Implications and challenges of tuberculosis in wildlife ungulates in Portugal: A molecular epidemiology perspective

Population structure and history of Mycobacterium bovis European 3 clonal complex reveal transmission across ecological corridors of unrecognized importance in Portugal

Mycobacterium bovis causes animal tuberculosis in livestock and wildlife, with an impact on animal health and production, wildlife management, and public health. In this work, we sampled a multi-host tuberculosis community from the official hotspot risk area of Portugal over 16 years, generating the largest available data set in the country. Using phylogenetic and ecological modeling, we aimed to reconstruct the history of circulating lineages across the livestock-wildlife interface to inform intervention and the implementation of genomic surveillance within the official eradication plan. We find evidence for the co-circulation of M. bovis European 1 (Eu1), Eu2, and Eu3 clonal complexes, with Eu3 providing sufficient temporal signal for further phylogenetic investigation. The Eu3 most recent common ancestor (bovine) was dated in the 1990s, subsequently transitioning to wildlife (red deer and wild boar). Isolate clustering based on sample metadata was used to inform phylogenetic inference, unravelng frequent transmission between two clusters that represent an ecological corridor of previously unrecognized importance in Portugal. The latter was associated with transmission at the livestock-wildlife interface toward locations with higher temperature and precipitation, lower agriculture and road density, and lower host densities. This is the first analysis of M. bovis Eu3 complex in Iberia, shedding light on background ecological factors underlying long-term transmission and informing where efforts could be focused within the larger hotspot risk area of Portugal.

IMPORTANCE

Efforts to strengthen surveillance and control of animal tuberculosis (TB) are ongoing worlwide. Here, we developed an eco-phylodynamic framework based on discrete phylogenetic approaches informed by M. bovis whole-genome sequence data representing a multi-host transmission system at the livestock-wildlife interface, within a rich ecological landscape in Portugal, to understand transmission processes and translate this knowledge into disease management benefits. We find evidence for the co-circulation of several M. bovis clades, with frequent transmission of the Eu3 lineage among cattle and wildlife populations. Most transition events between different ecological settings took place toward host, climate and land use gradients, underscoring animal TB expansion and a potential corridor of unrecognized importance for M. bovis maintenance. Results stress that animal TB is an established wildlife disease without ecological barriers, showing that control measures in place are insufficient to prevent long-distance transmission and spillover across multi-host communities, demanding new interventions targeting livestock-wildlife interactions.

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.

Genomic epidemiology sheds light on the emergence and spread of Mycobacterium bovis Eu2 Clonal Complex in Portugal

ABSTRACTAnimal tuberculosis (TB) remains a serious concern for animal and human health. Mycobacterium bovis circulates in multi-host systems, dominated by the European 2 clonal complex (Eu2) in Iberia. In this work, we use genomic epidemiology to infer the emergence, spread, and spatiotemporal patterns of Eu2 in the official epidemiological risk area of animal TB in Portugal. Phylogenetic analysis of 144 M. bovis whole-genome sequences from cattle, wild boar, and red deer, representing the 2002-2021 period, distinguished three Eu2 clades that evolved independently. The major Eu2 clade underwent phylodynamic inferences to estimate the time and location of outbreaks, host transitions, and spatial diffusion as well. The origin of this Eu2 clade was attributed to the red deer population in the Castelo Branco district, near the border with Spain. Most host transitions were intraspecific (80%), while interspecific transmissions between wildlife species (wild boar-red deer), and between wild boar and cattle, were highly supported. Phylogeographic reconstruction evidenced that most transitions (82%) occur within municipalities, highlighting local transmission corridors.Our study indicates that M. bovis continues to spread at the cattle-wildlife interface within the animal TB hotspot area, possibly driven by the foraging behaviour of wild boar near agricultural lands. Red deer seems to be an important driver of TB within wildlife hosts, while the wild boar links the multi-host wildlife community and livestock. This work highlights the value of combining genomic epidemiology with phylodynamic inference to resolve host jumps and spatial patterns of M. bovis, providing real-time clues about points of intervention.

Biocomputational characterisation of MBO_200107 protein of Mycobacterium tuberculosis variant caprae: a molecular docking and simulation study

The principal objective of this study was to delineate the potentiality of the MBO_200107 protein from the Mycobacterium tuberculosis variant caprae in cancer research. It is a cytoplasmic protein, comprised of a 354-long amino acid chain, alkaline, had a molecular weight of 39089.37 Da, an isoelectric point of 9.62 and a grand average of hydropathicity of -0.345. One of the functional domains was predicted as Gammaglutamylcyclotransferase (GGCT). Among tertiary structures, the Modeller and Phyre2 model satisfied all the quality parameters, though they are truncated; contrarily, the I-TASSER model is full length and contains the sequence for the GGCT domain, though it did not meet all the quality parameters. It also has significant sequence similarities (47.5% by EMBOSS Water and 72.4% by EMBOSS Matcher) with a human GGCT, and the conserved sequences are confined to the GGCT domain of the MBO_200107. According to molecular docking analyses, the protein has a binding affinity of -4.8 kcal/mol by Autodock Vina and -56.465 kcal/mol by HPEPDOCK to the human glutathione (GSH), an essential metabolite for GGCT metabolism. The Molecular dynamic simulation of the docked complex showed the binding efficiency of the GSH to MBO_200107 with a minimal structural alteration. The in silico findings mentioned above revealed that the protein could be used as a supplementary tool in cancer research, such as designing vaccines or drugs where the role of GGCT has been implicated. Further, we recommend fully characterising the protein and conducting essential in vitro and in vivo experiments to determine its detailed usefulness.Communicated by Ramaswamy H. Sarma.

Hepatitis E Virus in the Wild Boar Population: What Is the Real Zoonotic Risk in Portugal?

Hepatitis E virus (HEV) is an important zoonosis in wild boar. Reported zoonotic cases are mainly associated with the consumption of raw/undercooked meat and/or liver. This study aims to determine the occurrence of HEV in the Portuguese wild boar population. During the hunting season 2021/2022, 123-matched samples (liver, faeces, and blood) were collected from hunted wild boars throughout Portugal. An RT-PCR assay tested liver and faeces samples to detect HEV-RNA. From blood samples, an ELISA test was performed. Only one liver sample was positive for HEV (0,8%) and one other from faeces. A total of 34 sera were seropositive (26.7%). At the same time, in a survey of 106 hunters, 21 consumed/ate the liver of wild boars (19.8%). Only three recognised the possibility of consuming it undercooked. Contrary to previous studies in Portugal, the prevalence of HEV in liver and faeces is low, but the seropositivity is higher. But, when analyzing in detail, it could be observed that an HEV hotspot exists in the southeast of central Portugal and that it is a zoonotic risk for hunters of this region. The data of this study reinforce the importance of including HEV in surveillance programs for wildlife diseases to expand the potential zoonotic information.

Risk Practices for Occupational Zoonotic Exposure to Tuberculosis in a High-Risk Population in Portugal

Concerning large game in Portugal, there is an epidemiological risk area for tuberculosis where the pressure of tuberculosis infection in wild animals is high. Hunters and other people involved in managing carcasses (evisceration and/or initial examination) of these animals should be considered as a high-risk population for sporadic occupational zoonotic infection. This study aims to evaluate and indicate these stakeholders’ main risk practices. The survey was carried out in two phases: a first phase with an anonymous survey to hunters about self-consumption of game meat and carcass handling practices, and a second phase of evaluation in loco of the practices carried out at collection points after driven hunts. As the main results suggested in this study, bad practices and improper handling of hunted carcasses potentially infected with tuberculosis were marked in both phases of the survey, mostly related to the lack of recognition of tuberculosis-like lesions and the non-use of individual protection material, such as gloves and masks. It is evident that stakeholders are interested in learning more about how to perform initial examination properly and what kind of biosecurity measures can be adopted to minimize zoonotic infection risk.

Use of Whole-Genome Sequencing to Unravel the Genetic Diversity of a Prevalent Mycobacterium bovis Spoligotype in a Multi-Host Scenario in Spain

Despite the efforts invested in the eradication of bovine tuberculosis in Spain, herd prevalence has remained constant in the country during the last 15 years (~1.5–1.9%) due to a combination of epidemiological factors impairing disease control, including between-species transmission. Here, our aim was to investigate the molecular diversity of Mycobacterium bovis isolates belonging to the highly prevalent SB0339 spoligotype in the cattle-wildlife interface in different regions of Spain using whole-genome sequencing (WGS). Genomic data of 136 M. bovis isolates recovered from different animal species (cattle, wild boar, fallow deer, and red deer) and locations between 2005 and 2018 were analyzed to investigate between- and within-species transmission, as well as within-herds. All sequenced isolates differed by 49–88 single nucleotide polymorphisms from their most recent common ancestor. Genetic heterogeneity was geographic rather than host species-specific, as isolates recovered from both cattle and wildlife from a given region were more closely related compared to isolates from the same species but geographically distant. In fact, a strong association between the geographic and the genetic distances separating pairs of M. bovis isolates was found, with a significantly stronger effect when cattle isolates were compared with wildlife or cattle-wildlife isolates in Spain. The same results were obtained in Madrid, the region with the largest number of sequenced isolates, but no differences depending on the host were observed. Within-herd genetic diversity was limited despite the considerable time elapsed between isolations. The detection of closely related strains in different hosts demonstrates the complex between-host transmission dynamics present in endemic areas in Spain. In conclusion, WGS results a valuable tool to track bTB infection at a high resolution and may contribute to achieve its eradication in Spain.

GIS as an Epidemiological Tool to Monitor the Spatial-Temporal Distribution of Tuberculosis in Large Game in a High-Risk Area in Portugal

Simple Summary

Hunting of large game is an activity of great social and economic importance. However, it can cause public health problems due to the zoonotic diseases of these animals, such as tuberculosis. Regular space–time monitoring of hunted animals’ health status allows both the hunters and competent authorities to understand the geographic location of the hunted animals, as well as the occurrence of possible diseases in these animals. This investigation presents the results of the assessment of the spatial–temporal distribution of tuberculosis in large game in a tuberculosis high-risk area in Portugal in the form of maps, which allow any interested party to quickly analyse the hunting situation regardless of their technical or scientific knowledge.

Abstract

Since April 2011, Portugal has implemented specific national legislation (Notice No. 1/2011), defining “Epidemiologic Risk Areas for Bovine Tuberculosis in Large Game” and mitigation measures in these areas, including Idanha-a-Nova county. A GIS project was created to record information that would allow us to analyse the spatial–temporal distribution, both for hunting bags and tuberculosis occurrence, in hunted wild boar and red deer in Idanha-a-Nova. Hunting bag and tuberculosis-like lesion data were recorded during post-mortem inspection across 11 hunting seasons, totalling 9844 animals. The difference in tuberculosis occurrence for these species was statistically significant in nearly all 11 seasons, with wild boars presenting approximately twice the occurrence of red deer. No significant difference was noted before and after the Notice No. 1/2011 implementation. These results, following GIS-based spatial analysis, enable us to state that both large game species displayed an irregular tuberculosis pattern for the 2006–2016 period, and we identified some specific areas of high risk for both species. Southern areas of the county may be considered the priority for intervention. This research demonstrates the potential of GIS tools to evaluate, in the field, the results and efficacy of legislation such as Notice No. 1/2011, and to ensure the correct implementation of cost-effective mitigation strategies for tuberculosis in large game species.

Whole Genome Sequencing Refines Knowledge on the Population Structure of Mycobacterium bovis from a Multi-Host Tuberculosis System

Classical molecular analyses of Mycobacterium bovis based on spoligotyping and Variable Number Tandem Repeat (MIRU-VNTR) brought the first insights into the epidemiology of animal tuberculosis (TB) in Portugal, showing high genotypic diversity of circulating strains that mostly cluster within the European 2 clonal complex. Previous surveillance provided valuable information on the prevalence and spatial occurrence of TB and highlighted prevalent genotypes in areas where livestock and wild ungulates are sympatric. However, links at the wildlife-livestock interfaces were established mainly via classical genotype associations. Here, we apply whole genome sequencing (WGS) to cattle, red deer and wild boar isolates to reconstruct the M. bovis population structure in a multi-host, multi-region disease system and to explore links at a fine genomic scale between M. bovis from wildlife hosts and cattle. Whole genome sequences of 44 representative M. bovis isolates, obtained between 2003 and 2015 from three TB hotspots, were compared through single nucleotide polymorphism (SNP) variant calling analyses. Consistent with previous results combining classical genotyping with Bayesian population admixture modelling, SNP-based phylogenies support the branching of this M. bovis population into five genetic clades, three with apparent geographic specificities, as well as the establishment of an SNP catalogue specific to each clade, which may be explored in the future as phylogenetic markers. The core genome alignment of SNPs was integrated within a spatiotemporal metadata framework to further structure this M. bovis population by host species and TB hotspots, providing a baseline for network analyses in different epidemiological and disease control contexts. WGS of M. bovis isolates from Portugal is reported for the first time in this pilot study, refining the spatiotemporal context of TB at the wildlife-livestock interface and providing further support to the key role of red deer and wild boar on disease maintenance. The SNP diversity observed within this dataset supports the natural circulation of M. bovis for a long time period, as well as multiple introduction events of the pathogen in this Iberian multi-host system.

Long-term molecular surveillance provides clues on a cattle origin for Mycobacterium bovis in Portugal

Animal tuberculosis (TB), caused by Mycobacterium bovis, is maintained in Portugal in a multi-host system, with cattle, red deer and wild boar, playing a central role. However, the ecological processes driving transmission are not understood. The main aim of this study was thus to contribute to the reconstruction of the spatiotemporal history of animal TB and to refine knowledge on M. bovis population structure in order to inform novel intervention strategies. A collection of 948 M. bovis isolates obtained during long-term surveillance (2002–2016, 15 years) of cattle (n = 384), red deer (n = 303) and wild boar (n = 261), from the main TB hotspot areas, was characterized by spoligotyping and 8 to 12-loci MIRU-VNTR. Spoligotyping identified 64 profiles and MIRU-VNTR distinguished 2 to 36 subtypes within each spoligotype, enabling differentiation of mixed or clonal populations. Common genotypic profiles within and among livestock and wildlife in the same spatiotemporal context highlighted epidemiological links across hosts and regions, as for example the SB0119-M205 genotype shared by cattle in Beja district or SB0121-M34 shared by the three hosts in Castelo Branco and Beja districts. These genomic data, together with metadata, were integrated in a Bayesian inference framework, identifying five ancestral M. bovis populations. The phylogeographic segregation of M. bovis in specific areas of Portugal where the disease persists locally is postulated. Concurrently, robust statistics indicates an association of the most probable ancient population with cattle and Beja, providing a clue on the origin of animal TB epidemics. This relationship was further confirmed through a multinomial probability model that assessed the influence of host species on spatiotemporal clustering. Two significant clusters were identified, one that persisted between 2004 and 2010, in Beja district, with Barrancos county at the centre, overlapping the central TB core area of the Iberian Peninsula, and highlighting a significant higher risk associated to cattle. The second cluster was predominant in the 2012–2016 period, holding the county Rosmaninhal at the centre, in Castelo Branco district, for which wild boar contributed the most in relative risk. These results provide novel quantitative insights beyond empirical perceptions, that may inform adaptive TB control choices in different regions.

Epidemiology of Tuberculosis in Multi-Host Wildlife Systems: Implications for Black (Diceros bicornis) and White (Ceratotherium simum) Rhinoceros

Cases of tuberculosis (TB) resulting from infection with Mycobacterium tuberculosis complex (MTBC) have been recorded in captive white (Ceratotherium simum) and black (Diceros bicornis) rhinoceros. More recently, cases have been documented in free-ranging populations of both species in bovine tuberculosis (bTB) endemic areas of South Africa. There is limited information on risk factors and transmission patterns for MTBC infections in African rhinoceros, however, extrapolation from literature on MTBC infections in other species and multi-host systems provides a foundation for understanding TB epidemiology in rhinoceros species. Current diagnostic tests include blood-based immunoassays but distinguishing between subclinical and active infections remains challenging due to the lack of diagnostic techniques. In other species, demographic risk factors for MTBC infection include sex and age, where males and adults are generally at higher risk than females and younger individuals. Limited available historical information reflects similar age- and sex-associated patterns for TB in captive black and white rhinoceros, with more reports of MTBC-associated disease in black rhinoceros than in white rhinoceros. The degree of MTBC exposure in susceptible wildlife depends on their level of interaction, either directly with other infected individuals or indirectly through MTBC contaminated environments, which is dependent on the presence and abundance of infected reservoir hosts and the amount of MTBC shed in their excreta. Captive African rhinoceros have shown evidence of MTBC shedding, and although infection levels are low in free-ranging rhinoceros, there is a risk for intraspecies transmission. Free-ranging rhinoceros in bTB endemic areas may be exposed to MTBC from other infected host species, such as the African buffalo (Syncerus caffer) and greater kudu (Tragelaphus strepsiceros), through shared environmental niches, and resource co-utilization. This review describes current knowledge and information gaps regarding the epidemiology of TB in African rhinoceros.

Polyclonal infection as a new scenario in Mycobacterium caprae epidemiology

Portugal is one of the European Union countries with an ongoing eradication program for bovine tuberculosis (TB), which does not include systematic goat testing. However, surveillance in small ruminants is increasingly important, since goat and sheep can harbour Mycobacterium caprae and be an infection source to cattle with impact in the success of bovine TB control. Furthermore, the information regarding the epidemiology and biology of M. caprae is quite limited comparing to the cognate bovine-adapted ecotype, M. bovis. In this work, we applied spoligotyping and MIRU-VNTR (Mycobacterial Interspersed Repetitive Units-Variable Number of Tandem Repeats) to M. caprae obtained between 2003 and 2014 from 55 animal hosts, including goat (n = 29), cattle (n = 21), sheep (n = 1) and wild boar (n = 4) from Portugal. The molecular analysis revealed a unique spoligotyping pattern (SB0157) and 24 MIRU types. Genotyping of serial M. caprae from herds with recurrent outbreaks enabled further discrimination of epidemiologically related isolates, supporting a clonal structure in Portugal and denoting the emergence of clonal diversity at the herd level, more apparent for MIRU4. Results suggest a founder effect and adaptive genotypic divergence, paving the way for sympatric speciation. Double allele findings at MIRU4 in over 20 % of infected animals indicates that co-infection and in vivo microevolution may be frequent in the goat-adapted ecotype. While polyclonal infection appears common in M. caprae epidemiology, the functional significance of subtle genotypic variations remains to be disclosed, namely at the interface with the host, to expand knowledge on the epidemiology and biology of this neglected ecotype.

Spatial Analysis of Wildlife Tuberculosis Based on a Serologic Survey Using Dried Blood Spots, Portugal

We investigated the spatial epidemiology of bovine tuberculosis (TB) in wildlife in a multihost system. We surveyed bovine TB in Portugal by serologic analysis of elutes of dried blood spots obtained from hunted wild boar. We modeled spatial disease risk by using areal generalized linear mixed models with conditional autoregressive priors. Antibodies against Mycobaterium bovis were detected in 2.4% (95% CI 1.5%-3.8%) of 678 wild boar in 2 geographic clusters, and the predicted risk fits well with independent reports of M. bovis culture. Results show that elutes are an almost perfect substitute for serum (Cohen unweighted κ = 0.818), indicating that serologic tests coupled with dried blood spots are an effective strategy for large-scale bovine TB surveys, using wild boar as sentinel species. Results also show that bovine TB is an emerging wildlife disease and stress the need to prevent further geographic spread and prevalence increase.

Bovine Tuberculosis in Britain and Ireland - A Perfect Storm? the Confluence of Potential Ecological and Epidemiological Impediments to Controlling a Chronic Infectious Disease

Successful eradication schemes for bovine tuberculosis (bTB) have been implemented in a number of European and other countries over the last 50 years. However, the islands of Britain and Ireland remain a significant aberration to this trend, with the recent exception of Scotland. Why have eradication schemes failed within these countries, while apparently similar programs have been successful elsewhere? While significant socio-economic and political factors have been discussed elsewhere as key determinants of disease eradication, here we review some of the potential ecological and epidemiological constraints that are present in these islands relative to other parts of Europe. We argue that the convergence of these potential factors may interact additively to diminish the potential of the present control programs to achieve eradication. Issues identified include heterogeneity of diagnostic testing approaches, the presence of an abundant wildlife reservoir of infection and the challenge of sustainably managing this risk effectively; the nature, size, density and network structure of cattle farming; potential effects of Mycobacterium bovis strain heterogeneity on disease transmission dynamics; possible impacts of concurrent endemic infections on the disclosure of truly infected animals; climatological differences and change coupled with environmental contamination. We further argue that control and eradication of this complex disease may benefit from an ecosystem level approach to management. We hope that this perspective can stimulate a new conversation about the many factors potentially impacting bTB eradication schemes in Britain and Ireland and possibly stimulate new research in the areas identified.

Exposure of Threatened Accipitridae to Mycobacterium bovis Calls for Active Surveillance

Anthropogenic activities have cumulatively led to the dramatic decline of world populations of vultures that currently face serious survival challenges in several regions of the world. In Portugal, the three resident species qualify as endangered and are under conservation efforts, mainly in the central east and south-east regions, where habitat protection and artificial feeding stations were implemented. Concurrently, the areas under protection are highly affected by tuberculosis (TB) in cattle and wild ungulates, whose potentially infected carcasses may naturally or artificially be used as feed by local vultures. In this work, we opportunistically surveyed populations of Eurasian griffon (Gyps fulvus) and Eurasian black vulture (Aegypius monachus) for the presence of Mycobacterium bovis. Nine pathogenic mycobacteria, including one M. bovis isolate, were cultured from the oropharynx of nine of the surveyed vultures (n = 55), sampled in recovery centres or in artificial feeding stations. Genotyping of the M. bovis strain indicated spoligotype SB0121, the most frequent type in Portugal, and a unique MIRU-VNTR profile that differed in two loci from the profiles of SB0121 bovine and deer strains from the same geographical area. The M. bovis-positive griffon exhibited poor clinical condition when admitted to the recovery centre; however, clinical evidence of TB was not present. Although the significance of M. bovis isolation in this vulture specimen could not be ascertained and despite the accepted notion that vultures are naturally resistant to microbial pathogens, the sanitary follow-up of Accipitridae vulture populations in TB-hotspot areas is essential to safeguard ongoing conservation efforts and also to evaluate the suitability of standing legislation on deliberate supplementary feeding schemes for menaced birds of prey.

Isolation and Potential for Transmission of Mycobacterium bovis at Human-livestock-wildlife Interface of the Serengeti Ecosystem, Northern Tanzania

Mycobacterium bovis, the causative agent of bovine tuberculosis (bTB), is a multihost pathogen of public health and veterinary importance. We characterized the M. bovis isolated at the human-livestock-wildlife interface of the Serengeti ecosystem to determine the epidemiology and risk of cross-species transmission between interacting hosts species. DNA was extracted from mycobacterial cultures obtained from sputum samples of 472 tuberculosis (TB) suspected patients and tissue samples from 606 livestock and wild animal species. M. bovis isolates were characterized using spoligotyping and Mycobacterial Interspersed Repetitive Units-Variable Tandem Repeats (MIRU-VNTR) on 24 loci. Only 5 M. bovis were isolated from the cultured samples. Spoligotyping results revealed that three M. bovis isolates from two buffaloes (Syncerus caffer) and 1 African civet (Civettictis civetta) belonged to SB0133 spoligotype. The two novel strains (AR1 and AR2) assigned as spoligotype SB2290 and SB2289, respectively, were identified from indigenous cattle (Bos indicus). No M. bovis was detected from patients with clinical signs consistent with TB. Of the 606 animal tissue specimens and sputa of 472 TB-suspected patients 43 (7.09%) and 12 (2.9%), respectively, yielded non-tuberculous mycobacteria (NTM), of which 20 isolates were M. intracellulare. No M. avium was identified. M. bovis isolates from wildlife had 45.2% and 96.8% spoligotype pattern agreement with AR1 and AR2 strains, respectively. This finding indicates that bTB infections in wild animals and cattle were epidemiologically related. Of the 24 MIRU-VNTR loci, QUB 11b showed the highest discrimination among the M. bovis strains. The novel strains obtained in this study have not been previously reported in the area, but no clear evidence for recent cross-species transmission of M. bovis was found between human, livestock and wild animals.

Spoligotype diversity and 5-year trends of bovine tuberculosis in Extremadura, southern Spain

Bovine tuberculosis (bTB) causes significant losses to farming economies worldwide. A better understanding on the epidemiology of this disease and the role that the different hosts develop in the maintenance and spread of bTB is vital to control this zoonotic disease. This study reports the spoligotype diversity and temporal evolution of Mycobacterium tuberculosis Complex (MTBC) isolates obtained from Extremadura (southern Spain). Genotyping data of Mycobacterium bovis (n = 2102) and Mycobacterium caprae (n = 96) isolates from cattle and wildlife species, collected between 2008 and 2012, were used in this study. The isolates resulted clustered into 88 spoligotypes which varied largely in frequency and occurrence in the three hosts. The 20 most frequent patterns represented 91.99 % of the isolates, the spoligotype SB0121 being the clearly predominant and most widely dispersed geographically. The major variety of the spoligotype patterns (78 out of 88) was isolated from the cattle, in fact 50 (56.83 %) of the patterns were found only in this species. Within the spoligotypes shared between the cattle and wildlife species, 17 patterns (1747 isolates) were shared with wild boar and Iberian red deer, 10 patterns (308 isolates) were exclusively shared with wild boar, and only one pattern (two isolates) was shared exclusively with Iberian red deer. The significant number of spoligotypes shared between the three hosts (79.49 %) highlights the components of the multi-host system that allows the bTB maintenance in our study area. The greater percentage of isolates shared by the wild boar and cattle (93.50 %) supports the role of wild boar as main maintenance host for bTB in cattle. These results could be extrapolated to areas with a similar epidemiological scenario and could be helpful for other countries where wild reservoirs represent a handicap for the successful eradication of bTB from livestock.

Widespread Environmental Contamination with Mycobacterium tuberculosis Complex Revealed by a Molecular Detection Protocol

Environmental contamination with Mycobacterium tuberculosis complex (MTC) has been considered crucial for bovine tuberculosis persistence in multi-host-pathogen systems. However, MTC contamination has been difficult to detect due to methodological issues. In an attempt to overcome this limitation we developed an improved protocol for the detection of MTC DNA. MTC DNA concentration was estimated by the Most Probable Number (MPN) method. Making use of this protocol we showed that MTC contamination is widespread in different types of environmental samples from the Iberian Peninsula, which supports indirect transmission as a contributing mechanism for the maintenance of bovine tuberculosis in this multi-host-pathogen system. The proportion of MTC DNA positive samples was higher in the bovine tuberculosis-infected than in presumed negative area (0.32 and 0.18, respectively). Detection varied with the type of environmental sample and was more frequent in sediment from dams and less frequent in water also from dams (0.22 and 0.05, respectively). The proportion of MTC-positive samples was significantly higher in spring (p<0.001), but MTC DNA concentration per sample was higher in autumn and lower in summer. The average MTC DNA concentration in positive samples was 0.82 MPN/g (CI₉₅ 0.70–0.98 MPN/g). We were further able to amplify a DNA sequence specific of Mycobacterium bovis/caprae in 4 environmental samples from the bTB-infected area.

Factors that Influence Mycobacterium bovis Infection in Red Deer and Wild Boar in an Epidemiological Risk Area for Tuberculosis of Game Species in Portugal

Bovine tuberculosis (bTB) is a worldwide zoonotic disease of domestic and wild animals. Eradication has proved elusive in those countries with intensive national programmes but with ongoing transmission between wildlife and cattle. In Portugal, a high-risk area for bTB was defined and specific measures implemented to assess and minimize the risk from wildlife. Data from the 2011 to 2014 hunting seasons for red deer (Cervus elaphus) and wild boar (Sus scrofa) were analysed with bovine demographic and bTB information to assess factors that determined the occurrence and distribution of bTB in both species. The likelihood of bTB-like lesions in wild boar was positively associated with density of red deer, wild boar and cattle, while for red deer, only their density and age were significant factors. The likelihood of Mycobacterium bovis isolation in wild boar was associated with density of cattle and red deer and also with the anatomical location of lesions, while for red deer, none of the variables tested were statistically significant. Our results suggest that, in the study area, the role of red deer and wild boar may be different from the one previously suggested by other authors for the Iberian Peninsula, as red deer may be the driving force behind M. bovis transmission to wild boar. These findings may assist the official services and game managing bodies for the management of hunting zones, what could also impact the success of the bTB eradication programme.

Multiple sampling and discriminatory fingerprinting reveals clonally complex and compartmentalized infections by M. bovis in cattle

The combination of new genotyping tools and a more exhaustive sampling policy in the analysis of infection by Mycobacterium tuberculosis has shown that infection by this pathogen is more complex than initially expected. Mixed infections, coexistence of clonal variants from a parental strain, and compartmentalized infections are all different modalities of this clonal complexity. Until recently, genotyping of Mycobacterium bovis in animal populations was based on spoligotyping and analysis of a single isolate per infection; therefore, clonal complexity is probably underdetected. We used multiple sampling combined with highly discriminatory MIRU-VNTR to study compartmentalized infections by M. bovis in a low-tuberculosis prevalence setting. We spoligotyped the M. bovis isolates from two or more anatomic locations sampled from 55 animals on 39 independent farms. Compartmentalized infections, with two different strains infecting independent lymph nodes in the same animal, were found in six cases (10.9%). MIRU-VNTR analysis confirmed that the compartmentalization was strict and that only one strain was present in each infected node. MIRU-VNTR analysis of additional infected animals on one of the farms confirmed that the compartmentalized infection was a consequence of superinfection, since the two strains were independently infecting other animals. This same analysis revealed the emergence of a microevolved clonal variant in one of the lymph nodes of the compartmentalized animal. Clonal complexity must also be taken into consideration in M. bovis infection, even in low-prevalence settings, and analyses must be adapted to detect it and increase the accuracy of molecular epidemiology studies.

Mycobacterium caprae infection in humans

Mycobacterium caprae, a member of the Mycobacterium tuberculosis complex, causes tuberculosis (TB) in man and animals. Some features distinguish M. caprae from its epidemiological twin, Mycobacterium bovis: M. caprae is evolutionarily older, accounts for a smaller burden of zoonotic TB and is not globally distributed, but primarily restricted to European countries. M. caprae occurs only in a low proportion of human TB cases and this proportion may even decrease, if progress toward eradication of animal TB in Europe continues. So why bother, if M. caprae is not an enigma for diagnostic TB tests and if resistance against first-line drugs is a rarity with M. caprae? This 'European' pathogen of zoonotic TB asks interesting questions regarding the definition of a species. The latter, seemingly only an academic question, particularly requires and challenges the collaboration between human and veterinary medicine.

Rapid identification of veterinary-relevant Mycobacterium tuberculosis complex species using 16S rDNA, IS6110 and Regions of Difference-targeted dual-labelled hydrolysis probes

Members of the Mycobacterium tuberculosis complex (MTC) are causative agents of tuberculosis (TB) in both humans and animals. MTC species are genetically very similar but may differ in their epidemiology, namely geographic distribution and host preferences, virulence traits and antimicrobial susceptibility patterns. However, the conventional laboratory diagnosis does not routinely differentiate between the species of the MTC. In this work we describe a rapid and robust two-step five-target probe-based real-time PCR identification algorithm, based on genomic deletion analysis, to identify the MTC species most commonly associated with TB in livestock and other animals. The first step allows the confirmation of the cultures as MTC members, by targeting their IS6110 element, or as a mycobacterial species, if only a 16S rDNA product is detected in the duplex amplification reaction. If a MTC member is identified, the second amplification step allows the assessment of the presence or absence of the RD1, RD4 and RD9 genomic regions. The correspondent pattern allows us to infer the species of the isolate as M. tuberculosis (if all RDs are present), Mycobacterium caprae (if only RD1 and RD4 are present) and Mycobacterium bovis (if only RD1 is present). The identification algorithm developed presented an almost perfect agreement with the results of the routine bacteriological analysis, with a kappa coefficient of 0.970 (CI(P95%) 0.929-1.000). The assay is able to be adaptable to automation and implementation in the routine diagnostic framework of veterinary diagnostic laboratories, with a particular focus for reference laboratories.

Mycobacterium bovis: characteristics of wildlife reservoir hosts

Mycobacterium bovis is the cause of tuberculosis in animals and sometimes humans. Many developed nations have long-standing programmes to eradicate tuberculosis in livestock, principally cattle. As disease prevalence in cattle decreases these efforts are sometimes impeded by passage of M. bovis from wildlife to cattle. In epidemiological terms, disease can persist in some wildlife species, creating disease reservoirs, if the basic reproduction rate (R0) and critical community size (CCS) thresholds are achieved. Recognized wildlife reservoir hosts of M. bovis include the brushtail possum (Trichosurus vulpecula) in New Zealand, European badger (Meles meles) in Great Britain and Ireland, African buffalo (Syncerus caffer) in South Africa, wild boar (Sus scrofa) in the Iberian Peninsula and white-tailed deer (Odocoileus virginianus) in Michigan, USA. The epidemiological concepts of R0 and CCS are related to more tangible disease/pathogen characteristics such as prevalence, pathogen-induced pathology, host behaviour and ecology. An understanding of both epidemiological and disease/pathogen characteristics is necessary to identify wildlife reservoirs of M. bovis. In some cases, there is a single wildlife reservoir host involved in transmission of M. bovis to cattle. Complexity increases, however, in multihost systems where multiple potential reservoir hosts exist. Bovine tuberculosis eradication efforts require elimination of M. bovis transmission between wildlife reservoirs and cattle. For successful eradication identification of true wildlife reservoirs is critical, as disease control efforts are most effective when directed towards true reservoirs.

Overview and phylogeny of Mycobacterium tuberculosis complex organisms: implications for diagnostics and legislation of bovine tuberculosis

Members of the Mycobacterium tuberculosis complex (MTBC) cause a serious disease with similar pathology, tuberculosis; in this review, bovine tuberculosis will be considered as disease caused by any member of the MTBC in bovids. Bovine tuberculosis is responsible for significant economic loss due to costly eradication programs and trade limitations and poses a threat to both endangered and protected species as well as to public health. We here give an overview on all members of the MTBC, focusing on their isolation from different animal hosts. We also review the recent advances made in elucidating the evolutionary and phylogenetic relationships of members of the MTBC. Because the nomenclature of the MTBC is controversial, its members have been considered species, subspecies or ecotypes, this review discusses the possible implications for diagnostics and the legal consequences of naming of new species.

Enhanced detection of tuberculous mycobacteria in animal tissues using a semi-nested probe-based real-time PCR

Bovine tuberculosis has been tackled for decades by costly eradication programs in most developed countries, involving the laboratory testing of tissue samples from allegedly infected animals for detection of Mycobacterium tuberculosis complex (MTC) members, namely Mycobacterium bovis. Definitive diagnosis is usually achieved by bacteriological culture, which may take up to 6–12 weeks, during which the suspect animal carcass and herd are under sanitary arrest. In this work, a user-friendly DNA extraction protocol adapted for tissues was coupled with an IS6110-targeted semi-nested duplex real-time PCR assay to enhance the direct detection of MTC bacteria in animal specimens, reducing the time to achieve a diagnosis and, thus, potentially limiting the herd restriction period. The duplex use of a novel β-actin gene targeted probe, with complementary targets in most mammals, allowed the assessment of amplification inhibitors in the tissue samples. The assay was evaluated with a group of 128 fresh tissue specimens collected from bovines, wild boars, deer and foxes. Mycobacterium bovis was cultured from 57 of these samples. Overall, the full test performance corresponds to a diagnostic sensitivity and specificity of 98.2% (CI_P95% 89.4–99.9%) and 88.7% (CI_P95% 78.5–94.7%), respectively. An observed kappa coefficient was estimated in 0.859 (CI_P95% 0.771–0.948) for the overall agreement between the semi-nested PCR assay and the bacteriological culture. Considering only bovine samples (n = 69), the diagnostic sensitivity and specificity were estimated in 100% (CI_P95% 84.0–100%) and 97.7% (CI_P95% 86.2–99.9%), respectively. Eight negative culture samples exhibiting TB-like lesions were detected by the semi-nested real-time PCR, thus emphasizing the increased potential of this molecular approach to detect MTC-infected animal tissues. This novel IS6110-targeted assay allows the fast detection of tuberculous mycobacteria in animal specimens with very high sensitivity and specificity, being amenable and cost effective for use in the routine veterinary diagnostic laboratory with further automation possibilities.

Splitting of a prevalent Mycobacterium bovis spoligotype by variable-number tandem-repeat typing reveals high heterogeneity in an evolving clonal group

Mycobacterium bovis populations in countries with persistent bovine tuberculosis usually show a prevalent spoligotype with a wide geographical distribution. This study applied mycobacterial interspersed repetitive-unit-variable-number tandem-repeat (MIRU-VNTR) typing to a random panel of 115 M. bovis isolates that are representative of the most frequent spoligotype in the Iberian Peninsula, SB0121. VNTR typing targeted nine loci: ETR-A (alias VNTR2165), ETR-B (VNTR2461), ETR-D (MIRU4, VNTR580), ETR-E (MIRU31, VNTR3192), MIRU26 (VNTR2996), QUB11a (VNTR2163a), QUB11b (VNTR2163b), QUB26 (VNTR4052), and QUB3232 (VNTR3232). We found a high degree of diversity among the studied isolates (discriminatory index [D] = 0.9856), which were split into 65 different MIRU-VNTR types. An alternative short-format MIRU-VNTR typing targeting only the four loci with the highest variability values was found to offer an equivalent discriminatory index. Minimum spanning trees using the MIRU-VNTR data showed the hypothetical evolution of an apparent clonal group. MIRU-VNTR analysis was also applied to the isolates of 176 animals from 15 farms infected by M. bovis SB0121; in 10 farms, the analysis revealed the coexistence of two to five different MIRU types differing in one to six loci, which highlights the frequency of undetected heterogeneity.

Spatial relationships between Eurasian badgers (Meles meles) and cattle infected with Mycobacterium bovis in Northern Spain

Recent studies suggest that badgers may be a potential reservoir of Mycobacterium bovis infection for cattle in Northern Spain. The objective of this study was to investigate potential epidemiological links between cattle and badgers. Culture and molecular typing data were available for cattle culled during the national tuberculosis (TB) eradication campaigns between 2008 and 2012, as well as from 171 necropsied badgers and 60 live animals trapped and examined over the same time period. Mycobacterium tuberculosis complex strains were isolated from pooled tissues of 14 (8.2%) necropsied badgers, of which 11 were identified as M. bovis: six different spoligotypes of M. bovis were subsequently identified. In two geographical locations where these isolates were shared between cattle and badgers, infected cattle herds and badgers lived in close contact. Although it remains unclear if badgers are a maintenance or spill-over host of M. bovis in this setting, it would appear prudent to have precautionary measures in place to reduce contact between cattle and badgers.

Multihost tuberculosis: insights from the portuguese control program

This paper describes the current situation of animal tuberculosis in Portugal, reviewing the accomplishments and constraints of the 2001–2009 period. Notwithstanding the substantial progress achieved with the implementation of a comprehensive test and cull scheme, notification, postmortem inspection and surveillance at slaughterhouses, herd and animal prevalence have unexpectedly increased in 2009. In parallel, the recent awareness of tuberculosis in local free-ranging wildlife species causes concern regarding the final steps towards eradication, demanding new approaches to the existing disease control policies.