Accurate automated annotation of DNA sequences related to antibiotic resistance in Gram-Negative bacteria

Abstract

Gram-negative bacteria resistant to multiple antibiotics are an increasing global health problem. This resistance is largely due to resistance genes ‘captured’ by mobile genetic elements that move them between DNA molecules in the same cell. Multi-resistance spreads because genes conferring resistance to different classes of antibiotics and associated mobile elements are found in complex modular clusters on resistance plasmids that can transfer between cells, including different species. Increasing numbers of such plasmids are being sequenced, including by next-generation methods, but are often poorly annotated as current analysis software only gives general names to genes and suggest putative functions. We have developed an automated annotation system (Attacca) for DNA sequences relating to antibiotic resistance in Gram-negative bacteria that accurately and precisely annotates resistance genes and associated mobile elements. Attacca uses a database of relevant ‘features’ and computational grammars derived known rules about the behaviour of different mobile elements to annotate fragments of features and find informative signals that give information about movement of mobile elements. Attacca also creates diagrams of annotated sequences that facilitate detailed comparative analysis to help understand the evolution and spread of multi-resistance. We plan to make Attacca available via a website.