Dissemination of novel Tn7 family transposons carrying genes for synthesis and uptake of fimsbactin siderophores among Acinetobacter baumannii isolates

Abstract

Acinetobacter baumannii is a successful opportunistic pathogen that can compete for iron under iron-limiting conditions. Here, large novel transposons that carry genes for synthesis and transport of the fimsbactin siderophores present in some A. baumannii strains were examined. Tn6171, originally found in the A. baumannii global clone 1 (GC1) lineage 2 isolate D36, includes tns genes encoding proteins related to the TnsA, TnsB, TnsC transposition proteins (50–59 % identity), TnsD targeting protein (43 % identity) and TnsE (31 % identity) of Tn7, and is found in the chromosome downstream of the glmS gene, the preferred location for Tn7, flanked by a 5 bp target site duplication. Tn6171 is bounded by 29 bp inverted repeats and, like Tn7, includes additional TnsB binding sites at each end. Tn6171 or minor variants were detected in the equivalent location in complete or draft genomes of several further A. baumannii isolates belonging to GC1 [sequence type (ST) 1, ST81, ST94, ST328, ST623, ST717], GC2 (ST2) and ST10. However, in some of these isolates the surrounding glmS region was clearly derived from a different A. baumannii lineage, indicating that the transposon may have been acquired by replacement of a segment of the chromosome. A recombination-free phylogeny revealed that there were several transposon acquisition events in GC1. The GC1 isolates were mainly lineage 2, but a potential third lineage was also detected. A related transposon, designated Tn6552, was detected in ATCC 17978 (ST437) and other ST437 isolates. However, the Tn6552 tnsD targeting gene was interrupted by an ISAba12, and Tn6552 is not downstream of glmS.

Phylogenomics of two ST1 antibiotic-susceptible non-clinical Acinetobacter baumannii strains reveals multiple lineages and complex evolutionary history in global clone 1

“…The four Indian isolates forming the previously proposed L3 lineage [38] cluster with two additional isolates not previously examined: SP2486 (recovered in India in 2019) and MRSN15049 (recovered in Afghanistan in 2013). The four Indian isolates have the same ST IP :ST OX :KL:OCL profiles, and establish the designation of L3 as the third major lineage of GC1 (), although MRSN15049 and 5457 appear to have further diverged as they include differences in their ST IP :ST OX :KL:OCL profile ().…”

“…Whole genome sequences for these isolates and those currently available in the public domain enabled an overall picture of the evolution of GC1 to be generated with a recombination-free phylogeny constructed with clinical and non-clinical isolates from different geographical regions and with varying antibiotic resistance profiles. A recent study examined diversity within the GC1 population, and proposed a new lineage, L3 [38,39]. However, this phylogenetic analysis did not exclude nucleotide variants found in regions acquired by recombination and those in accessory genomes [38,39] while inclusion of these variants often leads to a skewed tree topology given the high rate of horizontal gene transfer in GC1s.…”

“…A recent study examined diversity within the GC1 population, and proposed a new lineage, L3 [38,39]. However, this phylogenetic analysis did not exclude nucleotide variants found in regions acquired by recombination and those in accessory genomes [38,39] while inclusion of these variants often leads to a skewed tree topology given the high rate of horizontal gene transfer in GC1s. The addition of newly available GC1 genomes in our recombination-free phylogenetic tree revealed an expansion of established lineages (Fig.…”

“…L1 included a geographically and genetically diverse set of strains, whereas L2 was more homogeneous and associated with strains isolated in the Middle East or linked to this region via isolates recovered from soldiers or military personnel returning from the Middle East region. Recently, two studies proposed that four Indian isolates (VB24319, VB29123, VB2486 and 5457) might belong to a third lineage, designated L3 [38,39].…”

Cargo genes of Tn7-like transposons comprise an enormous diversity of defense systems, mobile genetic elements and antibiotic resistance genes

“…Along with the core genes, the cargo genes are mobilized from a donor site to a recipient site, making a substantial contribution to HGT Peters et al, 2014). Examination of the cargo carried by Tn7 and about 50 other Tn7-like transposons identified integrons with antibiotic resistance gene cassettes, heavy metal resistance genes, iron-sequestering siderophores, non-ribosomal peptide synthases, restriction-modification enzymes and many other genes of unknown function (Aprile et al, 2021;Hamidian and Hall, 2021;Peters, 2007, 2009). Therefore, a larger-scale analysis of the cargo carried by Tn7-like transposons has the potential to illuminate consistent trends in transposon-mediated HGT.…”