Table 3. Nucleotide polymorphisms shared by all CDC Philadelphia strains relative to the NCBI Philadelphia-1 reference sequence.
| Nucleotide Polymorphism | No. of Polymorphisms (nt) | Nucleotide position | Nucleotide position in NCBI Philadelphia-1 | Associated ORF's | Potential Translational Importance |
|---|---|---|---|---|---|
| Multiple SNPs | 44 | Ph-1: 685,979–688,613 | 685,979–688,614 | rtxA (lpg0644) | Various indels and amino acid changes |
| Ph-2: 723,869–726,503 | |||||
| Ph-3: 685,978–688,612 | |||||
| Ph-4: 723,869–726,503 | |||||
| ATCC Ph-1: 723,869–726,503 | |||||
| Insertion | 10,203 | Ph-1: 688,664 | 688,665 | rtxA (lpg0644-lpg0645) | Single, rtxA ORF of 6420 amino acids created from lpg0644 and lpg0655 |
| Ph-2: 726,554 | |||||
| Ph-3: 688,663 | |||||
| Ph-4: 726554 | |||||
| ATCC Ph-1: 726,554 | |||||
| G → A | 1 | Ph-1: 826,712 | 816,510 | Repeat region upstream of iraAB (lpg0746) | Unknown |
| Ph-2: 864,602 | |||||
| Ph-3: 826,711 | |||||
| Ph-4: 864,602 | |||||
| ATCC Ph-1: 864,602 | |||||
| Insertion | 158 | Ph-1: 826,741 | 816,539 | Repeat region upstream of iraAB (lpg0746) | Unknown |
| Ph-2: 864,631 | |||||
| Ph-3: 826,741 | |||||
| Ph-4: 826,741 | |||||
| ATCC Ph-1: 864,631 | |||||
| T → G | 1 | Ph-1: 826,922 | 816,562 | Repeat region upstream of iraAB (lpg0746) | Unknown |
| Ph-2: 864,812 | |||||
| Ph-3: 826,921 | |||||
| Ph-4: 864,812 | |||||
| ATCC Ph-1: 864,812 | |||||
| Multiple SNPs | 2 | Ph-1: 830,817 | 820,457 | LPS biosynthesis protein, PseA-like (lpg0748) | V368R |
| Ph-2: 868,707 | |||||
| Ph-3: 830,816 | |||||
| Ph-4: 868,707 | |||||
| ATCC Ph-1: 868,707 | |||||
| Del G | 1 | Ph-1: 859,606 | 849,246 | Glycosyl transferase (lpg0775) | Premature stop at codon 53, potential longer ORF created |
| Ph-2: 897,496 | |||||
| Ph-3: 859,605 | |||||
| Ph-4: 897,496 | |||||
| ATCC Ph-1: 897,496 | |||||
| N → T | 1 | Ph-1: 1,366,331 | 1,355,972 | Hypothetical protein (lpg1228) | Synonymous |
| Ph-2: 1,404,221 | |||||
| Ph-3: 1,366,329 | |||||
| Ph-4: 1,404,219 | |||||
| ATCC Ph-1: 1,404,221 | |||||
| Del G | 1 | Ph-1: 3,083,758 | 3,073,980 | Glutamine amidotransferase (lpg2721) | Frameshift creates premature stop at codon 34, potential upstream start creates longer ORF in with same lpg2721 frame |
| Ph-2: 3,122,281 | |||||
| Ph-3: 3,084,386 | |||||
| Ph-4: 3,122,280 | |||||
| ATCC Ph-1: 3,122,280 | |||||
| A → T | 1 | Ph-1: 3,111,785 | 3,102,008 | 16S rRNA (lpg2753) | Unknown |
| Ph-2: 3,150,308 | |||||
| Ph-3: 3,112,411 | |||||
| Ph-4: 3,150,303 | |||||
| ATCC Ph-1: 3,150,307 | |||||
| C → G | 1 | Ph-1: 3,111,912 | 3,102,135 | 16S rRNA (lpg2753) | Unknown |
| Ph-2: 3,150,435 | |||||
| Ph-3: 3,112,538 | |||||
| Ph-4: 3,150,430 | |||||
| ATCC Ph-1: 3,150,434 | |||||
| Insertion | 1,032 | Ph-1: 3,360,806 | 3,351,031 | mompS (lpg2961) | Addition of tandem MOMPS ORF |
| Ph-2: 3,499,329 | |||||
| Ph-3: 3,361,253 | |||||
| Ph-4: 3,399,330 | |||||
| ATCC Ph-1: 3,399,329 |
Ph-1, CDC Philadelphia-1; Ph-2, Philadelphia-2; Ph-3, Philadelphia-3; Ph-4, Philadelphia-4; ATCC Ph-1, ATCC Philadelphia-1