TABLE 2.
Structural variants and plasmid losses in infecting compared to colonizing strains in each patient
| Patient | Strain type | agr statusa | Type of event | Fragment length (bp) | No. of genes | Event description |
|---|---|---|---|---|---|---|
| Cases | ||||||
| 53 | Blood | − | Insertion | 4,156 | 7 | Insertion of 4 paralogs of essI and 4 genes encoding hypothetical proteins in the ess locus |
| Repeat expansion | 120 | 1 | Expansion in gene sdrD | |||
| Repeat contraction | 90 | 1 | Contraction in gene sdrE | |||
| Deletion | 21 | 0 | Deletion in intergenic region | |||
| Repeat contraction | 69 | 0 | 350 bp upstream of setC | |||
| Repeat expansion | 57 | 0 | Intergenic region | |||
| Repeat contraction | 56 | 0 | Intergenic region | |||
| Deletion | 1,674 | 0 | Deletion of 4 genes encoding hypothetical proteins and a partial deletion of 1 gene encoding a hypothetical protein | |||
| Repeat expansion | 59 | 0 | Intergenic region | |||
| Deletion | 43,046 | 66 | Deletion of a φSa3 prophage containing scn, sak, lytN, dnaC, xerC, and 61 genes encoding hypothetical proteins; excision restores hlb | |||
| Repeat contraction | 100 | 0 | Intergenic region | |||
| Repeat expansion | 6 | 1 | Expansion in swrC | |||
| Insertion | 1,152 | 0 | Intergenic region | |||
| Repeat expansion | 128 | 1 | Expansion in clfB | |||
| Plasmid loss | 23,160 | 24 | Loss of plasmid containing racA, entD, entA, entG, acuI, ohrR, bin3, cadC, and 16 genes encoding hypothetical proteins | |||
| 60 | Blood | − | None | |||
| 73 | Blood | − | Repeat expansion | 90 | 1 | Expansion in gene bbp |
| Repeat contraction | 23 | 1 | Expansion in a gene encoding a hypothetical protein | |||
| Insertion | 1,074 | 1 | Insertion of a gene encoding a hypothetical protein | |||
| Insertion | 60 | 0 | Insertion in the intergenic region | |||
| 117 | Focus | + | None | |||
| 117 | Blood | − | Deletion | 27 | 1 | In gene pepF |
| Deletion | 30 | 1 | In a gene encoding a hypothetical protein | |||
| 135 | Focus | − | Insertion | 462 | 1 | Insertion alters a gene encoding a hypothetical protein |
| Deletion | 462 | 1 | Deletion of a gene encoding a hypothetical protein | |||
| Deletion | 43,757 | 69 | Prophage deletion; contains atl, dnaC, hin, lytN, pezA, and ssb | |||
| Insertion | 20 | 0 | Insertion of 20 bp in the intergenic region | |||
| Deletion | 125 | 1 | Deletion alters a gene encoding a hypothetical protein | |||
| Repeat contraction | 22 | 1 | In a gene encoding a hypothetical protein | |||
| Insertion | 1,332 | 2 | Insertion in dpiB; contains a gene encoding a hypothetical protein | |||
| Insertion | 1,332 | 24 | Insertion of a gene encoding a hypothetical protein into plasmid pPS00077.1A.1 | |||
| 135 | Blood | − | Insertion | 462 | 1 | Insertion alters a gene encoding a hypothetical protein |
| Deletion | 462 | 1 | Deletion of a gene encoding a hypothetical protein | |||
| Deletion | 43,757 | 69 | Prophage deletion; contains atl, dnaC, hin, lytN, pezA, and ssb | |||
| Insertion | 20 | 0 | Insertion of 20 bp in the intergenic region | |||
| Deletion | 125 | 1 | Deletion alters a gene encoding a hypothetical protein | |||
| Repeat contraction | 22 | 1 | In a gene encoding a hypothetical protein | |||
| Insertion | 1,332 | 2 | Insertion in dpiB contains a gene encoding a hypothetical protein | |||
| Plasmid loss | 26,241 | 23 | Loss of a plasmid containing nhaX, dauA, hin, bin, tnsB, blaI, blaR1, blaZ, repB, qacC, norG, and 10 genes encoding hypothetical proteins | |||
| Controls | ||||||
| 35 | Blood | + | Repeat expansion | 56 | 0 | 238 bp upstream of the hslO gene |
| Plasmid loss | 39,353 | 41 | Loss of a plasmid containing etb, hin, yxlF, ccr, lagD, ltnA2, cadC, and 35 genes encoding hypothetical proteins | |||
| 36 | Blood | + | Repeat expansion | 1,548 | 3 | Alters a gene encoding a hypothetical protein |
| 45 | Blood | + | None | |||
| 63 | Blood | + | None | |||
| 108 | Blood | None | ||||
| 152 | Focus | + | Insertion | 1,332 | 2 | Deletion of gene encoding hypothetical protein alters another gene encoding a hypothetical protein |
| Deletion | 1,332 | 1 | Insertion alters a gene encoding a hypothetical protein | |||
| Variable region | 578/1,330 | Deletion of a gene encoding a hypothetical protein; the inserted sequence alters another gene encoding a hypothetical protein | ||||
| Deletion | 581 | Partial deletion of the mpr gene | ||||
| 152 | Blood | + | Insertion | 1,332 | 1 | Contains a gene encoding a hypothetical protein |
| Deletion | 1,332 | 2 | Deletion of a gene encoding a hypothetical protein; alters another gene encoding a hypothetical protein | |||
| 158 | Blood | + | Inversion | 6,939 | 1 | Contains aphA, aadK, ycgJ, and 6 genes encoding hypothetical proteins |
a
+, functional; −, nonfunctional.