Table 5 Non-synonymous SNPs among S. pneumoniae isolates found in genes associated with virulence, antibiotic resistance, and other regulatory functions

SP_0041

blpU; bacteriocin

1

1

1

1

1

1

1

1

–

2

SP_0346

cpsA; capsular polysaccharide biosynthesis protein

7

5

4

4

4

4

8

8

8

8

SP_0347

cpsB; capsular polysaccharide biosynthesis protein

1

2

–

–

–

–

1

1

1

5

SP_0348

cpsC; capsular polysaccharide biosynthesis protein

1

3

3

3

3

3

2

2

2

6

SP_0349

cpsD; capsular polysaccharide biosynthesis protein

7

–

11

11

12

12

5

5

9

–

SP_0350

cpsE; capsular polysaccharide biosynthesis protein

–

–

–

–

–

–

–

–

–

–

SP_0351

cpsF; capsular polysaccharide biosynthesis protein

–

–

–

–

–

–

–

–

–

–

SP_0352

cpsG; capsular polysaccharide biosynthesis protein

–

–

–

–

–

–

–

–

–

–

SP_0353

cpsH; capsular polysaccharide biosynthesis protein

–

–

–

–

–

–

–

–

–

–

SP_1837

capsular polysaccharide biosynthesis protein

4

3

–

–

–

–

3

3

4

4

SP_0117

pspA; pneumococcal surface protein A

2

–

4

2

3

4

5

5

4

3

SP_0377

cbpC; choline-binding protein C

6

3

5

5

5

5

1

1

–

1

SP_0930

cbpE; choline-binding protein E

7

8

12

11

13

12

3

3

11

5

SP_0378

cbpJ; choline-binding protein J

1

3

2

2

2

2

1

1

–

1

SP_0390

cbpG; choline-binding protein G

3

6

4

4

2

4

4

4

3

1

SP_0391

cbpF; choline-binding protein F

5

6

–

–

–

–

–

–

–

–

SP_0069

cbpI; choline-binding protein I

–

–

–

–

–

–

–

–

–

–

SP_0533

blpK; bacteriocin associated protein

–

–

–

–

–

–

–

–

–

–

SP_0545

blpY; Immunity protein

2

3

3

3

2

2

2

2

–

1

SP_0641

prtA; protective antigen A

16

14

13

12

12

13

14

14

9

13

SP_0730

spxB; pyruvate oxidase

1

1

–

–

–

–

–

–

1

–

SP_1002

lmb; adhesion lipoprotein

–

–

–

–

–

–

–

–

–

3

SP_1003

Conserved hypothetical protein

7

6

5

3

4

5

8

8

4

4

SP_1207

xseA; exodeoxyribonuclease VII, large subunit

–

–

–

–

–

–

–

–

–

–

SP_1923

pln; pneumolysin

1

1

–

–

–

–

2

2

2

3

SP_1937

lytA; autolysin

1

4

1

1

1

1

1

1

1

–

SP_2190

chpA; choline-binding protein A

6

11

9

10

7

8

2

2

4

9

SP_2201

chpD; choline-binding protein D

3

4

4

4

4

4

6

6

3

8

SP_2239

htrA; serine protease

–

1

–

–

–

–

1

1

2

2

SP_2240

spoJ; homologous to sporulation protein

1

–

2

2

2

2

1

1

1

1

SP_0457

bacA; bacitracin resistance protein

–

–

–

–

–

–

–

–

–

–

SP_0615

fibA; beta-lactam resistance factor

–

1

1

2

2

1

2

1

1

4

SP_1673

penA; penicillin-binding protein 2B

1

6

3

1

5

5

2

2

3

2

SP_0369

penicillin-binding protein 1A

3

2

1

2

1

1

2

2

–

3

SP_2099

penicillin-binding protein 1B

3

2

4

4

4

4

3

3

4

4

SP_2010

penicillin-binding protein 2A

4

5

5

5

5

5

1

1

7

5

SP_0336

penicillin-binding protein 2X

1

1

3

2

1

2

2

2

4

3

SP_0616

beta-lactam resistance factor

2

1

1

2

2

1

4

4

3

2

SP_1075

CpoA; glycosyl transferase

1

1

1

1

1

1

–

–

1

1

SP_0798

ciaR; DNA-binding response regulator

–

1

–

1

–

–

–

–

–

–

SP_0799

ciaH; sensor histidine kinase

–

–

–

–

–

–

1

1

–

–

SP_2084

pstS; phosphate ABC transporter, phosphate-bind

–

–

–

–

–

–

–

–

–

1

SP_2085

pstC; phosphate ABC transporter, permease protein

–

2

3

3

3

3

2

2

1

1

SP_2086

pstA; phosphate ABC transporter, permease protein

–

–

–

–

–

–

–

–

–

–

SP_2087

pstB; phosphate ABC transporter, ATP-binding protein

3

3

1

1

1

1

–

–

1

–

SP_1890

amiC; oligopeptide ABC transporter permease

2

3

3

3

3

3

4

4

4

2

SP_0010

beta-lactamase class C

4

–

1

1

1

1

–

–

1

1

SP_0314

hyaluronate lyase

14

14

15

15

15

15

16

16

10

14

SP_0071

metalloprotease ZmpC

–

–

–

–

–

–

–

–

–

–

SP_1650

manganese ABC transporter substrate-binding lipoprotein

1

1

1

1

1

1

1

1

1

1

SP_1687

neuraminidase B

7

7

8

4

4

8

5

5

5

4

SP_0357

UDP-N-acetyl glucosamine 2-epimerase CpsI

–

–

–

–

–

–

–

–

–

–

SP_0358

capsular polysaccharide biosynthesis protein CpsJ

–

–

–

–

–

–

–

–

–

–

SP_0359

capsular polysaccharide biosynthesis protein CpsK

–

–

–

–

–

–

–

–

–

–

SP_0360

UDP-N-acetyl glucosamine 2-epimerase CpsL

–

–

–

–

–

–

–

–

–

–

SP_0463

cell wall surface anchor protein

–

–

1

1

1

1

–

–

–

–

SP_0461

transcriptional regulator

–

–

–

–

1

–

–

–

–

–

SP_0468

sortase

–

–

–

–

–

–

–

–

–

–

SP_0965

endo-beta-N-acetylglucosaminidase LytB

2

2

2

2

2

2

1

1

1

2

SP_1783

DNA mismatch repair protein MutT

–

–

1

1

1

1

–

–

–

1

SP_0173

DNA mismatch repair protein HexB

–

–

–

–

–

–

–

–

–

–

SP_2218

MreC; rod shape-determining protein

–

–

–

–

–

–

–

–

–

–

SP_rrnaA23S

23S ribosomal RNA; K01980 23S ribosomal RNA

–

–

–

–

–

–

–

–

–

–

SP_rrnaB23S

23S ribosomal RNA; K01980 23S ribosomal RNA

–

–

–

–

–

–

–

–

–

–

SP_rrnaC23S

23S ribosomal RNA; K01980 23S ribosomal RNA

–

–

–

–

–

–

–

–

–

–

SP_rrnaD23S

23S ribosomal RNA; K01980 23S ribosomal RNA

–

–

–

–

–

–

–

–

–

–