Localization of AbaR4-type genomic islands and multidrug resistance plasmids in multiple Acinetobacter baumannii clones and Acinetobacter pittii from infections of dogs and cats.

Abstract

The genomes of 39 clinical carbapenemase-producing A. baumannii (CP-Ab) and 2 A. pittii (CP-Ap) isolates from dogs and cats in Thailand (2016-2019) were analyzed for phylogenetic relationship and antimicrobial resistance gene (ARG) localization. Resistome and core genome multilocus sequence typing (cgMLST) analysis identified distinct ARG patterns within CP-Ab sequence type (ST) 2 (n = 4) and ST1575 (n = 1) of clonal complex (CC) 2, ST25 (n = 6), ST1576 (n = 1), and ST1581 (n = 2) of CC25, ST16 (n = 13), ST23 (n = 2), ST149 (n = 9), ST1093 (n = 1), along with CP-Ap (n = 2). Complete genome analysis of one CP-Ap strain and 15 representative CP-Ab strains from each clone identified strains with one to three copies of blaassociated with Tn2006 and/or AbaR-type genomic islands (GIs). AbaR4 was chromosomally located in all other STs except CP-Ab of CC2, which carried AbaR4b. AbaR4 was found on conjugative bla-containing plasmids in CP-Ab ST1093 and CP-Ap strains. Conjugative bla-containing plasmids and multidrug resistance (MDR) mega-plasmids in CP-Ab ST149 and CC25 shared ancestry with the cryptic plasmid pCUVET16-467.1 in CP-Ab ST23. MDR mega-plasmids contained a bacteriophage exclusion (BREX) locus and Tn6172-derived elements. A Tn6172ISCR2::(ΔISCR2-ΔTn10-MARR) structure containing GR38 repM, a class 1 integron, and multiple ARGs were found in R3_T60 (GR38) MDR mega-plasmids of ST149 and formed an AbGRI1 structure in CC25 plasmids. These findings highlight the role of AbaR4 in carbapenem resistance and the evolution of Acinetobacter plasmids, facilitating the bladissemination and the development of extensive drug resistance in multiple clones of clinical CP-Ab and CP-Ap strains originating from companion animals.