Table 2. Associations between full-length and putatively full-length prophages and pneumococcal genetic lineages.
| Prophage frequency (years of isolation)a |
||||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Clonal complex | IPP32 (1977–1988) | MM1 (1984–2002) | IPPX302 (1978–1985) | SPN195_1 (1993–2008) | IPPX3 (1978–1984) | IPPX4 (1978–1987) | 3059_06_phage (1978–1985) | IPPX300 (1999–2003) | IPP57 (1992–2005) | IPP12 (1948–2002) | IPP29 (1978–2002) | IPPX328 (1978) | IPP34 (1939–1999) | IPP62 (1999–2006) | IPP67 (1957–1962) | SPN_1873 (1999–2000) | IPPX215 (1999–2006) | IPP8 (1989–2000) | IPPX100 (1965–1966) | Total |
| 1094 | 7 | 6 | 6 | 5 | 24 | |||||||||||||||
| 41/1605 | 14 | 3 | 17 | |||||||||||||||||
| 81 | 11 | 11 | ||||||||||||||||||
| 156/162 | 7 | 7 | ||||||||||||||||||
| 199 | 5 | 1 | 6 | |||||||||||||||||
| 124 | 1 | 4 | 5 | |||||||||||||||||
| 180 | 5 | 5 | ||||||||||||||||||
| 2090 | 3 | 1 | 4 | |||||||||||||||||
| 3122/5977 | 3 | 3 | ||||||||||||||||||
| 113 | 3 | 3 | ||||||||||||||||||
| 15 | 3 | 3 | ||||||||||||||||||
| 439 | 2 | 2 | ||||||||||||||||||
| Singleton | 1 | 1 | 2 | |||||||||||||||||
| 66 | 2 | 2 | ||||||||||||||||||
| 217 | 2 | 2 | ||||||||||||||||||
| 615 | 2 | 2 | ||||||||||||||||||
| 236/271/320 | 1 | 1 | ||||||||||||||||||
| 7232 | 1 | 1 | ||||||||||||||||||
| 68/1656 | 1 | 1 | ||||||||||||||||||
| Total | 16 | 11 | 7 | 7 | 6 | 6 | 6 | 5 | 5 | 4 | 4 | 3 | 3 | 3 | 3 | 3 | 3 | 3 | 3 | 101 |
aOnly the full-length and putatively full-length prophages present ≥3 times in the study dataset were included here. The years of isolation refer to when the host pneumococci were isolated.