Viral haemorrhagic fevers in the Middle East.

Viral haemorrhagic fevers (VHFs) are a group of infectious, devastating and severe diseases caused by enveloped single-stranded RNA viruses. The endemicity, emergence or re-emergence of different VHF viruses and lack of vaccines and antiviral therapy for most VHFs result in a significant global threat. Most VHF viruses are restricted to specific parts of the world, and the dramatic expansion of their geographical distribution beyond their original habitats would greatly affect global public health. In the past few decades alone, several outbreaks have affected the Middle East, a part of the world containing arid to semi-arid, hot and water-scarce countries. Political instability, natural and humanitarian crises, direct contact with domesticated animals and climate change are the main factors in the dissemination of different zoonotic diseases, including vector-borne diseases. Some VHF viruses have been introduced into the Middle East (e.g. Alkhurma haemorrhagic fever) and others have been re-introduced and have become endemic in the region. Dengue fever, Crimean Congo haemorrhagic fever, Rift Valley fever and hantavirus haemorrhagic fever with renal syndrome are examples of re-emerging or endemic viruses in the region. The temporal and spatial extension of VHF distribution mandates a particular engagement from all the actors in the fields of animal, human and environmental health. The One Health concept is a multidisciplinary and multisectoral approach for promoting collaboration, coordination and communication among different nations, sectors and disciplines, which is highly relevant to the fight against endemic, emerging and re-emerging infectious agents at the human-animal-environment interface. The adoption of the One Health approach is a promising solution to addressing public health threats in the Middle East.

Les fièvres hémorragiques virales constituent un groupe de maladies infectieuses graves et dévastatrices causées par des virus à ARN monocaténaire avec enveloppe. Du fait de leur caractère endémique, de l'existence dans ce groupe de plusieurs virus émergents et réémergents et de l'absence de vaccins et de thérapie antivirale contre la plupart d'entre eux, les fièvres hémorragiques virales représentent une menace importante à l'échelle mondiale. La plupart des virus responsables des fièvres hémorragiques virales étant présents dans des régions circonscrites de la planète, une extension incontrôlée de leur distribution géographique au-delà de leurs habitats d'origine serait un véritable danger pour la santé publique mondiale. Au cours des dernières décennies, plusieurs foyers se sont déclarés au Moyen-Orient. Les pays de cette région se caractérisent par un climat aride ou semi-aride et chaud et par de très faibles précipitations. L'instabilité politique, les catastrophes naturelles, les crises humanitaires, le contact direct avec des espèces domestiquées et le changement climatique sont les principaux facteurs de dissémination des maladies zoonotiques, y compris celles à transmission vectorielle. Certains virus responsables de fièvres hémorragiques (par exemple celui de la fièvre hémorragique d'Alkhurma) ont été détectés pour la première fois au MoyenOrient, tandis que d'autres y ont été réintroduits ou sont devenus endémiques. La dengue, la fièvre hémorragique de Crimée-Congo, la fièvre de la Vallée du Rift et la fièvre hémorragique à hantavirus avec syndrome rénal sont des exemples de maladies dues à des virus réémergents ou endémiques dans la région. En raison de leur distribution temporelle et spatiale, les fièvres hémorragiques virales demandent des efforts particuliers à l'ensemble des acteurs de la santé animale, publique et environnementale. Le concept Une seule santé désigne une méthode multidisciplinaire et multisectorielle visant à promouvoir la collaboration, la concertation et la communication entre différents pays, secteurs et disciplines ; elle se révèle particulièrement efficace dans la lutte contre les agents infectieux endémiques, émergents et réémergents à l'interface homme­animal­environnement. L'adoption de la méthode Une seule santé est une stratégie prometteuse pour le traitement des dangers qui menacent la santé publique au Moyen-Orient.

Las fiebres hemorrágicas víricas son un grupo de enfermedades infecciosas que revisten suma gravedad y resultan devastadoras, causadas por virus ARN monocatenarios dotados de envoltura. El carácter endémico, emergente o reemergente de distintos virus causantes de estas fiebres hemorrágicas y la falta de vacunas y tratamiento antivírico contra la mayoría de ellas se alían para hacer de estas patologías una importante amenaza de dimensión planetaria. La mayoría de los virus causantes de fiebres hemorrágicas están circunscritos a determinadas partes del mundo, y toda expansión sustancial de su distribución geográfica más allá de sus hábitats originales afectaría sobremanera la salud pública mundial. Solo en los últimos decenios se cuentan varios brotes que han afectado la región del Oriente Medio, una parte del mundo que alberga a países áridos o semiáridos, cálidos y con escasos recursos hídricos. La inestabilidad política, las crisis naturales y humanitarias, el contacto directo con animales domesticados y el cambio climático son los principales factores de diseminación de distintas enfermedades zoonóticas, entre ellas las enfermedades transmitidas por vectores. Algunos virus causantes de fiebres hemorrágicas han sido introducidos en el Oriente Medio (p.ej. el de la fiebre hemorrágica de Alkhurma) y otros, tras ser reintroducidos, han cobrado carácter endémico en la región. El dengue, la fiebre hemorrágica de Crimea-Congo, la fiebre del Valle del Rift y la fiebre hemorrágica por hantavirus con síndrome renal son otros tantos ejemplos de virus reemergentes o endémicos presentes en la región. La expansión temporal y espacial de la distribución de las fiebres hemorrágicas víricas obliga a redoblar esfuerzos a cuantos intervienen en los ámbitos de la salud animal, humana y ambiental. El concepto de Una sola salud supone un planteamiento pluridisciplinar y multisectorial para promover la colaboración, coordinación y comunicación entre diferentes naciones, sectores y disciplinas, lo que reviste suma importancia a la hora de combatir agentes infecciosos endémicos, emergentes o reemergentes en la interfaz de personas, animales y medio ambiente. La adopción de la lógica de trabajo de Una sola salud es una prometedora solución para abordar las amenazas que pesan sobre la salud pública en el Oriente Medio.

Whole-genome sequencing for rapid, reliable and routine investigation of Mycobacterium tuberculosis transmission in local communities.

Contact investigations following the diagnosis of active tuberculosis (TB) are paramount for the control of the disease. Epidemiological data are very powerful for contact tracing but might be delayed and/or difficult to integrate, especially in the setting of multiple contact-tracing investigations. The aim of this study was to address the added-value of whole-genome sequencing (WGS) to routine local TB surveillance systems. From November 2016 to July 2017, the local TB surveillance system identified three clusters that could constitute a unique larger outbreak. Epidemiological and clinical information were integrated with WGS genotyping data of Mycobacterium tuberculosis strains obtained using a simple DNA extraction method coupled with sequencing using an Illumina MiSeq platform and an in-house bioinformatics pipeline for single nucleotide polymorphism (SNP) analysis. Epidemiological investigations identified three putative TB clusters potentially interrelated including eight patients with active TB. Seven M. tuberculosis isolates were available and analysed by WGS. Using a 5-SNP threshold to define recent transmission, WGS-based genotyping supported the occurrence of the three clusters as well as a link between clusters 1 and 2 (SNP ≤1), constituting a larger outbreak. This outbreak was clearly delineated by refuting a potential link with the third cluster (SNP >500). Genotyping data did not support the belonging of patient 7 to any studied cluster. This study illustrates the usefulness of WGS genotyping for routine TB surveillance systems in local communities to rapidly confirm or disprove epidemiological hypotheses and delineate TB clusters, especially in the context of multiple contact-tracing investigations.

Rapid screening and diagnosis of tuberculosis: a real challenge for the mycobacteriologist.

Tuberculosis (TB) is an infectious, devastating and contagious disease, which infects third of the global population worldwide with high rates of incidence in the developing countries, where the health care providers face a serious problem and a real challenge during their clinical practice for controlling and preventing the transmission of this illness. Indeed the first step of control is the correct diagnosis and the initiation of the drug treatment regimen at the early stage of infection, which mandate the rapidity of screening and the accuracy of laboratory testing. In this paper we aim to highlight the different actual techniques, regarding the rapid screening and diagnosis of tuberculosis.

Mycobacterial species as case-study of comparative genome analysis.

The genus Mycobacterium represents more than 120 species including important pathogens of human and cause major public health problems and illnesses. Further, with more than 100 genome sequences from this genus, comparative genome analysis can provide new insights for better understanding the evolutionary events of these species and improving drugs, vaccines, and diagnostics tools for controlling Mycobacterial diseases. In this present study we aim to outline a comparative genome analysis of fourteen Mycobacterial genomes: M. avium subsp. paratuberculosis K­10, M. bovis AF2122/97, M. bovis BCG str. Pasteur 1173P2, M. leprae Br4923, M. marinum M, M. sp. KMS, M. sp. MCS, M. tuberculosis CDC1551, M. tuberculosis F11, M. tuberculosis H37Ra, M. tuberculosis H37Rv, M. tuberculosis KZN 1435 , M. ulcerans Agy99,and M. vanbaalenii PYR­1, For this purpose a comparison has been done based on their length of genomes, GC content, number of genes in different data bases (Genbank, Refseq, and Prodigal). The BLAST matrix of these genomes has been figured to give a lot of information about the similarity between species in a simple scheme. As a result of multiple genome analysis, the pan and core genome have been defined for twelve Mycobacterial species. We have also introduced the genome atlas of the reference strain M. tuberculosis H37Rv which can give a good overview of this genome. And for examining the phylogenetic relationships among these bacteria, a phylogenic tree has been constructed from 16S rRNA gene for tuberculosis and non tuberculosis Mycobacteria to understand the evolutionary events of these species.