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This paper investigates linkage to care following community‐based screening for hepatitis B virus (HBV) in rural Senegal. HBV‐positive participants who completed a biological and clinical examination to assess liver disease and treatment eligibility were referred to a regional hospital (if eligible for treatment), invited to join the Sen‐B research cohort study (adults with detectable viral load) or referred to their local health centre (all others). Logistic regressions were conducted to investigate factors associated with (i) uptake of the scheduled post‐screening examination, and (ii) HBV management initiation. Obstacles to HBV management were identified using thematic analysis of in‐depth patient interviews. Of the 206 HBV‐positive participants, 163 (79.1%) underwent the examination; 47 of the 163 (28.8%) initiated HBV management. Women, people not migrating for >6 months/year, individuals living in households with more agricultural and monetary resources, with other HBV‐positive participants, and beneficiaries of the national cash transfer program, were all more likely to undergo the examination. The likelihood of joining the Sen‐B cohort increased with household monetary resources, but decreased with agricultural resources. Initiation of HBV management in local health centre was higher among participants with a non‐agricultural economic activity. Individuals reported wariness and confusion about HBV management content and rationale at various stages of the care continuum, in particular with respect to venous blood sampling and management without treatment. In conclusion, HBV community‐based test‐and‐treat strategies are feasible, but early loss to follow‐up must be addressed through simplified, affordable management and community support and sensitization. [ABSTRACT FROM AUTHOR]

Background: In countries where hepatitis B virus (HBV) is endemic, including Senegal, the World Health Organization recommends systematic HBV screening of pregnant women and vaccination at birth to prevent mother-to-child transmission (MTCT). This study investigated healthcare workers' (HCW) knowledge and practices regarding HBV prevention and care in the rural region of Fatick in Senegal, as well as challenges they faced in implementing prevention activities related to HBV MTCT.Methods: A mixed-methods survey was conducted between May-July 2017 among 112 HCW working in 15 healthcare facilities in two districts of the Fatick region using face-to-face questionnaires and semi-structured interviews. Descriptive statistics and chi-square/Mann-Whitney tests were used to analyze quantitative data, while qualitative data were analyzed thematically.Results: The study population included 87 HCW in the quantitative component (83% women, median age [interquartile range, IQR] = 35 [31-40] years) and 11 in the qualitative component. A knowledge gap was observed in key areas of HBV infection: only 24, 51 and 38%, respectively, correctly reported that early HBV acquisition is associated with a high risk of developing chronic infection, that perinatal transmission is one of the main modes of HBV transmission in Senegal, and that three to four doses of HBV vaccine are required to ensure immunization in children. Despite good acceptability of systematic screening of pregnant women and vaccination at birth, only 48% of HCW mainly involved in prenatal care and 71% of those involved exclusively in vaccination routinely performed these two key interventions. HCW reported several structural barriers that may hinder their implementation: a lack of training in HBV and in counseling, poor availability of rapid diagnostic tests (RDT), high costs of both screening and treatment, a lack of adequate information on treatment options and missed opportunities for vaccination at birth.Conclusions: HCW working in the Fatick region may be insufficiently trained and supported to effectively implement HBV prevention strategies. Our findings suggest an urgent need to strengthen MTCT prevention in this region, by improving HCW knowledge in key areas of HBV infection, providing RDT and antiviral treatment at low cost, and enhancing community-based interventions for the timely vaccination of newborns. [ABSTRACT FROM AUTHOR]

Background: Although mother-to-child transmission (MTCT) of hepatitis B virus (HBV) is prevalent in West Africa, epidemiological data on HBV infection in women remain scarce. We studied i) hepatitis B surface antigen (HBsAg) prevalence and its correlates, ii) HBV screening history and serological status awareness, iii) MTCT risk and treatment needs in Senegalese women. Methods: A cross-sectional population-based serosurvey for HBsAg positivity was conducted in 2018–2019 in the rural area of Niakhar (Fatick region, Senegal). Participants were offered home-based HBV screening and answered face-to-face questionnaires. HBsAg-positive participants underwent clinical and biological assessments. Data were weighted and calibrated to be representative of the area's population. Logistic regression models helped identify factors associated with HBsAg-positivity in adult women (> 15 years old). Results: HBsAg prevalence in adult women was 9.2% [95% confidence interval: 7.0–11.4]. Factors associated with HBsAg-positivity were being 15–49 years old (ref: ≥ 50), living in a household with > 2 other HBsAg-positive members, and knowing someone with liver disease. Only 1.6% of women had already been tested for HBV; no one who tested HBsAg positive was already aware of their serological status. In women 15–49 years old, 5% risked MTCT and none were eligible for long-term antiviral treatment. Conclusions: Adult women have a high HBsAg prevalence but a low MTCT risk. Low rates of HBV screening and serological status awareness argue for the adoption of systematic screening during pregnancy using free and rapid diagnostic tests. Additionally, screening household members of HBsAg-positive women may greatly improve the cascade of care in rural Senegal. Trial registration: ClinicalTrials.gov identifier (NCT number): NCT03215732. [ABSTRACT FROM AUTHOR]

Objective:Detection of meningococcal carriers is key to understanding the epidemiology of Neisseria meningitidis, yet no gold standard has been established. Here, we directly compare two methods for collecting pharyngeal swabs to identify meningococcal carriers. Methods:We conducted cross-sectional surveys of schoolchildren at multiple sites in Africa to compare swabbing the posterior pharynx behind the uvula (U) to swabbing the posterior pharynx behind the uvula plus one tonsil (T). Swabs were cultured immediately and analyzed using molecular methods. Results:One thousand and six paired swab samples collected from schoolchildren in four countries were analyzed. Prevalence of meningococcal carriage was 6.9% (95% CI: 5.4-8.6%) based on the results from both swabs, but the observed prevalence was lower based on one swab type alone. Prevalence based on the T swab or the U swab alone was similar (5.2% (95% CI: 3.8-6.7%) versus 4.9% (95% CI: 3.6-6.4%) respectively (p=0.6)). The concordance between the two methods was 96.3% and the kappa was 0.61 (95% CI: 0.50-0.73), indicating good agreement. Conclusions:These two commonly used methods for collecting pharyngeal swabs provide consistent estimates of the prevalence of carriage, but both methods misclassified carriers to some degree, leading to underestimates of the prevalence. [ABSTRACT FROM AUTHOR]

Background: Urogenital schistosomiasis is a major public health concern in sub-Saharan Africa. In Senegal, the disease is endemic in all regions of the country. Recently, WHO strongly recommended including pre-school children and women of reproductive age during a mass drug administration campaign. It is important to describe the burden of the disease in these group at risk using innovative diagnostic tools. This study aimed to assess the use of real-time PCR in the detection of schistosomiasis cases at the community level in a seasonal transmission area. Methods: A cross-sectional survey was carried out in Niakhar located in the centre of Senegal. Pre-schoolchildren, school-aged children and female adolescents and adults were invited to participate in the study in April 2018. Urine samples were collected and examined using Hemastix reagent strips, filtration technique and real-time PCR. Schistosoma haematobium was detected, identified by targeting the Dra1 gene. The prevalence of urogenital schistosomiasis was determined for each group and the performance of the real-time PCR was compared with the conventional techniques. Results: A total of 428 participants were enrolled in this study including 87 (20.4%) pre-school children (1–5 years), 262 (61.3%) school-aged children between (5–14 years), 17 (3.9%) adolescents (15–17 years) and 62 (14.4%) female adults. The comparison of the diagnostic techniques has shown that the prevalence of urogenital schistosomiasis is higher using molecular technique (34.6%) compared to microscopy (20.3%). The percentage rate of haematuria using Hemastix was 23.1%. School-aged children between 5 and 14 years old were the most affected with 29.0% and 43.1% under microscopy and RT-PCR, respectively. In female participants, microscopic prevalence decreases with age, from 21.4% in school-aged children to 17.6% in adolescents and 9.7% in adults. There was good correlation between the number of eggs per 10 ml and the cycle threshold range. Conclusion: These results show the importance of using molecular tools in the surveillance of schistosomiasis particularly in pre-school children and women of reproductive age. [ABSTRACT FROM AUTHOR]

Using the culturomics approach, the previously unknown strain Marseille-P8953T, was isolated and classified within the Weizmannia genus. Strain Marseille-P8953T was isolated from the faeces of a healthy subject and consisted of Gram-stain positive, spore-forming, motile rod-shaped cells. A 99.2% similarity was observed between the 16S rRNA gene of strain Marseille-P8953T (accession number LR735539) and that of Weizmannia coagulans strain NBRC 12583T (accession number KX261624), its closest phylogenetic relative, while the genome of strain Marseille-P8953T (3.5 Mpb long, 46.5% GC content) shared the average nucleotide identity by Orthology and digital DNA-DNA Hybridisation values of 95 and 60.4%, respectively. Given the phylogenetic classification and phenotypic characteristics of strain Marseille-P8953T, we propose the creation of a new species within the Weizmannia genus named Weizmannia faecalis (= CSUR P8953T = CECT 9904 T). [ABSTRACT FROM AUTHOR]

Background: A meningococcal group A conjugate vaccine, PsA-TT (also known as MenAfriVac), was developed with the support of the Meningitis Vaccine Project. Around 280 million individuals aged 1-29 years have been immunised across the African meningitis belt. We analysed the kinetics of vaccine-induced antibody response and assessed the possible implications for duration of protection.Methods: We obtained data from two longitudinal studies done in The Gambia, Mali, and Senegal of antibody responses in 193 children aged 12-23 months and 604 participants aged 2-29 years following MenAfriVac vaccination. Antibodies were measured using two methods: group A serum bactericidal antibody (SBA) assay and group A-specific IgG ELISA. Data on antibody responses were analysed using a mixed-effects statistical model accounting for the mean response and variation in patterns of antibody kinetics. Determinants of antibody duration were investigated using regression analysis.Findings: In children age 12-23 months, the reduction in MenAfriVac-induced antibody levels assessed by SBA titres had two phases: with 97·0% (95% credible interval [CrI] 95·1-98·3) of the response being short lived and decaying within the first 6 months and the remainder being long lived and decaying with a half-life of 2690 days (95% CrI 1016-15 078). Antibody levels assessed by SBA titres in participants aged 2-29 years were more persistent, with 95·0% (85·7-98·1) of the response being short lived, and the long lived phase decaying with a half-life of 6007 days (95% CrI 2826-14 279). Greater pre-vaccination antibody levels were associated with greater immunogenicity following vaccination, as well as greater antibody persistence. Despite rapid antibody declines in the first phase, antibodies in the second phase persisted at SBA titres greater than 128. Although there is no strong evidence base for a correlate of protection against infection with Neisseria meningitidis serogroup A, we use an assumed SBA titre of 128 as a threshold of protection to predict that 20 years after vaccination with a single dose of MenAfriVac, vaccine efficacy will be 52% (29-73) in children vaccinated at age 12-23 months and 70% (60-79) in participants vaccinated at age 2-29 years.Interpretation: Population-level immunity induced by routine vaccination with the Expanded Programme on Immunization is predicted to persist at levels sufficient to confer more than 50% protection over a 20-year time period. Further increases in population-level immunity could be obtained via mass campaigns or by delaying the age of vaccination through the Expanded Programme on Immunization. However, the benefits of such a strategy would need to be weighed against the risks of leaving young children unvaccinated for longer.Funding: Meningitis Vaccine Project and Institut Pasteur. [ABSTRACT FROM AUTHOR]

Maryam Tidjani Alou, Dipankar Bachar, Anthony Levasseur, Souleymane Brah, and Daouda Alhousseini did not respond to correspondence from the Editors about this retraction. Retraction of: I Scientific Reports i https://doi.org/10.1038/s41598-019-45611-3, published online 24 June 2019 Editors have retracted this Article. [Extracted from the article]

These authors contributed equally: Matthieu Million and Maryam Tidjani Alou. Matthieu Million, Jean-Christophe Lagier, Souleymane Brah, Cheikh Sokhna, Philippe Parola, and Didier Raoult disagree with this retraction. Retraction of: I Scientific Reports i https://doi.org/10.1038/srep26051, published online 17 May 2016 Editors have retracted this Article. [Extracted from the article]

Genetic and phylogenetic studies indicated that Zika virus (ZIKV) has evolved into 2 major lineages, the African and Asian. However, ZIKV has been described as a single serotype. This study aimed at assessing the cross-neutralization between ZIKV African and Asian lineages strains. Sixthy-five samples collected in 2007 and 30 samples collected from the same subjects in 2011/2012 in West Africa and positive to neutralizing antibody against ZIKV MR-766 strain (African lineage) were tested against ZIKV H/PF/2013 strain (Asian lineage) by microneutralization assay. All samples showing neutralizing antibodies against MR-766 strain showed also neutralizing activity against H/PF/2013 strain, although with lower titers. This is consistent with about 120 amino acid differences between the two strains. Despite differences in the magnitude of neutralizing activity against different ZIKV strains, all samples showed neutralizing antibody titers considered to be protective. [ABSTRACT FROM AUTHOR]

Anaerococcus rubiinfantis sp. nov. strain mt16 T is a new species within the genus Anaerococcus , which was isolated by the culturomics approach from the gut microbiota of an infant suffering from kwashiorkor. A phenotypic, biochemical and proteomic description of this strain is hereby presented alongside a complete annotation of its genome. This strictly anaerobic species forms Gram-positive non-sporeforming cocci. The major fatty acid was hexadecanoic acid. The phylogenetic analysis of strain mt16 T showed a 97.9% similarity level with Anaerococcus vaginalis , the closest validly published species. Its genome is 1,929,161 bp long with 29.5% G + C content and contains 1808 protein-coding genes and 56 RNA genes, among which are six rRNA genes. Genomic analysis identified 41/1864 coding genes as ORFans (2.2%) and at least 620/1808 (34.9%) orthologous proteins which are not shared with the closest phylogenetic species. We believe that the extension of the human anaerobic gut compendium by culturomics is one of the first steps that will improve the understanding of the links between the microbiome and health or disease. [ABSTRACT FROM AUTHOR]

Two strains, designated as Marseille-P2918 T and Marseille-P3646 T , were isolated from a 14-week-old Senegalese girl using culturomics: Urmitella timonensis strain Marseille-P2918 T (= CSUR P2918, = DSM 103634) and Marasmitruncus massiliensis strain Marseille-P3646 T (= CSUR P3646, = CCUG72353). Both strains were rod-shaped, anaerobic, spore forming motile bacteria. The 16S rRNA gene sequences of strains Marseille-P2918 T (LT598554) and Marseille-P3646 T (LT725660) shared 93.25% and 94.34% identity with Tissierella praeacuta ATCC 25539 T and Anaerotruncus colihominis CIP 107754 T , their respective phylogenetically closest species with standing in nomenclature. Therefore, strain Marseille-P2918 T is classified within the family Tissierellaceae and order Tissierellales whereas strain Marseille-P3646 T is classified within the family Oscillospiraceae and order Eubacteriales. The genome of strain Marseille-P2918 T had a size of 2.13 Mb with a GC content of 50.52% and includes six scaffolds and six contigs, and that of strain Marseille-P3646 T was 3.76 Mbp long consisting of five contigs with a 50.04% GC content. The genomes of both strains presented a high percentage of genes encoding enzymes involved in genetic information and processing, suggesting a high growth rate and adaptability. These new taxa are extensively described and characterised in this paper, using the concept of taxono-genomic description., (© 2022. The Author(s).)

A novel strain, Mt12 T (=CSUR P1907 = DSM 100590), was isolated from the fecal sample of a 7-month-old girl from Senegal afflicted with severe acute malnutrition. This bacterium is a strictly anaerobic, spore-forming Gram-stain positive bacillus. The major cellular fatty acid was identified as tetradecanoic acid. Its 16S rRNA gene sequence exhibited 94.9% similarity with that of Crassaminicella profunda strain Ra1766H T , currently the closest species with a validly published name. The draft genome of strain Mt12 T is 3,497,275-bp long with a 30.45% of G+C content. 3397 genes were predicted, including 3268 protein-coding genes and 129 RNAs, including eight 16S rRNAs. Genomic comparison with closely related species with an available genome showed a lower quantitative genomic content. The phylogenetic analysis alongside the dDDH values under 30% and phenotypic characteristics suggest that strain Mt12 T represents a new genus within the family Clostridiaceae, for which the name Inediibacterium massiliense gen. nov., sp. nov. is proposed.

Background: Girls tend to have a lower risk of stunting than boys do in low-income countries. Objective: We evaluated differences in height status and complementary food (CF) intake between sexes from ages 2 to 39 mo in Senegal. Methods: Length and weight measurements were taken at ages 2-3, 4-5, 6-8, and 9-10 mo ( n = 7319). Qualitative 24-h and 7-d food recalls were conducted in a subgroup ( n = 2512). A smaller subsample was followed up to age 39 mo ( n = 512). Height was measured, and intake of CF was noted. Boys and girls were compared in terms of height-for-age z score (HAZ) of WHO standards and National Center for Health Statistics growth reference, height-for-age difference, stunting, and consumption of CF by using chi-square tests, general linear models, and mixed-effects linear models (MLMs). Results: By using WHO standards, the mean HAZ was lower for boys than for girls in infancy, i.e., at 2-3 mo of age (-0.65 compared with -0.57; P = 0.002) and beyond, i.e., at 24-29 mo of age (-2.01 compared with -1.65; P < 0.001). Overall risk of stunting was 24.5% and 19.4% for boys and girls, respectively, during infancy ( P < 0.001) compared with 59.2% and 47.9%, respectively, at 12-39 mo ( P = 0.010). In MLMs from ages 2 to 39 mo, boys had a lower mean HAZ than girls had at age 2 mo (β 0 = -0.19; P = 0.035), and sex differences increased with increasing age (β 1 = -0.007 z scores/mo; P < 0.001). At 2-3 mo of age, boys were more likely to have been fed CF every day during the past week (15.8% compared with 11.2% for girls; P = 0.005) and to have eaten ≥2 meals in the past 24 h (13.4% compared with 8.2% for girls; P < 0.001). Conclusions: In Senegalese infants, CF intake differed by sex, with boys more likely to consume CF. Boys had lower HAZs than girls had during infancy, and sex differences increased up to age 39 mo. The importance of sex in complementary feeding and growth warrants further attention in low-income countries., Competing Interests: 2: Author disclosures: KA Bork and A Diallo, no conflicts of interest., (© 2017 American Society for Nutrition.)

Malnutrition is the leading cause of death worldwide in children under the age of five, and is the focus of the first World Health Organization (WHO) Millennium Development Goal. Breastfeeding, food and water security are major protective factors against malnutrition and critical factors in the maturation of healthy gut microbiota, characterized by a transient bifidobacterial bloom before a global rise in anaerobes. Early depletion in gut Bifidobacterium longum, a typical maternal probiotic, known to inhibit pathogens, represents the first step in gut microbiota alteration associated with severe acute malnutrition (SAM). Later, the absence of the Healthy Mature Anaerobic Gut Microbiota (HMAGM) leads to deficient energy harvest, vitamin biosynthesis and immune protection, and is associated with diarrhea, malabsorption and systemic invasion by microbial pathogens. A therapeutic diet and infection treatment may be unable to restore bifidobacteria and HMAGM. Besides refeeding and antibiotics, future trials including non-toxic missing microbes and nutrients necessary to restore bifidobacteria and HMAGM, including prebiotics and antioxidants, are warranted in children with severe or refractory disease., (Copyright © 2016 Elsevier Ltd. All rights reserved.)

Background: Live attenuated influenza vaccines have been shown to significantly reduce influenza in diverse populations of children, but no efficacy studies have been done in resource-poor tropical settings. In Senegal, we assessed the efficacy and safety of a live attenuated influenza vaccine based on Russian-derived master donor viruses and licensed as a single dose., Methods: In this double-blind, placebo-controlled, parallel group, single-centre trial done near Niakhar, Senegal, generally healthy children aged 2-5 years were randomly allocated (2:1) to receive a single intranasal dose of masked trivalent live attenuated influenza vaccine or placebo. The allocation sequence was computer-generated by PATH with block sizes of three. The manufacturer provided vaccine and placebo in coded vials to preserve blinding. Participants were monitored through the predictable influenza season in Senegal for adverse events and signs and symptoms of influenza using weekly home visits and surveillance in clinics. The primary outcome was symptomatic laboratory-confirmed influenza caused by any strain and occurring from 15 days post-vaccination to the end of the study. The primary analysis was per protocol. This study is registered with ClinicalTrials.gov, number NCT01854632., Findings: Between May 23, and July 1, 2013, 1761 children were randomly assigned, 1174 to receive live attenuated influenza vaccine and 587 to receive placebo. The per-protocol set included 1173 vaccinees and 584 placebo recipients followed up to Dec 20, 2013. Symptomatic influenza was laboratory-confirmed in 210 (18%) of 1173 recipients of live attenuated influenza vaccine and 105 (18%) of placebo recipients, giving a vaccine efficacy of 0·0% (95% CI -26·4 to 20·9). Adverse events were balanced between the study groups. Two girls who had received live attenuated influenza vaccine died, one due to anasarca 12 days postvaccination and one due to malnutrition 70 days postvaccination., Interpretation: Live attenuated influenza vaccine was well tolerated in young children in Senegal, but did not provide protection against influenza. Further study in such populations, which might experience extended periods of influenza circulation, is warranted., Funding: US Centers for Disease Control and Prevention and Bill & Melinda Gates Foundation., (Copyright © 2016 The Author(s). Published by Elsevier Ltd. This is an Open Access article under the CC BY license. Published by Elsevier Ltd.. All rights reserved.)

Objectives: Neisseria meningitidis, together with the non-pathogenic Neisseria species (NPNs), are members of the complex microbiota of the human pharynx. This paper investigates the influence of NPNs on the epidemiology of meningococcal infection., Methods: Neisseria isolates were collected during 18 surveys conducted in six countries in the African meningitis belt between 2010 and 2012 and characterized at the rplF locus to determine species and at the variable region of the fetA antigen gene. Prevalence and risk factors for carriage were analyzed., Results: A total of 4694 isolates of Neisseria were obtained from 46,034 pharyngeal swabs, a carriage prevalence of 10.2% (95% CI, 9.8-10.5). Five Neisseria species were identified, the most prevalent NPN being Neisseria lactamica. Six hundred and thirty-six combinations of rplF/fetA&#95;VR alleles were identified, each defined as a Neisseria strain type. There was an inverse relationship between carriage of N. meningitidis and of NPNs by age group, gender and season, whereas carriage of both N. meningitidis and NPNs was negatively associated with a recent history of meningococcal vaccination., Conclusion: Variations in the prevalence of NPNs by time, place and genetic type may contribute to the particular epidemiology of meningococcal disease in the African meningitis belt., (Copyright © 2016 The Authors. Published by Elsevier Ltd.. All rights reserved.)

The pattern of epidemic meningococcal disease in the African meningitis belt may be influenced by the background level of population immunity but this has been measured infrequently. A standardised enzyme-linked immunosorbent assay (ELISA) for measuring meningococcal serogroup A IgG antibodies was established at five centres within the meningitis belt. Antibody concentrations were then measured in 3930 individuals stratified by age and residence from six countries. Seroprevalence by age was used in a catalytic model to determine the force of infection. Meningococcal serogroup A IgG antibody concentrations were high in each country but showed heterogeneity across the meningitis belt. The geometric mean concentration (GMC) was highest in Ghana (9.09 μg/mL [95% CI 8.29, 9.97]) and lowest in Ethiopia (1.43 μg/mL [95% CI 1.31, 1.57]) on the margins of the belt. The force of infection was lowest in Ethiopia (λ = 0.028). Variables associated with a concentration above the putative protective level of 2 μg/mL were age, urban residence and a history of recent vaccination with a meningococcal vaccine. Prior to vaccination with the serogroup A meningococcal conjugate vaccine, meningococcal serogroup A IgG antibody concentrations were high across the African meningitis belt and yet the region remained susceptible to epidemics.