Whole-genome analysis of Salmonella enterica serovar Typhimurium T000240 reveals the acquisition of a genomic island involved in multidrug resistance via IS1 derivatives on the chromosome

Abstract

Salmonella enterica serovar Typhimurium is frequently associated with life-threatening systemic infections, and the recent global emergence of multidrug resistance in S. enterica isolates from agricultural and clinical settings has raised concerns. In this study, we determined the whole-genome sequence of fluoroquinolone-resistant S. enterica serovar Typhimurium T000240 strain (DT12) isolated from human gastroenteritis in 2000. Comparative genome analysis revealed that T000240 displays high sequence similarity to strain LT2, which was originally isolated in 1940, indicating that progeny of LT2 might be reemerging. T000240 possesses a unique 82-kb genomic island, designated as GI-DT12, which is composed of multidrug resistance determinants, including a Tn2670-like composite transposon (class 1 integron [intI1, bla(oxa-30), aadA1, qacEΔ1, and sul1], mercury resistance proteins, and chloramphenicol acetyltransferase), a Tn10-like tetracycline resistance protein (tetA), the aerobactin iron-acquisition siderophore system (lutA and lucABC), and an iron transporter (sitABCD). Since GI-DT12 is flanked by IS1 derivatives, IS1-mediated recombination likely played a role in the acquisition of this genomic island through horizontal gene transfer. The aminoglycoside-(3)-N-acetyltransferase (aac(3)) gene and a class 1 integron harboring the dfrA1 gene cassette responsible for gentamicin and trimethoprim resistance, respectively, were identified on plasmid pSTMDT12_L and appeared to have been acquired through homologous recombination with IS26. This study represents the first characterization of the unique genomic island GI-DT12 that appears to be associated with possible IS1-mediated recombination in S. enterica serovar Typhimurium. It is expected that future whole-genome studies will aid in the characterization of the horizontal gene transfer events for the emerging S. enterica serovar Typhimurium strains.

FIG. 1.

Circular representation of the S. enterica serovar Typhimurium T000240 genome. From the outside inward, the outer circle 1 indicates the size in base pairs (Mb). Circles 2 and 3 show the positions of CDS transcribed in clockwise and anticlockwise directions, respectively (using color codes according to the COG classification table). Circle 4 shows genomic islands (yellow, GI-DT12; green, prophages). The purple bars on circle 5 indicate 13 IS1 derivatives. The light blue bars on circle 6 and red bars on circle 7 indicate ribosomal DNA loci and tRNAs, respectively. Circle 8 shows a plot of G+C content (in a 0.5-kb window). Circle 9 shows a plot of GC skew ([G - C]/[G + C]; in a 0.5-kb window).

FIG. 2.

Phylogenetic tree based on core genome SNVs among whole-genome sequenced S. enterica serovar Typhimurium strains using the maximum-likelihood method with 1,000-fold bootstrapping. The scale indicates that a branch length of 0.04 is four times as long as one that would show a 1% difference between the nucleotide sequences at the beginning and end of the branch. The number at each branch node represents the bootstrapping value. The sequence type (ST) 19 and 313 groups, as determined by MLST, are indicated by red and green circles, respectively. The SNV information is summarized in Table S2 in the supplemental material.

FIG. 3.

Phylogenetic analysis of the 13 IS1 derivatives identified, revealing four types of IS1 sequences. Alignment of the nucleotide sequences are shown in Fig. S5 in the supplemental material.

FIG. 4.

Schematic representation of multiple drug resistance determinants. (A) Pairwise comparison of GI-DT12 in T000240 with S. Typhimurium plasmid pUO-StVR2 and uncultured bacterium plasmid pRSB107 by a BLASTN homology search and visualized by the ACT program. The red and blue bars between the chromosomal DNA lines shown in gray represent individual nucleotide matches with forward or inverted direction, respectively. BLASTN match scores less than 200 are not shown. (B) Class 1 integron on plasmid pSTMDT12_L. (C) Plasmid pSTMDT12_S.