Background In 2006, South Africa documented its first outbreak of extensively drug-resistant (XDR-TB) in Tugela Ferry, Kwa-Zulu Natal. Delayed diagnosis of XDR-TB increases mortality, emphasizing the need or rapid diagnostics. The MTBDRsl assay rapidly identifies resistance to fluoroquinolones (FLQ) and aminoglycosides/capreomycin (AG/CP). Hospitalization provides the ideal opportunity for nosocomial infections of TB, including M/XDR-TB, with its associated morbidity and mortality. Occupational exposures amongst healthcare workers are also of concern. Rapid knowledge of second-line resistance patterns of these in-patients would allow for quick stratification and administration of individualized anti-chemotherapy treatment by clinicians, thereby reducing morbidity and mortality within this population. Methods ` A prospective cohort study was performed from admission sputum specimens collected from patients admitted to Sizwe Tropical Disease Hospital (Sizwe Hospital), the only M/XDR-TB referral hospital in Gauteng, South Africa. MTBDRplus (version 1) and MTBDRsl line probe assays (LPAs) were performed on all sputa, irrespective of smear positivity and subsequently on Mycobacteria Growth Indicator Tube (MGIT) isolates. The results from the LPAs were compared to the gold standard MGIT 960 culture and direct susceptibility testing (DST) results. Results From April 2011 to January 2012, 150 participants were recruited. Seventy-five (50.0%) were female, 91 (60.7%) were HIV-positive and 9 (6.00%) had an unknown HIV status. Of the MGIT cultures performed 71 (47.3%) were positive for Mycobacterium tuberculosis (MTB), 31 (20.7%) negative, 40 (26.7%) were contaminated and 8 (5.63%) were inadvertently discarded by the routinen laboratory. The proportion of smear-negative specimens in HIV- positive patients was not statistically significantly different to the smear-negatives in HIV-negative patients (57.1% vs. 46.0%; p=0.139). On phenotypic drug susceptibility testing, 47 (66.2%) were resistant to only isoniazid and rifampicin (MDR-TB), 10 (14.0%) were MDR-TB with added resistance to ofloxacin (pre-XDR-TB FLQ), 4 (5.63%) were MDR-TB with added resistance to kanamycin (pre-XDR-TB AG/CP), 4 (5.63%) were MDR-TB with added resistance to both ofloxacin and kanamycin (XDR-TB), 3 (4.23%) were mono-isoniazid resistant, 2 (2.82%) mono-rifampicin resistant, and 1 (1.41%) was TB-drug sensitive. No TB drug-sensitive sputum specimens were collected and used as a control group for the MTBDRplus (version 1) assay, thus only sensitivity indices and positive predictive values (PPVs) could be interpreted.All specimens collected were used as an inherent control group for the performance of the MTBDRsl assay, thus sensitivity and specificity indices together with the PPVs and NPVs, were calculated. From all sputum samples collected, including both smear-positives and smear-negative specimens, the sensitivity of the MTBDRplus (version 1) for RIF and INH was 98.1% for both drugs. Overall sensitivity for the MTBDRsl assay to detect ofloxacin (OFX) and kanamycin (KAN) resistance was 90.9% and 42.9%, respectively. The specificity was 100.0% and 95.7%, respectively. From smear-positive specimens, the sensitivity for OFX and KAN was 100.0% and 50.0%, respectively. The specificity was 100.0% and 96.8%, respectively. From smear-negative specimens the sensitivity was 50.0% and 33.3%, respectively. The specificity was 100.0% and 92.9%, respectively. From MGIT culture isolates, sensitivity for RIF and INH was 98.2% and 94.5% respectively. The sensitivity for OFX and KAN were 100.0% and 42.9%, respectively, whereas the specificity was 95.6% and 100.0%, respectively. Conclusion The performances of both LPAs correlate with other local and international publications. On direct, smear-positive sputa both LPAs perform well. From these, the MTBDRsl assay is a good rule-out test for detection of resistance to FLQ and AG/CP. For FLQ, it’s a good rule-in test: this indicates that the MTBDRsl assay can be used as a rapid screen for the onset of XDR-TB. As predicted, MTBDRsl does not perform well on smear-negative specimens, whereas the MTBDRplus (version 1) does. On cultures, both LPAs perform well.

Objective The consistent emerging of multidrug-resistant tuberculosis (MDR-TB) cases are increasingly becoming a major threat and challenge in global TB control, especially in some resource-limited settings like India, China, South Africa. Currently there is no widely acknowledged treatment strategy for MDR-TB. Effectiveness and of current DOTS-Plus strategy is remaining controversial. This systematic review aims to investigate treatment outcomes for MDR-TB under DOTS-Plus and potential factors associated with poor outcome (death, default and failure). Methodology The literatures were searched in Pubmed, Medline, the Cochrane library, Essential Evidence Plus, EMBASE and CNKI. Some manual search articles were also added and 164 literatures in total were founded related to treatment outcomes for multidrug resistant patients under DOTS-Plus. After basically screening and carefully full-text reading, nine studies meeting the inclusion criteria were included. A total of 3358 participants from 8 high MDR-TB countries were investigated. Result Baseline characters were varied across these nine studies, including HIV prevalence (0-1.6%), MDR-TB prevalence (0-4.7%), previous treatment history (without TB treatment, with TB treatment but not under directly observed therapy, short courses (DOTS) and with TB treatment under DOTS), and male/female ratio (54%-86.5%). All studies reported a successful outcome rate (cure and complete) higher than 60 percent, and three of the studies reported higher than 70 percent, which are comparatively high in MDR-TB treatment. Factors associated with poor outcomes that reported by these studies were including alcohol use/ abuse, homelessness, unemployment, imprisonment, BMI, cavitary and bilateral disease, missing doses, and resistant to some second-line drugs. Conclusion In sum, the overall treatment outcomes from these nine studies under DOTS-Plus were acceptable, and most of them were satisfactory. Nevertheless, in consideration of potential bias arising from these cohort analyses, conclusions should be drawn carefully. Several major challenges restrict low- and middle- income countries from implementing DOTS-Plus, which put high command on TB infrastructure, policy commitment, human resources and financial support. Further effort could be put on systematical review and meta-analysis on cost-effectiveness of DOTS-Plus programs. In China, policy makers should pay attention to arrive at national and provincial guidelines of MDR-TB treatment under DOTS-Plus. / published_or_final_version / Public Health / Master / Master of Public Health

Background: There is widespread concern about the rise of drug-resistant TB because treatment outcomes of affected patients remain poor and treatment options are limited. After more than a forty-year gap without any breakthrough discovery, several new (bedaquiline and delamanid) and repurposed drugs (linezolid) are increasingly becoming available for use. However, data regarding the efficacy and safety of these drugs in drug-resistant TB patients, with or without HIV infection, from a real-life programmatic setting are lacking. This thesis aims to address that knowledge gap and provide information for management of drug-resistant TB in countries with high disease burden. Methods: A total of 326 drug resistant TB patients were prospectively followed up between January 2008 and April 2018. The efficacy and safety of two new drugs (bedaquiline and delamanid) and one repurposed drug (linezolid) was determined in these patients in three studies. In the first study, 24 months treatment outcomes and adverse event profiles were compared between extensively drug resistant (XDR) TB patients who received programmatic treatment regimens with the backbone of second line injectables and fluoroquinolones (nonbedaquiline-based) and those who received a bedaquiline- and/ or linezolid-based treatment regimen. The second study determined the frequency of system-specific adverse events associated with linezolid. The third study interrogated the safety and effectiveness of a strengthened treatment regimen containing a combination of delamanid and bedaquiline in patients with poor prognostic features compared to bedaquiline-based regimen. Results: In the first study, patients who received a bedaquiline-based treatment regimen had a significantly greater favourable outcome rate (66.2% vs 13.2%; p<0.001) ), more than a fourfold reduction in treatment failure rate (5.9% vs 26%; p<0.001 ) and less than a half of mortality rate compared to patients who received a non-bedaquiline-based regimen. The bedaquiline survival and favourable outcome effect remained significant in HIV-infected patients (p<0.001). The second study showed that linezolid interruption was common in patients receiving a bedaquiline-based treatment regimen, and that system-specific toxicity occurred within predictable time frames. It also showed that anaemia (77.3% versus 7.3%; p<0.001), peripheral neuropathy (63.6% versus 14.6%; p=0.003), and optic neuritis (18.2% versus 9.8%; p=0.34) occurred more frequently in linezolid interrupters than in non-interrupters. The third study showed that the use of delamanid-bedaquiline combination regimen was safe and efficacious in drug resistant TB patients with poor prognosis when compared with outcomes in the less sick patients who received a bedaquiline-based regimen. It also showed no significant difference in culture conversion rate at 6 months (92.5% versus 81.8%; p=0.26) or favourable treatment outcome rate (63.4% versus 67.5%; p=0.66) between the two groups. Although patients who received the combination regimen had more frequent occurrence of QTcF prolongation greater than 60 ms from baseline (p=0.001) and more episodes of QTcF greater than 450 ms during treatment (p=0.001), none of them were symptomatic or had delamanid or bedaquiline withdrawn from their regimen. Conclusion: These data demonstrated that new and repurposed drugs remarkably improved treatment outcomes in patients with drug-resistant TB. Although linezolid, which is an important component of the bedaquiline-based treatment regimen, is often associated with system-specific adverse events, these occurred at predictable time frames thereby guiding physicians to make informed management decisions. Lastly, drug resistant TB patients with poor prognosis may benefit from a regimen containing delamanid and bedaquiline which seems relatively safe from an adverse event perspective. These data, despite some limitations, make a case for a widespread and accelerated roll-out of new and repurposed drugs for the treatment of drug resistant TB.

Until the recent introduction of short course regimens, treatment regimens for multidrug resistant TB (MDR-TB) were long and toxic. Consequently, only approximately half of MDRTB patients completed their treatment. TB dosing guidelines have historically been unrefined with little consideration for pharmacokinetic/pharmacodynamic relationships. Large knowledge gaps therefore exist in the understanding of pharmacokinetic/pharmacodynamic relationships for both efficacy and toxicity in MDR-TB. My PhD used clinical pharmacology approaches to improve the understanding of drug exposures, toxicity, and exposure-toxicity relationships during the first 12 weeks of MDR-TB therapy. Aims and methods 1. Using non-compartmental analyses, describe the pharmacokinetics of cycloserine and, using regression modelling, explore the association of covariates with cycloserine exposure. 2. Using validated screening tools, describe the incidence of neuropsychiatric toxicity in MDR-TB patients, and explore associations with cycloserine pharmacokinetics. 3. Using a validated pain-rating scale in a crossover study design, investigate whether the addition of a local anaesthetic reduces kanamycin-related injection pain, and explore effects on kanamycin pharmacokinetics. 4. Using geometric mean ratios, compare the exposures of crushed versus whole formulations of pyrazinamide, moxifloxacin, ethionamide, ethambutol, cycloserine, and isoniazid. Results and conclusions We found no measurable terizidone in plasma supporting the hypothesis that terizidone is hydrolysed pre-systemically to cycloserine. The cycloserine time-concentration profile supports once daily dosing of terizidone. We describe a high incidence of peripheral neuropathy in MDR-TB patients with both cycloserine clearance and high-dose pyridoxine significantly associated with neuropathy on multivariate analysis. The addition of a local anaesthetic reduced the pain experienced by MDR-TB patients in the first 15 minutes post intramuscular administration of kanamycin, which could improve adherence to MDR-TB treatment. We also found the bioavailability of crushed isoniazid to be approximately 42% less than the whole tablet formulation, and therefore recommend that the crushing of isoniazid be avoided. Although some recent treatment advances have improved MDR-TB outcomes, enhancing the understanding of drugs used to treat MDR-TB, which continues to have an unacceptably high mortality and treatment-related morbidity, is a public health priority. This thesis comprises four peer-reviewed publications, all of which made a pragmatic contribution to the fight against MDR-TB.

Emerging multidrug-resistant tuberculosis (MDR-TB) is one of the most urgent global public health issues. Recent advances in molecular techniques should enable the development of different rapid detection tests for drug-resistant TB. Large-scale comparative studies on the diagnostic accuracy and turn-around-time (TAT) of these novel assays may promote their smooth implementation as routine tests for TB in diagnostic laboratories. In a pilot evaluation of 30 clinical isolates and 202 sputum specimens, diagnostic performance of a novel in-house assay for MTB identification (IS6110 qPCR) was compared to a commercial COBAS TaqMan MTB test (Roche Diagnostics). The sensitivity, specificity, positive predictive value (PPV) and negative predictive value (NPV) of IS6110 qPCR were 100%, 94.6%, 85.2% and 100%, respectively, compared to 94.7%, 100%, 100% and 98.6% for COBAS TaqMan MTB. Large-scale validation using 2,350 sputum specimens revealed the optimal cut-off crossing point (Cp) value of IS6110 qPCR was 29.61 with 97.3% sensitivity and 98.3% specificity determined by receiver operating characteristics (ROC) curve analysis. The median TAT for IS6110 qPCR and COBAS TaqMan MTB test to the reporting of results was 0.9 and 1.2 days, respectively. Among the IS6110 qPCR-positive specimens in the large-scale validation, 287 samples were tested in-house by katG MAS-PCR and rpoB PCR sequencing assays and 159 samples were tested by GenoType® MTBDRplus assay (Hain LifeScience). The sensitivity and specificity of katG MAS-PCR for isoniazid (INH) resistance detection were 71.4% and 99.5%, respectively. The sensitivity and specificity of rpoB PCR sequencing for rifampicin (RIF) resistance detection were 100% and 99.6%, respectively. Commercial GenoType® MTBDRplus assay reached 100% sensitivity for both INH and RIF resistance detection at a specificity of 99.3% and 100%, respectively. The median TAT for the in-house assays and GenoType® MTBDRplus assay to the reporting of the results was 4.7 and 1.4 days, respectively. The findings from this study provide different implementation strategies for diagnostic test combinations. The most cost-effective drug-resistant TB diagnosis cascade was IS6110 qPCR followed by GenoType® MTBDRplus assay. The TAT for results is 2.3 days at a cost of US$49.7. Despite an additional cost of US$24.6, COBAS TaqMan MTB test should replace IS6110 qPCR in populations with high prevalence of IS6110-negative strains. The in-house katG MAS-PCR and rpoB PCR sequencing assays should be used in developing countries instead of the expensive GenoType® MTBDRplus assay. Subsequently, accurate diagnosis of drug-resistant tuberculosis can be achieved in 4.5 days with a reasonable reagent cost of US$9.3. In conclusion, excellent diagnostic accuracy and shorter TAT of the molecular diagnostic cascade for drug-resistant TB, in particular IS6110 qPCR, can serve to guide physicians in the prompt choice of chemotherapy. This leads to timely delivery of anti-TB treatments to patients and holds the promise of easing the MDR-TB burden. / published_or_final_version / Microbiology / Master / Master of Philosophy

Dissertation ( PhD)--University of Stellenbsoch, 2007. / Bibliography. Also available via the Internet.

Thesis (MTech (Biomedical Technology))--Cape Peninsula University of Technology, 2010 / The World Health Organisation estimates that nine million people are infected with tuberculosis (TB) every year of which ninety-five percent live in developing countries. Africa has one of the highest incidences of TB in the world. but few of its countries are equipped to diagnose drug-resistant TB. This study aimed to develop a robust. yet simple and cost-effective assay. which would require minimal sophisticated instrumentation and specialised personnel that would make drug sensitivity screening for multi-drug resistant tuberculosis (MDR-TB) and extensively drug-resistant tuberculosis (XDR-TB) accessible to resource-poor high-burden settings. A four-quadrant colorimetric agar plate method was developed which showed good specificity (97.3%-100%) and sensitivity (77.8%-100%) compared to the polymerase chain reaction (PCR) method used as gold standard. Agreement between the methods. using Simple Kappa Coefficients. ranged between very good and excellent. all with high statistical significance (P < 0.0001). The currently used BACTEC MGIT SIREN sensitivity assay coupled with the E-test® strip method. as routinely used in the TB reference laboratory. was compared and showed excellent comparison with the newlydeveloped plate method. for each antibiotic tested. as well as the resultant monoresistant, MDR- or XDR-TB diagnoses. Moreover. the new method was found to be extremely cost-effective. priced at half the cost of a peR assay. These four quadrant plates. with a colorimetric indicator and selected antibiotics. can be considered as an economic altemative or a complimentary method for laboratories wishing to reduce the cost and complexity for TB drug sensitivity testing. Routine diagnostic testing would thus be made more accessible and affordable to laboratories that are not presently diagnosing drug resistant TB. therefore enhancing case detection and treatment in the resource-poor settings hardest hit by this curable disease.

The study aimed to explore and describe the experiences of people treated for multidrug resistant tuberculosis (MDR-TB) in Omaheke region, Namibia in order to make relevant recommendations regarding their management. A descriptive qualitative design approach was used. Data was collected using in-depth individual interviews with six participants. The interview transcripts were analysed using thematic content analysis. Three themes emerged namely (1) Stressors related to MDR-TB diagnosis and treatment which involved nature of disease and compulsory hospitalisation (2) Impact of being treated for MDR-TB which related to emotional , social , spiritual and financial impact (3) Support structures for people treated for MDR-TB which included family members, health care professionals and friends. Systemic practical patient-centred, staff-centred and community-centred recommendations are suggested as well as recommendations for future research and an appraisal of the limitations of this study. / Health Studies / M.A. (Public Health)

A research report submitted to the Faculty of Health Sciences, University of the Witwatersrand, in part fulfillment of the requirements for the degree of MSc (Med) (Pharmaceutical Affairs) Johannesburg, 25 March 2013 / The emergence of resistant forms of tuberculosis (TB) has not only caused continuous challenges on the world populations’ health, but has also attracted increased costs of primary health care for the infected and society at large. In 2005, when the South African public came to learn about another resistant form of TB other than multi-drug resistant (MDR), 53 patients had just died in a rural hospital in KwaZulu-Natal (KZN). The reports (SA DoH, 2006) came to announce this form of TB as extreme drug resistant tuberculosis (XDR-TB).

Objectives: We aimed to assess the variation in patient body weight over time according to the treatment outcome among multidrug-resistant tuberculosis (MDR-TB) cases. Methods: This was a retrospective cohort study. The data of patients commencing MDR-TB therapy were analyzed. Data were collected from different public TB treatment facilities located in peri-urban areas to the south of Lima, Peru. The outcome was patient body weight (kilograms) from treatment commencement, measured monthly. A random effects model was fitted using robust standard errors to calculate 95% confidence intervals. Results: Of a total of 1242 TB cases, 243 (19.6%) were MDR-TB. Only 201 cases were included in the analysis; 127 (63.2%) were males and the mean patient age was 33.6 (standard deviation 16.2) years. Weight changes over time among the patients who were cured differed from changes in those who died during therapy (p < 0.001). Weight curve divergence was important at the end of the third, fourth, and fifth treatment months: on average, the weight difference was 2.18 kg (p < 0.001), 3.27 kg (p = 0.007), and 3.58 kg (p = 0.03), respectively, when cured patients were compared to those who died. Conclusions: Our results show that weight variation during treatment can be a useful surrogate for the treatment outcome, specifically death during therapy. MDR-TB patients with weight loss should be followed more closely, as they are at greater risk of death. / Revisión por pares