High Rates of Clustering of Strains Causing Tuberculosis in Harare, Zimbabwe: a Molecular Epidemiological Study

Abstract

We examined the pattern of tuberculosis (TB) transmission (i.e., reactivation versus recent transmission) and the impact of human immunodeficiency virus (HIV) infection in Harare, Zimbabwe. Consecutive adult smear-positive pulmonary TB patients presenting to an urban hospital in Harare were enrolled. A detailed epidemiological questionnaire was completed, and tests for HIV type 1 and CD4 cell counts were performed for each patient. Molecular fingerprinting of the genomic DNA recovered from cultures of sputum was performed by two molecular typing methods: spacer oligonucleotide typing (spoligotyping) and analysis of variable number of tandem DNA repeats (VNTRs). A cluster was defined as isolates from two or more patients that shared the same spoligotype pattern or the same VNTR pattern, or both. DNA suitable for typing was recovered from 224 patients. The prevalence of HIV infection was 79%. Of 187 patient isolates (78.6%) typed by both spoligotyping and analysis of VNTRs, 147 were identified as part of a cluster by both methods. By spoligotyping alone, 84.1% of patient isolates were grouped into 20 clusters. The cluster size was generally <8 patient isolates, although three large clusters comprised 68, 25, and 23 patient isolates. A total of 89.4% of the patient isolates grouped into 12 clusters defined by analysis of VNTRs, with 2 large clusters consisting of 127 and 13 patient isolates, respectively. Thirty-six percent of patient isolates with a shared spoligotype and 17% with a shared VNTR pattern were geographically linked within Harare, but they were not linked on the basis of the patient's home district. In a multivariate analysis, there were no independent predictors of clustering, including HIV infection status. Comparison with the International Spoligotype database (Pasteur Institute, Pointe à Pitre, Guadeloupe) demonstrated that our three largest spoligotype clusters are well recognized and ubiquitous in Africa. In this epidemiologically well characterized urban population with a high prevalence of HIV infection, we identified a very high level of strain clustering, indicating substantial ongoing recent TB transmission. Geographic linkage could be detected in a proportion of these clusters. A small group of actively circulating strains accounted for most of the cases of TB transmission.Tuberculosis (TB) has reemerged as an important public health problem in Zimbabwe. Following a stabilization of the TB rates in the early 1980s at approximately 50 per 100,000 population, since 1987 there has been a dramatic increase to 250 per 100,000 population, which is largely attributable to the human immunodeficiency virus (HIV) epidemic in sub-Saharan Africa (9, 28).Strain-specific markers for the differentiation of Mycobacterium tuberculosis complex strains are reliable tools for the identification of specific strains and are useful for epidemiological studies of TB. The most extensively used differentiation method is restriction fragment length polymorphism (RFLP) typing, which uses the insertion sequence IS6110...

Heterogeneity in tuberculosis transmission and the role of geographic hotspots in propagating epidemics

“…By contrast, the areas of highest TB incidence in Rio de Janeiro are centrally located and in close geographic proximity to commercial districts and other residential areas, making them potentially more important to ongoing city-wide TB transmission. Similar findings, in which the majority of cases attributed to recent transmission are not geographically aggregated, have been reported in Baltimore (25) and Harare, Zimbabwe (26). Although molecular epidemiology studies are unlikely to be undertaken on a sufficient scale to ascertain the relative rates of transmission within vs. across hotspots on a population level (10), further modeling and mapping studies may shed light on this question, which is of critical importance in determining the appropriate prioritization of hotspot-centered interventions in TB control.…”

“…We therefore set three independent TB transmission rates: hotspot-to-hotspot, community-to-community, and the relative rate of cross-population (compared with within-population) transmission. A focused review of the literature (SI Materials and Methods) suggested that 30-50% of recent TB transmission at the city level is geographically clustered (25,26,28), but a small study in a Rio de Janeiro hotspot (29) found a higher rate of geographic aggregation (70%). Thus, for our baseline scenario, we estimated that a case of active TB in the hotspot would generate 0.5 secondary transmission events outside the hotspot for every transmission event occurring within the hotspot-a scenario that would lead to 67% geographic clustering among secondary cases if linked to the index case.…”

Genetic profile of Mycobacterium tuberculosis and treatment outcomes in human pulmonary tuberculosis in Tanzania

“…The consistency of results also indicates relative temporal stability of this pattern, as isolates from this study were collected over a much longer time period (7 years) than previous studies. The LAM family has also been reported to predominate in Zimbabwe and Zambia (Easterbrook et al, 2004;Chihota et al, 2007). In contrast, one study in Kampala, Uganda showed predominance of the T2 family (Asiimwe et al, 2008).…”

Determinants of Cluster Size in Large, Population-Based Molecular Epidemiology Study of Tuberculosis, Northern Malawi

“…Spoligotype 59 was common in the Malawi population in all groups of patients, clustered and unique, and was associated with a wide diversity of RFLP patterns, which suggests that it may be a longstanding strain in this area. It was also the most common spoligotype found in studies in Zimbabwe and Zambia (18,19). However, spoligotype 59 was particularly common among the isolates from large clusters, with more closely related RFLP patterns, consistent with some variants having high transmissibility.…”

“…However, spoligotype 59 was particularly common among the isolates from large clusters, with more closely related RFLP patterns, consistent with some variants having high transmissibility. Spoligotype 59 has been classifi ed as belonging to the Latin-American-Mediterranean lineage (18), and as part of the strain family Southern Africa Family 1 (19). The large cluster strain kps97 had a Beijing spoligotype and in total, we have previously identifi ed 44 patients with Beijing strains in this dataset, with 12 different RFLP patterns (14).…”