Complex class 1 integrons with diverse variable regions, including aac(6')-Ib-cr, and a novel allele, qnrB10, associated with ISCR1 in clinical enterobacterial isolates from Argentina

Abstract

Transferable quinolone resistance has not previously been reported in Argentina. Here we describe three complex class 1 integrons harboring the novel allele qnrB10 in a unique region downstream of orf513, one of them also containing aac(6')-Ib-cr within the variable region of integrons. The three arrays differed from bla(CTX-M-2)-bearing integrons, which are broadly distributed in Argentina.

FIG. 1.

Genetic organization of qnrB10-containing complex class 1 integrons. (A) Genes are represented by arrowed boxes (qnr genes are in black), attC is represented by vertical ovals, and the putative origin of replication of ISCR1 (16) is represented by a black diamond. The 3′-CS and the second copy of this element (3′-CS2) are shown by white arrowed boxes. The hatched horizontal bar indicates the sequenced regions (13,281 bp in In37::ISCR1::qnrB10 and 10,762 bp in In131::ISCR1::qnrB10). Thick horizontal lines indicate the principal amplicons obtained by PCR cartography of the qnrB10-bearing integrons (numbers indicate the corresponding primers in Table 1). The integrons In37::ISCR1::qnrA1 (18) and In37::ISCR1::qnrB4-bla_DHA-1 (17), having essentially the same vr-1 as In37::ISCR1::qnrB10, were included for comparison (sequences were truncated at the two vertical thin lines). Shaded areas with percentages depict identities (id.) between vr-2s. The X, Y, and Z boxes indicate regions of no homology with GenBank sequences. (B) Comparison of the aac(6′)-Ib-cr cassettes of In37::ISCR1::qnrA1 and In37::ISCR1::qnrB10 (nucleotides 1492 to 2261 and 1040 to 1702 in the sequences with accession numbers AY259086 and EF636461, respectively). Sequences are numbered from the first nucleotide following the junction with the 5′-CS, and dashes represent gaps introduced to maximize alignment (ClustalX software, available at ftp://ftp-igbmc.u-strasbg.fr/pub/). Identical nucleotides in the two sequences are in bold. The 101-bp duplication of the 3′-CS is underlined. The start (boxed) and stop (*) codons of each aac(6′)Ib-cr gene are indicated, and the amino acid sequence of the deduced protein is shown below each nucleotide sequence (14). For brevity, other regions showing 100% nucleotide (or amino acid) identity are represented by dots. The silent CGG-to-AGG change (see the text for details) is also shown. (C) Deletions at the inner boundary of 3′-CS2. Nucleotide sequences correspond to In0 (normal 3′-CS, M73819), In131::ISCR1::qnrB10 (EU052800), In37::ISCR1::qnrB10 (EF636461), In35::ISCR1::bla_CTX-M-2 (AY079169), In7::ISCR1::dfrA10 (L06418), In37::ISCR1::qnrA1 (AY259086), and In6::ISCR1::cat2 (U04277). The deletion endpoint in 3′-CS2 is defined by the first base appearing in bold. Base 1 of In0 corresponds to the nucleotide at position 65 from the normal 3′-CS.