Scielo RSS <![CDATA[African Journal of Laboratory Medicine]]> vol. 8 num. 1 lang. <![CDATA[SciELO Logo]]> <![CDATA[<b>Review of molecular subtyping methodologies used to investigate outbreaks due to multidrug-resistant enteric bacterial pathogens in sub-Saharan Africa</b>]]> BACKGROUND: In sub-Saharan Africa, molecular epidemiological investigation of outbreaks caused by antimicrobial-resistant enteric bacterial pathogens have mostly been described for Salmonella species, Vibrio cholerae, Shigella species and Escherichia coli. For these organisms, I reviewed all publications describing the use of molecular subtyping methodologies to investigate outbreaks caused by multidrug-resistant (MDR) enteric bacterial infections. OBJECTIVES: To describe the use of molecular subtyping methodologies to investigate outbreaks caused by MDR enteric bacterial pathogens in sub-Saharan Africa and to describe the current status of molecular subtyping capabilities in the region. METHODS: A PubMed database literature search (English language only) was performed using the search strings: 'Africa outbreak MDR', 'Africa outbreak multi', 'Africa outbreak multidrug', 'Africa outbreak multi drug', 'Africa outbreak resistance', 'Africa outbreak resistant', 'Africa outbreak drug', 'Africa outbreak antibiotic', 'Africa outbreak antimicrobial'. These search strings were used in combination with genus and species names of the organisms listed above. All results were included in the review. RESULTS: The year 1991 saw one of the first reports describing the use of molecular subtyping methodologies in sub-Saharan Africa; this included the use of plasmid profiling to characterise Salmonella Enteritidis. To date, several methodologies have been used; pulsed-field gel electrophoresis analysis and multilocus sequence typing have been the most commonly used methodologies. Investigations have particularly highlighted the emergence and spread of MDR clones; these include Salmonella Typhi H58 and Salmonella Typhimurium ST313 clones. In recent times, whole-genome sequencing (WGS) analysis approaches have increasingly been used. CONCLUSION: Traditional molecular subtyping methodologies are still commonly used and still have their place in investigations; however, WGS approaches have increasingly been used and are slowly gaining a stronghold. African laboratories need to start adapting their molecular surveillance methodologies to include WGS, as it is foreseen that WGS analysis will eventually replace all traditional methodologies. <![CDATA[<b>Whole genome sequencing for drug resistance determination in <i>Mycobacterium tuberculosis</i></b>]]> South Africa remains challenged with a high tuberculosis burden accompanied by an increase in drug resistant cases. We assessed the use of the Illumina MiSeq, a next-generation sequencing platform for whole genome sequencing, followed by bioinformatic analysis using a commercial software package to determine resistance to selected drugs used for Mycobacterium tuberculosis treatment in our setting. Whole genome sequencing shows potential as a diagnostic platform for the detection of drug resistance in Mycobacterium tuberculosis with the provision of information for several drugs simultaneously.