Population-specific variations in KCNH2 predispose patients to delayed ventricular repolarization upon dihydroartemisinin-piperaquine therapy

Funding Information: The study was supported by European and Developing Countries Clinical Trial Partnership (grant number RIA2017T-2018), Medicines for Malaria Venture (Geneva, Switzerland), UK Medical Research Council, Swedish International Development Cooperation Agency, German Ministry for Education and Research, University Claude Bernard (Lyon, France), Malaria Research and Training Centre (Bamako, Mali), Centre National de Recherche et de Formation sur le Paludisme (Burkina Faso), Institut de Recherche en Sciences de la Sant. (Bobo-Dioulasso, Burkina Faso), and Centre National de Formation et de Recherche en Sant. Rurale (Republic of Guinea). In addition, the authors received support from the Swedish Research Council (grant numbers 2019-01837, 2021-02801, 2021-05666, and 2021-06048), the Grants, Innovation and Product Development Unit of the South African Medical Research Council with funds received from Novartis and GSK R&D for Project Africa GRADIENT (grant numbers GSKNVS2/202101/004), the Robert Bosch Foundation, Stuttgart, Germany, and Conselho Nacional de Desenvolvimento Cient\u00EDfico e Tecnol\u00F3gico (CNPq), Brazil (grant number 200075/2022\u20135). T.N.S. is a CNPq Research Productivity Fellow. M.D.C. performed sequencing, analyzed the data, and conducted statistical analyses. Y.Z. conducted computational variant analyses. M.M.T. was involved in the acquisition of drug concentrations. A.D. and S.S. contributed to bioinformatics analyses. N.O. was the cardiologist responsible for cardiac toxicity assessment. A.H.T, M.L.A., B.F., and I.S. oversaw clinical patient recruitment and management. A.A.D. coordinated and oversaw the WANECAM study and critically reviewed the manuscript. P.J.G. and V.M.L designed and supervised the study. M.D.C. and V.M.L. wrote the manuscript. All authors read, reviewed, and approved of the final version of the manuscript. Funding Information: The study was supported by European and Developing Countries Clinical Trial Partnership (grant number RIA2017T-2018), Medicines for Malaria Venture (Geneva, Switzerland), UK Medical Research Council, Swedish International Development Cooperation Agency, German Ministry for Education and Research, University Claude Bernard (Lyon, France), Malaria Research and Training Centre (Bamako, Mali), Centre National de Recherche et de Formation sur le Paludisme (Burkina Faso), Institut de Recherche en Sciences de la Sant. (Bobo-Dioulasso, Burkina Faso), and Centre National de Formation et de Recherche en Sant. Rurale (Republic of Guinea). In addition, the authors received support from the Swedish Research Council (grant numbers 2019-01837, 2021-02801, 2021-05666, and 2021-06048), the Grants, Innovation and Product Development Unit of the South African Medical Research Council with funds received from Novartis and GSK R&D for Project Africa GRADIENT (grant numbers GSKNVS2/202101/004), the Robert Bosch Foundation, Stuttgart, Germany, and Conselho Nacional de Desenvolvimento e Tecnol\u00F3gico (CNPq), Brazil (grant number 200075/2022\u20135). T.N.S. is a CNPq Research Productivity Fellow. Publisher Copyright: Copyright © 2024 Camara et al.Dihydroartemisinin-piperaquine is efficacious for the treatment of uncomplicated malaria and its use is increasing globally. Despite the positive results in fighting malaria, inhibition of the Kv11.1 channel (hERG; encoded by the KCNH2 gene) by piperaquine has raised concerns about cardiac safety. Whether genetic factors could modulate the risk of piperaquine-mediated QT prolongations remained unclear. Here, we first profiled the genetic landscape of KCNH2 variability using data from 141,614 individuals. Overall, we found 1,007 exonic variants distributed over the entire gene body, 555 of which were missense. By optimizing the gene-specific parametrization of 16 partly orthogonal computational algorithms, we developed a KCNH2-specific ensemble classifier that identified a total of 116 putatively deleterious missense variations. To evaluate the clinical relevance of KCNH2 variability, we then sequenced 293 Malian patients with uncomplicated malaria and identified 13 variations within the voltage sensing and pore domains of Kv11.1 that directly interact with channel blockers. Cross-referencing of genetic and electrocardiographic data before and after piperaquine exposure revealed that carriers of two common variants, rs1805121 and rs41314375, experienced significantly higher QT prolongations (ΔQTc of 41.8 ms and 61 ms, respectively, vs 14.4 ms in controls) with more than 50% of carriers having increases in QTc >30 ms. Furthermore, we identified three carriers of rare population-specific variations who experienced clinically relevant delayed ventricular repolarization. Combined, our results map population-scale genetic variability of KCNH2 and identify genetic biomarkers for piperaquine-induced QT prolongation that could help to flag at-risk patients and optimize efficacy and adherence to antimalarial therapy.publishersversionpublishe

Persistent Submicroscopic Plasmodium falciparum Parasitemia 72 Hours after Treatment with Artemether-Lumefantrine Predicts 42-Day Treatment Failure in Mali and Burkina Faso.

A recent randomized controlled trial, the WANECAM (West African Network for Clinical Trials of Antimalarial Drugs) trial, conducted at seven centers in West Africa, found that artemether-lumefantrine, artesunate-amodiaquine, pyronaridine-artesunate, and dihydroartemisinin-piperaquine all displayed good efficacy. However, artemether-lumefantrine was associated with a shorter interval between clinical episodes than the other regimens. In a further comparison of these therapies, we identified cases of persisting submicroscopic parasitemia by quantitative PCR (qPCR) at 72 h posttreatment among WANECAM participants from 5 sites in Mali and Burkina Faso, and we compared treatment outcomes for this group to those with complete parasite clearance by 72 h. Among 552 evaluable patients, 17.7% had qPCR-detectable parasitemia at 72 h during their first treatment episode. This proportion varied among sites, reflecting differences in malaria transmission intensity, but did not differ among pooled drug treatment groups. However, patients who received artemether-lumefantrine and were qPCR positive at 72 h were significantly more likely to have microscopically detectable recurrent Plasmodium falciparum parasitemia by day 42 than those receiving other regimens and experienced, on average, a shorter interval before the next clinical episode. Haplotypes of pfcrt and pfmdr1 were also evaluated in persisting parasites. These data identify a possible threat to the parasitological efficacy of artemether-lumefantrine in West Africa, over a decade since it was first introduced on a large scale

Assessment of breast milk microbiota

Malgré les progrès technologiques dans l'exploration du microbiote humain et les nombreuses études menées sur le microbiote du tube digestif, le microbiote du colostrum et du lait maternel demeure un microbiote négligé. Cependant, les résultats de quelques études ont montré une grande diversité de bactéries commensales qui constituent le microbiote du lait maternel qui pourrait coloniser l'intestin du nourrisson. Selon les auteurs de ces études, le colostrum et le lait maternel pourraient être impliqués dans la transmission verticale des phénotypes associés au microbiote intestinal maternel. Dans cette thèse, nous avons d'abord évalué la diversité bactérienne de 154 échantillons de colostrum et de lait maternel de 144 mères par culture à travers la «microbial culturomics» et par métagénomique ciblée à travers le séquençage du gène de L'ARN ribosomal 16S. Avec l'approche de la «culturomics microbienne», nous avons analysé 20 échantillons de colostrum et de lait et tous les échantillons ont été analysés par l’approche de métagénomique ciblée. Nous avons cultivé 20 échantillons de colostrum et de lait pour l'isolement des archées méthanogènes qui jouent un rôle important dans la digestion de certains aliments. Dans la deuxième partie, nous avons procédé à la description taxonogénomique des nouvelles bactéries isolées à partir du colostrum, du lait maternel et des selles des patients obèses. Nous avons observé une grande diversité bactérienne du colostrum et du lait maternel grâce aux approches de la «microbial culturomics» et de métagénomique ciblé. Nous avons pu cultiver deux espèces d'archée méthanogènes, Methanobrevibacter smithii et Methanobrevibacter oralis.Despite technological advances in human microbiota exploration and numerous studies on digestive tract microbiota, colostrum and breast milk microbiota remain neglected microbiotes. However, the results of few studies have shown a significant diversity of commensal bacteria that constitute the microbiota of colostrum and breast milk that could colonise infant gut. According to the authors of these studies, colostrum and breast milk could be involved in the vertical transmission of phenotypes associated to mother gut microbiota. In this thesis, we first evaluated the bacterial diversity of 154 colostrum and breast milk samples from 144 mothers using culture (culturomics) and targeted metagenomics (16S rRNA gene) approaches. With culturomics approach, we analysed 20 samples of colostrum and milk and all samples with targeted metagenomics. We also cultured 20 samples, including 9 colostrum and 11 mature milk, for the isolation of methanogenic archaea that play a key role in the digestion of certain foods. In the second part we proceeded to the taxonogenomic description of new bacteria isolated from colostrum, breast milk and stools of obese patients. We observed a high bacterial diversity of colostrum and breast milk through culturomics and metagenomics approaches. We have been able to cultivate two species of methanogenic archaea; Methanobrevibacter smithii is present in most people gut and Methanobrevibacter oralis colonizes the human oral cavity. We have thus increased the microbial repertoire associated with colostrum and human breast milk by discovering and describing several new bacterial species

‘Negativicoccus massiliensis’, a new species identified from human stool from an obese patient after bariatric surgery

International audienceWe report here the main characteristics of 'Negativicoccus massiliensis' strain AT7 (CSURP=P2082, DSM=100853) isolated from a stool sample collected from a 47-year-old obese French man before bariatric surgery

Draft genome and description of Negativicoccus massiliensis strain Marseille-P2082, a new species isolated from the gut microbiota of an obese patient

International audienceStrain Marseille-P2082, an anaerobic, non-motile, asporogenous, Gram-negative, coccoid bacterium was isolated from the faeces of a 33 year-old obese French woman before bariatric surgery. The isolate exhibits 98.65% 16S rRNA gene nucleotide sequence similarity with Negativicoccus succinicivorans strain ADV 07/08/06-B-1388(T), its current closest phylogenetic neighbour with standing in nomenclature. However, the dDDH relatedness between the new isolate and N. succinicivorans type strain ADV 07/08/06-B-1388(T) is 52.5 +/- 2.7%. Strain Marseille-P2082 has a genome of 1,360,589 bp with a 51.1% G+C content. Its major fatty acids were identified as C-18:1n9, C-18:0 and C-16:0. Based on its phenotypic, genomic and phylogenetic characteristics, strain Marseille-P2082(T) [= CSURP2082 (Collection de Souches de l'Unite des Rickettsies) = DSM 100853] is proposed as the type strain of the novel species Negativicoccus massiliensis sp. nov. The 16S rRNA gene sequence and whole-genome shotgun sequence have been deposited in EMBL-EBI under accession numbers LN876651 and LT700188, respectively

Listeria monocytogenes in human milk in Mali: A potential health emergency

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Fournierella massiliensis gen. nov., sp nov., a new human-associated member of the family Ruminococcaceae

International audienceAn anaerobic bacterium, strain AT2(T), was isolated from the fresh stool sample of a healthy French man using the culturomics approach. The 16S rRNA gene sequence analysis showed that strain AT2(T) had 95.2% nucleotide sequence similarity with Gemmiger formicilis ATCC 27749(T), the phylogenetically closest species with standing in nomenclature. Cells are Gram-stain-negative, catalase- and oxidase-negative, obligately anaerobic, non-motile, non-spore-forming, rod-shaped, and the bacilli were mesothermophilic. The major fatty acids were C-16 : 0 (43.8 %) and C-18 : 1n9 (20 %). The DNA G+C content of the strain based on its genome sequence was 56.8 mol%. Based on the phenotypic, biochemical and phylogenetic analysis, we propose the creation of the genus Fournierella gen. nov., which contains strain AT2(T) (=CSUR P2014(T)=DSM 100451(T)) as the type strain of the type species Fournierella massiliensis gen. nov., sp. nov

Clinical evidence of the role of Methanobrevibacter smithii in severe acute malnutrition

International audienceAbstract Gut microbial dysbiosis has been shown to be an instrumental factor in severe acute malnutrition (SAM) and particularly, the absence of Methanobrevibacter smithii, a key player in energy harvest. Nevertheless, it remains unknown whether this absence reflects an immaturity or a loss of the microbiota. In order to assess that, we performed a case–control study in Mali using a propensity score weighting approach. The presence of M. smithii was tested using quantitative PCR on faeces collected from SAM children at inclusion and at discharge when possible or at day 15 for controls. M. smithii was highly significantly associated with the absence of SAM, detected in 40.9% controls but only in 4.2% cases (p < 0.0001). The predictive positive value for detection of M. smithii gradually increased with age in controls while decreasing in cases. Among children providing two samples with a negative first sample, no SAM children became positive, while this proportion was 2/4 in controls (p = 0.0015). This data suggests that gut dysbiosis in SAM is not an immaturity but rather features a loss of M. smithii . The addition of M. smithii as a probiotic may thus represent an important addition to therapeutic approaches to restore gut symbiosis

Culture of Methanogenic Archaea from Human Colostrum and Milk

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