TABLE 3.
Specificity of general Bacteroidales and swine-associated PCR markers using fecal DNA extracts
| Fecal type (origin) | % Positive PCR resultsa (no. of positive PCR results/total no. of source type samples tested)
|
|||
|---|---|---|---|---|
| General Bacteroidales (Bac32) | Pig Prevotella (PF163) | Pig methanogen (P23-2) | Pig Prevotella (PigBac1) | |
| Pig feces (DE) | 100 (9/9) | 44 (4/9) | 78 (7/9) | 44 (4/9) |
| Pig feces (OH) | 100 (52/52) | 98 (51/52) | 42 (22/52) | 81 (42/52) |
| Pig feces (TX) | 100 (7/7) | 100 (7/7) | 29 (2/7) | 100 (7/7) |
| Pig feces (TX) | 100 (9/9) | 89 (8/9) | 22 (2/9) | 100 (9/9) |
| Pig feces (WV) | 90 (18/20) | 70 (14/20) | 90 (18/20) | 90 (18/20) |
| Cattle (WV) | 100 (20/20) | 40 (9/20) | 5 (1/20) | 10 (2/20) |
| Pig manure pits (OH) | 100 (3/3) | 100 (3/3) | 0 (0/3) | 33 (1/3) |
| Pig manure pit (IL) | 100 (1/1) | 100 (1/1) | 0 (0/1) | 0 (0/1) |
| Pig lagoons (IL) | 100 (2/2) | 100 (2/2) | 0 (0/2) | 0 (0/2) |
| Human feces (WV) | 100 (10/10) | 30 (3/10) | 30 (3/10) | 60 (6/10) |
| Chicken (DE) | 88 (7/8) | 50 (4/8) | 38 (3/8) | 63 (5/8) |
| Raccoon (NE) | 34 (23/68) | 4 (3/68) | 1 (1/68) | 29 (20/68) |
| Horse (WV) | 100 (12/12) | 67 (8/12) | 0 (0/12) | 50 (6/12) |
| Cattle lagoon (OH) | 100 (1/1) | 0 (0/1) | 0 (0/1) | 0 (0/1) |
a
Percent positive PCR results using a given marker on a given source type. Diagnostic specificity, the number of nonpig fecal source samples that produce negative PCR results divided by the total number of nonpig fecal source samples tested (n = 119), was 0.77, 0.93, and 0.67 for pig Prevotella (PF163), pig methanogen (P23-2), and pig Prevotella (PigBac1), respectively. Diagnostic sensitivity, the number of pig source samples testing positive divided by the total number of pig source samples tested (n = 103), was 0.87, 0.49, and 0.79 for pig Prevotella (PF163), pig methanogen (P23-2), and pig Prevotella (PigBac1), respectively.