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Zhang H, Tang M, Li D, Xu M, Ao Y, Lin L. Applications and advances in molecular diagnostics: revolutionizing non-tuberculous mycobacteria species and subspecies identification. Front Public Health 2024; 12:1410672. [PMID: 38962772 PMCID: PMC11220129 DOI: 10.3389/fpubh.2024.1410672] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2024] [Accepted: 06/10/2024] [Indexed: 07/05/2024] Open
Abstract
Non-tuberculous mycobacteria (NTM) infections pose a significant public health challenge worldwide, affecting individuals across a wide spectrum of immune statuses. Recent epidemiological studies indicate rising incidence rates in both immunocompromised and immunocompetent populations, underscoring the need for enhanced diagnostic and therapeutic approaches. NTM infections often present with symptoms similar to those of tuberculosis, yet with less specificity, increasing the risk of misdiagnosis and potentially adverse outcomes for patients. Consequently, rapid and accurate identification of the pathogen is crucial for precise diagnosis and treatment. Traditional detection methods, notably microbiological culture, are hampered by lengthy incubation periods and a limited capacity to differentiate closely related NTM subtypes, thereby delaying diagnosis and the initiation of targeted therapies. Emerging diagnostic technologies offer new possibilities for the swift detection and accurate identification of NTM infections, playing a critical role in early diagnosis and providing more accurate and comprehensive information. This review delineates the current molecular methodologies for NTM species and subspecies identification. We critically assess the limitations and challenges inherent in these technologies for diagnosing NTM and explore potential future directions for their advancement. It aims to provide valuable insights into advancing the application of molecular diagnostic techniques in NTM infection identification.
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Affiliation(s)
- Haiyang Zhang
- Department of Pediatrics, West China Second University Hospital, Sichuan University, Chengdu, China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children, Sichuan University, Ministry of Education, Chengdu, China
| | - Maoting Tang
- Department of Pediatrics, West China Second University Hospital, Sichuan University, Chengdu, China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children, Sichuan University, Ministry of Education, Chengdu, China
| | - Deyuan Li
- Department of Pediatrics, West China Second University Hospital, Sichuan University, Chengdu, China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children, Sichuan University, Ministry of Education, Chengdu, China
| | - Min Xu
- Department of Pediatrics, West China Second University Hospital, Sichuan University, Chengdu, China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children, Sichuan University, Ministry of Education, Chengdu, China
| | - Yusen Ao
- Department of Pediatrics, The Eighth Affiliated Hospital, Sun Yat-sen University, Shenzhen, China
| | - Liangkang Lin
- Department of Pediatrics, The Eighth Affiliated Hospital, Sun Yat-sen University, Shenzhen, China
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Bissonnette N, Brousseau JP, Ollier S, Byrne AS, Ibeagha-Awemu EM, Tahlan K. Systematic assessment of the reliability of quantitative PCR assays targeting IS900 for the detection of Mycobacterium avium ssp. paratuberculosis presence in animal and environmental samples. J Dairy Sci 2024:S0022-0302(24)00788-4. [PMID: 38754821 DOI: 10.3168/jds.2023-24566] [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: 12/18/2023] [Accepted: 03/27/2024] [Indexed: 05/18/2024]
Abstract
Mycobacterium avium ssp. paratuberculosis (MAP) is the bacterium responsible for causing Johne's Disease (JD), which is endemic to dairy cattle and also incriminated in the etiology of Crohn's disease. The difficulty in diagnosing asymptomatic cows for JD makes this disease hard to control. JD is considered a priority under the One Health approach to prevent the spread of the causative agent to humans. Environmental screening is a strategic approach aimed at identifying dairy herds with animals infected with MAP. It serves as the initial step toward implementing more intensive actions to control the disease. Quantitative polymerase chain reaction (qPCR) technology is widely used for diagnosis. Given that genome sequencing is now much more accessible than ever before, it is possible to target regions of the MAP genome that allow for the greatest diagnostic sensitivity and specificity. The aim of this study was to identify among the published qPCR assays targeting IS900 the more cost-effective options to detect MAP and to validate them in the diagnostic context of JD disease. MAP IS900 is a prime target because it is a multicopy genetic element. A total of 136 publications have reported on the use of IS900 qPCR assays over the past 3 decades. Among these records, 29 used the SYBR Green chemistry and TaqMan technology was used in 107 reports. Aside from the 9 reports using commercial assays, 72 TaqMan reports cited previously published work, leaving us with 27 TaqMan qPCR designs. Upon closer examination, 5 TaqMan designs contained mismatches in primer or probe sequences. Additionally, others exhibited high similarity to environmental microorganisms or non-MAP mycobacteria. We assessed the performance of 6 IS900 qPCR designs and their sensitivity when applied to clinical or environmental samples, which varied from 4 to 56 fold overall. Additionally, we provide recommendations for testing clinical and environmental samples, as certain strategies used previously should be avoided due to poor qPCR design (e.g., the presence of mismatches) or a lack of specificity.
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Affiliation(s)
- N Bissonnette
- Sherbrooke Research and Development Centre, Agriculture and Agri-Food Canada, Sherbrooke, QC, Canada J1M 0C8.
| | - J-P Brousseau
- Sherbrooke Research and Development Centre, Agriculture and Agri-Food Canada, Sherbrooke, QC, Canada J1M 0C8
| | - S Ollier
- Sherbrooke Research and Development Centre, Agriculture and Agri-Food Canada, Sherbrooke, QC, Canada J1M 0C8
| | - A S Byrne
- Department of Biology, Memorial University of Newfoundland, St. John's, NL, Canada A1C 5S7
| | - E M Ibeagha-Awemu
- Sherbrooke Research and Development Centre, Agriculture and Agri-Food Canada, Sherbrooke, QC, Canada J1M 0C8
| | - K Tahlan
- Department of Biology, Memorial University of Newfoundland, St. John's, NL, Canada A1C 5S7
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Bannantine JP, Duffy SC, Colombatti Olivieri MA, Behr MA, Biet F, Price NPJ. Genetic and chemical control of tuberculostearic acid production in Mycobacterium avium subspecies paratuberculosis. Microbiol Spectr 2024; 12:e0050824. [PMID: 38501867 PMCID: PMC11064506 DOI: 10.1128/spectrum.00508-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2024] [Accepted: 02/28/2024] [Indexed: 03/20/2024] Open
Abstract
Tuberculostearic acid (TBSA) is a fatty acid unique to mycobacteria and some corynebacteria and has been studied due to its diagnostic value, biofuel properties, and role in membrane dynamics. In this study, we demonstrate that TBSA production can be abrogated either by addition of pivalic acid to mycobacterial growth cultures or by a bfaA gene knockout encoding a flavin adenine dinucleotide (FAD)-binding oxidoreductase. Mycobacterium avium subspecies paratuberculosis (Map) growth and TBSA production were inhibited in 0.5-mg/mL pivalic acid-supplemented cultures, but higher concentrations were needed to have a similar effect in other mycobacteria, including Mycobacterium smegmatis. While Map C-type strains, isolated from cattle and other ruminants, will produce TBSA in the absence of pivalic acid, the S-type Map strains, typically isolated from sheep, do not produce TBSA in any condition. A SAM-dependent methyltransferase encoded by bfaB and FAD-binding oxidoreductase are both required in the two-step biosynthesis of TBSA. However, S-type strains contain a single-nucleotide polymorphism in the bfaA gene, rendering the oxidoreductase enzyme vestigial. This results in the production of an intermediate, termed 10-methylene stearate, which is detected only in S-type strains. Fatty acid methyl ester analysis of a C-type Map bfaA knockout revealed the loss of TBSA production, but the intermediate was present, similar to the S-type strains. Collectively, these results demonstrate the subtle biochemical differences between two primary genetic lineages of Map and other mycobacteria as well as explain the resulting phenotype at the genetic level. These data also suggest that TBSA should not be used as a diagnostic marker for Map.IMPORTANCEBranched-chain fatty acids are a predominant cell wall component among species belonging to the Mycobacterium genus. One of these is TBSA, which is a long-chain middle-branched fatty acid used as a diagnostic marker for Mycobacterium tuberculosis. This fatty acid is also an excellent biolubricant. Control of its production is important for industrial purposes as well as understanding the biology of mycobacteria. In this study, we discovered that a carboxylic acid compound termed pivalic acid inhibits TBSA production in mycobacteria. Furthermore, Map strains from two separate genetic lineages (C-type and S-type) showed differential production of TBSA. Cattle-type strains of Mycobacterium avium subspecies paratuberculosis produce TBSA, while the sheep-type strains do not. This important phenotypic difference is attributed to a single-nucleotide deletion in sheep-type strains of Map. This work sheds further light on the mechanism used by mycobacteria to produce tuberculostearic acid.
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Affiliation(s)
- John P. Bannantine
- National Animal Disease Center, USDA Agricultural Research Service, Ames, Iowa, USA
| | - Shannon C. Duffy
- Department of Microbiology and Immunology, McGill University, Montreal, Quebec, Canada
| | - María A. Colombatti Olivieri
- National Animal Disease Center, USDA Agricultural Research Service, Ames, Iowa, USA
- ARS Participation Program, Oak Ridge Institute for Science and Education (ORISE), Oak Ridge, Tennessee, USA
| | - Marcel A. Behr
- Department of Microbiology and Immunology, McGill University, Montreal, Quebec, Canada
| | - Franck Biet
- INRAE, ISP, Université de Tours, Nouzilly, France
| | - Neil P. J. Price
- National Center for Agricultural Utilization Research, USDA Agricultural Research Service, Peoria, Illinois, USA
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de Noronha Xavier A, de Sá LMN, de Nazaré Santos Ferreira M, de Oliveira PRF, de Moraes Peixoto R, Mota RA, Junior JWP. First serological diagnosis of Mycobacterium avium subsp. paratuberculosis infection in sheep in the state of Pernambuco, Brazil. Vet Res Commun 2024; 48:1293-1299. [PMID: 38206561 DOI: 10.1007/s11259-024-10300-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Accepted: 01/07/2024] [Indexed: 01/12/2024]
Abstract
This study aimed to diagnose Mycobacterium avium subsp. paratuberculosis (MAP) infections in sheep in the state of Pernambuco, Brazil. A total of 276 blood samples were analyzed using the enzyme-linked immunosorbent assay IDEXX Paratuberculosis Screening kit, and 261 fecal samples were submitted for bacterial culture and polymerase chain reaction tests. An animal-level sero-frequency of 0.72% (n = 2/276) and a farm-level sero-frequency of 20% (n = 2/10) were found. All fecal sample cultures were negative, and molecular analyses were also negative. To the best of our knowledge, this is the first study of MAP infection in sheep in the state of Pernambuco and one of the pioneers in the country. It is an asymptomatic disease that is difficult to diagnose in this species because the susceptibility of sheep to the organism is lower than that of other ruminant species. However, the sero-frequency found reveals that there is MAP exposure in sheep flocks in the region. In addition, serological monitoring can contribute to the observation of the organism's behavior in herds. Our results support the potential risk of MAP infection in sheep in the state of Pernambuco, Brazil.
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Affiliation(s)
- Amanda de Noronha Xavier
- Department of Veterinary Medicine, Federal Rural University of Pernambuco, Rua Dom Manuel de Medeiros, s/n- Dois Irmãos, Recife, PE, 52171-900, Brazil.
| | - Luenda Menezes Novaes de Sá
- Federal Institute of the Pernambuco Sertão, Floresta Campus, Rua Projetada, s/n - Caetano II, Floresta, PE, 56400-000, Brazil
| | - Maria de Nazaré Santos Ferreira
- Department of Veterinary Medicine, Federal Rural University of Pernambuco, Rua Dom Manuel de Medeiros, s/n- Dois Irmãos, Recife, PE, 52171-900, Brazil
| | - Pollyanne Raysa Fernandes de Oliveira
- Department of Veterinary Medicine, Federal Rural University of Pernambuco, Rua Dom Manuel de Medeiros, s/n- Dois Irmãos, Recife, PE, 52171-900, Brazil
| | - Rodolfo de Moraes Peixoto
- Federal Institute of the Pernambuco Sertão, Campus Petrolina - Rural Zone, PE 647, Km 22, PISNC N - 4, Zona Rural, Petrolina, PE, 56302-970, Brazil
| | - Rinaldo Aparecido Mota
- Department of Veterinary Medicine, Federal Rural University of Pernambuco, Rua Dom Manuel de Medeiros, s/n- Dois Irmãos, Recife, PE, 52171-900, Brazil
| | - José Wilton Pinheiro Junior
- Department of Veterinary Medicine, Federal Rural University of Pernambuco, Rua Dom Manuel de Medeiros, s/n- Dois Irmãos, Recife, PE, 52171-900, Brazil
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Pickrodt C, Köhler H, Moog U, Liebler-Tenorio EM, Möbius P. Molecular Diversity of Mycobacterium avium subsp. paratuberculosis in Four Dairy Goat Herds from Thuringia (Germany). Animals (Basel) 2023; 13:3542. [PMID: 38003160 PMCID: PMC10668697 DOI: 10.3390/ani13223542] [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: 10/05/2023] [Revised: 11/13/2023] [Accepted: 11/14/2023] [Indexed: 11/26/2023] Open
Abstract
This study investigated the intra- and inter-herd diversity of Mycobacterium avium subsp. paratuberculosis (MAP) isolates from four goat herds in Thuringia (Germany) that were affected by paratuberculosis for several years. The main focus was on the characterization and distribution of genotypes among animals and the environment of goat herd 1. This study included 196 isolates from the feces of 121 infected goats, various tissues from 13 clinically diseased goats, 29 environmental samples from herd 1, and additionally, 22 isolates of different origin from herds 2 to 4. The isolates, sampled between 2018 and 2022, were genotyped using short-sequence-repeat (SSR) analysis, mycobacterial-interspersed repetitive units-variable-number tandem repeat (MIRU-VNTR) analysis, and a single nucleotide polymorphism (SNP)-based assay for phylogenetic grouping. All the isolates belonged to the MAP-C group. In herd 1, one predominant genotype was determined, while two other genotypes were identified very rarely and only in fecal and environmental samples. One of three further genotypes was found in each of herds 2 to 4. The assignment of genotypes to different phylogenetic clades suggested six different infection strains. The results indicated no epidemiological links between the examined herds. Based on the current MAP genotyping data from Germany, possible sources of infection are MAP-contaminated barns previously used by infected cattle and the purchase of sub-clinically infected goats.
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Affiliation(s)
- Chris Pickrodt
- Institute of Molecular Pathogenesis, Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Naumburger Straße 96a, 07743 Jena, Germany; (C.P.); (E.M.L.-T.)
| | - Heike Köhler
- Institute of Molecular Pathogenesis, Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Naumburger Straße 96a, 07743 Jena, Germany; (C.P.); (E.M.L.-T.)
| | - Udo Moog
- Thuringian Animal Diseases Fund, Sheep and Goat Health Service, Victor-Goerttler-Straße 4, 07745 Jena, Germany;
| | - Elisabeth M. Liebler-Tenorio
- Institute of Molecular Pathogenesis, Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Naumburger Straße 96a, 07743 Jena, Germany; (C.P.); (E.M.L.-T.)
| | - Petra Möbius
- Institute of Molecular Pathogenesis, Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Naumburger Straße 96a, 07743 Jena, Germany; (C.P.); (E.M.L.-T.)
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Hodgeman R, Mann R, Djitro N, Savin K, Rochfort S, Rodoni B. The pan-genome of Mycobacterium avium subsp. paratuberculosis (Map) confirms ancestral lineage and reveals gene rearrangements within Map Type S. BMC Genomics 2023; 24:656. [PMID: 37907856 PMCID: PMC10619280 DOI: 10.1186/s12864-023-09752-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2023] [Accepted: 10/18/2023] [Indexed: 11/02/2023] Open
Abstract
BACKGROUND To date genomic studies on Map have concentrated on Type C strains with only a few Type S strains included for comparison. In this study the entire pan-genome of 261 Map genomes (205 Type C, 52 Type S and 4 Type B) and 7 Mycobacterium avium complex (Mac) genomes were analysed to identify genomic similarities and differences between the strains and provide more insight into the evolutionary relationship within this Mycobacterial species. RESULTS Our analysis of the core genome of all the Map isolates identified two distinct lineages, Type S and Type C Map that is consistent with previous phylogenetic studies of Map. Pan-genome analysis revealed that Map has a larger accessory genome than Mycobacterium avium subsp. avium (Maa) and Type C Map has a larger accessory genome than Type S Map. In addition, we found large rearrangements within Type S strains of Map and little to none in Type C and Type B strains. There were 50 core genes identified that were unique to Type S Map and there were no unique core genes identified between Type B and Type C Map strains. In Type C Map we identified an additional CE10 CAZyme class which was identified as an alpha/beta hydrolase and an additional polyketide and non-ribosomal peptide synthetase cluster. Consistent with previous analysis no plasmids and only incomplete prophages were identified in the genomes of Map. There were 45 hypothetical CRISPR elements identified with no associated cas genes. CONCLUSION This is the most comprehensive comparison of the genomic content of Map isolates to date and included the closing of eight Map genomes. The analysis revealed that there is greater variation in gene synteny within Type S strains when compared to Type C indicating that the Type C Map strain emerged after Type S. Further analysis of Type C and Type B genomes revealed that they are structurally similar with little to no genetic variation and that Type B Map may be a distinct clade within Type C Map and not a different strain type of Map. The evolutionary lineage of Maa and Map was confirmed as emerging after M. hominissuis.
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Affiliation(s)
- Rachel Hodgeman
- Agriculture Victoria, AgriBio, La Trobe University, Bundoora, VIC, Australia.
- School of Applied Systems Biology, AgriBio, La Trobe University, Bundoora, VIC, Australia.
| | - Rachel Mann
- Agriculture Victoria, AgriBio, La Trobe University, Bundoora, VIC, Australia
| | - Noel Djitro
- School of Applied Systems Biology, AgriBio, La Trobe University, Bundoora, VIC, Australia
| | - Keith Savin
- Agriculture Victoria, AgriBio, La Trobe University, Bundoora, VIC, Australia
| | - Simone Rochfort
- Agriculture Victoria, AgriBio, La Trobe University, Bundoora, VIC, Australia
- School of Applied Systems Biology, AgriBio, La Trobe University, Bundoora, VIC, Australia
| | - Brendan Rodoni
- Agriculture Victoria, AgriBio, La Trobe University, Bundoora, VIC, Australia
- School of Applied Systems Biology, AgriBio, La Trobe University, Bundoora, VIC, Australia
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Ingratta GG, Stempler A, Fernández B, Colavecchia SB, Jolly A, Minatel L, Paolicchi FA, Mundo SL. Early-stage findings in an experimental calf model infected with Argentinean isolates of Mycobacterium avium subsp. paratuberculosis. Vet Immunol Immunopathol 2023; 259:110595. [PMID: 37058952 DOI: 10.1016/j.vetimm.2023.110595] [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: 01/03/2023] [Revised: 03/30/2023] [Accepted: 04/10/2023] [Indexed: 04/16/2023]
Abstract
Mycobacterium avium subsp. paratuberculosis (MAP) is an important pathogen that causes granulomatous enteritis known as Johne's disease or paratuberculosis (PTB). In this study an experimental model of calves infected with Argentinean isolates of MAP for 180 days was used to provide more data of the early PTB stages. Calves were challenged by oral route with MAP strain IS900-RFLPA (MA; n = 3), MAP strain IS900-RFLPC (MC; n = 2) or mock infected (MI; n = 2), and response to infection was evaluated through peripheral cytokine expression, MAP tissue distribution and histopathological early-stage findings. Specific and varied levels of IFN-γ were only detected at 80 days post-infection in infected calves. These data indicate that specific IFN-γ is not a useful indicator for early detection of MAP infection in our calf model. At 110 days post-infection, TNF-α expression was higher than IL-10 in 4 of the 5 infected animals and a significant decrease of TNF-α expression was detected in infected vs. non-infected calves. All calves challenged were identified as infected by mesenteric lymph node tissue culture and real time IS900 PCR. In addition, for lymph nodes samples, the agreement between these techniques was almost perfect (κ = 0.86). Colonization of tissues and levels of tissue infection varied between individuals. Evidence of early MAP dissemination to extraintestinal tissues such as the liver was detected by culture in one animal (MAP strain IS900-RFLPA). In both groups microgranulomatous lesions were observed predominantly in the lymph nodes, with giant cells present only in the MA group. In summary, the findings described herein may indicate that local MAP strains induced specific immune responses with particularities that could suggest differences in their biological behavior. Further studies should be carried out in order to obtain an in-depth understanding of the influence of MAP strains in host-pathogen interactions and the outcome of disease.
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Affiliation(s)
- Giselle Gabriela Ingratta
- Universidad de Buenos Aires, Facultad de Ciencias Veterinarias, Cátedra de Inmunología, Av. Chorroarín 280, C1427CWO Ciudad Autónoma de Buenos Aires, Argentina
| | - Ana Stempler
- Universidad de Buenos Aires, Facultad de Ciencias Veterinarias, Cátedra de Inmunología, Av. Chorroarín 280, C1427CWO Ciudad Autónoma de Buenos Aires, Argentina
| | - Bárbara Fernández
- Universidad de Buenos Aires, Facultad de Ciencias Veterinarias, Cátedra de Inmunología, Av. Chorroarín 280, C1427CWO Ciudad Autónoma de Buenos Aires, Argentina; CONICET-Universidad de Buenos Aires, Instituto de Investigaciones en Producción Animal (INPA), Av. Chorroarín 280, C1427CWO Ciudad Autónoma de Buenos Aires, Argentina; Universidad de Buenos Aires, Facultad de Ciencias Veterinarias, Instituto de Investigación y Tecnología en Reproducción Animal (INITRA), Av. Chorroarín 280, C1427CWO Ciudad Autónoma de Buenos Aires, Argentina.
| | - Silvia Beatriz Colavecchia
- Universidad de Buenos Aires, Facultad de Ciencias Veterinarias, Cátedra de Inmunología, Av. Chorroarín 280, C1427CWO Ciudad Autónoma de Buenos Aires, Argentina
| | - Ana Jolly
- Universidad de Buenos Aires, Facultad de Ciencias Veterinarias, Cátedra de Inmunología, Av. Chorroarín 280, C1427CWO Ciudad Autónoma de Buenos Aires, Argentina
| | - Leonardo Minatel
- Universidad de Buenos Aires, Facultad de Ciencias Veterinarias, Cátedra de Patología, Av. San Martín 5285, C1417DSM Ciudad Autónoma de Buenos Aires, Argentina
| | - Fernando Alberto Paolicchi
- Instituto Nacional de Tecnología Agropecuaria (INTA), Estación Experimental Agropecuaria Balcarce, Laboratorio de Bacteriología, Ruta 226, Km 73.5, Balcarce B7620BEN, Provincia de Buenos Aires, Argentina; Universidad Nacional de Mar del Plata, Facultad de Ciencias Agrarias, Departamento de Producción Animal, Ruta 226, Km 73.5, Balcarce B7620BEN, Provincia de Buenos Aires, Argentina
| | - Silvia Leonor Mundo
- Universidad de Buenos Aires, Facultad de Ciencias Veterinarias, Cátedra de Inmunología, Av. Chorroarín 280, C1427CWO Ciudad Autónoma de Buenos Aires, Argentina; CONICET-Universidad de Buenos Aires, Instituto de Investigaciones en Producción Animal (INPA), Av. Chorroarín 280, C1427CWO Ciudad Autónoma de Buenos Aires, Argentina; Universidad de Buenos Aires, Facultad de Ciencias Veterinarias, Instituto de Investigación y Tecnología en Reproducción Animal (INITRA), Av. Chorroarín 280, C1427CWO Ciudad Autónoma de Buenos Aires, Argentina
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Mazzone P, Di Paolo A, Petrucci L, Torricelli M, Corneli S, Sebastiani C, Ciullo M, Sebastianelli M, Costarelli S, Scoccia E, Sbarra F, Gabbianelli F, Chillemi G, Valentini A, Pezzotti G, Biagetti M. Evaluation of Single Nucleotide Polymorphisms (SNPs) Associated with Genetic Resistance to Bovine Paratuberculosis in Marchigiana Beef Cattle, an Italian Native Breed. Animals (Basel) 2023; 13:ani13040587. [PMID: 36830374 PMCID: PMC9951665 DOI: 10.3390/ani13040587] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Revised: 01/26/2023] [Accepted: 02/01/2023] [Indexed: 02/11/2023] Open
Abstract
Mycobacterium avium ssp. paratuberculosis (MAP) is the causative agent of paratuberculosis (PTB), a widespread chronic enteritis of ruminants. The progression of the infection depends on the containment action of innate and cell-mediated immunity (CMI), and it is related to environmental and genetic factors. In particular, PTB susceptibility seems to be associated with specific genes coding for immune regulators involved in the cell-mediated response during the infection. The aim of this preliminary study was to verify, in Italian beef cattle, an association between MAP infectious status and the presence of single nucleotide polymorphisms (SNPs) in candidate genes. To the best of our knowledge, this is the first investigation conducted on a native beef cattle breed, known as Marchigiana, reared in Central Italy. The present research, based on a longitudinal study, aimed to identify and correlate phenotypic and genetic profiles characteristic of the subjects potentially able to contrast or contain PTB. In a MAP-infected herd, ELISA, IFN-γ tests, qPCR, and cultures were performed at a follow-up, occurring within a period ranging from three to six years, to evaluate the individual state of infection. Animals testing positive for at least one test were considered infected. DNA samples of 112 bovines, with known MAP statuses, were analyzed to verify an association with SNPs in the genes encoding gamma-interferon (BoIFNG), interleukin receptor 10 (IL10RA), interleukin receptor 12 (IL12RB2), and toll-like receptors (TLR1, TLR2, TLR4). Regarding statistical analysis, the differences among target genes and pairs of alleles in the analyzed groups of animals, were evaluated at a significance level of p < 0.05. For IL10RA and for IL12RB2 genes, relevant differences in genotypic frequencies among the considered cattle groups were observed. For all candidate genes studied in this investigation, SNP genotypes already associated with PTB resistance were found more frequently in our population, suggesting potential resistance traits in the Marchigiana breed.
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Affiliation(s)
- Piera Mazzone
- Istituto Zooprofilattico Sperimentale dell’Umbria e delle Marche “Togo Rosati”, Via Salvemini 1, 06126 Perugia, Italy
| | - Antonella Di Paolo
- Istituto Zooprofilattico Sperimentale dell’Umbria e delle Marche “Togo Rosati”, Via Salvemini 1, 06126 Perugia, Italy
| | - Linda Petrucci
- Istituto Zooprofilattico Sperimentale dell’Umbria e delle Marche “Togo Rosati”, Via Salvemini 1, 06126 Perugia, Italy
- Correspondence: (L.P.); (M.T.)
| | - Martina Torricelli
- Istituto Zooprofilattico Sperimentale dell’Umbria e delle Marche “Togo Rosati”, Via Salvemini 1, 06126 Perugia, Italy
- Correspondence: (L.P.); (M.T.)
| | - Sara Corneli
- Istituto Zooprofilattico Sperimentale dell’Umbria e delle Marche “Togo Rosati”, Via Salvemini 1, 06126 Perugia, Italy
| | - Carla Sebastiani
- Istituto Zooprofilattico Sperimentale dell’Umbria e delle Marche “Togo Rosati”, Via Salvemini 1, 06126 Perugia, Italy
| | - Marcella Ciullo
- Istituto Zooprofilattico Sperimentale dell’Umbria e delle Marche “Togo Rosati”, Via Salvemini 1, 06126 Perugia, Italy
| | - Martina Sebastianelli
- Azienda Sanitaria Unica Regionale Marche, Area Vasta 2, Servizio di Igiene degli Allevamenti e delle Produzioni Zootecniche, 60127 Ancona, Italy
| | - Silva Costarelli
- Istituto Zooprofilattico Sperimentale dell’Umbria e delle Marche “Togo Rosati”, Via Salvemini 1, 06126 Perugia, Italy
| | - Eleonora Scoccia
- Istituto Zooprofilattico Sperimentale dell’Umbria e delle Marche “Togo Rosati”, Via Salvemini 1, 06126 Perugia, Italy
| | - Fiorella Sbarra
- A.N.A.B.I.C. Associazione Nazionale Allevatori Bovini Italiani Carne, Strada del Vio Viscoloso 21, San Martino in Colle, 06132 Perugia, Italy
| | - Federica Gabbianelli
- Department for Innovation in Biological Agro-Food and Forest Systems (DIBAF), University of Tuscia, 01100 Viterbo, Italy
| | - Giovanni Chillemi
- Department for Innovation in Biological Agro-Food and Forest Systems (DIBAF), University of Tuscia, 01100 Viterbo, Italy
| | - Alessio Valentini
- Department for Innovation in Biological Agro-Food and Forest Systems (DIBAF), University of Tuscia, 01100 Viterbo, Italy
| | - Giovanni Pezzotti
- Istituto Zooprofilattico Sperimentale dell’Umbria e delle Marche “Togo Rosati”, Via Salvemini 1, 06126 Perugia, Italy
| | - Massimo Biagetti
- Istituto Zooprofilattico Sperimentale dell’Umbria e delle Marche “Togo Rosati”, Via Salvemini 1, 06126 Perugia, Italy
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9
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Byrne A, Ollier S, Tahlan K, Biet F, Bissonnette N. Genomic epidemiology of Mycobacterium avium subsp. paratuberculosis isolates from Canadian dairy herds provides evidence for multiple infection events. Front Genet 2023; 14:1043598. [PMID: 36816022 PMCID: PMC9934062 DOI: 10.3389/fgene.2023.1043598] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Accepted: 01/18/2023] [Indexed: 02/05/2023] Open
Abstract
Mycobacterium avium subsp. paratuberculosis (MAP) is the pathogen responsible for paratuberculosis or Johne's Disease (JD) in ruminants, which is responsible for substantial economic losses worldwide. MAP transmission primarily occurs through the fecal-oral route, and the introduction of an MAP infected animal into a herd is an important transmission route. In the current study, we characterized MAP isolates from 67 cows identified in 20 herds from the provinces of Quebec and Ontario, Canada. Whole genome sequencing (WGS) was performed and an average genome coverage (relative to K-10) of ∼14.9 fold was achieved. The total number of SNPs present in each isolate varied from 51 to 132 and differed significantly between herds. Isolates with the highest genetic variability were generally present in herds from Quebec. The isolates were broadly separated into two main clades and this distinction was not influenced by the province from which they originated. Analysis of 8 MIRU-VNTR loci and 11 SSR loci was performed on the 67 isolates from the 20 dairy herds and publicly available references, notably major genetic lineages and six isolates from the province of Newfoundland and Labrador. All 67 field isolates were phylogenetically classified as Type II (C-type) and according to MIRU-VNTR, the predominant type was INMV 2 (76.1%) among four distinct patterns. Multilocus SSR typing identified 49 distinct INMV SSR patterns. The discriminatory index of the multilocus SSR typing was 0.9846, which was much higher than MIRU-VNTR typing (0.3740). Although multilocus SSR analysis provides good discriminatory power, the resolution was not informative enough to determine inter-herd transmission. In select cases, SNP-based analysis was the only approach able to document disease transmission between herds, further validated by animal movement data. The presence of SNPs in several virulence genes, notably for PE, PPE, mce and mmpL, is expected to explain differential antigenic or pathogenetic host responses. SNP-based studies will provide insight into how MAP genetic variation may impact host-pathogen interactions. Our study highlights the informative power of WGS which is now recommended for epidemiological studies and to document mixed genotypes infections.
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Affiliation(s)
- Alexander Byrne
- Department of Biology, Memorial University of Newfoundland, St. John’s, NL, Canada
| | - Séverine Ollier
- Sherbrooke Research and Development Centre, Agriculture and Agri-Food Canada, Sherbrooke, QC, Canada
| | - Kapil Tahlan
- Department of Biology, Memorial University of Newfoundland, St. John’s, NL, Canada
| | - Franck Biet
- INRAE, ISP, Université de Tours, Nouzilly, France
| | - Nathalie Bissonnette
- Sherbrooke Research and Development Centre, Agriculture and Agri-Food Canada, Sherbrooke, QC, Canada,*Correspondence: Nathalie Bissonnette,
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10
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Rasper-Hössinger M, Biggel M, Stephan R, Seehusen F, Scherrer S. Strain diversity in Mycobacterium avium subsp. paratuberculosis-positive bovine fecal samples collected in Switzerland. Front Vet Sci 2023; 10:1154516. [PMID: 37180063 PMCID: PMC10171428 DOI: 10.3389/fvets.2023.1154516] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Accepted: 04/05/2023] [Indexed: 05/15/2023] Open
Abstract
Paratuberculosis or Johne's disease is a chronic intestinal disease in domestic and wild ruminants. It affects global dairy economy and is caused by Mycobacterium avium subsp. paratuberculosis (MAP). The objective of this study was to analyze strain diversity in MAP-positive fecal samples by using a particular single nucleotide polymorphism (SNP) distinguishing between cattle (C-) and sheep (S-) type MAP and analysis of SNPs within gyrA and gyrB genes differentiating between Types I, II, and III. Moreover, mycobacterial interspersed repetitive unit and variable-number tandem repeat (MIRU-VNTR) analysis using eight established loci was performed. A total of 90 fecal samples from diseased animals presenting diarrhea and/or weight loss, originating from 59 bovine herds across 16 cantons of Switzerland were screened by PCR for the MAP-specific F57 and IS900 genes and were further subtyped. 96.7% and 3.3% of the samples contained C- and S-type MAP, respectively. Ten INRA Nouzilly MIRU-VNTR (INMV) profiles, with a discriminatory index of 0.802, calculated based on 65 epidemiological independent genotypes, were detected: INMV 1 (33.8%), INMV 2 (23.1%), INMV 6 (16.9%), INMV 9 (9.2%), INMV 116 (4.6%), INMV 3 (3.1%), INMV 5 (3.1%) and INMV 72 (1.5%), including two novel INMV profiles, namely INMV 253 (3.1%; S-type III) and INMV 252 (1.5%; C-type). INMV 1, INMV 2, and INMV 6 comprised almost 75% of the F57- and IS900-positive samples. Typing data from 11 herds suggest that there are some herds with intra-herd diversity of genotypes. The results of this study indicate a heterogeneity of MAP in Switzerland.
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Affiliation(s)
| | - Michael Biggel
- Institute for Food Safety and Hygiene, University of Zurich, Zurich, Switzerland
| | - Roger Stephan
- Institute for Food Safety and Hygiene, University of Zurich, Zurich, Switzerland
- Section of Veterinary Bacteriology, Institute for Food Safety and Hygiene, University of Zurich, Zurich, Switzerland
| | - Frauke Seehusen
- Institute of Veterinary Pathology, University of Zurich, Zurich, Switzerland
| | - Simone Scherrer
- Section of Veterinary Bacteriology, Institute for Food Safety and Hygiene, University of Zurich, Zurich, Switzerland
- *Correspondence: Simone Scherrer,
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11
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Genetic Features of Mycobacterium avium subsp. paratuberculosis Strains Circulating in the West of France Deciphered by Whole-Genome Sequencing. Microbiol Spectr 2022; 10:e0339222. [PMID: 36445077 PMCID: PMC9769990 DOI: 10.1128/spectrum.03392-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022] Open
Abstract
Paratuberculosis is a chronic infection of the intestine, mainly the ileum, caused by Mycobacterium avium subsp. paratuberculosis in cattle and other ruminants. This enzootic disease is present worldwide and has a negative impact on the dairy cattle industry. For this subspecies, the current genotyping tools do not provide the needed resolution to investigate the genetic diversity of closely related strains. These limitations can be overcome by the application of whole-genome sequencing (WGS), particularly for clonal populations such as M. avium subsp. paratuberculosis. The purpose of the present study was to undertake a WGS analysis with a panel of 200 animal field M. avium subsp. paratuberculosis strains selected based on a previous large-scale longitudinal study of Prim'Holstein and Normande dairy breeds naturally infected with M. avium subsp. paratuberculosis in the West of France. The pangenome analysis revealed that M. avium subsp. paratuberculosis has a closed pangenome. The phylogeny, based on alignment of 2,786 nonhomoplasic single nucleotide polymorphisms (SNPs), showed that the strain population is structured into three clades independently of the cattle breed or geographic distribution. The increased resolution of phylogeny obtained by WGS confirmed the homoplasic nature of the markers variable-number tandem repeat (VNTR) and short sequence repeat (SSR) used for M. avium subsp. paratuberculosis genotyping. These phylogenetic data also revealed independent introductions of the different genotypes in two main waves since at least 2003. WGS applied to this sampling demonstrated the presence of mixed infections in herds and at the individual animal level. Collectively, the phylogeny results inferred with French isolates compared to M. avium subsp. paratuberculosis isolates from around the world suggest introductions of M. avium subsp. paratuberculosis genotypes through the animal trade. Relationships between genetic traits and epidemiological data can now be investigated to better understand transmission dynamics of the disease. IMPORTANCE Mycobacterium avium subsp. paratuberculosis causes Johne's disease in ruminants, which is present worldwide and has significant negative impacts on the dairy cattle industry and animal welfare. Prevention and control of M. avium subsp. paratuberculosis infection are hampered by knowledge gaps in strain virulence, genotype distribution, and transmission dynamics. This work has revealed new insights into M. avium subsp. paratuberculosis strains currently circulating in western France and how they are related to strains circulating globally. We applied whole-genome sequencing (WGS) to obtain comprehensive information on genome evolution and discrimination of closely related strains. This approach revealed the history of M. avium subsp. paratuberculosis infection in France, refined the pangenomic characteristics of M. avium subsp. paratuberculosis, and demonstrated the existence of mixed infection in animals. Finally, this study identified predominant genotypes, which allow a better understanding of disease transmission dynamics. This information will facilitate tracking of this pathogen on farms and across agricultural regions, thus informing transmission pathways and disease control points.
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12
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Eshraghisamani R, Mirto AJ, Wang J, Behr MA, Barkema HW, De Buck J. Identification of essential genes in Mycobacterium avium subsp. paratuberculosis genome for persistence in dairy calves. Front Microbiol 2022; 13:994421. [PMID: 36338087 PMCID: PMC9631821 DOI: 10.3389/fmicb.2022.994421] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Accepted: 09/05/2022] [Indexed: 11/02/2023] Open
Abstract
To cause disease Mycobacterium avium subsp. paratuberculosis needs to enter mammalian cells, arrest phagosomal maturation and manipulate the host immune system. The genetic basis of the bacterial capacity to achieve these outcomes remains largely unknown. Identifying these genes would allow us to gain a deeper understanding of MAP's pathogenesis and potentially develop a live attenuated Johne's disease vaccine by knocking out these genes. MAP genes demonstrated to be essential for colonization in the natural host, ruminants, are unknown. Genome-wide transposon mutagenesis and high-throughput sequencing were combined to evaluate the essentiality of each coding region in the bacterial genome to survive in dairy calves. A saturated library of 3,852 MAP Tn mutants, with insertions in 56% of TA sites, interrupting 88% of genes, was created using a MycoMarT7 phagemid containing a mariner transposon. Six calves were inoculated with a high dose of a library of MAP mutants, 1011 CFUs, (input) at 2 weeks of age. Following 2 months of incubation, MAP cells were isolated from the ileum, jejunum, and their associated lymph nodes of calves, resulting in approximately 100,000 colonies grown on solid media across 6 animals (output). Targeted next-generation sequencing was used to identify the disrupted genes in all the mutants in the input pool and the output pool recovered from the tissues to identify in vivo essential genes. Statistical analysis for the determination of essential genes was performed by a Hidden Markov Model (HMM), categorizing genes into essential genes that are devoid of insertions and growth-defect genes whose disruption impairs the growth of the organism. Sequence analysis identified 430 in vivo essential and 260 in vivo growth-defect genes. Gene ontology enrichment analysis of the in vivo essential and growth-defect genes with the highest reduction in the tissues revealed a high representation of genes involved in metabolism and respiration, cell wall and cell processing, virulence, and information pathway processes. This study has systematically identified essential genes for the growth and persistence of MAP in the natural host body.
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Affiliation(s)
- Razieh Eshraghisamani
- Department of Production Animal Health, Faculty of Veterinary Medicine, University of Calgary, Calgary, AB, Canada
| | - Amanda J. Mirto
- Environmental Health and Safety, University of Wisconsin-Madison, Madison, WI, United States
| | - Joyce Wang
- Department of Medicine, Faculty of Medicine, Health Centre, McGill University, Montréal, QC, Canada
| | - Marcel A. Behr
- Department of Medicine, Faculty of Medicine, Health Centre, McGill University, Montréal, QC, Canada
| | - Herman W. Barkema
- Department of Production Animal Health, Faculty of Veterinary Medicine, University of Calgary, Calgary, AB, Canada
| | - Jeroen De Buck
- Department of Production Animal Health, Faculty of Veterinary Medicine, University of Calgary, Calgary, AB, Canada
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13
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Zang X, Dang G, Cai Z, Shao M, Tang Y, Cao J, Cui Z, Liu S. Extracellular DNase MAP3916c attacks the neutrophil extracellular traps and is needed for Mycobacterium avium subsp. paratuberculosis virulence. Vet Microbiol 2022; 273:109529. [PMID: 35944391 DOI: 10.1016/j.vetmic.2022.109529] [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: 01/05/2022] [Revised: 07/29/2022] [Accepted: 08/02/2022] [Indexed: 11/27/2022]
Abstract
Extracellular DNases/nucleases are important virulence factors in many bacteria. However, no DNase/nucleases have been reported in Mycobacterium avium subsp. paratuberculosis (MAP), which is a pathogen of paratuberculosis. Genome analyses of MAP K-10 revealed that the map3916c gene putatively encodes a nuclease. In this study, we show that MAP3916c is an extracellular nonspecific DNase requiring a divalent cation, especially Mg2+. The optimum DNase activity of MAP3916c was exhibited at 41 °C and pH 9.0. Site-directed mutagenesis studies indicated that 125-Histidine is necessary for MAP3916c DNase activity. In addition, MAP3916c DNase could destroy the neutrophil extracellular traps (NETs) induced by Phorbol 12-myristate 13-acetate in vitro and degrade the NETs induced by MAP K-10 upon infection. Furthermore, MAP3916c DNase promoted the colonization of MAP K-10, induced the formation of granulomas in the liver and small intestine and promoted the release of IL-1β, IL-6 and TNF-α inflammatory cytokines during the infection of mice. These results indicated that MAP3916c is relevant to NETs escape and the pathogenicity of MAP. It also provides a basis for further study of the function of nuclease activity on the MAP immune evasion.
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Affiliation(s)
- Xinxin Zang
- State Key Laboratory of Veterinary Biotechnology, Division of Bacterial Diseases, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, 678 Haping Street, Harbin 150069, China
| | - Guanghui Dang
- State Key Laboratory of Veterinary Biotechnology, Division of Bacterial Diseases, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, 678 Haping Street, Harbin 150069, China
| | - Zhuming Cai
- State Key Laboratory of Veterinary Biotechnology, Division of Bacterial Diseases, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, 678 Haping Street, Harbin 150069, China
| | - Mingzhu Shao
- State Key Laboratory of Veterinary Biotechnology, Division of Bacterial Diseases, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, 678 Haping Street, Harbin 150069, China
| | - Yangyang Tang
- State Key Laboratory of Veterinary Biotechnology, Division of Bacterial Diseases, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, 678 Haping Street, Harbin 150069, China; College of Animal Science and Technology, Jilin Agricultural University, Changchun, China
| | - Jun Cao
- State Key Laboratory of Veterinary Biotechnology, Division of Bacterial Diseases, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, 678 Haping Street, Harbin 150069, China
| | - Ziyin Cui
- State Key Laboratory of Veterinary Biotechnology, Division of Bacterial Diseases, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, 678 Haping Street, Harbin 150069, China
| | - Siguo Liu
- State Key Laboratory of Veterinary Biotechnology, Division of Bacterial Diseases, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, 678 Haping Street, Harbin 150069, China.
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14
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Yu Y, Zhang S, Xu G, Xu D, Zheng H, Li B, Shen K, Fu L. Identification of Mycobacterium avium subspecies paratuberculosis in sheep farms in Bayannaoer, Inner Mongolia, China (short communication). BMC Vet Res 2022; 18:281. [PMID: 35842628 PMCID: PMC9287916 DOI: 10.1186/s12917-022-03293-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Accepted: 04/29/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Paratuberculosis is a widespread chronic infection of Mycobacterium avium subspecies paratuberculosis (MAP) that causes significant economic losses to the sheep industry. The current study investigated this disease, which causes diarrhea in sheep, particularly, in Bayannaoer, Inner Mongolia, China. Diagnosis was based on clinical symptoms, pathological autopsy, histopathological inspection, and serological and molecular methods. RESULTS MAP was confirmed using polymerase chain reaction using DNA extracted from tissue and fecal samples. Serum samples from 472 individual sheep were obtained to detect antibodies against MAP using an enzyme-linked immunosorbent assay. MAP antibodies were separately detected in 17.86% (35/196) and 18.48% (51/276) of sheep herds at approximately 6 months and ≥ 1 year of age, respectively. The tissue lesion and pathological section results were consistent with paratuberculosis infection. CONCLUSIONS To our knowledge, this is the first report of Mycobacterium avium subspecies paratuberculosis seroprevalence in Bayannaoer sheep in Inner Mongolia. Our findings show that MAP is not only prevalent, but also a potential threat to this region. Further investigations, including long-term epidemiological surveillance and isolation are needed for the awareness and effective treatment of paratuberculosis in sheep of Inner Mongolia.
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Affiliation(s)
- Yuandi Yu
- Chongqing Academy of Animal Sciences, Chongqing, China.,Chongqing Research Center of Veterinary Biologicals Engineering and Technology, Chongqing Academy of Animal Sciences, 51 Changlong Avenue, Rongchang District, ChongQing, 402460, China
| | - Suhui Zhang
- Chongqing Academy of Animal Sciences, Chongqing, China.,Chongqing Research Center of Veterinary Biologicals Engineering and Technology, Chongqing Academy of Animal Sciences, 51 Changlong Avenue, Rongchang District, ChongQing, 402460, China
| | - Guoyang Xu
- Chongqing Academy of Animal Sciences, Chongqing, China.,Chongqing Research Center of Veterinary Biologicals Engineering and Technology, Chongqing Academy of Animal Sciences, 51 Changlong Avenue, Rongchang District, ChongQing, 402460, China
| | - Dengfeng Xu
- Chongqing Academy of Animal Sciences, Chongqing, China.,Chongqing Research Center of Veterinary Biologicals Engineering and Technology, Chongqing Academy of Animal Sciences, 51 Changlong Avenue, Rongchang District, ChongQing, 402460, China
| | - Hua Zheng
- Chongqing Academy of Animal Sciences, Chongqing, China.,Chongqing Research Center of Veterinary Biologicals Engineering and Technology, Chongqing Academy of Animal Sciences, 51 Changlong Avenue, Rongchang District, ChongQing, 402460, China
| | - Bo Li
- Chongqing Academy of Animal Sciences, Chongqing, China.,Chongqing Research Center of Veterinary Biologicals Engineering and Technology, Chongqing Academy of Animal Sciences, 51 Changlong Avenue, Rongchang District, ChongQing, 402460, China
| | - Kefei Shen
- Chongqing Academy of Animal Sciences, Chongqing, China. .,Chongqing Research Center of Veterinary Biologicals Engineering and Technology, Chongqing Academy of Animal Sciences, 51 Changlong Avenue, Rongchang District, ChongQing, 402460, China.
| | - Lizhi Fu
- Chongqing Academy of Animal Sciences, Chongqing, China. .,Chongqing Research Center of Veterinary Biologicals Engineering and Technology, Chongqing Academy of Animal Sciences, 51 Changlong Avenue, Rongchang District, ChongQing, 402460, China.
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15
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Field NL, McAloon CG, Gavey L, Mee JF. Mycobacterium avium subspecies paratuberculosis infection in cattle - a review in the context of seasonal pasture-based dairy herds. Ir Vet J 2022; 75:12. [PMID: 35590382 PMCID: PMC9121589 DOI: 10.1186/s13620-022-00217-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2022] [Accepted: 04/24/2022] [Indexed: 11/17/2022] Open
Abstract
Johne’s disease is an infectious disease affecting cattle, other ruminants and non-ruminant wildlife worldwide, caused by Mycobacterium avium subspecies paratuberculosis (MAP). This review provides an up-to-date concise overview of the pathogenesis of MAP, the significance of Johne’s disease in cattle and the use of diagnostic testing at both animal and herd level in the context of seasonal pasture-based herds. While MAP can only replicate intracellularly, the bacterium is sufficiently robust to survive for months in the environment. Transmission of MAP is mostly via the faecal-oral route, however in-utero transmission in also possible. The bacteria evade the immune system by persisting in macrophages in the small intestine submucosa, with this latent stage of infection lasting, in most cases, for at least two years before bacterial shedding and clinical signs begin. The slowly progressive nature of MAP infection, poor performance of diagnostic tests and management systems that expose susceptible calves to infection make control of Johne’s disease challenging, particularly in seasonal calving herds. Testing of individual animals provides little assurance for farmers and vets due to the poor sensitivity and, in the case of ELISA, imperfect specificity of the available tests. Repeated herd-level testing is utilised by the IJCP to detect infected herds, identify high risk animals, and provide increasing confidence that test-negative herds are free of infection. The IJCP aims to control the spread of Johne’s disease in cattle in Ireland, in order to protect non-infected herds, limit the economic and animal health impact of the disease, improve calf health and reassure markets of Johne’s disease control in Ireland.
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Affiliation(s)
- Niamh L Field
- Animal and Bioscience Research Department, Teagasc, Moorepark Research Centre, Fermoy, Co. Cork, P61 P302, Ireland. .,UCD School of Veterinary Medicine, University College Dublin, Belfield, Dublin, D04 W6F6, Ireland.
| | - Conor G McAloon
- UCD School of Veterinary Medicine, University College Dublin, Belfield, Dublin, D04 W6F6, Ireland
| | | | - John F Mee
- Animal and Bioscience Research Department, Teagasc, Moorepark Research Centre, Fermoy, Co. Cork, P61 P302, Ireland
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16
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Li X, Ding N, Zhang Z, Tian D, Han B, Liu D, Liu S, Tian F, Fu D, Song X, Zhao K. Identification of SSTR5 Gene Polymorphisms and Their Association With Growth Traits in Hulun Buir Sheep. Front Genet 2022; 13:831599. [PMID: 35559027 PMCID: PMC9086292 DOI: 10.3389/fgene.2022.831599] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Accepted: 03/10/2022] [Indexed: 11/15/2022] Open
Abstract
The aim of this study was to locate SSTR5 polymorphisms and evaluate their association with growth traits in Hulun Buir sheep. The study followed up 884 Hulun Buir sheep from birth to 16 months of age, which were born in the same pasture and the same year, and a consistent grazing management strategy was maintained. The birth weight (BRW) was recorded at birth, and body weight (BW), body height (BH), body length (BL), chest circumference (ChC), chest depth (ChD), chest width (ChW), hip width (HW), and cannon circumference (CaC) were measured at 4 and 9 months of age. BW, BH, BL, ChD, HW, and CaC were also recorded at 16 months of age. Based on the growth traits, 233 sheep were selected as experimental animals. Sanger sequencing was performed, and seven single-nucleotide polymorphisms (SNPs) were identified. Association analyses of the SNPs and the growth traits were then conducted. Seven SNPs of the SSTR5 exhibited moderate polymorphism (0.25
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Affiliation(s)
- Xue Li
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Qinghai Provincial Key Laboratory of Animal Ecological Genomics, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Ning Ding
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Qinghai Provincial Key Laboratory of Animal Ecological Genomics, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Zhichao Zhang
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Qinghai Provincial Key Laboratory of Animal Ecological Genomics, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Dehong Tian
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Qinghai Provincial Key Laboratory of Animal Ecological Genomics, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, China
| | - Buying Han
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Qinghai Provincial Key Laboratory of Animal Ecological Genomics, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Dehui Liu
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Qinghai Provincial Key Laboratory of Animal Ecological Genomics, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Sijia Liu
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Qinghai Provincial Key Laboratory of Animal Ecological Genomics, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, China
| | - Fei Tian
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Qinghai Provincial Key Laboratory of Animal Ecological Genomics, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, China
| | - Dejun Fu
- Inner Mongolia Daxing 'anling Agricultural Reclamation Group Co. LTD., Hulun Buir, China
| | - Xiaoliang Song
- Inner Mongolia Daxing 'anling Agricultural Reclamation Group Co. LTD., Hulun Buir, China
| | - Kai Zhao
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Qinghai Provincial Key Laboratory of Animal Ecological Genomics, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, China
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17
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Abstract
Saccharibacteria (TM7), which are obligate episymbionts growing on the surface of host bacteria, may play an important role in oral disease, such as periodontitis (1, 2). As TM7 is a newly cultured lineage of bacteria, its research is limited by the small number of isolated representatives relative to the number of TM7 genomes assembled from culture-independent studies (3–5). A comprehensive view of both TM7 taxa and TM7 strain-level variations remains opaque. In this study, we expanded our previously developed TM7 baiting method into using many host bacteria in parallel, which allowed us to obtain 37 TM7 strains from the human oral cavity. These strains were further classified into low-enrichment (LE, n = 24) and high-enrichment (HE, n = 13) groups based on their proficiency at propagating on host bacteria. Of the 13 HE strains, 10 belong to “Candidatus Nanosynbacter sp.” strain HMT-352 (human microbial taxon) (6), enabling us to explore both the phenotypic and genomic strain variations within a single TM7 species. We show that TM7 HMT-352 strains exhibit a diverse host range and varied growth dynamics during the establishment of their episymbiotic relationship with host bacteria. Furthermore, despite HMT-352 strains sharing a majority of their genes, we identified several gene clusters that may play a pivotal role in host affinity. More importantly, our comparative analyses also provide TM7 gene candidates associated with strain-level phenotypic variation that may be important for episymbiotic interactions with host bacteria. IMPORTANCE Candidate phylum radiation (CPR) bacteria comprise a poorly understood phylum that is estimated to encompass ∼26% of all diversity of domain bacteria. Among CPR bacteria, the Saccharibacteria lineage (TM7) is of particular interest, as it is found in high abundance in the mammal microbiome and has been associated with oral disease. While many CPR genomes, TM7 included, have been acquired through culture-independent methods, only a small number of representatives have been isolated. Such isolated representatives, however, shed light on the physiology, pathogenesis, and episymbiotic interactions of TM7. Combined with genomic analyses, experiments involving isolated representatives can distinguish phylogenetic to phenotypic discrepancies and better identify genes of importance. In this study, we utilized multiple host bacteria in parallel to isolate TM7 bacteria and examined strain-level variation in TM7 to reveal key genes that may drive TM7-host interactions. Our findings accentuate that broad phylogenetic characterization of CPR is the next step in understanding these bacteria.
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18
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Identification of Somatostatin Receptor Subtype 1 (SSTR1) Gene Polymorphism and Their Association with Growth Traits in Hulun Buir Sheep. Genes (Basel) 2021; 13:genes13010077. [PMID: 35052417 PMCID: PMC8775034 DOI: 10.3390/genes13010077] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Revised: 12/22/2021] [Accepted: 12/27/2021] [Indexed: 12/19/2022] Open
Abstract
This study was conducted to evaluate SSTR1 gene polymorphisms and their association with growth traits in Hulun Buir sheep. We followed 233 Hulun Buir sheep from birth to 16 months of age, born in the same pasture and on the same year under a consistent grazing conditions. The body weight (BW), body height (BH), body length (BL), chest circumference (ChC), chest depth (ChD), chest width (ChW), hip width (HW), and cannon circumference (CaC) were measured and recorded at birth, 4 months, 9 months, and 16 months of age. The polymorphisms of the SSTR1 gene in Hulun Buir sheep were excavated using exon sequencing, and association analyses of between SNPs and growth traits at each growth stage were conducted. The results showed that there were four SNPs in Exon 2 of the SSTR1 gene, SNP1, SNP2, and SNP3 were low mutation sites, and SNP4 was a moderate mutation site. Four SNPs were consistent with Hardy–Weinberg equilibrium, and all of them were synonymous mutations. The association analyses found that the genotypes of SNP2 were significantly associated with WW and BH at 4 months of age, BW, BL, ChC, and HW at 9 months of age (p < 0.05), and extremely significantly associated with ChD at 4 and 9 months of age (p < 0.01). There were significant associations between SNP3 and BH at 9 months of age, between SNP4 and ChD, ChW, and CaC at 9 months of age, and BW and ChC at 16 months of age (p < 0.05). There were no detectable associations with growth traits among the seven haplotypes between the SNP1, 3, and 4 of a strong linkage disequilibrium (p > 0.05). These results indicated that SNP2, SNP3, and SNP4 may be used as molecular markers for growth traits of Hulun Buir sheep.
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Ssekitoleko J, Ojok L, Abd El Wahed A, Erume J, Amanzada A, Eltayeb E, Eltom KH, Okuni JB. Mycobacterium avium subsp. paratuberculosis Virulence: A Review. Microorganisms 2021; 9:2623. [PMID: 34946224 PMCID: PMC8707695 DOI: 10.3390/microorganisms9122623] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Revised: 12/08/2021] [Accepted: 12/16/2021] [Indexed: 11/17/2022] Open
Abstract
To propose a solution for control of Mycobacterium avium subsp. paratuberculosis (MAP) infections in animals as well as in humans, and develop effective prevention, diagnostic and treatment strategies, it is essential to understand the molecular mechanisms of MAP pathogenesis. In the present review, we discuss the mechanisms utilised by MAP to overcome the host defense system to achieve the virulence status. Putative MAP virulence genes are mentioned and their probable roles in view of other mycobacteria are discussed. This review provides information on MAP strain diversity, putative MAP virulence factors and highlights the knowledge gaps regarding MAP virulence mechanisms that may be important in control and prevention of paratuberculosis.
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Affiliation(s)
- Judah Ssekitoleko
- College of Veterinary Medicine, Animal Resources and Biosecurity, Makerere University, Kampala P. O. Box 7062, Uganda; (J.S.); (L.O.); (J.E.)
- Department of Livestock Health Research, Rwebitaba Zonal Agricultural Research and Development Institute, National Agricultural Research Organisation, Entebbe P. O. Box 295, Uganda
| | - Lonzy Ojok
- College of Veterinary Medicine, Animal Resources and Biosecurity, Makerere University, Kampala P. O. Box 7062, Uganda; (J.S.); (L.O.); (J.E.)
- Department of Pathology, Faculty of Medicine, Gulu University, Gulu P. O. Box 166, Uganda
| | - Ahmed Abd El Wahed
- Institute of Animal Hygiene and Veterinary Public Health, Leipzig University, D-04103 Leipzig, Germany
| | - Joseph Erume
- College of Veterinary Medicine, Animal Resources and Biosecurity, Makerere University, Kampala P. O. Box 7062, Uganda; (J.S.); (L.O.); (J.E.)
| | - Ahmad Amanzada
- Department of Gastroenterology and Gastrointestinal Oncology, University Medical Centre Goettingen, D-37075 Goettingen, Germany;
| | - ElSagad Eltayeb
- Ibn Sina Specialised Hospital, Mohammed Najeeb St., Khartoum 11560, Sudan;
- Faculty of Medicine, Al Neelain University, 52nd St., Khartoum 11112, Sudan
| | - Kamal H. Eltom
- Unit of Animal Health and Safety of Animal Products, Institute for Studies and Promotion of Animal Exports, University of Khartoum, Shambat, Khartoum North 13314, Sudan;
| | - Julius Boniface Okuni
- College of Veterinary Medicine, Animal Resources and Biosecurity, Makerere University, Kampala P. O. Box 7062, Uganda; (J.S.); (L.O.); (J.E.)
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Transmission patterns of a Mycobacterium avium subsp. paratuberculosis clone within a single heard investigated by Whole Genome Sequencing. Vet Microbiol 2021; 263:109272. [PMID: 34785477 DOI: 10.1016/j.vetmic.2021.109272] [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: 10/05/2020] [Accepted: 10/28/2021] [Indexed: 11/23/2022]
Abstract
Mycobacterium avium subsp. paratuberculosis (MAP) is characterized by a low genomic rate of mutation. Current subtyping tools, such as Mini-Micro-satellite analyses, do to have not sufficient discriminatory power to disclose MAP's evolution on small spatial and temporal scales. The aim of the study was to investigate the population structure of MAP inside a single dairy herd using whole genome sequencing (WGS) approaches. For this purpose, the genomes of 43 field isolates, recovered from the faeces of 36 cows of the same dairy herd from 2012 to 2016, were sequenced by WGS. The isolates' genomes showed a low number (43) of polymorphic sites (SNPs), confirming the clonal origin of the herd infection. However, despite the limited genomic diversity found in WGS, the phylogenetic analysis was discriminatory enough to detect the presence of different genomic clades and sub-clades inside the herd population. In addition, the phylodynamic reconstruction showed the existence of an ancestor clade from which the other clades and sub-clades originated. Moreover, by reconstructing the putative within-herd transmission networks using WGS data, we demonstrated that: (i) in a herd where MAP is endemic, multiple isolates recovered from a single animal and differing from each other by few (three/four) SNPs can originate from different transmission or passive shedding events and not from intra-host evolution; and (ii) variability of minisatellites coupled with a few microsatellites does not represent reliable tracers of within-herd infection chains. Our findings show that WGS, coupled with relevant epidemiological information, represents a valuable tool to work out fine epidemiological and micro-evolutionary relationships such as those at herd-level scale.
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Esteves A, Vieira-Pinto M, Quintas H, Orge L, Gama A, Alves A, Seixas F, Pires I, Pinto MDL, Mendonça AP, Lima C, Machado CN, Silva JC, Tavares P, Silva F, Bastos E, Pereira J, Gonçalves-Anjo N, Carvalho P, Sargo R, Matos A, Figueira L, Pires MDA. Scrapie at Abattoir: Monitoring, Control, and Differential Diagnosis of Wasting Conditions during Meat Inspection. Animals (Basel) 2021; 11:3028. [PMID: 34827761 PMCID: PMC8614523 DOI: 10.3390/ani11113028] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Revised: 10/15/2021] [Accepted: 10/18/2021] [Indexed: 01/10/2023] Open
Abstract
Wasting disease in small ruminants is frequently detected at slaughterhouses. The wasting disorder is manifested by the deterioration of the nutritional and physiological state of the animal indicated by thinness, emaciation, and cachexia. Evidence of emaciation and cachexia, alone, are pathological conditions leading to carcass condemnation during an inspection. Several diseases are associated with a wasting condition, including scrapie, pseudotuberculosis, tuberculosis, paratuberculosis, Maedi Visna, and tumor diseases. On the other hand, parasitic diseases, nutrition disorders, exposure or ingestion of toxins, metabolic conditions, inadequate nutrition due to poor teeth, or poor alimentary diet are conditions contributing to poor body condition. Classical and atypical scrapie is naturally occurring transmissible spongiform encephalopathies in small ruminants. The etiological agent for each one is prions. However, each of these scrapie types is epidemiologically, pathologically, and biochemically different. Though atypical scrapie occurs at low incidence, it is consistently prevalent in the small ruminant population. Hence, it is advisable to include differential diagnosis of this disease, from other possibilities, as a cause of wasting conditions detected during meat inspection at the abattoir. This manuscript is a review of the measures in force at the abattoir for scrapie control, focusing on the differential diagnosis of gross lesions related to wasting conditions detected in small ruminants during meat inspection.
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Affiliation(s)
- Alexandra Esteves
- Animal and Veterinary Research Centre (CECAV), University of Trás-os-Montes and Alto Douro (UTAD), 5000-801 Vila Real, Portugal; (M.V.-P.); (L.O.); (A.G.); (A.A.); (F.S.); (I.P.); (M.d.L.P.); (F.S.); (J.P.); (R.S.)
| | - Madalena Vieira-Pinto
- Animal and Veterinary Research Centre (CECAV), University of Trás-os-Montes and Alto Douro (UTAD), 5000-801 Vila Real, Portugal; (M.V.-P.); (L.O.); (A.G.); (A.A.); (F.S.); (I.P.); (M.d.L.P.); (F.S.); (J.P.); (R.S.)
| | - Hélder Quintas
- Centro de Investigação de Montanha (CIMO), Instituto Politécnico de Bragança, Campus de Santa Apolónia, 5300-253 Bragança, Portugal;
| | - Leonor Orge
- Animal and Veterinary Research Centre (CECAV), University of Trás-os-Montes and Alto Douro (UTAD), 5000-801 Vila Real, Portugal; (M.V.-P.); (L.O.); (A.G.); (A.A.); (F.S.); (I.P.); (M.d.L.P.); (F.S.); (J.P.); (R.S.)
- Pathology Laboratory, UEISPSA, National Institute for Agricultural and Veterinary Research (INIAV), I.P., 2780-157 Oeiras, Portugal; (A.P.M.); (C.N.M.); (J.C.S.); (P.C.)
| | - Adelina Gama
- Animal and Veterinary Research Centre (CECAV), University of Trás-os-Montes and Alto Douro (UTAD), 5000-801 Vila Real, Portugal; (M.V.-P.); (L.O.); (A.G.); (A.A.); (F.S.); (I.P.); (M.d.L.P.); (F.S.); (J.P.); (R.S.)
| | - Anabela Alves
- Animal and Veterinary Research Centre (CECAV), University of Trás-os-Montes and Alto Douro (UTAD), 5000-801 Vila Real, Portugal; (M.V.-P.); (L.O.); (A.G.); (A.A.); (F.S.); (I.P.); (M.d.L.P.); (F.S.); (J.P.); (R.S.)
| | - Fernanda Seixas
- Animal and Veterinary Research Centre (CECAV), University of Trás-os-Montes and Alto Douro (UTAD), 5000-801 Vila Real, Portugal; (M.V.-P.); (L.O.); (A.G.); (A.A.); (F.S.); (I.P.); (M.d.L.P.); (F.S.); (J.P.); (R.S.)
| | - Isabel Pires
- Animal and Veterinary Research Centre (CECAV), University of Trás-os-Montes and Alto Douro (UTAD), 5000-801 Vila Real, Portugal; (M.V.-P.); (L.O.); (A.G.); (A.A.); (F.S.); (I.P.); (M.d.L.P.); (F.S.); (J.P.); (R.S.)
| | - Maria de Lurdes Pinto
- Animal and Veterinary Research Centre (CECAV), University of Trás-os-Montes and Alto Douro (UTAD), 5000-801 Vila Real, Portugal; (M.V.-P.); (L.O.); (A.G.); (A.A.); (F.S.); (I.P.); (M.d.L.P.); (F.S.); (J.P.); (R.S.)
| | - Ana Paula Mendonça
- Pathology Laboratory, UEISPSA, National Institute for Agricultural and Veterinary Research (INIAV), I.P., 2780-157 Oeiras, Portugal; (A.P.M.); (C.N.M.); (J.C.S.); (P.C.)
| | - Carla Lima
- Pathology Laboratory, UEISPSA, National Institute for Agricultural and Veterinary Research (INIAV), I.P., 4485-655 Vila do Conde, Portugal; (C.L.); (P.T.)
| | - Carla Neves Machado
- Pathology Laboratory, UEISPSA, National Institute for Agricultural and Veterinary Research (INIAV), I.P., 2780-157 Oeiras, Portugal; (A.P.M.); (C.N.M.); (J.C.S.); (P.C.)
| | - João Carlos Silva
- Pathology Laboratory, UEISPSA, National Institute for Agricultural and Veterinary Research (INIAV), I.P., 2780-157 Oeiras, Portugal; (A.P.M.); (C.N.M.); (J.C.S.); (P.C.)
| | - Paula Tavares
- Pathology Laboratory, UEISPSA, National Institute for Agricultural and Veterinary Research (INIAV), I.P., 4485-655 Vila do Conde, Portugal; (C.L.); (P.T.)
| | - Filipe Silva
- Animal and Veterinary Research Centre (CECAV), University of Trás-os-Montes and Alto Douro (UTAD), 5000-801 Vila Real, Portugal; (M.V.-P.); (L.O.); (A.G.); (A.A.); (F.S.); (I.P.); (M.d.L.P.); (F.S.); (J.P.); (R.S.)
| | - Estela Bastos
- Centre for the Research and Technology of Agro-Environmental and Biological Sciences (CITAB), University of Trás-os-Montes and Alto Douro (UTAD), 5000-801 Vila Real, Portugal;
- Genetic Department, University of Trás-os-Montes and Alto Douro (UTAD), 5000-801 Vila Real, Portugal;
| | - Jorge Pereira
- Animal and Veterinary Research Centre (CECAV), University of Trás-os-Montes and Alto Douro (UTAD), 5000-801 Vila Real, Portugal; (M.V.-P.); (L.O.); (A.G.); (A.A.); (F.S.); (I.P.); (M.d.L.P.); (F.S.); (J.P.); (R.S.)
| | - Nuno Gonçalves-Anjo
- Genetic Department, University of Trás-os-Montes and Alto Douro (UTAD), 5000-801 Vila Real, Portugal;
| | - Paulo Carvalho
- Pathology Laboratory, UEISPSA, National Institute for Agricultural and Veterinary Research (INIAV), I.P., 2780-157 Oeiras, Portugal; (A.P.M.); (C.N.M.); (J.C.S.); (P.C.)
| | - Roberto Sargo
- Animal and Veterinary Research Centre (CECAV), University of Trás-os-Montes and Alto Douro (UTAD), 5000-801 Vila Real, Portugal; (M.V.-P.); (L.O.); (A.G.); (A.A.); (F.S.); (I.P.); (M.d.L.P.); (F.S.); (J.P.); (R.S.)
| | - Ana Matos
- Research Center for Natural Resources, Environment and Society (CERNAS), Polytechnic Institute of Castelo Branco (IPCB), 6000-767 Castelo Branco, Portugal;
- Quality of Life in the Rural World (Q-Rural), Polytechnic Institute of Castelo Branco (IPCB), 6000-767 Castelo Branco, Portugal;
| | - Luís Figueira
- Quality of Life in the Rural World (Q-Rural), Polytechnic Institute of Castelo Branco (IPCB), 6000-767 Castelo Branco, Portugal;
| | - Maria dos Anjos Pires
- Animal and Veterinary Research Centre (CECAV), University of Trás-os-Montes and Alto Douro (UTAD), 5000-801 Vila Real, Portugal; (M.V.-P.); (L.O.); (A.G.); (A.A.); (F.S.); (I.P.); (M.d.L.P.); (F.S.); (J.P.); (R.S.)
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Correa-Valencia NM, Moyano RD, Hernández-Agudelo M, Fernández-Silva JA. Mycobacterium avium subsp. paratuberculosis (MAP) molecular diversity in cattle, sheep, and goats from Latin America and the Caribbean: a systematic review. Trop Anim Health Prod 2021; 53:468. [PMID: 34546430 PMCID: PMC8453475 DOI: 10.1007/s11250-021-02923-9] [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: 01/28/2021] [Accepted: 09/10/2021] [Indexed: 11/08/2022]
Abstract
This study aimed to systematically collect and appraise the scientific evidence to answer the research question: What MAP genotypes have been isolated from cattle, sheep, and goats in Latin America and the Caribbean? An electronic search was conducted on three platforms (i.e., OVID®, Web of Science®, SciELO) as well as on the proceedings of the International Colloquium on Paratuberculosis. Inclusion and exclusion criteria were defined a priori and conserved through the systematic process and only articles published in peer-reviewed journals were considered. A total of 26 articles met the definitive inclusion criteria. All were published in English, in 15 different journals, and between 1989 and 2020. The relevant articles reported the use of six different genotyping techniques (i.e., polymerase chain reaction-restriction endonuclease analysis, restriction fragment length polymorphism, type-specific-PCR, mycobacterial interspersed repetitive units-variable number of tandem repeats, multi-locus short sequence repeat, single nucleotide polymorphism) in isolates from seven countries. Genotypes found so far in the region using typing techniques were mainly C type. MIRU-VNTR mostly reported INMV 1, INMV 2, and INMV 11 subtypes, among others. MLSSR reported genotypes from four different countries, reporting nine different subtypes of which 7g–10g–4ggt was the most common for loci 1, 2, and 8, respectively. Regardless the high diversity of techniques used so far to genotype Latin American and Caribbean MAP isolates, the original question of this systematic review has been answered. In addition, a relative genetic similarity between MAP strains recovered from cattle, goats, and sheep unrelatedly of the matrix and geographic origin was identified.
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Affiliation(s)
- Nathalia M Correa-Valencia
- Centauro, Escuela de Medicina Veterinaria, Facultad de Ciencias Agrarias, Universidad de Antioquia, Medellín, Colombia.
| | - Roberto Damián Moyano
- Instituto de Agrobiotecnología y Biología Molecular (IABIMO), INTA-CONICET, Buenos Aires, Argentina
| | - Miguel Hernández-Agudelo
- Centauro, Escuela de Medicina Veterinaria, Facultad de Ciencias Agrarias, Universidad de Antioquia, Medellín, Colombia
| | - Jorge A Fernández-Silva
- Centauro, Escuela de Medicina Veterinaria, Facultad de Ciencias Agrarias, Universidad de Antioquia, Medellín, Colombia
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Zhao L, Wang Y, Wang JL, Zhao WH, Cheng HX, Ma YM, Chai HL, Zhang ZS, Wang LF, Miao ZQ, Ding YL, Sulijid J, Dang GH, Liu SY, Wang FL, Liu SG, Liu YH. Serological investigation and genotyping of Mycobacterium avium subsp. paratuberculosis in sheep and goats in Inner Mongolia, China. PLoS One 2021; 16:e0256628. [PMID: 34492040 PMCID: PMC8423245 DOI: 10.1371/journal.pone.0256628] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2021] [Accepted: 08/12/2021] [Indexed: 11/18/2022] Open
Abstract
Paratuberculosis a contagious and chronic disease in domestic and wild ruminants, is caused by Mycobacterium avium subspecies paratuberculosis (MAP). Typical clinical signs include intractable diarrhea, progressive emaciation, proliferative enteropathy, and mesenteric lymphadenitis. Paratuberculosis is endemic to many parts of the world and responsible for considerable economic losses. In this study, different types of paratuberculosis and MAP in sheep and goats were investigated in Inner Mongolia, a northern province in China contiguous with two countries and eight other provinces. A total of 4434 serum samples were collected from six cities in the western, central, and eastern regions of Inner Mongolia and analyzed using the ELISA test. In addition, tissue samples were collected from seven animals that were suspected to be infected with MAP. Finally, these tissues samples were analyzed by histopathological examination followed by polymerase chain reaction (PCR), IS1311 PCR-restriction enzyme analysis (PCR-REA), and a sequence analysis of five genes. Among all 4434 ruminant serum samples collected from the six cities in the western, central, and eastern regions of Inner Mongolia, 7.60% (337/4434) measured positive for the MAP antibody. The proportions of positive MAP antibody results for serum samples collected in the western, central, and eastern regions were 5.10% (105/2058), 6.63% (85/1282), and 13.44% (147/1094), respectively. For the seven suspected infected animals selected from the herd with the highest rate of positivity, the gross pathology and histopathology of the necropsied animals were found to be consistent with the pathological features of paratuberculosis. The PCR analysis further confirmed the diagnosis of paratuberculosis. The rest of the results demonstrated that herds of sheep and goats in Inner Mongolia were infected with both MAP type II and type III. To the best of our knowledge, this is the first study of the two subtypes of MAP strains in sheep and goats in Inner Mongolia.
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Affiliation(s)
- Li Zhao
- College of Veterinary Medicine, Inner Mongolia Agricultural University, Hohhot, China
- Key Laboratory of Clinical Diagnosis and Treatment Technology in Animal Disease, Ministry of Agriculture and Rural Affairs, Hohhot, China
| | - Yu Wang
- College of Veterinary Medicine, Inner Mongolia Agricultural University, Hohhot, China
- Key Laboratory of Clinical Diagnosis and Treatment Technology in Animal Disease, Ministry of Agriculture and Rural Affairs, Hohhot, China
| | - Jin-Ling Wang
- College of Veterinary Medicine, Inner Mongolia Agricultural University, Hohhot, China
- Key Laboratory of Clinical Diagnosis and Treatment Technology in Animal Disease, Ministry of Agriculture and Rural Affairs, Hohhot, China
| | - Wei-Hong Zhao
- College of Veterinary Medicine, Inner Mongolia Agricultural University, Hohhot, China
| | - Hui-Xin Cheng
- College of Veterinary Medicine, Inner Mongolia Agricultural University, Hohhot, China
| | - Yi-Min Ma
- College of Veterinary Medicine, Inner Mongolia Agricultural University, Hohhot, China
| | - Hai-Liang Chai
- College of Veterinary Medicine, Inner Mongolia Agricultural University, Hohhot, China
| | - Zhan-Sheng Zhang
- College of Veterinary Medicine, Inner Mongolia Agricultural University, Hohhot, China
| | - Li-Feng Wang
- College of Veterinary Medicine, Inner Mongolia Agricultural University, Hohhot, China
| | - Zeng-Qiang Miao
- College of Veterinary Medicine, Inner Mongolia Agricultural University, Hohhot, China
| | - Yu-Lin Ding
- College of Veterinary Medicine, Inner Mongolia Agricultural University, Hohhot, China
- Key Laboratory of Clinical Diagnosis and Treatment Technology in Animal Disease, Ministry of Agriculture and Rural Affairs, Hohhot, China
| | - Jirintai Sulijid
- College of Veterinary Medicine, Inner Mongolia Agricultural University, Hohhot, China
- Key Laboratory of Clinical Diagnosis and Treatment Technology in Animal Disease, Ministry of Agriculture and Rural Affairs, Hohhot, China
| | - Guang-Hui Dang
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, China
| | - Shu-Ying Liu
- College of Veterinary Medicine, Inner Mongolia Agricultural University, Hohhot, China
- Key Laboratory of Clinical Diagnosis and Treatment Technology in Animal Disease, Ministry of Agriculture and Rural Affairs, Hohhot, China
| | - Feng-Long Wang
- College of Veterinary Medicine, Inner Mongolia Agricultural University, Hohhot, China
- Key Laboratory of Clinical Diagnosis and Treatment Technology in Animal Disease, Ministry of Agriculture and Rural Affairs, Hohhot, China
| | - Si-Guo Liu
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, China
| | - Yong-Hong Liu
- College of Veterinary Medicine, Inner Mongolia Agricultural University, Hohhot, China
- Key Laboratory of Clinical Diagnosis and Treatment Technology in Animal Disease, Ministry of Agriculture and Rural Affairs, Hohhot, China
- * E-mail:
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Hosseiniporgham S, Biet F, Ganneau C, Bannantine JP, Bay S, Sechi LA. A Comparative Study on the Efficiency of Two Mycobacterium avium subsp. paratuberculosis (MAP)-Derived Lipopeptides of L3P and L5P as Capture Antigens in an In-House Milk ELISA Test. Vaccines (Basel) 2021; 9:vaccines9090997. [PMID: 34579234 PMCID: PMC8471605 DOI: 10.3390/vaccines9090997] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Revised: 09/01/2021] [Accepted: 09/02/2021] [Indexed: 02/07/2023] Open
Abstract
Mycobacterium avium subsp. paratuberculosis (MAP) surface-exposed lipopeptides could be specific capture-antigen molecules targeting antibodies against MAP, in milk, through ELISA. Previous studies have revealed that MAP strains, isolated from sheep (S) or cow (C), could produce specific lipopeptides, L3P or L5P, respectively. In this study, we used L3P and L5P as capture antigens in an in-house milk ELISA (H-MELISA) to assess how these antigens perform, in comparison with other ELISA tests, on well-defined milk samples from MAP-infected sheep. The overall positivity rates of H-MELISA via L3P and L5P varied by the source of milk samples, in which, at bulk-tank-milk (BTM) level, the majority of positive cases (63.83%) reacted more against L5P, whereas a predominant number (69.14%) of milk samples were more responsive against L3P at the individual level. To clarify whether the positivity status of milk samples in H-MELISA L3P/L5P were predictive of MAP strain-types (S/C), strain-typing was carried out using PCR IS1311-restriction enzyme analysis. Although the presence of three MAP strains (S/C/bison types) was detected among the milk samples, the C-type (46.67%) and S-type (75%) MAP strains were detected with higher incidence among BTMs and individual milk samples, respectively. However, further examination on the H-MELISA L3P/L5P-positivity pattern of each C/S-type-MAP sample revealed that some samples had a reverse reactivity against both L3P and L5P. These results could be the consequence of either cross-reactivity between L3P and L5P (due to the similarity in the structures of the two epitopes) or simply a within-herd mixed infection with MAP strains of C and S types. These findings suggest that lipopeptide antigens could contribute a diagnostic test with optimal performance, considering the diversity of MAP strains.
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Affiliation(s)
| | - Franck Biet
- UMR1282, Infectiologie et Santé Publique (ISP-311), INRAE Centre Val de Loire, 37380 Nouzilly, France;
| | - Christelle Ganneau
- Unité de Chimie Des Biomolécules, Département de Biologie Structurale et Chimie, Institut Pasteur, 75015 Paris, France; (C.G.); (S.B.)
- CNRS UMR 3523, 75015 Paris, France
| | - John P. Bannantine
- USDA-Agricultural Research Service, National Animal Disease Center, Ames, IA 50010, USA;
| | - Sylvie Bay
- Unité de Chimie Des Biomolécules, Département de Biologie Structurale et Chimie, Institut Pasteur, 75015 Paris, France; (C.G.); (S.B.)
- CNRS UMR 3523, 75015 Paris, France
| | - Leonardo A. Sechi
- Dipartimento di Scienze Biomediche, Università di Sassari, 07100 Sassari, Italy;
- SC Microbiologia e Virologia, Azienda Ospedaliera Universitaria, 07100 Sassari, Italy
- Mediterraneam Center for Disease Control, 07100 Sassari, Italy
- Correspondence:
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Links IJ, Denholm LJ, Evers M, Kingham LJ, Greenstein RJ. Is vaccination a viable method to control Johne's disease caused by Mycobacterium avium subsp. paratuberculosis? Data from 12 million ovine vaccinations and 7.6 million carcass examinations in New South Wales, Australia from 1999-2009. PLoS One 2021; 16:e0246411. [PMID: 34125838 PMCID: PMC8202914 DOI: 10.1371/journal.pone.0246411] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Accepted: 05/11/2021] [Indexed: 02/01/2023] Open
Abstract
BACKGROUND Mycobacterium avium subsp. paratuberculosis (MAP) causes Johne's disease (or paratuberculosis), a chronic wasting disease of ruminants and other animals resulting from granulomatous enteritis. There are increasing concerns that MAP is zoonotic. The prevalence of Johne's disease is increasing worldwide. In an attempt to control an epidemic of ovine Johne's disease (OJD) in New South Wales (NSW), a government/industry sponsored voluntary vaccination/on-farm management program commenced in 2000. We report herein an observational study of changes in disease prevalence as vaccination progressed, based on abattoir surveillance data for OJD from 1999 to 2009. We also discuss the epidemiological, policy, regulatory, research, economic and sociological elements that contributed to the development of a mature control program, whose aim was to halt the epidemic spread of OJD in a naïve sheep population. METHODS NSW was divided into areas of "High" (HPA), "Medium" (MPA) and "Low" (LPA) OJD prevalence. A killed whole cell vaccine (Gudair®) was administered to sheep from 2000 to 2009. Trained examiners evaluated the viscera of adult sheep carcasses at slaughter for gross evidence of OJD. MAP infection was confirmed by histopathology. PRINCIPAL FINDINGS From 2000-2009, 12 million vaccine doses were administered in NSW (91%; 10.9 million in the HPA). Many of the vaccinated flocks were suffering > 5% annual mortality in adult sheep, with some individual flocks with 10-15% losses attributable to OJD. A total of 7.6 million carcasses were examined (38%; 2.9 million from the HPA). Overall, 16% of slaughter consignments (sheep consigned to the abattoir from a single vendor) were positive for OJD, of which 94% were from the HPA. In the HPA, the percentage of animals with lesions attributable to OJD at slaughter fell progressively from 2.4% (10,406/432,860) at commencement of vaccination in 2000 to 0.8% (1,573/189,564) by 2009. Herd immunity from vaccination in the HPA was estimated at 70% by 2009, the target commonly espoused for an effective control program based on vaccination. This coincided with a progressive decrease in reports of clinical disease and mortalities in vaccinated flocks. SIGNIFICANCE We show a decrease in the prevalence of lesions attributable to OJD in NSW concomitant with initiation of voluntary vaccination, on-farm management plans, abattoir monitoring and feedback of animal prevalence data to sheep producers. We conclude that a target of ≤ 1% regional prevalence of OJD affected sheep at slaughter is achievable using these interventions.
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Affiliation(s)
- Ian J. Links
- Graham Centre for Agricultural Innovation (An alliance of Charles Sturt University and NSW Department of Primary Industries), Wagga Wagga, New South Wales, Australia
| | - Laurence J. Denholm
- Strategy and Delivery Group, NSW Department of Premier and Cabinet, Orange, New South Wales, Australia
| | - Marilyn Evers
- Formerly NSW Department of Primary Industries, Orange, New South Wales, Australia
| | - Lloyd J. Kingham
- NSW Department of Primary Industries, Orange, New South Wales, Australia
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Dhand NK, Plain KM, Green AC, Martinez E, Eppleston J, Ly A, Arif S, Emery D. Factors influencing the effectiveness of the Gudair vaccine for controlling Johne's disease in sheep flocks in Australia. Prev Vet Med 2021; 193:105394. [PMID: 34119857 DOI: 10.1016/j.prevetmed.2021.105394] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Revised: 05/14/2021] [Accepted: 05/25/2021] [Indexed: 11/15/2022]
Abstract
Ovine Johne's disease is a chronic debilitating disease of sheep caused by Mycobacterium avium subsp. paratuberculosis (Mptb) which results in diarrhoea, emaciation and mortalities in infected animals. Vaccination with Gudair® has been a key strategy for controlling the disease in Australia since its approval in 2002. Previous research conducted in Australia has demonstrated that the vaccine is quite effective in reducing sheep mortalities. While some farms have also been successful in reducing the prevalence of the disease in their flocks to undetectable levels, sheep in other flocks continue to shed Mptb in faeces even after an ongoing vaccination program . This study was conducted to investigate management, husbandry and biosecurity factors associated with paratuberculosis infection in Gudair® vaccinated sheep flocks in Australia. We enrolled 64 sheep farmers and interviewed them to obtain information about their management and biosecurity practices. Pooled faecal samples were collected from sheep at each farm and cultured to create two outcome variables: Mptb positive (yes/no) and disease prevalence level (nil, < 1 %, ≥ 1 %). Binary and ordinal logistic regression analyses were conducted to evaluate the association of management, husbandry and biosecurity factors with these outcome variables. Farms were more likely to have Mptb positive sheep and a higher disease prevalence in their flocks if they: (a) provided supplementary feed on the ground (instead of in a trough); (b) had a greater number of neighbours with sheep; and (c) had introduced rams from a greater number of sources. The results suggest the effectiveness of Gudair® vaccination to control OJD can be improved if sheep producers maintain other risk management strategies and biosecurity practices. Extension agencies should advise farmers not to relax their biosecurity practices and to purchase rams from only low-risk sources, even if they are continuing to vaccinate their flocks.
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Affiliation(s)
- Navneet K Dhand
- Sydney School of Veterinary Science, The University of Sydney, Australia.
| | - Karren M Plain
- Sydney School of Veterinary Science, The University of Sydney, Australia
| | - Alexandra C Green
- Sydney School of Veterinary Science, The University of Sydney, Australia
| | - Esteban Martinez
- Sydney School of Veterinary Science, The University of Sydney, Australia
| | - Jeff Eppleston
- Sydney School of Veterinary Science, The University of Sydney, Australia
| | - Anna Ly
- Sydney School of Veterinary Science, The University of Sydney, Australia
| | - Shumaila Arif
- Sydney School of Veterinary Science, The University of Sydney, Australia
| | - David Emery
- Sydney School of Veterinary Science, The University of Sydney, Australia
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Nigsch A, Robbe-Austerman S, Stuber TP, Pavinski Bitar PD, Gröhn YT, Schukken YH. Who infects whom?-Reconstructing infection chains of Mycobacterium avium ssp. paratuberculosis in an endemically infected dairy herd by use of genomic data. PLoS One 2021; 16:e0246983. [PMID: 33983941 PMCID: PMC8118464 DOI: 10.1371/journal.pone.0246983] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Accepted: 04/30/2021] [Indexed: 12/18/2022] Open
Abstract
Recent evidence of circulation of multiple strains within herds and mixed infections of cows marks the beginning of a rethink of our knowledge on Mycobacterium avium ssp. paratuberculosis (MAP) epidemiology. Strain typing opens new ways to investigate MAP transmission. This work presents a method for reconstructing infection chains in a setting of endemic Johne’s disease on a well-managed dairy farm. By linking genomic data with demographic field data, strain-specific differences in spreading patterns could be quantified for a densely sampled dairy herd. Mixed infections of dairy cows with MAP are common, and some strains spread more successfully. Infected cows remain susceptible for co-infections with other MAP genotypes. The model suggested that cows acquired infection from 1–4 other cows and spread infection to 0–17 individuals. Reconstructed infection chains supported the hypothesis that high shedding animals that started to shed at an early age and showed a progressive infection pattern represented a greater risk for spreading MAP. Transmission of more than one genotype between animals was recorded. In this farm with a good MAP control management program, adult-to-adult contact was proposed as the most important transmission route to explain the reconstructed networks. For each isolate, at least one more likely ancestor could be inferred. Our study results help to capture underlying transmission processes and to understand the challenges of tracing MAP spread within a herd. Only the combination of precise longitudinal field data and bacterial strain type information made it possible to trace infection in such detail.
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Affiliation(s)
- Annette Nigsch
- Department of Animal Sciences, Wageningen University, Wageningen, The Netherlands
- * E-mail:
| | - Suelee Robbe-Austerman
- USDA APHIS National Veterinary Services Laboratories, Ames, Iowa, United States of America
| | - Tod P. Stuber
- USDA APHIS National Veterinary Services Laboratories, Ames, Iowa, United States of America
| | - Paulina D. Pavinski Bitar
- Department of Population Medicine and Diagnostic Sciences, College of Veterinary Medicine, Cornell University, Ithaca, NY, United States of America
| | - Yrjö T. Gröhn
- Department of Population Medicine and Diagnostic Sciences, College of Veterinary Medicine, Cornell University, Ithaca, NY, United States of America
| | - Ynte H. Schukken
- Department of Animal Sciences, Wageningen University, Wageningen, The Netherlands
- Royal GD, Deventer, The Netherlands
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Conde C, Price-Carter M, Cochard T, Branger M, Stevenson K, Whittington R, Bannantine JP, Biet F. Whole-Genome Analysis of Mycobacterium avium subsp. paratuberculosis IS 900 Insertions Reveals Strain Type- Specific Modalities. Front Microbiol 2021; 12:660002. [PMID: 34040595 PMCID: PMC8141618 DOI: 10.3389/fmicb.2021.660002] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Accepted: 04/07/2021] [Indexed: 01/14/2023] Open
Abstract
Mycobacterium avium subsp. paratuberculosis (Map) is the etiological agent of Johne’s disease in ruminants. The IS900 insertion sequence (IS) has been used widely as an epidemiological marker and target for PCR diagnosis. Updated DNA sequencing technologies have led to a rapid increase in available Map genomes, which makes it possible to analyze the distribution of IS900 in this slow-growing bacterium. The objective of this study is to characterize the distribution of the IS900 element and how it affects genomic evolution and gene function of Map. A secondary goal is to develop automated in silico restriction fragment length polymorphism (RFLP) analysis using IS900. Complete genomes from the major phylogenetic lineages known as C-type and S-type (including subtypes I and III), were chosen to represent the genetic diversity of Map. IS900 elements were located in these genomes using BLAST software and the relevant fragments extracted. An in silico RFLP analysis using the BstEII restriction site was performed to obtain exact sizes of the DNA fragments carrying a copy of IS900 and the resulting RFLP profiles were analyzed and compared by digital visualization of the separated restriction fragments. The program developed for this study allowed automated localization of IS900 sequences to identify their position within each genome along with the exact number of copies per genome. The number of IS900 copies ranged from 16 in the C-type isolate to 22 in the S-type subtype I isolate. A loci-by-loci sequence alignment of all IS900 copies within the three genomes revealed new sequence polymorphisms that define three sequevars distinguishing the subtypes. Nine IS900 insertion site locations were conserved across all genomes studied while smaller subsets were unique to a particular lineage. Preferential insertion motif sequences were identified for IS900 along with genes bordering all IS900 insertions. Rarely did IS900 insert within coding sequences as only three genes were disrupted in this way. This study makes it possible to automate IS900 distribution in Map genomes to enrich knowledge on the distribution dynamics of this IS for epidemiological purposes, for understanding Map evolution and for studying the biological implications of IS900 insertions.
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Affiliation(s)
- Cyril Conde
- INRAE, ISP, Université de Tours, Nouzilly, France
| | | | | | | | | | - Richard Whittington
- School of Veterinary Science, The University of Sydney, Sydney, NSW, Australia
| | | | - Franck Biet
- INRAE, ISP, Université de Tours, Nouzilly, France
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Matthews C, Cotter PD, O’ Mahony J. MAP, Johne's disease and the microbiome; current knowledge and future considerations. Anim Microbiome 2021; 3:34. [PMID: 33962690 PMCID: PMC8105914 DOI: 10.1186/s42523-021-00089-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Accepted: 03/20/2021] [Indexed: 12/17/2022] Open
Abstract
Mycobacterium avium subsp. paratuberculosis is the causative agent of Johne's disease in ruminants. As an infectious disease that causes reduced milk yields, effects fertility and, eventually, the loss of the animal, it is a huge financial burden for associated industries. Efforts to control MAP infection and Johne's disease are complicated due to difficulties of diagnosis in the early stages of infection and challenges relating to the specificity and sensitivity of current testing methods. The methods that are available contribute to widely used test and cull strategies, vaccination programmes also in place in some countries. Next generation sequencing technologies have opened up new avenues for the discovery of novel biomarkers for disease prediction within MAP genomes and within ruminant microbiomes. Controlling Johne's disease in herds can lead to improved animal health and welfare, in turn leading to increased productivity. With current climate change bills, such as the European Green Deal, targeting livestock production systems for more sustainable practices, managing animal health is now more important than ever before. This review provides an overview of the current knowledge on genomics and detection of MAP as it pertains to Johne's disease.
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Affiliation(s)
- Chloe Matthews
- Cork Institute of Technology, Bishopstown, Co. Cork, Ireland
- Teagasc, Food Research Centre, Food Biosciences Department, Fermoy, Co. Cork, Ireland
| | - Paul D. Cotter
- Teagasc, Food Research Centre, Food Biosciences Department, Fermoy, Co. Cork, Ireland
- APC Microbiome Institute, University College Cork, Co. Cork, Ireland
| | - Jim O’ Mahony
- Cork Institute of Technology, Bishopstown, Co. Cork, Ireland
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Marete A, Ariel O, Ibeagha-Awemu E, Bissonnette N. Identification of Long Non-coding RNA Isolated From Naturally Infected Macrophages and Associated With Bovine Johne's Disease in Canadian Holstein Using a Combination of Neural Networks and Logistic Regression. Front Vet Sci 2021; 8:639053. [PMID: 33969037 PMCID: PMC8100051 DOI: 10.3389/fvets.2021.639053] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2020] [Accepted: 02/15/2021] [Indexed: 01/15/2023] Open
Abstract
Mycobacterium avium ssp. paratuberculosis (MAP) causes chronic enteritis in most ruminants. The pathogen MAP causes Johne's disease (JD), a chronic, incurable, wasting disease. Weight loss, diarrhea, and a gradual drop in milk production characterize the disease's clinical phase, culminating in death. Several studies have characterized long non-coding RNA (lncRNA) in bovine tissues, and a previous study characterizes (lncRNA) in macrophages infected with MAP in vitro. In this study, we aim to characterize the lncRNA in macrophages from cows naturally infected with MAP. From 15 herds, feces and blood samples were collected for each cow older than 24 months, twice yearly over 3–5 years. Paired samples were analyzed by fecal PCR and blood ELISA. We used RNA-seq data to study lncRNA in macrophages from 33 JD(+) and 33 JD(–) dairy cows. We performed RNA-seq analysis using the “new Tuxedo” suite. We characterized lncRNA using logistic regression and multilayered neural networks and used DESeq2 for differential expression analysis and Panther and Reactome classification systems for gene ontology (GO) analysis. The study identified 13,301 lncRNA, 605 of which were novel lncRNA. We found seven genes close to differentially expressed lncRNA, including CCDC174, ERI1, FZD1, TWSG1, ZBTB38, ZNF814, and ZSCAN4. None of the genes associated with susceptibility to JD have been cited in the literature. LncRNA target genes were significantly enriched for biological process GO terms involved in immunity and nucleic acid regulation. These include the MyD88 pathway (TLR5), GO:0043312 (neutrophil degranulation), GO:0002446 (neutrophil-mediated immunity), and GO:0042119 (neutrophil activation). These results identified lncRNA with potential roles in host immunity and potential candidate genes and pathways through which lncRNA might function in response to MAP infection.
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Affiliation(s)
- Andrew Marete
- Agriculture and Agri-Food Canada, Sherbrooke Research and Development Centre, Sherbrooke, QC, Canada
| | - Olivier Ariel
- Agriculture and Agri-Food Canada, Sherbrooke Research and Development Centre, Sherbrooke, QC, Canada.,Faculty of Science, Sherbrooke University, Sherbrooke, QC, Canada
| | - Eveline Ibeagha-Awemu
- Agriculture and Agri-Food Canada, Sherbrooke Research and Development Centre, Sherbrooke, QC, Canada
| | - Nathalie Bissonnette
- Agriculture and Agri-Food Canada, Sherbrooke Research and Development Centre, Sherbrooke, QC, Canada
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Hodgeman R, Mann R, Savin K, Djitro N, Rochfort S, Rodoni B. Molecular characterisation of Mycobacterium avium subsp. paratuberculosis in Australia. BMC Microbiol 2021; 21:101. [PMID: 33789575 PMCID: PMC8012159 DOI: 10.1186/s12866-021-02140-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2020] [Accepted: 02/23/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Mycobacterium avium subsp. paratuberculosis (Map) causes Johne's disease (JD), a chronic enteritis widespread in ruminants, resulting in substantial economic losses, especially to the dairy industry. Understanding the genetic diversity of Map in Australia will assist epidemiological studies for tracking disease transmission and identify subtype characteristics for use in development of improved diagnostic typing methods. Here we investigated the phylogenetic relationships of 351 Map isolates and compared different subtyping methods to assess their suitability for use in diagnostics and accuracy. RESULTS SNP-based phylogenetic analysis of 228 Australian isolates and 123 publicly available international isolates grouped Type S and Type C strains into two distinct lineages. Type C strains were highly monomorphic with only 20 SNP differences separating them. Type S strains, when aligned separately to the Telford strain, fell into two distinct clades: The first clade contained seven international isolates while the second clade contained one international isolate from Scotland and all 59 Australian isolates. The Australian Type B strain clustered with US bison strains. IS1311 PCR and Restriction Enzyme Analysis (REA) intermittently generated incorrect results when compared to Long Sequence Polymorphism (LSP) analysis, whole genome SNP-based phylogenetic analysis, IS1311 sequence alignment and average nucleotide identity (ANI). These alternative methods generated consistent Map typing results. A published SNP based assay for genotyping Map was found to be unsuitable for differentiating between Australian and international strain types of Map. CONCLUSION This is the first phylogenetic analysis of Australian Map isolates. The Type C lineage was highly monomorphic, and the Type S lineage clustered all Australian isolates into one clade with a single Scottish sheep strain. The Australian isolate classified as Type B by IS1311 PCR and REA is likely to be descended from bison and most closely related to US bison strains. Limitations of the current typing methods were identified in this study.
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Affiliation(s)
- Rachel Hodgeman
- Agriculture Victoria, AgriBio, La Trobe University, Bundoora, Victoria, Australia. .,School of Applied Systems Biology, AgriBio, La Trobe University, Bundoora, Victoria, Australia.
| | - Rachel Mann
- Agriculture Victoria, AgriBio, La Trobe University, Bundoora, Victoria, Australia
| | - Keith Savin
- Agriculture Victoria, AgriBio, La Trobe University, Bundoora, Victoria, Australia
| | - Noel Djitro
- School of Applied Systems Biology, AgriBio, La Trobe University, Bundoora, Victoria, Australia
| | - Simone Rochfort
- Agriculture Victoria, AgriBio, La Trobe University, Bundoora, Victoria, Australia.,School of Applied Systems Biology, AgriBio, La Trobe University, Bundoora, Victoria, Australia
| | - Brendan Rodoni
- Agriculture Victoria, AgriBio, La Trobe University, Bundoora, Victoria, Australia.,School of Applied Systems Biology, AgriBio, La Trobe University, Bundoora, Victoria, Australia
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32
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Bhat AM, Malik HU, Chaubey KK, Hussain T, Mir AQ, Nabi SU, Gupta S, Singh SV. Bio-typing of Mycobacterium avium subspecies paratuberculosis isolates recovered from the Himalayan sheep and goats. Trop Anim Health Prod 2021; 53:237. [PMID: 33791865 DOI: 10.1007/s11250-021-02682-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2019] [Accepted: 03/22/2021] [Indexed: 12/01/2022]
Abstract
Information on bio-type profile of Mycobacterium avium subspecies paratubeculosis (MAP) in sheep flocks and goat herds of Himalayan region is not reported earlier. The aim of our study was to determine the bio-type of MAP infecting livestock of this region. A total of 71 faecal samples (sheep-57, goats-14) were screened by Ziehl-Neelsen (ZN) staining and IS900 PCR, and then processed for culture on Herrold's egg yolk medium (HEYM) having mycobactin J (MJ). Out of 71 faecal samples, MAP colonies were seen only in four samples (sheep-3 and goat-1). Isolates were confirmed as MAP on the basis of slow growth, acid fastness, MJ dependency, IS900 and IS1311 PCR. All the IS900 and IS1311 PCR positive samples were bio-typed by IS1311 PCR-REA (restriction endonuclease analysis), which confirmed all four isolates as 'bison type.' In IS1311 based phylogeny of MAP isolates by ClustalW method of the MegAlign program of DNASTAR Lasergene software, the four sequences of MAP isolates (NCBI sequence nos. MH988763, MH988765, MH988766 and MH988764) did not show any distinct clustering/grouping pattern. However, these four isolates showed a bit of closeness to the MAP sequences (KC990353.1 and KC990352.1) of 'bison type' isolated from wood bison in Canada. In conclusion, this is the first report on isolation and bio-type profile of MAP infecting sheep and goats of Himalayan region. Study will help in devising prevention and control strategies against spread of MAP infection in livestock population of Himalayan region.
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Affiliation(s)
- Adil Majid Bhat
- Division of Clinical Veterinary Medicine, Ethics and Jurisprudence, Faculty of Veterinary Sciences and Animal Husbandry, Shuhama, Srinagar, Jammu and Kashmir, India. .,Department of Veterinary Medicine, Guru Angad Dev Veterinary and Animal Sciences University, Ludhiana, Punjab, India.
| | - Hamid Ullah Malik
- Division of Clinical Veterinary Medicine, Ethics and Jurisprudence, Faculty of Veterinary Sciences and Animal Husbandry, Shuhama, Srinagar, Jammu and Kashmir, India
| | - Kundan Kumar Chaubey
- Microbiology Lab, Animal Health Division, Central Institute for Research on Goats, Mathura, U.P., India.,Mountain Research Centre for Sheep and Goats, Faculty of Veterinary Sciences and Animal Husbandry, Shuhama, Srinagar, Jammu and Kashmir, India
| | - Tufail Hussain
- Division of Clinical Veterinary Medicine, Ethics and Jurisprudence, Faculty of Veterinary Sciences and Animal Husbandry, Shuhama, Srinagar, Jammu and Kashmir, India
| | - Abdul Qayoom Mir
- Mountain Research Centre for Sheep and Goats, Faculty of Veterinary Sciences and Animal Husbandry, Shuhama, Srinagar, Jammu and Kashmir, India
| | - Showkat Un Nabi
- Division of Clinical Veterinary Medicine, Ethics and Jurisprudence, Faculty of Veterinary Sciences and Animal Husbandry, Shuhama, Srinagar, Jammu and Kashmir, India
| | - Saurabh Gupta
- Microbiology Lab, Animal Health Division, Central Institute for Research on Goats, Mathura, U.P., India.,Department of Biotechnology, GLA University, Mathura, U.P., India
| | - Shoor Vir Singh
- Microbiology Lab, Animal Health Division, Central Institute for Research on Goats, Mathura, U.P., India.,Department of Biotechnology, GLA University, Mathura, U.P., India
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Evolutionary genomic and bacteria GWAS analysis of Mycobacterium avium subsp. paratuberculosis and dairy cattle Johne's disease phenotypes. Appl Environ Microbiol 2021; 87:AEM.02570-20. [PMID: 33547057 PMCID: PMC8091108 DOI: 10.1128/aem.02570-20] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Mycobacterium avium subsp. paratuberculosis (MAP) is the causative agent of Johne's disease in ruminants, which has important health consequences for dairy cattle. The Regional Dairy Quality Management Alliance (RDQMA) project is a multistate research program involving MAP isolates taken from three intensively studied commercial dairy farms in the northeastern United States, which emphasized longitudinal data collection of both MAP isolates and animal health in three regional dairy herds for a period of about 7 years. This paper reports the results of a pan-GWAS analysis involving 318 MAP isolates and dairy cow Johne's disease phenotypes, taken from these three farms. Based on our highly curated accessory gene count the pan-GWAS analysis identified several MAP genes associated with bovine Johne's disease phenotypes scored from these three farms, with some of the genes having functions suggestive of possible cause/effect relationships to these phenotypes. This paper reports a pan-genomic comparative analysis between MAP and Mycobacterium tuberculosis, assessing functional Gene Ontology category enrichments between these taxa. Finally, we also provide a population genomic perspective on the effectiveness of herd isolation, involving closed dairy farms, in preventing MAP inter-farm cross infection on a micro-geographic scale.IMPORTANCE Mycobacterium avium subsp. paratuberculosis (MAP) is the causative agent of Johne's disease in ruminants, which has important health consequences for dairy cattle, and enormous economic consequences for the dairy industry. Understanding which genes in this bacterium are correlated with key disease phenotypes can lead to functional experiments targeting these genes and ultimately lead to improved control strategies. This study represents a rare example of a prolonged longitudinal study of dairy cattle where the disease was measured and the bacteria were isolated from the same cows. The genome sequences of over 300 MAP isolates were analyzed for genes that were correlated with a wide range of Johne's disease phenotypes. A number of genes were identified that were significantly associated with several aspects of the disease and suggestive of further experimental follow-up.
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Lim J, Park HT, Ko S, Park HE, Lee G, Kim S, Shin MK, Yoo HS, Kim D. Genomic diversity of Mycobacterium avium subsp. paratuberculosis: pangenomic approach for highlighting unique genomic features with newly constructed complete genomes. Vet Res 2021; 52:46. [PMID: 33736686 PMCID: PMC7977185 DOI: 10.1186/s13567-021-00905-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Accepted: 01/26/2021] [Indexed: 01/25/2023] Open
Abstract
Mycobacterium avium subsp. paratuberculosis (MAP) is a causative agent of Johne’s disease, which is a chronic granulomatous enteropathy in ruminants. Determining the genetic diversity of MAP is necessary to understand the epidemiology and biology of MAP, as well as establishing disease control strategies. In the present study, whole genome-based alignment and comparative analysis were performed using 40 publicly available MAP genomes, including newly sequenced Korean isolates. First, whole genome-based alignment was employed to identify new genomic structures in MAP genomes. Second, the genomic diversity of the MAP population was described by pangenome analysis. A phylogenetic tree based on the core genome and pangenome showed that the MAP was differentiated into two major types (C- and S-type), which was in keeping with the findings of previous studies. However, B-type strains were discriminated from C-type strains. Finally, functional analysis of the pangenome was performed using three virulence factor databases (i.e., PATRIC, VFDB, and Victors) to predict the phenotypic diversity of MAP in terms of pathogenicity. Based on the results of the pangenome analysis, we developed a real-time PCR technique to distinguish among S-, B- and C-type strains. In conclusion, the results of our study suggest that the phenotypic differences between MAP strains can be explained by their genetic polymorphisms. These results may help to elucidate the diversity of MAP, extending from genomic features to phenotypic traits.
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Affiliation(s)
- Jaewon Lim
- School of Life Sciences, Ulsan National Institute of Science and Technology (UNIST), Ulsan, Korea
| | - Hong-Tae Park
- Department of Infectious Disease, College of Veterinary Medicine, Seoul National University, Seoul, Korea
| | - Seyoung Ko
- School of Life Sciences, Ulsan National Institute of Science and Technology (UNIST), Ulsan, Korea
| | - Hyun-Eui Park
- Department of Microbiology, Research Institute of Life Science, College of Medicine, Gyeongsang National University, Jinju, Korea
| | - Gyumin Lee
- School of Energy and Chemical Engineering, Ulsan National Institute of Science and Technology (UNIST), Ulsan, Korea
| | - Suji Kim
- Department of Infectious Disease, College of Veterinary Medicine, Seoul National University, Seoul, Korea
| | - Min-Kyoung Shin
- Department of Microbiology, Research Institute of Life Science, College of Medicine, Gyeongsang National University, Jinju, Korea
| | - Han Sang Yoo
- Department of Infectious Disease, College of Veterinary Medicine, Seoul National University, Seoul, Korea. .,Bio-MAX/N-Bio Institute, Seoul National University, Seoul, 08826, Korea.
| | - Donghyuk Kim
- School of Life Sciences, Ulsan National Institute of Science and Technology (UNIST), Ulsan, Korea. .,School of Energy and Chemical Engineering, Ulsan National Institute of Science and Technology (UNIST), Ulsan, Korea.
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Mizzi R, Timms VJ, Price-Carter ML, Gautam M, Whittington R, Heuer C, Biggs PJ, Plain KM. Comparative Genomics of Mycobacterium avium Subspecies Paratuberculosis Sheep Strains. Front Vet Sci 2021; 8:637637. [PMID: 33659287 PMCID: PMC7917049 DOI: 10.3389/fvets.2021.637637] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2020] [Accepted: 01/25/2021] [Indexed: 12/15/2022] Open
Abstract
Mycobacterium avium subspecies paratuberculosis (MAP) is the aetiological agent of Johne's disease (JD), a chronic enteritis that causes major losses to the global livestock industry. Further, it has been associated with human Crohn's disease. Several strains of MAP have been identified, the two major groups being sheep strain MAP, which includes the Type I and Type III sub-lineages, and the cattle strain or Type II MAP lineage, of which bison strains are a sub-grouping. Major genotypic, phenotypic and pathogenic variations have been identified in prior comparisons, but the research has predominately focused on cattle strains of MAP. In countries where the sheep industries are more prevalent, however, such as Australia and New Zealand, ovine JD is a substantial burden. An information gap exists regarding the genomic differences between sheep strain sub-lineages and the relevance of Type I and Type III MAP in terms of epidemiology and/or pathogenicity. We therefore investigated sheep MAP isolates from Australia and New Zealand using whole genome sequencing. For additional context, sheep MAP genome datasets were downloaded from the Sequence Read Archive and GenBank. The final dataset contained 18 Type III and 16 Type I isolates and the K10 cattle strain MAP reference genome. Using a pan-genome approach, an updated global phylogeny for sheep MAP from de novo assemblies was produced. When rooted with the K10 cattle reference strain, two distinct clades representing the lineages were apparent. The Australian and New Zealand isolates formed a distinct sub-clade within the type I lineage, while the European type I isolates formed another less closely related group. Within the type III lineage, isolates appeared more genetically diverse and were from a greater number of continents. Querying of the pan-genome and verification using BLAST analysis revealed lineage-specific variations (n = 13) including genes responsible for metabolism and stress responses. The genetic differences identified may represent important epidemiological and virulence traits specific to sheep MAP. This knowledge will potentially contribute to improved vaccine development and control measures for these strains.
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Affiliation(s)
- Rachel Mizzi
- Farm Animal Health Group, Sydney School of Veterinary Science, Faculty of Science, The University of Sydney, Camden, NSW, Australia
| | - Verlaine J Timms
- Centre for Infectious Diseases and Microbiology, Public Health, Westmead Hospital, Westmead, NSW, Australia
| | | | - Milan Gautam
- School of Veterinary Science, Massey University, Palmerston North, New Zealand
| | - Richard Whittington
- Farm Animal Health Group, Sydney School of Veterinary Science, Faculty of Science, The University of Sydney, Camden, NSW, Australia
| | - Cord Heuer
- School of Veterinary Science, Massey University, Palmerston North, New Zealand
| | - Patrick J Biggs
- School of Veterinary Science, Massey University, Palmerston North, New Zealand.,School of Fundamental Sciences, Massey University, Palmerston North, New Zealand
| | - Karren M Plain
- Farm Animal Health Group, Sydney School of Veterinary Science, Faculty of Science, The University of Sydney, Camden, NSW, Australia
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Villaamil FJ, Yus E, Benavides B, Allepuz A, Moya SJ, Casal J, Ortega C, Diéguez FJ. Factors Associated with the Introduction of Mycobacterium avium spp. Paratuberculosis (MAP) into Dairy Herds in Galicia (North-West Spain): The Perception of Experts. Animals (Basel) 2021; 11:ani11010166. [PMID: 33445689 PMCID: PMC7828141 DOI: 10.3390/ani11010166] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2020] [Revised: 12/23/2020] [Accepted: 01/04/2021] [Indexed: 11/30/2022] Open
Abstract
Simple Summary Paratuberculosis remains one of the most important diseases of cattle worldwide. Control of disease is difficult and offers important challenges at both diagnostic and management levels. This paper describes a study aimed at quantification of expert opinion on risk factors for paratuberculosis infection in dairy herds in Spain. For this purpose, a panel of nine experts working in the field of paratuberculosis was selected. Risk factors were also included into a questionnaire that was responded to by 93 farms whose sanitary status was known. The most important risk factors for the introduction of MAP, according to expert opinions, were related to purchase and grazing practices. The scores obtained for each farm, based on the expert opinions, allowed MAP positive/MAP negative farms to be discriminated with 68.8% sensitivity and 68.7% specificity. Despite increased awareness of the disease and the fact that several countries are implementing control programs, there is still incomplete understanding of the epidemiology of the disease. This, together with the lack of completely reliable diagnostic methods, makes it of vital importance considering the inter-herd transmission factors in order to prevent the introduction of the disease. Prioritizing the most important factors should be useful for focusing future training initiatives and improving risk-reduction strategies in this economically important industry. Abstract This study aimed at quantifying expert opinions on the risk factors involved in Mycobacterium avium subsp. paratuberculosis (MAP) infection in dairy cattle herds. For this purpose, potential risk factors associated with the introduction of MAP into dairies were chosen based on a literature review and discussions with researchers and veterinarians. For each factor, a decision tree was developed, and key questions were included in each. Answers to these key questions led to different events within each decision tree. An expert opinion workshop was organized (following the recommendations of the OIE), and ordinal values ranging from 0 to 9 (i.e., a null to very high likelihood of infection) were assigned to each event. The potential risk factors were also incorporated into a structured questionnaire that was responded to by 93 farms where the sanitary status against MAP was known. Thereby, based on the values given by the experts and the information collected in the questionnaires, each farm was assigned a score based on their MAP entry risk. From these scores (contrast variable) and using a ROC curve, the cut-off that best discriminated MAP-positive and -negative farms was estimated. The most important risk factors for the introduction of MAP, according to expert opinions, involved purchase and grazing practices related to animals under six months of age. The scores obtained for each farm, also based on the expert opinions, allowed MAP positive/MAP negative farms to be discriminated with 68.8% sensitivity and 68.7% specificity. These data should be useful for focusing future training initiatives and improving risk-reduction strategies in the dairy industry.
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Affiliation(s)
| | - Eduardo Yus
- Institute of Food Analysis and Research, Santiago de Compostela University, 27002 Lugo, Spain;
| | - Bibiana Benavides
- Animal Health Department, Universidad de Nariño, San Juan de Pasto 52001, Colombia;
| | - Alberto Allepuz
- Department of Health and Animal Anatomy, Autonomous University of Barcelona, 08193 Barcelona, Spain; (A.A.); (S.J.M.); (J.C.)
- Centre de Recerca en Sanitat Animal (CReSA), UAB, IRTA, 08193 Barcelona, Spain
| | - Sebastián Jesús Moya
- Department of Health and Animal Anatomy, Autonomous University of Barcelona, 08193 Barcelona, Spain; (A.A.); (S.J.M.); (J.C.)
| | - Jordi Casal
- Department of Health and Animal Anatomy, Autonomous University of Barcelona, 08193 Barcelona, Spain; (A.A.); (S.J.M.); (J.C.)
- Centre de Recerca en Sanitat Animal (CReSA), UAB, IRTA, 08193 Barcelona, Spain
| | - Carmelo Ortega
- Animal Pathology Department, Veterinary Faculty, Zaragoza University, 50013 Zaragoza, Spain;
| | - Francisco Javier Diéguez
- Anatomy, Animal Production and Clinical Veterinary Sciences Department, Veterinary Faculty, Santiago de Compostela University, 27002 Lugo, Spain
- Correspondence: ; Tel.: +34-9828-22400
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37
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Wibberg D, Price-Carter M, Rückert C, Blom J, Möbius P. Complete Genome Sequence of Ovine Mycobacterium avium subsp. paratuberculosis Strain JIII-386 (MAP-S/type III) and Its Comparison to MAP-S/type I, MAP-C, and M. avium Complex Genomes. Microorganisms 2020; 9:microorganisms9010070. [PMID: 33383865 PMCID: PMC7823733 DOI: 10.3390/microorganisms9010070] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Revised: 12/21/2020] [Accepted: 12/24/2020] [Indexed: 02/07/2023] Open
Abstract
Mycobacterium avium (M. a.) subsp. paratuberculosis (MAP) is a worldwide-distributed obligate pathogen in ruminants causing Johne’s disease. Due to a lack of complete subtype III genome sequences, there is not yet conclusive information about genetic differences between strains of cattle (MAP-C, type II) and sheep (MAP-S) type, and especially between MAP-S subtypes I, and III. Here we present the complete, circular genome of MAP-S/type III strain JIII-386 (DE) closed by Nanopore-technology and its comparison with MAP-S/type I closed genome of strain Telford (AUS), MAP-S/type III draft genome of strain S397 (U.S.), twelve closed MAP-C strains, and eight closed M.-a.-complex-strains. Structural comparative alignments revealed clearly the mosaic nature of MAP, emphasized differences between the subtypes and the higher diversity of MAP-S genomes. The comparison of various genomic elements including transposases and genomic islands provide new insights in MAP genomics. MAP type specific phenotypic features may be attributed to genes of known large sequence polymorphisms (LSPSs) regions I–IV and deletions #1 and #2, confirmed here, but could also result from identified frameshifts or interruptions of various virulence-associated genes (e.g., mbtC in MAP-S). Comprehensive core and pan genome analysis uncovered unique genes (e.g., cytochromes) and genes probably acquired by horizontal gene transfer in different MAP-types and subtypes, but also emphasized the highly conserved and close relationship, and the complex evolution of M.-a.-strains.
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Affiliation(s)
- Daniel Wibberg
- Center for Biotechnology (CeBiTec), Bielefeld University, 33501 Bielefeld, Germany; (D.W.); (C.R.)
| | - Marian Price-Carter
- AgResearch, Hopkirk Research Institute, Grasslands Research Centre, Palmerston North 4442, New Zealand;
| | - Christian Rückert
- Center for Biotechnology (CeBiTec), Bielefeld University, 33501 Bielefeld, Germany; (D.W.); (C.R.)
| | - Jochen Blom
- Bioinformatics and Systems Biology, Justus Liebig University Gießen, D-35390 Gießen, Germany;
| | - Petra Möbius
- Friedrich-Loeffler-Institut/Federal Research Institute for Animal Health, Institute of Molecular Pathogenesis, 07743 Jena, Germany
- Correspondence: ; Tel.: +49-(0)3641-8042280
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38
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Roller M, Hansen S, Knauf-Witzens T, Oelemann WMR, Czerny CP, Abd El Wahed A, Goethe R. Mycobacterium avium Subspecies paratuberculosis Infection in Zoo Animals: A Review of Susceptibility and Disease Process. Front Vet Sci 2020; 7:572724. [PMID: 33426014 PMCID: PMC7785982 DOI: 10.3389/fvets.2020.572724] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Accepted: 11/30/2020] [Indexed: 12/14/2022] Open
Abstract
Mycobacterium avium subspecies paratuberculosis (MAP) is the causative agent of paratuberculosis (ParaTB or Johne's disease), a contagious, chronic and typically fatal enteric disease of domestic and non-domestic ruminants. Clinically affected animals present wasting and emaciation. However, MAP can also infect non-ruminant animal species with less specific signs. Zoological gardens harbor various populations of diverse animal species, which are managed on limited space at higher than natural densities. Hence, they are predisposed to endemic trans-species pathogen distribution. Information about the incidence and prevalence of MAP infections in zoological gardens and the resulting potential threat to exotic and endangered species are rare. Due to unclear pathogenesis, chronicity of disease as well as the unknown cross-species accuracy of diagnostic tests, diagnosis and surveillance of MAP and ParaTB is challenging. Differentiation between uninfected shedders of ingested bacteria; subclinically infected individuals; and preclinically diseased animals, which may subsequently develop clinical signs after long incubation periods, is crucial for the interpretation of positive test results in animals and the resulting consequences in their management. This review summarizes published data from the current literature on occurrence of MAP infection and disease in susceptible and affected zoo animal species as well as the applied diagnostic methods and measures. Clinical signs indicative for ParaTB, pathological findings and reports on detection, transmission and epidemiology in zoo animals are included. Furthermore, case reports were re-evaluated for incorporation into accepted consistent terminologies and case definitions.
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Affiliation(s)
- Marco Roller
- Zoological-Botanical Gardens Wilhelma, Stuttgart, Germany
- Department of Animal Sciences, Faculty of Agricultural Science, Institute of Veterinary Medicine, Division of Microbiology and Animal Hygiene, Georg-August-University Göttingen, Göttingen, Germany
- Institute for Microbiology, University of Veterinary Medicine Hannover Foundation, Hannover, Germany
| | - Sören Hansen
- Department of Animal Sciences, Faculty of Agricultural Science, Institute of Veterinary Medicine, Division of Microbiology and Animal Hygiene, Georg-August-University Göttingen, Göttingen, Germany
| | | | - Walter M. R. Oelemann
- Institute for Microbiology, University of Veterinary Medicine Hannover Foundation, Hannover, Germany
- Department of Immunology, Institute of Microbiology, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Claus-Peter Czerny
- Department of Animal Sciences, Faculty of Agricultural Science, Institute of Veterinary Medicine, Division of Microbiology and Animal Hygiene, Georg-August-University Göttingen, Göttingen, Germany
| | - Ahmed Abd El Wahed
- Department of Animal Sciences, Faculty of Agricultural Science, Institute of Veterinary Medicine, Division of Microbiology and Animal Hygiene, Georg-August-University Göttingen, Göttingen, Germany
| | - Ralph Goethe
- Institute for Microbiology, University of Veterinary Medicine Hannover Foundation, Hannover, Germany
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Abstract
Mycobacterium avium paratuberculosis is responsible for paratuberculosis or Johne's disease in cows, having economic impacts on the dairy industry and a prevalence rate exceeding 50% in dairy herds. The economic burden of Johne's disease relates to decreased milk production and costs of disease prevention, treatment, and management, while having an economic impact on dairy producers, processors, consumers, and stakeholders of the dairy industry. Determining the true economic impact of the disease is difficult at regional and farm level as symptoms are not evident in subclinically infected animals. At present, the virulence, pathogenicity, persistence, and infectious dose of M. avium paratuberculosis are poorly understood, consequently effective paratuberculosis control measures remain obscure. M. avium paratuberculosis is potentially zoonotic with foodborne transmission a public health risk due to a possible causative link with inflammatory bowel disease in humans. A preventive approach is necessary to reduce the presence of this drug-resistant pathogen in dairy herds and subsequently dairy food. The use of inefficient diagnostic tests coupled with the long latency period of infection results in delayed animal culling and trade of asymptomatic animals, leading to regional transmission and increased disease prevalence. To date, there has been limited success at controlling and treating this terminal endemic disease, leading to significant prevalence rates. This study aims to outline the key factors associated with Johne's' disease while outlining its significant impact on the dairy sector.
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Affiliation(s)
- Mary Garvey
- Department of Life Science, Sligo Institute of Technology, F91 YW50 Sligo, Ireland
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40
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Mycobacterium Avium Paratuberculosis: A Disease Burden on the Dairy Industry. Animals (Basel) 2020; 10:ani10101773. [PMID: 33019502 PMCID: PMC7601789 DOI: 10.3390/ani10101773] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Revised: 09/21/2020] [Accepted: 09/26/2020] [Indexed: 12/22/2022] Open
Abstract
Mycobacterium avium paratuberculosis is responsible for paratuberculosis or Johne's disease in cows, having economic impacts on the dairy industry and a prevalence rate exceeding 50% in dairy herds. The economic burden of Johne's disease relates to decreased milk production and costs of disease prevention, treatment, and management, while having an economic impact on dairy producers, processors, consumers, and stakeholders of the dairy industry. Determining the true economic impact of the disease is difficult at regional and farm level as symptoms are not evident in subclinically infected animals. At present, the virulence, pathogenicity, persistence, and infectious dose of M. avium paratuberculosis are poorly understood, consequently effective paratuberculosis control measures remain obscure. M. avium paratuberculosis is potentially zoonotic with foodborne transmission a public health risk due to a possible causative link with inflammatory bowel disease in humans. A preventive approach is necessary to reduce the presence of this drug-resistant pathogen in dairy herds and subsequently dairy food. The use of inefficient diagnostic tests coupled with the long latency period of infection results in delayed animal culling and trade of asymptomatic animals, leading to regional transmission and increased disease prevalence. To date, there has been limited success at controlling and treating this terminal endemic disease, leading to significant prevalence rates. This study aims to outline the key factors associated with Johne's' disease while outlining its significant impact on the dairy sector.
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41
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Volpe R, Fett T, Cassart D, Godfroid J, Linden A. Mixed
Mycobacterium avium
subspecies
avium
and
M avium
subspecies
paratuberculosis
infection in a wild red deer (
Cervus elaphus
) in Belgium. VETERINARY RECORD CASE REPORTS 2020. [DOI: 10.1136/vetreccr-2020-001130] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Affiliation(s)
- Rosario Volpe
- Department of Infectious and Parasitic DiseasesUniversity of LiegeLiegeBelgium
| | - Thomas Fett
- Department of Infectious and Parasitic DiseasesUniversity of LiegeLiegeBelgium
| | - Dominique Cassart
- Department of Infectious and Parasitic DiseasesUniversity of LiegeLiegeBelgium
| | - Jacques Godfroid
- Biosciences, Fisheries and EconomicsUiT The Arctic University of NorwayTromsøNorway
- Department of Arctic and Marine BiologyThe Arctic University of NorwayTromsøNorway
| | - Annick Linden
- Department of Infectious and Parasitic DiseasesUniversity of LiegeLiegeBelgium
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42
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Cochard T, Branger M, Supply P, Sreevatsan S, Biet F. MAC-INMV-SSR: a web application dedicated to genotyping members of Mycobacterium avium complex (MAC) including Mycobacterium avium subsp. paratuberculosis strains. INFECTION GENETICS AND EVOLUTION 2019; 77:104075. [PMID: 31634642 DOI: 10.1016/j.meegid.2019.104075] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/11/2019] [Revised: 10/11/2019] [Accepted: 10/16/2019] [Indexed: 01/27/2023]
Abstract
Genotyping of Mycobacterium avium subsp. paratuberculosis (Map) is an indispensable tool for surveillance of this significant veterinary pathogen. For Map, multi-locus variable number tandem repeat analysis (MLVA) targeting mycobacterial interspersed repetitive units (MIRUs) and other variable number variable-number tandem repeats (VNTRs) was established using 8 markers. In the recent past this standard, portable, reproducible and discriminatory typing method has been frequently applied alone or in combinations with multi-locus short-sequence-repeat (MLSSR) sequencing. With the widespread use of these genotyping methods, standardization between laboratories needs to be managed, and knowledge of existing profiles and newly defined genotypes should be indexed and shared. To meet this need, a web application called "MAC-INMV-SSR database" was developed. This freely accessible service allows users to compare MLVA and MLSSR subtype data of their strains with those of existing reference strains analyzed with the same genotyping methods.
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Affiliation(s)
- Thierry Cochard
- ISP, INRA, Université de Tours, UMR 1282, 37380 Nouzilly, France
| | - Maxime Branger
- ISP, INRA, Université de Tours, UMR 1282, 37380 Nouzilly, France
| | - Philip Supply
- INSERM U1019, F-59019 Lille Cedex, France; CNRS UMR 8204, F-59019, Lille Cedex, France; Institut Pasteur de Lille, France; Univ Lille Nord de France, F-59019 Lille Cedex, France
| | - Srinand Sreevatsan
- Department of Pathobiology and Diagnostic Investigation, Michigan State University, East Lansing 48824, USA
| | - Franck Biet
- ISP, INRA, Université de Tours, UMR 1282, 37380 Nouzilly, France.
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43
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Scherrer S, Stephan R, Zumthor JP, Kipar A, Seehusen F. Morphological and Molecular Characterization of a New Mycobacterium avium Subsp. paratuberculosis S-Type Strain Genotype in Goats. Front Vet Sci 2019; 6:250. [PMID: 31417916 PMCID: PMC6684744 DOI: 10.3389/fvets.2019.00250] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2019] [Accepted: 07/10/2019] [Indexed: 11/13/2022] Open
Abstract
Paratuberculosis is a chronic bacterial disease of global importance mainly in domestic and wild ruminants, caused by Mycobacterium avium subsp. paratuberculosis (MAP). In goats, paratuberculosis is mostly caused by the "C-type" (cattle) and in a few cases by the "S-type" (sheep) strain of MAP. In 2017, a caprine S-type III isolate with a new VNTR profile was identified in a Swiss alpine region. In 2018, new caprine isolates with the same novel VNTR profile originating from a farm of a close by neighboring valley were analyzed. Here we report on this MAP S-type III outbreak in a Swiss dairy goat farm in which we investigated the pathological changes, distribution and genotype of MAP tissue homogenates. Full necropsy and histological examination were undertaken on two female adult goats with a history of weight loss and intermitting diarrhea. Routine and special stains were applied to characterize the morphological changes. DNA was extracted from 33 different tissue samples and tested for MAP by qPCR targeting IS900 and F57. Subtyping was performed, using the variable number tandem repeats (VNTR) and mycobacterial interspersed repetitive units (MIRU) approach. The goats showed moderate to marked emaciation and displayed typical clinical features of paratuberculosis. A moderate granulomatous enteritis and regional lymphadenitis with a small to moderate number of acid-fast bacteria within macrophages was detected. MAP detection was mainly restricted to the gastrointestinal tract, mesenteric and hepatic lymph nodes. Subtyping the S-type isolates using a panel of eight established MIRU-VNTR loci identified a new genotype, INMV 218.
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Affiliation(s)
- Simone Scherrer
- Section of Veterinary Bacteriology, University of Zurich, Zurich, Switzerland
| | - Roger Stephan
- Institute for Food Safety and Hygiene, University of Zurich, Zurich, Switzerland
| | | | - Anja Kipar
- Institute for Veterinary Pathology, University of Zurich, Zurich, Switzerland
| | - Frauke Seehusen
- Institute for Veterinary Pathology, University of Zurich, Zurich, Switzerland
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Sohal JS, Arsenault J, Leboeuf A, Hélie P, Buczinski S, Robinson Y, Labrecque O, Lachapelle V, Fecteau G, L'Homme Y. Molecular characterization of Mycobacterium avium subspecies paratuberculosis C-type and S-type isolated from sheep and goats by using a combination of MIRU-VNTR loci. CANADIAN JOURNAL OF VETERINARY RESEARCH = REVUE CANADIENNE DE RECHERCHE VETERINAIRE 2019; 83:160-167. [PMID: 31308587 PMCID: PMC6587881] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Received: 03/21/2018] [Accepted: 06/06/2018] [Indexed: 06/10/2023]
Abstract
Mycobacterium avium subspecies paratuberculosis (Map) is the etiological agent of paratuberculosis of domestic and wild ruminants. Map strains are segregated into 2 main groups or strain types referred to as sheep (S) type and cattle (C) type. Few small ruminant Map strains have been genetically characterized to date. The present study was undertaken to genetically characterize a panel of 30 small ruminant Map strains in the province of Quebec, Canada. Mycobacterial Interspersed Repetitive Units - Variable-Number Tandem Repeat analysis (MIRU-VNTR) were used as genetic markers in addition to IS1311 PCR-REA. S-type and C-type strains were found in both sheep and goats, although C-type strains were more frequently isolated from goats and S-type strains were more common in sheep. A total of 12 distinct Map genotypes were uncovered in the present collection of strains using these markers. Considering the genetic diversity reported here, molecular characterization of Map stains in small ruminants using MIRU-VNTR markers represent an interesting avenue for both epidemiological investigations regarding the sources of herd infection and association studies between Map strains and their virulence, persistence and host-specific adaptation characteristics.
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Affiliation(s)
- Jagdip Singh Sohal
- Canadian Food Inspection Agency, 3400 Casavant, St-Hyacinthe (Sohal, Robinson, Lachapelle, L'Homme); Faculté de Médecine Vétérinaire, Université de Montréal, 3200 Sicotte, St-Hyacinthe (Arsenault, Hélie, Buczinski, Fecteau, L'Homme); Ministère de l'Agriculture, des pêcheries et de l'alimentation du Quebec, 200 chemin Ste-Foy (Leboeuf); Laboratoire de santé animale du Quebec, Ministère de l'Agriculture, des pêcheries et de l'alimentation du Quebec, 3220 Sicotte, St-Hyacinthe, Quebec (Labrecque)
| | - Julie Arsenault
- Canadian Food Inspection Agency, 3400 Casavant, St-Hyacinthe (Sohal, Robinson, Lachapelle, L'Homme); Faculté de Médecine Vétérinaire, Université de Montréal, 3200 Sicotte, St-Hyacinthe (Arsenault, Hélie, Buczinski, Fecteau, L'Homme); Ministère de l'Agriculture, des pêcheries et de l'alimentation du Quebec, 200 chemin Ste-Foy (Leboeuf); Laboratoire de santé animale du Quebec, Ministère de l'Agriculture, des pêcheries et de l'alimentation du Quebec, 3220 Sicotte, St-Hyacinthe, Quebec (Labrecque)
| | - Anne Leboeuf
- Canadian Food Inspection Agency, 3400 Casavant, St-Hyacinthe (Sohal, Robinson, Lachapelle, L'Homme); Faculté de Médecine Vétérinaire, Université de Montréal, 3200 Sicotte, St-Hyacinthe (Arsenault, Hélie, Buczinski, Fecteau, L'Homme); Ministère de l'Agriculture, des pêcheries et de l'alimentation du Quebec, 200 chemin Ste-Foy (Leboeuf); Laboratoire de santé animale du Quebec, Ministère de l'Agriculture, des pêcheries et de l'alimentation du Quebec, 3220 Sicotte, St-Hyacinthe, Quebec (Labrecque)
| | - Pierre Hélie
- Canadian Food Inspection Agency, 3400 Casavant, St-Hyacinthe (Sohal, Robinson, Lachapelle, L'Homme); Faculté de Médecine Vétérinaire, Université de Montréal, 3200 Sicotte, St-Hyacinthe (Arsenault, Hélie, Buczinski, Fecteau, L'Homme); Ministère de l'Agriculture, des pêcheries et de l'alimentation du Quebec, 200 chemin Ste-Foy (Leboeuf); Laboratoire de santé animale du Quebec, Ministère de l'Agriculture, des pêcheries et de l'alimentation du Quebec, 3220 Sicotte, St-Hyacinthe, Quebec (Labrecque)
| | - Sébastien Buczinski
- Canadian Food Inspection Agency, 3400 Casavant, St-Hyacinthe (Sohal, Robinson, Lachapelle, L'Homme); Faculté de Médecine Vétérinaire, Université de Montréal, 3200 Sicotte, St-Hyacinthe (Arsenault, Hélie, Buczinski, Fecteau, L'Homme); Ministère de l'Agriculture, des pêcheries et de l'alimentation du Quebec, 200 chemin Ste-Foy (Leboeuf); Laboratoire de santé animale du Quebec, Ministère de l'Agriculture, des pêcheries et de l'alimentation du Quebec, 3220 Sicotte, St-Hyacinthe, Quebec (Labrecque)
| | - Yves Robinson
- Canadian Food Inspection Agency, 3400 Casavant, St-Hyacinthe (Sohal, Robinson, Lachapelle, L'Homme); Faculté de Médecine Vétérinaire, Université de Montréal, 3200 Sicotte, St-Hyacinthe (Arsenault, Hélie, Buczinski, Fecteau, L'Homme); Ministère de l'Agriculture, des pêcheries et de l'alimentation du Quebec, 200 chemin Ste-Foy (Leboeuf); Laboratoire de santé animale du Quebec, Ministère de l'Agriculture, des pêcheries et de l'alimentation du Quebec, 3220 Sicotte, St-Hyacinthe, Quebec (Labrecque)
| | - Olivia Labrecque
- Canadian Food Inspection Agency, 3400 Casavant, St-Hyacinthe (Sohal, Robinson, Lachapelle, L'Homme); Faculté de Médecine Vétérinaire, Université de Montréal, 3200 Sicotte, St-Hyacinthe (Arsenault, Hélie, Buczinski, Fecteau, L'Homme); Ministère de l'Agriculture, des pêcheries et de l'alimentation du Quebec, 200 chemin Ste-Foy (Leboeuf); Laboratoire de santé animale du Quebec, Ministère de l'Agriculture, des pêcheries et de l'alimentation du Quebec, 3220 Sicotte, St-Hyacinthe, Quebec (Labrecque)
| | - Virginie Lachapelle
- Canadian Food Inspection Agency, 3400 Casavant, St-Hyacinthe (Sohal, Robinson, Lachapelle, L'Homme); Faculté de Médecine Vétérinaire, Université de Montréal, 3200 Sicotte, St-Hyacinthe (Arsenault, Hélie, Buczinski, Fecteau, L'Homme); Ministère de l'Agriculture, des pêcheries et de l'alimentation du Quebec, 200 chemin Ste-Foy (Leboeuf); Laboratoire de santé animale du Quebec, Ministère de l'Agriculture, des pêcheries et de l'alimentation du Quebec, 3220 Sicotte, St-Hyacinthe, Quebec (Labrecque)
| | - Gilles Fecteau
- Canadian Food Inspection Agency, 3400 Casavant, St-Hyacinthe (Sohal, Robinson, Lachapelle, L'Homme); Faculté de Médecine Vétérinaire, Université de Montréal, 3200 Sicotte, St-Hyacinthe (Arsenault, Hélie, Buczinski, Fecteau, L'Homme); Ministère de l'Agriculture, des pêcheries et de l'alimentation du Quebec, 200 chemin Ste-Foy (Leboeuf); Laboratoire de santé animale du Quebec, Ministère de l'Agriculture, des pêcheries et de l'alimentation du Quebec, 3220 Sicotte, St-Hyacinthe, Quebec (Labrecque)
| | - Yvan L'Homme
- Canadian Food Inspection Agency, 3400 Casavant, St-Hyacinthe (Sohal, Robinson, Lachapelle, L'Homme); Faculté de Médecine Vétérinaire, Université de Montréal, 3200 Sicotte, St-Hyacinthe (Arsenault, Hélie, Buczinski, Fecteau, L'Homme); Ministère de l'Agriculture, des pêcheries et de l'alimentation du Quebec, 200 chemin Ste-Foy (Leboeuf); Laboratoire de santé animale du Quebec, Ministère de l'Agriculture, des pêcheries et de l'alimentation du Quebec, 3220 Sicotte, St-Hyacinthe, Quebec (Labrecque)
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Brauning R, Plain K, Gautam M, Russell T, Correa CC, Biggs P, Whittington R, Murray A, Price-Carter M. Complete Genome Sequence of the Telford Type S Strain of Mycobacterium avium subsp. paratuberculosis. Microbiol Resour Announc 2019; 8:e00004-19. [PMID: 30938318 PMCID: PMC6424202 DOI: 10.1128/mra.00004-19] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2019] [Accepted: 02/08/2019] [Indexed: 11/20/2022] Open
Abstract
Mycobacterium avium subsp. paratuberculosis is the causative agent of Johne's disease (JD). Here, we report the complete genome sequence of Telford 9.2, a well-characterized representative strain of the M. avium subsp. paratuberculosis S subtype that is endemic in New Zealand and Australian sheep.
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Affiliation(s)
- Rudiger Brauning
- AgResearch Ltd., Invermay Agricultural Centre, Mosgiel, New Zealand
| | - Karren Plain
- University of Sydney, Camden, New South Wales, Australia
| | - Milan Gautam
- School of Veterinary Science, EpiCentre, Massey University, Palmerston North, New Zealand
| | - Tonia Russell
- Ramaciotti Centre for Genomics, University of New South Wales (UNSW), Sydney, Australia
| | - C Carolina Correa
- Ramaciotti Centre for Genomics, University of New South Wales (UNSW), Sydney, Australia
| | - Patrick Biggs
- Infectious Disease Research Centre, School of Veterinary Science, Hopkirk Research Institute, and School of Fundamental Sciences, Massey University, Palmerston North, New Zealand
| | | | - Alan Murray
- School of Veterinary Science, Hopkirk Research Institute, Massey University, Palmerston North, New Zealand
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What counts? A review of in vitro methods for the enumeration of Mycobacterium avium subsp. paratuberculosis. Vet Microbiol 2019; 230:265-272. [DOI: 10.1016/j.vetmic.2019.02.011] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2018] [Revised: 02/03/2019] [Accepted: 02/05/2019] [Indexed: 11/24/2022]
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Mycobacterium avium subspecies paratuberculosis is able to manipulate host lipid metabolism and accumulate cholesterol within macrophages. Microb Pathog 2019; 130:44-53. [PMID: 30831227 DOI: 10.1016/j.micpath.2019.02.031] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2018] [Revised: 02/12/2019] [Accepted: 02/26/2019] [Indexed: 12/17/2022]
Abstract
Johne's disease is a chronic wasting disease of ruminants caused by Mycobacterium avium subspecies paratuberculosis (MAP). Closely related pathogenic mycobacteria such as M. tuberculosis are capable of altering host lipid metabolism, highlighting the need to explore the role of lipid metabolism contributing to intracellular survival. This study aimed to identify whether MAP is able to manipulate host lipid metabolic pathways and accumulate host cholesterol during early infection. Macrophages were exposed to four different MAP strains and non-pathogenic M. phlei for up to 72 h, with changes to lipid metabolism examined using fluorescent microscopy and gene expression. MAP-infected macrophages displayed strain-dependent differences to intracellular cholesterol levels during early infection, however showed similarly increased intracellular cholesterol at later timepoints. Gene expression revealed that MAP strains similarly activate the host immune response in a conserved manner compared to M. phlei. MAP significantly upregulated host genes associated with lipid efflux and endocytosis. Moreover, lipid biosynthesis genes were differentially regulated in a strain-dependent manner following MAP infection. Collectively, these results demonstrate that MAP manipulates host lipid metabolism during early infection, however the extent of these modulations are strain-dependent. These findings reflect a conserved pathway contributing to intracellular MAP survival.
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McAloon CG, Roche S, Ritter C, Barkema HW, Whyte P, More SJ, O'Grady L, Green MJ, Doherty ML. A review of paratuberculosis in dairy herds - Part 1: Epidemiology. Vet J 2019; 246:59-65. [PMID: 30902190 DOI: 10.1016/j.tvjl.2019.01.010] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2018] [Revised: 01/24/2019] [Accepted: 01/25/2019] [Indexed: 11/24/2022]
Abstract
Bovine paratuberculosis is a chronic infectious disease of cattle caused by Mycobacterium avium subspecies paratuberculosis (MAP). This is the first in a two-part review of the epidemiology and control of paratuberculosis in dairy herds. Paratuberculosis was originally described in 1895 and is now considered endemic among farmed cattle worldwide. MAP has been isolated from a wide range of non-ruminant wildlife as well as humans and non-human primates. In dairy herds, MAP is assumed to be introduced predominantly through the purchase of infected stock with additional factors modulating the risk of persistence or fade-out once an infected animal is introduced. Faecal shedding may vary widely between individuals and recent modelling work has shed some light on the role of super-shedding animals in the transmission of MAP within herds. Recent experimental work has revisited many of the assumptions around age susceptibility, faecal shedding in calves and calf-to-calf transmission. Further efforts to elucidate the relative contributions of different transmission routes to the dissemination of infection in endemic herds will aid in the prioritisation of efforts for control on farm.
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Affiliation(s)
- Conor G McAloon
- Section of Herd Health and Animal Husbandry, School of Veterinary Medicine, University College Dublin, Ireland.
| | - Steven Roche
- Department of Population Medicine, University of Guelph, 50 Stone Rd., Guelph, ON, N1G 2W1, Canada
| | - Caroline Ritter
- Department of Production Animal Health, Faculty of Veterinary Medicine, University of Calgary, 2500 University Drive, Calgary, AB, T2N 1N4, Canada
| | - Herman W Barkema
- Department of Production Animal Health, Faculty of Veterinary Medicine, University of Calgary, 2500 University Drive, Calgary, AB, T2N 1N4, Canada
| | - Paul Whyte
- Section of Herd Health and Animal Husbandry, School of Veterinary Medicine, University College Dublin, Ireland
| | - Simon J More
- Section of Herd Health and Animal Husbandry, School of Veterinary Medicine, University College Dublin, Ireland
| | - Luke O'Grady
- Section of Herd Health and Animal Husbandry, School of Veterinary Medicine, University College Dublin, Ireland
| | - Martin J Green
- School of Veterinary Medicine and Science, University of Nottingham, Sutton Bonington Campus, Leicestershire, LE12 5RD, United Kingdom
| | - Michael L Doherty
- Section of Herd Health and Animal Husbandry, School of Veterinary Medicine, University College Dublin, Ireland
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de Albuquerque PPF, de Melo RPB, de Farias Brito M, Bovino F, de Souza MA, Lima AMC, de Oliveira EAA, de Moraes Pereira H, Mota RA. First molecular epidemiological study of Mycobacterium avium subsp. paratuberculosis in cattle and buffalo from different regions of Brazil. Trop Anim Health Prod 2018; 50:1929-1935. [PMID: 29946985 DOI: 10.1007/s11250-018-1650-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2018] [Accepted: 06/15/2018] [Indexed: 01/28/2023]
Abstract
Paratuberculosis is an incurable disease in ruminants with great worldwide economic impact, caused by Mycobacterium avium subsp. paratuberculosis (MAP). The objective of this study was to carry out a study of the molecular epidemiology of the MAP using the restriction enzyme analysis (REA) technique of IS1311 MAP region in biological samples of feces, intestinal tissue, and mesenteric lymph nodes of cattle and buffaloes from six Brazilian states. In total, 109 samples of feces and tissues of cattle and buffaloes were collected from animal paratuberculosis suspected. Twenty-five samples were positive in the detection of the DNA of the IS900 region of MAP and it was possible to type 18 strains in the analysis of the region IS1311, being 100% of them identified as belonging to subtype Bison MAP strain. This is the first epidemiological molecular study of MAP in Brazil. The results indicate that paratuberculosis is widespread in cattle and in buffaloes in several regions of Brazil, and the subtype Bison MAP strain was the only one identified in the samples analyzed in this study, demonstrating the similarity between the strains from different states tested. These results provide the necessary support for the implementation of paratuberculosis control strategies in cattle and buffaloes in Brazil.
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Affiliation(s)
| | | | - Marilene de Farias Brito
- Department of Epidemiology and Public Health, Federal University of Rio de Janeiro, Rio de Janeiro, RJ, Brazil
| | - Fernanda Bovino
- Faculty of Agrarian Sciences of Andradina, Educational Foundation of Andradina, Andradina, SP, Brazil
| | | | | | | | | | - Rinaldo Aparecido Mota
- Department of Veterinary Medicine, Federal Rural University of Pernambuco, Recife, PE, Brazil
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Rani M, Narang D, Kumar D, Chandra M, Singh ST, Filia G. ISMap 02 element targeted nested polymerase chain in the detection of Mycobacterium avium subsp. paratuberculosis in fecal samples of cattle and buffaloes. Vet World 2018; 11:397-401. [PMID: 29657435 PMCID: PMC5891858 DOI: 10.14202/vetworld.2018.397-401] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2017] [Accepted: 02/21/2018] [Indexed: 11/16/2022] Open
Abstract
Background and Aim Johne's disease is chronic granulomatous enteritis which affects ruminants. There are many diagnostic approaches for the detection of Mycobacterium avium subsp. paratuberculosis (MAP) of which molecular detection methods using various elements are less time consuming and more accurate. The present study was conducted using ISMap02 element for nested polymerase chain reaction (nPCR) based detection of MAP in fecal samples. The aim was to test the sensitivity and specificity of the ISMap02 element and also to use this element for the detection of MAP in fecal samples of cattle and buffaloes. Materials and Methods A total of 211 fecal samples of cattle and buffaloes from different herds around Ludhiana aged between 2 and 13 years were collected, and DNA extraction was done from these samples. The nPCR was carried out for the detection of MAP in fecal samples. Results The ISMap02 element was specific for the detection of MAP only and showed a sensitivity of detection of 7.6 fg/µL of the standard genomic DNA. Among the 211 fecal samples of cattle and buffaloes tested for the ISMap02 element, 18 samples (8.5%) were positive for MAP. Conclusion The ISMap02 element is specific and sensitive for the detection of MAP in various samples, and when used in nPCR format, it can increase the sensitivity of detection.
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Affiliation(s)
- Mamta Rani
- Department of Veterinary Microbiology, College of Veterinary Science, Guru Angad Dev Veterinary and Animal Sciences University, Ludhiana, Punjab, India
| | - Deepti Narang
- Department of Veterinary Microbiology, College of Veterinary Science, Guru Angad Dev Veterinary and Animal Sciences University, Ludhiana, Punjab, India
| | - Dinesh Kumar
- Department of Veterinary Microbiology, College of Veterinary Science, Guru Angad Dev Veterinary and Animal Sciences University, Ludhiana, Punjab, India
| | - Mudit Chandra
- Department of Veterinary Microbiology, College of Veterinary Science, Guru Angad Dev Veterinary and Animal Sciences University, Ludhiana, Punjab, India
| | - Sikh Tejinder Singh
- Directorate of Livestock Farms, College of Veterinary Science, Guru Angad Dev Veterinary and Animal Sciences University, Ludhiana, Punjab, India
| | - G Filia
- Animal Disease Research Centre, College of Veterinary Science, Guru Angad Dev Veterinary and Animal Sciences University, Ludhiana, Punjab, India
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