Comparative Genomics of Two ST 195 Carbapenem-Resistant Acinetobacter baumannii with Different Susceptibility to Polymyxin Revealed Underlying Resistance Mechanism

Abstract

Acinetobacter baumannii is a Gram-negative nosocomial pathogen of importance due to its uncanny ability to acquire resistance to most antimicrobials. These include carbapenems, which are the drugs of choice for treating A. baumannii infections, and polymyxins, the drugs of last resort. Whole genome sequencing was performed on two clinical carbapenem-resistant A. baumannii AC29 and AC30 strains which had an indistinguishable ApaI pulsotype but different susceptibilities to polymyxin. Both genomes consisted of an approximately 3.8 Mbp circular chromosome each and several plasmids. AC29 (susceptible to polymyxin) and AC30 (resistant to polymyxin) belonged to the ST195 lineage and are phylogenetically clustered under the International Clone II (IC-II) group. An AbaR4-type resistance island (RI) interrupted the comM gene in the chromosomes of both strains and contained the blaOXA−23 carbapenemase gene and determinants for tetracycline and streptomycin resistance. AC29 harbored another copy of blaOXA−23 in a large (~74 kb) conjugative plasmid, pAC29b, but this gene was absent in a similar plasmid (pAC30c) found in AC30. A 7 kb Tn1548::armA RI which encodes determinants for aminoglycoside and macrolide resistance, is chromosomally-located in AC29 but found in a 16 kb plasmid in AC30, pAC30b. Analysis of known determinants for polymyxin resistance in AC30 showed mutations in the pmrA gene encoding the response regulator of the two-component pmrAB signal transduction system as well as in the lpxD, lpxC, and lpsB genes that encode enzymes involved in the biosynthesis of lipopolysaccharide (LPS). Experimental evidence indicated that impairment of LPS along with overexpression of pmrAB may have contributed to the development of polymyxin resistance in AC30. Cloning of a novel variant of the blaAmpC gene from AC29 and AC30, and its subsequent expression in E. coli also indicated its likely function as an extended-spectrum cephalosporinase.

Emergence of different Acinetobacter baumannii clones in a Croatian hospital and correlation with antibiotic susceptibility

“…Population structure of the isolates was quite variable with five different STs reported. ST 195 was previously reported in China and associated with OXA-23 β-lactamase in contrast with our study in which this ST was found in OXA-40 positive isolates [46][47] . In both studies ST195 isolates belonged to IC II.…”

Abundance of Colistin-Resistant, OXA-23- and ArmA-Producing Acinetobacter baumannii Belonging to International Clone 2 in Greece

“…Consistently, all the strains carrying armA (35/40, 87.5%) were resistant to gentamicin and tobramycin. The armA gene was located in the chromosome aboard on the widely disseminated Tn1548, and it was found downstream of a cluster of genes encoding proteins annotated as paraquat-inducible protein A and protein B, as previously described for ST195 strain AC29 (Lean et al, 2016).…”

Intercellular Transfer of Chromosomal Antimicrobial Resistance Genes between Acinetobacter baumannii Strains Mediated by Prophages

“…We used one representative A. baumannii clinical isolate to evaluate the phagemediated intercellular transfer of chromosomal ARGs. Although the presence of an identical NU60-I prophage (50 kb), carrying the capsid 1 gene found in the NU-60 genome, has not been admitted in any A. baumannii genome deposited in the database, the core capsid 1 protein gene involved in ARG transfer has been widely presented in A. baumannii strains isolated from geographically different areas, such as Japan (50), South Korea (51), China (52), Malaysia (53), and the United Kingdom (54). A similar phenomenon concerning the transfer of ARGs, using pelleted particles obtained through ultracentrifugation of culture supernatants, was identified when we used other A. baumannii clinical isolates (data not shown).…”