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Mycobacterial infections caused by the Mycobacterium tuberculosis complex (MTC) and non-tuberculous mycobacteria (NTM) are of great medical and veterinary relevance. The aim of this research was to study whether small mammals play a role in the epidemiology of mycobacterioses. Four samplings of 100 traps were performed in each of three cattle farms with previous history of tuberculosis or NTM between 2017 and 2018. A total of 108 animals belonging to seven species were trapped, classified, and necropsied, and tissues were submitted to microbiological and molecular methods for mycobacteria identification. The wood mouse (Apodemus sylvaticus) was the most abundant species (87%). No MTC was detected but six different NTM were identified (M. intracellulare, M. avium subsp. paratuberculosis, M. gordonae, M. celatum, M. fortuitum, and a not determined Mycobacterium sp.), showing a prevalence of 6.5%. No significant association was found between mycobacteria prevalence and the analyzed factors. Although a role in the epidemiology of MTC could not be attributed to small mammals, A. sylvaticus carries NTM that could be pathogenic or interfere with the diagnosis of tuberculosis. According to our results, there is a risk of NTM transmission at the wildlife–livestock interface through potential indirect contacts between small mammals and cattle. © 2020 by the authors. Licensee MDPI, Basel, Switzerland. ; Funding: This investigation received financial support from the National Institute for Agricultural and Food Research and Technology (INIA) (Research Project RTA2014-00002-C02-02) and the Basque Government. LV holds a pre-doctoral fellowship from the National Institute for Agricultural and Food Research and Technology (INIA) (CPD2016-0006).

11 páginas, 3 tablas, 3 figuras ; Rabbits are susceptible to infection by different species of the genus Mycobacterium. Particularly, development of specific lesions and isolation of Mycobacterium avium subsp. avium and Mycobacterium avium subsp. paratuberculosis, both subspecies of the M. avium complex, has been reported in wildlife conditions. Although, rabbit meat production worldwide is 200 million tons per year, microbiological data on this source of meat is lacking and more specifically reports of mycobacterial presence in industrially reared rabbit for human consumption have not been published. To this end, we sought mycobacteria by microbiological and histopathological methods paying special attention to Mycobacterium avium subsp. paratuberculosis in rabbits from commercial rabbitries from the North East of Spain. ; This study was supported by grants (AGL2012-39818-CO2-02) and (INIA, RTA2010-00022) from the Spanish Ministry of Economy and Competitiveness (MINECO) and the Spanish National Institute for Agricultural and Food Research and Technology, respectively. Rakel Arrazuria held a pre doctoral fellowship (BFI-2012-237) from the Basque Government. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. ; Peer Reviewed

Animal tuberculosis (TB) remains a major problem in some countries despite the existence of control programmes focused mainly on cattle. In this species, aerogenous transmission is accepted as the most frequent infection route, affecting mainly the respiratory system. Under the hypothesis that the oral route could be playing a more relevant role in transmission, diagnosis and disease persistence than previously thought, this study was performed to assess the course of TB infection in cattle and its effects on diagnosis depending on the route of entry of Mycobacterium bovis. Two groups of five calves each were either endotracheally (EC) or orally (OC) challenged. Necropsies were carried out 12 weeks after challenge except for three OC calves slaughtered 8 weeks later. All animals reacted to the tuberculin skin test and the entire EC group was positive to the interferon-gamma release assay (IGRA) 2 weeks after challenge and thereafter. The first positive IGRA results for OC calves (3/5) were recorded 4 weeks after challenge. Group comparison revealed significant differences in lesion and positive culture location and scoring. TB-compatible gross lesions and positive cultures were more frequently found in the thorax (p < 0.001) and lung (p < 0.05) of EC animals, whereas OC animals presented lesions (p = 0.23) and positive cultures (p < 0.05) mainly located in the abdomen. These results indicate that the infection route seems to be a determining factor for both the distribution and the time needed for the development of visible lesions. Our study suggests that confirmation of TB infection in some skin reactor animals can be problematic if current post-mortem examination and diagnostics are not improved. ; This study was supported with funds from the Spanish Ministry of Economy and Competitiveness (Research Project AGL2014-56305-C3-3-R) and the Department of Economic Development and Competitiveness of the Basque Government. MS holds a fellowship from the Department of Education of the Basque Government (PRE_2017_2_0043). ; Peer Reviewed

This is an open access article distributed under the terms of the Creative Commons Attribution License.-- et al. ; Mycobacteria of the Mycobacterium tuberculosis complex (MTBC) greatly affect humans and animals worldwide. The life cycle of mycobacteria is complex and the mechanisms resulting in pathogen infection and survival in host cells are not fully understood. Recently, comparative genomics analyses have provided new insights into the evolution and adaptation of the MTBC to survive inside the host. However, most of this information has been obtained using M. tuberculosis but not other members of the MTBC such as M. bovis and M. caprae. In this study, the genome of three M. bovis (MB1, MB3, MB4) and one M. caprae (MB2) field isolates with different lesion score, prevalence and host distribution phenotypes were sequenced. Genome sequence information was used for whole-genome and protein-targeted comparative genomics analysis with the aim of finding correlates with phenotypic variation with potential implications for tuberculosis (TB) disease risk assessment and control. At the whole-genome level the results of the first comparative genomics study of field isolates of M. bovis including M. caprae showed that as previously reported for M. tuberculosis, sequential chromosomal nucleotide substitutions were the main driver of the M. bovis genome evolution. The phylogenetic analysis provided a strong support for the M. bovis/M. caprae clade, but supported M. caprae as a separate species. The comparison of the MB1 and MB4 isolates revealed differences in genome sequence, including gene families that are important for bacterial infection and transmission, thus highlighting differences with functional implications between isolates otherwise classified with the same spoligotype. Strategic protein-targeted analysis using the ESX or type VII secretion system, proteins linking stress response with lipid metabolism, host T cell epitopes of mycobacteria, antigens and peptidoglycan assembly protein identified new genetic markers and candidate vaccine antigens that warrant further study to develop tools to evaluate risks for TB disease caused by M. bovis/M.caprae and for TB control in humans and animals. ; This research was supported by grants AGL2014-56305 and IPT-2011-0735-010000 from Ministerio de Economía y Competitividad, Spain, and the European Union FP7 ANTIGONE grant 278976 and Horizon 2020 COMPARE Grant 377/14. ; Peer Reviewed