CARD 2017: expansion and model-centric curation of the Comprehensive Antibiotic Resistance Database

Authors: JIA, BAOFENG - University Of Georgia; RAPHENYA, AMOGELANG - University Of Georgia; ALCOCK, BRIAN - University Of Georgia; WAGLECHNER, NICHOLAS - University Of Georgia; GUO, PEIYAO - University Of Georgia; TSANG, KARA - University Of Georgia; LAGO, BRIONY - University Of Georgia; DAVE, BIREN - University Of Georgia; PEREIRA, SHELDON - University Of Georgia; SHARMA, ARJUN - University Of Georgia; DOSHI, SACHIN - University Of Georgia; COURTOT, MELANIE - Simon Fraser University; LO, RAYMOND - Simon Fraser University; WILLIAMS, LAURA - Former ARS Employee; Frye, Jonathan

Submitted to: Nucleic Acids Research
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 10/17/2016
Publication Date: 10/26/2016
Citation: Jia, B., Raphenya, A., Alcock, B., Waglechner, N., Guo, P., Tsang, K., Lago, B., Dave, B., Pereira, S., Sharma, A., Doshi, S., Courtot, M., Lo, R., Williams, L., Frye, J.G. 2016. CARD 2017: expansion and model-centric curation of the Comprehensive Antibiotic Resistance Database. Nucleic Acids Research. doi:10.1093/nar/gkw1004.

Interpretive Summary: The development of Antimicrobial Resistant (AMR) bacteria in food animals presents a threat to food safety and human and animal health. To understand what is causing AMR, DNA sequencing of genes or whole bacterial genomes has been used to identify and characterize the genes that encode AMR. The DNA sequence from the bacterium being analyzed is compared to a database of AMR genes, and AMR genes in the strain are identified by DNA sequence homology. Therefore, the ability to detect and analyze AMR genes is highly dependent on using a complete and carefully annotated database of known AMR genes. To achieve this, we have developed the Comprehensive Antibiotic Resistance Database (CARD; http://arpcard.mcmaster.ca), which is a manually curated database containing high quality reference data on the molecular basis of AMR including the genes, proteins, and mutations involved in AMR. Its design allows the development of novel genome analysis tools, such as the Resistance Gene Identifier (RGI) for resistome prediction from raw genome sequences. CARD is a crucial tool in the research used to fight AMR and as such its development and continual update is key to understanding AMR and discovering ways to reduce AMRs impact on human health and food safety.

Technical Abstract: The Comprehensive Antibiotic Resistance Database (CARD; http://arpcard.mcmaster.ca) is a manually curated resource containing high quality reference data on the molecular basis of antimicrobial resistance (AMR), with an emphasis on the genes, proteins, and mutations involved in AMR. CARD is ontologically structured, model centric, and spans the breadth of AMR drug classes and resistance mechanisms, including intrinsic, mutation-driven, and acquired resistance. It is built upon the Antibiotic Resistance Ontology (ARO), a custom built, interconnected, and hierarchical controlled vocabulary allowing advanced data sharing and organization. Its design allows the development of novel genome analysis tools, such as the Resistance Gene Identifier (RGI) for resistome prediction from raw genome sequence. Recent improvements include extensive curation of additional reference sequences and mutations, development of a unique Model Ontology and accompanying AMR detection models to power sequence analysis, new visualization tools, and expansion of the RGI for detection of emergent AMR threats. CARD curation is updated monthly based on an interplay of manual literature curation, computational text mining, and genome analysis.