Table 3 includes an overview of the genetic and phenotypic characteristics of the bacterial isolates obtained from recruited animals. Additionally, the toxinotypes, PCR ribotypes (only for C. difficile isolates), amplified fragment length polymorphism (AFLP) genotypes and antimicrobial susceptibility profiles of C. perfringens and C. difficile isolates are detailed in Table 4, Table 5, respectively.Table 4Characteristics of the Clostridium perfringens isolates obtained in the study.Table 4IsolateaToxinotypebAFLP genotypecAntibiotic susceptibility (MIC, µg/ml)dAMCCLIERYIPMLVXLZDMTZPENRIFTECTETTGCVANA/02P1A (cpe, cpb2*)p0630.1250.2520.0640.54160.50.0080.064811A/02P2A (cpb2*)p0640.0320.0320.0640.0640.250.12580.1250.0040.03240.1250.5A/02P3A (cpe)p0650.0320.0320.0320.0640.250.12580.0640.0020.0320.1250.0640.5B/02P1Ap0670.0320.06420.0640.254160.0640.008<0.0160.1250.0640.5B/06P1A (cpb2*)p0270.0640.06420.0640.254160.0320.004<0.01640.250.5B/06P2A (cpb2*)p0280.0320.12520.50.254160.1250.0040.03240.50.5B/06P3A (cpb2*)p028<0.0160.520.50.254160.0640.0080.03240.50.5B/07P1A (cpe)p0110.0320.12510.0320.254160.0320.004<0.01620.1250.25B/07P2A (cpe)p0120.0320.12520.0640.254160.0640.0080.03240.1250.25B/07P3A (cpe)p023<0.0160.12520.0640.252160.1250.0080.03240.1250.25B/08P1A (cpb2*)p0470.0320.06420.1250.254160.0640.004<0.01640.1250.5B/08P2A (cpb2*)p0020.0320.2520.0640.252160.0640.0080.03220.50.5B/08P3A (cpb2*)p0510.0160.12520.1250.254160.0640.0080.03240.250.5B/11P1A (cpb2*)p0350.1250.01610.0640.251160.1250.004<0.01640.1250.5B/11P2A (cpb2*)p0360.0160.2520.0640.25280.1250.0040.01640.50.5B/11P3A (cpb2*)p0360.0320.2520.0080.52160.1250.0040.03240.50.5B/12P1Ap0370.0320.0160.1250.0640.25180.0320.004<0.01610.1250.5B/13P1A (cpb2*)p0030.0640.06420.0320.5432 (R)0.0640.0080.03220.0640.5B/13P2Ap0060.0320.06420.250.54160.1250.0040.06480.1250.5B/13P3Ap0310.0640.2520.0640.254160.1250.008<0.01680.1250.5B/14P1Ap0690.0640.12520.0640.52160.250.0080.03240.250.5B/14P2Ap0720.032220.0320.25<0.01680.0640.004<0.01640.250.5D/02P1E (cpe)p0870.064<0.01610.50.25232 (R)0.0640.0020.03240.0640.5D/02P2E (cpe)p0880.0640.06440.1250.258 (R)80.1250.0040.03240.251D/02P3E (cpe)p0950.0320.03210.0640.51160.1250.0040.03220.250.5F/09P2Ap0040.1250.0640.50.250.250.580.250.0040.0320.1250.0640.5F/09P3Ap0050.0640.064210.25480.250.0080.06440.0641G/01P1Ap1050.0640.0640.0640.0640.51160.0640.004<0.01610.1250.5G2/01P1†A (cpb2*)p0920.0640.06440.1250.25480.1250.0080.06440.250.5G2/01P2†A (cpb2*)p0970.064<0.0160.0640.1250.254160.1250.0080.01640.0640.5G2/01P3†A (cpb2*)p0410.0320.12520.0640.25480.1250.0040.01680.250.5G/05P1A (cpb2*)p0300.1250.06420.0640.25432 (R)0.1250.0080.03280.1250.5G/05P2A (cpb2*)p0500.0640.2510.0640.25280.50.004<0.01640.250.5G/05P3Ap096<0.0160.12510.0320.5440.1250.004<0.01640.1250.5G/06P1Ap0260.1250.12520.0640.54160.1250.0080.03280.251H/03P1Ap10280.1252≥32 (R)0.254168 (R)0.0040.03280.1250.5H/03P2Ap07840.032210.254168 (R)0.0040.03240.1250.5H/03P3Ap1030.0320.06410.1252280.0640.0040.06480.50.5H/05P1Ap07980.1252≥32 (R)0.258 (R)168 (R)0.0040.03280.50.5H/05P2Ap0080.0320.12510.0640.25140.0640.0020.01640.1250.5H/05P3Ap034<0.0160.06420.1250.254160.0320.0080.03240.1250.5I/02P1Ap0540.0640.06420.1250.252160.1250.0040.01640.1250.5I/02P2Ap0550.032<0.01640.0640.50.25160.064<0.002<0.01640.0640.5I/04P1A (cpe)P0990.1250.0320.250.1250.251160.1250.0040.0320.1250.0320.5I/04P2Ap0820.0320.2520.0320.250.5160.125<0.002<0.01640.1250.5I2/04P1†A (cpe)p0520.0320.12520.0640.258 (R)160.1250.0080.03240.250.5J/01P1A (cpb2*)p0530.0640.12520.0640.54160.1250.0080.03280.51J/01P2A (cpb2*)p0580.0640.2532 (R)0.125≥32 (R)2160.1250.0080.03240.1250.5J/03P1Ap0180.0640.03220.0640.54160.0640.004<0.0160.1250.0640.5J/03P2A (cpb2*)p0130.1250.0320.1250.0640.254160.064<0.002210.0322J/03P3A (cpb2*)p0170.0160.0320.1250.0320.252160.0640.004<0.01620.0320.5J/07P1A (cpb2)p1010.016<0.0160.1250.0640.251160.0320.0080.0320.1250.0320.5K/02P1Ap0890.0320.12520.50.254160.1250.0040.03240.1250.5M/04P1A (cpe)p0900.0640.12520.0640.254160.1250.0080.06480.50.5M/04P2A (cpe)p0900.0320.125210.54160.0640.0040.06440.50.5M/04P3A (cpe)p0910.032<0.016<0.0160.50.254160.0640.0160.06440.1250.5M2/04P1†A (cpb2*)p0430.0320.03220.250.254160.0320.0040.01616 (R)10.5M2/04P2†A (cpb2*)p0760.0320.06420.50.25480.0640.0080.01616 (R)0.50.5M2/04P3†A (cpb2*)p0770.0320.0320.0640.0640.5280.0640.0040.01640.250.5M/06P1A (cpb2*)p0660.1250.06420.0640.254160.50.0080.064821M/06P2A (cpb2*)p0600.0320.06410.0640.252160.1250.0040.03240.250.5M/06P3A (cpe, cpb2*)p0610.0320.0320.50.1250.254160.1250.0040.03240.1250.5M2/06P1†Ap0680.0640.06420.50.54160.250.0080.03280.1250.5M2/06P2†Ap0700.0160.12520.0320.254160.1250.0040.03216 (R)0.50.5M2/06P3†Ap1040.0640.0320.250.1250.25480.1250.0080.01640.50.5M/07P1Ap0810.250.03220.1250.254810.0080.03240.50.5M2/07P1†A (cpb2*)p042<0.0160.03220.0640.254160.1250.0080.01616 (R)10.5M2/07P2†Ap0560.0320.06440.1250.25480.1250.0040.03240.250.5M2/07P3†Ap0330.0320.06410.1250.5480.250.0080.03280.250.5M/08P1A (cpb2*)p0620.0640.520.0640.254160.25<0.0020.032820.5M/08P2Ap0400.0320.0640.250.0640.254160.1250.0080.01610.0640.5M/08P3Ap0800.032<0.0160.0320.0640.5180.064<0.0020.03240.1250.5M/13P1A (cpb2*)p0290.1250.2520.0640.254160.0640.0040.032841M/13P2A (cpb2*)p0250.0320.0320.0320.0320.250.12580.064<0.0020.03240.0320.5M/13P3A (cpe)p0710.032120.1250.5280.0640.0020.03240.1250.5M/14P1A (cpe)p0160.0160.06420.0640.25480.0640.0040.0160.1250.0640.5M/14P2A (cpe)p0200.1250.520.0640.25240.1250.004<0.01620.0320.5M/14P3A (cpe)p0210.0320.12520.0320.25280.0640.0080.01640.1250.5M2/14P1†A (cpb2*)p014<0.0160.03220.1250.25180.064<0.0020.01640.1250.5M2/14P2†A (cpb2*)p0150.0640.0320.0320.0640.252160.0640.0040.01640.50.5M2/14P3†A (cpb2*)p0140.0640.03220.1250.252160.0640.0040.01640.50.5M/23P1A (cpb2)p0320.0640.2520.0160.252160.250.0080.03240.1251M/25P1Ap0010.125240.0640.54160.250.0080.12516 (R)21M/25P2Ap0570.0320.01620.0640.25280.0320.0020.06480.1250.5M2/25P1†Ap0830.0320.12520.0640.5480.1250.0040.06416 (R)10.5M2/25P2†Ap0840.0320.12520.1250.258 (R)80.1250.0080.03216 (R)20.5M2/25P3†Ap0850.0320.12520.1250.258 (R)80.1250.0040.03216 (R)10.5M/26P1Ap0390.1250.12540.0640.254160.250.0040.03280.251M/26P2Ap0380.032<0.01610.0640.25280.0640.0020.01680.0640.5M2/26P1†Ap1000.0320.032210.254160.1250.0040.03240.250.5M2/26P2†Ap0860.0160.06420.1250.5432 (R)0.1250.0080.03220.1250.5M2/26P3†A (cpb2*)p0930.0160.06420.50.5480.0640.0040.03240.250.5N/01P1A (cpb2*)p0440.1250.12520.0640.254160.0640.004<0.01680.251N/01P2A (cpb2*)p0450.0320.06420.0640.54160.250.0040.06480.50.5N/01P3A (cpb2*)p0460.0320.12540.0640.5180.1250.004<0.01680.250.5N/12P1A (cpe)p0240.0640.06420.1250.254160.0640.0080.03240.50.5N/14P1Ap0190.0320.0320.250.1250.25280.0320.004<0.01640.1250.5O/04P1Ap0940.1250.06420.250.2541610.0080.03240.1250.5O/11P1A (cpb2*)p0070.064<0.0160.0640.0640.25480.125<0.0020.01640.1250.5O/11P2Ap0090.0320.06410.0320.25180.0320.0040.03280.1250.5O/11P3Ap0100.0320.06420.0640.25280.0640.0040.03280.1250.5Q/03P1Ap0730.1250.01620.0640.25432 (R)0.0640.004<0.01640.1250.5Q/03P2Ap0750.0640.03220.1250.258 (R)80.250.0080.03240.1250.5Q/03P3Ap0740.0320.12520.1250.254160.1250.0080.03240.250.5Q/04P2Ap0590.0320.12520.1250.254160.1250.0040.01640.1250.5Q2/04P1†A (cpb2*)p022<0.0160.12520.0640.254160.1250.0040.01640.250.5Q2/04P3†Ap0980.0320.01640.0640.254160.1250.0040.03220.1250.5Q/05P1A (cpb2*)p0480.016<0.0160.250.0640.51160.016<0.002<0.01610.1250.5Q/05P2A (cpb2*)p049<0.0160.12520.0640.52160.250.0040.01640.1250.5aIsolates whose names only differ in the last number were retrieved from the same animal (e.g. H/05P1, H/05P2 and H/05P3; see Table 3). Daggers (and the number 2 after the clinic's code) indicate isolates that were obtained in the follow-up analysis.bcpe: possession of the gene encoding for enterotoxin. cpb2: possession of the gene encoding for β2 toxin, with asterisks indicating atypical forms of the gene (as determined by PCR amplification).cAccording to the UPGMA dendrogram shown in Fig. 1 of Álvarez-Pérez et al. .dMinimum inhibitory concentration (MIC). AMC, amoxicillin/clavulanic acid; CLI, clindamycin; ERY, erythromycin; IPM, imipenem; LVX, levofloxacin; LZD, linezolid; MTZ, metronidazole; PEN, benzylpenicillin; RIF, rifampicin; TEC, teicoplanin; TET, tetracycline; TGC, tigecycline; VAN, vancomycin. R: MIC value above the breakpoint for in vitro resistance.Table 5Characteristics of the Clostridium difficile isolates obtained in the study.Table 5IsolateaPCR ribotypebAFLP genotypecAntibiotic susceptibility (MIC, µg/ml)dAMCCLIERYIPMLVXLZDMTZPENRIFTECTETTGCVANB/08D1RT154d0610.1250.25≥32 (R)≥32 (R)0.250.064≥32 (R)<0.0020.0640.0320.0160.25B/08D2RT154d070.250.0640.25≥32 (R)≥32 (R)0.250.0322 (R)<0.0020.0320.0320.0320.125B/08D3RT154d050.1250.0320.064≥32 (R)≥32 (R)0.1250.03232 (R)<0.0020.064<0.016<0.0160.125E/03D1RT?d130.5≥256 (R)≥256 (R)≥32 (R)≥32 (R)10.032≥32 (R)<0.0020.0640.5<0.0160.125E/03D2RT?d130.25≥256 (R)≥256 (R)≥32 (R)≥32 (R)0.50.064≥32 (R)0.0040.03210.0320.125E/03D3RT?d140.5≥256 (R)≥256 (R)≥32 (R)≥32 (R)10.125≥32 (R)<0.0020.0320.50.0320.125M/14D1RT106d150.50.0640.125≥32 (R)≥32 (R)0.250.064≥32 (R)<0.0020.032<0.016<0.0160.125M/14D2RT106d010.250.251≥32 (R)≥32 (R)0.1250.0644 (R)0.0040.032<0.016<0.0160.25M/14D3RT106d030.50.1250.25≥32 (R)≥32 (R)0.50.1252 (R)<0.0020.0320.032<0.0160.125N/19D1RT009-liked080.50.0640.25≥32 (R)≥32 (R)0.50.0324 (R)<0.0020.0640.032<0.0160.25N/19D2RT009-liked040.064<0.0160.016≥32 (R)≥32 (R)0.064<0.0161<0.0020.032<0.016<0.0160.125N/19D3RT009-liked090.25<0.0160.064≥32 (R)≥32 (R)0.125<0.0164 (R)<0.0020.0320.032<0.0160.125N/20D1RT009-liked100.250.0640.125≥32 (R)≥32 (R)0.250.032≥32 (R)<0.0020.0320.032<0.0160.25N/20D2RT009-liked1110.0160.032≥32 (R)≥32 (R)0.250.064≥32 (R)<0.0020.032<0.0160.0320.125N/20D3RT009-liked1210.1250.25≥32 (R)≥32 (R)0.1250.0641<0.0020.064<0.016<0.0160.125Q/03D1RT106d010.250.0640.064≥32 (R)≥32 (R)0.1250.032≥32 (R)<0.0020.032<0.016<0.0160.125Q/03D2RT106d020.250.0640.25≥32 (R)≥32 (R)0.1250.0322 (R)<0.0020.0640.0320.0320.25Q/03D3RT106d010.250.1250.125≥32 (R)≥32 (R)0.250.0322 (R)<0.0020.0640.064<0.0160.25aIsolates were retrieved from the same animal (B/08D1, B/08D2 and B/08D3; see Table 3).bToxin profiles: RT009-like, A-B-CDT- (but with a positive PCR result for tcdB); RT106, A+B+CDT-; RT154, A+B+CDT-; RT? (unknown ribotype), A-B-CDT-.cAccording to the UPGMA dendrogram shown in Fig. 2 of Álvarez-Pérez et al. .dMinimum inhibitory concentration (MIC). AMC, amoxicillin/clavulanic acid; CLI, clindamycin; ERY, erythromycin; IPM, imipenem; LVX, levofloxacin; LZD, linezolid; MTZ, metronidazole; PEN, benzylpenicillin; RIF, rifampicin; TEC, teicoplanin; TET, tetracycline; TGC, tigecycline; VAN, vancomycin. R: MIC value above the breakpoint for in vitro resistance.