DELEAT: gene essentiality prediction and deletion design for bacterial genome reduction.

BACKGROUND: The study of gene essentiality is fundamental to understand the basic principles of life, as well as for applications in many fields. In recent decades, dozens of sets of essential genes have been determined using different experimental and bioinformatics approaches, and this information has been useful for genome reduction of model organisms. Multiple in silico strategies have been developed to predict gene essentiality, but no optimal algorithm or set of gene features has been found yet, especially for non-model organisms with incomplete functional annotation. RESULTS: We have developed DELEAT v0.1 (DELetion design by Essentiality Analysis Tool), an easy-to-use bioinformatic tool which integrates an in silico gene essentiality classifier in a pipeline allowing automatic design of large-scale deletions in any bacterial genome. The essentiality classifier consists of a novel logistic regression model based on only six gene features which are not dependent on experimental data or functional annotation. As a proof of concept, we have applied this pipeline to the determination of dispensable regions in the genome of Bartonella quintana str. Toulouse. In this already reduced genome, 35 possible deletions have been delimited, spanning 29% of the genome. CONCLUSIONS: Built on in silico gene essentiality predictions, we have developed an analysis pipeline which assists researchers throughout multiple stages of bacterial genome reduction projects, and created a novel classifier which is simple, fast, and universally applicable to any bacterial organism with a GenBank annotation file.

[Wolbachia pipientis infections in populations of Aedes albopictus in the city of València (Spain): implications for mosquito control.] / Infecciones por Wolbachia pipientis en poblaciones de Aedes albopictus en la ciudad de València (España): implicaciones para el control de mosquitos.

OBJECTIVE: The presence of Aedes albopictus, of high sanitary and social impact, was first reported in Valencia (Eastern Spain) in 2015. Innovative tools for its control include the use of the endosymbiotic bacterium Wolbachia pipientis. The release of mosquito males infected with the wPip strain, has proven very promising for large-scale Incompatible Insect Technique (IIT) applications. Before this strategy can be implemented in Valencia, it is important to know whether the natural local mosquito populations are Wolbachia-infected and, if so, identifying the infecting strains/supergroups, these being the objectives of the present work. METHODS: Eggs were collected from the 19 districts of the València city between May and October 2019. A total of 50 lab-reared adult Ae. albopictus individuals were processed and analyzed for Wolbachia detection and molecular characterization. These actions took place within the framework of a collaboration established with the Department of Health and Consumer Affairs of the city council of Valencia. Fisher's exact test was used to detect the statistical significance of the differences between groups. RESULTS: Our study revealed that 94% of the analyzed samples were naturally infected with Wolbachia. Both wAlbA and wAlbB supergroups were identified, with most samples (72% of the infected ones) carrying co-infections. CONCLUSIONS: These data provide the first characterization of the Wolbachia presence in natural populations of Ae. albopictus in the Mediterranean area of Spain. This information is relevant to evaluate the potential use of Wolbachia strains in order to achieve the suppression of the Asian tiger mosquito populations through massive release of artificially-infected males.

OBJETIVO: La presencia de Aedes albopictus, de alto impacto sanitario y social, se informó por primera vez en Valencia en 2015. Las herramientas innovadoras para su control incluyen el uso de la bacteria endosimbiótica Wolbachia pipientis. La liberación de mosquitos machos infectados con la cepa wPip ha demostrado ser muy prometedora para aplicar la Técnica de Insectos Incompatibles (IIT) a gran escala. Antes de que esta estrategia pueda implementarse, es importante saber si las poblaciones locales de mosquitos silvestres están infectadas por Wolbachia y, de ser así, identificar las cepas/supergrupos infectantes, siendo estos los objetivos del presente trabajo. METODOS: Se recolectaron huevos de los diecinueve distritos de València entre mayo y octubre de 2019, y se mantuvieron en el laboratorio hasta llegar a adultos. Un total de cincuenta individuos adultos de Ae albopictus fueron procesados y analizados para detectar la presencia de Wolbachia y su caracterización molecular. Estas acciones se enmarcaron en la colaboración establecida con la Concejalía de Salud y Consumo del Ayuntamiento de València. La prueba exacta de Fisher fue utilizada para detectar la significación estadística de las diferencias entre grupos. RESULTADOS: El 94% de las muestras analizadas estaban infectadas de forma natural con Wolbachia. Se identificaron los supergrupos wAlbA y wAlbB, y la mayoría de las muestras (72% de las infectadas) presentaban coinfecciones. CONCLUSIONES: Los datos proporcionan la primera caracterización de la presencia de Wolbachia en poblaciones naturales de Ae. albopictus en el área mediterránea de España. Esta información es relevante para evaluar el potencial uso de cepas de Wolbachia de cara a la supresión de poblaciones de mosquito tigre asiático mediante la liberación masiva de machos infectados artificialmente.