Table S1.
Mycobacterial strains used in this study
| Strain name | Genotype | How constructed | Source |
| Parental strains | |||
| H37Rv | WT | N/A | Trudeau Institute |
| mc26230 | H37Rv ΔRD1 ΔpanCD | SpTr and unmarking | (24, 25) |
| H37Rv background | |||
| Hygromycin-marked strains | |||
| mc27788 | Δesx-3 (Rv0282–Rv0292)::res-sacB-hygR-res | SpTr of H37Rv | This work |
| mc27789 | ΔesxG (Rv0287)::res-sacB-hygR-res | SpTr of H37Rv | This work |
| mc27790 | ΔesxH (Rv0288)::res-sacB-hygR-res | SpTr of H37Rv | This work |
| mc27791 | ΔesxG–esxH (Rv0287–Rv0288)::res-sacB-hygR-res | SpTr of H37Rv | This work |
| mc27792 | Δpe5–ppe4 (Rv0285–Rv0286)::res-sacB-hygR-res | SpTr of H37Rv | This work |
| mc27808 | ΔmbtB (Rv2383c)::res-sacB-hygR-res | SpTr of H37Rv | This work |
| mc27809 | Δmbt-1 (Rv2377c–Rv2386c)::res-sacB-hygR-res | SpTr of H37Rv | This work |
| Hygromycin-marked, complemented strains | |||
| mc27827 | Δesx-3 (Rv0282–Rv0292)::res-sacB-hygR-res, attBL5::pYUB1335 | Transformation (pYUB1335) | This work |
| mc27828 | Δesx-3 (Rv0282–Rv0292)::res-sacB-hygR-res, attBL5::pYUB2076 | Transformation (pYUB2076) | This work |
| mc27829 | Δesx-3 (Rv0282–Rv0292)::res-sacB-hygR-res, attBL5::pJP148 | Transformation (pJP148) | This work |
| mc27830 | ΔesxG (Rv0287)::res-sacB-hygR-res, attBL5::pJP148 | Transformation (pJP148) | This work |
| mc27831 | Δesx-3 (Rv0282–Rv0292)::res-sacB-hygR-res, attBL5::pMV361 | Transformation (pMV361) | This work |
| Unmarked strains (sacB-hygR cassette removed) | |||
| mc27844 | Δesx-3 (Rv0282–Rv0292)::res | Phage delivery of γδ-resolvase | This work |
| mc27845 | ΔesxG (Rv0287)::res | Phage delivery of γδ-resolvase | This work |
| mc27846 | ΔesxH (Rv0288)::res | Phage delivery of γδ-resolvase | This work |
| mc27847 | ΔesxG–esxH (Rv0287-Rv0288)::res | Phage delivery of γδ-resolvase | This work |
| mc27848 | Δpe5–ppe4 (Rv0285-Rv0286)::res | Phage delivery of γδ-resolvase | This work |
| mc27850 | ΔmbtB (Rv2383c)::res | Phage delivery of γδ-resolvase | This work |
| Double-deletion strains (second deletion introduced into unmarked strain) | |||
| mc27851 | ΔesxG–esxH (Rv0287–Rv0288)::res; Δmbt-1 (Rv2377c–Rv2386c)::res-sacB-hygR-res | SpTr of mc27847 | |
| mc27852 | Δesx-3 (Rv0282–Rv0292)::res;Δmbt-1 (Rv2377c–Rv2386c)::res-sacB-hygR-res | SpTr of mc27844 | |
| Unmarked complemented strains | |||
| mc27856 | Δesx-3 (Rv0282–Rv0292)::res, attBL5::pYUB1335 | Phage delivery of γδ-resolvase | This work |
| mc27857 | Δesx-3 (Rv0282–Rv0292)::res, attBL5::pYUB2076 | Phage delivery of γδ-resolvase | This work |
| mc27866 | ΔesxG (Rv0287)::res, attBL5::pYUB1944 | Transformation (pYUB1944) | This work |
| mc27867 | ΔesxH (Rv0288)::res, attBL5::pYUB1944 | Transformation (pYUB1944) | This work |
| mc27868 | Δpe5–ppe4 (Rv0285-Rv0286)::res, attBL5::pYUB1945 | Transformation (pYUB1945) | This work |
| mc27874 | ΔmbtB (Rv2383c)::res, attBL5::pYUB1940 | Transformation (pYUB1940) | This work |
| mc26230 background | |||
| Hygromycin-marked strains | |||
| mc27818 | Δesx-3 (Rv0282–Rv0292)::res-sacB-hygR-res | Sptr of mc26230 | This work |
| mc27819 | ΔesxH (Rv0288)::res-sacB-hygR-res | Sptr of mc26230 | This work |
| mc27820 | ΔmbtB (Rv2383c)::res-sacB-hygR-res | Sptr of mc26230 | This work |
| Hygromycin-marked complemented strains | |||
| mc27838 | Δesx-3 (Rv0282–Rv0292)::res-sacB-hygR-res, attBL5::pYUB1335 | Transformation (pYUB1335) | This work |
| Unmarked strains (sacB-hygR cassette removed) | |||
| mc27860 | Δesx-3 (Rv0282–Rv0292)::res | Phage delivery of γδ-resolvase | This work |
| mc27861 | ΔesxH (Rv0288)::res | Phage delivery of γδ-resolvase | This work |
| mc27862 | ΔmbtB (Rv2383c)::res | Phage delivery of γδ-resolvase | This work |
| Unmarked complemented strain | |||
| mc27863 | Δesx-3 (Rv0282–Rv0292)::res, attBL5::pYUB1335 | Phage delivery of γδ-resolvase | This work |
The table lists strain names and relevant genotypes for the mycobacterial strains used in this study; the methods of construction are also indicated as well as the source where appropriate. SpTr, specialized transduction.