Table 1.
Single nucleotide polymorphisms (SNPs) that differentiate the reference, chlorhexidine susceptible, Salmonella Typhimurium ST24WT and the isogenic, chlorhexidine tolerant, mutant ST24CHX detected (A) within coding genes and (B) in intergenic regions.
| (A) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| Position | Nucleotide* | Gene name | Reference ID | Gene locations | Strand | ST24WT aa* (codon) | ST24CHX aa* (codon) | Gene function | Functional category | ||
| SL1344 | ST24WT | ST24CHX | |||||||||
| NON-SYNONYMOUS | |||||||||||
| 319066 | G | G | C | sciK1 | SL1344_0274 | 318655..319140 | + | V(GTG) | Q(CAG) | SPI-6 associated, Hcp like protein, component of type VI secretory system | Virulence |
| 319067 | T | T | A | sciK1 | SL1344_0274 | 318655..319140 | + | V(GTG) | |||
| 3504469 | T | T | G | lptC | SL1344_3289 | 3503949..3504524 | + | L(CTG) | R(CGG) | Lipopolysaccharide export system protein, forms ABC transporter with LptBFG | Transport and permeability |
| 638182 | C | C | T | ramR | SL1344_0568 | 637634..638215 | − | A(GCA) | T(ACA) | TetR family transcriptional regulator, repressor of ramA | Drug transport/ metabolism |
| 3781244 | G | G | A | pitA | SL1344_3554 | 3779941..3781314 | + | W(TGG) |
 (TAG) |
Low-affinity inorganic phosphate transporter, PiT family | Inorganic ion transport and metabolism |
| 2502787 | G | A | G | yfdC | SL1344_2362 | 2502523..2503464 | + | G(GGC) | S(AGC) | Putative formate/nitrate transporter | Anaerobic metabolism, transport and permeability |
| 3542329 | C | T | C | oadA2 | SL1344_3324 | 3541466..3543241 | − | G(GGC) | S(AGC) | Oxaloacetate decarboxylase subunit alpha, involved in pyruvate metabolism, conversion of oxaloacetate to pyruvate and carbon dioxide | Amino acid metabolism, energy production |
| 4182738 | A | A | T | − | SL1344_4465 | 4812650..4815415 | + | Y(TAT) | F(TTT) | NtrC family of transcriptional regulator, involved in activation of nitrogen metabolism related promoters and sigma 54 | Regulation |
| 4812741 | T | C | T | L(CTG) | P(CCG) | ||||||
| 2043305 | A | C | A | − | SL1344_1929 | 2041795..2042394 | V(GTT) | A(GCT) | Bacteriophage SLP203, putative bacteriophage tail protein | Bacteriophage | |
| 2043305 | A | C | A | − | SL1344_1930 | 2042364..2043959 | − | S(TCT) | A(GCT) | Bacteriophage SLP203, putative bacteriophage tail fiber protein | Bacteriophage |
| 2042368 | A | A | G | − | V(GTA) | G(GGA) | |||||
| 2045590 | T | T | C | − | SL1344_1934 | 2045576..2045989 | − | K(AAA) | Q(CAA) | Bacteriophage SLP203, bacteriophage protein | Bacteriophage |
| 2066438 | C | A | C | − | SL1344_1960 | 2065512..2066507 | − | A(GCG) | S(TCG) | Bacteriophage SLP203, bacteriophage protein | Bacteriophage |
| 2766226 | A | A | G | gpP | SL1344_2590 | 2766099..2766791 | − | V(GTT) | A(GCT) | Bacteriophage SLP272, replication protein P | Bacteriophage |
| DEGENERATIVE | |||||||||||
| 334377 | C | S | C | − | SL1344_0286 | 332521..336123 | + | G(GGC) | SPI 6 associated. Rhs family protein- membrane protein of unknown function | Virulence | |
| 3032926 | G | R | G | avrA | SL1344_2845 | 3032477..3033382 | − | L(CTG) | SPI 1 associated. Type III secretion system effector protein- regulator | Virulence | |
| 2509924 | C | S | C | pgtP | SL1344_2367 | 2509846..2511237 | + | R(CGT) | Phosphoglycerate transporter protein, induced by pgtBC | Inorganic ion transport and metabolism | |
| 4404698 | T | K | T | nudC | SL1344_4105 | 4404662..4405435 | + | W(TGG) | Hypothetical NADH pyrophosphatase | Inorganic ion transport and metabolism | |
| 699483 | A | M | A | rlpA | SL1344_0626 | 699240..700307 | − | A(GCT) | Rare lipoprotein A, role in cell division, contains SPOR domain, may bind peptidoglycan | ||
| 2733943 | T | Y | T | SL1344_2552 | 2732413..2734785 | − | A(GCA) | Bacteriophage SLP272, tail fiber- like protein | Bacteriophage | ||
| NON-CODING | |||||||||||
| 4372550 | A | T | A | − | rRNA | 3588585.. 3591592 | − | 23S ribosomal RNA | Transcription, ribosomal structure and translation | ||
| 4415836 | G | A | G | − | rRNA | 4372578..4374122 | + | 16S ribosomal RNA | Transcription, ribosomal structure and translation | ||
| 1282541 | A | R | A | STnc150 | SL1344_ncRNA_25 | 1282521..1282678 | − | Experimentally verified small RNA (Sittka et al., 2008) | Regulation | ||
| 3099732 | G | T | G | ||||||||
*
Nucleotide denoted by S is either C or G; R is either G or A; K is either T or G; M is either A of C; Y is either T or C.