Table 1.
Pathogen prevalence at the submission level, and details of pre-set microbiology tests employed in a small poultry flock surveillance study in Ontario, over a 2-y period.
| Pathogen | Type of test | Pooled samples for each submission | Species tested | Submissions tested (N) | Submissions positive (n) | Prevalence (%) |
|---|---|---|---|---|---|---|
| Avian bornavirus10 | RT-rtPCR | Brains | All species | 160 | 0 | 0 |
| Influenza A virus17 | RT-rtPCR | Tracheal and cloacal swabs | All species | 160 | 1 | 0.6 (0.02–3) |
| Avian avulavirus 134 | RT-rtPCR | Tracheal and cloacal swabs | All species | 160 | 1 | 0.6 (0.02–3) |
| Fowl adenovirus (A/C, D, E)‡ | RT-rtPCR | Cloacal swabs | Chickens | 134 | 47 | 35 (27–44) |
| Infectious bronchitis virus7 | RT-rtPCR | Tracheal and cloacal swabs | Chickens | 134 | 52 | 39 (31–48) |
| Infectious laryngotracheitis virus6 | RT-rtPCR | Tracheal swabs | Chickens and game birds | 142 | 22 | 15 (10–23) |
| Infectious bursal disease virus | RT-rtPCR | Cloacal swabs | Chickens | 134 | 2 | 1 (0.2–5) |
| Avian reovirus | RT-rtPCR | Cloacal swabs | Chickens and turkeys | 144 | 6 | 4 (2–9) |
| Mycoplasma gallisepticum | rtPCR | Tracheal swabs | All species except ducks | 151* | 35 | 23 (17–31) |
| Mycoplasma synoviae | Standard PCR | Tracheal swabs | All species except ducks | 151* | 54 | 36 (28–44) |
| Mycoplasma meleagridis | rtPCR | Tracheal swabs | Turkeys | 10 | 0 | 0 |
| Mycoplasma iowae | rtPCR | Tracheal swabs | Turkeys and game birds | 18 | 0 | 0 |
| Mycoplasma spp. | Culture | Airsac swabs | Ducks | 8 | 1 | 13 (0.3–53) |
| Campylobacter total‡ | Enrichment and isolation | Cecal tissue | All species | 158† | 56 | 35 (28–43) |
| C. jejuni | 29 | 18 (13–25) | ||||
| C. coli | 31 | 20 (14–27) | ||||
| Salmonella spp. | Enrichment and isolation | Cecal tissue | All species | 159* | 5 | 3 (1–7) |
| Brachyspira total‡ | rtPCR | Cecal tissue | All species | 159* | 59 | 37 (30–45) |
| Brachyspira spp. | 58 | 36 (29–44) | ||||
| B. innocens | 26 | 16 (11–23) | ||||
| B. intermedia | 16 | 10 (6–16) | ||||
| B. murdochii | 9 | 6 (3–10) | ||||
| B. pilosicoli | 1 | 0.6 (0.02–3) |
Prevalence estimates were calculated by dividing the number of submissions that tested positive for the pathogen by the total number of submissions tested for the pathogen (n/N). Exact binomial 95% confidence intervals (CI) for the non-zero prevalence estimates were computed, in parentheses. Superscripts by the name of the pathogen indicate references. All species = chickens, turkeys, ducks, pheasants, peafowl, and quail; game birds = pheasants, peafowl, and quail; rtPCR = real-time PCR; RT-rtPCR = reverse-transcription rtPCR.
Sample from one chicken submission not available.
Sample from 1 chicken and 1 peafowl submission not available.
At least one submission positive for species- or genotype-specific test.