Due to the depth and breadth of sample collection and processing (up to 96 samples a day), this study was limited by the number of farms evaluated (n=6). However, the focused assessment on several farms allowed for an in-depth evaluation of
transmission and contamination pathways from farms to processing plants.
Selection bias existed in the ‘Top 7’ STEC results from NeoSEEK, as most samples that had previously been screened as potential STEC using RT-PCR were eligible for
NeoSEEK testing. This strategy was due to resource limitations for the NeoSEEK testing of all samples (n=2580). However, our method used random selection of pre- screened samples, as well as the inclusion of a cohort of bobby calves, to help identify potential transmission routes and risk factors for STEC colonisation and
contamination.
Our advanced molecular detection methods (NeoSEEK, RT-PCR) only allowed for prevalence estimates of STEC, rather than the concentration of bacteria in the samples. Understanding concentration of bacteria may be useful for chemical
interventions to decrease STEC contamination. While this may be a limitation, these types of molecular methods are used to screen and confirm the presence of 'Top 7' STEC in beef trim for the export market; these methods are directly relevant to the New Zealand meat industry.
Finally, our analysis of the effect of transport and lairage of bobby calves to processing plants was limited by not sampling bobby calves from other farms that were
transported with our cohort calves. However, our investigation identified increased cross-contamination during transport and lairage, as well as the increasing risk of cross-contamination with each farm visited; this would be an important factor to fully evaluate in further studies.
4.7
Conclusion
The key driver for colonisation of very young calves appears to be a combination of dam-to-calf, calf-to-calf, and environment-to-calf factors. Several dam-related pathways, including cow colonisation (RAMS) and contamination of colostrum and milk filters, strongly indicate cows are part of the transmission cycle. The
contamination of calf hides, while indicative of shedding of 'Top 7' STEC within the pen, may also act as a transmission route, due to calves nuzzling behaviour with other calves. Our genomic analyses support the conclusion that cows, calves, the
environment, and feed sources are contaminated or colonised by the same strains of STEC, indicating that multiple transmission pathways are in action.
Transport and lairage led to significant increases in the prevalence and genomic diversity of 'Top 7' STEC on calf hides at the plant, suggesting cross-contamination of hides had occurred. Visually detectable contamination of hides, as well as
contamination of calf hides on farms increased the risk of eventual pre-intervention carcass contamination. The increase in farms visited by the transport truck increased the risk for pre-intervention carcass contamination. This would suggest that calf hide contamination or calf colonisation with STEC from one farm could lead to increased contamination of calf hides and pre-intervention carcasses of calves from other farms.
Due to the large number of potential transmission routes identified in this study, preventing exposure of very young calves to STEC on dairy farms is likely to be difficult to achieve. Even within the first three days of life, 10% of calves had 'Top 7' STEC hide contamination and some were already colonised and shedding STEC. Higher numbers of calves in shared pens has been identified both in this study and a larger cross-sectional study (Chapter 3) as a risk factor for STEC carriage, suggesting that transmission between calves could be reduced by decreasing pen-occupancy rates. Fewer calves in pens would result in decreased amplification of STEC in the environment. Calf pen faecal contamination could lead to hide contamination on the ventral surface of the calf; the ventral surface is where opening cuts are made in the hide during processing, and faecal contamination in this area may pose a higher risk for contamination of veal carcasses. Random clinical trials should be designed to evaluate the influence of decreasing pen-occupancy of calves on the contamination and colonisation of veal calves on farms.
Reduced contamination of calf hides may lead to decreased transmission of STEC on farms, as well as a decreased opportunity for initial contamination of carcasses during slaughter and dressing. Decreasing persistence of STEC in the calf pen environment, as well as on transport trucks and in lairage, may further decrease the level of
contamination. Sanitizers and local disinfection could be applied, but enlisting farmers to participate may be impractical; several opportunities for chemical interventions exist during transport and lairage: loading into a transport truck, unloading from a transport truck, and while in lairage.
As opposed to interventions to try and minimise the level of contamination associated with veal calves presented for slaughter and dressing, the value of meat hygiene
training at cattle processing plants cannot be overlooked. An assessment of current processing plant practices in the Netherlands revealed half the plants had structural and procedural inadequacies that led to a higher level of microbial contamination of carcasses (209). This study led to significant improvements in hygiene practices. A USDA study in veal processing plants found that after three processors improved their harvest process as recommended by the FSIS, there were significant drops of almost 50% in the contamination levels of hides compared to carcasses (202). In 2016, the Meat Industry Association in New Zealand worked together with the Ministry of Primary Industries to introduce nine initiatives aimed at reducing the risk of veal carcass contamination with ‘Top 7’ STEC, including hosting workshops targeted at senior operators, supervisors, technical staff and on-site verification staff (14).
Continued educational efforts at meat processing plants in New Zealand may reduce the risk of veal carcass contamination.
These results suggest that ‘Top 7’ STEC is likely to be maintained to some degree in the farm environment throughout the year, and there are a number of risk factors that have the potential to increase the level of colonisation of young calves on dairy farms, as well as hide and pre-intervention carcass contamination during transport and lairage. This research has provided evidence that is useful for risk mitigation of 'Top 7' STEC on farms and at processing plants, and can be used for future studies and