IS6100-mediated genetic rearrangement within the complex class 1 integron In104 of the Salmonella genomic island 1

Sir, Multidrug-resistant Salmonella enterica serovar Typhimurium DT104 (where DT stands for definitive type) emerged during the 1980s as a cause of many outbreaks in humans and animals, most isolates exhibiting resistance to a core group of antimicrobials including ampicillin/amoxicillin, chloramphenicol/florfenicol, streptomycin/spectinomycin, sulphonamides and tetracyclines (ACSSuT phenotype).1 The genes responsible were shown to be located on a 13 kb multidrug resistance region (MDR region) that constitutes a complex class 1 integron. This cluster, recently named In104, belongs to the integron In4 group and is located in a 43 kb genomic island named Salmonella genomic island 1 (SGI1).1 Several variants of SGI1 have also been described over time in a wide variety of S. enterica serovars and in Proteus mirabilis.1 In this study, we examined an S. enterica serovar Typhimurium strain 72-21880-11 isolated from the faeces of a healthy cow in Denmark in 2000, which displayed resistance to chloramphenicol/florfenicol, streptomycin/spectinomycin and tetracycline. To assess whether this strain harbours SGI1, PCRs were performed using primers corresponding to the left and right junctions of SGI1 in the Salmonella chromosome as described previously.2 PCR results were positive for the left junction with the chromosomal thdF gene and for the right junction with the int2 gene of the retron sequence specifically found downstream of SGI1 in the serovar Typhimurium, indicating that this strain contained SGI1 at the same location as in other isolates.2 To confirm the presence of the entire SGI1, PCR mapping of the 5′ region of SGI1 (the first 10 kb) was performed as described previously.3 All of the PCR results were positive. The presence of the remaining non-MDR region of SGI1 was assessed by Southern blot hybridization of XbaI-digested genomic DNA with the p1-9 probe as previously described.2 The Southern blot profile of the serovar strain 72-21880-11 was similar to that obtained for the control strain of serovar Typhimurium DT104 harbouring SGI1 with two XbaI fragments of 4 and 9 kb (data not shown). To confirm the location of the MDR region within SGI1, PCRs were performed using primers S026-FW/int-RV and DB-T1/MDR-B4 corresponding to the boundaries of the integron with the SGI1 backbone. The two PCRs gave positive results, indicating that the MDR region was at the normal position within the SGI1 backbone, i.e. between the res gene and the open reading frame S044.