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 position | Region | Isolates | SNP | Substitution | Antibiotic |
| 7254 | DNA gyrase subunit A (GyrA) | HUSA304, (S85, S130, S87) | T→G | Ser84→Ala84 (Ser84Ala)* | |
| 7255 | GyrA | (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→T | Ser84Leu | Quinolone (23) |
| 7266 | GyrA | (HU109, HUR18), AGT120, HU106, (ICP5014, ICP5062) | G→A | Lys88Glu | Quinolone (23) |
| 133864 | Immunoglobulin G binding protein A precursor | HU25, GRE108 | G→A | Synonymous | – |
| 134787 | 92 bp upstream of immunoglobulin G binding protein A precursor | 3HK, (HU25, BZ48, BRA2, CHL1, AGT120, HGSA142, HSJ216, AGT67, AGT9, AGT1) | G→T | Intergenic | – |
| 278498 | 129 bp upstream of putative acetyl–coenzyme A transferase | (ANS46, BK2421, LHH1, R35, GRE18, GRE317, GRE4, TUR9, TUR1, HU109, HUR18, TUR27, 3HK), GRE108 | T→C | Intergenic | – |
| 436474 | 34 bp upstream of putative dioxygenase | (TUR9, TUR1, HU109, HUR18, TUR27, 3HK), HSA10 | C→T | Intergenic | – |
| 594883 | Tetrapyrrole (corrin/porphyrin) methylase family protein | (BK24210, LHH1), TUR9 | C→T | Pro49Ser | – |
| 657696 | DNA-directed RNA polymerase beta chain protein (RpoB) | GRE4, HSJ216, GRE108, HDG2 | C→A | Asp471Glu | Rifampin (25) |
| 657724 | RpoB | (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→A | His481Asn | Rifampin (25) |
| 657869 | DNA-directed RNA polymerase beta chain protein RpoB | AGT67, (S93, S71, S102, S40) | C→T | Ser529Leu | Rifampin (25) |
| 666536 | Translation elongation factor G (FusA) | (GRE18, GRE317, GRE4), GRE108 | T→A | Leu461Lys† | Fusidic acid (20) |
| 666537 | FusA | (GRE18, GRE317, GRE4), GRE108 | T→A | ||
| 681826 | 48 bp upstream of serine-aspartate repeat-containing protein C | CHI61, (S26, S97, S2, S78, S39) | C→A | Intergenic | – |
| 862898 | Putative membrane protein | GRE4, (S87, S130) | A→C | Ser160Ala | – |
| 1130135 | 63 bp upstream of FolD bifunctional protein | URU110, HGSA9 | G→T | Intergenic | – |
| 1138698 | Phosphoribosylglycinamide formyltransferase (PurN) | (GRE18, GRE317, GRE4), (HUSA304, HU106), (HSA10, FFP103) | T→A | Leu174Met | – |
| 1172434 | 50 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→G | Intergenic | – |
| 1172436 | 52 bp upstream of probable manganese transport protein | (BK24210, LHH1), HSA11 | T→C | Intergenic | – |
| 1172444 | 60 bp upstream of probable manganese transport protein | (R35, GRE18, GRE317, GRE4), (HDG2, HSA10, FFP103, ICP5011, ICP5014, ICP5062) | C→G | Intergenic | – |
| 1206826 | ribonuclease HIII | (HU25, 2A8, BRA36, BZ48, BRA2, CHL1, CHL151, AGT120, HGSA9, HGSA142, HSJ216, AGT67, AGT9, URU34, AGT1), (TW20) | C→T | Glu199Lys | – |
| 1261219 | Isoleucyl-tRNA synthetase | CHI59, TW20 | G→T | Val588Phe | Mupirocin (22) |
| 1448063 | Topoisomerase IV subunit A (GrlA) | ANS46, R35, (HDG2, HSA10, FFP103), ICP5011 | T→C | Ser80Phe | Quinolone (23) |
| 1524413 | Dihydrofolate reductase type I (DfrB) | GRE18, (URU110, HU25, 2A8, BRA36, BZ48, BRA2, CHL1, CHL151, AGT120, HGSA9, HGSA142, HSJ216, AGT67, AGT9, URU34, AGT1) | T→C | His150Arg | Trimethoprim (24) |
| 1524566 | DfrB | (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→T | Phe99Tyr | Trimethoprim (21) |
| 1524789 | DfrB | LHH1, 2A8 | G→A | Synonymous | – |
| 1525796 | Thymidylate synthase (ThyA) | LHH1, 2A8, GRE108 | G→A | Synonymous | – |
| 1525817 | ThyA | LHH1, 2A8, GRE108 | G→A | Synonymous | – |
| 1525832 | ThyA | LHH1, 2A8, GRE108 | G→A | Synonymous | – |
| 1640281 | Glyoxalase/bleomycin resistance protein/dioxygenase superfamily protein | ICP5014, (CHI59, CHI61) | T→G | Synonymous | – |
| 1689862 | Putative transcriptional repressor (CcpN) | (BK24210, LHH1), (HU106, HUSA304) | C→T | Synonymous | – |
| 1755814 | Probable 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→G | Pro63Ser | – |
| 1921379 | Bifunctional riboflavin biosynthesis protein (RibD) | ANS46, URU110 | G→T | Asn208Lys | – |
| 2334865 | Protein SprT-like | TUR1, S40 | G→A | Ser43Phe | – |
| 2753531 | 458 bp upstream of conserved hypothetical protein | (BK24210, LHH1), GRE18 | A→T | Intergenic | – |
| 2828688 | 200 bp downstream of putative exported protein | (TUR9, TUR1, HU109, TUR27, 3HK), GRE108, CHI59 | T→C | Intergenic | – |
| 2828714 | 226 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→T | Intergenic | – |
| 2859765 | 39 bp upstream of O-acetyltransferase (OatA) | 3HK, S106 | C→T | Intergenic | – |
*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.