A peptide-mediated capture PCR for the detection of Mycobacterium avium subsp. paratuberculosis in bulk milk samples was developed and characterized. Capture of the organism was performed using peptide aMptD, which had been shown to bind to the M. avium subsp. Paratuberculosis (Johne's disease) is a chronic and incurable granulomatous enteritis of ruminants caused by Mycobacterium avium subsp. paratuberculosis (29). The disease occurs worldwide with increasing frequency (32) and has a considerable economic impact on the livestock industry (21). Calves are mostly infected in early life, with high shedding and clinical disease commonly occurring at 2 to 5 years of age (37). Previous attempts to eradicate the disease from infected herds have frequently failed, despite a high degree of organizational and financial efforts (3,26). This is most likely due to the ubiquitous presence of the pathogen in the environments of infected herds (39) and its very great tenacity (7,20,52).An economically feasible alternative to eradication would be a control program aiming at the early identification and removal of high shedders, thereby reducing environmental contamination and infectious pressure on the herd. High shedders are more likely to secrete M. avium subsp. paratuberculosis in milk (50), and in addition, in herds with high shedders the pathogen is more likely to enter the milk by fecal contamination (8). Therefore, bulk milk might be a suitable diagnostic substrate for such an approach. Since the general infrastructure for testing of bulk milk from farms (i.e., untreated raw milk) is established (25), regular testing of this milk for the presence of M. avium subsp. paratuberculosis could allow early detection of herds with high shedders. The most convenient and amenable methods for such detection of M. avium subsp. paratuberculosis DNA in milk are enrichment via immunomagnetic separation (17,28,38) and peptide-mediated capture (47) followed by PCR, as these methods can be adapted to high-throughput testing using standard laboratory automation.In the study presented here, we followed this approach, using the phage display-derived peptide aMptD (46) for the capture of M. avium subsp. paratuberculosis in milk samples. The aMptD peptide was shown to bind to the surface-exposed MptD protein of M. avium subsp. paratuberculosis (ORF 3733C) (31), which is part of an M. avium subsp. paratuberculosis-specific pathogenicity island (46), and therefore this method, in contrast to the previously described peptide-mediated capture assay (47), is based on a defined receptor-ligand interaction. Furthermore, we thoroughly elucidated the strain and species cross-specificity of peptide aMptD for M. avium subsp. paratuberculosis by performing competitive capture assays, and we determined the kinetics and affinity of the receptor-ligand interaction by surface plasmon resonance (SPR) (27) in BIAcore biosensor experiments. Finally, in order to