Table 1.

Closely related pairs of samples from separate countries. Column “D” is the number of genomic SNPs between this pair of samples. “Lin” indicates phylogenomic lineage for both samples in the pair. “DR Class” indicates drug resistance classification. The substitution rate used for Lineage 2.2.1 samples was 2.0175×10⁻⁷ substitutions/site/year ([1.1115×10⁻⁷,3.003×10⁻⁷] 95% HPD). The substitution rate used for Lineage 4 samples was 5.7694×10⁻⁸ substitutions/site/year ([4.0324×10⁻⁸,7.3311×10⁻⁸] 95% HPD). “Exp SNPs” are the lower and upper bounds of the 95% HPD for expected number of SNPs between pairs of samples. Boldface rows are paired samples where number of genomic SNPs between samples is within the 95% HPD limits of the expected number of SNPs for a direct ancestral relationship.

SRR ID1	SRR ID2	D	Country 1	Country 2	Lin	DR Class 1	DR Class 2	ΔT - years	Exp SNPs, Lower	Exp SNPs, Upper
SRR7655790	SRR10303352	1	Azerbaijan	Kazakhstan	2.2.1	MDR	MDR	0.79	0.77	2.09
SRR7654034	SRR11033773	2	Azerbaijan	Georgia	4.8	Sensitive	Sensitive	1.19	0.42	0.77
SRR6356966	SRR10397096	3	Azerbaijan	Georgia	2.2.1	MDR	MDR	0.95	0.93	2.51
SRR1159053	SRR10397096 *	5	Belarus	Georgia	2.2.1	XDR	MDR	3.30	3.23	8.73
SRR7516307	SRR10379886	6	Georgia	Moldova	2.2.1	MDR	MDR	2.15	2.11	5.69
SRR1159053	SRR6384965	7	Belarus	Azerbaijan	2.2.1	XDR	MDR	4.50	4.41	11.90
SRR5153222	SRR5153718	7	Georgia	Azerbaijan	2.2.1	MDR	MDR	0.09	0.09	0.23
SRR5153222	SRR6356966	7	Georgia	Azerbaijan	2.2.1	MDR	MDR	0.19	0.19	0.51
SRR6356966	SRR5153279	7	Azerbaijan	Georgia	2.2.1	MDR	MDR	0.04	0.04	0.10
SRR10397096	SRR6384965	7	Georgia	Azerbaijan	2.2.1	MDR	MDR	1.20	1.17	3.17
SRR1159053	SRR5153222	7	Belarus	Georgia	2.2.1	XDR	MDR	2.16	2.11	5.71
SRR1159053	SRR5153279	7	Belarus	Georgia	2.2.1	XDR	MDR	2.39	2.34	6.33
SRR5153830	SRR7516307	7	Moldova	Georgia	2.2.1	MDR	MDR	0.51	0.50	1.35
SRR10379966	SRR10397218	7	Moldova	Georgia	4.2.1	MDR	MDR	0.48	0.17	0.31
SRR7516307	SRR10380089	7	Georgia	Moldova	2.2.1	MDR	MDR	1.96	1.92	5.18
SRR10380072	SRR9738492	7	Moldova	Romania	4.2.1	MDR	MDR	4.77	1.69	3.08
SRR3743405	SRR9738492	7	Moldova	Romania	4.2.1	MDR	MDR	1.05	0.37	0.68
SRR1159053	SRR6356966	8	Belarus	Azerbaijan	2.2.1	XDR	MDR	2.36	2.30	6.23
SRR1163177	SRR7655469	8	Belarus	Azerbaijan	2.2.1	MDR	MDR	6.59	6.45	17.43
SRR5153718	SRR5153279	8	Azerbaijan	Georgia	2.2.1	MDR	MDR	0.15	0.14	0.38
SRR5153279	SRR6384965	8	Georgia	Azerbaijan	2.2.1	MDR	MDR	2.11	2.06	5.57
SRR6356966	SRR11033734	8	Azerbaijan	Georgia	2.2.1	MDR	Poly DR	2.47	2.42	6.53
SRR6807742	SRR9738492	8	Moldova	Romania	4.2.1	MDR	MDR	3.83	1.36	2.47
SRR1163140	SRR5153707	9	Belarus	Azerbaijan	4.3.3	XDR	MDR	2.57	0.91	1.66
SRR1159053	SRR5153718	9	Belarus	Azerbaijan	2.2.1	XDR	MDR	2.25	2.20	5.94
SRR1163140	SRR7655952	9	Belarus	Azerbaijan	4.3.3	XDR	MDR	4.97	1.76	3.21
SRR1163140	SRR7657747	9	Belarus	Azerbaijan	4.3.3	XDR	MDR	4.97	1.76	3.20
SRR5153329	SRR6356966	9	Georgia	Azerbaijan	2.2.1	XDR	MDR	0.51	0.50	1.35
SRR5153619	SRR6356977	9	Georgia	Azerbaijan	2.2.1	XDR	XDR	0.38	0.37	1.01
SRR7516458	SRR6357007	9	Georgia	Azerbaijan	2.2.1	XDR	MDR	0.48	0.47	1.28
SRR6384965	SRR10397106	9	Azerbaijan	Georgia	2.2.1	MDR	MDR	0.23	0.23	0.62
SRR10380139	SRR10397218	9	Moldova	Georgia	4.2.1	MDR	MDR	0.71	0.25	0.46
SRR11033734	SRR10380214	9	Georgia	Moldova	2.2.1	Poly DR	MDR	0.54	0.53	1.43
SRR10380234	SRR6384965	9	Moldova	Azerbaijan	2.2.1	MDR	MDR	2.82	2.75	7.44
SRR5153877	SRR9738492	9	Moldova	Romania	4.2.1	MDR	MDR	1.15	0.41	0.74
SRR6807719	SRR9738492	9	Moldova	Romania	4.2.1	MDR	MDR	2.98	1.06	1.92
SRR1159002	SRR7655952	10	Belarus	Azerbaijan	4.3.3	MDR	MDR	5.90	2.09	3.81
SRR1159290	SRR7655952	10	Belarus	Azerbaijan	4.3.3	MDR	MDR	4.71	1.67	3.04
SRR1159002	SRR7657747	10	Belarus	Azerbaijan	4.3.3	MDR	MDR	5.90	2.09	3.80
SRR1159290	SRR7657747	10	Belarus	Azerbaijan	4.3.3	MDR	MDR	4.71	1.67	3.04
SRR7516382	SRR6356982	10	Georgia	Azerbaijan	2.2.1	Sensitive	Sensitive	0.59	0.58	1.57
SRR6356988	SRR7516382	10	Azerbaijan	Georgia	2.2.1	MDR	Sensitive	2.63	2.58	6.96
SRR7516399	SRR6356977	10	Georgia	Azerbaijan	2.2.1	MDR	XDR	0.46	0.45	1.22
SRR5153718	SRR10397096	10	Azerbaijan	Georgia	2.2.1	MDR	MDR	1.05	1.03	2.79
SRR6356966	SRR11033716	10	Azerbaijan	Georgia	2.2.1	MDR	MDR	2.80	2.74	7.39
SRR6807730	SRR10397096	10	Moldova	Georgia	2.2.1	Sensitive	MDR	3.29	3.22	8.70
SRR10380234	SRR10397106	10	Moldova	Georgia	2.2.1	MDR	MDR	3.05	2.98	8.06
SRR5153860	SRR10397218	10	Moldova	Georgia	4.2.1	MDR	MDR	2.18	0.77	1.40
SRR10379908	SRR10397218	10	Moldova	Georgia	4.2.1	MDR	MDR	1.73	0.61	1.11
SRR10380080	SRR10397218	10	Moldova	Georgia	4.2.1	MDR	MDR	4.01	1.42	2.59
SRR10380120	SRR10397218	10	Moldova	Georgia	4.2.1	MDR	MDR	2.90	1.03	1.87
SRR11033734	SRR10380199	10	Georgia	Moldova	2.2.1	Poly DR	Mono DR	0.58	0.57	1.54
SRR7516428	SRR10379886	10	Georgia	Moldova	2.2.1	Sensitive	MDR	1.67	1.64	4.42
SRR9738492	SRR10379966	10	Romania	Moldova	4.2.1	MDR	MDR	0.70	0.25	0.45
SRR10380160	SRR9738492	10	Moldova	Romania	4.2.1	MDR	MDR	0.51	0.18	0.33
SRR10380245	SRR9738492	10	Moldova	Romania	4.2.1	XDR	MDR	4.83	1.71	3.12

The asterisk (*) indicates the sample with a possible mixed infection.