Evaluation of PacBio sequencing for full-length bacterial 16S rRNA gene classification.

BACKGROUND: Currently, bacterial 16S rRNA gene analyses are based on sequencing of individual variable regions of the 16S rRNA gene (Kozich, et al Appl Environ Microbiol 79:5112-5120, 2013).This short read approach can introduce biases. Thus, full-length bacterial 16S rRNA gene sequencing is needed to reduced biases. A new alternative for full-length bacterial 16S rRNA gene sequencing is offered by PacBio single molecule, real-time (SMRT) technology. The aim of our study was to validate PacBio P6 sequencing chemistry using three approaches: 1) sequencing the full-length bacterial 16S rRNA gene from a single bacterial species Staphylococcus aureus to analyze error modes and to optimize the bioinformatics pipeline; 2) sequencing the full-length bacterial 16S rRNA gene from a pool of 50 different bacterial colonies from human stool samples to compare with full-length bacterial 16S rRNA capillary sequence; and 3) sequencing the full-length bacterial 16S rRNA genes from 11 vaginal microbiome samples and compare with in silico selected bacterial 16S rRNA V1V2 gene region and with bacterial 16S rRNA V1V2 gene regions sequenced using the Illumina MiSeq. RESULTS: Our optimized bioinformatics pipeline for PacBio sequence analysis was able to achieve an error rate of 0.007% on the Staphylococcus aureus full-length 16S rRNA gene. Capillary sequencing of the full-length bacterial 16S rRNA gene from the pool of 50 colonies from stool identified 40 bacterial species of which up to 80% could be identified by PacBio full-length bacterial 16S rRNA gene sequencing. Analysis of the human vaginal microbiome using the bacterial 16S rRNA V1V2 gene region on MiSeq generated 129 operational taxonomic units (OTUs) from which 70 species could be identified. For the PacBio, 36,000 sequences from over 58,000 raw reads could be assigned to a barcode, and the in silico selected bacterial 16S rRNA V1V2 gene region generated 154 OTUs grouped into 63 species, of which 62% were shared with the MiSeq dataset. The PacBio full-length bacterial 16S rRNA gene datasets generated 261 OTUs, which were grouped into 52 species, of which 54% were shared with the MiSeq dataset. Alpha diversity index reported a higher diversity in the MiSeq dataset. CONCLUSION: The PacBio sequencing error rate is now in the same range of the previously widely used Roche 454 sequencing platform and current MiSeq platform. Species-level microbiome analysis revealed some inconsistencies between the full-length bacterial 16S rRNA gene capillary sequencing and PacBio sequencing

Working from home and intimate partner violence among cis-women during the COVID-19 pandemic: evidence from a global, cross-sectional study

Background Intimate partner violence (IPV) may have been exacerbated during the COVID-19 pandemic. This analysis aimed to determine how employment disruption during COVID-19, including working from home, was associated with IPV experience among cis-gendered women. Methods The International Sexual Health and Reproductive health (I-SHARE) study is a cross-sectional online survey implemented in 30 countries during the pandemic. Samples used convenience, online panel, and population-representative methods. IPV was a pre-specified primary outcome, measured using questions from a validated World Health Organisation instrument. Conditional logistic regression modelling was used to quantify the associations between IPV and changes to employment during COVID-19, adjusted for confounding. Results 13,416 cis-gender women, aged 18–97, were analysed. One third were from low and middle income countries, and two thirds from high income countries. The majority were heterosexual (82.7%), educated beyond secondary-level (72.4%) and childless (62.7%). During COVID-19 33.9% women worked from home, 14.6% lost employment, and 33.1% continued to work on-site. 15.5% experienced some form of IPV. Women working from home experienced greater odds of IPV than those working on-site (adjusted OR 1.40, 95% CI 1.12–1.74, p = 0.003). This finding was robust independent of sampling strategy and country income. The association was primarily driven by an increase in psychological violence, which was more prevalent than sexual or physical violence. The association was stronger in countries with high gender inequality. Conclusions Working from home may increase IPV risk globally. Workplaces offering working from home should collaborate with support services and research interventions to strengthen resiliency against IPV. Supplementary Information The online version contains supplementary material available at 10.1186/s12889-023-15785-7

ARK: Aggregation of Reads by K-Means for Estimation of Bacterial Community Composition.

MOTIVATION: Estimation of bacterial community composition from high-throughput sequenced 16S rRNA gene amplicons is a key task in microbial ecology. Since the sequence data from each sample typically consist of a large number of reads and are adversely impacted by different levels of biological and technical noise, accurate analysis of such large datasets is challenging. RESULTS: There has been a recent surge of interest in using compressed sensing inspired and convex-optimization based methods to solve the estimation problem for bacterial community composition. These methods typically rely on summarizing the sequence data by frequencies of low-order k-mers and matching this information statistically with a taxonomically structured database. Here we show that the accuracy of the resulting community composition estimates can be substantially improved by aggregating the reads from a sample with an unsupervised machine learning approach prior to the estimation phase. The aggregation of reads is a pre-processing approach where we use a standard K-means clustering algorithm that partitions a large set of reads into subsets with reasonable computational cost to provide several vectors of first order statistics instead of only single statistical summarization in terms of k-mer frequencies. The output of the clustering is then processed further to obtain the final estimate for each sample. The resulting method is called Aggregation of Reads by K-means (ARK), and it is based on a statistical argument via mixture density formulation. ARK is found to improve the fidelity and robustness of several recently introduced methods, with only a modest increase in computational complexity. AVAILABILITY: An open source, platform-independent implementation of the method in the Julia programming language is freely available at https://github.com/dkoslicki/ARK. A Matlab implementation is available at http://www.ee.kth.se/ctsoftware

Knowledge, use (misuse) and perceptions of over-the-counter analgesics in sub-Saharan Africa: a scoping review.

BACKGROUND: Over-the-counter (OTC) analgesics are safe for pain-management when used as recommended. Misuse can increase the risk of hypertension and gastrointestinal problems. OBJECTIVE: To conduct a scoping review of the uses and misuses of OTC analgesics in sub-Saharan Africa, to inform strategies for correct use. METHOD: Following guidelines for conducting a scoping review, we systematically searched Pubmed, ResearchGate and Google Scholar databases for published articles on OTC analgesic drug use in sub-Saharan Africa, without restrictions on publication year or language. Search terms were 'analgesics', 'non-prescription drugs', 'use or dependence or patterns or misuse or abuse' and 'sub-Saharan Africa'. Articles focusing on prescription drugs were excluded. RESULTS: Of 1381 articles identified, 35 papers from 13 countries were eligible for inclusion. Most were quantitative cross-sectional studies, two were mixed-methods studies, and one used qualitative methods only. About half (n = 17) the studies recorded prevalence of OTC drug use above 70%, including non-analgesics. Headache and fever were the most common ailments for which OTC drugs were taken. Primary sources of OTC drugs were pharmacy and drug shops, and family, friends and relatives as well as leftover drugs from previous treatment. The main reasons for OTC drug use were challenges in health service access, perception of illness as minor, and knowledge gained from treating a previous illness. Information regarding self-medication came from family, friends and neighbours, pharmacies and reading leaflets either distributed in the community or at institutions of learning. OTC drug use tended to be more commonly reported among females, those with an education lower than secondary level, and participants aged ≥50 years. CONCLUSION: Self-medicating with OTC drugs including analgesics is prevalent in sub-Saharan Africa. However, literature on reasons for this, and misuse, is limited. Research is needed to educate providers and the public on safe use of OTC drugs

Reported oral and anal sex among adolescents and adults reporting heterosexual sex in sub-Saharan Africa: a systematic review.

BACKGROUND: Oral and anal sexual behaviours are increasingly reported among adolescents and adults reporting heterosexual sex in peer-reviewed journals in high income countries, but less is known about these behaviours in low and middle-income countries, especially in sub-Saharan Africa. The aim of this systematic review is to describe the prevalence of, and motivations for, oral and anal sex among adolescents and adults reporting heterosexual sex in sub-Saharan Africa. METHODS: A systematic review of published articles that reported oral and or anal sex in sub-Saharan Africa was conducted from seven databases up to and including 30th August 2018. RESULTS: Of 13,592 articles, 103 met the inclusion criteria. The prevalence of reporting ever practising oral sex among adolescents, university students and a combined population of adolescents/adults ranged from 1.7-26.6%, 5.0-46.4% and 3.0-47.2% respectively. Similarly, prevalences of reported ever practising anal sex ranged from 6.4-12.4% among adolescents, 0.3-46.5% among university students and 4.3-37.8% amongst combined population of adolescents and adults. Higher prevalences of oral and anal sex were reported among populations at high-risk for sexually transmitted infections and HIV and university students and, in most studies, both behaviours were more commonly reported by males than females. Heterosexual oral and anal sexual acts were associated with some high-risk behaviours such as inconsistent condom use and multiple sexual partners. CONCLUSION: Reported oral and anal sex between men and women are prevalent behaviours in sub-Saharan Africa. Health professionals and policy makers should be aware of these behaviours and their potential associated health risks

Bacterial vaginosis among women at high risk for HIV in Uganda: high rate of recurrent diagnosis despite treatment.

OBJECTIVES: Bacterial vaginosis (BV) is associated with increased risk for sexually transmitted infections (STIs) and HIV acquisition. This study describes the epidemiology of BV in a cohort of women at high risk for STI/HIV in Uganda over 2 years of follow-up between 2008-2011. METHODS: 1027 sex workers or bar workers were enrolled and asked to attend 3-monthly follow-up visits. Factors associated with prevalent BV were analysed using multivariate random-effects logistic regression. The effect of treatment on subsequent episodes of BV was evaluated with survival analysis. RESULTS: Prevalences of BV and HIV at enrolment were 56% (573/1027) and 37% (382/1027), respectively. Overall, 905 (88%) women tested positive for BV at least once in the study, over a median of four visits. Younger age, a higher number of previous sexual partners and current alcohol use were independently associated with prevalent BV. BV was associated with STIs, including HIV. Hormonal contraception and condom use were protective against BV. Among 853 treated BV cases, 72% tested positive again within 3 months. There was no difference in time to subsequent BV diagnosis between treated and untreated women. CONCLUSIONS: BV was highly prevalent and persistent in this cohort despite treatment. More effective treatment strategies are urgently needed

Prevalence and genotype specific concordance of oro-genital and anal human papillomavirus infections among sexually active Nigerian women

Background: Human papillomavirus (HPV) associated cancers are increasingly reported globally, including in sub-Saharan Africa (SSA). However, with the exception of cervical HPV infection, data from SSA on the epidemiology of oral and genital HPV infections are limited. This study assessed the prevalence and concordance of oro-genital and anal HPV genotype specific infections among women in the general population. Methods: We conducted a cross-sectional study in sexually active women aged 18-45 years in Ibadan, Nigeria. After a face-to-face interview and clinical examination, oral, cervical, vulvar, and anal samples were collected from participants and tested by the Anyplex II 28 HPV assay. Descriptive and multivariable analyses were used to report prevalence and risk factors associated with HPV infections. Results: The prevalence of any vulva, cervical, anal, and oral HPV infections was 68.0% (210/309), 59.7% (182/305), 56.8% (172/303), and 16.1% (14/286), respectively. There was an inverse relationship between age-group and HPV prevalence of HPV in all anatomic sites except for the oral HPV infections. HPV 35 was the most prevalent high-risk HPV genotype in the vulva, cervix and oral cavity. Associated risk factors for HPV infection in each of the anatomic sites were reported. Overall, 10.0% (31/310) women had concordance of any HPV type in the four anatomic sites. Conclusion: There was a high prevalence of oro-genital and anal HPV infections among sexually active Nigerian women, with concordance of HPV types in the cervix, vulva, anus and oral cavity. We advocate large longitudinal studies that will involve sampling of multiple anatomic sites and inclusion of other women in the community for better understanding of HPV epidemiology in this region

Prevalence of sexually transmitted infections among young people in South Africa: A nested survey in a health and demographic surveillance site.

BACKGROUND: Sexually transmitted infections (STIs) and bacterial vaginosis (BV) are associated with increased transmission of HIV, and poor reproductive and sexual health. The burden of STIs/BV among young people is unknown in many high HIV prevalence settings. We conducted an acceptability, feasibility, and prevalence study of home-based sampling for STIs/BV among young men and women aged 15-24 years old in a health and demographic surveillance site (HDSS) in rural KwaZulu-Natal, South Africa. METHODS AND FINDINGS: A total of 1,342 young people, stratified by age (15-19 and 20-24 years) and sex were selected from the HDSS sampling frame; 1,171/1,342 (87%) individuals had ≥1 attempted home visit between 4 October 2016 and 31 January 2017, of whom 790 (67%) were successfully contacted. Among the 645 who were contacted and eligible, 447 (69%) enrolled. Consenting/assenting participants were interviewed, and blood, self-collected urine (men), and vaginal swabs (women) were tested for herpes simplex virus type 2 (HSV-2), chlamydia, gonorrhoea, syphilis, trichomoniasis, and BV. Both men and women reported that sample collection was easy. Participants disagreed that sampling was painful; more than half of the participants disagreed that they felt anxious or embarrassed. The weighted prevalence of STIs/BV among men and women, respectively, was 5.3% and 11.2% for chlamydia, 1.5% and 1.8% for gonorrhoea, 0% and 0.4% for active syphilis, 0.6% and 4.6% for trichomoniasis, 16.8% and 28.7% for HSV-2, and 42.1% for BV (women only). Of the women with ≥1 curable STI, 75% reported no symptoms. Factors associated with STIs/BV included having older age, being female, and not being in school or working. Among those who participated in the 2016 HIV serosurvey, the prevalence of HIV was 5.6% among men and 19% among women. Feasibility was impacted by the short study duration and the difficulty finding men at home. CONCLUSIONS: A high prevalence of STIs/BV was found in this rural setting with high HIV prevalence in South Africa. Most STIs and HIV infections were asymptomatic and would not have been identified or treated under national syndromic management guidelines. A nested STI/BV survey within a HDSS proved acceptable and feasible. This is a proof of concept for population-based STI surveillance in low- and middle-income countries that could be utilised in the evaluation of STI/HIV prevention and control programmes

Menstrual health intervention and school attendance in Uganda (MENISCUS-2): a pilot intervention study.

OBJECTIVES: Achieving good menstrual health and hygiene (MHH) is a public health challenge and there is little evidence to inform interventions. The aim of this study was to pilot test an intervention to improve MHH and school attendance in Uganda, in preparation for a future cluster-randomised trial. DESIGN: Longitudinal study with pre-post evaluation of a pilot intervention. SETTING: Two secondary schools in Entebbe, Uganda. PARTICIPANTS: Of the 473 eligible students in secondary 2 (S2) at baseline, 450 (95.1%; 232 girls and 218 boys) consented/assented. 369 students (188 girls; 81.0%; and 181 boys; 83.0%) participated in the endline survey. INTERVENTION: The intervention comprised training teachers to improve delivery of government guidelines for puberty education, training in use of a menstrual kit and pain management, a drama skit, provision of analgesics and improvements to school water and sanitation hygiene facilities. PRIMARY AND SECONDARY OUTCOME MEASURES: Feasibility and acceptability of delivering the intervention. Baseline and endline quantitative surveys were conducted, with qualitative interviews conducted at endline. School attendance was assessed using self-completed daily diaries among a nested cohort of 100 female students. RESULTS: There were high levels of uptake of the individual and behavioural intervention components (puberty education, drama skit, menstrual hygiene management (MHM) kit and pain management). The proportion of girls reporting anxiety about next period decreased from 58.6% to 34.4%, and reported use of effective pain management increased from 76.4% to 91.4%. Most girls (81.4%) reported improved school toilet facilities, which improved their comfort managing menstruation. The diary data and qualitative data indicated a potential intervention impact on improving menstrual-related school absenteeism. CONCLUSIONS: The pilot study showed that the multicomponent MHM intervention was acceptable and feasible to deliver, and potentially effective in improving menstruation knowledge and management. A cluster-randomised trial is needed to evaluate rigorously the intervention effects on MHM and school attendance. TRIAL REGISTRATION NUMBER: NCT04064736; Pre-results