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.

IntroductionCorynebacteria have an important place among the commensal flora of the skin and mucous membranes. Except for Corynebacterium diphtheriae, they were once considered contaminants of mucosa. Recent publications in medical bacteriology have highlighted the importance of several species, such as C. aurimucosum. To the best of our knowledge, we report the first isolation of this strain from urine.Case presentationWe report a case of a patient with a urinary tract infection with C. aurimucosum. We isolated this bacterium from a 52-year-old man of Wolof ethniticity (an ethnic group in Senegal, West Africa) at the regional hospital of Saint Louis, Senegal. Microscopic examination of his total urine sample showed coryneform Gram-positive bacilli associated with a high leukocyte reaction. After repeated isolation of the corynebacteria in three samples from the patient’s urine, it was identified by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry. The strain was susceptible to antibiotics, except for penicillin and co-trimoxazole. The potential infectious role of these commensal species in several infections should be taken into consideration.ConclusionsThis case highlights the significant proportion of species in the genus Corynebacterium other than dyphteriae in the infectious process. The use of mass spectrometry for identification highlights the originality of this work and the importance of these new diagnostic tools that are unavailable in most health facilities of countries with limited resources. We share the results of our method of identification of the isolated bacteria. This case should prompt attention to these rare bacteria, which can cause severe infections.

IntroductionThis report documents a rare case of Chryseobacterium indologenes urinary tract infection in Senegal. Chryseobacterium indologenes is an uncommon human pathogen reported in hospital outbreaks in Taiwan and there have been some sporadic cases reported in Europe and in the USA mainly from immune-suppressed patients.Case presentationThis case report describes a 42-year-old woman of Wolofa ethnicity who was hospitalized in our Department of Internal Medicine in a Senegalese university teaching hospital, with acute leukemia who died of severe sepsis 10 days following her hospitalization. A strain of Chryseobacterium indologenes isolated from her urine sample was resistant to several beta-lactams including ampicillin (minimum inhibitory concentrations ≥256μg/mL), cefotaxime (minimum inhibitory concentrations 32μg/mL) and imipenem (minimum inhibitory concentrations ≥32μg/mL), whereas it was susceptible to piperacillin (minimum inhibitory concentrations 16μg/mL), cefepime (minimum inhibitory concentrations 4μg/mL), ceftazidime (minimum inhibitory concentrations 4μg/mL), trimethoprim-sulfamethoxazole (minimum inhibitory concentrations ≤0.25μg/mL) and all tested quinolones including nalidixic acid (minimum inhibitory concentrations ≤2μg/mL).ConclusionsChryseobacterium indologenes although uncommon, is an important pathogen causing infection in hospitalized patients. The management of this infection needs better identification, drug susceptibility testing and monitoring of immunosuppressed patients with long hospitalizations.

Background: Bacterial vaginosis (BV) is associated with a high risk of complications, particularly during pregnancy. Objectives: The aims of this study were to determine the prevalence of BV in pregnant women in Dakar, Senegal, and to identify its associated risk factors. Patients and Methods: This prospective cross-sectional study was conducted from July 2020 to March 2021 in pregnant women with 34 to 38 weeks of gestation and seen for their routine prenatal consultation at the Nabil Choucair health center in Dakar, Senegal. Vaginal swabs were taken and examined using the Nugent scoring system for the diagnosis of the BV. Data analysis on SPSS (version 25) was done using the chi-square test to measure the strength of association. A value of p ≤ 0.05 was considered statistically significant. Results: BV was found in 28.0% (112/400) of the screened women with a median age 24 (21-29) years. A pH >4.5 predictive of BV was found in 80.4% (90/112) of samples. BV was associated with vaginal candidiasis in 49.1% (55/112) while Trichomonas vaginitis was found in 1.8% (02/112). In 80.4% (90/112) of affected women, BV was caused by Gardnerella vaginalis. Mobiluncus spp. was found in 19.6% (22/112) pregnant women in association with G. vaginalis. Symptoms characterized by episodes of pruritus, pelvic pain, burning and/or dyspareunia were seen among 59.8% (67/112) of these women with BV while 40.1% (45/112) of them reported no symptoms. Conclusion: In view of these results and in order to reduce gestational complications and adverse outcomes in the newborn, screening for BV in pregnant women should be favored in developing countries.

Cephalosporinases, which are naturally present in some enterobacterial species, can be mobilized by transposons, migrate to plasmids, and spread into other species such as Escherichia coli. The aim of this study was to characterize genes responsible for the production of extended-spectrum β-lactamases (ESBL) in E. coli isolates from urinary origin isolated in two hospitals in Senegal. Thus, a fortuitous discovery of plasmidic cephalosporinase in two isolates was noted. One of the isolates produced dha-1 associated with ESBL CTX-M-14, the other produced cmy-2, ESBL CTXM-15, tem-1 penicillinase, and oxa-1. This confirms the circulation of multidrug-resistant bacteria producing plasmidic cephalosporinase in Senegal. However, a large study is needed to better understand the prevalence and the nature of the genes involved.