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.
Genes and genomic elements have been identified using AMRFinderPlus , and MicroBIGG-E contains detailed AMRFinderPlus results and associated metadata for individual AMRFinderPlus hits. Every row in the MicroBIGG-E display represents an anti-microbial resistance (AMR), stress response, and/or virulence-associated genetic element that has been identified in an isolate, and also includes information about how the element was identified, supporting evidence, and the element’s type, subtype, class, subclass, and more (Figure 1).
MicroBIGG-E supports the following analyses:
- Identification of contigs that contain sets of AMR, virulence or stress response genes, which could be associated with a mobile element, using the genes_on_contig feature as shown in Figure 1.
- Identification of genetic elements based on isolation source or other metadata. For example, you can show only genetic elements from environmental sources using the Isolation type filters.
- Cross-Browser selection that will open an Isolates Browser display with every isolate found in your MicroBIGG-E search where you can see the SNP-based clustering with other isolates; or, if you have a set of isolates you have identified in the Isolates Browser, Cross Browser selectin will display the MicroBIGG-E output for every selected isolate that is published in GenBank.
- Downloading a metadata table or an NCBI Datasets custom dataset, containing the nucleotide and protein sequences of the genetic elements, the contigs on which they are found, and a data report with key metadata in JSON lines format. For downloads of element sequences, you may include up to 2 kb of flanking sequence. The current contig download limit is 1,000 contigs.
As with other Pathogen Detection tools, MicroBIGG-E uses a new filter system that makes it easy to select the isolates you want.
If you have any suggestions or questions, please contact the NCBI Pathogen Detection team at pd-help@ncbi.nlm.nih.gov.