Sounkalo Dao

Confirmation of immunogenic consensus sequence HIV-1 T-cell epitopes in Bamako, Mali and Providence, Rhode Island.

The design of epitope-driven vaccines for HIV has been significantly hampered by concerns about conservation of vaccine epitopes across clades of HIV. In previous work, we have described a computer-driven method for a cross-clade HIV vaccine comprised of overlapping, highly conserved helper T-cell epitopes or “immunogenic consensus sequence epitopes” (ICS epitopes). Here, we evaluated and compared the immunogenicity of 20 ICS HIV epitopes in ELISpot assays performed using peripheral blood monocytes (PBMC) from HIV-infected donors in Providence, Rhode Island, USA and in Bamako, Mali, West Africa. Each core 9-mer HIV sequence contained in a given consensus peptide was conserved in at least 105 to as many as 2,250 individual HIV-1 strains. Nineteen of the 20 ICS epitopes (95%) were confirmed in ELISpot assays using PBMC obtained from 13 healthy, HIV-1 infected subjects in Providence, and thirteen of the epitopes (65%) were confirmed in ELISpot assays using PBMC derived from 42 discarded blood units obtained at the Central Blood Bank in Bamako. Twelve of the epitopes were confirmed in ELISpot assays performed both in Providence and Bamako. These data confirm the utility of bioinformatics tools to select and design novel vaccines containing “immunogenic consensus sequence” T-cell epitopes for a globally relevant vaccine against HIV; a similar approach may also be useful for any pathogen that exhibits high variability (influenza, HCV, or variola for example). An HIV vaccine containing these immunogenic consensus sequences is currently under development.

Polymorphisms of HIV-2 integrase and selection of resistance to raltegravir.

BackgroundHuman Immunodeficiency Virus type 2 is naturally resistant to some antiretroviral drugs, restricting therapeutic options for patients infected with HIV-2. Regimens including integrase inhibitors (INI) seem to be effective, but little data on HIV-2 integrase (IN) polymorphisms and resistance pathways are available.Materials and methodsThe integrase coding sequence from 45 HIV-2-infected, INI-naïve, patients was sequenced and aligned against the ROD (group A) or EHO (group B) reference strains and polymorphic or conserved positions were analyzed.To select for raltegravir (RAL)-resistant variants in vitro, the ROD strain was cultured under increasing sub-optimal RAL concentrations for successive rounds. The phenotype of the selected variants was assessed using an MTT assay.ResultsWe describe integrase gene polymorphisms in HIV-2 clinical isolates from 45 patients. Sixty-seven percent of the integrase residues were conserved. The HHCC Zinc coordination motif, the catalytic triad DDE motif, and AA involved in IN-DNA binding and correct positioning were highly conserved and unchanged with respect to HIV-1 whereas the connecting residues of the N-terminal domain, the dimer interface and C-terminal LEDGF binding domain were highly conserved but differed from HIV-1. The N155 H INI resistance-associated mutation (RAM) was detected in the virus population from one ARV-treated, INI-naïve patient, and the 72I and 201I polymorphisms were detected in samples from 36 and 38 patients respectively. No other known INI RAM was detected.Under RAL selective pressure in vitro, a ROD variant carrying the Q91R+I175M mutations was selected. The Q91R and I175M mutations emerged simultaneously and conferred phenotypic resistance (13-fold increase in IC50). The Q91R+I175M combination was absent from all clinical isolates. Three-dimensional modeling indicated that residue 91 lies on the enzyme surface, at the entry of a pocket containing the DDE catalytic triad and that adding a positive charge (Gln to Arg) might compromise IN-RAL affinity.ConclusionsHIV-2 polymorphisms from 45 INI-naïve patients are described. Conserved regions as well as frequencies of HIV-2 IN polymorphisms were comparable to HIV-1. Two new mutations (Q91R and I175M) that conferred high resistance to RAL were selected in vitro, which might affect therapeutic outcome.

Effect of Seasonality and Ecological Factors on the Prevalence of the Four Malaria Parasite Species in Northern Mali

Background. We performed 2 cross-sectional studies in Ménaka in the Northeastern Mali across 9 sites in different ecological settings: 4 sites have permanent ponds, 4 without ponds, and one (City of Ménaka) has a semipermanent pond. We enrolled 1328 subjects in May 2004 (hot dry season) and 1422 in February 2005 (cold dry season) after the rainy season. Objective. To examine the seasonality of malaria parasite prevalence in this dry northern part of Mali at the edge of the Sahara desert. Results. Slide prevalence was lower in hot dry than cold dry season (4.94 versus 6.85%, P = 0.025). Gametocyte rate increased to 0.91% in February. Four species were identified. Plasmodium falciparum was most prevalent (74.13 and 63.72%). P. malariae increased from 9.38% to 22.54% in February. In contrast, prevalence of P. vivax was higher (10.31%) without seasonal variation. Smear positivity was associated with splenomegaly (P = 0.007). Malaria remained stable in the villages with ponds (P = 0.221); in contrast, prevalence varied between the 2 seasons in the villages without ponds (P = 0.004). Conclusion. Malaria was mesoendemic; 4 species circulates with a seasonal fluctuation for Plasmodium falciparum.

Identification and Characterization of CRF02_AG, CRF06_cpx, and CRF09_cpx Recombinant Subtypes in Mali, West Africa

Abstract Multiple HIV-1 subtypes and circulating recombinant forms (CRFs) are known to cocirculate in Africa. In West Africa, the high prevalence of CRF02_AG, and cocirculation of subtype A, CRF01_AE, CRF06_cpx, and other complex intersubtype recombinants has been well documented. Mali, situated in the heart of West Africa, is likely to be affected by the spread of recombinant subtypes. However, the dynamics of the spread of HIV-1 recombinant subtypes as well as nonrecombinant HIV-1 group M subtypes in this area have not been systematically assessed. Herein, we undertook genetic analyses on full-length env sequences derived from HIV-1-infected individuals living in the capital city of Mali, Bamako. Of 23 samples we examined, 16 were classified as CRF02_AG and three had a subsubtype A3. Among the remaining HIV-1 strains, CRF06_cpx and CRF09_cpx were each found in two patients. Comparison of phylogenies for six matched pol and full-length env sequences revealed that two strains had discordant subtype/CRF designations between the pol and env regions: one had A3(pol)CRF02_AG(env) and the other had CRF02_AG(pol)A3(env). Taken together, our study demonstrated the high prevalence of CRF02_AG and complexity of circulating HIV-1 strains in Mali. It also provided evidence of ongoing virus evolution of CRF02_AG, as illustrated by the emergence of more complex CRF02_AG/A3 intersubtype recombinants in this area.

Very high prevalence of extended-spectrum beta-lactamase-producing Enterobacteriaceae in bacteriemic patients hospitalized in teaching hospitals in Bamako, Mali

The worldwide dissemination of extended-spectrum beta-lactamase producing Enterobacteriaceae, (ESBL-E) and their subset producing carbapenemases (CPE), is alarming. Limited data on the prevalence of such strains in infections from patients from Sub-Saharan Africa are currently available. We determined, here, the prevalence of ESBL-E/CPE in bacteriemic patients in two teaching hospitals from Bamako (Mali), which are at the top of the health care pyramid in the country. During one year, all Enterobacteriaceae isolated from bloodstream infections (E-BSI), were collected from patients hospitalized at the Point G University Teaching Hospital and the pediatric units of Gabriel Touré University Teaching Hospital. Antibiotic susceptibility testing, enzyme characterization and strain relatedness were determined. A total of 77 patients had an E-BSI and as many as 48 (62.3%) were infected with an ESBL-E. ESBL-E BSI were associated with a previous hospitalization (OR 3.97 95% IC [1.32; 13.21]) and were more frequent in hospital-acquired episodes (OR 3.66 95% IC [1.07; 13.38]). Among the 82 isolated Enterobacteriaceae, 58.5% were ESBL-E (20/31 Escherichia coli, 20/26 Klebsiella pneumoniae and 8/15 Enterobacter cloacae). The remaining (5 Salmonella Enteritidis, 3 Morganella morganii 1 Proteus mirabilis and 1 Leclercia adecarboxylata) were ESBL negative. CTX-M-1 group enzymes were highly prevalent (89.6%) among ESBLs; the remaining ones being SHV. One E. coli produced an OXA-181 carbapenemase, which is the first CPE described in Mali. The analysis of ESBL-E relatedness suggested a high rate of cross transmission between patients. In conclusion, even if CPE are still rare for the moment, the high rate of ESBL-BSI and frequent cross transmission probably impose a high medical and economic burden to Malian hospitals.

Confirmation of Xanthomonas axonopodis pv. manihotis Causing Cassava Bacterial Blight in Ivory Coast

D. Kone, Université Félix Houphouët-Boigny, UFR Biosciences, Laboratoire de Physiologie Végétale, 22 BP582 Abidjan, Côte d’Ivoire; S. Dao, C. Tekete, I. Doumbia, and O. Koita, Université des Sciences Techniques et Technologiques, Faculté des Sciences et Techniques, LBMA, Bamako, Mali; K. Abo, Institut National Polytechnique Félix Houphouët-Boigny (INPHB), ESA, Département ARA, Laboratoire de Phytopathologie, Yamoussoukro, Côte d’Ivoire; E. Wicker, CIRAD, UMR Peuplements Végétaux et Bioagresseurs en Milieu Tropical (PVBMT) Pôle de Protection des Plantes 7, chemin de l’IRAT F-97410 Saint Pierre La Réunion, France; and V. Verdier, IRD, Cirad, Univ. Montpellier, Interactions Plantes Microorganismes Environnement (IPME), 34394 Montpellier, France.

Patient-provider communication styles in HIV treatment programs in Bamako, Mali: A mixed-methods study to define dimensions and measure patient preferences

Effective patient-provider communication (PPC) promotes patient adherence and retention in long-term care. Sub-Saharan Africa faces unprecedented demand for chronic care for HIV patients on antiretroviral therapy (ART), yet adherence and retention remain challenging. In high-income countries, research describing patient preferences for different PPC styles has guided interventions to improve PPC and patient outcomes. However, research on PPC preferences in sub-Saharan Africa is limited. We sought to define PPC dimensions relevant to ART programs in Bamako, Mali through recordings of clinical interactions, in-depth interviews and focus-group discussions with 69 patients and 17 providers. To assess preferences toward contrasting PPC styles within dimensions, we conducted a vignette-based survey with 141 patients across five ART facilities. Qualitative analysis revealed two PPC dimensions similar to those described in the literature on patient-centered communication (level of psychosocial regard, balance of power), and one unique dimension that emerged from the data (guiding patient behavior: easy/tough/sharp). Significantly more survey participants chose the vignette demonstrating high psychosocial regard (52.2%) compared to a biomedical style (22.5%) (p<0.001). Within balance of power, a statistically similar proportion of participants chose the vignette demonstrating shared power (40.2%) compared to a provider-dominated style (35.8%). In guiding patient behavior, a similar proportion of participants preferred the vignette depicting the “easy” (38.4%) and/or “tough” style (40.6%), but significantly fewer preferred the “sharp” style (14.5%) (p<0.001). Highly educated participants chose biomedical and shared power styles more frequently, while less educated participants more frequently indicated “no preference”. Working to understand, develop, and tailor PPC styles to patients in chronic care may help support patient retention and ultimately, clinical outcomes. Emphasis on developing skills in psychosocial regard and on adapting styles of power balance and behavioral guidance to individual patients is likely to yield positive results and should be considered a high priority for ART providers.

Relationship between HIV Positive Status Announcement and Smoking among Infected-Individuals in Bamako, 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.

Tuberculosis drug resistance in Bamako, Mali, from 2006 to 2014

BackgroundAlthough Drug resistance tuberculosis is not a new phenomenon, Mali remains one of the “blank” countries without systematic data.MethodsBetween 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.ResultsA 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.ConclusionThe 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.

Stool microbiome reveals diverse bacterial ureases as confounders of oral urea breath testing for Helicobacter pylori and Mycobacterium tuberculosis in Bamako, Mali.

Detection of bacterial urease activity has been utilized successfully to diagnose Helicobacter pylori (H. pylori). While Mycobacterium tuberculosis (M. tuberculosis) also possesses an active urease, it is unknown whether detection of mycobacterial urease activity by oral urease breath test (UBT) can be exploited as a rapid point of care biomarker for tuberculosis (TB) in humans. We enrolled 34 individuals newly diagnosed with pulmonary TB and 46 healthy subjects in Bamako, Mali and performed oral UBT, mycobacterial sputum culture and H. pylori testing. Oral UBT had a sensitivity and specificity (95% CI) of 70% (46-88%) and 11% (3-26%), respectively, to diagnose culture-confirmed M. tuberculosis disease among patients without H. pylori, and 100% sensitivity (69-100%) and 11% specificity (3-26%) to diagnose H. pylori among patients without pulmonary TB. Stool microbiome analysis of controls without TB or H. pylori but with positive oral UBT detected high levels of non-H. pylori urease producing organisms, which likely explains the low specificity of oral UBT in this setting and in other reports of oral UBT studies in Africa.