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. 2021 May 28;21(1):157.
doi: 10.1186/s12866-021-02232-z.

Distribution and Clonality of drug-resistant tuberculosis in South Africa

Halima Said  1   2 , John Ratabane  3 , Linda Erasmus  4 , Yasmin Gardee  3 , Shaheed Omar  3 , Andries Dreyer  5 , Farzana Ismail  3   6 , Zaheda Bhyat  3 , Tiisetso Lebaka  4 , Minty van der Meulen  3 , Thabisile Gwala  3 , Adeboye Adelekan  6 , Karidia Diallo  6 , Nazir Ismail  3   7
Affiliations

Distribution and Clonality of drug-resistant tuberculosis in South Africa

Halima Said et al. BMC Microbiol. .

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.

Keywords: 24-loci MIRU-VNTR typing; Genotyping; RR-TB; Spoligotyping.

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Conflict of interest statement

All authors declare no conflict of interest.

Figures

Fig. 1
Fig. 1
Distribution of RR-TB families in South Africa by province (2014–2018). FS, Free State; NC, Northern Cape; GP, Gauteng; KZN, KwaZulu-Natal; NW, North West; MP, Mpumalanga; EC, Eastern Cape; WC, Western Cape; Orphan, unknown genotype
Fig. 2
Fig. 2
Number of clusters by size in South Africa (2014–2018)
See this image and copyright information in PMC

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