TABLE 1 .

List of mutations that fixed in the infecting population and their association with phylogenetic clades C1 to C4, as shown in Fig. 1^a

Gene locus	Annotation	Mutation category	Type of mutation	Effect in protein	Presence of mutation in clade:
					C1	C2	C3	C4
BMD20_16520	ACP S-malonyltransferase FabD	CDS	SNP, nonsyn	Y89H	+	+	+	+
BMD20_24750	Cell division protein FtsK	CDS	Indel, 76-aa insertion		+	+	+	+
BMD20_24880	DNA-binding regulatory protein, YebC/PmpR family	INT (181-bp upstream CDS)	SNP		+	+	+	+
BMD20_02495	Diguanylate cyclase/phosphodiesterase RpfR	CDS	SNP, nonsyn	E185D	−	+	+	+
BMD20_04285	Acetyl-CoA carboxylase, carboxyl transferase subunit beta AccD	CDS	SNP, nonsyn	T240M	−	+	+	+
BMD20_05445	Transcriptional regulator/2-aminoadipate aminotransferase	CDS	SNP, syn	A362A	−	+	+	+
BMD20_06065	Two-component heavy-metal response transcriptional regulator	CDS	SNP, nonsyn	E229D	−	+	+	+
BMD20_08755	LysR transcriptional regulator	CDS	SNP, nonsyn	A24E	−	+	+	+
BMD20_10060	DNA-binding protein	CDS	SNP, nonsyn	I228M	−	+	+	+
BMD20_11660	OmpR-like response regulator	INT (16-bp upstream CDS)	SNP		−	+	+	+
BMD20_14360	ABC transporter permease	CDS	SNP, nonsyn	P12T	−	+	+	+
BMD20_14695	Multidrug resistance efflux pump membrane protein EmrA	CDS	SNP, nonsyn	Q97H	−	+	+	+
BMD20_16530	Glycerol-3-phosphate acyltransferase PlsX	INT (9-bp upstream CDS)	SNP		−	+	+	+
BMD20_16530	Glycerol-3-phosphate acyltransferase PlsX	INT (10-bp upstream CDS)	SNP		−	+	+	+
BMD20_17700	Nucleoside-diphosphate sugar epimerase WbiI	CDS	Indel, frameshift		−	+	+	−

^aCDS, coding sequence; INT, intergenic region; aa, amino acid; nonsyn, nonsynonymous; syn, synonymous.