Investment in SARS-CoV-2 sequencing in Africa over the past year has led to a major increase in the number of sequences generated, now exceeding 100,000 genomes, used to track the pandemic on the continent. Our results show an increase in the number of African countries able to sequence domestically, and highlight that local sequencing enables faster turnaround time and more regular routine surveillance. Despite limitations of low testing proportions, findings from this genomic surveillance study underscore the heterogeneous nature of the pandemic and shed light on the distinct dispersal dynamics of Variants of Concern, particularly Alpha, Beta, Delta, and Omicron, on the continent. Sustained investment for diagnostics and genomic surveillance in Africa is needed as the virus continues to evolve, while the continent faces many emerging and re-emerging infectious disease threats. These investments are crucial for pandemic preparedness and response and will serve the health of the continent well into the 21st century.

Group A Streptococcus (GAS) is one of the major causes of respiratory tract infections. The objectives of this study were to identify isolates of S. pyogenes obtained from respiratory tract infections, and to assess their susceptibility to several antibiotics. A total of 40 strains were isolated and their susceptibility to 17 antibiotics was tested using a standard disk diffusion method. The minimum inhibitory concentrations (MICs) were determined using the E-test. All isolates were sensitive to β-lactam antibiotics including penicillin, amoxicillin, and cephalosporins. Macrolides remain active with the exception of spiramycin, which showed reduced susceptibility. Out of the 40 isolates, 100% of the isolates were resistant to tetracycline. Interestingly, isolates were sensitive to chloramphenicol, teicoplanin, vancomycine, and levofloxacin, providing potential alternative choices of treatment against infections with S. pyogenes.

Acute respiratory infections (ARIs) are the leading cause of infectious disease–related morbidity, hospitalization, and morbidity among children worldwide. This study aimed to assess the viral and bacterial causes of ARI morbidity and mortality in children under 5 years in Senegal. Nasopharyngeal samples were collected from children under 5 years who had ARI. Viruses and bacteria were identified using multiplex real-time reverse transcription-polymerase chain reaction and conventional biochemical techniques, respectively. Adenovirus was the most prevalent virus (50%; n = 81), followed by influenza virus (45.68%, n = 74), rhinovirus (40.12%; n = 65), enterovirus (25.31%; n = 41), and respiratory syncytial virus (16.05%; n = 26), whereas Streptococcus pneumoniae (17%; n = 29), Moraxella catarrhalis (15.43%; n = 25), and Haemophilus influenzae (8.02%; n = 13) were the most commonly isolated bacteria. Virus pathogens seem more likely to be more prevalent in our settings and were often associated with bacteria and S. pneumoniae (6%; 16) coinfection.

Introduction: While acute respiratory tract infections are the main cause of paediatric mortality and morbidity worldwide, pathogen patterns shift due to factors such as hygiene, vaccinations, and antibiotic resistance. Knowledge about current cause of respiratory infections is lacking, particularly in low- and middle-income countries. The aim of this study was to identity the various respiratory pathogens causing acute respiratory tract infections in children below 5 years of age visiting a sub-urban primary care clinic in Senegal. Methods: A case-control study was performed in September and October 2018. Oropharyngeal swabs were collected from cases; infants with fever and respiratory symptoms, and controls; children involved in the vaccination programme. Viral identification was conducted by polymerase chain reaction for 21 different viruses; bacteria were identified by culture studies. Associations between microorganisms, acute respiratory infection and severity of disease were calculated by multivariate regression adjusting for confounders such as age, sex, and living area. Results: Overall, 102 cases and 96 controls were included. Microorganisms were detected in 90.1% of cases and 53.7% of controls ( P < .001). Influenza virus A (including H1N1), influenza virus B, respiratory syncytial virus (RSV), and Streptococcus pneumoniae were independently associated with acute respiratory tract infections. Co-detection of two or more pathogens was present in 49.5% of cases; 31.7% of cases had a pneumonia and 90.2% was treated with antibiotics. Conclusions: This case-control study in a primary care setting in sub-Saharan Africa found influenza virus A and B, RSV, and S pneumoniae to be the main causes of acute respiratory tract infections in children below 5 years of age. We recommend evaluation of antibiotics prescription behaviour in this setting.

Currently, the abundance of Pasteuria penetrans in soils, an unculturable bacterial parasite of root-knot nematodes (Meloidogyne spp,). is estimated by the percentage of nematode juveniles infected with bacteria and the number of spores attached to their cuticle. Indirect immunofluorescence led to detection of free spores directly in soil suspensions using UV light and polyclonal antibodies raised against two P. penetrans populations (ORS-21414-Sen and PPI). Three extraction methods were compared in order to improve spore recovery. A gentle shaking/sieving method recovered more than 90% of the spores inoculated in soils and was more efficient and simple than aqueous two-phase partitioning and polyethylene glycol extractions. All the spores inoculated in sandy or sandy-clay soils were detected with immunofluorescence microscopy. The quantification of the spores was improved using an ELISA technique that showed a good correlation between optical density and spore concentration in inoculated soils. Specific antibodies provide a suitable method to quantify A penetrans and may be used to follow the evolution of the real pool of bacteria either in native suppressive soils or in inoculated ones. (C) 2001 Federation of European Microbiological Societies. Published by Elsevier Science B.V. All rights reserved

Background: Acute respiratory infections (ARI) continue to be the leading cause of pediatric morbidity and mortality worldwide.

Detarium senegalense, Detarium microcarpum et Piliostigma reticulatum sont trois plantes de la flore sénégalaise, utilisées en médecine traditionnelle pour la prise en charge de maladies infectieuses. Cette étude visait à déterminer in vitro l’activité antimicrobienne d’extraits et de fractions de feuilles de ces plantes sur différentes souches (Escherichia coli, Klebsiella oxytoca, Pseudomonas aeruginosa, Enterococus faecalis, Staphylococcus aureus et Candida albicans). Les méthodes de diffusion en milieu solide et de dilution en milieu liquide ont été utilisées pour la détermination des Diamètres d’Inhibition (DI) et des Concentrations Minimales Inhibitrices (CMI). Le screening phytochimique a été réalisé par des tests de caractérisation reposant sur des réactions physico-chimiques et par chromatographie sur couche mince. Sur l’ensemble des échantillons testés, seule la fraction dichlorométhanique de P. reticulatum était inactive sur les souches bactériennes étudiées. Les DI variaient entre 10 et 23 mm pour les échantillons actifs. Les CMI étaient comprises entre 0,0293 et 2,50 mg/mL. Les fractions d’acétate d’éthyle étaient les plus actives. Les familles de molécules suivantes ont été identifiées : tanins, flavonoïdes et saponosides. Les teneurs en polyphénols totaux variaient de 0,66 à 19 mg équivalent acide tannique/g. Cette étude a montré que les extraits des trois plantes sont dotés d’un fort pouvoir antimicrobien et contiennent plusieurs familles de composés chimiques.

SummaryBackground and aims. Streptococcus pneumoniae, Haemophilus influenzae and Moraxella catarrhalis are the most common causative agents of acute respiratory tract infections (RTIs). The objective of this study was to assess their susceptibility to several antibiotics.Materials and methods. A total of 58 strains (16 S. pneumoniae, 19 H. influenzae and 23 M. catarrhalis) were isolated from samples collected in two paediatric centres, and their susceptibility to commonly used antibiotics tested by E-test.Results. Among H. influenzae isolates, 10.5% were resistant to ampicillin (all β-lactamase-positive), and 88.9% were susceptible to cefaclor. High β-lactam resistance rates (penicillin: 31.3% and cephalosporins: 18.7 to 31.3%) had been observed among S. pneumonia strains. Only 50% of isolates were susceptible to azithromycine. 91.3% of M. catarrhalis isolates β-lactamases producers were resistant to ampicillin while susceptible to the most tested antibiotics.Conclusions. Except M. catarrhalis β-lactamases producing strains, frequency of antibiotic resistance was mainly observed among S. pneumoniae, and to a lesser extent among H. influenzae clinical isolates, suggesting the need for continuous surveillance of antimicrobial resistance patterns in the management of RTIs.