Table 1

Homoplasies identified in the core regions of ST239 isolates. The SNP substitutions listed relate to the predicted forward strand of the TW20 chromosome. Isolates where homoplasies were detected are indicated, and where the isolates share the same node as illustrated in the phylogenic tree in Fig. 1 they are in parentheses. bp indicates base pairs.

SNP positionRegionIsolatesSNPSubstitutionAntibiotic
7254DNA gyrase subunit A (GyrA)HUSA304, (S85, S130, S87)T→GSer84→Ala84
(Ser84Ala)*
7255GyrA(BK2421, LHH1), (GRE18, GRE317, GRE4), (TUR9, TUR1), (TUR27, 3HK), (URU110, HU25, 2A8, BRA36, BZ48, BRA2, CHL1, CHL151, HGSA9, HGSA142, HSJ216, AGT67, AGT9, URU34, AGT1), HUSA304, GRE108, (CHI59, CHI61), (S102, S40, S71, S93, TW20, S38, S7, DEN907, S26, S25, S97, S106, S2, S78, S42, S24, S81, S39, S21)C→TSer84LeuQuinolone (23)
7266GyrA(HU109, HUR18), AGT120, HU106, (ICP5014, ICP5062)G→ALys88GluQuinolone (23)
133864Immunoglobulin G binding protein A precursorHU25, GRE108G→ASynonymous
13478792 bp upstream of immunoglobulin G binding protein A precursor3HK, (HU25, BZ48, BRA2, CHL1, AGT120, HGSA142, HSJ216, AGT67, AGT9, AGT1)G→TIntergenic
278498129 bp upstream of putative acetyl–coenzyme A transferase(ANS46, BK2421, LHH1, R35, GRE18, GRE317, GRE4, TUR9, TUR1, HU109, HUR18, TUR27, 3HK), GRE108T→CIntergenic
43647434 bp upstream of putative
dioxygenase
(TUR9, TUR1, HU109, HUR18, TUR27, 3HK), HSA10C→TIntergenic
594883Tetrapyrrole (corrin/porphyrin) methylase family protein(BK24210, LHH1), TUR9C→TPro49Ser
657696DNA-directed RNA polymerase beta chain protein (RpoB)GRE4, HSJ216, GRE108, HDG2C→AAsp471GluRifampin (25)
657724RpoB(GRE18, GRE317, GRE4), (TUR9, TUR1, HU109, HUR18, TUR27, 3HK), (HU25, 2A8, BRA36, BZ48, BRA2, CHL1, CHL151, AGT120, HGSA9, HGSA142, HSJ216, AGT67, AGT9, URU34, AGT1), (HDG2, HSA10, FFP103), (S85, S87, S130, S93, S71, S102, S40)C→AHis481AsnRifampin (25)
657869DNA-directed RNA polymerase beta chain protein RpoBAGT67, (S93, S71, S102, S40)C→TSer529LeuRifampin (25)
666536Translation elongation factor G (FusA)(GRE18, GRE317, GRE4), GRE108T→ALeu461LysFusidic acid (20)
666537FusA(GRE18, GRE317, GRE4), GRE108T→A
68182648 bp upstream of serine-aspartate repeat-containing protein CCHI61, (S26, S97, S2, S78, S39)C→AIntergenic
862898Putative membrane proteinGRE4, (S87, S130)A→CSer160Ala
113013563 bp upstream of FolD bifunctional proteinURU110, HGSA9G→TIntergenic
1138698Phosphoribosylglycinamide
formyltransferase (PurN)
(GRE18, GRE317, GRE4), (HUSA304, HU106), (HSA10, FFP103)T→ALeu174Met
117243450 bp upstream of probable
manganese transport protein
(TUR27, 3HK), (HU25, 2A8, BRA36, BZ48, BRA2, CHL1, CHL151, AGT120, HGSA9, HGSA142, HSJ216, AGT67, AGT9, URU34, AGT1), (TW20, S38, S7, DEN907, S26, S97, S25, S2, S106, S78, S24, S81, S39)T→GIntergenic
117243652 bp upstream of probable
manganese transport protein
(BK24210, LHH1), HSA11T→CIntergenic
117244460 bp upstream of probable
manganese transport protein
(R35, GRE18, GRE317, GRE4), (HDG2, HSA10, FFP103, ICP5011, ICP5014, ICP5062)C→GIntergenic
1206826ribonuclease HIII(HU25, 2A8, BRA36, BZ48, BRA2, CHL1, CHL151, AGT120, HGSA9, HGSA142, HSJ216, AGT67, AGT9, URU34, AGT1), (TW20)C→TGlu199Lys
1261219Isoleucyl-tRNA synthetaseCHI59, TW20G→TVal588PheMupirocin (22)
1448063Topoisomerase IV subunit A (GrlA)ANS46, R35, (HDG2, HSA10, FFP103), ICP5011T→CSer80PheQuinolone (23)
1524413Dihydrofolate reductase type I (DfrB)GRE18, (URU110, HU25, 2A8, BRA36, BZ48, BRA2, CHL1, CHL151, AGT120, HGSA9, HGSA142, HSJ216, AGT67, AGT9, URU34, AGT1)T→CHis150ArgTrimethoprim (24)
1524566DfrB(ANS46, BK2421, LHH1), (GRE18, GRE317, GRE4), (URU110, HU25, 2A8, BRA36, BZ48, BRA2, CHL1, CHL151, AGT120, HGSA9, HGSA142, HSJ216, AGT67, AGT9, URU34, AGT1), (HU106, HUSA304, HDG2, HSA10, FFP103, ICP5011, ICP5014, ICP5062)A→TPhe99TyrTrimethoprim (21)
1524789DfrBLHH1, 2A8G→ASynonymous
1525796Thymidylate synthase (ThyA)LHH1, 2A8, GRE108G→ASynonymous
1525817ThyALHH1, 2A8, GRE108G→ASynonymous
1525832ThyALHH1, 2A8, GRE108G→ASynonymous
1640281Glyoxalase/bleomycin resistance protein/dioxygenase superfamily proteinICP5014, (CHI59, CHI61)T→GSynonymous
1689862Putative transcriptional repressor (CcpN)(BK24210, LHH1), (HU106, HUSA304)C→TSynonymous
1755814Probable cell wall amidase (LytH)HDG2, (S85, S87, S130, S93, S71, S102, S40, TW20, S38, S7, DEN907, S26, S25, S97, S106, S2, S78, S42, S24, S81, S39, S21)A→GPro63Ser
1921379Bifunctional riboflavin biosynthesis protein (RibD)ANS46, URU110G→TAsn208Lys
2334865Protein SprT-likeTUR1, S40G→ASer43Phe
2753531458 bp upstream of conserved hypothetical protein(BK24210, LHH1), GRE18A→TIntergenic
2828688200 bp downstream of putative exported protein(TUR9, TUR1, HU109, TUR27, 3HK), GRE108, CHI59T→CIntergenic
2828714226 bp downstream of putative exported protein(TUR9, TUR1, HU109, TUR27, 3HK), GRE108, CHI59, (S38, DEN907, S26, S25, S97, S106, S2, S78, S42, S24, S81, S39, S21)G→TIntergenic
285976539 bp upstream of
O-acetyltransferase (OatA)
3HK, S106C→TIntergenic

*Change from serine to alanine occurs due to accompanying SNP (7255) within the same codon. †Change from leucine to lysine due to the presence of both SNPs (666536, 666537) within the same codon.