae In addition, this typing scheme allows for quick identification of outbreak-related isolates that can guide subsequent analyses, serving as an important first step in epidemiological research. This scheme is also easily scalable to analyze thousands of isolates at various levels of resolution, making it an invaluable tool for large-scale ecological and evolutionary analyses.
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Affiliation(s)
- Kevin Y H Liang
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta, Canada
| | - Fabini D Orata
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta, Canada
| | | | - Tania Nasreen
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta, Canada
| | - Munirul Alam
- Infectious Diseases Division, International Centre for Diarrhoeal Disease Research, Dhaka, Bangladesh
| | - Cheryl L Tarr
- Enteric Diseases Laboratory Branch, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Yann F Boucher
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta, Canada
- Saw Swee Hock School of Public Health, National University of Singapore, Singapore, Singapore
- Singapore Center for Environmental Life Sciences Engineering, National University of Singapore, Singapore, Singapore
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Abd El-Hamid MI, Abd El-Aziz NK, Samir M, El-Naenaeey ESY, Abo Remela EM, Mosbah RA, Bendary MM. Genetic Diversity of Campylobacter jejuni Isolated From Avian and Human Sources in Egypt. Front Microbiol 2019; 10:2353. [PMID: 31681217 PMCID: PMC6813243 DOI: 10.3389/fmicb.2019.02353] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2019] [Accepted: 09/27/2019] [Indexed: 11/17/2022] Open
Abstract
Campylobacter jejuni (C. jejuni) are able to colonise and infect domestic poultry and also pose a risk for humans. The aim of this study was to determine the extent of genotypic diversity among C. jejuni isolates recovered from avian and human sources in Egypt. Furthermore, the short variable region (SVR) of flagellin A (flaA) gene was analysed for the presence of allelic variants. Our results showed that C. jejuni isolates differ in their capacity to harbour each of the virulence genes alone or when present in various combinations. The flaA gene was detected in all C. jejuni strains and none of the strains had all the studied virulence genes together. When considering C. jejuni strains from the investigated sources, the cdtC gene was the most similar, while the cdtB and iam genes were the most dissimilar. We could identify 13 novel alleles in the analysed strains. The analyses of virulence gene patterns, flaA gene sequences and allelic variants showed that C. jejuni strains from different sources overlapped largely suggesting potential involvement of poultry in transmitting C. jejuni to humans. We also found that the strains isolated from the same host were highly heterogeneous, with chicken strains exhibiting the highest diversity. Moreover, the human strains were clustered closer to chicken ones than to those from pigeon. The results of this study should be taken into consideration when assessing the epidemiology and risk potential of Egyptian C. jejuni not only in poultry, but also in humans.
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Affiliation(s)
- Marwa I. Abd El-Hamid
- Department of Microbiology, Faculty of Veterinary Medicine, Zagazig University, Zagazig, Egypt
| | - Norhan K. Abd El-Aziz
- Department of Microbiology, Faculty of Veterinary Medicine, Zagazig University, Zagazig, Egypt
| | - Mohamed Samir
- Department of Zoonoses, Faculty of Veterinary Medicine, Zagazig University, Zagazig, Egypt
| | - El-sayed Y. El-Naenaeey
- Department of Microbiology, Faculty of Veterinary Medicine, Zagazig University, Zagazig, Egypt
| | - Etab M. Abo Remela
- Department of Bacteriology, Mycology and Immunology, Faculty of Veterinary Medicine, Kafrelsheikh University, Kafrelsheikh, Egypt
- Department of Biology, College of Science, Taibah University, Medina, Saudi Arabia
| | - Rasha A. Mosbah
- Fellow Pharmacist at Zagazig University Hospital, Zagazig, Egypt
| | - Mahmoud M. Bendary
- Department of Microbiology and Immunology, Faculty of Pharmacy, Port Said University, Port Said, Egypt
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6
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Discriminative power of Campylobacter phenotypic and genotypic typing methods. J Microbiol Methods 2016; 125:33-9. [PMID: 26996762 DOI: 10.1016/j.mimet.2016.03.004] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2016] [Revised: 03/07/2016] [Accepted: 03/07/2016] [Indexed: 01/31/2023]
Abstract
The aim of this study was to compare different typing methods, individually and combined, for use in the monitoring of Campylobacter in food. Campylobacter jejuni (n=94) and Campylobacter coli (n=52) isolated from different broiler meat carcasses were characterized using multilocus sequence typing (MLST), flagellin gene A restriction fragment length polymorphism typing (flaA-RFLP), antimicrobial resistance profiling (AMRp), the presence/absence of 5 putative virulence genes; and, exclusively for C. jejuni, the determination of lipooligosaccharide (LOS) class. Discriminatory power was calculated by the Simpson's index of diversity (SID) and the congruence was measured by the adjusted Rand index and adjusted Wallace coefficient. MLST was individually the most discriminative typing method for both C. jejuni (SID=0.981) and C. coli (SID=0.957). The most discriminative combination with a SID of 0.992 for both C. jejuni and C. coli was obtained by combining MLST with flaA-RFLP. The combination of MLST with flaA-RFLP is an easy and feasible typing method for short-term monitoring of Campylobacter in broiler meat carcass.
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Bronowski C, James CE, Winstanley C. Role of environmental survival in transmission of Campylobacter jejuni. FEMS Microbiol Lett 2014; 356:8-19. [PMID: 24888326 DOI: 10.1111/1574-6968.12488] [Citation(s) in RCA: 115] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2014] [Revised: 05/20/2014] [Accepted: 05/24/2014] [Indexed: 11/29/2022] Open
Abstract
Campylobacter species are the most common cause of bacterial gastroenteritis, with C. jejuni responsible for the majority of these cases. Although it is clear that livestock, and particularly poultry, are the most common source, it is likely that the natural environment (soil and water) plays a key role in transmission, either directly to humans or indirectly via farm animals. It has been shown using multilocus sequence typing that some clonal complexes (such as ST-45) are more frequently isolated from environmental sources such as water, suggesting that strains vary in their ability to survive in the environment. Although C. jejuni are fastidious microaerophiles generally unable to grow in atmospheric levels of oxygen, C. jejuni can adapt to survival in the environment, exhibiting aerotolerance and starvation survival. Biofilm formation, the viable but nonculturable state, and interactions with other microorganisms can all contribute to survival outside the host. By exploiting high-throughput technologies such as genome sequencing and RNA Seq, we are well placed to decipher the mechanisms underlying the variations in survival between strains in environments such as soil and water and to better understand the role of environmental persistence in the transmission of C. jejuni directly or indirectly to humans.
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Affiliation(s)
- Christina Bronowski
- Institute of Infection and Global Health, University of Liverpool, Liverpool, UK
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Kovanen SM, Kivistö RI, Rossi M, Hänninen ML. A combination of MLST and CRISPR typing reveals dominant Campylobacter jejuni types in organically farmed laying hens. J Appl Microbiol 2014; 117:249-57. [PMID: 24655229 DOI: 10.1111/jam.12503] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2013] [Revised: 03/05/2014] [Accepted: 03/19/2014] [Indexed: 11/27/2022]
Abstract
AIM To elucidate the Campylobacter jejuni population in organically farmed laying hens in Finland, multilocus sequence typing (MLST) was combined with characterization of clustered regularly interspaced short palindromic repeat (CRISPR) sequences. METHODS AND RESULTS A total of 147 Camp. jejuni isolates, collected from organically farmed laying hens from 18 farms in 2003-2004, were previously analysed by pulsed-field gel electrophoresis. In the present study, subsets of the isolates were further analysed by MLST and CRISPR sequences. Fourteen STs were found by MLST. ST-50 (27%, 7/18 farms), ST-3272 (20%, 8/18 farms), ST-45 (12%, 7/18 farms) and ST-356 (12%, 5/18 farms) were the most common STs. CRISPR types were identical among all isolates of ST-50 (ST-21 clonal complex (CC)) and the most variable among ST-45 (ST-45 CC). CONCLUSIONS ST-3272 (UA), a common ST in this study, has been infrequently detected in other hosts. Other major STs (ST-50 and ST-45) have been common in several hosts such as conventional poultry and bovines. CRISPR typing provided additional discrimination between isolates of certain dominant STs and could be useful in further epidemiological studies. SIGNIFICANCE AND IMPACT OF THE STUDY This study gives new information about MLST and CRISPR types of Camp. jejuni among organically farmed laying hens.
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Affiliation(s)
- S M Kovanen
- Department of Food Hygiene and Environmental Health, Faculty of Veterinary Medicine, University of Helsinki, Helsinki, Finland
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Lévesque S, Fournier E, Carrier N, Frost E, Arbeit RD, Michaud S. Campylobacteriosis in urban versus rural areas: a case-case study integrated with molecular typing to validate risk factors and to attribute sources of infection. PLoS One 2013; 8:e83731. [PMID: 24386265 PMCID: PMC3873381 DOI: 10.1371/journal.pone.0083731] [Citation(s) in RCA: 70] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2013] [Accepted: 11/15/2013] [Indexed: 11/26/2022] Open
Abstract
Campylobacter infection is a leading cause of bacterial gastroenteritis worldwide, and most clinical cases appear as isolated, sporadic infections for which the source is rarely apparent. From July 2005 to December 2007 we conducted a prospective case-case study of sporadic, domestically-acquired Campylobacter enteritis in rural versus urban areas and a prevalence study of Campylobacter in animal and environmental sources in the Eastern Townships, Quebec. Isolates were typed using Multilocus Sequence Typing (MLST) to reinforce the case-case findings and to assign a source probability estimate for each human isolate. The risk of human campylobacteriosis was 1.89-fold higher in rural than urban areas. Unconditional multivariate logistic regression analysis identified two independent risk factors associated with human Campylobacter infections acquired in rural area: occupational exposure to animals (OR = 10.6, 95% CI: 1.2–91, p = 0.032), and household water coming from a private well (OR = 8.3, 95% CI: 3.4–20.4, p<0.0001). A total of 851 C. jejuni isolates (178 human, 257 chicken, 87 bovine, 266 water, 63 wild bird) were typed using MLST. Among human isolates, the incidence rates of clonal complexes (CC) CC-21, CC-45, and CC-61 were higher in rural than urban areas. MLST-based source attribution analysis indicated that 64.5% of human C. jejuni isolates were attributable to chicken, followed by cattle (25.8%), water (7.4%), and wild birds (2.3%). Chicken was the attributable source for the majority of cases, independent of residential area, sex and age. The increased incidence in rural compared to urban areas was associated with occupational exposure to animals, particularly cattle among those aged 15–34 years, and with consumption of private well water. Both bovine and water exposure appeared to contribute to the seasonal variation in campylobacteriosis. These results provide a basis for developing public education and preventive programs targeting the risk factors identified.
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Affiliation(s)
- Simon Lévesque
- Department of Microbiology and Infectious Diseases, Faculté de Médecine de l'Université de Sherbrooke, Québec, Canada
| | - Eric Fournier
- Laboratoire de santé publique du Québec, Institut national de santé publique du Québec, Sainte-Anne-de-Bellevue, Québec, Canada
| | - Nathalie Carrier
- Centre de Recherche Clinique Étienne-Le Bel du Centre Hospitalier Universitaire de Sherbrooke, Sherbrooke, Québec, Canada
| | - Eric Frost
- Department of Microbiology and Infectious Diseases, Faculté de Médecine de l'Université de Sherbrooke, Québec, Canada
- Centre de Recherche Clinique Étienne-Le Bel du Centre Hospitalier Universitaire de Sherbrooke, Sherbrooke, Québec, Canada
| | - Robert D. Arbeit
- Infectious Diseases Section, Tufts University School of Medicine, Boston, Massachusetts, United States of America
| | - Sophie Michaud
- Department of Microbiology and Infectious Diseases, Faculté de Médecine de l'Université de Sherbrooke, Québec, Canada
- * E-mail:
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Ioannidou V, Ioannidis A, Magiorkinis E, Bagos P, Nicolaou C, Legakis N, Chatzipanagiotou S. Multilocus sequence typing (and phylogenetic analysis) of Campylobacter jejuni and Campylobacter coli strains isolated from clinical cases in Greece. BMC Res Notes 2013; 6:359. [PMID: 24010733 PMCID: PMC3844450 DOI: 10.1186/1756-0500-6-359] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2013] [Accepted: 09/04/2013] [Indexed: 01/25/2023] Open
Abstract
Background The molecular epidemiology of C. jejuni and C. coli clinical strains isolated from children with gastroenteritis, was investigated using the multilocus sequence typing method (MLST). This analysis establishes for the first time in Greece and constitutes an important tool for the epidemiological surveillance and control of Campylobacter infection in our country. Methods The MLST genotypes were compared with those gained by other typing methods (HS-typing, PFGE and FlaA typing) and were also phylogenetically analyzed, in order to uncover genetic relationships. Results Among 68 C. jejuni strains, 41 different MLST-Sequence Types (MLST-STs) were found. Fifty six strains or 34 MLST-STs could be sorted into 15 different MLST-Sequence Type Complexes (MLST-STCs), while twelve strains or seven MLST-STs did not match any of the MLST-STCs of the database. Twenty C. coli strains belonged to 14 different MLST-STs. Eleven MLST-STs were classified in the same MLST-STC (828), and three were unclassifiable. There was no significant association between the MLST-STs and the results of the other typing methods. Phylogenetic analysis revealed that some strains, classified to the species of C. jejuni, formed a separate, phylogenetically distinct group. In eight strains some alleles belonging to the taxonomic cluster of C. jejuni, were also detected in C. coli and vice versa, a phenomenon caused by the genetic mosaic encountered inside the genus Campylobacter. Conclusions The MLST-ST determination proved to be a very useful tool for the typing as well as the identification of Campylobacter on the species level.
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Affiliation(s)
- Vasiliki Ioannidou
- Department of Biopathology and Clinical Microbiology, Athens Medical School, Aeginition Hospital, Vass, Sophias av, 72-74, Athens 115 28, Greece.
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Bell JA, Jerome J, Plovanich-Jones AE, Smith EJ, Gettings JR, Kim HY, Landgraf JR, Lefébure T, Kopper JJ, Rathinam VA, St. Charles JL, Buffa BA, Brooks AP, Poe SA, Eaton KA, Stanhope MJ, Mansfield LS. Outcome of infection of C57BL/6 IL-10(-/-) mice with Campylobacter jejuni strains is correlated with genome content of open reading frames up- and down-regulated in vivo. Microb Pathog 2013; 54:1-19. [PMID: 22960579 PMCID: PMC4118490 DOI: 10.1016/j.micpath.2012.08.001] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2012] [Accepted: 08/07/2012] [Indexed: 12/12/2022]
Abstract
Human Campylobacter jejuni infection can result in an asymptomatic carrier state, watery or bloody diarrhea, bacteremia, meningitis, or autoimmune neurological sequelae. Infection outcomes of C57BL/6 IL-10(-/-) mice orally infected with twenty-two phylogenetically diverse C. jejuni strains were evaluated to correlate colonization and disease phenotypes with genetic composition of the strains. Variation between strains was observed in colonization, timing of development of clinical signs, and occurrence of enteric lesions. Five pathotypes of C. jejuni in C57BL/6 IL-10(-/-) mice were delineated: little or no colonization, colonization without disease, colonization with enteritis, colonization with hemorrhagic enteritis, and colonization with neurological signs with or without enteritis. Virulence gene content of ten sequenced strains was compared in silico; virulence gene content of twelve additional strains was compared using a C. jejuni pan-genome microarray. Neither total nor virulence gene content predicted pathotype; nor was pathotype correlated with multilocus sequence type. Each strain was unique with regard to absences of known virulence-related loci and/or possession of point mutations and indels, including phase variation, in virulence-related genes. An experiment in C. jejuni 11168-infected germ-free mice showed that expression levels of ninety open reading frames (ORFs) were significantly up- or down-regulated in the mouse cecum at least two-fold compared to in vitro growth. Genomic content of these ninety C. jejuni 11168 ORFs was significantly correlated with the capacity to colonize and cause enteritis in C57BL/6 IL-10(-/-) mice. Differences in gene expression levels and patterns are thus an important determinant of pathotype in C. jejuni strains in this mouse model.
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Affiliation(s)
- J. A. Bell
- Comparative Enteric Diseases Laboratory, Department of Large Animal Clinical Sciences, College of Veterinary Medicine, Michigan State University, East Lansing, MI 48824
| | - J.P. Jerome
- Comparative Enteric Diseases Laboratory, Department of Large Animal Clinical Sciences, College of Veterinary Medicine, Michigan State University, East Lansing, MI 48824
- Department of Microbiology and Molecular Genetics, College of Natural Sciences, Michigan State University, East Lansing, MI 48824
| | - A. E. Plovanich-Jones
- Comparative Enteric Diseases Laboratory, Department of Large Animal Clinical Sciences, College of Veterinary Medicine, Michigan State University, East Lansing, MI 48824
| | - E. J. Smith
- Comparative Enteric Diseases Laboratory, Department of Large Animal Clinical Sciences, College of Veterinary Medicine, Michigan State University, East Lansing, MI 48824
- Comparative Medicine and Integrative Biology Program, College of Veterinary Medicine, Michigan State University, East Lansing, MI 48824
| | - J. R. Gettings
- Comparative Enteric Diseases Laboratory, Department of Large Animal Clinical Sciences, College of Veterinary Medicine, Michigan State University, East Lansing, MI 48824
| | - H. Y. Kim
- Comparative Enteric Diseases Laboratory, Department of Large Animal Clinical Sciences, College of Veterinary Medicine, Michigan State University, East Lansing, MI 48824
| | - J. R. Landgraf
- Research Technology Support Facility, Michigan State University, East Lansing, MI 48824
| | - T. Lefébure
- Department of Population Medicine and Diagnostic Science, College of Veterinary Medicine, Cornell University, Ithaca, NY 14853
| | - J. J. Kopper
- Comparative Enteric Diseases Laboratory, Department of Large Animal Clinical Sciences, College of Veterinary Medicine, Michigan State University, East Lansing, MI 48824
- Cell and Molecular Biology Program, College of Natural Sciences, Michigan State University, East Lansing, MI 48824
| | - V. A. Rathinam
- Comparative Enteric Diseases Laboratory, Department of Large Animal Clinical Sciences, College of Veterinary Medicine, Michigan State University, East Lansing, MI 48824
- Comparative Medicine and Integrative Biology Program, College of Veterinary Medicine, Michigan State University, East Lansing, MI 48824
| | - J. L. St. Charles
- Comparative Enteric Diseases Laboratory, Department of Large Animal Clinical Sciences, College of Veterinary Medicine, Michigan State University, East Lansing, MI 48824
- Comparative Medicine and Integrative Biology Program, College of Veterinary Medicine, Michigan State University, East Lansing, MI 48824
| | - B. A. Buffa
- Comparative Enteric Diseases Laboratory, Department of Large Animal Clinical Sciences, College of Veterinary Medicine, Michigan State University, East Lansing, MI 48824
| | - A. P. Brooks
- Comparative Enteric Diseases Laboratory, Department of Large Animal Clinical Sciences, College of Veterinary Medicine, Michigan State University, East Lansing, MI 48824
| | - S. A. Poe
- Laboratory Animal Medicine Unit, University of Michigan Medical School, Ann Arbor, MI 48109; Laboratory Animal Medicine Unit, University of Michigan Medical School, Ann Arbor, MI 48109
| | - K. A. Eaton
- Laboratory Animal Medicine Unit, University of Michigan Medical School, Ann Arbor, MI 48109; Laboratory Animal Medicine Unit, University of Michigan Medical School, Ann Arbor, MI 48109
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI 48109
| | - M. J. Stanhope
- Department of Population Medicine and Diagnostic Science, College of Veterinary Medicine, Cornell University, Ithaca, NY 14853
| | - L. S. Mansfield
- Comparative Enteric Diseases Laboratory, Department of Large Animal Clinical Sciences, College of Veterinary Medicine, Michigan State University, East Lansing, MI 48824
- Comparative Medicine and Integrative Biology Program, College of Veterinary Medicine, Michigan State University, East Lansing, MI 48824
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12
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Colles FM, Maiden MCJ. Campylobacter sequence typing databases: applications and future prospects. Microbiology (Reading) 2012; 158:2695-2709. [DOI: 10.1099/mic.0.062000-0] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Affiliation(s)
- F. M. Colles
- Department of Zoology, University of Oxford, South Parks Road, Oxford OX1 3PS, UK
| | - M. C. J. Maiden
- Department of Zoology, University of Oxford, South Parks Road, Oxford OX1 3PS, UK
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Ahmed MU, Dunn L, Ivanova EP. Evaluation of Current Molecular Approaches for Genotyping ofCampylobacter jejuniStrains. Foodborne Pathog Dis 2012; 9:375-85. [DOI: 10.1089/fpd.2011.0988] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Affiliation(s)
- Monir U. Ahmed
- Faculty of Life & Social Sciences, Swinburne University of Technology, Hawthorn, Australia
| | - Louise Dunn
- Faculty of Life & Social Sciences, Swinburne University of Technology, Hawthorn, Australia
| | - Elena P. Ivanova
- Faculty of Life & Social Sciences, Swinburne University of Technology, Hawthorn, Australia
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Comparison of molecular typing methods useful for detecting clusters of Campylobacter jejuni and C. coli isolates through routine surveillance. J Clin Microbiol 2011; 50:798-809. [PMID: 22162562 DOI: 10.1128/jcm.05733-11] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
Campylobacter spp. may be responsible for unreported outbreaks of food-borne disease. The detection of these outbreaks is made more difficult by the fact that appropriate methods for detecting clusters of Campylobacter have not been well defined. We have compared the characteristics of five molecular typing methods on Campylobacter jejuni and C. coli isolates obtained from human and nonhuman sources during sentinel site surveillance during a 3-year period. Comparative genomic fingerprinting (CGF) appears to be one of the optimal methods for the detection of clusters of cases, and it could be supplemented by the sequencing of the flaA gene short variable region (flaA SVR sequence typing), with or without subsequent multilocus sequence typing (MLST). Different methods may be optimal for uncovering different aspects of source attribution. Finally, the use of several different molecular typing or analysis methods for comparing individuals within a population reveals much more about that population than a single method. Similarly, comparing several different typing methods reveals a great deal about differences in how the methods group individuals within the population.
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Magnússon S, Guðmundsdóttir S, Reynisson E, Rúnarsson Á, Harðardóttir H, Gunnarson E, Georgsson F, Reiersen J, Marteinsson V. Comparison of Campylobacter jejuni isolates from human, food, veterinary and environmental sources in Iceland using PFGE, MLST and fla-SVR sequencing. J Appl Microbiol 2011; 111:971-81. [DOI: 10.1111/j.1365-2672.2011.05100.x] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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16
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Hepworth PJ, Ashelford KE, Hinds J, Gould KA, Witney AA, Williams NJ, Leatherbarrow H, French NP, Birtles RJ, Mendonca C, Dorrell N, Wren BW, Wigley P, Hall N, Winstanley C. Genomic variations define divergence of water/wildlife-associated Campylobacter jejuni niche specialists from common clonal complexes. Environ Microbiol 2011; 13:1549-60. [PMID: 21418497 PMCID: PMC3569610 DOI: 10.1111/j.1462-2920.2011.02461.x] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Although the major food-borne pathogen Campylobacter jejuni has been isolated from diverse animal, human and environmental sources, our knowledge of genomic diversity in C. jejuni is based exclusively on human or human food-chain-associated isolates. Studies employing multilocus sequence typing have indicated that some clonal complexes are more commonly associated with particular sources. Using comparative genomic hybridization on a collection of 80 isolates representing diverse sources and clonal complexes, we identified a separate clade comprising a group of water/wildlife isolates of C. jejuni with multilocus sequence types uncharacteristic of human food-chain-associated isolates. By genome sequencing one representative of this diverse group (C. jejuni 1336), and a representative of the bank-vole niche specialist ST-3704 (C. jejuni 414), we identified deletions of genomic regions normally carried by human food-chain-associated C. jejuni. Several of the deleted regions included genes implicated in chicken colonization or in virulence. Novel genomic insertions contributing to the accessory genomes of strains 1336 and 414 were identified. Comparative analysis using PCR assays indicated that novel regions were common but not ubiquitous among the water/wildlife group of isolates, indicating further genomic diversity among this group, whereas all ST-3704 isolates carried the same novel accessory regions. While strain 1336 was able to colonize chicks, strain 414 was not, suggesting that regions specifically absent from the genome of strain 414 may play an important role in this common route of Campylobacter infection of humans. We suggest that the genomic divergence observed constitutes evidence of adaptation leading to niche specialization.
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Affiliation(s)
- Philip J Hepworth
- Institute of Infection and Global Health Institute of Integrative Biology National Centre for Zoonosis Research, University of Liverpool, Liverpool L69 3GA, UK
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Lévesque S, Michaud S, Arbeit RD, Frost EH. High-resolution melting system to perform multilocus sequence typing of Campylobacter jejuni. PLoS One 2011; 6:e16167. [PMID: 21297862 PMCID: PMC3026018 DOI: 10.1371/journal.pone.0016167] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2010] [Accepted: 12/08/2010] [Indexed: 11/18/2022] Open
Abstract
Multi-locus sequence typing (MLST) has emerged as the state-of-the-art method for resolving bacterial population genetics but it is expensive and time consuming. We evaluated the potential of high resolution melting (HRM) to identify known MLST alleles of Campylobacter jejuni at reduced cost and time. Each MLST locus was amplified in two or three sub fragments, which were analyzed by HRM. The approach was investigated using 47 C. jejuni isolates, previously characterized by classical MLST, representing isolates from diverse environmental, animal and clinical sources and including the six most prevalent sequence types (ST) and the most frequent alleles. HRM was then applied to a validation set of 84 additional C. jejuni isolates from chickens; 92% of the alleles were resolved in 35 hours of laboratory time and the cost of reagents per isolate was $20 compared with $100 for sequence-based typing. HRM has the potential to complement sequence-based methods for resolving SNPs and to facilitate a wide range of genotyping studies.
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Affiliation(s)
- Simon Lévesque
- Department of Microbiology and Infectious Diseases, Faculté de Médecine et des Sciences de la Santé de l'Université de Sherbrooke, Sherbrooke, Québec, Canada
| | - Sophie Michaud
- Department of Microbiology and Infectious Diseases, Faculté de Médecine et des Sciences de la Santé de l'Université de Sherbrooke, Sherbrooke, Québec, Canada
| | - Robert D. Arbeit
- Infectious Diseases Section, Tufts University School of Medicine, Boston, Massachusetts, United States of America
| | - Eric H. Frost
- Department of Microbiology and Infectious Diseases, Faculté de Médecine et des Sciences de la Santé de l'Université de Sherbrooke, Sherbrooke, Québec, Canada
- * E-mail:
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Isolation of a novel Campylobacter jejuni clone associated with the bank vole, Myodes glareolus. Appl Environ Microbiol 2010; 76:7318-21. [PMID: 20851991 DOI: 10.1128/aem.00511-10] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Campylobacter jejuni can be isolated from different animal hosts. Various studies have used multilocus sequence typing to look for associations between particular clones of C. jejuni and specific hosts. Here, we describe the isolation of a novel clone (sequence type 3704 [ST-3704]) of C. jejuni associated with the bank vole (Myodes glareolus).
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Scientific Opinion on Quantification of the risk posed by broiler meat to human campylobacteriosis in the EU. EFSA J 2010. [DOI: 10.2903/j.efsa.2010.1437] [Citation(s) in RCA: 158] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
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Multiplex strategy for multilocus sequence typing, fla typing, and genetic determination of antimicrobial resistance of Campylobacter jejuni and Campylobacter coli isolates collected in Switzerland. J Clin Microbiol 2009; 47:1996-2007. [PMID: 19439549 DOI: 10.1128/jcm.00237-09] [Citation(s) in RCA: 58] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
We present an optimized multilocus sequence typing (MLST) scheme with universal primer sets for amplifying and sequencing the seven target genes of Campylobacter jejuni and Campylobacter coli. Typing was expanded by sequence determination of the genes flaA and flaB using optimized primer sets. This approach is compatible with the MLST and flaA schemes used in the PubMLST database and results in an additional typing method using the flaB gene sequence. An identification module based on the 16S rRNA and rpoB genes was included, as well as the genetic determination of macrolide and quinolone resistances based on mutations in the 23S rRNA and gyrA genes. Experimental procedures were simplified by multiplex PCR of the 13 target genes. This comprehensive approach was evaluated with C. jejuni and C. coli isolates collected in Switzerland. MLST of 329 strains resulted in 72 sequence types (STs) among the 186 C. jejuni strains and 39 STs for the 143 C. coli isolates. Fourteen (19%) of the C. jejuni and 20 (51%) of the C. coli STs had not been found previously. In total, 35% of the C. coli strains collected in Switzerland contained mutations conferring antibiotic resistance only to quinolone, 15% contained mutations conferring resistance only to macrolides, and 6% contained mutations conferring resistance to both classes of antibiotics. In C. jejuni, these values were 31% and 0% for quinolone and macrolide resistance, respectively. The rpoB sequence allowed phylogenetic differentiation between C. coli and C. jejuni, which was not possible by 16S rRNA gene analysis. An online Integrated Database Network System (SmartGene, Zug, Switzerland)-based platform for MLST data analysis specific to Campylobacter was implemented. This Web-based platform allowed automated allele and ST designation, as well as epidemiological analysis of data, thus streamlining and facilitating the analysis workflow. Data networking facilitates the exchange of information between collaborating centers. The described approach simplifies and improves the genotyping of Campylobacter, allowing cost- and time-efficient routine monitoring.
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Bell JA, St Charles JL, Murphy AJ, Rathinam VAK, Plovanich-Jones AE, Stanley EL, Wolf JE, Gettings JR, Whittam TS, Mansfield LS. Multiple factors interact to produce responses resembling spectrum of human disease in Campylobacter jejuni infected C57BL/6 IL-10-/- mice. BMC Microbiol 2009; 9:57. [PMID: 19296832 PMCID: PMC2669091 DOI: 10.1186/1471-2180-9-57] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2008] [Accepted: 03/18/2009] [Indexed: 12/19/2022] Open
Abstract
BACKGROUND Campylobacter jejuni infection produces a spectrum of clinical presentations in humans--including asymptomatic carriage, watery diarrhea, and bloody diarrhea--and has been epidemiologically associated with subsequent autoimmune neuropathies. This microorganism is genetically variable and possesses genetic mechanisms that may contribute to variability in nature. However, relationships between genetic variation in the pathogen and variation in disease manifestation in the host are not understood. We took a comparative experimental approach to explore differences among different C. jejuni strains and studied the effect of diet on disease manifestation in an interleukin-10 deficient mouse model. RESULTS In the comparative study, C57BL/6 interleukin-10-/- mice were infected with seven genetically distinct C. jejuni strains. Four strains colonized the mice and caused disease; one colonized with no disease; two did not colonize. A DNA:DNA microarray comparison of the strain that colonized mice without disease to C. jejuni 11168 that caused disease revealed that putative virulence determinants, including loci encoding surface structures known to be involved in C. jejuni pathogenesis, differed from or were absent in the strain that did not cause disease. In the experimental study, the five colonizing strains were passaged four times in mice. For three strains, serial passage produced increased incidence and degree of pathology and decreased time to develop pathology; disease shifted from watery to bloody diarrhea. Mice kept on an ~6% fat diet or switched from an approximately 12% fat diet to an approximately 6% fat diet just before infection with a non-adapted strain also exhibited increased incidence and severity of disease and decreased time to develop disease, although the effects of diet were only statistically significant in one experiment. CONCLUSION C. jejuni strain genetic background and adaptation of the strain to the host by serial passage contribute to differences in disease manifestations of C. jejuni infection in C57BL/6 IL-10-/- mice; differences in environmental factors such as diet may also affect disease manifestation. These results in mice reflect the spectrum of clinical presentations of C. jejuni gastroenteritis in humans and contribute to usefulness of the model in studying human disease.
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Affiliation(s)
- Julia A Bell
- Comparative Enteric Diseases Laboratory, National Food Safety and Toxicology Center, Michigan State University, East Lansing, Michigan 48824, USA.
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Sheppard SK, Dallas JF, MacRae M, McCarthy ND, Sproston EL, Gormley FJ, Strachan NJC, Ogden ID, Maiden MCJ, Forbes KJ. Campylobacter genotypes from food animals, environmental sources and clinical disease in Scotland 2005/6. Int J Food Microbiol 2009; 134:96-103. [PMID: 19269051 DOI: 10.1016/j.ijfoodmicro.2009.02.010] [Citation(s) in RCA: 117] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2008] [Revised: 01/23/2009] [Accepted: 02/02/2009] [Indexed: 10/21/2022]
Abstract
A nationwide multi-locus sequence typing (MLST) survey was implemented to analyze patterns of host association among Campylobacter jejuni and Campylobacter coli isolates from clinical disease in Scotland (July 2005-September 2006), food animals (chickens, cattle, sheep, pigs and turkey), non-food animals (wild birds) and the environment. Sequence types (STs) were determined for 5247 clinical isolates and 999 from potential disease sources (augmented with 2420 published STs). Certain STs were over represented among particular sample sets/host groups. These host-associated STs were identified for all sample groups in both Campylobacter species and host associated clonal complexes (groups of related STs) were characterized for C. jejuni. Some genealogical lineages were present in both human disease and food animal samples. This provided evidence for the relative importance of different infection routes/food animal sources in human disease. These results show robust associations of particular genotypes with potential infection sources supporting the contention that contaminated poultry is a major source of human disease.
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Affiliation(s)
- Samuel K Sheppard
- Department of Zoology, University of Oxford, Oxford. OX1 3SY, United Kingdom
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Multilocus sequence typing of Campylobacter jejuni isolates from humans, chickens, raw milk, and environmental water in Quebec, Canada. J Clin Microbiol 2008; 46:3404-11. [PMID: 18701662 DOI: 10.1128/jcm.00042-08] [Citation(s) in RCA: 103] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Molecular strain typing is essential for deciphering the epidemiology of Campylobacter jejuni infections. We applied two different methods, multilocus sequence typing (MLST) and analysis of the flaA short variable repeat (SVR), to 289 isolates (163 human, 56 chicken, 34 raw milk, and 36 environmental water isolates) collected in the province of Québec, Canada, over 3 years; in addition, the analysis included the pulsed-field gel electrophoresis (PFGE) typing results for a subset of 131 isolates studied previously. MLST defined 96 sequence types (STs) and 20 clonal complexes (CCs), including 49 STs (73 isolates, 25%) and 39 alleles not previously documented in an international database. The frequency of new STs was significantly higher among water isolates than among isolates from other sources (18/36 [50%] and 55/253 [22%], respectively; P < 0.001). Nine of the 10 most prevalent CCs included isolates from humans and at least one other source; five CCs comprised exclusively or mostly human and chicken isolates. However, water and milk were the predominant nonhuman sources among the remaining CCs, suggesting that sporadic C. jejuni infections in humans may frequently arise from sources other than chickens. All three typing systems were discriminatory (discriminatory index > 0.9). Among 131 isolates analyzed by PFGE, each of the 20 types represented by two or more isolates corresponded to a single CC. In contrast, among the 14 most prevalent types detected by analysis of the flaA SVR (5 to 27 isolates each), 8 (57%) included isolates that represented multiple different CCs. The basis for these discordant results was uncertain. Antimicrobial resistance was randomly distributed among the CCs and appeared to be more closely related to the source of an isolate than its genotype. Although MLST is labor-intensive and expensive, it remains the single best method for the genotyping of C. jejuni isolates and deciphering the epidemiologic relationships among isolates.
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Rodin S, Andersson AF, Wirta V, Eriksson L, Ljungström M, Björkholm B, Lindmark H, Engstrand L. Performance of a 70-mer oligonucleotide microarray for genotyping of Campylobacter jejuni. BMC Microbiol 2008; 8:73. [PMID: 18462507 PMCID: PMC2396164 DOI: 10.1186/1471-2180-8-73] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2007] [Accepted: 05/08/2008] [Indexed: 12/05/2022] Open
Abstract
BACKGROUND Campylobacter jejuni is widespread in the environment and is the major cause of bacterial gastroenteritis in humans. In the present study we use microarray-based comparative genomic hybridizations (CGH), pulsed-field gel electrophoresis (PFGE) and multilocus sequence typing (MLST) to analyze closely related C. jejuni isolates from chicken and human infection. RESULTS With the exception of one isolate, the microarray data clusters the isolates according to the five groups determined by PFGE. In contrast, MLST defines only three genotypes among the isolates, indicating a lower resolution. All methods show that there is no inherit difference between isolates infecting humans and chicken, suggesting a common underlying population of C. jejuni. We further identify regions that frequently differ between isolates, including both previously described and novel regions. Finally, we show that genes that belong to certain functional groups differ between isolates more often than expected by chance. CONCLUSION In this study we demonstrated the utility of 70-mer oligonucleotide microarrays for genotyping of Campylobacter jejuni isolates, with resolution outperforming MLST.
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Affiliation(s)
- Sandra Rodin
- Swedish Institute for Infectious Disease Control, SE-17182 Solna, Sweden
| | - Anders F Andersson
- Swedish Institute for Infectious Disease Control, SE-17182 Solna, Sweden
- Limnology/Department of Ecology & Evolution, Uppsala University, Box 573, SE-75123 Uppsala, Sweden
| | - Valtteri Wirta
- Swedish Institute for Infectious Disease Control, SE-17182 Solna, Sweden
| | - Lena Eriksson
- Swedish Institute for Infectious Disease Control, SE-17182 Solna, Sweden
| | | | - Britta Björkholm
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, SE-17177 Stockholm, Sweden
| | - Hans Lindmark
- National Food Administration, P.O. Box 622, SE-75126 Uppsala, Sweden
| | - Lars Engstrand
- Swedish Institute for Infectious Disease Control, SE-17182 Solna, Sweden
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, SE-17177 Stockholm, Sweden
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Emergence of a tetracycline-resistant Campylobacter jejuni clone associated with outbreaks of ovine abortion in the United States. J Clin Microbiol 2008; 46:1663-71. [PMID: 18322054 DOI: 10.1128/jcm.00031-08] [Citation(s) in RCA: 90] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
Campylobacter infection is one of the major causes of ovine abortions worldwide. Historically, Campylobacter fetus subsp. fetus was the major cause of Campylobacter-associated abortion in sheep; however, Campylobacter jejuni is increasingly associated with sheep abortions. We examined the species distribution, genotypes, and antimicrobial susceptibilities of abortion-associated Campylobacter isolates obtained from multiple lambing seasons on different farms in Iowa, Idaho, South Dakota, and California. We found that C. jejuni has replaced C. fetus as the predominant Campylobacter species causing sheep abortion in the United States. Most strikingly, the vast majority (66 of 71) of the C. jejuni isolates associated with sheep abortion belong to a single genetic clone, as determined by pulsed-field gel electrophoresis, multilocus sequence typing, and cmp gene (encoding the major outer membrane protein) sequence typing. The in vitro antimicrobial susceptibilities of these isolates to the antibiotics that are routinely used in food animal production were determined using the agar dilution test. All of the 74 isolates were susceptible to tilmicosin, florfenicol, tulathromycin, and enrofloxacin, and 97% were sensitive to tylosin. However, all were resistant to tetracyclines, the only antibiotics currently approved in the United States for the treatment of Campylobacter abortion in sheep. This finding suggests that feeding tetracycline for the prevention of Campylobacter abortions is ineffective and that other antibiotics should be used for the treatment of sheep abortions in the United States. Together, these results indicate that a single tetracycline-resistant C. jejuni clone has emerged as the major cause of Campylobacter-associated sheep abortion in the United States.
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Mickan L, Doyle R, Valcanis M, Dingle KE, Unicomb L, Lanser J. Multilocus sequence typing of Campylobacter jejuni isolates from New South Wales, Australia. J Appl Microbiol 2007; 102:144-52. [PMID: 17184329 DOI: 10.1111/j.1365-2672.2006.03049.x] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
AIMS Multilocus sequence typing (MLST) was used to examine the diversity and population structure of Campylobacter jejuni isolates associated with sporadic cases of gastroenteritis in Australia, and to compare these isolates with those from elsewhere. METHODS AND RESULTS A total of 153 Camp. jejuni isolates were genotyped. Forty sequence types (STs) were found, 19 of which were previously undescribed and 21 identified in other countries. The 19 newly described STs accounted for 43% of isolates, 16 of which were assigned to known clonal complexes. Eighty-eight percent of isolates were assigned to a total of 15 clonal complexes. Of these, four clonal complexes accounted for 60% of isolates. Three STs accounted for nearly 40% of all isolates and appeared to be endemic, while 21 STs were represented by more than one isolate. Seven infections were acquired during international travel, and the associated isolates all had different STs, three of which were exclusive to the travel-acquired cases. Comparison of serotypes among isolates from clonal complexes revealed further diversity. Eight serotypes were identified among isolates from more than one clonal complex, while isolates from six clonal complexes displayed serotypes not previously associated with those clonal complexes. CONCLUSIONS Multilocus sequence typing is a useful tool for the discrimination of subtypes and examination of the population structure of Camp. jejuni associated with sporadic infections. SIGNIFICANCE AND IMPACT OF THE STUDY This study highlights the genotypic diversity of Camp. jejuni in Australia, demonstrating that STs causing disease have both a global and a local distribution evident from the typing of domestically and internationally acquired Camp. jejuni isolates.
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Affiliation(s)
- L Mickan
- Infectious Diseases Laboratories, Institute of Medical and Veterinary Science, Adelaide, SA, Australia.
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Malik-Kale P, Raphael BH, Parker CT, Joens LA, Klena JD, Quiñones B, Keech AM, Konkel ME. Characterization of genetically matched isolates of Campylobacter jejuni reveals that mutations in genes involved in flagellar biosynthesis alter the organism's virulence potential. Appl Environ Microbiol 2007; 73:3123-36. [PMID: 17369342 PMCID: PMC1907099 DOI: 10.1128/aem.01399-06] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2006] [Accepted: 02/28/2007] [Indexed: 11/20/2022] Open
Abstract
Phenotypic and genotypic evidence suggests that not all Campylobacter jejuni isolates are pathogenic for humans. We hypothesized that differences in gene content or gene expression alter the degree of pathogenicity of C. jejuni isolates. A C. jejuni isolate (Turkey) recovered from a turkey and a second C. jejuni isolate (CS) recovered from a chicken differed in their degrees of in vitro and in vivo virulence. The C. jejuni Turkey isolate invaded INT 407 human epithelial cells and secreted the Cia (Campylobacter invasion antigen) proteins, while the C. jejuni CS isolate was noninvasive for human epithelial cells and did not secrete the Cia proteins. Newborn piglets inoculated with the C. jejuni Turkey isolate developed more severe clinical signs of campylobacteriosis than piglets inoculated with the C. jejuni CS isolate. Additional work revealed that flagellin was not expressed in the C. jejuni CS isolate. Microarray and real-time reverse transcription-PCR analyses revealed that all flagellar class II genes were significantly downregulated in the C. jejuni CS isolate compared to the C. jejuni Turkey isolate. Finally, nucleotide sequencing of the flgR gene revealed the presence of a single residue that was different in the FlgR proteins of the C. jejuni Turkey and CS isolates. Complementation of the C. jejuni CS isolate with a wild-type copy of the flgR gene restored the isolate's motility. Collectively, these findings support the hypothesis that critical differences in gene content or gene expression can alter the pathogenic potential of C. jejuni isolates.
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Affiliation(s)
- Preeti Malik-Kale
- School of Molecular Biosciences, Washington State University, Pullman, WA 99164-4233, USA
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Use of suppression subtractive hybridisation to extend our knowledge of genome diversity in Campylobacter jejuni. BMC Genomics 2007; 8:110. [PMID: 17470265 PMCID: PMC1868759 DOI: 10.1186/1471-2164-8-110] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2006] [Accepted: 04/30/2007] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND Previous studies have sought to identify a link between the distribution of variable genes amongst isolates of Campylobacter jejuni and particular host preferences. The genomic sequence data available currently was obtained using only isolates from human or chicken hosts. In order to identify variable genes present in isolates from alternative host species, five subtractions between C. jejuni isolates from different sources (rabbit, cattle, wild bird) were carried out, designed to assess genomic variability within and between common multilocus sequence type (MLST) clonal complexes (ST-21, ST-42, ST-45 and ST-61). RESULTS The vast majority (97%) of the 195 subtracted sequences identified had a best BLASTX match with a Campylobacter protein. However, there was considerable variation within and between the four clonal complexes included in the subtractions. The distributions of eight variable sequences, including four with putative roles in the use of alternative terminal electron acceptors, amongst a panel of C. jejuni isolates representing diverse sources and STs, were determined. CONCLUSION There was a clear correlation between clonal complex and the distribution of the metabolic genes. In contrast, there was no evidence to support the hypothesis that the distribution of such genes may be related to host preference. The other variable genes studied were also generally distributed according to MLST type. Thus, we found little evidence for widespread horizontal gene transfer between clonal complexes involving these genes.
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Hiett KL, Seal BS, Siragusa GR. Campylobacter spp. subtype analysis using gel-based repetitive extragenic palindromic-PCR discriminates in parallel fashion to flaA short variable region DNA sequence analysis. J Appl Microbiol 2006; 101:1249-58. [PMID: 17105555 DOI: 10.1111/j.1365-2672.2006.03026.x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
AIMS The repetitive extragenic palindromic-PCR (rep-PCR) subtyping technique, which targets repetitive extragenic DNA sequences in a PCR, was optimized for Campylobacter spp. These data were then used for comparison with the established genotyping method of flaA short variable region (SVR) DNA sequence analysis as a tool for molecular epidemiology. METHODS AND RESULTS Uprime Dt, Uprime B1 or Uprime RI primers were utilized to generate gel-based fingerprints from a set of 50 Campylobacter spp. isolates recovered from a variety of epidemiological backgrounds and sources. Analysis and phenogram tree construction, using the unweighted pair group method with arithmetic mean, of the generated fingerprints demonstrated that the Uprime Dt primers were effective in providing reproducible patterns (100% typability, 99% reproducibility) and at placing isolates into epidemiological relevant groups. Genetic stability of the rep-PCR Uprime Dt patterns under nonselective, short-term transfer conditions revealed a Pearson's correlation approaching 99%. These same 50 Campylobacter spp. isolates were analysed by flaA SVR DNA sequence analysis to obtain phylogenetic relationships. CONCLUSIONS The Uprime Dt primer-generated rep-PCR phenogram was compared with a phenogram generated from flaA SVR DNA sequence analysis of the same isolates. Comparison of the two sets of resulting genomic relationships revealed that both methods segregated isolates into similar groups. SIGNIFICANCE AND IMPACT OF THE STUDY These results indicate that rep-PCR analysis performed using the Mo Bio Ultra Clean Microbial Genomic DNA Isolation Kit for DNA isolation and the Uprime DT primer set for amplification is a useful and effective tool for accurate differentiation of Campylobacter spp. for subtyping and epidemiological analyses.
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Affiliation(s)
- K L Hiett
- U.S. Department of Agriculture, Agricultural Research Service, Poultry Microbiological Safety Research Unit, Russell Research Center, Athens, GA 30604-5677, USA.
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Thakur S, Morrow WEM, Funk JA, Bahnson PB, Gebreyes WA. Molecular epidemiologic investigation of Campylobacter coli in swine production systems, using multilocus sequence typing. Appl Environ Microbiol 2006; 72:5666-9. [PMID: 16885327 PMCID: PMC1538767 DOI: 10.1128/aem.00658-06] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Multilocus sequence typing of 151 Campylobacter coli isolates from swine reared in conventional (n = 74) and antimicrobial-free (n = 77) production systems revealed high genotypic diversity. Sequence type (ST) 1413 was predominant and observed among ciprofloxacin-resistant strains. We identified a C. coli ST 828 clonal complex consisting of isolates from both production systems.
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Affiliation(s)
- Siddhartha Thakur
- Department of Population Health and Pathobiology, College of Veterinary Medicine, North Carolina State University, Raleigh, NC 27606, USA
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31
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Pinheiro ET, Anderson MJ, Gomes BPFA, Drucker DB. Phenotypic and genotypic identification of enterococci isolated from canals of root-filled teeth with periapical lesions. ACTA ACUST UNITED AC 2006; 21:137-44. [PMID: 16626369 DOI: 10.1111/j.1399-302x.2006.00285.x] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
The objectives of the present study were to identify enterococcal species isolated from the canals of root-filled teeth with periapical lesions using biochemical and molecular techniques, and to investigate the genetic diversity of the isolates. Twenty-two Enterococcus strains, isolated from the canals of root-filled teeth with persisting periapical lesions, were identified to species level using rapid ID 32 STREP galleries and partial 16S rDNA sequencing. To subtype the strains, genomic DNA from the isolates was analyzed by pulsed field gel electrophoresis (PFGE) after digestion with SmaI. Intragenic regions of two genes, ace and salA, were sequenced for further differentiation of the isolates. All strains were identified as Enterococcus faecalis by both commercial kit and partial 16S rDNA sequencing. PFGE with SmaI of 22 isolates demonstrated 18 macrorestriction profiles, whereas 13 distinct genotypes were identified after analysis of the ace and salA composite sequences. Most of the isolates from distinct patients had different PFGE profiles. Moreover, in two cases, different E. faecalis strains were found in different root-filled teeth from the same mouth. E. faecalis was the only enterococcal species isolated from the canals of root-filled teeth with periapical lesions. Genetic heterogeneity was observed among the E. faecalis isolates following PFGE and sequence-based typing method. Furthermore, the genetic diversity within root canal strains was similar to previous reports regarding E. faecalis isolates from different clinical and geographic origins.
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Affiliation(s)
- E T Pinheiro
- Endodontic Area, Dental School of Piracicaba, University of Campinas - UNICAMP, Piracicaba, São Paulo, Brazil
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32
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van Bergen MAP, Dingle KE, Maiden MCJ, Newell DG, van der Graaf-Van Bloois L, van Putten JPM, Wagenaar JA. Clonal nature of Campylobacter fetus as defined by multilocus sequence typing. J Clin Microbiol 2006; 43:5888-98. [PMID: 16333072 PMCID: PMC1317208 DOI: 10.1128/jcm.43.12.5888-5898.2005] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Campylobacter fetus can be divided into the subspecies C. fetus subsp. fetus and C. fetus subsp. venerealis. C. fetus subsp. fetus causes sporadic infections in humans and abortion in cattle and sheep and has been isolated from a variety of sites in different hosts. C. fetus subsp. venerealis is host restricted, being isolated mainly from the genital tracts of cattle, and is the causative agent of bovine genital campylobacteriosis. Despite differences in niche preference, microbiological subspecies differentiation has proven difficult. Different typing methods divided C. fetus isolates into different subgroups, depending on the methods used. The relative value of these methods can be assessed by the evolutionary relationship of isolates belonging to the genus; therefore, we developed a multilocus sequence typing (MLST) scheme for C. fetus. This scheme was applied to 140 C. fetus isolates previously typed by amplified fragment length polymorphism (AFLP) analysis. A total of 14 different sequence types (STs) were identified, and these exhibited low levels of inter-ST genetic diversity, with only 22 variable sites in 3,312 nucleotides. These MLST data indicate that C. fetus is genetically homogeneous compared to the homogeneity of other Campylobacter species. The two C. fetus subspecies were extremely closely related genetically, but ST-4 was associated only with C. fetus subsp. venerealis, which represents a "bovine" clone. The C. fetus subsp. fetus isolates studied were more diverse in terms of their STs, and the STs correlated with epidemiological relationships. Congruence was observed among C. fetus subspecies, sap type, and ST; therefore, MLST confirms that mammalian C. fetus is genetically stable, probably as result of the introduction of a single ancestral clone into a mammalian niche.
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Affiliation(s)
- Marcel A P van Bergen
- Animal Sciences Group, Division of Infectious Diseases, P.O. Box 65, 8200 AB Lelystad, The Netherlands
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Thakur S, Gebreyes WA. Campylobacter coli in swine production: antimicrobial resistance mechanisms and molecular epidemiology. J Clin Microbiol 2005; 43:5705-14. [PMID: 16272508 PMCID: PMC1287812 DOI: 10.1128/jcm.43.11.5705-5714.2005] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2005] [Revised: 07/05/2005] [Accepted: 08/15/2005] [Indexed: 11/20/2022] Open
Abstract
The aim of this study was to determine antimicrobial resistance, to evaluate and compare the use of two genotyping methods for molecular epidemiology purposes, and to determine the genotypic diversity of Campylobacter coli of porcine origin. A total of 100 C. coli isolates from swine were tested for susceptibility to six antimicrobials using the agar dilution method and genotyped using two high-resolution fingerprinting approaches: multilocus sequence typing (MLST) and pulsed-field gel electrophoresis (PFGE). Evaluation of the methods was based on their resistance patterns, discriminatory indexes (DI), high test throughputs, costs, and turnaround times. Resistance to erythromycin and tetracycline was the most common. Both genotypic methods were found to have high discriminatory power, although MLST had a higher DI (0.936) than PFGE (DI = 0.889). It also had a higher throughput than PFGE. Isolates were clustered into 27 groups by MLST compared to 11 by PFGE. MLST was able to further discriminate the isolates grouped under the same cluster by PFGE. Out of the 65 MLST sequence types (STs) identified among the total isolates, 50 were reported for the first time. Most STs were found to be specific to the farm (n = 38) and to slaughter (n = 22). Resistance against tetracycline and erythromycin was encoded by the tet(O) gene and a A2075G point mutation in the 23S rRNA gene, respectively. A high ciprofloxacin MIC (>64 microg/liter) was conferred by a point mutation in the gyrA gene. The weak clonal structure of the C. coli population among swine was further highlighted by the index of association value of 0.293. The findings of this study indicate that multidrug-resistant diverse C. coli strains exhibiting resistance to ciprofloxacin and erythromycin are concerning, since these are the drugs of choice for treating invasive campylobacteriosis cases in humans.
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Affiliation(s)
- Siddhartha Thakur
- Department of Population Health and Pathobiology, College of Veterinary Medicine, North Carolina State University, 4700 Hillsborough St., Raleigh, NC 27606, USA
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Best EL, Fox AJ, Frost JA, Bolton FJ. Real-time single-nucleotide polymorphism profiling using Taqman technology for rapid recognition of Campylobacter jejuni clonal complexes. J Med Microbiol 2005; 54:919-925. [PMID: 16157544 DOI: 10.1099/jmm.0.45971-0] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The rapid identification of Campylobacter jejuni isolates to strain level would significantly inform the public health investigation of C. jejuni infection. Conceptual advances provided by multilocus sequence typing (MLST) have established the clonal complex as an important epidemiological group at the strain level, enabling accurate and phylogenetically valid strain identification for C. jejuni. The development of real-time PCR assays for allelic discrimination of strain-associated single-nucleotide polymorphisms (SNPs) based upon MLST locus alleles offers one possible approach for rapid strain detection. SNPs defining key alleles diagnostic for the most prevalent clonal complexes were identified following a detailed analysis of the available MLST data. Real-time Taqman allelic discrimination assays designed to detect the SNPs specific for six major clonal complexes, ST-21, ST-45, ST-48, ST-61, ST-206 and ST-257, were developed, allowing the rapid detection of C. jejuni isolates and preliminary strain identification. This will provide an important complementary technique to sequence typing for rapid detection and strain characterization to inform in real-time the public health management and investigation of C. jejuni infections.
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Affiliation(s)
- E L Best
- Campylobacter and Helicobacter Reference Unit, Laboratory of Enteric Pathogens, Centre For Infections, Health Protection Agency, 61 Colindale Avenue, London NW9 5HT, UK 2Health Protection Agency North West Laboratory, Manchester Medical Microbiology Partnership, Manchester Royal Infirmary, Manchester, UK
| | - A J Fox
- Campylobacter and Helicobacter Reference Unit, Laboratory of Enteric Pathogens, Centre For Infections, Health Protection Agency, 61 Colindale Avenue, London NW9 5HT, UK 2Health Protection Agency North West Laboratory, Manchester Medical Microbiology Partnership, Manchester Royal Infirmary, Manchester, UK
| | - J A Frost
- Campylobacter and Helicobacter Reference Unit, Laboratory of Enteric Pathogens, Centre For Infections, Health Protection Agency, 61 Colindale Avenue, London NW9 5HT, UK 2Health Protection Agency North West Laboratory, Manchester Medical Microbiology Partnership, Manchester Royal Infirmary, Manchester, UK
| | - F J Bolton
- Campylobacter and Helicobacter Reference Unit, Laboratory of Enteric Pathogens, Centre For Infections, Health Protection Agency, 61 Colindale Avenue, London NW9 5HT, UK 2Health Protection Agency North West Laboratory, Manchester Medical Microbiology Partnership, Manchester Royal Infirmary, Manchester, UK
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Clark CG, Bryden L, Cuff WR, Johnson PL, Jamieson F, Ciebin B, Wang G. Use of the oxford multilocus sequence typing protocol and sequencing of the flagellin short variable region to characterize isolates from a large outbreak of waterborne Campylobacter sp. strains in Walkerton, Ontario, Canada. J Clin Microbiol 2005; 43:2080-91. [PMID: 15872226 PMCID: PMC1153734 DOI: 10.1128/jcm.43.5.2080-2091.2005] [Citation(s) in RCA: 57] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The Walkerton (Ontario, Canada) outbreak of waterborne Escherichia coli O157:H7 and Campylobacter jejuni was quite limited in both space and time, making it a good model for exploring the utility of different typing and subtyping methods for the characterization of relationships among isolates of these organisms. We have extended previous work with these organisms through analysis by the Oxford multilocus sequence typing (MLST) and the flagellin short variable region (fla-SVR) sequencing methods. Additional isolates not epidemiologically related to the Walkerton outbreak have also been included. Both sequencing methods identified and differentiated between Walkerton outbreak strains 1 and 2. When these strains were compared with isolates that were not part of the outbreak, the information produced by the fla-SVR method more often correlated with epidemiological findings than that produced by MLST, though both methods were required for optimal discrimination. The MLST data were more relevant in terms of the overall population structure of the organisms. Both mutation and recombination appeared to be responsible for generating diversity among the isolates tested.
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Affiliation(s)
- Clifford G Clark
- Bacteriology and Enteric Pathogens Program, National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Canada.
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36
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Miller WG, On SLW, Wang G, Fontanoz S, Lastovica AJ, Mandrell RE. Extended multilocus sequence typing system for Campylobacter coli, C. lari, C. upsaliensis, and C. helveticus. J Clin Microbiol 2005; 43:2315-29. [PMID: 15872261 PMCID: PMC1153752 DOI: 10.1128/jcm.43.5.2315-2329.2005] [Citation(s) in RCA: 172] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
A multilocus sequence typing (MLST) system has been reported previously for Campylobacter jejuni to both differentiate strains and identify clonal lineages. However, sequence variation at the MLST loci prevents its use for closely related Campylobacter species. We describe herein an expanded MLST method to include three clinically relevant Campylobacter species, C. coli, C. lari, and C. upsaliensis, and a fourth Campylobacter species, C. helveticus. The C. coli and C. helveticus methods use the same seven C. jejuni loci (aspA, atpA, glnA, gltA, glyA, pgm, and tkt); however, adk and pgi were substituted for aspA and gltA in C. lari and for gltA and pgm in C. upsaliensis. Multiple C. coli (n = 57), C. lari (n = 20), C. upsaliensis (n = 78), and C. helveticus (n = 9) isolates, representing both clinical and environmental sources, were typed. All four species were genetically diverse: the majority (> 80%) of the isolates had unique sequence types (STs). Using this method, mixed C. lari, C. upsaliensis, and C. helveticus isolates were identified; upon separation, each isolate was shown to contain two strains of the same species with distinct STs. Additionally, the expanded MLST method was able to detect potential lateral transfer events between C. jejuni and either C. coli or C. lari and between C. upsaliensis and C. helveticus. Thus, the expanded MLST method will prove useful in differentiating strains of five Campylobacter species, identifying mixed Campylobacter cultures, and detecting genetic exchange within the genus.
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Affiliation(s)
- William G Miller
- USDA, ARS, WRRC, Produce Safety and Microbiology Research Unit, 800 Buchanan St., Albany, CA 94710, USA.
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Höök H, Fattah MA, Ericsson H, Vågsholm I, Danielsson-Tham ML. Genotype dynamics of Campylobacter jejuni in a broiler flock. Vet Microbiol 2005; 106:109-17. [PMID: 15737480 DOI: 10.1016/j.vetmic.2004.12.017] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2004] [Revised: 12/14/2004] [Accepted: 12/17/2004] [Indexed: 11/25/2022]
Abstract
We investigated the genotype diversity and dynamics of Campylobacter in a commercial broiler flock during rearing and slaughter. In total, 220 Campylobacter jejuni isolates collected on four sampling occasions during rearing and from routine sampling during slaughter were subtyped by SmaI macrorestriction and pulsed-field gel electrophoresis, PFGE. Eight different SmaI types were found. During rearing, a subsequent addition of genotypes occurred, with two SmaI types found at 2 weeks of age and six types on the day before slaughter. All types that were detected in more than one isolate were also found on all succeeding sampling occasions, including the slaughter sampling. Two new types were found in the slaughter samples. In two-thirds of the individual birds sampled the day before slaughter, more than one SmaI type were found, although there was a clear tendency for dominance of one type in individual birds. Our results show that multiple genotypes of C. jejuni may be present in a commercial broiler flock during rearing and even in gastrointestinal tracts of individual birds. Both recurring environmental exposure and genetic changes within the population may explain the genotype diversity. Although the distribution of genotypes varied between different sampling occasions, we found no indication that any subtype excluded another during the rearing of the broiler flock.
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Affiliation(s)
- Helena Höök
- Division of Food Hygiene and Bacteriology, Department of Biomedical Sciences and Veterinary Public Health, Swedish University of Agricultural Sciences, Box 7009, S-750 07 Uppsala, Sweden.
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Poly F, Threadgill D, Stintzi A. Identification of Campylobacter jejuni ATCC 43431-specific genes by whole microbial genome comparisons. J Bacteriol 2004; 186:4781-95. [PMID: 15231810 PMCID: PMC438563 DOI: 10.1128/jb.186.14.4781-4795.2004] [Citation(s) in RCA: 57] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
This study describes a novel approach to identify unique genomic DNA sequences from the unsequenced strain C. jejuni ATCC 43431 by comparison with the sequenced strain C. jejuni NCTC 11168. A shotgun DNA microarray was constructed by arraying 9,600 individual DNA fragments from a C. jejuni ATCC 43431 genomic library onto a glass slide. DNA fragments unique to C. jejuni ATCC 43431 were identified by competitive hybridization to the array with genomic DNA of C. jejuni NCTC 11168. The plasmids containing unique DNA fragments were sequenced, allowing the identification of up to 130 complete and incomplete genes. Potential biological roles were assigned to 66% of the unique open reading frames. The mean G+C content of these unique genes (26%) differs significantly from the G+C content of the entire C. jejuni genome (30.6%). This suggests that they may have been acquired through horizontal gene transfer from an organism with a G+C content lower than that of C. jejuni. Because the two C. jejuni strains differ by Penner serotype, a large proportion of the unique ATCC 43431 genes encode proteins involved in lipooligosaccharide and capsular biosynthesis, as expected. Several unique open reading frames encode enzymes which may contribute to genetic variability, i.e., restriction-modification systems and integrases. Interestingly, many of the unique C. jejuni ATCC 43431 genes show identity with a possible pathogenicity island from Helicobacter hepaticus and components of a potential type IV secretion system. In conclusion, this study provides a valuable resource to further investigate Campylobacter diversity and pathogenesis.
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Affiliation(s)
- Frédéric Poly
- Department of Veterinary Pathobiology, College of Veterinary Medicine, Oklahoma State University, Stillwater, OK 74078, USA
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Best EL, Fox AJ, Frost JA, Bolton FJ. Identification of Campylobacter jejuni multilocus sequence type ST-21 clonal complex by single-nucleotide polymorphism analysis. J Clin Microbiol 2004; 42:2836-9. [PMID: 15184486 PMCID: PMC427879 DOI: 10.1128/jcm.42.6.2836-2839.2004] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Conserved single-nucleotide polymorphisms (SNPs) which characterize the allelic profile of the major epidemiological lineage ST-21 were identified from the alleles within the current Campylobacter jejuni multilocus sequence typing (MLST) database. Allelic discrimination assays were designed for the detection of SNPs, enabling rapid strain profiling for clonal complex ST-21. This method is suitable for epidemiological investigations and is complementary to full MLST.
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Affiliation(s)
- E L Best
- Campylobacter Reference Unit, Laboratory of Enteric Pathogens, Specialist and Reference Microbiology Division, Health Protection Agency, 61 Colindale Ave., London NW9 5HT, United Kingdom.
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