The Pathogen Detection project now offers the Microbial Browser for Identification of Genetic and Genomic Elements (MicroBIGG-E) that lets you browse anti-microbial resistance (AMR), stress response, virulence genes and genomic elements found in GenBank published isolate genomes from the NCBI Isolates Browser. Unlike the Isolates Browser that provides only a strain-level view of both published and unpublished genomes, MicroBIGG-E shows the location of these genes, how they were identified, plus phenotypic information (Figure 1).
Figure 1. Top panel. Portion of the MicroBIGG-E table display showing the results of a search (genes_on_contig:blaTEM-1 AND genes_on_contig:blaKPC*) for isolates that contain two different beta lactamase genes (blaTEM-1 and any of the carbapenem-hydrolyzing , blaKPC* ) on a single contig. Available columns include the element’s type, subtype, and class as well as information about how the element was identified and supporting evidence. Bottom panel. Graphical view of the annotation on a contig from one of the isolates, the assembled Serratia marcescens record NZ_CP020507 showing the two beta-lactamases in the search (blaTEM-1 and blaKPC-3) as well as an oxacillin-hydrolyzing gene (blaOXA-9). All three genes and some other AMR and stress response genes are part a mobile element on the assembled contig.