Short communication: Mycolicibacterium smegmatis, basonym Mycobacterium smegmatis, causing pyogranulomatous mastitis and its cross-reactivity in bovine (para)tuberculosis testing

Performance of the PhoP (Rv0757/Mb0780) protein as diagnostic antigen for bovine tuberculosis

Bovine tuberculosis (bTB), a global zoonotic disease, causes negative effects on human and animal health. PhoP protein is a key regulator of pathogenic phenotypes in members of the Mycobacterium tuberculosis complex, which includes the causative agent of bTB. Despite extensive research on this protein focused in deciphering its regulatory role, little was explored about it as a diagnostic antigen. In humans, a novel role of anti-PhoP antibodies as a possible marker for the diagnosis of TB was demonstrated. However, this issue was not addressed in bovines. In this study, antigenic properties of the PhoP protein were evaluated in naturally Mycobacterium bovis (M. bovis) infected bovines. A high homology of PhoP (≥ 75 %) was observed in environmental mycobacterial species and other genera such as Salmonella and Pasteurella. Using the IFN-gamma release assay (IGRA), we detected cell-mediated immune response against PhoP in cattle from infected herds (25 %; IC 95 % 3.2-65.1), although it was significantly lower than that evoked by the reference antigens, ESAT-6/CFP-10/Rv3615c (75 %; IC95 % 34.9-96.8), and the purified protein derivative (87.5 %; IC 95 % 47.4-99.7) (p < 0.05)). Animals from a bTB free area showed no response against PhoP when analyzed by IGRA. Although, the humoral response detected 62.5 % (CI95% 24.5-91.5) of naturally infected animals, there was 100 % cross-reactivity among TB-free cattle. These results suggest that the PhoP protein is not a promising candidate for bTB diagnosis, due to it had relatively low levels of test sensitivity in the IGRA test, and very low specificity in a humoral antibody western blot assay.

Rescue of Mycobacterium bovis DNA Obtained from Cultured Samples during Official Surveillance of Animal TB: Key Steps for Robust Whole Genome Sequence Data Generation

Epidemiological surveillance of animal tuberculosis (TB) based on whole genome sequencing (WGS) of Mycobacterium bovis has recently gained track due to its high resolution to identify infection sources, characterize the pathogen population structure, and facilitate contact tracing. However, the workflow from bacterial isolation to sequence data analysis has several technical challenges that may severely impact the power to understand the epidemiological scenario and inform outbreak response. While trying to use archived DNA from cultured samples obtained during routine official surveillance of animal TB in Portugal, we struggled against three major challenges: the low amount of M. bovis DNA obtained from routinely processed animal samples; the lack of purity of M. bovis DNA, i.e., high levels of contamination with DNA from other organisms; and the co-occurrence of more than one M. bovis strain per sample (within-host mixed infection). The loss of isolated genomes generates missed links in transmission chain reconstruction, hampering the biological and epidemiological interpretation of data as a whole. Upon identification of these challenges, we implemented an integrated solution framework based on whole genome amplification and a dedicated computational pipeline to minimize their effects and recover as many genomes as possible. With the approaches described herein, we were able to recover 62 out of 100 samples that would have otherwise been lost. Based on these results, we discuss adjustments that should be made in official and research laboratories to facilitate the sequential implementation of bacteriological culture, PCR, downstream genomics, and computational-based methods. All of this in a time frame supporting data-driven intervention.