Conceived and designed the experiments: HSC CM VA DC GC GvC EG. Performed the experiments: HSC OM JS MB. Analyzed the data: HSC VA OM DC JS MB. Contributed reagents/materials/analysis tools: JS MB GC. Wrote the paper: HSC CM DC GvC EG.
The authors have declared that no competing interests exist.
Although multidrug-resistant tuberculosis (MDR-TB) is emerging as a significant threat to tuberculosis control in high HIV prevalence countries such as South Africa, limited data is available on the burden of drug resistant tuberculosis and any association with HIV in such settings. We conducted a community-based representative survey to assess the MDR-TB burden in Khayelitsha, an urban township in South Africa with high HIV and TB prevalence.
A cross-sectional survey was conducted among adult clinic attendees suspected for pulmonary tuberculosis in two large primary care clinics, together constituting 50% of the tuberculosis burden in Khayelitsha. Drug susceptibility testing (DST) for isoniazid and rifampicin was conducted using a line probe assay on positive sputum cultures, and with culture-based DST for first and second-line drugs. Between May and November 2008, culture positive pulmonary tuberculosis was diagnosed in 271 new and 264 previously treated tuberculosis suspects (sample enriched with previously treated cases). Among those with known HIV status, 55% and 71% were HIV infected respectively. MDR-TB was diagnosed in 3.3% and 7.7% of new and previously treated cases. These figures equate to an estimated case notification rate for MDR-TB of 51/100,000/year, with new cases constituting 55% of the estimated MDR-TB burden. HIV infection was not significantly associated with rifampicin resistance in multivariate analyses.
There is an extremely high burden of MDR-TB in this setting, most likely representing ongoing transmission. These data highlight the need to diagnose drug resistance among all TB cases, and for innovative models of case detection and treatment for MDR-TB, in order to interrupt transmission and control this emerging epidemic.
There are an estimated 13,000 cases of multidrug-resistant tuberculosis (MDR-TB) emerging in South Africa each year
Drug-resistant tuberculosis (DR-TB) requires much longer and more costly treatment regimens than drug-susceptible tuberculosis, and in most high HIV prevalence settings, there is limited capacity for diagnosis. Thus, in many settings, few patients are diagnosed with DR-TB and even fewer receive adequate treatment. The HIV epidemic has driven dramatic increases in tuberculosis case notifications in southern Africa
To date, there have been limited data available on the prevalence of DR-TB in high HIV prevalence settings. Only 12 countries in the African region have conducted nationwide surveys since 2000, with few disaggregating by HIV status
Khayelitsha is a high population density township situated 30 km from Cape Town with a population estimated at more than 500,000. Poverty and unemployment are high and the majority live in informal housing. In 2006, the prevalence of HIV among antenatal clinic attendees was 33% and close to 6,000 tuberculosis cases were notified in 2008, giving an estimated case notification rate of 1158/100,000/year (based on an estimated population of 500,000)
A cross-sectional survey among clinic attendees suspected for pulmonary tuberculosis was conducted in two large primary care clinics in Khayelitsha between May and November 2008. These clinics combined account for 50% of the TB case burden in Khayelitsha. Clinic attendees, aged 18 years and over, not currently receiving TB treatment and in whom tuberculosis was suspected clinically, were eligible to participate. The study was explained by clinic staff and written informed consent was obtained from each participant. The study was approved by the University of Cape Town Ethical Review Committee and by both the City of Cape Town and the Western Cape Province Health Department.
The desired sample size was determined separately for new and previously treated culture positive TB cases. Previous tuberculosis treatment was defined as 1 month or more of anti-tuberculosis treatment. Based on estimated proportions of MDR-TB of 2% and 4% respectively in South Africa
Two sputum samples were collected one hour apart and were transported the same day to the National Health Laboratory Service (NHLS) TB laboratory in Cape Town as per routine practice. Fluorescence sputum smear microscopy was performed on both sputum specimens in accordance with guidelines from the International Union Against Tuberculosis and Lung Disease (IUATLD)
Resistance to rifampicin and isoniazid was determined on positive cultures using a rapid line probe assay (LPA) (Hain GenoType MTBDRplus) as previously trialled in this laboratory
Data on previous TB treatment, demographics, HIV status and antiretroviral treatment at the time of TB diagnosis were recorded routinely during the clinical assessment by a primary care nurse. Data on previous TB treatment was additionally verified among patients starting treatment through a medical record review. All data were entered on a database using Excel (Microsoft Office 2003). Data analysis, including multivariate logistic regression models, was conducted with SPSS (Release 17.0.0, 2008).
To investigate factors potentially associated with rifampicin resistance, both univariate and multivariate logistic regression analyses were conducted. Previous TB treatment was classified as either: new (not previously treated), the most recent TB treatment episode in 2007/08 (the survey was conducted between May and November 2008) or the most recent treatment episode prior to 2007. Factors significant or approaching significance (p = 0.05) on univariate analysis were entered into the multivariate logistic regression models. Factors were coded as categorical variables with missing data included as a category. All factors were entered as a block into multivariate logistic regression models and goodness of fit was assessed with the Hosmer and Lemeshow statistic
The MDR-TB burden in Khayelitsha was estimated by applying the proportions of MDR-TB found through the survey to the case notification data for the whole of Khayelitsha in 2008
During the study period, 1,842 (96%) of the 1,928 eligible clinic attendees suspected for pulmonary tuberculosis seen in the two clinics were recruited to the survey (
New TB suspects were recruited from May through August, while previously treated suspects were recruited May through November, 2008. * Valid culture results include negative and positive cultures and exclude contaminated cultures, those found to be non-tuberculous mycobacteria or those with no growth.
In TB suspects for whom valid culture results were obtained (including valid positive and negative cultures), culture positive tuberculosis was diagnosed in 271/732 (37%) cases among those not previously treated and 264/843 (31%) cases among those with more than one month of previous tuberculosis treatment (
HIV status was known for 88% of new and 90% of previously treated cases (
New TB | Previously treated TB | |
Total | 271 | 264 |
HIV negativeHIV positiveHIV status unknown | 106132 (55% of known HIV status)33 (12%) | 70168 (71% of known HIV status)26 (10%) |
MaleFemale | 155116 (43%) | 16796 (36%) |
Median age (IQR)Age 18–25Age 26–35Age 36+ | 32 (13)58 (21%)118 (44%)95 (35%) | 36 (13)34 (13%)102 (39%)128 (48%) |
Valid LPA results were obtained for 267 (98.5%) of the 271 new TB cases and 259 (98.1%) of the 264 previously treated TB cases. Valid culture-based DST results were available for 237 (87.5%) and 221 (83.7%) of new and previously treated cases respectively (
New TB cases | Previously treated TB cases | |
Total (positive culture) | 271 | 264 |
LPA results available | 267 | 259 |
Susceptible | 244 (91%) | 223 (86%) |
H-mono | 11 (4.1%) | 7 (2.7%) |
R-mono | 4 (1.5%) | 11 (4.2%) |
MDR-TB | 8 (3.0%) | 18 (6.9%) |
12 (4.5%) | 29 (11.2%) | |
19 (7.1%) | 25 (9.7%) | |
Culture-based DST available | 237 | 221 |
Susceptible to first-line | 186 (79%) | 167 (76%) |
First-line mono-resistance | 35 (14.8%) | 38 (17.2%) |
H-mono | 8 (3.4%) | 15 (6.8%) |
R-mono | 2 (0.8%) | 2 (0.9%) |
First-line poly-resistance | 9 (3.8%) | 5 (2.3%) |
MDR-TB Total | 7 (3.0%) | 11 (5.0%) |
MDR-TB with second line resistance | 3 (1.3%) | 5 (2.3%) |
XDR-TB | 1 (0.4%) | 1 (0.5%) |
9 (3.8%) | 13 (5.9%) | |
22 (9.3%) | 31 (14.0%) | |
Either LPA and culture DST | 269 | 261 |
MDR-TB | 9 (3.3%) | 20 (7.7%) |
14 (5.2%) | 29 (11.1%) | |
28 (10.4%) | 41 (15.7%) |
The line probe assay identified more rifampicin resistant cases than did culture-based DST, while more isoniazid resistance was identified through culture-based DST (
Resistance profile – culture-based DST | LPA MDR-TB | LPA Susc | LPA R-mono |
no culture DST available | 7 | ||
Susceptible | 1 | ||
H | 1 | 1 | |
HR | 2 | ||
HRE | 1 | 1 | |
HRS | 1 | ||
HREZ | 3 | ||
HRSZ | 2 | ||
HREZ Eto | 1 | ||
HRESZ Eto | 1 | ||
HZ Amk | 1 | ||
HRS Km | 1 | ||
HRESZ Ofx | 1 | ||
HRESZ Eto Km Amk Cm | 1 | ||
HRESZ Eto Ofx | 1 | ||
HRESZ Eto Ofx Km Amk Cm | 2 | ||
Total | 26 | 1 | 2 |
Among the 22 MDR-TB cases with culture-based DST available, 9 (41%) were found to have additional second-line resistance, including 7 (32%) with resistance to a fluoroquinolone or a second-line injectable agent or both (
Resistance profile | Number |
R Eto | 1 |
H Eto | 3 |
HS Eto | 2 |
HZ Amk | 1 |
Eto | 7 |
Cm | 6 |
Amk Cm Eto | 1 |
Cm Ofx | 1 |
In 2008, 5,791 cases of pulmonary tuberculosis were reported from primary care clinics in Khayelitsha. When the percentages of MDR-TB are applied to these case notification figures, 257 MDR-TB cases would have been diagnosed if all TB cases were tested: 4.4% of the notified TB cases in that year (
Given the significant burden of rifampicin resistance not defined as MDR-TB, associations with HIV infection and other factors were assessed with rifampicin resistance. Among HIV infected new cases, 5.3% (7/131) were rifampicin resistant, compared to 3.8% (4/105) among HIV negative new cases. For HIV infected previously treated cases, 13.9% (23/165) were rifampicin resistant compared to 5.7% (4/70) among HIV negative cases. For the total combined sample, there was a significant association between HIV infection and rifampicin resistance on univariate analysis, but this did not reach significance in the multivariate analysis (OR = 2.26, 95% CI 0.91–5.61); a recent TB treatment episode and female sex were significant predictors (
Univariate | Multivariate | |||||||
Factor | Categories | Rifampicin resistant TB (%) | OR | 95% CI | P value | OR | 95% CI | P value |
Previous TB treatment | New (ref)Prev. TB 2006 or beforePrev. TB 2007/08Missing | 14 (5.2%)10 (6.5%)15 (18.3%)4 (15.4%) | 1.274.083.31 | 0.55–2.941.88–8.861.00–10.92 | 0.57<0.00010.049 | 1.404.424.23 | 0.59–3.321.97–9.931.22–14.59 | 0.45<0.00010.023 |
HIV status | Negative (ref)PositiveMissing | 7 (4.0%)30 (10.1%)6 (10.2%) | 2.712.71 | 1.16–6.300.88–8.44 | 0.0210.084 | 2.262.89 | 0.91–5.610.90–9.33 | 0.0790.075 |
Sex | Male (ref)Female | 18 (5.6%)25 (12.0%) | 2.30 | 1.22–4.33 | 0.010 | 2.03 | 1.01–4.06 | 0.047 |
Age | 26+ (ref)18–25 | 31 (7.1%)12 (13.2%) | 2.00 | 0.98–4.06 | 0.055 | 2.16 | 1.0–4.70 | 0.051 |
Most recent TB episode | 2006 or bef (ref)2007/08Missing | 10 (6.5%)15 (18.3%)4 (15.4%) | 3.202.60 | 1.3–7.50.75–9.02 | 0.0070.13 | 3.423.02 | 1.43–8.150.85–10.80 | 0.0060.089 |
HIV status | Negative (ref)PositiveMissing | 3 (4.3%)23 (13.9%)3 (11.1%) | 3.622.91 | 1.1–12.50.55–15.46 | 0.040.21 | 3.103.17 | 0.85–11.330.57–17.5 | 0.0870.19 |
Sex | Male (ref)Female | 13 (7.8%)16 (17.0%) | 2.41 | 1.1–5.3 | 0.03 | 1.97 | 0.85–4.56 | 0.11 |
Age | 26+ (ref)18–25 | 22 (8.7%)6 (18.2%) | 1.98 | 0.74–5.30 | 0.17 | |||
Previous TB treatment | New (ref)Prev. TB 2006 or beforePrev. TB 2007/08Missing | 7 (5.3%)7 (7.1%)14 (26.9%)2 (13.3%) | 1.366.532.73 | 0.46–4.022.46–17.340.51–14.51 | 0.58<0.00010.24 | 1.677.274.26 | 0.53–5.232.61–20.250.74–24.37 | 0.38<0.00010.103 |
ART at TB diagnosis | No ART (ref)On ART at diagMissing | 18 (8.7%)9 (17.3%)3 (7.9%) | 2.190.89 | 0.92–5.200.25–3.20 | 0.0770.87 | 1.590.88 | 0.62–4.080.23–3.33 | 0.340.85 |
Sex | Male (ref)Female | 10 (6.9%)20 (13.2%) | 2.05 | 0.92–4.54 | 0.078 | 1.90 | 0.81–4.50 | 0.14 |
Age | 26+ (ref)18–25 | 23 (8.9%)7 (18.4%) | 2.31 | 0.92–5.82 | 0.077 | 2.18 | 0.75–6.33 | 0.15 |
CD4 at TB diagnosis | CD4 >100 (ref)CD4 <100CD4 missing | 11 (8.5%)12 (15.8%)7 (7.8%) | 2.030.91 | 0.84–4.860.34–2.45 | 0.110.86 | |||
Eastern Europe and the former Soviet Union have been described as global “hot spots” for tuberculosis drug resistance
The data presented here show that in Khayelitsha, a densely populated urban township in South Africa, the estimated burden of MDR-TB is extremely high, at 51/100,000/year based on notified TB cases, with incidence likely to be considerably higher taking into account incomplete tuberculosis case detection in the community. A large proportion of MDR-TB cases have pre-existing second-line tuberculosis resistance and indeed XDR-TB in the absence of extensive previous second-line treatment (data not shown). These data suggest a burden of MDR-TB more than twice that previously estimated for South Africa. Given the high population density, poverty, high HIV and TB prevalence in Khayelitsha, these data are unlikely to be representative nationally. However the living conditions in Khayelitsha are reflective of the large proportion of South Africans who are most at risk for tuberculosis. Urban and peri-urban townships like Khayelitsha therefore should be the focus of particular attention for both surveillance and epidemic control.
Currently available diagnostics for tuberculosis drug resistance rely on culture and are therefore slow, cumbersome and commonly only available through centralised laboratories. As a result, DST is only selectively available if at all and even in South Africa is only available for previously treated TB cases. The data from Khayelitsha suggest that a large proportion of MDR-TB cases occur in new TB suspects, who are not routinely tested for drug resistance. These patients are therefore likely to receive ineffective first-line anti-tuberculosis treatment resulting in likely amplification of resistance, poor treatment outcomes including increased mortality, and not least fuelling increasing transmission through remaining infectious and inadequately treated in the community. If DST is only accessible for those failing treatment, a large proportion of cases will be missed due to the high risk of death among HIV positive patients with untreated DR-TB
The extent of MDR-TB among new, previously untreated TB cases in this survey suggests that at least half of all MDR-TB is due to ongoing primary transmission in Khayelitsha. Transmission may be even higher; up to 80% of cases may be transmitted, as it cannot be assumed that MDR-TB among previously treated cases is always due to resistance amplification. While this is a gross approximation of transmission, clearly transmission remains a substantial cause of incident MDR-TB cases in this setting.
Tuberculosis drug resistance has traditionally been blamed on poor TB control programmes and poor patient compliance with treatment. However, HIV infection has also been suggested to contribute to both an increased risk of acquiring resistance and to the risk of direct infection with DR-TB. Acquired rifamycin resistance has been demonstrated among HIV positive TB patients in well controlled clinical trials and other studies
HIV infection was not significantly associated with rifampicin resistant TB in multivariate analyses, either overall or among previously treated TB cases in this large community based representative survey. Rather, consistent significant associations were found between recent TB treatment and rifampicin resistance. These data suggest that any observed associations between HIV infection and DR-TB may be mediated through the propensity for HIV infected individuals to be repeatedly treated for TB and that HIV is not an independent risk factor for infection and development of active DR-TB disease. However, without prospective data and molecular genotyping of strains from subsequent TB episodes, it is not possible to differentiate the extent of acquisition of resistance during TB treatment, and the impact of HIV infection and concomitant ART on resistance acquisition, from reinfection with a DR-TB strain. It may be that HIV infected individuals who have been treated for TB previously are more exposed to DR-TB in nosocomial settings. Indeed, nosocomial transmission is suggested to be a significant cause of MDR- and XDR-TB transmission in Msinga district, KwaZulu Natal, South Africa
This survey is subject to the usual limitations in survey design and data collection. While restricted to two primary care clinics in Khayelitsha, these two clinics were responsible for diagnosing and treating approximately 50% of TB cases in Khayelitsha in 2008. Nonetheless, if nosocomial transmission is a significant factor driving DR-TB transmission, the risk of DR-TB infection through a larger clinic may be greater than that in the smaller primary care clinics in Khayelitsha. While previous tuberculosis treatment was verified through medical record review when possible, there is likely to be a tendency for patients to not report previous treatment in order to avoid receiving daily streptomycin injections and the longer treatment course. While such a bias could lower our estimate of overall MDR-TB prevalence, the data still suggest a substantial number of MDR-TB cases would be diagnosed if all TB cases were to be tested.
The Khayelitsha tuberculosis treatment programme reports reasonable treatment outcomes for 2008; currently treatment success stands at 82% for new TB cases and 50% for previously treated cases
Although HIV infection, along with previous sub-optimal tuberculosis treatment programmes, may have contributed to the initial emergence of tuberculosis drug resistance, the high community HIV prevalence in Khayelitsha does not appear to be a significant factor
The authors wish to acknowledge the contribution of health care workers from the 2 clinics involved in this study. We also thank Tim Spelman for advice on the statistical analyses used in this article, and Zaheda Bhyat for laboratory analyses. Finally, we acknowledge the patients suffering from tuberculosis in Khayelitsha.