Identification of New Mycobacterium bovis antigens and development of a multiplexed serological bead-immunoassay for the diagnosis of bovine tuberculosis in cattle.

Serological assays for bovine tuberculosis diagnosis require the use of multiple Mycobacterium bovis specific antigens to ensure the detection of infected animals. In the present study, identification and selection process of antigens, based on data from published proteomic studies and involving the use of bioinformatics tools and an immuno-screening step, was firstly performed for identifying novel antigens that elicit an antibody response in M. bovis infection. Based on this approach, a panel of 10 M. bovis antigens [with known relevance (MPB70, MPB83, MPB70/83, and ESAT6/CFP10) and novel (Mb1961c, Mb1301c, Mb3871, Mb1403, Mb0592, and PE25/PPE41)] were constructed and thenused to develop a new multiplexed serological assay based on Luminex technology. The performance of the Luminex-bTB immunoassay was evaluated using sera from cattle with known tuberculosis status. Among the proteins whose ability to detect bovine tuberculosis was evaluated for the first time, PE25/PPE41 and Mb1403, but not Mb3871, showed good detection capacity. Following multiple antigen combination, the final Luminex-bTB immunoassay included seven antigens (MPB70, MPB83, MPB70/83, ESAT6/CFP10, PE25/PPE41, Mb1403, and Mb0592) and showed better global performance than the immunoassay using the four usual antigens (MPB70, MPB70/83, MPB83 and ESAT6/CFP10). The specificity and sensitivity values were, respectively, of 97.6% and 42.8% when the cut-off of two-positive antigens was used to classify samples as positive. With the use of the more-restrictive criterion of three-positive antigens, the specificity increased to 99.2% but the sensitivity decreased to 23.9%. The analysis of antigen profiles generated with the Luminex-bTB immunoassay showed that mainly serodominant proteins were recognized in samples from infected cattle. The detection of Mb1961c and Mb1301c appeared to be associated with presumed false-positive results. Moreover, sera from cattle originating from bTB-outbreaks but having inconclusive or negative skin test results were identified as positive by the Luminex-bTB immunoassay and showed an antigen pattern associated with M. bovis infection. The Luminex-bTB immunoassay including seven antigens may be useful as adjunct test for the detection of M. bovis-infected herds, and different cut-offs could be applied according to the bovine tuberculosis epidemiological context.

Performance of two commercial serological assays for bovine tuberculosis using plasma samples.

In the bovine tuberculosis diagnosis, the use of plasma samples (already available for IFNÉ£ assays) in serological tests might facilitate the work in the field. Here, the performance of two commercial serological tests (ELISA IDEXX M. bovis Ab test and Enferplex Bovine TB antibody test) were evaluated using plasma samples from cattle in Belgium. Specificity values estimated from 567 plasma samples collected from bTB-free cattle were 98.4% when using the ELISA IDEXX M. bovis Ab test, and were 96.5% and 93.3% when using the high specificity and high sensitivity settings of the Enferplex Bovine TB antibody test, respectively. Sensitivity values were calculated relative to SICCT-positive (N = 117) and IFNÉ£-positive (N = 132) animals originating from M. bovis-infected herds. Overall, the multiplexed Enferplex Bovine TB antibody test had better sensitivity (mean: 32.5% and 43.4% for the high specificity and sensitivity settings, respectively) compared to the ELISA IDEXX M. bovis Ab test (mean: 12%). Data obtained from plasma samples in the current study were compared to a previous study using both serological tests with sera. In conclusion, both serological tests showed comparable performance with both matrix; although overall specificity values with the Enferplex Bovine TB antibody test were lower when using plasma samples than sera.

Field evaluation of two commercial serological assays for detecting bovine tuberculosis.

Diagnosis of bovine tuberculosis in cattle is challenging due to complex immune host response to infection that limit the performance of available diagnostic tests. In this study, performance of two commercial serological assays developed to detect bovine tuberculosis were evaluated: Enferplex Bovine TB antibody kit including 11 antigens (EnferGroup, Ireland) and IDEXX M. bovis Ab kit (IDEXX, USA). The specificity value obtained with the ELISA IDEXX M. bovis Ab test was 97.1%, whereas it was 97.1% and 95.1% for the high specificity and sensitivity settings, respectively, with the Enferplex Bovine TB antibody kit. The sensitivity of the multiplexed Enferplex Bovine TB antibody test for SICCT-positive animals was higher (N = 172; 51.7% and 58.7% with high specificity and sensitivity settings, respectively) compared to the ELISA IDEXX M. bovis Ab test (sensitivity of 36.6%). "Antigen profiles" generated by the multiplexed Enferplex method showed that five out of 11 antigens present in the test were mostly identified as positive sera in cattle originating from bTB-outbreaks. In comparison, unique profiles appeared to be correlated with false positive results. However additional studies are needed to confirm the observed antigen profiles, and their potential use as an additional diagnostic tool. Serial interpretation of the two serological tests produced higher diagnostic specificity (>99%), reducing false positive results, which is essential for a screening test when the prevalence of bovine tuberculosis is low.

Domestic canaries (Serinus canaria forma domestica) are susceptible to low pathogenic avian influenza virus infections.

Avian influenza viruses have been isolated from many bird species; however, little is known about the susceptibility of pet birds to low pathogenic avian influenza (LPAI) viruses. To address this research gap, domestic canaries (Serinus canaria forma domestica) were experimentally infected with H5 and H7 LPAI viruses to determine susceptibility and to evaluate samples for diagnostic purposes. Clinical evidence of infection (e.g. ruffled plumage and apathy) and mortality were noted for the canaries inoculated with chicken-adapted LPAI viruses. Real-time reverse transcription-polymerase chain reaction (RRT-PCR) demonstrated higher viral RNA levels in buccal compared to faecal samples. No clinical signs or mortality were observed in canaries inoculated with LPAI virus originating from wild birds; however, the canaries in this group did have evidence of viral RNA in buccal and faecal samples. Overall, this study showed that domestic canaries are susceptible to LPAI virus infections and that they can shed large amounts of viral RNA, primarily through the respiratory route. Thus, buccal swabs might be better samples than faeces for efficient detection of some LPAI virus infections in these birds. Although canaries have not been identified as a significant reservoir for LPAI viruses, they may be infected by LPAI viruses. Thus, the importance of the control of domestic canaries for detection of LPAI viruses should not be underestimated, especially in the contexts of international commercial exchange and outbreaks. RESEARCH HIGHLIGHTS Canaries are susceptible to infection with H5/H7 LPAI viruses. Canaries inoculated with LPAI viruses excrete large amounts of viral RNA. Buccal swabs may be appropriate specimens for AI virus detection in canaries. The control of canaries for LPAI virus detection should not be overlooked.

Complete Coding Sequences of One H9 and Three H7 Low-Pathogenic Influenza Viruses Circulating in Wild Birds in Belgium, 2009 to 2012.

The complete coding sequences of four avian influenza A viruses (two H7N7, one H7N1, and one H9N2) circulating in wild waterfowl in Belgium from 2009 to 2012 were determined using Illumina sequencing. All viral genome segments represent viruses circulating in the Eurasian wild bird population.

First TBEV serological screening in Flemish wild boar.

In the frame of a Flemish wildlife surveillance in 2013, a serological screening was performed on sera from wild boar (Sus scrofa; n=238) in order to detect tick-borne encephalitis virus (TBEV)-specific antibodies. Neutralising antibodies were titrated with a seroneutralisation test (SNT), using two cut-off titres (1/10-1/15). Seven wild boars were found TBEV-seropositive and showed moderate (>1/15) to high (>1/125) SNT-titres; three individuals had borderline results (1/10-1/15). This study demonstrated the presence of TBEV-specific antibodies in wild boar and highlighted potential TBEV-foci in Flanders. Additional surveillance including direct virus testing is now recommended.

Evaluation of the kinetics of anti-NP and anti-HA antibody after infection of Pekin ducks with low pathogenic avian influenza virus.

Serological monitoring is a feature of surveillance programmes for the detection of the circulation of notifiable low pathogenic avian influenza (LPAI) viruses in commercial poultry holdings. Commercial multispecies nucleoprotein (NP) enzyme-linked immunosorbent assays (ELISAs) have been replacing the haemagglutination inhibition (HI) test as pre-screening tools. Few comparative studies have been conducted to test sera from domestic ducks for diagnostic purposes. Therefore, we evaluated the correlation between commercial NP ELISAs and the HI test. Anti-NP and anti-haemagglutinin (HA) antibodies were measured in sera from domestic ducks that had undergone serological screening and from juvenile domestic Pekin ducks that were experimentally infected with LPAI viruses. The findings highlight an absence of a correlation between NP ELISA and HI results with both field and experimental duck sera. Dissimilar kinetics of the antibodies detected during the follow-up evaluation of the humoral immune responses in experimentally infected ducks may explain this lack of correlation. Indeed, anti-NP titres decreased over time, whereas anti-HA titres remained unchanged after inoculation with the H3N1 LPAI virus isolated from domestic duck or the H7N1 LPAI virus isolated from chicken. Despite these differences, the NP ELISA may serve as a valid pre-screening tool to detect circulating LPAI viruses in domestic duck populations at the flock level.

Multiyear Serological Surveillance of Notifiable Influenza A Viruses in Belgian Poultry: A Retrospective Analysis.

Surveillance of notifiable avian influenza (NAI) virus is mandatory in European member states, and each year a serological survey is performed to detect H5 and H7 circulation in poultry holdings. In Belgium, this serological monitoring is a combination of a stratified and a risk-based approach and is applied to commercial holdings with more than 200 birds. Moreover, a competitive nucleoprotein (NP) ELISA has been used as first screening method since 2010. A retrospective analysis of the serological monitoring performed from 2007 through 2013 showed sporadic circulation of notifiable low-pathogenicity avian influenza (LPAI) viruses in Belgian holdings with a fluctuating apparent flock seroprevalence according to years and species. Overall, the highest apparent flock seroprevalence was detected for the H5 subtype in domestic Anatidae, with 20%-50% for breeding geese and 4%-9% for fattening ducks. Positive serology against non-H5/H7 viruses was also observed in the same species with the use of the IDScreen influenza A antibody competition ELISA kit (ID-vet NP ELISA), and confirmed by isolation of H2, H3, H6, and H9 LPAI viruses. Among Galliformes, the apparent flock seroprevalence was lower, ranging between 0.3% and 1.3%. Circulation of notifiable LPAI viruses was only observed in laying hens with a similar seroprevalence for H5 and H7. Based on ID-vet NP ELISA results, no circulation of LPAI viruses, regardless the subtype, was observed in breeding chickens and fattening turkeys. Retrospectively, the use of an ELISA as first-line test not only reduced the number of hemagglutination inhibition tests to be performed, but also gave a broader evaluation of the prevalence of LPAI viruses in general, and might help to identify the most at-risk farms.

Evaluation of four enzyme-linked immunosorbent assays for the serologic survey of avian influenza in wild bird species.

Wild birds that reside in aquatic environments are the major reservoir of avian influenza viruses (AIVs). Since this reservoir of AIVs forms a constant threat for poultry, many countries have engaged in AIV surveillance. More and more commercial enzyme-linked immunosorbent assays (ELISA) are available for serologic surveillance, but these tests are often developed and validated for use in domestic poultry. However, for a correct interpretation of ELISA test results from wild bird sera, more information is needed. In the present study, four ELISA test kits (ID-Vet IDScreen, IDEXX FlockChek AI MultiS-Screen Ab Test Kit, Synbiotics FluDETECTBE, and BioChek AIMSp) were compared for the serologic analysis of 172 serum samples from mallard, mute swan, and Canada goose. Samples were selected based on ID-Vet IDScreen results to obtain an approximately equal number of positive and negative samples. In addition, 92 serum samples from experimentally infected specific-pathogen-free (SPF) chickens and Pekin ducks were included in the tests for validation purposes. Cohen's kappa statistics and Spearman correlation coefficients were calculated for each combination of two tests and for each bird species. Test agreement for mallard sera varied from poor to moderate, while test results for Canada goose and swan sera agreed from fair to almost perfect. The best agreement was obtained with sera from experimentally infected SPF chickens and Pekin ducks. This study shows that some care must be taken before using nucleoprotein ELISAs for the testing of sera from wild birds and that more reliable validation studies should be considered before their use in the serologic surveillance of wild birds.

Different replication profiles in specific-pathogen-free chickens of two H7 low pathogenic avian influenza viruses isolated from wild birds.

During an active wild bird survey conducted in Belgium from 2007 to 2011, two low pathogenic avian influenza (LPAI) H7 viruses were isolated from wild birds: an H7N1 virus from a common shelduck (Tadorna tadorna) and an H7N7 virus from a Canada goose (Branta canadensis). The H7 sequence analyses and intravenous pathogenicity indices indicated that they were both low pathogenic isolates and genetically related to other recent European H7 LPAIs isolated from wild birds. Interestingly, the two isolates showed different replication profiles in specific-pathogen-free (SPF) chickens, but poultry can be at risk from both. Indeed, the H7N1 isolated from the common shelduck had the ability to infect and to replicate efficiently in SPF chickens as indicated by high oropharyngeal and cloacal excretions compatible with efficient transmission as well as strong immune responses. On the other hand, the H7N7 isolated from the Canada goose presented a lower replication profile because the inoculated chickens excreted less virus, mostly via the oropharyngeal route, and only three chickens seroconverted. None of the chickens showed clinical signs during the entire infection. Our study using an SPF chicken model underlines that the mechanisms of adaptation of LPAIs in poultry remain unpredictable and are still poorly understood but it represents a powerful tool to gain a better evaluation of the risks of LPAI circulation in poultry.

Redesigning the serological surveillance program for notifiable avian influenza in Belgian professional poultry holdings.

This study was aimed at redesigning the Belgian active surveillance program for domestic birds in professional poultry holdings based on a risk analysis approach. A stochastic quantitative analysis, combining all data sources, was run to obtain sensitivity estimates for the detection of an infected bird in the different risk groups identified. An optimal number of holdings for each risk group was then estimated on the basis of the different sensitivities obtained. This study proved to be a useful tool for decision makers, providing insight on how to reallocate the total amount of samples to be taken in the coming year(s) in Belgium, thus optimizing the field resources and improving efficiency of disease surveillance such as required by the international standards.

Evaluation of different strategies for the use of ELISA tests as first screening tools for serologic surveillance of low pathogenic avian influenza in the Belgian poultry sector.

Since the emergence of the highly pathogenic avian influenza H5N1, avian influenza surveillance has been expanded in Europe. The serologic monitoring of domestic poultry is usually accomplished using the reference hemagglutination inhibition (HI) test for the detection of H5 and H7 subtypes. However, as the number of tested sera has been increasing, there is a need for another serologic method that could be used as a preliminary screening test. A comparison of four enzyme-linked immunosorbent assay (ELISA) tests (two indirect and two competitive) was conducted, and they showed good specificity and higher sensitivity than the HI test. The selected ELISA tests were then tested using approximately 800 field sera representative of different poultry species, and a simulation was done to determine the best strategy for screening. The first strategy was testing both gallinaceous and nongallinaceous sera with a competitive ELISA and using the HI test for H5 and H7 as a confirmatory test. The second strategy was testing only gallinaceous bird sera with the indirect ELISA with confirmatory H5 and H7 HI and all nongallinaceous sera by the H5 and H7 HI test. In the Belgian poultry context, the best strategy seems to be the use of a blocking ELISA as the primary screening tool to test all the poultry sera, followed by confirmation by H5 and H7 HI test subtyping.

Evaluation of rapid antigen detection kits for the diagnosis of highly pathogenic avian influenza H5N1 infection.

Early detection of highly pathogenic (HP) strains of avian influenza, especially the HP H5N1, is important in terms of controlling and minimizing the spread of the virus. Several rapid antigen detection kits that are able to detect influenza A viruses in less than 1 hr are commercially available, but only a few of them have been evaluated. In this study, four commercially available rapid tests for veterinary usage and two tests for human usage were evaluated and compared. The evaluation of the detection limits of the different tests established with serial dilution of HP H5N1 indicated that most of them have a detection limit of about 10(5) to 10(6) 50% tissue culture infectious dose/ml. None of the tests was able to detect virus in oral and cloacal swabs 24 hr post-experimental infection of specific-pathogen-free chickens with HP H5N1. However, 48 hr postinfection, almost all of the rapid tests were able to detect infected birds (dead or alive). Moreover, organs were also successful samples for detection of H5N1 with the rapid tests. Unexpectedly, the specificity was not very high for some tests. However, in general in this study, the tests for veterinary usage showed better sensitivity. To conclude, these tests offer good indicative value in the event of an outbreak, but as a result of their low sensitivity and some aspecific reactions, test results always need to be confirmed by other methods.

Evaluation of different serologic markers for the early detection of avian influenza infection in chickens.

Viruses of all subtypes may be introduced into domestic poultry, but only H5 and H7 low pathogenicity avian influenza viruses can mutate during circulation in poultry and emerge as high pathogenicity avian influenza variants. It is therefore essential to monitor the field situation continuously to detect low pathogenicity notifiable avian influenza (LPNAI) as soon as possible. With the emergence of the highly pathogenic H5N1, markers of infection of avian influenza are becoming more and more significant. They are important as early warning systems, and they can also be valuable tools as companion tests of vaccines (differentiating infected from vaccinated animals), but they might also be informative about the evaluation of the degree of adaptation and the timing of infection. Therefore, several experimental infections of specific-pathogen-free chickens were conducted to follow the kinetics of antibody responses against the hemagglutinin, the neuraminidase, the nucleoprotein, and the M2e after infections with LPNAI viruses isolated from waterfowl or already adapted to chicken. Overall, the immune responses against the different antigens showed similar kinetics in the different infected animals, but they were lower when the animals were infected with AI viruses originating from waterfowl, and the kinetics of the M2e antibodies was quite different. Indeed, it was rather shorter and disappeared more rapidly (approximately 35 days postinfection) compared to the kinetics of the other antibodies. Therefore, the detection of the antibodies against M2e peptide could be an interesting tool to detect recent infection, and these preliminary results indicated that the production of M2e antibodies might be correlated with the degree of adaptation of LPNAIs.

H5N1 high pathogenicity avian influenza virus survival in different types of water.

Persistence of H5N1 high pathogenicity avian influenza virus (HPAIV), isolated during the epidemic in wild birds in Poland in 2006, was evaluated in three water samples derived from the sources known to host wild water birds (city pond, Vistula river mouth, and Baltic Sea). The virus was tested at two concentrations (10(4) and 10(6) median tissue culture infective dose per milliliter) and at three temperatures (4 C, 10 C, and 20 C), representing average seasonal temperatures in Poland. All tested water samples were filtered before virus inoculation, and one unfiltered sample (Baltic seawater) was also tested. Infectivity was determined twice a week over a 60-day trial period by microtiter endpoint titration. The persistence of the virus varied considerably depending on its concentration and also on physico-chemical parameters of the water, such as temperature and salinity. Avian influenza virus survival was the highest at 4 C and the lowest at 20 C. Prolonged infectivity of the virus in Baltic seawater (brackish, 7.8 ppt) was also seen. In distilled water, the virus retained its infectivity beyond the 60-day study period. Interestingly, a devastating effect of the unfiltered fraction of seawater was seen as the virus disappeared in this fraction the quickest in all studied combinations; thus, biologic factors may also affect infectivity of HPAIV.

Influenza vaccines and vaccination strategies in birds.

Although it is well accepted that the present Asian H5N1 panzootic is predominantly an animal health problem, the human health implications and the risk of human pandemic have highlighted the need for more information and collaboration in the field of veterinary and human health. H5 and H7 avian influenza (AI) viruses have the unique property of becoming highly pathogenic (HPAI) during circulation in poultry. Therefore, the final objective of poultry vaccination against AI must be eradication of the virus and the disease. Actually, important differences exist in the control of avian and human influenza viruses. Firstly, unlike human vaccines that must be adapted to the circulating strain to provide adequate protection, avian influenza vaccination provides broader protection against HPAI viruses. Secondly, although clinical protection is the primary goal of human vaccines, poultry vaccination must also stop transmission to achieve efficient control of the disease. This paper addresses these differences by reviewing the current and future influenza vaccines and vaccination strategies in birds.

Antigen mining with iterative genome screens identifies novel diagnostics for the Mycobacterium tuberculosis complex.

The definition of antigens for the diagnosis of human and bovine tuberculosis is a research priority. If diagnosis is to be used alongside Mycobacterium bovis BCG-based vaccination regimens, it will be necessary to have reagents that allow the discrimination of infected and vaccinated animals. A list of 42 potential M. bovis-specific antigens was prepared by comparative analysis of the genomes of M. bovis, M. avium subsp. avium, M. avium subsp. paratuberculosis, and Streptomyces coelicolor. Potential antigens were tested by applying them in a high-throughput peptide-based screening system to M. bovis-infected and BCG-vaccinated cattle and to cattle without prior exposure to M. bovis. A response hierarchy of antigens was established by comparing responses in infected animals. Three antigens (Mb2555, Mb2890, and Mb3895) were selected for further study, as they were strongly recognized in experimentally infected animals but with low or no frequency in BCG-vaccinated and naïve cows. Interestingly, all three antigens were recognized in animals vaccinated against Johne's disease, suggesting the presences of epitopes cross-reacting with M. avium subsp. paratuberculosis antigens. Eight peptides from the three antigens studied in detail were identified as immunodominant and were characterized in terms of major histocompatibility complex class II restriction element usage and shown to be restricted through both DR and DQ molecules. Reasons for antigenic cross-reactivity with M. avium subsp. paratuberculosis and refinement of the in silico strategy to predict such cross-reactivity from the primary protein sequence will be discussed. Evaluation of the peptides identified from the three dominant antigens by use of larger field studies is now a priority.

Members of the 30- to 32-kilodalton mycolyl transferase family (Ag85) from culture filtrate of Mycobacterium avium subsp. paratuberculosis are immunodominant Th1-type antigens recognized early upon infection in mice and cattle.

The characterization of protective antigens is essential for the development of an effective, subunit-based vaccine against paratuberculosis. Surface-exposed and secreted antigens, present abundantly in mycobacterial culture filtrate (CF), are among the well-known protective antigens of Mycobacterium tuberculosis and Mycobacterium bovis. Culture filtrate, prepared from Mycobacterium avium subsp. paratuberculosis ATCC 19698 grown as a surface pellicle on synthetic Sauton medium, was strongly and early recognized in experimentally infected B6 bg/bg beige mice and cattle, as indicated by elevated spleen cell gamma interferon (IFN-gamma) secretion and lymphoproliferative responses of peripheral blood mononuclear cells, respectively. Strong proliferative and ex vivo IFN-gamma responses against antigen 85 (Ag85) complex (a major protein component from M. bovis BCG culture filtrate) could be detected in cattle as early as 10 weeks after oral M. avium subsp. paratuberculosis infection. Synthetic peptides from the Ag85A and Ag85B components of this complex were strongly recognized, whereas T-cell responses were weaker against peptides from the Ag85C protein. A promiscuous T-cell epitope spanning amino acids 145 to 162 of Ag85B (identical sequence in M. bovis and M. avium subsp. paratuberculosis) was identified in experimentally infected cattle. Finally, young calves, born from cows with confirmed paratuberculosis, demonstrated proliferative responses to purified, recombinant Ag85A and Ag85B from M. avium subsp. paratuberculosis. These results indicate that the M. avium subsp. paratuberculosis Ag85 homologues are immunodominant T-cell antigens that are recognized early in experimental and natural infection of cattle.

Definitive differentiation between single and mixed mycobacterial infections in red deer (Cervus elaphus) by a combination of duplex amplification of p34 and f57 sequences and Hpy188I enzymatic restriction of duplex amplicons.

Severe emaciation and mortalities suggestive of mycobacterial infections were recently reported for both adult and young wild red deer (Cervus elaphus) in the southeastern part of Belgium. In deer, tuberculous lesions are not pathognomonic of Mycobacterium bovis infection due to gross and microscopic similarities with lesions caused by Mycobacterium avium subsp. paratuberculosis or M. avium subsp. avium. The aim of this study was to improve molecular methods for the species-specific identification of M. bovis, M. avium subsp. avium, and M. avium subsp. paratuberculosis in mycobacterial infections of deer. DNA banding patterns were assessed prior to and after Hpy188I restriction of f57-upstream (us)-p34 duplex amplicons. The duplex f57-us-p34 PCR differentiated M. bovis from M. avium subsp. paratuberculosis and M. avium subsp. avium infections, whereas the restriction step differentiated single M. avium subsp. paratuberculosis or M. avium subsp. avium infections from mixed M. avium subsp. paratuberculosis/M. avium subsp. avium infections. The endonuclease Hpy188I cleaves DNA between nucleotides N and G in the unique TCNGA sequence. This restriction site was found at position 168 upstream of the us-p34 initiation codon in all M. avium subsp. avium strains tested, regardless of their origin and the results of IS901 PCR. In contrast, the restriction site was abrogated in all M. avium subsp. paratuberculosis strains tested, independent of their origin, Mycobactin J dependency, and IS900 PCR results. Consequently, a two-step strategy, i.e., duplex us-p34-f57 PCR and Hpy188I restriction, allowed us to exclude M. bovis infection and to identify single (M. avium subsp. paratuberculosis or M. avium subsp. avium) or mixed (M. avium subsp. paratuberculosis/M. avium subsp. avium) infections in wild red deer in Belgium. Accordingly, we propose to integrate, in a functional molecular definition of M. avium subsp. paratuberculosis, the absence of the Hpy188I restriction site from the us-p34 amplicon.