TABLE 1.

Regions of diversity correlated with the invasive or noninvasive phenotype

RD and TIGR IDSTMbCGH correlationaTIGR annotation or gene name
IPDNoninvasive
RD2
    SP01636ATranscriptional regulator PlcR, putative
    SP0164U, 6AHypothetical protein
    SP0165U, 6AFlavoprotein
    SP0166U, 6APyridoxal-dependent decarboxylase, Orn/Lys/Arg family
    SP0167U, 6AHypothetical protein
    SP0168U, 6AMacrolide efflux protein, putative
    SP0169U, 6ALactose phosphotransferase system repressor, degenerate
    SP0171U, 6AROK family protein
RD5
    SP0691146AHypothetical protein
    SP0692146AHypothetical protein
    SP0694146AConserved domain protein
    SP0695146AHesA/MoeB/ThiF family protein
    SP0696146AHypothetical protein
    SP0697146AABC transporter, ATP-binding protein
    SP0698146AHypothetical protein
    SP0700146ATransposase, IS30 family, degenerate
RD6
    SP1046U, 6Aα-Amylase family protein, authentic point mutation
    SP10476AHypothetical protein
    SP1048Hypothetical protein
    SP1049Hypothetical protein
    SP1050Transcriptional regulator, putative
    SP1051Conserved hypothetical protein
    SP10526APhosphoesterase, putative
    SP10536AConserved domain protein
    SP1054Tn5252, Orf 10 protein
    SP1055Tn5252, Orf 9 protein
    SP1056Tn5252, relaxase
    SP1057Transcriptional regulator PlcR, putative
    SP1058Hypothetical protein
    SP1059Hypothetical protein
    SP1060UHypothetical protein
    SP1061U, 14Protein kinase, putative
    SP1062U, 14ABC transporter, ATP-binding protein
    SP1063ABC-2 transporter, permease protein, putative
    SP1064U, 6A, 14Transposase, IS200 family
    SP10656A14Hypothetical protein
RD7
    SP1129U, 6BIntegrase/recombinase, phage integrase family
    SP1130Transcriptional regulator
    SP1131Transcriptional regulator, putative
    SP1132U, 6BHypothetical protein
    SP1133U, 6BHypothetical protein
    SP1134U, 6BHypothetical protein
    SP11356BHypothetical protein
    SP1136U, 6BConserved domain protein
    SP1137UGTP-binding protein, putative
    SP1138Hypothetical protein
    SP1139Hypothetical protein
    SP1140Hypothetical protein
    SP1141Hypothetical protein
    SP1142Hypothetical protein
    SP1143HConserved hypothetical protein
    SP1144Conserved hypothetical protein
    SP1145Hypothetical protein
    SP1146Hypothetical protein
    SP1147U, 14Integrase/recombinase, phage integrase family, truncation
RD8
    SP1315U, 6B, 14V-type sodium ATP synthase, subunit D
    SP1316U, 6B, 14V-type sodium ATP synthase, subunit B
    SP1317U, 6B, 14V-type sodium ATP synthase, subunit A
    SP1318U, 6BV-type sodium ATP synthase, subunit G
    SP1319U, 6B, 14V-type sodium ATP synthase, subunit C
    SP1320U, 6B, 14V-type sodium ATP synthase, subunit E
    SP1321HU, 6B, 14V-type sodium ATP synthase, subunit K
    SP1322U, 6BV-type sodium ATP synthase, subunit I
    SP13236BHypothetical protein
    SP1324U, 6B, 14ROK family protein
    SP1325U, 6BOxidoreductase, Gfo/Idh/MocA family
    SP1326U, 6B, 14Neuraminidase, putative
    SP1327U, 6B, 14Conserved hypothetical protein
    SP1328HU, 6B, 14Sodium:solute symporter family protein
    SP1329U, 6B, 14N-Acetylneuraminate lyase
    SP1330U, 6B, 14N-Acetylmannosamine-6-P epimerase, putative
    SP1331U, 6B, 14Phosphosugar-binding transcriptional regulator, putative
    SP1332Conserved domain protein
    SP1333Hypothetical protein
    SP133414Conserved hypothetical protein
    SP133514Hypothetical protein
    SP1336Type II DNA modification methyltransferase Spn5252IP
    SP1337U, 14IS1380-Spn1, transposase
    SP1338U, 6B, 14Hypothetical protein
    SP1340U, 6B, 14Hypothetical protein
    SP1341U, 6B, 14ABC transporter, ATP-binding protein
    SP1342U, 6B, 14Toxin secretion ABC transporter, ATP-binding/permease protein
    SP1343H6AU, 6B, 14Prolyl oligopeptidase family protein
    SP1344HU, 6B, 14Conserved hypothetical protein
    SP1345U, 6B, 14Hypothetical protein
    SP1346Conserved hypothetical protein
    SP1347U, 14Hypothetical protein
    SP1348U, 14Conserved hypothetical protein
    SP1349U, 14Hypothetical protein
    SP1350U, 14Conserved domain protein
    SP1351U, 14Hypothetical protein
RD9
    SP1612U, 14Conserved domain protein
    SP1613U, 14IS3-Spn1, transposase, authentic point mutation
    SP1614IS3-Spn1, hypothetical protein, degenerate
    SP16156ATransketolase, authentic frameshift
    SP16166ARibulose-phosphate 3-epimerase family protein
    SP16176APTS system, IIC component
    SP16186APTS system, IIB component
    SP16196APTS system, IIA component
    SP16206APTS system, nitrogen regulatory component IIA, putative
    SP16216ATranscription antiterminator BglG family protein, authentic frameshift
    SP1622U, 6A, 14Transposase, IS200 family
RD10
    SP1755U, 6A, 14Hypothetical protein
    SP1756U, 6A, 14Conserved domain protein
    SP1757U, 6A, 14Conserved hypothetical protein
    SP1758U, 6A, 14Glycosyl transferase, group 1
    SP1759U, 6A, 14Preprotein translocase, SecA subunit
    SP1760HU, 6A, 6BConserved domain protein
    SP1761U, 6A, 6BHypothetical protein
    SP1762U, 6A, 6BHypothetical protein
    SP1765U, 6A, 6BGlycosyl transferase, family 8
    SP1766U, 6A, 6BGlycosyl transferase, family 8
    SP1767U, 6AGlycosyl transferase, family 8
    SP1768U, 6A, 6BConserved hypothetical protein
    SP1769U, 6BGlycosyl transferase, authentic frameshift
    SP1770HGlycosyl transferase, family 8
    SP1771HGlycosyl transferase, family 2/glycosyl transferase family 8
    SP1772HU, 6A, 6BCell wall surface anchor family protein
    SP1773U, 6A, 14IS630-Spn1, transposase Orf1/Orf2 degenerate
RD13
    SP215814l-Fucose isomerase
    SP2159H6A14Lucolectin-related protein
    SP21606A14Conserved hypothetical protein
    SP21616A14PTS system, IID component
    SP2162H6A14PTS system, IIC component
    SP21636A14PTS system, IIB component
    SP2164H6A14PTS system, IIA component
    SP21656A14Fucose operon FucU protein
    SP21666A14l-Fuculose phosphate aldotase
  • a 6A, 6B, and 14 indicate genes whose presence is correlated with the invasive cohort or the noninvasive cohort. U indicates genes whose presence is correlated with either cohort in a serotype-independent manner.

  • b H indicates genes determined by STM to be required for in vivo passage (Hava and Camilli [24]).