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Said H, Kachingwe E, Gardee Y, Bhyat Z, Ratabane J, Erasmus L, Lebaka T, van der Meulen M, Gwala T, Omar S, Ismail F, Ismail N. Determining the risk-factors for molecular clustering of drug-resistant tuberculosis in South Africa. BMC Public Health 2023; 23:2329. [PMID: 38001453 PMCID: PMC10668341 DOI: 10.1186/s12889-023-17234-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2022] [Accepted: 11/15/2023] [Indexed: 11/26/2023] Open
Abstract
BACKGROUND Drug-resistant tuberculosis (DR-TB) epidemic is driven mainly by the effect of ongoing transmission. In high-burden settings such as South Africa (SA), considerable demographic and geographic heterogeneity in DR-TB transmission exists. Thus, a better understanding of risk-factors for clustering can help to prioritise resources to specifically targeted high-risk groups as well as areas that contribute disproportionately to transmission. METHODS The study analyzed potential risk-factors for recent transmission in SA, using data collected from a sentinel molecular surveillance of DR-TB, by comparing demographic, clinical and epidemiologic characteristics with clustering and cluster sizes. A genotypic cluster was defined as two or more patients having identical patterns by the two genotyping methods used. Clustering was used as a proxy for recent transmission. Descriptive statistics and multinomial logistic regression were used. RESULT The study identified 277 clusters, with cluster size ranging between 2 and 259 cases. The majority (81.6%) of the clusters were small (2-5 cases) with few large (11-25 cases) and very large (≥ 26 cases) clusters identified mainly in Western Cape (WC), Eastern Cape (EC) and Mpumalanga (MP). In a multivariable model, patients in clusters including 11-25 and ≥ 26 individuals were more likely to be infected by Beijing family, have XDR-TB, living in Nelson Mandela Metro in EC or Umgungunglovo in Kwa-Zulu Natal (KZN) provinces, and having history of imprisonment. Individuals belonging in a small genotypic cluster were more likely to infected with Rifampicin resistant TB (RR-TB) and more likely to reside in Frances Baard in Northern Cape (NC). CONCLUSION Sociodemographic, clinical and bacterial risk-factors influenced rate of Mycobacterium tuberculosis (M. tuberculosis) genotypic clustering. Hence, high-risk groups and hotspot areas for clustering in EC, WC, KZN and MP should be prioritized for targeted intervention to prevent ongoing DR-TB transmission.
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Affiliation(s)
- Halima Said
- Centre for Tuberculosis, National Institute of Communicable Diseases, Moderfontein Road, Sandringham, Johannesburg, code 2131, South Africa.
| | - Elizabeth Kachingwe
- Centre for Tuberculosis, National Institute of Communicable Diseases, Moderfontein Road, Sandringham, Johannesburg, code 2131, South Africa
| | - Yasmin Gardee
- Centre for Tuberculosis, National Institute of Communicable Diseases, Moderfontein Road, Sandringham, Johannesburg, code 2131, South Africa
| | - Zaheda Bhyat
- Centre for Tuberculosis, National Institute of Communicable Diseases, Moderfontein Road, Sandringham, Johannesburg, code 2131, South Africa
| | - John Ratabane
- Centre for Tuberculosis, National Institute of Communicable Diseases, Moderfontein Road, Sandringham, Johannesburg, code 2131, South Africa
| | - Linda Erasmus
- Centre for Enteric Diseases, National Institute of Communicable Diseases, Sandringham, Johannesburg, South Africa
| | - Tiisetso Lebaka
- Division of Surveillance and Outbreak Response, National Institute of Communicable Diseases, Sandringham, Johannesburg, South Africa
| | - Minty van der Meulen
- Centre for Tuberculosis, National Institute of Communicable Diseases, Moderfontein Road, Sandringham, Johannesburg, code 2131, South Africa
| | - Thabisile Gwala
- Centre for Tuberculosis, National Institute of Communicable Diseases, Moderfontein Road, Sandringham, Johannesburg, code 2131, South Africa
| | - Shaheed Omar
- Centre for Tuberculosis, National Institute of Communicable Diseases, Moderfontein Road, Sandringham, Johannesburg, code 2131, South Africa
| | - Farzana Ismail
- Centre for Tuberculosis, National Institute of Communicable Diseases, Moderfontein Road, Sandringham, Johannesburg, code 2131, South Africa
| | - Nazir Ismail
- Centre for Tuberculosis, National Institute of Communicable Diseases, Moderfontein Road, Sandringham, Johannesburg, code 2131, South Africa
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Said H, Ratabane J, Erasmus L, Gardee Y, Omar S, Dreyer A, Ismail F, Bhyat Z, Lebaka T, van der Meulen M, Gwala T, Adelekan A, Diallo K, Ismail N. Distribution and Clonality of drug-resistant tuberculosis in South Africa. BMC Microbiol 2021; 21:157. [PMID: 34044775 PMCID: PMC8161895 DOI: 10.1186/s12866-021-02232-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Accepted: 05/13/2021] [Indexed: 11/29/2022] Open
Abstract
Background Studies have shown that drug-resistant tuberculosis (DR-TB) in South Africa (SA) is clonal and is caused mostly by transmission. Identifying transmission chains is important in controlling DR-TB. This study reports on the sentinel molecular surveillance data of Rifampicin-Resistant (RR) TB in SA, aiming to describe the RR-TB strain population and the estimated transmission of RR-TB cases. Method RR-TB isolates collected between 2014 and 2018 from eight provinces were genotyped using combination of spoligotyping and 24-loci mycobacterial interspersed repetitive-units-variable-number tandem repeats (MIRU-VNTR) typing. Results Of the 3007 isolates genotyped, 301 clusters were identified. Cluster size ranged between 2 and 270 cases. Most of the clusters (247/301; 82.0%) were small in size (< 5 cases), 12.0% (37/301) were medium sized (5–10 cases), 3.3% (10/301) were large (11–25 cases) and 2.3% (7/301) were very large with 26–270 cases. The Beijing genotype was responsible for majority of RR-TB cases in Western and Eastern Cape, while the East-African-Indian-Somalian (EAI1_SOM) genotype accounted for a third of RR-TB cases in Mpumalanga. The overall proportion of RR-TB cases estimated to be due to transmission was 42%, with the highest transmission-rate in Western Cape (64%) and the lowest in Northern Cape (9%). Conclusion Large clusters contribute to the burden of RR-TB in specific geographic areas such as Western Cape, Eastern Cape and Mpumalanga, highlighting the need for community-wide interventions. Most of the clusters identified in the study were small, suggesting close contact transmission events, emphasizing the importance of contact investigations and infection control as the primary interventions in SA. Supplementary Information The online version contains supplementary material available at 10.1186/s12866-021-02232-z.
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Affiliation(s)
- Halima Said
- Centre for Tuberculosis, National Institute of Communicable Diseases, 1 Moderfontein Road, Sandringham, Johannesburg, 2131, South Africa. .,Department of Medical Microbiology, Faculty of Health Science, University of Free State, Bloemfontein, South Africa.
| | - John Ratabane
- Centre for Tuberculosis, National Institute of Communicable Diseases, 1 Moderfontein Road, Sandringham, Johannesburg, 2131, South Africa
| | - Linda Erasmus
- Division of Public Health Surveillance and Response, National Institute of Communicable Diseases, Johannesburg, South Africa
| | - Yasmin Gardee
- Centre for Tuberculosis, National Institute of Communicable Diseases, 1 Moderfontein Road, Sandringham, Johannesburg, 2131, South Africa
| | - Shaheed Omar
- Centre for Tuberculosis, National Institute of Communicable Diseases, 1 Moderfontein Road, Sandringham, Johannesburg, 2131, South Africa
| | | | - Farzana Ismail
- Centre for Tuberculosis, National Institute of Communicable Diseases, 1 Moderfontein Road, Sandringham, Johannesburg, 2131, South Africa.,Centers for Disease Control and Prevention, Pretoria, South Africa
| | - Zaheda Bhyat
- Centre for Tuberculosis, National Institute of Communicable Diseases, 1 Moderfontein Road, Sandringham, Johannesburg, 2131, South Africa
| | - Tiisetso Lebaka
- Division of Public Health Surveillance and Response, National Institute of Communicable Diseases, Johannesburg, South Africa
| | - Minty van der Meulen
- Centre for Tuberculosis, National Institute of Communicable Diseases, 1 Moderfontein Road, Sandringham, Johannesburg, 2131, South Africa
| | - Thabisile Gwala
- Centre for Tuberculosis, National Institute of Communicable Diseases, 1 Moderfontein Road, Sandringham, Johannesburg, 2131, South Africa
| | - Adeboye Adelekan
- Centers for Disease Control and Prevention, Pretoria, South Africa
| | - Karidia Diallo
- Centers for Disease Control and Prevention, Pretoria, South Africa
| | - Nazir Ismail
- Centre for Tuberculosis, National Institute of Communicable Diseases, 1 Moderfontein Road, Sandringham, Johannesburg, 2131, South Africa.,Department of Medical Microbiology, Faculty of Health Science, University of Pretoria, Pretoria, South Africa
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Ismail N, Ismail F, Omar SV, Blows L, Gardee Y, Koornhof H, Onyebujoh PC. Drug resistant tuberculosis in Africa: Current status, gaps and opportunities. Afr J Lab Med 2018; 7:781. [PMID: 30568900 PMCID: PMC6295755 DOI: 10.4102/ajlm.v7i2.781] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2018] [Accepted: 09/12/2018] [Indexed: 11/24/2022] Open
Abstract
Background The World Health Organization End TB Strategy targets for 2035 are ambitious and drug resistant tuberculosis is an important barrier, particularly in Africa, home to over a billion people. Objective We sought to review the current status of drug resistant tuberculosis in Africa and highlight key areas requiring improvement. Methods Available data from 2016 World Health Organization global tuberculosis database were extracted and analysed using descriptive statistics. Results The true burden of drug resistant tuberculosis on the continent is poorly described with only 51% of countries having a formal survey completed. In the absence of this data, modelled estimates were used and reported 92 629 drug resistant tuberculosis cases with 42% of these occurring in just two countries: Nigeria and South Africa. Of the cases estimated, the majority of patients (70%) were not notified, representing ‘missed cases’. Mortality among patients with multi-drug resistant tuberculosis was 21%, and was 43% among those with extensively drug resistant tuberculosis. Policies on the adoption of new diagnostic tools was poor and implementation was lacking. A rifampicin result was available for less than 10% of tuberculosis cases in 23 of 47 countries. Second-line drug resistance testing was available in only 60% of countries. The introduction of the short multi-drug resistant tuberculosis regimen was a welcome development, with 40% of countries having implemented it in 2016. Bedaquiline has also been introduced in several countries. Conclusion Drug resistant tuberculosis is largely missed in Africa and this threatens prospects to achieve the 2035 targets. Urgent efforts are required to confirm the true burden of drug resistant tuberculosis in Africa. Adoption of new tools and drugs is essential if the 2035 targets are to be met.
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Affiliation(s)
- Nazir Ismail
- Center for Tuberculosis, National Institute for Communicable Diseases, National Health Laboratory Services, Johannesburg, South Africa.,Department of Medical Microbiology, University of Pretoria, Pretoria, South Africa.,Department of Internal Medicine, University of Witwatersrand, Johannesburg, South Africa
| | - Farzana Ismail
- Center for Tuberculosis, National Institute for Communicable Diseases, National Health Laboratory Services, Johannesburg, South Africa.,Department of Medical Microbiology, University of Pretoria, Pretoria, South Africa
| | - Shaheed V Omar
- Center for Tuberculosis, National Institute for Communicable Diseases, National Health Laboratory Services, Johannesburg, South Africa
| | - Linsay Blows
- Center for Tuberculosis, National Institute for Communicable Diseases, National Health Laboratory Services, Johannesburg, South Africa
| | - Yasmin Gardee
- Center for Tuberculosis, National Institute for Communicable Diseases, National Health Laboratory Services, Johannesburg, South Africa
| | - Hendrik Koornhof
- Center for Tuberculosis, National Institute for Communicable Diseases, National Health Laboratory Services, Johannesburg, South Africa
| | - Philip C Onyebujoh
- Africa Centres for Disease Control and Prevention, Addis Ababa, Ethiopia
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Said HM, Kushner N, Omar SV, Dreyer AW, Koornhof H, Erasmus L, Gardee Y, Rukasha I, Shashkina E, Beylis N, Kaplan G, Fallows D, Ismail NA. A Novel Molecular Strategy for Surveillance of Multidrug Resistant Tuberculosis in High Burden Settings. PLoS One 2016; 11:e0146106. [PMID: 26752297 PMCID: PMC4713439 DOI: 10.1371/journal.pone.0146106] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2015] [Accepted: 12/14/2015] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND In South Africa and other high prevalence countries, transmission is a significant contributor to rising rates of multidrug resistant tuberculosis (MDR-TB). Thus, there is a need to develop an early detection system for transmission clusters suitable for high burden settings. We have evaluated the discriminatory power and clustering concordance of a novel and simple genotyping approach, combining spoligotyping with pncA sequencing (SpoNC), against two well-established methods: IS6110-RFLP and 24-loci MIRU-VNTR. METHODS A total of 216 MDR-TB isolates collected from January to June 2010 from the NHLS Central TB referral laboratory in Braamfontein, Johannesburg, representing a diversity of strains from South Africa, were included. The isolates were submitted for genotyping, pncA sequencing and analysis to the Centre for Tuberculosis in South Africa and the Public Health Research Institute Tuberculosis Center at Rutgers University in the United States. Clustering rates, Hunter-Gaston Discriminatory Indexes (HGI) and Wallace coefficients were compared between the methods. RESULTS Overall clustering rates were high by both IS6110-RFLP (52.8%) and MIRU-VNTR (45.8%), indicative of on-going transmission. Both 24-loci MIRU-VNTR and IS6110-RFLP had similar HGI (0.972 and 0.973, respectively), with close numbers of unique profiles (87 vs. 70), clustered isolates (129 vs. 146), and cluster sizes (2 to 26 vs. 2 to 25 isolates). Spoligotyping alone was the least discriminatory (80.1% clustering, HGI 0.903), with 28 unique types. However, the discriminatory power of spoligotyping was improved when combined with pncA sequencing using the SpoNC approach (61.8% clustering, HGI 0.958). A high proportion of MDR-TB isolates had mutations in pncA (68%, n = 145), and pncA mutations were significantly associated with clustering (p = 0.007 and p = 0.0013 by 24-loci MIRU-VNTR and IS6110-RFLP, respectively), suggesting high rates of resistance to pyrazinamide among all MDR-TB cases and particularly among clustered cases. CONCLUSION We conclude that SpoNC provides good discrimination for MDR-TB surveillance and early identification of outbreaks in South Africa, with 24-loci MIRU-VNTR applied for pncA wild-type strains as needed.
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Affiliation(s)
- Halima M. Said
- Centre for Tuberculosis, National Institute of Communicable Diseases, Sandringham, South Africa
- * E-mail:
| | - Nicole Kushner
- Public Health Research Institute, Rutgers University, Newark, New Jersey, United States of America
| | - Shaheed V. Omar
- Centre for Tuberculosis, National Institute of Communicable Diseases, Sandringham, South Africa
| | - Andries W. Dreyer
- Centre for Tuberculosis, National Institute of Communicable Diseases, Sandringham, South Africa
| | - Hendrik Koornhof
- Centre for Tuberculosis, National Institute of Communicable Diseases, Sandringham, South Africa
| | - Linda Erasmus
- Centre for Tuberculosis, National Institute of Communicable Diseases, Sandringham, South Africa
| | - Yasmin Gardee
- Centre for Tuberculosis, National Institute of Communicable Diseases, Sandringham, South Africa
| | - Ivy Rukasha
- Centre for Tuberculosis, National Institute of Communicable Diseases, Sandringham, South Africa
| | - Elena Shashkina
- Public Health Research Institute, Rutgers University, Newark, New Jersey, United States of America
| | - Natalie Beylis
- National Health Laboratory Service, Groote Schuur Hospital, Cape Town, South Africa
| | - Gilla Kaplan
- The Bill & Melinda Gates Foundation, Seattle, Washington, United States of America
| | - Dorothy Fallows
- Public Health Research Institute, Rutgers University, Newark, New Jersey, United States of America
| | - Nazir A. Ismail
- Centre for Tuberculosis, National Institute of Communicable Diseases, Sandringham, South Africa
- Department of Medical Microbiology, Faculty of Health Science, University of Pretoria, Pretoria, South Africa
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Gardee Y, Kirby R. The incidence of inducible macrolide-lincosamide-streptogramin B resistance in methicillin-resistant staphylococci in clinical isolates from the Eastern Cape area of South Africa. Lett Appl Microbiol 1993; 17:264-8. [PMID: 7764379 DOI: 10.1111/j.1472-765x.1993.tb01462.x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
The incidence of inducible macrolide-lincosamide-streptogramin B resistance in methicillin-resistant staphylococci in clinical isolates from the Eastern Cape area of South Africa is shown to be higher than might be expected. A significant difference in the frequency between different hospital and different population groups was identified. RAPD fingerprinting of the strains suggests that this difference is mirrored in the presence of different Staphylococcus aureus strains in the different hospitals. It is proposed that the significantly higher level of overcrowding in certain hospitals in worsening the problem of multiple antibiotic resistance in the Eastern Cape.
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Affiliation(s)
- Y Gardee
- Department of Biochemistry and Microbiology, Rhodes University, Grahamstown, South Africa
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