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Paintsil EK, Ofori LA, Adobea S, Akenten CW, Phillips RO, Maiga-Ascofare O, Lamshöft M, May J, Obiri Danso K, Krumkamp R, Dekker D. Prevalence and Antibiotic Resistance in Campylobacter spp. Isolated from Humans and Food-Producing Animals in West Africa: A Systematic Review and Meta-Analysis. Pathogens 2022; 11:pathogens11020140. [PMID: 35215086 PMCID: PMC8877155 DOI: 10.3390/pathogens11020140] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Revised: 01/14/2022] [Accepted: 01/17/2022] [Indexed: 12/30/2022] Open
Abstract
Campylobacter species are one of the leading causes of gastroenteritis in humans. This review reports on the prevalence and antibiotic resistance data of Campylobacter spp. isolated from humans and food-producing animals in West Africa. A systematic search was carried out in five databases for original articles published between January 2000 and July 2021. Among 791 studies found, 38 original articles from seven (41%) out of the 17 countries in West Africa met the inclusion criteria. For studies conducted in food-producing animals, the overall pooled prevalence of Campylobacter spp. was 34% (95% CI: 25–45). The MDR prevalence was 59% (95% CI: 29–84) and half (50%, 13/26) of the animal studies had samples collected from the market. The human studies recorded a lower pooled prevalence of Campylobacter spp. (10%, 95% CI: 6–17), but a considerably higher rate of MDR prevalence (91%; 95% CI: 67–98). The majority (85%, 11/13) of the human studies took place in a hospital. Campylobacter jejuni and Campylobacter coli were the most common species isolated from both animals and humans. Our findings suggest that Campylobacter spp. is highly prevalent in West Africa. Therefore, improved farm hygiene and ‘One Health’ surveillance systems are needed to reduce transmission.
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Affiliation(s)
- Ellis Kobina Paintsil
- Kumasi Centre for Collaborative Research in Tropical Medicine (KCCR), South-End, Asuogya Road, Kumasi 039-5028, Ghana; (C.W.A.); (R.O.P.); (O.M.-A.)
- Department of Theoretical and Applied Biology, Kwame Nkrumah University of Science and Technology, Kumasi 039-5028, Ghana; (L.A.O.); (K.O.D.)
- Correspondence: (E.K.P.); (R.K.); Tel.: +233-202-700-486 (E.K.P.); +49-(0)40-42818-535 (R.K.)
| | - Linda Aurelia Ofori
- Department of Theoretical and Applied Biology, Kwame Nkrumah University of Science and Technology, Kumasi 039-5028, Ghana; (L.A.O.); (K.O.D.)
| | - Sarah Adobea
- Department of Emergency Medicine, Komfo Anokye Teaching Hospital, Okomfo Anokye Road, Kumasi 034-9094, Ghana;
| | - Charity Wiafe Akenten
- Kumasi Centre for Collaborative Research in Tropical Medicine (KCCR), South-End, Asuogya Road, Kumasi 039-5028, Ghana; (C.W.A.); (R.O.P.); (O.M.-A.)
- Department of Theoretical and Applied Biology, Kwame Nkrumah University of Science and Technology, Kumasi 039-5028, Ghana; (L.A.O.); (K.O.D.)
| | - Richard Odame Phillips
- Kumasi Centre for Collaborative Research in Tropical Medicine (KCCR), South-End, Asuogya Road, Kumasi 039-5028, Ghana; (C.W.A.); (R.O.P.); (O.M.-A.)
| | - Oumou Maiga-Ascofare
- Kumasi Centre for Collaborative Research in Tropical Medicine (KCCR), South-End, Asuogya Road, Kumasi 039-5028, Ghana; (C.W.A.); (R.O.P.); (O.M.-A.)
- Department of Infectious Disease Epidemiology, Bernhard Nocht Institute for Tropical Medicine (BNITM), Bernhard-Nocht-Str. 74, 20359 Hamburg, Germany; (M.L.); (J.M.); (D.D.)
- German Centre for Infection Research (DZIF), Partner Site Hamburg-Lübeck-Borstel-Riems, 20359 Hamburg, Germany
| | - Maike Lamshöft
- Department of Infectious Disease Epidemiology, Bernhard Nocht Institute for Tropical Medicine (BNITM), Bernhard-Nocht-Str. 74, 20359 Hamburg, Germany; (M.L.); (J.M.); (D.D.)
- German Centre for Infection Research (DZIF), Partner Site Hamburg-Lübeck-Borstel-Riems, 20359 Hamburg, Germany
| | - Jürgen May
- Department of Infectious Disease Epidemiology, Bernhard Nocht Institute for Tropical Medicine (BNITM), Bernhard-Nocht-Str. 74, 20359 Hamburg, Germany; (M.L.); (J.M.); (D.D.)
- German Centre for Infection Research (DZIF), Partner Site Hamburg-Lübeck-Borstel-Riems, 20359 Hamburg, Germany
- Tropical Medicine II, University Medical Center Hamburg-Eppendorf (UKE), 20251 Hamburg, Germany
| | - Kwasi Obiri Danso
- Department of Theoretical and Applied Biology, Kwame Nkrumah University of Science and Technology, Kumasi 039-5028, Ghana; (L.A.O.); (K.O.D.)
| | - Ralf Krumkamp
- Department of Infectious Disease Epidemiology, Bernhard Nocht Institute for Tropical Medicine (BNITM), Bernhard-Nocht-Str. 74, 20359 Hamburg, Germany; (M.L.); (J.M.); (D.D.)
- German Centre for Infection Research (DZIF), Partner Site Hamburg-Lübeck-Borstel-Riems, 20359 Hamburg, Germany
- Correspondence: (E.K.P.); (R.K.); Tel.: +233-202-700-486 (E.K.P.); +49-(0)40-42818-535 (R.K.)
| | - Denise Dekker
- Department of Infectious Disease Epidemiology, Bernhard Nocht Institute for Tropical Medicine (BNITM), Bernhard-Nocht-Str. 74, 20359 Hamburg, Germany; (M.L.); (J.M.); (D.D.)
- German Centre for Infection Research (DZIF), Partner Site Hamburg-Lübeck-Borstel-Riems, 20359 Hamburg, Germany
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Pena-Fernández N, Cano-Terriza D, García-Bocanegra I, Horcajo P, Vázquez-Arbaizar P, Cleofé-Resta D, Pérez-Arroyo B, Ortega-Mora LM, Collantes-Fernández E. Prevalence of Bovine Genital Campylobacteriosis, Associated Risk Factors and Spatial Distribution in Spanish Beef Cattle Based on Veterinary Laboratory Database Records. Front Vet Sci 2021; 8:750183. [PMID: 34957276 PMCID: PMC8692666 DOI: 10.3389/fvets.2021.750183] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Accepted: 11/15/2021] [Indexed: 12/04/2022] Open
Abstract
Bovine genital campylobacteriosis (BGC) is a sexually transmitted disease that causes early reproductive failure in natural breeding cattle that are managed extensively. The aim of this study was to assess the BGC prevalence in Spain from 2011 to 2019 using data collected cross-sectionally from the diagnostic reports issued by the SALUVET veterinary diagnostic laboratory from a total of 5,182 breeding bulls from 1,950 herds managed under “dehesa” systems (large herds within fenced pastures and all-year breeding season) or mountain systems (smaller herds with seasonal breeding management and grazing in communal mountain pastures). Infection was detected by PCR in 7.7 and 12.2% of the bulls and herds tested, respectively. The “dehesa” herd management system (OR = 2.078, P = < 0.001, 95% CI = 1.55–1.77), bovine trichomonosis status of the herd (OR = 1.606, P = 0.004, 95% CI = 1.15–2.22), and bulls ≥3 years old (OR = 1.392, P = 0.04, 95% CI = 1.01–1.92) were identified as risk factors associated with Campylobacter fetus venerealis infection. We also studied the high-risk areas for circulation of the infection in extensive beef cattle herds in Spain, showing four significant clusters in “dehesa” areas in the south-western provinces of the country and a fifth cluster located in a mountain area in northern Spain. The results obtained in the present study indicate that BGC is endemic and widely distributed in Spanish beef herds. Specifically, “dehesa” herds are at greater risk for introduction of Cfv based on relatively high local prevalence of the infection and the use of specific management practices.
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Affiliation(s)
- Nerea Pena-Fernández
- Servicio Regional de Investigación y Desarrollo Agroalimentario, Villaviciosa, Spain.,Animal Health and Zoonoses Group (SALUVET), Animal Health Department, Faculty of Veterinary Sciences, Complutense University of Madrid, Madrid, Spain
| | - David Cano-Terriza
- Animal Health and Zoonosis Research Group (GISAZ), Animal Health Department, Faculty of Veterinary Sciences, University of Cordoba-Agrifood Excellence International Campus (ceiA3), Córdoba, Spain
| | - Ignacio García-Bocanegra
- Animal Health and Zoonosis Research Group (GISAZ), Animal Health Department, Faculty of Veterinary Sciences, University of Cordoba-Agrifood Excellence International Campus (ceiA3), Córdoba, Spain
| | - Pilar Horcajo
- Animal Health and Zoonoses Group (SALUVET), Animal Health Department, Faculty of Veterinary Sciences, Complutense University of Madrid, Madrid, Spain
| | - Patricia Vázquez-Arbaizar
- Animal Health and Zoonoses Group (SALUVET)-Innova S.L. Faculty of Veterinary Sciences, Complutense University of Madrid, Madrid, Spain
| | - Darío Cleofé-Resta
- Animal Health and Zoonoses Group (SALUVET), Animal Health Department, Faculty of Veterinary Sciences, Complutense University of Madrid, Madrid, Spain
| | - Bárbara Pérez-Arroyo
- Animal Health and Zoonoses Group (SALUVET), Animal Health Department, Faculty of Veterinary Sciences, Complutense University of Madrid, Madrid, Spain
| | - Luis M Ortega-Mora
- Animal Health and Zoonoses Group (SALUVET), Animal Health Department, Faculty of Veterinary Sciences, Complutense University of Madrid, Madrid, Spain.,Animal Health and Zoonoses Group (SALUVET)-Innova S.L. Faculty of Veterinary Sciences, Complutense University of Madrid, Madrid, Spain
| | - Esther Collantes-Fernández
- Animal Health and Zoonoses Group (SALUVET), Animal Health Department, Faculty of Veterinary Sciences, Complutense University of Madrid, Madrid, Spain.,Animal Health and Zoonoses Group (SALUVET)-Innova S.L. Faculty of Veterinary Sciences, Complutense University of Madrid, Madrid, Spain
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Hlashwayo DF, Sigaúque B, Bila CG. Epidemiology and antimicrobial resistance of Campylobacter spp. in animals in Sub-Saharan Africa: A systematic review. Heliyon 2020; 6:e03537. [PMID: 32181402 PMCID: PMC7063338 DOI: 10.1016/j.heliyon.2020.e03537] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2019] [Revised: 11/20/2019] [Accepted: 03/02/2020] [Indexed: 01/05/2023] Open
Abstract
Introduction Low sanitary conditions characterize the rural and urban households in Sub-Saharan African region. Those environmental conditions propitiate the transmission of bacterial infections between animals and humans. Campylobacter spp. is a zoonotic bacterium and cause of human gastroenteritis worldwide, whose main symptom is diarrhea. It is normally found in the digestive tract of many farm animals as a commensal but some species cause diseases in animals. It is important to understand the occurrence of these bacteria in animals, as they may also play a role in transmission to humans. The main objective of this review was to describe the prevalence of Campylobacter in animals in Sub-Saharan Africa. We also report findings on antibiotic resistance. Methods We followed PRISMA guidelines to find studies about occurrence of Campylobacter spp. in animals in all countries from Sub-Saharan Africa. PubMed, Cochrane Library, CINAHL, African Index Medicus, African Journals Online, Google Scholar and Science Direct were searched for studies published between 2000 and 2019. Results We found 70 studies that described occurrence of Campylobacter spp. in animals in 18 out of 53 countries of Sub-Saharan Africa. Campylobacter jejuni and C. coli were the predominant species isolated. The majority of studies were found in Western Africa. Middle Africa had the lowest amount of data. Most records presented data from Nigeria (n = 25), South Africa (n = 14) and Tanzania (n = 11). Cattle and chickens appear to be important hosts and may be playing an important role in transmitting to humans. Most Campylobacter isolates were resistant to erythromycin (44%), ampicillin (39%), tetracycline (33%), nalidixic acid (31%) and ciprofloxacin (30%). Conclusion Several studies about Campylobacter spp. in animals have been published in the last 19 years but information on the epidemiology of campylobacteriosis is scarce in most Sub-Saharan African countries. Antibiotic resistance is an increasing concern in many countries. Measures should be taken to prevent infection by this pathogen in the region and to control antibiotic resistance.
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Affiliation(s)
- Delfina Fernandes Hlashwayo
- Department of Biological Sciences, Faculty of Sciences, Eduardo Mondlane University, Maputo, Mozambique.,Faculty of Veterinary Science, Eduardo Mondlane University, Maputo, Mozambique
| | - Betuel Sigaúque
- Centro de Investigação em Saúde de Manhiça, Maputo, Mozambique
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More S, Bøtner A, Butterworth A, Calistri P, Depner K, Edwards S, Garin-Bastuji B, Good M, Gortázar Schmidt C, Michel V, Miranda MA, Nielsen SS, Raj M, Sihvonen L, Spoolder H, Stegeman JA, Thulke HH, Velarde A, Willeberg P, Winckler C, Baldinelli F, Broglia A, Candiani D, Beltrán-Beck B, Kohnle L, Bicout D. Assessment of listing and categorisation of animal diseases within the framework of the Animal Health Law (Regulation (EU) No 2016/429): bovine genital campylobacteriosis. EFSA J 2017; 15:e04990. [PMID: 32625287 PMCID: PMC7010193 DOI: 10.2903/j.efsa.2017.4990] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
Bovine genital campylobacteriosis has been assessed according to the criteria of the Animal Health Law (AHL), in particular criteria of Article 7 on disease profile and impacts, Article 5 on the eligibility of bovine genital campylobacteriosis to be listed, Article 9 for the categorisation of bovine genital campylobacteriosis according to disease prevention and control rules as in Annex IV and Article 8 on the list of animal species related to bovine genital campylobacteriosis. The assessment has been performed following a methodology composed of information collection and compilation, expert judgement on each criterion at individual and, if no consensus was reached before, also at collective level. The output is composed of the categorical answer, and for the questions where no consensus was reached, the different supporting views are reported. Details on the methodology used for this assessment are explained in a separate opinion. According to the assessment performed, bovine genital campylobacteriosis can be considered eligible to be listed for Union intervention as laid down in Article 5(3) of the AHL. The disease would comply with the criteria as in sections 4 and 5 of Annex IV of the AHL, for the application of the disease prevention and control rules referred to in points (d) and (e) of Article 9(1). The assessment here performed on compliance with the criteria as in section 3 of Annex IV referred to in point (c) of Article 9(1) is inconclusive. The animal species to be listed for bovine genital campylobacteriosis according to Article 8(3) criteria is mainly cattle as susceptible and reservoir.
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Prevalence and risk factors associated with bovine genital campylobacteriosis and bovine trichomonosis in the state of Pernambuco, Brazil. Trop Anim Health Prod 2015; 47:549-55. [PMID: 25633914 DOI: 10.1007/s11250-015-0761-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2014] [Accepted: 01/09/2015] [Indexed: 10/24/2022]
Abstract
The aim of the present study was to determine the prevalence and risk factors associated with Campylobacter fetus subsp. venerealis and Tritrichomonas foetus infection in cows from dairy herds in the state of Pernambuco, Brazil. In total, 383 samples of cervico-vaginal mucus were collected from cows on 21 herds in 19 districts. Genomic DNA was extracted from the samples and submitted for polymerase chain reaction analysis. An investigative questionnaire was used to analyze the risk factors, using questions related to reproductive and hygiene/sanitation management. A prevalence of 1.8% (0.8-3.9%; confidence interval (CI) 95%) and 33.4% (28.7-38.4%; CI 95%) was found for C. fetus subsp. venerealis and T. foetus, respectively. In terms of the number of foci, 28.6% of the herds contained at least one animal that was positive for C. fetus subsp. venerealis and 90.5% for T. foetus. The present study identified herds larger than 100 animals as a risk factor for bovine genital campylobacteriosis (OR = 7.2; CI 1.3-38.4%; p = 0.020) and the use of natural breeding as a risk factor for bovine trichomonosis (OR = 2.4; CI 1.1-5.9%; p = 0.041). In conclusion, C. fetus subsp. venerealis and T. foetus infections occurred in the region studied and high numbers of foci were found. Thus, prophylaxis and control measures, such as diagnosis, separation, and sexual rest for infected females, are suggested. An artificial insemination program with early rigorous sanitary care should be implemented on the properties in order to avoid the spread of agents in the herds.
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Barkallah M, Gharbi Y, Hassena AB, Slima AB, Mallek Z, Gautier M, Greub G, Gdoura R, Fendri I. Survey of infectious etiologies of bovine abortion during mid- to late gestation in dairy herds. PLoS One 2014; 9:e91549. [PMID: 24662769 PMCID: PMC3963856 DOI: 10.1371/journal.pone.0091549] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2013] [Accepted: 02/10/2014] [Indexed: 11/30/2022] Open
Abstract
Bovine abortion of unknown infectious etiology still remains a major economic problem. Thus, we investigated whether Brucella spp., Listeria monocytogenes, Salmonella spp., Campylobacter spp. and Coxiella burnetii are associated with abortion and/or stillbirth in Tunisian dairy cattle. Using a pan-Chlamydiales PCR, we also investigated the role of Chlamydiaceae, Waddlia chondrophila, Parachlamydia acanthamoebae and other members of the Chlamydiales order in this setting. Veterinary samples taken from mid to late-term abortions from twenty dairy herds were tested. From a total of 150 abortion cases collected, infectious agents were detected by PCR in 73 (48.66%) cases, 13 (8.66%) of which represented co-infections with two infectious agents. Detected pathogens include Brucella spp (31.3%), Chlamydiaceae (4.66%), Waddlia chondrophila (8%), Parachlamydia acanthamoebae (5.33%), Listeria monocytogenes (4.66%) and Salmonella spp. (3.33%). In contrast, Campylobacter spp. and Coxiella burnetii DNA were not detected among the investigated veterinary samples. This demonstrates that different bacterial agents may cause bovine abortion in Tunisia. This is the first report suggesting the role of Parachlamydia acanthamoebae in bovine abortion in Africa. Further studies with a larger number of samples are necessary to confirm whether this emerging pathogen is directly linked to abortion in cattle.
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Affiliation(s)
- Mohamed Barkallah
- Unité de recherche Toxicologie – Microbiologie Environnementale et Santé (UR11ES70), Faculté des Sciences de Sfax, Université de Sfax-Tunisia, Sfax, Tunisia
| | - Yaakoub Gharbi
- Unité de recherche Toxicologie – Microbiologie Environnementale et Santé (UR11ES70), Faculté des Sciences de Sfax, Université de Sfax-Tunisia, Sfax, Tunisia
| | - Amal Ben Hassena
- Unité de recherche Toxicologie – Microbiologie Environnementale et Santé (UR11ES70), Faculté des Sciences de Sfax, Université de Sfax-Tunisia, Sfax, Tunisia
| | - Ahlem Ben Slima
- Unité de recherche Toxicologie – Microbiologie Environnementale et Santé (UR11ES70), Faculté des Sciences de Sfax, Université de Sfax-Tunisia, Sfax, Tunisia
| | | | - Michel Gautier
- Laboratoire de Microbiologie, Département agroalimentaire, Agrocampus Ouest, Rennes, France
| | - Gilbert Greub
- Institute of Microbiology, University Hospital Center and University of Lausanne, Lausanne, Switzerland
| | - Radhouane Gdoura
- Unité de recherche Toxicologie – Microbiologie Environnementale et Santé (UR11ES70), Faculté des Sciences de Sfax, Université de Sfax-Tunisia, Sfax, Tunisia
| | - Imen Fendri
- Unité de recherche Toxicologie – Microbiologie Environnementale et Santé (UR11ES70), Faculté des Sciences de Sfax, Université de Sfax-Tunisia, Sfax, Tunisia
- Laboratoire de Microbiologie, Département agroalimentaire, Agrocampus Ouest, Rennes, France
- * E-mail:
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Mai HM, Irons PC, Kabir J, Thompson PN. Prevalence of bovine genital campylobacteriosis and trichomonosis of bulls in northern Nigeria. Acta Vet Scand 2013; 55:56. [PMID: 23927676 PMCID: PMC3751741 DOI: 10.1186/1751-0147-55-56] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2012] [Accepted: 08/01/2013] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND A survey was conducted to determine the prevalence of campylobacteriosis and trichomonosis, and their concurrence with brucellosis, in cattle in three states of northern Nigeria. METHODS A total of 602 preputial samples was collected from bulls in 250 herds and tested using culture and identification. Various indigenous and exotic breeds were studied and four major management systems were encountered. Age of the cattle was estimated using dentition, farm records or cornual rings. RESULTS The estimated true animal-level prevalence of Campylobacter fetus infection was 16.4% (95% CI: 13.0-20.7), of which 18.5% was C. f. fetus and 81.5% was C. f. venerealis. Of the latter, 92% were C. f. venerealis biovar intermedius strains. Animal-level prevalences in Adamawa, Kano and Kaduna states were 31.8%, 11.6% and 8.3% respectively, and were highest in bulls>7 years old (33.4%) and in the Gudali breed (28.8%). Of the 250 herds, 78 (25.5%, 95% CI: 19.4-32.7) had at least one infected bull, and herd prevalence was highest in the pastoral management system (43.5%). After adjustment for confounding using multivariable analysis, the odds of C. fetus infection were highest in Adamawa state (P<0.01), in the pastoral management system (P<0.01), and in bulls>7 years old (P=0.01), and tended to be higher in Bos taurus breeds (P=0.06). There was a strong positive association between the presence of campylobacteriosis and brucellosis (P<0.01), both within bulls (OR=8.3) and within herds (OR=16.0). Trichomonosis was not detected in any herds. CONCLUSION Bovine genital campylobacteriosis is prevalent particularly in the pastoral management system in northern Nigeria, with C. f. venerealis biovar intermedius as the major aetiology. There was a strong positive correlation between the occurrence of campylobacteriosis and brucellosis. No evidence of trichomonosis was found in herds in this study.
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Zhou Y, Bu L, Guo M, Zhou C, Wang Y, Chen L, Liu J. Comprehensive genomic characterization of campylobacter genus reveals some underlying mechanisms for its genomic diversification. PLoS One 2013; 8:e70241. [PMID: 23940551 PMCID: PMC3734277 DOI: 10.1371/journal.pone.0070241] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2013] [Accepted: 06/19/2013] [Indexed: 11/18/2022] Open
Abstract
Campylobacter species.are phenotypically diverse in many aspects including host habitats and pathogenicities, which demands comprehensive characterization of the entire Campylobacter genus to study their underlying genetic diversification. Up to now, 34 Campylobacter strains have been sequenced and published in public databases, providing good opportunity to systemically analyze their genomic diversities. In this study, we first conducted genomic characterization, which includes genome-wide alignments, pan-genome analysis, and phylogenetic identification, to depict the genetic diversity of Campylobacter genus. Afterward, we improved the tetranucleotide usage pattern-based naïve Bayesian classifier to identify the abnormal composition fragments (ACFs, fragments with significantly different tetranucleotide frequency profiles from its genomic tetranucleotide frequency profiles) including horizontal gene transfers (HGTs) to explore the mechanisms for the genetic diversity of this organism. Finally, we analyzed the HGTs transferred via bacteriophage transductions. To our knowledge, this study is the first to use single nucleotide polymorphism information to construct liable microevolution phylogeny of 21 Campylobacter jejuni strains. Combined with the phylogeny of all the collected Campylobacter species based on genome-wide core gene information, comprehensive phylogenetic inference of all 34 Campylobacter organisms was determined. It was found that C. jejuni harbors a high fraction of ACFs possibly through intraspecies recombination, whereas other Campylobacter members possess numerous ACFs possibly via intragenus recombination. Furthermore, some Campylobacter strains have undergone significant ancient viral integration during their evolution process. The improved method is a powerful tool for bacterial genomic analysis. Moreover, the findings would provide useful information for future research on Campylobacter genus.
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Affiliation(s)
| | - Lijing Bu
- Biology Department of University of New Mexico, Albuquerque, New Mexico, United States of America
| | - Min Guo
- BGI-Shenzhen, Shenzhen, Guangdong Province, China
| | - Chengran Zhou
- Department of Biology, Sichuan University, Chengdu, Sichuan Province, China
| | - Yongdong Wang
- Key Discipline Laboratory for National Defense for Biotechnology in Uranium Mining and Hydrometallurgy, University of South China, Hengyang, Hunan Province, China
| | - Liyu Chen
- Department of Microbiology, Xiangya School of Medicine, Central South University, Changsha, Hunan Province, China
- * E-mail: (LC); (JL)
| | - Jie Liu
- Translational Center for Stem Cell Research, Tongji Hospital, Stem Cell Research Center, Tongji University School of Medicine, Shanghai, China
- * E-mail: (LC); (JL)
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