Table 1.
KEGG pathways altered in ST416/ST417
| Pathway | Pathway name | Pan-genome | SNP |
|---|---|---|---|
| stm01100 | Metabolic pathways | 46 | 30 |
| stm01120 | Microbial metabolism in diverse environments | 35 | 9 |
| stm02020 | Two-component system | 20 | 9 |
| stm05132 | Salmonella infection | 13 | 5 |
| stm02060 | Phosphotransferase system (PTS) | 12 | – |
| stm01110 | Biosynthesis of secondary metabolites | 12 | 7 |
| stm03070 | Bacterial secretion system | 12 | – |
| stm00350 | Tyrosine metabolism | 10 | 2 |
| stm00030 | Pentose phosphate pathway | 9 | – |
| stm01220 | Degradation of aromatic compounds | 7 | – |
| stm01200 | Carbon metabolism | 6 | 2 |
| stm02024 | Quorum sensing | 6 | – |
| stm02010 | ABC transporters | 5 | 5 |
| stm00051 | Fructose and mannose metabolism | 5 | 4 |
| stm00520 | Amino sugar and nucleotide sugar metabolism | 5 | 4 |
| stm00910 | Nitrogen metabolism | 5 | – |
| stm00010 | Glycolysis/gluconeogenesis | 5 | – |
| stm01230 | Biosynthesis of amino acids | 4 | – |
| stm00310 | Lysine degradation | 4 | 3 |
| stm05100 | Bacterial invasion of epithelial cells | 3 | – |
| stm00330 | Arginine and proline metabolism | 3 | – |
| stm00630 | Glyoxylate and dicarboxylate metabolism | 3 | 2 |
| stm00650 | Butanoate metabolism | 3 | 2 |
| stm00680 | Methane metabolism | 3 | 2 |
| stm00620 | Pyruvate metabolism | 3 | – |
| stm00260 | Glycine, serine and threonine metabolism | 3 | – |
| stm03430 | Mismatch repair | 3 | – |
| stm00760 | Nicotinate and nicotinamide metabolism | – | 3 |
| stm00250 | Alanine, aspartate and glutamate metabolism | – | 3 |
| stm01503 | Cationic antimicrobial peptide (CAMP) resistance | - | 3 |
| stm03010 | Ribosome | 2 | – |
| stm00071 | Fatty acid degradation | 2 | – |
| stm00400 | Phenylalanine, tyrosine and tryptophan biosynthesis | 2 | – |
| stm00633 | Nitrotoluene degradation | 2 | – |
| stm00640 | Propanoate metabolism | 2 | – |
| stm00500 | Starch and sucrose metabolism | 2 | 4 |
| stm02030 | Bacterial chemotaxis | 2 | - |
| stm00564 | Glycerophospholipid metabolism | 2 | – |
| stm00562 | Inositol phosphate metabolism | 2 | – |
| stm00541 | O-Antigen nucleotide sugar biosynthesis | – | 2 |
| stm00540 | Lipopolysaccharide biosynthesis | – | 2 |
| stm02060 | Phosphotransferase system (PTS) | – | 2 |
| stm00052 | Galactose metabolism | – | 2 |
| stm00230 | Purine metabolism | – | 2 |
KEGG pathways significantly enriched for presence/absence variation in isolates of ST416/ST417 compared to the S. enterica type strain LT2 as determined by pan-genome analysis and identification of high impact (i.e., presumed loss of function) SNPs.