TABLE 1.
Results of chlamydia detection in avian and environmental samples from five duck farmsa
| Flock and sample | Action | Date (day/mo/yr) | Place | Age (days) |
Chlamydiaceae detection |
Bacteriophage detection |
Amoeba detectionc |
||||||||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Cloacal swabs |
Air samples |
Dusters |
Water samples |
Soil samples |
Cloacal swabs |
Air samples |
Dusters |
Water samples |
Soil samples |
Water |
Soil |
||||||||||||||||||||
| 23S-rtPCR |
IncA-rtPCR |
Genotype | |||||||||||||||||||||||||||||
| No. pos/total | Mean Cq | No. pos/totalb | Mean Cq | No. pos/total | Cq | No. pos/total | Mean Cq | No. pos/total | Mean Cq | No. pos/total | Mean Cq | No. pos/total | Mean Cq | No. pos/total | Cq | No. pos/total | Mean Cq | No. pos/total | Mean Cq | No. pos/total | Mean Cq | Amo | Vahl | Amo | Vahl | ||||||
| A1 | |||||||||||||||||||||||||||||||
| 13-0273/1 | Implementation | 24/01/13 | Starter building | 1 | 0/15 | NA | 0/2 | NA | 0/1 | NA | 0/2 | NA | 2/5 | 37.7 | 0/15 | NA | 0/2 | NA | 1/1 | 35.4 | 0/2 | NA | 3/5 | 34.6 | + | – | + | + | |||
| 13-0458/1 | Nail trimming | 06/02/13 | Starter building | 14 | 1/15 | 35.9 | 0/1 | NA | 0/2 | NA | 0/1 | NA | 0/2 | NA | ND | 3/15 | 38.5 | 1/2 | 38.2 | 1/1 | 36.8 | 0/2 | NA | ND | + | – | |||||
| 13-0550/1 | Vaccination | 19/02/13 | Starter building + enclosures | 27 | 15/15 | 24.2 | 15/15 | 28.9 | E/B_06-859 | 1/2 | 35.7 | 1/1 | 28.0 | 0/2 | NA | 5/5 | 28.3 | 14/15 | 35.5 | 2/2 | 37.3 | 1/1 | 30.2 | 0/2 | NA | 5/5 | 33.7 | + | + | – | – |
| 13-0904/1 | Vaccination boost | 21/03/13 | Outdoor area | 57 | 13/15 | 34.6 | 13/13 | 34.1 | 0/2 | NA | 2/2 | 36.8 | 0/2 | NA | 1/5 | 40.0 | 14/15 | 35.3 | 0/2 | NA | 2/2 | 35.2 | 0/2 | NA | 1/5 | 37.4 | + | + | + | – | |
| 13-1159/1 | Transfer | 16/04/13 | Outdoor area | 83 | 10/15 | 32.2 | 10/10 | 33.2 | 0/2 | NA | 0/1 | NA | ND | ND | 13/15 | 35.7 | 0/2 | NA | 1/1 | 36.8 | ND | ND | |||||||||
| 13-1159/2 | Start of force-feeding | 16/04/13 | 0/2 | NA | ND | ND | ND | 0/2 | NA | ND | ND | ND | |||||||||||||||||||
| 13-1328/1 | Force-feeding | 23/04/13 | 90 | 6/15 | 37.0 | 5/6 | 36.4 | 0/2 | NA | ND | ND | ND | 6/15 | 35.7 | 0/2 | NA | ND | ND | ND | ||||||||||||
| 13-1328/2 | Transfer | 29/04/13 | 96 | 1/15 | 35.9 | 1/1 | 35.6 | 0/2 | NA | ND | ND | ND | 4/15 | 34.5 | 0/2 | NA | ND | ND | ND | ||||||||||||
| 13-1328/3 | Slaughtering | 29/04/13 | 1/15 | 39.3 | 1/1 | 38.9 | 0/4 | NA | ND | ND | ND | 4/15 | 35.8 | 0/4 | NA | ND | ND | ND | |||||||||||||
| A2 | |||||||||||||||||||||||||||||||
| 13-0749/1 | Implementation | 07/03/13 | Starter building | 1 | 0/15 | NA | 0/2 | NA | 0/1 | NA | 0/2 | NA | 2/5 | 38.9 | 0/15 | NA | 0/2 | NA | 1/1 | 37.4 | 0/2 | NA | 2/5 | 38.4 | – | – | + | + | |||
| 13-0904/2 | Nail and beak trimming | 18/03/13 | Starter building | 12 | 0/15 | NA | 0/2 | NA | 0/1 | NA | 0/2 | NA | ND | 2/15 | 38.3 | 1/2 | 39.3 | 0/1 | NA | 0/2 | NA | ND | + | – | |||||||
| 13-1030/1 | Vaccination | 04/04/13 | Starter building + enclosures | 29 | 15/15 | 26.9 | 15/15 | 26.9 | E/B_06-859 | 1/2 | 37.8 | 2/2 | 31.3 | 2/2 | 32.0 | 5/5 | 31.6 | 12/15 | 37.2 | 2/2 | 36.2 | 2/2 | 34.7 | 0/2 | NA | 5/5 | 35.2 | + | + | – | – |
| 13-1376/1 | Vaccination boost | 02/05/13 | Outdoor area | 57 | 7/15 | 33.8 | 6/7 | 32.9 | 0/2 | NA | 0/2 | NA | 0/2 | NA | 2/5 | 38.6 | 10/15 | 35.6 | 1/2 | 37.2 | 0/2 | NA | 0/2 | NA | 2/5 | 38.5 | + | + | + | – | |
| 13-1598/1 | Slaughtering | 03/06/13 | 89 | 3/15 | 37.7 | 3/3 | 37.6 | 0/4 | NA | ND | ND | ND | 4/15 | 36.3 | 1/4 | 39.5 | ND | ND | ND | ||||||||||||
| B | |||||||||||||||||||||||||||||||
| 13-0273/2 | Implementation | 31/01/13 | Starter building | 1 | 0/15 | NA | 0/2 | NA | 0/1 | NA | 0/2 | NA | 0/5 | NA | 0/15 | NA | 0/2 | NA | 1/1 | 33.2 | 0/2 | NA | 0/5 | NA | + | – | + | + | |||
| 13-0458/2 | Nail trimming | 14/02/13 | Starter building | 15 | 0/15 | NA | 0/2 | NA | 0/1 | NA | 0/2 | NA | ND | 0/15 | NA | 0/2 | NA | 0/1 | NA | 0/2 | NA | ND | + | – | |||||||
| 13-0550/2 | Vaccination | 25/02/13 | Starter building + enclosures | 26 | 6/15 | 32.9 | 3/6 | 32.7 | E/B_06-859 | 0/2 | NA | 1/1 | 36.2 | 0/2 | NA | 0/5 | NA | 10/15 | 38.0 | 0/2 | NA | 1/1 | 32.8 | 0/2 | NA | 0/5 | NA | – | – | + | – |
| 13-1030/2 | Vaccination boost | 28/03/13 | Outdoor area | 57 | 11/15 | 35.1 | 10/11 | 34.4 | E/B_06-859 | 0/2 | NA | 0/2 | NA | 0/2 | NA | 3/5 | 37.1 | 15/15 | 33.7 | 0/2 | NA | 2/2 | 33.3 | 0/2 | NA | 5/5 | 36.9 | + | – | + | + |
| 13-1328/4 | Transfer | 23/04/13 | Outdoor area | 83 | 5/15 | 33.0 | 5/5 | 33.0 | 0/2 | NA | 0/1 | NA | ND | ND | 8/15 | 33.7 | 1/2 | 38.0 | 1/1 | 36.7 | ND | ND | |||||||||
| 13-1328/5 | Start of force-feeding | 23/04/13 | 0/2 | NA | ND | ND | ND | 1/2 | 38.1 | ND | ND | ND | |||||||||||||||||||
| 13-1328/6 | Force-feeding | 30/04/13 | 90 | 1/15 | 38.0 | 1/1 | 37.8 | 0/2 | NA | ND | ND | ND | 5/15 | 32.8 | 0/2 | NA | ND | ND | ND | ||||||||||||
| 13-1376/2 | Transfer | 06/05/13 | 96 | 5/15 | 39.1 | 1/5 | 37.2 | 0/2 | NA | ND | ND | ND | 5/15 | 33.7 | 0/2 | NA | ND | ND | ND | ||||||||||||
| 13-1376/3 | Slaughtering | 06/05/13 | 1/15 | 39.7 | 0/1 | NA | 0/4 | NA | ND | ND | ND | 3/15 | 35.7 | 0/4 | NA | ND | ND | ND | |||||||||||||
| C | |||||||||||||||||||||||||||||||
| 13-0458/3 | Implementation | 14/02/13 | Starter building | 1 | 2/15 | 35.8 | 0/2 | NA | 0/2 | NA | 0/1 | NA | 0/2 | NA | 0/5 | NA | 1/15 | 39.9 | 0/2 | NA | 0/1 | NA | 0/2 | NA | 1/5 | 35.6 | + | – | + | – | |
| 13-0749/2 | Nail trimming | 26/02/13 | Starter building | 13 | 0/15 | NA | 0/1 | NA | 0/1 | NA | 0/2 | NA | ND | 2/15 | 39.1 | 0/1 | NA | 1/1 | 39.1 | 0/2 | NA | ND | + | – | |||||||
| 13-0749/3 | Vaccination | 07/03/13 | Starter building | 22 | 15/15 | 25.4 | 15/15 | 25.5 | E/B_E30 | 1/2 | 36.6 | 1/1 | 28.7 | 2/2 | 27.9 | 5/5 | 28.8 | 15/15 | 28.9 | 2/2 | 34.4 | 1/1 | 26.4 | 2/2 | 35.5 | 5/5 | 31.4 | + | – | – | + |
| 13-1030/3 | Vaccination boost | 28/03/13 | Outdoor area | 43 | 14/15 | 33.7 | 14/14 | 33.4 | 0/2 | NA | 2/2 | 35.0 | 2/2 | 38.2 | 4/5 | 36.0 | 15/15 | 31.3 | 2/2 | 36.1 | 2/2 | 34.9 | 0/2 | NA | 3/5 | 38.4 | + | – | + | – | |
| 13-1376/4 | Transfer | 07/05/13 | Outdoor area | 83 | 5/15 | 36.9 | 4/5 | 37.1 | 0/2 | NA | 0/1 | NA | ND | ND | 11/15 | 34.4 | 0/2 | NA | 1/1 | 28.5 | ND | ND | |||||||||
| 13-1376/5 | Start of force-feeding | 07/05/13 | 0/2 | NA | ND | ND | ND | 1/2 | 38.9 | ND | ND | ND | |||||||||||||||||||
| 13-1458/1 | Force-feeding | 13/05/13 | 89 | 1/15 | 37.6 | 0/1 | NA | 0/2 | NA | ND | ND | ND | 7/15 | 35.5 | 0/2 | NA | ND | ND | ND | ||||||||||||
| 13-1458/2 | Transfer | 21/05/13 | 97 | 3/15 | 37.0 | 2/3 | 37.0 | 0/2 | NA | ND | ND | ND | 7/15 | 34.2 | 0/2 | NA | ND | ND | ND | ||||||||||||
| 13-1458/3 | Slaughtering | 21/05/13 | 1/15 | 39.9 | 0/1 | NA | 0/4 | NA | ND | ND | ND | 6/15 | 37.5 | 0/4 | NA | ND | ND | ND | |||||||||||||
| D1 | |||||||||||||||||||||||||||||||
| 13-0458/4 | Implementation | 14/02/13 | Starter building | 1 | 2/15 | 36.8 | 0/2 | NA | 0/2 | NA | 0/1 | NA | 0/2 | NA | 0/5 | NA | 0/15 | NA | 0/2 | NA | 0/1 | NA | 0/2 | NA | 0/5 | NA | + | + | + | + | |
| 13-0749/4 | Vaccination | 07/03/13 | Starter building | 22 | 0/15 | NA | 0/2 | NA | 0/1 | NA | 0/2 | NA | 0/5 | NA | 0/15 | NA | 1/2 | 38.1 | 1/1 | 36.9 | 0/2 | NA | 1/5 | 36.0 | + | + | + | + | |||
| 13-1030/4 | Vaccination boost | 04/04/13 | Outdoor area | 50 | 0/15 | NA | 0/2 | NA | 0/2 | NA | 0/2 | NA | 0/5 | NA | 3/15 | 39.2 | 0/2 | NA | 1/2 | 35.5 | 0/2 | NA | 0/5 | NA | + | + | + | + | |||
| 13-1376/6 | Transfer | 10/05/13 | Outdoor area | 86 | 7/15 | 37.0 | 5/7 | 37.0 | 0/2 | NA | 0/1 | NA | ND | ND | 11/15 | 32.1 | 2/2 | 34.8 | 1/1 | 30.9 | ND | ND | |||||||||
| 13-1376/7 | Start of force-feeding | 10/05/13 | 0/2 | NA | ND | ND | ND | 1/2 | 33.8 | ND | ND | ND | |||||||||||||||||||
| 13-1458/4 | Force-feeding | 15/05/13 | 91 | 4/15 | 37.4 | 3/4 | 37.5 | 0/2 | NA | ND | ND | ND | 14/15 | 32.6 | 1/2 | 35.6 | ND | ND | ND | ||||||||||||
| 13-1458/5 | Transfer | 22/05/13 | 98 | 5/15 | 37.7 | 4/5 | 36.5 | 0/2 | NA | ND | ND | ND | 13/15 | 34.2 | 2/2 | 38.7 | ND | ND | ND | ||||||||||||
| 13/1458/6 | Slaughtering | 22/05/13 | 1/15 | 39.0 | 1/1 | 39.0 | 0/4 | NA | ND | ND | ND | 14/15 | 34.3 | 2/4 | 39.4 | ND | ND | ND | |||||||||||||
| D2 | |||||||||||||||||||||||||||||||
| 13-1159/3 | Implementation | 11/04/13 | Starter building | 1 | 0/15 | NA | 0/2 | NA | 0/1 | NA | 0/2 | NA | 0/5 | NA | 0/15 | NA | 0/2 | NA | 1/1 | 39.7 | 0/2 | NA | 0/5 | NA | + | + | – | + | |||
| 13-1376/8 | Vaccination | 06/05/13 | Starter building + enclosures | 26 | 0/15 | NA | 0/1 | NA | 0/1 | NA | 0/2 | NA | 0/5 | NA | 2/15 | 39.6 | 0/1 | NA | 1/1 | 38.8 | 0/2 | NA | 0/5 | NA | + | – | + | + | |||
| 13-1598/2 | Vaccination boost | 03/06/13 | Outdoor area | 55 | 14/15 | 32.8 | 13/14 | 32.1 | E/B_06-859 | 0/2 | NA | 0/2 | NA | 2/2 | 39.4 | 1/5 | 37.9 | 14/15 | 34.5 | 2/2 | 36.8 | 2/2 | 34.8 | 0/2 | NA | 1/5 | 35.1 | + | + | + | + |
| 13-2060/1 | Transfer | 05/07/13 | Outdoor area | 86 | 4/15 | 36.7 | 3/4 | 37.1 | 0/2 | NA | 1/1 | 39.7 | ND | ND | 5/15 | 32.7 | 1/2 | 38.9 | 1/1 | 33.9 | ND | ND | |||||||||
| 13-2060/2 | Start of force-feeding | 05/07/13 | 0/2 | NA | ND | ND | ND | 0/2 | NA | ND | ND | ND | |||||||||||||||||||
| 13-2060/3 | Force-feeding | 08/07/13 | 89 | 2/15 | 37.3 | 2/2 | 37.4 | 0/2 | NA | ND | ND | ND | 4/15 | 35.9 | 0/2 | NA | ND | ND | ND | ||||||||||||
| 13-2060/4 | Transfer | 18/07/13 | 99 | 2/15 | 35.3 | 2/2 | 35.7 | 0/2 | NA | ND | ND | ND | 2/15 | 37.1 | 0/2 | NA | ND | ND | ND | ||||||||||||
| 13-2060/5 | Slaughtering | 18/07/13 | 1/15 | 34.5 | 1/1 | 35.5 | 0/4 | NA | ND | ND | ND | 2/15 | 36.1 | 0/4 | NA | ND | ND | ND | |||||||||||||
| E | |||||||||||||||||||||||||||||||
| 13-0749/5 | Implementation | 28/02/13 | Starter building | 1 | 0/15 | NA | 0/2 | NA | 0/1 | NA | 0/2 | NA | 0/5 | NA | 0/15 | NA | 0/2 | NA | 1/1 | 37.8 | 0/2 | NA | 1/5 | 35.8 | + | – | – | + | |||
| 13-0904/3 | Nail trimming | 08/03/13 | Starter building + enclosures | 9 | 0/15 | NA | 0/1 | NA | 0/1 | NA | 0/2 | NA | ND | 1/15 | 39.9 | 0/1 | NA | 1/1 | 36.5 | 0/2 | NA | ND | – | – | |||||||
| 13-0904/4 | Vaccination | 21/03/13 | Outdoor area | 22 | 0/15 | NA | 0/2 | NA | 0/1 | NA | 0/2 | NA | 0/5 | NA | 0/15 | NA | 0/2 | NA | 1/1 | 36.0 | 0/2 | NA | 0/5 | NA | + | – | – | – | |||
| 13-1159/4 | Vaccination boost | 11/04/13 | Outdoor area | 43 | 0/15 | NA | 0/2 | NA | 0/2 | NA | 2/2 | 38.7 | 1/5 | 37.6 | 9/15 | 39.1 | 0/2 | NA | 2/2 | 35.9 | 2/2 | 38.3 | 1/5 | 37.1 | + | + | + | – | |||
| 13-1458/7 | Transfer | 17/05/13 | Outdoor area | 79 | 15/15 | 32.3 | 15/15 | 32.7 | E/B_06-859 | ND | ND | ND | ND | 14/15 | 28.5 | ND | ND | ND | ND | ||||||||||||
| 13-1458/8 | Start of force-feeding | 17/05/13 | 0/2 | NA | ND | ND | ND | 2/2 | 33.5 | ND | ND | ND | |||||||||||||||||||
| 13-1598/3 | Force-feeding | 22/05/13 | 84 | 12/15 | 35.6 | 10/12 | 34.7 | E/B_06-859 | 0/2 | NA | ND | ND | ND | 15/15 | 29.5 | 2/2 | 37.2 | ND | ND | ND | |||||||||||
| 13-1598/4 | Transfer | 29/05/13 | 91 | 6/15 | 36.9 | 5/6 | 36.4 | 0/2 | NA | ND | ND | ND | 14/15 | 32.1 | 2/2 | 35.9 | ND | ND | ND | ||||||||||||
| 13-1598/5 | Slaughtering | 29/05/13 | 7/15 | 38.0 | 7/7 | 38.0 | 0/4 | NA | ND | ND | ND | 15/15 | 33.0 | 3/4 | 37.9 | ND | ND | ND | |||||||||||||
a
ND, not done; NA, not applicable. No. pos/total = number of positive swabs/total number of tested swabs (except as noted in footnote b).
b
No. pos/total = number of positive swabs/number of Chlamydiaceae PCR-positive swabs.
c
–, no amplification on electrophoresis; +, amplification on electrophoresis.