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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