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Dlamini TC, Mkhize BT, Sydney C, Maningi NE, Malinga LA. Molecular investigations of Mycobacterium tuberculosis genotypes among baseline and follow-up strains circulating in four regions of Eswatini. BMC Infect Dis 2023; 23:566. [PMID: 37644382 PMCID: PMC10466871 DOI: 10.1186/s12879-023-08546-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2022] [Accepted: 08/18/2023] [Indexed: 08/31/2023] Open
Abstract
BACKGROUND The tuberculosis (TB) epidemic remains a major global health problem and Eswatini is not excluded. Our study investigated the circulating genotypes in Eswatini and compared them at baseline (start of treatment) and follow-up during TB treatment. METHODS Three hundred and ninety (n = 390) participants were prospectively enrolled from referral clinics and patients who met the inclusion criteria, were included in the study. A total of 103 participants provided specimens at baseline and follow-up within six months. Mycobacterium tuberculosis (M.tb) strains were detected by GeneXpert® MTB/RIF assay (Cephied, USA) and Ziehl -Neelsen (ZN) microscopy respectively at baseline and follow-up time-points respectively. The 206 collected specimens were decontaminated and cultured on BACTEC™ MGIT™ 960 Mycobacteria Culture System (Becton Dickinson, USA). Drug sensitivity testing was performed at both baseline and follow-up time points. Spoligotyping was performed on both baseline and follow-up strains after DNA extraction. RESULTS Resistance to at least one first line drug was detected higher at baseline compared to follow-up specimens with most of them developing into multidrug-resistant (MDR)-TB. A total of four lineages and twenty genotypes were detected. The distribution of the lineages varied among the different regions in Eswatini. The Euro-American lineage was the most prevalent with 46.12% (95/206) followed by the East Asian with 24.27% (50/206); Indo-Oceanic at 9.71% (20/206) and Central Asian at 1.94% (4/206). Furthermore, a high proportion of the Beijing genotype at 24.27% (50/206) and S genotype at 16.50% (34/206) were detected. The Beijing genotype was predominant in follow-up specimens collected from the Manzini region with 48.9% (23/47) (p = 0.001). A significant proportion of follow-up specimens developed MDR-TB (p = 0.001) with Beijing being the major genotype in most follow-up specimens (p < 0.000). CONCLUSION Eswatini has a high M.tb genotypic diversity. A significant proportion of the TB infected participants had the Beijing genotype associated with MDR-TB in follow-up specimens and thus indicate community wide transmission.
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Affiliation(s)
- Talent C Dlamini
- Department of Medical Laboratory Sciences, Southern Africa Nazarene University, Manzini, Eswatini.
- Biomedical and Clinical Technology, Department, Durban University of Technology, Durban, South Africa.
| | - Brenda T Mkhize
- Biomedical and Clinical Technology, Department, Durban University of Technology, Durban, South Africa
| | - Clive Sydney
- Biomedical and Clinical Technology, Department, Durban University of Technology, Durban, South Africa
| | | | - Lesibana A Malinga
- Department of Medical Microbiology, Faculty of Health Sciences, University of Pretoria, Pretoria, South Africa
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Ndhlovu V, Kiran A, Sloan DJ, Mandala W, Nliwasa M, Everett DB, Kumwenda B, Mwapasa M, Kontogianni K, Kamdolozi M, Corbett E, Caws M, Davies G. Characterization of DNA methylation in Malawian Mycobacterium tuberculosis clinical isolates. PeerJ 2020; 8:e10432. [PMID: 33362962 PMCID: PMC7749660 DOI: 10.7717/peerj.10432] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2020] [Accepted: 11/05/2020] [Indexed: 11/23/2022] Open
Abstract
Background Although Mycobacterium tuberculosis (Mtb) strains exhibit genomic homology of >99%, there is considerable variation in the phenotype. The underlying mechanisms of phenotypic heterogeneity in Mtb are not well understood but epigenetic variation is thought to contribute. At present the methylome of Mtb has not been completely characterized. Methods We completed methylomes of 18 Mycobacterium tuberculosis (Mtb) clinical isolates from Malawi representing the largest number of Mtb genomes to be completed in a single study using Single Molecule Real Time (SMRT) sequencing to date. Results We replicate and confirm four methylation disrupting mutations in 4 lineages of Mtb. For the first time we report complete loss of methylation courtesy of C758T (S253L) mutation in the MamB gene of Indo-oceanic lineage of Mtb. Additionally, we report a novel missense mutation G454A (G152S) in the MamA gene of the Euro-American lineage which could potentially be attributed to total disruption of methylation in the CCCAG motif but partial loss in a partner motif. Through a genomic and methylome comparative analysis with a global sample of sixteen, we report previously unknown mutations affecting the pks15/1 locus in L6 isolates. We confirm that methylation in Mtb is lineage specific although some unresolved issues still remain.
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Affiliation(s)
- Victor Ndhlovu
- University of Malawi, College of Medicine, Blantyre, Malawi
- University of Liverpool, Liverpool, United Kingdom
- Helse Nord Tuberculosis Initiative Project, University of Malawi, College of Medicine, Blantyre, Malawi
| | - Anmol Kiran
- Malawi-Liverpool Welcome Trust, Blantyre, Malawi
- University of Edinburgh, Edinburgh, United Kingdom
| | - Derek J. Sloan
- Department of Medicine, University of St. Andrews, St. Andrews, United Kingdom
| | - Wilson Mandala
- Malawi-Liverpool Welcome Trust, Blantyre, Malawi
- Academy of Medical Sciences, Malawi University of Science and Technology, Thyolo, Malawi
| | - Marriott Nliwasa
- University of Malawi, College of Medicine, Blantyre, Malawi
- Helse Nord Tuberculosis Initiative Project, University of Malawi, College of Medicine, Blantyre, Malawi
| | - Dean B. Everett
- Malawi-Liverpool Welcome Trust, Blantyre, Malawi
- University of Edinburgh, Edinburgh, United Kingdom
| | | | - Mphatso Mwapasa
- Helse Nord Tuberculosis Initiative Project, University of Malawi, College of Medicine, Blantyre, Malawi
| | | | | | - Elizabeth Corbett
- Helse Nord Tuberculosis Initiative Project, University of Malawi, College of Medicine, Blantyre, Malawi
- Malawi-Liverpool Welcome Trust, Blantyre, Malawi
- London School of Hygiene & Tropical Medicine, University of London, London, United Kingdom
| | - Maxine Caws
- Liverpool School of Tropical Medicine, Liverpool, United Kingdom
- Birat Nepal Medical Trust, Lazimpat, Kathmandu, Kathmandu, Nepal
| | - Gerry Davies
- University of Liverpool, Liverpool, United Kingdom
- Malawi-Liverpool Welcome Trust, Blantyre, Malawi
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