Comparing IS6110‐RFLP, PGRS‐RFLP and IS6110‐Mtb1/Mtb2 PCR methods for genotyping of Mycobacterium tuberculosis isolates
Aims Tuberculosis (TB) is still an important disease in the world, especially in developing countries. Applying efficient and suitable methods for genotyping Mycobacterium tuberculosis (MTB) isolates is a crucial step for identifying the MTB transmission mode and controlling its subsequent outcomes....
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| Veröffentlicht in: | Journal of applied microbiology 2020-10, Vol.129 (4), p.1062-1070 |
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| container_title | Journal of applied microbiology |
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| creator | Ansarin, Kh Sahebi, L. Aftabi, Y. Khalili, M. Seyyedi, M. |
| description | Aims
Tuberculosis (TB) is still an important disease in the world, especially in developing countries. Applying efficient and suitable methods for genotyping Mycobacterium tuberculosis (MTB) isolates is a crucial step for identifying the MTB transmission mode and controlling its subsequent outcomes. Considering the complexity of IS6110‐RFLP and PGRS‐RFLP methods for MTB classification, suggesting other simple but reliable techniques could be helpful in the MTB studies, especially in low‐income countries.
Methods and Results
This study aimed to evaluate the capabilities of three methods for genotyping MTB isolates collected from Iran through comparing our previously published results for IS6110‐RFLP and PGRS‐RFLP methods and current results obtained from IS6110‐Mtb1/Mtb2 PCR technique. A strong concordance was observed between the results of clustering by three techniques. Calculated Kendall’s Tau concordance value for correlation of IS6110‐RFLP and IS6110‐Mtb1/Mtb2 PCR, for IS6110‐RFLP and PGRS‐RFLP, and for IS6110‐Mtb1/Mtb2 PCR and PGRS‐RFLP techniques was equal to 0·943, 0·898 and 0·85 respectively.
Conclusions
A strong correlation between IS6110‐Mtb1/Mtb2 PCR, and IS6110‐RFLP and PGRS‐RFLP methods was observed and therefore IS6110‐Mtb1/Mtb2 PCR discriminates MTBs capably.
Significance and Impact of the Study
The study showed that IS6110‐Mtb1/Mtb2 PCR, which is a simple and economical MTB genotyping approach, could be a more appropriate method to be applied in the low‐budget research programmes. |
| doi_str_mv | 10.1111/jam.14676 |
| format | Article |
| fullrecord | <record><control><sourceid>proquest_cross</sourceid><recordid>TN_cdi_proquest_miscellaneous_2394893455</recordid><sourceformat>XML</sourceformat><sourcesystem>PC</sourcesystem><sourcerecordid>2394893455</sourcerecordid><originalsourceid>FETCH-LOGICAL-c3536-a1df9b9fc5800c83046538abd7b06626760f96bd2e291f076780f20dd700c50d3</originalsourceid><addsrcrecordid>eNp1kdFKHDEUhkOxVGt70RcoAW8sdNyTZJKZXMqi1rJLl7W9DplJorPMTNZkBtmLQh_BZ_RJGt2tgtBcnOSQj4-T_Ah9InBC0pqsdHdCclGIN-iAMMEzKgq693TOMw4F3UfvY1wBEAZcvEP7jDIGLOcH6PfUd2sdmv4aX14JQuDhz_3yfLb4ihcXy6tdg3VvXq7nQ0UmqVC8mC5xZ4cbbyJ2PuBr2_ths36UeYfnm9pXuh5saMYOD2NlQz22PjYRN9G3erDxA3rrdBvtx91-iH6dn_2cfstmPy4up6ezrGaciUwT42QlXc1LgLpkkAvOSl2ZogIh0mMFOCkqQy2VxEEhihIcBWOKhHMw7BAdb73r4G9HGwfVNbG2bat768eoKJN5KdOH8IQevUJXfgx9mk7RPGcSJJUiUV-2VB18jME6tQ5Np8NGEVCPmaiUiXrKJLGfd8ax6qx5Jv-FkIDJFrhrWrv5v0l9P51vlX8BrmCUyQ</addsrcrecordid><sourcetype>Aggregation Database</sourcetype><iscdi>true</iscdi><recordtype>article</recordtype><pqid>2443909296</pqid></control><display><type>article</type><title>Comparing IS6110‐RFLP, PGRS‐RFLP and IS6110‐Mtb1/Mtb2 PCR methods for genotyping of Mycobacterium tuberculosis isolates</title><source>MEDLINE</source><source>Wiley Journals</source><source>Oxford University Press Journals All Titles (1996-Current)</source><creator>Ansarin, Kh ; Sahebi, L. ; Aftabi, Y. ; Khalili, M. ; Seyyedi, M.</creator><creatorcontrib>Ansarin, Kh ; Sahebi, L. ; Aftabi, Y. ; Khalili, M. ; Seyyedi, M.</creatorcontrib><description>Aims
Tuberculosis (TB) is still an important disease in the world, especially in developing countries. Applying efficient and suitable methods for genotyping Mycobacterium tuberculosis (MTB) isolates is a crucial step for identifying the MTB transmission mode and controlling its subsequent outcomes. Considering the complexity of IS6110‐RFLP and PGRS‐RFLP methods for MTB classification, suggesting other simple but reliable techniques could be helpful in the MTB studies, especially in low‐income countries.
Methods and Results
This study aimed to evaluate the capabilities of three methods for genotyping MTB isolates collected from Iran through comparing our previously published results for IS6110‐RFLP and PGRS‐RFLP methods and current results obtained from IS6110‐Mtb1/Mtb2 PCR technique. A strong concordance was observed between the results of clustering by three techniques. Calculated Kendall’s Tau concordance value for correlation of IS6110‐RFLP and IS6110‐Mtb1/Mtb2 PCR, for IS6110‐RFLP and PGRS‐RFLP, and for IS6110‐Mtb1/Mtb2 PCR and PGRS‐RFLP techniques was equal to 0·943, 0·898 and 0·85 respectively.
Conclusions
A strong correlation between IS6110‐Mtb1/Mtb2 PCR, and IS6110‐RFLP and PGRS‐RFLP methods was observed and therefore IS6110‐Mtb1/Mtb2 PCR discriminates MTBs capably.
Significance and Impact of the Study
The study showed that IS6110‐Mtb1/Mtb2 PCR, which is a simple and economical MTB genotyping approach, could be a more appropriate method to be applied in the low‐budget research programmes.</description><identifier>ISSN: 1364-5072</identifier><identifier>EISSN: 1365-2672</identifier><identifier>DOI: 10.1111/jam.14676</identifier><identifier>PMID: 32330345</identifier><language>eng</language><publisher>England: Oxford University Press</publisher><subject>Clustering ; detection ; Developing countries ; diversity ; DNA, Bacterial - genetics ; Genotype ; Genotyping ; Humans ; Iran - epidemiology ; LDCs ; molecular epidemiology ; Molecular Typing - methods ; mycobacteria ; Mycobacterium tuberculosis ; Mycobacterium tuberculosis - classification ; Mycobacterium tuberculosis - genetics ; Mycobacterium tuberculosis - isolation & purification ; Polymerase Chain Reaction ; Polymorphism, Restriction Fragment Length ; Repetitive Sequences, Nucleic Acid - genetics ; Tuberculosis ; Tuberculosis - epidemiology ; Tuberculosis - microbiology</subject><ispartof>Journal of applied microbiology, 2020-10, Vol.129 (4), p.1062-1070</ispartof><rights>2020 The Society for Applied Microbiology</rights><rights>2020 The Society for Applied Microbiology.</rights><rights>Copyright © 2020 The Society for Applied Microbiology</rights><lds50>peer_reviewed</lds50><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c3536-a1df9b9fc5800c83046538abd7b06626760f96bd2e291f076780f20dd700c50d3</citedby><cites>FETCH-LOGICAL-c3536-a1df9b9fc5800c83046538abd7b06626760f96bd2e291f076780f20dd700c50d3</cites><orcidid>0000-0002-3114-5224 ; 0000-0002-0133-4788 ; 0000-0002-8692-8867 ; 0000-0001-9848-4274 ; 0000-0001-5162-2174</orcidid></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://onlinelibrary.wiley.com/doi/pdf/10.1111%2Fjam.14676$$EPDF$$P50$$Gwiley$$H</linktopdf><linktohtml>$$Uhttps://onlinelibrary.wiley.com/doi/full/10.1111%2Fjam.14676$$EHTML$$P50$$Gwiley$$H</linktohtml><link.rule.ids>314,780,784,1417,27924,27925,45574,45575</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/32330345$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Ansarin, Kh</creatorcontrib><creatorcontrib>Sahebi, L.</creatorcontrib><creatorcontrib>Aftabi, Y.</creatorcontrib><creatorcontrib>Khalili, M.</creatorcontrib><creatorcontrib>Seyyedi, M.</creatorcontrib><title>Comparing IS6110‐RFLP, PGRS‐RFLP and IS6110‐Mtb1/Mtb2 PCR methods for genotyping of Mycobacterium tuberculosis isolates</title><title>Journal of applied microbiology</title><addtitle>J Appl Microbiol</addtitle><description>Aims
Tuberculosis (TB) is still an important disease in the world, especially in developing countries. Applying efficient and suitable methods for genotyping Mycobacterium tuberculosis (MTB) isolates is a crucial step for identifying the MTB transmission mode and controlling its subsequent outcomes. Considering the complexity of IS6110‐RFLP and PGRS‐RFLP methods for MTB classification, suggesting other simple but reliable techniques could be helpful in the MTB studies, especially in low‐income countries.
Methods and Results
This study aimed to evaluate the capabilities of three methods for genotyping MTB isolates collected from Iran through comparing our previously published results for IS6110‐RFLP and PGRS‐RFLP methods and current results obtained from IS6110‐Mtb1/Mtb2 PCR technique. A strong concordance was observed between the results of clustering by three techniques. Calculated Kendall’s Tau concordance value for correlation of IS6110‐RFLP and IS6110‐Mtb1/Mtb2 PCR, for IS6110‐RFLP and PGRS‐RFLP, and for IS6110‐Mtb1/Mtb2 PCR and PGRS‐RFLP techniques was equal to 0·943, 0·898 and 0·85 respectively.
Conclusions
A strong correlation between IS6110‐Mtb1/Mtb2 PCR, and IS6110‐RFLP and PGRS‐RFLP methods was observed and therefore IS6110‐Mtb1/Mtb2 PCR discriminates MTBs capably.
Significance and Impact of the Study
The study showed that IS6110‐Mtb1/Mtb2 PCR, which is a simple and economical MTB genotyping approach, could be a more appropriate method to be applied in the low‐budget research programmes.</description><subject>Clustering</subject><subject>detection</subject><subject>Developing countries</subject><subject>diversity</subject><subject>DNA, Bacterial - genetics</subject><subject>Genotype</subject><subject>Genotyping</subject><subject>Humans</subject><subject>Iran - epidemiology</subject><subject>LDCs</subject><subject>molecular epidemiology</subject><subject>Molecular Typing - methods</subject><subject>mycobacteria</subject><subject>Mycobacterium tuberculosis</subject><subject>Mycobacterium tuberculosis - classification</subject><subject>Mycobacterium tuberculosis - genetics</subject><subject>Mycobacterium tuberculosis - isolation & purification</subject><subject>Polymerase Chain Reaction</subject><subject>Polymorphism, Restriction Fragment Length</subject><subject>Repetitive Sequences, Nucleic Acid - genetics</subject><subject>Tuberculosis</subject><subject>Tuberculosis - epidemiology</subject><subject>Tuberculosis - microbiology</subject><issn>1364-5072</issn><issn>1365-2672</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2020</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><recordid>eNp1kdFKHDEUhkOxVGt70RcoAW8sdNyTZJKZXMqi1rJLl7W9DplJorPMTNZkBtmLQh_BZ_RJGt2tgtBcnOSQj4-T_Ah9InBC0pqsdHdCclGIN-iAMMEzKgq693TOMw4F3UfvY1wBEAZcvEP7jDIGLOcH6PfUd2sdmv4aX14JQuDhz_3yfLb4ihcXy6tdg3VvXq7nQ0UmqVC8mC5xZ4cbbyJ2PuBr2_ths36UeYfnm9pXuh5saMYOD2NlQz22PjYRN9G3erDxA3rrdBvtx91-iH6dn_2cfstmPy4up6ezrGaciUwT42QlXc1LgLpkkAvOSl2ZogIh0mMFOCkqQy2VxEEhihIcBWOKhHMw7BAdb73r4G9HGwfVNbG2bat768eoKJN5KdOH8IQevUJXfgx9mk7RPGcSJJUiUV-2VB18jME6tQ5Np8NGEVCPmaiUiXrKJLGfd8ax6qx5Jv-FkIDJFrhrWrv5v0l9P51vlX8BrmCUyQ</recordid><startdate>202010</startdate><enddate>202010</enddate><creator>Ansarin, Kh</creator><creator>Sahebi, L.</creator><creator>Aftabi, Y.</creator><creator>Khalili, M.</creator><creator>Seyyedi, M.</creator><general>Oxford University Press</general><scope>CGR</scope><scope>CUY</scope><scope>CVF</scope><scope>ECM</scope><scope>EIF</scope><scope>NPM</scope><scope>AAYXX</scope><scope>CITATION</scope><scope>7QL</scope><scope>7QO</scope><scope>7T7</scope><scope>7TM</scope><scope>7U7</scope><scope>8FD</scope><scope>C1K</scope><scope>FR3</scope><scope>M7N</scope><scope>P64</scope><scope>RC3</scope><scope>7X8</scope><orcidid>https://orcid.org/0000-0002-3114-5224</orcidid><orcidid>https://orcid.org/0000-0002-0133-4788</orcidid><orcidid>https://orcid.org/0000-0002-8692-8867</orcidid><orcidid>https://orcid.org/0000-0001-9848-4274</orcidid><orcidid>https://orcid.org/0000-0001-5162-2174</orcidid></search><sort><creationdate>202010</creationdate><title>Comparing IS6110‐RFLP, PGRS‐RFLP and IS6110‐Mtb1/Mtb2 PCR methods for genotyping of Mycobacterium tuberculosis isolates</title><author>Ansarin, Kh ; Sahebi, L. ; Aftabi, Y. ; Khalili, M. ; Seyyedi, M.</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c3536-a1df9b9fc5800c83046538abd7b06626760f96bd2e291f076780f20dd700c50d3</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2020</creationdate><topic>Clustering</topic><topic>detection</topic><topic>Developing countries</topic><topic>diversity</topic><topic>DNA, Bacterial - genetics</topic><topic>Genotype</topic><topic>Genotyping</topic><topic>Humans</topic><topic>Iran - epidemiology</topic><topic>LDCs</topic><topic>molecular epidemiology</topic><topic>Molecular Typing - methods</topic><topic>mycobacteria</topic><topic>Mycobacterium tuberculosis</topic><topic>Mycobacterium tuberculosis - classification</topic><topic>Mycobacterium tuberculosis - genetics</topic><topic>Mycobacterium tuberculosis - isolation & purification</topic><topic>Polymerase Chain Reaction</topic><topic>Polymorphism, Restriction Fragment Length</topic><topic>Repetitive Sequences, Nucleic Acid - genetics</topic><topic>Tuberculosis</topic><topic>Tuberculosis - epidemiology</topic><topic>Tuberculosis - microbiology</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Ansarin, Kh</creatorcontrib><creatorcontrib>Sahebi, L.</creatorcontrib><creatorcontrib>Aftabi, Y.</creatorcontrib><creatorcontrib>Khalili, M.</creatorcontrib><creatorcontrib>Seyyedi, M.</creatorcontrib><collection>Medline</collection><collection>MEDLINE</collection><collection>MEDLINE (Ovid)</collection><collection>MEDLINE</collection><collection>MEDLINE</collection><collection>PubMed</collection><collection>CrossRef</collection><collection>Bacteriology Abstracts (Microbiology B)</collection><collection>Biotechnology Research Abstracts</collection><collection>Industrial and Applied Microbiology Abstracts (Microbiology A)</collection><collection>Nucleic Acids Abstracts</collection><collection>Toxicology Abstracts</collection><collection>Technology Research Database</collection><collection>Environmental Sciences and Pollution Management</collection><collection>Engineering Research Database</collection><collection>Algology Mycology and Protozoology Abstracts (Microbiology C)</collection><collection>Biotechnology and BioEngineering Abstracts</collection><collection>Genetics Abstracts</collection><collection>MEDLINE - Academic</collection><jtitle>Journal of applied microbiology</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Ansarin, Kh</au><au>Sahebi, L.</au><au>Aftabi, Y.</au><au>Khalili, M.</au><au>Seyyedi, M.</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Comparing IS6110‐RFLP, PGRS‐RFLP and IS6110‐Mtb1/Mtb2 PCR methods for genotyping of Mycobacterium tuberculosis isolates</atitle><jtitle>Journal of applied microbiology</jtitle><addtitle>J Appl Microbiol</addtitle><date>2020-10</date><risdate>2020</risdate><volume>129</volume><issue>4</issue><spage>1062</spage><epage>1070</epage><pages>1062-1070</pages><issn>1364-5072</issn><eissn>1365-2672</eissn><abstract>Aims
Tuberculosis (TB) is still an important disease in the world, especially in developing countries. Applying efficient and suitable methods for genotyping Mycobacterium tuberculosis (MTB) isolates is a crucial step for identifying the MTB transmission mode and controlling its subsequent outcomes. Considering the complexity of IS6110‐RFLP and PGRS‐RFLP methods for MTB classification, suggesting other simple but reliable techniques could be helpful in the MTB studies, especially in low‐income countries.
Methods and Results
This study aimed to evaluate the capabilities of three methods for genotyping MTB isolates collected from Iran through comparing our previously published results for IS6110‐RFLP and PGRS‐RFLP methods and current results obtained from IS6110‐Mtb1/Mtb2 PCR technique. A strong concordance was observed between the results of clustering by three techniques. Calculated Kendall’s Tau concordance value for correlation of IS6110‐RFLP and IS6110‐Mtb1/Mtb2 PCR, for IS6110‐RFLP and PGRS‐RFLP, and for IS6110‐Mtb1/Mtb2 PCR and PGRS‐RFLP techniques was equal to 0·943, 0·898 and 0·85 respectively.
Conclusions
A strong correlation between IS6110‐Mtb1/Mtb2 PCR, and IS6110‐RFLP and PGRS‐RFLP methods was observed and therefore IS6110‐Mtb1/Mtb2 PCR discriminates MTBs capably.
Significance and Impact of the Study
The study showed that IS6110‐Mtb1/Mtb2 PCR, which is a simple and economical MTB genotyping approach, could be a more appropriate method to be applied in the low‐budget research programmes.</abstract><cop>England</cop><pub>Oxford University Press</pub><pmid>32330345</pmid><doi>10.1111/jam.14676</doi><tpages>9</tpages><orcidid>https://orcid.org/0000-0002-3114-5224</orcidid><orcidid>https://orcid.org/0000-0002-0133-4788</orcidid><orcidid>https://orcid.org/0000-0002-8692-8867</orcidid><orcidid>https://orcid.org/0000-0001-9848-4274</orcidid><orcidid>https://orcid.org/0000-0001-5162-2174</orcidid></addata></record> |
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| source | MEDLINE; Wiley Journals; Oxford University Press Journals All Titles (1996-Current) |
| subjects | Clustering detection Developing countries diversity DNA, Bacterial - genetics Genotype Genotyping Humans Iran - epidemiology LDCs molecular epidemiology Molecular Typing - methods mycobacteria Mycobacterium tuberculosis Mycobacterium tuberculosis - classification Mycobacterium tuberculosis - genetics Mycobacterium tuberculosis - isolation & purification Polymerase Chain Reaction Polymorphism, Restriction Fragment Length Repetitive Sequences, Nucleic Acid - genetics Tuberculosis Tuberculosis - epidemiology Tuberculosis - microbiology |
| title | Comparing IS6110‐RFLP, PGRS‐RFLP and IS6110‐Mtb1/Mtb2 PCR methods for genotyping of Mycobacterium tuberculosis isolates |
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