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Background: The emergence and spread of carbapenem-resistant Acinetobacter baumannii are critical in hospitals, particularly in intensive care units (ICUs), which represents a public health concern worldwide. In this study, we investigated the molecular epidemiology of multi-drug resistant A. baumannii (MDR-AB) in Dakar, Senegal. Methods. The A. baumannii was isolated from Eosin Methylene Blue Agar culture and identified using API 20NE strip test and MALDI-TOF. The antimicrobial susceptibility testing was performed using the disk diffusion method. Simplex and multiplex-polymerase chain reactions with appropriate primers were used to detect and sequence the following β-lactamase genes: Two class D carbapenem hydrolyzing oxacillinases (blaOXA-51 and blaOXA-23), three class B metallo-β-lactamase genes (blaIMP, blaVIM and blaNDM), and five class A β-lactamase genes (blaPER, blaSHV, blaVEB, blaTEM, and blaGES). Results: A total of 29 strains of MDR-AB were isolated from patients hospitalized at Aristide Le Dantec University teaching hospital in Dakar, Senegal. Among the 29 MDR-AB strains isolated, 11 (37.9%) were isolated from ICUs, 5 (17.2%) from pediatric surgery, and 13 (44.8%) from other departments. The MDR strains were isolated from urine and pus samples with 12 (41.4%) and 9 (31.0%), respectively. All isolates were positive for the A. baumannii specific gene blaOXA-51. The blaOXA-51 and blaOXA-23 genes coexisted in 26 (89.65%) of the strains. The blaIMP and blaVIM genes were not detected among the selected strains. Moreover1 (3.4%) strain elicited the gene coding for metallo-β-lactamase NDM-1. 2 (6.9%) isolates turned out to produce the penicillinase TEM-2. Conclusions: Carbapenem resistance in Senegalese strains of A. baumannii is predominantly due to the worldwide disseminated gene blaOXA-23, with a subset of strains due to NDM-1 and TEM-2. Systemic molecular surveillance network should be established for further efficient monitoring of MDR strains in Senegal.

Extra-intestinal pathogenic Escherichia coli (ExPEC), a predominant Gram-negative bacterial pathogen, express a wide range of virulence factors and is responsible of several diseases including urinary tract infections (UTI), nosocomial pneumonia, bacteremia, and neonatal meningitis. ExPEC isolates are often multidrug resistant (MDR) and clones producing extended-spectrum beta-lactamases (ESBL) are increasingly reported all over the world.Seventy-eight clinical ExPEC strains were selected for this study. The majority was from UTIs (n=51), while the rest (n=27) was from pus, sputum, bronchial fluid and vaginal samples (non-uropathogenic ExPEC). Interestingly, 49 out of the 78 ExPEC isolates where considered as community-acquired (CA) and 29 hospital-acquired (HA) bacteria. Antibiotic susceptibility testing was performed using the Kirby-Bauer disc diffusion method. Standard polymerase chain reaction (PCR) was used to screen major ESBL genes (blaCTX-M, blaOXA-1, blaTEM, blaSHV) and blaCTX-M variants (blaCTX-M-1, blaCTX-M-9, blaCTX-M-15, blaCTX-M-25).All the ExPEC strains were resistant to ampicillin, ticarcillin, amoxicillin/clavulanic acid combination, cefalotin, cefotaxime, ceftazidime, cefepime and aztreonam, but showed a high susceptibity to fosfomycin (98.7%, n = 77), ertapenem (96.2%, n = 75), and imipenem (100%). Moreover, isolates harbored at least one ESBL gene, including blaCTX-M (98.7%), blaOXA-1 (78.2%), blaTEM (44.9%) and blaSHV (3.8%). The CTX-M variants were also found with the predominance of blaCTX-M-1 (90.9%) and blaCTX-M-15 (90.9%) followed by blaCTX-M-9 (11.7%), while blaCTX-M-25 was not detected.Despite the resistance to most of the tested antibiotics, ExPEC isolates showed fortunately a good susceptibility to fosfomycin and carbapenems. blaCTX-M (blaCTX-M1, blaCTX-M15) and blaOXA-1 seem to be E. coli major ESBL genes circulating in Senegal. No significant difference was noted when comparing prevalence of ESBL genes detected from CA and HA strains, and from UPEC and non-uropathogenic ExPEC. The high level of resistance to antimicrobials observed stresses the need of establishing an epidemiological surveillance of antimicrobial resistance in both community and hospital settings.

Enterobactericeae producing extended spectrum b-lactamases (ESBL) are likely to express carbapenemases OXA-48 which have hydrolytic activity on carbapenems. The aim of this work was to evaluate prevalence of blaOXA-48 for Klebsiella pneumoniae isolates producing ESBL. This work was conducted at the French Reference Center for Antibiotic Resistance with strains from Senegalese Hospital. Standard antibiogram was performed in accordance to CA-SFM/EUCAST 2016 and presence of ESBL was confirmed by synergistic image. Polymerase chain reaction (PCR) was performed to detect systematically blaOXA-1, blaTEM-1, blaCTX-M-1, blaCTX-M-9 and blaOXA-48 gene in case of decrease sensitivity to carbapenem. PCR products were extracted, purified, sequenced and whole-genome sequence (WGS) were used for the analyses. Plasmids extraction was performed by Kado and Liu method. Five isolates harbored a decreased susceptibility to carbapenems. They were positive for blaOXA-48 gene and also expressed blaCTX-M-15. Analysis of the five plasmids by WGS identified a single IncL/M type plasmid of 63 kb and other genes for aminoglycosides and quinolones resistance. Carbapenemase-producing Enterobacteriaceae represent new threat to public health. Decrease in carbapenem susceptibility should be an alert for rapid detection of carbapenemases and to prevent their spread. Phenotypic or molecular methods should be available in many laboratories to take appropriate preventive and therapeutic measures. Key words: Klebsiella pneumoniae, extended spectrum b-lactamases (ESBL), carbapenemase, blaOXA-48, Senegal.

Extended spectrum β-lactamase (ESBL) and carbapenemase-producing Enterobacteriaceae (CPE) have been increasingly reported worldwide. The objective of this study is to determine the prevalence of these multidrug-resistant strains in a major university teaching hospital in Dakar, Senegal. A total of 1205 Enterobacteriaceae stains were tested for ESBL and carbapenemase production. Antibiotics susceptibility test was performed with disk diffusion method. ESBL was detected using a double-disk synergy method. Carbapenemase production was detected with ertapenem 10 µg disk charge. The overall prevalence of ESBL- and carbapenemase-producing Enterobacteriaceae was 26.2 (316/1205) and 5.1% (62/1205), respectively. Interestingly, 3.8% of these pathogens were both ESBL-carbapenemase producers. Among the Enterobacteriaceae ESBL positive, Escherichia coli (45.2%, 143/316), Klebsiella pneumoniae (26.3%, 83/316), Enterobacter cloacae (12.7%, 40/316), and Proteus vulgaris (9.2%, 29/316) were the most prevalent. These strains were mainly isolated from urine (56.6%) and pus (22.7%) specimen. The most prevalent CPEs were E. coli (45.2%, 28/62), K. pneumoniae (27.4%, 17/62), and E. cloacae (16.1%, 10/62), particularly isolated from urine (58%) and pus (19.3%). The majority of these MDR strains were isolated from patients hospitalized in urology (32.4%), surgery (27.7%), internal medicine (18.5%), and intensive care units (10%). ESBL-producing Enterobacteriaceae remain highly susceptible to fosfomycin (94.1%), amikacin (92.5%) and ertapenem (88.6%), while carbapenemase producers were fully susceptible to amikacin (100%), and to a lesser extent, fosfomycin (66.7%) and colistin (60%). This study revealed increasing prevalence of ESBL- and carbapenemase-producing Enterobacteriaceae with limited therapeutic options, suggesting a need for continuous multi-drug resistant (MDR) surveillance patterns particularly in hospital settings. Key words: Extended spectrum β-lactamase, carbapenemase, Enterobacteriaceae.

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).

In the context of early infant diagnosis (EID) decentralization in sub-Saharan Africa, dried blood spot (DBS) is now widely used for HIV proviral DNA detection in resource-limited settings. A new version of CAP/CTM (version 2) has been introduced, recently by Roche Diagnosis as a new real-time PCR assay to replace previous technologies on qualitative detection of HIV-1 DNA using whole blood and DBS samples. The objective of this study was to evaluate CAP/CTM version 2 compared to CAP/CTM version 1 and Amplicor on DBS. A total of 261 DBS were collected from children aged 4 weeks to 17 months born from HIV-seropositive mothers and tested by the three techniques. CAP/CTM version 2 showed 100% of agreement with Amplicor including 74 positive results and 187 negative results. CAP/CTM version 2 versus CAP/CTM version 1 as well as CAP/CTM version 1 versus Amplicor showed two discordant results giving a sensitivity of 98.6%, specificity of 99.5%, positive predictive value of 98.6% and negative predictive value of 99.5%. The concordance was 99.12% (95% of confidence interval) giving a Kappa coefficient of 0.97 (p

Background: To improve the care and treatment of HIV-exposed children, early infant diagnosis (EID) using dried blood spot (DBS) sampling has been performed in Senegal since 2007, making molecular diagnosis accessible for patients living in decentralized settings. This study aimed to determine the evolution of the HIV transmission rate in children from 2008 to 2015 and to analyze associated factors, particularly the mother’s treatment status and/or child’s prophylaxis status and the feeding mode. Methods: The data were analyzed using EID reports from the reference laboratory. Information related to sociodemographic characteristics, HIV profiles, the mother’s treatment status, the child’s prophylaxis status, and the feeding mode was included. Descriptive statistics were calculated, and bivariate and multivariate logistic regression analyses were performed. Results: During the study period, a total of 5418 samples (5020 DBS and 398 buffy coat) from 168 primary prevention of HIV mother-to-child transmission (PMTCT) intervention sites in Senegal were tested. The samples were collected from 4443 children with a median age of 8 weeks (1-140 weeks) and a sex ratio (M/F) of 1.1 (2309/2095). One-third (35.2%; N = 1564) of the children were tested before 6 weeks of age. Twenty percent (N = 885) underwent molecular diagnostic testing more than once. An increased number of mothers receiving treatment (57.4%; N = 2550) and children receiving prophylaxis (52.1%; N = 2315) for protection against HIV infection during breastfeeding was found over the study period. The transmission rate decreased from 14.8% (95% confidence interval (CI): 11.6-18.7) in 2008 to 4.1% (95% CI: 2.7-6.2) in 2015 (p < 0.001). Conclusion: This study demonstrates the effectiveness of PMTCTinterventions in Senegal and indicates that increased effortsshould be continued to reduce the MTCT rate to less than 2%.

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

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.

The aim of this study was to compare four HIV-1 viral quantitation platforms, Nuclisens EasyQ v2.0 ® (EQ), COBAS AmpliPreP/Cobas Taqman ® HIV-1 test v 2.0 (CTM), GENERIC HIV CHARGE VIRALE ® (GEN), with Abbott Real Time HIV-1 ® (m2000sp/rt) as reference technique. The study had first evaluated m2000sp/rt performances and then compared quantitation between techniques. Discordant samples were genotyped on gag and pol gene and sequences were analyzed using Sequence locator and SeqPublish to detect eventual mismatches. Performance analysis of m2000sp/rt showed good results with coefficients of variation values (CV) of 1.35%, 0.65%, and 0.54% for repeatability testing of low, intermediate and high concentrations, respectively. Reproducibility tests showed low CV values with 2.36% and 1.42% for low and high concentration levels, respectively and contamination test was very low value with 0.94%. Correlation and concordance between techniques ranged from r 2 = 0.98 and bias = −0.00185 (for m 2000sp/rt vs CTM) to r 2 = 0.90 and bias = −0.135 (for EQ vs GEN). Discrepancies were observed on 37 samples mostly CRF02_AG but despite some mismatches, sequence analysis (26/37) did not show any remarkable differences between CRF02_AG queries and references. This study showed good correlation and good concordance between techniques. However, EQ yielded under-quantitation of CRF02_AG.

The study aimed to estimate the prevalence of Hepatitis B virus (HBV) infection and to describe the HBV virological profiles among Senegalese HIV-1-infected patients. We conducted a retrospective study between 2006 and 2010 among Senegalese HIV-1-infected patients from the antiretroviral therapy cohort. Samples were screened using Determine® HBsAg or MONOLISA® POC test. The HBsAg positivity status was confirmed by Architect® HBsAg. Detection of HBeAg, anti-HBe Ab, and HBV DNA load were done for the HBsAg-positive samples. Then, Anti-HBcAb was tested for the HBsAg-negative samples. Microsoft Excel was used for data collection and statistical analyses were performed using Epi info 3.5.1. Overall, 466 HIV-infected patients were enrolled including 271 women (58.4%), and 193 men (41.6%) with a median age of 39 years (19–74 years). The global prevalence of HIV/HBV coinfection (HBsAg positive) was 8.8% (41/466). For HBsAg positives samples, the prevalence of HBeAg and the anti-HBeAb were, respectively, 24.4 and 69.2% and the median of HBV DNA viral load, for 27 HBsAg-positive samples, was 3.75 log10 copies/ml. The virological profiles were the following: 7, 15, and 5 patients infected, respectively, by a replicative virus, an inactive virus and a probably mutant virus. For HBsAg-negative samples, 83 out of 109 were positive for anti-HBcAb. This study showed a significant decrease of the prevalence of HBV/HIV coinfection between 2004 and 2014 (P = 0.003), which highlighted the performance of the Senegalese HBV vaccine program. However, implementing a systematic quantification of HBV DNA viral load could improve the monitoring of HBV-infected patient. J. Med. Virol. © 2015 Wiley Periodicals, Inc.

Cephalosporinases, which are naturally present in some enterobacterial species, can be mobilized by transposons, migrate to plasmids, and spread into other species such as Escherichia coli. The aim of this study was to characterize genes responsible for the production of extended-spectrum β-lactamases (ESBL) in E. coli isolates from urinary origin isolated in two hospitals in Senegal. Thus, a fortuitous discovery of plasmidic cephalosporinase in two isolates was noted. One of the isolates produced dha-1 associated with ESBL CTX-M-14, the other produced cmy-2, ESBL CTXM-15, tem-1 penicillinase, and oxa-1. This confirms the circulation of multidrug-resistant bacteria producing plasmidic cephalosporinase in Senegal. However, a large study is needed to better understand the prevalence and the nature of the genes involved.

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.

Cephalosporinases, which are naturally present in some enterobacterial species, can be mobilized by transposons, migrate to plasmids, and spread into other species such as Escherichia coli. The aim of this study was to characterize genes responsible for the production of extended-spectrum β-lactamases (ESBL) in E. coli isolates from urinary origin isolated in two hospitals in Senegal. Thus, a fortuitous discovery of plasmidic cephalosporinase in two isolates was noted. One of the isolates produced dha-1 associated with ESBL CTX-M-14, the other produced cmy-2, ESBL CTXM-15, tem-1 penicillinase, and oxa-1. This confirms the circulation of multidrug-resistant bacteria producing plasmidic cephalosporinase in Senegal. However, a large study is needed to better understand the prevalence and the nature of the genes involved.

Introduction: Chlamydia trachomatis and Neisseria gonorrhoeae are the most common causes of sexually transmitted disease in Senegal and worldwide. Molecular techniques have become the standard for their detection, and due to the frequency of co-infections, these tests can detect both agents and can be used on urine samples, vaginal swabs, or endocervical samples. In developing countries, the use of these molecular techniques is very limited and there is a need for evaluations of these techniques to be done. Methodology: A total of 181 samples were tested with the Abbott RealTime CT/NG assay and compared with the Roche Cobas Amplicor CT/NG assay. Specimens were collected from the key population of men having sex with men (urine, n = 60), female sex workers (genital swabs, n = 60) and from women visiting the laboratory for a gynecological checkup (urine, n = 60 and endocervical samples, n = 61). Results: The agreement between the two techniques was 98.90% with a Kappa coefficient of 0.98. A sensitivity of 93.3%, a specificity of 100%, a positive predictive value of 100%, and a negative predictive value of 93.3% were found for both Chlamydia trachomatis and Neisseria gonorrhoeae . Conclusion: These results showed that both methods are similar and suitable for the detection of CT/NG in all types of samples examined in this study.

Background To improve the care and treatment of HIV-exposed children, early infant diagnosis (EID) using dried blood spot (DBS) sampling has been performed in Senegal since 2007, making molecular diagnosis accessible for patients living in decentralized settings. This study aimed to determine the evolution of the HIV transmission rate in children from 2008 to 2015 and to analyze associated factors, particularly the mother’s treatment status and/or child’s prophylaxis status and the feeding mode. Methods The data were analyzed using EID reports from the reference laboratory. Information related to sociodemographic characteristics, HIV profiles, the mother’s treatment status, the child’s prophylaxis status, and the feeding mode was included. Descriptive statistics were calculated, and bivariate and multivariate logistic regression analyses were performed. Results During the study period, a total of 5418 samples (5020 DBS and 398 buffy coat) from 168 primary prevention of HIV mother-to-child transmission (PMTCT) intervention sites in Senegal were tested. The samples were collected from 4443 children with a median age of 8 weeks (1–140 weeks) and a sex ratio (M/F) of 1.1 (2309/2095). One-third (35.2%; N = 1564) of the children were tested before 6 weeks of age. Twenty percent (N = 885) underwent molecular diagnostic testing more than once. An increased number of mothers receiving treatment (57.4%; N = 2550) and children receiving prophylaxis (52.1%; N = 2315) for protection against HIV infection during breastfeeding was found over the study period. The transmission rate decreased from 14.8% (95% confidence interval (CI): 11.4–18.3) in 2008 to 4.1% (95% CI: 2.5–7.5) in 2015 (p < 0.001). However, multivariate logistic regression analysis revealed that independent predictors of HIV mother-to-child transmission included lack of mother’s treatment (adjusted odd ratio (aOR) = 3.8, 95% CI: 1.9–7.7; p˂0.001), lack of child’s prophylaxis (aOR = 7.8, 95% CI: 1.7–35.7; p = 0.009), infant age at diagnosis (aOR = 2.2, 95% CI: 1.1–4.3 for ≤6 weeks versus 12–24 weeks; p = 0.025) and protective effect of breastfeeding on ART against formula feeding (aOR = 0.4, 95% CI: 0.2, 0.7; p = 0.005). Conclusion This study demonstrates the effectiveness of PMTCT interventions in Senegal but indicates also that increased efforts should be continued to reduce the MTCT rate to less than 2%.

BackgroundRecent advances in molecular diagnostics, especially the Xpert MTB/Rif test, have reduced the time to diagnose rifampicin resistant tuberculosis (RR-TB). However, with this test only rifampicin resistance is diagnosed, leading to presumptive diagnosis of resistance to isoniazid and maybe other drugs. In addition, culture on monthly sputum samples is currently recommended by the World Health Organization (WHO) for follow-up of RR-TB patients under treatment. Unfortunately, culture is often not locally available, and samples need to be shipped from field to culture laboratories. The associated transport delays lead to high rates of contamination and false-negative culture, particularly in laboratories in low-resource settings. Many gaps for the diagnosis and management of RR-TB patients still need to be addressed and the DIAMA project (Diagnostics for multidrug-resistant tuberculosis in Africa) aims to address some of them.MethodsThe TB Supranational Reference Laboratory of Benin leads a consortium of 11 partners involved in multiple-drug resistant TB care in Africa. The DIAMA project will explore the feasibility and accuracy of: i) diagnosing TB resistance to first and second line drugs through novel molecular multiplex assays developed by the company Genoscreen; ii) setting-up alternative culture-free approaches for the monitoring of patients’ response to rifamipcin-resistant treatment; iii) piloting whether the implementation of software by Data2Care Technologies for real-time monitoring of molecular test results can reduce delays between diagnosis and treatment of RR-TB patients. This project is funded by EDCTP for a period of five years.ConclusionTogether, these advances could dramatically improve the currently dismal prognosis of multiple-drug resistant TB in health systems in resource-poor settings. Through this presentation, we will share the background information, the design of this project and its progress.

BACKGROUND: Drug-resistant tuberculosis (TB) is a global public health problem. Adequate management requires baseline drug-resistance prevalence data. In West Africa, due to a poor laboratory infrastructure and inadequate capacity, such data are scarce. Therefore, the true extent of drug-resistant TB was hitherto undetermined. In 2008, a new research network, the West African Network of Excellence for Tuberculosis, AIDS and Malaria (WANETAM), was founded, comprising nine study sites from eight West African countries (Burkina Faso, The Gambia, Ghana, Guinea-Bissau, Mali, Nigeria, Senegal and Togo). The goal was to establish Good Clinical Laboratory Practice (GCLP) principles and build capacity in standardised smear microscopy and mycobacterial culture across partnering laboratories to generate the first comprehensive West African drug-resistance data. METHODS: Following GCLP and laboratory training sessions, TB isolates were collected at sentinel referral sites between 2009-2013 and tested for first- and second-line drug resistance. RESULTS: From the analysis of 974 isolates, an unexpectedly high prevalence of multi-drug-resistant (MDR) strains was found in new (6 %) and retreatment patients (35 %) across all sentinel sites, with the highest prevalence amongst retreatment patients in Bamako, Mali (59 %) and the two Nigerian sites in Ibadan and Lagos (39 % and 66 %). In Lagos, MDR is already spreading actively amongst 32 % of new patients. Pre-extensively drug-resistant (pre-XDR) isolates are present in all sites, with Ghana showing the highest proportion (35 % of MDR). In Ghana and Togo, pre-XDR isolates are circulating amongst new patients. CONCLUSIONS: West African drug-resistance prevalence poses a previously underestimated, yet serious public health threat, and our estimates obtained differ significantly from previous World Health Organisation (WHO) estimates. Therefore, our data are reshaping current concepts and are essential in informing WHO and public health strategists to implement urgently needed surveillance and control interventions in West Africa.

The objective of this study was to compare the performance of the NucliSENS EasyQ HIV-1 v1.2 platform (bioMérieux, France) to the Amplicor HIV-1 DNA test v1.5 (Roche Molecular Systems, Switzerland) in detecting HIV-1 infection in infants using venipuncture-derived whole blood in tubes and dried blood spots. A total of 149 dried blood spots and 43 EDTA-anticoagulated peripheral blood samples were collected throughout Dakar and other areas in Senegal from infants and children aged 3 weeks to 24 months who were born to HIV-1-infected mothers. Samples were tested using the NucliSENS and Amplicor technologies. The NucliSENS and Amplicor results were 100% concordant using either EDTA-anticoagulated peripheral blood or dried blood spots. Compared to Amplicor, the sensitivity and specificity of the NucliSENS test were 100%. The NucliSENS EasyQ HIV-1 RNA assay performed as well as the Amplicor HIV-1 DNA test in detecting HIV-1 infection in infants. In addition, this platform can give an indication of the viral load baseline. The NucliSENS EasyQ platform is a good alternative for early infant diagnosis of HIV-1 infection.

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.

A total of 343 HIV-1-positive samples obtained between June 1996 and March 1999 was genetically characterized in the envelope region by HMA and/or sequencing. The env subtype distribution was as follows: 290 (84.6%) A, 22 (6.5%) B, 16 (4.7%) C, 8 (2.5%) D, 1 (0.03%) E, 1 (0.03%) F1, 4 (1.2%) G, and 1 (0.03%) H. For 77 samples the p24 region from the gag gene was also sequenced, and for 9 (11.6%) the subtypes between env and gag were different. Phylogenetic tree analysis showed the predominance of AG-IBNG-like viruses among gag and env subtype A sequences. HMA is relatively simple and requires less sophisticated technical facilities compared with sequencing, and in Senegal 323 (94.2%) of the 343 samples could be identified by this technique. However, in the actual configuration of the assay, discrimination between the recombinant AG-IBNG-like recombinant viruses, which are predominant in Senegal, and the nonrecombinant subtype A viruses is not possible.