Skip to main content

Table 3 Presence and absence of genes involved in virulence and antibiotic-resistance in each of the 10 clinical isolates

From: Comparative genomic analysis of ten clinical Streptococcus pneumoniae collected from a Malaysian hospital reveal 31 new unique drug-resistant SNPs using whole genome sequencing

Locus namea

Gene name and/or description

Presence of virulent genes in Pneumococcal isolates

SPS01

SPS02

SPS03

SPS04

SPS05

SPS06

SPS07

SPS08

SPS09

SPS10

SP_0531

blpI; bacteriocin

1

1

0

0

0

0

0

0

1

0

SP_0041

blpU; bacteriocin

1

1

1

1

1

1

1

1

0

1

SP_0109

bacteriocin

1

1

0

0

0

0

1

1

1

1

SP_0544

immunity protein BlpX

1

1

0

0

0

0

1

1

0

1

SP_1315

V-type ATP synthase subunit D

1

1

0

0

0

0

1

0

0

0

SP_1318

V-type ATP synthase subunit F

1

1

0

0

0

0

1

0

0

0

SP_1319

V-type ATP synthase subunit C

1

1

0

0

0

0

1

0

0

0

SP_1320

V-type ATP synthase subunit E

1

1

0

0

0

0

1

0

0

0

SP_1321

V-type ATP synthase subunit K

1

1

0

0

0

0

1

0

0

0

SP_1322

V-type ATP synthase subunit I

1

1

0

0

0

0

1

0

0

0

SP_0346

cpsA; capsular polysaccharide biosynthesis protein

1

1

1

1

1

1

1

1

1

1

SP_0347

cpsB; capsular polysaccharide biosynthesis protei

1

1

1

1

1

1

1

1

1

1

SP_0348

cpsC; capsular polysaccharide biosynthesis protein

1

1

1

1

1

1

1

1

1

1

SP_0349

cpsD; capsular polysaccharide biosynthesis protein

1

1

1

1

1

1

1

1

1

1

SP_0350

cpsE; capsular polysaccharide biosynthesis protein

1

1

1

1

1

1

1

1

1

1

SP_0117

pspA; pneumococcal surface protein A

1

1

1

1

1

1

1

1

1

1

SP_0377

cbpC; choline-binding protein C

1

1

1

1

1

1

1

1

1

1

SP_0378

cbpJ; choline-binding protein J

1

1

1

1

1

1

1

1

1

1

SP_0390

cbpG; choline-binding protein G

1

1

1

1

1

1

1

1

1

1

SP_0391

cbpF; choline-binding protein F

1

1

1

1

1

1

1

1

1

1

SP_0533

blpK; bacteriocin associated protein

1

1

1

1

1

1

1

1

1

1

SP_0545

blpY; Immunity protein

1

1

1

1

1

1

1

1

1

1

SP_0641

prtA; protective antigen A

1

1

1

1

1

1

1

1

1

1

SP_1638

PsaR; transcriptional regulator

1

1

1

1

1

1

1

1

1

1

SP_0966

pavA; adherence and virulence protein A

1

1

1

1

1

1

1

1

1

1

SP_1923

pln; pneumolysin

1

1

1

1

1

1

1

1

1

1

SP_1937

lytA; autolysin

1

1

1

1

1

1

1

1

1

1

SP_2190

chpA; choline-binding protein A

1

1

1

1

1

1

1

1

1

1

SP_2201

chpD; choline-binding protein D

1

1

1

1

1

1

1

1

1

1

SP_0457

bacA; bacitracin resistance protein

1

1

1

1

1

1

1

1

1

1

SP_0615

fibA; beta-lactam resistance factor

1

1

1

1

1

1

1

1

1

1

SP_1673

penA; penicillin-binding protein 2B

1

1

1

1

1

1

1

1

1

1

SP_0369

penicillin-binding protein 1A

1

1

1

1

1

1

1

1

1

1

SP_2099

penicillin-binding protein 1B

1

1

1

1

1

1

1

1

1

1

SP_2010

penicillin-binding protein 2A

1

1

1

1

1

1

1

1

1

1

SP_0336

penicillin-binding protein 2X

1

1

1

1

1

1

1

1

1

1

SP_0616

beta-lactam resistance factor

1

1

1

1

1

1

1

1

1

1

SP_0798

ciaR; DNA-binding response regulator

1

1

1

1

1

1

1

1

1

1

SP_0799

ciaH; sensor histidine kinase

1

1

1

1

1

1

1

1

1

1

SP_0972

pmrA; multi-drug resistance efflux pump

1

1

1

1

1

1

1

1

1

1

SP_0461

transcriptional regulator

0

0

1

1

1

1

0

0

0

0

  1. All S. pneumoniae loci number (sp_#) are according to the annotation of reference strain TIGR4. 1 indicates presence and 0 indicates absence of the gene from the pneumococcal isolates