The shortcut of mycobacterial interspersed repetitive unit-variable number tandem repeat typing for Mycobacterium tuberculosis differentiation
The 24-loci mycobacterial interspersed repetitive unit-variable number tandem repeat (MIRU-VNTR) genotyping has been used as an international standard method for Mycobacterium tuberculosis (Mtb) genotyping. However, different optimized VNTR loci sets for improving the discrimination of specific Mtb...
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| Format: | Article |
| Language: | English |
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Frontiers Media S.A.
2022-09-01
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| Series: | Frontiers in Microbiology |
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| Online Access: | https://www.frontiersin.org/articles/10.3389/fmicb.2022.978355/full |
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| author | Shima Hadifar Shima Hadifar Mansour Kargarpour Kamakoli Mansour Kargarpour Kamakoli Sana Eybpoosh Mehran Nakhaeizadeh Mehran Nakhaeizadeh Mohammad Ali Kargarpour Kamakoli Nasim Ebrahimifard Nasim Ebrahimifard Abolfazl Fateh Abolfazl Fateh Seyed Davar Siadat Seyed Davar Siadat Farzam Vaziri Farzam Vaziri |
| author_facet | Shima Hadifar Shima Hadifar Mansour Kargarpour Kamakoli Mansour Kargarpour Kamakoli Sana Eybpoosh Mehran Nakhaeizadeh Mehran Nakhaeizadeh Mohammad Ali Kargarpour Kamakoli Nasim Ebrahimifard Nasim Ebrahimifard Abolfazl Fateh Abolfazl Fateh Seyed Davar Siadat Seyed Davar Siadat Farzam Vaziri Farzam Vaziri |
| author_sort | Shima Hadifar |
| collection | DOAJ |
| description | The 24-loci mycobacterial interspersed repetitive unit-variable number tandem repeat (MIRU-VNTR) genotyping has been used as an international standard method for Mycobacterium tuberculosis (Mtb) genotyping. However, different optimized VNTR loci sets for improving the discrimination of specific Mtb genotypes have been proposed. In this regard, we investigated the efficacy of accumulation of the percentage differences (APDs) compared with the least absolute shrinkage and selection operator (LASSO) regression strategy to identify a customized genotype-specific VNTR loci set which provides a resolution comparable to 24-loci MIRU-VNTR in divergent Mtb populations. We utilized Spoligotyping and 24-loci MIRU-VNTR typing for genotyping 306 Mtb isolates. The APD and LASSO regression approaches were used to identify a customized VNTR set in our studied isolates. Besides, the Hunter-Gaston discriminatory index (HGDI), sensitivity, and specificity of each selected loci set were calculated based on both strategies. The selected loci based on LASSO regression compared with APD-based loci showed a better discriminatory power for identifying all studied genotypes except for T genotype, which APD-based loci showed promising discriminative power. Our findings suggested the LASSO regression rather than the APD approach is more effective in the determination of possible discriminative VNTR loci set to precise discrimination of our studied Mtb population and may be beneficial to be used in finding reduced number loci sets in other Mtb genotypes or sublineages. Moreover, we proposed customized genotype-specific MIRU-VNTR loci sets based on the LASSO regression and APD approaches for precise Mtb strains identification. As the proposed VNTR sets offered a comparable discriminatory power to the standard 24 MIRU-VNTR loci set could be promising alternatives to the standard genotyping for using in resource-limited settings. |
| first_indexed | 2024-04-12T23:38:08Z |
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| id | doaj.art-5d3e133b9ac541e98ea3569dea19f0d7 |
| institution | Directory Open Access Journal |
| issn | 1664-302X |
| language | English |
| last_indexed | 2024-04-12T23:38:08Z |
| publishDate | 2022-09-01 |
| publisher | Frontiers Media S.A. |
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| series | Frontiers in Microbiology |
| spelling | doaj.art-5d3e133b9ac541e98ea3569dea19f0d72022-12-22T03:12:04ZengFrontiers Media S.A.Frontiers in Microbiology1664-302X2022-09-011310.3389/fmicb.2022.978355978355The shortcut of mycobacterial interspersed repetitive unit-variable number tandem repeat typing for Mycobacterium tuberculosis differentiationShima Hadifar0Shima Hadifar1Mansour Kargarpour Kamakoli2Mansour Kargarpour Kamakoli3Sana Eybpoosh4Mehran Nakhaeizadeh5Mehran Nakhaeizadeh6Mohammad Ali Kargarpour Kamakoli7Nasim Ebrahimifard8Nasim Ebrahimifard9Abolfazl Fateh10Abolfazl Fateh11Seyed Davar Siadat12Seyed Davar Siadat13Farzam Vaziri14Farzam Vaziri15Department of Mycobacteriology and Pulmonary Research, Pasteur Institute of Iran, Tehran, IranMicrobiology Research Center, Pasteur Institute of Iran, Tehran, IranDepartment of Mycobacteriology and Pulmonary Research, Pasteur Institute of Iran, Tehran, IranMicrobiology Research Center, Pasteur Institute of Iran, Tehran, IranDepartment of Epidemiology and Biostatistics, Research Centre for Emerging and Reemerging Infectious Diseases, Pasteur Institute of Iran, Tehran, IranModeling in Health Research Center, Institute for Futures Studies in Health, Kerman University of Medical Sciences, Kerman, IranDepartment of Biostatistics and Epidemiology, School of Public Health, Kerman University of Medical Sciences, Kerman, IranDepartment of Mechanical Engineering, Quchan University of Technology, Quchan, IranDepartment of Mycobacteriology and Pulmonary Research, Pasteur Institute of Iran, Tehran, IranMicrobiology Research Center, Pasteur Institute of Iran, Tehran, IranDepartment of Mycobacteriology and Pulmonary Research, Pasteur Institute of Iran, Tehran, IranMicrobiology Research Center, Pasteur Institute of Iran, Tehran, IranDepartment of Mycobacteriology and Pulmonary Research, Pasteur Institute of Iran, Tehran, IranMicrobiology Research Center, Pasteur Institute of Iran, Tehran, IranDepartment of Mycobacteriology and Pulmonary Research, Pasteur Institute of Iran, Tehran, IranMicrobiology Research Center, Pasteur Institute of Iran, Tehran, IranThe 24-loci mycobacterial interspersed repetitive unit-variable number tandem repeat (MIRU-VNTR) genotyping has been used as an international standard method for Mycobacterium tuberculosis (Mtb) genotyping. However, different optimized VNTR loci sets for improving the discrimination of specific Mtb genotypes have been proposed. In this regard, we investigated the efficacy of accumulation of the percentage differences (APDs) compared with the least absolute shrinkage and selection operator (LASSO) regression strategy to identify a customized genotype-specific VNTR loci set which provides a resolution comparable to 24-loci MIRU-VNTR in divergent Mtb populations. We utilized Spoligotyping and 24-loci MIRU-VNTR typing for genotyping 306 Mtb isolates. The APD and LASSO regression approaches were used to identify a customized VNTR set in our studied isolates. Besides, the Hunter-Gaston discriminatory index (HGDI), sensitivity, and specificity of each selected loci set were calculated based on both strategies. The selected loci based on LASSO regression compared with APD-based loci showed a better discriminatory power for identifying all studied genotypes except for T genotype, which APD-based loci showed promising discriminative power. Our findings suggested the LASSO regression rather than the APD approach is more effective in the determination of possible discriminative VNTR loci set to precise discrimination of our studied Mtb population and may be beneficial to be used in finding reduced number loci sets in other Mtb genotypes or sublineages. Moreover, we proposed customized genotype-specific MIRU-VNTR loci sets based on the LASSO regression and APD approaches for precise Mtb strains identification. As the proposed VNTR sets offered a comparable discriminatory power to the standard 24 MIRU-VNTR loci set could be promising alternatives to the standard genotyping for using in resource-limited settings.https://www.frontiersin.org/articles/10.3389/fmicb.2022.978355/fullMycobacterium tuberculosisMIRU-VNTRLASSO regressionaccumulation of the percentage differencesgenotyping |
| spellingShingle | Shima Hadifar Shima Hadifar Mansour Kargarpour Kamakoli Mansour Kargarpour Kamakoli Sana Eybpoosh Mehran Nakhaeizadeh Mehran Nakhaeizadeh Mohammad Ali Kargarpour Kamakoli Nasim Ebrahimifard Nasim Ebrahimifard Abolfazl Fateh Abolfazl Fateh Seyed Davar Siadat Seyed Davar Siadat Farzam Vaziri Farzam Vaziri The shortcut of mycobacterial interspersed repetitive unit-variable number tandem repeat typing for Mycobacterium tuberculosis differentiation Frontiers in Microbiology Mycobacterium tuberculosis MIRU-VNTR LASSO regression accumulation of the percentage differences genotyping |
| title | The shortcut of mycobacterial interspersed repetitive unit-variable number tandem repeat typing for Mycobacterium tuberculosis differentiation |
| title_full | The shortcut of mycobacterial interspersed repetitive unit-variable number tandem repeat typing for Mycobacterium tuberculosis differentiation |
| title_fullStr | The shortcut of mycobacterial interspersed repetitive unit-variable number tandem repeat typing for Mycobacterium tuberculosis differentiation |
| title_full_unstemmed | The shortcut of mycobacterial interspersed repetitive unit-variable number tandem repeat typing for Mycobacterium tuberculosis differentiation |
| title_short | The shortcut of mycobacterial interspersed repetitive unit-variable number tandem repeat typing for Mycobacterium tuberculosis differentiation |
| title_sort | shortcut of mycobacterial interspersed repetitive unit variable number tandem repeat typing for mycobacterium tuberculosis differentiation |
| topic | Mycobacterium tuberculosis MIRU-VNTR LASSO regression accumulation of the percentage differences genotyping |
| url | https://www.frontiersin.org/articles/10.3389/fmicb.2022.978355/full |
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