Table 3.
Genetic clusters identified among pathogenic E. coli through cgMLST analyses.
| Global cgMLST Analysis (n = 2567 loci) a | ST-Specific cgMLST Analysis b | |||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| Cluster | Cluster Length | Isolates | Animal Species | Timespan (Days) | Pathotype | MLST_ST | Serotype | Antibiotic Resistance Phenotype | Extended Schema Size | Cluster Confirmation |
| cluster_5 | 7 | Ec-TM1,Ec-TM28,Ec-TM29-4,Ec-TM31,Ec-TM56,Ec-TM87,Ec-TM92 | fallow deer (100.0%) | 120 | STEC | 13 | O75:H8 (71.4%), OND:H8 (28.6%) | Susceptible (100.0%) | 3321 | Yes. Cluster isolates connected by ≤ 9 ADs (0.27%) |
| cluster_7 | 2 | Ec-TM15,Ec-TM74 | fallow deer (100.0%) | 112 | STEC | 13 | O75:H8 (100.0%) | Susceptible (100.0%) | 3321 | Yes. Cluster isolates differ by 11 ADs (0.33%) |
| cluster_9 | 2 | Ec-TM26,Ec-TM69 | fallow deer (50.0%), wild boar (50.0%) | 112 | EPEC | 137 | O145:HND (50.0%), OND:HND (50.0%) | AMP, CHL, SMX (50.0%), Susceptible (50.0%) | 3333 | Yes. Cluster isolates differ by 5 ADs (0.15%) |
| cluster_3 | 2 | Ec-TM30-2,Ec-TM101 | fallow deer (100.0%) | 106 | EPEC | 300 | O156:H25 (100.0%) | Susceptible (100.0%) | 3387 | Yes. Cluster isolates differ by 5 ADs (0.15%) |
| cluster_6 | 6 | Ec-TM2,Ec-TM3,Ec-TM23,Ec-TM73,Ec-TM82,Ec-TM95 | fallow deer (83.3%), wild boar (16.7%) | 120 | STEC | 442 c | O146:H21 (100.0%) | Susceptible (100.0%) | 3248 | Yes, consolidating the potential link with cluster_4 (12 ADs/0.37%). Ec-TM95 slightly split apart (15 ADs/0.46%) |
| cluster_4 | 4 | Ec-TM27,Ec-TM84,Ec-TM97,Ec-TM99 | fallow deer (75.0%), wild boar (25.0%) | 106 | STEC | 442 c | O146:H21 (100.0%) | Susceptible (100.0%) | 3248 | Yes, consolidating the potential link with cluster_6 (12 ADs/0.37%). Ec-TM99 slightly split apart (12 ADs/0.37%) |
| cluster_1 | 3 | Ec-TM14,Ec-TM55,Ec-TM64 | fallow deer (66.7%), red deer (33.3%) | 105 | EPEC | 655 | O121:HND (100.0%) | Susceptible (100.0%) | 3349 | Yes. Cluster isolates connected by 5 ADs (0.15%) |
| cluster_2 | 2 | Ec-TM25,Ec-TM30-1 | red deer (50.0%), fallow deer (50.0%) | 7 | STEC | 738 | O146:H28 (50.0%), OND:H28 (50.0%) | Susceptible (100.0%) | 3334 | Yes. Cluster isolates differ by 7 ADs (0.21%) |
| cluster_8 | 2 | Ec-TM81,Ec-TM96 | fallow deer (50.0%), wild boar (50.0%) | 1 | STEC | 753 | O27:H30 (100.0%) | Susceptible (100.0%) | 3208 | Yes. Cluster isolates differ by 8 ADs (0.25%). |
a cgMLST analysis based on the core-genome of the 52 isolates (i.e., a sub-schema of the original 7601-loci wgMLST schema comprising loci called in all samples); b Dynamic cgMLST analysis based on ST-specific core-genome schema (i.e., a sub-schema comprising the loci called in all the isolates of the same ST); c Given the genetic proximity of the isolates previously identified as ST442-like and ST11692-like (Figure 1), the ST11692-like isolate was included in the analysis of the ST442.