AcCNET (Accessory Genome Constellation Network): comparative genomics software for accessory genome analysis using bipartite networks

AcCNET (Accessory genome Constellation Network) is a Perl application that aims to compare accessory genomes of a large number of genomic units, both at qualitative and quantitative levels. Using the proteomes extracted from the analysed genomes, AcCNET creates a bipartite network compatible with standard network analysis platforms. AcCNET allows merging phylogenetic and functional information about the concerned genomes, thus improving the capability of current methods of network analysis. The AcCNET bipartite network opens a new perspective to explore the pangenome of bacterial species, focusing on the accessory genome behind the idiosyncrasy of a particular strain and/or population.This work was supported by the European Commission, Seven Framework Program (EVOTARFP7-HEALTH-282004 for VFL, FB, FdlC and TMC (PI15-00466) and PLASWIRES-612146/FP7-ICT-2013-10 for FdlC). Authors also acknowledge the European Development Regional Fund ‘A way to achieve Europe’ (ERDF) for cofounding the Plan Nacional de I + D+ I 2012-2015 (PI12-01581 to TMC and BFU2014-55534-C2-1-P for FdlC) and CIBER actions (CIBER in Epidemiology and Public Health, CIBERESP; CB06/02/0053 to FB) and the Regional Government of Madrid (PROMPT-S2010/BMD2414). Val F. Lanza is further supported by a Research Award Grant 2016 of the European Society for Clinical Microbiology and Infectious Diseases (ESCMID).Peer Reviewe

Enterococcus faecalis: nuevas perspectivas sobre la estructura poblacional y el impacto de los elementos genéticos móviles en la evolución

Enterococcus faecalis es una especie bacteriana generalista que habita en una amplia variedad de hospedadores como mamíferos, reptiles insectos y aves, siendo la causa potencial de graves infecciones en todos ellos. Esta especie es también uno de los principales patógenos nosocomiales y uno de los mayores vehículos de transmisión de genes de resistencia a antibióticos. Para definir la estructura poblacional de E. faecalis es importante identificar las principales líneas clonales causantes de infecciones en hospedadores relevantes. Existen estudios basados en el análisis de datos de MLST mediante la aplicación de herramientas como eBURST (Based Upon Related Sequence Types) o BAPS (Análisis Bayesiano de la Estructura Poblacional) así como de cgMLST (Core Genome Multilocus sequencing), los cuales revelan una estructura epidémica con una alta tasa de recombinación/ mutación. Estos estudios destacan las dificultades para establecer una estructura poblacional y para elucidar la historia evolutiva de algunos de los linajes clonales. Además el limitado número de genomas provenientes de hospedadores no-humanos y las escasas herramientas para analizar especies con alta recombinación impide la confirmación de esta hipótesis. Estudiar cepas de animales salvajes es una buena aproximación para expandir el conocimiento disponible sobre la estructura poblacional de E. faecalis. Estos hospedadores están sometidos a una gran variedad de presiones selectivas (como antibióticos, metales pesados, biocidas u otros compuestos) y tienen una amplia red de contactos en los distintos ambientes que promueven el intercambio y el flujo entre diferentes comunidades bacterianas. Además, recientemente hemos creado nuevas herramientas en nuestro grupo y con los consorcios en los que participamos que nos permiten un estudio profundo del pangenoma de E. faecalis..

Pangenome-guided tools for investigating the role of epsilonproteobacteria in human gastroenteritis : a thesis presented in partial fulfilment of the requirements for the degree of Doctor of Philosophy (PhD) in Veterinary Science at Massey University, Manawatu, New Zealand

Gastroenteritis affects billions of people every year and current testing methods fail to identify the cause for approximately half of the samples submitted for microbiological testing. Epsilonproteobacteria contains Campylobacter jejuni, the most commonly reported cause of bacterial gastroenteritis in the world, and Helicobacter pylori, a gastric pathogen and class I carcinogen. This bacterial class also contains ≥20 additional species known, or suspected, of being human pathogens. To better understand the role some of these species play in human gastroenteritis, novel rapid, cost effective methods are needed. The growing number of whole genome sequences available for this class were exploited to first evaluate the classification of the genetically heterogeneous species C. concisus and then to identify taxon-specific CDS for a range of Epsilonproteobacterial taxa. Probes were designed to detect 28 of these CDS and incorporated into a single multiplex ligation-dependent probe amplification (MLPA) assay which was tested against DNA from 43 Epsilonproteobacterial species and then applied to DNA extracts from stool samples from a childhood gastroenteritis case control study undertaken in Belgium. The 22 C. concisus genomes consistently clustered into two genomospecies (GS) represented by ATCC 33237T (GS1) and CCUG 19995 (GS2). Taxon-specific genes were identified for 28 taxa, including the two C. concisus genomospecies, and concordant results were observed for the majority of MLPA probes and DNA extracts from pure cultures. The probes designed to detect C. lari subsp. concheus and H. pullorum failed to detect the target DNA; all of the urease positive thermophilic Campylobacter DNA extracts were also positive for the probe designed to detect C. subantarcticus, some probes lacked repeatability in the presence of elevated EDTA and the size differences between some probes needs to be optimised. C. jejuni was the most common Epsilonproteobacterial species isolated by culture and C. concisus was the most common species detected by MLPA. Both C. jejuni and C. concisus GS2 were detected in significantly higher numbers in cases than controls in a Belgian childhood case control study. This demonstrated the utility of the Epsilonproteobacteria MLPA assay and provides some evidence that C. concisus GS2 may have a role in childhood gastroenteritis