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

Abstract

Salmonella genomic island 1 was identified for the first time in Salmonella enterica serovar Virchow isolated from humans in Taiwan. The complex class 1 integron conferring multidrug resistance was shown to be inserted within open reading frame (ORF) S023 and contains for the first time a partial transpositional module. The 5-bp target duplication flanking the complex integron suggests that its insertion in ORF S023 was by transposition.

Early Strains of Multidrug-Resistant Salmonella enterica Serovar Kentucky Sequence Type 198 from Southeast Asia Harbor Salmonella Genomic Island 1-J Variants with a Novel Insertion Sequence

“…SGI1 and its chromosomal location were detected using primers corresponding to the left and right junctions (DR-L and DR-R) in the chromosome as described previously (4-7). PCR mapping of the SGI1 scaffold (outside complex integron) was performed using PCRs and primers previously described (3,4,7). The atypical insertion site of the complex integrons InSGI1-J (in ORF S023) was further assessed by Southern blot hybridization of whole genomic DNA cut by XbaI (Promega, Charbonnières, France) by using probe p1-9 as previously described (1,4,5,7).…”

“…This probe corresponds to a 2-kb EcoRI fragment comprising parts of the S023 and S024 ORFs. To assess variant SGI1 MDR regions and their insertion sites identified in this study, a complete integron PCR mapping and integron junction PCR were also performed using primers previously described (3,4,7). Integron cassette arrays were amplified by PCR using primers CS1 and CS2 (13).…”

“…In the great majority of these variants, except the SGI1-J subgroup, the complex In104 integron or variants of it are found always at the same position in the SGI1 scaffold, i.e., between the resolvase gene res (also named tnpR) and the open reading frame (ORF) S044 at the 3= end of SGI1 ( Fig. 1) (3,4,11,19).…”

“…1) (3,4,14,15,24). Levings et al have proposed to classify this subgroup as a derivative named SGI2; nevertheless, according to high nucleotide identity of the SGI1 backbone, the classification as in SGI1-J1 to -J5 is more advisable and is related to different complex integrons, genetic rearrangements, and the presence of resistance genes floR2 (also called cmlA9) for chloramphenicol resistance, tetR(G) and tetA(G) for tetracycline resistance, and sul1 and dfrA1 for sulfamethoxazole/trimethoprim resistance (3,4,14,15).…”

“…The SGI1-J subgroup is represented by the unique and peculiar SGI1 variants that have been characterized in two S. enterica serovars, i.e., Emek and Virchow, isolated from Southeast Asia and Oceania from 1993 to 2006 (3,4,14,15,24). The main characteristic of SGI1-J relies in that different complex integrons are inserted by transposition within the ORF S023 and not in the classical SGI1 integron insertion site, i.e., between the res gene and ORF S044 that is left empty (Fig.…”