TABLE 2.

Primers used in this study

Primer	Sequence (5′→3′)	Purpose
Kan F	AGGTGATAGGTAAGATTATACCG	irvR; irvR irvA deletions
Kan R	CCCTATCTAGCGAACTTTTAGA	irvR; irvR irvA deletions
irvR Up F	CGCTGCAGTTTCCTTGTGTGTGACTTTC	irvR deletion
irvR Up R	GCGAATTCAGCCTTCATTGCTTCTAAATC	irvR deletion
irvR Dn F	GCGAATTCATCGGAACGGTCATTACCTAA	irvR; irvR irvA deletions
irvR Dn R	CCACTAGTCCTGTAATTTTTCATAAGGAAGAGG	irvR; irvR irvA deletions
irvR-c F	CATATGAAATACTTTTAATT	irvR complementation
irvR-c R	CCGCTCGAGTTAGGTAATGACCGTTCC	irvR complementation
gbpC F	GTCGACATCTGGGCGTGTTGAAAAAG	gbpC insertion
gbpC R	GGATCCAATGGCATTATTGCCGCTTA	gbpC insertion
irvA RT F	CCCTCAACACACTCTGCTAAGCT	irvA RT-PCR
irvA RT R	CCAAATCATTGGCCAGTTGAA	irvA RT-PCR
comEA RT F	AGGAACAATCCCTTCAGGTAACC	comEA RT-PCR
comEA RT R	CAGTCGTCTGCGTCTTCTTCTG	comEA RT-PCR
dprA RT F	GCGGTTTAGCGCGTGGTAT	dprA RT-PCR
dprA RT R	GCTCCACCGCTTTTAAGACTTG	dprA RT-PCR
comY RT F	CTTTTTTCTGGACGTCACGATTT	comYA RT-PCR
comY RT R	TCGCCCCTTGATTTCATTTAA	comYA RT-PCR
gbpC RT F	AATTCTGATACTGTTGCAGCACCTA	gbpC RT-PCR
gbpC RT R	TTCTGTTGCAGCCGGTTCT	gbpC RT-PCR
16S RT F	ATCACTAGTAGATGGACCTG	RT-PCR normalization
16S RT R	TGTATCGTCGCCTTGGTAAG	RT-PCR normalization