Novel variants of AbaR resistance islands with a common backbone in Acinetobacter baumannii isolates of European clone II

Abstract

In this study, the genetic organization of three novel genomic antibiotic resistance islands (AbaRs) in Acinetobacter baumannii isolates belonging to group of European clone II (EC II) comM integrated sequences of 18-, 21-, and 23-kb resistance islands were determined. These resistance islands carry the backbone of AbaR-type transposon structures, which are composed of the transposition module coding for potential transposition proteins and other genes coding for the intact universal stress protein (uspA), sulfate permease (sul), and proteins of unknown function. The antibiotic resistance genes strA, strB, tetB, and tetR and insertion sequence CR2 element were found to be inserted into the AbaR transposons. GenBank homology searches indicated that they are closely related to the AbaR sequences found integrated in comM in strains of EC II (A. baumannii strains 1656-2 and TCDC-AB0715) and AbaR4 integrated in another location of A. baumannii AB0057 (EC I). All of the AbaRs showed structural similarity to the previously described AbaR4 island and share a 12,008-bp backbone. AbaRs contain Tn1213, Tn2006, and the multiple fragments which could be derived from transposons Tn3, Tn10, Tn21, Tn1000, Tn5393, and Tn6020, the insertion sequences IS26, ISAba1, ISAba14, and ISCR2, and the class 1 integron. Moreover, chromosomal DNA was inserted into distinct regions of the AbaR backbone. Sequence analysis suggested that the AbaR-type transposons have evolved through insertions, deletions, and homologous recombination. AbaR islands, sharing the core structure similar to AbaR4, appeared to be distributed in isolates of EC I and EC II via integration into distinct genomic sites, i.e., pho and comM, respectively.

Fig 1

Structure of AbaR4a, AbaR4b, and AbaR4c islands. AbaR-type transposon backbone is shown by filled boxes bounded by inverted terminal repeats (IR_AbaR) shown as black bars. The additional inserted regions are indicated by vertical arrows indicating the insertion site. Boxes of different thickness distinguish the various segments: antibiotic resistance genes, ISCR2, and ISAba1. Vertical bars indicate the ori and ter sites of ISCR2 element and the inverted repeats (IR) with a subscript note, indicating the identity of IR. The genes are shown by horizontal arrows with the gene name below. An angled style at the beginning and the head of the arrow indicate 5′ and 3′ truncated genes, respectively. Genes named m, h, g, and r potentially encode a DNA methylase, helicase, phosphoglucosamine mutase (glmM), and the transcription regulator of ArsR family, respectively. Note that orf5 is 85% identical to orf4. The sizes of individual AbaRs are drawn to scale. Sequences of AbaR4a, AbaR4b, and AbaR4c are available from GenBank under accession numbers JN129845, JN129846, and JN129847, respectively.

Fig 2

Structure of AbaR4, AbaR4d, and AbaR4e islands. Features are as described in Fig. 1. The gene pac potentially encodes a puromycin N-acetyltransferase (usually designated orf5 in class 1 integrons). The sizes of individual AbaRs are drawn to scale. Sequences of AbaR4, AbaR4d, and AbaR4e are available from GenBank under accession numbers NC_011586, CP001921, and CP002522, respectively.