Browsing by Author "Victor, T. C."

Now showing 1 - 5 of 5
  • Thumbnail Image
    Item
    Evidence that the spread of Mycobacterium tuberculosis strains with the Beijing genotype is human population dependent
    (American Society for Microbiology, 2007-07) Hanekom, M.; Van der Spuy, G. D.; Gey van Pittius, N. C.; McEvoy, C. R. E.; Ndabambi, S. L.; Victor, T. C.; Hoal, E. G.; Van Helden, Paul D.; Warren, Robin M.
    This study describes a comparative analysis of the Beijing mycobacterial interspersed repetitive unit types of Mycobacterium tuberculosis isolates from Cape Town, South Africa, and East Asia. The results show a significant association between the frequency of occurrence of strains from defined Beijing sublineages and the human population from whom they were cultured (P < 0.0001). Copyright © 2007, American Society for Microbiology. All Rights Reserved.
  • Thumbnail Image
    Item
    Molecular epidemiological interpretation of the epidemic of extensively drug-resistant tuberculosis in South Africa
    (American Society for Microbiology, 2015) Streicher, Elizabeth M.; Sampson, S. L.; Dheda, K.; Dolby, T.; Simpson, J. A.; Victor, T. C.; Gey van Pittius, Nicolaas C.; Van Helden, Paul D.; Warren, Robin M.
    We show that the interpretation of molecular epidemiological data for extensively drug-resistant tuberculosis (XDR-TB) is dependent on the number of different markers used to define transmission. Using spoligotyping, IS6110 DNA fingerprinting, and DNA sequence data, we show that XDR-TB in South Africa (2006 to 2008) was predominantly driven by the acquisition of second-line drug resistance.
  • No Thumbnail Available
    Item
    Mutations and other Risk indicators for Oesophageal Cancer among two distinct groups.
    (2005) Burger, H.; Barnard, D.; Van Helden, P. D.; Victor, T. C.; Abel, S.; Gelderblom, W. C. A.; Rossouw, G.; Wilken, E.; Marasas, W. F.O
  • Thumbnail Image
    Item
    Rifampicin resistance in Mycobacterium tuberculosis : rapid detection and implications in chemotherapy
    (Health & Medical Publishing Group, 1996-01) Pretorius, G. S.; Sirgel, F. A.; Schaaf, H. Simon; Van Helden, P. D.; Victor, T. C.
    Objectives. Tuberculosis treatment and susceptibility testing are cumbersome, especially in the case of multidrug-resistant (MDR) Mycobacterium tuberculosis. It is known that mutations in the rpoB gene of M. tuberculosis lead to resistance to rifampicin (RMP). In this study an attempt was made to apply molecular techniques for rapid detection of antibiotic resistance in clinical isolates of M. tuberculosis. Design. settings and subjects. RMP-resistant clinical isolates of M. tuberculosis from South Africa (N = 120) with unique resistant patterns were selected for calculation of resistance frequencies, and 74 MDR isolates of M. tuberculosis from different geographical origins were used for microbiological and molecular analysis. The polymerase chain reaction (PCR) technique was applied for amplification of a previously described region around a cluster of mutations in the rpoB gene, and single-stranded conformational polymorphism (SSCP) analysis was optimised to screen for mutations in the amplified region. Results. The results showed that an optimised PCR-SSCP procedure could detect a cluster of mutations in the rpoB gene (for RMP resistance) in 95% of RMP-resistant isolates. This procedure could therefore be used in the prediction of RMP resistance. Evidence was obtained that these mutations can be screened for directly from BACTEC cultures or even directly from Ziehl-Neelsen-positive sputum samples. Statistical analysis also showed that this locus can be used to predict the presence of an MDR isolate, which may have important implications in decisions concerning chemotherapy. Conclusions. It is currently not feasible to test all tuberculosis cases, but application of the PCR-SSCP technology in the prediction of multidrug resistance in M. tuberculosis isolates may be important in patients, especially where frequencies are high for drug-resistant isolates. This methodology could reduce the time required for sensitivity testing from approximately 6-12 weeks to a few days.
  • Thumbnail Image
    Item
    Whole genome sequencing reveals genomic heterogeneity and antibiotic purification in Mycobacterium tuberculosis isolates
    (BioMed Central, 2015-10) Black, P. A.; De Vos, M.; Louw, G. E.; Van der Merwe, R. G.; Dippenaar, A.; Streicher, Elizabeth M.; Abdallah, A. M.; Sampson, S. L.; Victor, T. C.; Dolby, T.; Simpson, J. A.; Van Helden, P. D.; Warren, Robin M.; Pain, A.
    Background: Whole genome sequencing has revolutionised the interrogation of mycobacterial genomes. Recent studies have reported conflicting findings on the genomic stability of Mycobacterium tuberculosis during the evolution of drug resistance. In an age where whole genome sequencing is increasingly relied upon for defining the structure of bacterial genomes, it is important to investigate the reliability of next generation sequencing to identify clonal variants present in a minor percentage of the population. This study aimed to define a reliable cut-off for identification of low frequency sequence variants and to subsequently investigate genetic heterogeneity and the evolution of drug resistance in M. tuberculosis. Methods: Genomic DNA was isolated from single colonies from 14 rifampicin mono-resistant M. tuberculosis isolates, as well as the primary cultures and follow up MDR cultures from two of these patients. The whole genomes of the M. tuberculosis isolates were sequenced using either the Illumina MiSeq or Illumina HiSeq platforms. Sequences were analysed with an in-house pipeline. Results: Using next-generation sequencing in combination with Sanger sequencing and statistical analysis we defined a read frequency cut-off of 30 % to identify low frequency M. tuberculosis variants with high confidence. Using this cut-off we demonstrated a high rate of genetic diversity between single colonies isolated from one population, showing that by using the current sequencing technology, single colonies are not a true reflection of the genetic diversity within a whole population and vice versa. We further showed that numerous heterogeneous variants emerge and then disappear during the evolution of isoniazid resistance within individual patients. Our findings allowed us to formulate a model for the selective bottleneck which occurs during the course of infection, acting as a genomic purification event. Conclusions: Our study demonstrated true levels of genetic diversity within an M. tuberculosis population and showed that genetic diversity may be re-defined when a selective pressure, such as drug exposure, is imposed on M. tuberculosis populations during the course of infection. This suggests that the genome of M. tuberculosis is more dynamic than previously thought, suggesting preparedness to respond to a changing environment.