Table 3.

Mutations identified in ST896 strains compared with the HBSJRP7 reference (Ref) genome

Strain/Ref contig	Ref position (bp)	Variant type	Ref allele	Mutant allele	Amino acid change	Annotation
HBSJRP9 (daptomycin MIC 8 mg/L)
25	866	insertion	—	CTTGGTCTTCT	frame shift	hypothetical protein
32	5333	deletion	T	—	NA	intergenic (between sensor histidine kinase VanS and contig break)
41	19814	SNP	T	A	NA	intergenic (between mobile element protein and contig break)
75	8628	NSY SNP	C	T	Gly106Glu	PTS system, sucrose-specific
106	26313	SNP	T	C	NA	intergenic (between S-adenosylmethionine:tRNA ribosyltransferase-isomerase and contig break)
123	30223	NSY SNP	C	T	Thr112Ile	cell division protein FtsI
144	5948	NSY SNP	G	A	Arg208His	SSU ribosomal protein S2p
145	9634	insertion	—	ATCTGTCTCGCAG	NA	intergenic (between methionine ABC transporter ATP-binding protein and CsbD-like protein)
HBSJRP10 (daptomycin MIC 4 mg/L)
59	22691	NSY SNP	A	T	Lys233Ile	multimodular transpeptidase-transglycosylase
66	29793	deletion	G	—	NA	intergenic (between GCN5-related N-acetyltransferase and PTS system, cellobiose-specific IIC component)
75	13399	SYN SNP	G	A	NA	mobile element protein
130	23788	SYN SNP	T	C	NA	ribosomal protein S18
HBSJRP12 (daptomycin MIC 8 mg/L)
17	7425	SYN SNP	G	A	NA	hypothetical protein
17	19639	NSY SNP	T	A	Asp518Glu	metal-transporting ATPase
32	5333	deletion	T	—	NA	intergenic (downstream of sensor histidine kinase VanS, upstream of contig break)
106	26313	SNP	T	C	NA	intergenic (between S-adenosylmethionine:tRNA ribosyltransferase-isomerase and contig break)
HBSJRP13 (daptomycin MIC 2 mg/L)
106	6463	NSY SNP	C	T	Thr316Met	d-alanine-d-alanine ligase

NSY SNP, non-synonymous SNP; SYN SNP, synonymous SNP; NA, not applicable (no change in coding sequence; shared between strains).

Bold text indicates that this change is hypothesized to cause the lower daptomycin MIC.