Table 3.
Characteristics of clusters identified with cgMLST using a cut-off of ≤5 alleles, including their relatedness to international MSM-associated reference genomes
|
ID |
#isolates |
Species |
Serotype SF/ |
Male/female |
MSM* |
Travel history |
Related to international |
|---|---|---|---|---|---|---|---|
|
genotype SS |
yes/no |
MSM references/subclades |
|||||
|
1 |
15† |
1b |
12/0† |
10-Feb |
None |
No |
|
|
2 |
5‡ |
3.6.2 |
2/2‡ |
01-Jan |
1 x Morocco, |
No |
|
|
1 x Greece | |||||||
|
3 |
4 |
3.6.1.1 |
4/0 |
4/0 |
None |
No |
|
|
4 |
4 |
2a |
02-Feb |
0/2 |
4 x The Ghana |
No |
|
|
5 |
3 |
2a |
3/0 |
3/0 |
None |
UK_Major MSMclade (10 AD); Australia_flexneri_BAPS2 (15 AD) |
|
|
6 |
3‡ |
3.6.1.1.2 |
2/0‡ |
0/1‡ |
1 x Spain |
BEL_I (8 AD) |
|
|
7 |
3 |
3a |
3/0 |
3/0 |
None |
UK_MSM sublineageA (13 AD); Australia_flexneri_BAPS3 (18 AD) |
|
|
8 |
2 |
3a |
2/0 |
2/0 |
1 x Spain |
Spain_flexneri_clade5 (1 AD) |
|
|
9 |
2 |
3.6.2 |
01-Jan |
0/1 |
1 x Morocco |
No |
|
|
10 |
2 |
3a |
2/0 |
2/0 |
1 x Spain |
UK_MSM sublineageA (15 AD); Australia_flexneri_BAPS3 (20 AD) |
|
|
11 |
2 |
3.7.18 |
2/0 |
01-Jan |
1 x Peru |
No |
|
|
12 |
2 |
3.6.1.1.2 |
2/0 |
2/0 |
None |
BEL_I (11 AD) |
|
|
13 |
2 |
3.6.4 |
01-Jan |
0/1 |
2 x Sri Lanka |
No |
|
|
14 |
2‡ |
3.7.29.1.4.1 |
1/0c |
1/0 |
None |
BEL_II (4 AD); Spain_sonnei_clade1 (5 AD) |
*Among male cases.
†No data about sex, MSM, travel available for three cases
‡No data about sex, MSM, travel available for one case.
SF, Shigella flexneri ; SS, Shigella sonnei .