Human cytomegalovirus prevalence and distribution of glycoprotein B, O genotypes among hospitalized children with respiratory infections in West China, 2009-2014.

OBJECTIVES: Human cytomegalovirus (HCMV) is an important pathogen causing morbidity and mortality in children. HCMV prevalence in children with respiratory infections has not been investigated in West China. Previous studies have suggested that glycoproteins genotypes may be associated with different clinical presentations, but the associations were controversial. The aim of this study was to determine the prevalence of HCMV infection in children with respiratory infections, the distributions of gB, gO genotypes among these isolates and their potential predictive roles for the development of symptoms in children. METHODS: A total of 1709 respiratory specimens were obtained from hospitalised children with respiratory symptoms from 2009 to 2014 for the confirmation of HCMV infection. Glycoprotein B,O genotyping was carried out by multiplex nested PCR and sequencing. RESULTS: The overall infection rate was 10.8%, and dominant genotypes were gB1 (74.2%) and gO1 (37.1%). Clinical characteristics differed between infants and children >1 year of age. Infants infected with HCMV had a higher frequency of fever (P < 0.001), cough (P < 0.001), rhinorrhea (P < 0.001), expectoration (P = 0.001) and diarrhoea (P = 0.005). Children <1 year age infected with gB1 had a higher rate of cough (P = 0.0192). CONCLUSIONS: Infants infected with HCMV had a severe clinical outcome. gB1 may negatively associate with clinical presentations and quality of life in these children. The prevalence of HCMV infection and genotype distribution emphasises the importance of HCMV screening, vaccination and control for transmission.

Standard finishing categories for high-throughput sequencing of viral genomes.

Viral genome sequencing has become the cornerstone of almost all aspects of virology. In particular, high-throughput, next-generation viral genome sequencing has become an integral part of molecular epidemiological investigations into outbreaks of viral disease, such as the recent outbreaks of Middle Eastern respiratory syndrome, Ebola virus disease and Zika virus infection. Multiple institutes have acquired the expertise and necessary infrastructure to perform such investigations, as evidenced by the accumulation of thousands of novel viral sequences over progressively shorter time periods. The authors recently proposed a nomenclature comprised of five high-throughput sequencing standard categories to describe the quality of determined viral genome sequences. These five categories (standard draft, high quality, coding complete, complete and finished) cover all levels of viral genome finishing and can be applied to sequences determined by any technology platform or assembly technique.

Le séquençage des génomes viraux est devenu la pierre angulaire de pratiquement toutes les facettes de la virologie. En particulier, le séquençage à haut débit de nouvelle génération est désormais une partie intégrante des enquêtes d'épidémiologie moléculaire relatives aux foyers de maladies virales, par exemple les récentes épidémies du syndrome respiratoire du Moyen-Orient, la maladie due au virus Ebola ou l'infection par le virus Zika. Nombre d'institutions ont acquis les compétences techniques et les infrastructures nécessaires pour réaliser ce type d'enquêtes, comme en témoigne l'accumulation de milliers de séquences virales nouvelles obtenues en un laps de temps de plus en plus court. Les auteurs ont récemment élaboré une nomenclature constituée de cinq catégories de référence décrivant la qualité des séquences d'un génome viral obtenues par séquençage à haut débit. Ces cinq catégories (ébauche de référence, séquence de haute qualité, séquence codante complète, séquence complète et séquence finie) couvrent toutes les étapes de la finition du génome viral et s'appliquent quelle que soit la plateforme technologique ou la technique d'assemblage utilisée pour déterminer la séquence.

La secuenciación del genoma vírico se ha erigido a día de hoy en la piedra angular de casi todos los aspectos de la virología. La secuenciación de alto rendimiento de próxima generación, en particular, es ahora un componente integral de las investigaciones de epidemiología molecular sobre brotes de enfermedades víricas como los registrados últimamente de síndrome respiratorio de Oriente Medio, enfermedad por el virus del Ebola o infección por el virus Zika. Numerosas instituciones se han dotado de las competencias técnicas y la infraestructura necesaria para llevar a cabo tales investigaciones, como deja patente la acumulación de miles de nuevas secuencias víricas en periodos de tiempo cada vez más cortos. En fechas recientes los autores han propuesto una nomenclatura compuesta de cinco categorías de referencia que sirven para describir la calidad de las secuencias de genoma vírico determinadas por secuenciación de alto rendimiento. Estas cinco categorías (borrador normal, gran calidad, codificación completa, completa y acabada) cubren toda la gradación de acabados en la secuenciación de genoma vírico y pueden ser aplicadas a las secuencias obtenidas por cualquier dispositivo técnico o cualquier técnica de ensamblaje.

Using genomics data to reconstruct transmission trees during disease outbreaks.

Genetic sequence data from pathogens present a novel means to investigate the spread of infectious disease between infected hosts or infected premises, complementing traditional contact-tracing approaches, and much recent work has gone into developing methods for this purpose. The objective is to recover the epidemic transmission tree, which identifies who infected whom. This paper reviews the various approaches that have been taken. The first step is to define a measure of difference between sequences, which must be done while taking into account such factors as recombination and convergent evolution. Three broad categories of method exist, of increasing complexity: those that assume no withinhost genetic diversity or mutation, those that assume no within-host diversity but allow mutation, and those that allow both. Until recently, the assumption was usually made that every host in the epidemic could be identified, but this is now being relaxed, and some methods are intended for sparsely sampled data, concentrating on the identification of pairs of sequences that are likely to be the result of direct transmission rather than inferring the complete transmission tree. Many of the procedures described here are available to researchers as free software.

L'accès aux données sur les séquences génétiques des agents pathogènes ouvre de nouvelles perspectives pour étudier la manière dont les maladies infectieuses se propagent entre différents hôtes ou établissements infectés, en complément des méthodes traditionnelles d'évaluation de l'exposition ; de grands efforts ont donc été déployés pour mettre au point des techniques permettant d'arriver à cette fin. Leur objectif est de reconstituer l'arborescence de la transmission d'une épidémie, ce qui permet d'identifier chaque individu ayant infecté d'autres individus. Les auteurs passent en revue les différentes méthodes appliquées. La première étape consiste à définir les modalités de mesure des différences entre séquences, ainsi que les facteurs à prendre en compte, par exemple les phénomènes de recombinaison ou d'évolution convergente. Les méthodes disponibles se répartissent en trois catégories principales, par ordre de complexité croissante : celles qui présupposent qu'il ne peut y avoir de diversité ni de mutation génétiques chez l'hôte ; celles qui présupposent qu'il peut y avoir une diversité génétique mais pas de mutation ; enfin celles qui présupposent qu'il peut y avoir les deux. Jusqu'à une période récente, le présupposé le plus courant était que tous les hôtes intervenant dans un foyer pouvaient être identifiés ; cette exigence s'est considérablement assouplie et de nouvelles méthodes ont été conçues pour travailler à partir d'un échantillon de données plus clairsemé, ce qui permet de se concentrer sur l'identification de paires de séquences révélatrices d'une transmission directe au lieu de déduire l'intégralité de l'arbre de transmission. La plupart des procédures décrites par les auteurs existent sous forme de logiciels libres accessibles aux chercheurs.

Los datos de la secuencia genética de patógenos ofrecen un medio novedoso para investigar la propagación de enfermedades infecciosas entre individuos o establecimientos infectados, medio que viene a complementar la fórmula tradicional consistente en rastrear los contactos. De ahí que últimamente se haya dedicado un ingente trabajo a definir métodos útiles para ese fin. El objetivo radica en desentrañar el árbol de transmisión epidémica, que permite determinar quién infectó a quién. Los autores pasan revista a los diferentes planteamientos adoptados. El primer paso consiste en definir una medida de la diferencia entre secuencias, para lo cual hay que tener en cuenta factores como la recombinación o la convergencia evolutiva. Existen tres grandes clases de métodos, que presentan un grado creciente de complejidad: aquellos que presuponen que no hay diversidad genética ni mutaciones dentro del individuo infectado; aquellos que presuponen que no hay diversidad, pero admiten la posibilidad de mutaciones; y aquellos que postulan que ambas cosas pueden producirse. Hasta hace poco, en general se partía de la premisa de que era posible identificar a todos los individuos infectados en una epidemia. Ahora, sin embargo, se está flexibilizando este postulado, y existen métodos que se aplican específicamente a datos obtenidos con muestreos dispersos, con los cuales se trata de determinar pares de secuencias que probablemente sean resultado de la transmisión directa, y no tanto de inferir el árbol de transmisión completo. Muchos de los procedimientos aquí descritos están a disposición de los investigadores en forma de programas informáticos gratuitos.

Genomics and outbreaks: foot and mouth disease.

Foot and mouth disease virus (FMDV) is an animal pathogen of global economic significance. Identifying the sources of outbreaks plays an important role in disease control; however, this can be confounded by the ease with which FMDV can spread via movement of infected livestock and animal products, aerosols or fomites, e.g. contaminated persons and objects. As sequencing technologies have advanced, this review highlights the uses of viral genomic data in helping to understand the global distribution and transboundary movements of FMDV, and the role that these approaches have played in control and surveillance programmes. The recent application of next-generation sequencing platforms to address important epidemiological and evolutionary challenges is discussed with particular reference to the advent of 'omics' technologies.

Le virus de la fièvre aphteuse est un agent pathogène affectant les animaux d'élevage, avec des conséquences économiques considérables à l'échelle mondiale. La détection des sources des foyers est un aspect important de la lutte contre cette maladie ; l'efficacité de cette stratégie est toutefois compromise par la facilité avec laquelle le virus de la fièvre aphteuse se propage à la faveur des mouvements d'animaux ou de produits d'origine animale infectés, d'aérosols ou de personnes ou matières contaminées. Les auteurs décrivent, au fur et à mesure des avancées des technologies du séquençage, les données de la génomique virale qui ont permis de mieux comprendre la distribution mondiale et la propagation transfrontalière du virus de la fièvre aphteuse et le rôle que ces approches ont commencé à jouer dans les programmes de contrôle et de surveillance. Les auteurs examinent également les applications récentes des plates-formes de séquençage de nouvelle génération pour résoudre des problèmes épidémiologiques et évolutifs importants, en se référant particulièrement à l'avènement des technologies dites «­omiques ¼.

El virus de la fiebre aftosa es un patógeno animal que reviste importancia planetaria. A la hora de combatir la enfermedad es útil poder determinar el origen de los brotes, tarea que sin embargo puede verse frustrada por la facilidad con que el virus es capaz de diseminarse siguiendo los desplazamientos de animales o derivados animales infectados o por aerosoles o fómites (por ejemplo personas u objetos contaminados). Los autores hacen hincapié en la utilización de datos de genómica vírica para ayudar a aprehender la distribución mundial y los movimientos transfronterizos del virus de la fiebre aftosa, lo cual es posible gracias a los avances que han conocido las técnicas de secuenciación, así como en la función que pueden cumplir estos métodos dentro de los programas de control y vigilancia. También examinan la reciente aplicación de dispositivos de secuenciación de próxima generación para abordar importantes problemas epidemiológicos y evolutivos, refiriéndose especialmente al advenimiento de las técnicas «ómicas¼.

Molecular epidemiology of tuberculosis in Havana, Cuba, 2009.

OBJECTIVES: To estimate the proportion of tuberculosis cases attributable to recent transmission and the risk factors possibly associated with tuberculosis clustering. METHODS: Population-based study combining information from epidemiological investigation of tuberculosis cases notified to the National Tuberculosis Control Program in Havana, Cuba, in 2009 with the results of genotyping of Mycobacterium tuberculosis isolates with variable number tandem repeat of mycobacterial interspersed repetitive units (MIRU-VNTR) typing. RESULTS: Of 186 cases, 61 were genotyped: 33 patterns and five clusters with 19, 7, 3, 2 and 2 cases were found. The proportion of cases due to recent transmission was 45% (95% confidence interval 33-58%). Routine contact investigation failed to identify a substantial number of epidemiological links. A history of living in a closed setting was strongly associated with clustering. CONCLUSIONS: The proportion of cases due to recent transmission in Havana in 2009 is high. The existing control measures in closed settings should be strengthened. A study on a larger number of cases and for a longer time period should be carried out to obtain more precise estimates. Further studies on the utility and cost-effectiveness of the addition of molecular epidemiology techniques to support the progress towards tuberculosis elimination in Cuba, a low-incidence resource-limited setting, are also needed.

Identifying locations of recent TB transmission in rural Uganda: a multidisciplinary approach.

OBJECTIVES: Targeting high Tuberculosis (TB) transmission sites may offer a novel approach to TB prevention in sub-Saharan Africa. We sought to characterise TB transmission sites in a rural Ugandan township. METHODS: We recruited adults starting TB treatment in Tororo, Uganda, over 1 year. Fifty four TB cases provided names of frequent contacts, sites of residence, health care, work and social activities, and two sputum samples. Mycobacterium tuberculosis (MTB) culture-positive specimens underwent spoligotyping to identify strains with shared genotypes. We visualised TB case social networks, and obtained, mapped and geo-coded global positioning system measures for every location that cases reported frequenting 1 month before treatment. Locations of spatial overlap among genotype-clustered cases were considered potential transmission sites. RESULTS: Six distinct genotypic clusters were identified involving 21 of 33 (64%) MTB culture-positive, genotyped cases; none shared a home. Although 18 of 54 (33%) TB cases shared social network ties, none of the genotype-clustered cases shared social ties. Using spatial analysis, we identified potential sites of within-cluster TB transmission for five of six genotypic clusters. All sites but one were healthcare and social venues, including sites of drinking, worship and marketplaces. Cases reported spending the largest proportion of pre-treatment person-time (22.4%) at drinking venues. CONCLUSIONS: Using molecular epidemiology, geospatial and social network data from adult TB cases identified at clinics, we quantified person-time spent at high-risk locations across a rural Ugandan community and determined the most likely sites of recent TB transmission to be healthcare and social venues. These sites may not have been identified using contact investigation alone.

Staphylococcus aureus native arthritis over 10 years.

OBJECTIVES: Septic arthritis is associated with significant case fatality and morbidity. Staphylococcus aureus is the most common cause of arthritis. We aimed to analyze the microbiological features of S. aureus causing native arthritis and to investigate their influence on the clinical outcome of the infection. PATIENTS AND METHODS: We conducted a retrospective study including all episodes of S. aureus native arthritis between 2005-2015. Phenotypic (antimicrobial susceptibility, ß-hemolysis, agr functionality, biofilm formation) and genotypic characteristics (pulsed-field gel electrophoresis, DNA microarrays) were investigated. The primary endpoint was microbiological failure of treatment, including infection relapse, persistence, or attributable death. RESULTS: Twenty-nine patients were included (65.5% of men, mean age: 59): seven (24.1%) patients presenting with methicillin-resistant S. aureus (MRSA) native arthritis and 19 with methicillin-susceptible S. aureus (MSSA) native arthritis. Treatment failure occurred in seven (26.9%) patients (4/7 patients [57.1%] among MRSA infections vs. 3/19 [15.8%] among MSSA infections). The persistence rate was similar in MRSA and MSSA infections (1/7 vs. 3/19). However, the case fatality was significantly higher in patients with MRSA infection (3/7 vs. 0/19). The most frequent clonal complex (CC) was CC5 (38.1%). MSSA showed higher genetic variability (nine CCs) versus MRSA (3 CCs). CONCLUSIONS: Beyond methicillin resistance, we did not find phenotypic or genotypic factors associated with the poor outcome of S. aureus native arthritis. CC5 was the major CC, showing the higher genetic variability of MSSA versus MRSA.

[The virological and epidemiological aspects of human adenoviral conjunctivitis in Tunisia]. / Aspects épidémiologiques et virologiques de la conjonctivite à adénovirus en Tunisie.

Human adenoviruses (HAdV) are the main cause of viral conjunctivitis. In Tunisia and North Africa more generally, there is no regular nationwide surveillance program that monitors viruses causing conjunctivitis and keratoconjunctivitis. In this study, we report the results of HAdV screening in conjunctival samples collected for over 14 years in Tunisia. A total of 282 conjunctival samples received between 2000 and 2013 were investigated. Detection and identification of genotype were performed by PCR-sequencing at the hexon gene; 64.5% of samples (n=182) revealed positive by PCR detection without correlation noted between infection, age, sex, social class or clinical manifestations of viral conjunctivitis. HAdV-D8 was the largely predominant genotype in Tunisia, representing 81.3% of all isolates, and was detected continuously from 2000 to 2013. Minor co-circulating genotypes were also identified - HAdV-E4, HAdV-B3, B55 and HAdV-B7 - accounting for 10.7%, 4.9%, 1.9% and 0.9% of isolates, respectively. In conclusion, this work reports epidemiological data on adenoviral conjunctivitis from a region where such information is very scarce and contributes to a better knowledge of the worldwide distribution of causative genotypes. It also presents an approach for the identification of circulating HAdV in the country and demonstrates the importance of molecular tools for both detection and identification of genotypes, which allow rapid virological investigation, especially during epidemics.