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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: 8] [Impact Index Per Article: 8.0] [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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2
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Phylogenetic and Multiple-Locus Variable number tandem repeat analysis of Mycobacterium avium subsp. paratuberculosis isolates from Argentina. Vet Res Commun 2022; 46:1121-1129. [PMID: 35948855 DOI: 10.1007/s11259-022-09983-8] [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: 02/24/2022] [Accepted: 08/03/2022] [Indexed: 10/15/2022]
Abstract
Paratuberculosis is a worldwide chronic enteric disease of ruminants, caused by Mycobacterium avium subsp. paratuberculosis (MAP). While MAP has been widely investigated all around the world, little is known about the different strains that circulate in each country. This study describes the genetic diversity of MAP isolates from different bovine and deer herds from Argentina, analyzed by Multiple-Locus Variable number tandem repeat Analysis (MLVA), as well as the phylogenetic relatedness between geographically distant isolates through Whole Genome Sequencing (WGS) and core-genome analysis. A total of 90 MAP isolates were analyzed. The results showed seven different MLVA genotypes, with almost 75% of them belonging to pattern INMV 1, described in all the herds studied. WGS results suggested the presence of a common INMV 1 strain circulating throughout the country. Our results allow confirming the coexistence of different strains in time and space and the mixed infections identified in some animals. These observations suggest the absence of animal monitoring prior to introduction to the herds and the need for a control program in the country. This study represents the first to report WGS of MAP strains in Argentina.
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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: 4] [Impact Index Per Article: 1.3] [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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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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5
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Park HT, Park HE, Park WB, Kim S, Hur TY, Jung YH, Yoo HS. Genetic diversity of bovine Mycobacterium avium subsp. paratuberculosis discriminated by IS 1311 PCR-REA, MIRU-VNTR, and MLSSR genotyping. J Vet Sci 2018; 19:627-634. [PMID: 29929361 PMCID: PMC6167339 DOI: 10.4142/jvs.2018.19.5.627] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2018] [Revised: 06/01/2018] [Accepted: 06/04/2018] [Indexed: 11/29/2022] Open
Abstract
The aim of this study was to describe the genetic diversity of Mycobacterium avium subsp. paratuberculosis (MAP) obtained from individual cows in Korea. Twelve MAP-positive fecal DNA samples and 19 MAP isolates were obtained from 10 cattle herds located in 5 provinces in Korea. In addition, 5 MAP isolates obtained from the Czech Republic and Slovakia and 3 isolates from Australia were genotyped for comparison with the domestic isolates. The most prevalent strains in Korea were of the “bison-type” genotype (23 of 31 fecal DNA/isolates) and were distributed nationwide. The remaining MAP isolates (8) and all of the foreign isolates were identified as “cattle-type”. The bison-type strains which were discriminated only as INMV 68 in variable-number tandem repeats of mycobacterial interspersed repetitive units (MIRU-VNTR) typing. Multilocus short sequence repeat (MLSSR) typing differentiated the bison-type strains into 3 different subtypes. The cattle-type strains were divided into 3 subtypes by MIRU-VNTR and 8 subtypes by MLSSR. The allelic diversities in the MIRU-VNTR and MLSSR results were calculated as 0.567 and 0.866, respectively. These results suggest that MIRU-VNTR typing cannot provide a sufficient description of the epidemiological situation of MAP. Therefore, an alternative method, such as MLSSR, is needed for typing of MAP strains to elucidate the molecular epidemiology of MAP infections. Overall, this study is the first epidemiological survey report in Korea using both MIRU-VNTR and MLSSR typing methods, and it has provided basic data necessary to elucidate the characteristics of MAP infections in Korea.
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Affiliation(s)
- Hong-Tae Park
- Department of Infectious Disease, College of Veterinary Medicine, Seoul National University, Seoul 08826, Korea
| | - Hyun-Eui Park
- Department of Infectious Disease, College of Veterinary Medicine, Seoul National University, Seoul 08826, Korea
| | - Woo Bin Park
- Department of Infectious Disease, College of Veterinary Medicine, Seoul National University, Seoul 08826, Korea
| | - Suji Kim
- Department of Infectious Disease, College of Veterinary Medicine, Seoul National University, Seoul 08826, Korea
| | - Tai Young Hur
- Department of Animal Resources Development, National Institute of Animal Science, Rural Development Administration, Cheonan 31000, Korea
| | - Young-Hoon Jung
- Department of Animal Resources Development, National Institute of Animal Science, Rural Development Administration, Cheonan 31000, Korea
| | - Han Sang Yoo
- Department of Infectious Disease, College of Veterinary Medicine, Seoul National University, Seoul 08826, Korea.,Institute of Green Bio Science and Technology, Seoul National University, Pyeongchang 25354, Korea
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6
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Fawzy A, Zschöck M, Ewers C, Eisenberg T. Genotyping methods and molecular epidemiology of Mycobacterium avium subsp. paratuberculosis (MAP). Int J Vet Sci Med 2018; 6:258-264. [PMID: 30564606 PMCID: PMC6286618 DOI: 10.1016/j.ijvsm.2018.08.001] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2018] [Revised: 08/02/2018] [Accepted: 08/02/2018] [Indexed: 12/22/2022] Open
Abstract
Mycobacterium avium subsp. paratuberculosis (MAP) is the causative agent of Johne’s disease (JD) which affects mainly ruminants and is characterized by chronic diarrhea and emaciation. Johne’s disease is highly prevalent in many countries around the world and leads to high economic losses associated with decreased production. Genotyping of the involved pathogen could be used in the study of population genetics, pathogenesis and molecular epidemiology including disease surveillance and outbreak investigation. Principally, researchers have first assumed the presence of two different MAP strains that are associated with the animal host species (cattle and sheep). However, nowadays MAP characterization depends mainly upon genetic testing using genetic markers such as insertion elements, repetitive sequences and single nucleotide polymorphisms. This work aims to provide an overview of the advances in molecular biological tools used for MAP typing in the last two decades, discuss how these methods have been used to address interesting epidemiological questions, and explore the future prospects of MAP molecular epidemiology given the ever decreasing costs of the high throughput sequencing technology.
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Affiliation(s)
- Ahmad Fawzy
- Faculty of Veterinary Medicine, Department of Medicine and Infectious Diseases, Cairo University, Egypt
- Hessian State Laboratory (LHL), Giessen, Germany
- Institute of Hygiene and Animal Infectious Diseases, Justus-Liebig University, Giessen, Germany
- Corresponding author at: Institute of Hygiene and Animal Infectious Diseases, Justus-Liebig University, Giessen, Germany.
| | | | - Christa Ewers
- Institute of Hygiene and Animal Infectious Diseases, Justus-Liebig University, Giessen, Germany
| | - Tobias Eisenberg
- Hessian State Laboratory (LHL), Giessen, Germany
- Institute of Hygiene and Animal Infectious Diseases, Justus-Liebig University, Giessen, Germany
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7
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Galiero A, Leo S, Garbarino C, Arrigoni N, Russo S, Giacomelli S, Bianchi A, Trevisiol K, Idrizi I, Daka G, Fratini F, Turchi B, Cerri D, Ricchi M. Mycobacterium aviumsubsp. paratuberculosis isolated from wild red deer (Cervus elaphus) in Northern Italy. Vet Microbiol 2018; 217:167-172. [PMID: 29615250 DOI: 10.1016/j.vetmic.2018.03.015] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2018] [Revised: 03/15/2018] [Accepted: 03/15/2018] [Indexed: 01/19/2023]
Abstract
Paratuberculosis (or Johne's disease) is an infectious disease which affects mainly ruminants and it is caused by Mycobacterium avium subsp. paratuberculosis (MAP). During a culling program (years 2011-2015) aimed at controlling the red deer (Cervus elaphus) population in Stelvio National Park (Italian Alps), where paratuberculosis was already described in this species, 382 tissue samples from the Lombardy Region and 102 fecal specimens from the Autonomous Province of Bolzano were analyzed by PCR. Of these, 77 samples (20.16%) from the Lombardy area and 19 specimens (18.63%) from the Bolzano area resulted PCR positive. The cultural test was carried out on PCR positive samples (n = 96), enabling the isolation of 19 MAP field strains which were genotyped using MIRU-VNTR typing and Short Sequence repeats (SSRs). Our results suggest that all isolates share an identical VNTR profile corresponding to the INMV1 genotype. The only variation was on the locus SSR2, but the utility of this last locus has already been questioned because of its instability. Overall, these data suggest a common clonal origin and host adaptation during the diffusion of paratuberculosis in this population. Finally, this profile is the same as that which has already been described in the cattle population in Northern Italy, suggesting a possible inter-species disease transmission pattern from wildlife to domestic ruminants and vice versa.
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Affiliation(s)
- Alessia Galiero
- Istituto Zooprofilattico Sperimentale dell'Emilia Romagna e della Lombardia, Sezione di Piacenza-Gariga, Strada della Faggiola 1, 29027, National Reference Centre for Paratuberculosis, Gariga di Podenzano, (PC), Italy.
| | - Simone Leo
- Istituto Zooprofilattico Sperimentale dell'Emilia Romagna e della Lombardia, Sezione di Piacenza-Gariga, Strada della Faggiola 1, 29027, National Reference Centre for Paratuberculosis, Gariga di Podenzano, (PC), Italy
| | - Chiara Garbarino
- Istituto Zooprofilattico Sperimentale dell'Emilia Romagna e della Lombardia, Sezione di Piacenza-Gariga, Strada della Faggiola 1, 29027, National Reference Centre for Paratuberculosis, Gariga di Podenzano, (PC), Italy
| | - Norma Arrigoni
- Istituto Zooprofilattico Sperimentale dell'Emilia Romagna e della Lombardia, Sezione di Piacenza-Gariga, Strada della Faggiola 1, 29027, National Reference Centre for Paratuberculosis, Gariga di Podenzano, (PC), Italy
| | - Simone Russo
- Istituto Zooprofilattico Sperimentale dell'Emilia Romagna e della Lombardia, Sezione di Piacenza-Gariga, Strada della Faggiola 1, 29027, National Reference Centre for Paratuberculosis, Gariga di Podenzano, (PC), Italy
| | - Stefano Giacomelli
- Istituto Zooprofilattico Sperimentale dell'Emilia Romagna e della Lombardia, Sezione di Brescia, Via Bianchi 7/9, 25124, Brescia, Italy
| | - Alessandro Bianchi
- Istituto Zooprofilattico Sperimentale dell'Emilia Romagna e della Lombardia, Sezione di Sondrio, Via Bormio 30, 23100, Sondrio, Italy
| | - Karin Trevisiol
- Istituto Zooprofilattico Sperimentale delle Venezie, Sezione di Bolzano, Via Laura Conti 4, 39100, Bolzano, Italy
| | - Ilda Idrizi
- Istituto Zooprofilattico Sperimentale delle Venezie, Sezione di Bolzano, Via Laura Conti 4, 39100, Bolzano, Italy
| | - Gezim Daka
- Istituto Zooprofilattico Sperimentale delle Venezie, Sezione di Bolzano, Via Laura Conti 4, 39100, Bolzano, Italy
| | - Filippo Fratini
- Department of Veterinary Sciences, University of Pisa, Viale delle Piagge, 2, 56124 Pisa, Italy
| | - Barbara Turchi
- Department of Veterinary Sciences, University of Pisa, Viale delle Piagge, 2, 56124 Pisa, Italy
| | - Domenico Cerri
- Department of Veterinary Sciences, University of Pisa, Viale delle Piagge, 2, 56124 Pisa, Italy
| | - Matteo Ricchi
- Istituto Zooprofilattico Sperimentale dell'Emilia Romagna e della Lombardia, Sezione di Piacenza-Gariga, Strada della Faggiola 1, 29027, National Reference Centre for Paratuberculosis, Gariga di Podenzano, (PC), Italy
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8
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Barkema HW, Orsel K, Nielsen SS, Koets AP, Rutten VPMG, Bannantine JP, Keefe GP, Kelton DF, Wells SJ, Whittington RJ, Mackintosh CG, Manning EJ, Weber MF, Heuer C, Forde TL, Ritter C, Roche S, Corbett CS, Wolf R, Griebel PJ, Kastelic JP, De Buck J. Knowledge gaps that hamper prevention and control of Mycobacterium avium subspecies paratuberculosis infection. Transbound Emerg Dis 2017; 65 Suppl 1:125-148. [PMID: 28941207 DOI: 10.1111/tbed.12723] [Citation(s) in RCA: 77] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2017] [Indexed: 12/17/2022]
Abstract
In the last decades, many regional and country-wide control programmes for Johne's disease (JD) were developed due to associated economic losses, or because of a possible association with Crohn's disease. These control programmes were often not successful, partly because management protocols were not followed, including the introduction of infected replacement cattle, because tests to identify infected animals were unreliable, and uptake by farmers was not high enough because of a perceived low return on investment. In the absence of a cure or effective commercial vaccines, control of JD is currently primarily based on herd management strategies to avoid infection of cattle and restrict within-farm and farm-to-farm transmission. Although JD control programmes have been implemented in most developed countries, lessons learned from JD prevention and control programmes are underreported. Also, JD control programmes are typically evaluated in a limited number of herds and the duration of the study is less than 5 year, making it difficult to adequately assess the efficacy of control programmes. In this manuscript, we identify the most important gaps in knowledge hampering JD prevention and control programmes, including vaccination and diagnostics. Secondly, we discuss directions that research should take to address those knowledge gaps.
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Affiliation(s)
- H W Barkema
- Department of Production Animal Health, Faculty of Veterinary Medicine, University of Calgary, Calgary, AB, Canada
| | - K Orsel
- Department of Production Animal Health, Faculty of Veterinary Medicine, University of Calgary, Calgary, AB, Canada
| | - S S Nielsen
- University of Copenhagen, Copenhagen, Denmark
| | - A P Koets
- Utrecht University, Utrecht, The Netherlands.,Wageningen Bioveterinary Research, Wageningen, The Netherlands
| | - V P M G Rutten
- Utrecht University, Utrecht, The Netherlands.,Department of Veterinary Tropical Diseases, Faculty of Veterinary Science, University of Pretoria, Private Bag X04, Onderstepoort, 0110, South Africa
| | | | - G P Keefe
- University of Prince Edward Island, Charlottetown, Canada
| | | | - S J Wells
- University of Minnesota, Minneapolis, MN, USA
| | | | | | | | - M F Weber
- GD Animal Health, Deventer, The Netherlands
| | - C Heuer
- Massey University, Palmerston North, New Zealand
| | | | - C Ritter
- Department of Production Animal Health, Faculty of Veterinary Medicine, University of Calgary, Calgary, AB, Canada
| | - S Roche
- University of Guelph, Guelph, Canada
| | - C S Corbett
- Department of Production Animal Health, Faculty of Veterinary Medicine, University of Calgary, Calgary, AB, Canada
| | - R Wolf
- Amt der Steiermärkischen Landesregierung, Graz, Austria
| | | | - J P Kastelic
- Department of Production Animal Health, Faculty of Veterinary Medicine, University of Calgary, Calgary, AB, Canada
| | - J De Buck
- Department of Production Animal Health, Faculty of Veterinary Medicine, University of Calgary, Calgary, AB, Canada
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9
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Möbius P, Liebler-Tenorio E, Hölzer M, Köhler H. Evaluation of associations between genotypes of Mycobacterium avium subsp. paratuberculsis and presence of intestinal lesions characteristic of paratuberculosis. Vet Microbiol 2017; 201:188-194. [PMID: 28284609 DOI: 10.1016/j.vetmic.2017.01.026] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2016] [Revised: 12/15/2016] [Accepted: 01/18/2017] [Indexed: 10/20/2022]
Abstract
Mycobacterium avium subsp. paratuberculosis (MAP) is the causative agent of paratuberculosis affecting ruminants worldwide. Depending on the MAP-Type (MAP-C or MAP-S, cattle or sheep type), strains differ in virulence and host preference. There is not yet any strong evidence indicating that individual field strains of the same MAP-subgroup exhibit differences in virulence. The aim of this study was to evaluate a potential association between the genotype of individual field strains belonging to the MAP-C group and the presence of macroscopic intestinal lesions characteristic of paratuberculosis in the infected animals. 88 MAP-C isolates were sampled from clinically healthy cows at slaughter. Cows were grouped as A (n=46) with, and B (n=42) without macroscopic intestinal lesions. Sampled cows from both the A and B groups came from different farms and had a similar age distribution. MAP isolates were characterized by MIRU-VNTR and IS900-RFLP analysis. Resulting genotypes were examined for an association with the presence of macroscopic intestinal lesions characteristic of paratuberculosis. MAP isolates from groups A and B exhibited similar strain diversity: 20 and 18 combined genotypes, altogether 32 genotypes. Six of these genotypes were detected in both groups. Although no association was found between individual combined genotypes and presence of macroscopic intestinal lesions, IS900-RFLP-(BstEII)-Type-C1 (the most common type worldwide) was found more often in group A (p<0.01). The data give only weak indication for the existence of differences in virulence among MAP-cattle type isolates. Differences in the development and severity of lesions may rather depend on unknown host factors or inoculation dose. Virulence properties of IS900-RFLP-(BstEII)-Type-C1 isolates should be examined in more detail.
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Affiliation(s)
- Petra Möbius
- Friedrich-Loeffler-Institut (Federal Research Institute for Animal Health), Institute of Molecular Pathogenesis, 07743 Jena, Naumburger Str. 96a, Germany.
| | - Elisabeth Liebler-Tenorio
- Friedrich-Loeffler-Institut (Federal Research Institute for Animal Health), Institute of Molecular Pathogenesis, 07743 Jena, Naumburger Str. 96a, Germany.
| | - Martin Hölzer
- Friedrich Schiller University Jena, Faculty of Mathematics and Computer Science, RNA Bioinformatics and High Throughput Analysis, 07743 Jena, Leutragraben 1, Germany.
| | - Heike Köhler
- Friedrich-Loeffler-Institut (Federal Research Institute for Animal Health), Institute of Molecular Pathogenesis, 07743 Jena, Naumburger Str. 96a, Germany.
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10
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Davidson FW, Ahlstrom C, De Buck J, Whitney HG, Tahlan K. Examination of Mycobacterium avium subspecies paratuberculosis mixed genotype infections in dairy animals using a whole genome sequencing approach. PeerJ 2016; 4:e2793. [PMID: 27994984 PMCID: PMC5160890 DOI: 10.7717/peerj.2793] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2016] [Accepted: 11/14/2016] [Indexed: 11/20/2022] Open
Abstract
Many pathogenic mycobacteria are known to cause severe disease in humans and animals. M. avium subspecies paratuberculosis (Map) is the causative agent of Johne’s disease—a chronic wasting disease affecting ruminants such as cattle and sheep, responsible for significant economic losses in the dairy and beef industries. Due to the lack of treatment options or effective vaccines, mitigating losses can be difficult. In addition, the early stages of Map infection may occur in asymptomatic hosts that continue to shed viable bacteria in their faeces, leading to the infection of other healthy animals. Using multi-locus short sequence repeat (ML-SSR) analysis we previously reported that individual Johne’s positive dairy cattle from farms across the island of Newfoundland were infected by Map with multiple SSR-types simultaneously. The occurrence of multiple mixed genotype infections has the potential to change pathogen and disease dynamics as well as reduce the efficacy of treatments and vaccines. Therefore, we conducted whole genome sequencing (WGS) and single nucleotide polymorphism (SNP) analysis on a subset of these isolates for a more in-depth examination. We also implemented a PCR assay using two discriminatory SNPs and demonstrated the incidence of a mixed infection by three genotypically diverse Map isolates in a single animal. In addition, results show that WGS and SNP analysis can provide a better understanding of the relationship between Map isolates from individual and different animals. In the future such studies on the occurrence of mixed genotype infections could potentially lead to the identification of variable pathogenicity of different genotypes and allow for better tracking of Map isolates for epidemiological studies.
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Affiliation(s)
- Fraser W Davidson
- Department of Biology, Memorial University of Newfoundland , St. John's , NL , Canada
| | - Christina Ahlstrom
- Faculty of Veterinary Medicine, University of Calgary , Calgary , AB , Canada
| | - Jeroen De Buck
- Faculty of Veterinary Medicine, University of Calgary , Calgary , AB , Canada
| | - Hugh G Whitney
- Department of Biology, Memorial University of Newfoundland , St. John's , NL , Canada
| | - Kapil Tahlan
- Department of Biology, Memorial University of Newfoundland , St. John's , NL , Canada
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11
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Li L, Katani R, Schilling M, Kapur V. Molecular Epidemiology ofMycobacterium aviumsubsp.paratuberculosison Dairy Farms. Annu Rev Anim Biosci 2016; 4:155-76. [DOI: 10.1146/annurev-animal-021815-111304] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Lingling Li
- Department of Veterinary and Biomedical Sciences, The Pennsylvania State University, University Park, Pennsylvania 16802; , , ,
| | - Robab Katani
- Department of Veterinary and Biomedical Sciences, The Pennsylvania State University, University Park, Pennsylvania 16802; , , ,
| | - Megan Schilling
- Department of Veterinary and Biomedical Sciences, The Pennsylvania State University, University Park, Pennsylvania 16802; , , ,
| | - Vivek Kapur
- Department of Veterinary and Biomedical Sciences, The Pennsylvania State University, University Park, Pennsylvania 16802; , , ,
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12
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Fawzy A, Zschöck M, Ewers C, Eisenberg T. New polymorphisms within the variable number tandem repeat (VNTR) 7 locus of Mycobacterium avium subsp. paratuberculosis. Mol Cell Probes 2016; 30:132-7. [PMID: 26872530 DOI: 10.1016/j.mcp.2016.02.002] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2015] [Revised: 02/04/2016] [Accepted: 02/04/2016] [Indexed: 02/07/2023]
Abstract
Variable number tandem repeat (VNTR) is a frequently employed typing method of Mycobacterium avium paratuberculosis (MAP) isolates. Based on whole genome sequencing in a previous study, allelic diversity at some VNTR loci seems to over- or under-estimate the actual phylogenetic variance among isolates. Interestingly, two closely related isolates on one farm showed polymorphism at the VNTR 7 locus, raising concerns about the misleading role that it might play in genotyping. We aimed to investigate the underlying basis of VNTR 7-polymorphism by analyzing sequence data for published genomes and field isolates of MAP and other M. avium complex (MAC) members. In contrast to MAP strains from cattle, strains from sheep displayed an "imperfect" repeat within VNTR 7, which was identical to respective allele types in other MAC genomes. Subspecies- and strain-specific single nucleotide polymorphisms (SNPs) and two novel (16 and 56 bp) repeats were detected. Given the combination of the three existing repeats, there are at least five different patterns for VNTR 7. The present findings highlight a higher polymorphism and probable instability of VNTR 7 locus that needs to be considered and challenged in future studies. Until then, sequencing of this locus in future studies is important to correctly assign the underlying allele types.(1).
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Affiliation(s)
- Ahmad Fawzy
- Justus Liebig Universität, Institut für Hygiene und Infektionskrankheiten der Tiere, Frankfurter Straße 85-89 35392, Gießen, Germany; Landesbetrieb Hessisches Landeslabor, Schubertstraße 60 D-35392 Gießen, Germany; Cairo University, Faculty of Veterinary Medicine, Department of Medicine and Infectious Diseases, Giza Square 12211, Egypt.
| | - Michael Zschöck
- Landesbetrieb Hessisches Landeslabor, Schubertstraße 60 D-35392 Gießen, Germany
| | - Christa Ewers
- Justus Liebig Universität, Institut für Hygiene und Infektionskrankheiten der Tiere, Frankfurter Straße 85-89 35392, Gießen, Germany
| | - Tobias Eisenberg
- Justus Liebig Universität, Institut für Hygiene und Infektionskrankheiten der Tiere, Frankfurter Straße 85-89 35392, Gießen, Germany; Landesbetrieb Hessisches Landeslabor, Schubertstraße 60 D-35392 Gießen, Germany
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13
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Genetic diversity of Mycobacterium avium subspecies paratuberculosis and the influence of strain type on infection and pathogenesis: a review. Vet Res 2015; 46:64. [PMID: 26092160 PMCID: PMC4473831 DOI: 10.1186/s13567-015-0203-2] [Citation(s) in RCA: 71] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2014] [Accepted: 01/16/2015] [Indexed: 12/12/2022] Open
Abstract
Mycobacterium avium subspecies paratuberculosis (Map) is an important pathogen that causes a chronic, progressive granulomatous enteritis known as Johne's disease or paratuberculosis. The disease is endemic in many parts of the world and responsible for considerable losses to the livestock and associated industries. Diagnosis and control are problematic, due mostly to the long incubation period of the disease when infected animals show no clinical signs and are difficult to detect, and the ability of the organism to survive and persist in the environment. The existence of phenotypically distinct strains of Map has been known since the 1930s but the genetic differentiation of Map strain types has been challenging and only recent technologies have proven sufficiently discriminative for strain comparisons, tracing the sources of infection and epidemiological studies. It is important to understand the differences that exist between Map strains and how they influence both development and transmission of disease. This information is required to develop improved diagnostics and effective vaccines for controlling Johne's disease. Here I review the current classification of Map strain types, the sources of the genetic variability within strains, growth characteristics and epidemiological traits associated with strain type and the influence of strain type on infection and pathogenicity.
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14
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Podder MP, Banfield SE, Keefe GP, Whitney HG, Tahlan K. Typing of Mycobacterium avium subspecies paratuberculosis isolates from Newfoundland using fragment analysis. PLoS One 2015; 10:e0126071. [PMID: 25927612 PMCID: PMC4415927 DOI: 10.1371/journal.pone.0126071] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2014] [Accepted: 03/28/2015] [Indexed: 01/12/2023] Open
Abstract
Short Sequence Repeat (SSR) typing of Mycobacterium avium subspecies paratuberculosis (Map) isolates is one of the most commonly used method for genotyping this pathogen. Currently used techniques have challenges in analyzing mononucleotide repeats >15 bp, which include some of the Map SSRs. Fragment analysis is a relatively simple technique, which can accurately measure the size of DNA fragments and can be used to calculate the repeat length of the target SSR loci. In the present study, fragment analysis was used to analyze 4 Map SSR loci known to provide sufficient discriminatory power to determine the relationship between Map isolates. Eighty-five Map isolates from 18 animals from the island of Newfoundland were successfully genotyped using fragment analysis. To the best of our knowledge, this is the first report on Map SSR diversity from Newfoundland dairy farms. Previously unreported Map SSR-types or combinations were also identified during the course of the described work. In addition, multiple Map SSR-types were isolated from a single animal in many cases, which is not a common finding.
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Affiliation(s)
- Milka P. Podder
- Department of Biology, Memorial University of Newfoundland, St. John’s, Newfoundland and Labrador, Canada
| | - Susan E. Banfield
- Department of Biology, Memorial University of Newfoundland, St. John’s, Newfoundland and Labrador, Canada
| | - Greg P. Keefe
- Department of Health Management, Atlantic Veterinary College, University of Prince Edward Island, Charlottetown, Prince Edward Island, Canada
| | - Hugh G. Whitney
- Animal Health Division, Newfoundland and Labrador Department of Natural Resources, St. John's, Newfoundland and Labrador, Canada
- * E-mail: (KT); (HGW)
| | - Kapil Tahlan
- Department of Biology, Memorial University of Newfoundland, St. John’s, Newfoundland and Labrador, Canada
- * E-mail: (KT); (HGW)
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15
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Fernández M, Delgado L, Sevilla IA, Fuertes M, Castaño P, Royo M, Ferreras MC, Benavides J, Pérez V. Virulence attenuation of a Mycobacterium avium subspecies paratuberculosis S-type strain prepared from intestinal mucosa after bacterial culture. Evaluation in an experimental ovine model. Res Vet Sci 2015; 99:180-7. [DOI: 10.1016/j.rvsc.2015.02.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2014] [Revised: 01/19/2015] [Accepted: 02/06/2015] [Indexed: 10/24/2022]
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16
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Amin AS, Hsu CY, Darwish SF, Ghosh P, AbdEl-Fatah EM, Behour TS, Talaat AM. Ecology and genomic features of infection with Mycobacterium avium subspecies paratuberculosis in Egypt. MICROBIOLOGY-SGM 2015; 161:807-18. [PMID: 25667007 DOI: 10.1099/mic.0.000051] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/08/2014] [Accepted: 02/02/2015] [Indexed: 01/27/2023]
Abstract
Mycobacterium avium subspecies paratuberculosis (M. paratuberculosis) is the causative agent of paratuberculosis, or Johne's disease, in cattle, with potential involvement in cases of Crohn's disease in humans. Johne's disease is found worldwide and is economically important for both beef and dairy industries. In an effort to characterize this important infection in Egypt, we analysed the ecological and genomic features of recent isolates of M. paratuberculosis. In this report, we examined 26 Holstein dairy herds distributed throughout Egypt, from 2010 to 2013. Using PCR analysis of faecal samples, we estimated a mean herd-level prevalence of 65.4 %, with animal-level infection that reached a mean of 13.6 % among animals suffering from diarrhoea. Whole genome sequencing of field isolates identified numerous single nucleotide polymorphisms among field isolates relative to the standard M. paratuberculosis K10 genome. Interestingly, the virulence of M. paratuberculosis isolates from Egypt revealed diverse virulence phenotypes in the murine model of paratuberculosis, with significant differences in tissue colonization, particularly during the chronic stage of infection. Overall, our analysis confirmed that Johne's disease is a newly identified problem in Egypt and indicated that M. paratuberculosis has potentially diverse genotypes that impact its virulence. Further ecological mapping and genomic analysis of M. paratuberculosis will enhance our understanding of the transmission and evolutionary dynamics of this pathogen under natural field conditions.
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Affiliation(s)
- Adel S Amin
- Biotechnology Research Unit, Animal Reproduction Research Institute (ARRI), Giza, Egypt
| | - Chung-Yi Hsu
- Department of Pathobiological Sciences, University of Wisconsin-Madison, Madison, WI, USA
| | - Samah F Darwish
- Biotechnology Research Unit, Animal Reproduction Research Institute (ARRI), Giza, Egypt
| | - Pallab Ghosh
- Department of Pathobiological Sciences, University of Wisconsin-Madison, Madison, WI, USA
| | - Eman M AbdEl-Fatah
- Biotechnology Research Unit, Animal Reproduction Research Institute (ARRI), Giza, Egypt
| | - Tahani S Behour
- Biotechnology Research Unit, Animal Reproduction Research Institute (ARRI), Giza, Egypt
| | - Adel M Talaat
- Department of Pathobiological Sciences, University of Wisconsin-Madison, Madison, WI, USA Department of Food Hygiene and Control, Faculty of Veterinary Medicine Cairo University, Giza, Egypt
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Oakey J, Gavey L, Singh SV, Platell J, Waltisbuhl D. Variable-number tandem repeats genotyping used to aid and inform management strategies for a bovine Johne’s disease incursion in tropical and subtropical Australia. J Vet Diagn Invest 2014; 26:651-7. [DOI: 10.1177/1040638714547257] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
The application of variable-number tandem repeats (VNTR) genotyping of Mycobacterium avium subsp. paratuberculosis isolates to assist in investigating incidents of bovine Johne’s disease in a low-prevalence region of Australia is described in the current study. Isolates from a response to detection of bovine Johne’s disease in Queensland were compared with strains from national and international sources. The tandem application of mycobacterial interspersed repetitive unit (MIRU) and multilocus short sequence repeats (MLSSR) genotyping identified 2 strains, 1 that infected cattle on multiple properties with trace-forward histories from a common infected property, and 1 genotypically different strain recovered from a single property. The former strain showed an identical genotype to an isolate from India. Neither strain showed a genotypic link to regions of Australia with a higher prevalence of the disease. Genotyping has indicated incursions from 2 independent sources. This intelligence has informed investigations into potential routes of entry and the soundness of ongoing control measures, and supported strategy and policy decisions regarding management of Mycobacterium avium subsp. paratuberculosis incursions for Queensland.
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Affiliation(s)
- Jane Oakey
- Biosecurity Sciences Laboratory, Biosecurity Queensland, Queensland Department of Agriculture, Fisheries and Forestry, Coopers Plains, Queensland, Australia (Oakey, Platell, Waltisbuhl)
- Biosecurity Queensland, Queensland Department of Agriculture, Fisheries and Forestry, Toowoomba, Queensland, Australia (Gavey)
- Central Institute for Research on Goats, Makhdoom, District of Mathura, Uttar Pradesh, India (Singh)
| | - Lawrence Gavey
- Biosecurity Sciences Laboratory, Biosecurity Queensland, Queensland Department of Agriculture, Fisheries and Forestry, Coopers Plains, Queensland, Australia (Oakey, Platell, Waltisbuhl)
- Biosecurity Queensland, Queensland Department of Agriculture, Fisheries and Forestry, Toowoomba, Queensland, Australia (Gavey)
- Central Institute for Research on Goats, Makhdoom, District of Mathura, Uttar Pradesh, India (Singh)
| | - Shoor Vir Singh
- Biosecurity Sciences Laboratory, Biosecurity Queensland, Queensland Department of Agriculture, Fisheries and Forestry, Coopers Plains, Queensland, Australia (Oakey, Platell, Waltisbuhl)
- Biosecurity Queensland, Queensland Department of Agriculture, Fisheries and Forestry, Toowoomba, Queensland, Australia (Gavey)
- Central Institute for Research on Goats, Makhdoom, District of Mathura, Uttar Pradesh, India (Singh)
| | - Joanne Platell
- Biosecurity Sciences Laboratory, Biosecurity Queensland, Queensland Department of Agriculture, Fisheries and Forestry, Coopers Plains, Queensland, Australia (Oakey, Platell, Waltisbuhl)
- Biosecurity Queensland, Queensland Department of Agriculture, Fisheries and Forestry, Toowoomba, Queensland, Australia (Gavey)
- Central Institute for Research on Goats, Makhdoom, District of Mathura, Uttar Pradesh, India (Singh)
| | - David Waltisbuhl
- Biosecurity Sciences Laboratory, Biosecurity Queensland, Queensland Department of Agriculture, Fisheries and Forestry, Coopers Plains, Queensland, Australia (Oakey, Platell, Waltisbuhl)
- Biosecurity Queensland, Queensland Department of Agriculture, Fisheries and Forestry, Toowoomba, Queensland, Australia (Gavey)
- Central Institute for Research on Goats, Makhdoom, District of Mathura, Uttar Pradesh, India (Singh)
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18
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Atreya R, Bülte M, Gerlach GF, Goethe R, Hornef MW, Köhler H, Meens J, Möbius P, Roeb E, Weiss S. Facts, myths and hypotheses on the zoonotic nature of Mycobacterium avium subspecies paratuberculosis. Int J Med Microbiol 2014; 304:858-67. [PMID: 25128370 DOI: 10.1016/j.ijmm.2014.07.006] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Mycobacterium avium subspecies paratuberculosis (MAP) is the causative agent of paratuberculosis (Johne's disease [JD]), a chronic granulomatous enteritis in ruminants. JD is one of the most widespread bacterial diseases of domestic animals with significant economic impact. The histopathological picture of JD resembles that of Crohn's disease (CD), a human chronic inflammatory bowel disease of still unresolved aetiology. An aetiological relevance of MAP for CD has been proposed. This and the ambiguity of other published epidemiological findings raise the question whether MAP represents a zoonotic agent. In this review, we will discuss evidence that MAP has zoonotic capacity.
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Affiliation(s)
- Raja Atreya
- Medical Clinic 1, University of Erlangen-Nuermberg, Ulmenweg 18, D-91054 Erlangen, Germany
| | - Michael Bülte
- Institute of Veterinary Food Science, Faculty of Veterinary Medicine, Justus Liebig University, Frankfurter Straße 92, 35392 Gießen, Germany
| | | | - Ralph Goethe
- Institute for Microbiology, Department of Infectious Diseases, University of Veterinary Medicine Hannover, Bischofsholer Damm 15, 30173 Hannover, Germany.
| | - Mathias W Hornef
- Department of Microbiology, Hannover Medical School, Carl-Neuberg-Str. 1, 30625 Hannover, Germany
| | - Heike Köhler
- Institute of Molecular Pathogenesis, Friedrich-Loeffler-Institut (Federal Research Institute for Animal Health), Naumburger Str. 96a, 07743 Jena, Germany
| | - Jochen Meens
- Institute for Microbiology, Department of Infectious Diseases, University of Veterinary Medicine Hannover, Bischofsholer Damm 15, 30173 Hannover, Germany
| | - Petra Möbius
- Institute of Molecular Pathogenesis, Friedrich-Loeffler-Institut (Federal Research Institute for Animal Health), Naumburger Str. 96a, 07743 Jena, Germany
| | - Elke Roeb
- Justus-Liebig-University Giessen, Department of Gastroenterology, Klinikstr.33, 35392 Giessen, Germany
| | - Siegfried Weiss
- Helmholtz Centre for Infection Research, Molecular Immunology, Inhoffenstraße 7, 38124 Braunschweig, Germany
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Improved short-sequence-repeat genotyping of Mycobacterium avium subsp. paratuberculosis by using matrix-assisted laser desorption ionization-time of flight mass spectrometry. Appl Environ Microbiol 2013; 80:534-9. [PMID: 24212568 DOI: 10.1128/aem.03212-13] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Accurate sequence analysis of mononucleotide repeat regions is difficult, complicating the use of short sequence repeats (SSRs) as a tool for bacterial strain discrimination. Although multiple SSR loci in the genome of Mycobacterium avium subsp. paratuberculosis allow genotyping of M. avium subsp. paratuberculosis isolates with high discriminatory power, further characterization of the most discriminatory loci is limited due to inherent difficulties in sequencing mononucleotide repeats. Here, a method was evaluated using matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) as an alternative to Sanger sequencing to further differentiate the dominant mycobacterial interspersed repetitive-unit (MIRU)-variable-number tandem-repeat (VNTR) M. avium subsp. paratuberculosis type (n = 37) in Canadian dairy herds by targeting a highly discriminatory mononucleotide SSR locus. First, PCR-amplified DNA was digested with two restriction enzymes to yield a sufficiently small fragment containing the SSR locus. Second, MALDI-TOF MS was performed to identify the mass, and thus repeat length, of the target. Sufficiently intense, discriminating spectra were obtained to determine repeat lengths up to 15, an improvement over the limit of 11 using traditional sequencing techniques. Comparison to synthetic oligonucleotides and Sanger sequencing results confirmed a valid and reproducible assay that increased discrimination of the dominant M. avium subsp. paratuberculosis MIRU-VNTR type. Thus, MALDI-TOF MS was a reliable, fast, and automatable technique to accurately resolve M. avium subsp. paratuberculosis genotypes based on SSRs.
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