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Table 3 43 Variable genes found within a clonal lineage of Salmonella Montevideo.

From: High resolution clustering of Salmonella enterica serovar Montevideo strains using a next-generation sequencing approach

Gene LT Locus Drain Locus Nuc AA Position Clade Feature
lig STM2427 SEEM020_00085 C/T T 1974 b DNA ligase, NAD-dependent
perM STM2493 SEEM020_00410 C/T A 1034 d,e,f permease PerM
aroB STM3486 SEEM020_01090 C/T V/A 488 b,c,d,e,f shikimate kinase I
yrfI STM3498 SEEM020_01145 C/T T/I 353 b,c,d,e,f heat shock protein
gntK STM3542 SEEM020_01330 G/A H/Q 93 a1 1) gluconate transporter GntU, 2) shikimate kinase
dppA STM3630 SEEM020_01925 C/T H 282 a1 dipeptide transport protein
tolB STM0748 SEEM020_01960 G/T A/S 64 a1 tolB protein precursor
citG STM0619 SEEM020_04239 C/T R/C 181 b,c,d,e,f triphosphoribosyl-dephospho-CoA synthase
citF STM0621 SEEM020_04249 C/T V/A 602 b,c,d,e,f citrate lyase alpha chain
ydfZ STM1509 SEEM020_04749 G/A P 174 b putative selenium-binding protein YdfZ
  STM1546 SEEM020_04939 C/T L 1473 d,e,f 1) putative multidrug efflux protein, 2) hypothetical protein
  SeSA_A1664 SEEM020_05139 C/T L 667 a1 LysR substrate binding domain protein
  STM1627 SEEM020_05529 C/T T 543 a1 alcohol dehydrogenase class III
  STM1628 SEEM020_05534 T/G L/R 155 a1 putative cytoplasmic protein
  STM1671 SEEM020_05759 A/C V 122 a1 putative regulatory protein
  STM1856 SEEM020_06993 G/T E/Stop 316   putative cytoplasmic protein
fliC STM1959 SEEM020_07518 T/A N/K 723 a1 phase 1 flagellin
uhpA STM3790 SEEM020_08264 A/G l 60 a1 1) sensor histidine kinase UhpB, 2)transcriptional regulatory protein UhpA
nuoL STM2318 SEEM020_09061 C/T F 291 f2 NADH dehydrogenase I
  STM4534 SEEM020_10120 C/T A/V 14 b putative transcriptional regulator
ytfG STM4401 SEEM020_10825 C/T S/F 503 f3 conserved hypothetical protein
yjeM STM4345 SEEM020_11085 C/T L 1179 a1 putative APC family amino-acid transport protein
  STM4261 SEEM020_11575 G/A V/I 4684   putative inner membrane protein
araD STM0101 SEEM020_12590 C/A Q/K 466 b L-ribulose-5-phosphate 4-epimerase
araB STM0103 SEEM020_12600 G/A L 702 e,f L-ribulokinase
  STM3260 SEEM020_13557 G/A V/M 70 b PTS family galactitol-specific enzyme IIC
  SeD_A3648 SEEM020_13697 A/G D/G 263 d,e,f hypothetical protein
pduV STM2056 SEEM020_14356 G/A D/G 353 b,c,d,e,f propanediol utilization protein
orf408 STM1382 SEEM020_15066 G/A T/A 1096 a1 putative regulatory protein, deoR family
ydiA STM1348 SEEM020_15231 C/T F 126 b,c,d,e,f putative inner membrane protein
envE STM1242 SEEM020_15746 T/C I/T 446 a1 EnvE
ycfX STM1220 SEEM020_15941 C/T G 24 d,e,f N-acetylglucosamine kinase
  STM4097 SEEM020_16375 G/A S/N 119 a1 putative outer membrane lipoprotein
uvrD STM3951 SEEM020_17067 G/A G/E 2111 f2 DNA helicase II
  STM2404 SEEM020_17529 G/T A/S 394 b putative chloride channel permease
recB STM2994 SEEM020_17950 G/A S/G 901 d,e,f exodeoxyribonuclease V
stdB STM3028 SEEM020_18130 C/T L 2433 f2 putative outer membrane usher protein
yqjI STM3215 SEEM020_19095 C/A H/N 562 e,f 1) transcriptional regulator (PadR), 2) family methyl-accepting chemotaxis protein II
ybhK STM0801 SEEM020_19330 G/A L 618 a1 conserved hypothetical protein
  STM0818 SEEM020_19410 G/T A/S 277 e,f 1) putative ABC-type multidrug transport system, 2) membrane permease predicted cation efflux pump
yliD STM0851 SEEM020_19565 T/C W/R 760   putative ABC transporter inner membrane component
invE STM2897 SEEM020_21151 C/G L/V 757 f invasion protein
yejM STM2228 SEEM020_21392 G/A A/E 395 a1 putative hydrolase of alkaline phosphatase superfamily
  1. Variable genes are listed by their Genbank abbreviated and full name (feature) and by the blast locus hit to either a reference isolate LT2 or the Drain swab isolate. A representative nucleotide change observed within each gene is listed as well as whether this caused an AA change and to which phylogenetic group it was associated with from Figure 3 (A-F). These SNPs were the most useful for the spiced meat outbreak investigation and will be useful for both targeted resequencing efforts and for rapid subtyping methods for traceback of future S. Montevideo investigation and diagnosis.