Thesis (MScMedSc)--Stellenbosch University, 2014. / ENGLISH ABSTRACT: Mycobacterium tuberculosis is the etiological agent for tuberculosis, an infectious disease which is one of the leading causes of morbidity and mortality in developing countries. The emergence of drug resistant tuberculosis has negatively impacted the efficacy of current treatment regimens and threatens to undermine tuberculosis control programs worldwide. Rifampicin forms the backbone of the World Health Organization’s recommended treatment regimen for the treatment of drug susceptible tuberculosis. Resistance to rifampicin is caused by mutations in the 81 bp core region of the rpoB gene which encodes the β subunit of RNA polymerase. Numerous studies have shown that mutations at codons 531 and 526 are the most frequent in clinical isolates, yet little is known concerning the mechanistic effect of these mutations on the fidelity of RNA polymerase. In the present study, we aimed to determine the influence of rpoB mutations on the gene expression profile of M. tuberculosis cultured in vitro. To accomplish this, rifampicin resistant clinical isolates and spontaneous mutants (selected in vitro from H37Rv and a drug-sensitive clinical strain) harbouring rpoB H526Y and S531L mutations were subjected to whole genome sequencing and genome-wide transcriptional profiling. When comparing the transcription profile of H37Rv to the in vitro rpoB mutants, a large proportion of the differentially expressed genes were found to encode for proteins involved in intermediary metabolism and respiration; and cell wall and cell processes. The majority of these differentially expressed genes were downregulated. Prominent differential expression in the same functional categories was also evident when comparing the clinical isolates with these mutations; however, a greater number of genes were differentially expressed in this case. Furthermore, expression of genes that are part of the WhiB7 regulon were found to be upregulated in the rpoB526 mutants, and downregulated in the rpoB531 mutants. These findings indicate that both the position of the rpoB mutation, as well as the genetic background of the strain, play an important role in the gene expression profile of rpoB mutants. Surprisingly, transcriptional profiling of cultures that were exposed to the critical concentration of rifampicin for 24 hours did not exhibit significant differential gene expression. Whole genome sequencing, followed by bioinformatic analysis, revealed that the in vitro mutants harbour synonymous and non-synonymous single nucleotide polymorphisms in addition to the respective rpoB mutations. This suggests that the mycobacterial genome is constantly evolving, challenging previous assumptions of relatively static mycobacterial genomes. The findings from this research have provided novel insight into understanding the influence of resistance-conferring mutations on the biology of M. tuberculosis and have shown that further studies are urgently needed to better understand the complex physiology of this pathogen. This knowledge will be critical for the success of future drug development endeavours. / AFRIKAANSE OPSOMMING: Mycobacterium tuberculosis is die etiologiese agent vir tuberkulose, een van die grootste oorsake van morbiditeit en sterftes in ontwikkelende lande. Die verskyning van middelweerstandige tuberkulose het 'n negatiewe impak op die effektiwiteit van die huidige behandeling van tuberkulose en dreig om tuberkulose beheerprogramme wêreldwyd te ondermyn. Weerstandigheid teen rifampisien, een van die eerste-lyn anti-tuberkulose middels, word veroorsaak deur mutasies in die 81 bp kerngedeelte van die rpoB geen. Die mees algemene mutasies in kliniese isolate word gevind in kodons 531 en 526; alhoewel daar min inligting beskikbaar is oor die effek van hierdie mutasies op die funksie van RNS polimerase. Die doel van hierdie studie was om die effek van verskillende rpoB mutasies op die geen-uitdrukkingsprofiel van M. tuberculosis te bepaal. Rifampisien-weerstandige kliniese isolate en in vitro mutante (geselekteer vanaf H37Rv en 'n rifampisien-sensitiewe kliniese isolaat) met rpoB H526Y en S531L mutasies was vir hierdie doel geselekteer en gebruik om die heel genoom volgorde te bepaal en geenuitdrukking te kwantifiseer. Vergelyking van die H37Rv transkripsieprofiel met in vitro geselekteerde rpoB mutante het getoon dat 'n groot aantal gene wat differensieel uitgedruk is, vir proteïene kodeer wat betrokke is in selwand-prosesse en intermediêre metabolisme en respirasie. Die meerderheid van hierdie differensieel uitgedrukte gene was afgereguleer. ’n Soortgelyke verskynsel is ook waargeneem in kliniese isolate, met die verskil dat 'n groter aantal gene in hierdie geval differensieel-uitgedruk was. Gene wat deel vorm van die WhiB7 regulon is opgereguleer in die rpoB526 mutante, terwyl dit afgereguleer was in die rpoB531 mutante. Hierdie resultate is ’n baie sterk aanduiding dat beide die posisie van die rpoB mutasie, asook die genetiese agtergrond van die organisme, ’n belangrike rol speel in die uitdrukking van gene in rifampisin weerstandige M. tuberculosis. Kulture wat aan die kritiese konsentrasie van rifampisien vir 24 uur blootgestel is, het teenverwagting geen differensiële geen-uitdrukking getoon nie. Verder het die heel genoom volgorde bepaling van die in vitro mutante getoon dat sinonieme en nie-sinonieme enkel-nukleotied polimorfismes teenwoordig is in die onderskeie rpoB mutante. Dit dui daarop dat die mikobakteriële genoom voortdurend verander, moontlik nie so stadig as wat voorheen vermoed is nie. Die bevindinge van hierdie navorsing bied nuwe insigte om die invloed van mutasies wat middel-weerstandigheid veroorsaak op die biologie van M. tuberculosis te verstaan. Dit het ook getoon dat verdere studies dringend nodig is om die komplekse fisiologie van hierdie patogeen te verstaan. Hierdie kennis sal van kardinale belang wees vir die sukses van toekomstige ondernemings om nuwe anti-tuberkulose middels te ontwikkel.

Thesis (PhD)--Stellenbosch University, 2014. / ENGLISH ABSTRACT: Mycobacterium tuberculosis (M. tuberculosis) is the causative agent of tuberculosis (TB), a disease that affects millions of people world-wide. The species M. tuberculosis consists of a large number of different strains that can be grouped into at least 40 different known strain families. Many of the strains present with different pathogenic characteristics and host adaptations. The F11 LAM strains and Beijing strains currently have a nearly equal representation in the population of Cape Town, making up a total of 45% of all strains in this setting. The Latin-American Mediterranean (LAM) family of M. tuberculosis is proved to be the cause of a large percentage of TB cases worldwide and it is the predominant strain in high-prevalence regions such as the Western Cape and KwaZulu-Natal regions of South Africa, Zambia, Zimbabwe, and South America. This project aimed to investigate the evolution and biological characteristics of the members of the principle genetic group (PGG) 2 Latin-American Mediterranean (LAM) genotype of M. tuberculosis using a combination of whole genomic and proteomic analyses, coupled to mycobacterial molecular epidemiological techniques. The evolution of M. tuberculosis strain families from the Western Cape Province of South Africa proved to be consistent with previous evolutionary scenarios for M. tuberculosis isolated from other parts of the world. This genome-wide SNP-based phylogeny for the evolution of M. tuberculosis offers novel insight into the unique global representation of the M. tuberculosis isolates from the Western Cape, South Africa. The evolutionary scenario presented confirms six LAM sub-lineages, namely IS6110 RFLP families F9, F11, F13, F14, F15, and F26. A subset of sub-lineage defining SNPs was determined for each of the six LAM sub-lineages. The genomic changes in the LAM genotype strains observed through the SNP analysis presented here mostly occur in the genes involved in the cell wall, cell processes, intermediary metabolism and respiration. The same phenomenon was observed when the non-redundant SNPs of the non-LAM isolates were functionally annotated. The functional classification of the regulated proteins in the representative of the LAM RDRio lineage of M. tuberculosis suggests that proteins involved in the lipid metabolism, intermediary metabolism and respiration may be the key to the pathogenic effectiveness of the RDRio LAM lineage. A combination of the LAM SNP analysis and the LAM RDRio/non-RDRio comparison showed that the overall genomic- and proteomic features involved in the cell wall and cell processes of the LAM genotype differ to a large extent from what is seen in the reference strain, M. tuberculosis H37Rv. This genome wide phylogenetic study is the first of its kind in a South African context, and not only presents a robust phylogeny of the M. tuberculosis strain families, and specifically the LAM lineage, but also gives the first ever insight into the protein differences which distinguishes RDRio and non-RDRio M. tuberculosis strains from each other. / AFRIKAANSE OPSOMMING: Mycobacterium tuberculosis (M. tuberculosis) is die mikrobiese agent wat tuberkulose (TB), 'n siekte wat miljoene mense wêreldwyd affekteer, veroorsaak. Die spesie M. tuberculosis bestaan uit 'n groot aantal verskillende stamme wat in ten minste 40 verskillende bekende stam-families gegroepeer word. Baie van die stamme toon verskillende patogeniese eienskappe en gasheer aanpassings. Die F11 LAM stam en Beijing stam het tans 'n byna gelyke verteenwoordiging in die bevolking van Kaapstad, wat 'n totaal opmaak van 45% van stamme wat in hierdie gebied gevind word. Die Latyns-Amerikaanse Meditereense (LAM) familie van M. tuberculosis is bewys om die oorsaak van 'n groot persentasie van TB-gevalle wêreldwyd te wees, en dit is die oorheersende stam in hoë voorkoms streke soos die Wes-Kaap en KwaZulu-Natal streke van Suid-Afrika, Zambië, Zimbabwe en Suid-Amerika. Hierdie projek het ten doel gehad om die evolusie en biologiese eienskappe van die lede van die basiese genetiese groep (BGG) 2 Latyns-Amerikaanse Meditereense (LAM) genotipe van M. tuberculosis te ondersoek deur gebruik te maak van 'n kombinasie van heel genoom en proteoom analise, gekoppel aan mikobakteriële molekulêre epidemiologiese tegnieke. Die evolusie van M. tuberculosis stam families van die Wes-Kaap Provinsie van Suid-Afrika blyk om in ooreenstemming te wees met vorige evolusionêre scenario's vir M. tuberculosis wat in ander dele van die wêreld geïsoleer is. Die genoom-wye enkelnukleotied polimorfisme-gebaseerde filogenetiese hipotese vir die evolusie van M. tuberculosis bied nuwe insig in die unieke wêreldwye verteenwoordiging van die M. tuberculosis isolate van die Wes-Kaap, Suid-Afrika. Die evolusionêre scenario wat hier aangetoon word bevestig ses LAM sub-lyne, naamlik IS6110 RFLP families F9, F11, F13, F14, F15, en F26. 'n Versameling sub-lyn definiërende enkelnukleotied polimorfismes was bepaal vir elk van die ses LAM sub-afstammelinge. Die genomiese veranderinge wat waargeneem is in die LAM-genotipe isolate deur die enkelnukleotied polimorfisme analise wat hier aangebied word, is meestal in die gene wat betrokke is in die selwand, selprosesse, intermediêre metabolisme en respirasie. Dieselfde verskynsel is waargeneem wanneer die nie-oorbodige enkelnukleotied polimorfismes van die nie-LAM isolate funksioneel geannoteer is. Die funksionele klassifikasie van die gereguleerde proteïene in die verteenwoordiger van die LAM RDRio-lyn van M. tuberculosis dui daarop dat die proteïene wat betrokke is in die lipiedmetabolisme, intermediêre metabolisme en respirasie die sleutel tot die patogene doeltreffendheid van die RDRio-LAM-lyn kan wees. 'n Kombinasie van die LAM enkelnukleotied polimorfisme analise en die LAM-RDRio/nie-RDRio vergelyking het getoon dat die totale genomiese- en proteomiese kenmerke wat verwant is aan selwand en selprosesse van die LAM genotipe tot ʼn groot mate verskil van wat gesien word in die verwysing stam, M. tuberculosis H37Rv. Hierdie genoom-wye filogenetiese studie is die eerste van sy soort in 'n Suid-Afrikaanse konteks, en bied nie net ‗n robuuste filogenie van die M. tuberculosis stam families, en spesifiek die LAM genotipe van M. tuberculosis nie, maar gee ook die eerste keer ooit insig in die proteïen verskille wat RDRio en nie-RDRio M. tuberculosis stamme van mekaar onderskei.

published_or_final_version / Pathology / Doctoral / Doctor of Philosophy

published_or_final_version / abstract / Microbiology / Doctoral / Doctor of Philosophy

published_or_final_version / abstract / Microbiology / Master / Master of Philosophy

published_or_final_version / abstract / Microbiology / Doctoral / Doctor of Philosophy

published_or_final_version / Microbiology / Master / Master of Medical Sciences

One third of the world’s population is affected by Tuberculosis (TB), a disease caused by infection with Mycobacterium tuberculosis (MtB). The emergence of multidrug-resistant MtB makes this disease a major public health concern. New agents are needed to treat TB infections in a manner that circumvents existing pathways of resistance. One strategy is to target the organism at the translational level by inhibiting vital modifications of RNA. One gene responsible for these modifications is the tRNA (guanosine-1)-methyltransferase, trmD, which has been shown to be essential in several bacteria. The eukaryotic and bacterial m1G methyltransferases are structurally dissimilar, making this enzyme an ideal target for selective anti-TB agents. One strategy for TrmD inhibitor design is to target the catalytic center of the enzyme. Existing inhibitors such as Sinefungin exhibit poor selectivity due to the substrate’s role, SAM, as a universal methyl donor in many biological processes. Structure/activity relationships for inhibitory compounds are sparse, impeding the design of novel antimicrobials. Crystallographic data would identify molecular features unique to TrmD, and allow design of agents complimentary to the TrmD active site with minimal differential toxicity. Presently, no crystal structure for Mycobacterium tuberculosis TrmD exists. As a first step in this direction, the MtB gene has been cloned and expressed by using a His-tagged T7 expression vector. The recombinant protein was characterized through kinetic and preliminary inhibitor assays. The native enzyme displays a mass of 50 kDa, proving this enzyme is a dimer of two identical subunits. This is similar to data found on other TrmD orthologs. Crystallization of MtB TrmD has been achieved and preliminary x-ray diffraction studies conducted.

Objetivo: Determinar los factores de riesgo para el desarrollo de tuberculosis multidrogorresistente (TBC-MDR) en pacientes del Hospital Nacional “Dos de Mayo”, de junio de 2015 a junio de 2016. Materiales y métodos: Estudio observacional, analítico, longitudinal, retrospectivo, comparativo de casos y controles. La muestra fue de 120 pacientes diagnosticados con tuberculosis en el Programa de Control de la Tuberculosis en el Hospital Nacional “Dos de Mayo”, de junio de 2015 a junio de 2016, de los cuales 40 fueron casos y 80, controles. Se realizó un análisis bivariado, usando el software IBM SPSS Statistics versión 24. En él, se cruzaron las variables edad, sexo, ocupación, contacto con TBC-MDR, antecedente de tratamiento antituberculoso, presencia de comorbilidad, co-infección con VIH e IMC; utilizando X2 y la medida de asociación odds ratio. Resultados: Se encontró que el contacto con TBC-MDR, el antecedente de tratamiento antituberculoso, la presencia de alguna comorbilidad, la co-infección con VIH y la desnutrición son factores de riesgo para el desarrollo de TBC-MDR. Por otro lado, no se pudo establecer la edad menor a 40 años, el sexo masculino o el desempleo como factores de riesgo. Conclusión: Hay una serie de factores de riesgo para el desarrollo de tuberculosis multidrogorresistente que son manejables, por lo que se podrían establecer nuevos programas o estrategias a fin de evitar, o de no ser posible, asegurar el correcto manejo de estos factores, lo que podría ayudar a frenar el incremento de casos que se ha visto en los últimos años.

Identifica los linajes de Mycobacterium tuberculosis (MTB) en la región Callao mediante el uso de la metodología MIRU-VNTR. El estudio comprende 133 muestras de DNA obtenidas a partir de aislamientos de MTB en medio sólido Löwenstein - Jensen (LJ). Utiliza 24 MIRU-VNTR para la genotipificación de MTB. Los resultados reportan un alto poder discriminatorio de este método con un HGDI de 0.995. El linaje LAM es el más prevalente (51.1 %), seguido por Haarlem (18.8 %), el linaje asiático Beijing (8.3 %), el linaje Uganda se identificó en el 6% y los linajes T y S se observaron con un 2.3 % y 0.8 %, respectivamente. Identifica como Orphans (huérfanos) un 8.3 % de las cepas analizadas. La región Callao muestra una gran diversidad de linajes; así como, la presencia de patrones huérfanos endémicos. Esta información permite reconocer los linajes que se encuentran circulando en toda la región, así mismo su posible relación con multidrogorresistencia, lo cual será de gran utilidad al sector salud, para establecer programas de control y prevención oportuna de casos de tuberculosis. / Tesis