Phylogenetic analysis of integrases of Acinetobacter baumannii genomic islands

Abstract

Acinetobacter baumannii among other pathogens is capable of acquiring new virulence determinants via mobile genetic elements (MGE). Analysis of the distribution of genomic islands (GIs) has shown in many species that most MGEs cluster tightly with specific lineages on a phylogenetic core genome tree. This study aims to address the questions on the association between GIs distribution among certain clonal lineagesand to test the contribution of G08 and G62 in A. baumannii to metal susceptibility phenotypes. The whole genome phylogenetic single nucleotide polymorphism (SNP) tree was build using the feature frequency profile. As input, the 101 complete A. baumannii genomes deposited in GenBank were used. The matrix was generated using command line blast and the R platform to generate the output. Susceptibility testing of heavy metals was performed on wild-type and GI-deletion mutants using eight different heavy metals. Whole genome phylogenetic SNP tree constructed on all complete deposited A. baumannii genomes showed that the integrase of the metal resistance G08 and G62 are present only in single or very few sequence types (STs). To test the hypothesis that these GI seven if present only in defined lineage are still mobile, G08 and G62 were selected respectively in strains AB0057 and ATCC17978. Phylogenetic analysis of the respective GI integrases confirmed that the G08int and G62int belong to a separate clade within the Acinetobacter tyrosine recombinases. Susceptibility testing in A. baumannii strain ATCC 17978, AB0057 and their respective ΔG62 and ΔG08 mutants confirmed the contribution of the GI-encoded efflux transporters to heavy metal decreased susceptibility.