Deep Sequencing of the Vaginal Microbiota of Women with HIV

BACKGROUND: Women living with HIV and co-infected with bacterial vaginosis (BV) are at higher risk for transmitting HIV to a partner or newborn. It is poorly understood which bacterial communities constitute BV or the normal vaginal microbiota among this population and how the microbiota associated with BV responds to antibiotic treatment. METHODS AND FINDINGS: The vaginal microbiota of 132 HIV positive Tanzanian women, including 39 who received metronidazole treatment for BV, were profiled using Illumina to sequence the V6 region of the 16S rRNA gene. Of note, Gardnerella vaginalis and Lactobacillus iners were detected in each sample constituting core members of the vaginal microbiota. Eight major clusters were detected with relatively uniform microbiota compositions. Two clusters dominated by L. iners or L. crispatus were strongly associated with a normal microbiota. The L. crispatus dominated microbiota were associated with low pH, but when L. crispatus was not present, a large fraction of L. iners was required to predict a low pH. Four clusters were strongly associated with BV, and were dominated by Prevotella bivia, Lachnospiraceae, or a mixture of different species. Metronidazole treatment reduced the microbial diversity and perturbed the BV-associated microbiota, but rarely resulted in the establishment of a lactobacilli-dominated microbiota. CONCLUSIONS: Illumina based microbial profiling enabled high though-put analyses of microbial samples at a high phylogenetic resolution. The vaginal microbiota among women living with HIV in Sub-Saharan Africa constitutes several profiles associated with a normal microbiota or BV. Recurrence of BV frequently constitutes a different BV-associated profile than before antibiotic treatment

Global diversity and antimicrobial resistance of typhoid fever pathogens: Insights from a meta-analysis of 13,000 Salmonella Typhi genomes

Background: The Global Typhoid Genomics Consortium was established to bring together the typhoid research community to aggregate and analyse Salmonella enterica serovar Typhi (Typhi) genomic data to inform public health action. This analysis, which marks 22 years since the publication of the first Typhi genome, represents the largest Typhi genome sequence collection to date (n=13,000). Methods: This is a meta-analysis of global genotype and antimicrobial resistance (AMR) determinants extracted from previously sequenced genome data and analysed using consistent methods implemented in open analysis platforms GenoTyphi and Pathogenwatch. Results: Compared with previous global snapshots, the data highlight that genotype 4.3.1 (H58) has not spread beyond Asia and Eastern/Southern Africa; in other regions, distinct genotypes dominate and have independently evolved AMR. Data gaps remain in many parts of the world, and we show the potential of travel-associated sequences to provide informal ‘sentinel’ surveillance for such locations. The data indicate that ciprofloxacin non-susceptibility (>1 resistance determinant) is widespread across geographies and genotypes, with high-level ciprofloxacin resistance (=3 determinants) reaching 20% prevalence in South Asia. Extensively drug-resistant (XDR) typhoid has becomedominant in Pakistan (70% in 2020) but has not yet become established elsewhere. Ceftriaxone resistance has emerged in eight non-XDR genotypes, including a ciprofloxacin-resistant lineage (4.3.1.2.1) in India. Azithromycin resistance mutations were detected at low prevalence in South Asia, including in two common ciprofloxacin-resistant genotypes. Conclusions: The consortium’s aim is to encourage continued data sharing and collaboration to monitor the emergence and global spread of AMR Typhi, and to inform decision-making around the introduction of typhoid conjugate vaccines (TCVs) and other prevention and control strategies

Worksite intervention study to prevent diabetes in Nepal: a randomised trial protocol

Introduction In Nepal, approximately 31% of adult industrial employees have diabetes. While the prevention of type 2 diabetes through behavioural intervention has been disseminated, worksite could be an effective platform for the translation of this knowledge into action as employed adults spend most of their workday waking hours at workplaces. Methods and analysis We will conduct a randomised controlled trial to assess the effectiveness of a behavioural and a canteen intervention on diabetes risk reduction among those who are prediabetic at two worksites in eastern Nepal. We will recruit 162 adult full-time factory workers with haemoglobin A1c (HbA1c) of 5.7%–6.4% at baseline or fasting blood sugar of 100–125 mg/dL. The 8–14 months’ control period will be followed by the behavioural intervention where half of the participants will be randomised to receive the behavioural intervention and half will act as a control and will not receive any intervention. Then, all participants will receive the canteen intervention. The analysis will be intent-to-treat, comparing the difference in the change in HbA1c% between the behavioural intervention group and the control group using a two-sample t-test. The within-participant changes in HbA1c after 6 or more months on the canteen intervention among those not randomised to the behavioural intervention in the previous period will be assessed using the paired t-test. Ethics and dissemination Ethical approval was obtained from the Institutional Review Board at Yale School of Public Health, New Havens, USA and the Nepal Health Research Council. Trial registration number NCT04161937 (https://clinicaltrials.gov/ct2/show/NCT04161937)