Introduction: Access to antiretroviral treatment (ART) becomes more and more effective in resource‐limited settings (RLS). However, this global effort would be even more profitable if the access to laboratory services especially in decentralized settings was strengthened. We report the virological outcome and HIV‐1 drug resistance in three West African countries using dried blood spots (DBS) samples.Methods: We included HIV‐1‐infected adults on ART ≥6 months and followed up in capital cities and decentralized sites in Senegal, Mali and Guinea‐Conakry. Patients were consecutively enrolled and DBS were collected in field conditions and kept at ambient temperature before transfer to the reference laboratory. Viral load (VL) was quantified using the NucliSENS EasyQ HIV‐1 v1.2. Genotyping of HIV‐1 pol gene was performed using in‐house protocol.Results: Of the 407 participants, 119, 152 and 136 were from Senegal, Mali and Guinea‐Conakry, respectively. The median treatment duration was 36 months [IQR: 6–136]. Virological failure (VF) (VL≥3log₁₀ copies/mL) was observed in 26% (95% confidence interval (CI), 18–35; n=31), 11% (95% CI, 6–17; n=16) and 24% (95% CI, 17–32; n=33) of patients in Senegal, Mali and Guinea‐Conakry, respectively (p=0.001). Of samples presenting VL≥3log₁₀ copies/mL (n=80), 70 were successfully genotyped. At least one drug resistance mutation (DRM) was detected in the following proportions: 70% (95% CI, 50–86; n=19), 93% (95% CI, 68–100; n=14) and 68% (95% CI, 48–84; n=19) in Senegal, Mali and Guinea‐Conakry, respectively (p=0.22). Twenty‐six per cent (26%; 95% CI, 16–38; n=18) of patients in VF harboured wild‐type viruses, which is likely indicative of weak adherence. Phylogenetic analysis showed the predominance of CRF02_AG subtype (73%; 95% CI, 61–83; n=51).Conclusions: We describe the ART outcome in capital and rural settings of Senegal, Mali and Guinea‐Conakry. Our results in all of the three countries highlight the need to reinforce the ART adherence in order to minimize the occurrence of drug resistance. In addition, these findings provide additional evidence that the use of DBS as a sampling support could assist virological monitoring of patients on ART in remote areas.

Integrase inhibitors (INIs) are a potent option for HIV treatment. Limited data exist on INI resistance in West Africa, particularly in children living with HIV/AIDS. We determined the prevalence of integrase gene polymorphisms and the frequency of naturally occurring amino acid (aa) substitutions at positions associated with INI resistance. Dried blood spot (DBS) samples were obtained from one hundred and seven (107) HIV-1-infected children aged less than 15 years old in two West African countries, Benin and Mali. All children were naïve to INI treatment, 56 were naïve to anti-retroviral therapy (ART), and 51 had received ART. Genetic sequencing of HIV integrase was successful in 75 samples. The aa changes at integrase positions associated with INI resistance were examined according to the Stanford HIV Genotypic Resistance database. The median ages were 2.6 and 10 years for ART-naïve and -treated children, respectively. The most common subtypes observed were CRF02_AG (74.7%) followed by CRF06_cpx (20%). No major INI-resistance mutations at positions 66, 92, 121, 143, 147, 148, 155, and 263 were detected. The most prevalent INI accessory resistance mutations were: L74I/M (14/75, 18.6%) followed by E157Q (8/75, 10.6%), G163E/N/T/Q (5/75, 6.6%), Q95A/H/P (2/75, 2.6%), and T97A (4/75, 5.3%). Other substitutions observed were M50I/L/P, H51E/P/S/Q, I72V, T112V, V201I, and T206S. Polymorphisms at positions which may influence the genetic barrier and/or drive the selection of specific INI-resistance pathways were detected. However, no transmitted drug resistance (TDR) to INI was detected among samples of INI-naïve patients. These findings support the use of this treatment class for children with HIV-1, particularly in West Africa.

Background: Antimicrobial resistance (AMR) is a global health concern, with extended-spectrum β-lactamases (ESBLs) and carbapenemases being major contributors. Pleural infection (PI) is a severe condition in West Africa, complicated by AMR. This study aimed to investigate the prevalence and molecular characteristics of ESBL and carbapenemase-producing enterobacteria in pleural effusions in Mali. Materials and methods: Pleural fluid samples from 526 patients with pleuritis were analyzed. Enterobacterial species were isolated and identified, and the prevalence of resistance genes (blaOXA-48, blaNDM-1, blaKPC, blaTEM, blaSHV) and virulence factors was determined. Results: Among the patients, 110 were diagnosed with enterobacterial pleuritis. Escherichia coli, Klebsiella pneumoniae, and Proteus mirabilis were the main pathogens identified. Resistance to β-lactams and cephalosporins was high, while carbapenems showed good activity. ESBL production was detected in 33.6% of isolates, with blaTEM being the most common gene. Carbapenemase gene (blaNDM-1) was found in three isolates. Conclusion: The study highlights the high prevalence of multidrug-resistant bacteria and the need for appropriate antibiotic selection based on local resistance patterns. Understanding the molecular characteristics of resistance is crucial for optimizing patient care and developing effective therapeutic strategies. Further research is needed to monitor and control AMR in PIs in Mali.

Background: Underdeveloped and underused medical laboratories in sub-Saharan Africa negatively affect the diagnosis and appropriate treatment of ailments.Objective: We identified political, disease-related and socio-economic factors that have shaped the laboratory sector in Senegal, Mali and Burkina Faso to inform laboratory-strengthening programmes.Methods: We searched peer-reviewed and grey literature from February 2015 to December 2018 on laboratory and health systems development from colonial times to the present and conducted in-depth interviews with 73 key informants involved in (inter)national health or laboratory policy, organisation, practice or training. This article depended on the key informants’ accounts due to the paucity of literature on laboratory development in francophone West African countries. Literature and interview findings were triangulated and are presented chronologically.Results: Until around 1990 there were a few disease-specific research laboratories; only the larger hospitals and district health facilities housed a rudimentary laboratory. The 1990s brought the advent of donor-dictated, vertical, endemic and epidemic disease programmes and laboratories. Despite decentralising from the national level to the regional and district levels, these vertical laboratory programmes biased national health resource allocation deleteriously neglecting the development of the horizontal, general-health laboratory. After the year 2000, the general-health laboratory system received more attention when, influenced by the World Health Organization, national networks and (sub-)directorates of laboratories were installed.Conclusion: To advance national general healthcare, as opposed to disease-specific healthcare, national laboratory directors and experts in general laboratory development should be consulted when national policies are made with potential laboratory donors.

Mpox is a zoonosis caused by the monkeypox virus. Here, we report Mali’s index Mpox case, which was clinically identified at the Mali–Guinea border by the national telemedicine center and confirmed by PCR. The library prepared with NextGenPCR™ MPXV Sequencing Library Prep and sequenced on Minion MK1C revealed a genome length of 197,122 bp with an average depth of 1284.4×. The strain belonged to Clade IIb G1 lineage and exhibited 85 mutations relative to NC_063383.1. To decipher genomic epidemiology, genomes ≥ 195 kb were retrieved from NCBI and aligned with MAFFT. Time-resolved phylogenetic reconstruction and ancestral trait inference were performed with TreeTime v0.11.4. A median joining network was built with Popart v1.7. Phylogeographic analysis revealed clustering with Clade IIb (G.1 lineage) linked to the May 2025 outbreak in Sierra Leone.

Background Diarrheal diseases constitute a serious public health problem, particularly in developing countries and it is the second leading cause of child mortality. Self-medication and overuse of antibiotics due to the scarcity of complementary diagnostic systems can lead to the development of multi-resistant bacteria causing diarrhea. The objective of this work was to identify the bacteria responsible for diarrhea in children and to characterize their sensitivity to a panel of antibiotics used in Mali. Methods This study involved 554 children seen in outpatient visits at the Yirimadio community health center and diagnosed with diarrhea. Yirimadio is a peripheral district area of Bamako the capital city of Mali. Stool samples were collected and analyzed by stool culture and antibiotic susceptibility was determined by the disk diffusion method on agar medium. Results The bacteria responsible for diarrheal were Escherichia coli (31.8%) and Salmonella (2.9%). In Escherichia coli strain, amoxicillin and cotrimoxazole were the most resistant antibiotics, 93.8% and 92.6%, respectively. The Extented Spectrum Beta Lactamase resistance phenotype accounted for 39.8% in Escherichia coli. A resistance of 12.5% to cotrimoxazole and cefoxitin was found to Salmonella strains. Conclusion This study showed that Escherichia coli is the most frequent bacteria involved in diarrhea in children under 3 years of age in Yirimadio, which are resistant to amoxicillin and co-trimoxazole, two antibiotics commonly prescribed in this setting.