1.4 MicroBIGG E

The Microbial Browser for Identification of Genetic and Genomic Elements (MicroBIGG-E) has a feature, genes_on_contig, which allows users to identify contigs that contain a set of genetic elements. To demonstrate this feature, we will use a subset of genes that co-occur in a common mobile element of Pseudomonas aeruginosa (sul1, qacEdelta1, aadA1, blaOXA-10) associated with an outbreak of NDM-1 carbapenemase-containing P. aeruginosa; more information available on this outbreak can be found here.

Go to MicroBIGG-E: https://www.ncbi.nlm.nih.gov/pathogens/microbigge/

Use the line command below to identify contigs containing sul1, qacEdelta1, aadA1, blaOXA-10.

line command:

genes_on_contig:sul1 AND genes_on_contig:qacEdelta1 AND genes_on_contig:aadA1 AND genes_on_contig:blaOXA-10

link: https://www.ncbi.nlm.nih.gov/pathogens/microbigge/#genes_on_contig:sul1%20AND%20genes_on_contig:qacEdelta1%20AND%20genes_on_contig:aadA1%20AND%20genes_on_contig:blaOXA-10

As with the tables in other browsers, the table can be downloaded as a .tsv file, but users also can download the contigs themselves, along with the sequences (protein and nucleotide) of the elements themselves:

Do any of these contigs also contain blaNDM-1?

Go to Filters, select "Element symbol", and then enter "blaNDM-1" into the search bar. This will display the number of the selected contigs with blaNDM-1.