Insights into the complete genomes of carbapenem-resistant Acinetobacter baumannii harbouring bla OXA-23, bla OXA-420 and bla NDM-1 genes using a hybrid-assembly approach

Abstract

Carbapenem resistance in Acinetobacter baumannii is due to bla OXA-23, which is endemic in India. Recently, the sporadic presence of bla OXA-58 as well as the occurrence of dual carbapenemases were observed. The mobility as well as the dissemination of these resistance genes were mainly mediated by various mobile genetic elements. The present study was aimed at characterizing the genetic arrangement of bla OXA-23, bla NDM-1 and bla OXA-58 identified in two complete genomes of carbapenem-resistant A. baumannii (CRAB). Complete genomes obtained using a hybrid-assembly approach revealed the accurate arrangement of Tn2006 with bla OXA-23, ISAba125 with bla NDM and ISAba3 with bla OXA-58. In addition, the association of IntI1 integrase with the bla CARB-2 gene and several virulence factors required for type-IV pili assembly, motility and biofilm formation have been identified. The current study provided deeper insight into the complete characterization of insertion sequences and transposons associated with the carbapenem-resistant genes using short reads of IonTorrent PGM and long reads of MinIon in A. baumannii .

Genomic Characterization of Extensively Drug-Resistant NDM-Producing Acinetobacter baumannii Clinical Isolates With the Emergence of Novel blaADC-257

“…This genetic organization is similar to that of Tn125like transposon previously reported by Bonnin et al (2013). BLAST analysis of the contigs harboring bla NDM-1 showed highest similarity to the chromosome of A. baumannii strain ACN21 (GenBank accession: CP038644.1; Vijayakumar et al, 2020).…”

“…This was previously documented by Bonnin et al (2013) who failed to identify a downstream second copy of ISAba125 by PCR and suggested loss of functionality of this truncated transposon (ΔTn125). WGS of bla NDM -positive isolates by a later study (Vijayakumar et al, 2020) uncovered the existence of a second copy of ISAba125 downstream to the ISAba14-interrupted transposon. Interestingly, analysis of the upstream region to the truncated transposon revealed the existence of the amikacin resistance gene AphA6 preceded by another copy of ISAba14 in ST85 Pas Intrinsic to all A. baumannii, cephalosporin resistance is mediated by ADC (formerly known as bla AmpC ).…”

Surveillance of antimicrobial resistance in low- and middle-income countries: a scattered picture

“…[ 110 , 111 ], Shigella spp. [ 104 , 112 , 113 ], Pseudomonas spp. [ 102 , 105 , 108 , 109 ], and Acinetobacter spp.…”

Emergence of a multidrug-resistant plasmid encoding bla NDM-1, bla OXA-420 and armA in a clinical isolate of Acinetobacter variabilis in Japan

“…The main genetic structures of pRYU24, nucleotides 1-38 198 containing armA and nucleotides 46 459-53 186 containing bla OXA-420 , were 99.82 and 99.78 % similar to those of nucleotides 1-38 188 and 48 634-55 368, respectively, of the ACN21 plasmid present in an isolate of A. baumannii obtained in 2018 in India (Fig. 3) [33]. Another genetic structure of pRYU24, nucleotides 57 553-66 524 containing bla NDM-1 , had 99.77% similarity to nucleotides 4043-13 029 of the pNDM-GJ02 plasmid present in an isolate of Acinetobacter towneri strain G295 obtained in 2011 in PR China [34].…”