Key resources table.
| Reagent type (species) or resource | Designation | Source or reference | Identifiers | Additional information |
|---|---|---|---|---|
| Strain and strain background (S. pneumoniae) | D39V | doi:10.1093/nar/gky725 | VL001 | Serotype 2 and wildtype |
| Strain and strain background (S. pneumoniae) | 19F | This paper | VL4303 | Serotype 19F and clinical isolate |
| Strain and strain background (S. pneumoniae) | Spain-23F | German National Reference Center for Streptococci | VL1306 | Serotype 23F, PMEN1, and clinical isolate |
| Strain and strain background (S. pneumoniae) | 11A | German National Reference Center for Streptococci, doi:10.1093/jac/dky305 | VL1313 | Serotype 11A, PMEN3, and clinical isolate |
| Strain and strain background (Mus musculus) | C57BL/6JRj, male, 8 weeks old | Janvier Laboratories, Saint Berthevin, France | ||
| Genetic reagent (S. pneumoniae) | VL333 | Veening lab collection | VL333 | D39V prs1::lacI-tetR-Gm |
| Genetic reagent (S. pneumoniae) | VL567 | doi:10.1038/s41467-017-00903-y | VL567 | D39V Δcps::Cm |
| Genetic reagent (S. pneumoniae) | VL1630 | Veening lab collection | VL1630 | D39V ftsZ-mCherry-Ery bgaA::Pzn-gfp-stkP |
| Genetic reagent (S. pneumoniae) | VL1998 | doi:10.15252/msb.20167449 | VL1998 | D39V prs1::F6-lacI-Gm bgaA::Plac-dCas9-Tc |
| Genetic reagent (S. pneumoniae) | VL2226 | doi:10.1128/JB.02221-14 | VL2226 | D39V hlpA-gfp-Cm |
| Genetic reagent (S. pneumoniae) | VL3117 | This paper | VL3117 | VL1998 hlpA-gfp-Cm ftsZ-mCherry-Ery |
| Genetic reagent (S. pneumoniae) | VL3404 | This paper | VL3404 | VL333 hlpA-gfp-Cm ftsZ-mCherry-Ery |
| Genetic reagent (S. pneumoniae) | VL3565 | This paper | VL3565 | VL3404 zip::Plac-mvk-mvaD- mvaK2-fni-Spec Δmvk-mvaD-mvaK2-fni::Km |
| Genetic reagent (S. pneumoniae) | VL3567 | This paper | VL3567 | VL3404 zip::Plac-mvaS- mvaA-Spec ΔmvaS-mvaA::Km |
| Genetic reagent (S. pneumoniae) | VL3584 | This paper | VL3584 | VL3404 zip::Plac-uppS- Spec ΔuppS::Km |
| Genetic reagent (S. pneumoniae) | VL3585 | This paper | VL3585 | VL3404 zip::Plac-mraY-Spec ΔmraY::Km |
| Genetic reagent (S. pneumoniae) | VL3586 | This paper | VL3586 | VL3404 zip::Plac-SPV_1620- Trm ΔSPV_1620::Km |
| Genetic reagent (S. pneumoniae) | VL3671 | This paper | VL3671 | VL3117 zip::P3-sgRNA035 |
| Genetic reagent (S. pneumoniae) | VL3672 | This paper | VL3672 | VL3117 zip::P3-sgRNA036 |
| Genetic reagent (S. pneumoniae) | VL3673 | This paper | VL3673 | VL3117 zip::P3-sgRNA046 |
| Genetic reagent (S. pneumoniae) | VL3674 | This paper | VL3674 | VL3117 zip::P3-sgRNA087 |
| Genetic reagent (S. pneumoniae) | VL3675 | This paper | VL3675 | VL3117 zip::P3-sgRNA100 |
| Genetic reagent (S. pneumoniae) | VL3676 | This paper | VL3676 | VL3117 zip::P3-sgRNA121 |
| Genetic reagent (S. pneumoniae) | VL3677 | This paper | VL3677 | VL3117 zip::P3-sgRNA135 |
| Genetic reagent (S. pneumoniae) | VL3678 | This paper | VL3678 | VL3117 zip::P3-sgRNA355 |
| Genetic reagent (S. pneumoniae) | VL3679 | This paper | VL3679 | VL3117 zip::P3-sgRNA432 |
| Genetic reagent (S. pneumoniae) | VL3680 | This paper | VL3680 | VL3117 zip::P3-sgRNA455 |
| Genetic reagent (S. pneumoniae) | VL3681 | This paper | VL3681 | VL3117 zip::P3-sgRNA460 |
| Genetic reagent (S. pneumoniae) | VL3682 | This paper | VL3682 | VL3117 zip::P3-sgRNA461 |
| Genetic reagent (S. pneumoniae) | VL3683 | This paper | VL3683 | VL3117 zip::P3-sgRNA503 |
| Genetic reagent (S. pneumoniae) | VL3684 | This paper | VL3684 | VL3117 zip::P3-sgRNA573 |
| Genetic reagent (S. pneumoniae) | VL3685 | This paper | VL3685 | VL3117 zip::P3-sgRNA583 |
| Genetic reagent (S. pneumoniae) | VL3686 | This paper | VL3686 | VL3117 zip::P3-sgRNA590 |
| Genetic reagent (S. pneumoniae) | VL3687 | This paper | VL3687 | VL3117 zip::P3-sgRNA628 |
| Genetic reagent (S. pneumoniae) | VL3688 | This paper | VL3688 | VL3117 zip::P3-sgRNA673 |
| Genetic reagent (S. pneumoniae) | VL3689 | This paper | VL3689 | VL3117 zip::P3-sgRNA757 |
| Genetic reagent (S. pneumoniae) | VL3690 | This paper | VL3690 | VL3117 zip::P3-sgRNA780 |
| Genetic reagent (S. pneumoniae) | VL3691 | This paper | VL3691 | VL3117 zip::P3-sgRNA785 |
| Genetic reagent (S. pneumoniae) | VL3692 | This paper | VL3692 | VL3117 zip::P3-sgRNA796 |
| Genetic reagent (S. pneumoniae) | VL3693 | This paper | VL3693 | VL3117 zip::P3-sgRNA813 |
| Genetic reagent (S. pneumoniae) | VL3694 | This paper | VL3694 | VL3117 zip::P3-sgRNA822 |
| Genetic reagent (S. pneumoniae) | VL3695 | This paper | VL3695 | VL3117 zip::P3-sgRNA824 |
| Genetic reagent (S. pneumoniae) | VL3696 | This paper | VL3696 | VL3117 zip::P3-sgRNA900 |
| Genetic reagent (S. pneumoniae) | VL3697 | This paper | VL3697 | VL3117 zip::P3-sgRNA1019 |
| Genetic reagent (S. pneumoniae) | VL3699 | This paper | VL3699 | VL3117 zip::P3-sgRNA1064 |
| Genetic reagent (S. pneumoniae) | VL3700 | This paper | VL3700 | VL3117 zip::P3-sgRNA1236 |
| Genetic reagent (S. pneumoniae) | VL3701 | This paper | VL3701 | VL3117 zip::P3-sgRNA1240 |
| Genetic reagent (S. pneumoniae) | VL3702 | This paper | VL3702 | VL333 ΔmvaS-mvaA::Km |
| Genetic reagent (S. pneumoniae) | VL3708 | This paper | VL3708 | VL333 zip::Plac-mvk-mvaD- mvaK2-fni-Spec Δmvk- mvaD-mvaK2-fni::Km |
| Genetic reagent (S. pneumoniae) | VL3709 | This paper | VL3709 | VL333 zip::Plac-mvaS- mvaA-Spec ΔmvaS-mvaA::Km |
| Genetic reagent (S. pneumoniae) | VL3710 | This paper | VL3710 | VL333 zip::Plac-uppS- Spec ΔuppS::Km |
| Genetic reagent (S. pneumoniae) | VL3711 | This paper | VL3711 | VL333 zip::Plac-mraY-Spec ΔmraY::Km |
| Genetic reagent (S. pneumoniae) | VL3712 | This paper | VL3712 | VL333 zip::Plac-SPV_1620- Trm ΔSPV_1620::Km |
| Genetic reagent (S. pneumoniae) | VL3834 | This paper | VL3834 | VL1998 ΔmvaS-mvaA::Km |
| Genetic reagent (S. pneumoniae) | VL4273 | This paper | VL4273 | VL333 bgaA::Ptet-pbp2x-Tc Δpbp2x::Ery |
| Genetic reagent (S. pneumoniae) | VL4274 | This paper | VL4274 | VL3709 bgaA::Ptet-pbp2x-Tc Δpbp2x::Ery |
| Genetic reagent (S. pneumoniae) | LD0001 | This paper | LD0001 | VL333 bgaA::Ptet-divIVA-Tc ΔdivIVA::Cm |
| Genetic reagent (S. pneumoniae) | LD0002 | This paper | LD0002 | VL3709 bgaA::Ptet-divIVA-Tc ΔdivIVA::Cm |
| Sequence-based reagent | OVL47 | This paper | PCR primer | GATTGTAACCGATTCATCTG |
| Sequence-based reagent | OVL48 | This paper | PCR primer | GGAATGCTTGGTCAAATCTA |
| Sequence-based reagent | OVL898 | This paper | PCR primer | CCAACAAGCTTCA CAAAATAAACCG |
| Sequence-based reagent | OVL901 | This paper | PCR primer | CTTATCCGTTGCACGCTGACTC |
| Sequence-based reagent | OVL1369 | This paper | PCR primer | GTCTTCTTTTTTACCTT TAGTAACTACTAATCCTGCAC |
| Sequence-based reagent | OVL2077 | This paper | PCR primer | ATTCCTTCTTAA CGCCCCAAGTTC |
| Sequence-based reagent | OVL2181 | This paper | PCR primer | GCGTCACGTCTCA GCATTATTTTTC CTCCTTATTTAT |
| Sequence-based reagent | OVL2182 | This paper | PCR primer | GCGTCACGTCTCACG GATCCCTCCAGT AACTCGAGAA |
| Sequence-based reagent | OVL2933 | This paper | PCR primer | GATCGGTCTCGAG GAATTTTCATATGAA CAAAAATATAAAATATTCTCAA |
| Sequence-based reagent | OVL2934 | This paper | PCR primer | GATCGGTCTCGTT ATTTCCTCCCGTTAA ATAATAGATAAC TATTAAAAAT |
| Sequence-based reagent | OVL3493 | This paper | PCR primer | GCCAATAAATTGC TTCCTTGTTTT |
| Sequence-based reagent | OVL3496 | This paper | PCR primer | ATGACACGGATTTT AAGAATAATTCTTTC |
| Sequence-based reagent | OVL3649 | This paper | PCR primer | TGTGTGGCTCTTCG AGAACTCGAGAAAA AAAAACCGCGCCC |
| Sequence-based reagent | OVL3650 | This paper | PCR primer | TGTGTGGCTCTTCG GTTTCATTATTTTT CCTCCTTATTTATTT AGATCTTAATTGTGAGC |
| Sequence-based reagent | OVL3671 | This paper | PCR primer | CTGGTAGCTCTTCCA ACATGCTGAAATGGG AAGACTTGCCTG |
| Sequence-based reagent | OVL3672 | This paper | PCR primer | CTGGTAGCTCTTCCT CTTTATTTTAGTACCT CAAACACGGTT |
| Sequence-based reagent | OVL3677 | This paper | PCR primer | GTATAGTAAGCTGG CAGAGAATATC |
| Sequence-based reagent | OVL3680 | This paper | PCR primer | ATACTTTTTAGGGA CAGGATCAC |
| Sequence-based reagent | OVL3958 | This paper | PCR primer | GCGTCACGTCTCAAT GCTCGTCTAGTAAAA GGAAAAAATGACAAAAAAA |
| Sequence-based reagent | OVL3959 | This paper | PCR primer | GCGTCACGTCTCATC CGTTACGCCTTTTTC ATCTGATCATTTG |
| Sequence-based reagent | OVL3962 | This paper | PCR primer | GCGTCACGTCTCAATG CAGTATAGAACGATTTT TTACATGAATGATAAAACAG |
| Sequence-based reagent | OVL3963 | This paper | PCR primer | GCGTCACGTCTCATCC GTTATGATCTTAAATTT TCGAGATAGCGCT |
| Sequence-based reagent | OVL3981 | This paper | PCR primer | GCGTCACGTCTCAAT GGCTAAAATGAGAA TATCACCGG |
| Sequence-based reagent | OVL3982 | This paper | PCR primer | GCGTCACGTCTCACTA AAACAATTCATCCAGTA AAATATAATATTTTATTTTCTCC |
| Sequence-based reagent | OVL3983 | This paper | PCR primer | GCGTCACGTCTCAGA GGACGCGCAAGCTG |
| Sequence-based reagent | OVL4061 | This paper | PCR primer | CACTACCAATTGG TGAAGTTGCT |
| Sequence-based reagent | OVL4062 | This paper | PCR primer | GCGTCACGTCTCACCT CTTTTTCCTTTTACTA GACGAAAAAACGTC |
| Sequence-based reagent | OVL4063 | This paper | PCR primer | GCGTCACGTCTCAT TAGGGCGTAACCAGCGCC |
| Sequence-based reagent | OVL4064 | This paper | PCR primer | TACAGGTACGAT GATTTTGGTCGT |
| Sequence-based reagent | OVL4069 | This paper | PCR primer | AGCTGAAGATAAA GCCTGTAACCA |
| Sequence-based reagent | OVL4070 | This paper | PCR primer | GCGTCACGTCTCAC CATGTAAAAAATCGT TCTATACTATTTT ATCACAAATGG |
| Sequence-based reagent | OVL4071 | This paper | PCR primer | GCGTCACGTCTCATT AGCATAAAAACTCA GACGAATCGGTCT |
| Sequence-based reagent | OVL4072 | This paper | PCR primer | ACAGCGCCGATTATTTCCTTTG |
| Sequence-based reagent | OVL4341 | This paper | PCR primer | GCGTCACGTCTCAAT TTATTTAGATCTTAA TTGTGAGCGCTC |
| Sequence-based reagent | OVL4583 | This paper | PCR primer | GCGTCACGTCTCAAAA TTTTTGAATAGGAATAA GATCATGTTTGGATTTT |
| Sequence-based reagent | OVL4584 | This paper | PCR primer | GCGTCACGTCTCATCC GCTAAACTCCTCCA AATCGGCG |
| Sequence-based reagent | OVL4585 | This paper | PCR primer | TCCAGATTTTTCTTAT GAGGAAACCTTATT |
| Sequence-based reagent | OVL4586 | This paper | PCR primer | GCGTCACGTCTCAC CATGATCTTATTCCT ATTCAAAAATCTA TCGTTTCATT |
| Sequence-based reagent | OVL4587 | This paper | PCR primer | GCGTCACGTCTCATT AGGGAGGAGTTTAG GAGGAAATATGACC |
| Sequence-based reagent | OVL4588 | This paper | PCR primer | CTGTACTGTCAACT ATCATAAAGATAATGGT |
| Sequence-based reagent | OVL4595 | This paper | PCR primer | GCGTCACGTCTCAAA ATATTAACTTTAGGAG ACTAATATGTTTATTTCCATCAG |
| Sequence-based reagent | OVL4596 | This paper | PCR primer | GCGTCACGTCTCATC CGTTACATCAAATAC AAAATTGCGAGGGT |
| Sequence-based reagent | OVL4597 | This paper | PCR primer | AGATTGCTGACGA GAAAAATGGTG |
| Sequence-based reagent | OVL4598 | This paper | PCR primer | GCGTCACGTCTCACC ATATTAGTCTCCTAAA GTTAATGTAATTTT TTTAATGTCC |
| Sequence-based reagent | OVL4599 | This paper | PCR primer | GCGTCACGTCTCATT AGGAATGGCACCC TGATGTTTCA |
| Sequence-based reagent | OVL4600 | This paper | PCR primer | AATAAATCATCCATG TTGTTAAAATTATT AAAATTGTTGT |
| Sequence-based reagent | OVL4601 | This paper | PCR primer | GCGTCACGTCTCAC CATGCTGTTCTCC TTTGTTTTTATTATAC |
| Sequence-based reagent | OVL4602 | This paper | PCR primer | GCGTCACGTCTCATT AGAGTAGTCATAAG AAAATGAGTACAG |
| Sequence-based reagent | OVL5705 | This paper | PCR primer | GCGTCAGGTCTCAAT TTATTTAGATCTACTCT ATCAATGATAGAG TTATTATACTCT |
| Sequence-based reagent | OVL5706 | This paper | PCR primer | GCGTCAGGTCTCAGC GTAAGGAAATCCATTA TGTACTATTTCTG |
| Sequence-based reagent | OVL5707 | This paper | PCR primer | GCGTCAGGTCTCAAAA TTTAAGTAAGTGAGGA ATAGAATGCCAATTACA |
| Sequence-based reagent | OVL5708 | This paper | PCR primer | GCGTCAGGTCTCAAC GCCTACTTCTGGTTC TTCATACATTGGG |
| Sequence-based reagent | OVL5717 | This paper | PCR primer | GCGTCACGTCTCAAT TTATTTAGATCTACTCT ATCAATGATAGAG TTATTATACTCT |
| Sequence-based reagent | OVL5718 | This paper | PCR primer | GCGTCACGTCTCAGC GTAAGGAAATCCATT ATGTACTATTTCTG |
| Sequence-based reagent | OVL5727 | This paper | PCR primer | GCGTCAGGTCTCAAT GAACTTTAATAAAATT GATTTAGACAATTGGAAGAG |
| Sequence-based reagent | OVL5728 | This paper | PCR primer | GCGTCAGGTCTCAT TATAAAAGCCAGTC ATTAGGCCTATCT |
| Sequence-based reagent | OVL5729 | This paper | PCR primer | CTCCTTTTTTAACTCC TTTTATCAATCCTCA |
| Sequence-based reagent | OVL5730 | This paper | PCR primer | GCGTCAGGTCTCATCAT TCTATTCCTCACTTACT TAATAATAACTGGACG |
| Sequence-based reagent | OVL5731 | This paper | PCR primer | GCGTCAGGTCTCAATAA CTCCAGTGCATCCGACAGG |
| Sequence-based reagent | OVL5732 | This paper | PCR primer | ACCAAGTCCATTTCTTTACGTTTGAC |
| Sequence-based reagent | OVL6214 | This paper | PCR primer | GCGCGTAAGATTGAGCAA |
| Sequence-based reagent | OVL6215 | This paper | PCR primer | GATCGGTCTCATCCT ATCTTACTCCGCT ATTCTAATATTTTCA |
| Sequence-based reagent | OVL6216 | This paper | PCR primer | GATCGGTCTCGATAAAT CAAGGACATTAAAAA AATTACATTAACTT |
| Sequence-based reagent | OVL6217 | This paper | PCR primer | ACATCACCCATAAAGACCTTG |
| Sequence-based reagent | OVL6276 | This paper | PCR primer | GCGTCACGTCTCAAAA TTTAGAATAGCGGAG TAAGATATGAAGTGG |
| Sequence-based reagent | OVL6277 | This paper | PCR primer | GCGTCACGTCTCAAC GCTTAGTCTCCTAAAGT TAATGTAATTTTTTTAATGTCC |
| Chemical compound and drug | Mevalonic acid lithium salt | Bio-Connect BV (BIPP) | HY-113071A | |
| Chemical compound and drug | Clomiphene citrate salt | Sigma - Aldrich | C6272 | |
| Chemical compound and drug | Clomid | Sanofi-Aventis | Clomiphene citrate tablets USP, 50 mg tablets, used for in vivo assays |
|
| Chemical compound and drug | Amoxicillin | GlaxoSmithKline | Clamoxyl for injection, used for in vivo assays |
|
| Chemical compound and drug | sBADA | Tocris Bioscience | 6659 | Work concentration 250 µM |
| Chemical compound and drug | RADA | Tocris Bioscience | 6649 | Work concentration 250 µM RRID:SCR_014237 |
| Software and algorithm | 2FAST2Q | doi:10.1101/2021.12.17.473121 |
https://github.com/veeninglab/2FAST2Q; Veening Lab, 2022a |
|
| Software and algorithm | DESeq2 | doi:10.1186/s13059-014-0550-8 | https://bioconductor.org/packages/release/bioc/html/DESeq2.html | |
| Software and algorithm | Fiji (Fiji Is Just ImageJ) | doi:10.1038/nmeth.2019 | https://imagej.net/software/fiji/downloads | |
| Software and algorithm | Huygens software | Scientific Volume Imaging | https://svi.nl/Huygens-Software | |
| Software and algorithm | MicrobeJ | doi:10.1038/nmicrobiol.2016.77 | https://www.microbej.com/ | |
| Software and algorithm | BactMAP | doi:10.1111/mmi.14417 |
https://github.com/veeninglab/BactMAP; Veening Lab, 2022b |