Détection des troupeaux laitiers infectés par Mycobacterium avium ssp. paratuberculosis via la culture fécale et impact des mesures de contrôle des maladies entériques contagieuses sur l’incidence d’excrétion fécale individuelle

Paratuberculosis is a chronic and contagious enteric disease of ruminants caused by Mycobacterium avium subsp. paratuberculosis (MAP). This disease is responsible for significant economic losses and the bacteria itself has been associated to Crohn’s disease in humans; even though the causal link has not been established. Paratuberculosis control programs focus on reducing MAP transmission by implementing better management practices that target infection routes. In Québec, a Voluntary Paratuberculosis Prevention and Control Program (QVPPCP) was launched in 2007. Upon enrolment in the QVPPCP, a risk assessment questionnaire is administered to determine the risk of introduction and transmission of MAP into the herd. Herd status is then determined by environmental sampling (ES). The ES has been previously evaluated mostly in large free-stall dairy herds in the US. Microbial overgrowth can interfere with the correct assessment of MAP herd status when non-interpretable (NI) results are obtained from environmental samples. The objectives of this thesis are: 1) to determine the impact of enrolment in the QVPPCP on the incidence of fecal excretion of MAP and 2) to improve the detection of MAP infected tie-stall dairy herds. A cohort study was design to answer to the first objective. The incidence of fecal excretion of cows born before and after the enrolment of the farms in the QVPPCP was compared using a Cox proportional hazards model. The second objective included two other studies. In one study, 7 environmental and 2 targeted pool samples were collected from 24 herds with MAP known status (19 positive and 5 negative herds) and compared with serum and fecal individual samples from all the adult cows in the herd. The other study evaluated the performance of the polymerase chain reaction (PCR) before and after the incubation of the samples in the automated system. The PCR was performed on 154 samples (62 NI, 62 negative and 30 positive). It was demonstrated that the incidence and hazard of fecal excretion were significantly lower for cows born after the enrolment of the farm in the QVPPCP than for cows born before (incidence rate ratio=0.4; 95% CI: 0.2-0.8 and hazard ratio (HR)=0.48; 95% CI: 0.23-0.98). Poor calving cow hygiene (HR=3.4; 95% CI: 1.4-8.3) and contact between pre-weaned heifers and adult cows or their feces (HR=2.7; 95% CI: 1.1-6.6) were significantly associated with an increased hazard of fecal excretion of MAP. In addition, the sensitivity of environmental culture was 44% (95% CI: 20%-70%) when combining results from 2 different samplings and 32% (95% CI: 13%-57%) when results from only 1 random sampling were analyzed. It was found that the best sampling strategy was to combine samples from the manure pit, gutter, sick cows, and cows with poor body condition. Finally, a total of 1.6% of the NI environmental samples had detectable MAP DNA. The PCR had a significantly greater performance when applied after the culture than before the culture (P = 0.004). Thus, the results of this thesis show a reduction of the fecal excretion of MAP in cows born after enrolment of farms in the QVPPCP. The lower fecal excretion is probably a consequence of the reduction of the risk of within-herd transmission of MAP which is likely achieved through the implementation of better management practices aiming to reduce the contact of calves with adult cows or their feces. ES is the best sampling strategy as compared to costly individual tests (culture or ELISA) for detecting MAP-infected tie-stall dairy herds. It is a non-expensive and non-invasive technique for detecting mainly high MAP prevalence herds. However, our results show that it also detects low MAP prevalence herds. Performing a PCR on overgrown environmental samples contributes to MAP culture process improvement increasing the sensitivity and specificity, and reducing the turnaround laboratory time.

Keyphrases: Tie-stall dairy herds, Incidence of fecal excretion, Prevention and control program, Environmental sampling, Microbial overgrowth, Herd status