Comparative analysis of Mycobacterium avium subsp. paratuberculosis isolates from cattle, sheep and goats by short sequence repeat and pulsed-field gel ... View Full Text


Ontology type: schema:ScholarlyArticle      Open Access: True


Article Info

DATE

2008-12

AUTHORS

Iker Sevilla, Lingling Li, Alongkorn Amonsin, Joseba M Garrido, Maria V Geijo, Vivek Kapur, Ramón A Juste

ABSTRACT

BACKGROUND: Mycobacterium avium subsp. paratuberculosis (Map) causes the chronic enteritis called paratuberculosis mainly in cattle, sheep and goats. Evidences that point out an association between Map and Crohn's Disease in humans are increasing. Strain differentiation among Map isolates has proved to be difficult and has limited the study of the molecular epidemiology of paratuberculosis. In order to asses the usefulness of the PCR based short sequence repeat (SSR) analysis of locus 1 and locus 8 in the epidemiological tracing of paratuberculosis strains we here compare for the first time the results of SSR and SnaBI-SpeI pulsed-field gel electrophoresis (PFGE) typing methods in a set of 268 Map isolates from different hosts (cattle, sheep, goats, bison, deer and wild boar). RESULTS: A total of nineteen different multi-locus SSR (SSR1_SSR8) types were identified amongst the 268 isolates compared to the 37 multiplex profiles differentiated by the SnaBI-SpeI PFGE. SSR type 7_4 was the predominant genotype (51.2% of all isolates and 54.3% of cattle isolates), but combined with PFGE results the abundance of the most prevalent genotype (7_4&{2-1}) dropped down to 37.7%. SSR types 7_3 and 14_3 were significantly spread amongst isolates recovered from small ruminants. The comparison of SSR1_SSR8 and SnaBI-SpeI PFGE typing of these isolates has shown that both methods perform at similar discriminatory level. These were 0.691 and 0.693, respectively for SSR and PFGE as indicated Simpson's Index of Diversity, and 0.82 when calculated for combined SSR and PFGE genotypes. Overall, SSR1_SSR8 analysis seemed to detect higher levels of within-farm strain diversity and seemed to give higher year-related information. Combination of both typing methods revealed 20 multi-type farms out of the 33 bovine farms studied with more than one isolate. CONCLUSION: The particular SSR and PFGE typing approaches described here are in general agreement but they showed some discrepancies that might reflect differing evolutionary processes of Map strains. Both methods are able to reciprocally complement their results and neither should be replaced with the other if sufficient material and time is available. Overall, the results of our comparative analyses suggest that, based on current methodologies available, a combined approach that includes SSR and PFGE seems to provide the highest level of discrimination for Map strain typing with meaningful epidemiological information. More... »

PAGES

204

Identifiers

URI

http://scigraph.springernature.com/pub.10.1186/1471-2180-8-204

DOI

http://dx.doi.org/10.1186/1471-2180-8-204

DIMENSIONS

https://app.dimensions.ai/details/publication/pub.1049554618

PUBMED

https://www.ncbi.nlm.nih.gov/pubmed/19032737


Indexing Status Check whether this publication has been indexed by Scopus and Web Of Science using the SN Indexing Status Tool
Incoming Citations Browse incoming citations for this publication using opencitations.net

JSON-LD is the canonical representation for SciGraph data.

TIP: You can open this SciGraph record using an external JSON-LD service: JSON-LD Playground Google SDTT

[
  {
    "@context": "https://springernature.github.io/scigraph/jsonld/sgcontext.json", 
    "about": [
      {
        "id": "http://purl.org/au-research/vocabulary/anzsrc-for/2008/0707", 
        "inDefinedTermSet": "http://purl.org/au-research/vocabulary/anzsrc-for/2008/", 
        "name": "Veterinary Sciences", 
        "type": "DefinedTerm"
      }, 
      {
        "id": "http://purl.org/au-research/vocabulary/anzsrc-for/2008/07", 
        "inDefinedTermSet": "http://purl.org/au-research/vocabulary/anzsrc-for/2008/", 
        "name": "Agricultural and Veterinary Sciences", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Animals", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Bacterial Typing Techniques", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Cattle", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Electrophoresis, Gel, Pulsed-Field", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Goats", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Microsatellite Repeats", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Mycobacterium avium subsp. paratuberculosis", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Sheep", 
        "type": "DefinedTerm"
      }
    ], 
    "author": [
      {
        "affiliation": {
          "name": [
            "Instituto Vasco de Investigaci\u00f3n y Desarrollo Agrario (NEIKER), Berreaga, 1, 48160, Derio, Bizkaia, Spain"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Sevilla", 
        "givenName": "Iker", 
        "id": "sg:person.011546513207.12", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.011546513207.12"
        ], 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "alternateName": "University of Minnesota", 
          "id": "https://www.grid.ac/institutes/grid.17635.36", 
          "name": [
            "Departments of Microbiology and Biomedical Genomics Center, University of Minnesota, 55108, MN, USA"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Li", 
        "givenName": "Lingling", 
        "id": "sg:person.0634544476.38", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0634544476.38"
        ], 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "alternateName": "University of Minnesota", 
          "id": "https://www.grid.ac/institutes/grid.17635.36", 
          "name": [
            "Departments of Microbiology and Biomedical Genomics Center, University of Minnesota, 55108, MN, USA"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Amonsin", 
        "givenName": "Alongkorn", 
        "id": "sg:person.01002436054.12", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01002436054.12"
        ], 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "name": [
            "Instituto Vasco de Investigaci\u00f3n y Desarrollo Agrario (NEIKER), Berreaga, 1, 48160, Derio, Bizkaia, Spain"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Garrido", 
        "givenName": "Joseba M", 
        "id": "sg:person.01353250306.86", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01353250306.86"
        ], 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "name": [
            "Instituto Vasco de Investigaci\u00f3n y Desarrollo Agrario (NEIKER), Berreaga, 1, 48160, Derio, Bizkaia, Spain"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Geijo", 
        "givenName": "Maria V", 
        "id": "sg:person.0614533757.20", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0614533757.20"
        ], 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "alternateName": "University of Minnesota", 
          "id": "https://www.grid.ac/institutes/grid.17635.36", 
          "name": [
            "Departments of Microbiology and Biomedical Genomics Center, University of Minnesota, 55108, MN, USA"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Kapur", 
        "givenName": "Vivek", 
        "id": "sg:person.0631114411.35", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0631114411.35"
        ], 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "name": [
            "Instituto Vasco de Investigaci\u00f3n y Desarrollo Agrario (NEIKER), Berreaga, 1, 48160, Derio, Bizkaia, Spain"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Juste", 
        "givenName": "Ram\u00f3n A", 
        "id": "sg:person.01323473621.85", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01323473621.85"
        ], 
        "type": "Person"
      }
    ], 
    "citation": [
      {
        "id": "https://doi.org/10.1006/mcpr.1998.0194", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1004614084"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1128/jcm.42.4.1694-1702.2004", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1007539369"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1111/j.1751-0813.2000.tb10590.x", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1009242118"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1128/jcm.42.11.5345-5348.2004", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1012828596"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1128/jcm.41.5.2015-2026.2003", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1015677815"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1111/j.1751-0813.2001.tb11980.x", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1017927696"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1111/j.1365-2672.2005.02598.x", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1018328164"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1111/j.1365-2672.2005.02598.x", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1018328164"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1128/jcm.01801-07", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1020867250"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1016/s1473-3099(03)00724-2", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1021106696"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1016/s1473-3099(03)00724-2", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1021106696"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1186/1471-2180-7-18", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1021601027", 
          "https://doi.org/10.1186/1471-2180-7-18"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1128/jcm.42.4.1703-1712.2004", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1023894978"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1016/s0167-7012(99)00091-3", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1028102825"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1097/mog.0b013e3282f1dcc4", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1031906399"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1097/mog.0b013e3282f1dcc4", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1031906399"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1128/jcm.43.5.2111-2117.2005", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1031939720"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1186/1751-0147-46-13", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1035595166", 
          "https://doi.org/10.1186/1751-0147-46-13"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1128/aem.71.12.8934-8936.2005", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1039577046"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1111/j.1751-0813.1997.tb11259.x", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1039619301"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1371/journal.pone.0002537", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1044323595"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1016/j.micinf.2005.12.003", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1045052246"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1016/j.ijid.2008.06.034", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1047075561"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1128/jcm.40.5.1798-1804.2002", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1047563327"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1128/jcm.00476-07", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1050579832"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1016/j.vetmic.2006.01.008", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1053061731"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.20506/rst.20.1.1274", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1068791838"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.20506/rst.20.1.1274", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1068791838"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.20506/rst.24.3.1634", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1068792198"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.20506/rst.24.3.1634", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1068792198"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.4315/0362-028x-68.5.966", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1072509254"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://app.dimensions.ai/details/publication/pub.1074693565", 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://app.dimensions.ai/details/publication/pub.1078408327", 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://app.dimensions.ai/details/publication/pub.1082954029", 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.17221/5631-vetmed", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1100967193"
        ], 
        "type": "CreativeWork"
      }
    ], 
    "datePublished": "2008-12", 
    "datePublishedReg": "2008-12-01", 
    "description": "BACKGROUND: Mycobacterium avium subsp. paratuberculosis (Map) causes the chronic enteritis called paratuberculosis mainly in cattle, sheep and goats. Evidences that point out an association between Map and Crohn's Disease in humans are increasing. Strain differentiation among Map isolates has proved to be difficult and has limited the study of the molecular epidemiology of paratuberculosis. In order to asses the usefulness of the PCR based short sequence repeat (SSR) analysis of locus 1 and locus 8 in the epidemiological tracing of paratuberculosis strains we here compare for the first time the results of SSR and SnaBI-SpeI pulsed-field gel electrophoresis (PFGE) typing methods in a set of 268 Map isolates from different hosts (cattle, sheep, goats, bison, deer and wild boar).\nRESULTS: A total of nineteen different multi-locus SSR (SSR1_SSR8) types were identified amongst the 268 isolates compared to the 37 multiplex profiles differentiated by the SnaBI-SpeI PFGE. SSR type 7_4 was the predominant genotype (51.2% of all isolates and 54.3% of cattle isolates), but combined with PFGE results the abundance of the most prevalent genotype (7_4&{2-1}) dropped down to 37.7%. SSR types 7_3 and 14_3 were significantly spread amongst isolates recovered from small ruminants. The comparison of SSR1_SSR8 and SnaBI-SpeI PFGE typing of these isolates has shown that both methods perform at similar discriminatory level. These were 0.691 and 0.693, respectively for SSR and PFGE as indicated Simpson's Index of Diversity, and 0.82 when calculated for combined SSR and PFGE genotypes. Overall, SSR1_SSR8 analysis seemed to detect higher levels of within-farm strain diversity and seemed to give higher year-related information. Combination of both typing methods revealed 20 multi-type farms out of the 33 bovine farms studied with more than one isolate.\nCONCLUSION: The particular SSR and PFGE typing approaches described here are in general agreement but they showed some discrepancies that might reflect differing evolutionary processes of Map strains. Both methods are able to reciprocally complement their results and neither should be replaced with the other if sufficient material and time is available. Overall, the results of our comparative analyses suggest that, based on current methodologies available, a combined approach that includes SSR and PFGE seems to provide the highest level of discrimination for Map strain typing with meaningful epidemiological information.", 
    "genre": "research_article", 
    "id": "sg:pub.10.1186/1471-2180-8-204", 
    "inLanguage": [
      "en"
    ], 
    "isAccessibleForFree": true, 
    "isPartOf": [
      {
        "id": "sg:journal.1024253", 
        "issn": [
          "1471-2180"
        ], 
        "name": "BMC Microbiology", 
        "type": "Periodical"
      }, 
      {
        "issueNumber": "1", 
        "type": "PublicationIssue"
      }, 
      {
        "type": "PublicationVolume", 
        "volumeNumber": "8"
      }
    ], 
    "name": "Comparative analysis of Mycobacterium avium subsp. paratuberculosis isolates from cattle, sheep and goats by short sequence repeat and pulsed-field gel electrophoresis typing", 
    "pagination": "204", 
    "productId": [
      {
        "name": "readcube_id", 
        "type": "PropertyValue", 
        "value": [
          "ec10ce23e4c49084f5481e318f483c78eaba5177eee44b0d42a8d73d37b05f5b"
        ]
      }, 
      {
        "name": "pubmed_id", 
        "type": "PropertyValue", 
        "value": [
          "19032737"
        ]
      }, 
      {
        "name": "nlm_unique_id", 
        "type": "PropertyValue", 
        "value": [
          "100966981"
        ]
      }, 
      {
        "name": "doi", 
        "type": "PropertyValue", 
        "value": [
          "10.1186/1471-2180-8-204"
        ]
      }, 
      {
        "name": "dimensions_id", 
        "type": "PropertyValue", 
        "value": [
          "pub.1049554618"
        ]
      }
    ], 
    "sameAs": [
      "https://doi.org/10.1186/1471-2180-8-204", 
      "https://app.dimensions.ai/details/publication/pub.1049554618"
    ], 
    "sdDataset": "articles", 
    "sdDatePublished": "2019-04-10T14:08", 
    "sdLicense": "https://scigraph.springernature.com/explorer/license/", 
    "sdPublisher": {
      "name": "Springer Nature - SN SciGraph project", 
      "type": "Organization"
    }, 
    "sdSource": "s3://com-uberresearch-data-dimensions-target-20181106-alternative/cleanup/v134/2549eaecd7973599484d7c17b260dba0a4ecb94b/merge/v9/a6c9fde33151104705d4d7ff012ea9563521a3ce/jats-lookup/v90/0000000001_0000000264/records_8660_00000508.jsonl", 
    "type": "ScholarlyArticle", 
    "url": "http://link.springer.com/10.1186%2F1471-2180-8-204"
  }
]
 

Download the RDF metadata as:  json-ld nt turtle xml License info

HOW TO GET THIS DATA PROGRAMMATICALLY:

JSON-LD is a popular format for linked data which is fully compatible with JSON.

curl -H 'Accept: application/ld+json' 'https://scigraph.springernature.com/pub.10.1186/1471-2180-8-204'

N-Triples is a line-based linked data format ideal for batch operations.

curl -H 'Accept: application/n-triples' 'https://scigraph.springernature.com/pub.10.1186/1471-2180-8-204'

Turtle is a human-readable linked data format.

curl -H 'Accept: text/turtle' 'https://scigraph.springernature.com/pub.10.1186/1471-2180-8-204'

RDF/XML is a standard XML format for linked data.

curl -H 'Accept: application/rdf+xml' 'https://scigraph.springernature.com/pub.10.1186/1471-2180-8-204'


 

This table displays all metadata directly associated to this object as RDF triples.

239 TRIPLES      21 PREDICATES      67 URIs      29 LITERALS      17 BLANK NODES

Subject Predicate Object
1 sg:pub.10.1186/1471-2180-8-204 schema:about N4c1ecd21ada84b6db5e12383493a2ede
2 N58e695c3a988470c9830eb67966346f7
3 N5fd4b0873b914404a7071f43918d4d70
4 N6ae5e7928ba345c38402c85b82f56a22
5 N79450dbb2c0b4def9bfba3e13b1e8f6b
6 N89acd406851e4d1997a5c6d0cdd69281
7 N9aa1428297d843ad90946f979a0e3066
8 Nd36f717d36e645ea8df2b1a8a70b0452
9 anzsrc-for:07
10 anzsrc-for:0707
11 schema:author Nc8600910caa24133899ffe2c40730fb7
12 schema:citation sg:pub.10.1186/1471-2180-7-18
13 sg:pub.10.1186/1751-0147-46-13
14 https://app.dimensions.ai/details/publication/pub.1074693565
15 https://app.dimensions.ai/details/publication/pub.1078408327
16 https://app.dimensions.ai/details/publication/pub.1082954029
17 https://doi.org/10.1006/mcpr.1998.0194
18 https://doi.org/10.1016/j.ijid.2008.06.034
19 https://doi.org/10.1016/j.micinf.2005.12.003
20 https://doi.org/10.1016/j.vetmic.2006.01.008
21 https://doi.org/10.1016/s0167-7012(99)00091-3
22 https://doi.org/10.1016/s1473-3099(03)00724-2
23 https://doi.org/10.1097/mog.0b013e3282f1dcc4
24 https://doi.org/10.1111/j.1365-2672.2005.02598.x
25 https://doi.org/10.1111/j.1751-0813.1997.tb11259.x
26 https://doi.org/10.1111/j.1751-0813.2000.tb10590.x
27 https://doi.org/10.1111/j.1751-0813.2001.tb11980.x
28 https://doi.org/10.1128/aem.71.12.8934-8936.2005
29 https://doi.org/10.1128/jcm.00476-07
30 https://doi.org/10.1128/jcm.01801-07
31 https://doi.org/10.1128/jcm.40.5.1798-1804.2002
32 https://doi.org/10.1128/jcm.41.5.2015-2026.2003
33 https://doi.org/10.1128/jcm.42.11.5345-5348.2004
34 https://doi.org/10.1128/jcm.42.4.1694-1702.2004
35 https://doi.org/10.1128/jcm.42.4.1703-1712.2004
36 https://doi.org/10.1128/jcm.43.5.2111-2117.2005
37 https://doi.org/10.1371/journal.pone.0002537
38 https://doi.org/10.17221/5631-vetmed
39 https://doi.org/10.20506/rst.20.1.1274
40 https://doi.org/10.20506/rst.24.3.1634
41 https://doi.org/10.4315/0362-028x-68.5.966
42 schema:datePublished 2008-12
43 schema:datePublishedReg 2008-12-01
44 schema:description BACKGROUND: Mycobacterium avium subsp. paratuberculosis (Map) causes the chronic enteritis called paratuberculosis mainly in cattle, sheep and goats. Evidences that point out an association between Map and Crohn's Disease in humans are increasing. Strain differentiation among Map isolates has proved to be difficult and has limited the study of the molecular epidemiology of paratuberculosis. In order to asses the usefulness of the PCR based short sequence repeat (SSR) analysis of locus 1 and locus 8 in the epidemiological tracing of paratuberculosis strains we here compare for the first time the results of SSR and SnaBI-SpeI pulsed-field gel electrophoresis (PFGE) typing methods in a set of 268 Map isolates from different hosts (cattle, sheep, goats, bison, deer and wild boar). RESULTS: A total of nineteen different multi-locus SSR (SSR1_SSR8) types were identified amongst the 268 isolates compared to the 37 multiplex profiles differentiated by the SnaBI-SpeI PFGE. SSR type 7_4 was the predominant genotype (51.2% of all isolates and 54.3% of cattle isolates), but combined with PFGE results the abundance of the most prevalent genotype (7_4&{2-1}) dropped down to 37.7%. SSR types 7_3 and 14_3 were significantly spread amongst isolates recovered from small ruminants. The comparison of SSR1_SSR8 and SnaBI-SpeI PFGE typing of these isolates has shown that both methods perform at similar discriminatory level. These were 0.691 and 0.693, respectively for SSR and PFGE as indicated Simpson's Index of Diversity, and 0.82 when calculated for combined SSR and PFGE genotypes. Overall, SSR1_SSR8 analysis seemed to detect higher levels of within-farm strain diversity and seemed to give higher year-related information. Combination of both typing methods revealed 20 multi-type farms out of the 33 bovine farms studied with more than one isolate. CONCLUSION: The particular SSR and PFGE typing approaches described here are in general agreement but they showed some discrepancies that might reflect differing evolutionary processes of Map strains. Both methods are able to reciprocally complement their results and neither should be replaced with the other if sufficient material and time is available. Overall, the results of our comparative analyses suggest that, based on current methodologies available, a combined approach that includes SSR and PFGE seems to provide the highest level of discrimination for Map strain typing with meaningful epidemiological information.
45 schema:genre research_article
46 schema:inLanguage en
47 schema:isAccessibleForFree true
48 schema:isPartOf N6309c345a38f47249e7e91535141c043
49 Nb1afef38992c47bc9fae7ac647eaf6c1
50 sg:journal.1024253
51 schema:name Comparative analysis of Mycobacterium avium subsp. paratuberculosis isolates from cattle, sheep and goats by short sequence repeat and pulsed-field gel electrophoresis typing
52 schema:pagination 204
53 schema:productId N60d6d2efb7984a069feb34a2cd9fa89e
54 N6dcc3b2da19142a19039ff82ec53e636
55 N72696df806fc48c892473ce63daaa229
56 N75f9dbe2356e4370b3697718936ab180
57 N7d9439e4230b4bd1a6b4f9ba7122a835
58 schema:sameAs https://app.dimensions.ai/details/publication/pub.1049554618
59 https://doi.org/10.1186/1471-2180-8-204
60 schema:sdDatePublished 2019-04-10T14:08
61 schema:sdLicense https://scigraph.springernature.com/explorer/license/
62 schema:sdPublisher N149e6ab2ecff4f69a303d542d7997c9f
63 schema:url http://link.springer.com/10.1186%2F1471-2180-8-204
64 sgo:license sg:explorer/license/
65 sgo:sdDataset articles
66 rdf:type schema:ScholarlyArticle
67 N149e6ab2ecff4f69a303d542d7997c9f schema:name Springer Nature - SN SciGraph project
68 rdf:type schema:Organization
69 N326962f4683b402e81f1588be0607c30 rdf:first sg:person.01323473621.85
70 rdf:rest rdf:nil
71 N3fc76f251883492d8d8446217a78a3fb rdf:first sg:person.0631114411.35
72 rdf:rest N326962f4683b402e81f1588be0607c30
73 N40611aac3e2d41f4bf73dee679b536a3 schema:name Instituto Vasco de Investigación y Desarrollo Agrario (NEIKER), Berreaga, 1, 48160, Derio, Bizkaia, Spain
74 rdf:type schema:Organization
75 N43ff726c86394ccf9a962a33f41e34e5 schema:name Instituto Vasco de Investigación y Desarrollo Agrario (NEIKER), Berreaga, 1, 48160, Derio, Bizkaia, Spain
76 rdf:type schema:Organization
77 N4c1ecd21ada84b6db5e12383493a2ede schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
78 schema:name Cattle
79 rdf:type schema:DefinedTerm
80 N58e695c3a988470c9830eb67966346f7 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
81 schema:name Sheep
82 rdf:type schema:DefinedTerm
83 N5fd4b0873b914404a7071f43918d4d70 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
84 schema:name Electrophoresis, Gel, Pulsed-Field
85 rdf:type schema:DefinedTerm
86 N60d6d2efb7984a069feb34a2cd9fa89e schema:name doi
87 schema:value 10.1186/1471-2180-8-204
88 rdf:type schema:PropertyValue
89 N6309c345a38f47249e7e91535141c043 schema:volumeNumber 8
90 rdf:type schema:PublicationVolume
91 N6ae5e7928ba345c38402c85b82f56a22 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
92 schema:name Animals
93 rdf:type schema:DefinedTerm
94 N6dcc3b2da19142a19039ff82ec53e636 schema:name dimensions_id
95 schema:value pub.1049554618
96 rdf:type schema:PropertyValue
97 N72696df806fc48c892473ce63daaa229 schema:name pubmed_id
98 schema:value 19032737
99 rdf:type schema:PropertyValue
100 N75f9dbe2356e4370b3697718936ab180 schema:name readcube_id
101 schema:value ec10ce23e4c49084f5481e318f483c78eaba5177eee44b0d42a8d73d37b05f5b
102 rdf:type schema:PropertyValue
103 N79450dbb2c0b4def9bfba3e13b1e8f6b schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
104 schema:name Microsatellite Repeats
105 rdf:type schema:DefinedTerm
106 N7d9439e4230b4bd1a6b4f9ba7122a835 schema:name nlm_unique_id
107 schema:value 100966981
108 rdf:type schema:PropertyValue
109 N89acd406851e4d1997a5c6d0cdd69281 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
110 schema:name Bacterial Typing Techniques
111 rdf:type schema:DefinedTerm
112 N95d9b172e4ed4ce0a0e0faafff113b93 rdf:first sg:person.0614533757.20
113 rdf:rest N3fc76f251883492d8d8446217a78a3fb
114 N9aa1428297d843ad90946f979a0e3066 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
115 schema:name Mycobacterium avium subsp. paratuberculosis
116 rdf:type schema:DefinedTerm
117 Nb1afef38992c47bc9fae7ac647eaf6c1 schema:issueNumber 1
118 rdf:type schema:PublicationIssue
119 Nb3c0e0ce742e48978b61ecbda59d6f83 schema:name Instituto Vasco de Investigación y Desarrollo Agrario (NEIKER), Berreaga, 1, 48160, Derio, Bizkaia, Spain
120 rdf:type schema:Organization
121 Nc8600910caa24133899ffe2c40730fb7 rdf:first sg:person.011546513207.12
122 rdf:rest Nd261bf7ff4af404799a46a44715328f1
123 Nca69223047c446949ac30db555bf91ea rdf:first sg:person.01353250306.86
124 rdf:rest N95d9b172e4ed4ce0a0e0faafff113b93
125 Nd261bf7ff4af404799a46a44715328f1 rdf:first sg:person.0634544476.38
126 rdf:rest Ne1aacca9520147dc9e960ecec7612c79
127 Nd36f717d36e645ea8df2b1a8a70b0452 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
128 schema:name Goats
129 rdf:type schema:DefinedTerm
130 Ne1aacca9520147dc9e960ecec7612c79 rdf:first sg:person.01002436054.12
131 rdf:rest Nca69223047c446949ac30db555bf91ea
132 Nf10f675d3e9e42c2bc52e8dc6afdea18 schema:name Instituto Vasco de Investigación y Desarrollo Agrario (NEIKER), Berreaga, 1, 48160, Derio, Bizkaia, Spain
133 rdf:type schema:Organization
134 anzsrc-for:07 schema:inDefinedTermSet anzsrc-for:
135 schema:name Agricultural and Veterinary Sciences
136 rdf:type schema:DefinedTerm
137 anzsrc-for:0707 schema:inDefinedTermSet anzsrc-for:
138 schema:name Veterinary Sciences
139 rdf:type schema:DefinedTerm
140 sg:journal.1024253 schema:issn 1471-2180
141 schema:name BMC Microbiology
142 rdf:type schema:Periodical
143 sg:person.01002436054.12 schema:affiliation https://www.grid.ac/institutes/grid.17635.36
144 schema:familyName Amonsin
145 schema:givenName Alongkorn
146 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01002436054.12
147 rdf:type schema:Person
148 sg:person.011546513207.12 schema:affiliation Nb3c0e0ce742e48978b61ecbda59d6f83
149 schema:familyName Sevilla
150 schema:givenName Iker
151 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.011546513207.12
152 rdf:type schema:Person
153 sg:person.01323473621.85 schema:affiliation N40611aac3e2d41f4bf73dee679b536a3
154 schema:familyName Juste
155 schema:givenName Ramón A
156 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01323473621.85
157 rdf:type schema:Person
158 sg:person.01353250306.86 schema:affiliation N43ff726c86394ccf9a962a33f41e34e5
159 schema:familyName Garrido
160 schema:givenName Joseba M
161 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01353250306.86
162 rdf:type schema:Person
163 sg:person.0614533757.20 schema:affiliation Nf10f675d3e9e42c2bc52e8dc6afdea18
164 schema:familyName Geijo
165 schema:givenName Maria V
166 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0614533757.20
167 rdf:type schema:Person
168 sg:person.0631114411.35 schema:affiliation https://www.grid.ac/institutes/grid.17635.36
169 schema:familyName Kapur
170 schema:givenName Vivek
171 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0631114411.35
172 rdf:type schema:Person
173 sg:person.0634544476.38 schema:affiliation https://www.grid.ac/institutes/grid.17635.36
174 schema:familyName Li
175 schema:givenName Lingling
176 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0634544476.38
177 rdf:type schema:Person
178 sg:pub.10.1186/1471-2180-7-18 schema:sameAs https://app.dimensions.ai/details/publication/pub.1021601027
179 https://doi.org/10.1186/1471-2180-7-18
180 rdf:type schema:CreativeWork
181 sg:pub.10.1186/1751-0147-46-13 schema:sameAs https://app.dimensions.ai/details/publication/pub.1035595166
182 https://doi.org/10.1186/1751-0147-46-13
183 rdf:type schema:CreativeWork
184 https://app.dimensions.ai/details/publication/pub.1074693565 schema:CreativeWork
185 https://app.dimensions.ai/details/publication/pub.1078408327 schema:CreativeWork
186 https://app.dimensions.ai/details/publication/pub.1082954029 schema:CreativeWork
187 https://doi.org/10.1006/mcpr.1998.0194 schema:sameAs https://app.dimensions.ai/details/publication/pub.1004614084
188 rdf:type schema:CreativeWork
189 https://doi.org/10.1016/j.ijid.2008.06.034 schema:sameAs https://app.dimensions.ai/details/publication/pub.1047075561
190 rdf:type schema:CreativeWork
191 https://doi.org/10.1016/j.micinf.2005.12.003 schema:sameAs https://app.dimensions.ai/details/publication/pub.1045052246
192 rdf:type schema:CreativeWork
193 https://doi.org/10.1016/j.vetmic.2006.01.008 schema:sameAs https://app.dimensions.ai/details/publication/pub.1053061731
194 rdf:type schema:CreativeWork
195 https://doi.org/10.1016/s0167-7012(99)00091-3 schema:sameAs https://app.dimensions.ai/details/publication/pub.1028102825
196 rdf:type schema:CreativeWork
197 https://doi.org/10.1016/s1473-3099(03)00724-2 schema:sameAs https://app.dimensions.ai/details/publication/pub.1021106696
198 rdf:type schema:CreativeWork
199 https://doi.org/10.1097/mog.0b013e3282f1dcc4 schema:sameAs https://app.dimensions.ai/details/publication/pub.1031906399
200 rdf:type schema:CreativeWork
201 https://doi.org/10.1111/j.1365-2672.2005.02598.x schema:sameAs https://app.dimensions.ai/details/publication/pub.1018328164
202 rdf:type schema:CreativeWork
203 https://doi.org/10.1111/j.1751-0813.1997.tb11259.x schema:sameAs https://app.dimensions.ai/details/publication/pub.1039619301
204 rdf:type schema:CreativeWork
205 https://doi.org/10.1111/j.1751-0813.2000.tb10590.x schema:sameAs https://app.dimensions.ai/details/publication/pub.1009242118
206 rdf:type schema:CreativeWork
207 https://doi.org/10.1111/j.1751-0813.2001.tb11980.x schema:sameAs https://app.dimensions.ai/details/publication/pub.1017927696
208 rdf:type schema:CreativeWork
209 https://doi.org/10.1128/aem.71.12.8934-8936.2005 schema:sameAs https://app.dimensions.ai/details/publication/pub.1039577046
210 rdf:type schema:CreativeWork
211 https://doi.org/10.1128/jcm.00476-07 schema:sameAs https://app.dimensions.ai/details/publication/pub.1050579832
212 rdf:type schema:CreativeWork
213 https://doi.org/10.1128/jcm.01801-07 schema:sameAs https://app.dimensions.ai/details/publication/pub.1020867250
214 rdf:type schema:CreativeWork
215 https://doi.org/10.1128/jcm.40.5.1798-1804.2002 schema:sameAs https://app.dimensions.ai/details/publication/pub.1047563327
216 rdf:type schema:CreativeWork
217 https://doi.org/10.1128/jcm.41.5.2015-2026.2003 schema:sameAs https://app.dimensions.ai/details/publication/pub.1015677815
218 rdf:type schema:CreativeWork
219 https://doi.org/10.1128/jcm.42.11.5345-5348.2004 schema:sameAs https://app.dimensions.ai/details/publication/pub.1012828596
220 rdf:type schema:CreativeWork
221 https://doi.org/10.1128/jcm.42.4.1694-1702.2004 schema:sameAs https://app.dimensions.ai/details/publication/pub.1007539369
222 rdf:type schema:CreativeWork
223 https://doi.org/10.1128/jcm.42.4.1703-1712.2004 schema:sameAs https://app.dimensions.ai/details/publication/pub.1023894978
224 rdf:type schema:CreativeWork
225 https://doi.org/10.1128/jcm.43.5.2111-2117.2005 schema:sameAs https://app.dimensions.ai/details/publication/pub.1031939720
226 rdf:type schema:CreativeWork
227 https://doi.org/10.1371/journal.pone.0002537 schema:sameAs https://app.dimensions.ai/details/publication/pub.1044323595
228 rdf:type schema:CreativeWork
229 https://doi.org/10.17221/5631-vetmed schema:sameAs https://app.dimensions.ai/details/publication/pub.1100967193
230 rdf:type schema:CreativeWork
231 https://doi.org/10.20506/rst.20.1.1274 schema:sameAs https://app.dimensions.ai/details/publication/pub.1068791838
232 rdf:type schema:CreativeWork
233 https://doi.org/10.20506/rst.24.3.1634 schema:sameAs https://app.dimensions.ai/details/publication/pub.1068792198
234 rdf:type schema:CreativeWork
235 https://doi.org/10.4315/0362-028x-68.5.966 schema:sameAs https://app.dimensions.ai/details/publication/pub.1072509254
236 rdf:type schema:CreativeWork
237 https://www.grid.ac/institutes/grid.17635.36 schema:alternateName University of Minnesota
238 schema:name Departments of Microbiology and Biomedical Genomics Center, University of Minnesota, 55108, MN, USA
239 rdf:type schema:Organization
 




Preview window. Press ESC to close (or click here)


...