Internet-Based Solutions for Analysis of Next-Generation Sequence Data

LETTER

I have with great interest read the paper “Outbreak Investigation Using High-Throughput Genome Sequencing within a Diagnostic Microbiology Laboratory” by Sherry and colleagues (1). A point of this paper is that there is a paucity of user-friendly and clinically focused bioinformatics platforms for analysis of next-generation sequencing (NGS) data. Furthermore, the authors state, “No automated method to screen NGS data for a wide range of antimicrobial resistance determinants is freely available.” We would like to draw attention to the services provided by the Center for Genomic Epidemiology, Technical University of Denmark (http://www.genomicepidemiology.org/). The aim of this center is to provide user-friendly and Internet-based solutions for the global scientific and medical communities for rapid analysis of prokaryotic whole-genome sequence data. We published the first service, which enables multilocus sequence typing of 66 different bacterial species based on NGS data, in the Journal of Clinical Microbiology in April 2012 (2) (the service is available at http://cge.cbs.dtu.dk/services/MLST/). Since then, we have published the ResFinder method (3) (http://cge.cbs.dtu.dk/services/resfinder/) for the identification of acquired antimicrobial resistance genes and the snpTree method (4) (http://cge.cbs.dtu.dk/services/snptree/) for the identification of single-nucleotide polymorphisms (SNPs) and the construction of phylogenetic trees. We are currently in the process of developing additional services, e.g., for species identification, plasmid identification and typing, detection of virulence genes, and prediction of pathogenic potential. All services are free to use and aim at being simple and easy to use, even for people without an informatics background.