Phylodynamic analysis of an emergent Mycobacterium bovis outbreak in an area with no previously known wildlife infections

1. Understanding how an emergent pathogen successfully establishes itself and persists in a previously unaffected population is a crucial problem in disease ecology, with important implications for disease management. In multi-host pathogen systems this problem is particularly difficult, as the importance of each host species to transmission is often poorly characterised, and the disease epidemiology is complex. Opportunities to observe and analyse such emergent scenarios are few. 2. Here, we exploit a unique dataset combining densely-collected data on the epidemiological and evolutionary characteristics of an outbreak of Mycobacterium bovis (the causative agent of bovine tuberculosis, bTB) in a population of cattle and badgers in an area considered low-risk for bTB, with no previous record of either persistent infection in cattle, or of any infection in wildlife. We analyse the outbreak dynamics using a combination of mathematical modelling, Bayesian evolutionary analyses, and machine learning. 3. Comparison to M. bovis whole-genome sequences from Northern Ireland confirmed this to be a single introduction of the pathogen from the latter region, with evolutionary analysis supporting an introduction directly into the local cattle population six years prior to its first discovery in badgers. 4. Once introduced, the evidence supports M. bovis epidemiological dynamics passing through two phases, the first dominated by cattle-to-cattle transmission before becoming established in the local badger population. 5. Synthesis and applications. The raw data object of this analysis were used to support decisions regarding the control of a M. bovis emergent outbreak, of considerable concern because of the geographical distance from previously known high-risk areas. Our further analyses, estimating the time of introduction (and therefore the likely magnitude of any hidden outbreak) and the rates of cross-species transmission, provided valuable confirmation that the extent and focus of the imposed controls were appropriate. Not only these findings strengthen the call for genomic surveillance, but they also pave the path for future outbreaks control, providing insights for more rapid and decisive evidence-based decision-making. As the methods we used and developed are agnostic to the disease itself, they are also valuable for other slowly transmitting pathogens

O Departamento De Ciências Agronômicas

O Departamento de Ciências Agronômicas foi criado em 1975, pelo ex-Diretor do INPA, Prof. Dr. Warwick E. Kerr. A Divisão de Genética e Melhoramento concentra suas atividades no melhoramento de hortaliças e leguminosas e na coleta, análise, testes de adaptação e desenvolvimento de variedades de espécies indígenas com potencial olerícola. Aproxima-se, no momento, de seus primeiros resultados de real expressão prática, com perspectiva do lançamento de 4 novas variedades. A Divisão de Fruticultura iniciou suas atividades com experimentos de sistemas de produção de frutíferas em consorciação em 1976 e 1977 e com as primeiras coletas de germoplasma de espécies indígenas. Atualmente dedica atenção prioritária às seguintes espéciespupunha, graviola, cupuaçu, sapota, mapati, araçá-boi, araçá-pera, camu-camu e lucuma. Foram instalados diversos experimentos de adubação e espaçamento e feitas novas introduções de pupunha e sapota. A Divisão de Fitossanidade iniciou suas atividades em meados de 1980, concentrando-se na constatação e confirmação das doenças nas principais culturas estudadas pelo INPA, para posterior estudos de métodos de controle ecologicamente aceitáveis. A Divisão de Agricultura de Sobrevivência tem como objetivo desenvolver uma agricultura mais apropriada para a região, conhecida pela sua ecologia frágil e que sofre os efeitos da agricultura convencional. Assim, estão sendo desenvolvidos vários trabalhos básicos sobre utilização de biomassa, ciclagem de nutrientes, os efeitos do homem sobre essa ciclagem, sistemas agroflorestais e experiências práticas sobre sistemas alternativos de agricultura. A Divisão de Solos realiza no momento pesquisas sobre o comportamento dos solos da Amazônia, conservação dos solos e controle da erosão, levantamento de nodulação de leguminosas florestais e outras, fixação de nitrogênio em plantas aquáticas e cupins e solubilização de fosfatos naturais. A Divisão de Fontes Alternativas de Energia desenvolve projetos de uso de correnteza de rios como fonte de energia, gasogênio com carvão vegetal, estufa solar e biogás

Genomic epidemiology of Mycobacterium bovis infection in sympatric badger and cattle populations in Northern Ireland

Bovine tuberculosis (bTB) is a costly, epidemiologically complex, multi-host, endemic disease. Lack of understanding of transmission dynamics may undermine eradication efforts. Pathogen whole-genome sequencing improves epidemiological inferences, providing a means to determine the relative importance of inter- and intra-species host transmission for disease persistence. We sequenced an exceptional data set of 619 Mycobacterium bovis isolates from badgers and cattle in a 100 km2 bTB 'hotspot' in Northern Ireland. Historical molecular subtyping data permitted the targeting of an endemic pathogen lineage, whose long-term persistence provided a unique opportunity to study disease transmission dynamics in unparalleled detail. Additionally, to assess whether badger population genetic structure was associated with the spatial distribution of pathogen genetic diversity, we microsatellite genotyped hair samples from 769 badgers trapped in this area. Birth death models and TransPhylo analyses indicated that cattle were likely driving the local epidemic, with transmission from cattle to badgers being more common than badger to cattle. Furthermore, the presence of significant badger population genetic structure in the landscape was not associated with the spatial distribution of M. bovis genetic diversity, suggesting that badger-to-badger transmission is not playing a major role in transmission dynamics. Our data were consistent with badgers playing a smaller role in transmission of M. bovis infection in this study site, compared to cattle. We hypothesize, however, that this minor role may still be important for persistence. Comparison to other areas suggests that M. bovis transmission dynamics are likely to be context dependent, with the role of wildlife being difficult to generalize.ISSN:2057-585

Genomic epidemiology of Mycobacterium bovis infection in sympatric badger and cattle populations in Northern Ireland

Publication history: Accepted - 29 March 2023; Published - 25 May 2023.Bovine tuberculosis (bTB) is a costly, epidemiologically complex, multi-host, endemic disease. Lack of understanding of transmission dynamics may undermine eradication efforts. Pathogen whole-genome sequencing improves epidemiological inferences, providing a means to determine the relative importance of inter- and intra-species host transmission for disease persistence. We sequenced an exceptional data set of 619 Mycobacterium bovis isolates from badgers and cattle in a 100 km2 bTB 'hotspot' in Northern Ireland. Historical molecular subtyping data permitted the targeting of an endemic pathogen lineage, whose long-term persistence provided a unique opportunity to study disease transmission dynamics in unparalleled detail. Additionally, to assess whether badger population genetic structure was associated with the spatial distribution of pathogen genetic diversity, we microsatellite genotyped hair samples from 769 badgers trapped in this area. Birth death models and TransPhylo analyses indicated that cattle were likely driving the local epidemic, with transmission from cattle to badgers being more common than badger to cattle. Furthermore, the presence of significant badger population genetic structure in the landscape was not associated with the spatial distribution of M. bovis genetic diversity, suggesting that badger-to-badger transmission is not playing a major role in transmission dynamics. Our data were consistent with badgers playing a smaller role in transmission of M. bovis infection in this study site, compared to cattle. We hypothesize, however, that this minor role may still be important for persistence. Comparison to other areas suggests that M. bovis transmission dynamics are likely to be context dependent, with the role of wildlife being difficult to generalize.This work was funded by the Department of Agriculture, Environment and Rural Affairs for Northern Ireland (DAERA-NI) through its Evidence and Innovation programme – project no. 15/3/07. Additional funding was provided by the UK’s Biotechnology and Biological Sciences Research Council (BBSRC) – grant numbers BB/P0105598 and BB/M01262X. A. A. is supported by a Bolashak International Scholarship

Should Innovation Always be OPEN?

<p>Roland Harwood will reference how many large organisations are now embracing open innovation, open source and open data because it is proven to be a better way to solve complex problems, attract and retain talent, and to maintain accountability through transparency. And yet he will highlight the<br> significant challenges this still poses to most organisations, particularly in terms of intellectual property but also regarding collaborative cultures. However he will argue that anything that can be shared will be eventually and that those that do so by default will benefit more than those who have openness<br> forced upon them.</p> <p>Roland Harwood is Co-founder and Networks Partner at 100%Open, the global open innovation agency that works with the likes of LEGO, P&G, Oxfam and Ordnance Survey to coinnovate with partners. It was a spin-out from NESTA in 2010, the UK Innovation Agency and Investment Fund, where he was Director of Open Innovation. Graduating with a PhD in Physics from Edinburgh University, he has held senior innovation roles in the public and private sector. In addition has worked with hundreds of start-ups to raise venture capital and comercialise technology. He is a keen piano player and has produced TV and film music for SonyBMG. Last but not least, he is a proud and often exhausted dad of 3 kids under 7.</p> <p>Linked In: http://uk.linkedin.com/in/rolandharwood</p

Bibliography of published COVID-19 in children literature

Background: the COVID-19 pandemic is the biggest worldwide health challenge in this century. Research concerning the role of children in the spread of SARS-CoV-2, and investigating the clinical effects of infection in children, has been vital. This paper describes the publication trend for pertinent scientific literature relating to COVID-19 in children during the first 6 months of the pandemic. Methods: a comprehensive search of preprint and published literature was conducted daily across four databases (PubMed, Scopus, Ovid-Embase and MedRXiv) between 1 January 2020 and 30 June 2020. Titles and abstracts were screened against predefined inclusion and exclusion criteria. Findings: over the study period, a total of 45 453 papers were retrieved, of which 476 met our inclusion criteria. The cumulative number of children described in included publications totalled (at most) 41 396. The median number of children per paper was 6 (IQR 1-33). Nearly one-third of papers (30.2%) reported on a single child, and a further 28.3% reported on between 1 and 9 children. Half of all the publications originated from Asia. Interpretation: our prospective bibliographic analysis of paediatric COVID-19 publications demonstrated a steady increase in the number of papers over time. Understanding and policy evolved with new information that was gathered over the course of the study period. However, over half of publications were individual case reports or small case series, which may have had a limited contribution to advancement of knowledge. During a pandemic, literature should be interpreted with great caution, and clinical/policy decisions should be continually reviewed in light of emerging evidence.</p