Transferable Acinetobacter baumannii plasmid pDETAB2 encodes OXA-58 and NDM-1 and represents a new class of antibiotic resistance plasmids

Abstract

Objectives To characterize a blaOXA-58- and blaNDM-1-containing MDR plasmid from a rare Acinetobacter baumannii lineage and compare it with related plasmids to explore the distribution and evolution of a new plasmid group. Methods A. baumannii DETAB-P2 was isolated from a rectal swab of an intensive care patient. Antibiotic susceptibility was determined using broth microdilution. DETAB-P2 was mated with A. baumannii ATCC 17978 and putative transconjugants were characterized by S1/PFGE and Southern hybridization. WGS was performed on the Illumina and Oxford Nanopore platforms. MLST was performed with the Pasteur and Oxford schemes. Antibiotic resistance genes were identified with ABRicate. Plasmid sequence annotation was performed manually. Complete plasmids in GenBank with the same rep gene were used for comparative analyses. Results A. baumannii DETAB-P2 was ST138 by the Pasteur scheme and a novel Oxford type, ST2209. It transferred blaOXA-58 and blaNDM-1 to ATCC 17978 in the 100 072 bp plasmid pDETAB2 that also carried bleMBL, sul2, aacC2d, tet(39), msr(E)-mph(E) and putative mercury resistance and RND efflux system determinants. pDETAB2 represents a new plasmid type, GR34, and contained 16 pdif sites and several novel dif modules. Only a 10 kbp core sequence is shared amongst pDETAB2 and 18 further GR34 plasmids in GenBank, with diverse accessory regions comprised of various dif modules. Conclusions GR34 plasmids are found in several Acinetobacter species from diverse environments. They display considerable variation in accessory content owing to the presence of pdif sites and an array of dif modules, some of which contain antibiotic resistance genes.

GR13-type plasmids in Acinetobacter potentiate the accumulation and horizontal transfer of diverse accessory genes

“…Plasmids in Acinetobacter are typed according to replication initiation gene ( rep ) identity (Bertini et al ., 2010). A recent review listed 33 rep groups (GRs) (Salgado-Camargo et al ., 2020), and we have since described an additional group, GR34 (Liu et al ., 2021). Plasmids carrying clinically-significant antibiotic resistance genes (ARGs) have been reported in A. baumannii (Blackwell and Hall, 2017; Hamidian et al ., 2016; Hamidian and Hall, 2014; Liu et al ., 2015; Nigro and Hall, 2014) and in other Acinetobacter species (Alattraqchi et al ., 2021; Hayashi et al ., 2021; Li et al ., 2021; Silva et al ., 2018; Yang et al ., 2021), clearly indicating their important role in the emergence and transmission of antimicrobial resistance in this genus.…”

“…These have been called plasmid- dif (p dif ) sites (Blackwell and Hall, 2017), and have been shown to be recognised by A. baumannii XerC and XerD (Lin et al ., 2020). ARGs have been found in p dif -flanked structures called dif modules, including the carbapenemase genes bla OXA-24 (D’Andrea et al ., 2009), bla OXA-58 (Bertini et al ., 2007), and bla OXA-72 (Kuo et al ., 2016), the tetracycline resistance gene tet (39) (Blackwell and Hall, 2017), the macrolide resistance genes msr (E)- mph (E) (Blackwell and Hall, 2017), the aminoglycoside resistance gene aacC2d and the sulphonamide resistance gene sul2 (Liu et al ., 2021). Identical ARG-containing dif modules have been found in multiple contexts and in different types of plasmids (Blackwell and Hall, 2017).…”

“…Identical ARG-containing dif modules have been found in multiple contexts and in different types of plasmids (Blackwell and Hall, 2017). Further dif modules, including those carrying genes for chromium resistance, a serine recombinase, RND efflux system and multiple toxin-antitoxin systems have also been described (Blackwell and Hall, 2017; Hamidian and Hall, 2018; Liu et al ., 2021; Mindlin et al ., 2018). Given the apparent importance of dif modules to the evolution of some Acinetobacter plasmids, it is important to understand the breadth of genetic cargo they carry and which types of plasmids can interact with them.…”

“…We recently described the GR34 family of plasmids that share a 10 kbp core segment but can grow to as large as 190 kbp through the acquisition of dif modules (Liu et al ., 2021). The exemplar GR34 plasmid, pDETAB2, is from an A. baumannii isolated in an intensive care unit (ICU) in Hangzhou, China, and carries six ARGs in a series of dif modules (Liu et al ., 2021).…”

“…We recently described the GR34 family of plasmids that share a 10 kbp core segment but can grow to as large as 190 kbp through the acquisition of dif modules (Liu et al ., 2021). The exemplar GR34 plasmid, pDETAB2, is from an A. baumannii isolated in an intensive care unit (ICU) in Hangzhou, China, and carries six ARGs in a series of dif modules (Liu et al ., 2021). Here, we report two GR13-type plasmids found in unrelated A. baumannii isolated one and two months later in that same ICU, one cryptic and the other carrying ARG-containing dif modules identical to ones in pDETAB2.…”