Johnes Disease in Dairy Herds

• aka Paratuberculosis • enteritis (inflamation of small intestine) of ruminant animals • granulomas: form when immune system attempts to wall off foreign substances but cant eliminate = thickening of intestine, inhibits nutrient absorption • initial signs subtle: ~ decreased milk yield ~ reduced BCS ~ low fertility ~ roughening of hair/coat • many animals removed from herds before diagnosed

• loose manure • weight loss • chronic and progressive • as progress lead to ~ intermandibular odema (bottle jaw) = as a result of protein loss from bloodstream into digestive tract • no cure = dehydration, cachexia and death • causative bac found on 70% of US dairy farms • UK = >50%

= Mycobacterium Avium subsp. Paratuberculosis (MAP) • difficult to treat e.g mycobacterium bovis • genus slow growing, resilient • resistant to acids, alkalis and detergents • encased by thick layer of mycolic acids = fungus like growth pattern on culture media

• characterised by long incubation periods ~ infected between 2 and 10 years before CS apear ~ subclinical animals shed MAP into manure and milk, spread througout enviro w/o farmers knowing • calves most susceptable (esp via faecal-oral route) • MAP often goes undetected - lengthy incubation, intermittent shedding, delay before antibody production (evade diagnostic test detection), variety of other explanations for consequences of subclinical infections

• cow has clinical johnes disease • other subclinical cows in herd (stage 2) infected and shedding but no CS • more cows stage one = infected

• susceptability to other diseases • lose money from ~ breeding problems ~ decreasd milk production ~ loss of investment in infected younstock ~ vet costs ~ cull rate ~ relacement costs

• internal route (direct) shed into milk by infected animals • enviro route (indirect) faecal contamination during milking • MAP can survive pasturation if present at high threshold = >10^3 CFU/L (colony forming units • calves sometimes fed bulk milk • MAP and potential cause of human chrons disease - important to keep contamination level below threshold

• ELIZA, PCR, Culture • ELIZA = detects MAP antibodies • PCR and culture = detect causal organism • diagnostic matrices for ante-mortem testing are: serum, milk, feaces (when cow alive)

• culture = takes 16 weeks and alot can go wrong in that time, lacks sensitivity (map fussy about what it requires to grow) • ELIZA = lacks sensitivity (no ab production in early stages) • PCR = some of targets arnt specific to MAP , found in other mycobacterial species (may give =ve result but actually got diff mycobacterial species), can be bad at differentiating between live and dead bac

• 14 MAP infected cows on 2 low prevalence dairy herds for 180 days • repeated milk and faecal sample measuremens overtime • used ELISA, milk and faecal qPCR and faecal culture • weekly bulk milk qPCR and bulk milk ELISA • qPCR alow to know what bacterial load was rather than just +/- • lack of research between tests and majority focus at single point in time across large no. herds and focused on agrement of 2 dichotamus outcomes (+/-) and no adjustment for individual cow/herd characteristics

• ELIZA ab level • scale for all possible eliza values • cut off level. after = +ve result • 2 ab levels can be very similar but either side of cut off point • ab level is continuous scale and should be seen as liklyhood than animal is infected • For PCR: sample that has one colony forming unit of MAP = +ve sample ~ what use for famrer? inform whether to cull cow depending on level of sheding

• strong associations between milk ELISA, faecal culture and faecal qPCR • temporal relationships between faecal shedding and subsequent high ELISA ~ spikes in shedding may predict ELISA results taken up to 2 months later • bulk tank milk supply never positive (not a main concern for farms with low prevalence of infection

= simplified representation of a complex phenomenon - SIR model (susceptible, infected, recovered) - provides an abstraction to reduce a problem to its essential characteristics ~ biology and catagories of infection, catagories of population itself ~ relavent time period ~ main research question

• Deteminstic: ~ parameter values fixed ~ describes what happens on average in population • Stochastic ~ randomness present ~ certain perameters vary around given distribution

• (not suitable for real world implementation) But adding years may correspond to a fraction of a second in computation time • altering value of a model parameter vs decades of herd monitoring to observe the true impact of control strategy (dont waste time in real world with strategies with no potential) • mathematical models may be continuously refined to incorporate new insights and mimic real-word scenarios

• study between 3 production types (organis, conventional non-grazing, conventional grazing) • cross sectional • data from 300 dairy herds • production types yet to be compared for johnes transmission risk • growing demand for organic products • safety of organic dairy practices for MAP control not yet evaluates • also looked at conventional herds that use organic practices (grazing) • risk factors scored 0-3 (no-high risk) • each farm scored on each risk factor, scores tallied E.g. calving area ~dedicated calving area = 0 ~ area separate from lactating cows = 1 ~ area houses sick or lactating cows = 3 • Results = organic herds had higher total risk scores, esp calving area and pre-weaned calves

(in study) - 40% allowed calves to nurse - 89% allowed calves to spend >6hours with dam after birth ~ practices may be important to philosophies of organic dairy farmer ~ perceived and substantiated welfare benefits for cow-calf contact - control programs consistently recomend prompt cow-calf separation to mitigate spread of MAP bacteria - studies contradict findings (beaver) - participation in JD control programs diminished for organic herds = counselled to abandon practices

• specific interactions may interact, producing synergism of risk (heightened risk) goal = evaluate production types based on compaound risk factors (logistic regression, adjustment for herd size, state) • e.g. risk of calves remain with dam links to poor hygiene of cows, other animals present at calving and livestock entering from other herds • organic herds permiting extended cow-calf contactmore at risk e.g 36x greater odds allowing sick cows in calving area compared to conventional

• rather than councle farmers to abandon practices (did not show increased vigilance to prevent risk inflation), advise how to better accommodate practices ~ improve calving area hygiene/management ~ clean fresh cow udders, improve overall udder hygiene, provide footbaths ~ provide dedicated calving area with minimal manure = increase participation of organic herds in JD control programs