TABLE 6.
Final mixed-effect negative binomial hurdle model of risk factors associated with the count of generic Escherichia coli (log10 CFU/g) on spinach (with the random effects farm and date)a
| Variable (comparison level) | Reference or unit | Coeffb | SEc | OR or RRd | 95% CIe | P value |
|---|---|---|---|---|---|---|
| Binary part (binomial with logit link) | ||||||
| Intercept | −5.97 | 1.58 | NAf | NA | <.001 | |
| Hygiene-field status (level 1)g | 0 | −2.88 | 0.86 | 0.06 | 0.01–0.30 | 0.001 |
| pd29h | mm | 1.24 | 0.38 | 3.5 | 1.7–7.2 | 0.001 |
| Manure_application (yes) | No | 3.96 | 1.37 | 52.2 | 3.6–761.4 | 0.004 |
| State (Texas) | Colorado | 4.68 | 1.52 | 108.1 | 5.5–2128.7 | 0.002 |
| P_count part (zero-truncated negative binomial with log link) | ||||||
| Intercept | −29.08 | 12.02 | NA | NA | 0.016 | |
| pd29i | mm | 0.38 | 0.11 | 1.5 | 1.2–1.8 | <.001 |
| txd9j | °C | 2.50 | 1.04 | 12.2 | 1.6–94.2 | 0.017 |
| txd92 | °C | −0.0523 | 0.02 | NA | NA | 0.021 |
Variance component values (standard deviation) were 3.53 (1.88) for date and 0.10 (0.32) for farm in the binary part and 1.62e−7 (4.00e−4) for date and 0.77e−7 (2.77e−4) for farm in the P_count part; in the final P_count part, the random effects were dropped because their effect was negligible. For the intercept-only model, variance component values were 6.11 (2.47) for date and 0.94 (0.97) for farm in the binary part and 0.16 (0.40) for date and 0.11 (0.33) for farm in the P_count model.
Coeff, value of the regression coefficient.
SE, standard error.
OR, odds ratio; RR, relative risk. In the column, ORs are shown for the binary part and RRs are shown for the P_count part.
CI, confidence interval.
NA, not applicable.
The estimated OR (95% CI) applies to all factors within the composite variable “hygiene-field status” group. Here, “level 1” indicates the presence of toilet training and use of toilets and washing stations but absence of field grazing and hay production before planting of the spinach during the current growing season.
pd29, mean amount of rain between the day of sample collection (SC) and day 29 prior to SC.
Estimate for the variable pd29 when txd9 is 0.
Mean of the maximum daily temperatures between the day of SC and day 9 prior to SC; here the estimate is for the variable txd9 when pd29 is 0.