TABLE 4.
Epidemiologically relevant phylogenetic clades from the retail deli study
| Phylogeographic clade classificationa | Clade ID | PFGE type or SNP group subtype represented within cladeb | 95% HPD for date of clade divergence from MRCA (yr)c | Deli ID of isolates putatively: |
Median SNP count differences among isolates of the same PFGE type or SNP group: |
|||
|---|---|---|---|---|---|---|---|---|
| Persistent | Sporadic | Within a putative persistence event (no. of isolates within deli) | Among isolates from a given deli and all other delis (no. of isolates in other delis) | FDR-corrected P value for significantly fewer median SNP differencesf | ||||
| Deli specific | M | CU-11-282 | 1.3–4.3 | 13 | NAd | 3 (4) | NA | NA |
| J | CU-262-334 | 0.8–2.6 | 23 | NA | 2 (2) | NA | NA | |
| C | CU-55-266 | 1.2–4.3 | 2 | NA | 3 (4) | NA | NA | |
| O | CU-8-340 | 1.8–7.0 | 8 | NA | 10.5 (5) | NA | NA | |
| E | CU-258-69 | 1.2–8.4 | 23 | NA | 13 (2) | 77 (16) | 0.025 | |
| G | CU-262-318 | 1.0–3.5 | 21 | NA | 2 (3) | 102 (1) | 0.357 | |
| U | SNP group 1 (CU-11-320 and CU-8-96) | 2.2–7.0 | 2 | NA | 9 (11) | 24 (53) | 0.023 | |
| K | SNP group 3 (CU-262-79) | 1.4–3.7 | 2 | NA | 2 (10) | 10 (18) | <0.001 | |
| H | SNP group 3 (CU-262-79) | 0.9–3.8 | 29 | NA | 4 (2) | 25 (22) | 0.008 | |
| X | CU-296-330 | NEe | 23 | NA | 4 (2) | NA | NA | |
| Y | CU-182-173 | NE | 19 | NA | 1 (2) | NA | NA | |
| State specific | N | CU-11-326 | 1.3–3.1 | 8 | 11 | 2 (2) | 1 (1) | 1.000 |
| B | CU-57-267 | 1.6–5.6 | 10 | 7, 28 | 3 (3) | 5 (9) | 0.159 | |
| 16 | 0 (2) | 3.5 (10) | 0.071 | |||||
| 23 | 3 (2) | 4 (10) | 0.433 | |||||
| 4 | 5 (3) | 5 (9) | 0.784 | |||||
| P | SNP group 1 (CU-11-320) | 1.5–7.7 | 13 | 29 | 12 (2) | 41 (62) | 0.082 | |
| R | SNP group 1 (CU-8-96) | 2.6–10.8 | 16 | 7 | 22 (6) | 51 (58) | <0.001 | |
| S | SNP group 1 (CU-11-320 and CU-8-96) | 1.5–5.1 | 24 | 16 | 4 (10) | 18 (54) | 0.007 | |
| D | SNP group 2 (CU-258-323, CU-258-322, and CU-259-322) | 1.9–6.6 | 23 | 10, 21 | 7 (18) | 9 (2) | 0.159 | |
| I | SNP group 3 (CU-262-79 and CU-262-319) | 1.6–4.4 | 23 | 21, 24 | 10 (2) | 8.5 (22) | 0.784 | |
| 28 | 4 (12) | 9 (12) | <0.001 | |||||
| Multistate | F | CU-258-69 | 2.2–7.8 | 24 | 4, 10, 22, 27, 28 | 10 (2) | 8 (16) | 0.808 |
| 7 | 5 (9) | 8 (9) | 0.025 | |||||
| A | CU-294-321 | 1.4–4.3 | 10 | 2, 4, 7, 12 | 2 (3) | 2 (8) | 0.808 | |
| 16 | 2 (2) | 2 (9) | 0.808 | |||||
| 21 | 3 (2) | 3 (9) | 0.959 | |||||
| T | SNP group 1 (CU-11-320 and CU-8-96) | 2.0–6.8 | 10 | 25 | 6 (10) | 20 (54) | 0.004 | |
| V | SNP group 1 (CU-40-96) | 1.8–7.0 | 18 | 2, 3, 8, 11, 26 | 6 (3) | 46 (61) | 0.008 | |
| 29 | 3 (3) | 43 (59) | <0.001 | |||||
| Q | SNP group 1 (CU-11-320) | 1.4–5.7 | 21 | 12, 17 | 4 (6) | 22 (58) | 0.004 | |
Deli-specific clade, all isolates in a clade were isolated from a single deli; state-specific clade, all isolates in a given clade were isolated from the same states; multistate clade, all isolates in a given clade were isolated from multiple delis across multiple states.
A SNP group subtype is comprised of two or three individual PFGE types (indicated in parentheses where applicable), See the text for details.
HPD, highest posterior density; MCRA, most recent common ancestor.
NA, not applicable. A deli-specific clade cannot contain any isolates from other delis.
NE, not estimated (due to insufficient lineage II isolates for tip-dated phylogenetics).
Significantly different values are indicated in boldface.