A new STM report has been evaluated from the 2019-2020 call.  Vicente López Chavarrías from VISAVET - Health Surveillance Centre (UCM), Spain visited Prof. Andres Pereez, Dr Ehud Elnekave and Seunghyun Lim at the Centre for Animal Health and Food Safety (CAHFS), University of Minnesota (UMN), United States from 12th October to 12th December 2019 to study Use of NGS to characterize co-resistance to critically important antimicrobials in thermophilic Campylobacter from livestock in Spain and the US.

Vicente Lopez Charvarrias


Training in the design and use of Next Generation Sequencing (NGS) pipelines for analysis of whole genome sequencing information from foodborne pathogens. Analysis of sets of WGS data from the US and Spain to acquire skills to be able to compare data sets from both countries, that in turn will help to frame results/conclusions of applicant PhD project in a European epidemiological context.


Vicente was trained in the different steps involved in the analysis of whole genome sequences from bacteria, taking as a model Salmonella serovar Kentucky with the goal of applying the same steps on Campylobacter strains as part of his PhD project. The work was performed using the services of the Minnesota Supercomputing Institute and its big data processing capabilities.

The analysis carried out focused on:

- alignment of WGS of isolates from Spain and the US to a reference genome, which enabled the reconstruction of phylogeny trees based on similarity

- assemblies of genomes, obtaining ‘contigs’ that were used for detection of genes, plasmids, and virulence factors, among others, and

- building of phylo-genetic trees with the analysed Salmonella Kentucky sequences

The expected outputs of the short-term mission (receiving training on WGS analysis and characterizing sequences of Salmonella Kentucky strains from Spain and compared those with strains from the US) were successfully achieved.

 Building where I workedEntrance to campusOn the way to uni autumn

Building where I worked     Entrance to campus          On the way to the uni-autumn

On the way to the uni winterUniversity of MinnesotaVicente Lopez Chavarrias

On the way to uni-Winter                University of Minnesota       Vicente López Chavarrías