University of Wisconsin–Madison


2021-09-15 15:23:40


Lawrence Gavey and colleagues from Animal Health Ireland and the Centre for Veterinary Epidemiology and Risk Analysis, UCD School of Veterinary Medicine, University College Dublin published an article describing the Irish Johne’s disease (JD) control program. Their Open Access article appeared August 27, 2021, in the journal Frontiers in Veterinary Science.


The Irish Johne's Control Programme (IJCP) provides a long-term approach to the voluntary control of Johne's disease (JD) in Ireland, strongly supported by Irish cattle industry leadership. It leverages the establishment of Animal Health Ireland for control of animal diseases not regulated by the European Union. The IJCP has four objectives: facilitate protection against spread of JD to uninfected farms; reduce the level of infection when present; assure markets of JD control in Ireland; and improve calf health and farm biosecurity. Key IJCP elements are an annual veterinary risk assessment and management plan (VRAMP), annual whole herd test (WHT) by ELISA on blood or milk samples with ancillary faecal PCR testing of ELISA reactors, and Targeted Advisory Service on Animal Health (TASAH) investigations of infected herds. There are pathways for assurance of herds with continuing negative tests and for management of test-positive herds. Herdowners are responsible for on-farm activities, and specifically-trained (approved) veterinary practitioners have a pivotal role as technical advisors and service providers. The programme is supported by training of veterinarians, performance of testing in designated laboratories, documentation of policies and procedures, innovative data management for herd and test activities and for programme administration, training, and broad communication and awareness activities. Tools and systems are refined to address emerging issues and enhance the value of the programme. An Implementation Group comprising industry, government and technical leaders sets strategic direction and policy, advised by a Technical Working Group. Shared funding responsibilities are agreed by key stakeholders until 2022 to support herds in the programme to complete requirements. Herd registrations have increased steadily to exceed 1,800. National bulk tank milk surveillance is also being deployed to identify and recruit test-positive herds with the expectation that they have a relatively high proportion of seropositive animals. The programme will continue to innovate and improve to meet farmer and industry needs.

Website editor’s note: According to the Irish Cooperative Organisation Society’s website, “There are 18,000 dairy farmers in Ireland, producing milk of an outstanding quality from over 1.2 million dairy cows. Irish dairy farms are family run enterprises, supplying 6.4 billion litres of milk in 2015.” This means that the Irish Johne’s Control Programme has enrolled roughly 10% of Irish dairy herds this far.


The Irish JD program has all the same elements found in most national Johne’s disease programs:
1. Education of producers and veterinarians.
2. Herd risk assessments to identify when and where MAP transmission occurs on the farm.
3. Changes to animal husbandry methods to limit MAP transmission.
4. Regular application of diagnostic tests to all adults in the herd for many years.
5. Consistent actions based on the diagnostic test results.
6. Monitoring progress.

The program is also available for beef cattle producers.

The authors of this publication discuss the challenges for sustaining and growing the program stating: “The judgement of insufficient reward for the risk, inconvenience and expense of participation, especially for low-risk herds, remains a constant limitation and is recognised as an inhibitor to uptake of programmes internationally”.

This impediment could be addressed by paying farmers more for milk from herds that are test-negative or deemed to be low-risk. Currently, according to the Animal Health Ireland (AHI) website, Irish milk processors pay dairy farmers a set amount per cow each year depending on whether they are in the test-negative pathway or the test-positive pathway and the number of years in the program, as shown below (copied from the AHI website).

Funding Support per Eligible Animal by Year of Registration 

Test-negative pathway

  1. €2.75 ($3.25)**
  2. €2.06 ($2.43)
  3. €1.38 ($1.63)
  4. Nil*

Test-positive pathway

  1. €2.75 ($3.25)
  2. €2.75 ($3.25)
  3. €2.75 ($3.25)
  4. €2.75 ($3.25)

*It is anticipated that after four consecutive years of test-negative results, herds in the text-negative pathway will move to a lower-intensity maintenance testing programme – details of which are to be announced in the near future.
** Currency conversion based on values on 11-SEP-2021.

There are two problems with this. First, while I am sure the financial support is welcome, it represents a very small portion of the actual costs that dairy producers incur when trying to control JD. For more on the costs of a JD control program see Table 6 in Roch, et al. Journal of Dairy Science, 2020 (Open Access).

Secondly, in this plan for test-negative herds there appears to be a financial disincentive to remain in the program. It seems to me that test-negative herds should be paid an increasing amount for each year they remain in the program and the test-positive herds that do not show progress in the program after 3 years should have a decreasing rate of financial support. Farmers must spend money not only on annual diagnostic testing of their herd but also the management changes necessary to limit MAP transmission. They do this for the health and welfare of their animals but also for the health and safety of the public and the profitability of the Irish dairy industry as a whole.

In 2019, according to the Irish Dairy Board website, Irish dairy exports reached €4.4 billion, making it the largest food and drink export category. This was the third consecutive year in which the value of dairy exports exceeded the €4bn mark. Protection and expansion of export markets are a major driver for the Irish dairy industry as the graphic below shows.

Profits from the export of dairy products, that rely on the eco-friendly, wholesome and healthy image of Irish dairy products with a zero or very low MAP infection rate, need to be equitably shared with the people who make this possible, the Irish dairy producers.



2021-09-09 14:43:31


In 2009 Dairy UK, milk processor body set up an industry initiative with stakeholders from the dairy industry called Action Johne's. All UK dairy farms have a single supply contract with a designated buyer, who has control over the standards to which the milk is produced. This has progressed over the years from a Johne's Disease (JD) education and engagement program to a more structured framework for the control and management of Johne's Disease in the UK dairy herd called the National Johne's Management Plan (NJMP).

In 2017 the scheme structure involved the training or more than 1000 veterinarians to be Approved JD Advisors through the British Cattle Vet Association and a campaign through the milk buyers to ensure their farmers had undertaken an annual risk assessment in conjunction with a trained and accredited Johne's Veterinary Adviser and selected an appropriate control strategy from six possible options. The UK national farm assurance program (Red Tractor) incorporated the NJMP into the dairy farm standards in 2020, effectively making it mandatory to be part of the NJMP, resulting in 95% of all UK dairy farmers now being included in the scheme.

Dr. Pete Orpin, Chair of the Johne’s Technical Action Group has provided the document updating the UK National Johne's Management Plan and a link to videos describing the UK program and the progress it has made to date.


The UK program has all the same elements found in most national Johne’s disease programs:

  1. Education of producers and veterinarians.
  2. Herd risk assessments to identify when and where MAP transmission occurs on the farm.
  3. Changes to animal husbandry methods to limit MAP transmission.
  4. Regular application of diagnostic tests to all adults in the herd for many years.
  5. Consistent actions based on the diagnostic test results.
  6. Monitoring progress.

What is special about the UK program is that the main costs of implementing the program have been born by the farmers and milk processors, and indirectly by the milk market. There has not been any State involvement.



2021-09-01 15:46:37


Pamela Steuer, working on the laboratory of Miguel Salgado at the Universidad Austral de Chile, published a series of three articles on the effects of copper ions on Mycobacterium avium subsp. paratuberculosis (MAP). This news story summarizes those three articles.


The first study, published in2018 in BMC Microbiology, showed that copper ions resulted in a significant reduction of MAP in suspended in saline (PBS), although some MAP survival on some occasions was observed.

The second study, published in 2020 in the Journal of Applied Microbiology, showed that copper ions have a significant inactivating effect on MAP as well as certain other bacterial communities found in naturally contaminated cow’s milk. However, there were some copper-tolerant MAP strains.

The third study, published in the July 2021 issue of Animals (Open Access), attempted to use copper treatment of milk to prevent infection of calves on farm. Below is the full abstract of that publication.


One of the important routes of Mycobacterium avium subsp. paratuberculosis (MAP) transmission in dairy calves is milk. The aim of the present study was to assess the efficacy of milk treatments to prevent MAP infection transmission to calves. A one-year longitudinal study was carried out. Newborn calves were assigned to one of four experimental groups: 5 calves received naturally MAP-contaminated milk, 5 calves received copper treated milk, 4 calves were fed calf milk replacer, and 3 were fed UHT pasteurized milk. MAP load in milk was estimated. Infection progression was monitored monthly. After one year, calves were euthanized, and tissue samples were cultured and visually examined. MAP was undetectable in milk replacer and UHT milk. Copper ion treatment significantly reduced the number of viable MAP in naturally contaminated milk. Fecal shedding of MAP was observed in all study groups but began earlier in calves fed naturally contaminated milk. Paratuberculosis control programs must place multiple hurdles between the infection source, MAP-infected adult cows, and the most susceptible animals on the farm, young calves. As our study shows, strict dependence on a single intervention to block infection transmission, no matter how important, fails to control this insidious infection on dairy farms.


This series of studies opens new avenues of investigation on use of copper to control of MAP. There are many applications of copper to kill MAP in settings other than the farm that can be explored. However, as the on-farm study showed, controlling MAP in dairy cattle requires multiple complimentary strategies to be effective.

The fact that a Chilean institution studied the effect of copper on MAP is no surprise. Chile produces more than one quarter of the world's copper and is also by far the country with the largest copper reserves.



2021-08-06 15:05:54


Dr. C.T. Dow has published a thought-provoking article (11 pages with 169 references) proposing that the inflammatory response to a MAP infection of humans could lead to Alzheimer’s disease. The article appears in the August issue of Frontiers in Immunology.


This article prosecutes a case against the zoonotic pathogen Mycobacterium avium ss. paratuberculosis (MAP) as a precipitant of Alzheimer’s disease (AD). Like the other major neurodegenerative diseases AD is, at its core, a proteinopathy. Aggregated extracellular amyloid protein plaques and intracellular tau protein tangles are the recognized protein pathologies of AD. Autophagy is the cellular housekeeping process that manages protein quality control and recycling, cellular metabolism, and pathogen elimination. Impaired autophagy and cerebral insulin resistance are invariant features of AD. With a backdrop of age-related low-grade inflammation (inflammaging) and heightened immune risk (immunosenescence), infection with MAP subverts glucose metabolism and further exhausts an already exhausted autophagic capacity. Increasingly, a variety of agents have been found to favorably impact AD; they are agents that promote autophagy and reduce insulin resistance. The potpourri of these therapeutic agents: mTOR inhibitors, SIRT1 activators and vaccines are seemingly random until one recognizes that all these agents also suppress intracellular mycobacterial infection. The zoonotic mycobacterial MAP causes a common fatal enteritis in ruminant animals. Humans are exposed to MAP from contaminated food products and from the environment. The enteritis in animals is called paratuberculosis or Johne’s disease; in humans, it is the putative cause of Crohn’s disease. Beyond Crohn’s, MAP is associated with an increasing number of inflammatory and autoimmune diseases: sarcoidosis, Blau syndrome, autoimmune diabetes, autoimmune thyroiditis, multiple sclerosis, and rheumatoid arthritis. Moreover, MAP has been associated with Parkinson’s disease. India is one county that has extensively studied the human bio-load of MAP; 30% of more than 28,000 tested individuals were found to harbor, or to have harbored, MAP. This article asserts an unfolding realization that MAP infection of humans 1) is widespread in its presence, 2) is wide-ranging in its zoonosis and 3) provides a plausible link connecting MAP to AD.


(excerpt from the discussion section of the article)

This article suggests steps to further investigate this potentially fertile line of inquiry: 1) determine population-based MAP “bio-load”, 2) use optimized blood-based biomarkers to determine AD risk, 3) test for MAP in those with elevated AD risk vs. healthy controls. Concurrently, interventions could be initiated to 1) eliminate MAP from animals, the environment, and the food chain, 2) initiate clinical trials to test iterations of anti-mycobacterial agents shown to have benefit for AD. Parsimoniously, when searching for new directions in the efforts against AD, look at the MAP.



2021-07-15 11:00:47


Lauren and John Todd Kuenstner have published an article titled: Mycobacterium avium ssp. paratuberculosis in the Food Supply: A Public Health Issue which appears in the most current issue of Frontiers in Public Health.

Article Description

This article examines the policy implications of Mycobacterium avium subspecies paratuberculosis (MAP) as a zoonotic pathogen and the public health risks posed by the presence of MAP in food, particularly milk products. Viable MAP has been cultured from commercially pasteurized milk in the US. Dairy pasteurization standards and regulations are examined in light of this finding. On the basis of the precautionary principle, the authors suggest options to reduce exposure to MAP, including (1) increased federal authority to regulate pasteurization of all dairy products, (2) modification of pasteurization standards in order to more effectively kill MAP, (3) removal of the Pasteurized Milk Ordinance (PMO) provision that allows states to override federal policy in intrastate dairy sales, and (4) creation of a mandatory Johne's Disease Control Program. These measures would reduce human exposure to MAP and may reduce the risk of diseases associated with MAP.


The Precautionary Principle is used in EU countries but less so in the US.  Wikipedia does an excellent job describing this principle that guides development of many governmental regulations.  It is worth reading the entire article, including criticisms are the very end.




2021-06-23 01:00:12


Researchers in Mexico surveyed sheep flocks in the state of Aguascalientes in Mexico. Their findings were published in Abanico Veterinario.


With the objective of identifying the presence of Paratuberculosis (PTB), an infectious disease caused by Mycobacterium avium ssp paratuberculosis (MAP), in sheep, through pathological studies, bacterial culture and IS900 PCR, as well as estimating seroprevalence to MAP. The present cross-sectional study, was conducted in 16 different flocks, with the serum of 2415 adult sheep, and analyzed by Enzyme-Linked ImmunoSorbent Assay (ELISA); nine sheep were used with clinical signs suggestive of PTB, from which samples were obtained for the identification studies; obtaining 51.3% of animals seropositive to MAP (1239/2415), in 100% of the herds (16/16); Bacterial isolation and its identification by PCR IS900 were founded in five of the nine cases (5/9) corresponding to 31.25% of the herds (5/16). Confirming the presence of Mycobacterium avium ssp paratuberculosis, and a high frequency of seropositive animals to MAP in flocks of Aguascalientes.


Con el objetivo de identificar la presencia de Paratuberculosis (PTB), enfermedad infecciosa causada por el Mycobacterium avium subsp paratuberculosis (MAP), en ovinos, a través de estudios anatomopatológicos, cultivo bacteriano y PCR IS900, así como estimar la seroprevalencia a MAP. El presente estudio, de tipo transversal, se realizó en 16 diferentes rebaños con el suero de 2415 animales adultos y analizados por Ensayo por Inmunoabsorción Ligado a Enzimas (ELISA); se emplearon nueve ovinos con signos clínicos sugerentes a PTB, de los cuales se obtuvieron muestras para la realización de los estudios de identificación; obteniendo un 51.3 % de animales seropositivos a MAP (1239/2415), en el 100% de los rebaños (16/16); el aislamiento bacteriano y su identificación por PCR IS900 en cinco de los nueve casos hallados (5/9) correspondiendo al 31.25% de los rebaños (5/16). Conformando la presencia del Mycobacterium avium subsp paratuberculosis, así como una elevada frecuencia de animales seropositivos a MAP en rebaños de Aguascalientes.


Johne’s disease is far more common than most sheep owners realize. Biosecurity regarding animal purchasing is critical to prevention of this economically important disease. This is especially true for sheep breeders. MAP infection prevention is far less costly than MAP infection control. In other words: PREVENTION PAYS. Sheep breeders should only buy animals from flocks that are 100% negative by fecal PCR. Breeders that don’t follow this practice will eventually have sheep that look like the one shown above from publication and then spend years and a lot of money trying to eradicate the infection.



2021-06-17 16:17:57


Australian researchers have published the results of a large scale 10-year effort to control Johne’s disease in sheep, also known as ovine JD (OJD). The study was published in PLOS ONE (38 pages with 106 references). It is one of the most comprehensive and extensive field studies on JD vaccination and the publication is comprehensive in its discussion of OJD and the role of vaccination; highly recommended reading.



Mycobacterium avium subsp. paratuberculosis (MAP) causes Johne’s disease (or paratuberculosis), a chronic wasting disease of ruminants and other animals resulting from granulomatous enteritis. There are increasing concerns that MAP is zoonotic. The prevalence of Johne’s disease is increasing worldwide. In an attempt to control an epidemic of ovine Johne’s disease (OJD) in New South Wales (NSW), a government/industry sponsored voluntary vaccination/on-farm management program commenced in 2000. We report herein an observational study of changes in disease prevalence as vaccination progressed, based on abattoir surveillance data for OJD from 1999 to 2009. We also discuss the epidemiological, policy, regulatory, research, economic and sociological elements that contributed to the development of a mature control program, whose aim was to halt the epidemic spread of OJD in a naïve sheep population.


NSW was divided into areas of “High” (HPA), “Medium” (MPA) and “Low” (LPA) OJD prevalence. A killed whole cell vaccine (Gudair®) was administered to sheep from 2000 to 2009. Trained examiners evaluated the viscera of adult sheep carcasses at slaughter for gross evidence of OJD. MAP infection was confirmed by histopathology.

Principal findings

From 2000–2009, 12 million vaccine doses were administered in NSW (91%; 10.9 million in the HPA). Many of the vaccinated flocks were suffering > 5% annual mortality in adult sheep, with some individual flocks with 10–15% losses attributable to OJD. A total of 7.6 million carcasses were examined (38%; 2.9 million from the HPA). Overall, 16% of slaughter consignments (sheep consigned to the abattoir from a single vendor) were positive for OJD, of which 94% were from the HPA. In the HPA, the percentage of animals with lesions attributable to OJD at slaughter fell progressively from 2.4% (10,406/432,860) at commencement of vaccination in 2000 to 0.8% (1,573/189,564) by 2009. Herd immunity from vaccination in the HPA was estimated at 70% by 2009, the target commonly espoused for an effective control program based on vaccination. This coincided with a progressive decrease in reports of clinical disease and mortalities in vaccinated flocks.


We show a decrease in the prevalence of lesions attributable to OJD in NSW concomitant with initiation of voluntary vaccination, on-farm management plans, abattoir monitoring and feedback of animal prevalence data to sheep producers. We conclude that a target of ≤ 1% regional prevalence of OJD affected sheep at slaughter is achievable using these interventions.


As the authors noted, the decline in OJD animal-level prevalence was achieved “by the combination of voluntary vaccination, abattoir monitoring, feedback of surveillance data to sheep producers and the implementation of appropriate disease management strategies on farm”. The study was not designed to define the extent to which each of these practices contributed to OJD control, although there is a tendency to give the vaccine most of the credit.

Only 7 countries (31.8% of 22 countries with JD control programs) use vaccination as part of their JD control program (Whittington, 2019). This is due in part to conflicting data on the efficacy of vaccination, interference with TB testing and eradication programs, and the hazards of using the current vaccines. Presently, the widest use of JD vaccines is in countries with a significant small ruminant animal agriculture and then primarily in commercial production systems, as opposed to breeder flocks. This is largely due to economics, i.e., other JD control methods are deemed not affordable.

This important publication shows the economic value of vaccination as part of a comprehensive JD control effort at a regional or national level. Having lost the opportunity in most countries to eradicate JD before it became endemic, vaccination may become necessary for protection of both animal and human health. However, there is significant room for improvement in the safety and efficacy of current JD vaccines.



2021-06-01 16:02:56


Portuguese researchers found high levels of MAP in domestic water supplies in parts of Portugal with a high incidence of inflammatory bowel diseases, such as Crohn’s disease, in humans. The article by Sousa and colleagues was published in AIMS Microbiology.


Mycobacterium avium subsp. paratuberculosis (MAP) may play a role in the pathology of human inflammatory bowel disease (IBD). Previously, we found a high frequency (98% in patients with active disease) of MAP DNA detection in the blood of Portuguese Crohn’s Disease patients, suggesting this cohort has high exposure to MAP organisms. Water is an important route for MAP dissemination, in this study we therefore aimed to assess MAP contamination within water sources in Porto area (the residential area of our IBD study cohort).

Water and biofilms were collected in a wide variety of locations within the Porto area, including taps connected to domestic water sources and from municipal water distribution systems. Baseline samples were collected in early autumn plus further domestic water samples in early winter, to assess the effect of winter rainfall. DNA was extracted from all 131 samples and IS900-based nested PCR used to assess the frequency of MAP presence.

Our results show high MAP positivity in municipal water sources (20.7% of water samples and 41.4% of biofilm samples) and even higher amongst domestic sources (30.8% of water samples and 50% of biofilm samples). MAP positivity in biofilms correlated with positivity in water samples from the same sources. A significantly higher frequency of MAP-positivity was observed during winter rains as compared with samples collected in autumn prior to the winter rainfall period (61.9% versus 30.8%). We conclude that domestic and municipal water sources of Porto region have a high burden of MAP contamination and this prevalence increases with rainfall. We hypothesize that human exposure to MAP from local water supplies is commonplace and represents a major route for MAP transmission and challenge which, if positively linked to disease pathology, may contribute to the observed high prevalence of IBD in Porto district.


MAP is spilling over from animals to humans through contaminated food and water leading to human disease. In other words, MAP is a zoonotic infection, and it is a global problem. The most effective means of protecting human health is to control the infection in food-producing animals. Doing so will not only improve human health, it also will improve animal health and welfare as well as farm profitability. Seems like a “no-brainer”.



2021-05-22 01:00:09


Ninety-nine years ago today, two University of Wisconsin faculty published a seminal article on Johne’s disease. The full article is provided here for Johne’s history enthusiasts. Although published so long ago, the descriptions of the pathology and epidemiology of the disease are remarkably accurate. Today’s Johne’s news highlights some of the prophetic statements made by those authors.

Johne’s disease is one that is not at all widespread in Wisconsin or in any part of our country at present. It does occur, however, and as the years go by it will become more and more common and will place a greater tax on the cattle industry unless some consideration is given to it by those engaged in the raising and sale of cattle.”

The affected animals lose flesh very slowly until they become virtually walking skeletons. The unthrifty condition of animals, in spite of abundant feed, is occasioned in part by this disease.”

…it is likely to be present in pure bred herds from which animals are being sold in great numbers. A few such distributing centers will thus spread with a constantly increasing rapidity unless more attention is paid too it that is done at present.

The aim of this bulletin is to call the attention of veterinarians and breeders to Johne’s disease, which, it is felt, is not recognized by many, in order that steps may be taken to prevent its introduction into still healthy herds, and to gradually eliminate it from affected herds.

These statements were published by B.A. Beach and E.G. Hastings in 1922 in the Wisconsin Bulletin, a publication by the Wisconsin Agriculture Experiment Station. Their warnings remain true today and their aim, to raise awareness, is the same aim as that of this website.


Fast forward 99 years and, based on USDA survey data from 2007, we find that over 90% of U.S. dairy herds are now MAP-infected (Lombard et al., 2013), and the situation in most other major dairy-producing countries is similar. Millions of animals have died or been culled from herds due to this disease. Millions of dollars in farm income are lost annually because we failed to heed these warnings. And, we now find the cause of Johne’s disease, MAP, spilling into humans through contaminated food and water.

  • More indications that JD is common and MAP is in raw meat:
    A Georgia, USA a survey of cattle sold at sale barns using ELISA found that 9.58% of dairy cattle and 3.95% of beef cattle tested ELISA-positive. Given the accuracy of ELISAs, the actual infection rates are roughly double these figures (Pence, 2003). Most of these cattle were headed to slaughterhouses (abattoirs) and then into the food supply.
  • A survey of culled dairy cows in Atlantic Canada and Maine, USA found that 16.1% of the cows were culture-positive for MAP. The meat from these animals also was headed into the human food chain (McKenna, 2004).
  • A Colorado, USA study of 40 cull dairy cows found that 21 had MAP disseminated infection. Moreover, 57% (12/21) of cows with disseminated infection had average to heavy body condition and no diarrhea. Cows with disseminated infection had no to minimal gross pathologic evidence of infection in 37% (8/21) of cases. Only 76% (16/21) of cows with disseminated infection had positive historical ELISA results and only 62% (13/21) had a positive ELISA at slaughter (Antognoli, 2008). Thus, further verifying that ELISAs underestimate the number of MAP-infected cows with disseminated MAP infections that enter the food supply.

Side note:
The University of Wisconsin (UW) has remains a leader in Johne’s disease diagnosis and research. Ekundayo and Okoh provided a review of paratuberculosis literature published from 1911 to 2019 (Microoganisms, 2020). The graphic below from their publication indicates, by size of the circle, the number of scientific publications and collaborations between UW and other institutions working on paratuberculosis. The purple circle for the University of Wisconsin is the largest and most interconnected. This website is a legacy of the UW tradition in paratuberculosis research and outreach.



2021-03-26 16:58:46


Surveillance of cattle herds for MAP infections can be costly if individual cows are tested by fecal PCR. Some countries, such as the U.S., have adopted methods allowing pooling of fecal samples from 5 cattle before doing culture of PCR testing. If the pooled fecal sample tests PCR-negative, then all cattle contributing to that pooled sample are considered PCR-negative.

Australian researchers published a simulation modelling study indicating that the pool size can be increased to 10. Their study was published in the journal Preventive Veterinary Medicine.


Johne’s disease is a chronic intestinal disease affecting livestock. It leads to the shedding of Mycobacterium avium subspecies paratuberculosis (MAP) in the faeces, wasting and eventually death, with animal welfare, economic, and trade implications. The Johne’s Beef Assurance Scheme, used in Australia to determine the risk of Johne’s disease on beef properties and facilitate trade, is based on testing a subset of the herd with pooled faecal quantitative PCR. This study aimed to model the herd-sensitivity of pooled faecal testing under different Australian farming scenarios. Animals from simulated herds were randomly sampled and allocated into their respective pools. Each tested pool was provided a test outcome, with herd-sensitivity estimated as the probability of detecting a truly infected herd. The models simulated the test performance for the ‘Sample’ and ‘Check’ tests used in the assurance schemes (recommended sample sizes of 300 and 50, respectively) for a range of herd sizes, infection prevalence and MAP faecal shedding levels for the pool sizes of 5, 10, 15 and 20. Sensitivity and specificity input values of each pool size were obtained from a previous laboratory investigation. The herd-sensitivity estimate increased with herd size and infection prevalence levels, regardless of the pool size. Higher herd-sensitivity was also achieved for testing scenarios involving larger sample sizes. A pool size of 10 achieved similar herd-sensitivity to that of the current pool size for the majority of the Sample test and Check test scenarios. This was particularly evident when pool-specificity was assumed to be perfect. The overall herd-sensitivity of the Check test was very low for all infection prevalence levels and pool sizes, but it more than doubled, when the sample size increased from 50 to 100 animals (11%  versus 26% for a herd size of 500 cattle with a 2% infection prevalence). The results show that the majority of beef producers participating in the assurance scheme can benefit from using a larger pool size for the pooled faecal quantitative PCR testing of their herd, in comparison to the pool size currently used.


Kalis et al. (2000) first demonstrated that fecal sample pooling (5/pool) was effective at detecting MAP-infected dairy herds. Importantly, he showed that samples should be pooled based on animal age. He called this “strategic pooling”. The importance of this cannot be stressed enough. Animals born around the same time experience similar risks of acquiring a MAP infection. Therefore age-based (strategic) pooling helps insure that the least number of sample pools test positive and thus the fewest number of individual cattle require follow-up PCR testing.

Wells et al. (2002) compared dairy cattle fecal pools of 5 and 10 and concluded that pools of 5 were slightly more sensitive than pools of 10 when using fecal culture as the diagnostic test. This was a small study that used feces from only 10 cows to construct various fecal combinations in pools.

Van Schaik et al. (2007) collected 50 fecal samples from each of 12 Chilean dairy herds and compared pools of 5 and 10 samples finding that pools of 10 were as good or better than pools of 5 at detecting MAP-infected dairy herds.

It is challenging for veterinary diagnostic laboratories to change protocols but perhaps the time has come to consider using age-based pooling of 10 fecal samples in cattle herds that have a very low or zero rate of MAP-infections. Unless a herd is trying to meet US. or other Johne's disease program standards for herd classification, there is no mandate to test fecal samples in pools of 5. Standards may differ in other countries.

Below are cost calculations for a herd of 100 cattle tested by fecal PCR using pools of 5 or 10 cattle/pool. Only laboratory fees are calculated, and prices are based on the rates posted on the Wisconsin Veterinary Diagnostic Laboratory (WVDL) website 26-MAR-2021 (individual feal PCR @ $30.89 and pooled PCR @ $35.02). It does not include the $10 accession fee, veterinary costs, or sample shipping. Costs are rounded to the nearest U.S. dollar. Note: The WVDL has no extra cost for Johne’s disease tests for samples originating from states or than Wisconsin.

For comparison, the cost of testing 100 cattle individually by fecal PCR would be $3,502.

This table illustrates that:

  1. Sample pooling can save money. Even if 5 fecal pools test PCR-positive the total cost for testing a herd of 100 cows would be less than testing each cow individually by fecal PCR.
  2. Sample pooling is most advantageous for herds with a low MAP infection prevalence, i.e., few PCR-positive pools.

It is important to stress that to have the fewest number of positive pools, samples should be pooled based on animal age. This will tend to group fecal samples from MAP-infected cows into the same sample pool results in in fewer pools requiring individual fecal sample testing.

How does this compare to testing by ELISA (blood sample testing)?

The cost for testing a herd of 100 cows by ELISA would be $600 at current WVDL prices. In most instances, cows testing ELISA-positive would have to be retested by individual fecal PCR to confirm the diagnosis. This makes the per head cost of doing pooled fecal PCR equal to or less than that of testing by ELISA for low prevalence herds. This is especially true if pools of 10 are tested. Given that the fecal PCR is roughly 2 to 3 times more sensitive than the ELISA, herd owners get a better return on their investment in Johne’s disease diagnostics by using fecal PCR on pooled samples; no need to resample and test ELISA-positive cows by fecal PCR and greater confidence in that the PCR-negative cattle are truly not MAP-infected.

Not all laboratories offer pooled fecal PCR testing and prices vary considerably among veterinary diagnostic laboratories. Talk to your herd veterinarians and consult with testing laboratories before sending samples. This website provides a list of laboratories that are USDA-approved to perform pooled fecal testing: scroll down to the PDF file named “Johne’s Disease-pooling methods”.

What about sheep and goats?

Sample pooling studies have not been reported for goats, but cattle-based studies are a good guide.  In Australia, fecal samples from 50 sheep are pooled before PCR testing.




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