Thesis(PhD)--Stellenbosch University, 2013. / ENGLISH ABSTRACT: The epidemic levels of drug-resistant tuberculosis (DR-TB) in high-burden countries such as South Africa, which is currently ranked as third highest in the world, is the result of a synergistic relationship between the increased transmission of DR strains, poor patient adherence as well as Human-Immunodeficiency Virus (HIV)-coinfection. The impact of these combined factors on the rise of DR-TB led to an urgent need for the development of new diagnostic tools to rapidly detect TB and its associated drug susceptibility profile. The Foundation for Innovative New Diagnostics (FIND) has taken the onus upon them to ensure that laboratory strengthening becomes a reality by having developed, and still developing, new diagnostic assays in order to improve the laboratory turn-around time (TAT), whereby the transmission of DR-TB strains can be stopped. Laboratory strengthening does not solely rely on new diagnostic assays alone, and thus a Quality Management System, discussed in the dissertation, must be in place to ensure that the rapid result is accurate and reliable. The series of studies encompassed in this dissertation includes methodological validations (both technical and operational) of rapid TB diagnostic assays in order to rapidly and accurately diagnose the disease, and thus reducing the diagnostic delay associated with conventional diagnostic platforms. The studies were conducted “in-house” at the National Health Laboratory Service (NHLS) Reference TB laboratory in Green Point, Cape Town, which is a high-volume public health laboratory. The need to rapidly detect resistance to the first line anti-tubercular drugs Isoniazid and Rifampicin was a priority and thus the performance of a commercial line probe assay (LPA), the GenoType®MTBDRplus Ver1.0 LPA, was assessed for use on smear positive direct patient material. The performance characteristics was superior to that of conventional drug susceptibility testing, where the sensitivity and specificity for the detection of multi-drug resistant TB (MDR-TB) was 98.8 and 100%, respectively, with results in 1-2 days. Based on this study, the World Health Organization (WHO) endorsed the use of molecular LPA for the rapid detection of DR-TB. Furthermore, the need for quality assurance associated with the GenoType®MTBDRplus LPA in the diagnostic laboratory is essential and thus a user manual for the molecular detection of Drug Resistant Tuberculosis in resource-limited settings has also been developed (http://www.finddiagnostics.org/export/sites/default/resource-center/reports brochures/docs/LPA LaboratoryManual22Mar2012.pdf) for which Global Laboratory Initiative (GLI) status is pending. With the outbreak of extensively drug resistant TB (XDR-TB) in Tugela Ferry area in KwaZulu-Natal and the rest of the world, the need to rapidly detect resistance to the second line drugs arose, and thus the performance characteristics of the GenoType®MTBDRsl LPA was assessed for use on smear positive direct patient material. The performance characteristics proved to be excellent once again, with a 93.3% reduction in TAT. The data was scrutinized by the WHO, where it may be used as a triage test to guide treatment, but to date, no final policies on the use thereof has been finalized. The need for rapid point-of-care (POC) testing led to the implementation of the Xpert®MTB/RIF assay in the referral laboratories, for use on both smear positive and smear negative direct patient material. In order to accommodate for laboratories where the LPA has been implemented already, the GenoType®MTBDRplus Ver2.0 LPA was developed, which is aimed for use on all smear types as well. A head-to-head assessment was done between these assays to determine their performance characteristics and it was shown to be equally good. In this study we have shown the utility of molecular diagnostic assays to rapidly diagnose TB and its associated drug susceptibility patterns. This will have a significant impact on diagnostic delay and clinical decision making as well as patient outcome. / AFRIKAANSE OPSOMMING: Die epidemiese vlakke van middel-weerstandige tuberkulose (MW-TB) in hoë-lading lande, soos Suid Afrika wat tans derde hoogste op die wêreld ranglys is, is die nagevolge van 'n sinergistiese verband tussen die verhoogde voorkoms van transmissie van MW stamme, swak pasiënt deelname aan die voorgeskrewe behandelings programme, asook Menslike Immuniteitsgebreksvirus (MIV) ko-infeksie. Die impak van hierdie drie faktore saam, gee aanleiding tot 'n verhoging in MW-TB en dus was daar 'n daadwerklike behoefte vir die ontwikkeling van nuwe diagnostiese toetse wat nie net TB kan identifiseer nie, maar wat ook die gepaardgaande middel-weerstandigheids profiel aandui. Die “Foundation for Innovative New Diagnostics” (FIND) het die onus van laboratorium versterking op hulself geneem, deur te verseker dat die nuut ontwikkelde diagnostiese toetse, asooks steeds ontwikkelende diagnostiese toetse, gebruik kan word om die konsep van laboratorium versterking 'n realiteit te maak. Die doel is dus om sodoende die tyd-tot-resultaat tussen geneesheer en laboratorium te verbeter, terwyl die transmissie van MW-TB ook die hok geslaan kan word. Nietemin, laboratorium versterking berus nie net op nuwe diagnostiese toetse nie, en dus is dit noodsaaklik dat 'n Kwaliteitbestuursisteem, soos bespreek in hierdie verhandeling, in plek is om te verseker dat die resultaat spoedig, akkuraat en betroubaar is. Die samevattende reeks studies in hierdie verhandeling behels metodologiese validasies (beide tegnies en operasioneel van aard) van spoedige TB diagnostiese toetse met die doel om die siekte so vinnig en akkuraat as moontlik te diagnoseer en dus die diagnostiese vertraging, wat histories met konvensionele metodes geassosiëerd is, te verminder. Al die studies is uitgevoer in die “National Health Laboratory Service (NHLS)” TB verwysingslaboratorium in Groenpunt, Kaapstad, wat 'n hoë-volume publieke gesondheidslaboratorium is. Die noodsaaklikheid om weerstandigheid teenoor die eerste-linie antituberkulose middels isoniasied en rifampisien so spoedig moontlik te diagnoseer het 'n groot bekommernis geword, en dus is die laboratorium daartoe genoop om die prestasie eienskappe van 'n kommersiëel beskikbare “line probe assay” (LPA), die “Genotype®MTBDRplus Ver1.0 LPA”, te asseseer vir die gebruik daarvan op direkte pasientmateriaal wat smeer positief is. Die prestasie eienskappe was beter as die van konvensionele middelvatbaarheidstoetse, waar die sensitiwiteit en spesifisiteit vir die diagnosering van MW-TB 98.8 en 100%, respektiewelik, was. Verder was die resultate ook binne 1-2 dae beskikbaar. Op grond van dié bevindinge het die Wêreldgesondheidsorganisasie (WGO) die gebruik van hierdie molekulêre “LPA” vir die spoedige diagnose van MW-TB onderskryf. Nietemin, die belangrikheid van gehalteversekering wat met die “GenoType®MTBDRplus LPA” in die diagnostiese laboratorium geassosieerd is, is essentiëel en dus is 'n gebruikershandleiding vir die molekulêre diagnose van MW-TB in beperkte hulpbron-instellings ontwikkel (http://www.finddiagnostics.org/export/sites/default/resource-center/reports brochures/docs/LPA LaboratoryManual22Mar2012.pdf) waarvoor daar op„n “Global Laboratory Initiative (GLI)” status in afwagting is. Met die uitbraak van ekstensiewemiddelweerstandige TB (EMW-TB) in die Tugela Ferry distrik in KwaZulu-Natal asook in die res van die wêreld, het die noodsaaklikheid onstaan om weerstandigheid teenoor die tweede-linie middels ook so spoedig moontlik te diagnoseer, en die laboratorium is dus weereens daartoe genoop om die prestasie eienskappe van die “GenoType®MTBDRsl LPA” (ook vir die gebruik op direkte pasient materiaal wat smeer positief is) te asseseer. Die prestasie eienskappe was weereens verbysterend, en het „n 93.3% afname in tyd-tot-resultaat getoon. Die data is deur die WGO aangevra, en daar is besluit dat die toets gebruik kan word om behandeling in werking te stel, maar geen finale onderskrywings is tot op hede nog gemaak nie. Die behoefte aan 'n punt-van-sorg toets het gelei tot die implementering van die “Xpert®MTB/RIF” toets in die verwysingslaboratorium, en is geoogmerk vir die gebruik op beide smeer positiewe en -negatiewe direkte pasient materiaal. Omrede die “LPA” al in verskeie laborotoriums geimplementeer was, is die “GenoType®MTBDRplus Ver2.0 LPA” ontwikkel, waarvan die gebruik onafhanklik is van die smeerresultaat. 'n Direkte assesering tussen die twee toetse was gedoen en daar is bevind dat beide se prestasie eienskappe vergelykend was. In hierdie studies het ons bewys dat die gebruik van molekulêre diagnostiese toetse in staat is om TB en die gepaargaande middel-weerstandigheids profiel spoedig te diagnoseer. Hierdie bevindinge sal 'n groot impak hê op die vetraging van tyd-tot-resultaat, op die mediese besluitneming asook op die uitkoms van die pasiënt. / FIND (Foundation for Innovative New Diagnostics) / Hain Lifescience / National Health Laboratory Service (NHLS)