Evolution of AbGRI2-0, the Progenitor of the AbGRI2 Resistance Island in Global Clone 2 of Acinetobacter baumannii

Abstract

A320, isolated in the Netherlands in 1982 and also known as RUH134, is the earliest available multiply antibiotic-resistant (MAR) Acinetobacter baumannii isolate belonging to global clone 2 (GC2) and is the reference strain for this clone. The draft genome sequence of A320 was used to investigate the original location and configuration of the IS26-bounded AbGRI2 resistance island found in current GC2 isolates. PCR mapping and sequencing were used to order contigs composing the resistance islands. A320 contains two IS26-bounded resistance islands, AbGRI2-0a and AbGRI2-0b, of 7.8 kb and 25.4 kb, respectively. Together they contain bla TEM , aacC1, aadA1, sul1, catA1, and aphA1b genes, which confer resistance to antibiotics used clinically in the 1970s, as well as an incomplete mercury resistance module. Tracking the continuity of the chromosome and the target site duplications revealed that the two resistance islands were originally together as AbGRI2-0, an island of 32.4 kb, and were subsequently separated via an IS26-mediated intramolecular inversion that reversed the orientation of 1.54 Mb of the chromosome and duplicated an IS26. A320 contains an ancestral form of AbGRI2, and the original insertion site of the AbGRI2 island was identified. Many of the AbGRI2 versions present in the completed GC2 genomes can be derived from it via the variant AbGRI2-1. IS26-mediated inversions have also played a part in forming AbGRI2-0, and, upon reversal, large regions of AbGRI2-0 are identical to parts of AbaR0, the ancestral version of the AbaR islands present in GC1 isolates. This indicates a common source.

Variants of AbGRI3 carrying thearmAgene in extensively antibiotic-resistantAcinetobacter baumanniifrom Singapore

“…The presence of an 8 bp TSD surrounding AbGRI3 demonstrates that, like AbGRI2, 20 , 36 this island entered the chromosome of a GC2 isolate through the action of IS 26 . What is less clear is if both Tn 6180 and Tn 6179 entered together or individually 33 .…”

“…AbGRI2 variants on the other hand generally contain some or all of the following genes, bla TEM (resistance to ampicillin), aphA1b in Tn 6020 (kanamycin and neomycin resistance) 18 and sul1 , aacC1 and aadA1 in a class 1 integron (conferring resistance to sulphonamides, gentamicin and streptomycin, respectively) 19–21 . Hence, the armA transposon represents a third chromosomally located resistance island, and for simplicity and consistency we recently called it AbGRI3 20 . The three resistance islands are widely separated on the chromosome (see Figure 1 in Blackwell et al 20 ).…”

Genomic epidemiology of multidrug‐resistant Gram‐negative organisms

“…While ECI and ECII strains carry resistance plasmids, the defining features of these strains are massive chromosomally encoded resistance islands that contain multiple antibiotic‐resistance determinants that are associated with mobile genetic elements . These resistance islands have proved to be extremely dynamic, with many different configurations reported . In addition to horizontally acquired elements, A. baumannii also has several intrinsic resistance genes, including β‐lactamases and efflux pumps, which can become activated under antibiotic pressure by mobilization of Insertion Sequence (IS) elements that carry strong promoters .…”

“…[82][83][84] These resistance islands have proved to be extremely dynamic, with many different configurations reported. 85 In addition to horizontally acquired elements, A. baumannii also has several intrinsic resistance genes, including ␤-lactamases and efflux pumps, which can become activated under antibiotic pressure by mobilization of Insertion Sequence (IS) elements that carry strong promoters. 83,86 Similar to A. baumannii, resistance in MDR epidemic clones ST235 and ST111 of P. aeruginosa is also attributable to a combination of intrinsic resistance elements and chromosomally associated mobile elements.…”

Targeted conservative formation of cointegrates between two DNA molecules containing IS26 occurs via strand exchange at either IS end

“…The insertion sequence IS26 (Mollet et al, 1983(Mollet et al, , 1985 plays a central role in generating genetic diversity in the plasmids and chromosomes of Gram-negative bacteria and particularly in the dissemination of antibiotic resistance genes (Wrighton and Strike, 1987;Colonna et al, 1988;Allard et al, 1993;Miriagou et al, 2005;Post and Hall, 2009;Cain et al, 2010;Nigro and Hall, 2012;Blackwell et al, 2016). IS26 is 820 bp long, with 14 bp perfect inverted repeats and a single gene, tnp26, that encodes the 234 amino acid Tnp26 transposase ( Fig.…”