TABLE 1.
Bacterial strains and plasmids used in this work
| Strain or plasmid | Relevant characteristics | Sources or references |
|---|---|---|
| STRAINS | ||
| E. coli TOP10 | F–mcrA Δ(mrr-hsdRMS-mcrBC) Φ80lacZΔM15 ΔlacX74 recA1 araD139 Δ(ara leu) 7697 galU galK rpsL (StrR) endA1 nupG | Invitrogen |
| EC958 | ST131 reference strain (Clade C2). Presence of an ISCro1insertion sequence in the afa promoter region and the afaE-IX allelic variant. | (7, 48, 84) |
| EC958Δlac | EC958lacI-Z::gfp | (79) |
| EC958Δhns | EC958hns::cm; Cmr | (78) |
| EC958ΔihfA | EC958ihfA::cm; Cmr | This study |
| EC958ΔafaE | EC958afaE::cm; Cmr | This study |
| EC958ΔafaC | EC958afaC::cm; Cmr | This study |
| S10EC | ST131 UPEC isolate (Clade C2). Presence of an ISCro1 and IS1 insertion sequences in the afa promoter region and the afaE-IX allelic variant. Presence of an IS1 upstream of the osmB gene. | (7) |
| S10ECΔlac | S10EC lacI-Z::gfp. Cmr cassette removed. | This study |
| S10ECΔIS1 | S10EC IS1. Cmr cassette removed | This study |
| S10ECΔIS1Δlac | S10EC IS1 lacI-Z::gfp. Cmr cassette removed | This study |
| S10ECΔhns | S10EChns::cm; Cmr | This study |
| S10ECΔihfA | S10ECihfA::cm; Cmr | This study |
| S10ECΔafaE | S10ECafaE::cm; Cmr | This study |
| S10ECΔafaC | S10ECafaC::cm; Cmr | This study |
| S103EC | ST131 UPEC isolate (Clade C2). Presence of an ISEc10 insertion sequence in the afa promoter region and the afaE-XIII allelic variant. | (7) |
| S21EC | ST131 UPEC isolate (Clade B). Absence of insertion sequences in the afa promoter region and presence of the daaE allelic variant. | (7) |
| S22EC | ST131 UPEC isolate (Clade B). Presence of a 118 bp unknown sequence in the afa promoter region and the afaE-I allelic variant. | (7) |
| HVM52 | ST131 UPEC isolate (Clade B). Presence of an IS1 upstream of the ugd gene. | (7) |
| HVM277 | ST131 UPEC isolate (Clade B). Presence of an IS1 upstream of the ugd gene. | (7) |
| HVM2044 | ST131 UPEC isolate (Clade B). Presence of an IS1 upstream of the ugd gene. | (7) |
| S12EC | ST131 UPEC isolate (Clade C2). Presence of an IS1 upstream of the afaA and osmB genes. | (7) |
| PLASMIDS | ||
| pKD3 | Template plasmid for cm gene amplification; Cmr | (85) |
| pKOBEG-Gm | λ-red recombinase expressing plasmid; Gmr | (84, 86) |
| pCP20-Gm | FLP expressing plasmid; Gmr | (80) |
| pQF50-Cm | Promoterless lacZ reporter plasmid; Cmr | (87) |
| pQF50-Cm-afa/dr_EC958 | afa promoter region of EC958 cloned in pQF50-Cm | This study |
| pQF50-Cm-afa/dr_S10EC | afa promoter region of S10EC cloned in pQF50-Cm | This study |
| pQF50-Cm-afa/dr_S10ECΔIS1 | pQF50-Cm-afa/dr_S10EC without the IS1 element | This study |
| pQF50-Cm-afa/dr_S103EC | afa promoter region of S103EC cloned in pQF50-Cm | This study |
| pQF50-Cm-afa/dr_S21EC | afa promoter region of S21EC cloned in pQF50-Cm | This study |
| pQF50-Cm-afa/dr_S22EC | afa promoter region of S22EC cloned in pQF50-Cm | This study |