Table 1. Strains, plasmids, and oligonucleotides used in this study.

Strain, plasmid, or oligo	Relevant characteristics or sequence	Source
WAM2266	CFT073 gyrA S83L, nalR	H. Mobley
WAM2267	CFT073 rpoS am	H. Mobley
WAM2615	WAM2266 derivative, dsdA Δ445bp gyrA S83L, nalR	[28]
WAM2880	WAM2267 derivative, CFT074 ΔlacZYA rpoS am	[50]
WAM2914	WAM2267 derivative, CFT073 ΔdsdA rpoS am	P. Roesch
WAM2966	WAM2267 derivative, CFT073 dsdX::CmR rpoS am	A. Anfora
WAM3707	WAM2267 derivative, CFT073 sdaA::CmR sdaB::KmR rpoS am	A. Anfora
WAM4248	WAM2267 derivative, CFT073 cycA::KmR rpoS am	G. Baisa
WAM4505	CFT073, original patient isolate	H. Mobley
WAM4520	WAM4505 derivative, CFT073 ΔlacZYA	[45]
WAM4567	WAM4505 derivative, CFT073 ΔdsdA	This study
WAM5311	WAM4505 derivative, CFT073 ΔdsdA sdaA::CmR sdaB::KmR	This study
WAM5314	WAM4505 derivative, CFT073 ΔcycA ΔdsdX	This study
ΦEB49	Generalized transducing phage	[48]
pKD46	Expresses λ RED recombination functions, ApR	[47]
pKD3	Template for λ RED-mediated replacement, CmR	[47]
pKD4	Template for λ RED-mediated replacement, KmR	[47]
pCP20	Encodes FLP recombinase, ApR	[47]
cycA F Check	5’-GAC TAT CCC GCA GGA ACT GG-3’	Our laboratory
cycA R Check	5’-CGG CAT TAA TGA ACT GAT TGA TGA C-3’	Our laboratory
dsdA λ RED F	5’-CCT GCT GTC ATT TAT CAT CTA AGC GCA AAG AGACGT ACT TGT GTA GGC TGG AGC TGC TTC G-3’	This study
dsdA λ RED R	5’-CAC CCA GGG AAA GGA TGG CGA TGC TGC GTT GAA ACG TTA CAT ATG AAT ATC CTC CTT AG-3’	This study
dsdA F Check	5’-GGT TCC GGT GCG ATT GGC TGC-3’	This study
dsdA R Check	5’-GGA TGG CGA TGC TGC GTT G-3’	This study
dsdX F Check	5’-GAA TTG GTC TGA CAC TTC AAC GCT GC-3’	Our laboratory
dsdX R Check	5’-GCA ACC AGT TCT GAT TCA ATA ATC CCC-3’	Our laboratory
rpoS sequencing F	5’-CTG AGT GCC TAC GCC CAT AAC GAC-3’	This study
rpoS sequencing R	5’-CAA TTA CTG TGC GCT TAA AAT GAT GAT TG-3’	This study
sdaA F Check	5’-CGG GAA ACC CTA AAT CAT CGT CAG G-3’	Our laboratory
sdaA R Check	5’-GGT TGC GGA AGG GAA TCT ACC A-3’	Our laboratory
sdaB F Check	5’-GCG TGG CAA TCA CCA ATA CAG TTG A-3’	Our laboratory
sdaB R Check	5’-CGC TAG CCG CGT CTT ATC CG-3’	Our laboratory