Molecular Epidemiology of <i>Mycobacterium tuberculosis</i> Complex Strains in Urban and Slum Settings of Nairobi, Kenya
Kenya is a country with a high tuberculosis (TB) burden. However, knowledge on the genetic diversity of <i>Mycobacterium tuberculosis</i> complex (MTBC) strains and their transmission dynamics is sparsely available. Hence, we used whole-genome sequencing (WGS) to depict the genetic diver...
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| Format: | Article |
| Language: | English |
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MDPI AG
2022-03-01
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| Series: | Genes |
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| Online Access: | https://www.mdpi.com/2073-4425/13/3/475 |
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| author | Glennah Kerubo Perpetua Ndungu Yassir Adam Shuaib Evans Amukoye Gunturu Revathi Susanne Homolka Samuel Kariuki Matthias Merker Stefan Niemann |
| author_facet | Glennah Kerubo Perpetua Ndungu Yassir Adam Shuaib Evans Amukoye Gunturu Revathi Susanne Homolka Samuel Kariuki Matthias Merker Stefan Niemann |
| author_sort | Glennah Kerubo |
| collection | DOAJ |
| description | Kenya is a country with a high tuberculosis (TB) burden. However, knowledge on the genetic diversity of <i>Mycobacterium tuberculosis</i> complex (MTBC) strains and their transmission dynamics is sparsely available. Hence, we used whole-genome sequencing (WGS) to depict the genetic diversity, molecular markers of drug resistance, and possible transmission clusters among MTBC strains in urban and slum settings of Nairobi. We analyzed 385 clinical MTBC isolates collected between 2010 and 2015 in combination with patients’ demographics. We showed that the MTBC population mainly comprises strains of four lineages (L1–L4). The two dominating lineages were L4 with 55.8% (<i>n</i> = 215) and L3 with 25.7% (<i>n</i> = 99) of all strains, respectively. Genome-based cluster analysis showed that 30.4% (117/385) of the strains were clustered using a ≤5 single-nucleotide polymorphism (SNP) threshold as a surrogate marker for direct patient-to-patient MTBC transmission. Moreover, 5.2% (20/385) of the strains were multidrug-resistant (MDR), and 50.0% (<i>n</i> = 10) were part of a genome-based cluster (i.e., direct MDR MTBC transmission). Notably, 30.0% (6/20) of the MDR strains were resistant to all first-line drugs and are part of one molecular cluster. Moreover, TB patients in urban living setting had 3.8 times the odds of being infected with a drug-resistant strain as compared to patients from slums (<i>p</i>-value = 0.002). Our results show that L4 strains are the main causative agent of TB in Nairobi and MDR strain transmission is an emerging concern in urban settings. This emphasizes the need for more focused infection control measures and contact tracing of patients with MDR TB to break the transmission chains. |
| first_indexed | 2024-03-09T19:48:15Z |
| format | Article |
| id | doaj.art-5b477249100140248c6e80448158bf04 |
| institution | Directory Open Access Journal |
| issn | 2073-4425 |
| language | English |
| last_indexed | 2024-03-09T19:48:15Z |
| publishDate | 2022-03-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Genes |
| spelling | doaj.art-5b477249100140248c6e80448158bf042023-11-24T01:18:47ZengMDPI AGGenes2073-44252022-03-0113347510.3390/genes13030475Molecular Epidemiology of <i>Mycobacterium tuberculosis</i> Complex Strains in Urban and Slum Settings of Nairobi, KenyaGlennah Kerubo0Perpetua Ndungu1Yassir Adam Shuaib2Evans Amukoye3Gunturu Revathi4Susanne Homolka5Samuel Kariuki6Matthias Merker7Stefan Niemann8Molecular and Experimental Mycobacteriology, Research Center Borstel, 23845 Borstel, GermanyJomo Kenyatta University of Agriculture and Technology, Nairobi 62000-00200, KenyaMolecular and Experimental Mycobacteriology, Research Center Borstel, 23845 Borstel, GermanyCentre for Respiratory Disease Research, Kenya Medical Research Institute, Nairobi 54840-00200, KenyaAga Khan University Hospital, Nairobi 30270-00100, KenyaMolecular and Experimental Mycobacteriology, Research Center Borstel, 23845 Borstel, GermanyCentre for Microbiology Research, Kenya Medical Research Institute, Nairobi 54840-00200, KenyaMolecular and Experimental Mycobacteriology, Research Center Borstel, 23845 Borstel, GermanyMolecular and Experimental Mycobacteriology, Research Center Borstel, 23845 Borstel, GermanyKenya is a country with a high tuberculosis (TB) burden. However, knowledge on the genetic diversity of <i>Mycobacterium tuberculosis</i> complex (MTBC) strains and their transmission dynamics is sparsely available. Hence, we used whole-genome sequencing (WGS) to depict the genetic diversity, molecular markers of drug resistance, and possible transmission clusters among MTBC strains in urban and slum settings of Nairobi. We analyzed 385 clinical MTBC isolates collected between 2010 and 2015 in combination with patients’ demographics. We showed that the MTBC population mainly comprises strains of four lineages (L1–L4). The two dominating lineages were L4 with 55.8% (<i>n</i> = 215) and L3 with 25.7% (<i>n</i> = 99) of all strains, respectively. Genome-based cluster analysis showed that 30.4% (117/385) of the strains were clustered using a ≤5 single-nucleotide polymorphism (SNP) threshold as a surrogate marker for direct patient-to-patient MTBC transmission. Moreover, 5.2% (20/385) of the strains were multidrug-resistant (MDR), and 50.0% (<i>n</i> = 10) were part of a genome-based cluster (i.e., direct MDR MTBC transmission). Notably, 30.0% (6/20) of the MDR strains were resistant to all first-line drugs and are part of one molecular cluster. Moreover, TB patients in urban living setting had 3.8 times the odds of being infected with a drug-resistant strain as compared to patients from slums (<i>p</i>-value = 0.002). Our results show that L4 strains are the main causative agent of TB in Nairobi and MDR strain transmission is an emerging concern in urban settings. This emphasizes the need for more focused infection control measures and contact tracing of patients with MDR TB to break the transmission chains.https://www.mdpi.com/2073-4425/13/3/475tuberculosis<i>Mycobacterium tuberculosis</i>whole-genome sequencingmolecular epidemiologyNairobi |
| spellingShingle | Glennah Kerubo Perpetua Ndungu Yassir Adam Shuaib Evans Amukoye Gunturu Revathi Susanne Homolka Samuel Kariuki Matthias Merker Stefan Niemann Molecular Epidemiology of <i>Mycobacterium tuberculosis</i> Complex Strains in Urban and Slum Settings of Nairobi, Kenya Genes tuberculosis <i>Mycobacterium tuberculosis</i> whole-genome sequencing molecular epidemiology Nairobi |
| title | Molecular Epidemiology of <i>Mycobacterium tuberculosis</i> Complex Strains in Urban and Slum Settings of Nairobi, Kenya |
| title_full | Molecular Epidemiology of <i>Mycobacterium tuberculosis</i> Complex Strains in Urban and Slum Settings of Nairobi, Kenya |
| title_fullStr | Molecular Epidemiology of <i>Mycobacterium tuberculosis</i> Complex Strains in Urban and Slum Settings of Nairobi, Kenya |
| title_full_unstemmed | Molecular Epidemiology of <i>Mycobacterium tuberculosis</i> Complex Strains in Urban and Slum Settings of Nairobi, Kenya |
| title_short | Molecular Epidemiology of <i>Mycobacterium tuberculosis</i> Complex Strains in Urban and Slum Settings of Nairobi, Kenya |
| title_sort | molecular epidemiology of i mycobacterium tuberculosis i complex strains in urban and slum settings of nairobi kenya |
| topic | tuberculosis <i>Mycobacterium tuberculosis</i> whole-genome sequencing molecular epidemiology Nairobi |
| url | https://www.mdpi.com/2073-4425/13/3/475 |
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