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International audience; Mycobacterium tuberculosis complex (MTBC) Lineage 3 (L3) strains are abundant in world regions with the highest tuberculosis burden. To investigate the population structure and the global diversity of this major lineage, we analyzed a dataset comprising 2682 L3 strains from 38 countries over 5 continents, by employing 24-loci mycobacterial interspersed repetitive unit-variable number of tandem repeats genotyping (MIRU-VNTR) and drug susceptibility testing. We further combined whole-genome sequencing (WGS) and phylogeographic analysis for 373 strains representing the global L3 genetic diversity. Ancestral state reconstruction confirmed that the origin of L3 strains is located in Southern Asia and further revealed multiple independent introduction events into North-East and East Africa. This study provides a systematic understanding of the global diversity of L3 strains and reports phylogenetic variations that could inform clinical trials which evaluate the effectivity of new drugs/regimens or vaccine candidates.

Breast cancer is a complex disease characterized by the accumulation of multiple molecular alterations giving each tumor phenotype and an own evolutionary potential. This study aimed to describe the distribution of the profile and molecular subtypes of breast cancers followed at Surgical Oncology Unit of Donka National Hospital. This was retrospective and descriptive study on cases of breast cancer in which the hormone receptor status and expression of the Her2 oncogene have been performed from 2007 to 2016. We recorded 58 cases including 56 (96.6%) women and 2 (3.4%) men. The average age was 48.2 ± 10.9. Invasive ductal carcinoma accounted for 50 (86.2%) cases. The SBR grade was II in 31(53.4%) cases, III in 21 (36.2%) cases and I in 6 (10.3%) cases. The tumor was classified as T4 in 36 (62.1%) cases; it was metastatic in 11(19.0%) cases. Estrogen receptors were positive in 29 (50.0%) cases, progesterone receptors positive in 25 (43.1%) cases, the Her2 oncogene was positive in 22 (39.3%) cases. The distribution of molecular sub-types was: 20 (34.5%) luminal A, 15 (25.9%) triple negative, 13 (22.4%) Her2 overexpressed, 8 (13.8%) luminal B and 2 (3.2%) undetermined. This preliminary study showed the poor accessibility of immunohistochemistry for the molecular diagnosis of breast cancer in our country. Luminal A subtypes and triple negatives were more common. The determination of molecular subtypes is a rational basis for hormone therapy and targeted therapy, thus personalizing the treatment of breast cancer.

Tuberculosis is a contagious infectious disease, in which epidemiologic monitoring by molecular approaches is a critical element of prevention and control. The population structure of the Mycobacterium tuberculosis complex (MTBc) in Senegal was last described in the 1970’s using biochemical methods. In this present study, we applied molecular approaches to genotype M. tuberculosis isolates from active pulmonary tuberculosis patients who participated in a prospective cohort study between 2004 to 2006. Genetic characterization, using standard spoligotype analysis and Line Probe Assay for resistance to isoniazid and rifampicin, was applied after culture on egg based solid media. The prevalence of resistance to isoniazid was 1.0% and to rifampicin 0.0% among 203 isolates tested. Of the 203 isolates, spoligotype patterns present in the TB-insight database were identified in 178 (87.6%) while 25 (12.3%) showed patterns suggestive of mixed infection. The major spoligotypes identified were the Haarlem lineage (22%), followed by the T (19%), Beijing (12%), LAM (12%), and M. africanum West African 2 (10%). Patterns suggestive of mixed infections, such as the sole lack of spacers 33 and 34, suggested a combination of Euro-American M. tuberculosis and Beijing lineage, which were confirmed by polymerase chain reactions (PCRs) for lineage defining deletions in a subset of isolates. The population structure of the M. tuberculosis complex in Dakar reflects a predominance of Euro-American M. tuberculosis (Haarlem, T and LAM), with a decreased prevalence of M. africanum West African 2, compared with reports from the 1970’s based on biochemical speciation, which reported prevalence of M. africanum around 20% in Dakar. Key words: Tuberculosis, Mycobacterium tuberculosis complex, polymerase chain reactions (PCRs).

OBJECTIVE To assess the effectiveness of the WHO syndromic algorithm in the management of vaginal discharge among women of reproductive age in Dakar. METHODS Cross-sectional study of consecutive female patients (aged 18-49 years) presenting with vaginal symptoms at six selected study sites in Dakar; of these, 276 patients were included in the analysis. Vaginal and cervical swab samples were collected and analysed to establish an aetiological diagnosis of any infection. Syndrome-based diagnosis was compared with the laboratory results to evaluate its accuracy based on sensitivity, specificity and positive and negative predictive values. The degree of agreement between the two approaches was assessed using the Cohen's kappa concordance analysis. RESULTS Overall prevalence of vaginal infections was 56.9% (157/276); 5.4% (15/276) of the patients had cervical infection. Using the syndromic approach, 51% of patients were correctly managed for Trichomonas vaginalis (TV)/Gardnerella vaginalis (GV); 61% for Candida albicans (CA) and 54% for Chlamydia trachomatis (CT)/Neisseria gonorrhoea (NG) infections. Consequently, 31% of patients with TV/GV, 51% with CA and 53% with CT/NG infections would have missed treatment. Further, the kappa value was

Background Emergence of Multidrug-resistant (MDR) strains constitutes a significant public health problem worldwide. Prevalence of MDR tuberculosis from Chad is unavailable to date. Methods We collected samples from consecutive TB patients nationwide in the seven major cities of Chad between 2007 and 2012 to characterize drug resistance and the population structure of circulating Mycobacterium tuberculosis complex (MTBC) strains. We tested drug sensitivity using Line Probe Assays and phenotypic drug susceptibility testing (DST) were used for second line drugs. We genotyped the isolates using spoligotype analysis and MIRU-VNTR. Results A total of 311 cultures were isolated from 593 patients. The MDR prevalence was 0.9% among new patients and 3.5% among retreatment patients, and no second line drug resistance was identified. The distribution of genotypes suggests a dissemination of MDR strains in the Southern city of Moundou, bordering Cameroon and Central African Republic. Conclusion Emerging MDR isolates pose a public health threat to Southern Chad, with risk to neighboring countries. This study informs public health practitioners, justifying the implementation of continuous surveillance with DST for all retreatment cases as well as contacts of MDR patients, in parallel with provision of adequate 2nd line regimens in the region. Electronic supplementary material The online version of this article (doi:10.1186/s12879-017-2671-7) contains supplementary material, which is available to authorized users.

Background: Lower reproductive tract infections in women are important causes of morbidity but can also lead to complications and sequelae. This study aimed to establish the prevalence and risk factors of lower genital tract infections among women of reproductive age in Dakar (Senegal). Methods: This was a prospective study conducted in 6 maternity hospitals from July to November 2015. Participants ranged in age from 18 to 49 years and presented at health facilities with signs and symptoms of genital infection. Consenting individuals who met the inclusion criteria were recruited for the study. Results: During the reporting period, 276 patients were enrolled. According to the laboratory results, the prevalence of any genital infection was 69.6% (192 of 276). The most common vaginal infections were bacterial vaginosis (39.5%) and vaginal candidiasis (29%), with the third most common cause, trichomoniasis, trailing behind in terms of prevalence (2.5%). Among the microorganisms responsible for cervical infections, Ureaplasma urealyticum was the most frequent (27.5%), followed by Mycoplasma hominis (14.5%), Chlamydia trachomatis (4.7%), and Neisseria gonorrhoeae (1.1%). Multivariate analysis showed that young women and women with low levels of education were at increased risk for vaginal/cervical infections. Conclusions: This study revealed a high prevalence of bacterial vaginosis and vaginal candidiasis and suggests that health care providers should increase awareness and communication to improve vaginal hygiene practices. If infection with Trichomonas vaginalis, C trachomatis or N gonorrhoeae is suspected, we also recommend systematically performing laboratory diagnostic confirmation.

Hepatitis B is a major public health problem in Senegal, a country with high prevalence and a transmission occurring mainly during infancy. Only, one 6-8 weeks vaccination campaign was initiated in 2005 and it was part of the expanded program of immunization. The aim of this study was to determine the prevalence of HBsAg in children born from HIV-seropositive mothers by using dried blood specimens. Specimens were collected between July 2007 and November 2012 from children aged 2-48 weeks in Dakar and decentralized sites working on HIV mother-to-child transmission prevention. HBsAg detection was performed using Architect HBsAg Qualitative II kit (Abbott Diagnostics, Ireland) and for all reactive samples confirmation was done using Architect HBsAg Qualitative II Confirmatory kit (Abbott Diagnostics, Ireland). Nine hundred thirty samples were collected throughout the country with 66% out of Dakar, the capital city. The median age was 20 weeks and 88% of children were less than 1 year of age with a sex ratio of 1.27 in favor of boys. HBsAg was detected in 28 cases giving a global prevalence of 3%. According to age, HBsAg prevalences were 5.1% for children less than 6 weeks, 4.1% and 4.6%, respectively, for those aged 12-18 weeks and 18-24 weeks of age. The HIV prevalence was 2.6% with no HIV/HBV co-infection. This study showed a high rate of HBV infection in children under 24 months, highlighting the need to promote birth-dose HBV vaccination as recommended by WHO.

Background Multidrug-resistant tuberculosis (MDR-TB) remains a clear threat to TB control. There is a paucity of data on DR-TB for many countries especially in sub-Saharan Africa. The study was undertaken to measure the prevalence of DR-TB, including MDR-TB, from West Africa. Methods Mycobacterial isolates were obtained from consecutive new and previously treated TB patients from Burkina Faso, Ghana, Guinea-Bissau, Mali, Nigeria, Senegal, The Gambia and Togo from December 2012 to December 2014. Phenotypic drug susceptibility testing to first- and second-line anti-TB drugs was performed using BACTEC MGIT 960 system. Results Viable isolates from a total of 44% (416/950) new and 56% (534/950) previously treated TB patients were included. HIV results were available for 599 (63%) with estimated HIV-TB co-infection of 21% (95% CI: 18.2−24.9%). Pooled estimate of any DR-TB prevalence among new TB patients was 20% (95% CI: 16.4−24.4%) while for MDR-TB this was 6% (95% CI: 4.1−9.0%). Among previously treated TB patients, these were 53% (95% CI: 48.3−56.9%) and 34% (95% CI: 30.1−38.3%), respectively. Significant factor for the development of MDR-TB was the history of previous anti-TB treatment (Crude OR=0.13; 95% CI: 0.08−0.20; p= Mono-resistance was detected in 12% (95% CI: 10.2−14.5%) with the highest resistance to streptomycin 6% (95% CI: 4.8−7.9%). Pooled estimate of pre-XDR-TB prevalence rate among MDR-TB patients was 21% (95% CI: 15.2−26.9%). Estimated resistance to ofloxacin, kanamycin, capreomycin and kanamycin and capreomycin were 7% (95% CI: 3.5−10.9%), 2% (95% CI: 0.6−5.1%), 9% (95% CI: 5.8−14.5%), and 3% (95% CI: 0.8−5.8%), respectively. Conclusions The reported prevalence of MDR-TB and pre-XDR-TB are high compared to WHO estimates. Resistance to streptomycin may indicate a high risk of failure for the WHO standard regimen. MDR-TB patients with resistance to either the fluoroquinolone or injectables may have suboptimal response; thus the need for continuous surveillance of TB resistance.

A total of 24 cases of hospitalized, laboratory-confirmed Haemophilus influenzae type b (Hib) meningitis were identified through a regional pediatric bacterial meningitis surveillance system. Each case was matched by age and residence to 4 neighborhood controls. The adjusted vaccine effectiveness for ≥ 2 doses was 95.8% (95% confidence interval, 67.9%-99.4%). Hib vaccine appears to be highly effective in preventing Hib meningitis in Senegal.

In a polygamous marriage in Senegal, the husband and his two spouses were infected with HIV-1 group O. This study provides new full-length genome sequences for the two spouses (99SE-MP1299 and 99SE-MP1300) and the 3'-end LTR-tat fragment (6084 bp) for the husband (98SE-42HALD). Phylogenetic tree and diversity plot analysis revealed that the new viruses belong to HIV-1 group O and that they are closely related to each other in a cluster around ANT-70. The intrafamilial transmission occurred at most 6 years ago. The interpatient variability was highest in the envelope region, and in some regions of the envelope the strains from the two spouses do not cluster together anymore. The source of infection was in Cameroon and confirms a slow but continuous spread of HIV-1 group O viruses.

Bacterial meningitis is an important cause of morbidity and mortality in children living in low-resource settings. Pediatric bacterial meningitis cases < 5 years of age were identified through a regional hospital surveillance system for 3 years after introduction of routine immunization with Haemophilus influenzae type b (Hib) conjugate vaccine in Senegal in July 2005. Cases from the national pediatric hospital were also tracked from 2002 to 2008. The regional surveillance system recorded 1,711 suspected pediatric bacterial meningitis cases. Of 214 laboratory-confirmed cases, 108 (50%) were caused by Streptococcus pneumoniae, 42 (20%) to Hib, and 13 (6%) to Neisseria meningitidis. There was a 98% reduction in the number of hospitalized Hib meningitis cases from Dakar Region in 2008 compared with 2002. The surveillance system provides important information to the Ministry of Health as they consider self-funding Hib vaccine and introducing pneumococcal vaccine.

To document the actual genetic diversity of HIV-1 strains in the Republic of Congo, 114 HIV-1 positives persons were sampled in 2003 and 2004 after their informed consent. They were attending the teaching hospital, the reference health center in Makelekele, Brazzaville and the regional hospital centers in Pointe-Noire, Gamboma and Ouesso. A total of 104 samples were genetically characterized by direct sequencing of the p24 gag region and 80 were also subtyped in the V3-V5 env region. The genetic subtype distribution of the Congolese strains showed the predominance of subtype A (36.5% and 32.5% in gag and env, respectively) and G (30.8% and 21.25%), whereas subtype D strains represented 12.5% and 15%. Subtypes C, F, H, J, K and the CRFs-01, -02, -05 -06, and also the recently characterized CRF18 were seen at lower rates. Finally, 4.8% (gag) and 6.25% (env) of the strains could not be classified. Moreover, a high intra-subtype diversity was observed in our study. Among 70 strains which have been characterized in the two genomic regions, 14 (20%) appeared to be unique recombinants. These data show a high genetic variability in the Republic of Congo, where all the subtypes have been documented together with certain subsubtypes and several CRFs. (c) 2006 B.V. All rights reserved.