Quantitative assessment of insertion sequence impact on bacterial genome architecture

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.

The plasmid diversity ofAcinetobacter bereziniaeHPC229 provides clues on the ability of the species to thrive on both clinical and environmental habitats

“…A search for mobile genetic elements in pAbe229-114 indicated the existence of 15 different IS (including complete IS and IS remnants) assigned to 7 different families (Table 2). The presence among them of IS Aba12 and IS Aba22 in multiple copies is consistent with previous observations indicating the ubiquitous distribution of these two IS among Acinetobacter genomes [59]. This suggested that pAbe229-114 has undergone several structural rearrangements, some resulting from IS insertions.…”

“…This suggested that pAbe229-114 has undergone several structural rearrangements, some resulting from IS insertions. Most of the IS shown in Table 2 have been reported previously in different members of the Acinetobacter genus [59]. However, we identified a novel IS element, which received the designation IS Abe18 by the ISSaga database [36].…”

“…Moreover, this region is contiguous in pAbe229-114 to a genetic element encompassing a gshR glutathione reductase gene (region 11, Fig 1, S4 Table) which is surrounded by an IS Aba12 copy and a defective IS Aba22 element that is immediately followed in turn by a complete IS Aba1 copy (Fig 1, Table 2). IS Aba1 exhibits a large impact on A. baumannii genomes [59], and therefore we hypothesize that the two IS Aba1 elements bracketing the 22,744 bp region represent a composite transposon encompassing the oxidative stress resistance genes, the incomplete conjugal-transfer region, and the gshR gene. Supporting this notion, the two IS Aba1 elements at the borders are limited by identical 9 bp-duplications immediately next to their external inverted-repeats, a hallmark of a recent IS Aba1 transposition event [62].…”

Challenges and opportunities for whole‐genome sequencing–based surveillance of antibiotic resistance

“…Alternatively, transposon insertions can increase the expression of intrinsic resistance genes, as illustrated by transposon‐mediated upregulation of ampC in A. baumannii , causing third‐generation cephalosporin resistance, or increased expression of an efflux system in E. coli , which contributes to fluoroquinolone resistance . In cases where transposon‐mediated resistance has been experimentally verified, these events may be predicted from genome data, using either read‐based tools (ISMapper) or assembly‐based analysis (ISseeker) to identify transposon insertion sites in microbial genomes.…”

SVants – A long-read based method for structural variation detection in bacterial genomes

“…Historically, the study of MGEs and their insertion sites has been restricted to short-read sequencing technologies, where a number of innovative bioinformatic methods have been developed to assess structural variations in bacterial genomes [4,5]. While these methods have helped demonstrate the importance and diversity of MGEs, limitations inherent to short reads have impeded the study of the full variety of MGEs and the structural variants they create when inserted into the genome.…”