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Table 3 Distribution of the virulence factor and regulation genes of S. pneumoniae

From: The variome of pneumococcal virulence factors and regulators

Virulence Factors

TIGR4

D39

R6

70,585

Hungary19A 6

SPN994038

SPN994039

SPN034183

OXC141

SPN034156

ST556

Taiwan19F-14

TCH8431/19A

A026

INV200

CGSP14

INV104

G54

AP200

P1031

gamPNI0373

SPNA45

ATCC 700669

JJA

670-6B

LPxTG - Proteins

bgaA

1

1

1

1

1

1

1

1

1

1

1

1

1

1

1

1

1

1

1

1

1

1

1

1

1

endoD

1

1

1

1

1

1

1

1

1

1

1

1

1

1

1

1

1

1

1

1

1

1

1

1

1

pclA

1

1

1

1

1

1

1

1

1

1

1

1

1

1

1

1

1

1

1

1

1

1

1

1

1

spGH101

1

1

1

1

1

1

1

1

1

1

1

1

1

1

1

1

1

1

1

1

1

1

1

1

1

strH

1

1

1

1

1

1

1

1

1

1

1

1

1

1

1

1

1

1

1

1

1

1

1

1

1

nanA

1

1

1

1

1

1

1

1

1

1

1

1

1

1

1

1

1

1

1

1

1

1

1

1

1

pfbA

1

1

1

1

1

1

1

1

1

1

1

1

1

1

1

1

1

1

1

1

1

0

1

1

1

prtA

1

1

1

1

1

1

1

1

1

1

1

1

1

1

1

1

1

1

1

1

1

0

1

1

1

pavB

1

1

1

1

1

1

1

1

1

1

1

1

1

1

1

1

1

1

1

1

0

1

0

1

1

ksgA

1

1

1

1

1

1

1

1

0

1

1

1

1

1

1

1

1

1

1

1

0

1

0

1

1

spuA

1

1

1

1

1

1

1

1

1

0

1

1

1

1

1

1

1

1

1

1

1

1

1

1

1

hysA

1

1

1

1

1

0

0

0

0

0

1

1

1

1

1

1

1

1

1

1

1

1

1

1

1

SP_1492

1

1

1

1

1

0

0

0

0

0

1

1

1

1

1

0

1

1

1

1

1

1

0

1

1

zmpA

1

1

1

1

1

1

1

1

1

1

1

1

1

1

0

0

1

0

1

0

0

0

0

0

1

zmpB

1

1

1

1

1

1

1

1

1

1

1

1

1

1

1

1

1

1

1

1

1

0

1

0

1

zmpC

1

0

0

0

0

0

0

0

0

0

0

0

0

0

0

0

0

1

1

0

0

0

0

0

0

zmpD

0

0

0

0

0

0

0

0

0

0

0

0

0

0

1

1

0

1

0

1

1

0

1

1

0

psrP

1

0

0

1

1

0

0

0

0

0

0

0

0

0

0

1

1

0

0

0

0

0

0

0

0

rrgA

1

0

0

0

1

0

0

0

0

0

1

1

1

1

0

0

0

0

0

0

0

0

0

0

1

rrgB

1

0

0

0

1

0

0

0

0

0

1

1

1

1

0

0

0

0

0

0

0

0

0

0

1

rrgC

1

0

0

0

1

0

0

0

0

0

1

1

1

1

0

0

0

0

0

0

0

0

0

0

1

pitA

0

0

0

0

0

1

0

0

0

0

1

1

1

0

0

0

1

0

1

0

0

0

0

0

0

pitB

0

0

0

0

0

1

0

0

0

0

1

1

1

0

0

0

1

0

1

0

0

0

0

0

0

Choline-Binding Proteins (CBPs)

lytA

1

1

1

2

2

2

2

2

2

2

2

1

1

1

1

1

1

1

2

2

2

2

2

3

3

lytB

1

1

1

1

1

1

1

1

1

1

1

1

1

1

1

1

1

1

1

1

1

1

1

1

1

lytC

1

1

1

1

1

1

0

0

0

0

1

1

1

0

1

1

1

1

1

1

1

1

1

1

1

pce

1

1

1

1

1

1

1

1

1

1

1

1

1

1

1

1

1

1

1

1

1

1

1

1

1

pcpA

1

1

1

1

1

0

0

0

0

0

1

1

1

1

1

1

1

1

1

0

0

1

1

1

1

pspA

1

1

1

1

1

1

1

1

1

1

1

1

1

1

1

1

1

1

1

1

1

0

1

0

1

pspC

1

1

1

1

1

0

0

0

0

1

1

1

1

1

0

1

1

0

1

1

1

1

1

1

1

cbpC

1

1

1

1

1

1

1

1

1

1

1

1

1

1

1

0

1

1

1

1

1

0

0

1

1

cbpD

1

1

1

1

1

1

1

1

1

1

1

1

1

1

1

1

1

1

1

1

1

1

1

1

1

cbpF

1

1

1

1

1

0

0

0

0

0

0

0

0

0

0

0

0

0

0

0

0

0

1

1

1

cbpG

1

0

0

0

0

0

0

0

1

1

1

1

1

1

1

1

1

1

1

1

1

1

1

1

0

cbpI

1

0

0

0

0

0

0

0

0

0

0

0

0

0

0

0

0

1

1

0

0

0

0

0

0

cbpJ

1

0

0

0

0

1

1

1

1

1

1

1

1

1

1

1

0

0

0

0

0

0

1

1

1

SP_0667

1

1

1

1

1

1

1

1

1

1

1

1

1

1

1

1

1

1

1

0

0

0

0

0

0

Lipoproteins

glnQ

1

1

1

1

1

1

1

1

1

1

1

1

1

1

1

1

1

1

1

1

1

1

1

1

1

piaA

1

1

1

1

1

1

1

1

1

1

1

1

1

1

1

1

1

1

1

1

1

1

1

1

1

piuA

1

1

1

1

1

1

1

1

1

1

1

1

1

1

1

1

1

1

1

1

1

1

1

1

1

ppiA

1

1

1

1

1

1

1

1

1

1

1

1

1

1

1

1

1

1

1

1

1

1

1

1

1

psaA

1

1

1

1

1

1

1

1

1

1

1

1

1

1

1

1

1

1

1

1

1

1

1

1

1

ppmA

1

1

1

1

1

1

1

1

1

1

1

1

1

1

0

1

1

0

0

1

1

1

1

1

1

aliA

1

1

1

1

1

0

0

0

0

0

1

1

1

1

1

1

1

1

1

1

1

0

1

1

1

phtA

1

1

1

1

0

0

0

0

0

0

0

0

0

0

0

0

1

0

1

1

1

0

0

0

1

phtB

1

0

0

0

0

0

0

0

0

0

1

1

0

0

1

0

1

1

1

0

1

0

0

0

0

phtD

1

1

1

1

1

1

1

1

1

0

1

1

1

0

1

1

1

1

1

1

1

1

1

1

1

phtE

1

1

1

1

1

1

1

1

1

1

1

1

1

1

1

1

1

1

1

1

1

1

1

1

1

Non-Classical Surface-Exposed Proteins

eno

1

1

1

1

1

1

1

1

1

1

1

1

1

1

1

1

1

1

1

1

1

1

1

1

1

gap

1

1

1

1

1

1

1

1

1

1

1

1

1

1

1

1

1

1

1

1

1

1

1

1

1

htrA

1

1

1

1

1

1

1

1

1

1

1

1

1

1

1

1

1

1

1

1

1

1

1

1

1

pavA

1

1

1

1

1

1

1

1

1

1

1

1

1

1

1

1

1

1

1

1

1

1

1

1

1

pbp1B

1

1

1

1

1

1

1

1

1

1

1

1

1

1

1

1

1

1

1

1

1

1

1

1

1

stkP

1

1

1

1

1

1

1

1

1

1

1

1

1

1

1

1

1

1

1

1

1

1

1

1

1

usp45

1

1

1

1

1

1

1

1

1

1

1

1

1

1

1

1

1

1

1

1

1

1

1

1

1

nanB

1

1

1

1

0

1

1

1

1

1

1

1

1

1

1

1

1

1

1

1

1

1

1

1

1

pppA

1

1

1

1

1

1

1

0

1

1

1

1

1

1

1

1

1

1

1

1

1

1

1

1

1

fic-Like

1

1

1

1

1

1

1

1

1

1

1

1

1

1

1

1

1

1

0

1

1

1

1

1

1

gnd

1

1

1

1

1

1

1

1

1

1

1

1

1

1

1

1

1

1

1

1

1

2

1

1

1

ply

1

1

1

1

1

1

1

1

1

1

1

1

1

1

1

1

1

1

1

1

1

1

1

1

1

nanC

1

0

0

0

1

0

0

0

0

0

0

0

0

0

1

1

1

1

1

0

0

0

1

1

1

Regulators

mgrA

1

1

1

1

1

1

1

1

1

1

1

1

1

1

1

1

1

1

1

1

1

1

1

1

1

psaR

1

1

1

1

1

1

1

1

1

1

1

1

1

1

1

1

1

1

1

1

1

1

1

1

1

merR

1

0

1

0

0

1

1

1

1

1

1

0

1

1

1

1

0

1

1

1

1

0

1

1

1

rlrA

1

0

0

0

1

0

0

0

0

0

1

1

1

1

0

0

0

0

0

0

0

0

0

0

1

  1. The present table shows the absence (0) or presence (1, 2 or 3) of each considered genes in the 25 strains selected for this study. The number (1, 2 or 3) indicates the amount of copies of each gene in the genome. lytA is the only factor with more than one copy per genome. In the strain SPNA45, the gene gnd was found duplicated (2) and fused with a duplication of its neighbor gene (rr14) downstream. In the gene nanA of TIGR4 (1) a shift in its ORF was found. However, it has also been reported that NanA is expressed in this pneumoccoccal strain. Gene defective copies (genes with any alteration in their primary DNA sequences) are depicted in bold and italics: In the SPNA45 strain ply is fused with a copy of lytA, and pspA is defective in the ATCC700669 pneumococcal strain