Table 2.
Prophage carriage in the study strains.
| Localization (Gene Name) | Localization (cg MLST) | Strain ED133, CP001996 | Strain X22, CP042650 | Swan Isolate 15V8707 | Duck Isolate V315 | Duck Isolate V482 | Goat Isolate 17CS1042 | Comments |
|---|---|---|---|---|---|---|---|---|
| Between lip2 and A5IPQ2 | SAUR0317 (SAR_RS01585), SAUR0318 (SAR_RS01590) | Positive (ca. 47,400 nt) |
Positive (ca. 41,500 nt) |
Negative | Negative | Negative | Negative | - |
| Between sufB and MW0800 | SAUR0895 (SAR_RS04475), SAUR0896 (SAR_RS04480): | Negative | Positive (ca. 46,600 nt) |
Negative | Negative | Negative | Negative | - |
| Between rpmF and isdB | SAUR1124 (SAR_RS05620), SAUR1125 (SAR_RS05625) | Positive (ca. 40,500 nt) |
Negative | Negative | Negative | Negative | Positive (ca. 43,700 nt) |
In ED133, the phage in this position carried a variant of the Enterotoxin A gene, sea-320E (GenBank: AY196686.1). |
| Between Q7A4X2 = DUF1828 and ydeN | N/A, and SAUR1973 (SAR_RS09865) | Incomplete (ca. 1600 nt) |
Incomplete (ca. 1600 nt) |
Positive (ca. 45,700 nt) |
Incomplete (ca. 1600 nt) |
Positive (ca. 42,800 nt) |
Incomplete (ca. 1600 nt) |
“Incomplete” means that there were only genes for Q99T51, a “putative DUF2871 domain-containing protein” and a phage integrase. |
| Between Q5HEP8 and A5IU43 = yfkAB | SAUR2053 (SAR_RS10265), SAUR2054 (SAR_RS10270) | Positive (ca. 44,700 nt) |
Negative | Negative | Negative | Negative | Positive (ca. 40,600 nt) |
The prophage in ED133 carried leukocidin genes lukM/lukF-P83, while the one in 17CS1042 harbored a variant thereof. |
| Within hlb | SAUR2190 (SAR_RS10950) | Negative | Positive (ca. 52,100 nt) |
Positive * (ca. 62,800 nt) |
Positive ** (ca. 45,700 nt) |
Negative | Negative | Prophages in this position carried “bird-specific” virulence factors D0K6J8 and D0K6J9. |
* The Austrian duck isolate 511525-22 was also positive, with the same prophage as in 15V8707 (see Supplemental Files S4a–c). ** IMT40427 was also positive, with the same prophage as in V315 (see Supplemental Files S4a–c), but 511509-22 and 511510-22 were negative.