TABLE 1.
Single nucleotide polymorphisms that specifically distinguished clade I isolates from the cheese isolate from New York (CFSAN009740) and clinical isolate from California (PNUSAL000355)a
| SNP position | Nucleotide at the position in isolate(s) from: |
Synonymous change? | Amino acid at the position in isolate(s) from: |
Gene locus tag, putative protein function, and corresponding gene locus tag in wgMLST pan-genome | ||||
|---|---|---|---|---|---|---|---|---|
| Clade I | NY | CA | Clade I | NY | CA | |||
| 479720 | T | Cb | C | Yes | CG42_RS02440, ZIP family metal transporter, lmo0414 | |||
| 607603 | G | G | T | No | A | A | E | CG42_RS02995, LacI family transcriptional regulator, lmo0535 |
| 782555 | T | C | C | Yes | CG42_RS03880, flagellar cap protein FliD, lmo0707 | |||
| 1080475 | A | G | G | No | E | G | G | CG42_RS05405, copper homeostasis protein CutC, lmo1018 |
| 1298795c | C | C | A | No | P | P | Q | CG42_RS06585, DNA primase, LMON_1266 |
| 1334724 | C | T | C | No | T | I | T | CG42_RS06775, histidine phosphatase family protein, lmo1244 |
| 1740888 | T | C | C | Yes | CG42_RS08730, VOC family protein, lmo1635 | |||
| 1762440 | C | G | G | Intergenic | ||||
| 1775838 | C | A | C | No | A | D | A | CG42_RS08875, rRNA methyltransferase, lmo1662 |
| 2275331 | T | T | G | Yes | CG42_RS11330, sugar ABC transporter substrate-binding protein, lmo2125 | |||
| 2311944 | A | A | G | Yes | CG42_RS11530, xylose isomerase, lmo2160 | |||
| 2532881 | C | C | A | No | W | W | L | CG42_RS12665, glutamate decarboxylase, lmo2434 |
a
The reported SNP position, protein ID, and putative functions are based on the complete and annotated chromosome of isolate CFSAN010068 (GenBank accession number NZ_CP014250.1). All specific SNPs are located on the chromosome.
b
Underlining indicates that the nucleotide is different from that in clade I isolate.
c
The locus is in the putative prophage region.