Complete nucleotide sequence of a 43-kilobase genomic island associated with the multidrug resistance region of Salmonella enterica serovar Typhimurium DT104 and its identification in phage type DT120 and serovar Agona

Abstract

This study describes the characterization of the recently described Salmonella genomic island 1 (SGI1) (D. A. Boyd, G. A. Peters, L.-K. Ng, and M. R. Mulvey, FEMS Microbiol. Lett. 189:285-291, 2000), which harbors the genes associated with the ACSSuT phenotype in a Canadian isolate of Salmonella enterica serovar Typhimurium DT104. A 43-kb region has been completely sequenced and found to contain 44 predicted open reading frames (ORFs) which comprised approximately 87% of the total sequence. Fifteen ORFs did not show any significant homology to known gene sequences. A number of ORFs show significant homology to plasmid-related genes, suggesting, at least in part, a plasmid origin for the SGI1, although some with homology to phage-related genes were identified. The SGI1 was identified in a number of multidrug-resistant DT120 and S. enterica serovar Agona strains with similar antibiotic-resistant phenotypes. The G+C content suggests a potential mosaic structure for the SGI1. Emergence of the SGI1 in serovar Agona strains is discussed.

FIG. 1

Cloning strategy of the complete SGI1. Letters above the map indicate restriction enzyme sites. X, XbaI; E, EcoRI; S, SalI; A, AvrII. Boxes above the map depict previously characterized regions (4) and are not drawn to scale. Arrows denote the direction of transcription.

FIG. 2

Linear representation of the complete SGI1 and flanking regions. Upper rectangles indicate ORFs transcribed from right to left, and lower rectangles are transcribed left to right. GenBank entries of ORFs were assigned unique identifiers in the form SXXX. Color coding indicates ORFs with similar function as follows: green, DNA recombination; black, DNA replication; yellow, conjugal transfer; blue, regulatory; red, drug resistance; white, not known or other functions.

FIG. 3

G+C content of the SGI1. MDR and RT represent the multidrug resistance and retron sequences, respectively.

FIG. 4

Clustering of Salmonella isolates by analysis of IRS-PCR patterns. The dendrogram was constructed by UPGMA on a matrix based on Jaccard's coefficient. Strains were isolated in Belgium (B), France (F), or Scotland (S).

FIG. 5

Alignment of the direct repeats (DR) flanking the SGI1 in serovars Typhimurium and Agona. Asterisks represent nucleotide substitutions (see the text). sen, sensitive; res, resistant.