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Over the past 12 years, culturomics, a high-throughput culture method, has been developed, considerably widening the repertoire of known cultured bacteria. An exhaustive database, including a list of microbes isolated by culture from human skin, was recently established by performing a review of the literature. The aim of the present study was to use the culturomics approach to explore the African skin microbiota. Skin swabs from the palms of human hands were collected between January and December 2016 from healthy subjects from the villages of Dielmo and Ndiop in rural Senegal. Three culture media were selected for the isolation of bacteria in aerobic conditions. Bacterial colonies were subjected to matrix-assisted laser desorption ionization-time of flight mass spectroscopy and the 16 S rRNA gene was sequenced for unidentified colonies. A total of 176 bacterial species were isolated. This increased the repertoire of bacterial species on the skin by 14.0%, by adding 71 bacteria, including seven new species. The culturomics approach characterizing microbial diversity has significantly changed our view of the skin microbiota, raising many important questions about the host-microorganism relationship and its relevance to skin diseases. In particular, the difference between the palm microbiota of these African populations (composed mainly of the genera Staphylococcus, Arthrobacter, Bacillus, and Microbacterium) and that of Western populations, whose main genera are Staphylococcus, Propionibacterium, Micrococcus, Corynebacterium, Enhydrobacter, and Streptococcus. This study demonstrates the need to continue to explore the skin microbiome using the culturomics approach.

Respiratory infections, mainly due to viruses, are among the leading causes of worldwide morbidity and mortality. We investigated the prevalence of viruses and bacteria in a cross-sectional survey conducted in Dielmo, a village in rural Senegal with a population of 481 inhabitants. Nasopharyngeal sampling was performed in 50 symptomatic subjects and 101 asymptomatic subjects. Symptomatic subjects were defined as individuals presenting with clinical signs of respiratory infection, whereas asymptomatic subjects were recruited in the same households. The identification of pathogens was performed by polymerase chain reaction for 18 respiratory viruses and eight respiratory bacteria. The prevalence results for respiratory viruses detected in each study group demonstrated that 83.6% of symptomatic samples were positive for at least one respiratory virus, and 21.8% were detected in asymptomatic samples. Influenza A (P = 0.0001), metapneumovirus (P = 0.04), and enterovirus (P = 0.001) were significantly more prevalent in symptomatic patients. Overall, 82.0% of symptomatic subjects and 26.9% of asymptomatic subjects were positive for at least one respiratory bacterium. The most frequent pathogenic bacteria detected were Moraxella catarrhalis (56%) and Streptococcus pneumoniae (48.0%) among symptomatic individuals, whereas in asymptomatic subjects Corynebacterium propinquum was more prevalent (18%). A principal component analysis showed that parainfluenzas 2 and 4 were associated with asymptomatic subjects, whereas influenza A was associated with the presence of symptoms. Considering these results, a large epidemiological surveillance of the circulation of these respiratory pathogens in the general population should be conducted to provide a better understanding of their carriage and to potentially prevent epidemics.

West Africa faced the COVID-19 pandemic in early March 2020 and, as of March 31, 2022, had more than 900,000 confirmed cases and more than 12,000 deaths. During this period, SARS-CoV-2 genomes evolved genetically, resulting in the emergence of distinct lineages. This review was conducted to provide the epidemiological profile of COVID-19, the mutational profile of SARS-CoV-2, and the dynamics of its lineages in the 16 west African countries by analyzing data from 33 studies and seven situation reports. For a more complete representation of the epidemiology and genetic diversity of SARS-CoV-2, we used reliable public data in addition to eligible studies. As of March 31, 2022, the 16 west African countries experienced four epidemic waves with variable intensities. Higher mortality was noted during the third wave with a case fatality rate (CFR) of 1.9%. After these four epidemic waves, Liberia recorded the highest CFR (4.0%), whereas Benin had the lowest CFR (0.6%). Through mutational analysis, a high genetic heterogeneity of the genomes was observed, with a predominance of mutations in the spike protein. From this high mutational rate, different lineages emerged. Our analysis of the evolutionary diversity allowed us to count 205 lineages circulating in west Africa. This study has provided a good representation of the mutational profile and the prevalence of SARS CoV-2 lineages beyond the knowledge of the global epidemiology of the 16 African countries.

In endemic malaria areas, Plasmodium is currently diagnosed mainly through the use of rapid diagnostic tests (RDTs). However, in Senegal, many causes of fever remain unknown. Tick-borne relapsing fever, an often-neglected public health problem, is the main cause of consultation for acute febrile illness after malaria and flu in rural areas. Our objective was to test the feasibility of extracting and amplifying DNA fragments by quantitative polymerase chain reaction (qPCR) from malaria-negative RDTs for Plasmodium falciparum (malaria Neg RDTs P.f) to detect Borrelia spp. and other bacteria. Between January and December 2019, malaria Neg RDTs P.f were collected on a quarterly basis in 12 health facilities in four regions of Senegal. The DNA extracted from the malaria Neg RDTs P.f was tested using qPCR and the results were confirmed by standard PCR and sequencing. Only Borrelia crocidurae DNA was detected in 7.22% (159/2,202) of RDTs. The prevalence of B. crocidurae DNA was higher in July (16.47%, 43/261) and August (11.21%, 50/446). The annual prevalence was 9.2% (47/512) and 5.0% (12/241) in Ngayokhem and Nema-Nding, respectively, health facilities in the Fatick region. Our study confirms that B. crocidurae infection is a frequent cause of fever in Senegal, with a high prevalence of cases in health facilities in the regions of Fatick and Kaffrine. Malaria Neg RDTs P.f are potentially a good source of pathogen sampling for the molecular identification of other causes of fever of unknown origin, even in the most remote areas.

The occurrence of malaria resurgences could threaten progress toward elimination of the disease. This study investigated the impact of repeated renewal of long-lasting insecticide-treated net (LLIN) universal coverage on malaria resurgence over a period of 10 years of net implementation in Dielmo (Senegal). A longitudinal study was carried out in Dielmo between August 2007 and July 2018. In July 2008, LLINs were offered to all villagers through universal campaign distribution which was renewed in July 2011, August 2014, and May 2016. Malaria cases were treated with artemisinin-based combination therapy. Two resurgences of malaria occurred during the 10 years in which LLINs have been in use. Since the third renewal of the nets, malaria decreased significantly compared with the first year the nets were implemented (adjusted incidence rate ratio) (95% CI) = 0.35 (0.15-0.85), during the ninth year after net implementation). During the tenth year of net implementation, no cases of malaria were observed among the study population. The use of nets increased significantly after the third time the nets were renewed when compared with the year after the first and the second times the nets were renewed ( P < 0.001). The third renewal of nets, which took place after 2 years instead of 3 years together with a higher use of LLINs especially among the young, probably prevented the occurrence of a third malaria upsurge in this village.

The Grand Magal of Touba (GMT) is an annual 1-day Muslim religious event that takes place in Touba in Senegal. The city of Touba swells from 800,000 to four million people during the GMT. All patients who attended one of the 154 dedicated medical care public healthcare structures of the medical region of Diourbel during the GMT were included in a cross-sectional survey from November 16 to November 21, 2016. Demographic, morbidity, and mortality data were collected on a daily basis using a standardized article form that allows data to be recorded in a free-text format. Data were obtained from a total of 20,850 healthcare encounters, and 30.9% patients were aged ≤ 15 years. The most frequent conditions were gastrointestinal and respiratory diseases. Most frequent gastrointestinal symptoms were abdominal and gastric pain, nausea and vomiting, and diarrhea, suggesting that most patients suffered gastroenteritis. The predominance of cough, rhinitis, influenza-like illness, and sore throat among patients with respiratory symptoms suggests that most patients suffered from upper respiratory tract infections. Other frequent symptoms were headaches and pain in various organs. Three percentage of patients were considered to have malaria, 29.8% of patients were prescribed antibiotics and 2.6% antimalarial drugs, and 1.5% of patients were hospitalized. Only one death was recorded. Preparedness of the medical infrastructure should target these syndromic features, in terms of diagnostic tools and specific treatments, including pediatric formulations. It is also essential to improve the quality and rapid availability of data to enable real-time analysis of medical events at the GMT and to implement a rapid response, if necessary.

Vaginal self-sampling and human papillomavirus (HPV) DNA testing can be useful tools for women with limited access to health care living in sub-Saharan Africa. To assess the feasibility and acceptability of vaginal self-sampling and high-risk HPV prevalence in two villages of central Senegal, women were asked to self-sample vaginal swabs for HPV detection in May, 2016. Vaginal swabs were collected from 133 women and were tested for HPV genotyping. The acceptability rate of vaginal self-sampling was 98.5%, and 99.2% of the women (133/134) used the device correctly. The quality of self-sampling was satisfactory in 100% of the samples; 10.5% of the samples were positive for HPV, including 6% with high-risk HPV types and 4% with low-risk HPV types. This preliminary study indicates that vaginal self-sampling is a valuable strategy for high-risk HPV detection and cervical cancer screening in a population of women not attending gynecologic screening in rural areas of Senegal.

In the context of the pre-elimination of malaria, biological control may provide an alternative or additional tool to current malaria control strategies. During their various stages of development, mosquitoes undergo subsequent changes in their associated microbiota, depending on their environment and nutritional status. Although Anopheles gambiae s.l. and Anopheles funestus are the two major malaria vectors in Senegal, the composition of their microbiota is not yet well known. In this study, we explored the microbiota of mosquitoes naturally infected or not by Plasmodium falciparum ( Pf ) using the 16S ribosomal RNA gene-based bacterial metagenomic approach. In both vector species, the microbiota was more diverse in Pf- infected samples than in the noninfected ones, although the total number of reads appeared to be higher in noninfected mosquitoes. Overall, the microbiota was different between the two vector species. Noteworthy, the bacterial microbiota was significantly different between Pf -positive and Pf -negative groups whatever the species, but was similar between individuals of the same infection status within a species. Overall, the phylum of Proteobacteria was the most predominant in both species, with bacteria of the genus Burkholderia outweighing the others in noninfected vectors. The presence of some specific bacterial species such as Asaia bogorensis , Enterobacter cloacae , Burkholderia fungorum , and Burkholderia cepacia was also observed in Pf -free samples only. These preliminary observations pave the way for further characterization of the mosquito microbiota to select promising bacterial candidates for potential use in an innovative approach to controlling malaria and overcoming the challenges to achieving a malaria-free world.

Rickettsia felis is a common emerging pathogen in sub-Saharan Africa. Comparing dynamics of morbidities due to malaria and R. felis infections in two Senegalese villages, we found a strong and significant correlation between them. Malaria morbidity is strongly decreasing because of the implementation of long-lasting insecticidal nets, so we hypothesize that the same measure may decrease the R. felis infections.

The implementation of long-lasting insecticidal-treated bed nets (LLINs) has contributed to halving the mortality rate due to malaria since 2000 in sub-Saharan Africa. These tools are highly effective against indoor-feeding malaria vectors. Thus, to achieve the World Health Assembly's new target to reduce the burden of malaria over the next 15 years by 90%, it is necessary to understand how the spatiotemporal dynamics of malaria vectors and human exposure to bites is modified in the context of scaling up global efforts to control malaria transmission. This study was conducted in Dielmo, a Senegalese village, after the introduction of LLINs and two rounds of LLINs renewals. Data analysis showed that implementation of LLINs correlated with a significant decrease in the biting densities of the main malaria vectors, Anopheles gambiae s.l. and Anopheles funestus , reducing malaria transmission. Other environment factors likely contributed to the decrease in An. funestus , but this trend was enhanced with the introduction of LLINs. The bulk of bites occurred during sleeping hours, but the residual vector populations of An. gambiae s.l. and An. funestus had an increased propensity to bite outdoors, so a risk of infectious bites remained for LLINs users. These results highlight the need to increase the level and correct use of LLINs and to combine this intervention with complementary control measures against residual exposure, such as spatial repellents and larval source management, to achieve the goal of eliminating malaria transmission.

AbstractSome observations and recent publications demonstrated, particularly in Africa, the potential influence that low-cost motorcycles, cell phones, and even widespread electrification could have on the evolution of infectious diseases, particularly zoonoses. Our reflections support the conclusion that we should focus on the real-time surveillance systems including alerting systems leading to a rapid and flexible response rather than the strongly limited modeling of infectious diseases because of the continuous evolution of microorganisms, as well as changes in the environment and human habits that are unpredictable.

In Senegal, tick-borne relapsing fever (TBRF) is a major cause of morbidity and a neglected public health problem. Borreliosis cases commonly detected in two villages led us to implement a borreliosis preventive control including cementing of floors in bedrooms and outbuildings attended by inhabitants to avoid human contacts with tick vectors. Epidemiological and medical monitoring of the TBRF incidence was carried out at Dielmo and Ndiop by testing the blood of febrile patients since 1990 and 1993, respectively. Intra-domiciliary habitat conditions were improved by cementing, coupled with accompanying measures, from March 2013 to September 2015. Application of this strategy was associated with a significant reduction of borreliosis incidence. This was more evident in Dielmo, dropping from 10.55 to 2.63 cases per 100 person-years (P < 0.001), than in Ndiop where it changed from 3.79 to 1.39 cases per 100 person-years (P < 0.001). Thirty-six cases of TBRF were estimated to be prevented at a cost of €526 per infection. The preventive control strategy was successful in Dielmo and Ndiop, being associated with decreased incidence by 89.8% and 81.5%, respectively, suggesting that TBRF may be widely decreased when the population is involved. Public health authorities or any development stakeholders should adopt this effective tool for promoting rural health through national prevention programs., (© The American Society of Tropical Medicine and Hygiene.)

Matrix-assisted laser desorption ionization time-of-flight (MALDI-TOF) mass spectrometry (MS) represents a revolution in routine pathogen identification in clinical microbiology laboratories. A MALDI-TOF MS was introduced to tropical Africa in the clinical microbiology laboratory of the Hôpital Principal de Dakar (Senegal) and used for routine pathogen identification. Using MS, 2,429 bacteria and fungi isolated from patients were directly assayed, leading to the identification of 2,082 bacteria (85.7%) and 206 fungi (8.5%) at the species level, 109 bacteria (4.5%) at the genus level, and 16 bacteria (0.75%) at the family level. Sixteen isolates remained unidentified (0.75%). Escherichia coli was the most prevalent species (25.8%) followed by Klebsiella pneumoniae (14.8%), Streptococcus agalactiae (6.2%), Acinetobacter baumannii (6.1%), Pseudomonas aeruginosa (5.9%), and Staphylococcus aureus (5.9%). MALDI-TOF MS has also enabled the detection of rare bacteria and fungi. MALDI-TOF MS is a powerful tool for the identification of bacterial and fungal species involved in infectious diseases in tropical Africa., (© The American Society of Tropical Medicine and Hygiene.)

Direct skin feeding experiments are sensitive assays to determine human infectiousness to mosquitoes but are rarely used in malaria epidemiological surveys. We determined the infectiousness of inhabitants of a malaria hypoendemic area in Senegal. Gametocyte prevalence by microscopy was 13.5% (26 of 192). Of all individuals who were gametocyte positive, 44.4% (11 of 25) infected ≥ 1 Anopheles arabiensis mosquito and 10.8% (54 of 500) of mosquitoes became infected. Of all individuals who were gametocyte negative by microscopy, 4.3% (7 of 162) infected ≥ 1 mosquito and 0.4% (12 of 3240) of mosquitoes became infected. The 18.2% (12 of 66) of all mosquito infections was a result of submicroscopic gametocyte carriage and two individuals without asexual parasites or gametocytes by microscopy were infectious to mosquitoes. When infectivity and local demography was taken into account, children 5-14 years of age contributed 50.8% of the human infectious reservoir for malaria. Adults and submicroscopic gametocyte carriers may contribute considerably to onward malaria transmission in our setting., (© The American Society of Tropical Medicine and Hygiene.)

The incidence of malaria has decreased recently in parts of Africa, coinciding with the widespread use of long-lasting insecticide-treated nets (LLINs) and artemisinin-based combination therapy (ACT). This reduction was also observed in Dielmo, our study area, and it was associated with the use of ACT as the first-line treatment against malaria beginning in 2006 and the implementation of LLINs in 2008. However, an unexplained slight increase in malaria incidence was observed in October and November of 2013. The aim of this study was to identify individual and environmental risk factors for malaria using a case-control study approach. Thirty cases and sixty controls were investigated. The use of LLINs was protective against malaria (adjusted odds ratio [AOR] = 0.10; 95% confidence interval [95% CI] = 0.02-0.45; P = 0.003). The risk of malaria transmission was high among villagers who watched television outside the house or the bedroom during the night (AOR = 8.83; 95% CI = 1.39-56.22; P = 0.021). The use of LLINs should be reinforced by the use of individual protection measures to avoid malaria transmission outside of the home., (© The American Society of Tropical Medicine and Hygiene.)

Fever caused by Rickettsia felis was recently shown to play an important role in infectious diseases morbidity in sub-Saharan Africa. We collected 68 cotton swabs from fever-associated eschars in four different regions of Senegal. In 5 of 68 eschar samples (7.4%), we have identified DNA from R. felis. In 49 of 68 eschar samples (72.1%), we have identified DNA from Staphylococcus aureus. In 35 of 68 eschar samples (51.5%), we have identified DNA from Streptococcus pyogenes, and in 4 of 68 eschar samples (5.9%), we have identified DNA from Streptococcus pneumoniae. In 34 cases, S. aureus was found together with S. pyogenes. DNA from R. felis was also found in swabs from the skin of the healthy Senegalese villagers (3 of 60; 5%) but not French urbanites. The presence of S. aureus and S. pyogenes was significantly associated with the presence of eschars in febrile patients compared with the healthy skin from the control group. Finally, we confirmed that Senegal is an endemic region for R. felis, which is found in both eschars and healthy skin swabs., (© The American Society of Tropical Medicine and Hygiene.)

Trench fever is poorly known by the staff of health facilities that manage febrile patients in Senegal. Bartonella quintana DNA was identified in 5 of 274 (2%) febrile patients from two rural dispensaries and 2 of 71 (3%) head lice specimens collected from the same villages., (© The American Society of Tropical Medicine and Hygiene.)

Oropharyngeal swabs collected from patients with Q fever from France and from febrile patients from Senegal were tested by molecular assays for Coxiella burnetii. One positive result (0.08%) occurred for only one patient with acute Q fever. Throat swabs cannot replace blood serum samples as diagnostic tools for Q fever.

Tropheryma whipplei, the bacterium linked to Whipple's disease, is involved in acute infections and asymptomatic carriage. In rural Senegal, the prevalence of T. whipplei is generally high but is not homogeneous throughout households in the same village. We studied environmental samples collected in two Senegalese villages and conducted the survey to investigate the difference between households. Overall, the comparison between five households with very high T. whipplei prevalence and three households without any registered cases showed that the only difference was the presence of toilets in the latter (1/5 versus 3/3; P = 0.01423). Among the 1,002 environmental specimens (including domestic and synanthropic animals and dust sampled in households) tested for T. whipplei DNA, only four specimens were slightly positive. Humans are currently the predominant identified reservoir and source of T. whipplei in these populations. Limited access to toilets and exposure to human feces facilitate the fecal-oral transmission of T. whipplei.

In sub-Saharan Africa, malaria and malnutrition are major causes of morbidity and mortality in children less than five years of age. To explore the impact of malnutrition on subsequent susceptibility to malaria, a cohort of 874 rural preschool children in Senegal was followed-up during one malaria transmission season from July through December. Data on nutritional status and Plasmodium falciparum parasitemia were collected at baseline. Malaria morbidity was monitored through weekly home visits. Wasted children (weight-for-height z-score < -2) were at lower risk of having at least one subsequent clinical malaria attack (odds ratio = 0.33; 95% confidence interval = 0.13-0.81, P = 0.02), whereas stunting (height-for-age z-score < -2) or being underweight (weight-for-age z-score < -2) was not associated with clinical malaria. Although non-biological explanations such as overprotection of wasted children by their mothers should be considered, immunomodulation according to nutritional status could explain the lower risk of malaria attack among wasted children.

Negative consequences of malaria might account for seasonality in nutritional status in children in the Sahel. We report the impact of a randomized, double-blind, placebo-controlled trial of seasonal intermittent preventive anti-malarial treatment on growth and nutritional status in 1,063 Senegalese preschool children. A combination of artesunate and sulfadoxine-pyrimethamine was given monthly from September to November. In the intervention arm, mean weight gain was significantly greater (122.9 +/- 340 versus 42.9 +/- 344 [SD] g/mo, P < 0.0001) and losses in triceps and subscapular skinfold measurements were less (-0.39 +/- 1.01 versus -0.66 +/- 1.01 mm/mo, and -0.15 +/- 0.64 versus -0.36 +/- 0.62 mm/mo, respectively, P < 0.0001 for both). There was no difference in height increments. The prevalence of wasting increased significantly in the control arm (4.6% before versus 9.5% after, P < 0.0001), but remained constant in intervention children: 5.6% versus 7.0% (P = 0.62). The prevention of malaria would improve child nutritional status in areas with seasonal transmission.

To investigate the relationship between the entomologic inoculation rate (EIR) and time to reappearance of malaria parasites after radical treatment under moderate seasonal transmission conditions, a study was undertaken in a mesoendemic area of Senegal where malaria transmission is concentrated over an annual three-month period and averages 12 infective bites per person per year. A three-day course of quinine was administered to 48 asymptomatic adults between 19 and 66 years of age. Malaria transmission and parasitemia were monitored every week for two months and cases of fever or symptoms were investigated as part of a daily clinical surveillance. The proportion of persons reinfected at Days 28, 35, and 56 was 25%, 38%, and 54%, respectively. Adults less than 40 years of age had a shorter time to reinfection. In this age group, the median Plasmodium falciparum reappearance time was 28 days, and it was estimated that only one infected mosquito bite was able to induce a patent infection among half of the subjects. Only 8% (2 of 26) of the reinfections caused a clinical attack. These data are discussed in the light of previous studies conducted among adults naturally exposed to intense perennial transmission or among naive volunteers receiving artificial challenges. Rapid reinfection occurs at very low EIRs and dramatic differences in actual and cumulated exposure to infected mosquito bites poorly affect the median time to reappearance of malaria parasites in endemic populations.

We conducted a three-year entomologic study in Dielmo, a village of 250 inhabitants in a holoendemic area for malaria in Senegal. Anophelines were captured on human bait and by pyrethrum spray collections. The mosquitoes belonging to the Anopheles gambiae complex were identified using the polymerase chain reaction. Malaria vectors captured were An. funestus, An. arabiensis, and An. gambiae. Anopheles funestus was the most abundant mosquito captured the first year, An. arabiensis in the following years. The annual entomologic inoculation rates calculated by enzyme-linked immunosorbent assay were 238, 89, and 150 for the first, second, and third years, respectively. Each year there was a peak of transmission at the end of the rainy season, but transmission occurred year round. The heterogeneity of transmission was found at four different levels: 1) the relative vector proportion according to the place and method of capture, 2) the human biting rate and relative proportion of vectors by month and year, 3) the infection rate of each vector by year, and 4) the number of infected bites for all vectors, and for each species, for the year. Our data show that even in areas of intense and perennial transmission, there exist large longitudinal variations and strong heterogeneity in entomologic parameters of malaria transmission. It is important to take these into account for the study of the variations in clinical and biological parameters of human malaria, and to evaluate this relationship, a very thorough investigation of transmission is necessary.