Environmental determinants of the Mycobacterium bovis concomitant infection in cattle and badgers in France

Intra- and interspecies infectious neighbourhoods as determinant parameters for Mycobacterium bovis infection among badgers in southwestern France

The epidemiological system for Mycobacterium bovis in France involves cattle and, in some areas, wildlife species (mainly badgers and wild boar). This multi-host aspect complicates the control and eradication prospects for bovine tuberculosis in endemic areas, despite the surveillance and control measures implemented for decades in this officially tuberculosis-free European country. To improve control measures, and to manage spillback transmission from badgers to cattle, it is necessary to clarify the transmission mechanisms of M. bovis in these epidemiological systems. We modelled a badger population from a southwestern endemic area by a Dirichlet tessellation based on a sett census conducted by local hunters and trappers between 2013 and 2015. We then used a logistic regression model to test the association between the infection status of setts and computed variables depicting three types of transmission (intraspecific, interspecific and landscape-associated). The apparent prevalence of infected setts was of 40.5%. Two variables were significantly associated with the probability for a sett to be infected: the proportion of neighbouring setts that were infected (OR: 3.19 [2.04-5.17]95%) and the presence of nearby pastures belonging to an infected farm (OR: 2.33 [1.13-4.89]95%]. While badger culling measures have been implemented according to the national TB control plan in the study area since 2012 (in the vicinity of infected farms and their pastures), our results clearly highlight the need to reinforce measures aimed at reducing both intraspecific and interspecific infection pressure. For this purpose, the promising prospect of badger vaccination could be considered, along with biosecurity measures.

Spatial association of Mycobacterium bovis infection in cattle and badgers at the pasture interface in an endemic area in France

Despite control and surveillance programmes, Mycobacterium bovis, the main aetiologic agent of bovine tuberculosis (bTB), is still detected on cattle farms and in wildlife populations in France, especially in badgers in the French Côte-d'Or département. The aim of our study was to find out if infected badgers were trapped significantly closer to pastures of infected farms than non-infected badgers and, if so, to determine the most efficient distance around those pastures for badger trapping, particularly for surveillance purposes. We studied two subareas (southern and northern), chosen based on natural barriers to badger movements and according to the presence of pastures belonging to infected farms (POIFs) and infected or non-infected badgers. In each subarea, we computed the shortest distances D0 and D between badgers trapped a given year n between 2015 and 2019 (n = 59 infected and n = 1535 non-infected badgers for D0; n = 53 infected and n = 1476 non-infected badgers for D) and POIFs designated as infected between the year n - 4 and n + 1 (respectively n = 373 and n = 388 POIFs). D0 was calculated without considering spoligotypes, while D was calculated considering the possible epidemiological link between infected badgers and POIFs by using bTB spoligotype information. Then, we computed the observed mean and median of the D0 and D distances and used a bootstrap analysis to test if infected badgers were found significantly closer to POIFs than non-infected badgers. We observed that infection of badgers was not independent of distance from POIF in both subareas but distances (D0 or D) were different between the northern and southern subarea. In the northern subarea, which displays a mosaic landscape (mean and median D distances were respectively 612 m and 303 m for infected badgers), infected badgers indeed were trapped closer to POIFs, considering D0 and D. In the southern subarea, predominantly forested, infected badgers were significantly closer to POIFs than non-infected badgers when considering D0 but not for D (mean and median D distances were respectively 7148 m and 4831 m for infected badgers). These results will help to determine the most efficient distance from POIFs to trap badgers to determine their infection status in countryside landscapes. They also highlight the need to better understand the epidemiological systems at play in more forested landscapes where badgers may behave differently or other susceptible sympatric wild species might play a more important role in the circulation of M. bovis, both phenomena contributing to badger infection at greater distances from POIFs.

Analysis of a multi-type resurgence of Mycobacterium bovis in cattle and badgers in Southwest France, 2007-2019

Although control measures to tackle bovine tuberculosis (bTB) in cattle have been successful in many parts of Europe, this disease has not been eradicated in areas where Mycobacterium bovis circulates in multi-host systems. Here we analyzed the resurgence of 11 M. bovis genotypes (defined based on spoligotyping and MIRU-VNTR) detected in 141 farms between 2007 and 2019, in an area of Southwestern France where wildlife infection was also detected from 2012 in 65 badgers. We used a spatially-explicit model to reconstruct the simultaneous diffusion of the 11 genotypes in cattle farms and badger populations. Effective reproduction number R was estimated to be 1.34 in 2007-2011 indicating a self-sustained M. bovis transmission by a maintenance community although within-species Rs were both < 1, indicating that neither cattle nor badger populations acted as separate reservoir hosts. From 2012, control measures were implemented, and we observed a decrease of R below 1. Spatial contrasts of the basic reproduction ratio suggested that local field conditions may favor (or penalize) local spread of bTB upon introduction into a new farm. Calculation of generation time distributions showed that the spread of M. bovis has been more rapid from cattle farms (0.5-0.7 year) than from badger groups (1.3-2.4 years). Although eradication of bTB appears possible in the study area (since R < 1), the model suggests it is a long-term prospect, because of the prolonged persistence of infection in badger groups (2.9-5.7 years). Supplementary tools and efforts to better control bTB infection in badgers (including vaccination for instance) appear necessary.

A Bayesian evolutionary model towards understanding wildlife contribution to F4-family Mycobacterium bovis transmission in the South-West of France

In two “départements” in the South-West of France, bovine tuberculosis (bTB) outbreaks due to Mycobacterium bovis spoligotype SB0821 have been identified in cattle since 2002 and in wildlife since 2013. Using whole genome sequencing, the aim of our study was to clarify badger contribution to bTB transmission in this area. We used a Bayesian evolutionary model, to infer phylogenetic trees and migration rates between two pathogen populations defined by their host-species. In order to account for sampling bias, sub-population structure was inferred using the marginal approximation of the structured coalescent (Mascot) implemented in BEAST2. We included 167 SB0821 strains (21 isolated from badgers and 146 from cattle) and identified 171 single nucleotide polymorphisms. We selected a HKY model and a strict molecular clock. We estimated a badger-to-cattle transition rate (median: 2.2 transitions/lineage/year) 52 times superior to the cattle-to-badger rate (median: 0.042 transitions/lineage/year). Using the maximum clade credibility tree, we identified that over 75% of the lineages from 1989 to 2000 were present in badgers. In addition, we calculated a median of 64 transition events from badger-to-cattle (IQR: 10–91) and a median of zero transition event from cattle-to-badger (IQR: 0–3). Our model enabled us to infer inter-species transitions but not intra-population transmission as in previous epidemiological studies, where relevant units were farms and badger social groups. Thus, while we could not confirm badgers as possible intermediaries in farm-to-farm transmission, badger-to-cattle transition rate was high and we confirmed long-term presence of M.bovis in the badger population in the South-West of France.

Environmental DNA: A promising factor for tuberculosis risk assessment in multi-host settings

Attaining and maintaining the Official Tuberculosis Free status continues to be a challenge when several domestic and wild hosts contribute to the maintenance of the Mycobacterium tuberculosis complex (MTC). Local tuberculosis hotspots are sometimes identified in cattle in low-prevalence regions. We have, therefore, studied one such hotspot in depth in order to produce an epidemiological diagnosis. Host population size and MTC prevalence were estimated in selected wildlife and in livestock, while on-cattle environmental DNA detection was additionally used as a proxy for risk of exposure at the farm (herd) level. Positive skin test reactors were found on16 of the 24 cattle farms studied in the period 2012–2016. Although all goats tested negative to the skin test during this period, MTC was confirmed in four sheep at slaughter, thus indicating an unknown prevalence of infection in this host species. With regard to wildlife, the prevalence of MTC infection based on culture was 8.8% in the case of wild boar (Sus scrofa), and the only road-killed badger (Meles meles) submitted for culture tested positive. Two criteria were employed to divide the cattle farms into higher or lower risk: tuberculosis testing results and environmental DNA detection. Environmental MTC DNA detection yielded significant differences regarding “use of regional pastures” and “proximity to woodland”. This study suggests that on-animal environmental DNA sampling may help when assessing contact risk as regards MTC in livestock at the herd level. This tool opens up new avenues of epidemiological research in complex multi-host settings.

New serological platform for detecting antibodies against Mycobacterium tuberculosis complex in European badgers

European badgers (Meles meles) have been identified as wildlife reservoirs for Mycobacterium bovis in the UK and Ireland, and may also have a role in the epidemiology of animal tuberculosis in other European regions. Thus, detection of M. bovis‐infected badgers may be required for the purposes of surveillance and monitoring of disease levels in infected populations. Current serological assays to detect M. bovis infection in live badgers, while rapid and inexpensive, show limited diagnostic sensitivity. Here we describe and evaluate new ELISA platforms for the recognition of the P22 multiprotein complex derived from the purified protein derivative (PPD) of M. bovis. The recognition of IgG against P22 multiprotein complex derived from PPD‐B was tested by ELISA in the serum of badgers from the UK, Ireland and Spain. TB infection in the badgers was indicated by the presence of M. bovis in tissues by culture and histology at post‐mortem examination and TB‐free status was established by repeated negativity in the interferon γ release assay (IGRA). In experimentally infected badgers, humoral antibody responses against P22 developed within 45 days post‐infection. The ELISA tests showed estimated sensitivity levels of 74–82% in experimentally and naturally infected badgers with specificities ranging from 75% to 100% depending on the badger population tested. The P22 multi‐antigen based ELISAs provide a sensitive and specific test platform for improved tuberculosis surveillance in badgers.

Outbreak of tuberculosis caused by Mycobacterium bovis in a cattery of Abyssinian cats in Italy

Mycobacterium bovis is a re-emerging zoonosis; it was diagnosed in five Abyssinian cats in a breeding cattery in Italy. The infection entered the cattery with an imported kitten (cat A); it had a suspected bite wound on its leg that had been treated at a veterinary clinic in Kiev, Ukraine, which is probably where it became infected with M. bovis. When the kitten arrived in Italy, there were four cats in the cattery; an adult female, her two kittens and a kitten imported from Russia. These were all healthy, and had no outdoor access. All five cats developed tuberculous interstitial pneumonia; in cat A this occurred 6 weeks after importation, the others were diagnosed 4-6 weeks later. Three cats were euthanised with deteriorating pneumonia while two cats remained clinically well on antibiotic therapy (marbofloxacin, doxycycline and azithromycin). The latter cases were euthanised after 5 weeks, as required by Italian law once M. bovis infection was suspected. Changes consistent with tuberculosis on gross post-mortem examination included mesenteric and mediastinal lymphadenopathy, splenomegaly and hepatomegaly, and the presence of disseminated focal white lesions on the cut surface of the spleen, liver and lungs. Visible acid-fast bacteria (cats A, B and C) were confirmed as Mycobacterium tuberculosis complex by PCR (cats A, B, C, D and E), refined to M. bovis (cats A, B and D), spoligotype SB0950 (cats A and D).

The Distribution of Bovine Tuberculosis in Cattle Farms Is Linked to Cattle Trade and Badger-Mediated Contact Networks in South-Western France, 2007-2015

Bovine tuberculosis (bTB), mainly caused by Mycobacterium bovis, can affect domestic and wild animals as well as humans. Identifying the major transmission mechanisms in an area is necessary for disease control and management. In this study, we aimed to evaluate the involvement of different types of contact in M. bovis transmission between cattle farms of south-western France between 2007 and 2015. We analyzed an empirical contact network of cattle farms as nodes, with known infection status and molecular types (16 circulated during the study period of which 14 affected only cattle and two both badgers and cattle). Edges were based on cattle trade data (T-edges) and on spatial neighborhood relationships between farms, either direct (P-edges) or badger-mediated, when two farms neighbored the same badger home range (B-edges), or two distinct but neighboring badger home ranges (D-edges). Edge types were aggregated so that the contact network contained only unique edges labeled by one or several edge types. The association between the contact network structure and bTB infection status was assessed using a non-parametric test, each molecular type being considered a marker of an independent epidemic. Using a logistic regression model, we estimated the contribution of each edge type to the probability for an edge originating from an infected farm to end at another infected farm. A total number of 1946 cattle farms were included in the study and were linked by 54,243 edges. Within this contact network, infected farms (whatever the molecular type) always belonged to the same component, suggesting the contact network may have supported bTB spread among those farms. A significant association between the pattern of bTB-infected farms and the structure of the contact network was observed when all the molecular types were simultaneously considered. The logistic regression model showed a significant association between M. bovis infection in direct neighbors of infected farms and the connection by T-, B- and D-edges, with odds-ratios of 7.4, 1.9, and 10.4, respectively. These results indicate a multifactorial M. bovis transmission between cattle farms of the studied area, with varying implication levels of the trade, pasture and badger networks according to the molecular type.