Genomic Context of SARS-CoV-2 Outbreaks in Farmed Mink in Spain during Pandemic: Unveiling Host Adaptation Mechanisms.

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infects various mammalian species, with farmed minks experiencing the highest number of outbreaks. In Spain, we analyzed 67 whole genome sequences and eight spike sequences from 18 outbreaks, identifying four distinct lineages: B.1, B.1.177, B.1.1.7, and AY.98.1. The potential risk of transmission to humans raises crucial questions about mutation accumulation and its impact on viral fitness. Sequencing revealed numerous not-lineage-defining mutations, suggesting a cumulative mutation process during the outbreaks. We observed that the outbreaks were predominantly associated with different groups of mutations rather than specific lineages. This clustering pattern by the outbreaks could be attributed to the rapid accumulation of mutations, particularly in the ORF1a polyprotein and in the spike protein. Notably, the mutations G37E in NSP9, a potential host marker, and S486L in NSP13 were detected. Spike protein mutations may enhance SARS-CoV-2 adaptability by influencing trimer stability and binding to mink receptors. These findings provide valuable insights into mink coronavirus genetics, highlighting both host markers and viral transmission dynamics within communities.

Antibodies against the Mycobacterium tuberculosis complex and Brucella spp. in captive and free-living European bison (Bison bonasus) in Poland.

BACKGROUND: The European bison (Bison bonasus), a symbol of Polish nature, is a protected species that requires active health monitoring. However, conservation efforts are made difficult by the zoonotic diseases such as brucellosis and tuberculosis. OBJECTIVE: The aim of this study was to screen the Polish European bison population for exposure to the Mycobacterium tuberculosis complex (MTC) and Brucella spp. METHODS: A total of 323 free-living and captive European bison from 13 localities were tested serologically for antibodies against the M. bovis P22 multi-protein complex (in-house ELISA) and against Brucella spp. (commercial ELISA). RESULTS: Antibodies against the MTC (P22) were detected in 7% (22/323) of the tested European bison. Anti-MTC antibody positivity was not significantly different by sex, age, and captive/free range status. Anti-MTC antibodies were found in six of 13 populations sampled, always in populations with larger sample sizes including the four free-living ones. Antibodies against Brucella spp. were detected in 36% (116/323) of the tested bison. While Brucella spp. antibody prevalence was not different by sex, it was significantly different by age (lower in adults) and captive/free-living status. Brucella spp. seroprevalence decreased with sample size and seropositive bison were found in 12 of 13 sampling populations. CONCLUSIONS: Our findings identify potential emerging threats to the European bison population and confirm the first serological response to P22 in European bison. As Poland is currently officially free of brucellosis and bovine tuberculosis, our results require careful interpretation. Further studies are needed to establish the presence of cross-reactions with atypical mycobacteria in the case of MTC and other bacteria (e.g. Yersinia enterocolitica O:9) in the case of Brucella spp.

Evaluation of P22 Antigenic Complex for the Immuno-Diagnosis of Tuberculosis in BCG Vaccinated and Unvaccinated Goats.

Current eradication strategies of tuberculosis (TB) in goats mainly rely on the single intradermal tuberculin test (SIT) and single intradermal cervical comparative tuberculin tests (SICCTs). TB vaccination has been proposed as a cost-effective option in high-prevalence herds or countries where economic compensation for the slaughter of positive animals is not affordable. However, TB vaccination compromises the efficiency of tuberculin-based diagnostic tests. In this study, the performance of a new diagnostic platform, based on the P22 antigenic complex, was assessed for skin test (ST), interferon-gamma release assay (IGRA), and serology under different TB scenarios. The sensitivity (Se) of diagnostic tests was assessed in TB-infected goats from the same farm (herd A, N = 77). The specificity (Sp) was assessed in two TB-negative farms (both vaccinated against paratuberculosis): one TB unvaccinated (herd B, N = 77) and another vaccinated with bacille Calmette-Guérin (BCG) (herd C, N = 68). The single (s) P22-IGRA showed the highest Se among IGRA tests (91%), and the comparative (c) P22-ST showed the highest Sp (100% in herd B and 98% in herd C). Combined interpretation of techniques enabled the best diagnostic performances. Combining the SICCT + sP22-IGRA improved Se (97%) compared to SICCT + tuberculin-based IGRA (95%), with a reduction of Sp (95 and 100%, respectively). Besides, combination of P22-ELISA with cP22-ST or SICCT elicited a similar performance in the non-vaccination context (Se: 94 and 95%; Sp: 95 and 95%, respectively), but Sp was significantly higher for the combination with cP22-ST compared to SICCT in the TB vaccination context (95 and 79%, respectively). The combination of serological tests based on P22 and MPB83 showed higher complementarity and improved 13 percentage points the Se of P22-ELISA alone. These findings suggest that either cell-mediated or antibody-based diagnostic techniques, using the P22 antigen complex, can contribute to improve the immunodiagnostics of TB in goats under different TB control strategies.

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.

Protective Effect of Oral BCG and Inactivated Mycobacterium bovis Vaccines in European Badgers (Meles meles) Experimentally Infected With M. bovis.

In Europe, badgers (Meles meles) are recognized as major tuberculosis (TB) reservoir hosts with the potential to transmit infection to associated cattle herds. Recent studies in Spain have demonstrated that vaccination with a heat-inactivated Mycobacterium bovis vaccine (HIMB) successfully protects captive wild boar and red deer against progressive disease. The aim of this study was to evaluate the efficacy of two oral vaccines against TB in a badger model: the live-attenuated M. bovis bacillus Calmette-Guérin BCG vaccine (Danish strain) and a HIMB vaccine. Twenty-four badgers were separated in three treatment groups: oral vaccinated with live BCG (108 CFU, n = 5), oral vaccinated with HIMB (107 CFU, n = 7), and unvaccinated controls (n = 12). All badgers were experimentally infected with M. bovis (103 CFU) by the endobronchial route targeting the right middle lung lobe. Throughout the study, clinical, immunological, pathological, and bacteriological parameters of infection were measured. Both vaccines conferred protection against experimental TB in badger, as measured by a reduction of the severity and lesion volumes. Based on these data, HIMB vaccination appears to be a promising TB oral vaccine candidate for badgers in endemic countries.

Serological technique for detecting tuberculosis prevalence in sheep in Atlantic Spain.

Recent studies show that sheep could be considered to be a maintenance host for the causative agents of animal tuberculosis (TB). The performance of diagnostic tests is not well established, and new tests need to be developed for this species. In addition, information about TB prevalence in sheep is scarce. Our objectives were to evaluate a new P22 ELISA for detection of specific antibodies against Mycobacterium tuberculosis Complex (MTC), and to assess the seropositivity in 3998 sheep from herds sampled in TB hotspot areas of northern Atlantic Spain with a low TB prevalence in cattle. Results based on 80 sheep of known infection status suggest excellent sensitivity and specificity (100% and 98%, respectively) even in a M. avium susbsp. paratuberculosis infected flock. The observed TB seroprevalence was 17.96% (698/3998; CI95% 16.31-18.67). Our results indicate that the P22 ELISA may constitute a good option for TB screening at the herd level in sheep, and that sheep are an important host and control programs should be implemented at least in hotspots or when cohabiting with other TB-infected species, i.e. cattle and goats.

Tuberculosis Epidemiology and Badger (Meles meles) Spatial Ecology in a Hot-Spot Area in Atlantic Spain.

: We provide a temporal overview (from 2012 to 2018) of the outcomes of tuberculosis (TB) in the cattle and badger populations in a hot-spot in Asturias (Atlantic Spain). We also study the badger's spatial ecology from an epidemiological perspective in order to describe hazardous behavior in relation to TB transmission between cattle and badgers. Culture and single intradermal tuberculin test (SITT) were available for cattle as part of the National Program for the Eradication of TB. A field survey was also carried out in order to determine the paddocks and buildings used by each farm, and the information obtained was stored by using geographic information systems. Moreover, eighty-three badgers were submitted for necropsy and subsequent bacteriological studies. Ten badgers were also tracked, using global positioning system (GPS) collars. The prevalence of TB in cattle herds in the hot-spot increased from 2.2% in 2012 to 20% in 2016; it then declined to 0.0% in 2018. In contrast, the TB prevalence in badgers increased notably (from 5.55% in 2012-2015 to 10.64% in 2016-2018). Both cattle and badgers shared the same strain of Mycobacterium bovis. The collared badgers preferred paddocks used by TB-positive herds in spring and summer (when they were more active). The males occupied larger home ranges than the females (Khr95: males 149.78 ± 25.84 ha and females 73.37 ± 22.91 ha; Kcr50: males 29.83 ± 5.69 ha and females 13.59 ± 5.00 ha), and the home ranges were smaller in autumn and winter than in summer. The averages of the index of daily and maximum distances traveled by badgers were 1.88 ± (SD) 1.20 km and 1.99 ± 0.71 km, respectively. One of them presented a dispersive behavior with a maximum range of 18.3 km. The most preferred habitat was apple orchards in all seasons, with the exception of winter, in which they preferred pastures. Land uses and landscape structure, which have been linked with certain livestock-management practices, provide a scenario of great potential for badger-cattle interactions, thus enhancing the importance of the badgers' ecology, which could potentially transmit TB back to cattle in the future.

Temporal analysis of the interference caused by paratuberculosis vaccination on the tuberculosis diagnostic tests in goats.

Vaccination against paratuberculosis (PTB) in goats is a cost-effective control strategy, and is also effective as regards preventing the onset of clinical cases. However, it causes interference in the diagnostic tests used in the control of tuberculosis (TB). A group of 99 goats from a herd with no history of TB or PTB infection was vaccinated against PTB at seven months of age. They then underwent consecutive intradermal tests [single (SIT) and comparative (CIT) intradermal tuberculin tests), interferon-gamma release assays (IGRA) and two serological tests (p22_CE and DR-ELISA) every three months, until the interference disappeared. When using the SIT test, a variable number of positive reactors were observed at 3 months (T3; 32.3%, 95% CI 23.9-42.1), 6 months (T6; 11.5%, 95% CI 6.5-19.4), 9 months (T9; 6.4%, 95% CI 3.0-13.2) and 12 months (T12; 0%, 95% CI 0-4.0) post-vaccination. In contrast, the CIT test had a specificity (Sp) of 100% (95%, CI 96.0-100, regardless of the time post-vaccination. The IGRA also obtained high Sp values throughout the study period. No significant interference in the serological tests was recorded at T3 [p22_CE, Sp = 96% (95% CI 90.1-98.4) and DR-ELISA, Sp = 98% (95% CI 92.9-99.4)], although an increase in antibody titers was observed in the following herd testing events. In conclusion, the use of the SIT test causes the onset of false-positive reactors if applied before 12 months post-vaccination in a TB-free/PTB-vaccinated herd. Nevertheless, the CIT test and IGRA obtained high Sp values under these epidemiological circumstances. The serological tests were also highly specific in the case of PTB-vaccinated goats, although their Sp decreased significantly after several intradermal tests.

The use of serological tests in combination with the intradermal tuberculin test maximizes the detection of tuberculosis infected goats.

The diagnosis of tuberculosis (TB) in goats is based mainly on the single and comparative intradermal tuberculin (SIT and CIT) tests and, exceptionally, on the interferon-gamma (IFN-γ) assay, however they are not perfect in terms of sensitivity and specificity. Nevertheless, various serological assays that provide a potential cost-effective approach for the control of TB are also available or under development, and a variety of results have been reported regarding the ability of these tests to detect infected animals, particularly in the early stages of infection. In the present study, SIT/CIT and IFN-γ tests and three different serological assays were evaluated during two consecutive herd testing events in a recently infected caprine herd (n = 447) with a high prevalence of infection in order to evaluate their performance and provide field data with which to improve the TB control programs in this species. The proportion of infected animals that tested positive among all the infected goats (T+/I+ value) in the last herd testing event ranged from 26.2% (IC95%; 19.3-34.5) to 85.7% (IC95%; 78.5-90.7) using cell-based diagnostic tests. The SIT/SCIT tests detected more infected goats than the IFN-γ test, regardless of the interpretation criteria. The T+/I+ value of serology was 83.2 (IC95%; 75.2-89), although it increased significantly (P < 0.05) when using samples collected 15 days after the intradermal test (100%, IC95%; 97-100). In general, a parallel interpretation of intradermal tests with serology maximized the detection of infected goats. These results demonstrate that serological tests are valuable diagnostic tools to maximize the detection of TB infected goats, even in recent outbreaks, accelerating the eradication process.

Proteomic characterisation of bovine and avian purified protein derivatives and identification of specific antigens for serodiagnosis of bovine tuberculosis.

BACKGROUND: Bovine purified protein derivative (bPPD) and avian purified protein derivative (aPPD) are widely used for bovine tuberculosis diagnosis. However, little is known about their qualitative and quantitative characteristics, which makes their standardisation difficult. In addition, bPPD can give false-positive tuberculosis results because of sequence homology between Mycobacterium bovis (M. bovis) and M. avium proteins. Thus, the objective of this study was to carry out a proteomic characterisation of bPPD, aPPD and an immunopurified subcomplex from bPPD called P22 in order to identify proteins contributing to cross-reactivity among these three products in tuberculosis diagnosis. METHODS: Trypsin digests of bPPD, aPPD and P22 were analysed by nanoscale liquid chromatography-electrospray ionization tandem mass spectrometry. Mice were immunised with bPPD or aPPD, and their serum was tested by indirect ELISA for reactivity against these preparations as well as against P22. RESULTS: A total of 456 proteins were identified in bPPD, 1019 in aPPD and 118 in P22; 146 of these proteins were shared by bPPD and aPPD, and 43 were present in all three preparations. Candidate proteins that may cause cross-reactivity between bPPD and aPPD were identified based on protein abundance and antigenic propensity. Serum reactivity experiments indicated that P22 may provide greater specificity than bPPD with similar sensitivity for ELISA-type detection of antibodies against M. tuberculosis complex. CONCLUSION: The subpreparation from bPPD called P22 may be an alternative to bPPD for serodiagnosis of bovine tuberculosis, since it shares fewer proteins with aPPD than bPPD does, reducing risk of cross-reactivity with anti-M. avium antibodies.