Rapidly rising cases with Omicron in Senegal.

•Omicron variant continues to progress in Senegal with the appearance of new contaminations.•IRESSEF detected the first positive case of the Omicron variant on Friday, December 3, 2021.•Since this date, the number of Omicron variant infections has increased over the weeks.•Molecular surveillance of the Omicron variant is carried out in real time to inform the medical authorities.

The Genomics of Cannabis and Its Close Relatives.

Cannabis sativa L. is an important yet controversial plant with a long history of recreational, medicinal, industrial, and agricultural use, and together with its sister genus Humulus, it represents a group of plants with a myriad of academic, agricultural, pharmaceutical, industrial, and social interests. We have performed a meta-analysis of pooled published genomics data, andwe present a comprehensive literature review on the evolutionary history of Cannabis and Humulus, including medicinal and industrial applications. We demonstrate that current Cannabis genome assemblies are incomplete, with ∼10% missing, 10-25% unmapped, and 45S and 5S ribosomal DNA clusters as well as centromeres/satellite sequences not represented. These assemblies are also ordered at a low resolution, and their consensus quality clouds the accurate annotation of complete, partial, and pseudogenized gene copies. Considering the importance of genomics in the development of any crop, this analysis underlines the need for a coordinated effort to quantify the genetic and biochemical diversity of this species.

Genome-wide differentiation in closely related populations: the roles of selection and geographic isolation.

Population divergence in geographic isolation is due to a combination of factors. Natural and sexual selection may be important in shaping patterns of population differentiation, a pattern referred to as 'isolation by adaptation' (IBA). IBA can be complementary to the well-known pattern of 'isolation by distance' (IBD), in which the divergence of closely related populations (via any evolutionary process) is associated with geographic isolation. The barn swallow Hirundo rustica complex comprises six closely related subspecies, where divergent sexual selection is associated with phenotypic differentiation among allopatric populations. To investigate the relative contributions of selection and geographic distance to genome-wide differentiation, we compared genotypic and phenotypic variation from 350 barn swallows sampled across eight populations (28 pairwise comparisons) from four different subspecies. We report a draft whole-genome sequence for H. rustica, to which we aligned a set of 9493 single nucleotide polymorphisms (SNPs). Using statistical approaches to control for spatial autocorrelation of phenotypic variables and geographic distance, we find that divergence in traits related to migratory behaviour and sexual signalling, as well as geographic distance, together explain over 70% of genome-wide divergence among populations. Controlling for IBD, we find 42% of genomewide divergence is attributable to IBA through pairwise differences in traits related to migratory behaviour and sexual signalling alone. By (i) combining these results with prior studies of how selection shapes morphological differentiation and (ii) accounting for spatial autocorrelation, we infer that morphological adaptation plays a large role in shaping population-level differentiation in this group of closely related populations.

Epidemiologie des souches de Klebsiella pneumoniae productrices de Beta-lactamases a spectre elargi dans un hopital universitaire au Senegal; 2011

Objectifs : Au cours de ces dix dernieres annees; la resistance bacterienne aux antibiotiques; particulierement par production de ?-lactamases a spectre elargi (BLSE); est devenue un probleme majeur de sante publique. L'objectif de cette etude est de determiner la prevalence des souches de Klebsiella pneumoniae BLSE au CHNU Le Dantec; Dakar; Senegal. Methodes : Il s'agit d'une etude retrospective sur une periode de 12 mois portant sur 139 souches de K. pneumoniae. La detection des BLSE a ete effectuee par la methode de diffusion par double disque. Resultats : Parmi les 139 souches de K. pneumoniae etudiees; 44 (31;7) etaient productrices de BLSE. Trente trois (75) de ces 44 souches etaient d'origine nosocomiale (p = 0;016). Ces souches etaient surtout isolees chez les patients hospitalises dans les unites de soins intensifs (USI : 45;4 ; p = 0;031) et provenaient principalement de prelevements d'urines (59) et de pus (25). Toutes les souches de K. pneumoniae etaient resistantes a l'Amoxicilline; a la Piperacilline et a la Cefalotine. La majorite des souches de K. pneumoniae BLSE avait en outre une resistance a l'association sulfamethoxazole/trimethoprime (95;2); a la Gentamicine (78;6); a la Ciprofloxacine (67;4) et a l'Amikacine (41). Par contre; elles demeurent tres sensibles a l'Imipeneme et a la Fosfomycine. Conclusion : La resistance des enterobacteries; notamment K. pneumoniae; aux fluoroquinolones par production de BLSE devient de plus en plus preoccupante. Ceci suggere une utilisation plus rationnelle des fluoroquinolones; en particulier dans les traitements de premiere intension des infections du tractus urinaire

Genomic islands of divergence are not affected by geography of speciation in sunflowers.

Genomic studies of speciation often report the presence of highly differentiated genomic regions interspersed within a milieu of weakly diverged loci. The formation of these speciation islands is generally attributed to reduced inter-population gene flow near loci under divergent selection, but few studies have critically evaluated this hypothesis. Here, we report on transcriptome scans among four recently diverged pairs of sunflower (Helianthus) species that vary in the geographical context of speciation. We find that genetic divergence is lower in sympatric and parapatric comparisons, consistent with a role for gene flow in eroding neutral differences. However, genomic islands of divergence are numerous and small in all comparisons, and contrary to expectations, island number and size are not significantly affected by levels of interspecific gene flow. Rather, island formation is strongly associated with reduced recombination rates. Overall, our results indicate that the functional architecture of genomes plays a larger role in shaping genomic divergence than does the geography of speciation.

[HIV sentinel surveillance of pregnant women in Mauritania from 2001 to 2007]. / Surveillance sentinelle du VIH chez les femmes enceintes en Mauritanie entre 2001 et 2007.

According to the 2008 report on global AIDS epidemic, 33 millions of people are living with HIV/AIDS. Subsaharian Africa is the most affected part of the world. The first case of AIDS in Mauritania was reported in 1987. The national prevalence of HIV/AIDS in the country is estimated at less than 1%. The HIV serosurveillance among pregnant women started in country in 2001. This work has focused on HIV sentinel surveillance among pregnant women in antenatal clinics, attending health centres in different wilayas (regions) of the country in order to assess evolution of prevalence between 2001 and 2007. An anonymous and non-correlated method is used for this survey. A questionnaire was administered and venous sampling made for eligible women. Analyses were performed with an algorithm based on two screening tests (ELISA) and another test for confirmation (New Lav Blot). Despite some disparities between the sites considered, the results have shown a low prevalence rate (between 0.1 and 1.48). The average prevalence of HIV infection samples collected increased from 0.57% [0.34-0.80] in 2001 to 0.61% [0.40-0.82] in 2007 with 95% confidence interval. Statistical analysis showed no significant changes between 2001 and 2007 at all these sites. HIV1 is the most frequent type with a proportion of 93.5% in 2007. After several years of classic HIV sentinel surveillance, and to better understand disparities between sites, we recommend a second generation sentinel surveillance (behavioural and serological) approach.

Permanent Genetic Resources added to the Molecular Ecology Resources Database 1 February 2010-31 March 2010.

This article documents the addition of 228 microsatellite marker loci to the Molecular Ecology Resources Database. Loci were developed for the following species: Anser cygnoides, Apodemus flavicollis, Athene noctua, Cercis canadensis, Glis glis, Gubernatrix cristata, Haliotis tuberculata, Helianthus maximiliani, Laricobius nigrinus, Laricobius rubidus, Neoheligmonella granjoni, Nephrops norvegicus, Oenanthe javanica, Paramuricea clavata, Pyrrhura orcesi and Samanea saman. These loci were cross-tested on the following species: Apodemus sylvaticus, Laricobius laticollis and Laricobius osakensis (a proposed new species currently being described).

[Preliminary study of human Herpesvirus type 8 infection in pregnant women in Dakar (Senegal)]. / Etude préliminaire de l'infection à Herpesvirus humain type 8 chez les femmes enceintes à Dakar (Sénégal).

HHV8 was discovered in 1994 and few studies on this virus have been conducted in Africa. The virus is related to Kaposi sarcoma, an opportunistic affection occurring during HIV infection. No studies have been carried out on this subject in Senegal, a country known for its low KS prevalence even among people living with HIV/AIDS. Thus it will be interesting to explore this field. The aim of our study has been first, to demonstrate the presence of HHV8; second, to evaluate sero-prevalence of the infection in Senegal and third, to determine the specificities of HHV8 infection in our country. We performed our study on 407 pregnant women whose average age was 29.24 years, the majority of whom were Senegalese. HIV serology was done by dot blot for the screening and western blot for the confirmation. For the diagnosis of HHV8 infection, we used the indirect immunofluorescence kit of ABI. HIV infection was low among this study population; 0.5% and no HIV1 infection was mentioned. Among the 407 women, 58 or 14.3% were HHV8 positive and there was no HHV8/HIVco-infection. Regarding marital status, no significant difference was found between HHV8 positive and HHV8 negative among unmarried, monogamous or polygamous women. However, women having had 4 to 5 children were more likely to test positive for HHV8. The difference is significant and a relationship has been established with a p value of 0.02. Regarding pregnancy, HHV8 infection is more closely related to abortion: 17.2% of women who had aborted were HHV8 positive versus 4.9% seronegative. The odds ratio calculation shows a strong correlation with a p value of 0.01. No correlation was found between HHV8 infection of the mother and neonate mortality or Apgar score. However, a relationship did show up between HHV8 infection of the mother and low birth weight. 29.2% of seropositive women had had a child with a birth weight under 2600 g whereas only 16.3% of seronegative women had had babies with low birth weight. We determined that HHV8 is indeed present in Senegal. Further studies should focus on transmission routes as well as the molecular epidemiology of this virus and diseases related to HHV8 infection in Senegal.

[Improvement of tuberculosis diagnosis by the Mycobacteria Growth Indicator Tube (MGIT) in a developing country laboratory]. / Amélioration du diagnostic de la tuberculose par le Mycobacteria Growth Indicator tube (MGIT) dans un laboratoire de pays en développement.

In order to improve tuberculosis diagnosis in a developing country (Senegal), we evaluated a new liquid-based medium and nonradioactive system, Mycobacteria Growth Indicator Tube (MGIT), with individual clinical specimens collected in Dakar. The main purpose was to compare the time to detection and the rate of recovery of Mycobacterium tuberculosis complex and to determine its importance with respect to Lowenstein-Jensen (LJ), a liquid-based-medium for isolation of M. tuberculosis complex. 531 specimens were processed with Mycoprep kit containing NaOH-N-acetyl L-cystein and inoculated on both LJ and MGIT and incubated at 37 degrees C for 60 days. For each medium, the recovery rate and the time to detection were recorded. Among the 531 specimens, of which 121 smears were positive, 32.5% (173/531) grew the M. tuberculosis complex. Of these, 103 were smear positive (S+) and 70 smear negative (S-). LJ recovered 54.9% (95/173) and MGIT recovered 91.9% (159/173). Disagreements were observed with 92 isolates, LJ failed to recover 78 while MGIT failed to recover 14. The overall mean time to detection was 20.1 days for LJ and 10.5 days for MGIT. MGIT has shown a better sensitivity in isolation with significant reduction in reporting culture for M. tuberculosis complex. As a simple and a nonradiometric system, it could be used in conjunction with egg-based media in developing countries laboratories.

Rapid susceptibility testing of Mycobacterium tuberculosis by the Mycobacteria Growth Indicator Tube (MGIT AST SIRE).

OBJECTIVE: To evaluate the reliability of the Mycobacteria Growth Indicator Tube (MGIT AST) for susceptibility testing of Mycobacterium tuberculosis. METHODS: Seventy strains of M. tuberculosis were tested for susceptibility to streptomycin, isoniazid, rifampicin and ethambutol by comparing MGIT AST results to those obtained by the method of proportion (MOP) on Lowenstein-Jensen (LJ) and Middlebrook 7H10 media. The 7H10 MOP was considered the method of reference. RESULTS: The turnaround time for MGIT AST was 6.2 days (5-10 days) and for MOP it was 18-21 days. With rifampicin, MGIT AST agreed for all isolates with both MOP. For streptomycin, MGIT AST and 7H10 MOP agreed for 64 isolates (91.4%); 61 were susceptible and three resistant. LJ MOP and 7H10 MOP agreed for 64 isolates (92.2%); 62 were susceptible and three resistant. With isoniazid, both MOP agreed for all isolates, while MGIT AST and 7H10 MOP had two discrepancies. For ethambutol, MGIT AST and 7H10 MOP were concordant for 66 isolates; 65 were susceptible and one resistant. Both MOP were concordant for 67 isolates; 66 were susceptible and one resistant. CONCLUSIONS: Based on these results, MGIT AST is a time-saving method and can be used as an alternative to the BACTEC System. MGIT AST is reliable as far as rifampicin and isoniazid are concerned; however, additional studies are needed for streptomycin and ethambutol.

[Importance of culture media choice in the isolation of Haemophilus ducreyi. Experience in Senegal]. / Importance du choix d'un milieu de culture dans l'isolement de Haemophilus ducreyi. Expérience du Sénégal.

Genital ulcerations typify one of the major reasons clients seek STD consultation in developing countries. The usual etiologies are syphilis, chancroid and herpes. The ideal diagnostic approach is to undertake complete laboratory examination that are rarely possible in structure destitute of laboratory analysis possibilities which is the case for most of the STD transmission agents. Chancroid is caused by Haemophilus ducreyi, a short Gram negative bacteria. The bacteriological diagnosis is based on direct examination, isolation and identification of the bacteria. The nutritive exigence of the bacteria required 3 medium of isolation (PPLO base Pasteur), GC base (GIBCO) and Muller Hinton base (Becton & Dickinson, with "chocolate" agar) have been tested from the chancre samples of 108 male patients who had a median age of 31 years. Direct exams were positive in 66 cases (61%) and culture exams positive in 53 cases (49%). The Muller Hinton base with "chocolate" agar produced the best results and seems to be the medium of choice for isolated strains in Senegal. The culture mediums currently used in Europe are apparently inappropriate for the germ culture in Senegal. We have also observed that all the isolated strains were producers of beta-lactamase. Antibiotic treatment before the sample swab is taken seems to have an inhibiting effect on the culture. Direct examination with a sensibility of 94.3% and a specificity of 70.9% remains sufficient in routine presumptive diagnosis in endemic areas.