Nora Zidane

Background: An outbreak of diphtheria, declared in Yemen in October 2017, is still ongoing. Methods. Probable cases were recorded through an electronic diseases early warning system. Microbiological culture, genomic sequencing, antimicrobial susceptibility and toxin production testing were performed. Methods: Probable cases were recorded through an electronic diseases early warning system. Microbiological culture, genomic sequencing, antimicrobial susceptibility and toxin production testing were performed. Findings: The Yemen diphtheria outbreak developed in three epidemic waves, which affected nearly all governorates (provinces) of Yemen, with 5701 probable cases and 330 deaths (October 2017 - April 2020). The median age of patients was 12 years (range, 0.17-80). Virtually all outbreak isolates (40 of 43 tested ones) produced the diphtheria toxin. We observed low level of antimicrobial resistance to penicillin. We identified six separate Corynebacterium diphtheriae phylogenetic sublineages, three of which are genetically related to isolates from Saudi Arabia and Somalia. The predominant sublineage was resistant to trimethoprim and was associated with unique genomic features, more frequent neck swelling ( p =0.002) and a younger age of patients ( p =0.06). Its evolutionary rate was estimated at 1.67 × 10 ⁻⁶ substitutions per site year ^-1 , placing its most recent common ancestor in 2015, and indicating silent circulation of C. diphtheriae in Yemen earlier than outbreak declaration. Interpretation: We disclose clinical, epidemiological and microbiological characteristics of one of the largest contemporary diphtheria outbreaks and demonstrate clinically relevant heterogeneity of C. diphtheriae isolates, underlining the need for laboratory capacity and real-time microbiological analyses to inform prevention, treatment and control of diphtheria. Funding: This work was supported by institutional funding from the National Centre of the Public Health Laboratories (Sanaa, Yemen) and Institut Pasteur (Paris, France) and by the French Government Investissement d ‘Avenir Program.

DNA methylation is influenced by both environmental and genetic factors and is increasingly thought to affect variation in complex traits and diseases. Yet, the extent of ancestry-related differences in DNA methylation, their genetic determinants, and their respective causal impact on immune gene regulation remain elusive. We report extensive population differences in DNA methylation between 156 individuals of African and European descent, detected in primary monocytes that are used as a model of a major innate immunity cell type. Most of these differences (~ 70%) are driven by DNA sequence variants nearby CpG sites, which account for ~ 60% of the variance in DNA methylation. We also identify several master regulators of DNA methylation variation in trans, including a regulatory hub nearby the transcription factor-encoding CTCF gene, which contributes markedly to ancestry-related differences in DNA methylation. Furthermore, we establish that variation in DNA methylation is associated with varying gene expression levels following mostly, but not exclusively, a canonical model of negative associations, particularly in enhancer regions. Specifically, we find that DNA methylation highly correlates with transcriptional activity of 811 and 230 genes, at the basal state and upon immune stimulation, respectively. Finally, using a Bayesian approach, we estimate causal mediation effects of DNA methylation on gene expression in ~ 20% of the studied cases, indicating that DNA methylation can play an active role in immune gene regulation. Using a system-level approach, our study reveals substantial ancestry-related differences in DNA methylation and provides evidence for their causal impact on immune gene regulation.

DNA methylation is influenced by both environmental and genetic factors and is increasingly thought to affect variation in complex traits and diseases. Yet, the extent of ancestry-related differences in DNA methylation, its genetic determinants, and their respective causal impact on immune gene regulation remain elusive. We report extensive population differences in DNA methylation between individuals of African and European descent — detected in primary monocytes that were used as a model of a major innate immunity cell type. Most of these differences (~70%) were driven by DNA sequence variants nearby CpG sites (meQTLs), which account for ~60% of the variance in DNA methylation. We also identify several master regulators of DNA methylation variation in trans , including a regulatory hub nearby the transcription factor-encoding CTCF gene, which contributes markedly to ancestry-related differences in DNA methylation. Furthermore, we establish that variation in DNA methylation is associated with varying gene expression levels following mostly, but not exclusively, a canonical model of negative associations, particularly in enhancer regions. Specifically, we find that DNA methylation highly correlates with transcriptional activity of 811 and 230 genes, at the basal state and upon immune stimulation, respectively. Finally, using a Bayesian approach, we estimate causal mediation effects of DNA methylation on gene expression in ~20% of the studied cases, indicating that DNA methylation can play an active role in immune gene regulation. Using a system-level approach, our study reveals substantial ancestry-related differences in DNA methylation and provides evidence for their causal impact on immune gene regulation.

Dengue fever is the most important vector-borne viral disease. Four serotypes of dengue virus, DENV1 to DENV4, coexist. Infection by one serotype elicits long-lasting immunity to that serotype but not the other three. Subsequent infection by a different serotype is a risk factor for severe dengue. Domain III (ED3) of the viral envelope protein interacts with cell receptors and contains epitopes recognized by neutralizing antibodies. We determined the serotype specificity and cross-reactivity of human IgMs directed against ED3 by using a well-characterized collection of 90 DENV-infected and 89 DENV-uninfected human serums. The recognitions between the four serotypes of ED3 and the serums were assayed with an IgM antibody-capture ELISA (MAC-ELISA) and artificial homodimeric antigens. The results were analyzed with Receiving Operator Characteristic (ROC) curves. The DENV-infected serums contained IgMs that reacted with one or several ED3 serotypes. The discrimination by ED3 between serums infected by the homotypic DENV and uninfected serums varied with the serotype in the decreasing order DENV1 > DENV2 > DENV3 > DENV4. The ED3 domain of DENV1 gave the highest discrimination between DENV-infected and DENV-uninfected serums, whatever the infecting serotype, and thus behaved like a universal ED3 domain for the detection of IgMs against DENV. Some ED3 serotypes discriminated between IgMs directed against the homotypic and heterotypic DENVs. The patterns of cross-reactivities and discriminations varied with the serotype. The results should help better understand the IgM immune response and protection against DENV since ED3 is widely used as an antigen in diagnostic assays and an immunogen in vaccine candidates.