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Table 7. GAS genes upregulated (+Z) and downregulated (-Z) on day 32 in comparison to day 16 of infection.

M5005_gene Gene Description Function mean difference Z NFD Analysis Probe-set Probe # M5005_Spy1808 argS Arginyl-tRNA synthetase (EC 6.1.1.19) Protein synthesis -1.72298 -4.95958 0.14279 PPA1&2 SpM1_ChORF2151_s_at 8 M5005_Spy0317 hlyX putative hemolysin Virulence -2.02534 -4.71231 0.30786 PPA1&2 SpM1_ChORF0378_s_at 5 M5005_Spy0475 - PTS system, beta-glucoside-specific IIABC component (EC 2.7.1.69) Carbohydrate metabolism -1.47813 -4.48425 0.62109 PPA1&2 SpM1_ChORF0572_s_at 4 M5005_Spy0577 atpF ATP synthase B chain (EC 3.6.3.14) Carbohydrate metabolism -1.7496 -4.45203 0.68541 PPA1&2 SpM1_ChORF0756_s_at 11 M5005_Spy1637 lacB.2 Galactose-6-phosphate lacB subunit (EC 5.3.1.26) Carbohydrate metabolism -1.94768 -4.37397 0.86962 PPA1&2 SpM18_ChORF1990_s_at 15 M5005_Spy1485 accA Acetyl-coenzyme A carboxylase carboxyl subunit beta (EC 6.4.1.2) Lipid metabolism -1.67854 -4.23953 1.30699 PPA1&2 SpM1_ChORF1743_s_at 4 M5005_Spy0500 - N-acetylmuramoyl-L-alanine amidase (EC 3.5.1.28) Cell wall metabolism -1.54852 -4.2346 1.32657 PPA1&2 SpM1_ChORF0601_s_at 12 M5005_Spy0608 rgpFc alpha-L-Rha alpha-1,3-L-rhamnosyltransferase (EC 2.4.1.-) Cell wall metabolism -0.77914 -4.07772 0.58709 PPA3 SpM1_ChORF0792_s_at M5005_Spy1697 - 4-amino-4-deoxychorismate (EC 4.-.-.-) Unknown -1.55045 -4.04336 2.35339 PPA1&2 SpM18_ChORF2056_at 12 M5005_Spy1108 metK S-adenosylmethionine synthetase (EC 2.5.1.6) Cellular processing -1.57308 -3.94036 3.19399 PPA1&2 SpM1_ChORF1359_s_at 15 M5005_Spy0111 - Hypothetical protein Unknown -1.56285 -3.91447 3.44739 PPA1&2 SpM1_ChORF0130_at 16 M5005_Spy0212 - N-acetylmannosamine-6-phosphate 2-epimerase (EC 5.1.3.9) Carbohydrate metabolism -1.77146 -3.90173 3.5792 PPA1&2 SpM1_ChORF0251_s_at 14 M5005_Spy0782 ptsC PTS system, mannose/fructose family IIC component Carbohydrate metabolism -1.59495 -3.87937 3.82247 PPA1&2 SpM1_ChORF1059_s_at 1 M5005_Spy0839 - Hypothetical membrane spanning protein Unknown -2.16174 -3.8708 3.9199 PPA1&2 SpM18_ChORF1077_s_at 10 M5005_Spy1500 hrcA Heat-inducible transcription repressor hrcA Information processing -1.39281 -3.85739 4.07718 PPA1&2 SpM1_ChORF1763_s_at 15 M5005_Spy1075 uvrB Excinuclease ABC subunit B Information processing -1.44698 -3.85117 4.15223 PPA1&2 SpM1_ChORF1314_s_at 6 M5005_Spy0317 hlyX putative hemolysin Virulence -1.35882 -3.8256 4.47503 PPA1&2 SpM1_ChORF0378_s_at 1 M5005_Spy1723 isp Immunogenic secreted protein Virulence -1.73905 -3.80643 4.73273 PPA1&2 SpM12_ChORF249-5_s_at 2 M5005_Spy1388 nagA N-acetylglucosamine-6-phosphate deacetylase (EC 3.5.1.25) Carbohydrate metabolism -1.41297 -3.75556 5.48859 PPA1&2 SpM1_ChORF1694_s_at 11 M5005_Spy1372 proB ABC transporter permease protein Amino acid metabolism -0.57535 -3.741 1.58237 PPA3 SpM1_ChORF1673_at M5005_Spy0760 - UDP-N-acetylmuramoylalanyl-D-glutamate--2,6-diaminopimelate (EC 6.3.2.13) Cell wall metabolism -2.07773 -3.67455 6.9386 PPA1&2 SpM12_ChORF281-1_s_at 6 M5005_Spy0694 clpL ATP-dependent protease ATP-binding subunit clpL Stress -1.5096 -3.64816 7.48621 PPA1&2 SpM1_ChORF0888_s_at 9 M5005_Spy0111 - Hypothetical protein Unknown -1.43271 -3.64533 7.54751 PPA1&2 SpM1_ChORF0130_at 10 M5005_Spy0006 trcF Transcription-repair coupling factor Cellular processing -1.9486 -3.6416 7.6287 PPA1&2 SpM1_ChORF0008_s_at 12 M5005_Spy0762 - Hypothetical membrane associated protein Unknown -1.27144 -3.63905 7.68488 PPA1&2 SpM1_ChORF1037_s_at 2 M5005_Spy1365 - Phospho-N-acetylmuramoyl-pentapeptide-transferase (EC 2.7.8.13) Cell wall metabolism -1.43042 -3.56309 9.55004 PPA1&2 SpM1_ChORF1662_s_at 4 M5005_Spy0866 - Phosphinothricin N-acetyltransferase (EC 2.3.1.-) Unknown -1.79138 -3.5538 9.80621 PPA1&2 SpM1_ChORF1144_s_at 12 M5005_Spy0915 ffh SIGNAL RECOGNITION PARTICLE, SUBUNIT FFH/SRP54 Secretion -1.78818 -3.55266 9.83814 PPA1&2 SpM1_ChORF1200_s_at 16 M5005_Spy1129 - CAAX amino terminal protease family Information processing -1.65336 -3.52596 10.6135 PPA1&2 SpM1_ChORF1384_s_at 3 M5005_Spy0957 - Myo-inositol-1(or 4)-monophosphatase (EC 3.1.3.25) Carbohydrate metabolism -1.96256 -3.52313 10.69928 PPA1&2 SpM1_ChORF1247_s_at 5 M5005_Spy0502 - Hypothetical exported protein Unknown -1.34858 -3.50463 11.27514 PPA1&2 SpM1_ChORF0604_s_at 1 M5005_Spy0826 potA Spermidine/putrescine transport ATP-binding protein potA Membrane transport -1.45833 -3.50146 11.37667 PPA1&2 SpM1_ChORF1102_s_at 1 M5005_Spy1007 - Phage protein Phage -0.80443 -3.48346 3.30834 PPA3 SpM49_ChORF7585-33_at M5005_Spy1699 - ATPase, AAA family Unknown -1.04994 -3.46541 12.59614 PPA1&2 SpM1_ChORF1992_s_at 12 M5005_Spy0103 - Deoxyadenosine (EC 2.7.1.76) / Deoxyguanosine kinase (EC 2.7.1.113) Nucleotide metabolism -1.64916 -3.42762 14.00838 PPA1&2 SpM1_ChORF0121_s_at 11 M5005_Spy1164 gpmA Phosphoglycerate mutase (EC 5.4.2.1) Carbohydrate metabolism -1.43632 -3.40918 14.75147 PPA1&2 SpM1_ChORF1429_s_at 7 M5005_Spy1133 surA, prsA Peptidyl-prolyl cis-trans isomerase (EC 5.2.1.8) Unknown -1.51792 -3.40244 15.0323 PPA1&2 SpM1_ChORF1390_s_at 1 M5005_Spy1426 - Phage protein Phage -1.29811 -3.40119 15.08484 PPA1&2 SpM12_ChORF299-4_at 14 M5005_Spy1365 - Phospho-N-acetylmuramoyl-pentapeptide-transferase (EC 2.7.8.13) Cell wall metabolism -1.64969 -3.35533 17.1434 PPA1&2 SpM1_ChORF1662_s_at 16 M5005_Spy0762 - Hypothetical membrane associated protein Unknown -1.16777 -3.32837 18.47587 PPA1&2 SpM1_ChORF1037_s_at 6 M5005_Spy0769 - Hypothetical cytosolic protein Unknown -1.90343 -3.32384 18.70902 PPA1&2 SpM1_ChORF1046_s_at 7 M5005_Spy0671 - Mobile genetic element -1.55554 -3.26954 21.73493 PPA1&2 SpM1_ChORF0864_s_at 3 M5005_Spy1108 metK S-adenosylmethionine synthetase (EC 2.5.1.6) Cellular processing -1.43151 -3.22981 24.23765 PPA1&2 SpM1_ChORF1359_s_at 9 M5005_Spy1082 - PTS system, cellobiose-specific IIB component (EC 2.7.1.69) Carbohydrate metabolism -0.54801 -3.21765 6.92509 PPA3 SpM1_ChORF1324_s_at M5005_Spy0877 - Hypothetical protein Unknown -1.4767 -3.21674 25.11969 PPA1&2 SpM1_ChORF1156_s_at 11 M5005_Spy1500 hrcA Heat-inducible transcription repressor hrcA Information processing -1.29882 -3.16996 28.53123 PPA1&2 SpM1_ChORF1763_s_at 10 M5005_Spy1753 pbp2A Multimodular transpeptidase-transglycosylase PBP 2A Cell wall metabolism -1.71042 -3.1658 28.85535 PPA1&2 SpM1_ChORF2059_s_at 12 M5005_Spy0805 srtK Nisin biosynthesis sensor protein nisK (EC 2.7.3.-) Signal transduction -1.38837 -3.1526 29.90571 PPA1&2 SpM1_ChORF1082_at 8 M5005_Spy0614 pepT Peptidase T (EC 3.4.11.14) Amino acid metabolism -1.48608 -3.13959 30.97731 PPA1&2 SpM1_ChORF0799_s_at 3 M5005_Spy0890 ddh D-lactate dehydrogenase (EC 1.1.1.28) Carbohydrate metabolism -0.68219 -3.1307 8.76916 PPA3 SpM1_ChORF1170_s_at M5005_Spy0539 - ATP-binding protein (contains P-loop) Membrane transport -1.34349 -3.12677 32.06771 PPA1&2 SpM1_ChORF0652_s_at 6 M5005_Spy1126 - Transposase Mobile genetic element -0.50305 -3.11936 9.04149 PPA3 SpM1_ChORF0195_x_at M5005_Spy1118 - Peptidoglycan N-acetylglucosamine deacetylase (EC 3.5.1.-) Cell wall metabolism -1.68072 -3.11456 33.14006 PPA1&2 SpM1_ChORF1370_s_at 10 M5005_Spy0245 nifU, yurV IscU protein Coenzyme and metabolism -1.0746 -3.10643 33.87371 PPA1&2 SpM1_ChORF0289_s_at 10 M5005_Spy0618 cmk Cytidylate kinase (EC 2.7.4.14) Nucleotide metabolism -0.49742 -3.10238 9.46398 PPA3 SpM1_ChORF0803_s_at M5005_Spy1647 rplM LSU ribosomal protein L13P Protein synthesis -0.60018 -3.07786 10.10752 PPA3 SpM5_ChORF125g-172_at M5005_Spy1117 deaD2 ATP-dependent RNA helicase Stress -1.34055 -3.07013 37.33685 PPA1&2 SpM1_ChORF1369_s_at 13 M5005_Spy0477 - Hypothetical membrane spanning protein Unknown -1.87098 -3.06993 37.35691 PPA1&2 SpM1_ChORF0575_s_at 16 M5005_Spy1504 - Hypothetical membrane spanning protein Unknown -0.59699 -3.06489 10.46442 PPA3 SpM1_ChORF1768_s_at M5005_Spy0663 mur1.1 Autolysin (EC 3.5.1.28) Cell wall metabolism -1.65847 -3.05701 38.66882 PPA1&2 SpM1_ChORF0856_s_at 13 M5005_Spy0986 glmS Glucosamine--fructose-6-phosphate aminotransferase [isomerizing] (EC 2.6.1.16) Cell wall metabolism -1.32876 -3.05323 39.06074 PPA1&2 SpM1_ChORF1280_s_at 3 M5005_Spy0633 rplU LSU ribosomal protein L21P Protein synthesis -1.6243 -3.04644 39.7751 PPA1&2 SpM1_ChORF0819_s_at 3 M5005_Spy1722 - Hypothetical protein Unknown -1.50638 -3.01978 42.69681 PPA1&2 SpM1_ChORF2023_s_at 8

Page 1 of 5 Table 7. GAS genes upregulated (+Z) and downregulated (-Z) on day 32 in comparison to day 16 of infection.

M5005_gene Gene Description Function mean difference Z NFD Analysis Probe-set Probe # M5005_Spy0746 - ABC transporter ATP-binding protein Membrane transport -1.2132 -3.00848 43.99601 PPA1&2 SpM1_ChORF1019_s_at 5 M5005_Spy1134 - O-methyltransferase (EC 2.1.1.-) Unknown -0.53901 -2.95233 14.10049 PPA3 SpM1_ChORF1391_s_at M5005_Spy1542 scrA PTS system, sucrose-specific IIABC component (EC 2.7.1.69) Carbohydrate metabolism -0.54474 -2.94861 14.23877 PPA3 SpM1_ChORF1815_s_at M5005_Spy1288 - Hypothetical cytosolic protein Unknown -0.64533 -2.92063 15.3214 PPA3 SpM1_ChORF1564_s_at M5005_Spy0688 thyA Thymidylate synthase (EC 2.1.1.45) Unknown -0.58896 -2.84554 18.61936 PPA3 SpM1_ChORF0882_s_at M5005_Spy0589 - Salt-stress induced protein Unknown -0.44126 -2.81444 20.17038 PPA3 SpM1_ChORF0770_s_at M5005_Spy1420 - Phage protein Phage -0.51926 -2.76782 22.72204 PPA3 SpM1_ChORF0999_at M5005_Spy1764 ctsR Transcriptional regulator ctsR Information processing -0.45532 -2.76421 22.93151 PPA3 SpM1_ChORF2074_s_at M5005_Spy1540 endoS Endo-beta-N-acetylglucosaminidase F2 precursor (EC 3.2.1.96) Carbohydrate metabolism -0.67472 -2.73562 24.65626 PPA3 SpM1_ChORF1813_at M5005_Spy1555 rpsF SSU ribosomal protein S6P Protein synthesis -0.34383 -2.73236 24.8602 PPA3 SpM1_ChORF1831_s_at M5005_Spy0910 citC [Citrate [pro-3S]-lyase] ligase (EC 6.2.1.22) Carbohydrate metabolism -0.44181 -2.72389 25.39781 PPA3 SpM1_ChORF1192_s_at M5005_Spy1158 ddlA D-alanine--D-alanine ligase (EC 6.3.2.4) Cell wall metabolism -0.57783 -2.69318 27.43881 PPA3 SpM1_ChORF1421_s_at M5005_Spy1050 - Phage transcriptional repressor Phage -0.36667 -2.6839 28.08517 PPA3 SpM18_ChORF1306_at M5005_Spy1240 clpE ATP-dependent clp protease ATP-binding subunit clpE Stress -0.49997 -2.6832 28.13419 PPA3 SpM1_ChORF1509_s_at M5005_Spy1421 - Phage infection protein Phage -0.50746 -2.66555 29.40406 PPA3 SpM12_ChORF299-1_at M5005_Spy1261 - Radical SAM family Unknown -0.54041 -2.66452 29.47969 PPA3 SpM1_ChORF1533_s_at M5005_Spy1243 ileS Isoleucyl-tRNA synthetase (EC 6.1.1.5) Protein synthesis -0.4209 -2.64479 30.96511 PPA3 SpM3_ChORF1166_at M5005_Spy1200 - Phage protein Phage -0.52141 -2.64017 31.32255 PPA3 SpM1_ChORF0962_s_at M5005_Spy1027 - Phage protein Phage -0.50749 -2.62135 32.81905 PPA3 SpM18_ChORF1786_at M5005_Spy1525 - ABC transporter ATP-binding protein Membrane transport -0.41337 -2.61581 33.27176 PPA3 SpM1_ChORF1793_s_at M5005_Spy0630 nifS, yrvO Cysteine desulfhydrase (EC 4.4.1.-) / Selenocysteine lyase (EC 4.4.1.16) Amino acid metabolism -0.41901 -2.61017 33.73862 PPA3 SpM1_ChORF0816_s_at M5005_Spy0036 - Protein tyrosine phosphatase (EC 3.1.3.48) Cellular processing -0.40981 -2.60999 33.75391 PPA3 SpM1_ChORF0039_s_at M5005_Spy1469 - enzyme family Unknown -0.42916 -2.59629 34.91376 PPA3 SpM1_ChORF1727_s_at M5005_Spy0881 - Hypothetical cytosolic protein Virulence -0.50733 -2.5859 35.81746 PPA3 SpM1_ChORF1159_s_at M5005_Spy1200 - Phage protein Phage -0.39069 -2.5817 36.18907 PPA3 SpM1_ChORF1474_s_at M5005_Spy0038 - Acyltransferase family Unknown -0.423 -2.55807 38.34588 PPA3 SpM1_ChORF0041_s_at M5005_Spy1840 trmU tRNA (5-methylaminomethyl-2-thiouridylate)-methyltransferase (EC 2.1.1.61) Protein synthesis -0.41186 -2.54666 39.42939 PPA3 SpM1_ChORF2188_s_at M5005_Spy0183 - Hypothetical membrane associated protein Unknown -0.49289 -2.54475 39.61299 PPA3 SpM18_ChORF0202_s_at M5005_Spy1435 - Phage scaffold protein Phage -0.48599 -2.54099 39.9783 PPA3 SpM12_ChORF299-52_s_at M5005_Spy1296 - Hypothetical protein Unknown -0.41821 -2.51628 42.4508 PPA3 SpM1_ChORF1572_s_at M5005_Spy1019 - Phage scaffold protein Phage -0.47798 -2.50566 43.55593 PPA3 SpM49_ChORF7585-21_at M5005_Spy1382 - Hypothetical membrane associated protein Unknown -0.50717 -2.45651 49.02215 PPA3 SpM1_ChORF1686_s_at M5005_Spy1552 - Hypothetical membrane spanning protein Unknown -0.4027 -2.45413 49.30146 PPA3 SpM1_ChORF1828_s_at M5005_Spy0206 fasA Response regulator FasA Signal transduction -0.46462 -2.44536 50.34578 PPA3 SpM1_ChORF0245_s_at M5005_Spy0025 purM Phosphoribosylformylglycinamidine cyclo-ligase (EC 6.3.3.1) Nucleotide metabolism -0.58713 -2.43358 51.77834 PPA3 SpM1_ChORF0027_s_at M5005_Spy1792 - Hypothetical protein Unknown -0.3584 -2.41165 54.54629 PPA3 SpM18_ChORF2167_x_at M5005_Spy0331 dnaX DNA III, delta' subunit (EC 2.7.7.7) Information processing -0.48822 -2.38491 58.10339 PPA3 SpM1_ChORF0400_s_at M5005_Spy1389 - Sodium-dependent phosphate transporter Membrane transport -0.39758 -2.38274 58.40056 PPA3 SpM1_ChORF1695_s_at M5005_Spy1798 - Arsenate reductase family protein Unknown -0.40315 -2.36099 61.45997 PPA3 SpM1_ChORF2115_s_at M5005_Spy0272 - ABC transporter ATP-binding protein Membrane transport -0.42165 -2.3528 62.64854 PPA3 SpM1_ChORF0320_s_at M5005_Spy0186 - Transcriptional regulator Information processing -0.55466 -2.34018 64.52144 PPA3 SpM3_ChORF0158_s_at M5005_Spy1381 glpK (EC 2.7.1.30) Carbohydrate metabolism -0.5368 -2.32815 66.35415 PPA3 SpM1_ChORF1684_s_at M5005_Spy1568 dinP DNA polymerase IV (EC 2.7.7.7) Cellular processing -0.44017 -2.32675 66.57118 PPA3 SpM1_ChORF1846_s_at M5005_Spy1132 alaS Alanyl-tRNA synthetase (EC 6.1.1.7) Protein synthesis -0.51869 -2.32243 67.24148 PPA3 SpM18_ChORF1397_at M5005_Spy1179 - Phage protein Phage -0.47758 -2.30616 69.8249 PPA3 SpM1_ChORF1449_s_at M5005_Spy0581 atpD ATPase, beta subunit Carbohydrate metabolism -0.49094 -2.30001 70.82377 PPA3 SpM12_ChORF269-12_s_at M5005_Spy1167 - Lead, cadmium, zinc and mercury transporting ATPase (EC 3.6.3.-) Membrane transport -0.49579 -2.27128 75.66372 PPA3 SpM3_ChORF1093_at M5005_Spy1507 gatA Aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase subunit A (EC 6.3.5.-) Protein synthesis -0.51619 -2.2666 76.48086 PPA3 SpM1_ChORF1771_s_at M5005_Spy0551 rplS LSU ribosomal protein L19P Protein synthesis -0.44634 -2.24174 80.94708 PPA3 SpM1_ChORF0724_s_at M5005_Spy0792 - NAD(P)H-dependent quinone reductase (EC 1.-.-.-) Carbohydrate metabolism -0.45144 -2.22451 84.17989 PPA3 SpM1_ChORF1069_s_at M5005_Spy0633 rplU LSU ribosomal protein L21P Protein synthesis -0.52304 -2.2141 86.18652 PPA3 SpM1_ChORF0819_s_at M5005_Spy1111 - Hypothetical protein Unknown -0.37251 -2.20587 87.80404 PPA3 SpM1_ChORF1363_s_at M5005_Spy1004 - Phage protein Phage -0.49901 -2.19967 89.04055 PPA3 SpyM3_1308_x_at M5005_Spy0239 mecA Negative regulator of genetic competence mecA Virulence -0.57171 -2.19442 90.09882 PPA3 SpM1_ChORF0281_s_at M5005_Spy0231 rpsG SSU ribosomal protein S7P Protein synthesis -0.55758 -2.1825 92.54578 PPA3 SpM1_ChORF0272_s_at M5005_Spy0973 - General stress protein, Gls24 family Stress -0.47584 -2.17548 94.01325 PPA3 SpM1_ChORF1262_s_at M5005_Spy1173 - Phage protein Phage -0.41783 -2.16908 95.36833 PPA3 SpM3_ChORF0729_s_at M5005_Spy1000 - Phage protein Phage -0.48225 -2.16256 96.76922 PPA3 SpM49_ChORF7585-41_at M5005_Spy0313 - Riboflavin transporter Membrane transport -0.44017 -2.16216 96.85477 PPA3 SpM1_ChORF0373_s_at M5005_Spy0203 gltX Glutamyl-tRNA synthetase (EC 6.1.1.17) Protein synthesis -0.41987 -2.16007 97.30808 PPA3 SpM1_ChORF0239_s_at M5005_Spy0522 - Unsaturated glucuronyl (EC 3.2.1.-) Unknown -0.39109 -2.15228 99.01069 PPA3 SpM5_ChORFJ7578C-260_s_at M5005_Spy0213 - N-acetylneuraminate-binding protein Membrane transport -0.39323 -2.15094 99.30632 PPA3 SpM12_ChORF295-17_s_at M5005_Spy0295 - 60 kDa inner membrane protein YIDC Cellular processing -0.46715 -2.14062 101.61092 PPA3 SpM1_ChORF0351_s_at

Page 2 of 5 Table 7. GAS genes upregulated (+Z) and downregulated (-Z) on day 32 in comparison to day 16 of infection.

M5005_gene Gene Description Function mean difference Z NFD Analysis Probe-set Probe # M5005_Spy1424 - Phage endopeptidase Phage -0.44062 -2.14034 101.67362 PPA3 SpM12_ChORF299-2_x_at M5005_Spy0969 - Hypothetical protein Unknown -0.3274 -2.13253 103.4508 PPA3 SpM18_ChORF1209_x_at M5005_Spy1506 gatB Aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase subunit B (EC 6.3.5.-) Protein synthesis -0.39412 -2.12621 104.90745 PPA3 SpM1_ChORF1769_s_at M5005_Spy1518 - Transporter Membrane transport -0.47594 -2.12503 105.18119 PPA3 SpM1_ChORF1784_s_at M5005_Spy1409 infB Bacterial Protein Translation Initiation Factor 2 (IF-2) Cellular processing -0.44595 -2.11772 106.89239 PPA3 SpM18_ChORF1729_at M5005_Spy1637 lacB.2 Galactose-6-phosphate isomerase lacB subunit (EC 5.3.1.26) Carbohydrate metabolism -0.47939 -2.11342 107.91064 PPA3 SpM1_ChORF1922_s_at M5005_Spy1258 - Hypothetical cytosolic protein Unknown -0.40078 -2.10577 109.74454 PPA3 SpM1_ChORF1530_s_at M5005_Spy1256 - Rhodanese-related sulfurtransferases Unknown -0.40811 -2.07354 117.77023 PPA3 SpM1_ChORF1528_s_at M5005_Spy0724 - Cystathionine beta-lyase (EC 4.4.1.8) / Cystathionine gamma-lyase (EC 4.4.1.1) Amino acid metabolism -0.43495 -2.06182 120.81391 PPA3 SpM1_ChORF0923_s_at M5005_Spy1156 - Hypothetical Membrane Spanning Protein Unknown -0.36476 -2.06164 120.86109 PPA3 SpM1_ChORF1419_s_at M5005_Spy0164 - ParB-like nuclease Unknown -0.40023 -2.04865 124.31578 PPA3 SpM1_ChORF0190_s_at M5005_Spy0751 acoA Pyruvate dehydrogenase E1 component alpha subunit (EC 1.2.4.1) Carbohydrate metabolism -0.50732 -2.0272 130.21092 PPA3 SpM1_ChORF1026_s_at M5005_Spy1523 - Permease Unknown -0.32558 -2.0089 135.43174 PPA3 SpM1_ChORF1789_s_at M5005_Spy0031 purK Phosphoribosylaminoimidazole carboxylase ATPase subunit (EC 4.1.1.21) Nucleotide metabolism -0.5345 -2.00558 136.39781 PPA3 SpM1_ChORF0034_at M5005_Spy0761 - Hypothetical membrane spanning protein Unknown 2.23896 5.29118 0.05052 PPA1&2 SpM1_ChORF1036_s_at 11 M5005_Spy0982 - Histidine-binding protein Membrane transport 1.80726 4.86604 0.19109 PPA1&2 SpM1_ChORF1274_s_at 15 M5005_Spy1131 - Transcriptional regulator, Cro/CI family Information processing 1.77279 4.39504 0.81559 PPA1&2 SpM1_ChORF1386_s_at 5 M5005_Spy0732 - NIF3-related protein Information processing 1.35987 4.31653 1.03537 PPA1&2 SpM1_ChORF0931_s_at 7 M5005_Spy1547 efp Protein Translation Elongation Factor P (EF-P) Cellular processing 0.67591 4.28432 0.31548 PPA3 SpM1_ChORF1821_s_at M5005_Spy1519 recG ATP-dependent DNA helicase recG (EC 3.6.1.-) Information processing 2.00232 4.24461 1.2871 PPA1&2 SpM12_ChORF294-6_s_at 6 M5005_Spy1178 - Phage protein Phage 0.71236 4.2437 0.35669 PPA3 SpM18_ChORF1460_s_at M5005_Spy0712 parC Topoisomerase IV subunit A (EC 5.99.1.-) Information processing 1.61753 4.14909 1.71579 PPA1&2 SpM1_ChORF0910_s_at 15 M5005_Spy0618 cmk Cytidylate kinase (EC 2.7.4.14) Nucleotide metabolism 1.21684 4.03317 2.42586 PPA1&2 SpM1_ChORF0803_s_at 14 M5005_Spy1022 - Portal protein Phage 1.56069 3.99449 2.72116 PPA1&2 SpM49_ChORF7585-19_at 3 M5005_Spy0078 adcC High-affinity zinc uptake system ATP-binding protein znuC Membrane transport 1.5939 3.98576 2.79252 PPA1&2 SpM1_ChORF0093_s_at 2 M5005_Spy0497 - Phosphoglycerate mutase (EC 5.4.2.1) Carbohydrate metabolism 0.61573 3.98247 0.77935 PPA3 SpM1_ChORF0598_s_at M5005_Spy1804 mutL DNA mismatch repair protein mutL Information processing 0.60223 3.87698 1.06389 PPA3 SpM1_ChORF2121_s_at M5005_Spy1223 hlpA DNA-binding protein HU Cellular processing 1.65908 3.82455 4.48873 PPA1&2 SpM1_ChORF1489_s_at 1 M5005_Spy0933 - Probable NADH-dependent flavin yqiG (EC 1.-.-.-) Unknown 1.40392 3.79144 4.9443 PPA1&2 SpM1_ChORF1218_s_at 11 M5005_Spy1748 - Transcriptional regulator, DeoR family Unknown 0.81478 3.78649 1.38631 PPA3 SpM5_ChORF125g-81_s_at M5005_Spy1131 - Transcriptional regulator, Cro/CI family Information processing 1.59506 3.78191 5.08348 PPA1&2 SpM1_ChORF1386_s_at 9 M5005_Spy1550 uvrA Excinuclease ABC subunit A Cellular processing 0.57752 3.68612 1.8547 PPA3 SpM18_ChORF1890_s_at M5005_Spy0942 - Nucleoside-binding protein Unknown 1.11528 3.68166 6.79777 PPA1&2 SpM1_ChORF1228_s_at 15 M5005_Spy1123 nrdE.2 Ribonucleoside-diphosphate reductase alpha chain (EC 1.17.4.1) Nucleotide metabolism 1.26683 3.64538 7.54624 PPA1&2 SpM1_ChORF1375_s_at 16 M5005_Spy0232 fus Protein Translation Elongation Factor G (EF-G) Cellular processing 1.41047 3.63588 7.75523 PPA1&2 SpM1_ChORF0273_s_at13 M5005_Spy0612 amrA Transcriptional activator amrA Information processing 1.1961 3.63535 7.76685 PPA1&2 SpM1_ChORF0797_s_at 10 M5005_Spy0957 - Myo-inositol-1(or 4)-monophosphatase (EC 3.1.3.25) Carbohydrate metabolism 1.47148 3.61836 8.15482 PPA1&2 SpM1_ChORF1248_s_at 13 M5005_Spy0479 - Hypothetical membrane spanning protein Unknown 0.71456 3.60547 2.33851 PPA3 SpM1_ChORF0577_at M5005_Spy1088 obg GTP-binding protein OBG family Unknown 1.79354 3.55915 9.65789 PPA1&2 SpM1_ChORF1333_s_at 5 M5005_Spy0318 pflC Pyruvate formate-lyase activating enzyme (EC 1.97.1.4) Carbohydrate metabolism 1.1494 3.55342 9.81678 PPA1&2 SpM1_ChORF0379_s_at 15 M5005_Spy1721 - Hypothetical protein Unknown 0.52153 3.53953 2.82239 PPA3 SpyM3_1729_x_at M5005_Spy1146 - DNA polymerase III, delta subunit (EC 2.7.7.7) Information processing 1.04605 3.53407 10.37192 PPA1&2 SpM3_ChORF1072_s_at 2 M5005_Spy0458 - Hypothetical cytosolic protein Unknown 1.03873 3.52133 10.75409 PPA1&2 SpM18_ChORF0618_s_at 6 M5005_Spy0833 - NAD-dependent malic enzyme (EC 1.1.1.38) Carbohydrate metabolism 1.50532 3.47016 12.42838 PPA1&2 SpM1_ChORF1110_s_at 10 M5005_Spy1025 - Phage encoded transcriptional regulator, ArpU family Phage 1.74302 3.43696 13.64592 PPA1&2 SpM1_ChORF0677_s_at 3 M5005_Spy1123 nrdE.2 Ribonucleoside-diphosphate reductase alpha chain (EC 1.17.4.1) Nucleotide metabolism 1.64905 3.4015 15.07167 PPA1&2 SpM1_ChORF1375_s_at 5 M5005_Spy0841 - Glutamine amidotransferase, class I Unknown 1.56343 3.38325 15.86021 PPA1&2 SpM1_ChORF1119_s_at 3 M5005_Spy1411 - Hypothetical cytosolic protein Unknown 1.49671 3.37485 16.23635 PPA1&2 SpM1_ChORF1722_s_at 14 M5005_Spy0926 - Cardiolipin synthetase (EC 2.7.8.-) Lipid metabolism 2.02698 3.37016 16.44979 PPA1&2 SpM1_ChORF1212_s_at 7 M5005_Spy0758 lplB Lipoate-protein ligase A (EC 6.-.-.-) Coenzyme and cofactor metabolism 0.68376 3.36927 4.5575 PPA3 SpM1_ChORF1033_s_at M5005_Spy0745 - ABC transporter permease protein Membrane transport 0.7773 3.36787 4.57535 PPA3 SpM1_ChORF1018_s_at M5005_Spy0322 fhuB Ferrichrome transport system permease protein fhuB Membrane transport 1.22872 3.36342 16.76139 PPA1&2 SpM1_ChORF0383_s_at 5 M5005_Spy0755 acoL, pdhD Dihydrolipoamide dehydrogenase (EC 1.8.1.4) Carbohydrate metabolism 1.6824 3.36293 16.78465 PPA1&2 SpM1_ChORF1031_s_at 6 M5005_Spy1192 - Phage protein Phage 1.31841 3.32733 18.52923 PPA1&2 SpM1_ChORF1463_s_at 8 M5005_Spy1761 groEL 60 kDa chaperonin GroEL Stress 0.78644 3.29276 5.63456 PPA3 SpM1_ChORF2070_s_at M5005_Spy0101 adhE tRNA binding domain protein Protein synthesis 1.35674 3.28959 20.56668 PPA1&2 SpM18_ChORF0119_s_at 16 M5005_Spy0383 - D-alanyl-D-alanine carboxypeptidase (EC 3.4.16.4) Cell wall metabolism 1.11737 3.2817 21.01918 PPA1&2 SpM1_ChORF0467_s_at 2 M5005_Spy0994 - Putative membrane-associated alkaline phosphatase Membrane transport 1.37155 3.24166 23.46381 PPA1&2 SpM1_ChORF1289_s_at 11 M5005_Spy0509 tpi Triosephosphate isomerase (EC 5.3.1.1) Carbohydrate metabolism 2.02353 3.2288 24.30492 PPA1&2 SpM1_ChORF0613_s_at 12 M5005_Spy0602 rmlD dTDP-4-dehydrorhamnose reductase (EC 1.1.1.133) Cell wall metabolism 1.31835 3.2108 25.53032 PPA1&2 SpM1_ChORF0784_s_at 7 M5005_Spy1223 hlpA DNA-binding protein HU Cellular processing 1.52085 3.20886 25.66591 PPA1&2 SpM1_ChORF1489_s_at 4 M5005_Spy1215 - Phage protein Phage 1.58037 3.20625 25.84872 PPA1&2 SpM1_ChORF0948_s_at 9 M5005_Spy0933 - Probable NADH-dependent flavin oxidoreductase yqiG (EC 1.-.-.-) Unknown 1.74097 3.19809 26.43057 PPA1&2 SpM1_ChORF1218_s_at 4

Page 3 of 5 Table 7. GAS genes upregulated (+Z) and downregulated (-Z) on day 32 in comparison to day 16 of infection.

M5005_gene Gene Description Function mean difference Z NFD Analysis Probe-set Probe # M5005_Spy0024 purF Amidophosphoribosyltransferase (EC 2.4.2.14) Nucleotide metabolism 1.85516 3.19033 26.99486 PPA1&2 SpM1_ChORF0026_s_at 6 M5005_Spy0320 - Hypothetical cytosolic protein Unknown 1.64061 3.18899 27.09313 PPA1&2 SpM1_ChORF0382_s_at 5 M5005_Spy0418 - Permease Unknown 1.35539 3.18151 27.65047 PPA1&2 SpM1_ChORF0507_s_at 4 M5005_Spy0368 mtsA Manganese-binding protein Membrane transport 1.42576 3.16163 29.18305 PPA1&2 SpM1_ChORF0453_s_at 13 M5005_Spy1451 - Phage protein Phage 1.30058 3.11943 32.70845 PPA1&2 SpM12_ChORF299-42_at 13 M5005_Spy1364 - ATP-dependent RNA helicase Stress 1.78211 3.09038 35.36526 PPA1&2 SpM12_ChORF274-19_s_at 8 M5005_Spy1232 xseB Exodeoxyribonuclease VII small subunit (EC 3.1.11.6) Information processing 0.60119 3.07154 10.27992 PPA3 SpM1_ChORF1500_s_at M5005_Spy0389 dgk (EC 2.7.1.107) Lipid metabolism 1.2286 3.07116 37.23449 PPA1&2 SpM1_ChORF0475_s_at 11 M5005_Spy1576 - Transcription regulator, crp family Information processing 1.36069 3.06274 38.08153 PPA1&2 SpM1_ChORF1857_s_at 5 M5005_Spy0612 amrA Transcriptional activator amrA Information processing 1.33346 3.04305 40.13533 PPA1&2 SpM1_ChORF0797_s_at 8 M5005_Spy1731 - Hypothetical cytosolic protein Unknown 0.61393 3.03675 11.2799 PPA3 SpM18_ChORF2095_s_at M5005_Spy1823 - Integral membrane protein Phage 0.55764 3.03393 11.36496 PPA3 SpyM3_1824_at M5005_Spy0542 pepD Dipeptidase (EC 3.4.-.-) Amino acid metabolism 1.43729 3.01029 43.78604 PPA1&2 SpM1_ChORF0713_s_at 10 M5005_Spy0331 dnaX DNA polymerase III, delta' subunit (EC 2.7.7.7) Information processing 1.40631 3.00578 44.31226 PPA1&2 SpM1_ChORF0400_s_at 15 M5005_Spy1332 hk03 Two-component response regulator yvqC Signal transduction 0.65211 3.00077 12.41016 PPA3 SpM1_ChORF1622_s_at M5005_Spy0991 - Transcriptional regulator, GntR family Information processing 1.63123 3.00006 44.98791 PPA1&2 SpM1_ChORF1285_s_at 15 M5005_Spy1439 - Portal protein Phage 0.63606 2.90966 15.76636 PPA3 SpM5_ChORF270b-357_at M5005_Spy1771 hutU Urocanate hydratase (EC 4.2.1.49) Amino acid metabolism 0.64879 2.88785 16.68734 PPA3 SpM12_ChORF298-25_s_at M5005_Spy0411 - Multidrug resistance protein B Membrane transport 0.63628 2.86866 17.53906 PPA3 SpM1_ChORF0501_s_at M5005_Spy1562 - Colicin V production protein Unknown 0.5549 2.80546 20.63971 PPA3 SpM1_ChORF1839_s_at M5005_Spy0260 - Putative lipase Unknown 0.59976 2.76792 22.71588 PPA3 SpM1_ChORF0305_s_at M5005_Spy1484 accD Acetyl-coenzyme A carboxylase carboxyl transferase subunit alpha (EC 6.4.1.2) Lipid metabolism 0.61034 2.76648 22.79926 PPA3 SpM1_ChORF1744_s_at M5005_Spy1673 proS Prolyl-tRNA synthetase (EC 6.1.1.15) Protein synthesis 0.50899 2.75924 23.22327 PPA3 SpM1_ChORF1962_s_at M5005_Spy0687 mvaS.1 Hydroxymethylglutaryl-CoA synthase (EC 4.1.3.5) Lipid metabolism 0.39151 2.71301 26.10446 PPA3 SpM1_ChORF0881_s_at M5005_Spy0666 - Hypothetical protein Unknown 0.56744 2.66998 29.08005 PPA3 SpM12_ChORF291-52_s_at M5005_Spy0850 pta putative phosphotransacetylase Cellular processing 0.56297 2.64411 31.01723 PPA3 SpM1_ChORF1128_s_at M5005_Spy0202 - Hypothetical protein Unknown 0.39892 2.63046 32.08654 PPA3 SpM1_ChORF0238_s_at M5005_Spy1746 - PTS system, cellobiose-specific IIA component (EC 2.7.1.69) Carbohydrate metabolism 0.47439 2.61082 33.68474 PPA3 SpM1_ChORF2052_s_at M5005_Spy0225 - Thiamin pyrophosphokinase (EC 2.7.6.2) Coenzyme and cofactor metabolism 0.41265 2.60446 34.21762 PPA3 SpM1_ChORF0265_s_at M5005_Spy1009 - Phage protein Phage 0.5428 2.5942 35.09415 PPA3 SpM49_ChORF7585-31_at M5005_Spy0624 aroD 3-dehydroquinate dehydratase (EC 4.2.1.10) Carbohydrate metabolism 0.42061 2.58164 36.19477 PPA3 SpM1_ChORF0809_s_at M5005_Spy1203 - Phage protein Phage 0.53197 2.5465 39.44432 PPA3 SpM3_ChORF1132_at M5005_Spy1428 - Phage protein Phage 0.44032 2.54437 39.64961 PPA3 SpM12_ChORF299-58_s_at M5005_Spy0159 polA DNA polymerase I (EC 2.7.7.7) Cellular processing 0.58968 2.48805 45.44759 PPA3 SpM1_ChORF0185_at M5005_Spy0800 - DNA-cytosine methyltransferase (EC 2.1.1.73) Cellular processing 0.5735 2.47456 46.94588 PPA3 SpM1_ChORF1077_s_at M5005_Spy1663 - PTS SYSTEM, IIB COMPONENT (EC 2.7.1.69) Carbohydrate metabolism 0.47725 2.47003 47.45907 PPA3 SpM1_ChORF1952_s_at M5005_Spy0974 - Small integral membrane protein Unknown 0.51625 2.45366 49.35677 PPA3 SpM18_ChORF1214_s_at M5005_Spy1377 - trans-acting positive regulator Information processing 0.4605 2.44447 50.4527 PPA3 SpM1_ChORF1680_s_at M5005_Spy0191 - Integral membrane protein (Rhomboid family) Unknown 0.52911 2.43672 51.39264 PPA3 SpM12_ChORF279-21_s_at M5005_Spy1012 - Antigen A Phage 0.43977 2.3596 61.66043 PPA3 SpM49_ChORF7585-27_at M5005_Spy0670 rpsU Nucleoside diphosphate kinase (EC 2.7.4.6) Cellular processing 0.50953 2.3372 64.97137 PPA3 SpM3_ChORF0584_s_at M5005_Spy1203 - Phage protein Phage 0.46478 2.31915 67.7554 PPA3 SpM18_ChORF0733_s_at M5005_Spy0568 sagG Streptolysin S export ATP-binding protein SagG Membrane transport 0.47121 2.31827 67.89313 PPA3 SpM1_ChORF0744_s_at M5005_Spy1284 - Cytochrome c-type biogenesis protein ccdA Unknown 0.56265 2.314 68.56865 PPA3 SpM5_ChORF270b-69_at M5005_Spy1370 - Gamma-glutamyl phosphate reductase (EC 1.2.1.41) Unknown 0.48171 2.29932 70.93621 PPA3 SpM1_ChORF1670_s_at M5005_Spy0994 - Putative membrane-associated alkaline phosphatase Membrane transport 0.58437 2.29869 71.04031 PPA3 SpM1_ChORF1289_s_at M5005_Spy0540 - Transporter Membrane transport 0.4943 2.2935 71.89494 PPA3 SpM1_ChORF0653_s_at M5005_Spy0783 ptsD PTS system, mannose/fructose family IID component Carbohydrate metabolism 0.27405 2.28885 72.66956 PPA3 SpM1_ChORF1060_s_at M5005_Spy1854 - Hypothetical cytosolic protein Cellular processing 0.45667 2.27693 74.68955 PPA3 SpM1_ChORF2203_s_at M5005_Spy0133 ntpD V-type sodium ATP synthase subunit D (EC 3.6.3.15) Membrane transport 0.51572 2.26756 76.31312 PPA3 SpM1_ChORF0157_s_at M5005_Spy0882 - GTP-binding protein Unknown 0.41666 2.25911 77.80256 PPA3 SpM1_ChORF1161_s_at M5005_Spy0400 silD Hypothetical protein Virulence 0.49851 2.25622 78.31859 PPA3 SpM18_ChORF0547_s_at M5005_Spy1813 aspS Aspartyl-tRNA synthetase (EC 6.1.1.12) Protein synthesis 0.52233 2.24479 80.38761 PPA3 SpM1_ChORF2156_s_at M5005_Spy0356 speJ Exotoxin type J precursor Virulence 0.46868 2.24325 80.66994 PPA3 SpM1_ChORF0436_at M5005_Spy0041 - Na+ driven multidrug efflux pump Membrane transport 0.29139 2.23786 81.66676 PPA3 SpM1_ChORF0045_s_at M5005_Spy0544 - Transcriptional regulator, GntR family Information processing 0.44161 2.23471 82.25222 PPA3 SpM12_ChORF293-41_s_at M5005_Spy1500 hrcA Heat-inducible transcription repressor hrcA Information processing 0.64736 2.23102 82.94465 PPA3 SpM1_ChORF1763_s_at M5005_Spy1836 rplI LSU ribosomal protein L9P Protein synthesis 0.36534 2.22059 84.93081 PPA3 SpM1_ChORF2184_s_at M5005_Spy1379 glpF Glycerol uptake facilitator protein Carbohydrate metabolism 0.45977 2.21226 86.54751 PPA3 SpM1_ChORF1682_s_at M5005_Spy1100 aroK (EC 2.7.1.71) Amino acid metabolism 0.4848 2.17546 94.01644 PPA3 SpM1_ChORF1351_s_at M5005_Spy1814 hisS Histidyl-tRNA synthetase (EC 6.1.1.21) Protein synthesis 0.36084 2.15996 97.33106 PPA3 SpM1_ChORF2157_s_at M5005_Spy1278 - Hypothetical protein Unknown 0.41949 2.15383 98.66954 PPA3 SpM1_ChORF1551_s_at M5005_Spy1598 - Hypothetical protein Unknown 0.34705 2.15149 99.18561 PPA3 SpM1_ChORF1879_s_at

Page 4 of 5 Table 7. GAS genes upregulated (+Z) and downregulated (-Z) on day 32 in comparison to day 16 of infection.

M5005_gene Gene Description Function mean difference Z NFD Analysis Probe-set Probe # M5005_Spy0044 rplC LSU ribosomal protein L3P Protein synthesis 0.55954 2.11846 106.71924 PPA3 SpM1_ChORF0049_s_at M5005_Spy0303 glr Glutamate racemase (EC 5.1.1.3) Cellular processing 0.3909 2.11371 107.84206 PPA3 SpM1_ChORF0361_s_at M5005_Spy0858 xpt Xanthine phosphoribosyltransferase (EC 2.4.2.-) Unknown 0.49189 2.11243 108.14834 PPA3 SpM1_ChORF1136_s_at M5005_Spy0460 - Hypothetical protein Unknown 0.45901 2.11005 108.71549 PPA3 SpM1_ChORF0556_s_at M5005_Spy0055 rplX LSU ribosomal protein L24P Protein synthesis 0.33801 2.09128 113.29121 PPA3 SpM1_ChORF0062_s_at M5005_Spy1286 - DNA polymerase (EC 2.7.7.7) Unknown 0.36962 2.08323 115.30613 PPA3 SpM1_ChORF1563_s_at M5005_Spy1370 proA Gamma-glutamyl phosphate reductase (EC 1.2.1.41) Amino acid metabolism 0.41991 2.07122 118.36699 PPA3 SpM1_ChORF1672_s_at M5005_Spy0778 csrA Peptide methionine sulfoxide reductase msrB (EC 1.8.4.6) Unknown 0.44335 2.05848 121.69361 PPA3 SpM1_ChORF1055_s_at M5005_Spy1365 - Phospho-N-acetylmuramoyl-pentapeptide-transferase (EC 2.7.8.13) Cell wall metabolism 0.47236 2.04802 124.4864 PPA3 SpM18_ChORF1673_s_at M5005_Spy1249 ftsZ Cell division protein ftsZ Cellular processing 0.38152 2.03766 127.30824 PPA3 SpM1_ChORF1520_s_at M5005_Spy1390 - Hypothetical protein Unknown 0.50775 2.03761 127.32025 PPA3 SpM1_ChORF1697_s_at M5005_Spy1016 - Phage protein Phage 0.46689 2.03604 127.75253 PPA3 SpM49_ChORF7585-23_at M5005_Spy0841 - Glutamine amidotransferase, class I Unknown 0.49181 2.03258 128.70912 PPA3 SpM1_ChORF1119_s_at M5005_Spy0769 - Hypothetical cytosolic protein Unknown 0.33675 2.01683 133.14727 PPA3 SpM1_ChORF1046_s_at M5005_Spy1703 - Hypothetical cytosolic protein Unknown 0.39468 2.01313 134.20842 PPA3 SpM18_ChORF2065_x_at

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