Assignment of Streptococcus agalactiae isolates to clonal complexes using a small set of single nucleotide polymorphisms

Table 5 Relationship between CCs identified by SNP typing, and genotype

CLONAL COMPLEX	SNP PROFILE	MOLECULAR SEROTYPE (MS)¹	PROTEIN GENE PROFILE (PGP)¹	MOBILE GENETIC ELEMENTS (MGE)¹	N = 116 (SSI)²
CC 1 (n = 22)	CTAG	V	Alp3	1S1381	10 (3)
		V	Alp3	None	1
		V	-	GBSi1	1
		Ia	Alp1	GBSi1	2
		Ia	Alp1	IS861-GBSi1	1
		Ia	Alp1	None	1
		II	Alp1	IS1381-ISsAg4-GBSi1	1 (1)
		II	Alp1	IS1381-ISsAg4	1
		III	Alp3	IS1381-GBSi1	1
		VII	Alp3	1S1381	2
		VII	A	IS1381	1
CC 10 (n = 16)	CTAA	Ib	A	IS1381-IS861	13
		II	A	IS1381-IS861-IS1548	1
		II	A	IS1381-IS861-ISsAg4	1
		V	A	IS1381-IS861	1
CC 17 (n = 7)	CCGG	III	R	IS861-GBSi1	6 (1)³
		Ia	Alp1	IS1381	1⁴
CC 19 (n = 50)	CCAG	III	R	IS1381-IS861-GBSi1	38 (4)⁵
		II	R	IS1381-IS861-IS1548	8
		V	-	GBSi1	1
		V	Alp3	IS861-GBSi1	1 (1)
		V	Alp3	GBSi1	1
CC 23 (n = 21)	TCGG	Ia	Alp1	IS1381	16 (2)
		Ia	Alp1	IS1381-IS861	1
		Ia	Alp2	-	1
		V	Alp1	IS1381-IS861	2
		II	Alp2	-	1
New profile⁶	TCAG	III	R	IS1381-IS861-IS1548	1

¹For description of methods of identification of molecular serotype (MS), protein gene profiles (pgp) and mobile genetic elements (mge) see [5].
²SSI – sterile site isolates. Figures in brackets indicate the small subset of isolates from blood or CSF cultures from patients of varying ages. All others were from routine antenatal vaginal swabs or their sites of isolates were unknown (5 isolates). No attempt was made to identify differences between invasive and colonising isolates among those studied.
³The profile MS III-pgp R-mge IS861-GBSi1 is typical of the virulent serotype III subtype, which we have found previously to be associated with late onset neonatal sepsis) [6].
⁴This isolate was shown to not be CC17 by interrogation of the safety net SNP.
⁵The profile MSIII-pgp R-mge IS1381-IS861-GBSi1 is typical of the most common serotype III subtype, which is commonly found among vaginal isolates and is also a common cause of neonatal sepsis.
⁶This profile was derived from a mixed DNA sample and is likely an artefact.

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