Table 3.
Genetic clusters including Clostridioides difficile isolates from Portugal.
| Cluster ID | Cluster length (n°of isolates) | Samples |
Ribo
type |
Country | Source | Collection date | Moxifloxacin resistance |
|---|---|---|---|---|---|---|---|
| CL01 | 15 | PT_CD00043, PT_CD00057, ERR3276441, ERR3276506, ERR3278163, ERR3278167, ERR3288184, ERR3288190, ERR3288338, ERR3289201, ERR3289202, ERR3289206, ERR3289207, ERR3289212, ERR3299518 | 106 | Spain (86.7%), Portugal (13.3%) | Human (93.3%), Canine (6.7%) | 2015 (46.7%), 2014 (33.3%), 2021 (13.3%), 2016 (6.7%) | No data (86.7%), R (13.3%) |
| CL02 | 2 | PT_CD00053, PT_CD00055 | 106 | Portugal (100.0%) | Feline (50.0%), Canine (50.0%) | 2021 (100.0%) | S (100.0%) |
| CL03 | 6 | PT_CD00064, PT_CD00030, PT_CD00031, PT_CD00048, PT_CD00049, PT_CD00044 | 106 | Portugal (100.0%) | Canine (50.0%), Feline (33.3%), Human (16.7%) | 2021 (66.7%), 2020 (33.3%) | S (83.3%), R (16.7%) |
| CL04 | 6 | PT_CD00059, PT_CD00060, PT_CD00062, PT_CD00066, PT_CD00046, ERR3288329 | 106 | Portugal (83.3%), Spain (16.7%) | Human (83.3%), Canine (16.7%) | 2021 (83.3%), 2014 (16.7%) | S (66.7%), R (16.7%), No data (16.7%) |
| CL05 | 2 | PT_CD00027, PT_CD00028 | 106 | Portugal (100.0%) | Feline (100.0%) | 2020 (100.0%) | S (100.0%) |
| CL06 | 2 | PT_CD00036, PT_CD00029 | 106 | Portugal (100.0%) | Canine (100.0%) | 2021 (50.0%), 2020 (50.0%) | S (100.0%) |
| CL07 | 4 | PT_CD00050, PT_CD00051, PT_CD00052, PT_CD00054 | 106 | Portugal (100.0%) | Canine (100.0%) | 2021 (100.0%) | R (100.0%) |
| CL08 | 2 | PT_CD00094, PT_CD00095 | 014/020 | Portugal (100.0%) | Feline (50.0%), Canine (50.0%) | 2021 (100.0%) | S (100.0%) |
| CL09 | 2 | PT_CD00086, PT_CD00098 | 014/020 | Portugal (100.0%) | Canine (50.0%), Human (50.0%) | 2021 (100.0%) | R (50.0%), S (50.0%) |
| CL10 | 3 | PT_CD00075, PT_CD00077, PT_CD00085 | 014/020 | Portugal (100.0%) | Human (100.0%) | 2021 (100.0%) | S (100.0%) |
| CL11 | 2 | PT_CD00099, PT_CD00100 | 014/020 | Portugal (100.0%) | Human (100.0%) | 2021 (100.0%) | S (100.0%) |
| CL12 | 6 | PT_CD00089, PT_CD00091, PT_CD00093, ERR1307028, SRR7308801, SRR7309218 | 014/020 | Portugal (50.0%), Australia (16.7%), Ireland (16.7%), Italy (16.7%) | Canine (50.0%), Human (50.0%) | 2021 (50.0%), 2013 (33.3%), 2012 (16.7%) | No data (50.0%), S (33.3%), R (16.7%) |
| CL13 | 2 | PT_CD00108, PT_CD00107 | 014/020 | Portugal (100.0%) | Feline (50.0%), Canine (50.0%) | 2021 (100.0%) | S (100.0%) |
| CL14 | 2 | PT_CD00088, ERR3465438 | 014/020 | Portugal (50.0%), Germany (50.0%) | Canine (50.0%), Human (50.0%) | 2021 (50.0%), 2014 (50.0%) | S (50.0%), No data (50.0%) |
| CL15 | 3 | PT_CD00071, PT_CD00073, PT_CD00074 | 014/020 | Portugal (100.0%) | Human (100.0%) | 2021 (100.0%) | S (100.0%) |
R, Resistant; S, Susceptible. Genetic clusters were defined at a threshold of ≤ 2 SNPs, as previously proposed (29).
All isolates from Portugal were collected in 2021, except samples from two felines from CL03 that were collected in 2020.