Phylogenomic and epidemiological insights into two clinical Mycobacterium bovis BCG strains circulating in South Africa.

BACKGROUND: Mycobacterium bovis BCG is a live, attenuated tuberculosis vaccine. While the vaccine protects infants from tuberculosis, complications including disseminated infections have been reported following vaccination. Genetically diverse BCG sub-strains now exist following continuous passaging of the original Pasteur strain for vaccine manufacture. This genetic diversity reportedly influences the severity of disseminated BCG infections and the efficacy of BCG immunization. METHODS: M. bovis BCG was isolated from infants suspected of being infected with tuberculosis. The whole genome of the clinical isolates and BCG Moscow were sequenced using Illumina Miseq and the sequences were analysed using CLC Genomics Workbench 7.0, PhyResSE v1.0, and Parsnp. RESULTS AND CONCLUSIONS: Genetic variations between the clinical strains and the reference BCG Copenhagen were identified. The clinical strains shared only one mutation in a secretion protein. Mutations were identified in various antibiotic resistance genes in the BCG isolates, which suggests their potential as multidrug-resistant (MDR) phenotypes. Phylogenetic analysis showed that the two isolates were distantly related, and the M1_S48 clinical isolate was closely related to M. bovis BCG Moscow. The phylogenomics results imply that two different BCG strains may be circulating in South Africa. However, it is difficult to associate the BCG vaccine strain administered and the BCG strain supplied with specific adverse events, as BCGiosis is under-reported. This study presents background genomic information for future surveillance and tracking of the distribution of BCGiosis-associated mycobacteria. It is also the first to report on the genomes of clinical BCG strains in Africa.

A molecular ecological approach to the detection and designation of the etiological agents of a model polymicrobial disease.

The application of the original Koch postulates and the molecular Koch postulates in the definition of the etiological agents of polymicrobial diseases has received little or no attention. In the present study, denaturing gradient gel electrophoresis (DGGE) of oral samples (n = 3) from each of 3 categories of animals (healthy, diseased [gingivitis], and then oxytetracycline-treated) was used and revealed different bacterial community structures in a model polymicrobial disease (gingivitis) and after clinical cure. Potential microbes associated with the disease and belonging to the following families were identified: Fusobacteriaceae, Porphyromonadaceae, Flavobacteriaceae, Alcanivoracaceae, Bacteroidaceae, Xanthomonadaceae, and Neisseriaceae. Liquid chromatography-mass spectrophotometric analysis of culturable anaerobic bacteria culture supernatant revealed 3 major compounds (2-hydroxycaproic acid, phenyllactic acid, and indole acetic acid) that differentiated the healthy and disease groups. Results indicate that different microbial community structures were associated with the healthy and disease oral states. The results demonstrate the potential of DGGE as a tool in the detection and designation of etiological agents of polymicrobial diseases.