TABLE 4.
Strains, phages, and plasmids used for phage propagation and molecular genetic validation of GWAS results
| Strain, phage, or plasmid | Characteristics/description | Reference(s) |
|---|---|---|
| E. coli strains | ||
| DH5ɑ | E. coli cloning strain; F− endA1 glnV44 thi-1 recA1 relA1 gyrA96 deoR nupG purB20 φ80dlacZΔM15 Δ(lacZYA-argF)U169 hsdR17 (rK– mK+) λ− | 119 |
| IM08B | E. coli cloning strain with S. aureus CC8 DNA modification; DNA cytosine methyltransferase (dcm)-negative mutant of E. coli K-12 DH10B; mcrA Δ(mrr-hsdRMS-mcrBC) φ80lacZΔM15 ΔlacX74 recA1 araD139 Δ(ara-leu)7697 galU galK rpsL endA1 nupG Δdcm ΩPhelp-hsdMS (CC8-2) ΩPN25-hsdS (CC8-1) | 114 |
| S. aureus strains | ||
| RN4220 | Phage propagation strain; background for transducing tarM::Tn; cloning intermediate for pOS1-Plgt-fmtC | 120 |
| RN4220 tarM::Tn | Podovirus (p0017) propagation strain; generated by transducing RN4220 with USA300 JE2 tarM::Tn (NE611) phage 0045 lysate | This study |
| USA300 JE2 | Wild-type for genetic validation experiments and background for transposon mutant backcrossing | 49 |
| USA300 JE2 tarM::Tn (NE611) | Transposon mutant transduced into RN4220 to make RN4220 tarM::Tn by a NE611 phage 0045 lysate | 49 |
| USA300 JE2 trpA::Tn | Mutant NE304 backcrossed into USA300 JE2 | This study |
| USA300 JE2 trpA::Tn pOS1 | Complemented backcrossed mutant with empty vector | This study |
| USA300 JE2 trpA::Tn pOS1 trpA | Complemented backcrossed mutant with trpA from USA300 JE2 | This study |
| USA300 JE2 phoR::Tn | Mutant NE618 backcrossed into USA300 JE2 | This study |
| USA300 JE2 phoR::Tn pOS1 | Complemented backcrossed mutant with empty vector | This study |
| USA300 JE2 phoR::Tn pOS1 phoR | Complemented backcrossed mutant with phoR from USA300 JE2 | This study |
| USA300 JE2 isdB::Tn | Mutant NE1102 backcrossed into USA300 JE2 | This study |
| USA300 JE2 isdB::Tn pOS1 | Complemented backcrossed mutant with empty vector | This study |
| USA300 JE2 isdB::Tn pOS1 isdB | Complemented backcrossed mutant with isdB from USA300 JE2 | This study |
| USA300 JE2 sodM::Tn | Mutant NE1224 backcrossed into USA300 JE2 | This study |
| USA300 JE2 sodM::Tn pOS1 | Complemented backcrossed mutant with empty vector | This study |
| USA300 JE2 sodM::Tn pOS1 sodM | Complemented backcrossed mutant with sodM from USA300 JE2 | This study |
| USA300 JE2 fmtC::Tn | Mutant NE1360 backcrossed into USA300 JE2 | This study |
| USA300 JE2 fmtC::Tn pOS1 | Complemented backcrossed mutant with empty vector | This study |
| USA300 JE2 fmtC::Tn pOS1 fmtC | Complemented backcrossed mutant with fmtC from USA300 JE2 | This study |
| USA300 JE2 fmtC::Tn pOS1 fmtC209 | Complemented backcrossed mutant with fmtC from NRS209 | This study |
| USA300 JE2 relA::Tn | Mutant NE1714 backcrossed into USA300 JE2 | This study |
| USA300 JE2 relA::Tn pOS1 | Complemented backcrossed mutant with empty vector | This study |
| USA300 JE2 relA::Tn pOS1 relA | Complemented backcrossed mutant with relA from USA300 JE2 | This study |
| Phages | ||
| p0045 (80α-like) | Siphoviridae phage; also used for backcrossing and pOS1-Plgt-fmtC transduction from RN4220 into USA300 fmtC::Tn | 5, 6, 121 |
| p0006 (K) | Myoviridae phage; GenBank accession no. NC_005880.2 | 30, 31, 122 |
| p0017 (HER49/p66) | Podoviridae phage; GenBank accession no. NC_007046.1 | This study |
| p0017S | Siphoviridae phage | This study |
| p002y (DI) | Siphoviridae phage | This study |
| p003p (Mourad 87) | Siphoviridae phage | This study |
| p0040 (Mourad 2) | Siphoviridae phage | This study |
| pyo | Myoviridae phage; BioProject accession no. PRJNA477834 | 81, 123 |
| Plasmids | ||
| pOS1-Plgt | Empty complementation vector | 50 |
| pOS1-Plgt-trpA | Complementation vector with trpA cloned downstream of Plgt | This study |
| pOS1-Plgt-phoR | Complementation vector with phoR cloned downstream of Plgt | This study |
| pOS1-Plgt-isdB | Complementation vector with isdB cloned downstream of Plgt | This study |
| pOS1-Plgt-sodM | Complementation vector with sodM cloned downstream of Plgt | This study |
| pOS1-Plgt-fmtC | Complementation vector with fmtC cloned downstream of Plgt | This study |
| pOS1-Plgt-fmtC209 | Complementation vector with fmtC from NRS209 cloned downstream of Plgt | This study |
| pOS1-Plgt-relA | Complementation vector with relA cloned downstream of Plgt | This study |