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

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 No. of SNPs in Pneumococcal isolates
SPS01 SPS02 SPS03 SPS04 SPS05 SPS06 SPS07 SPS08 SPS09 SPS10
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
  1. aAll S. pneumoniae loci number (sp_#) are according to the annotation of reference strain TIGR4