Variant Salmonella genomic island 1 antibiotic resistance gene clusters in Salmonella enterica serovar Derby isolates from humans in Taiwan

Abstract

Sir, A chromosomal genomic island called Salmonella genomic island 1 (SGI1) has been initially described in epidemic multidrug-resistant (MDR) Salmonella enterica serovar Typhimurium phage type DT104 strains (Salmonella Typhimurium DT104). SGI1 contains an antibiotic resistance gene cluster and most often confers resistance to ampicillin, chloramphenicol/ florfenicol, streptomycin/spectinomycin, sulphonamides and tetracyclines. The 43 kb SGI1 is located between the thdF and int2 genes of the chromosome of Salmonella Typhimurium. The int2 gene is part of a retron sequence that has been reported to date only in Salmonella Typhimurium. In other S. enterica serovars, SGI1 is located between the thdF and yidY genes. The antibiotic resistance gene cluster is located near the 30 end of SGI1 and constitutes a complex class 1 integron (Figure 1). At the first attI1 site of this complex integron, the cassette carries the aadA2 gene, which confers resistance to streptomycin and spectinomycin, and a 30-conserved segment (30-CS) with a truncated sul1 (sul1delta) gene is present. At the second attI1 site, the cassette contains the b-lactamase gene blaPSE-1 conferring resistance to ampicillin and the 30-CS comprises a complete sul1 gene conferring resistance to sulphonamides. Flanked by the two cassettes are the floR gene, which confers cross-resistance to chloramphenicol and florfenicol, and the tetracycline-resistance genes tetR and tet(G). SGI1 has been recently demonstrated to be an integrative mobilizable element. Variant SGI1 antibiotic resistance gene clusters have been described in a wide variety of S. enterica serovars. SGI1 variant antibiotic resistance gene clusters were accordingly classified from SGI1-A to SGI1-L. These gene clusters were probably generated after chromosomal recombinational events or by antibiotic resistance gene cassette replacement at one of the attI1 sites. We reasoned that MDR of Salmonella Derby isolated in Taiwan might be due to the spread of SGI1 and the presence of SGI1 antibiotic resistance gene clusters was thus investigated. The 22 MDR isolates of Salmonella Derby isolated in 2003 and 2004 from humans examined in this study were provided by the Center of Disease Control, Taiwan. Detection of SGI1, its location, and mapping of antibiotic resistance genes were performed by PCR on extracted genomic DNA using primers and conditions described previously (Figure 1). Among the 22 Salmonella Derby isolates examined, 13 isolates showed three different MDR resistance phenotypes indicative of the presence of SGI1 antibiotic resistance gene clusters. SGI1 was detected in these 13 isolates based on PCRs using primer pairs corresponding to the left junction and right junction of SGI1 in the Salmonella chromosome. PCR results were positive for the left junction of SGI1 with the chromosomal thdF gene and for the right junction with the chromosomal yidY gene, but negative for the junction with the int2 gene. Thus, the 13 Salmonella Derby strains were shown to harbour SGI1 at the same chromosomal location, i.e. between the thdF and yidY genes, as in non-Typhimurium serovars. In seven Salmonella Derby strains showing the typical Salmonella Typhimurium DT104 MDR phenotype, PCR mapping of the antibiotic resistance gene cluster showed the presence of fragments A, B, C, D, E, F and floR of the sizes expected (Figure 1). These isolates thus carried the SGI1 antibiotic resistance gene cluster classically found in MDR Salmonella Typhimurium DT104. For the five Salmonella Derby strains showing the chloramphenicol/florfenicol, streptomycin/spectinomycin, sulphonamides, tetracycline and trimethoprim MDR phenotype, PCR mapping yielded fragments A–D and floR. However, fragment E specific for the blaPSE-1 gene cassette was negative whereas a PCR using the forward primer of PCR E and the reverse primer of PCR H was positive, with a size slightly different from that expected from an SGI1-carrying Salmonella Typhimurium DT104 control strain, suggesting the presence of another gene cassette(s) at the second attI1 site of the SGI1 antibiotic resistance gene cluster. To confirm this result and to identify the gene cassette(s), PCR amplification of class 1 integrons using primers 50-conserved segment and 30-CS was performed as described previously. This PCR yielded two fragments, one of 1 kb corresponding to the aadA2 gene cassette and one of 1.3 kb, which was sequenced. Nucleotide sequencing identified the dfrA1 (conferring resistance to trimethoprim) and orfC (unknown function) gene cassettes. This array of gene cassettes was previously identified in the SGI1 antibiotic resistance gene cluster called SGI1-I of a Salmonella Derby human isolate from Malaysia. Thus, in these five Salmonella Derby strains the blaPSE-1 gene was replaced by the dfrA1 and orfC gene cassettes and corresponded to the SGI1-I antibiotic resistance gene cluster.