Distribution and Clonality of drug-resistant tuberculosis in South Africa

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.

Spatial Distribution of Drug-Resistant Mycobacterium tuberculosis Infections in Rural Eastern Cape Province of South Africa

“…A comparison of lineages among all clinics/hospitals in this study shows that the Beijing family was the commonest genotype found in all the hospitals/clinics, with HCF 2, HCF 3, HCF 5, and HCF 6 having a higher proportion of Beijing isolates. The Beijing family is known to be more transmissible than other families and more prevalent in Eastern Cape and Western Cape provinces, which are neighbors [ 42 , 43 ]; this confirms its high prevalence in this study (42%). This family has been detected in studies reported from other parts of South Africa, including Limpopo, the Western Cape, and Mpumalanga [ 43 , 44 ].…”

“…The Beijing family is known to be more transmissible than other families and more prevalent in Eastern Cape and Western Cape provinces, which are neighbors [ 42 , 43 ]; this confirms its high prevalence in this study (42%). This family has been detected in studies reported from other parts of South Africa, including Limpopo, the Western Cape, and Mpumalanga [ 43 , 44 ]. Nelson et al [ 45 ] reported that human movement between rural and urban areas in search of employment in South Africa is common and serves as a bridge for transporting pathogens across long distances.…”

Spatial Distribution and Clustering of Drug-Resistant <em>Mycobacterium Tuberculosis</em> Infections in Rural Eastern Cape Province of South Africa

“…A comparison of lineages among all clinics/ hospitals in the study shows that the Beijing family was the only genotype found in all the hospitals/ clinics, with HCF 2, HCF 3, HCF 5 and HCF 6 having the highest number of Beijing isolates. The Beijing family is known to be more transmissible than other families and more prevalent in Eastern Cape and Western Cape Provinces which are neighbors [48,49] this confirms its high prevalence in this study (42%). This family has been detected in studies reported from other parts of South Africa including Limpopo, Western Cape and Mpumalanga [49,50].…”

“…The Beijing family is known to be more transmissible than other families and more prevalent in Eastern Cape and Western Cape Provinces which are neighbors [48,49] this confirms its high prevalence in this study (42%). This family has been detected in studies reported from other parts of South Africa including Limpopo, Western Cape and Mpumalanga [49,50]. Nelson et al [51] reported that human movement between rural and urban areas in search of employment in South Africa is common and serves as a bridge for transporting pathogen across long distances.…”

Variants in Bedaquiline-Candidate-Resistance Genes: Prevalence in Bedaquiline-Naive Patients, Effect on MIC, and Association with Mycobacterium tuberculosis Lineage

“…Second, we could not assess the BDQ MIC for four of the 36 unique variants as some samples failed to grow. Third, reflecting the epidemiology of Mtb in South Africa (41), isolates of lineage 5, 6 or 7 were absent and isolates of lineages 1 and 3 were rare. Lastly, CFZ exposure, which can result in BDQ cross-resistance through mutations in the Rv0678 gene, was not considered because data on CFZ exposure status was not available (42).…”