Table 1. Primer and probe sequences for qPCR assays and sequencing.

Primer/Probe	Sequence (5’ → 3’)	Target	Ref.
leadpGRG36	GGGGTGGAAATGGAGTTTTT	pGRG36	McKenzie and Craig (18)
Tn7-F	GATGCTGGTGGCGAAGCTGT	tn7
Tn7-R	GATGACGGTTTGTCACATGGA	tn7
staG-Frt	CGCGAAGTCAGAGTCGACATAG	S. Typhi	Nga, Karkey (17)
staG-Rrt	AAGACCTCAACGCCGATCAC	S. Typhi
staG-Probe a	FAM-CATTTGTTCTGGAGCAGGCTGACGG-TAMRA	S. Typhi
STmod-Probe	HEX-GCACGAGATGTCTCAGTCCCGCATT-BHQ	PCO	This manuscript
ttr-F	CTCACCAGGAGATTACAACATGG	Pan Salmonella	Nair, Patel (22)
ttr-R	AGCTCAGACCAAAAGTGACCATC	Pan Salmonella
ttr-Probe	FAM-CACCGACGGCGAGACCGACTTT-BHQ1	Pan Salmonella
tviB-F	TGTGGTAAAGGAACTCGGTAAA	S. Typhi
tviB-R	GACTTCCGATACCGGGATAATG	S. Typhi
tviB-Probe	TET-TGGATGCCGAAGAGGTAAGACGAGA-BHQ1	S. Typhi

^a The LSTM staG probe contained Cy5 on the 5’ end rather than FAM.