Table 1.
Information of outgroups and models used to construct maximum likelihood phylogenetic trees for each bacterial species in this study.
| Bacteria | Outgroup (GenBank accession no.) | Substitution models for MLST treesa |
|---|---|---|
| Burkholderia pseudomallei | Burkholderia thailandensis E254 (CP004381) | TIM1 + I + G |
| Campylobacter jejuni | Campylobacter coli 15-537360 (CP006702) | TIM1 + I + G |
| Chlamydia trachomatis | Chlamydia muridarum Nigg (AE002160) | TIM3 + I + G |
| Escherichia coli 1 | Escherichia fergusonii ATCC 35469 (CU928158) | TIM3 + I + G |
| Escherichia coli 2 | Escherichia fergusonii ATCC 35469 (CU928158) | GTR + I + G |
| Helicobacter pylori | Helicobacter acinonychis str. Sheeba (AM260522) | GTR + I + G |
| Helicobacter pylori SouthAfrica20 (CP006691) | ||
| Helicobacter pylori SouthAfrica7 (CP002336) | ||
| Klebsiella pneumoniae | Klebsiella variicola strain DSM 15968 (CP010523) | TIM1 + I + G |
| Listeria monocytogenes | Listeria innocua Clip11262 (AL592022) | TIM3 + I + G |
| Staphylococcus aureus | Staphylococcus capitis subsp. capitis strain AYP1020 (CP007601) | GTR + I + G |
| Salmonella enterica | Salmonella bongori serovar 48:z41:–str. RKS3044 (CP006692) | TrN + I + G |
| Streptococcus pyogenes | Streptococcus dysgalactiae subsp. equisimilis 167 (AP012976) | TrN + I + G |
aG, gamma distributed rate of heterogeneity; I, proportion of invariant sites.