TABLE 1.

Oligonucleotide primer sequences used in PCRs for species and subspecies identification and MLST

Primer purpose and name	Sequence	Target region	Reference
Species identification
16S_Fa	5′-AGAGTTTGATCCTGGCTCAGG-3′	16S rRNA	18
16S_R	5′-ACGGCAACCTTGTTACGAGTT-3′	16S rRNA
Subspecies identification
LacF	5′-GTACTTGTACCGACTGGAT-3′	16S rRNA	13
CreF	5′-GTGCTTGCACCGATTTGAA-3′	16S rRNA
LacreR	5′-GGGATCATCTTTGAGTGAT-3′	16S rRNA
Lhis5F	5′-CTTCGTTATGATTTTACA-3′	Histidine operon	11
Lhis6R	5′-AATATCAACAATTCCATG-3′	Histidine operon
MLSTb
rpoA_F	5′-ATGATYGARTTTGAAAAACC-3′	RNA polymerase	5
rpoA_R	5′-ACHGTRTTRATDCCDGCRCG-3′	RNA polymerase
atpA_F	5′-TAYRTYGGKGAYGGDATYGC-3′	ATP synthase
atpA_R	5′- CCRCGRTTHARYTTHGCYTG-3′	ATP synthase
bcaT_F	5′-TTTKSHRTGCCDGTWGG-3′	BCAAc aminotransferase
bcaT_R	5′-GGWCCHACTTCYGTYTC-3′	BCAA aminotransferase
pepN_F	5′-ATKTCTTAYGCWGAYRTYGT-3′	Aminopeptidase N
pepN_R	5′-TTKCTTCAAGSMAWGSCC-3′	Aminopeptidase N
pepX_F	5′-TTTGGGTTGAAAGTCCAGT-3′	X-prolyl peptidase
pepX_R	5′-CCAAGAAGAAATTCCAGC-3′	X-prolyl peptidase
pheS_F	5′-CAYCCNGCHCGYGAYATGC-3′	Phe tRNA synthetase
pheS_R	5′-CCWARVCCRAARGCAAARCC-3′	Phe tRNA synthetase
SSU rRNA_F	5′-GCGGCGTGCCTAATACATGC-3′	16S rRNA
SSU rRNA_R	5′-ATCTACGCATTTCACCGCTAC-3′	16S rRNA

^aF, forward; R, reverse.

^bR represents A or G, Y represents C or T, M represents A or C, K represents G or T, S represents C or G, W represents A or T, H represents A, C, or T, B represents C, G, or T, V represents A, C, or G, D represents A, G, or T, and N represents A, C, G, or T.

^cBCAA, branched-chain amino acid.