Table 1.
Epidemiological characteristics of 44 satellite prophages identified among pneumococci
| Prophage | Cluster | Isolation | Genomes (n) | CC (n) | Country (n) | Serotype (n) | Site | Int |
|---|---|---|---|---|---|---|---|---|
| SpnSP16 | A | 1939–1982 | 4 | 3 | 2 | 4 | b | I |
| SpnSP3 | A | 1981–2004 | 3 | 2 | 2 | 2 | b | I |
| SpnSP26 | A | 1985–2000 | 3 | 2 | 1 | 2 | b | I |
| SpnSP35 | A | 1952–1952 | 2 | 2 | 1 | 2 | b | I |
| SpnSP43 | A | 1939–2004 | 2 | 2 | 2 | 2 | b | I |
| SpnSP30 | A | 1978–1978 | 5 | 1 | 1 | 1 | b | I |
| SpnSP44 | A | 1939–1962 | 2 | 1 | 1 | 1 | b | I |
| SpnSP7 | A | 1968 | 1 | 1 | 1 | 1 | b | I |
| SpnSP25 | A | 1999 | 1 | 1 | 1 | 1 | b | I |
| SpnSP19 | A | 1939–1952 | 2 | S | 2 | 2 | b | V |
| SpnSP11 | A | 1952 | 1 | S | 1 | 1 | b | I |
| SpnSP5 | B | 1939–2007 | 15 | 5 | 3 | 7 | d, g | I |
| SpnSP29 | B | 1978–1988 | 15 | 1 | 1 | 2 | b | I |
| SpnSP27 | B | 2006 | 1 | 1 | 1 | 1 | b | I |
| SpnSP20 | B | 1954 | 1 | S | 1 | 1 | b | I |
| SpnSP2 | C | 1984–2005 | 4 | 2 | 3 | 2 | f | VII |
| SpnSP31 | C | 1983–2005 | 2 | 2 | 1 | 2 | b | I |
| SpnSP12 | C | 1968 | 1 | 1 | 1 | 1 | b | I |
| SpnSP15 | C | 1943 | 1 | 1 | 1 | 1 | b | I |
| SpnSP32 | C | 1986 | 1 | 1 | 1 | 1 | f | VII |
| SpnSP37 | D | 1939–1988 | 9 | 5 | 4 | 7 | c | II |
| SpnSP38 | D | 1972–2006 | 30 | 4 | 6 | 5 | c | II |
| SpnSP6 | D | 1939–1991 | 8 | 3 | 3 | 3 | c | II |
| SpnSP23 | D | 1962–2008 | 11 | 2 | 3 | 4 | a | III |
| SpnSP39 | D | 2005–2007 | 2 | 1 | 1 | 1 | a | III |
| SpnSP18 | D | 1939–1952 | 2 | S | 2 | 2 | c | II |
| SpnSP24 | E | 1939–2006 | 23 | 6 | 6 | 4 | a | III |
| SpnSP33 | E | 1952–1998 | 3 | 2 | 1 | 2 | a | III |
| SpnSP1 | E | 1978–1988 | 5 | 1 | 1 | 1 | b | I |
| SpnSP40 | E | 2001 | 3 | 1 | 2 | 2 | a | III |
| SpnSP8 | E | 1988 | 1 | 1 | 1 | 1 | a | III |
| SpnSP9 | E | 1957 | 1 | 1 | 1 | 1 | a | III |
| SpnSP13 | E | 1943 | 1 | 1 | 1 | 1 | a | III |
| SpnSP14 | E | 1995 | 1 | 1 | 1 | 1 | a | III |
| SpnSP17 | E | 1972 | 1 | 1 | 1 | 1 | a | IV |
| SpnSP22 | E | 1971 | 1 | 1 | 1 | 1 | a | III |
| SpnSP28 | E | 2003 | 1 | 1 | 1 | 1 | a | III |
| SpnSP34 | E | 1990 | 1 | 1 | 1 | 1 | a | III |
| SpnSP36 | E | 1963 | 1 | 1 | 1 | 1 | a | III |
| SpnSP42 | E | 1994 | 1 | 1 | 1 | 1 | a | III |
| SpnSP4 | E | 1982 | 1 | S | 1 | 1 | e | I |
| SpnSP10 | E | N/A | 1 | S | 1 | 1 | h | I |
| SpnSP21 | E | 1954 | 1 | S | 1 | 1 | e | VI |
| SpnSP41 | E | 1983 | 1 | S | 1 | 1 | a | III |
Note: Prophage = name of each satellite prophage; Cluster = satellite prophage cluster (see Fig. 3); Isolation = isolation date(s) of the pneumococci that harboured the satellite prophage; Genomes = number of pneumococcal genomes in which the satellite prophage was identified; CC = clonal complex (genetic lineage) of the host pneumococcus; Country = the number of countries in which the pneumococci were recovered; Serotype = number of different serotypes of the host pneumococci; Site = prophage insertion site within the pneumococcal genome (see Fig. 4); Int = integrase sequence of the satellite prophage; S = singleton, a genotype with no closely related variants