chewBBACA: A complete suite for gene-by-gene schema creation and strain identification

posted Aug 9, 2017, 6:36 AM by Mirko Rossi   [ updated Aug 9, 2017, 6:36 AM ]

Mickael Silva, Miguel P. Machado, Mirko Rossi, Jacob Moran-Gilad, Sergio Santos, Mario Ramirez, Joao Andre Carrico

Motivation: Gene-by-gene (GbG) approaches are becoming increasingly popular in bacterial genomic epidemiology and outbreak detection. However, there is a lack of open source software for schema definition and allele calling. Results: The chewBBACA suite was designed to assist users in the creation and evaluation of novel whole-genome or core-genome GbG schemas and allele calling in bacterial strains of interest. The alleles called by chewBBACA are potential coding sequences, allowing the user to evaluate the possible consequences of the observed diversity. The software can run in a laptop or in high performance clusters making it useful for both small laboratories and large reference centers. Availability:

link to bR

Whole-genome sequencing in the epidemiology of Campylobacter jejuni infections

posted Mar 15, 2017, 1:24 AM by Mirko Rossi   [ updated Mar 15, 2017, 1:25 AM ]

Llarena AK, Taboada E, Rossi M. J Clin Microbiol. 2017 Mar 1. pii: JCM.00017-17. doi: 10.1128/JCM.00017-17

This review provides the current state of knowledge on the application of whole-genome sequencing (WGS) in the epidemiology of Campylobacter jejuni, the leading cause of bacterial gastroenteritis worldwide. We describe how WGS has increased our understanding of the evolutionary and epidemiological dynamics of this pathogen and how WGS has the potential to improve surveillance and outbreak detection. We have identified hurdles towards the full implementation of WGS in public health settings. However, despite these challenges, we believe that ample evidence is available to support the benefit of integrating WGS in the routine monitoring of C. jejuni infections and outbreak investigations.

Monomorphic genotypes within a generalist lineage of Campylobacter jejuni show signs of global dispersion

posted Mar 15, 2017, 1:21 AM by Mirko Rossi

Llarena A, Zhang J, Vehkala M, Välimäki N, Hakkinen M, Hänninen M, Roasto M, Mäesaar M, Taboada E, Barker D, Garofolo G, Cammà C, Di Giannatale E, Corander J, Rossi M. 01/10/2016. M Gen 2(10): doi:10.1099/mgen.0.000088

The decreased costs of genome sequencing have increased the capability to apply whole-genome sequencing to epidemiological surveillance of zoonotic Campylobacter jejuni. However, knowledge of the genetic diversity of this bacteria is vital for inferring relatedness between epidemiologically linked isolates and a necessary prerequisite for correct application of this methodology. To address this issue in C. jejuni we investigated the spatial and temporal signals in the genomes of a major clonal complex and generalist lineage, ST-45 CC, by analysing the population structure and genealogy as well as applying genome-wide association analysis of 340 isolates from across Europe collected over a wide time range. The occurrence and strength of the geographical signal varied between sublineages and followed the clonal frame when present, while no evidence of a temporal signal was found. Certain sublineages of ST-45 formed discrete and genetically isolated clades containing isolates with extremely similar genomes regardless of time and location of sampling. Based on a separate data set, these monomorphic genotypes represent successful C. jejuni clones, possibly spread around the globe by rapid animal (migrating birds), food or human movement. In addition, we observed an incongruence between the genealogy of the strains and multilocus sequence typing (MLST), challenging the existing clonal complex definition and the use of whole-genome gene-by-gene hierarchical nomenclature schemes for C. jejuni.

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