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.

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-P3515^T (=CSURP3515), Bacillus sinesaloumensis strain Marseille-P3516^T (=CSURP3516), and Bacillus massiliogabonensis strain Marseille-P2639^T (=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.

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.

Hepatitis B vaccination status and vaccine immune response among children in rural Senegal

Background

Hepatitis B vaccination during childhood is key to reduce the prevalence of Hepatitis B virus (HBV) infection. In Senegal, a highly endemic country, the three-dose hepatitis B vaccine and the birth dose vaccine were introduced in the Expanded Programme on Immunization (EPI) in 2004 and 2016 respectively. This study aimed to determine chronic HBV infection prevalence, hepatitis B vaccination status and vaccine immunity among children in Senegal.

Methods

A cross-sectional study including HBV screening was conducted at home among children aged 6 months to 15 years (i.e. born after the introduction of the HBV vaccine in the EPI) in the rural zone of Niakhar. Dried Blood Spot (DBS) samples were collected for the detection of HBsAg, anti-HBc Ab and anti-HBs Ab using chemoluminescence. Vaccination status was assessed using information on vaccination cards. Detectable vaccine immunity was defined with an adjusted DBS threshold of DOI≥0.36 IU/mL (corresponding to 10 IU/mL in venous blood sampling).

Results

Between October and December 2018, 455 children were enrolled. Preliminary results show that 7/455 (1.5%) had been in contact with HBV (positive anti-HBc Ab) and 5/455 (1.1%) had chronic HBV infection (positive HBsAg).

Only 161/455 (35.4%) children had a vaccination card available. Among those, 150/161 (93.2%) received at least 3 doses of hepatitis B vaccine, of which 83/150 (55.3%) had detectable vaccine immunity. The proportion of children with detectable vaccine immunity was significantly higher in children <5 years than in children aged 5-9 and 10-15 (72.3% versus 47.3%, p = 0.006 and 72.3% versus 14.3%, p < 0.001).

Conclusions

Preliminary results suggest a low prevalence of HBV chronic infection among children born after the introduction of HBV vaccination in Senegal. However, detectable vaccine immunity rapidly decreases with age among vaccinated children, signalling a need for further studies on the immune response to HBV vaccination in this context.

Key messages

HBV chronic infection is low among children born after the introduction of HBV vaccination in Senegal. Further studies on the immune response to HBV vaccination in this context are needed.

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

Strain Marseille-P5643^T was isolated from a vaginal sample of a healthy Senegalese woman. It is an anaerobic Gram-negative, rod-shaped bacterium. Strain Marseille-P5643^T exhibits 93.7% similarity levels with the Facklamia hominis strain ATCC 700628^T, the phylogenetically closest related species with standing in nomenclature. The draft genome size of strain Marseille-P5643^T 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.

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-P4329^T (= CSURP4329) and Arthrobacter senegalensis strain Marseille-P4329^T (= CSURP4198) are new species first isolated from human skin. A culturomics approach and taxonogenomics methods were used for these new bacterial species.

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-P5727^T (=CSURP5727), Microbacterium timonense strain Marseille-P5731^T (=CSURP5731) and Erwinia mediterraneensis strain Marseille-P5165^T (=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-P5647^T, Varibaculum vaginae sp. nov. strain Marseille-P5644^T and Tessaracoccus timonensis sp. nov. strain Marseille-P5995^T, which we describe according to the concept of taxonogenomics.

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.

'Helcococcus massiliensis' sp. nov., a new bacterial species isolated from the vaginal sample of a woman with bacterial vaginosis living in Dielmo, Senegal

We report here the isolation of a new bacterial species ‘Helcococcus massiliensis’ strain Marseille P4590 (CSURP4590), isolated from the vaginal sample of a woman with bacterial vaginosis.

Mobile populations across the Mediterranean Sea and beyond: travel medicine, mass gathering medicine and homeless health

The Méditerranée Infection institute is internationally recognized for its expertise in infectious diseases and tropical medicine, and is one of the most active research centres for infectious diseases in Europe. Surveillance and research addressing infectious diseases in globally mobile populations is one of the strong components of the research conducted at the institute. A significant amount of clinical, microbiologic and epidemiologic works have been conducted in international travellers, pilgrims participating in large international religious gatherings, economic migrants and homeless migrant people over the last decades by our group. Our strong anchoring in several countries around the Mediterranean Sea and beyond, as well as the pivotal role of Marseille in the EuroTravNet and GeoSentinel international networks that monitor travel-associated diseases, reinforce our leading position in the fields of travel and tropical medicine, mass gathering medicine and homeless health.

'Citricoccus massiliensis' sp. nov., a new bacterial species isolated from human skin by culturomics

We report the main characteristics of 'Citricoccus massiliensis'strain Marseille-P4330, a new species within the genus Citricoccus. This strain was isolated from the skin of a healthy human man living in Dielmo, Senegal, Western Africa.

Th1/Th2 Dichotomy in Obese Women with Gestational Diabetes and Their Macrosomic Babies

The aim of the study was to assess T cell differentiation and the modulation of inflammatory cytokines in obese and gestational diabetes mellitus (GDM) women and their macrosomic newborns. Hence, immediately after delivery, blood samples were collected through the mother's arm vein and the umbilical cordon vein. Biochemical parameters measured were HbA1C, glucose, insulin, triglyceride (TG), total cholesterol (Tchol), HDL cholesterol (HDLchol), and LDL cholesterol (LDLchol). T lymphocytes were purified from the total blood with Ficoll-Paque. The mRNA expression of inflammatory markers in T cells was determined by RT-qPCR. We observed that diabetic mothers exhibited higher HbA1C, glycemia, insulinemia, TG, Tchol, HDLchol, and LDLchol levels than control mothers. Glycemia was not significantly different between macrosomic and control newborns. However, insulinemia was high in macrosomic babies. TG, Tchol, HDLchol, and LDLchol were not significantly different between macrosomic and control babies. In diabetic mothers, mRNA expression of the Th1 cell subtype was significantly increased. Th1 markers were upregulated in babies born to diabetic women than in control newborns. However, expression of two Th2 markers (GATA3 and IL-4) was not significantly different between control and GDM women and between their respective newborns. Interestingly, IL-10 mRNA expression was decreased in diabetic mothers and their offsprings. The Th1/Th2 cytokine ratio was increased in GDM obese mothers and their macrosomic newborns, suggesting a proinflammatory status in these subjects.

Taxonogenomic description of four new Clostridium species isolated from human gut: 'Clostridium amazonitimonense', 'Clostridium merdae', 'Clostridium massilidielmoense' and 'Clostridium nigeriense'

Culturomics investigates microbial diversity of the human microbiome by combining diversified culture conditions, matrix-assisted laser desorption/ionization time-of-flight mass spectrometry and 16S rRNA gene identification. The present study allowed identification of four putative new Clostridium sensu stricto species: ‘Clostridium amazonitimonense’ strain LF2^T, ‘Clostridium massilidielmoense’ strain MT26^T, ‘Clostridium nigeriense’ strain Marseille-P2414^T and ‘Clostridium merdae’ strain Marseille-P2953^T, which we describe using the concept of taxonogenomics. We describe the main characteristics of each bacterium and present their complete genome sequence and annotation.

'Gracilibacillus phocaeensis' sp. nov., 'Sediminibacillus massiliensis' sp. nov. and 'Virgibacillus ndiopensis' sp. nov., three halophilic species isolated from salty human stools by culturomics

We report the isolation of three bacterial strains that could not be identified by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry screening. ‘Gracilibacillus phocaeensis’ sp. nov., ‘Sediminibacillus massiliensis’ sp. nov. and ‘Virgibacillus ndiopensis’ sp. nov. are halophilic species isolated from salty human stools by culturomics.

Noncontiguous finished genome sequences and descriptions of 'Paenibacillus bouchesdurhonensis,' 'Paenibacillus rubinfantis,' 'Paenibacillus senegalimassiliensis' and 'Paenibacillus tuaregi' identified by culturomics

Microbial culturomics represents a completely new approach to investigate microbial diversity by using different optimized culture conditions, mass spectrometry, genome sequencing and annotation and phenotypic description that allow for an extensive characterization of new species and the study of the human microbiome. Here we present four new species within the genus Paenibacillus: ‘Paenibacillus bouchesdurhonensis’ strain Marseille-P3071^T, ‘Paenibacillus rubinfantis’ strain MT18^T, ‘Paenibacillus senegalimassiliensis’ strain SIT18^T and ‘Paenibacillus tuaregi’ strain Marseille-P2472^T, which are all facultatively aerobic and Gram-positive bacilli.

'Marasmitruncus massiliensis' gen. nov., sp. nov., 'Clostridium culturomicum' sp. nov., 'Blautia provencensis' sp. nov., 'Bacillus caccae' sp. nov. and 'Ornithinibacillus massiliensis' sp. nov., isolated from stool samples of undernourished African children

We report here the main characteristics of five new species, ‘Marasmitruncus massiliensis’ strain Marseille-P3646^T (CSUR P3646), ‘Clostridium culturomicum’ strain Marseille-P3545^T (CSUR P3545), ‘Blautia provencensis’ strain Marseille-P3502^T (CSUR P3502), ‘Bacillus caccae’ strain Marseille-P3604^T (CSUR P3604) and ‘Ornithinibacillus massiliensis’ strain Marseille-P3601^T (CSUR P3601), which were isolated recently from undernourished children's stool samples from Niger using microbial culturomics.

'Khelaifiella massiliensis', 'Niameybacter massiliensis', 'Brachybacterium massiliense', 'Enterobacter timonensis', 'Massilibacillus massiliensis', new bacterial species and genera isolated from the gut microbiota of healthy infants

The main characteristics of 'Khelaifiella massiliensis' strain Mt13^T (= CSUR P1935, = DSM100591), 'Niameybacter massiliensis' strain Mt14^T (= CSUR P1909, = DSM100592), 'Brachybacterium massiliense' strain MT5^T (= CSUR P2240, = DSM101766), 'Enterobacter timonensis' strain mt20^T (= CSUR P2201, = DSM 101775) and 'Massilibacillus massiliensis' strain Marseille-P2411^T (= CSUR P2411, = DSM102838), new species isolated from the gut of healthy African infants, are presented.

'Urmitella timonensis' gen. nov., sp. nov., 'Blautia marasmi' sp. nov., 'Lachnoclostridium pacaense' sp. nov., 'Bacillus marasmi' sp. nov. and 'Anaerotruncus rubiinfantis' sp. nov., isolated from stool samples of undernourished African children

We report here the main characteristics of five new species ‘Urmitella timonensis’ strain Marseille-P2918^T (CSUR P2918), ‘Blautia marasmi’ strain Marseille-P2377^T (CSUR P2377), ‘Lachnoclostridium pacaense’ strain Marseille-P3100^T (CSUR P3100), ‘Bacillus marasmi’ strain Marseille-P3556^T (CSUR P3556) and ‘Anaerotruncus rubiinfantis’ strain MT15^T (CSUR P2276), which were isolated recently from stool samples taken from undernourished children in Niger and Senegal using microbial culturomics.

Description of 'Bacillus dakarensis' sp. nov., 'Bacillus sinesaloumensis' sp. nov., 'Gracilibacillus timonensis' sp. nov., 'Halobacillus massiliensis' sp. nov., 'Lentibacillus massiliensis' sp. nov., 'Oceanobacillus senegalensis' sp. nov., 'Oceanobacillus timonensis' sp. nov., 'Virgibacillus dakarensis' sp. nov. and 'Virgibacillus marseillensis' sp. nov., nine halophilic new species isolated from human stool

We report the main characteristics of 'Bacillus dakarensis' P3515^T sp. nov., 'Bacillus sinesaloumensis' P3516^T sp. nov., 'Gracilibacillus timonensis' P2481^T sp. nov., 'Halobacillus massiliensis' P3554^T sp. nov., 'Lentibacillus massiliensis' P3089^T sp. nov., 'Oceanobacillus senegalensis' P3587^T sp. nov., 'Oceanobacillus timonensis' P3532^T sp. nov., 'Virgibacillus dakarensis' P3469^T sp. nov. and 'Virgibacillus marseillensis' P3610^T sp. nov., that were isolated in 2016 from salty stool samples (≥1.7% NaCl) from healthy Senegalese living at Dielmo and N'diop, two villages in Senegal.

Genome sequence and description of Anaeromassilibacillus senegalensis gen. nov., sp. nov., isolated from the gut of patient with kwashiorkor

Using the culturomics strategy, a wide range of anaerobic bacteria was discovered including Anaeromassilibacillus senegalensis strain mt9^T (= CSUR P1511 = DSM 102954), isolated from the gut microbiota of a 1-year-old Senegalese patient with kwashiorkor. This Gram-negative strain is a strictly anaerobic, spore-forming rod motile by a polar flagellum. The 3 511 289 bp long genome of this strain contains 3046 protein-coding and 49 RNA genes, including 45 tRNA and four rRNA genes, and exhibits a G+C content of 52.94%. Here we describe the features of this organism, together with the complete genome sequence and annotation.

Marseillibacter massiliensis gen. nov., sp. nov., a new bacterial genus isolated from the human gut

In this manuscript, we report the main characteristics of Marseillibacter massiliensis gen. nov., sp. nov., strain Marseille-P2840^T (CSUR P2840), a new member of the family Oscillospiraceae that was isolated from the stool of a healthy 29-year-old Senegalese woman.

[Effectiveness of three biological larvicides and of an insect growth regulator against Anopheles arabiensis in Senegal]

Urban malaria is a major public health problem in Africa. In Senegal, the environmental changes seem to favor the persistence of malaria transmission in Dakar suburbs by creating, throughout the year, potential breeding sites of malaria vectors. In such a situation and in a context of a growing threat of insecticide resistance in anopheline vectors, the larval control making use of products from biological origin or growth regulators could represent an additional tool to the current strategies developed against anophelines. In this study conducted in 2012, the efficiency and residual effect of three biological larvicides (VectoBac^® WG, Vecto-Max^® CG, and VectoBac^® GR) and an insect growth regulator (MetaLarv™) were evaluated on Anopheles gambiae s.l. larvae in seminatural conditions (experimental station) and natural breeding sites in the suburbs of Dakar. The formulations were tested according to the manufacturer recommendations, namely 0.03 g/m² for VectoBac^® WG, 0.5 g/m² for VectoBac^® GR, 0.75 g/m² for VectoMax^® CG, and 0.5 g/m² for MetaLarv™. In experimental station, the treatment with larvicides was effective over a period of 14 days with a mortality ranging between 92% and 100%. The insect growth regulator remained effective up to 55 days with a single emergence recorded in the 27th day after treatment. In natural conditions, a total effectiveness (100% mortality) of larvicides was obtained 48 hours after treatment, then a gradual recolonization of breeding sites was noted. However, the insect growth regulator has reduced adult emergence higher than 80% until the end of follow-up (J28). This study showed a good efficiency of the larvicides and of the growth regulator tested. These works provide current data on potential candidates for the implementation of larval control interventions in addition to that of chemical adulticide for control of urban malaria.

Correction: Safety of Seasonal Malaria Chemoprevention (SMC) with Sulfadoxine-Pyrimethamine plus Amodiaquine when Delivered to Children under 10 Years of Age by District Health Services in Senegal: Results from a Stepped-Wedge Cluster Randomized Trial

[This corrects the article DOI: 10.1371/journal.pone.0162563.].

Rubeoparvulum massiliense gen. nov., sp. nov., a new bacterial genus isolated from the human gut of a Senegalese infant with severe acute malnutrition

Rubeoparvulum massiliense strain mt6^T was isolated from the gut microbiota of a severely malnourished boy from Senegal and consisted of facultative anaerobic, spore-forming, nonmotile and Gram-negative rods. R. massiliense showed a 92% similarity with the 16S rRNA of Bacillus mannanilyticus. The genome of strain mt6^T is 2 843 796 bp long with a 43.75% G+C content. It contains 2735 protein-coding genes and 76 RNA genes, among which are nine rRNA genes.

Safety of Seasonal Malaria Chemoprevention (SMC) with Sulfadoxine-Pyrimethamine plus Amodiaquine when Delivered to Children under 10 Years of Age by District Health Services in Senegal: Results from a Stepped-Wedge Cluster Randomized Trial

Background

It is recommended that children aged 3 months to five years of age living in areas of seasonal transmission in the sub-Sahel should receive Seasonal Malaria Chemoprevention (SMC) with sulfadoxine-pyrimethamine plus amodiaquine (SPAQ) during the malaria transmission season. The purpose of this study was to evaluate the safety of SMC with SPAQ in children when delivered by community health workers in three districts in Senegal where SMC was introduced over three years, in children from 3 months of age to five years of age in the first year, then in children up to 10 years of age.

Methods

A surveillance system was established to record all deaths and all malaria cases diagnosed at health facilities and a pharmacovigilance system was established to detect adverse drug reactions. Health posts were randomized to introduce SMC in a stepped wedge design. SMC with SPAQ was administered once per month from September to November, by nine health-posts in 2008, by 27 in 2009 and by 45 in 2010.

Results

After three years, 780,000 documented courses of SMC had been administered. High coverage was achieved. No serious adverse events attributable to the intervention were detected, despite a high level of surveillance.

Conclusions

SMC is being implemented in countries of the sub-Sahel for children under 5 years of age, but in some areas the age distribution of cases of malaria may justify extending this age limit, as has been done in Senegal. Our results show that SMC is well tolerated in children under five and in older children. However, pharmacovigilance should be maintained where SMC is implemented and provision for strengthening national pharmacovigilance systems should be included in plans for SMC implementation.

Trial Registration

ClinicalTrials.gov NCT 00712374

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.

"Lagierella massiliensis," a new bacterium detected in human feces

We report here the main characteristics of “Lagierella massiliensis” strain SIT14 (CSUR P2012), which was isolated from a stool specimen from a healthy 28-month-old Senegalese boy.

Noncontiguous finished genome sequence and description of Bacillus testis strain SIT10 sp. nov

Bacillus testis strain SIT10 (= CSUR P1492 = DSMZ 101190) is the new type strain collected from stool from a 2-year-old boy from Senegal during a culturomics study. This Gram-positive bacterium is a facultative anaerobic rod and a member of the Bacillaceae family. We describe here the features of this bacterium, together with the complete genome sequence and annotation. The 3 987 349 bp long genome (one chromosome but no plasmid) with 42.8% GC content contains 4005 protein-coding and 171 sRNA genes, including 19 5S rRNA gene, 15 16S rRNA genes and ten 23S rRNA genes.

Massilibacterium senegalense gen. nov., sp. nov., a new bacterial genus isolated from the human gut

Massilibacterium senegalense gen. nov., sp. nov., strain mt8^T, is the type strain of Massilibacterium gen. nov., a new genus within the Bacillaceae family. This Gram-negative facultative anaerobic rod was isolated from the gut microbiota of a severely malnourished boy. Its phenotypic description is hereby presented with a complete annotation of its genome sequence. This genome is 5 697 950 bp long and contains 5615 protein-coding genes and 178 RNA genes, among which are 40 rRNA genes.

High-quality genome sequence and description of Bacillus ndiopicus strain FF3(T) sp. nov

Strain FF3^T was isolated from the skin-flora of a 39-year-old healthy Senegalese man. Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry did not allow any identification. This strain exhibited a 16S rRNA sequence similarity of 96.8% with Bacillus massiliensis, the phylogenetically closest species with standing nomenclature. Using a polyphasic study made of phenotypic and genomic analyses, strain FF3^T was Gram-positive, aeroanaerobic and rod shaped and exhibited a genome of 4 068 720 bp with a G+C content of 37.03% that coded 3982 protein-coding and 67 RNA genes (including four rRNA operons). On the basis of these data, we propose the creation of Bacillus ndiopicus sp. nov.

[Changes in malaria prevalence and management of fevers from 2000 to 2012 in Casamance, Senegal]

Before 2006 in Senegal, in the absence of clinical diagnosis, all fever cases were considered as malaria and treated with chloroquine. Between 2004-2006, to face the dramatic increase of Plasmodium falciparum resistance to chloroquine, the combination of amodiaquine plus sulfadoxine-pyriméthamine was recommended for treatment. In 2006, rapid diagnostic tests were introduced and the treatment with a combination of artesunate plus amodiaquine (ASAQ) became the national recommendation for malaria treatment in 2007. This coincided with a decrease of the prevalence of malaria cases and change in fever management. Since 1995 in Mlomp in Casamance, thin and thick blood smear examination has systematically been done in patients with fever and clinical signs of malaria, and treatment with ASAQ given as experimental procedure. Between 2000 and 2012, 70,892 outpatients were attending the health center, and 51.2% of them for fever. Among these fever cases, 72.4% were suspected of malaria and 27.6% were identified as bacterial and viral infections. Confirmed malaria cases decreased dramatically from 1365 in 2000 to 53 in 2012. While comparing the 2 periods 2000-2006 and 2007-2012, the number of fever cases decreased by half, the number of fever identified as non malaria doubled and malaria treatment given decreased by 86%. Improvement of fever management in Mlomp has contributed to a better identification of their cause and to a decrease of inappropriate malaria treatments.

The changes in mosquito vector behaviour and the emerging resistance to insecticides will challenge the decline of malaria

The preventive measures against malaria recommended by the WHO include anti-vector procedures such as indoor residual spraying, the use of long-lasting insecticide-treated bed-nets, and the destruction of larval breeding sites. The presence of insecticide-treated materials inside the mosquito habitat has consequences for the vector's population, reducing density, survival, contact with humans, and feeding frequency. However, the effectiveness of these tools is being challenged by the emergence of insecticide resistance. The evolution of resistance to insecticides in Anopheles threatens to thwart the goal of decreasing malaria transmission, in an arms race between malaria control programmes and the vector populations. Multiple mechanisms of resistance to insecticides have been observed in Anopheles populations, including target site mutation (knockdown resistance), increased metabolic detoxification, and remarkable behavioural adaptation. These disturbing observations all show the capacity of Anopheles to adapt to and circumvent strategies aimed at reducing malaria transmission. Thus, by using nets to protect ourselves, are we providing Anopheles with the entire arsenal needed to hit much harder?

[Assessment of a rapid diagnostic test for malaria in rural health care facilities in Senegal]

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

[Comparison of PCR, ELISA-CSP and direct microscopic observation methods for the detection of Plasmodium falciparum sporozoites in Anopheles gambiae M in Senegal]

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.

[Assessing the reliability of clinical malaria diagnosis in children consulting in three peripheral health care facilities, in Niakhar rural area, Senegal]

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.

In vitro activity of iron-binding compounds against Senegalese isolates of Plasmodium falciparum

OBJECTIVES

The in vitro activities of FR160, a synthetic catecholate siderophore, and two iron-binding agents, desferrioxamine and doxycycline, were evaluated against Plasmodium falciparum isolates. Correlations between these compounds and standard antimalarial drugs (chloroquine, quinine, amodiaquine, pyronaridine, artemether, artesunate, atovaquone, cycloguanil and pyrimethamine) were assessed to determine any degree of cross-resistance.

METHODS

Between October 1997 and February 1998, and September and November 1998, 189 P. falciparum isolates were obtained in Dielmo and Ndiop (Dakar). Their susceptibilities were assessed using an isotopic, microwell format, drug susceptibility test.

RESULTS

The 137 inhibitory concentrations (IC(50)) values of FR160 ranged from 0.1 to 10 microM and the geometric mean IC(50) was 1.48 microM (95% CI = 1.29-1.68 microM). The geometric mean IC(50) of doxycycline for 121 isolates was 18.9 microM (95% CI = 16.8-21.3 microM) and that of desferrioxamine for 73 isolates was 20.7 microM (95% CI = 17.3-24.8 microM). FR160 was significantly less active against the chloroquine-resistant isolates (P < 0.0001). The mean IC(50)s of doxycycline were significantly higher for the chloroquine-susceptible isolates than for the resistant parasites (P = 0.0447). There was a weak correlation between the responses to FR160, desferrioxamine or doxycycline and those to the other antimalarial compounds (r(2) < 0.22).

CONCLUSIONS

The activities of FR160 and desferrioxamine, determined for P. falciparum clones, were confirmed against 137 isolates. The coefficients of determination between the responses to FR160, doxycycline or desferrioxamine and those to all the antimalarial drugs tested are too weak to suggest cross-resistance. FR160 could be a rationale partner to use in combination with doxycycline.

Four years' entomological study of the transmission of seasonal malaria in Senegal and the bionomics of Anopheles gambiae and A. arabiensis

From 1993 to 1996, an entomological survey was conducted in the village of Ndiop, Senegal, as part of a research programme on malaria epidemiology and the mechanisms of protective immunity. Mosquitoes were captured on human bait and by indoor spraying. Species from the Anopheles gambiae complex were identified using the polymerase chain reaction, and Plasmodium falciparum infections were detected by enzyme-linked immunosorbent assay for circumsporozoite protein. The vector species identified were A. gambiae (33.9%), A. arabiensis (63.2%), A. melas (0.3%) and A. funestus (2.5%). Similar proportions of A. gambiae (74.2%) and A. arabiensis (73.8%) contained human blood; 27.0% of A. gambiae and 28.3% of A. arabiensis had fed on cattle. The sporozoite rates were similar for A. gambiae (3.2%) and A. arabiensis (3.7%). The annual entomological inoculation rates varied greatly depending on the year. There were 63, 17, 37 and 7 infected bites per person per year in 1993, 1994, 1995 and 1996 respectively. Transmission was highly seasonal, from July to October. A. arabiensis was responsible for 66% of malaria transmission, A. gambiae for 31%, and A. funestus for 3%.

High annual and seasonal variations in malaria transmission by anophelines and vector species composition in Dielmo, a holoendemic area in Senegal

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.