TABLE 1.

Genome characteristics among sequence types (STs) of invasive serotype 1 pneumococcus, South Africa, 1989 to 2013

MLST	No. of isolates	Mean genome length (bp)	Mean (±SD) no. of SNPs outside recombination sitesa	Mean (±SD) no. of recombination blocksb	Mean rho/thetac	P valued	Mean r/me	P valued
ST-217 (All)	382	1,918,345	8 (±9)	0.24 (±1)	0.015		0.283
ST-217C1	353	1,919,081	7 (±8)	0.16 (±0.7)	0.013	Ref	0.091	Ref
ST-217C2	15	1,903,232	13 (±11)	0.67 (±0.2)	0.035	0.253	0.934	0.220
ST-217C3	14	1,915,989	26 (±16)	1.64 (±4)	0.032	0.360	4.436	<0.001
ST-304	1	2,042,749	330	52	0.157	0.051	11.524	<0.001
ST-306	4	2,033,949	8 (±5)	0.25 (±0.43)	0.019	0.871	0.173	0.950
ST-611	5	1,934,828	16 (±22)	0.20 (±0.4)	0.009	0.911	0.076	0.990
ST-612f	101	1,915,591	8 (±8)	0.26 (±1)	0.012	0.866	0.610	0.078
ST-618	17	1,917,230	19 (±18)	0.06 (±0.2)	0.001	0.514	0.081	0.987
ST-8314f	8	1,900,792	7 (±4)	0.04 (±1)	0.038	0.357	0.625	0.567
ST-9067f	16	1,907,652	6 (±6)	0.56 (±1)	0.086	<0.001	0.813	0.279

^aSNP, single nucleotide polymorphism.

^bA recombination block was defined as ≥3 consecutive SNPs.

^crho/theta is the ratio of the number of recombination events to point mutations, a measure of the relative rates of recombination and point mutation (6, 11).

^dST-217_C1 was the reference group for comparing rho/theta and r/m between sequence types.

^er/m is the ratio of base substitutions predicted to have been imported through recombination to those occurring through point mutation.

^fSingle-locus variant of ST-217.