Salt in stools is associated with obesity, gut halophilic microbiota and Akkermansia muciniphila depletion in humans.

BACKGROUND/OBJECTIVES: High salt intake has been linked to several diseases including obesity and an increased risk of death; however, fecal salinity and the ability of salt to alter the gut microbiota, which was recently identified as an instrumental factor for health and disease, remains poorly explored. METHODS/SUBJECTS: We analyzed the fecal samples of 1326 human individuals for salinity by refractometry, 572 for gut microbiota by culturomics, and 164 by 16S rRNA-targeted metagenomics. Geographical origin, age, gender, and obesity were tested as predictors of fecal salinity and halophilic diversity. All halophilic isolates were characterized by taxonogenomics and their genome sequenced. RESULTS: Fecal salinity was associated with obesity independently of geographical origin, gender, and age. The first 2 human-associated halophilic archaeal members were isolated along with 64 distinct halophilic species, including 21 new species and 41 known in the environment but not in humans. No halophiles grow in less than 1.5% salinity. Above this threshold, the richness of the halophilic microbiota was correlated with fecal salinity (r = 0.58, p < 0.0001). 16S metagenomics linked high fecal salinity to decreased diversity (linear regression, p < .035) and a depletion in anti-obesity Akkermansia muciniphila and Bifidobacterium, specifically B. longum and B. adolescentis. Genomics analysis suggested that halophilic microbes are not only transient passengers but may be residents of the human gut. CONCLUSIONS: High salt levels are associated with alteration of the gut microbial ecosystem and halophilic microbiota, as discovered during this study. Further studies should clarify if the gut microbiota alterations associated with high salt levels and the human halophilic microbiota could be causally related to human disease, such as obesity.

Shift in species composition in the Anopheles gambiae complex after implementation of long-lasting insecticidal nets in Dielmo, Senegal.

Long-lasting insecticidal nets (LLINs) and indoor residual spraying (IRS) are the cornerstones of malaria vector control. However, the effectiveness of these control tools depends on vector ecology and behaviour, which also largely determine the efficacy of certain Anopheles mosquitoes (Diptera: Culicidae) as vectors. Malaria vectors in sub-Saharan Africa are primarily species of the Anopheles gambiae complex, which present intraspecific differences in behaviour that affect how they respond to vector control tools. The focus of this study is the change in species composition in the An. gambiae complex after the implementation of LLINs in Dielmo, Senegal. The main findings referred to dramatic decreases in the proportions of Anopheles coluzzii and An. gambiae after the introduction of LLINs, and an increase in the proportion of Anopheles arabiensis. Two years after LLINs were first introduced, An. arabiensis remained the most prevalent species and An. gambiae had begun to rebound. This indicated a need to develop additional vector control tools that can target the full range of malaria vectors.

Taxonogenomics description of Bacillus marasmi sp. nov., a new species isolated from the stool sample.

Using the culturomics method, two strains were isolated, identified, and characterised following the taxonogenomics concept. Bacillus marasmi sp. nov. strain Marseille-P3556 (= CSURP3556) is isolated from a 13-month-old girl living in Niger. The phylogenetic tree, phenotypic criteria, and genomic analysis described here clearly show that this bacterium is different from previously known bacterial species withstanding in nomenclature and new members of Bacillus genus.

Amodiaquine dosage and tolerability for intermittent preventive treatment to prevent malaria in children.

Sulfadoxine-pyrimethamine with amodiaquine (SP-AQ) is a highly efficacious regimen for intermittent preventive treatment to prevent malaria in children (IPTc), but the amodiaquine component is not always well tolerated. We determined the association between amodiaquine dosage by body weight and mild adverse events (AEs) and investigated whether alternative age-based regimens could improve dosing accuracy and tolerability, using data from two trials of IPTc in Senegal, one in which AQ dose was determined by age and the other in which it was determined by weight category. Both dosage strategies resulted in some children receiving AQ doses above the recommended therapeutic range. The odds of vomiting increased with increasing amodiaquine dosage. In one study, incidence of fever also increased with increasing dosage. Anthropometric data from 1,956 children were used to predict the dosing accuracy of existing and optimal alternative regimens. Logistic regression models describing the probability of AEs by dosage were used to predict the potential reductions in mild AEs for each regimen. Simple amendments to current AQ dosing schedules based on the child's age could substantially increase dosing accuracy and thus improve the tolerability of IPTc using SP-amodiaquine in situations where weighing the child is impractical.

What could explain the late emergence of COVID-19 in Africa?

At the end of November 2019, a novel coronavirus responsible for respiratory tract infections emerged in China. Despite drastic containment measures, this virus, known as severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), spread in Asia and Europe. The pandemic is ongoing with a particular hotspot in southern Europe and America in spring 2020. Many studies predicted an epidemic in Africa similar to that currently seen in Europe and the USA. However, reported data do not confirm these predictions. Several hypotheses that could explain the later emergence and spread of the coronavirus disease 2019 (COVID-19) pandemic in African countries are being discussed, including the lack of health-care infrastructure capable of clinically detecting and confirming COVID-19 cases, the implementation of social distancing and hygiene, international air traffic flows, the climate, the relatively young and rural population, the genetic polymorphism of the angiotensin-converting enzyme 2 receptor, cross-immunity and the use of antimalarial drugs.

Taxonogenomics description of Bacillus dakarensis sp. nov., Bacillus sinesaloumensis sp. nov. and Bacillus massiliogabonensis sp. nov., three new species isolated from human stools.

Using microbial culturomics, three Bacillus strains were isolated, identified and characterized following the taxonogenomics strategy. Bacillus dakarensis strain Marseille-P3515T (=CSURP3515), Bacillus sinesaloumensis strain Marseille-P3516T (=CSURP3516), and Bacillus massiliogabonensis strain Marseille-P2639T (=CSURP2639) were isolated from human stool samples. The phylogenetic analysis, phenotypic characteristics and genotypic data presented here prove that these three bacteria are different from previously known bacterial species with standing in nomenclature and represent new Bacillus species.

Detailed description of Senegalia massiliensis strain SIT17T , a bacterium isolated from the human gut.

Strain SIT17T was isolated from the stool of a healthy 13-month-old Senegalese boy. It is a Gram-positive, anaerobic, rod-shaped, non-spore-forming and mobile bacterium. It exhibited 92.74% 16S rRNA gene sequence similarity with the Brassicibacter thermophilus strain Cel2f, the phylogenetically most closely related species. Its genome is about 2.87 Mb long with 27.39 mol% G + C content. We provide more details of Senegalia massiliensis strain SIT17T (= CSURP2130 = DSM 103071), the creation of which was previously announced.

Description of Gracilibacillus phocaeensis sp. nov., a new halophilic bacterium isolated from Senegalian human stool.

Using the taxonogenomics method, we describe Gracilibacillus phocaeensis strain Marseille-P3801, a new species previously isolated from a salty stool of a 20-year-old man from N'Diop, Senegal. It is a Gram-positive, aerobic and motile bacillus. The major fatty acids are C15:0-anteiso (59%), C16:0 (16%) and C17:0-anteiso (11%). Strain Marseille-P3801 exhibits a 98.45% sequence similarity with Gracilibacillus thailandensis strain TP2-8, the phylogenetically closest species. Its genome is 4.66 Mb with 39.6 mol% G + C content.

Epidemic of venereal treponematosis in wild monkeys: a paradigm for syphilis origin.

Treponema pallidum infections have been primarily known as slightly contagious mucocutaneous infections called yaws (tropical Africa and America) and bejel (subtropical North Africa). T. pallidum emerged as a highly infectious venereal syphilis agent in South America, probably about 500 years ago, and because of its venereal transmission, it quickly caused a worldwide pandemic. The disease manifests as lesions, including a chancre; then antibodies become detectable when or slightly after the chancre appears, and before the development of a rash and other systemic manifestations. Venereal diseases are poorly known in monkeys. During fieldwork in Senegal, we discovered an epizootic outbreak of venereal disease that we explored. We detected a venereal form of T. pallidum subsp. pertenue infection in green monkeys (Chlorocebus sabaeus), then observed an epizootic outbreak in Senegal and its spread among baboons a year later. Comparative analysis of T. pallidum genomes from the monkeys' chancres and other Treponema genomes showed an acceleration of the number of single nucleotide polymorphisms, comparable to that observed in syphilis. Identified T. pallidum clones seem to be epizootic through the acceleration of their mutation rate, which is linked to their larger diffusion.

[Assessing the reliability of clinical malaria diagnosis in children consulting in three peripheral health care facilities, in Niakhar rural area, Senegal]. / Evaluation de la fiabilité du diagnostic clinique de paludisme chez les enfants consultant dans trois postes de santé périphériques, dans la zone rurale de Niakhar au Sénégal.

A demographic survey site has been implemented in Niakhar rural zone in Senegal since the 1960s and many epidemiological and demographic studies have been conducted in this context. In this Sahelo-Sudanese area, malaria transmission is mesoendemic and mainly seasonal. In health care facilities, malaria real burden is poorly known as malaria diagnosis only relies on patients' clinical signs. The aim of our study was to measure the reliability of malaria diagnosis in these health centres by performing a parasitological confirmation of presumptive malaria cases and by assessing the validity of diagnosis according to child's age. A cross-sectional study was conducted in August-December 2006 (rainy season) and in February-June 2007 (dry season) in three health care facilities of the area (2 public centres and one private dispensary). Children aged 1 to 14 years old and accompanied by an adult were included. Two thick blood smears were carried out for each patient. A total of 474 children were included; among them 208 (43.9%) had a positive blood smear. Among the 335 (70.7%) presumptive malaria cases, 182 (54.3%) were confirmed by thick smear. Sensitivity specificity positive and negative predictive values were respectively 87.5%, 42.6%, 55.3% and 80.7%. Clinical signs which were predictive of confirmed malaria were vomiting and body temperature > or =38 degrees C. Clinical diagnosis performances decreased significantly during the dry season and in children under the age of two. The proportion of true malaria cases (54.3%) confirms the results of previous studies described in literature and shows a consistency for the last twenty years. Malaria is the main diagnosis attributed to patients by health care agents, regardless of the child's age or the season, whereas thick smear results are predominantly negative among children aged less than 2 and during dry season. A better knowledge of malaria morbidity in these health care facilities is an asset for setting up further epidemiological studies in this area and implementing interventions aiming at improving patients' care.

[Comparison of PCR, ELISA-CSP and direct microscopic observation methods for the detection of Plasmodium falciparum sporozoites in Anopheles gambiae M in Senegal]. / Comparaison des méthodes de la PCR, d'ELISA-CSP et d'observation microscopique directe pour la détection des sporozoïtes de Plasmodium falciparum chez Anopheles gambiae M au Sénégal.

A comparative study between the Enzyme-Linked Immuno Sorbent Assay (ELISA-CSP) for circumsporozoitic antigen detection method, the direct observation after dissection and the polymerase chain reaction (PCR) technique used to identify Plasmodium falciparum genomic DNA markers was carried out. This to evaluate the sensibility and the specificity of the PCR, for the determination of both sporozoitic index (ICSP) and the entomological inoculation rate (EIR). The study is conducted in laboratory on eighty six specimens of Anopheles gambiae M infected after being fed with the blood of a gametocytes carrier from Dielmo (Senegal). Salivary glands of forty-eight specimens randomly selected (test A) among the infected eighty six are microscopically observed after manual dissection for the sporozoites detection. The content of these salivary glands and the crushed head/thorax of the remaining 38 specimens (test B) are tested in ELISA-CSP and PCR. The positive and negative results obtained were recorded and summarized for each method. A pair-comparison of the results obtained with each method generally revealed a good sensibility and an excellent specificity The kappa coefficient (K) of test A indicated a "moderate" to "excellent" concordance between the three different methods performed. By using the crushed head/thorax sample, generally used to determine the transmission parameters (ICSP and EIR), the PCR/ELISA-CSP concordance was excellent. In the light of the values of sensibility and specificity obtained, this PCR is comparable to the other methods for the assessment of sporozoitic index and entomological inoculation rate.

[Assessment of a rapid diagnostic test for malaria in rural health care facilities in Senegal]. / Evaluation d'un test de diagnostic rapide du paludisme dans les postes de santé ruraux au Sénégal.

PURPOSE: The aim of the study was to determine the accuracy of a rapid diagnostic test in confirming presumptive malaria diagnosis in a rural zone of Senegal. Thick blood smear was used as the reference technique for comparison. METHOHDOLOGY: Testing was conducted on children between the ages of 1 and 14 years at three health care facilities located in the Niakhar are from August 2006 to June 2007. If malaria was suspected by the nurse based on clinical findings, two thick smears and one rapid diagnostic test (Core Malaria Pf) were performed. Blood slides were stained in Niakhar and read in Dakar. RESULTS: A total of 474 patients were examined. Three-fourths (75%) of these patients were seen during the rainy season. Malaria was suspected in 335 patients (71%). Rapid tests and thick smears were obtained in 330 of these patients with positive results in 194 (59%) and 180 (55%) respectively. The sensitivity, specificity, positive predictive value and negative predictive value of the rapid test were 96%, 87%, 90% and 95% respectively. CONCLUSION: Our data show that the rapid diagnostic test used in this study exhibits good sensitivity and positive predictive value. Despite its cost this test could be helpful in confirming malaria diagnosis in outlying health care facilities without the necessary resources to perform blood smears. Confirmation is necessary to avoid unwarranted prescription of malaria treatment due to inaccurate clinical diagnosis

Lysinibacillus timonensis sp. nov., Microbacterium timonense sp. nov., and Erwinia mediterraneensis sp. nov., three new species isolated from the human skin.

Lysinibacillus timonensis strain Marseille-P5727T (=CSURP5727), Microbacterium timonense strain Marseille-P5731T (=CSURP5731) and Erwinia mediterraneensis strain Marseille-P5165T (=CSURP5165) are three new species isolated from the human skin.

Arcanobacterium ihumii sp. nov., Varibaculum vaginae sp. nov. and Tessaracoccus timonensis sp. nov., isolated from vaginal swabs from healthy Senegalese women.

Culturomics studies the microbial variety of the human microbiome by combining diversified culture conditions, matrix-assisted laser desorption/ionization time-of-flight mass spectrometry and 16S rRNA gene identification. This study identifies three putative new bacterial species: Arcanobacterium ihumii sp. nov. strain Marseille-P5647T, Varibaculum vaginae sp. nov. strain Marseille-P5644T and Tessaracoccus timonensis sp. nov. strain Marseille-P5995T, which we describe according to the concept of taxonogenomics.

Corynebacterium senegalense sp. nov. and Arthrobacter senegalensis sp. nov., two new Actinobacteria isolated from skin swab from the palm of hand.

Corynebacterium senegalense strain Marseille-P4329T (= CSURP4329) and Arthrobacter senegalensis strain Marseille-P4329T (= CSURP4198) are new species first isolated from human skin. A culturomics approach and taxonogenomics methods were used for these new bacterial species.

The University Hospital Institute Mediterrannée Infection from Marseille to Dakar.

In Senegal, we have developed technology-driven research based on observation and technology transfer especially in molecular biology, genomics, culturomics, and proteomics with the use of the first Maldi-TOF mass spectrometer in clinical microbiology in Africa. This strategy is associated with a policy of training students from the South and helping them to return back. This technology transfer and expertise has enabled us to explore the causes of non-malarial fevers of unknown causes, with the study of the repertoire of infectious pathogens in humans and arthropod vectors, to diagnose infectious diseases in rural areas with Point of Care laboratories, to isolate new bacteria, and to study pathologies linked to mass gatherings. They have also allowed us to develop transdisciplinary research including the study of the microbiota in malnourished children. We wish to continue this technological development, which provides the foundation for high-level research in Senegal.

Vaginisenegalia massiliensis gen. nov., sp. nov., a new bacterium isolated from the vagina flora and its taxono-genomic description.

Strain Marseille-P5643T was isolated from a vaginal sample of a healthy Senegalese woman. It is an anaerobic Gram-negative, rod-shaped bacterium. Strain Marseille-P5643T exhibits 93.7% similarity levels with the Facklamia hominis strain ATCC 700628T, the phylogenetically closest related species with standing in nomenclature. The draft genome size of strain Marseille-P5643T is 1.79 Mb with 39.0 mol% of G+C content. We propose here the creation of Vaginisenegalia massiliensis gen. nov., sp. nov., as a new bacterial genus from the phylum Firmicutes.

Treponema species enrich the gut microbiota of traditional rural populations but are absent from urban individuals.

There is a significant gap in our knowledge of the microbe-host relationship between urban and traditional rural populations. We conducted a large-scale study to examine the gut microbiota of different traditional rural and urban lifestyles in human populations. Using high-throughput 16S ribosomal RNA gene amplicon sequencing, we tested urban French, Saudi, Senegalese, Nigerian and Polynesian individuals as well as individuals living in traditional rural societies, including Amazonians from French Guiana, Congolese Pygmies, Saudi Bedouins and Algerian Tuaregs. The gut microbiota from individuals living in traditional rural settings clustered differently and presented significantly higher diversity than those of urban populations (p 0.01). The bacterial taxa identified by class analysis as contributing most significantly to each cluster were Phascolarctobacterium for traditional rural individuals and Bifidobacterium for urban individuals. Spirochaetae were only present in the gut microbiota of individuals from traditional rural societies, and the gut microbiota of all traditional rural populations was enriched with Treponema succinifaciens. Cross-transmission of Treponema from termites or swine to humans or the increased use of antibiotics in nontraditional populations may explain why Treponema is present only in the gut microbiota of traditional rural populations.

MALDI-TOF MS and point of care are disruptive diagnostic tools in Africa.

We review reviewing our experience of point-of-care and mass spectrometry in Senegal as two disruptive technologies promoting the rapid diagnosis of infection, permitting better medical management of patients.