TABLE 1.
Bacterial strains and plasmids used in this study
| Strain or plasmid | Genotype or description | Source or reference |
|---|---|---|
| Strains | ||
| E. coli | ||
| NEB-10 beta | Δ(ara-leu)7697 araD139 fhuA ΔlacX74 galK16 galE15 e14 mutant ϕ80dlacZΔM15 recA1 relA1 endA1 nupG rpsL (Strr) rph spoT1 Δ(mrr hsdRMS-mcrBC) | New England Biolabs |
| HB101(RP4) | supE44 aa14 galK2 lacY1 Δ(gpt-proA)62 rpsL20 (Strr) xyl-5 mtl-1 recA13 Δ(mcrC-mrr) hsdSB(rB− mB−) RP4 (Tra+ IncP Apr Kmr Tcr) | Laboratory stock |
| C. difficile | ||
| 630Δerm | Sequenced reference strain, ΔermB | Laboratory stock (52) |
| R20291 | PCR ribotype 027 epidemic strain | Laboratory stock |
| wt/p | 630Δerm or R20291 carrying the pRPFΔgus plasmid | This work |
| Δhfq/p | 630Δerm Δhfq or R20291 Δhfq carrying the pRPFΔgus plasmid | This work |
| Δhfq/p-hfq | 630Δerm Δhfq or R20291 Δhfq carrying the p-hfq plasmid | This work |
| Plasmid | ||
| pRPF185Δgus | pRPF185Δgus vector derivative | 14, 47 |
| pECrF_hfq | pRPF185Δgus carrying the hfq gene targeting the CRISPR miniarray with the full leader sequence | This work |
| pECrP_hfq | pRPF185Δgus carrying the hfq gene targeting the CRISPR miniarray with the partial leader sequence under the control of the Ptet promoter | This work |
| pECrFA_hfq630 | pECrF_hfq carrying arms for recombination in the 630Δerm strain | This work |
| pECrPA_hfq630 | pECrP_hfq carrying arms for recombination in the 630Δerm strain | This work |
| pECrPA_hfqR20291 | pECrP_hfq carrying arms for recombination in the R20291 strain | This work |
| p-hfq | pRPF185Δgus carrying the hfq gene under the control of the Ptet promoter | This work |