Bacterial vaginosis, vaginal flora patterns and vaginal hygiene practices in patients presenting with vaginal discharge syndrome in The Gambia, West Africa

BACKGROUND: Bacterial vaginosis (BV) – a syndrome characterised by a shift in vaginal flora – appears to be particularly common in sub-Saharan Africa, but little is known of the pattern of vaginal flora associated with BV in Africa. We conducted a study aimed at determining the prevalence of BV and patterns of BV-associated vaginal micro-flora among women with vaginal discharge syndrome (VDS) in The Gambia, West Africa. METHODS: We enrolled 227 women with VDS from a large genito-urinary medicine clinic in Fajara, The Gambia. BV was diagnosed by the Nugent's score and Amsel's clinical criteria. Vaginal swabs were collected for T vaginalis and vaginal flora microscopy, and for Lactobacillus spp, aerobic organisms, Candida spp and BV-associated bacteria (Gardnerella vaginalis, anaerobic bacteria, and Mycoplasma spp) cultures; and cervical swabs were collected for N gonorrhoeae culture and C trachomatis PCR. Sera were tested for HIV-1 and HIV-2 antibodies. Sexual health history including details on sexual hygiene were obtained by standardised questionnaire. RESULTS: BV prevalence was 47.6% by Nugent's score and 30.8% by Amsel's clinical criteria. Lactobacillus spp were isolated in 37.8% of women, and 70% of the isolates were hydrogen-peroxide (H(2)0(2))-producing strains. Prevalence of BV-associated bacteria were: G vaginalis 44.4%; Bacteroides 16.7%; Prevotella 15.2%; Peptostretococcus 1.5%; Mobiluncus 0%; other anaerobes 3.1%; and Mycoplasma hominis 21.4%. BV was positively associated with isolation of G vaginalis (odds-ratio [OR] 19.42, 95%CI 7.91 – 47.6) and anaerobes (P = 0.001 [OR] could not be calculated), but not with M hominis. BV was negatively associated with presence of Lactobacillus (OR 0.07, 95%CI 0.03 – 0.15), and H(2)O(2)-producing lactobacilli (OR 0.12, 95% CI 0.05 – 0.28). Presence of H(2)O(2)-producing lactobacilli was associated with significantly lower prevalence of G vaginalis, anaerobes and C trachomatis. HIV prevalence was 12.8%. Overall, there was no association between BV and HIV, and among micro-organisms associated with BV, only Bacteroides spp. and Prevotella spp. were associated with HIV. BV or vaginal flora patterns were not associated with any of the factors relating to sexual hygiene practices (vaginal douching, menstrual hygiene, female genital cutting). CONCLUSION: In this population, BV prevalence was higher than in corresponding populations in industrialised countries, but the pattern of vaginal micro-flora associated with BV was similar. BV or vaginal flora patterns were not associated with HIV nor with any of the vaginal hygiene characteristics

The evolving SARS-CoV-2 epidemic in Africa: Insights from rapidly expanding genomic surveillance

INTRODUCTION Investment in Africa over the past year with regard to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) sequencing has led to a massive increase in the number of sequences, which, to date, exceeds 100,000 sequences generated to track the pandemic on the continent. These sequences have profoundly affected how public health officials in Africa have navigated the COVID-19 pandemic. RATIONALE We demonstrate how the first 100,000 SARS-CoV-2 sequences from Africa have helped monitor the epidemic on the continent, how genomic surveillance expanded over the course of the pandemic, and how we adapted our sequencing methods to deal with an evolving virus. Finally, we also examine how viral lineages have spread across the continent in a phylogeographic framework to gain insights into the underlying temporal and spatial transmission dynamics for several variants of concern (VOCs). RESULTS Our results indicate that the number of countries in Africa that can sequence the virus within their own borders is growing and that this is coupled with a shorter turnaround time from the time of sampling to sequence submission. Ongoing evolution necessitated the continual updating of primer sets, and, as a result, eight primer sets were designed in tandem with viral evolution and used to ensure effective sequencing of the virus. The pandemic unfolded through multiple waves of infection that were each driven by distinct genetic lineages, with B.1-like ancestral strains associated with the first pandemic wave of infections in 2020. Successive waves on the continent were fueled by different VOCs, with Alpha and Beta cocirculating in distinct spatial patterns during the second wave and Delta and Omicron affecting the whole continent during the third and fourth waves, respectively. Phylogeographic reconstruction points toward distinct differences in viral importation and exportation patterns associated with the Alpha, Beta, Delta, and Omicron variants and subvariants, when considering both Africa versus the rest of the world and viral dissemination within the continent. Our epidemiological and phylogenetic inferences therefore underscore the heterogeneous nature of the pandemic on the continent and highlight key insights and challenges, for instance, recognizing the limitations of low testing proportions. We also highlight the early warning capacity that genomic surveillance in Africa has had for the rest of the world with the detection of new lineages and variants, the most recent being the characterization of various Omicron subvariants. CONCLUSION Sustained investment for diagnostics and genomic surveillance in Africa is needed as the virus continues to evolve. This is important not only to help combat SARS-CoV-2 on the continent but also because it can be used as a platform to help address the many emerging and reemerging infectious disease threats in Africa. In particular, capacity building for local sequencing within countries or within the continent should be prioritized because this is generally associated with shorter turnaround times, providing the most benefit to local public health authorities tasked with pandemic response and mitigation and allowing for the fastest reaction to localized outbreaks. These investments are crucial for pandemic preparedness and response and will serve the health of the continent well into the 21st century

Evaluation of a new rapid diagnostic kit (FemExam) for bacterial vaginosis in patients with vaginal discharge syndrome in The Gambia.

BACKGROUND: Diagnosis of bacterial vaginosis (BV) in resource-poor primary health care settings is often overlooked; there is a need for a cheap, rapid, objective point-of-care diagnostic test. GOAL: The goal was to determine the prevalence of BV and to evaluate the performance of a new commercial diagnostic test kit in a developing country environment. STUDY DESIGN: Vaginal and cervical swabs were collected from 230 consecutive women attending a genitourinary medicine clinic with reported symptoms of vaginal discharge and/or itching. Etiological testing was carried out. BV was diagnosed on the basis of the Nugent score, the Amsel clinical criteria, and results of FemExam card tests. Card 1 is for pH and amines, and card 2 measures proline iminopeptidase (PIP) activity. RESULTS: BV prevalence was 47.9% according to the Nugent score. When compared with the Nugent score, the Amsel clinical criteria had a sensitivity of 77.9% and specificity of 58.4%, FemExam card 1 had a sensitivity of 71.4% and specificity of 72.8%, FemExam card 2 had a sensitivity of 70% and specificity of 81.0%, and FemExam cards 1 and 2 combined had a sensitivity of 91.0% and specificity of 61.5%. Cost per patient and cost per true case detected ranged from US $0.74 and US$1.54, respectively, for Gram stain diagnosis, to US $8.32 and US$18.49 for the FemExam two-card method. CONCLUSIONS: In a setting where BV was frequently associated with vaginal discharge, the FemExam test compared favorably with conventional clinical diagnosis, and it has the advantage of being rapid, less subjective, and easily performed. Cutting its cost would provide wider accessibility in developing countries

Molecular identification of unexposed <i>An</i>. <i>gambiae s</i>.<i>l</i>. mosquitoes collected in six rounds of collection between 2008 and 2010.

<p>Molecular identification of unexposed <i>An</i>. <i>gambiae s</i>.<i>l</i>. mosquitoes collected in six rounds of collection between 2008 and 2010.</p

Spatial and Temporal Trends in Insecticide Resistance among Malaria Vectors in Chad Highlight the Importance of Continual Monitoring

<div><p>Background</p><p>A longitudinal <i>Anopheles gambiae</i> s.l. insecticide resistance monitoring programme was established in four sentinel sites in Chad 2008–2010. When this programme ended, only sporadic bioassays were performed in a small number of sites.</p><p>Methods</p><p>WHO diagnostic dose assays were used to measure the prevalence of insecticide resistance to 0.1% bendiocarb, 4% DDT, 0.05% deltamethrin, 1% fenitrothion, and 0.75% permethrin in the main malaria vectors at the beginning and end of the malaria transmission season for three years 2008–2010, with subsequent collections in 2011 and 2014. Species and molecular identification of <i>An</i>. <i>gambiae</i> M and S forms and <i>kdr</i> genotyping was performed using PCR-RLFP; circumsporozoite status was assessed using ELISA.</p><p>Results</p><p>Between 2008 and 2010, significant changes in insecticide resistance profiles to deltamethrin and permethrin were seen in 2 of the sites. No significant changes were seen in resistance to DDT in any site during the study period. Testing performed after the period of routine monitoring had ended showed dramatic increases to DDT and pyrethroid resistance in 3 sites. No resistance to organophosphate or carbamate insecticides was detected. <i>An</i>. <i>arabiensis</i> was the predominate member of the <i>An</i>. <i>gambiae</i> complex in all 4 sites; adult collections showed temporal variation in species composition in only 1 site. <i>Kdr</i> analysis identified both 1014F and 1014S alleles in <i>An</i>. <i>gambiae</i> S only. Circumsporozoite analysis showed the highest vector infection rates were present in Donia, a site with extensive use of agricultural insecticides.</p><p>Conclusions</p><p>During the monitoring gap of four years, significant changes occurred in resistance prevalence in 3 of the 4 sites (p = <0.001), endangering the efficacy of currently implemented malaria control interventions. Significant changes in insecticide resistance profiles and a lack of <i>kdr</i> resistance alleles in adult populations highlight the urgent need for comprehensive entomological monitoring to be implemented and sustained in country.</p></div

Results from adult collections.

<p>A) PSC B) Pit traps. Different coloured series represent different species: Green = Other Anopheles; Red = <i>An</i>. <i>funestus</i>; Blue = <i>An</i>. <i>gambiae</i>.</p

Sentinel sites for biannual resistance monitoring.

<p>Green dots indicate the geographic locations of each of the four sites. Sites were chosen to represent a range of different selection pressures for insecticide resistance. Embedded charts show the baseline percentage mortality for the year in which monitoring began (2008), where BC = bendiocarb, DDT = DDT, DM = deltamethrin, FT = Fenitrothion, and PT = Permethrin. Green lines represent 98% mortality and red lines indicate 90% mortality. Map source <a href="https://commons.wikimedia.org/wiki/File:Chad_sat.jpg" target="_blank">https://commons.wikimedia.org/wiki/File:Chad_sat.jpg</a>.</p

Insecticide bioassay results for <i>Anopheles gambiae s</i>.<i>l</i>. in 2008, 2010 and 2014 in four sentinel sites in Chad.

<p>Insecticide bioassay results for <i>Anopheles gambiae s</i>.<i>l</i>. in 2008, 2010 and 2014 in four sentinel sites in Chad.</p