PATRIC May 2016 Release Features Over 700 New Genomes and AMR Panel Data for Approximately 1800 Genomes¶

Published on 2016-06-01 00:00:00

In this release, we have added 748 new genomes from NCBI GenBank, bringing the total number of genomes in PATRIC to over 70,000. The full list of available bacterial genomes can be accessed from the Genomes Tab for all bacteria, and from the Genomes Data Landing Page.

This release includes a special genome, corresponding to the first U.S. case of Colistin-resistant E. coli MRSN 388634. Sequence reads for MRSN388634 have been deposited in the NCBI Short Read Archive by researchers at the Walter Reed Army Institute of Research and Walter Reed National Military Medical Center under Accession number SRP075674. The authors report the presence of mcr-1 in an E. coli cultured from a patient with a urinary tract infection in the United States. The early version of the publication can be found here. A provisional assembly and annotation is provided in PATRIC using the PATRIC Genome Assembly and Genome Annotation services and can be accessed here.

This release also includes AMR panel data curated from publications for 1832 genomes. The AMR panel data is displayed on the corresponding genome overview pages. All available AMR panel data can be downloaded from here.

Finally, we have also added 10 eukaryotic host genomes in PATRIC, available available here. These mark our first step in supporting host response data linked to bacterial infection. After further refinements, these genomes will provide anchor for the host-pathogen protein-protein interactions and host response RNA-seq analysis capabilities we plan to provide later this year.