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

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.

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Phylogenomics Sheds Light on the population structure of Mycobacterium bovis from a Multi-Host Tuberculosis System

10.1101/2021.04.26.441523 ◽

2021 ◽

Author(s):

Ana C. Reis ◽

Liliana C.M. Salvador ◽

Suelee Robbe-Austerman ◽

Rogério Tenreiro ◽

Ana Botelho ◽

...

Keyword(s):

Wild Boar ◽

Mycobacterium Bovis ◽

Red Deer ◽

Evolutionary Dynamics ◽

Genetic Relatedness ◽

Variable Number Tandem Repeat ◽

Variant Calling ◽

Pathogen Transmission ◽

Whole Genome ◽

Host System

AbstractMolecular analyses of Mycobacterium bovis based on spoligotyping and Variable Number Tandem Repeat (MIRU-VNTR) brought 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. The genetic relatedness of M. bovis isolates from cattle and wildlife have also suggested sustained transmission within this multi-host system. However, while previous surveillance highlighted prevalent genotypes in areas where livestock and wild ungulates are sympatric and provided valuable information on the prevalence and spatial occurrence of TB, links at the wildlife-livestock interfaces were established mainly via genotype associations. Therefore, evidence at a local fine scale of transmission events linking wildlife hosts and cattle remains lacking. Here, we explore the advantages of whole genome sequencing (WGS) applied to cattle, red deer and wild boar isolates to reconstruct the evolutionary dynamics of M. bovis and to identify putative pathogen transmission events. 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 geographic specificities, as well as the establishment of a SNPs 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 reconstruct transmission networks, which together with inferred secondary cases, further structured this M. bovis population by host species and geographic location.WGS of M. bovis isolates from Portugal is reported for the first time, refining the spatiotemporal context of transmission events and providing further support to the key role of red deer and wild boar on the persistence of animal TB in this Iberian multi-host system.

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

Animals ◽

10.3390/ani11082374 ◽

2021 ◽

Vol 11 (8) ◽

pp. 2374

Author(s):

José Aranha ◽

Ana Carolina Abrantes ◽

Raquel Gonçalves ◽

Rui Miranda ◽

João Serejo ◽

...

Keyword(s):

High Risk ◽

Red Deer ◽

Temporal Distribution ◽

Cost Effective ◽

Mitigation Strategies ◽

Mitigation Measures ◽

Risk Area ◽

Game Species ◽

High Risk Area ◽

Significant Difference

Since April 2011, Portugal has implemented specific national legislation (Notice N.º1/2011), 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 N.º1/2011 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 N.º1/2011, and to ensure the correct implementation of cost-effective mitigation strategies for tuberculosis in large game species.

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

Scientific Reports ◽

10.1038/s41598-020-77713-8 ◽

2020 ◽

Vol 10 (1) ◽

Author(s):

Ana C. Reis ◽

Rogério Tenreiro ◽

Teresa Albuquerque ◽

Ana Botelho ◽

Mónica V. Cunha

Keyword(s):

Wild Boar ◽

Mycobacterium Bovis ◽

Red Deer ◽

Robust Statistics ◽

Probability Model ◽

Ecological Processes ◽

Spatiotemporal Clustering ◽

History Of ◽

Bayesian Inference Framework

AbstractAnimal 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.

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A correlation of Mycobacterium bovis SB0134 infection between cattle and a wild boar (Sus Scrofa) in Campania region

Veterinary and Animal Science ◽

10.1016/j.vas.2021.100182 ◽

2021 ◽

pp. 100182

Author(s):

Emanuela Sannino ◽

Lorena Cardillo ◽

Rubina Paradiso ◽

Anna Cerrone ◽

Paolo Coppa ◽

...

Keyword(s):

Wild Boar ◽

Mycobacterium Bovis ◽

Sus Scrofa ◽

Campania Region

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Use of ethanol extract of Mycobacterium bovis for detection of specific antibodies in sera of farmed red deer (Cervus elaphus) with bovine tuberculosis

BMC Veterinary Research ◽

10.1186/1746-6148-9-256 ◽

2013 ◽

Vol 9 (1) ◽

pp. 256 ◽

Cited By ~ 6

Author(s):

Ashutosh Wadhwa ◽

Rachel E Johnson ◽

Colin G Mackintosh ◽

J Frank T Griffin ◽

W Waters ◽

...

Keyword(s):

Mycobacterium Bovis ◽

Cervus Elaphus ◽

Bovine Tuberculosis ◽

Red Deer ◽

Ethanol Extract ◽

Specific Antibodies

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The response of red deer to oral administration of heat-inactivated Mycobacterium bovis and challenge with a field strain

Veterinary Microbiology ◽

10.1016/j.vetmic.2017.08.007 ◽

2017 ◽

Vol 208 ◽

pp. 195-202 ◽

Cited By ~ 13

Author(s):

Jobin Thomas ◽

María Ángeles Risalde ◽

Miriam Serrano ◽

Iker Sevilla ◽

Mariví Geijo ◽

...

Keyword(s):

Oral Administration ◽

Mycobacterium Bovis ◽

Red Deer ◽

Field Strain

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Lesion Distribution and Epidemiology ofMycobacterium bovisin Elk and White-Tailed Deer in South-Western Manitoba, Canada

Veterinary Medicine International ◽

10.4061/2011/591980 ◽

2011 ◽

Vol 2011 ◽

pp. 1-11 ◽

Cited By ~ 18

Author(s):

Todd K. Shury ◽

Doug Bergeson

Keyword(s):

Mycobacterium Bovis ◽

Geographic Distribution ◽

Cervus Elaphus ◽

Red Deer ◽

Core Area ◽

Age Classes ◽

Small Core ◽

The Core ◽

Free Ranging ◽

Culture Positive

Surveillance forMycobacterium bovisin free-ranging elk (Cervus elaphus) and white-tailed deer (Odocoileus virginianus) from south-western Manitoba was carried out from 1997 to 2010 to describe the lesions, epidemiology, and geographic distribution of disease. Tissues were cultured from animals killed by hunters, culled for management, blood-tested, or found opportunistically. Period prevalence in elk was approximately six times higher than deer, suggesting a significant reservoir role for elk, but that infected deer may also be involved. Prevalence was consistently higher in elk compared to deer in a small core area and prevalence declines since 2003 are likely due to a combination of management factors instituted during that time. Older age classes and animals sampled from the core area were at significantly higher risk of being culture positive. Positive elk and deer were more likely to be found through blood testing, opportunistic surveillance, and culling compared to hunting. No non-lesioned, culture-positive elk were detected in this study compared to previous studies in red deer.

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Retrospective screening of routine respiratory samples revealed undetected community transmission and missed intervention opportunities for SARS-CoV-2 in the United Kingdom

Journal of General Virology ◽

10.1099/jgv.0.001595 ◽

2021 ◽

Vol 102 (6) ◽

Author(s):

Joseph G. Chappell ◽

Theocharis Tsoleridis ◽

Gemma Clark ◽

Louise Berry ◽

Nadine Holmes ◽

...

Keyword(s):

Sequence Data ◽

Infected Individual ◽

Case Definition ◽

Case Definitions ◽

Risk Area ◽

High Risk Area ◽

Epidemiological Risk ◽

Distinct Lineage ◽

The Uk ◽

Archival Specimens

In the early phases of the SARS coronavirus type 2 (SARS-CoV-2) pandemic, testing focused on individuals fitting a strict case definition involving a limited set of symptoms together with an identified epidemiological risk, such as contact with an infected individual or travel to a high-risk area. To assess whether this impaired our ability to detect and control early introductions of the virus into the UK, we PCR-tested archival specimens collected on admission to a large UK teaching hospital who retrospectively were identified as having a clinical presentation compatible with COVID-19. In addition, we screened available archival specimens submitted for respiratory virus diagnosis, and dating back to early January 2020, for the presence of SARS-CoV-2 RNA. Our data provides evidence for widespread community circulation of SARS-CoV-2 in early February 2020 and into March that was undetected at the time due to restrictive case definitions informing testing policy. Genome sequence data showed that many of these early cases were infected with a distinct lineage of the virus. Sequences obtained from the first officially recorded case in Nottinghamshire - a traveller returning from Daegu, South Korea – also clustered with these early UK sequences suggesting acquisition of the virus occurred in the UK and not Daegu. Analysis of a larger sample of sequences obtained in the Nottinghamshire area revealed multiple viral introductions, mainly in late February and through March. These data highlight the importance of timely and extensive community testing to prevent future widespread transmission of the virus.

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