Phenotypic and genotypic drug susceptibility patterns of Mycobacterium tuberculosis isolates from pulmonary tuberculosis patients in Central and Southern Ethiopia
The persistence of tuberculosis (TB) infection in some patients after treatment has highlighted the importance of drug susceptibility testing (DST). This study aimed to determine the drug susceptibility patterns of Mycobacterium tuberculosis (M. tuberculosis) isolates from pulmonary TB (PTB) patient...
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| Veröffentlicht in: | PloS one 2023-09, Vol.18 (9), p.e0285063-e0285063 |
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| creator | Tilahun, Melaku Wegayehu, Teklu Wondale, Biniam Gebresilase, Tewdros Tariku Gebreyohannes, Tesfaye Tekola, Abraham Alemu, Mekdes Neway, Sebsib Adnew, Bethlehem Nassir, Maeruf Fetu Kassahun, Yonas Aseffa, Abraham Bobosha, Kidist |
| description | The persistence of tuberculosis (TB) infection in some patients after treatment has highlighted the importance of drug susceptibility testing (DST). This study aimed to determine the drug susceptibility patterns of Mycobacterium tuberculosis (M. tuberculosis) isolates from pulmonary TB (PTB) patients in Central and Southern Ethiopia.
A health institution-based cross-sectional study was conducted between July 2021 and April 2022. Sputum samples were collected from newly diagnosed smear microscopy and/or Xpert MTB/RIF-positive PTB patients. The samples were processed and cultivated in Lowenstein-Jensen (LJ) pyruvate and glycerol medium. M. tuberculosis isolates were identified using polymerase chain reaction (PCR) based region of difference 9 (RD9) deletion typing. Phenotypic DST patterns of the isolates were characterized using the BACTEC MGIT™ 960 instrument with SIRE kit. Isoniazid (INH) and Rifampicin (RIF) resistant M. tuberculosis isolates were identified using the GenoType® MTBDRplus assay.
Sputum samples were collected from 350 PTB patients, 315 (90%) of which were culture-positive, and phenotypic and genotypic DST were determined for 266 and 261 isolates, respectively. Due to invalid results and missing data, 6% (16/266) of the isolates were excluded, while 94% (250/266) were included in the paired analysis. According to the findings, 14.4% (36/250) of the isolates tested positive for resistance to at least one anti-TB drug. Gene mutations were observed only in the rpoB and katG gene loci, indicating RIF and high-level INH resistance. The GenoType® MTBDRplus assay has a sensitivity of 42% and a specificity of 100% in detecting INH-resistant M. tuberculosis isolates, with a kappa value of 0.56 (95%CI: 0.36-0.76) compared to the BACTEC MGIT™ DST. The overall discordance between the two methods was 5.6% (14/250) for INH alone and 0% for RIF resistance and MDR-TB (resistance to both INH and RIF) detection.
This study reveals a higher prevalence of phenotypic and genotypic discordant INH-resistant M. tuberculosis isolates in the study area. The use of whole-genome sequencing (WGS) is essential for gaining a comprehensive understanding of these discrepancies within INH-resistant M. tuberculosis strains. |
| doi_str_mv | 10.1371/journal.pone.0285063 |
| format | Article |
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A health institution-based cross-sectional study was conducted between July 2021 and April 2022. Sputum samples were collected from newly diagnosed smear microscopy and/or Xpert MTB/RIF-positive PTB patients. The samples were processed and cultivated in Lowenstein-Jensen (LJ) pyruvate and glycerol medium. M. tuberculosis isolates were identified using polymerase chain reaction (PCR) based region of difference 9 (RD9) deletion typing. Phenotypic DST patterns of the isolates were characterized using the BACTEC MGIT™ 960 instrument with SIRE kit. Isoniazid (INH) and Rifampicin (RIF) resistant M. tuberculosis isolates were identified using the GenoType® MTBDRplus assay.
Sputum samples were collected from 350 PTB patients, 315 (90%) of which were culture-positive, and phenotypic and genotypic DST were determined for 266 and 261 isolates, respectively. Due to invalid results and missing data, 6% (16/266) of the isolates were excluded, while 94% (250/266) were included in the paired analysis. According to the findings, 14.4% (36/250) of the isolates tested positive for resistance to at least one anti-TB drug. Gene mutations were observed only in the rpoB and katG gene loci, indicating RIF and high-level INH resistance. The GenoType® MTBDRplus assay has a sensitivity of 42% and a specificity of 100% in detecting INH-resistant M. tuberculosis isolates, with a kappa value of 0.56 (95%CI: 0.36-0.76) compared to the BACTEC MGIT™ DST. The overall discordance between the two methods was 5.6% (14/250) for INH alone and 0% for RIF resistance and MDR-TB (resistance to both INH and RIF) detection.
This study reveals a higher prevalence of phenotypic and genotypic discordant INH-resistant M. tuberculosis isolates in the study area. The use of whole-genome sequencing (WGS) is essential for gaining a comprehensive understanding of these discrepancies within INH-resistant M. tuberculosis strains.</description><identifier>ISSN: 1932-6203</identifier><identifier>EISSN: 1932-6203</identifier><identifier>DOI: 10.1371/journal.pone.0285063</identifier><identifier>PMID: 37682820</identifier><language>eng</language><publisher>United States: Public Library of Science</publisher><subject>Analysis ; Biology and Life Sciences ; Coronaviruses ; Cross-Sectional Studies ; Diagnosis ; Discordance ; Drug resistance ; Drug therapy ; Ethiopia - epidemiology ; Gene deletion ; Gene mutations ; Gene sequencing ; Genes ; Genomes ; Genotype ; Genotype & phenotype ; Genotypes ; Glycerin ; Glycerol ; Health aspects ; Hospitals ; Humans ; Infectious diseases ; Isoniazid ; KatG gene ; Laboratories ; Latent Tuberculosis ; Medical diagnosis ; Medicine and Health Sciences ; Microbial Sensitivity Tests ; Microscopy ; Missing data ; Mutation ; Mycobacterium tuberculosis ; Mycobacterium tuberculosis - genetics ; People and Places ; Phenotype ; Polymerase chain reaction ; Public health ; Pyruvic acid ; Regions ; Rifampin ; RNA polymerase ; RpoB protein ; Sputum ; Tuberculosis ; Tuberculosis, Pulmonary - diagnosis ; Tuberculosis, Pulmonary - drug therapy ; Tuberculosis, Pulmonary - epidemiology ; Whole genome sequencing</subject><ispartof>PloS one, 2023-09, Vol.18 (9), p.e0285063-e0285063</ispartof><rights>Copyright: © 2023 Tilahun et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.</rights><rights>COPYRIGHT 2023 Public Library of Science</rights><rights>2023 Tilahun et al. This is an open access article distributed under the terms of the Creative Commons Attribution License: http://creativecommons.org/licenses/by/4.0/ (the “License”), which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Notwithstanding the ProQuest Terms and Conditions, you may use this content in accordance with the terms of the License.</rights><rights>2023 Tilahun et al 2023 Tilahun et al</rights><rights>2023 Tilahun et al. This is an open access article distributed under the terms of the Creative Commons Attribution License: http://creativecommons.org/licenses/by/4.0/ (the “License”), which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. 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This study aimed to determine the drug susceptibility patterns of Mycobacterium tuberculosis (M. tuberculosis) isolates from pulmonary TB (PTB) patients in Central and Southern Ethiopia.
A health institution-based cross-sectional study was conducted between July 2021 and April 2022. Sputum samples were collected from newly diagnosed smear microscopy and/or Xpert MTB/RIF-positive PTB patients. The samples were processed and cultivated in Lowenstein-Jensen (LJ) pyruvate and glycerol medium. M. tuberculosis isolates were identified using polymerase chain reaction (PCR) based region of difference 9 (RD9) deletion typing. Phenotypic DST patterns of the isolates were characterized using the BACTEC MGIT™ 960 instrument with SIRE kit. Isoniazid (INH) and Rifampicin (RIF) resistant M. tuberculosis isolates were identified using the GenoType® MTBDRplus assay.
Sputum samples were collected from 350 PTB patients, 315 (90%) of which were culture-positive, and phenotypic and genotypic DST were determined for 266 and 261 isolates, respectively. Due to invalid results and missing data, 6% (16/266) of the isolates were excluded, while 94% (250/266) were included in the paired analysis. According to the findings, 14.4% (36/250) of the isolates tested positive for resistance to at least one anti-TB drug. Gene mutations were observed only in the rpoB and katG gene loci, indicating RIF and high-level INH resistance. The GenoType® MTBDRplus assay has a sensitivity of 42% and a specificity of 100% in detecting INH-resistant M. tuberculosis isolates, with a kappa value of 0.56 (95%CI: 0.36-0.76) compared to the BACTEC MGIT™ DST. The overall discordance between the two methods was 5.6% (14/250) for INH alone and 0% for RIF resistance and MDR-TB (resistance to both INH and RIF) detection.
This study reveals a higher prevalence of phenotypic and genotypic discordant INH-resistant M. tuberculosis isolates in the study area. The use of whole-genome sequencing (WGS) is essential for gaining a comprehensive understanding of these discrepancies within INH-resistant M. tuberculosis strains.</description><subject>Analysis</subject><subject>Biology and Life Sciences</subject><subject>Coronaviruses</subject><subject>Cross-Sectional Studies</subject><subject>Diagnosis</subject><subject>Discordance</subject><subject>Drug resistance</subject><subject>Drug therapy</subject><subject>Ethiopia - epidemiology</subject><subject>Gene deletion</subject><subject>Gene mutations</subject><subject>Gene sequencing</subject><subject>Genes</subject><subject>Genomes</subject><subject>Genotype</subject><subject>Genotype & phenotype</subject><subject>Genotypes</subject><subject>Glycerin</subject><subject>Glycerol</subject><subject>Health aspects</subject><subject>Hospitals</subject><subject>Humans</subject><subject>Infectious diseases</subject><subject>Isoniazid</subject><subject>KatG 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Abstracts</collection><collection>Environmental Science Database</collection><collection>Materials Science Collection</collection><collection>Publicly Available Content Database</collection><collection>ProQuest One Academic Eastern Edition (DO NOT USE)</collection><collection>ProQuest One Academic</collection><collection>ProQuest One Academic UKI Edition</collection><collection>Engineering Collection</collection><collection>Environmental Science Collection</collection><collection>Genetics Abstracts</collection><collection>MEDLINE - Academic</collection><collection>PubMed Central (Full Participant titles)</collection><collection>DOAJ Directory of Open Access Journals</collection><jtitle>PloS one</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Tilahun, Melaku</au><au>Wegayehu, Teklu</au><au>Wondale, Biniam</au><au>Gebresilase, Tewdros Tariku</au><au>Gebreyohannes, Tesfaye</au><au>Tekola, Abraham</au><au>Alemu, Mekdes</au><au>Neway, Sebsib</au><au>Adnew, Bethlehem</au><au>Nassir, Maeruf Fetu</au><au>Kassahun, Yonas</au><au>Aseffa, Abraham</au><au>Bobosha, Kidist</au><au>Via, Laura Ellen</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Phenotypic and genotypic drug susceptibility patterns of Mycobacterium tuberculosis isolates from pulmonary tuberculosis patients in Central and Southern Ethiopia</atitle><jtitle>PloS one</jtitle><addtitle>PLoS One</addtitle><date>2023-09-08</date><risdate>2023</risdate><volume>18</volume><issue>9</issue><spage>e0285063</spage><epage>e0285063</epage><pages>e0285063-e0285063</pages><issn>1932-6203</issn><eissn>1932-6203</eissn><abstract>The persistence of tuberculosis (TB) infection in some patients after treatment has highlighted the importance of drug susceptibility testing (DST). This study aimed to determine the drug susceptibility patterns of Mycobacterium tuberculosis (M. tuberculosis) isolates from pulmonary TB (PTB) patients in Central and Southern Ethiopia.
A health institution-based cross-sectional study was conducted between July 2021 and April 2022. Sputum samples were collected from newly diagnosed smear microscopy and/or Xpert MTB/RIF-positive PTB patients. The samples were processed and cultivated in Lowenstein-Jensen (LJ) pyruvate and glycerol medium. M. tuberculosis isolates were identified using polymerase chain reaction (PCR) based region of difference 9 (RD9) deletion typing. Phenotypic DST patterns of the isolates were characterized using the BACTEC MGIT™ 960 instrument with SIRE kit. Isoniazid (INH) and Rifampicin (RIF) resistant M. tuberculosis isolates were identified using the GenoType® MTBDRplus assay.
Sputum samples were collected from 350 PTB patients, 315 (90%) of which were culture-positive, and phenotypic and genotypic DST were determined for 266 and 261 isolates, respectively. Due to invalid results and missing data, 6% (16/266) of the isolates were excluded, while 94% (250/266) were included in the paired analysis. According to the findings, 14.4% (36/250) of the isolates tested positive for resistance to at least one anti-TB drug. Gene mutations were observed only in the rpoB and katG gene loci, indicating RIF and high-level INH resistance. The GenoType® MTBDRplus assay has a sensitivity of 42% and a specificity of 100% in detecting INH-resistant M. tuberculosis isolates, with a kappa value of 0.56 (95%CI: 0.36-0.76) compared to the BACTEC MGIT™ DST. The overall discordance between the two methods was 5.6% (14/250) for INH alone and 0% for RIF resistance and MDR-TB (resistance to both INH and RIF) detection.
This study reveals a higher prevalence of phenotypic and genotypic discordant INH-resistant M. tuberculosis isolates in the study area. The use of whole-genome sequencing (WGS) is essential for gaining a comprehensive understanding of these discrepancies within INH-resistant M. tuberculosis strains.</abstract><cop>United States</cop><pub>Public Library of Science</pub><pmid>37682820</pmid><doi>10.1371/journal.pone.0285063</doi><tpages>e0285063</tpages><orcidid>https://orcid.org/0000-0002-2033-5874</orcidid><orcidid>https://orcid.org/0000-0002-8028-1150</orcidid><orcidid>https://orcid.org/0000-0002-3101-3926</orcidid><orcidid>https://orcid.org/0000-0001-8993-5117</orcidid><oa>free_for_read</oa></addata></record> |
| fulltext | fulltext |
| identifier | ISSN: 1932-6203 |
| ispartof | PloS one, 2023-09, Vol.18 (9), p.e0285063-e0285063 |
| issn | 1932-6203 1932-6203 |
| language | eng |
| recordid | cdi_plos_journals_2862749011 |
| source | MEDLINE; DOAJ Directory of Open Access Journals; Public Library of Science (PLoS); EZB-FREE-00999 freely available EZB journals; PubMed Central; Free Full-Text Journals in Chemistry |
| subjects | Analysis Biology and Life Sciences Coronaviruses Cross-Sectional Studies Diagnosis Discordance Drug resistance Drug therapy Ethiopia - epidemiology Gene deletion Gene mutations Gene sequencing Genes Genomes Genotype Genotype & phenotype Genotypes Glycerin Glycerol Health aspects Hospitals Humans Infectious diseases Isoniazid KatG gene Laboratories Latent Tuberculosis Medical diagnosis Medicine and Health Sciences Microbial Sensitivity Tests Microscopy Missing data Mutation Mycobacterium tuberculosis Mycobacterium tuberculosis - genetics People and Places Phenotype Polymerase chain reaction Public health Pyruvic acid Regions Rifampin RNA polymerase RpoB protein Sputum Tuberculosis Tuberculosis, Pulmonary - diagnosis Tuberculosis, Pulmonary - drug therapy Tuberculosis, Pulmonary - epidemiology Whole genome sequencing |
| title | Phenotypic and genotypic drug susceptibility patterns of Mycobacterium tuberculosis isolates from pulmonary tuberculosis patients in Central and Southern Ethiopia |
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