Table 3. Genetic differentiation of serotypes within serogroups.
Description of variants present in the CTV database.
| Serogroup | Serotype | Distinguishing genetic features | Functional effect |
|---|---|---|---|
| 6 | 6A/6B and 6C/6D | A > G 583 in wciP | Amino acid substitution (Ser195Asn) which results to different rhamnose-ribitol linkages (1 → 3 in 6A/6C and 1 → in 6B/6D) (Mavroidi et al., 2007; Sheppard et al., 2010; Baek et al., 2014) |
| 6A/6C and 6B/6D and 6E | wciNα in 6A and 6B / wciNβin 6C and 6B / wciNγ in 6E | Allele wciNα encodes for galactosyl-transferase whereas wciNβ is 200 bp shorter and encodes for a glycosyl-transferase—consistent with changes in structure (Park et al., 2007). WciNγ is a chimeric form of wciNα (75%) and wciNβ (25%). | |
| 7 and serotype 40 | 7A/7F | Frameshift mutation insT 587 in 7A wcwD gene | Loss of function of glycosyltransferase leading to loss of side branch for 7A (Mavroidi et al., 2007). ∗“Mixed: [‘07A’,‘07F’]” result corresponds to 7A phenotype (see ‘Results’) |
| 7B/7C/40 | SNPs in wcwK (Table S1) | Amino acid changes—wcwK encodes for a GT but 7C and 40 structure not known | |
| 9 | 9A/9V | Frameshift mutation delG 722 in 9A wcjE | Loss of function of O-acetyltranferase leads to differences in acetylation |
| 9L/9N | SNPs in genes wchA, wcjA, wcjB and wzy (Table S2) | Amino acid changes—wcjA and wcjB encode for glycosyltranferases (GT) and changes in these are consistent with presence of glucose in 9N instead of galactose present in residue 3 of the polysaccharide repeat unit of the other three serotypes (Mavroidi et al., 2007) | |
| 9A/9V/9L/9N | presence of an additional O-acetyltransferase encoded by wcjD in 9A-9V | Differences in acetylation | |
| 10 | 10A/10B/10C/10F | 10A/10B carries gene wcrG, whereas 10C/10F carries genes wcrH and wciG | wcrH encodes for GT and is responsible for side branch linkage Galf(1-6)Galp present in 10F but not in 10A; wcrG encodes for GT and it catalyzes the linkage of Galp( 1-6) side branch in 10A (Aanensen et al., 2007) |
| 10A/10B/10C/10F | 10A/10C have wcrCα whereas 10B/10F have wcrCβ | wcrCβ allele is described as wcrF and both genes encode for glucosyltransferases and are responsible for the differences observed in the linkage between galactose and ribitol-5-phosphate (Yang et al., 2011) | |
| 11 | 11A/11B/11C/11D/11F | Genes wcwC and wcjE are present in 11A, 11D and 11F whereas gene wcwR is present in 11B and 11C (Mavroidi et al., 2007) | wcwC, wcjE and wcwR are acetyltransferase genes—differences in acetylation |
| 11A/11B/11C/11D/11F | Frameshift mutation delA 130 in gct in 11B and 11F | Presence of Gro-1P correlates with an intact gct gene in types 11A and 11C; gct is frameshifted in types 11F and 11B, and Rib-ol is present in the CPS instead of Gro (Mavroidi et al., 2007) | |
| 11A/11D/11F | wcrL pos 334: codon AAT (Asn) in 11A; codon ACT (Ser) in 11D (Oliver et al., 2013) and codon GCT (Ala) in 11F | wcrL encodes for a GT—donor sugar for WcrL is GlcpNAc in types 11F, 11B, and 11C but Glcp in type 11A (Mavroidi et al., 2007) | |
| 12 and serotypes 44 and 46 | 12A/12B/12F/44/46 | SNPs in genes wcxD and wcxF (Table S3) | Both genes encode for GTs present only in this genogroup (Mavroidi et al., 2007)—effect on sugar chain unknown (no structure for 12B, 44 and 46) |
| 15 | 15A/15B/15C/15F | 15F has 4 additional genes; glf, rmlB, rmlD and wcjE (Bentley et al., 2006) | glf, rmlB and rmlD are involved in sugar biosynthesis; wcjE encodes for an acetyltraferase. |
| 15A/15B/15C | 15A wchL has 81% identity in the first 300 bps compare to the allele found in 15B/15C, whereas 15A wzd has 69% identity in the last 300 bps when compared to the 15B/C allele | wchL encodes for a GT; wzd is involved in translocation of mature CPS to the cell surface and thus is responsible for determining the length of the capsule polysaccharide chain (Bentley et al., 2006) | |
| 15B/15C | Difference in TA tandem repeat region near position 413 of wciZ, leading to frameshift in 15C (Bentley et al., 2006) | wciZ encodes for an O-acetyltransferase—differences in acetylation. ∗15B, 15B/C and 15C results can be assigned (see ‘Results’) | |
| 16 | 16A, 16F | Mapping only | |
| 17 | 17A, 17F | Mapping only | |
| 18 | 18A/18B/18C/18F | 18F has an extra acetyltransferase gene (wcxM) and type 18A lacks the acetyltransferase gene wciX(Mavroidi et al., 2007) | Differences in acetylation |
| 18B/18C | G > T 168 in wciX leads to early stop codon in 18B (Mavroidi et al., 2007) | wciX encodes for an acetylotranferase—difference in acetylation | |
| 19 | 19A, 19F | Mapping only | |
| 19B/19C | 19B lacks genes wchU, HG264 and glf | wchU encodes for a putative GT and could be responsible for the additional glucose in the capsular polysaccharide repeat unit of 19C; glf encodes for a UDP-galactopyranose mutase whereas HG264 has no functional product | |
| 22 | 22A/22F | wcwA and wcwC share no similarity between 22A and 22F. | wcwA, encoding for a putative glycosyl-transferase and wcwC, encoding for a putative O-acetyltranferase—structure for 22A unknown |
| 23 | 23A/23B/23F | distinct wzy sequence in all serotypes | wzy encodes for a polymerase and differences in sequence should account for the different polymerization linkages (Mavroidi et al., 2007)—structures for 23A and 23B unknown |
| 23A/23B/23F | wchA is identical in 23B and 23F but distinct in 23A. | wchA encodes for a glycosyl-1-phosphatase transferase (Aanensen et al., 2007)—structures for 23A and 23B unknown | |
| 25 and serotype 38 | 25A/25F/38 | wcyV missing in 38 (Mavroidi et al., 2007) | wcyV, wcyD and wcyC encode for GTs (Aanensen et al., 2007)—no structures available for 25A, 25F or 38 |
| 25A/25F/38 | wcyDα in serogroup 25 and wcyDβ in serotype 38 | ||
| 25A/25F/38 | SNPs in wcyC (Table S4) | ||
| 28 | 28A/28F | SNPs in wciU (Table S5) | wciU encodes for a GT—no structures available |
| 33 and serotype 37 | 33A/33F/37 | 37 carries tts - a transferase gene | tts is responsible for the polysaccharide capsule synthesis in 37 (Waite et al., 2003) |
| 33A/33F | Frameshift mutation insT 433 in 33F wcjE gene | Loss of function of O-acetyltranferase leads to differences in acetylation (Mavroidi et al., 2007) | |
| 33B/33D | wciNα in 33B/wciNβin 33C | wciNα encodes for a putative glycosyltranferase whereas wciNα encodes for a putative galactosyltransferase—consistent with differences in structure | |
| 33C | Mapping only | ||
| 35 and serotype 42 | 35B, 35F | Mapping only | |
| 35A/35C/42 | SNPs in genes mnp1, wcrL and wzh (Table S6) | mnp1 encodes for a putative nucleotidyltranferase (NDP-mannitol pathway), wcrL, a GT and wzh, a protein-tyrosine phosphatase—consistent with differences in structure | |
| 35A/35C/42 | Frameshift mutation insA 248 in 35A wcrK (Mavroidi et al., 2007) | wcrK encodes for a GT—consistent with differences in structure | |
| 41 | 41A/41F | Frameshift mutation delG 23 in 41A wcrX (Mavroidi et al., 2007) | wcrX encodes for a acetyltranferase—differences in acetylation |
| 47 | 47A, 47F | Mapping only |