Table 2.
Properties of ICE elements in strains with complete genome sequences
| Strain | ICE type | Integration site (P12) | Pos. LJ | Pos. RJ | Size (kb) 14 | Complete T4SS? |
|---|---|---|---|---|---|---|
|
52 |
none |
|
|
|
|
|
|
B38 |
none2 |
|
|
|
|
|
|
F16 |
none |
|
|
|
|
|
|
HPAG1 |
none |
|
|
|
|
|
|
Sat464 |
none |
|
|
|
|
|
|
v225d |
none |
|
|
|
|
|
|
26695 |
ICEHptfs33 |
hpp12_981 |
1049829 |
473989 |
(16.0) |
N |
|
26695 |
ICEHptfs4a/4b3 |
hpp12_13285 |
1071598 |
464996 |
(18.3) |
N |
|
35A |
ICEHptfs4a |
hpp12_92-91 |
359215 |
309788 |
(10.0)15 |
N |
|
51 |
ICEHptfs3/4a3 |
hpp12_999 |
none |
1034232 |
(32.2) |
N |
|
83 |
ICEHptfs3 |
hpp12_65 |
7908512 |
106931 |
(27.8) |
N |
|
83 |
ICEHptfs4b |
hpp12_1495 |
1522267 |
150317212 |
(19.1) |
N |
|
908, 2017, 2018
1
|
ICEHptfs4a/b4 |
hpp12_995-9796 |
99180112 |
none |
(14.6) |
N |
|
B8 |
ICEHptfs3 |
hpp12_439-438 |
487322 |
526844 |
39.516 |
Y |
|
B8 |
ICEHptfs4a |
hpp12_1380-5S-rRNA5,7 |
52870812 |
452245 |
(37.0) |
N |
|
Cuz20 |
ICEHptfs4b |
hpp12_210-211 |
266516 |
227821 |
38.5 |
Y |
|
ELS37 |
ICEHptfs3 |
hpp12_511-5128 |
884907 |
838572 |
46.3 |
Y |
|
ELS37 |
ICEHptfs4b |
hpp12_511-5128 |
838326 |
none |
(2.0) |
N |
|
F30 |
ICEHptfs4a |
hpp12_92-91 |
1239533 |
1287710 |
(10.0)15 |
N |
|
F32 |
ICEHptfs3 |
hpp12_312-313 |
328469 |
1058181 |
(4.1 + 25.5)17 |
N |
|
F57 |
ICEHptfs4a |
hpp12_92-91 |
152065 |
103732 |
(10.0)15 |
N |
|
F57 |
ICEHptfs4b |
hpp12_259 |
323634 |
284294 |
39.3 |
Y |
|
G27 |
ICEHptfs4b |
hpp12_1009-1010 |
1085072 |
1045702 |
39.4 |
Y |
|
Gambia 94/24 |
ICEHptfs3 |
hpp12_15085 |
1473904 |
1521243 |
47.3 |
Y |
|
Gambia 94/24 |
ICEHptfs4a/b4 |
hpp12_994-5S-rRNA |
106932212 |
none |
(35.2) |
N |
|
HUP-B14 |
ICEHptfs3 |
hpp12_1365 |
135565613 |
135565613 |
(10.8) |
N |
|
India 7 |
ICEHptfs3 |
hpp12_599 |
752074 |
798006 |
45.9 |
Y |
|
India 7 |
ICEHptfs4a |
hpp12_1391-152810 |
none |
none |
(7.3) |
N |
|
J99 |
ICEHptfs33 |
hpp12_444-445 |
104487813 |
104487813 |
(16.7) |
N |
|
J99 |
ICEHptfs4a/b4 |
hpp12_994-5S-rRNA |
none |
none |
(25.3) |
N |
|
Lithuania 75 |
ICEHptfs3 |
hpp12_1508 |
1516637 |
none |
(34.8) |
N |
|
Lithuania 75 |
ICEHptfs4c |
n.a. (plasmid integration) |
352813 |
352813 |
(10.1) |
N |
|
P12 |
ICEHptfs3 |
hp1354 |
1424780 |
1394778 |
(30.0) |
N |
|
P12 |
ICEHptfs4a |
hp0464 |
452023 |
492769 |
40.7 |
Y |
|
PeCan4 |
ICEHptfs3 |
hpp12_1528-15235 |
1530039 |
1536824 |
(6.8) |
N |
|
PeCan4 |
ICEHptfs4a |
hpp12_1528-15235, 11 |
1578142 |
1537082 |
41.1 |
Y |
|
PeCan18 |
ICEHptfs3 |
hpp12_440-439 |
1015120 |
1064481 |
49.416 |
Y |
|
PeCan18 |
ICEHptfs4a |
hpp12_994-5S-rRNA |
1067535 |
none |
(3.1) |
N |
|
Puno120 |
ICEHptfs3 |
hpp12_994-5S-rRNA |
1004976 |
none |
(6.8 + 26.6)18 |
N |
|
Puno135 |
ICEHptfs3/4b3 |
hpp12_994-5S-rRNA |
1014870 |
1059997 |
(45.1) |
Y |
|
Shi112 |
ICEHptfs3 |
hpp12_226-225 |
281418 |
232869 |
48.616 |
Y |
|
Shi112 |
ICEHptfs4b |
hpp12_1380-5S-rRNA |
1412827 |
1451480 |
38.7 |
Y |
|
Shi169 |
ICEHptfs4b |
hpp12_211-210 |
240310 |
201136 |
39.2 |
Y |
|
Shi417 |
ICEHptfs3 |
hpp12_1510 |
1546576 |
1591512 |
(44.9) |
Y |
|
Shi417 |
ICEHptfs4b |
hpp12_1126-1125 |
1186887 |
1147709 |
39.2 |
Y |
|
Shi470 |
ICEHptfs4b |
hpp12_495 |
874710 |
913872 |
39.2 |
Y |
|
SJM180 |
ICEHptfs3 |
hpp12_454-453 |
1413941 |
none |
(23.2) |
N |
|
SJM180 |
ICEHptfs4a |
hpp12_1364-13659 |
1371932 |
141618012 |
(24.1) |
N |
|
SNT49 |
ICEHptfs4b |
hpp12_65 |
61216 |
100646 |
39.4 |
Y |
|
South Africa 7 |
ICEHptfs4c |
hpp12_1366 |
1568674 |
1527381 |
41.316 |
Y |
|
South Africa 7 |
ICEHptfs4b |
hpp12_943-944 |
934499 |
973788 |
39.3 |
Y |
|
XZ274 |
ICEHptfs4a |
hpp12_92-91 |
162178 |
111739 |
(10.0)15 |
N |
| XZ274 | ICEHptfs4b | hpp12_776 | 653446 | 612019 | (41.4)16 | Y |
1Strains 908, 2017 and 2018 are sequential isolates from a single patient [17] and do not show major differences in their ICEHptfs4 sequences. However, note that GenBank entries EF195724.1, EF195725.1 and EF195726.1 describe ICEHptfs3 clusters in these strains [17] that are not present in the genome sequences.
2HELPY0971 is possibly a vestige of hpp12_1321/pz7.
3resulting from insertions of 2-3 genomic islands and subsequent rearrangements.
4containing ICEHPtfs4a-type genes close to the left junction, and ICEHptfs4b-type genes close to the right junction.
5associated with genome rearrangement in comparison to strain P12.
6associated with deletion of hpp12_980 to hpp12_995 (5’) including one copy of 5S-23S-rRNA.
7associated with a recombination between the two 5S-23S-rRNA loci (including hpp12_1381-1384).
8partial duplication of both genes; ICEHptfs3 inserted into truncated ICEHptfs4b.
9within a restriction-modification system inserted into this region.
10integrated together with a 0.9 kb fragment of ICEHptfs3 and a putative toxin-antitoxin system.
11integration of ICEHptfs4a into remnant of ICEHptfs4b, which is in turn integrated into truncated ICEHptfs3.
12irregular integration, using internal AAGAATG motif.
13left and right junctions coincide due to irregular integration.
14numbers in parentheses indicate incomplete ICE elements.
15disrupted by a chromosomal inversion from hpp12_92 to hpp12_128.
16size of ICE increased by IS element insertion.
17interrupted by a chromosomal rearrangement between hpp12_312 and hpp12_1044 (including babC deletion).
18original integration probably in hpp12_994-5S-rRNA locus; from there, relocation of 26.6 kb fragment via internal AAGAATG motifs into hpp12_1510; 1.4 kb duplication (containing xerT) in both loci.