When exposed to antibiotics, microbial communities respond not only by changing composition, but also by evolving, optimizing and disseminating antibiotic resistance genes (ARGs), collectively termed resistomes. The human gut microbiota is considered a reservoir for ARGs, where microbes exchange these genes thereby propagating resistance. Development and spread of microbial antibiotic resistance is a serious health concern given that once reliable antibiotics now fail.
The effects on the microbiota depends on initial microbiota status. Together with other collaborators we have recently showed that after a multidrug combination the human gut microbiota of healthy young adults recovered to the initial state ~ 42 days after treatement. However, some species were lost (eg. Bifidobacterium spp.). Right after the antibiotic exposure we observed the increase of opportunistic pathogens with colonization and virulence potential.
Using shotgun metagenomics we can map sequence reads to our microbial gene catalogs annotated using curated ARG databases. This allows us to study the resistome of your study samples. Using the metagenomics species (MGS) concept we can link the ARGs to species and thus label these as resistant or non-resistant. Resistome analysis can be used for investigating:
- How antibiotics impact the level of resistance genes during and after treatment
- Effects of antibiotics on the gut microbiome composition and specific species
- How other treatments and interventions impact the level of antibiotic resistance genes
Albert Pallejà Caro, PhD, Bioinformatics Specialist
Resistome analysis expert at Clinical Microbiomics.
Antibiotic resistance databases
To annotate our microbial gene catalogs we use the Comprehensive Antibiotic Resistance Database (CARD). This database is a manually curated reference based resource containing genes, proteins and mutations related to antibiotic resistance. It is based on the Antibiotic Resistance Ontology (ARO) - interconnected and hierarchical controlled vocabulary of antimicrobial molecules and their targets, resistance mechanisms, genes and mutations, and their relationships. CARD currently gathers 2540 antimicrobial resistance models and the database curation is updated monthly based on manual literature curation, computational text mining, and genome analysis