Sandringham, South Africa
Sandringham, South Africa

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Gray C.M.,Foundation for Innovative New Diagnostics FIND | Katamba A.,Makerere University | Narang P.,Mahatma Gandhi Institute | Giraldo J.,Cayetano Heredia Peruvian University | And 8 more authors.
Journal of Clinical Microbiology | Year: 2016

Currently available nucleic acid amplification platforms for tuberculosis (TB) detection are not designed to be simple or inexpensive enough to implement in decentralized settings in countries with a high burden of disease. The loop-mediated isothermal amplification platform (LAMP) may change this. We conducted a study in adults with symptoms suggestive of TB in India, Uganda, and Peru to establish the feasibility of using TB-LAMP (Eiken Chemical Co.) in microscopy laboratories compared with using smear microscopy against a reference standard of solid and liquid cultures. Operational characteristics were evaluated as well. A total of 1,777 participants met the eligibility criteria and were included for analysis. Overall, TB-LAMP sensitivities among culture-positive samples were 97.2% (243/250; 95% confidence interval [CI], 94.3% to 98.2%) and 62.0% (88/142; 95% CI, 53.5% to 70.0%) for smear-positive and smear-negative TB, respectively, but varied widely by country and operator. Specificities ranged from 94.5% (446/472; 95% CI, 92.0% to 96.4%) to 98.0% (350/357; 95% CI, 96.0% to 99.2%) by country. A root cause analysis identified high temperatures, high humidity, and/or low reaction volumes as possible causes for false-positive results, as they may result in nonspecific amplification. The study was repeated in India with training focused on vulnerable steps and an updated protocol; 580 participants were included for analysis. Specificity in the repeat trial was 96.6% (515/533; 95% CI, 94.7% to 97.9%). To achieve acceptable performance of LAMP at the microscopy center level, significant training and infrastructure requirements are necessary. Copyright © 2016 David et al.


Lukoye D.,National Tuberculosis | Lukoye D.,Management science for Health MSH | Ssengooba W.,Makerere University | Ssengooba W.,Amsterdam Institute for Global Heath and Development | And 10 more authors.
BMC Public Health | Year: 2015

Background: Prevalence of multidrug resistant tuberculosis (MDR-TB), defined as in vitro resistance to both rifampicin and isoniazid with or without resistance to other TB drugs, in sub-Saharan Africa (SSA) is reportedly low compared to other regions. These estimates are based on data reported to the World Health Organization (WHO) on drug resistance surveys, which may suffer from a reporting bias. We set out to evaluate the variation in prevalence of drug resistant tuberculosis (DR-TB) and its determinants across SSA countries among new and previously treated TB patients. Methods: The aim was to perform a systematic review and meta-analysis of DR-TB prevalence and associated risk factors in SSA. PubMed, EMBASE, Cochrane and bibliographies of DR-TB studies were searched. Surveys at national or sub-national level, with reported DR-TB prevalence (or sufficient data to calculate a prevalence) to isoniazid (INH), rifampicin (RMP), ethambutol (EMB), and streptomycin (SM) conducted in SSA excluding the Republic of South Africa, published between 2003 and 2013 with no language restriction were considered. Two authors searched and reviewed the studies for eligibility and extracted the data in pre-defined forms. Forest plots of all prevalence estimates by resistance outcome were performed. Summary estimates were calculated using random effects models, when appropriate. Associations between any DR-TB and MDR-TB with potential risk factors were examined through subgroup analyses stratified by new and previously treated patients. Results: A total of 726 studies were identified, of which 27 articles fulfilled the inclusion criteria. Studies reported drug susceptibility testing (DST) results for a total of 13,465 new and 1,776 previously treated TB patients. Pooled estimate of any DR-TB prevalence among the new cases was 12.6% (95% CI 10.6-15.0) while for MDR-TB this was 1.5% (95% CI 1.0-2.3). Among previously treated patients, these were 27.2% (95% CI 21.4-33.8) and 10.3% (95% CI 5.8-17.4%), respectively. DR-TB (any and MDR-TB) did not vary significantly with respect to study characteristics. Conclusions: The reported prevalence of DR-TB in SSA is low compared to WHO estimates. MDR-TB in this region does not seem to be driven by the high HIV prevalence rates. © 2015 Lukoye et al.; licensee BioMed Central.


Barnard M.,Point of Reference | Barnard M.,Stellenbosch University | Barnard M.,University of Cape Town | Warren R.,Stellenbosch University | And 10 more authors.
American Journal of Respiratory and Critical Care Medicine | Year: 2012

Rationale: Conventional culture-based drug susceptibility testing (DST) for the second-line antituberculosis drugs is slow, leading to diagnostic delay with associated exacerbation of transmission, amplification of resistance, and increased mortality. Objectives: To assess the diagnostic performance of the GenoType MTBDRsl line probe assay (LPA) for the rapid detection of mutations conferring resistance to ofloxacin (OFX), amikacin (AMK), and ethambutol and to determine the impact of implementation on the turnaround time in a high-throughput diagnostic laboratory. Methods: Six hundred and fifty-seven direct patient acid-fast bacilli smear-positive specimens resistant to isoniazid, rifampin, or both according to the GenoType MTBDRplus assay were consecutively tested, using the GenoType MTBDRsl LPA. The diagnostic performance was assessed relative to the "gold standard" culture-based method, and the laboratory turnaround times for bothmethods were determined. Measurements and Main Results: A total of 516 of 657 patient specimens had valid results for both tests. The sensitivity for detecting OFX, AMK, and extensive drug resistance, using the GenoType MTBDRsl LPA, was 90.7% (95% confidence interval [CI], 80.1-96.0%), 100% (95% CI, 91.8-100%), and 92.3% (95% CI, 75.9-97.9%), respectively, and the specificity for detection was 98.1% (95% CI, 96.3-99.0%), 99.4% (95% CI, 98.2-99.8%), and 99.6% (95% CI, 98.5-99.9%), respectively. Implementation of this test significantly reduced the turnaround time by 93.3% (P < 0.001), calculated from the date that the specimen was received at the laboratory to reporting second-line results. In addition, a significant increase in diagnostic yield of 20.1% and 19.3% (P < 0.001) for OFX and AMK resistance, respectively, was obtained for isolates that were either contaminated or had lost viability. Conclusions: The GenoType MTBDRsl LPA is a rapid and reliable DST that can be easily incorporated into the diagnostic algorithm. This assay significantly improved diagnostic yield (P < 0.001) while simultaneously decreasing diagnostic delay for reporting second-line DST. The rapid dissemination of second-line DST results will guide initiation of appropriate treatment, thereby reducing transmission and improving treatment outcome. Copyright © 2012 by the American Thoracic Society.


Erasmus L.,National TB Reference Laboratory | Koornhof H.,National TB Reference Laboratory | Coetzee G.,National TB Reference Laboratory
PLoS ONE | Year: 2012

Introduction: Globally, multidrug resistant tuberculosis (MDR-TB) remains underdiagnosed. The Genotype MTBDRplus®, a rapid drug susceptibility testing (DST) assay used to detect resistance to isoniazid and rifampicin in the diagnosis of MDR-TB, has good diagnostic accuracy, but its impact on patient outcomes in routine practice is unproven. We assessed the clinical impact of routine DST using MTBDRplus in a single health district in South Africa. Methods: Data were collected on all adult pulmonary TB patients registered at 25 public health clinics in the periods before and after introduction of an expanded DST algorithm using MTBDRplus version 1.0. Results: We collected data on 1176 TB patients before implementation and 1177 patients afterwards. In the before period, measured MDR-TB prevalence among new cases was 0.7% (95% CI1.4-3.1%), and among retreatment cases 6.2% (95% CI:3.5-8.8%), versus 3.7% (95% CI:2.4-5.0, p<0.01) and 6.6% (95% CI:3.8-9.4%, p = 0.83) respectively after MTBDRplus introduction. The median times from sputum collection to MDR treatment in the before and after periods were 78 days (IQR:52-93) and 62 days (IQR:32-86, p = 0.05), respectively. Among MDR-TB cases, 27% (95%CI:10-44) in the before period converted sputum cultures to negative by 8 months following treatment initiation, while 52% (95%CI:38-66) converted in the intervention period (p = 0.04). Conclusions: The expanded use of MTBDRplus DST resulted in a substantial increase in the proportion of new cases identified as MDR-TB; though time to MDR treatment was reduced, it was still over two months. Culture conversion for MDR-TB patients improved after introduction of MTBDRplus. This work illustrates the mixture of successes and challenges resulting from increased access to rapid DST in a setting with a high TB burden. © 2012 Hanrahan et al.


Lukoye D.,Management science for Health MSH | Ssengooba W.,Makerere University | Musisi K.,National TB Reference Laboratory | Kasule G.W.,National TB Reference Laboratory | And 2 more authors.
BMC public health | Year: 2015

BACKGROUND: Prevalence of multidrug resistant tuberculosis (MDR-TB), defined as in vitro resistance to both rifampicin and isoniazid with or without resistance to other TB drugs, in sub-Saharan Africa (SSA) is reportedly low compared to other regions. These estimates are based on data reported to the World Health Organization (WHO) on drug resistance surveys, which may suffer from a reporting bias. We set out to evaluate the variation in prevalence of drug resistant tuberculosis (DR-TB) and its determinants across SSA countries among new and previously treated TB patients.METHODS: The aim was to perform a systematic review and meta-analysis of DR-TB prevalence and associated risk factors in SSA. PubMed, EMBASE, Cochrane and bibliographies of DR-TB studies were searched. Surveys at national or sub-national level, with reported DR-TB prevalence (or sufficient data to calculate a prevalence) to isoniazid (INH), rifampicin (RMP), ethambutol (EMB), and streptomycin (SM) conducted in SSA excluding the Republic of South Africa, published between 2003 and 2013 with no language restriction were considered. Two authors searched and reviewed the studies for eligibility and extracted the data in pre-defined forms. Forest plots of all prevalence estimates by resistance outcome were performed. Summary estimates were calculated using random effects models, when appropriate. Associations between any DR-TB and MDR-TB with potential risk factors were examined through subgroup analyses stratified by new and previously treated patients.RESULTS: A total of 726 studies were identified, of which 27 articles fulfilled the inclusion criteria. Studies reported drug susceptibility testing (DST) results for a total of 13,465 new and 1,776 previously treated TB patients. Pooled estimate of any DR-TB prevalence among the new cases was 12.6% (95% CI 10.6-15.0) while for MDR-TB this was 1.5% (95% CI 1.0-2.3). Among previously treated patients, these were 27.2% (95% CI 21.4-33.8) and 10.3% (95% CI 5.8-17.4%), respectively. DR-TB (any and MDR-TB) did not vary significantly with respect to study characteristics.CONCLUSIONS: The reported prevalence of DR-TB in SSA is low compared to WHO estimates. MDR-TB in this region does not seem to be driven by the high HIV prevalence rates.


Barnard M.,Point of Reference | Barnard M.,Stellenbosch University | Gey Van Pittius N.C.,Stellenbosch University | Van Helden P.D.,Stellenbosch University | And 3 more authors.
Journal of Clinical Microbiology | Year: 2012

Molecular diagnostics for Mycobacterium tuberculosis have recently been endorsed by the World Health Organization. The Xpert MTB/RIF assay was endorsed for use on patient material, regardless of smear gradation, while the GenoType MTBDRplus (version 1) has been limited for use on smear-positive patient material. In this study, we evaluated the diagnostic performance of the Xpert MTB/RIF and GenoType MTBDRplus (version 2) assays on smear-positive and smear-negative patient specimens submitted to a high-throughput diagnostic laboratory. A total of 282 consecutive specimens were subjected to the two new molecular assays, and their performance characteristics were assessed relative to the routine diagnostic standard. Both assays showed similar diagnostic performance characteristics. The sensitivities of the GenoType MTBDRplus (v2.0) and Xpert MTB/RIF assays for the detection of culture-positive M. tuberculosis were 73.1% and 71.2%, respectively, while the specificities of both assays were 100%. Both assays were able to diagnose the presence of M. tuberculosis in 57 to 58% of smear-negative cases, suggesting that the performance characteristics were dependent on bacillary load. The detection of M. tuberculosis in culture-negative specimens confirmed that molecular assays should not be used for treatment monitoring. The sensitivity and specificity for rifampin resistance detection were 100% in both assays; however, the GenoType MTBDRplus (v2.0) assay provided additional information on isoniazid susceptibility. The GenoType MTBDRplus (v2.0) assay will complement the Xpert MTB/RIF screening assay by validating rifampin susceptibility and providing information on isoniazid susceptibility. In addition, the GenoType MTBDRplus (v2.0) assay will provide pharmacogenetic information that may be critical in guiding appropriate treatment. Copyright © 2012, American Society for Microbiology. All Rights Reserved.


PubMed | National TB Reference Laboratory, National Tuberculosis and Leprosy Program and Makerere University
Type: | Journal: BMC public health | Year: 2015

Prevalence of multidrug resistant tuberculosis (MDR-TB), defined as in vitro resistance to both rifampicin and isoniazid with or without resistance to other TB drugs, in sub-Saharan Africa (SSA) is reportedly low compared to other regions. These estimates are based on data reported to the World Health Organization (WHO) on drug resistance surveys, which may suffer from a reporting bias. We set out to evaluate the variation in prevalence of drug resistant tuberculosis (DR-TB) and its determinants across SSA countries among new and previously treated TB patients.The aim was to perform a systematic review and meta-analysis of DR-TB prevalence and associated risk factors in SSA. PubMed, EMBASE, Cochrane and bibliographies of DR-TB studies were searched. Surveys at national or sub-national level, with reported DR-TB prevalence (or sufficient data to calculate a prevalence) to isoniazid (INH), rifampicin (RMP), ethambutol (EMB), and streptomycin (SM) conducted in SSA excluding the Republic of South Africa, published between 2003 and 2013 with no language restriction were considered. Two authors searched and reviewed the studies for eligibility and extracted the data in pre-defined forms. Forest plots of all prevalence estimates by resistance outcome were performed. Summary estimates were calculated using random effects models, when appropriate. Associations between any DR-TB and MDR-TB with potential risk factors were examined through subgroup analyses stratified by new and previously treated patients.A total of 726 studies were identified, of which 27 articles fulfilled the inclusion criteria. Studies reported drug susceptibility testing (DST) results for a total of 13,465 new and 1,776 previously treated TB patients. Pooled estimate of any DR-TB prevalence among the new cases was 12.6% (95% CI 10.6-15.0) while for MDR-TB this was 1.5% (95% CI 1.0-2.3). Among previously treated patients, these were 27.2% (95% CI 21.4-33.8) and 10.3% (95% CI 5.8-17.4%), respectively. DR-TB (any and MDR-TB) did not vary significantly with respect to study characteristics.The reported prevalence of DR-TB in SSA is low compared to WHO estimates. MDR-TB in this region does not seem to be driven by the high HIV prevalence rates.


PubMed | Médecins Sans Frontières, National Diagnostics, Swaziland Health Laboratory Services, London School of Hygiene and Tropical Medicine and 5 more.
Type: Journal Article | Journal: Public health action | Year: 2015

All 19 public health laboratories in Swaziland that had Xpert() MTB/RIF machines installed as part of a countrywide roll-out between June 2011 and June 2014.To evaluate the utilisation and functionality of Xpert from 2011 to mid-2014.Descriptive study of Xpert implementation using routinely collected data.Of 48 829 Xpert tests conducted, 93% were successful: 14% detected Mycobacterium tuberculosis and 12% showed rifampicin resistance. The most common cause of unsuccessful tests was an Error result (62%). Similar findings were obtained in government-supported and partner-supported laboratories. Annual utilisation of Xpert improved from 51% of maximum capacity in 2011 and 2012 to 74% in 2013 and 2014. A monitoring and supervision exercise of all Xpert testing sites in 2014 showed a generally good performance, with over 50% of laboratories achieving a 80% score on most components. However, poor scores were obtained with equipment use and maintenance (6% achieving a score of 80%), internal audit (19% achieving a score of 80%) and process control (25% achieving a score of 80%).Countrywide roll-out of Xpert in Swaziland has been successful, although operational issues have been identified and need to be resolved.


Jamal W.,Kuwait University | Jamal W.,Mubarak Al Kabeer Hospital | Salama M.F.,Mubarak Al Kabeer Hospital | Al Hashem G.,Mubarak Al Kabeer Hospital | And 6 more authors.
Pediatric Infectious Disease Journal | Year: 2014

Background: Mycobacterium abscessus has been associated with respiratory tract infections, localized skin and soft tissue infections and sepsis. However, outbreaks of M. abscessus are rare. Aim: to report an outbreak of M. abscessus causing respiratory tract infections in a Pediatric Intensive Care Unit (PICU) in Kuwait, its investigation and control measures. Methods: Respiratory secretions were obtained from ventilator-dependent patients showing signs of sepsis, including fever, malaise and weight loss. The specimens were cultured on appropriate routine media. After the results of the sample taken from the index case as acid-fast bacilli positive, all patients were screened for M. abscessus carriage. Isolates were identified by INNO-LiPA Mycobacteria v2 line probe assay and DNA sequencing. Molecular fingerprinting DiversiLab strain typing was performed on the isolates. Epidemiologic investigation was conducted during the outbreak. Findings: the outbreak affected 5 patients, 4 of whom had severe infections including 1 patient with septicemia. Asymptomatic carriage of outbreak strain was found in 1 patient. All environmental samples were negative for M. abscessus but some were positive for M. gordonae and M. fortuitum. The source could not be identified. Stringent infection control measures were put in place, including reemphasizing hand hygiene and closure of the Pediatric Intensive Care Unit to new admissions. A year later, no further case has occurred after the last case. Conclusion: To our knowledge, this is the first report of a hospital-acquired outbreak of respiratory tract infection caused by M. abscessus in a Pediatric Intensive Care Unit. In the absence of definite source identification, reinforcement of standard infection control guidelines was successful in containing the outbreak. Copyright © 2013 by Lippincott Williams & Wilkins.


Kasule G.W.,National Tuberculosis and Leprosy Program | Kasule G.W.,National TB Reference Laboratory | Kateete D.P.,Makerere University | Joloba M.L.,National Tuberculosis and Leprosy Program | And 2 more authors.
BMC Infectious Diseases | Year: 2016

Background: Mycobacterium tuberculosis Uganda family is the predominant cause of tuberculosis in Uganda. Reasons for this are not clear but are likely to be due to the rampant person-to-person transmission or delayed susceptibility of the organism to drugs during treatment, which may lead to continuous shedding of infectious bacilli, among others. The objective of this study was to determine in vitro, the susceptibility patterns of M. tuberculosis Uganda family compared with Beijing and Delhi/CAS, other M. tuberculosis sub-lineages that also circulate in Uganda but are not as prevalent. The comparisons were made after 10 days of exposure of the strains to Rifampicin and Isoniazid, the most important first-line anti-tuberculosis drugs. Methods: Minimum inhibitory concentrations (MICs) for three Isoniazid- and Rifampicin-susceptible M. tuberculosis strains (Uganda II, Beijing and Delhi/CAS families) were determined by micro-dilution plate assay. Killing curves for each strain were deduced from colony forming units after exposure to Isoniazid and Rifampicin on days 0, 2, 4, 6, 8, and 10 under aerobic and oxygen-depleted conditions. Data were analyzed with GraphPad Prism 5 software. Results: The MIC for Isoniazid was 0.05 μg/ml for M. tuberculosis Uganda II, and 0.03 μg/ml for M. tuberculosis Beijing and Delhi/CAS. Rifampicin MIC was 1 μg/ml for M. tuberculosis Uganda II, and 0.12 μg/ml for Beijing and Delhi/CAS. At low Rifampicin (0.03-2.5 μg/ml) and Isoniazid (0.12-5 μg/ml) concentrations under aerobic conditions, there was no significant difference in susceptibility patterns between M. tuberculosis Uganda II and Beijing or Delhi/CAS. However, at high Rifampicin (5 μg/ml) and Isoniazid (1.25 μg/ml) concentrations under oxygen-depleted conditions, M. tuberculosis Uganda II was more susceptible to the drugs compared with Beijing or Delhi/CAS families. Conclusion: The predominance of M. tuberculosis Uganda II family as the main causative agent of tuberculosis in Uganda is not attributed to its susceptibility behavior to Isoniazid and Rifampicin. Probably, its predominance is due to differences in the immune defenses in the general population against the strains, given that Beijing and Delhi/CAS families may have been introduced more recently. Further research beyond susceptibility to anti-tuberculosis drugs is required to fully explore tuberculosis strain predominance in Uganda. © 2016 Kasule et al.

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