Genetic Environment of ISEcp 1 and bla ACC-1

Abstract

A recent paper (8) presented analyses of the genetic environments of the blaACC-1 β-lactamase gene, which originates from the Hafnia alvei chromosome (7), associated with truncated ISEcp1 elements in Enterobacteriaceae. In three Klebsiella pneumoniae isolates (SKL54 [GenBank accession no. {type:entrez-nucleotide,attrs:{text:AJ870922,term_id:56691986,term_text:AJ870922}}AJ870922], SKL55, and C5900 [{type:entrez-nucleotide,attrs:{text:AJ870923,term_id:56691992,term_text:AJ870923}}AJ870923]) ISEcp1 was described as having a 1,433-bp deletion due to insertion of IS26 (IS26R; Fig. ​Fig.1A).1A). A second copy of IS26 (IS26L) in the opposite orientation was found adjacent to a second truncated ISEcp1 (ISEcp1L) with the 3′ deletion “exactly complementary to that of ISEcp1 upstream from blaACC-1.” The authors suggested that a composite transposon with directly oriented flanking IS26 elements was inserted into ISEcp1, with subsequent unexplained events giving the observed configuration. FIG. 1. (A) Schematic representation of part of {type:entrez-nucleotide,attrs:{text:AJ870922,term_id:56691986,term_text:AJ870922}}AJ870922. (B) Inversion of the region between IS26L and IS26R restores matching DR. (C) Removal of IS26L plus one ... An alternative explanation for this configuration is suggested by the sequences adjacent to the ends of IS26, which produces 8-bp direct repeats (DR) of target DNA on transposition (2). In {type:entrez-nucleotide,attrs:{text:AJ870922,term_id:56691986,term_text:AJ870922}}AJ870922 and {type:entrez-nucleotide,attrs:{text:AJ870923,term_id:56691992,term_text:AJ870923}}AJ870923, 8-bp sequences that are the reverse complements of one another are found adjacent to one end of IS26L (AAAATGTC) and one end of IS26R (GACATTTT) (Fig. ​(Fig.1A),1A), suggesting that the region between these two IS26 elements could have been inverted by homologous recombination between them. Reversing this event would give the configuration shown in Fig. ​Fig.1B,1B, with matching DR flanking IS26L. Removal of IS26L plus one copy of this 8-bp DR sequence would regenerate a complete ISEcp1 (Fig. ​(Fig.1C1C). ISEcp1B (which differs from ISEcp1 by three nucleotides [10]) has been shown to mobilize an adjacent blaCTX-M-19 gene (10) and to transfer the blaCTX-M-2 gene from the Kluyvera ascorbata chromosome to plasmids (6). It appears that sequences other than the right inverted repeat (IRR) of ISEcp1, but which have some bases in common with this 14-bp IR, are used during the transposition process (6, 10). A presumed transposon consisting of ISEcp1, blaCTX-M, and the region up to and including the alternative IR is flanked by 5-bp DR (6, 10). A structure including ISEcp1-blaCTX-M-15 and flanked by 5-bp DR is also found in the plasmid pC15-1a (1). As mentioned by Doloy et al. (3), ISEcp1 may have been similarly responsible for mobilizing the blaACC-1 gene and adjacent DNA from H. alvei. GenBank entries of blaACC-1 from H. alvei (e.g., {type:entrez-nucleotide,attrs:{text:AF180952,term_id:9294813,term_text:AF180952}}AF180952 [4]) include insufficient flanking sequence to define the region that has been transferred. However, a plasmid from Salmonella enterica serovar Bareilly ({type:entrez-nucleotide,attrs:{text:AY856832,term_id:61677572,term_text:AY856832}}AY856832 [5]) also contains part of ISEcp1and blaACC-1 (Fig. ​(Fig.1D),1D), and alignment of the sequence beyond the 3′ end of blaACC-1 with the equivalent region from {type:entrez-nucleotide,attrs:{text:AY870922,term_id:58397751,term_text:AY870922}}AY870922/{type:entrez-nucleotide,attrs:{text:AY870923,term_id:58397753,term_text:AY870923}}AY870923 suggested a potential IR sequence (Fig. ​(Fig.1E1E). A search (http://www.ncbi.nlm.nih.gov/BLAST) with the sequence from {type:entrez-nucleotide,attrs:{text:AY870922,term_id:58397751,term_text:AY870922}}AY870922/{type:entrez-nucleotide,attrs:{text:AY870923,term_id:58397753,term_text:AY870923}}AY870923 beyond this putative IR identified GenBank accession no. {type:entrez-nucleotide,attrs:{text:EF104648,term_id:118776561,term_text:EF104648}}EF104648 (8), which includes a gene encoding a putative glycosidase, orf1 from the work of Doloy et al. (3), reidentified as a novel β-lactamase gene, blaSCO-1, and IS26 (Fig. ​(Fig.1D).1D). Part of the glycosidase gene and blaSCO-1, but not IS26, are also found in {type:entrez-nucleotide,attrs:{text:EF063111,term_id:119434064,term_text:EF063111}}EF063111 (9). A search with the corresponding sequence from {type:entrez-nucleotide,attrs:{text:AY856832,term_id:61677572,term_text:AY856832}}AY856832 identified {type:entrez-nucleotide,attrs:{text:AJ519722,term_id:37518395,term_text:AJ519722}}AJ519722 (11). An alignment of the four different sequences (Fig. ​(Fig.1E)1E) seemed to confirm the proposed IR and suggested that the same region of the H. alvei chromosome has been transferred to both K. pneumoniae and S. enterica serovar Bareilly plasmids. The origin of one T residue is ambiguous, but excluding this T from the IR gives 6/14 matches with the ISEcp1 IR (Fig. ​(Fig.1E).1E). The sequences thus predicted as DR for {type:entrez-nucleotide,attrs:{text:AY870922,term_id:58397751,term_text:AY870922}}AY870922/{type:entrez-nucleotide,attrs:{text:AY870923,term_id:58397753,term_text:AY870923}}AY870923 and {type:entrez-nucleotide,attrs:{text:AY856832,term_id:61677572,term_text:AY856832}}AY856832 (TTGAA and TAATA, respectively; Fig. ​Fig.1E)1E) are AT rich, as previously noted (6, 10), but these cannot be confirmed in the absence of sequence adjacent to IRL of ISEcp1. Thus, blaACC-1 may have been picked up from the H. alvei chromosome by ISEcp1 and inserted into different locations, including adjacent to blaSCO-1 and IS26. Subsequent events, such as the insertion of IS26 into ISEcp1 and IS26-mediated inversion described for SLK54 and SLK55/C5900, may also explain the other configurations seen by Doloy et al. (3).