Resistance to new tuberculosis drugs

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dc.contributor.advisorTheron, Granten_ZA
dc.contributor.advisorDerendinger, Brigittaen_ZA
dc.contributor.advisorVenter, Rouxjeaneen_ZA
dc.contributor.authorAlberts, Renciaen_ZA
dc.contributor.otherStellenbosch University. Faculty of Medicine and Health Sciences. Dept. of Biomedical Sciences. Molecular Biology and Human Genetics.en_ZA
dc.date.accessioned2024-03-06T09:09:53Zen_ZA
dc.date.accessioned2024-04-26T11:43:03Zen_ZA
dc.date.available2024-03-06T09:09:53Zen_ZA
dc.date.available2024-04-26T11:43:03Zen_ZA
dc.date.issued2024-03en_ZA
dc.descriptionThesis (MSc)--Stellenbosch University, 2024.en_ZA
dc.description.abstractENGLISH ABSTRACT: Introduction: Tuberculosis (TB) is a leading worldwide cause of death, further exacerbated by drug-resistant (DR)-TB. Therefore, new TB drugs are urgently needed. Bedaquiline (BDQ) is the first new TB drug in 40 years and is used for DR-TB treatment. BDQ resistance has, however, already been identified and, at the time of the study, routine phenotypic drug susceptibility testing (pDST) was not done on people initiating BDQ. Additionally, it's important to implement routine DR monitoring for BDQ and other companion drugs. Furthermore, little is known about phenotypic changes over time and whether increases in minimum inhibitory concentrations (MICs) could predict the later DR emergence. Additionally, we aimed to look at the performance of a molecular diagnostic assay for all 13 TB drugs (FLeXT) and determine its sensitivity and specificity. Methods: We determined how MICs from people who started on BDQ with sustained culture positivity changed over time from baseline (BL: closest isolate to BDQ treatment start) to follow up (FU: closest isolate to four-month sustained culture positivity) using a MIC microtitre plate from CRyPTIC. The plate included all 13 TB drugs, including new and repurposed drugs. Additionally, intercedent isolates were also tested using CRyPTIC to look at the change in MIC over time. Furthermore, we sequenced 720 sputa isolates using a manual extraction kit and the GenoXtract kit needed for the FLeXT machine. Results: BDQ MICs increased (p=0.0002) between BL [Median IQR: 0.008 (0.004-0.015)] and FU [Median IQR: 0.030 (0.015-0.019)]. The BDQ isolates had 14/17 (82.5%) isolates showing an increase in MIC over time. Isolates who had sustained culture positivity over time while on BDQ also showed larger increases in BDQ MIC over time compared to the BDQ susceptible https://scholar.sun.ac.za 6 group. Furthermore, for those isolates that indicated BDQ resistance at FU, companion drugs also indicated a higher level of variants and greater increases in CRyPTIC MIC over time. The largest increases in variants and CRyPTIC MICs were found for ethambutol (EMB), the fluoroquinolones (FQs), and ethionamide (ETH). No variants were found for the other new and repurposed drugs: clofazimine (CFZ, delamanid (DLM), or linezolid (LZD) at either timepoint, for both resistance groups. Lastly, FLeXT had a sensitivity of 87% using the manual extraction method (Fluorolyse) and aN 86% specificity for the automated extraction method (FleXT). Conclusion: This highlights the importance of doing routine testing for new drugs such as BDQ as well as companion drugs in people with DR-TB. Our results indicate that there is often a slow increase in CRyPTIC MIC that would lead to resistance over time, and this should be considered in patients with sustained culture positivity). Therefore, it is important to do resistance detection for TB drugs before initiating anyone on a regimen for the treatment to be effective. Furthermore, we proved that the FLeXT GenoXtract has great performance in the detection of DR for second-line TB drugs and serves as a much more efficient way of detecting second-line drug resistance. Molecular assays like this will improve the diagnosis pipeline and help clinicians form individualised treatment plans.en_ZA
dc.description.abstractAFRIKAANSE OPSOMMING: Inleiding Tuberkulose (TB) is 'n wêreldwye oorsaak van dood, wat verder vererger word deur weerstandige (DR)-TB. Daarom is nuwe TB-middels dringend nodig. Bedaquiline (BDQ) is die eerste nuwe TB-middel in 40 jaar en word vir DR-TB-behandeling gebruik. BDQweerstandigheid is egter reeds geïdentifiseer. Verder, is roetine fenotipiese dwelmvatbaarheids toetsing (pDST) nie gedoen op mense op BDQ is nie. Tans is min bekend oor fenotipiese veranderinge oor tyd en of toenames in minimum inhiberende konsentrasies (MIC's) die latere DR-opkoms kan voorspel. Verder het ons gemik om te kyk na die kwaliteit van 'n molekulêre diagnostiese toets vir al 13 TB-middels (FLeXT) en die sensitiwiteit en spesifisiteit daarvan bepaal. Metodes Ons het vasgestel dat CRyPTIC MIC's van mense wat op BDQ en wat volgehoue kultuur positiwiteit het ≥ vier maande, het met verloop van tyd verander het van begin (BL: naaste isolaat vanaf BDQ behandeling begin het) tot opvolg (FU: naaste isolaat ≥ as vier maande volgehoue kultuur positiwiteit). Dit was geevalueerd met behulp van 'n MIC mikrotiter plaat van CRyPTIC. Die plaat het al 13 TB-middels ingesluit, insluitend nuwe en hergebruikte middels. Verder is tussen in isolate ook getoets met behulp van CRyPTIC. Ons het ook 720 sputa-isolate gesequence met ‘n molekulere diagnose masjien deur die GenoXtract-stel wat nodig is vir die FLeXT-masjien. Resultate BDQ MIC's het aansienlik toegeneem (p=0.0002) tussen BL [Median IQR: 0.008 (0.004-0.015)] en FU [Median IQR: 0.030 (0.015-0.019)]. Veërtien uit seventien isolate (82.5%) van alle BDQisolate het 'n toename in MIC oor tyd getoon. Isolate wat kultuur positiwiteit oor tyd volgehou https://scholar.sun.ac.za 8 het, het ook groter toenames in BDQ MIC getoon met verloop van tyd; in vergelyking met die BDQ vatbare groep. Verder, vir daardie isolate wat BDQ-weerstandig by FU aangedui het, het metgesel medisyne ook 'n hoër vlak van weerstandigheid en groter toenames in CRyPTIC MIC oor tyd aangedui. Die grootste toenames invariante en CRyPTIC MIC's is gevind vir etambutol (EMB), die fluoroqinolone (FQ's) en ethionamied (ETH). Geen variante is gevind vir die ander nuwe en hergebruikte middels nie [klofazimien (CFZ, delamanied (DLM) of linezolid (LZD)] op enige tydpunt vir beide weerstandsgroepe nie. Laastens het FLeXT 'n sensitiwiteit van 87% gehad deur die manuele ekstraksiemetode (Fluorolyse) te gebruik en 'n 86% spesifisiteit vir die outomatiese ekstraksiemetode (FleXT). Gevolgtrekking Dit beklemtoon die belangrikheid daarvan om roetine-toetsing vir nuwe middels soos BDQ sowel as metgesel middels by mense met DR-TB te doen. Ons resultate dui aan dat daar dikwels 'n stadige toename in CRyPTIC MIC is wat mettertyd tot weerstand sal lei en dit moet oorweeg word by pasiënte met vertraagde patogeen opruiming. Daarom is dit belangrik om weerstandhigheids-toetsing vir TB-middels te doen voordat iemand met 'n behandeling begin, om die behandeling meer doeltreffend te maak. Verder het ons bewys dat die FLeXT GenoXtract die middelweerstand vir tweedelyn-medisyne kan vind. Molekulêre toetse soos hierdie sal die diagnose pyplyn verbeter en dokters help om geïndividualiseerde behandelingsplanne te vorm.af_ZA
dc.description.versionMastersen_ZA
dc.format.extent167 pagesen_ZA
dc.identifier.urihttps://scholar.sun.ac.za/handle/10019.1/130276en_ZA
dc.language.isoen_ZAen_ZA
dc.language.isoen_ZAen_ZA
dc.publisherStellenbosch : Stellenbosch University,en_ZA
dc.rights.holderStellenbosch University,en_ZA
dc.subject.lcshAdenosine triphosphateen_ZA
dc.subject.lcshTuberculosis -- Molecular diagnosisen_ZA
dc.subject.lcshMultidrug-resistant tuberculosisen_ZA
dc.titleResistance to new tuberculosis drugsen_ZA
dc.typeThesisen_ZA
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Masters Degrees (Molecular Biology and Human Genetics)