Patient recruitment started in May 2009 and was completed in July 2009 for NCs and February 2010 for PTCs. Of 988 screened patients, 840 (85%) met the study inclusion criteria (Figure 2). During the survey period, the national TB program registered 1,175 TB smear-positive case-patients (618 NCs and 557 PTCs). Therefore, 84% of all registered patients were screened for the survey. Reasons given by the health personnel for not screening were heavy workload in the health center and staff turnover. No significant differences in age and sex between screened and nonscreened patients were observed.

Of 822 samples shipped to the mycobacteriology laboratory in Germany, 814 were cultured (99%). Of these samples, 74 (9.1%) were negative and 74 (9.1%) were contaminated. Half the negative culture results (n = 37) were from the PTC subgroup of treatment failure patients.

Fifteen mycobacteria other than M. tuberculosis were isolated: M. avium (n = 6), M. avium complex (n = 5), M. fortuitum (n = 2), and M. kansaii (n = 2). In 13 cultures, >1 type of mycobacteria grew.

For baseline characteristics of the included patients (Table 1), overall male-to-female ratio was 0.9 and median age was 33 years (interquartile range 27–41 years). The patients were equally distributed among the 4 regions of Swaziland. Regarding socioeconomic aspects, 80.6% of the patients had either not attended school or had not reached high school, and 68.8% had no permanent job.

Among PTCs, most had received only 1 previous category I treatment course; 55.7% had a successful outcome (cured or treatment completed) in their last treatment, and 28.6% failed treatment. HIV status was known for 758 (90.2%) patients. Of these patients, 606 were HIV positive (79.9%).

Of 352 NCs tested, 54 (15.3%) had TB strains resistant to >1 first-line drug, and 47 (13.4%) had strains resistant to isoniazid (Table 2). An MDR strain was isolated in 27 NCs, resulting in MDR TB prevalence of 7.7% (95% CI 4.9%–10.5%). Almost half (45.2%) of the 281 PTCs had a TB strain resistant to >1 drug; 127 (45.2%) had a strain resistant to isoniazid, and 95 (33.8%) had MDR TB (95% CI 28.3%–39.3%). Among PTCs, all who had failures of category II treatment (6/6), 83.5% (40/48) who had failures of category I treatment, 23.2% (42/181) relapses, and 13.4% (4/30) who had default treatment were infected with an MDR strain. The proportion of resistance to pyrazinamide among MDR TB strains was 74.1% (20/27) for NCs and 67.4% (64/95) for PTCs.

Among strains resistant to isoniazid or rifampin, second-line drug resistance was most frequently seen with ethionamide (Table 3). Of the 10 strains resistant to ofloxacin, 8 were also resistant to moxifloxacin (3 in NCs, 5 in PTCs). Only 1 XDR TB strain was isolated; it was resistant to moxifloxacin.

In univariate analysis, past TB treatment (PTCs), female sex, HIV infection, and age 28–40 years were significantly associated with MDR TB (Table 4). In multivariate analysis, PTCs and HIV-infected patients were 4× and ≈2× more likely to be infected with an MDR TB strain, respectively, compared with NCs and HIV-noninfected patients. The youngest age group was close to being significantly associated with MDR TB regardless of HIV status and history of previous treatment.

In Swaziland, 7.7% and 33.8% of TB smear-positive NCs and PTCs, respectively, had MDR. This represents an 8.5-fold and 3.7-fold increase compared with MDR prevalence among NCs and PTCs, respectively, from the previous DST survey in 1995. This prevalence appears to be the highest MDR TB prevalence reported in an African country thus far. In neighboring countries, as in South Africa, the estimated MDR TB prevalence was 1.8% (95% CI 1.5–2.3) in NCs and 6.7% (95% CI 5.5–8.1) in PTCs in 2002 (5). In Mozambique, 3.5% (95% CI 2.5–4.7) of NCs and 11.2% (95% CI 4.2–30.0) of PTCs had MDR TB in 2006 (5). The next closest value of prevalence of MDR in new case-patients in an African country is nearly half the one observed in Swaziland (Rwanda, 3.9%) (5). If we consider the extremely high incidence of TB in the population, the prevalence of resistance observed would result in a high MDR TB population rate, comparable to that observed in former Soviet Union countries. Resistance to fluoroquinolones and second-line anti-TB injectable drugs was surprisingly low, however, with only 1 XDR TB patient seen.

Several factors may have contributed to the increase of MDR TB in Swaziland. First, health services are overwhelmed by a huge increase in TB patients due to the HIV epidemic and a lack of health personnel, which could result in poor TB case management and subsequent development of drug resistance. Second, many citizens from Swaziland regularly cross the border to work in mines in South Africa, where the prevalence of MDR TB is high (12). Third, the small size of the country (17,364 km²) enables the mobility of the population between regions.

High HIV rates might also play a role. In our study, HIV co-infection was independently associated with MDR TB. The correlation between HIV infection and anti-TB drug resistance remains controversial; there were more frequent associations reported in studies in North America than in studies in Africa (13–15). Several factors have been proposed to explain such an association. Malabsorption of anti-TB drugs has been documented for HIV-positive patients, which could increase the risk for acquired rifampin resistance (13). In settings where HIV infection is linked to socioeconomically vulnerable populations, poor treatment adherence and lack of access to proper treatment may contribute to the development of drug resistance (14). Also, persons with HIV/AIDS may be more exposed to patients with MDR TB during hospitalizations or consultations in health structures with insufficient infection control because the complexity of management of MDR TB patients entails frequent visits to health facilities, which also increases the risk for MDR TB nosocomial outbreaks among HIV-infected persons (16–18). Finally, TB progresses rapidly in HIV-infected patients, who are likely to reactivate an infection acquired recently, compared with HIV-negative patients, who usually reactivate latent infection acquired a long time ago.

Therefore, we could speculate that TB strains harbored by HIV-infected patients are more likely to reflect the strains currently circulating in the community. This suggestion could explain the more frequent association observed between HIV infection and primary MDR TB compared with acquired MDR TB (14). In our study, the adjusted prevalence ratio was higher for HIV-infected NCs than PTCs (2.14 versus 1.74), although estimates were not significantly different because of the small sample size (data not shown). We also observed an association between the youngest age group, which is more likely to be recently infected, and MDR TB after correcting for HIV status and history of previous TB treatment. Unfortunately, because of the small sample size, we were not able to further analyze this association by stratified analysis. Nonetheless, the role of HIV infection on the transmission of MDR TB could be further assessed in a cluster analysis of the MTB strains by using DNA fingerprinting data.

In eastern European countries, the specific phylogenetic lineage Beijing M. tuberculosis genotype has been identified as a particularly prevalent strain independently associated with MDR TB and transmission, indicating a potential role of this pathogen in the epidemiology of drug resistance in these regions (19,20). The Beijing strain has also been isolated in several African countries (21–26), and an association between this strain and the emergence of drug resistance has been reported in South Africa (27). Such molecular epidemiologic studies would be recommended in Swaziland.

This study had several limitations. First, the survey population only represented the population of patients diagnosed through the health system. Therefore, not much is known about patients lacking access to health services. The 15 clinics providing TB diagnosis and treatment in the country were included in the survey, but, despite free TB diagnosis and treatment in Swaziland, transport costs and user fees for health facility registration are factors that can limit access to care. Also, almost 16% of the registered smear-positive patients during the survey period were not screened. Although, basic demographic data between assessed and nonassessed patients were not statistically different, we cannot fully exclude the possibility of a selection bias. The proportion of patients with unknown HIV status could have also biased the association seen with MDR prevalence. Therefore, we conducted a sensitivity analysis under a pessimistic assumption that all patients with unknown HIV status were HIV positive and under an optimistic assumption that they were all HIV negative. Figures did not diverge from the original result.

Current WHO recommendations for countries with high anti-TB drug resistance rates and high HIV prevalence are to systematically perform DST at the time of initiation of anti-TB therapy to avoid deaths caused by unrecognized MDR TB (28,29). The use of rapid drug-resistance testing methods (i.e., PCR) is also recommended to enable a quick start to empirical treatment in potential case-patients while waiting for DST results (28). Such strategies require a major effort from national TB programs in terms of laboratory capacity. Line probe assays were recently introduced at the National Reference Laboratory in Swaziland. New technologies, such as the fully automated PCR method of Xpert MTB/RIF (Cepheid, Sunnyvale, CA, USA) would be useful in Swaziland to detect M. tuberculosis and resistance to rifampin at lower levels of health care services (30).

The national TB program in Swaziland should also consider implementing a surveillance system for anti-TB drug resistance to follow drug resistance trends over time, detect outbreaks in a timely manner, and monitor achievements in infection control and treatment measures (31,32). Periodic surveys may be a costly alternative in terms of logistics, human resources, and shipment costs (≈€137,000 for this survey). Similarly, the implementation of a treatment strategy able to effectively treat all case-patients with drug-resistant TB in contexts of limited health services capacity, lack of health personnel, and high risk of nosocomial drug resistance transmission is another challenge. The National MDR TB Program of Swaziland was approved in 2009 by the WHO Green Light Committee for a MDR TB pilot project, and organizations such as Médecins Sans Frontières provide support to the program in certain regions. However, the overall response for MDR TB and HIV treatment for co-infected patients still needs to be scaled up.

In conclusion, this study reports a very high prevalence of MDR TB in Swaziland, which currently appears to have the highest prevalence in Africa, and shows a rapid increase in the prevalence of MDR TB in the space of slightly more than a decade. The experience from Swaziland calls for further investigation into the effect of the HIV epidemic on TB drug resistance. These results also highlight the inappropriateness of drug resistance surveys to detect early increase of drug resistance in a country when the surveys are not performed regularly. The lack of recent representative data in many African countries probably underestimates the prevalence of drug-resistant TB in this region (5,33). The high prevalence of drug resistance in a country already facing a huge epidemic of TB and HIV shows an urgent need for major interventions in terms of detection, treatment, and infection control.