Bassirou Diarra

Introduction: The burden of arboviral infections remains underestimated in sub-Saharan Africa due to the similarity of symptoms with malaria and other tropical febrile illnesses. Simultaneous infection with three arboviruses sharing the same vector is rarely reported. Case presentation: We report here the case of a six-year-old girl diagnosed by multiplex real time-polymerase chain reaction for infection involving dengue, zika and chikungunya viruses with no severe symptoms and good clinical improvement with symptomatic treatment in Bamako, Mali. Conclusions: Co-circulation of different arboviruses is possible in urban context where Aedes mosquito vectors are emerging. Further studies are needed to explore the epidemiology and the clinical features of these coinfections.

: Dengue fever, a vector-borne disease caused by four serotypes of dengue virus (DENV), ranges from asymptomatic to severe illness, including hemorrhagic fever and shock syndrome. A 2023 outbreak (August 2023–May 2024) in Mali affected six districts in Bamako, causing 1,422 confirmed cases with a 2.7% fatality rate. In this study, viral sequencing provided insights into the molecular epidemiology and transmission dynamics of this outbreak. From September to October 2023, 23 of 42 suspected cases detected through national dengue surveillance activities were tested using the pan-vertebrate virus metagenomics method (virome capture sequencing platform for vertebrate viruses [VirCapSeq-VERT]). Sequencing data were analyzed using the Rapid Identification of Microbes pipeline, and Bayesian phylogenetic inference with Monte Carlo methods was used to assess viral genomic evolution. Among 23 patients, 61% were male, and the median age was 37 years (range: 20–74). The most common symptoms were fever (93.1%), headache (56.5%), and asthenia (47.8%). The largest proportion experienced dengue with warning signs (65.2%), followed by dengue without warning signs (30.4%) and severe dengue (4.4%). The successful sequencing of 19 samples revealed dengue virus serotype 3 (DENV-3; genotype III) in 15 (65.21%) samples and dengue virus serotype 1 (DENV-1; genotype III) in 4 (17.39%) samples. The DENV-1 sequences were analogous to West African sequences, and the DENV-3 were clustered with West African, Asian, and Caribbean sequences. In this study of DENV in Mali, we offer insights into the molecular epidemiology of the virus and underscore the benefits of the genomic surveillance of arboviruses in West Africa.

: Unexplained fever poses significant diagnostic challenges in resource-limited settings like Bamako, Mali, where overlapping endemic diseases include malaria, HIV/AIDS, yellow fever, typhoid, and others. This study aimed to elucidate the infectious etiologies of acute febrile illnesses in this context. Acute febrile patients of any age were enrolled after informed consent or assent. Baseline clinical and demographic data were collected, and samples were analyzed by using rapid diagnostic tests, reverse transcriptase polymerase chain reaction, ELISA, and virus-targeted metagenomic sequencing (virome capture sequencing platform for vertebrate viruses [VirCapSeq-VERT]). Among 108 enrolled subjects, most were male (51.9%) and under 15 years old (56.5%). Measles virus was identified in 39.8% of cases, primarily among children. Other findings included Plasmodium spp. (12%), Salmonella spp. (13%), and severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2; 8.7%). The virome capture sequencing platform for vertebrate viruses was used for 101 subjects, corroborating many routine test results and identifying additional cases of measles virus (1), SARS-CoV-2 (5), and numerous other agents. Notably, nearly all subjects showed evidence of herpesviruses (90%) and anelloviruses (98%). Hemorrhagic fever viruses were not observed. With the inclusion of VirCapSeq-VERT, identifiable pathogens were found in 79.6% of cases, leaving 20.4% without a clear etiology. The identification of more than one concurrent pathogen was common (41.5%). Integrating metagenomic sequencing with routine laboratory diagnostic testing enhances the detection of pathogens in acute febrile illnesses, highlighting its potential value in identifying infectious etiologies in resource-limited settings.

Background: Non-tuberculous mycobacteria (NTM) are environmental agents that can cause opportunistic pulmonary disease in humans and animals, often misdiagnosed as tuberculosis (TB). In this study, we describe the cases of NTM identified during the first national anti-TB drug resistance survey conducted in Mali and explore associated risk factors. Methods: Sputum was collected from people presenting for pulmonary TB diagnosis from April to December 2019, regardless of age. Microscopy-positive patients were enrolled and tested using the Xpert MTB/RIF assay. A patient who tested negative for the Mycobacterium tuberculosis complex (MTBC) was tested for the presence of mycobacteria by amplification of the IS6110 and 16SrRNA (16S) genes through double quantitative real-time PCR, followed by nested PCR and Sanger sequencing of the IS6110-negative samples for NTM species identification. Results: 1,418 sputum smear-positive patients were enrolled, including 1,199 new cases, 211 previously treated cases, and 8 whose previous treatment history was unknown. Based on the results of Xpert MTB/RIF assay and in-house PCR methods, 1,331 (93.9%) patients were positive for MTBC, 48 (3.4%) for NTM, and no species identification was possible for 39 (2.7%). Advanced age of 65 and over with an OR 8.8 (95% CI 2.3–33.2 and p = 0.001) and previous TB treatment with an OR 3.4 (95% CI 1.2–9.6 and p = 0.016) were the risk factors statistically associated with NTM detection. M. avium complex (MAC) was the predominant NTM species, detected in 20 cases. Conclusion: Detection of NTM in people presumed to have TB is an ongoing challenge, confounding correct TB diagnosis. Concomitant use of microscopy and GeneXpert testing among at-risk individuals could improve patient management.

Background: Non-tuberculosis mycobacteria (NTMs) are environmental agents that can cause opportunistic pulmonary disease in humans and animals which is often misdiagnosed as tuberculosis (TB). In this study, we describe the cases of NTMs identified during the first national anti-TB drug-resistance survey conducted in Mali, and associated risk factors. Methods: Sputum was collected from people presenting for pulmonary TB diagnosis, from April to December 2019, regardless of age. Microscopy-positive patients were enrolled and were tested by GeneXpert MTB/RIF. Cases that tested negative for the Mycobacterium tuberculosis complex (MTBc) were tested for presence of mycobacteria by amplification of the IS 6110 and 16SrRNA genes through double quantitative real-time PCR, followed by nested PCR and Sanger sequencing of the IS 6110 -negative samples for NTM species identification. Results: A total of 1,418 sputum smear-positive patients were enrolled, including 1,199 new cases, 211 previously treated cases and 8 whose previous treatment history was unknown. Based on the results of GeneXpert MTB/RIF and in-house PCR methods, 1331 (93.9%) patients were positive for MTBc, 48 (3.4%) for NTMs and for 39 (2.7%) no species identification was possible. Advanced age (65 and over) (OR 8.8, p=0.001) and previous TB treatment (OR 3.4 and p=0.016) were the risk factors statistically associated with NTM detection. M. avium complex (MAC) was the predominant NTM species, detected in 20 cases. Conclusion: Detection of NTMs in people presumed to have TB is an ongoing challenge, confounding correct TB diagnosis. Concomitant use of microscopy and GeneXpert testing among at-risk individuals could lessen confusion.

Introduction: While real-time reverse transcription PCR (RT-PCR) is the recommended laboratory method to diagnose severe acute respiratory syndrome Coronavirus 2 (SARS-CoV-2) infection, its use in resource limited settings can be difficult to maintain due to high testing demand and shortage of reagents. The aim of this study was to evaluate the performances of Realy Tech™ and Standard Q™ in comparison to RT-PCR in a relatively low COVID-19 prevalence setting, Mali.Methods: We conducted a cross-sectional study between January and April 2021 in Bamako and Kati regions to evaluate both rapid tests during a large SARS-CoV-2 prevalence study in Mali.Results: Of the 390 samples tested, the sensitivity and specificity of Realy Tech™ and Standard Q™ were 57.1% (95%CI: 44.1-69.2), 95.8% (95%CI: 93.1-97.5); 61.9% (95%CI: 46.8-75.0), and 94.1% (95%CI: 89.5-96.8) respectively. Using RT-PCR, the global prevalence of SARS-CoV-2 was 14.4% (56/390). In both rapid antigen tests, the performance was better when used in suspected patients compared to positive patients under treatment. Moreover, higher viral loads equivalent to Ct < 25 were associated with better detection rates.Conclusion: While waiting for more complete data, these preliminary studies suggest that Realy Tech™ and Standard Q™ should not be used alone for COVID-19 diagnosis in Mali.

Burden of HAI and its risk factors. Materials and Methods: This was a prospective cohort study from January to June 2021 at the CHU Gabriel TOURE, Bamako, Mali. The sample size was determined based on the CDC Atlanta criteria, used to confirm HAI in surgical settings. Demographic, clinical, and biological parameters were determined. For the confirmed case of infection, the incriminated bacteria were isolated and tests were performed for the choice of drugs. Results: Of the total 1001 patients included in this study, 195 patients (19.48%) have HAIs. The types of infections were as follows: 70 cases of surgical site infections, 54 infections on burns victims, 40 urinary tract infections, and 31 cases of bacteraemia. Germs such as Escherichia Coli, Klebsiella pneumoniae, and Acinetobacter were often isolated. We found increasing hospital stays as well as some postoperative mortality related to infections. At the end of this study, corrective efforts were implemented to prevent HAI. Among them are improvements in sterilisation techniques as far as surgical materials were concerned. In addition to a surgical checklist, locally used drapes were replaced with single-use surgical supplies. Advanced training of the surgical team on things such as bladder catheterisation was also conducted in the department. It is important to put in place a committee, to prevent nosocomial infection in our hospital. The selected committee will be responsible for planning and implementing diverse strategies to prevent infections. Conclusions: The prevention of HAIs will reduce health costs and improve the quality of surgical care....

Investment in severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) sequencing in Africa over the past year has led to a major increase in the number of sequences that have been generated and used to track the pandemic on the continent, a number that now exceeds 100,000 genomes. Our results show an increase in the number of African countries that are able to sequence domestically and highlight that local sequencing enables faster turnaround times 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 illuminate 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 reemerging 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.

: Men and women often respond differently to infectious diseases and their treatments. Tuberculosis (TB) is a life-threatening communicable disease that affects more men than women globally. Whether male sex is an independent risk factor for unfavorable TB outcomes, however, has not been rigorously investigated in an African context, where individuals are likely exposed to different microbial and environmental factors. We analyzed data collected from a cohort study in Mali by focusing on newly diagnosed active pulmonary TB individuals who were treatment naive. We gathered baseline demographic, clinical, and microbiologic characteristics before treatment initiation and also at three time points during treatment. More males than females were affected with TB, as evidenced by a male-to-female ratio of 2.4:1. In addition, at baseline, males had a significantly higher bacterial count and shorter time to culture positivity as compared with females. Male sex was associated with lower smear negativity rate after 2 months of treatment also known as the intensive phase of treatment, but not at later time points. There was no relationship between patients’ sex and mortality from any cause during treatment. This study suggests that sex-based differences in TB outcomes exist, with sex-specific effects on disease outcomes being more pronounced before treatment initiation and during the intensive phase of treatment rather than at later phases of treatment.