The genomic island SGI1, containing the multiple antibiotic resistance region of Salmonella enterica serovar Typhimurium DT104 or variants of it, is widely distributed in other S. enterica serovars

Abstract

The global dissemination of the multiply-antibiotic-resistant Salmonella enterica serovar Typhimurium DT104 clone with the resistance genes located in a class 1 integron, here designated In104, within genomic island SGI1 is a significant public health issue. Here, we have shown that SGI1 and variants of it carrying different combinations of resistance genes are found in several Salmonella enterica serovars. These are serovars Cerro, Derby, Dusseldorf, Infantis, Kiambu, and Paratyphi B dT(+) isolated from human infections and serovar Emek from sewage effluent. Two new variants, SGI1-I and SGI1-J, both of which include the dfrA1-orfC cassette array, were identified.

FIG. 1.

Structure of SGI1 regions. (A) The SGI1 region of serovar Typhimurium DT104 (from GenBank accession no. AF261825) is drawn to scale except for In104, which is to scale in B. The SGI1 backbone and the retron element (shown above) are represented by open boxes, and the chromosomal and In104 regions as lines of different thicknesses. Vertical bars indicate the IR bounding In104. Fragments amplified by PCR are shown as thin lines below, with the primer pairs used (Table 1) indicated underneath. (B) In104 region. Dashed lines represent the surrounding SGI1 backbone and narrow vertical bars represent the IRs (IRi and IRt). The 5′-CS, 3′-CS, and tni regions of class 1 integrons are indicated by lines of different thicknesses, with attI1 as a tall open box and gene cassettes as open boxes with a black bar at one end, indicating the 59-be. IS6100 and the central, non-integron-derived region are open boxes. Arrows indicate the position and orientation of genes and ORFs. Primer pairs used to detect the boundaries of In104 or to determine the size of the cassette array and the location of cassettes are indicated above or below.

FIG. 2.

Characterization of the cassette arrays. PCR amplification products (top panel) of cassette regions (using primers L1 and R1) and RsaI-generated restriction endonuclease fragments from them (bottom panel) were separated on agarose gels. Size markers are a 100-bp ladder.

FIG. 3.

Maps of In104 variants. Features are as in Fig. 1B, and the vertical arrow indicates the right-hand boundary of SGI1. Regions associated with the additional dfrA10 genes are indicated above, with CR1 as a shaded box and the unique region including the dfrA10 gene as a hatched box. The strain or strains from which each map is derived, together with the SGI1 designation, are indicated on the left.

FIG. 4.

Mapping the CR1-dfrA10 region. The primer combinations used to link genes in serovar Kiambu and serovar Infantis strains that possessed CR1 are shown. Primer sequences are listed in Table 1.