The complete sequence of Salmonella genomic island SGI1-K.

Sir, Multiple antibiotic resistance in Salmonella enterica is often caused by the presence of a class 1 integron or a complex class 1 integron, which is located inside a genomic island that integrates into the chromosome at the end of the 3′-end of the thdF gene (recently renamed trmE). The first form of this island to be identified was SGI1, which was found in S. enterica serovar Typhimurium DT104, and until recently it was the only completely sequenced example of this island type (GenBank accession number AF261825). However, this sequence is a confusing exemplar as serovar Typhimurium carries an additional element inserted between SGI1 and the downstream yidY gene that is not found in any other serovar that has been examined to date. Many SGI1 variants have been reported, most of which involve the loss, gain or replacement of antibiotic resistance genes within the boundaries of the complex class 1 integron (In104 in SGI1). A second independently created island form, SGI2, carries the integron in a different location. However, these various forms have generally been characterized using only PCR, hybridization and limited sequencing. SGI1-K was found in S. enterica serovar Kentucky strain SRC73 recovered in 2001 in Australia from spice imported from India. We originally reported that SGI1-K was different from most SGI1 variants as it carries a mercuric ion resistance module. We subsequently sequenced the remainder of the resistance island, which consists of a set of segments carrying an antibiotic resistance gene separated by copies of IS26 (GenBank accession number AY463797), and an IS26-mediated deletion had removed the right-hand end of the integron including the inverted repeat IRt and part of the adjacent backbone (S044 gene). A similar structure was reported for an SGI1 derivative, named SGI1-K1, that was also found in a serovar Kentucky isolate of North African origin isolated between 2001 and 2005, but again only part of the sequence was reported (GenBank accession number EU664602). SGI1-K1 was found to carry a copy of IS1359 (ISVch4) in its backbone that had displaced 2.8 kb of adjacent DNA extending from within S005 to within S009 and the same configuration was later found in SGI1-K (GenBank accession number AY463797). Hence, SGI1-K and SGI1-K1 are likely to be identical. To determine the precise relationship of SGI1-K to SGI1, and as the backbones of so few SGI1 family genomic islands have been reported, we sequenced the genome of SRC73 on an Illumina HiSeq at the Australian Genomic Research Facility and assembled the reads (36-fold average read depth) using Velvet. The complete sequence of SGI1-K was assembled using the relevant contigs and our available sequence for In104-K and part of the backbone. The structure of SGI1-K is shown in Figure 1. Compared with SGI1, 2779 bp are missing (from S005 to S009) and 292 bp are missing from S044 (see Figure 1), and there are eight single base differences in the remaining backbone. SGI1-K and its derivatives are part of a subgroup of the SGI1 genomic island family, all of which carry the aacCA5-aadA7 cassettes in a class 1 integron and IS1359 with the same surrounding deletion. This group includes SGI1-H and SGI1-L. A number of SGI1-type islands carrying the aacCA5-aadA7 gene cassettes found in Proteus mirabilis have been completely sequenced, and all have the right (IRt) end of the integron and S044 intact, but they share the remaining backbone differences with SGI1-K. Although named differently, one of the P. mirabilis islands corresponds to SGI1-H (GenBank accession number JX121639; SGIPmSCO) and another carries a large segment including a further integron with the dfrA15 gene cassette between the two integron-associated cassette arrays found in most SGI1 variants, and may represent SGI1-L (GenBank accession number JX121641; SGIPmGUE). A third is a variant of SGI1-H that has lost the central portion and right-hand integron (GenBank accession number JX121638; SGIPmABB), which for clarity and simplicity we have named SGI1-W. A further variant can be derived from SGI1-L by the IS26-mediated loss of a large region (GenBank accession number JX121640; SGIPmVER). SRC73 is ST198, and many S. enterica serovar Kentucky ST198 isolates have been reported to include SGI1-K or variants derived from it. The SGI1-K-carrying form of this clone is believed to have originated in North Africa Later, resistance to fluoroquinolones was acquired in two steps: first nalidixic acid resistance and then ciprofloxacin resistance. SRC73 is resistant to nalidixic acid and, consistent with that phenotype, carries a mutation (TCC to TTC) in codon 83 of gyrA causing a Ser83Phe substitution in GyrA. GyrA codon 87 (GAC) codes for the original Asp. Serovar Kentucky ST198 isolates carrying SGI2 (incorrectly named SGI1-J) have also been found, indicating that an SGI island has been acquired by the ST198 serovar Kentucky clone on two occasions.