Discovering a novel resistance gene for carbapenem resistance in Parabacteroides timonensis using Whole Genome Sequencing

Up to 95% of the human microbiome consists of anaerobic bacteria. However, they are not as well studied as the aerobic bacteria. Among all anaerobes, the Bacteroides group is the best known and most studied. There has been an increase in carbapenem resistance in Bacteroidales strains without a known cause.

We isolated a Parabacteroides timonensis strain, related to Bacteroides, resistant for amoxicillin, clindamycin and meropenem.

The strain was sequenced using the Miseq (Illumina, San Diego, CA), followed by a de novo assembly using CLC workbench to create a draft genome. Resistance genes were detected with ResFinder (https://cge.cbs.dtu.dk/services/ResFinder/). Genome annotation was performed by RAST (http://rast.nmpdr.org/). Protein modeling was performed, on genes of interest, using Phyre2 (http://www.sbg.bio.ic.ac.uk/phyre2/html/page.cgi?id=index) and 3DLigandSite (http://www.sbg.bio.ic.ac.uk/3dligandsite/). FatCat (http://fatcat.burnham.org/) was used to do a pairwise structure alignment to compare protein structures.

The draft genome had a size of 6,356,323 bp, present on 95 contigs. Using Resfinder 1 resistance gene was found, tetQ. A possible novel resistance gene for a metallo β-lactamase related to cfiA was found using RAST. The protein model showed similarities with the model for cfiA and includes several Zn2+ ions, used by metallo β-lactamase to hydrolyze carbapenems.

Our results indicate the presence of a not yet described metallo β-lactamase. There are also indications that a conjugative transposon is present, enabling horizontal gene transfer. No erm genes, encoding for clindamycin resistance, were detected in the draft genome.