Abstract
Insertion sequence (IS) elements are important mediators of genome plasticity and can lead to phenotypic changes with evolutionary significance. In multidrug-resistant Acinetobacter baumannii and Klebsiella pneumoniae, IS elements have contributed significantly to the mobilization of genes that encode resistance to antimicrobial drugs. A systematic analysis of IS elements is needed for a more comprehensive understanding of their evolutionary impact. We developed a computational approach (ISseeker) to annotate IS elements in draft genome assemblies and applied the method to analysis of IS elements in all publicly available A. baumannii(>1000) and K. pneumoniae(>800) genome sequences, in a phylogenetic context. Most IS elements in A. baumanniigenomes are species-specific ISAba elements, whereas K. pneumoniaegenomes contain significant numbers of both ISKpn elements and elements that are found throughout the Enterobacteriaceae. A. baumanniigenomes have a higher density of IS elements than K. pneumoniae, averaging ~33 vs ~27 copies per genome. In K. pneumoniae, several insertion sites are shared by most genomes in the ST258 clade, whereas in A. baumannii, different IS elements are abundant in different phylogenetic groups, even among closely related Global Clone 2 strains. IS elements differ in the distribution of insertion locations relative to genes, with some more likely to disrupt genes and others predominantly in intergenic regions. Several genes and intergenic regions had multiple independent insertion events, suggesting that those events may confer a selective advantage. Genome- and taxon-wide characterization of insertion locations revealed that IS elements have been active contributors to genome diversity in both species.
Highlights
Insertion sequences (IS) are mobile genetic elements smaller than ~2 kbp that encode only a transposase
One interesting case identified by ISseeker, but not ISmapper, involved the creation and mobilization of a compound transposon comprised of inverted repeat copies of ISAba1 in the ORAB01 genome (Fig. S1)
After correcting for the larger number of A. baumannii genomes in the analysis, there were about 40 % more total insertions observed in A. baumannii genomes than in K. pneumoniae genomes, and more than twice as many distinct insertion sites
Summary
Insertion sequences (IS) are mobile genetic elements smaller than ~2 kbp that encode only a transposase. IS elements can spread in a genome by transposition, creating genetic variation and playing important roles in adaptation (Bennett, 2004; Siguier et al, 2014). The density of coding content in bacterial genomes means that most random insertions occur in functional genome regions. Intragenic insertions can cause loss-of-function mutations, while intergenic insertions may disrupt promoter function or can result in up-regulation of adjacent genes in cases where the IS element encodes an outwardfacing promoter.
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