Evaluating transmission dynamics of Shiga toxin-producing E. coli (STEC) in New Zealand cattle from farm to slaughter using PCR/MALDI-TOF and genome sequencing.

Cattle are asymptomatic carriers of Shiga toxin-producing E. coli (STEC) that can cause serious illness or death in humans. In New Zealand, contact with cattle feces and living near cattle populations are known risk factors for human STEC infection. Contamination of fresh meat with STECs also has the potential for rejection of consignments by importing countries.We used a combination of PCR/MALDI-TOF and whole genome sequencing to evaluate the presence and transmission of STEC on farms and in processing plants to better understand the potential pathways for human exposure and thus mitigate risk.Animal and environmental samples (n=2,580) were collected from six farms and three meat processing plants in New Zealand during multiple sampling sessions in spring of 2015 and 2016. PCR/MALDI-TOF analysis revealed 6.2% were positive for 'Top 7' STEC. 'Top 7' STEC were identified in all sample sources (n=17) tested. A marked increase in 'Top 7' STEC prevalence was observed between calf hides on-farm (6.3% prevalence), and calf hides at processing plants (25.1% prevalence).Whole genome sequencing was performed on 'Top 7' STEC bacterial isolates (n=40). Analysis of STEC O26 (n=25 isolates) revealed relatively low genetic diversity on individual farms, consistent with the presence of a resident strain disseminated within the farm environment.Public health efforts should focus on minimizing human contact with fecal material on farms and during handling, transport and slaughter of calves. Meat processing plants should focus on minimizing cross-contamination between the hides of calves in a cohort during transport, lairage and slaughter.ImportanceCattle are asymptomatic carriers of Shiga toxin-producing E. coli (STEC), which can cause serious illness or death in humans. Contact with cattle feces and living near cattle are known risk factors for human STEC infection. This study evaluated STEC carriage in young calves and the farm environment with an in-depth evaluation of six farms and three meat processing plants over two years. An advanced molecular detection method and whole genome sequencing were used to provide a detailed evaluation of the transmission of STEC both within and between farms.The study revealed widespread STEC contamination within the farm environment, but no evidence of recent spread between farms. Contamination of young dairy calf hides increased following transport and holding at meat processing plants. The elimination of STEC in farm environments may be very difficult given the multiple transmission routes; interventions should be targeted at decreasing fecal contamination of calf hides during transport, lairage, and processing.