Second-line antiretroviral therapy failure and characterization of HIV-1 drug resistance patterns in children in Mali.

INTRODUCTION: In recent years, children born to HIV-infected mothers have been receiving antiretroviral treatment (ART) with limited or no virologic monitoring, which increases the likelihood of development and accumulation of drug resistance mutations, which itself may limit the effectiveness of future ART. The objective of this study was to evaluate the prevalence of resistance mutations in children infected with HIV-1 experiencing virological failure to second-line ART in the Pediatric Department of Gabriel Touré Hospital in Mali. METHODS: Children aged from 5 to 18 infected with HIV-1 on second-line antiretroviral therapy and whose viral load was greater than 1000 copies/mL after observance reinforcement were enrolled. The protease and reverse transcriptase genes were sequenced with ViroSeq®. The results were interpreted according to the last version of the Stanford algorithm in 2018. The study was approved by the Ethics Committee of the Faculty of Medicine and Dentistry, University of Sciences, Techniques and Technologies of Bamako (Mali). RESULTS: Of 216 children, 33 (15.3%) who had a viral load (VL)>1000 copies/mL in second line were recruited and included in the study. The median plasma viral load was 77,000 copies/mL [IQR (28,000-290,000)] and the median CD4 cell count was 310 cells/mm3 [IQR (152-412)]. The median age was 12 years; 48.5% of patients were treated with a combination of stavudine/lamivudine/nevirapine (Triomune®) for first-line treatment and 60.6% with abacavir/lamivudine/lopinavir/ritonavir for the second-line ART. The median treatment duration was 8.5 years [range, 3-13]. Of the 33 children whose treatment failed, the predominant HIV-1 subtype was CRF02_AG (66.7%). The prevalence of resistance to ART classes was 60.61% (20/33) to nucleoside reverse transcriptase inhibitors (NRTIs), 54.51% (18/33) to nonnucleoside reverse transcriptase inhibitors (NNRTIs), and 51.52% (17/33) to protease inhibitors (PIs). Of the patients studied, 90.9% were exposed to lopinavir/ritonavir (LPV/r) but only 15.2% (5/33) developed resistance to LPV/r. CONCLUSIONS: This study demonstrated that LPV/r remains active in most patients after second-line ART failure. In children whose second-line ART fails, particular attention should be paid to their ART and adherence history when considering the next treatment option.

Resistance profile and treatment outcomes in HIV-infected children at virological failure in Benin, West Africa.

Background: In Africa a high percentage of HIV-infected children continue to experience HIV treatment failure despite enormous progress. In Benin (West Africa), there are currently no data on HIV drug resistance at failure in paediatric populations. Objectives: To assess the frequency and patterns of HIV drug resistance among children with virological ART failures. Methods: Dried blood spots from 62 HIV-infected children with virological failure were collected at the paediatric clinic of the National Hospital Center in Cotonou for genotyping and plasma drug concentration determination. Results: Characteristics of the population show a median age of 10 years (IQR 6-13) and a median duration on ART of 5 years (IQR 3-7). Viruses from 53 children were successfully amplified. Of these, 76% of patients were on an NNRTI-based regimen and 24% on a boosted PI-based regimen. NRTI, NNRTI and dual-class resistance was present in 71%, 84% and 65% of cases, respectively. Only 4% of the children had major resistance mutations to PIs and none had major resistance mutations to integrase inhibitors. Among the participants, 25% had undetectable antiretroviral concentrations. Conclusions: Our results showed that the development of drug resistance could be one of the main consequences of high and continuous viral replication in HIV-infected children in Benin. Thus, inadequate attention to monitoring lifelong ART in children may prevent achievement of the goal of the United Nations Program on HIV and AIDS (UNAIDS) of 90% viral suppression among patients receiving ART.

Prevalence and clinical impact of minority resistant variants in patients failing an integrase inhibitor-based regimen by ultra-deep sequencing.

Background: Integrase strand transfer inhibitors (INSTIs) are recommended by international guidelines as first-line therapy in antiretroviral-naive and -experienced HIV-1-infected patients. Objectives: This study aimed at evaluating the prevalence at failure of INSTI-resistant variants and the impact of baseline minority resistant variants (MiRVs) on the virological response to an INSTI-based regimen. Methods: Samples at failure of 134 patients failing a raltegravir-containing (n = 65), an elvitegravir-containing (n = 20) or a dolutegravir-containing (n = 49) regimen were sequenced by Sanger sequencing and ultra-deep sequencing (UDS). Baseline samples of patients with virological failure (VF) (n = 34) and of those with virological success (VS) (n = 31) under INSTI treatment were sequenced by UDS. Data were analysed using the SmartGene platform, and resistance was interpreted according to the ANRS algorithm version 27. Results: At failure, the prevalence of at least one INSTI-resistant variant was 39.6% by Sanger sequencing and 57.5% by UDS, changing the interpretation of resistance in 17/134 (13%) patients. Among 53 patients harbouring at least one resistance mutation detected by both techniques, the most dominant INSTI resistance mutations were N155H (45%), Q148H/K/R (23%), T97A (19%) and Y143C (11%). There was no difference in prevalence of baseline MiRVs between patients with VF and those with VS. MiRVs found at baseline in patients with VF were not detected at failure either in majority or minority mutations. Conclusions: UDS is more sensitive than Sanger sequencing at detecting INSTI MiRVs at treatment failure. The presence of MiRVs at failure could be important to the decision to switch to other INSTIs. However, there was no association between the presence of baseline MiRVs and the response to INSTI-based therapies in our study.

[High prevalence of methicillin-resistant Staphylococcus aureus strains in the Point G teaching hospital in Bamako, Mali]. / Haute prevalence des souches de staphylococcus aureus resistantes a la meticilline au centre hospitalier universitaire du Point G a Bamako (Mali).

Our aim was to study the susceptibility of Staphylococcus aureus to antimicrobial agents and to determine the methicillin-resistant S. aureus (MRSA) prevalence in the Point G teaching hospital in Bamako. METHODS: Columbia blood agar with nalidixic acid and colistin was used for the isolation of S. aureus strains. The diffusion method was used for antimicrobial susceptibility testing. RESULTS: Of 434 non repetitive strains of S. aureus isolated from 2007 to 2009 in the Point G teaching hospital, 297 (68.6%) were from hospital area and 137 (31.4%) were from extra-hospital area. The hospital strains were more resistant to penicillin than the extra-hospital strains (95% versus 88%; p = 0,016). Tetracycline was more active against hospital clinical isolates than extra-hospital clinical isolates (32% versus 21%; p = 0.024). Among 297 S. aureus clinical isolates, 195 (66%) were MRSA and 102 (34%) were methicillin-susceptible S. aureus (MSSA). The MRSA clinical isolates prevalence was higher in hospital area than in extra-hospital area (66% versus 55.5%; p = 0.0418). The MRSA clinical isolates prevalence was higher in the medical wards than in the surgical wards (74.8% vs 34.3%; p < 10-6). Among 251 MRSA clinical isolates, 169 (67.3%) were from urine, 39 (15.5%) from pus, 30 (12%) from blood culture, 7 (2.9%) from vagina and 6 (2.5%) from other sites. The MRSA clinical isolates prevalence was 46% in 2007, 63% in 2008 and 80% in 2009. The MRSA clinical isolates were highly more resistant to penicillin (p < 10-6), to amoxicillin combined with clavulanic acid (p < 10-6), to aminoglycosides (p < 10-6), to macrolides, lincosamides and streptogramins (p < 10-6), to norfloxacin (p < 10-6), to chloramphenicol (p < 10-6), to tetracycline (p = 0,0042), to sulfonamides (p < 10-6), to trimethoprim (p < 10-6), to fusidic acid (p < 10-6), and to fosfomycin (p = 0,0103) than the MSSA strains. The high level resistance to aminoglycosides, fluoroquinolones, macrolides, lincosamides and streptogramins was more frequent in the MRSA strains than in the MSSA strains. CONCLUSION: The MRSA clinical isolates prevalence was very high in the Point G teaching hospital in Bamako, in the medical wards especially. The MRSA strains were drugs multiple resistant.

Notre objectif était d'étudier la sensibilité de Staphylococccus aureus aux antibiotiques et de déterminer la prévalence des souches résistantes à la méticilline au centre hospitalier universitaire du Point G à Bamako. MÉTHODES: L'isolement des souches de S. aureus a été réalisé sur la gélose Columbia additionnée de sang de mouton, d'acide nalidixique et de colistine. L'étude de la sensibilité aux antibiotiques a été faite par la méthode des disques. RÉSULTATS: Sur 434 souches non répétitives de S. aureus isolées de 2007 à 2009 au centre hospitalier universitaire du Point G, 297 (68,6 %) sont d'origine hospitalière et 137 (31,4 %) d'origine extrahospitalière. Les souches hospitalières ont été plus résistantes à la pénicilline G que les souches extrahospitalières (95 % versus 88 %; p = 0,016). La résistance de S. aureus à la méticilline (SARM) a été plus fréquente chez les souches hospitalières que chez les souches extrahospitalières (66 % versus 55,5 %; p = 0,0418). Les plus hautes prévalences de SARM ont été observées dans les services de néphrologie (90 %), de cardiologie (87,5 %) de médecine interne (71 %), d'hématologie-oncologie médicale (66 %) et des maladies infectieuses (65 %). La prévalence des souches de SARM a été de 46 % en 2007, 63 % en 2008 et 80 % en 2009 en milieu hospitalier. Les souches de SARM ont été plus résistantes à la pénicilline G (p < 10−6), à l'association amoxicilline + acide clavulanique (p < 10−6), aux aminosides (p < 10−6), aux macrolides, lincosamides et streptogramines (p < 10−6), à la norfloxacine (p < 10−6), au chloramphénicol (p < 10−6), à la tétracycline (p = 0,0042), aux sulfamides (p < 10−6), au triméthoprime (p < 10−6), à l'acide fusidique (p < 10−6), et à la fosfomycine (p = 0,0103) que les souches de S. aureus sensibles à la méticilline (SASM). Les phénotypes de résistance aux aminosides (KTG, S+ KTG) et aux macrolides, lincosamides et streptogramines (MLSB constitutif) ont été plus fréquents chez les souches de SARM que chez celles de SASM. CONCLUSION: La prévalence des souches de SARM a été très élevée au centre hospitalier universitaire du Point G, dans les services de médecine surtout. Les souches de SARM sont multirésistantes.

Performance of genotypic algorithms for predicting tropism of HIV-1CRF02_AG subtype.

BACKGROUND: Several genotypic rules for predicting HIV-1 non-B subtypes tropism are commonly used, but there is no consensus about their performances. OBJECTIVES: Three genotypic methods were compared for CRF02_AG HIV-1 tropism determination. STUDY DESIGN: V3 env region of 178HIV-1 CRF02_AG from Pitié-Salpêtrière and Saint-Antoine Hospitals was sequenced from plasma HIV-1 RNA. HIV-1 tropism was determined by Geno2Pheno algorithm, false positive rate (FPR) 5% or 10%, the 11/25 rule or the combined criteria of the 11/25 and net charge rule. RESULTS: A concordance of 91.6% was observed between Geno2pheno 5% and the combined criteria. The results were nearly similar for the comparison between Geno2pheno 5% and the 11/25 rule. More mismatches were observed when Geno2pheno was used with the FPR 10%. A lower nadir CD4 cell count was associated with a discordance of tropism prediction between Geno2pheno 5% and the combined criteria or the 11/25 rule (p=0.02 and p=0.03, respectively). A lower HIV-1 viral load was associated with some discordance for the comparison of Geno2pheno 10% and the combined rule (p=0.02). CONCLUSION: Geno2pheno FPR 5% or 10% predicted more X4-tropic viruses for this set of CRF02_AG sequences than the combined criteria or the 11/25 rule alone. Furthermore, Geno2pheno FPR 5% was more concordant with the 11/25 rule and the combined rule than Geno2pheno 10% to predict HIV-1 tropism. Overall, Geno2pheno 5% could be used to predict CRF02_AG tropism as well as other genotypic rules.

High level of HIV-1 resistance in patients failing long-term first-line antiretroviral therapy in Mali.

OBJECTIVES: In resource-limited settings, few data are available on virological failure after long-term first-line antiretroviral therapy. This study characterized the genotypic resistance patterns at the time of failure after at least 36 months of a first-line regimen in Mali, West Africa. METHODS: Plasma samples from 84 patients who were receiving first-line antiretroviral treatment and with an HIV-1 RNA viral load (VL) >1000 copies/mL were analysed. Genotypic resistance testing was performed and HIV-1 drug resistance was interpreted according to the latest version of the National Agency for HIV and Hepatitis Research algorithm. RESULTS: At the time of resistance testing, patients had been treated for a median of 60 months (IQR 36-132 months) and had a median CD4 cell count of 292 cells/mm(3) (IQR 6-1319 cells/mm(3)), a median HIV-1 RNA level of 28266 copies/mL (IQR 1000-2 93 495 copies/mL) and a median genotypic susceptibility score of 1 (IQR 1-4). The prevalence of nucleoside reverse transcriptase inhibitor (NRTI) and non-nucleoside reverse transcriptase inhibitor (NNRTI) resistance mutations was 78% and 82%, respectively. Viruses were resistant to at least one drug in 92% of cases. Although etravirine and rilpivirine were not used in the first-line regimens, viruses were resistant to etravirine in 34% of cases and to rilpivirine in 49% of cases. The treatment duration, median number of NRTI and NNRTI mutations and some reverse transcriptase mutations (T215Y/F/N, L210W, L74I, M41L and H221Y) were associated with the VL at virological failure. CONCLUSIONS: This study demonstrated a high level of resistance to NRTIs and NNRTIs, compromising second-generation NNRTIs, for patients who stayed on long-term first-line regimens. It is crucial to expand the accessibility of virological testing in resource-limited settings to limit the expansion of resistance and preserve second-line treatment efficacy.

Genetic barrier to the development of resistance to rilpivirine and etravirine between HIV-1 subtypes CRF02_AG and B.

OBJECTIVES: It has been demonstrated for some drugs that the genetic barrier, defined as the number of genetic transitions and/or transversions needed to produce a resistance mutation, can differ between HIV-1 subtypes. We aimed to assess differences in the genetic barrier for the evolution of resistance to the second-generation non-nucleoside reverse transcriptase inhibitors etravirine and rilpivirine in subtypes B and CRF02_AG in antiretroviral-naive patients. METHODS: An analysis was undertaken of 25 substitutions associated with etravirine and rilpivirine resistance at 12 amino acid positions in 267 nucleotide sequences (136 HIV-1 B and 131 HIV-1 CRF02_AG subtypes) of the reverse transcriptase gene. RESULTS: The majority (7/12) of amino acid positions studied were conserved between the two HIV-1 subtypes, leading to a similar genetic barrier. Different predominant codons between the subtypes were observed in 5/12 positions (90, 98, 179, 181 and 227), with an effect on the calculated genetic barrier only at the V179D and V179F codons (2.5 versus 3.5 for V179D, and 2.5 versus 5 for V179F, respectively, for subtype B versus subtype CRF02_AG). CONCLUSIONS: The majority of amino acids involved in etravirine and rilpivirine resistance showed a high degree of conservation of the predominant codon between the B and CRF02_AG subtypes. For rilpivirine, the genetic barrier was the same between the two subtypes. Nevertheless, subtype CRF02_AG showed a higher genetic barrier to acquiring mutations V179D and V179F (mutations associated with resistance to etravirine) compared with subtype B, suggesting that it would be more difficult to produce resistance to etravirine in the CRF02_AG subtype than the B subtype.

Prevalence of pre-existing resistance-associated mutations to rilpivirine, emtricitabine and tenofovir in antiretroviral-naive patients infected with B and non-B subtype HIV-1 viruses.

OBJECTIVES: The prevalence of rilpivirine, emtricitabine and tenofovir resistance-associated mutations (RAMs), described in vitro and in vivo, was determined in antiretroviral-naive patients. PATIENTS AND METHODS: From 2008 to 2011, 1729 treatment-naive patients were tested for resistance by bulk sequencing. We studied the primary rilpivirine RAMs (K101E/P, E138A/G/K/Q/R, V179L, Y181C/I/V, H221Y, F227C and M230I/L) and other potential rilpivirine-associated mutations (V90I, L100I, K101T, E138S, V179D/I, Y188L, V189I, G190A/E/S and M230V). We also studied the M184V/I and K65R mutations for emtricitabine and tenofovir, respectively. RESULTS: Among 1729 sequences, half of patients had B-subtype viruses and the other half non-B (with 26.7% CRF02, n=461). Primary rilpivirine RAMs were infrequent (4.6%, n=79) and the most prevalent were E138A (3%, n=52), E138K, (0.3%, n=5), H221Y (0.3%, n=5), E138G (0.2%, n=4) and Y181C (0.2%, n=4). The frequency of the primary rilpivirine RAMs was similar between B and non-B subtypes. The other potential rilpivirine-associated mutations that were most prevalent were V179I (8.4%, n=145), V90I (3.8%, n=65) and V189I (2.3%, n=40). The common V179I, V189I and V90I polymorphisms have not been associated with virological failure in Phase 3 clinical studies. By the ANRS algorithm, 4.9% (n=84) of samples were resistant to rilpivirine, 3.7% (n=32) of B-subtype viruses versus 6% (n=52) of non-B-subtype viruses (P=0.02, χ(2) test). The prevalence of K65R and M184I/V was 0.06% (1/1729) and 1% (18/1729), respectively. The prevalence of K103N was 2% (35/1729). CONCLUSIONS: The prevalence of rilpivirine, emtricitabine and tenofovir resistance mutations was very low in antiretroviral-naive patients. The prevalence of resistance to rilpivirine (4.9%, n=84) was not statistically different from the prevalence of efavirenz and nevirapine resistance in our population.

[Knowledge and attitudes of medical personnel in blood transfusion in Bamako, Mali]. / Connaissances et attitudes du personnel médical en matière de transfusion sanguine au Mali.

PURPOSE OF THE STUDY: We undertook a study to determine the level of knowledge and practice of medical staff personnel on transfusion medicine in Mali at Bamako and Kati. PATIENTS AND METHODS: The study was conducted from January to April 2010 in the three main teaching hospitals of Bamako and Kati and in the six referral health centers of the district of Bamako. Medical staff knowledge and practice were assessed using a questionnaire. The study population consisted of specialized practitioners (15%), general practitioners (21.4%), nurses (41.6%), and midwives (22%). RESULTS: Overall, 70.9% of the staff did not receive any training in blood transfusion since their graduation. The general knowledge about blood transfusion was insufficient in 53.9% of staff and excellent in 46.1%. Only 42.9% of medical staff has a good basic knowledge of blood products, their indications, and related accidents. CONCLUSION: Our study showed weaknesses in the transfusion system in Bamako, with insufficient knowledge of the medical staff in blood transfusion and little experience.