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Background: Despite an increase in health research conducted in Africa, there are still inadequate human resources with research ethics training and lack of local long-term training opportunities in research ethics. A research ethics training program named United States-Mali Research Ethics Training Program (US-Mali RETP) was established through a partnership between the George Washington University Milken Institute School of Public Health (GWSPH), USA and University of Sciences, Techniques & Technologies of Bamako (USTTB), to address the critical need for improved bioethics training, leadership, and policy in Mali. Methods: The aims of the capacity building programme are achieved by leveraging US and Africa-based expertise to strengthen research ethics education and capacity through: (1) intensive faculty development to design ethics training curricula; (2) development of a research ethics specialization within the existing Masters of Public Health program (MPH); and (3) establishing professional development courses through short-term training workshops and webinars to address research and professional needs in ethics. Results: The program will strengthen USTTB’s capacity of research ethics by training at least 15 MPH students over 5 years to prepare the next generation of ethics researchers. During the first two years of the program, a new ethics training curricula was developed, two cohorts of Master’s students were enrolled, and a series of webinars and workshops were conducted with participation of Malian and international researchers. Conclusions: US-Mali RETP will promote a sustainable bioethics enterprise at USTTB, and enable dissemination of research ethics training to increase health research capacity in Mali.

It is now recognized that to fully understand the role of host genetic variation on susceptibility to HIV-1 infection, investigations must be extended to African populations. We sought to determine...

Tuberculosis (TB) remains an important global health issue worldwide. Despite this scourge threatening many human lives, especially in developing countries, thus far, no advanced molecular epidemiology study using recent and more accurate tools has been conducted in Mali. Therefore, this study aimed to use variable-number tandem repeats of mycobacterial interspersed repetitive units (MIRU-VNTR) technology coupled with the spoligotyping method to accurately determine the hot spots and establish the epidemiological transmission links of TB in Bamako, Mali.In a cross-sectional study, 245 isolates of Mycobacterium tuberculosis complex (MTBC) were characterized using spoligotyping and MIRU-VNTR, and an epidemiological investigation was conducted.Of the 245 isolates, 184 (75.1%) were formally identified. The most widespread strain was the Cameroon strain (83; 45.1%). Eight major clusters were identified: Ghana (27; 14.7%), West African 2 (22; 12%), Haarlem (13; 7.1%), H37Rv (t) (8; 4.3%), Latin American Mediterranean (8; 4.3%), and Uganda I and II (6; 3.3%). Statistical analysis showed a significant difference between lineages from the respective referral health centers of Bamako, Mali (P = 0.01).This study establishes, for the first time, an accurate spatial distribution of circulating MTB strains in Bamako, Mali. The data was used to identify strains and "hot spots" causing TB infection and can also be used for more targeted public health responses, particularly for hot spots of drug-resistant strains.

The 2014-2016 Ebola epidemic in Guinea highlighted the need for more extensive evaluation of laboratories diagnostic capacities and preparedness in anticipation of future emerging viral disease outbreaks. We developed a questionnaire to assess the diagnostic capacities and preparedness of the four major medical laboratories in Guinea and Mali that are responsible for the provision of Ebola, Lassa, and Dengue diagnostics. The questionnaire inquired about the current state and need for equipment and reagents and adequacy of equipment and training received. In Guinea, all three diagnostic laboratories have the capacity and are well-prepared to perform Ebola diagnostics, however, only two have the capacity and trained staff to diagnose Lassa and none are currently prepared to diagnose Dengue infection. In Mali, the University Clinical Research Center (UCRC) laboratory, which was in charge of Ebola diagnostics during the last epidemic, currently has the capacity and is prepared to diagnose Ebola, Lassa, and Dengue infections. Combined, Guinea and Mali appear to have complementary capacity and preparedness to diagnose these Category A Priority Pathogens. While, the equipment, reagents and training efforts should be maintained, the gap in Dengue diagnostic capability in Guinea should be addressed with further equipping and training of additional district laboratories to strengthen the public health response for all viral diseases in these high-risk, yet, low-resource settings.

Mycobacterium africanum (MAF) is known to endemically cause up to 40-50% of all pulmonary TB in West Africa. The aim of this study was to compare MAF with Mycobacterium tuberculosis (MTB) with regard to time from symptom onset to TB diagnosis, and clinical and radiological characteristics. A cross-sectional study was conducted in Bamako, Mali, between August 2014 and July 2016. Seventy-seven newly diagnosed pulmonary TB patients who were naive to treatment were enrolled at Mali's University Clinical Research Center. Sputum cultures were performed to confirm the diagnosis and spoligotyping to identify the mycobacterial strain. Univariate and multivariate analyses were used to identify factors associated with disease progression. Overall, the frequency of female patients was 25% in MAF infection and only 10.0% in MTB infection (OR = 2.9), and MAF was more represented in patients aged ≥ 30 years (57.1% versus 36.7% [OR = 2.3]). More MAF- than MTB-infected patients had a history of a prior TB contact (32.1% versus 14.3% [OR = 2.8]). The mean duration between cough onset and TB diagnosis was 111 days (∼3.7 months) for MAF and 72 days (∼2.4 months) for MTB (P = 0.007). In a multivariate regression, weight loss (body mass index [BMI] 4 months) were strongly associated with MAF infection (OR = 5.20 [1.49-18.26], P = 0.010, and 4.74 [1.2-18.58], P = 0.02), respectively. Our data show that MAF infection was significantly associated with lower BMI and a longer time between symptom onset and TB diagnosis than MTB. This supports the concept that MAF infection may have slower disease progression and less severe cough symptoms than MTB.

Background: MDR-TB is a major threat to global TB control. In 2015, 580,000 were treated for MDR-TB worldwide. The worldwide roll-out of GeneXpert MTB/RIF® has improved diagnosis of MDR-TB; however, in many countries laboratories are unable to assess drug resistance and clinical predictors of MDR-TB could help target suspected patients. In this study, we aimed to determine the clinical factors associated with MDR-TB in Bamako, Mali. Methods: We performed a cross-sectional study of 214 patients with presumed MDR-TB admitted to University of Bamako Teaching Hospital, Point-G between 2007 and 2016. We calculated crude and adjusted odds ratios for MDR-TB disease diagnosis using SPSS. Results: We found that age ≤40 years (OR = 2.56. 95% CI: 1.44–4.55), two courses of prior TB treatment (OR = 3.25, 95% CI: 1.44–7.30), TB treatment failure (OR = 3.82, 95% CI 1.82–7.79), sputum microscopy with 3+ bacilli load (OR = 1.98, 95% CI: 1.13–3.48) and a history of contact with a TB patient (OR = 2.48, 95% CI: 1.11–5.50) were significantly associated with confirmation of MDR-TB disease. HIV was not a risk factor for MDR-TB (aOR = 0.88, 95% CI: 0.34–1.94). Conclusion: We identified several risk factors that could be used to identify MDR-TB suspects and prioritize them for laboratory confirmation. Prospective studies are needed to understand factors associated with TB incidence and clinical outcomes of TB treatment and disease. Keywords: Multi-Drug Resistant Tuberculosis, Risk factors, Mali

Background: Routine monitoring of HIV-1 Viral Load (VL) is important in patients on Antiretroviral Therapy (ART) management. Access to HIV VL remains a challenge in resource-limited settings, especially in rural areas. Universal access to VL requires more simplified and less restrictive alternatives to current conventional VL methods. The objective of this study was to evaluate the performance of the new rapid (2-hour turnaround time) Xpert HIV-1VL technique compared to Roche TaqMan and Abbott RT m2000 for HIV-1 RNA quantification in HIV- infected patients. Study design: We conducted a cross-sectional study in patients seen for routine VL monitoring between August and November 2018 in a HIV care site in Bamako. The performance of the Xpert HIV-1 VL assay was evaluated against the Roche TaqMan assay and Abbott m2000 RT assay. Performance, utility and reliability/reproducibility were verified using accuracy, sensitivity, specificity, positive and negative predictive values, Diagnostic Odds Ratio (DOR), Kappa coefficient, Pearson correlation coefficient, and Bland-Altman analysis. Results: The Xpert assay compared well with the two current referral assays (Roche TaqMan and Abbott m2000 RT assays). Compared to Roche TaqMan assay the sensitivity was 93.10%, specificity (97.01%) and accuracy (95.20%), the correlation coefficient of Pearson (r) was 0.98 (p

Introduction:the region of Segou recorded 36.8% of children were incompletely vaccinated in 2018. In 2019, the district of Segou was one of the districts with the lowest vaccination coverage in the region, with 85.1% coverage for the three doses of the pentavalent vaccine and 85.4% for the measles vaccine. This study was initiated to better understand this low vaccination coverage, in the absence of specific studies on vaccination coverage in the district of Segou. Methods:a prospective cross-sectional study was conducted from May to August 2020 with 30 clusters. We performed Kappa coefficient, bivariate, and multiple logistic regression analysis. Results:findings showed that 18.46% (101/547) [15.44-21.93] of children were incompletely vaccinated. Mothers correctly reported the vaccination status of their children in 67.30% of cases (Kappa coefficient). Uneducated (OR[IC95%]=2.13[1.30-3.50]), living in rural area (OR[IC95%]=2.07[1.23-3.47]), lack of knowledge of Expanded Program on Immunization (EPI) target diseases (OR[IC95%]=2.37[1.52-3.68]), lack of knowledge of vaccination schedule (OR[IC95%]=3.33[1.90-5.81]) and lack of knowledge of the importance of vaccination (OR[IC95%]=3.6[2.35-6.32]) were associated with incomplete vaccination. In multivariate analysis, uneducated (ORa[IC95%>]=1.68[1.004-2.810]) and lack of knowledge of the importance of vaccination were associated with incomplete vaccination (ORa[IC95%]=3.40[2.049-5.649]). Conclusion:findings showed a good concordance of the vaccination status. Living in a rural area, no education, lack of the knowledge of EPI target diseases, lack of the knowledge of vaccination schedule and lack of knowledge of the importance of vaccination were associated with incomplete vaccination.

It is now recognized that to fully understand the role of host genetic variation on susceptibility to HIV-1 infection, investigations must be extended to African populations. We sought to determine if genetic variation in IL10 are associated with HIV-1 infection in a West African cohort in Mali. HIV-infected and -uninfected individuals were genotyped for three common single nucleotide polymorphisms (SNPs) located at positions −592 (C/A), −819 (C/T), and −1082 (G/A) of the IL10 promoter. We found that the ATA haplotype, which has been previously associated with low IL-10 expression, was the most represented in the cohort. Although we observed a trend toward an increased frequency of ATA/ATA carriage in HIV-infected compared with -uninfected individuals, the difference was not statistically significant. Similarly, individual IL10 SNPs were not significantly enriched in the HIV-infected group, suggesting that IL10 genetic variants are not associated with HIV-1 in this West African cohort from Mali.

BACKGROUND: Non-conversion on auramine smear microscopy indicates a lack of treatment response, possibly associated with initial rifampicin-resistant tuberculosis (RR-TB). However, dead bacteria still stain positive and may be detected. Fluorescein diacetate smear microscopy (FDA) shows live mycobacteria only. Therefore, we studied the potential of 2-month (2M) FDA for the identification of initial RR-TB.METHODS: Between 2015 and 2018, we enrolled new smear-positive pulmonary TB patients from five local centres in Bamako, Mali. After baseline screening, sputum samples were collected at 1M, 2M, 5M and 18M. We used rpoB sequencing to identify initial RR-TB.RESULTS: Of 1359 patients enrolled, 1019 (75%) had rpoB sequencing results. Twenty-six (2.6%, 95%CI: 1.7–3.7) had mutations conferring rifampicin resistance. Most frequent rpoB mutations were located at the codons Asp435Val (42.4%) and Ser450Leu (34.7%). Among patients with initial RR-TB, 72.2% were FDA-negative at 2M (P = 0.2). The positive and negative predictive value of 5M FDA for culture-based failure was respectively 20.0% and 94.7%.CONCLUSION: FDA did not identify the majority of patients with initial RR-TB or culture-based failure. As the full spectrum of mutations identified on sequencing was identified using Xpert, our data support its rapid universal implementation in Mali.

Tuberculosis (TB) is caused by Mycobacterium tuberculosis complex (MTBC), however, the distribution and frequency of MTBC lineages and sublineages vary in different parts of the globe. Mycobacterium africanum, a member of MTBC is responsible for a large percentage of TB cases in West Africa, however, it is rarely identified outside of this part of the World. Whether or not differential HLA polymorphism (an important host factor) is contributing to the geographic restriction of M. africanum to West Africa is unknown. Here, we conducted a cohort study in Mali of newly diagnosed individuals with active pulmonary TB and normal healthy controls. The MTBC isolates were spoligotyped to determine the TB study groups (M. tuberculosis sensu stricto LAM10 and M. africanum), and HLA typing was performed on peripheral blood. Unlike previous reports on other populations, we found that HLA class-I alleles were significantly associated with active TB disease in this population. HLA-B alleles (B*07:02, B*08:01, B*14:02, B*15:03, B*15:10, B*18:01, B*42:01, B*42:02, B*51:01 and B*81:01) were significantly associated with M. africanum (40%-45%) and M. tuberculosis (75%) compared with healthy controls. Many HLA-A alleles (A*02:05, A*34:02, A*66:01 and A*68:02) were also associated with both TB groups (65%-70%). However, many class II HLA-DR variants were found to be associated with M. tuberculosis but not M. africanum with the exception of the DRB1*03:01, which was associated with both groups. The differential HLA distribution observed in this study might be at least partially responsible for the geographical restriction of M. africanum infections to West Africa.

Background: While, bacteria resistance mutations can affect competitive fitness, given our multidrug-resistant (MDR) prevalence, we conducted this study to determine the impact of MDR on the competitive fitness of Mycobacterium tuberculosis (MTB) complex MDR strains. We conducted a cross-sectional study at the University Clinical Research Center (UCRC) from January to December 2017. New TB patients over aged of 18 were recruited at University teaching hospital and health reference centers of Bamako in USTTB Ethical committee approved protocols. Methods: MDR and drug-susceptible (wild-type [WT]) MTB strains (T1 and Beijing) and MTB H37Rv were competed on solid media in UCRC's Tuberculosis Laboratory. Competitive and individual cultures were incubated for 14 days at 37°C with 7% CO2. Number of generation, generation time, and relative competitive fitness (W) of the strains were calculated. Data were analyzed with Epi-Info 7.1.5.2 software (CDC). P value was considered significant when it was

Resume Position du probleme Le depistage neonatal de la drepanocytose s’impose en Afrique ou la maladie est plus frequente. L’electrophorese de l’hemoglobine permet ce depistage, mais son usage est limite par un cout eleve et des difficultes d’acces. Le test d’Emmel, plus abordable et techniquement plus accessible est souvent demande dans le bilan prenatal des gestantes en Afrique, pour reserver le depistage aux nouveau-nes issus de meres chez qui le test positif atteste la presence d’hemoglobine S. Cette etude se propose d’evaluer le nombre de naissances drepanocytaires non reperees dans le cadre d’une politique de depistage ciblant les seules naissances issues de meres chez qui le test d’Emmel serait positif. Methodes De 2010 a 2012, a Bamako, Mali, 2489 nouveau-nes ont fait l’objet d’un depistage systematique de la drepanocytose, au niveau du cordon ombilical ou du talon, par isoelectrofocalisation, completee au besoin par une chromatographie liquide haute performance. Ces nouveau-nes etaient issus de 2420 meres dont l’hemoglobinique a ete etudiee par isoelectrofocalisation. Les donnees ont ete enregistrees et traitees a l’aide du logiciel Excel dans sa version 14.0.0. Nous avons calcule la frequence du gene drepanocytaire chez les populations des meres et des nouveau-nes depistes ainsi que le nombre de nouveau-nes drepanocytaires nes de meres heterozygotes ou homozygotes C. Resultats Parmi les 2489 nouveau-nes, 16 etaient drepanocytaires majeurs dont 6 SS et 10 SC ; 198 avaient le trait drepanocytaire ; 139 etaient AC et 1 etait CC. Parmi les 10 drepanocytaires majeurs SC, 3 etaient nes de meres n’ayant pas le drepanocytaire S, mais porteuses du gene C de l’hemoglobine et chez lesquelles, un test d’Emmel aurait ete negatif. Conclusion Un depistage neonatal cible, base sur les resultats du test d’Emmel chez les femmes enceintes, meconnaitrait plus d’un drepanocytaire majeur sur six qui serait ainsi prive d’une prise en charge adaptee precoce. Des etudes de rapport cout/efficacite d’un depistage neonatal systematique de la drepanocytose doivent conduire a une meilleure strategie de depistage a adopter dans les contextes ou la mutation S coexiste avec d’autres mutants hemoglobiniques.

Resume Introduction La retinopathie est une complication chronique a risque fonctionnel important chez le drepanocytaire, dont l’incidence est mal connue en Afrique subsaharienne, faute de depistage. Ce travail decrit les resultats d’un depistage systematique de la retinopathie drepanocytaire dans un centre de suivi des drepanocytaires au Mali. Methodes Tous les drepanocytaires âges de 10 ans et plus, suivis au centre, ont ete depistes entre 2010 et 2012 par un examen du fond d’œil complete si besoin par une angiographie. Les caracteristiques des patients porteurs d’une retinopathie ont ete comparees a celles de drepanocytaires sans retinopathie recrutes durant la meme periode et selectionnes au hasard. Resultats La retinopathie avait une prevalence globale de 8,8 % chez les 1604 drepanocytaires âges de 10 ans et plus et concernait 91/731 (12,4 %) drepanocytaires SC, 38/734 (5,2 %) SS, 5/53 (9,4 %) Sβ 0 thalassemiques et 8/86 (9,3 %) Sβ + thalassemiques. La forme proliferante de la retinopathie etait plus frequente chez les SC ( p 0 thalassemiques. Conclusion La retinopathie touche pres d’un patient drepanocytaire sur dix et sa prevalence est negativement associee au taux d’hemoglobine fœtale. L’efficience d’un depistage systematique de la retinopathie drepanocytaire doit etre etudiee en Afrique, ainsi que l’interet de la phlebotomie et de l’hydroxycarbamide en traitement preventif.

Mycobacterium africanum (MAF) is known to endemically cause up to 40–50% of all pulmonary TB in West Africa. The aim of this study was to compare MAF with Mycobacterium tuberculosis (MTB) with regard to time from symptom onset to TB diagnosis, and clinical and radiological characteristics. A cross-sectional study was conducted in Bamako, Mali, between August 2014 and July 2016. Seventy-seven newly diagnosed pulmonary TB patients who were naive to treatment were enrolled at Mali’s University Clinical Research Center. Sputum cultures were performed to confirm the diagnosis and spoligotyping to identify the mycobacterial strain. Univariate and multivariate analyses were used to identify factors associated with disease progression. Overall, the frequency of female patients was 25% in MAF infection and only 10.0% in MTB infection (OR = 2.9), and MAF was more represented in patients aged ≥ 30 years (57.1% versus 36.7% [OR = 2.3]). More MAF- than MTB-infected patients had a history of a prior TB contact (32.1% versus 14.3% [OR = 2.8]). The mean duration between cough onset and TB diagnosis was 111 days (∼3.7 months) for MAF and 72 days (∼2.4 months) for MTB (P = 0.007). In a multivariate regression, weight loss (body mass index [BMI] < 18.5 kg/m2) and cough duration (> 4 months) were strongly associated with MAF infection (OR = 5.20 [1.49–18.26], P = 0.010, and 4.74 [1.2–18.58], P = 0.02), respectively. Our data show that MAF infection was significantly associated with lower BMI and a longer time between symptom onset and TB diagnosis than MTB. This supports the concept that MAF infection may have slower disease progression and less severe cough symptoms than MTB.

Sputum smear microscopy (SSM), the most widely available tool for tuberculosis (TB) detection, has limited performance in paucibacillary patients and requires highly experienced technicians. The objective of this study was to determine whether the addition of sodium dodecyl sulfate (SDS), a detergent that thins sputum, at 4% and 10%, improves the detection of acid-fast bacilli (AFB), the clarity of slides, and the biosafety of the technique. Thirty participants with presumptive TB were enrolled. Three independent, blinded technicians examined the slides. Regular sputum concentrated AFB smear and sputum culture were used as standard control methods. Sputum culture was also performed before and after 10% SDS addition for safety analysis. We found that neither SSM with SDS 4% nor SSM with SDS 10% improved the test's performance. However, slides with 4% and 10% SDS, compared with slides prepared without SDS, had significantly better clarity scores. The 10% SDS-prepared sputum samples were all culture negative. While adding SDS detergent does not improve the performance of SSM slides, it does improve the clarity and biosafety. Where experienced technicians are scarce, especially in low resource settings, use of SDS may enhance the ease of slide reading in sputum smear microscopy.

As part of the scientific community's development of medical countermeasures against Ebola virus disease, optimization of standardized assays for product evaluation is paramount. The recent outbreak heightened awareness to the scarcity of available assays and limited information on performance and reproducibility. To evaluate the immunogenicity of vaccines entering Phase I-III trials and to identify survivors, two enzyme-linked immunosorbent assays, the Filovirus Animal Non-Clinical Group assay and the Alpha Diagnostics International assay, were evaluated for detection of immunoglobulin G against Ebola virus glycoprotein. We found that the Filovirus Animal Nonclinical Group assay produced a wider range of relative antibody concentrations, higher assay precision, larger relative accuracy range, and lower regional background. Additionally, to sufficiently power a vaccine trial, use of the Filovirus Animal Nonclinical Group assay would require one third the number of participants than the Alpha Diagnostics International assay. This reduction in needed study participants will require less money, fewer man hours, and much less time to evaluate vaccine immunogenicity.

To identify strains of Mycobacterium tuberculosis complex (MTBc) circulating in Bamako region during the past 10 years.From 2006 to 2016, we conducted a cross-sectional study to identify with spoligotyping, clinical isolates from tuberculosis (TB)-infected patients at different stages of their treatments in Bamako, Mali.Among the 904 suspected TB patients included in the study and thereafter tested in our BSL-3 laboratory, 492 (54.4%) had MTBc and therefore underwent spoligotyping. Overall, three subspecies, i.e., MTB T1 (31.9%) and MTB LAM10 (15.3%) from lineage 4 and M. africanum 2 (16.8%) from lineage 6 were the leading causes of TB in Bamako region during the past 10 years. Other spoligotypes such as MTB T3, MTB Haarlem 2, MTB EAI3, and MTB family 33 were also commonly seen from 2010 to 2016.This study showed a high genetic diversity of strains isolated in Bamako region and highlights that M. tuberculosis T1 strain was the most prevalent. Furthermore, the data indicate an increasing proportion of primary drug resistance overtime in Bamako.

Introduction: Diabetes Mellitus (DM) increases worldwide, mostly in low- and middle-income countries. In Mali, the prevalence in the adult population is estimated at 1.8%, but tuberculosis (TB) patients are not systematically screened. The goal of our study was to determine the prevalence of DM among newly diagnosed TB patients. Methods: We conducted a cross sectional study and a pilot prospective cohort study in four health centers in Bamako. All patients underwent fasting capillary-blood glucose (FCBG) test at Day 0, and repeated after one-week of TB treatment. Venous FBG test was performed for discrepancies between the two FCBG results. Thereafter, FCBG was performed for pilot study at month-2 (M2) and M5 of TB treatment. Results: Two hundred and one patients were enrolled in this study. Impaired fasting blood glucose was identified in 17 (8.5%), of whom 11 (5.5%) had DM (VFBG >7 mmol/L). Among patients with DM, seven (63.6%) had successful TB treatment outcome, versus 142 (74.7%) of those without DM (p = 0.64), and (OR: 1.69, 95%CI 0.47–6.02). Conclusion: The prevalence of DM among TB patients in Bamako exceeds that of the general population and screening at TB diagnosis suffices to identify those with DM. Systematic screening of both diseases will allow better treatment. Keywords: Diabetes Mellitus, Tuberculosis, Prevalence, Bamako, Mali

IntroductionXpert MTB/RIF assay is used extensively for the detection of rifampicin-resistant TB (RR-TB). RR-TB treatment monitoring is culture-based, although, in resource-limited settings, access to TB culture is poor. Alternative methods are needed. We therefore conducted a pilot study to determine the performance of fluorescein di-acetate FDA vital staining, a microscopy-based test that shows viable bacilli, and Xpert threshold cycle value (Ct) changes when assessing culture conversion at the end of the intensive phase of RR-TB treatment.MethodsBetween December 2015 and April 2018, we prospectively followed patients with RR-TB during the 6-month intensive phase of a 21-month standardised WHO treatment regimen. Sputum was collected and tested monthly with Auramine, FDA, Xpert MTB/RIF, and culture (Manual MGIT). Culture was considered to have converted to negative when two consecutive cultures, taken at least 30 days apart, were negative, including at least one culture between 4–6 months of treatment.ResultsForty-one patients were included in this study, 80% were male and 7% were HIV-co-infected. Conversion could not be assessed in 12 (29%) patients. Among the remaining 29 patients, 9 (31%) converted, and 11 (38%) did not convert. All 9 who converted on culture had a negative FDA, and most (6) had a Ct trend that showed a reduction of excreted DNA (increasing Ct trend). Three of these were still positive on Auramine (excretion of dead bacilli?). Of 11 patients with positive cultures, 8 tested negative on FDA, 5 tested ‘MTB not detected’ on Xpert MTB/RIF, and another 2 showed a reduction of excreted DNA.ConclusionResults from culture, FDA, and Xpert MTB/RIF provide similar results among converters but contrasting results among non-converters. Longer follow-up time is needed to assess the value of these tests to predict treatment outcome.

Background Although Drug resistance tuberculosis is not a new phenomenon, Mali remains one of the “blank” countries without systematic data. Methods Between 2006 and 2014, we enrolled pulmonary TB patients from local TB diagnostics centers and a university referral hospital in several observational cohort studies. These consecutive patients had first line drug susceptibility testing (DST) performed on their isolates. A subset of MDR was subsequently tested for second line drug resistance. Results A total of 1186 mycobacterial cultures were performed on samples from 522 patients, including 1105 sputa and 81 blood samples, yielding one or more Mycobacterium tuberculosis complex (Mtbc) positive cultures for 343 patients. Phenotypic DST was performed on 337 (98.3%) unique Mtbc isolates, of which 127 (37.7%) were resistant to at least one drug, including 75 (22.3%) with multidrug resistance (MDR). The overall prevalence of MDR-TB was 3.4% among new patients and 66.3% among retreatment patients. Second line DST was available for 38 (50.7%) of MDR patients and seven (18.4%) had resistance to either fluoroquinolones or second-line injectable drugs. Conclusion The drug resistance levels, including MDR, found in this study are relatively high, likely related to the selected referral population. While worrisome, the numbers remained stable over the study period. These findings prompt a nationwide drug resistance survey, as well as continuous surveillance of all retreatment patients, which will provide more accurate results on countrywide drug resistance rates and ensure that MDR patients access appropriate second line treatment. Electronic supplementary material The online version of this article (doi:10.1186/s12879-016-2060-7) contains supplementary material, which is available to authorized users.

Aware of the rapid spread of Ebola virus (EBOV) during the current West African epidemic, Mali took several proactive steps to rapidly identify cases within its borders. Under the Mali International Center for Excellence in Research program, a collaboration between the National Institute of Allergy and Infectious Diseases and the Malian Ministry of Higher Education and Scientific Research established a national EBOV diagnostic site at the University of Sciences, Techniques and Technologies of Bamako in the SEREFO Laboratory. Two separate introductions of EBOV occurred in Mali from neighboring Guinea, but both chains of transmission were quickly halted, and Mali was declared "Ebola free" on 18 January 2015 and has remained so since. The SEREFO Laboratory was instrumental in the success of Mali's Ebola response by providing timely and accurate diagnostics. As of today, the SEREFO Laboratory has tested 103 samples from 88 suspected cases, 10 of which were EBOV positive, since the Ebola diagnostics unit started in April 2014. The establishment of Ebola diagnostics in the SEREFO Laboratory, safety precautions, and diagnostics are described.

Objectives In Mali early detection and treatment of multidrug-resistant tuberculosis (MDR-TB) are still challenging due to the cost, time and/or complexity associated with regular tests. Microscopic Observation Drug Susceptibility (MODS) is a low-cost assay validated by WHO in 2010. It is a liquid-culture-based assay to detect the ‘cording' characteristic of Mycobacterium tuberculosis complex and to assess susceptibility to both isoniazid and rifampicin defining multidrug-resistant tuberculosis (MDR-TB). In this study we aimed to evaluate the performance of MODS as diagnostic tool compared with a validated method—Mycobacteria Growth Indicator Tube/Antimicrobial Susceptibility Testing/Streptomycin, Isoniazid, Rifampicin and Ethambutol (MGIT/AST/SIRE). Methods and Results Between January 2010 and October 2015 we included 98 patients with suspected TB in an observational cohort study. The sensitivity and specificity of MODS assay for detecting TB were respectively 94.12% and 85.71% compared with the reference MGIT/7H11 culture, with a Cohen κ coefficient of 0.78 (95% CI 0.517–1.043). The median time to culture positivity for MODS assay and MGIT (plus interquartile range, IQR) was respectively 8 days (IQR 5–11) and 6 days (IQR 5–6). In detecting patients with MDR-TB, the sensitivity and specificity of MODS assay were respectively 100% and 95.92%. The positive predictive value and negative predictive value were, respectively, 66.7% and 100%. The median turnaround times for obtaining MDR-TB results using MODS assay and MGIT/AST/SIRE was respectively 9 days and 35 days. Hence, the MODS assay rapidly identifies MDR-TB in Mali compared with the MGIT/AST/SIRE. Conclusion As an easy, simple, fast and affordable method, the MODS assay could significantly improve the management of TB.

Background Bovine tuberculosis (BTB) is a contagious, debilitating human and animal disease caused by Mycobacterium bovis, a member of the Mycobacterium tuberculosis complex. The study objective were to estimate the frequency of BTB, examine genetic diversity of the M. bovis population in cattle from five regions in Mali and to determine whether M. bovis is involved in active tuberculosis (TB) in humans. Samples from suspected lesions on cattle at the slaughterhouses were collected. Mycobacterial smear, culture confirmation, and spoligotyping were used for diagnosis and species identification. Mycobacterium DNA from TB patients was spoligotyped to identify M. bovis. Results In total, 675 cattle have been examined for lesions in the five regions of Mali. Out of 675 cattle, 79 specimens presented lesions and then examined for the presence of M. bovis. Thus, 19 (24.1 %) were identified as M. bovis; eight (10.1 %) were non-tuberculous Mycobacterium (NTM). Nineteen spoligotype patterns were identified among 79 samples with five novel patterns. One case of M. bovis (spoligotype pattern SB0300) was identified among 67 TB patients. Conclusion This study estimates a relatively true proportion of BTB in the regions of Mali and reveals new spoligotype patterns.

OBJECTIVE: To determine whether female genital mutilation (FGM) is a risk factor for intimate partner violence (IPV) and its subtypes (physical sexual and emotional). DESIGN: Population-based cross-sectional study. SETTING: The study used the 2006 Demographic and Health Survey (DHS) conducted in Mali. POPULATION: A total of 7875 women aged 15-49 years who responded to the domestic violence and female circumcision modules in the 2006 administration of the DHS in Mali. METHODS: Multivariable logistic regression was used to compute adjusted odds ratios (aOR) and 95% confidence intervals (CI) to measure risk for IPV. MAIN OUTCOME MEASURES: The outcomes of interest were IPV and its subtypes. RESULTS: Women with FGM were at heightened odds of IPV (aOR 2.71 95% CI 2.17-3.38) and IPV subtypes: physical (aOR 2.85 95% CI 2.22-3.66) sexual (aOR 3.24 95% CI 1.80-5.82) and emotional (aOR 2.28 95% CI 1.68-3.11). The odds of IPV increased with ascending FGM severity (P for trend

The National Centre for Blood Transfusion, Bamako, Mali has collected data that characterizes trend in HIV prevalence over 10 years by gender, age, occupation, marital status and donor category. These data help to describe national HIV prevalence and assist in formulating blood donation policies. Donations from 1993 to 2002 were categorized by donor age (decade), occupation (student, military and other), marital status (single, married and other), gender and donor status (volunteer, occasional and family). Comparisons were made using conservative estimates of donation frequency/donor category. Donations increased by more than 400%. By 1999, increased HIV prevalence in donations from women was consistently present. Donations from the age group of 30-39 years showed an increased prevalence beginning in 2000, which by 2002 was almost 10 times greater than in the low-prevalence (20 years) group (5.9 vs. 0.6%). By 2000, both categories - students and military were less likely to be HIV positive than those from other occupational categories, and donations from married persons were less likely to be HIV positive by 1997. The highest prevalence was observed in the 'occasional' donor category, which increased to14% by 2001; volunteer donation HIV positive peaked at 2.3% in 1999. HIV prevalence in blood donations in Bamako, Mali, demonstrates important trends from 1993 to 2002. The prevalence of14% in donations from occasional donors and significant trends by decade, gender, marital status and occupation argue for increased analysis of the blood donor population to improve blood safety and to understand the demographics of HIV infection in Mali.

Background: The announcement of HIV-positive status is a critical moment of psycho-social destabilization that can induce changes in the behavior of an individual such a beginning or increased tobacco consumption. Objective: The objective was to study the relationship between the HIV positive status announcement and smoking behavior among people living with human immunodeficiency virus (HIV) in Bamako after the discovering their status. Methods: We did a descriptive cross-sectional study over six months from January to June 2012. Data were collected by interviewing HIV infected patients in three health care centers, departments of pulmonary diseases, department of infectious and tropical diseases and the largest HIV clinic in Mali (CESAC of Bamako). All participants have signed an informed consent before the interview. Data were analyzed using Epi-Info version 7.1.5.2 software. Results: A total of 301 HIV-infected people were included, 24% patients were current smokers 6.3% former smokers and 69.7% non-smokers. Smokers were male in majority with 93.2%. After their HIV infection status announcement, 64.9% have increased their tobacco consumption while 10.8% have decreased their consumption. Majority of patients have a good knowledge of the health risks of smoking. Of those who continue to smoke, 83.8% reported that they tried and fail to stop smoking at least one time. The main reason of their cessation was the effect on their health. And the main reason for the failure was the constant thinking of the disease. Conclusion: The announcement of the HIV positivity status must be accompanied by psychosocial support helping to overcome the emotion and stress and a smoking cessation program must be added to HIV screening program.

Characterizing perturbations in the immune response to tuberculosis in HIV can develop insights into the pathogenesis of coinfection. HIV+ TB+ and TB monoinfected (TB+) subjects recruited from clinics in Bamako prior to initiation of TB treatment were evaluated at time-points following initiation of therapy. Flow cytometry assessed CD4+/CD8+ T cell subsets and activation markers CD38/HLA-DR. Antigen specific responses to TB proteins were assessed by intracellular cytokine detection and proliferation. HIV+ TB+ subjects had significantly higher markers of immune activation in the CD4+ and CD8+ T cells compared to TB+ subjects. HIV+ TB+ had lower numbers of TB-specific CD4+ T cells at baseline. Plasma IFNγ levels were similar between HIV+ TB+ and TB+ subjects. No differences were observed in in-vitro proliferative capacity to TB antigens between HIV+ TB+ and TB+ subjects. Subjects with HIV+ TB+ coinfection demonstrate in vivo expansion of TB-specific CD4+ T cells. Immunodeficiency associated with CD4+ T cell depletion may be less significant compared to immunosuppression associated with HIV viremia or untreated TB infection.

Hydroxyurea (HU) is the only drug which has demonstrated efficacy in terms of reduced incidence of VOC and ACS, reduced need for hospitalization and reduced number of blood transfusion in sickle cell disease. African countries are among those with highest rate of both malaria and sickle cell disease. Despite of that the heterozygous form (HbAS) is known to protect against malaria, there is no documented studies on the clinical effect of HU on malaria. 36 patients aged 4 to 60 years old and treated by HU at the sickle cell disease research and control center of Bamako for at least 2 years. The treated group was compared to a matched untreated sickle cell patients group. During the follow-up, malaria incidence and onset to clinical episode of malaria were compared between treated SCD patients and untreated group. Results of the comparison show that there is no increased incidence of malaria in the treated group after 2 years follow-up (P=0.9). However, a reduction on the time to first malaria episode within the sickle cell population treated with HU was observed (P=0002).Based on this observed reduced time to first malaria episode in HU treated SCD patients, the use of HU in malaria endemic areas needs to be revaluated. It is howether clear that a more comprehensive approach would hopefully reduce the morbidity due to HU use for SCD affected children. Disclosures No relevant conflicts of interest to declare.

Objective To identify strains of Mycobacterium tuberculosis complex (MTC) circulating in Bamako and to examine the relationship between the strains and their drug susceptibility profiles. Methods Between 2006 and 2010, we conducted a cross-sectional study using spoligotyping to identify strains of MTC recovered from 126 tuberculosis (TB) patients under treatment in Bamako, Mali. Result Three members of the MTC were isolated: M. tuberculosis (71.4%), M. africanum (27.8%) and M. bovis (0.8%). Of these, three strains were found to be the most prevalent: M. tuberculosis T1 (MTB T1; 38.9%), M. africanum F2 (MAF2; 26.2%) and M. tuberculosis Latin American and Mediterranean 10 (MTB LAM 10; 10.3%). MAF2 and MTB LAM 10 strains have a lower risk of multidrug resistance (MDR) than MTB T1 (respectively OR 0.1, 95%CI 0.03-0.4 and OR 0.1, 95%CI 0.01-0.8). Age ≥ 32 years (OR 1.4, 95%CI 0.4-3.9), negative human immunodeficiency virus status (OR 0.4, 95%CI 0.1-2.5) and male sex (OR 4, 95%CI 0.9-16.5) were not associated with MDR. The prevalence of MDR among treatment and retreatment failure patients was respectively 25% and 81.8% compared to new patients (2.9%). Conclusion This study indicates a low level of primary drug resistance in Bamako, affirms the importance of using correct drug regimens, and suggests that the MTB T1 strain may be associated with the development of resistance.

The objectives of this cross-sectional study were to assess the prevalence and identify predictors of HIV-1 and HIV-2 infection among students in three cities of Mali. Between January and June 2005, we assessed HIV knowledge, attitudes, associated sexual behaviors and tested HIV serostatus among 950 high school and university students in Sikasso, Bamako, and Koulikoro cities, using a combination of enzyme-linked immunosorbent assay (ELISA) and Western blot testing. Univariate and logistic regression analyses were used to determine predictors of infection among students. Mean HIV prevalence was 3.1%, ranging from 1.8% in Sikasso to 3.6% in Bamako. The results showed the presence of all three HIV subtypes in Bamako, though HIV-1 predominated in all cities. Infection rates were slightly higher among males (3.6%) than among females (2.8%), but the difference was not significant. The single significant predictor of HIV infection was knowledge of HIV routes of transmission (p=0.01). HIV prevalence rates observed in this population were higher than general adult prevalence rates previously reported for Mali. HIV/AIDS education and prevention campaigns should be targeted to students at both the secondary and university levels. Students may represent an informative HIV sentinel population for Mali.

Objectives. A cross-sectional study was conducted to assess the prevalence of human immunodeficiency virus (HIV), hepatitis B virus (HBV), and their coinfection among blood donors at the National Blood Transfusion Center in Bamako, Mali, from November 2001 to July 2002. Methods. Enzyme-linked immunosorbent assay techniques with reagents from Bio-Rad (France) were used to test the blood samples. Results. 11 592 blood donors were tested for HIV and HBV surface antigens. The prevalence of HIV was 4.5% and the prevalence of HBV was 14.9%. The HIV/HBV coinfection rate was only 1.13% in this population. Conclusion. The coinfection rate was unexpectedly low in this blood donor population where monoinfection with HIV or HBV prevalence was high.