Comparative genomics of Cluster O mycobacteriophages

Mycobacteriophages - viruses of mycobacterial hosts - are genetically diverse but morphologically are all classified in the Caudovirales with double-stranded DNA and tails. We describe here a group of five closely related mycobacteriophages - Corndog, Catdawg, Dylan, Firecracker, and YungJamal - designated as Cluster O with long flexible tails but with unusual prolate capsids. Proteomic analysis of phage Corndog particles, Catdawg particles, and Corndog-infected cells confirms expression of half of the predicted gene products and indicates a non-canonical mechanism for translation of the Corndog tape measure protein. Bioinformatic analysis identifies 8-9 strongly predicted SigA promoters and all five Cluster O genomes contain more than 30 copies of a 17 bp repeat sequence with dyad symmetry located throughout the genomes. Comparison of the Cluster O phages provides insights into phage genome evolution including the processes of gene flux by horizontal genetic exchange

Genomic and functional analyses of mycobacterium tuberculosis strains implicate ald in D-cycloserine resistance.

CAPRISA, 2016.Abstract available in PDF file

Evolution of extensively drug-resistant tuberculosis over four decades: whole genome sequencing and dating analysis of Mycobacterium tuberculosis isolates from KwaZulu-Natal.

CAPRISA, 2015.Abstract available in pdf

Prevalence and risk factors for myopia among school children in Aba, Nigeria

Aim: To study the prevalence of myopia among school children in Aba, Nigeria. Methods: This cross-sectional study was conducted in public and private (primary and secondary) schools. A multi-stage random sampling technique was used for selecting participants aged between 8 and 15 years from 12 schools in Aba, Nigeria. Data were analysed for 1197 children who underwent a comprehensive eye examination. The children were divided according to the following criteria: age groups (group 1 [8–11 years] or group 2 [12–15 years]), gender (male or female), level of education (primary or secondary) and type of school (public or private). Myopia was defined as spherical equivalent refraction (SER) ≤ -0.50 D in the poorer eye. Results: The prevalence of myopia was estimated to be 2.7%. Of the 96 children with refractive error, 78.1% were uncorrected. In using logistic regression analysis, risk of developing myopia was associated with older age groups (odds ratio [OR]: 1.20; 95% confidence interval [CI], 0.16–9.11; p < 0.010) and higher level of education (OR: 1.73; 95% CI, 1.05–2.86; p < 0.030). There was no significant difference in myopia prevalence between male and female children (p = 0.89). Conclusion: Although the prevalence of myopia and overall prevalence of refractive error in school children in Aba were low, the high prevalence of uncorrected refractive error is a significant public health problem. An effective and sustainable children’s vision screening programme is needed to prevent visual impairment and blindness

Dual-Reporter Mycobacteriophages (Φ2DRMs) Reveal Preexisting Mycobacterium tuberculosis Persistent Cells in Human Sputum

Persisters are the minor subpopulation of bacterial cells that lack alleles conferring resistance to a specific bactericidal antibiotic but can survive otherwise lethal concentrations of that antibiotic. In infections with Mycobacterium tuberculosis, such persisters underlie the need for long-term antibiotic therapy and contribute to treatment failure in tuberculosis cases. Here, we demonstrate the value of dual-reporter mycobacteriophages (Φ2DRMs) for characterizing M. tuberculosis persisters. The addition of isoniazid (INH) to exponentially growing M. tuberculosis cells consistently resulted in a 2- to 3-log decrease in CFU within 4 days, and the remaining ≤1% of cells, which survived despite being INH sensitive, were INH-tolerant persisters with a distinct transcriptional profile. We fused the promoters of several genes upregulated in persisters to the red fluorescent protein tdTomato gene in Φ2GFP10, a mycobacteriophage constitutively expressing green fluorescent protein (GFP), thus generating Φ2DRMs. A population enriched in INH persisters exhibited strong red fluorescence, by microscopy and flow cytometry, using a Φ2DRM with tdTomato controlled from the dnaK promoter. Interestingly, we demonstrated that, prior to INH exposure, a population primed for persistence existed in M. tuberculosis cells from both cultures and human sputa and that this population was highly enriched following INH exposure. We conclude that Φ2DRMs provide a new tool to identify and quantitate M. tuberculosis persister cells