WO2015077541A2 - Mycobacterium biomarkers and methods - Google Patents

Abstract

This disclosure provides a method for detecting infection of an animal by Mycobacterium bovis. The method generally includes obtaining a biological sample from a host animal at risk of being infected by Mycobacterium bovis and analyzing the sample for the presence or absence of at least one M. bovis polypeptide. In some embodiments, the method can further include analyzing the sample for the presence or absence of at least one M. bovis lipid. In some embodiments, the method can further include detecting at least one host polypeptide whose expression is greater in a host infected with M. bovis compared to expression in a host known to be uninfected with M. bovis.

Description

MYCOBACTERIUM BIOMARKERS AND METHODS

CROSS-REFERENCE TO RELATED APPLICATION This application claims priority to U.S. Provisional Patent Application Serial No.

61/907,686, filed November 22, 2013, which is incorporated herein by reference. GOVERNMENT FUNDING

This invention was made with government support under 2009-34427.19959 awarded by the USDA. The government has certain rights in the invention.

SUMMARY

This disclosure provides, in one aspect, a method for detecting infection of an animal by

Mycobacterium bovis. The method generally includes obtaining a biological sample from a host animal at risk of being infected by Mycobacterium bovis and analyzing the sample for the presence or absence of at least one bovis polypeptide.

In some embodiments, the biological sample can include serum, plasma, urine, or a fecal extract.

In some embodiments, the M. bovis polypeptide does not cross-react with serum from a host animal infected with another Mycobacterium spp. In some of these embodiments, the other

Mycobacterium spp. ca include M. avium subsp. paratuberculosis. In other embodiments, the other Mycobacterium spp. can include M. kansasii.

In some embodiments, the M. bovis polypeptide can include MB1895c, MB2515c,

MB0862, MB1482C, MB2883c, MB 1929, MB1192 MB 1886c, MB2441c, MB2275, MB2122c,

MB 1672c, MB3729c, MB1268, MB3017c, or Pks5.

In some embodiments, the method can further include detecting at least one host polypeptide whose expression is greater in a host infected with bovis compared to expression in a host known to be uninfected with M. bovis. In some of these embodiments, the host polypeptide can include vitamin D binding protein (VDBP), fetuin-A. In some embodiments, the method can further involve analyzing the sample for the presence or absence of at least one M. bovis lipid. In some of these embodiments, the M. bovis lipid can include lipoarabinomannan.

In some embodiments, the host animal can have a sub-clinical M. bovis infection.

In some embodiments, the host animal can exhibit no symptoms or clinical sign of infection by M. bovis.

In some embodiments, the method may be performed in a field location. In some of these embodiments, the method may be performed using a microfluidic device. In other embodiments, the method may be performed using portable surface-enhanced Raman spectroscopy.

The above summary of the present invention is not intended to describe each disclosed embodiment or every implementation of the present invention. The description that follows more particularly exemplifies illustrative embodiments. In several places throughout the application, guidance is provided through lists of examples, which examples can be used in various combinations. In each instance, the recited list serves only as a representative group and should not be interpreted as an exclusive list.

BRIEF DESCRIPTION OF THE FIGURES FIG. 1 : Receiver Operating Characteristic (ROC) curves for host biomarkers. Each point on ROC curves is the fraction of bTB positive cattle (true-positive rate) versus the corresponding fraction of negative exposed bTB cattle (false-positive rate). VDBP is the most reliable biomarker (AUC = 0.8860), fetuin-A is a moderately reliable biomarker (AUC = 0.7741), and alpha- 1 antitrypsin is an unreliable biomarker (AUC = 0.5425).

FIG. 2: Vitamin D binding protein (VDBP) histogram. Relative densities were collected from negative bTB exposed (n = 82) and infected (n = 128) animals. Cutoff value (38.50) was determined based on ROC analysis and true negative rate versus true positive rate.

FIG. 3: Vitamin D Binding Protein distinguished bovine tuberculosis positive and negative exposed animals. The true negative rate and true positive rate using VDPB as a biomarker were plotted against each other. The optimal cutoff value corresponded to 38.50 (raw density). Cutoff value corresponds to a sensitivity of 80.6% and specificity of 81.7%.

FIG. 4: Receiver Operating Characteristic (ROC) curves for pathogen biomarkers. Each point on ROC curves is the fraction of bTB positive cattle (true-positive rate) versus the corresponding fraction of negative exposed bTB cattle (false-positive rate). Pks5 is the most reliable biomarker (AUC = 0.9676) and MB 18952 and MB2515c are moderately reliable biomarkers (AUC = 0.8353 and 0.7671, respectively).

FIG. 5: Polyketide synthetase 5 (Pks5) histogram. Relative densities were collected from negative bTB exposed (n = 428) and infected (n = 128) animals. Cutoff value (0.4 nm) was determined based on ROC analysis and true negative rate versus true positive rate.

FIG. 6: Pks5 distinguished bovine tuberculosis positive and negative exposed animals. The true negative rate and true positive rate using Pks5 as a biomarker were plotted against each other. The optimal cutoff value corresponded to 0.4 nm. Cutoff value corresponds to a sensitivity of 92.2% and specificity of 93.2%.

FIG. 7: Vitamin D binding protein (VDBP) histogram. Relative densities were collected from negative control (n=38), negative bTB exposed (n= 82) and infected (n = 128) animals. Cutoff value (38.50) was determined based on ROC analysis and true negative rate versus true positive rate. Control, positive and exposed groups showed clear separation.

FIG. 8: Polyketide synthetase 5 (Pks5) histogram. Relative densities were collected from negative controls (n = 38), negative bTB exposed (n = 428) and infected (n = 128) animals. Cutoff value (0.4 nm) was determined based on ROC analysis and true negative rate versus true positive rate.

FIG. 9: Pks5 Positive and Negative Predictive Values and Cutoff Values Based on Bovine tuberculosis Prevalence. Positive and negative predictive values were plotted against percent prevalence. Cutoff values were assigned to 4 scenarios based on prevalence. Scenario 1 = High bTB prevalence, Scenario 2 = Moderate bTB prevalence, Scenario 3 = Moderate-low bTB prevalence, and Scenario 4 = Low bTB prevalence.

FIG. 10. Receiver operating characteristic (ROC) curves for LAM. (A) Each point on

ROC curves is the fraction of bTB positive cattle (true-positive rate) versus the corresponding fraction of bTB exposed (false-positive rate) with an AUC of 0.983; (B) Each point on ROC curves is the fraction of exposed bTB cattle (true-positive rate) versus negative controls (false- positive rate) with an AUC of 0.949.

FIG. 11. LAM distinguishes bovine tuberculosis positive and negative controls and exposed animals. The true negative rate and true positive rate using LAM as a biomarker were plotted against each other. (A) The optimal cutoff value for bTB positive versus bTB exposed corresponds to O.D.₄₅onm of 0.7901 (100% sensitivity and 91.7% specificity); (B) The optimal cutoff value for bTB exposed versus negative controls corresponds to O.D.₄₅₀nm of 0.0055 (100% sensitivity and 93.9% specificity).

DETAILED DESCRIPTION OF ILLUSTRATIVE EMBODIMENTS

One element to preventing and/or control of bovine tuberculosis (bTB) is early and unambiguous identification of subclinical infection. Many diagnostics for subclinical infections rely on immune responses, which may be confounded by previous exposure to the suspect pathogen and/or cross-reactivity to similar microbes. This disclosure describes compositions and methods that permit one to detect subclinical infection by Mycobacterium bovis. The

compositions and methods involve M. ^ovzs-specific molecular signatures that may be detected in individuals with a subclinical M. bovis infection. The M. ftovw-specific molecular signature can include one or more M. bovis polypeptide and/or M. bovis lipid.

Bovine tuberculosis, a prevalent disease of cattle worldwide caused by Mycobacterium bovis, is one example of detection failure and misidentification using conventional technologies. The United States Department of Agriculture (USDA) bTB eradication program relies on three main tests: caudal fold test (CFT), comparative cervical test (CCT), and a γ-interferon release assay (IGRA, Bovigam, Prionics AG, Schlieren, Switzerland) (USDA- APHIS. 2005. Bovine Tuberculosis Eradication.35). All three tests are labor intensive, have logistical challenges, and sensitivity/specificity issues. For example, CFT lacks biological specificity for M. bovis infection and often fails to detect all diseased cattle, which can be further confounded by high background infection with a different pathogenic mycobacterium, M. avium subsp. paratuberculosis . In addition, IGRAs require blood processing within 24 hours of collection, which may not be feasible on large herds located in areas where a specialized laboratory is not easily accessible. Current testing limitations, significant economic losses, and spillover to human and wildlife populations highlight the urgency for a multifaceted test that increases detection, limits disease exposure, and distinguishes M. bovis infection from other mycobacteria and diseases that impact animal and human health.

The public availability of the genomes of cattle and M. bovis have advanced our understanding of host responses to M. bovis and its genetic elements that may be regulated during infection (Gamier et al. 2003. Proc Natl Acad Sci USA 100:7877-7882). Host responses utilized for conventional bTB diagnostics include an array of cytokines, chemokines, and antibody responses to M. bovis proteins. Although these tools provide another layer of testing, results obtained are often confounded by cross-reactivity due to homology between

mycobacterial species. Furthermore, host response testing often relies on a single cut-off value for detection, which may not be applicable to the testing needs of all environments. For example, endemic bTB regions may require diagnostics with a high sensitivity to eliminate all infected cattle to control disease spread, while areas of low bTB prevalence may seek increased specificity to minimize false positives and avoid unnecessary economic losses.

Identification of M. bovis polypeptides

In order to minimize cross-reactivity, we have identified 32 host and 16 pathogen circulating peptides, unique to M. bovis infection over a five-month follow-up of experimentally infected calves, using a highly sensitive proteomics approach (Seth et al. 2009. PLoS One 4:e5478). During infection, mycobacteria specific proteins, peptides, DNA, and lipids are shed into circulation and are likely to provide unprecedented specificity to identify M. bovis infection. A panel of biomarkers that includes host and pathogen peptides can establish a precise test to detect subclinical bTB infection. Serum host proteins (vitamin D binding protein (VDBP), fetuin-A, alpha- 1 antitrypsin) and three pathogen peptides (MB1895c, MB2515c, and Pks5) were identified by iTRAQ and validated using a well characterized cattle serum repository including confirmed cases of M. bovis, negative bTB exposed (animals in contact with bTB positive cattle), and negative controls. Based on our findings, we describe methods, compositions, and kits for identifying circulating pathogen peptides and host response proteins in sera that may augment diagnostics and track disease progression across the spectra for other pathogenic infections.

VDBP distinguishes confirmed bTB from uninfected and exposed cattle

The top three candidates identified by our previous study, alpha- 1 antitrypsin, fetuin A, and VDBP, were validated for diagnostic potential in a large scale screen of control and M. bovis infected cattle. A total of 248 animals (negative control [n = 38], confirmed bTB [n = 128], and negative bTB exposed [n = 82]) were tested for reactivity to alpha- 1 antitrypsin, fetuin A, and VDBP via dot blot analysis. The area under the Receiver Operating Characteristic (ROC) curves (AUC) determined that VDBP was the most reliable biomarker capable of differentiation of negative, M. bovis infected, and negative bTb exposed animals (FIGS. 1-3, FIG. 7). Similar to VDPB, ROC curve analysis of fetuin-A showed a near perfect separation (0.9949) between negative controls and bTB infected animals; however, separation between negative bTB exposed and infected animals decreased to 0.7741 (FIG. 1). Although analysis of alpha-1 antitrypsin AUC exhibited a separation value of 0.7967 for infected versus uninfected animals, separation between infected and exposed groups could not be distinguished (AUC = 0.5425) (FIG. 1). Herds suspected of bTB will unlikely include pristine animals (i.e., those that are uninfected and unexposed). Therefore, we examined VDBP as a potential diagnostic marker as the AUC for infected versus exposed animals was 0.8860 (FIG. 1). ROC analysis identified 5 cutoff ODs that retained high sensitivity and specificity, which ranged from 33.25-40.25 nm. The true negative rate and true positive rate were plotted against the OD cutoffs and the optimal cutoff value was 38.50 nm with a sensitivity of 80.597% and specificity of 81.7073% (FIGS. 2-3). Together these data show that VDBP is a reliable host biomarker that distinguishes negative, exposed, and bTb infected animals. iTRAQ identification ofM. bovis specific proteins in serum

Sera from five M. bovis infected calves at one and four months post-infection and uninfected controls were pooled and analyzed by iTRAQ. Peptides were compared against the M. bovis strain AF2122/97 genome. iTRAQ analysis identified 16 unique M. bovis proteins present in sera from calves at 4 months PI (CI=95%) (Table 1).

Table 1 : Proteins identified in sera from M. bovis calves four months post- infection.

Locus ID predicted function subcellular location

MB2515c transcriptional regulator Cytoplasm

(LuxR family)

MB0862 methyltransferase activity Cytoplasm

MB 1482c glucose metabolism Cytoplasm

MB2883c aldehyde dehydrogenase Cytoplasm

activity

MB 1929 redox activity Cytoplasm

MB 1886c redox activity Cytoplasm

MB1 192 hydrolase activity Cytoplasm

MB2441c hydrolase activity Cytoplasm MB2275 FAD binding activity Cytoplasm

MB2122c transcriptional regulator Cytoplasm

MB 1672c conserved hypothetical protein Cytoplasm

MB 1554c (pks5) cell wall biosynthesis Cytoplasm

MB 1895c molybdenum ion binding Extracellular

MB3729c conserved hypothetical protein Periplasm

MB1268 transporter activity Transmembrane

MB3017c isomerase activity Transmembrane

M. bovis proteins MB 1895c, MB2515c and Pks5 are present in bTB positive and exposed animals

Three M. bovis proteins (MB 1895c, MB2515c, and Pks5) identified in iTRAQ analysis were selected for antibody production. Field (bTb [n=128], negative bTB exposed [n=428], and negative control [n=38]) animals were tested for detection with MB1895c, MB2515c, and Pks5 antibodies. AUC show that all three pathogen markers easily distinguish negative from infected animals (FIG. 4). Pks5 showed the greatest separation of bTB positive samples from negative bTB exposed and negative animals (FIGS. 8). Cutoff values from ROC, true positive rate, and true negative rate analyses determined that the maximum sensitivity (92.2%) and specificity

(93.2%) was achieved at 0.4 nm (FIGS. 4-6). MB1895c cutoff value that provided separation of exposed and infected animals while retaining a high degree of specificity was 0.3 nm. The MB2515c cutoff value of 0.2 had a sensitivity of 69.5% and specificity of 64.1%. Together these data show that circulating pathogen peptides are detected within M. bovis infected animal sera, which may be used to distinguish control, exposed, and infected cattle.

Application of Pks5 to detect bovine tuberculosis in a low prevalence region

Many infectious disease diagnostics rely on a single cutoff value to indicate infectious status. However, diagnostic requirements may differ between regions of low and high prevalence for bTB. Therefore, we determined the positive and negative predictive values of Pks5 to correctly diagnose bTB given known disease prevalence of ~10% (FIGS. 2 and 3). In regions of high bTB prevalence, scenarios 1 and 2 would be applicable given increased sensitivity, while low prevalence areas would require increased specificity (scenarios 3 and 4) (FIG. 9). In order to determine the utility of Pks5 in a low prevalence bTB region and the possibility of cross- reactivity with other pathogenic mycobacteria, we tested sera from cattle infected with either M. avium subsp. paratuberculosis or M. kansasii and considered the cutoff value from scenario 4 (FIG. 9). Ninety percent of M. avium subsp. paratuberculosis and M. kansasii sera tested were categorized as uninfected animals under scenario 4 (low prevalence) and only 1 animal from each group was categorized as bTb infected. Data suggest that multi-cutoff value testing based on prevalence can provide bTB testing in various locations and that Pks5 is specifically shed. There is minimal Pks5 cross-reactivity to other pathogenic mycobacteria infections.

We tested three host serum proteins (VDPB, alpha- 1 -antitrypsin, and fetuin-A) and three pathogen proteins (MB2515c, MB 1895c and Pks5) in a large-scale validation study using well- characterized field sera from M bovis infected, negative bTB exposed, and negative controls. Reliance exclusively on host-related biomarkers of infectious disease can, however, provide indeterminate results. This may be due, at least in part, to cross-reactivity with similar pathogenic and environmental bacteria and/or other diseases (e.g., potentially of a non-infectious nature). We therefore interrogated iTRAQ datasets for M. bovis- specific proteins in infected animal sera. Pathogen proteins MB2515c, MB1895c, and Pks5, were present in all infected animal sera. All three proteins were capable of distinguishing M. bovis infected and suspect cases from uninfected controls. Although all three pathogen peptides easily separated negative from infected animals, this alone may not necessarily be adequate for all possible testing applications.. For example, animals within a suspected bTB herd are likely to be of an exposed status (i.e., contact with infected animals) rather than a truly uninfected classification. Thus, comparisons between only bTB and negative animals could lead to an improperly low cutoff value that, when applied in the field, can produce a higher false positive rate. Therefore, we examined the ability of each pathogen protein to differentiate between infected and exposed animals (FIG. 4). Pks5 provided a high AUC and, therefore, the ability to distinguish between both (a) infected versus exposed animals, and (b) bTB and negative animals.

Current testing strategies are based on a single cutoff value to diagnosis bTB infection regardless of prevalence. Such a "one-size-fits-all" testing method is not necessarily appropriate for all testing applications. For example, in the United States, bTB affects less than 0.1% of all herds and diagnostics with a cutoff based on high sensitivity may incorrectly identify animals exposed to other mycobacteria (e.g. M. avium subsp. paratuberculosis) as bTB positive. This sort of misidentification can negatively impact the agricultural economy of a low prevalence area. In such scenarios, cutoff values can rely more on specificity than sensitivity. In contrast, areas with a high prevalence of bTB, such as China and India, it may be beneficial to have testing cutoffs that rely more on sensitivity than specificity in order to capture all infected cattle and minimize potential spillover to other animals and humans.

Pks5 proved to be an effective marker for testing methods that may employ more than one, or variable, cutoff values suitable for a particular application. We determined exemplary Pks5 cutoff values based on scenarios for high (scenarios 1 and 2) and low (scenarios 3 and 4) prevalence areas (FIG. 9).

To ensure that Pks5 did not react with other pathogenic mycobacteria, we tested sera from animals infected with M. avium subsp. paratuberculosis and kansasii. Pks5 exhibited limited cross-reactivity against M. avium subsp. paratuberculosis- fected and kansasii- infected sera.

Identification of M. bovis lipids

We validated the presence of mannosylated lipoarabinomannan (ManLAM), a major mycobacterial cell wall glycolipid, in the serum of M. ftovw-infected cattle. During the establishment and progression of M. bovis infection, mycobacterial-specific proteins and lipids, including those from the bacterial cell wall, are shed into host fluids. Lipoarabinomannan, which is a cell wall glycolipid found on pathogenic mycobacteria, can be detected in sera and urine of M. ftovw-infected animals.

Fifty-five animals (uninfected [n = 33], bTb [n = 10] and exposed cases [n = 12]) were screened for the presence of LAM using a commercially available ELISA. A LAM concentration curve was created and cross-reactivity to another glycolipid, non-capped lipoarabinomannan (AraLAM), found in environmental mycobacteria was assessed. AraLAM was not discernable from the kit negative control. Herds suspected of a bTB-positive status will likely include contact animals (exposed) rather than pristine animals (i.e., uninfected and unexposed). Therefore, ROC and AUC analyses compared bTB-positive and bTB-negative controls against bTB-exposed animals.

The AUC showed a near perfect separation for bTB-positive versus bTB-exposed animals (0.983) and bTB-exposed versus bTB-negative control animals (0.949) (FIG. 10A and FIG. 10B, respectively). Five cutoff ODs (0.3368-0.16089 nm) that retained high sensitivity and specificity were identified in bTB-positive and bTB-exposed comparison by ROC analysis. ROC analysis of bTB-exposed versus negative controls determined three cutoff ODs (0.0055-0.068 nm).

The true positive and negative rates were plotted against the OD cutoffs to determine optimal cutoff values. The optimal cutoff value was calculated at 0.7901 nm with a sensitivity of 100% and a specificity of 91.7% for bTB-positive versus bTB-exposed animals (FIG. 11 A). The optimal cutoff value to distinguish bTB-exposed animals from negative controls was calculated at 0.0055 with a sensitivity of 100% and specificity of 93.9% (FIG. 1 IB). Together, these data indicate that the LAM ELISA can be effectively applied for rapid detection of M. bovis infection and exposure.

While detection systems utilizing host responses provided a first layer in identification of suspect diseased animals, they lack the needed specificity to eliminate cross-reactivity with other non-pathogenic mycobacteria or confusion with chronic illnesses of a non-infectious nature. This disclosure describes M. bovis peptides circulating in the serum accurately predict bTB-infected from bTB-negative and exposed animals. This disclosure further describes another M. bovis component, lipoarabinomannan (LAM), that is present in serum of bTB-infected animals. These M. bovis components may be used, either alone or with with additional pathogen signature components, to provide a battery test for subclinical bTB.

We show that the presence of LAM correlates with bTb infection and is capable of separating infected from bTB-exposed and bTB-negative animals. A single cutoff value applied to the true negative and positive rates showed LAM with a sensitivity of 100% and specificity of 91.7% for bTB positive versus bTB exposed animals (FIG. 11). The identification of a glycolipid in infected serum also opens the possibility for identification of other pathogen-related lipid biomarkers.

Although host and pathogen serum proteins have served as diagnostic biomarkers of M. bovis infection, conventional tests— in the form of, for example, dot blots and ELISAs— are not feasible in the field. A diagnostic test for field use should provide sensitivity (to limit false negative results), specificity (to limit false positive results), rapid results, and ease of testing. Analyzing a sample for these biomarkers using appropriate point of care testing device such as, for example, a nanosensor microfluidic apparatus or portable surfaced-enhanced Raman spectroscopy can provide improved convenience and throughput compared to detection methods using conventional lab-based M. bovis detection methods. As used herein, therefore, the term "point of care" can include, for example, field locations— i.e., a location geographically closer to the animal being tested than a laboratory and/or clinic.

Thus, this disclosure provides a method of detecting infection of a host by M. bovis. Generally, the method includes obtaining a biological sample from a host animal at risk of being infected by Mycobacterium bovis, and analyzing the sample for the presence or absence of at least one M. bovis polypeptide. In some embodiments, the method can further include analyzing the sample for the presence or absence of at least one M. bovis lipid.

In some embodiments, the biological sample can include any suitable biological material such as, for example, serum, plasma, urine, or fecal extracts.

In some embodiments, the M. bovis polypeptide being detected is adequate to distinguish a subclinical M. bovis infection from infection by other Mycobacterium species such as, for example, M. avium subsp. paratuberculosis or M. kansasii. Thus, in an area where another Mycobacterium species is prevalent, the method can be designed so that the M. bovis polypeptide does not cross-react with proteins from the other Mycobacterium species. In other embodiments, however, it may be acceptable to design the method using a M. bovis polypeptide that cross- reacts with a protein from another Mycobacterium species if that other Mycobacterium species is not expected to be present (e.g., is not natively present) in the area where the method is being performed.

In some embodiments, the method can include detecting one or more of MB 1895c, MB2515c, MB0862, MB1482c, MB2883c, MB1929, MB1192 MB1886c, MB2441c, MB2275, MB2122c, MB1672c, MB3729c, MB1268, MB3017c, or Pks5.

In some embodiments, the method can include analyzing the sample for the presence or absence of at least one M. bovis lipid. In some cases, the M. bovis lipid being detected may be adequate to distinguish a subclinical M. bovis infect from infection by other Mycobacterium species such as, for example, M. avium subsp. paratuberculosis or M. kansasii. Thus, similar to embodiments that involve detecting the presence of a M. bovis polypeptide, in an area where another Mycobacterium species is prevalent, the method can be designed so that the M. bovis lipid does not cross-react with lipids produced by the other Mycobacterium species. In other embodiments, however, it may be acceptable to design the method using a M. bovis lipid that cross-reacts with a lipid from another Mycobacterium species if that other Mycobacterium species is not expected to be present (e.g., is not natively present) in the area where the method is being performed. In some embodiments, the M. bovis lipid can include lipoarabinomannan.

In some embodiments, the host animal may have, and the method may detect, a subclinical M. bovis infection. As used herein, the term "subclinical infection" refers to a status in which the host animal may harbor M. bovis microbes, but not yet manifest any symptoms or clinical signs of being infected by M. bovis. Consequently, in some embodiments, the method may be performed on a host who is or is at risk of being infected with M. bovis. "At risk" refers to a host that may or may not actually be infected with M. bovis. Thus, for example, a host "at risk" of infection by M. bovis is a host animal present in an area where individuals have been identified as infected by M. bovis and/or is likely to be exposed to M. bovis (e.g., the host is present within the known geographical range of M. bovis) even if the host has not yet manifested any detectable indication of infection by M. bovis and regardless of whether the host may harbor a subclinical amount of M. bovis. As used herein, the term "sign" or "clinical sign" refers to an objective physical finding relating to a particular condition capable of being found by one other than the patient; and the term "symptom" refers to any subjective evidence of disease or of a patient's condition.

In some embodiments, the methods described herein may be used in combination with other methods, including other methods that are described herein. Thus, for example, the method can include analyzing a sample for the presence or absence of one or more M. bovis polypeptides and one or more M. bovis lipids. The methods described herein also may be combined with conventional methods of bTB detection. For example, the methods described herein may be used in the field to provide early detection so that, for example, appropriate preliminary quarantine procedures may be implemented, which can later be confirmed using conventional laboratory- based methods of bTB detection. The preliminary quarantine procedures can limit spread of M. bovis within a herd (or larger geographical area) while the bTB-positive result is confirmed, thereby reducing the extent of economic loss of a positive result.

As used herein, the term "use in the field" and variations thereof refer to tests that may be performed at point of care— i.e., at or near the location of the animals being tested rather than in a laboratory setting. Thus, in some embodiments, the methods described herein may be performed as an ELISA, dot blot assay, or any test format that involves lateral flow in a portable device. Such a "point of care" or "in the field" test can typically provide a result in, for example, 10-15 minutes. In contrast, a conventional γ-interferon release assay (IGRA) typically requires 5- 6 hours and sophisticated laboratory equipment.

Thus, in some embodiments, the methods described herein can produce a result in a maximum time of no more than 250 minutes, such as, for example, no more than 230 minutes, no more than 200 minutes, no more than 180 minutes, no more than 150 minutes, no more than 120 minutes, no more than 90 minutes, no more than 60 minutes, no more than 50 minutes, no more than 40 minutes, no more than 30 minutes, no more than 25 minutes, no more than 20 minutes, or no more than 15 minutes. In some embodiments, the methods described herein can provide a result in a minimum time of no less than five minutes such as, for example, no less than 10 minutes, no less than 15 minutes, no less than 20 minutes, no less than 25 minutes, or no less than 30 minutes. In some embodiments, the methods described herein can provide a result with a range of time having endpoints defined be any maximum time listed above and any minimum time listed above that is less than the maximum time.

In the preceding description, particular embodiments may be described in isolation for clarity. Unless otherwise expressly specified that the features of a particular embodiment are incompatible with the features of another embodiment, certain embodiments can include a combination of compatible features described herein in connection with one or more

embodiments.

For any method disclosed herein that includes discrete steps, the steps may be conducted in any feasible order. And, as appropriate, any combination of two or more steps may be conducted simultaneously.

The present invention is illustrated by the following examples. It is to be understood that the particular examples, materials, amounts, and procedures are to be interpreted broadly in accordance with the scope and spirit of the invention as set forth herein.

EXAMPLES

Example 1

Sample Source.

All cattle used in this study were housed according to institutional guidelines and approved animal care protocols at the National Animal Disease Center (NADC; Ames, IA). Sera used for iTRAQ analyses were obtained from calves infected with M. bovis 95-1315 at the NADC. M. bovis infected calves were housed in a biosafety level 3 (BSL-3) facility. Sera were collected from M. bovis infected calves at baseline and prospectively for every month postinfection (PI) for five months. All calves were tested for disease associated immune response parameters, clinical signs and lesions characteristics identified at necropsy. Field samples from bTB infected and negative bTB exposed , M. avium subsp. paratuberculosis-mfected, and M. kansasii-mfected cattle (19, 22) were obtained from serum repositories at the National

Veterinary Services Laboratory (NVSL; United States Department of Agriculture, Ames, IA) and National Animal Disease Center (NADC, USDA, Ames, IA), respectively. bTB infection status of each animal was confirmed by a combination of antemortem caudal fold tests, pathogen culture and lesion histology at necropsy. Negative controls were collected from bTB free dairy herds in Minnesota. iTRAQ Data Analysis and Interpretation.

In our previous study, sera from M. bovis (n = 5), M. avium subsp. paratuberculosis (n =

5) infected calves and contemporary controls (n = 5) were pooled in equal concentrations (100 of 100 μg/ μί) and used in four individual iTRAQ experiments: 1) M. bovis infection versus contemporary controls; 2) M. bovis infection versus M. avium subsp. paratuberculosis infection; 3) early chronic M. avium subsp. paratuberculosis infection; and 4) late chronic M. avium subsp. paratuberculosis infection, as previously described. (Seth et al. 2009. PLoS One 4:e5478).

Host- specific peptides and relative abundance (> 95% Confidence Interval (CI)) were identified using ProteinPilot software™2.0 and 2.01 (Applied Biosystems Inc., Foster City, CA) and the nr_bos_CTM_20070802 FASTA database. Pathogen peptides were identified using the M. bovis strain AF2122/97 genome. At least two unique peptides per protein were used as a cutoff for analysis (P<0.05 and an error factor (EF) of < 2). The EF signifies the 95% CI for an average ratio of (EF = 10^{95% CI}, where 95% CI = (ratio x EF) - (ratio/EF)).

Immunoblotting for host response associated biomarkers during bTB infection.

All procedures were developed at room temperature (RT). Field samples (n = 128 confirmed bTB infected and n = 82 negative bTB exposed) and negative controls (n = 38) were spotted in duplicate and dried on 0.2 μιη nitrocellulose membranes. Nitrocellulose membranes were blocked using IX phosphate buffered saline (PBS)-0.05% Tween-20 (TW20) containing 5% nonfat dried milk powder for 1 h with subtle shaking and washed 5 times in IX PBS-TW20 in 5 min increments. Nitrocellulose membranes were separately incubated with rabbit polyclonal a- 1 -antitrypsin (Abeam, Cambridge, MA), goat polyclonal fetuin-A (M-17) (Santa Cruz

Biotechnology, Inc., Dallas, TX), and mouse anti-human VDBP (R&D systems, Minneapolis, MN) diluted 1 : 1 ,000 in PBS-TW20 containing 1 % nonfat dried milk powder for one hour with shaking and subsequently washed as described above. Binding of primary antibodies to sera was detected using a 1 : 10,000 dilution of anti-rabbit IgG (R&D systems, Minneapolis, MN), anti- mouse IgG (R&D systems, Minneapolis, MN) and anti-goat IgG (SantaCruz Biotechnology, Inc., Dallas, TX) conjugated to horseradish peroxidase (HRP) incubated for one hour with shaking followed by 5 PBS-TW20 washes and development with Western Lightening Enhanced

Chemiluminescence substrate (PerkinElmer, Waltham, MA) per manufacturer's instructions. Membranes were imaged using simple biochem acquisition from Labworks 4.6 software

(Labworks Inc., Costa Mesa, CA) and raw density values were calculated.

Production of monoclonal antibodies against M. bovis specific peptides present in the serum of animals infected with M. bovis.

MB2515c, MB 1895c, and MB 1554c (Pks5) antibodies were commercially produced by NEOBioscience (Cambridge, MA). Proteins were selected based on iTRAQ identification and potential for immunogenicity. Briefly, peptides were designed for each protein using

NEOBioscience software that considered hydrophilicity, flexibility, accessibility, rotation, surface exposed probability and antigenicity. A Basic Local Alignment Search Tool (BLAST) was performed on M. bovis proteins to eliminate homologous sequences. Mice (n = 5 for each peptide) were initially injected intraperitoneally with an emulsion of peptide (10-50 μg) and Complete Freund's Adjuvant (CFA, add source) in sterile saline. Immunizations were repeated 2 times using Incomplete Freund's Adjuvant (IF A, add source) and once using PBS in place of CFA in 14 and 21 day intervals post-immunization. Every 21 days post-immunization blood was drawn from mice and tested against appropriate peptides using indirect ELISA. All mice were euthanized 61 days post-immunization and spleens were harvested for splenocyte extraction. Splenocytes were fused with hybridomas, which were seeded into individual wells in a 96 well plate and screened by ELISA to detect positive clones. Clones 19-1-1 (MB1895c), 5-1-3 (Pks5) and 3-1-2 (MB2515c) were selected, subcloned by limiting dilution, and isotyped. Clones were expanded and the supernatant was collected. Monoclonal antibodies were kept at -70°C until further use. Development of an indirect ELISA to detect M. ^ovis-specific peptides in serum.

bTB confirmed (n = 128) , bTB negative exposed (n = 424), M. kansasii- fectGd (n = 10), M. avium subsp. paratuberculosis- fectGd (n = 10), and negative control sera (n = 38) were individually diluted in 0.05 M carbonate-bicarbonate buffer (pH = 9.6; Sigma-Aldrich, St. Louis, MO) at a 1 :50 (MB 1895c and MB2515c detection) and 1 : 100 dilution (Pks5 detection) and 50 μίΛνεΙΙ of each sample was transferred to separate wells in Nunc Maxisorp flat bottom ELISA plates. Each sample was plated in triplicate. Sera were allowed to absorb overnight at 4°C and plates were washed three times using 200 μΕΛνεΙΙ of PBS. Plates were blocked in 200 μΕΛνεΙΙ of Blocker™ BLOTTO in Tris-buffered saline (TBS) (Pierce, Rockford, IL) for two hours at 37°C, washed three times using 300 μΕΛνεΙΙ of l x Femto PBS containing 0.05% TW20 (G- Biosciences, St. Louis, MO), and incubated with either 100 μίΛνεΙΙ of a 1 :5,000 dilution of

MB2515c or MB1895c or a 1 : 10,000 dilution of Pks5 resuspended in a 1% solution of Blocker™ BLOTTO in TBS with 0.05% TW20 for one hour at room temperature. Plates were washed as described above and incubated with 100 μίΛνεΙΙ of goat anti-mouse IgG-HRP (Santa Cruz Biotechnology, Inc., Dallas, TX) diluted 1 :5,000 in 1% Blocker™ BLOTTO in TBS with 0.05% TW20 for one hour at room temperature and subsequently washed. ELISA plates were developed with 100 μΕ/well of 1-Step™ Ultra TMB-ELISA (Pierce, Rockford, IL) and incubated for 30 minutes at room temperature in the dark. TMB reaction was stopped with the addition of 50 μίΛνεΙΙ of 2 M sulfuric acid and optical densities were recorded at 450 nm using the SpectraMax M2 microplate reader and software (Molecular Devices, Sunnyvale, CA). Positive cut-off values were calculated from the negative control average and two standard deviations.

Statistical Analysis.

To construct receiver operating characteristic (ROC) curves for each biomarker, test results in each individual animal were averaged across replicates and the respective coefficient of variation calculated (Supplemental information). ROC curves for host response and bovis specific biomarkers were compared using the area under the ROC curve (AUC). Two comparisons were performed, positive versus within herd exposed negative controls (exposed) and positive versus not exposed negative controls (controls). For the best biomarker in each class, sensitivity (Se) and specificity (Sp) values were calculated at optimal cutoff values. For the best performing biomarker, positive (PPV) and negative predictive values (NPV) with respective cutpoint specific likelihood ratios (LR) were calculated at four different optimal combinations of Se and Sp, in order to develop a framework for a decision analysis algorithm in multiple scenarios of disease prevalence (Dohoo et al. 2010. Veterinary Epidemiologic Research. VER Inc.). ROC curves and sensitivity-specificity plots were generated using SAS 9.3 (SAS Institute Inc., Cary, NC, USA).

Example 2

Sample source

Field samples from bovine tuberculosis infected and exposed cases were generously provided by the National Veterinary Services Laboratory (NVSL; United States Department of Agriculture, Ames, IA) serum repositories. All field samples were collected from a single herd in California. Bovine tuberculosis disease status for each animal was validated using a combination of bacterial culture, antemortem caudal fold tests (CFT) and lesion histology at necropsy.

Johne's disease history for this herd was indeterminate. Bovine tuberculosis exposed cases were defined as animals that had contact with bovine tuberculosis infected animals but remained bovine tuberculosis negative (i.e. negative results for culture, CFT and histology). Negative controls were collected from a bovine tuberculosis free dairy herd in Minnesota. Negative controls tested negative for M. bovis (culture, histology, and CFT).

Lipoarabinomannan Enzyme-linked immunosorbent assay (ELISA)

Randomly selected field sera samples (bTB positive n = 10 and bTB exposed n = 12), negative controls (n = 33), and negative controls spiked with either M. tuberculosis strain H37Rv purified mannosylated lipoarabionmannan (ManLAM) (BEI Resources; NR- 14848) or M.

smegmatis purified non-mannose-capped lipoarabinomannan (AraLAM) (BEI Resources; NR- 14849) (Biodefense and Emerging Infections Research Resources Repository, NIAID, NIH) were diluted 1 :5 in PBS and analyzed for the presence of LAM using the human LAM ELISA kit (Biotang, Waltham, MA) according to the manufacturer's instructions. A LAM standard curve was included using kit controls and two-fold dilution series of ManLAM spiked sera. The standard curve was plotted using GraphPad Prism software (GraphPad Software, LaJolla, CA). The optical density was read at 450 nm with a wavelength correction at 570 nm. All samples were read in three wells. LAM ELISA was repeated twice.

Statistical analysis

Optical densities for each animal were averaged across the replicates. Receiver operating characteristic (ROC) curves were compared for 1) positive versus within-herd negative exposed (exposed) and 2) positive versus negative controls using the area under the ROC curves (AUC). Optimal cutoff values were determined by maximizing specificity and sensitivity by plotting the true negative rate against the true positive rate. ROC curves and specificity-sensitivity plots were created in SPSS® (IBM Corp. Released 2013, IBM SPSS Statistics for Windows, Version 22.0, Amonk, NY).

EXEMPLARY EMBODIMENTS

Embodiment 1. A method comprising: obtaining a biological sample from a host animal at risk of being infected by Mycobacterium bovis; and analyzing the sample for the presence or absence of at least one M. bovis polypeptide.

Embodiment 2. A method comprising: obtaining a biological sample from a host animal at risk of being infected by Mycobacterium bovis; and analyzing the sample for the presence or absence of at least one M. bovis lipid.

Embodiment 3. The method of Embodiment 1 further comprising analyzing the sample for the presence or absence of at least one M. bovis lipid.

Embodiment 4. The method of Embodiment 1 or Embodiment 3 wherein the M. bovis polypeptide does not cross-react with serum from a host animal exposed to another Mycobacterium spp.

Embodiment 5. The method of Embodiment 4 wherein the other Mycobacterium spp. comprises M. avium subsp. paratuberculosis .

Embodiment 6. The method of Embodiment 4 wherein the other Mycobacterium spp. comprises M. kansasii. Embodiment 7. The method of Embodiment 1 or Embodiment 3 wherein the M. bovis polypeptide comprises MB1895c, MB2515c, MB0862, MB1482c, MB2883c, MB1929, MB1192 MB1886c, MB2441c, MB2275, MB2122c, MB1672c, MB3729c, MB1268, MB3017c, or Pks5.

Embodiment s. The method of Embodiment 2 or Embodiment 3 wherein the M. bovis lipid does not cross-react with serum from a host animal exposed to another

Mycobacterium spp.

Embodiment 9. The method of Embodiment 8 wherein the other Mycobacterium spp. comprises M. avium subsp. paratuberculosis .

Embodiment 10. The method of Embodiment 8 wherein the other Mycobacterium spp. comprises M. kansasii.

Embodiment 11. The method of any one of Embodiments 2, 3, or 8-10 wherein the M. bovis lipid comprises lipoarabionmannan.

Embodiment 12. The method of any preceding Embodiment wherein the biological sample comprises serum, plasma, urine, or a fecal extract.

Embodiment 13. The method of any preceding Embodiment wherein the host animal has a subclinical M. bovis infection.

Embodiment 14. The method of any preceding Embodiment wherein the host animal exhibits no symptoms or clinical sign of infection by M. bovis.

Embodiment 15. The method of any preceding Embodiment performed at point of care.

Embodiment 16. The method of Embodiment 15 performed using a micro fluidic device.

Embodiment 17. The method of Embodiment 15 performed using portable surface- enhanced Raman spectroscopy.

Embodiment 18. The method of any preceding Embodiment further comprising detecting at least one host polypeptide whose expression is greater in a host infected with M. bovis compared to expression in a host known to be uninfected with M. bovis.

Embodiment 19. The method of Embodiment 18 wherein the host polypeptide comprises vitamin D binding protein (VDBP), fetuin-A. As used herein, the term "and/or" means one or all of the listed elements or a combination of any two or more of the listed elements; the terms "comprises" and variations thereof do not have a limiting meaning where these terms appear in the description and claims; unless otherwise specified, "a," "an," "the," and "at least one" are used interchangeably and mean one or more than one; and the recitations of numerical ranges by endpoints include all numbers subsumed within that range (e.g., 1 to 5 includes 1, 1.5, 2, 2.75, 3, 3.80, 4, 5, etc.).

The complete disclosure of all patents, patent applications, and publications, and electronically available material cited herein are incorporated by reference in their entirety. In the event that any inconsistency exists between the disclosure of the present application and the disclosure(s) of any document incorporated herein by reference, the disclosure of the present application shall govern. The foregoing detailed description and examples have been given for clarity of understanding only. No unnecessary limitations are to be understood therefrom. The invention is not limited to the exact details shown and described, for variations obvious to one skilled in the art will be included within the invention defined by the claims.

Unless otherwise indicated, all numbers expressing quantities of components, molecular weights, and so forth used in the specification and claims are to be understood as being modified in all instances by the term "about." Accordingly, unless otherwise indicated to the contrary, the numerical parameters set forth in the specification and claims are

approximations that may vary depending upon the desired properties sought to be obtained by the present invention. At the very least, and not as an attempt to limit the doctrine of equivalents to the scope of the claims, each numerical parameter should at least be construed in light of the number of reported significant digits and by applying ordinary rounding techniques.

Notwithstanding that the numerical ranges and parameters setting forth the broad scope of the invention are approximations, the numerical values set forth in the specific examples are reported as precisely as possible. All numerical values, however, inherently contain a range necessarily resulting from the standard deviation found in their respective testing measurements.

All headings are for the convenience of the reader and should not be used to limit the meaning of the text that follows the heading, unless so specified.

Claims

What is claimed is:

1. A method comprising:

obtaining a biological sample from a host animal at risk of being infected by

Mycobacterium bovis; and

analyzing the sample for the presence or absence of at least one M. bovis polypeptide.

2. A method comprising:

obtaining a biological sample from a host animal at risk of being infected by

Mycobacterium bovis; and

analyzing the sample for the presence or absence of at least one M. bovis lipid.

3. The method of claim 1 further comprising analyzing the sample for the presence or absence of at least one M. bovis lipid.

4. The method of claim 1 or claim 3 wherein the M. bovis polypeptide does not cross-react with serum from a host animal exposed to another Mycobacterium spp.

5. The method of claim 4 wherein the other Mycobacterium spp. comprises M. avium subsp. paratuberculosis.

6. The method of claim 4 wherein the other Mycobacterium spp. comprises M. kansasii.

7. The method of claim 1 or claim 3 wherein the M. bovis polypeptide comprises MB 1895c, MB2515c, MB0862, MB1482c, MB2883c, MB1929, MB1192 MB1886c, MB2441c, MB2275,

MB2122c, MB1672c, MB3729c, MB1268, MB3017c, or Pks5.

8. The method of claim 2 or claim 3 wherein the M. bovis lipid does not cross-react with serum from a host animal exposed to another Mycobacterium spp.

9. The method of claim 8 wherein the other Mycobacterium spp. comprises M. avium subsp. paratuberculosis .

10. The method of claim 8 wherein the other Mycobacterium spp. comprises M. kansasii.

11. The method of any one of claims 2, 3, or 8-10 wherein the M. bovis lipid comprises lipoarabionmannan.

12. The method of any preceding claim wherein the biological sample comprises serum, plasma, urine, or a fecal extract.

13. The method of any preceding claim wherein the host animal has a subclinical M. bovis infection.

14. The method of any preceding claim wherein the host animal exhibits no symptoms or clinical sign of infection by M. bovis.

15. The method of any preceding claim performed at point of care.

16. The method of claim 15 performed using a micro fluidic device.

17. The method of claim 15 performed using portable surface-enhanced Raman

spectroscopy.

18. The method of any preceding claim further comprising detecting at least one host polypeptide whose expression is greater in a host infected with M. bovis compared to expression in a host known to be uninfected with M. bovis.

19. The method of claim 18 wherein the host polypeptide comprises vitamin D binding protein (VDBP), fetuin-A.