Table 2.

PCR primers used in this study

Gene target	Primer sequence (5’-3’)		Probe	Ta*	Amplicon size (bp)	Reference
	Forward	Reverse
ompW	TCCTCAACGCTTCTGTGTGGTAT	ATTGATTTCAACATCCGTGGATT	FAM-TGAAACAACGGCAACCTACAAAGCAGG-BHQ1	55	92	This study
hlyA	AGTGGTCAACCGATGCGATT	TTCAGGATCTGCGCTTTATTGTT	ROX-CCCAAGATTATCGCTTCGTGTTTAACGCA- BHQ2	47-55	76	This study
toxR	GATTCGACAAAGTCCCCACAA	TCGGGCGATCAATTGGTAA	HEX-CGTCAAAACGGTTCCGAAACGCG-BHQ1	47-55	66	This study
ctxAB	CTCAGACGGGATTTGTTAGGCACG	TCTATCTCTGTAGCCCCTATTACG	-	55	303	[39]
tcpA (1)#	GTGACTGAAAGTCATCTCTTC	AATCCGACACCTTGTTGGTA	-	55	1248	[40]
tcpA (2)#	ATATGCAATTATTAAAACAGC	TTATTATTACCCGTTGTCGG	-	55	1052	[40]
ace	AGAGCGCTGCATTTATCCTTATTG	AACTCGGTCTCGGCCTCTCGTATC	-	55	655	[41]
zot	GCTATCGATATGCTGTCTCCTCAA	AAAGCCGACCAATACAAAAACCAA	-	55	1000	[41]
T3SS (vcsC2)	GGAAAGATCTATGCGTCGACGTTACCGATGCTATGGGT	CATATGGAATTCCCGGGATCCATGCTCT AGAAGTCGGTTGTTTCGGTAA	-	47-60	535	[16]
T3SS (vcsV2)	ATGCAGATCTTTTGGCTCACTTGATGGG	ATGCGTCGACGCCACATCATTGCTTGCT	-	47-55	742	[16]
NAG-ST	CCTATTCATTAGCATAATG	CCAAAGCAAGCTGGATTGC	-	47-55	215	[16]

^*Ta – Annealing temperature.

^# Two primer pairs of tcpA primers were used. These two primer pairs have been used previously to amplify divergent tcpA alleles [24].