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Artemisinin resistance (delayed P. falciparum clearance following artemisinin-based combination therapy), is widespread across Southeast Asia but to date has not been reported in Africa 1 – 4 . Here we genotyped the P. falciparum K13 ( Pfkelch13 ) propeller domain, mutations in which can mediate artemisinin resistance 5 , 6 , in pretreatment samples collected from recent dihydroarteminisin-piperaquine and artemether-lumefantrine efficacy trials in Rwanda 7 . While cure rates were >95% in both treatment arms, the Pfkelch13 R561H mutation was identified in 19 of 257 (7.4%) patients at Masaka. Phylogenetic analysis revealed the expansion of an indigenous R561H lineage. Gene editing confirmed that this mutation can drive artemisinin resistance in vitro. This study provides evidence for the de novo emergence of Pfkelch13 -mediated artemisinin resistance in Rwanda, potentially compromising the continued success of antimalarial chemotherapy in Africa. Identification in Rwanda of mutations in Plasmodium falciparum capable of conferring in vitro resistance to artemisinin, an essential medicine for the treatment of malaria, underscore the crucial need for surveillance in Africa to safeguard efficacy of life-saving therapies.

Background Comparing the composition of microbial communities among groups of interest (e.g., patients vs healthy individuals) is a central aspect in microbiome research. It typically involves sequencing, data processing, statistical analysis and graphical display. Such an analysis is normally obtained by using a set of different applications that require specific expertise for installation, data processing and in some cases, programming skills. Results Here, we present SHAMAN, an interactive web application we developed in order to facilitate the use of (i) a bioinformatic workflow for metataxonomic analysis, (ii) a reliable statistical modelling and (iii) to provide the largest panel of interactive visualizations among the applications that are currently available. SHAMAN is specifically designed for non-expert users. A strong benefit is to use an integrated version of the different analytic steps underlying a proper metagenomic analysis. The application is freely accessible at http://shaman.pasteur.fr/ , and may also work as a standalone application with a Docker container (aghozlane/shaman), conda and R. The source code is written in R and is available at https://github.com/aghozlane/shaman . Using two different datasets (a mock community sequencing and a published 16S rRNA metagenomic data), we illustrate the strengths of SHAMAN in quickly performing a complete metataxonomic analysis. Conclusions With SHAMAN, we aim at providing the scientific community with a platform that simplifies reproducible quantitative analysis of metagenomic data.

The mutation responsible for the black carbonaria morph of the peppered moth is identified as a transposable element within the cortex gene. The look of Lepidoptera driven by cortex The darkening of the peppered moth Biston betularia , the phenomenon known as industrial melanism, is a textbook example of evolutionary biology in action. However, the genetic background of the black or c arbonaria variants has remained unclear. Building on their earlier work that isolated the gene responsible to within a roughly 400-kilobase region containing 13 genes, Ilik Saccheri and colleagues have identified the melanism-causing event as the insertion of a class II transposable element into the first intron of a gene called cortex . Statistical inference indicates that the polymorphism occurred around 1819, when the Industrial Revolution was well under way. In a separate study, Nicola Nadeau et al . report that colour patterning in butterflies of the genus Heliconius is also mediated by expression of the cortex gene, apparently co-opted to control the rate of scale cell development, on which colour depends. Taken together, these two papers suggest that cortex , conserved widely within Lepidoptera, is a major target for natural selection acting on colour and pattern variation. Discovering the mutational events that fuel adaptation to environmental change remains an important challenge for evolutionary biology. The classroom example of a visible evolutionary response is industrial melanism in the peppered moth ( Biston betularia ): the replacement, during the Industrial Revolution, of the common pale typica form by a previously unknown black ( carbonaria ) form, driven by the interaction between bird predation and coal pollution 1 . The carbonaria locus has been coarsely localized to a 200-kilobase region, but the specific identity and nature of the sequence difference controlling the carbonaria – typica polymorphism, and the gene it influences, are unknown 2 . Here we show that the mutation event giving rise to industrial melanism in Britain was the insertion of a large, tandemly repeated, transposable element into the first intron of the gene cortex . Statistical inference based on the distribution of recombined carbonaria haplotypes indicates that this transposition event occurred around 1819, consistent with the historical record. We have begun to dissect the mode of action of the carbonaria transposable element by showing that it increases the abundance of a cortex transcript, the protein product of which plays an important role in cell-cycle regulation, during early wing disc development. Our findings fill a substantial knowledge gap in the iconic example of microevolutionary change, adding a further layer of insight into the mechanism of adaptation in response to natural selection. The discovery that the mutation itself is a transposable element will stimulate further debate about the importance of ‘jumping genes’ as a source of major phenotypic novelty 3 .

Drug-recalcitrant infections are a leading global-health concern. Bacterial cells benefit from phenotypic variation, which can suggest effective antimicrobial strategies. However, probing phenotypic variation entails spatiotemporal analysis of individual cells that is technically challenging, and hard to integrate into drug discovery. In this work, we develop a multi-condition microfluidic platform suitable for imaging two-dimensional growth of bacterial cells during transitions between separate environmental conditions. With this platform, we implement a dynamic single-cell screening for pheno-tuning compounds, which induce a phenotypic change and decrease cell-to-cell variation, aiming to undermine the entire bacterial population and make it more vulnerable to other drugs. We apply this strategy to mycobacteria, as tuberculosis poses a major public-health threat. Our lead compound impairs Mycobacterium tuberculosis via a peculiar mode of action and enhances other anti-tubercular drugs. This work proves that harnessing phenotypic variation represents a successful approach to tackle pathogens that are increasingly difficult to treat. Tuberculosis is a major global health threat. Here, the authors develop a single-cell drug discovery approach and identify a compound that tunes bacterial phenotypic variation. This enhances the activity of anti-tubercular drugs against the pathogen.

The voltage-gated sodium channel, para, is a target of DDT and pyrethroid class insecticides. Single nucleotide mutations in para , called knockdown resistant or kdr, which contribute to resistance against DDT and pyrethroid insecticides, have been correlated with increased susceptibility of Anopheles to the human malaria parasite Plasmodium falciparum . However, a direct role of para activity on Plasmodium infection has not yet been established. Here, using RNA-mediated silencing, we provide in vivo direct evidence for the requirement of wild-type (wt) para function for insecticide activity of deltamethrin. Depletion of wt para, which is susceptible to insecticide, causes deltamethrin tolerance, indicating that insecticide-resistant kdr alleles are likely phenocopies of loss of para function. We then show that normal para activity in An. coluzzii limits Plasmodium infection prevalence for both P. falciparum and P. berghei . A transcriptomic analysis revealed that para activity does not modulate the expression of immune genes. However, loss of para function led to enteric dysbiosis with a significant increase in the total bacterial abundance, and we show that para function limiting Plasmodium infection is microbiota dependent. In the context of the bidirectional “enteric microbiota-brain” axis studied in mammals, these results pave the way for studying whether the activity of the nervous system could control Anopheles vector competence.

Pyrethroid insecticides induce an excito-repellent effect that reduces contact between humans and mosquitoes. Insecticide use is expected to lower the risk of pathogen transmission, particularly when impregnated on long-lasting treated bednets. When applied at low doses, pyrethroids have a toxic effect, however the development of pyrethroid resistance in several mosquito species may jeopardize these beneficial effects. The need to find additional compounds, either to kill disease-carrying mosquitoes or to prevent mosquito contact with humans, therefore arises. In laboratory conditions, the effects (i.e., repellent, irritant and toxic) of 20 plant extracts, mainly essential oils, were assessed on adults of Anopheles gambiae, a primary vector of malaria. Their effects were compared to those of DEET and permethrin, used as positive controls. Most plant extracts had irritant, repellent and/or toxic effects on An. gambiae adults. The most promising extracts, i.e. those combining the three types of effects, were from Cymbopogon winterianus, Cinnamomum zeylanicum and Thymus vulgaris. The irritant, repellent and toxic effects occurred apparently independently of each other, and the behavioural response of adult An. gambiae was significantly influenced by the concentration of the plant extracts. Mechanisms underlying repellency might, therefore, differ from those underlying irritancy and toxicity. The utility of the efficient plant extracts for vector control as an alternative to pyrethroids may thus be envisaged.

Background Cervical cancer screening programs are increasingly relying on sensitive molecular approaches as primary tests to detect high-risk human papillomaviruses (hrHPV), the causative agents of cervix cancer. Although hrHPV infection is a pre-requisite for the development of most precancerous lesions, the mere detection of viral nucleic acids, also present in transient infections, is not specific of the underlying cellular state, resulting in poor positive predictive values (PPV) regarding lesional states. There is a need to increase the specificity of molecular tests for better stratifying individuals at risk of cancer and to adapt follow-up strategies. Methods HPV-RNA-SEQ, a targeted RNA next generation sequencing assay allowing the detection of up to 16 hrHPV splice events and key human transcripts, has previously shown encouraging PPV for the detection of precancerous lesions. Herein, on 302 patients with normal cytology (NILM, n  = 118), low-grade (LSIL, n  = 104) or high-grade squamous intraepithelial lesions (HSIL, n  = 80), machine learning-based model improvement was applied to reach 2-classes (NILM vs HSIL) or 3-classes (NILM, LSIL, HSIL) predictive models. Results Linear (elastic net) and nonlinear (random forest) approaches resulted in five 2-class models that detect HSIL vs NILM in a validation set with specificity up to 0.87, well within the range of PPV of other competing RNA-based tests in a screening population. Conclusions HPV-RNA-SEQ improves the detection of HSIL lesions and has the potential to complete and eventually replace current molecular approaches as a first-line test. Further performance evaluation remains to be done on larger and prospective cohorts.

Animal African trypanosomosis (AAT), caused by protist parasites of the genus Trypanosoma , puts upward of a million head of livestock at risk across 37 countries in Africa. The economic impact of AAT and the presence of human-infectious trypanosomes in animals place a clear importance on improving diagnostics for animal trypanosomes to map the distribution of the veterinary parasites and identify reservoirs of human-infectious trypanosomes. We have adapted the CRISPR-based detection toolkit SHERLOCK (Specific High-sensitivity Enzymatic Reporter unLOCKing) for trypanosomatid parasites responsible for AAT (SHERLOCK4AAT) including Pan-trypanosomatid, Trypanozoon , T. vivax , T. congolense , T. theileri , T. simiae, and T. suis assays. To test the applicability of this technique in the field, we analysed dried blood spots collected from 200 farm and 224 free-ranging pigs in endemic and historical human African trypanosomiasis foci in Guinea and Côte d’Ivoire, respectively. The results revealed that SHERLOCK4AAT can detect and discriminate between trypanosome species involved in multiple infections with a high sensitivity. 62.7% [58.1, 67.3] of pigs were found infected with at least one trypanosome species. T. brucei gambiense , a human-infectious trypanosome, was found in one animal at both sites, highlighting the risk that these animals may act as persistent reservoirs. These data suggest that, due to their proximity to humans and their attractiveness to tsetse flies, pigs could act as sentinels to monitor T. b. gambiense circulation using the SHERLOCK4AAT toolbox.

In the version of this article initially published, affiliation 2 (Malaria Genetics and Resistance Unit, Institut Pasteur, Paris, France) was incorrect. The correct affiliation is ‘Malaria Genetics and Resistance Unit–Institut Pasteur, INSERM U1201, CNRS ERL9195, Paris, France’. Also, in the first sentence in the first paragraph of the fifth subsection of Results (‘Origins of the Rwandan Pfkelch13 561H haplotype and its relationship to other P. falciparum populations’), the first part of the sample description (“350 samples, comprising 25 Rwandan sequences and 10 Eritrean P. falciparum sequences generated for this study”) was incorrect. The correct text is “...340 samples, comprising 25 Rwandan P. falciparum sequences generated for this study...”. Finally, Fig. 1 was incorrect, and the number of worldwide isolates in the legend title (325) was incorrect. The corrected figure is presented here, and the correct number of worldwide isolates is 315. The errors have been corrected in the HTML and PDF versions of the article

BackgroundInterferon beta (IFN β ) has been prescribed as a first-line disease-modifying therapy for relapsing-remitting multiple sclerosis (RRMS) for nearly three decades. However, there is still a lack of treatment response markers that correlate with the clinical outcome of patients.AimTo determine a combination of cellular and molecular blood signatures associated with the efficacy of IFN β treatment using an integrated approach.MethodsThe immune status of 40 RRMS patients, 15 of whom were untreated and 25 that received IFN β 1a treatment (15 responders, 10 non-responders), was investigated by phenotyping regulatory CD4+ T cells and naïve/memory T cell subsets, by measurement of circulating IFN α / β proteins with digital ELISA (Simoa) and analysis of ~600 immune related genes including 159 interferon-stimulated genes (ISGs) with the Nanostring technology. The potential impact of HLA class II gene variation in treatment responsiveness was investigated by genotyping HLA - DRB1, -DRB3,4,5, -DQA1 , and - DQB1 , using as a control population the Milieu Interieur cohort of 1,000 French healthy donors.ResultsClinical responders and non-responders displayed similar plasma levels of IFN β and similar ISG profiles. However, non-responders mainly differed from other subject groups with reduced circulating naïve regulatory T cells, enhanced terminally differentiated effector memory CD4+ TEMRA cells, and altered expression of at least six genes with immunoregulatory function. Moreover, non-responders were enriched for HLA-DQB1 genotypes encoding DQ8 and DQ2 serotypes. Interestingly, these two serotypes are associated with type 1 diabetes and celiac disease. Overall, the immune signatures of non-responders suggest an active disease that is resistant to therapeutic IFN β , and in which CD4+ T cells, likely restricted by DQ8 and/or DQ2, exert enhanced autoreactive and bystander inflammatory activities.