Stéphane Ranque

Background & Aims: The intestinal mycobiota constitutes a minor yet functionally relevant component of the gut microbiota and has been implicated in chronic liver diseases, including metabolic dysfunction–associated steatohepatitis (MASH). However, its characterization remains challenging because of low fungal biomass and the methodological dependence of culture-based approaches. Methods: Intestinal fungal communities were characterized in 20 patients with MASH and 20 healthy controls using a culturomics approach based on three fungal culture media. Isolates were identified by MALDI-TOF mass spectrometry and DNA sequencing. Antifungal susceptibility testing was performed using Sensititre YeastOne for yeasts and Etest for filamentous fungi. Results: A total of 111 fungal isolates were recovered, including 41 on FastFung medium. The most frequently isolated species in the MASH group were Aspergillus tubingensis, Geotrichum candidum, and Meyerozyma guilliermondii, whereas controls were dominated by Geotrichum candidum, Penicillium chrysogenum, and Aspergillus tubingensis. Rare multidrug-resistant fungal strains were isolated exclusively from controls. No significant differences in taxonomic diversity were observed, although marked inter-individual heterogeneity was evident. Conclusions: Intestinal fungal communities in MASH are diverse, with no major differences in the structure or diversity of the cultivable mycobiome. However, antifungal susceptibility profiles varied between individuals, warranting further investigation of additional functional traits.

Freshwater snails are the main intermediate hosts of trematodes, responsible for major neglected tropical diseases such as schistosomiasis. Traditional snail identification methods relied on morphological characteristics and DNA-based techniques, each with limitations in terms of accuracy, cost and time. This study used matrix-assisted laser desorption/ionisation-time-of-flight mass spectrometry (MALDI-TOF MS) and DNA-based methods to identify freshwater snail species from three regions of Senegal and update the description of Lanistes adansoni. A total of 154 snails from six morphologically described species Bulinus senegalensis, B. umbilicatus, B. globosus, Biomphalaria spp, Gyraulus costulatus and L. adansoni were analysed. MALDI-TOF MS technique provided high-quality spectra for 149 specimens. A blind test was performed on 125 specimens against an updated database and revealed 100.00% correct identification with high identification scores (mean= 2.35 ± 0.21). DNA analysis of COI and 16S sequences, as well as morphological/morphometric criteria, supported the classification of L. adansoni. The study demonstrated that MALDI-TOF MS is a rapid and effective tool for identifying frozen freshwater snails without specialist expertise. We also report the first record of L. adansoni in central Senegal, improving knowledge of snail biodiversity, which is essential in the fight against neglected tropical diseases as part of the ’One Health’ approach.

Background: Tick-borne relapsing fever (TBRF) is caused by Borrelia species transmitted to humans by soft ticks of the genus Ornithodoros . Very little is currently known about the morbidity of this disease in Mali, despite the risk of human co-infection with malaria. The lack of appropriate diagnostic services or technical expertise to differentiate suspected malaria from other causes of febrile illness of unknown origin means that this tick-borne disease remains neglected and under-diagnosed in febrile patients in Mali. Our study investigated the detection of Borrelia crocidurae DNA in febrile patients in Mali from malaria rapid diagnostic tests (RDTs) for Plasmodium falciparum . Methodology/Principal Findings: Between June and December 2021, negative and positive malaria RDTs were collected from 41 health centers in the nine regions of Mali. Both qPCR and standard PCR were used to detect the presence of B. crocidurae DNA. Results: Of the 1,496, malaria RDTs tested, B. crocidurae DNA was detected in 9 DNA extracts from malaria-negative RDTs. All of these were collected in the region of Kayes, where the prevalence rate was 5% (9/180) of the malaria RDTs . Conclusions/significance: This study demonstrates that tick-borne relapsing fever is an under-diagnosed condition in Mali.

Freshwater snails act as intermediate hosts for parasites affecting both humans and livestock, including schistosomes. In Mauritania, however, the diversity, distribution, and infection status of these snails remain poorly documented. This study aimed to identify freshwater snail species collected from two schistosomiasis-endemic areas in southern Mauritania, characterize their spatial distribution, and assess their infection rates using molecular tools. Malacological surveys were conducted in Kankossa and Oued Rawdha during the 2023 rainy season. A total of 806 snail specimens were collected and preserved in 70% ethanol at 4 °C prior to analysis. Five species were identified morphologically and confirmed by molecular analysis: Bulinus truncatus, B. forskalii, B. senegalensis, B. umbilicatus, and Melanoidestuberculata. MALDI-TOF MS generated high-quality spectra for 99.0% of specimens and correctly identified 99.9% of analyzable samples after molecular confirmation of discrepant cases. Preservation in ethanol at 4 °C markedly improved spectral quality compared with previously reported room-temperature storage conditions. Distinct ecological distributions were observed according to water body type. B. senegalensis and B. umbilicatus were exclusively collected from temporary ponds, whereas B. truncatus, B. forskalii, and M. tuberculata were found in permanent water bodies. Real-time PCR screening detected Schistosoma haematobium complex DNA in 239/798 (29.9%) specimens, with substantially higher infestation rates in Kankossa than in Oued Rawdha. These findings demonstrate that MALDI-TOF MS is a rapid, accurate, and field-compatible tool for freshwater snail identification, including closely related species that are difficult to distinguish morphologically. This approach could facilitate large-scale epidemiological surveillance and improve monitoring of schistosomiasis transmission dynamics in endemic settings.

Endogenous ethanol (EtOH) production is a newly identified pathophysiological mechanism involved in metabolic dysfunction-associated steatohepatitis (MASH) and liver disease associated with hepatitis B virus (HBV). Therefore, the characterization of EtOH-producing species associated with liver disease could contribute to the development of gut microbiota-targeted approaches. We investigated EtOH production and tolerance, antimicrobial susceptibility and antimicrobial resistance gene(s) in 33 strains isolated in previous culturomics studies and belonging to species enriched in MASH, alcoholic hepatitis (AH) and HBV patients. Enterocloster clostridioformis, Thomasclavelia ramosa and Peptinophilus grossensis were identified as new EtOH-producing species associated with liver diseases. A strong association between EtOH tolerance and production was detected (p < 0.05). Yeast, Enterocloster species (strictly anaerobic bacteria) and Limosilactobacillus fermentum produced the highest concentrations of EtOH (0.8 to 3.3 g/L). The poorly absorbed drugs, amphotericin B, rifaximin and vancomycin together showed high in vitro susceptibility. Furthermore, E. clostridioformis EC38 harbored the vanB operon. New EtOH-producing species associated with liver diseases were identified thanks to culturomics. Notably, most of them are anaerobic bacteria. These findings underscore the need to further investigate anaerobic gut microbiota species enriched in liver diseases with the aim of developing gut microbiota-targeted therapies.

Schistosomiasis is a major neglected tropical disease in sub-Saharan Africa. This study compared the epidemiology of urinary schistosomiasis among children living in two distinct ecosystems in Mauritania: the Senegal River Basin (Trarza region) and the arid oasis areas (Adrar and Tagant regions). A cross-sectional study was conducted between February 2023 and February 2024 involving 856 children across 14 sites. Urine samples were collected from school-aged children and subjected to macroscopic and microscopic examinations. A questionnaire was administered to each child to determine sociodemographic factors. Environmental and geographical factors were documented in the localities. The prevalence rate of urinary schistosomiasis among children in the Senegal River Valley was 32.4%. In the oases zone, prevalences were 6.43% and 3.35% in Tagant and Adrar, respectively. Macroscopic hematuria was 29.1%, 6.04%, and 4.18% in Trarza, Adrar, and Tagant, respectively. The intensities of infection were 48.9, 6.43, and 40 eggs/10 mL in the Trarza, Adrar, and Tagant regions, respectively. Based on sex, prevalence was higher among boys in the Trarza and Tagant regions, while in Adrar, it was higher among girls. Prevalence among children using polluted water sources with dense vegetation in the department of Tékane, in the Trarza region, was significantly higher (35.7%) than among those using cleaner water sources (21%). Urinary schistosomiasis remains highly prevalent among children living along the Senegal River, while considerably lower transmission was observed in oasis settings. These findings highlight the strong influence of environmental and water-related factors on transmission dynamics and underscore the need for targeted, context-specific control strategies.

This study explores the use of Matrix-Assisted Laser Desorption/Ionization Time-of-Flight mass spectrometry (MALDI-TOF MS) to identify and differentiate Biomphalaria snails infected with the parasite S. mansoni , which causes schistosomiasis. The study was conducted on two snail species, Biomphalaria pfeifferi (collected in the field in Senegal) and Biomphalaria glabrata (a laboratory strain). The snails were infected in the laboratory with S. mansoni miracidia, and their infection was confirmed by cercariae emission tests and quantitative PCR (qPCR). MALDI-TOF MS was then used to analyse proteins from infected and uninfected snails to identify spectral differences. Based on protein profiles, the results of MALDI-TOF mass spectrometry made it possible to accurately differentiate between S. mansoni-infected snails and uninfected snails. An increase in the number of peaks detected and their intensity was observed for the spectra of S. mansoni -infected snails compared to uninfected snails. The application of principal component analysis (PCA) to these mass spectrometry profiles confirmed the discrimination between the two groups according to their infection status. In addition, specific discriminating peaks were identified for each snail species, allowing for the distinction of infected from uninfected snails. The present study revealed, for the first time, that MALDI-TOF MS appears to be a rapid, reliable, and specific tool for the diagnosis of schistosomiasis in snails, offering promising prospects for the surveillance and control of this disease in endemic areas. However, further work is needed to establish a MALDI-TOF MS reference spectra database specific to Schistosoma parasites and to standardise sample collection, storage, and preparation in order to apply this technique in the field.

Tick-borne relapsing fever (TBRF) is caused by Borrelia species transmitted to humans by soft ticks of the genus Ornithodoros . Very little is currently known about the morbidity of this disease in Mali, despite the risk of human co-infection with malaria. The lack of appropriate diagnostic services or technical expertise to differentiate suspected malaria from other causes of febrile illness of unknown origin means that this tick-borne disease remains neglected and under-diagnosed in febrile patients in Mali. Our study investigated the detection of Borrelia crocidurae DNA in febrile patients in Mali from malaria rapid diagnostic tests (RDTs). Methods: Between June and December 2021, negative and positive malaria RDTs were collected from 41 sites in the nine regions of Mali. Both qPCR and standard PCR were used to detect the presence of B. crocidurae DNA. Results: Of the 1496 malaria RDTs tested, B. crocidurae DNA was detected in 9 malaria-negative RDTs. All of these were collected in the region of Kayes, where the prevalence rate was 6% (9/150) of the negative malaria RDTs. Conclusions: This study demonstrates that tick-borne relapsed fever is an under-diagnosed condition in febrile patients in Mali.