Table 1. S. pneumoniae strains and primers used in this study.

Strain/Primer	Description (Sequence type)	Source/Reference
WCH16	Capsular serotype 6A clinical isolate (4966)	Women’s and Children’s Hospital, North Adelaide, Australia
WCH43	Capsular serotype 4 clinical isolate (205)	Women’s and Children’s Hospital, North Adelaide, Australia
WCH16::ΔprtA	prtA deletion mutant of WCH16 [EryR]	Present study
WCH16::ΔsodA	sodA deletion mutant of WCH16 [EryR]	Present study
WCH16::ΔvanZ	vanZ deletion mutant of WCH16 [SpecR]	Present study
WCH43::ΔprtA	prtA deletion mutant of WCH43 [EryR]	Present study
WCH43::ΔsodA	sodA deletion mutant of WCH43 [EryR]	Present study
WCH43::ΔulaA	ulaA deletion mutant of WCH43 [SpecR]	Present study
WCH43::ΔvanZ	vanZ deletion mutant of WCH43 [SpecR]	Present study
prtA Ery X	5’-TTGTTCATGTAATCACTCCTTCTATTTATATAACTTCCAATAGATA-3’
prtA Ery Y	5’-CGGGAGGAAATAATTCTATGAGTATAGAAAAAAATGGTTTATGTACTGA-3’
prtA Flank F	5’-GAATGCATCTGATTTTTATCAGAC-3’
prtA Flank R	5’-TCTAAAACCTCTTTGTTTACGAGAG-3’
prtA UpSeq	5’-GAGCTTGGTTCCAAGTGGTTGATT-3’
sodA Ery X	5’-TTGTTCATGTAATCACTCCTTCTTTCTTTCTATATGAAAATGATAACGC-3’
sodA Ery Y	5’-CGGGAGGAAATAATTCTATGAGGAGGGAAGAATTGTTCTTCTCTTTTTAG-3’
sodA Flank F	5’-CTTTGCGGATGAGAAAATCGTGAT-3’
sodA Flank R	5’-GACAGATAAACCATAGTGTTGACGC-3’
sodA UpSeq	5’-GCCAATGTTCACGCCTTTTATCAAC-3’
ulaA Spec X	5’-TATGTATTCATATATATCCTCCTCTTGAATTGTTTTTGTAAGTTTATTATATA-3’
ulaA Spec Y	5’-AAATAACAGATTGAAGAAGGTATAATATCTAGAAAAGGAGAAATAAAATGGTT-3’
ulaA Flank F	5’-GCTATTAAAAAAATAGAGGAAGAAGGT-3’
ulaA Flank R	5’-GCTGGATCCACAGCCTCTGTAATTC-3’
ulaA UpSeq	5’-TCTTTGCAGTTTATGCGCCAGGTG-3’
vanZ Spec X	5’-TATGTATTCATATATATCCTCCTCGTTTGAAGCCGTCTTCAACAAACA-3’
vanZ Spec Y	5’-AAATAACAGATTGAAGAAGGTATAACTAATGATTAAAAAGGAGAATATAATG-3’
vanZ Flank F	5’-CTTAAGGAAGTTCTACTTGAGCCG-3’
vanZ Flank R	5’-GAAAACGCCGTGCATCTTCTCAGC-3’
vanZ UpSeq	5’-CAAGACTGGGGTTAAAGAACCCGT-3’