TABLE 1.
Summary of variants in infecting strains compared to the colonizing strain in each patient
| Patient | Strain type | agr statusa | No. of SNVs |
No. of insertions/deletions of ≤5 nt |
No. of structural variants of >5 nt |
Total no. of variantsd (no. of variants in core genome/no. of variants in accessory genome) | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Nonsynonymous (I/C/U)e | Stop gain (I/C)e | Stop loss (I/C)e | Synonymous (I/C/U)e | Intergenic (I/C/U)e | Otherb | Intergenic (I/C)e | Frameshift (I/C)e | Structural variant (I/C)e | Repeat expansion (I/C)e | Variable regionc | Inversion | Plasmid loss | ||||
| Cases | ||||||||||||||||
| 53 | Blood | − | 46/48/7 | 1/1 | 0/0 | 21/49/37 | 21/20/52 | 7 | 13/13 | 5/6 | 3/3 | 3/4 | 1 | 0 | 1 | 362 (137/225) |
| 60 | Blood | − | 0/1/0 | 0/0 | 0/1 | 0/0/0 | 0/0/1 | 1 | 0/0 | 0/1 | 0/0 | 0/0 | 0 | 0 | 0 | 5 (4/1) |
| 73 | Blood | − | 5/6/0 | 0/0 | 0/0 | 4/3/37 | 4/1/0 | 0 | 1/2 | 1/0 | 2/0 | 1/1 | 0 | 0 | 0 | 68 (22/46) |
| 117 | Blood | − | 0/0/2 | 0/0 | 0/0 | 0/1/0 | 2/0/0 | 0 | 1/0 | 0/0 | 0/2 | 0/0 | 0 | 0 | 0 | 8 (4/4) |
| 117 | Focus | + | 1/0/0 | 0/0 | 0/0 | 1/1/0 | 1/0/0 | 0 | 0/1 | 0/0 | 0/0 | 0/0 | 0 | 0 | 0 | 5 (3/2) |
| 135 | Blood | − | 1/3/2 | 0/0 | 0/0 | 0/1/1 | 0/3/1 | 0 | 3/4 | 0/1 | 3/3 | 0/1 | 0 | 0 | 1 | 28 (6/22) |
| 135 | Focus | − | 1/3/2 | 0/0 | 0/0 | 0/1/1 | 0/3/1 | 0 | 6/0 | 1/1 | 4/3 | 0/1 | 0 | 0 | 0 | 28 (5/23) |
| Controls | ||||||||||||||||
| 35 | Blood | + | 0/2/0 | 0/0 | 0/0 | 0/0/0 | 0/0/0 | 0 | 0/0 | 0/0 | 0/0 | 1/0 | 0 | 0 | 1 | 4 (0/4) |
| 36 | Blood | + | 0/2/0 | 0/0 | 0/0 | 0/0/0 | 0/0/0 | 1 | 1/1 | 0/0 | 0/0 | 1/0 | 0 | 0 | 0 | 6 (3/3) |
| 45 | Blood | + | 1/0/0 | 0/0 | 0/0 | 0/0/0 | 0/0/0 | 0 | 0/0 | 0/0 | 0/0 | 0/0 | 0 | 0 | 0 | 1 (1/0) |
| 63 | Blood | + | 2/2/0 | 0/0 | 0/0 | 0/0/0 | 0/0/0 | 0 | 0/0 | 0/0 | 0/0 | 0/0 | 0 | 0 | 0 | 4 (4/0) |
| 108 | Blood | + | 0/0/0 | 0/0 | 0/0 | 0/0/0 | 0/0/0 | 0 | 0/0 | 2/1 | 0/0 | 0/0 | 0 | 0 | 0 | 3 (2/1) |
| 152 | Blood | + | 0/0/0 | 0/0 | 0/0 | 0/1/0 | 0/0/0 | 0 | 0/0 | 0/0 | 1/1 | 0/0 | 0 | 0 | 0 | 3 (2/1) |
| 152 | Focus | + | 0/0/0 | 0/0 | 0/0 | 0/1/0 | 0/0/0 | 0 | 0/0 | 0/0 | 1/2 | 0/0 | 1 | 0 | 0 | 5 (1/4) |
| 158 | Blood | + | 1/1/0 | 0/0 | 0/0 | 0/0/0 | 0/0/0 | 0 | 0/0 | 0/0 | 0/0 | 0/0 | 0 | 1 | 0 | 3 (2/1) |
a
+, wild type; −, agr defective.
b
Uncategorized SNV in the gene in one strain but not in the gene in the other.
c
Variable region with a different sequence at the same position.
d
Variant counts in the total, core, and accessory genomes.
e
Ancestry of mutations was determined by PAML analysis. I, infecting strain (blood or infection focus); C, colonizing strain (nares); U, undetermined ancestry (i.e., associated with variably present repeat and/or mobile elements).