Comparative phylogenetics of ICEHin1056 family reveals deep evolutionary associations of mobile genetic elements responsible for transfer of antibiotic resistance genes

Abstract

BackgroundIntegrating and conjugating elements (ICEs) are self-transmissible mobile genetic elements. ICEs are composed of modules of conserved genes, with accessory genes at hotspots. Antibiotic resistance genes are often encoded on ICEs, leading to rapid intraspecific and interspecific spread of resistance. Our aim was to study ICEs with homology to ICEHin1056 in Haemophilus influenzae using the large number of whole genome sequences now available. MethodsMembers of the ICEHin1056 family were identified with tBLASTx searches on the National Center for Biotechnology Information genome database. The query sequences were concatenated core genes from ICEHin1056. Alignments were performed with the Artemis Comparison Tool. Sequences were stored in a BIGS (Bacterial Isolate Genome Sequence) database and homologues of core genes identified. Alignments were performed in ClustalW and phylogenetic trees drawn with MEGA (Molecular Evolutionary Genetics Analysis). Ancestral sequences were predicted with GASP (Gapped Ancestral Sequence Prediction). Predicted ancestral sequences were used as BLAST inputs to find further possible members of the ICE family and more distant relatives. FindingsWe identified over 100 whole or partial sequences in the ICEHin1056 family in a-proteobacteria, b-proteobacteria, and g-proteobacteria. This is the largest comparative phylogenetic study of ICEs performed to date and demonstrates extensive lateral gene transfer across the whole phylum. The three core ICE modules encode replication, type IV secretion, and excision/integration. The conservation of synteny implies a powerful selective advantage of the ICE. GC content of the core modules mirrors that of the host chromosome, suggesting coexistence deep in evolutionary history. Absence of core genes or modules represents lifestyle adaptations of the mobile genetic element. Absence of an integrase and presence of a replicative DNA helicase are markers of a plasmid lifestyle. A variety of accessory genes are found at hotspots; they confer a survival advantage in the ecological niche of the organism, which ranges from eukaryotic pathogens to extreme environments. InterpretationThis large comparative phylogenetic study of ICEs allows inference about evolutionary associations within the ICEHin1056 family. This evolutionary history is so ancient that it may link all mobile genetic elements transferred by conjugation in proteobacteria. This provides important insights into the mobile gene pool and may have implications for prediction of spread of antibiotic resistance and pathogenicity. FundingUK National Health Service.