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The global MDR-TB caseload is increasingly driven by primary transmission of MDR-TB in high burden countries. Control will require interruption of transmission through earlier detection, effective outbreak investigation, detailed resistance testing to guide tailored treatment for patients with highly resistant TB and development and rapid access to better drugs. Genomics research and the application of technologies enabled through genomic research and technological innovation can play a critical role in each of these areas. Early diagnosis is facilitated through rapid and sensitive molecular detection of resistance-conferring mutations, real-time whole genome sequencing is now being used to target outbreak investigation and to rapidly identify resistance to second-line drugs and drug development has been enabled through the development of sophisticated screening methods supported by genomic tools. However, the promise of the genomic revolution has not yet been translated to more effective control of MDR-TB, and significant obstacles and gaps in knowledge remain. This presentation will highlight recent advances in this area, describe where existing genomic technologies are already being applied in MDR-TB programmes and identify key knowledge gaps that remain. [ABSTRACT FROM AUTHOR]

Background: The explosion of interest in the human microbiome research was sparked in part by two research initiatives launched in 2008, the European and Chinese-led Metagenomics of the Human Intestinal Tract Consortium and the National Institutes of Health (NIH)-sponsored Human Microbiome Project. The new knowledge provided by these initiatives and others worldwide are transforming our understanding of the pathogenesis of several diseases, including asthma, inflammatory bowel diseases, obesity and Type 1 diabetes, as well as the development of the immune response linked to some vaccines. However, African populations are understudied in these initiatives, and there is no "African Microbiome Initiative". This systematic review aimed to summarize and discuss the state of research on the human microbiome in Africa, including the therapeutic role of the microbiome for the management of certain local diseases. Methods&Materials: Using predefined keywords, we searched in six electronic databases for human microbiome studies conducted in Africa. In addition, to find additional articles, we checked references cited in eligible studies. Two authors independently selected eligible studies published until 30 September 2015. Results: Eighty-nine human microbiome papers were identified from six electronic databases and other sources. There were 80 primary microbiome studies (including Khoi San (n= 1) and Hunter- Gatherers (n= 4)) and 9 nested microbiome studies within existing cohorts. 16S rRNA gene sequencing was the technique most widely used to characterize the microbiota. The main body sites studied were the gut (46%), vagina (25%) and the oral cavity (11%). The diseases targeted were malnutrition (n= 4), HIV/AIDS (n= 7), diarrhoea (n= 4), and periodontitis (n= 5). These microbiome studies were performed in individuals of all ages, with most of the studies being conducted in adults. Kenya, Uganda, South Africa and Nigeria were the sites of the majority of studies; however the principal investigators of most of the studies (87%) were from developed countries. TheUSANIHwasthemainfunding source (25%), followed by the Bill and Melinda Gates Foundation (9%) and the European Commision (8%). Conclusion: More studies of the microbiome including African participants, focusing on endemic diseases and led by African researchers are needed. [ABSTRACT FROM AUTHOR]

Background: We aimed to determine the prevalence and genetic characteristics of extended-spectrum beta-lactamase (ESBL)- and carbapenemase-producing Enterobacteriaceae in stools from healthy infants and their mothers, and to determine the risk factors associated with their carriage. Methods & Materials: This study was nested within the Drakenstein Child Health Study, South Africa. Maternal and infant faecal samples were collected at birth and at two additional time-points from the infants. Samples were screened for ESBLs and carbapenemase-producing organisms using ChromID ESBL and ChromID CARBA media, respectively. Vitek 2 was used for antibiotic susceptibility testing and identification of suspect ESBL/carbapenemase-producing isolates. ESBL production was confirmed using the combination disc test, and carbapenemase production using the modified Hodge test. Selected ESBL and carbapenemase genes were characterized by singleplex polymerase chain reaction and Sanger sequencing. Results: Maternal faecal carriage of ESBL-producing bacteria was 4.4%; 4/90 (95% confidence interval (CI): 1.5%-10.2%), and that of infants at birth was 3.5%; 4/116 (95% CI: 1.2%-8.0%). The infant faecal carriage of ESBL-producing bacteria at 5-12 and 20- 28 weeks was 4.4%; 3/68 (95% CI: 1.3%-11.3%) and 5.7%; 2/35 (95% CI: 1.2%-17.1%), respectively. ESBL genes were detected in six K. pneumoniae (blaCTX-M-15), five E. cloacae (blaSHV-12 and blaSHV-5) and three E. coli (blaCTX-M-14) isolates. No carbapenemaseproducing bacteria were identified in this study. Pulsed-field gel electrophoresis showed heterogeneous clones of CTX-M-15-producing K. pneumoniae isolates. In contrast, in a mother-infant pair, we observed clonal relations among ESBL-producing E. cloacae isolates. In addition, one infant was persistently colonized by SHV- 12-producing E. cloacae. Univariate analysis showed that infants born to HIV-positive mother, via elective caesarean section, and medication use before discharge were positively associated with ESBL faecal carriage. In contrast, breastfeeding prior to discharge was negatively associated with ESBL carriage. Conclusion: This is the first study to detect ESBL-producing bacteria inhumanmeconiumsamples in Africa, and raises questions on the source of such isolates and implications for community transmission. Further research is required to determine the spread of ESBL- and carbapenemase-producing bacteria in community settings in South Africa. [ABSTRACT FROM AUTHOR]