University of Wisconsin–Madison



Typically used when referring to diagnostic tests, accuracy means how often the test is correct. Since tests are usually interpreted as either positive or negative, and animals can either be infected or not infected, accuracy reflects the combined sensitivity (rate of being correct with the test is positive) and specificity (rate of being correct with the test is negative) of a test.

AGID (Agar Gel Immunodiffusion Assay)

A diagnostic test using serum (the fluid, non-cellular part of blood) that detects antibody produced in response to infection. Serum is placed in a well in the agar and a MAP antigen preparation is placed in a nearby well. These two test components passively diffuse out of the well into the agar. If the serum sample contains antibodies to antigens of MAP they bind, forming an interlaced antigen-antibody complex that precipitates in the agar. The precipitate is visible to the unaided eye as a thin white line. This same technology is used for diagnosis of other diseases. The test is best interpreted by using a known positive control serum sample (provided in commercial kits) in the assay for comparison. This test has largely been replaced with more sensitive ELISA technology and commercial AGID kits for Johne's disease are no longer available (in the US).


An immunoglobulin produced by an animal usually in response to an infection. Found in the blood (and other sites) it carries a specific amino acid sequence that binds to a portion of the infecting organism (antigen). This antibody - antigen interaction is the basis of serologic diagnostic testing. This image comes fro Wikipedia where much more detailed information is provided.



A commercial system sld by BD diagnostics for detection of mycobacteria in samples. The basis of the system is growth of mycobacteria in a liquid culture medium called MGIT ParaTB Medium. Mycobacteria grow and consume oxygen in the sealed tube. An instrument, known as a BACTEC MGIT 960, measures the amount of oxygen in each sealed tube hourly as an indicator of whether bacterial growth has occurred. If mycobacteria are detected by the BACTEC MGIT system, further testing is required to determine exactly what species of mycobacteria has been isolated from the sample. The MGIT 960 incubates and reads 960 cultures. The incubation period is typically 49 days.    


CF (complement fixation) assay

A diagnostic test for serum (the fluid, non-cellular part of blood) antibodies to MAP, produced in response to infection. The technique, also used for diagnosis of other infectious diseases, requires that the antibodies bind to antigens and then bind (fix) complement. An indicator system, involving red blood cells pre-coated with anti-red blood cell antibody, allows interpretation of whether complement was fixed thus indirectly indicating that antibody to MAP was present in the test serum sample. By testing serial dilutions of each serum sample to be tested it is possible to gauge how much antibody to MAP is present in the test sample. Results are reported as the highest serum dilution not "fixing" complement. This assay is not internationally standardized. Each laboratory or country uses its own MAP antigen formulation. In addition, other reagents are needed that must be prepared fresh (notably antibody coated red blood cells) with each new batch of assays. Criteria for interpretation of the CF test for paratuberculosis also may vary between countries. There is a move internationally toward replacing the CF test with ELISA as the basis for testing animals for international trade because ELISA can be better standardized and hence more reproducible between countries. For more information on paratuberculosis testing for international trade the visitor should refer to the OIE Manual of Standards for Diagnostic Tests & Vaccines.

Clinical diagnosis

Diagnosis of a disease, such as paratuberculosis, only by means of physical examination of the animal. For example cows with chronic diarrhea, rapid weight loss, but without fever and loss of appetite may warrant a clinical diagnosis of paratuberculosis. Clinical signs can vary somewhat among animal species but weight loss is the most consistent sign.


Diseases that spread among animals or humans. Often used synonymously, and inaccurately, with "infectious". A disease may be caused by an infectious agent and yet not be contagious. An example is Lyme disease. Among wild mice this infectious disease is contagious (with the help of ticks). However, when humans are infected, the infected human is not contagious for other humans. In this situation, humans are referred to as a "dead-end host" since the infectious agent has no capacity to move on to other susceptible humans or animals. Paratuberculosis is a contagious infectious disease of animals.


Growing MAP in artificial media made in the laboratory. To culture MAP from clinical samples from animals first requires treatment of the sample to destroy the many other microbes in the sample that could interfere with growth or detection of growth of MAP. In order to ensure that the mycobacteria are not killed off as well, control of contaminating microbes is not always successful. Hence, roughly 5-15% of fecal cultures for MAP become contaminated, that is, are over-grown with other microbes making it impossible to know if MAP was in the original sample. This is one drawback of using this diagnostic method. The other drawback is that the slow growth rate of MAP. On traditional culture media the organism does not produce colonies visible to the unaided eye for 12-16 weeks. An alternative to traditional culture methods on solid culture media are liquid culture systems such as the BACTEC MGIT system or Trek ESP system. Shown on the right is a common solid culture medium, Herrold's Egg Yolk Agar, with MAP colonies seen in the tube on the left and a control, uninoculated tube, on the right.


For diagnostic tests that produce a numerical result, the point above which test results are classified as positive is called the cut-off. These are usually established by testing a large number of infected and non-infected animals and selecting the value that maximizes the sensitivity and specificity of the test. For diagnostic kits the cut-off is established by the kit manufacturer. It is well-established that the quantity of antibody is is directly related to: 1) the likelihood of a MAP-infection, 2) the rate of fecal shedding of MAP, 3) the probability an animal will soon develop clinical signs of Johne's disease, and 4) the degree of decreased milk production for dairy cattle. Thus, knowing the magnitude of the ELISA result, not only the positive/negative interpretation, is important. All ELISA tests for antibody in serum or milk yield numerical results. ELISA kits typically provide a single cut-off for positive/negative interpretation. However, the numerical results can be interpreted as negative, low-positive, moderate-positive or high (strong)-positive which gives animal owners valuable information. Animal owners are encouraged to use laboratories that provide this quantitative data and multiple levels of results interpretation.



Impaired performance of the normal function of some part of the body. Generally this is evident in some clinical (overt) sign or, for humans, symptom. Infection often, but not always, leads to disease. For paratuberculosis, there is a long period of time while the animal is infected when no evidence of disease is apparent. This is sometimes called the "incubation period" of the infection.


ELISA - Enzyme-Linked Immunosorbent Assay

A diagnostic test using serum (the fluid, non-cellular part of blood) that detects antibody produced in response to infection. ELISA technology is widely used to diagnose infectious diseases. As for other serologic assays, the fundamental basis of the test is binding of antibody in the test sample (serum) to MAP antigens in the test container. An indicator system based on an enzymatic reaction generating a colored product distinguishes ELISAs from CF or AGID (other ways of detecting antibody). The amount of color produced in the reaction is directly related to the amount of antibody in the test sample. While the colored reaction resulting from the ELISA can be interpreted by the unaided eye, most often an instrument called and ELISA reader measures the amount of color in each well and reports the result as an optical density (OD) value. OD values for test samples can be compared to negative and positive control samples to derive ELISA results. For example, the ELISA kit for paratuberculosis sold in the USA by IDEXX uses the ratio between the OD value for the sample to the OD value for the positive control (provided in the kit). The resulting value, called the S/P ratio, standardizes results for tests done on different plates, or different days or different laboratories. The S/P is a reproducible, quantitative measure of the level of antibody in the original serum sample. S/P values can be used to gauge the probability a tested animal is infected once sufficient representative control populations of infected and non-infected animals are tested. See the section on diagnosis of MAP infections in dairy cattle in this website for more information. Also, see the information provided sponsors of this website with ELISA kits for paratuberculosis.


"Endemic" is often used to characterize diseases that are generally found in a particular area; malaria, for example, is said to be endemic to tropical and subtropical regions. MAP infections have sadly become endemic in most countries.



A diagnostic test result that is negative even though the tested subject IS infected/diseased. Test sensitivity is the measure of test accuracy that describes the rate of false-negative test results. For example, a test with 60% sensitivity has a 40% false-negative rate (100%-sensitivity). False-negative results are common with Johne's disease. This is not because of a failure of the testing technology. Rather, it is because the MAP infection progresses so slowly and during the incubation phase is very hard to detect because few if any MAP are being shed in feces and the animal has not yet mounted an antibody response.


A diagnostic test result that is positive even though the tested subject is NOT infected/diseased. Test specificity is the measure of test accuracy that describes the rate of false-positive test results. For example, a test with 99% specificity has a 1% false-positive rate (100%-specificity).


Gamma Interferon

A chemical released by various cells, in particular white blood cells to enhance the cellular immune response to an infectious agent. (The generic terms for such chemicals is cytokine). Animals that are, or have been infected with MAP have cells circulating in their blood that have been "trained" to recognize the antigens of this bacterium and respond by releasing significant amounts of gamma interferon. This can be tested for in the laboratory by mixing a blood sample, collected to preserve live leukocytes (white blood cells), with antigens of MAP. After overnight incubation the blood is then tested for gamma interferon using a commercially available kit. This test for cellular immunity to MAP shows considerable promise as a method for detecting the infection in young animals. Similar gamma interferon assays are under development for animals other than cattle.



The study of the microscopic structure, composition and function of diseased tissue.



A measure of the number of new cases of infection or disease divided by the population "at risk" of getting the infection or disease over a specified period of time. Incidence should not be confused with "prevalence" - a measure of the total number of infected or diseased individuals at a specific point in time. Example: Loftus et al. (Gastroenterology 114:1161, 1998) reported that the incidence of Crohn's disease in Olmstead County Minnesota was 5.8 per 100,000 persons / year. On January 1, 1991 the prevalence of Crohn's disease in that county was 133 per 100,000. For chronic diseases prevalence is always much higher than the incidence. There are many studies reporting prevalence of paratuberculosis, primarily in cattle, in different states, countries or regions of the world. Incidence of paratuberculosis, however, is much harder to measure and is seldom reported.


The invasion and replication of a disease causing microbe in the body.


Likelihood Ratio (LHR)

A likelihood ratio expresses the odds, for instance, that a Johne's disease test result at a given level would be expected in an animal infected with M. paratuberculosis as opposed to one not infected. LHR is a very powerful way to interpret test results when the test produces a quantitative result such as the ELISA S/P ratio. LHRs can only be defined by actual testing of large populations of truly infected and truly noninfected animals. This website provides a more comprehensive explanation of LHRs.


Mycobacterium avium subspecies hominissuis (MAH)

This species of mycobacterium is commonly found in soil and water but is generally of low virulence, meaning it has only a limited capacity to cause infection and disease. In animals, pigs have the highest rate of MAH infections. However, they are self-limited infections that cause no obvious disease and are restricted to lymph nodes of the neck region and only seen by meat inspectors at the time of slaughter. In humans children may occasionally get MAH infections in the lymph nodes in their neck. MAH can also infect the intestinal tract of people with AIDS due to the impairment the HIV virus causes to their immune system. The significance of MAH to understanding Johne's disease is that this microbe is very closely related to MAP and can cause interference with immunological diagnostic testing (cross reactions causing false-positive test results). Other mycobacteria can potentially cause this same problem. However, this is not a very common occurrence in most species.

Mycobacterium avium subspecies paratuberculosis

This bacterium is the cause of Johne's disease. Molecular taxonomists prefer to name this organism Mycobacterium avium subspecies paratuberculosis (MAP) in recognition of its close genetic similarity to other Mycobacterium avium subspecies, collectively known as the Mycobacterium Avium Complex. Three characteristics distinguish MAP from other mycobacteria: 1) an in vitro (laboratory culture) growth requirement for mycobactin, an iron transport chemical produced all other mycobacteria, 2) very slow growth rate (this is the slowest growing of all culturable mycobacteria known to microbiologists), and 3) presence of a genetic element in the chromosome of the organism called IS900.


Mycobactin is a commercially available siderophore. Siderophores are chemicals synthesized by living organisms for the purpose of binding and/or transporting iron into cells. The chemical structure of Mycobactin J (the commercially available mycobactin used as a supplement in bacteriological media to support growth of MAP) was described by Schwartz and De Voss (Tetrahedron Letters 42:3653-3655, May, 2001). MAP is considered incapable of synthesizing mycobactin and hence is dependent on the presence of mycobactin in culture media for growth. With minor exceptions, MAP is considered the only species of mycobacteria dependent on mycobactin for in vitro growth. Mycobactin-dependency is a characteristic used to distinguish MAP from other mycobacteria that may be isolated during the culture assay of manure or tissue samples.

Mycobactin Dependency

MAP requires a substance called mycobactin to grow in the laboratory setting. The organism therefore can be identified by using two types of media: one with mycobactin, one without it. If the bacteria grows on both types of media, the organism is not mycobactin dependent and thus is not MAP. If it grows only on the media with mycobactin, this is strong evidence that the organism is MAP.



Pasteurization is the use of heat to reduce the number of bacteria in a liquid. Developed by Louis Pasteur in 1864 as a technique to improve wine production, the process is now the primary method used to reduce bacterial pathogens in milk to levels that do not constitute a risk to human health. In the United States there are two standard time/temperature combinations used for milk pasteurization. The first is called vat or low-temperature long-time (LTLT) pasteurization which requires holding milk at 62.8 °C (145 °F) for 30 minutes. The second is called high-temperature short-time (HTST) pasteurization which requires keeping milk at 71.7 °C (161 °F) for 15 seconds. HTST pasteurization is done on a continuous flow basis and is favored by commercial manufacturers of fluid milk and cream. (Another continuous flow process called ultra-heat-treated (UHT) pasteurization is in use in Europe and Asia. UHT milk is heated to at least 135°C (275°F) for 1.0 seconds.) These definitions were adapted from Encyclopedia of Dairy Sciences, Roginski, Fuquay & Fox, editors, Academic Press, 2003.


Synonymous with sub-clinical, pre-clinical describes an animal infected with MAP that does not yet show any signs of disease. The pre-clinical phase of paratuberculosis in cattle can last 1 to 10 years.

Predictive Value

Positive and negative diagnostic test results can be expressed as probabilities (of being correct). These are called the positive predictive value (PVP) and negative predictive value (NPV), respectively. To calculate PVP or NPV one must know the sensitivity and specificity of the test being used and know or estimate the prevalence of infection in the population of animals being tested. Specific formulas are given in the part of the website concerning serologic diagnosis of paratuberculosis in cattle.


This is a measure of the total number of infected or diseased individuals at a specific point in time. For example, the U.S. Dept. of Agriculture found that the apparent prevalence of MAP infected U.S. dairy herds is 60% (observed rate of test-positive dairy herds). Prevalence can be either the true, actual, infection or disease rate, or it can be the apparent prevalence, often called the test prevalence, meaning percentage of a population that tests positive. True prevalence can only be estimated from the test prevalence if you know the performance characteristics (sensitivity and specificity) of the test. The estimated TRUE prevalence of MAP infected dairy herds in the U.S. is 91%.



Animals that have a complex, four-chambered, stomach and chew their cud. The cud is a lump of hay or grass that is regurgitated from the stomach into the animal's mouth where it is chewed more to break down the fibrous plant material and mix it with saliva to aid in its digestion.



The frequency that a test for paratuberculosis is POSITIVE when animals are infected: the true-positive rate. Tests on infected animals are either true-positive or false-negative. Diagnostic sensitivity as described here must be distinguished from analytical sensitivity: the number of analytes (things being measured) it takes to trigger a positive test result. Example: the number of antibody molecules in serum needed to trigger a positive ELISA.


Diagnostic testing based on the binding of antibody and antigen. The antibody is produced by an animal in response to infection and is found in serum (fluid portion of blood). The antigen, a portion of the infecting organism, is incorporated into the diagnostic test. In most cases of Johne's disease, serology is most likely to detect an infected animal during later stages of the infection when antibody is most likely to be produced.


In the context of paratuberculosis biology, shedding usually refers to the excretion of MAP in feces, milk or semen. Animals in the more advanced stage of the infection become fecal shedders.


Signs of disease are manifestations caused by the infection that can be observed. Examples, diarrhea and weight loss are signs of Johne's disease. Signs are distinct from symptoms. Symptoms are things that can only be perceived by humans, such as a headache or anxiety.


The frequency that a test for paratuberculosis is NEGATIVE when animals are NOT infected: the true-negative rate. Tests on NONinfected animals are either true-negative or false-positive. Diagnostic specificity as described here must be distinguished from analytical specificity: the ability of an assay to distinguish between similar analytes (things being measured). Example: the ability of an assay to distinguish M. avium subspecies avium (MAA) from MAP is the analytical specificity of the assay.


Synonymous with pre-clinical, sub-clinical describes an animal infected with MAP that does not yet show any signs of disease. The sub-clinical phase of paratuberculosis in cattle can last 1 to 10 years.


Symptoms are subjective evidence of disease. Humans can describe feelings they have of being sick that are not obvious to an observer. An example is the feeling of aching muscles and joints that come with the flu are symptoms. Since animals can not talk, they can not have symptoms; they only have signs of disease.



This defines the outcome of a diagnostic test. Only by knowing the true MAP-infection status of an animal can you know for certain if the negative test is correct (true-negative) or incorrect (false-negative).


This defines the outcome of a diagnostic test. Only by knowing the true MAP-infection status of an animal can you know for certain if the positive test is correct (true-positive) or incorrect (false-positive).


Spread of MAP from one animal (usually an adult) to another (usually a young animal). The primary modes of paratuberculosis transmission are via feces, milk, or across the placenta (called in utero).


Tuberculosis (TB) is a disease of animals and humans that is distinctly different from paratuberculosis. TB in humans usually is caused by Mycobacterium tuberculosis and TB in cattle and most other animals usually is caused by Mycobacterium bovis. In both animals and humans TB most often affects the lungs and lymph nodes near the respiratory tract.


Waste Milk

Waste milk is an informal term referring to fluid milk that is not appropriate for use in food production for humans. There are a number of reasons the milk may not be used (such as its coming from a cow with mastitis i.e. high somatic cell count). Such milk is a potential risk for transmission of MAP to calves since the organism is shed into milk by infected cows or the milk is contaminated by manure containing the organism. Waste milk can be made safe if pasteurized on-farm. Alternatively, milk replacer (commercially prepared powdered milk) can be fed to calves prior to weaning with little or no risk of infecting the calf with MAP.



A disease of animals that may be transmitted to humans under natural conditions.