SGI2, a Relative ofSalmonellaGenomic Island SGI1 with an Independent Origin

Abstract

Multiply antibiotic-resistant Salmonella enterica serovar Emek strains isolated in Australia and the United Kingdom had similar features, suggesting that they all belong to a single clone. These strains all contain SGI2 (formerly SGI1-J), an independently formed relative of Salmonella genomic island SGI1. In SGI2, the complex class 1 integron which includes all of the resistance genes is not located between tnpR (S027) and S044 as in SGI1 and SGI1 variants. Instead, tnpR was found to be adjacent to S044, and the integron is located 6.9 kb away, within S023. In both SGI1 and SGI2, the 25-bp inverted repeats that mark the outer ends of class 1 integrons are flanked by a 5-bp duplication of the target, indicating that incorporation of the integron was by transposition. A small number of differences between the sequences of the backbones of SGI1 and SGI2 were also found. Hence, a class 1 integron has entered two different variants of the SGI backbone to generate two distinct lineages. Despite this, the integron in SGI2 has a complex structure that is very similar to that of In104 in SGI1. Differences are in the cassette arrays and in the gene which encodes the chloramphenicol and florfenicol efflux protein. The CmlA9 protein, encoded by InEmek, is only 92.8% identical to FloRc (also a CmlA family protein) from SGI1. A variant form of SGI2, SGI2-A, which has lost the tet(G) and cmlA9 resistance determinants, was found in one strain.

Truncated tni Module Adjacent to the Complex Integron of Salmonella Genomic Island 1 in Salmonella enterica Serovar Virchow

“…1A). However, the right boundary PCR product was 2.1 kb larger than the size expected from the SGI1-J (SGI2) sequence with the GenBank accession number AY963803 (11). Sequence analysis revealed that, adjacent to the short segment of 152 bp derived from the IRt outer end of Tn402, the complex integron of serovar Virchow strains harbored the right outer end of the mercury resistance transposon Tn5058 (GenBank accession no.…”

“…Sequence analysis showed the presence of the trimethoprim resistance gene cassette dfrA1 and a gene cassette of unknown function, orfC. These results suggested the occurrence of the SGI1-J complex integron variant recently described in serovar Emek strains (11). Then, PCRs were carried out from the sul1⌬ gene to the tetR gene and the resulting product was sequenced.…”

“…The complex class 1 integron initially named SGI1-J contains the dfrA1-orfC cassette array in the first attI1 site and a deletion at the second attI1 site. Flanked by the two integron-like structures are a new variant of the floR gene called floR2 or cmlA9 and the tetracycline resistance genes tetR and tet(G) (8,11). For the first time, this complex integron, relative to In104, was found inserted within ORF S023 of the SGI1 backbone.…”

“…Recently, Levings et al have described an unusual SGI1 variant in Salmonella enterica serovar Emek strains isolated between 1999 and 2002 (11). The complex class 1 integron initially named SGI1-J contains the dfrA1-orfC cassette array in the first attI1 site and a deletion at the second attI1 site.…”

“…For the first time, this complex integron, relative to In104, was found inserted within ORF S023 of the SGI1 backbone. For this major reason, Levings et al chose to rename SGI1-J as SGI2 (9,11). This point of nomenclature will be further discussed below.…”