The fall armyworm Spodoptera frugiperda (J.E. Smith), a new pest of maize in Africa: monitoring, damage evaluation and identification of natural enemies on production areas of Senegal

The fall armyworm (FAW) Spodoptera frugiperda (J.E. Smith), an invasive pest of cereal crops in Africa, poses a real threat to food security in sub-Saharan African countries where cereals are the staple food. Since its appearance in Africa in 2016, the FAW has invaded almost all African countries due to its great dispersal capacity. Because of its resistance to a number of chemical pesticides but also the risks associated with the use of these, the search for an alternative method becomes essential. In order to report on the incidence of this pest and explore its associations with native natural enemies, a monitoring study of S. frugiperda populations, its damage as well as its natural enemies was carried out during the period of August to September 2020 in corn fields of two agro-ecological zones of Senegal and in the laboratory. Monitoring results show a heavy infestation with rates of up to nearly 75% of defoliated plants and more than 60% of attacked ears. The damage recorded remains low overall (score below 3/9). A wide range of auxiliary insects (17 families) made up of parasitoids and predators were identified in the field and in the laboratory as well as an endoparasitic nematode with a parasitism rate of 38.46% and a fungus in one of the sites. These results pave the way for the development of an approach to control CLA with these biological agents

Diagnostic accuracy of Xpert® MTB/RIF Ultra for childhood tuberculosis in West Africa - a multicentre pragmatic study

OBJECTIVE: To evaluate the performance of Xpert MTB/RIF Ultra ('Ultra') for diagnosis of childhood tuberculosis (TB) within public health systems. METHODS: In this cross-sectional study, children aged <15 years with presumptive pulmonary TB were consecutively recruited and evaluated for TB at tertiary-level hospitals in Benin, Mali and Ghana. Bivariate random-effects models were used to determine the pooled sensitivity and specificity of Ultra against culture. We also estimated its diagnostic yield against a composite microbiological reference standard (cMRS) of positive culture or Ultra. RESULTS: Overall, 193 children were included in the analyses with a median (IQR) age of 4.0 (1.1 - 9.2) years, 88 (45.6%) were female, and 36 (18.7%) were HIV-positive. Thirty-one (16.1%) children had confirmed TB, 39 (20.2%) had unconfirmed TB, and 123 (63.7%) had unlikely TB. The pooled sensitivity and specificity of Ultra verified by culture were 55.0% (95% CI: 28.0 - 79.0%) and 95.0% (95% CI: 88.0 - 98.0%), respectively. Against the cMRS, the diagnostic yield of Ultra and culture were 67.7% (95% CI: 48.6 - 83.3%) and 70.9% (95% CI: 51.9 - 85.8%), respectively. CONCLUSION: Ultra has suboptimal sensitivity in children with TB that were investigated under routine conditions in tertiary-level hospitals in three West African countries

Correction: A Seroepidemiological Study of Serogroup A Meningococcal Infection in the African Meningitis Belt.

[This corrects the article DOI: 10.1371/journal.pone.0147928.]

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

Prevalence and Risk Factors of Lower Reproductive Tract Infections in Symptomatic Women in Dakar, Senegal

Background: Lower reproductive tract infections in women are important causes of morbidity but can also lead to complications and sequelae. This study aimed to establish the prevalence and risk factors of lower genital tract infections among women of reproductive age in Dakar (Senegal). Methods: This was a prospective study conducted in 6 maternity hospitals from July to November 2015. Participants ranged in age from 18 to 49 years and presented at health facilities with signs and symptoms of genital infection. Consenting individuals who met the inclusion criteria were recruited for the study. Results: During the reporting period, 276 patients were enrolled. According to the laboratory results, the prevalence of any genital infection was 69.6% (192 of 276). The most common vaginal infections were bacterial vaginosis (39.5%) and vaginal candidiasis (29%), with the third most common cause, trichomoniasis, trailing behind in terms of prevalence (2.5%). Among the microorganisms responsible for cervical infections, Ureaplasma urealyticum was the most frequent (27.5%), followed by Mycoplasma hominis (14.5%), Chlamydia trachomatis (4.7%), and Neisseria gonorrhoeae (1.1%). Multivariate analysis showed that young women and women with low levels of education were at increased risk for vaginal/cervical infections. Conclusions: This study revealed a high prevalence of bacterial vaginosis and vaginal candidiasis and suggests that health care providers should increase awareness and communication to improve vaginal hygiene practices. If infection with Trichomonas vaginalis, C trachomatis or N gonorrhoeae is suspected, we also recommend systematically performing laboratory diagnostic confirmation

Additional file 1: Table S1. of Emergence and clonal transmission of multi-drug-resistant tuberculosis among patients in Chad

Individual spoligotyping data from isolates collected in Chad. a: The black and white boxes indicate the presence and absence, respectively, of the specific spacer at positions 1–43 in the DR locus; b: Lineage designations according to SITVIT2 using revised SpolDB4 rules; c: Clustered strains correspond to a similar spoligotype pattern shared by 2 or more strains “within this study”; as opposed to unique strains harboring a spoligotype pattern that does not match with another strain from this study. (DOCX 19 kb

HIV and Tuberculosis co-infection impacts T-cell activation markers but not the numbers subset of regulatory T-cells in HIV-1 infected patients

Background: Tuberculosis (TB) has been shown to accelerate the clinical course of HIV infection, but the mechanisms by which this occurs are not well understood. Regulatory T-cells (Tregs)are known to dampen hyperactivation of the immune cells, but it remains unclear whether hyperactivation of T-cells in HIV infection is associated with a decrease of Tregs and what the effect Mycobacterium tuberculosis (MTB) co-infection has on T-cell activation and Tregs. Objectives: In this study, we aim to evaluate whether active TB is associated with the increased expression of T-cell activation markers and reduced number of Treg cells in HIV-1-infected patients. Methods: This study was conducted on 69 subjects consisting of 20 HIV-infected patients,20 HIV and MTB co-infected patients, 19 MTB-infected patients and 10 uninfected control subjects negative for both MTB and HIV. The frequencies of T-cell activation markers (CD38 and HLA-DR) and Treg cells (CD4+CD25+CD127-) were measured by flow cytometry. Results: Significantly higher expression of CD38 and HLA-DR on CD4+ and CD8+ T-cells was found in MTB and HIV co-infected patients compared with HIV-infected patients. However,no significant difference in the percentage of Treg cells was reported between HIV patients with TB and those without. The study also showed a negative correlation between regulatoryT-cells frequency and CD4+ T-cell counts. Conclusion: These results suggest that TB enhances the expression of peripheral T-cell activation markers during HIV infection, whilst having no impact on the percentages of Tregcells

Half of rifampicin-resistant Mycobacterium tuberculosis complex isolated from tuberculosis patients in Sub-Saharan Africa have concomitant resistance to pyrazinamide

Besides inclusion in 1st line regimens against tuberculosis (TB), pyrazinamide (PZA) is used in 2nd line anti-TB regimens, including in the short regimen for multidrug-resistant TB (MDR-TB) patients. Guidelines and expert opinions are contradictory about inclusion of PZA in case of resistance. Moreover, drug susceptibility testing (DST) for PZA is not often applied in routine testing, and the prevalence of resistance is unknown in several regions, including in most African countries.Six hundred and twenty-three culture isolates from rifampicin-resistant (RR) patients were collected in twelve Sub-Saharan African countries. Among those isolates, 71% were from patients included in the study on the Union short-course regimen for MDR-TB in Benin, Burkina Faso, Burundi, Cameroon, Central Africa Republic, the Democratic Republic of the Congo, Ivory Coast, Niger, and Rwanda PZA resistance, and the rest (29%) were consecutive isolates systematically stored from 2014-2015 in Mali, Rwanda, Senegal, and Togo. Besides national guidelines, the isolates were tested for PZA resistance through pncA gene sequencing.Over half of these RR-TB isolates (54%) showed a mutation in the pncA gene, with a significant heterogeneity between countries. Isolates with fluoroquinolone resistance (but not with injectable resistance or XDR) were more likely to have concurrent PZA resistance. The pattern of mutations in the pncA gene was quite diverse, although some isolates with an identical pattern of mutations in pncA and other drug-related genes were isolated from the same reference center, suggesting possible transmission of these strains.Similar to findings in other regions, more than half of the patients having RR-TB in West and Central Africa present concomitant resistance to PZA. Further investigations are needed to understand the relation between resistance to PZA and resistance to fluoroquinolones, and whether continued use of PZA in the face of PZA resistance provides clinical benefit to the patients