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.

Bacterial bloodstream infections (BSI) account for considerable morbidity worldwide, but epidemiological data from resource-constrained tropical settings are scarce. We analysed 293 blood cultures from patients presenting to a regional referral hospital in Bouaké, central Côte d’Ivoire, to determine the aetiology of community-onset BSI. The prevalence of bacteraemia was 22.5%, with children being most commonly affected. Enterobacteriaceae (predominantly Klebsiella pneumoniae and Salmonella enterica) accounted for 94% of BSI. Staphylococcus aureus was the only relevant Gram-positive pathogen. Clinical signs and symptoms were not significantly associated with blood culture positivity after controlling for malaria.

The pharynx of the child may serve as a reservoir of pathogenic bacteria, including beta-haemolytic group A streptococci (GAS), which can give rise to upper airway infections and post-streptococcal diseases. The objective of this study was to determine the prevalence of beta-haemolytic Streptococcus spp. in pharyngeal samples stemming from children aged 3–14 years in Bouaké, central Côte d’Ivoire. Oropharyngeal throat swabs for microbiological culture and venous blood samples to determine the seroprevalence of antistreptolysin O antibodies (ASO) were obtained from 400 children in March 2017. Identification was carried out using conventional bacteriological methods. Serogrouping was performed with a latex agglutination test, while an immunological agglutination assay was employed for ASO titres. The mean age of participating children was 9 years (standard deviation 2.5 years). In total, we detected 190 bacteria in culture, with 109 beta-haemolytic Streptococcus isolates, resulting in an oropharyngeal carriage rate of 27.2%. Group C streptococci accounted for 82.6% of all isolates, whereas GAS were rarely found (4.6%). The ASO seroprevalence was 17.3%. There was no correlation between serology and prevalence of streptococci (p = 0.722). In conclusion, there is a high pharyngeal carriage rate of non-GAS strains in children from Bouaké, warranting further investigation.

Aims: The aims of the present study were to investigate the presence of Plasmid-Mediated Quinolone Resistance (PMQR) determinants and the association of these determinants with Extended Spectrum Beta-Lactamases (ESBLs) genes in ESBL-producing Klebsiella pneumoniae isolates from Teaching Hospital of Bouaké, Côte d’Ivoire. Study Design: It is a retrospective study. Place of Study: Bacteriology-Virology Laboratory of Teaching Hospital, Bouaké, Côte d'Ivoire. Methodology: From January 2015 to December 2016, 96 ESBL-producing Klebsiella pneumoniae isolates were collected from several specimens. Antimicrobial susceptibility of isolates was tested using the standard disk-diffusion method on Mueller-Hinton and interpretation according to recommendations of the 2017 EUCAST. These isolates analyzed for the detection of ESBL (blaCTX-M, blaTEM and blaSHV) and PMQR genes (aac(6’)-Ib-cr, qnrB and qnrS) using simplex PCR. Results: Of the 96 ESBL-producing strains, 85 (88.55%) harbored at least one of the ESBL genes tested. Out of the 85 strains encoding ESBL genes, 96.47% carried blaCTX-M and 92.94% blaSHV and blaTEM genes. Eighty nine (89.6%) of the 96 ESBL producing-isolates were resistant to ciprofloxacin and 84.4% to norfloxacin. Among the 96 strains, 80 (83.33%) were found harboring at least one PMQR gene consisting of 78 (81.3%) aac(6’)-Ib-cr, 61 (63.5%) qnrB and 15 (15.6%) qnrS. Among the PMQR-positive strains, 68.4% coharbored qnrB+acc(6’)-Ib-cr genes, 10.5% qnrB+qnrS+acc(6’)-Ib-cr and 6.6% qnrS+acc(6’)-Ib-cr. The qnrB gene was always linked to aac(6’)-Ib-cr gene. Aac(6’)-Ib-cr gene showed the highest association with three ESBL genes (87.6%), followed by qnrB gene (70.6%), then qnrS (17.7%). Conclusion: The PMQR genes were highly prevalent in ESBL-producing Klebsiella pneumoniae, primarily the aac(6’)-Ib-cr gene. The high associated was observed between ESBL and PMQR genes, notably with the aac(6’)-Ib-cr gene.

Aim: Determine the prevalence of serological markers and identify risk factors associated with Hepatitis B Virus (HBV) infection in patients screened at the Bouake teaching hospital. Study Design: Retrospective cross sectional study was conducted Study Site and Period: Bacteriology-Virology Laboratory/Bouake teaching hospital, Côte d´Ivoire, from April 2016 to January 2018. Methodology: In all 1076 study participants, venous blood sample was collected and screened for HBV surface antigen (HBsAg) and antibody against HBV core antigen (anti-HBc), by electrochemical-luminescence following the manufacturer protocols.  Additionally, questionnaires were used to collect information regarding sociodemographic variables and possible risk factors for hepatitis B infection.  Data were processed and analyzed using EPI INFO 7 software. Results: A total of 1076 participants were included in this study with a median age of 30.0 years (range: 3 months; 82 years). Of which, 514 (48%) were female and 562 (52%) were male with female / male ratio 1.09. HBsAg was detected in 24,3% of participants and 82 1 (76,3%) were exposed to the risk of HBV infection (anti-HBc positive). High rate of HBV infection was detected in male (27.93%) (p=0.003). The age group of 15–45 years were more infected (27.18%) (p<0.0001). The detection rate of HBe antigen (HBeAg), anti-HBe and anti-HBc (total antibodies) were respectively 12%; 86% and 7%. Of 938 participants who were not vaccinated against HBV, 240 (25.58%) were HBsAg-positive. HBV vaccine uptake was protective against HBV infection (AOR =0.580; 95% CI 0.359-0.938; p=0.024). Conclusion: The rate of carriage of HBs antigen was higer than national rate, which confirms that Bouake is a highly endemic area for HBV infection. Vaccination against Hepatitis B virus is the only way to prevent and to fight effectively against this infection. It is therefore important to encourage the screening and vaccination in the general population.