Guidance for populating GenomeTrakr metadata templates (BioSample and SRA) v2

2021 ◽  
Author(s):  
Ruth E Timme ◽  
Maria Balkey ◽  
William Wolfgang ◽  
Errol Strain
Keyword(s):  
One Health ◽  
Foodborne Pathogen ◽  
Incremental Update ◽  
The One ◽  
Pathogen Surveillance

PURPOSE: Guidance on how to populate NCBI's metadata packages, maximizing interoperability for foodborne pathogen surveillance. SCOPE: This protocol provides detailed instructions for populating the following two templates: 1. BioSample metadata: guidelines to populate the GenomeTrakr-extended pathogen package. 2. SRA metadata: NCBI's generic sequence metadata template for SRA submissions. Versions: v6: Added the One Health Enteric package presented at IAFP 2021 meeting. v7: Updated the picklists in the GenomeTrakr-extended pathogen package, "GT-pathogen package-OHE v0.2.2.xlsx" and added an incremental update file for the DRAFT One Health Enteric Package that includes extensive edits compared to v6.

scholarly journals Optimizing open data to support one health: best practices to ensure interoperability of genomic data from bacterial pathogens

2020 ◽  
Vol 2 (1) ◽  
Author(s):  
Ruth E. Timme ◽  
William J. Wolfgang ◽  
Maria Balkey ◽  
Sai Laxmi Gubbala Venkata ◽  
Robyn Randolph ◽  
...  
Keyword(s):  
Best Practices ◽  
One Health ◽  
Open Data ◽  
Holistic Approach ◽  
Interdisciplinary Cooperation ◽  
Health Goals ◽  
Public Data ◽  
Open Access Database ◽  
The One ◽  
Pathogen Surveillance

Abstract The holistic approach of One Health, which sees human, animal, plant, and environmental health as a unit, rather than discrete parts, requires not only interdisciplinary cooperation, but standardized methods for communicating and archiving data, enabling participants to easily share what they have learned and allow others to build upon their findings. Ongoing work by NCBI and the GenomeTrakr project illustrates how open data platforms can help meet the needs of federal and state regulators, public health laboratories, departments of agriculture, and universities. Here we describe how microbial pathogen surveillance can be transformed by having an open access database along with Best Practices for contributors to follow. First, we describe the open pathogen surveillance framework, hosted on the NCBI platform. We cover the current community standards for WGS quality, provide an SOP for assessing your own sequence quality and recommend QC thresholds for all submitters to follow. We then provide an overview of NCBI data submission along with step by step details. And finally, we provide curation guidance and an SOP for keeping your public data current within the database. These Best Practices can be models for other open data projects, thereby advancing the One Health goals of Findable, Accessible, Interoperable and Re-usable (FAIR) data.

scholarly journals Tick-borne zoonoses and commonly used diagnostic methods in human and veterinary medicine

2021 ◽  
Author(s):  
Andrea Springer ◽  
Antje Glass ◽  
Julia Probst ◽  
Christina Strube
Keyword(s):  
Veterinary Medicine ◽  
Diagnostic Tests ◽  
One Health ◽  
Animal Health ◽  
Diagnostic Techniques ◽  
Diagnostic Methods ◽  
Diagnostic Tools ◽  
Zoonotic Pathogens ◽  
Health Concept ◽  
The One

AbstractAround the world, human health and animal health are closely linked in terms of the One Health concept by ticks acting as vectors for zoonotic pathogens. Animals do not only maintain tick cycles but can either be clinically affected by the same tick-borne pathogens as humans and/or play a role as reservoirs or sentinel pathogen hosts. However, the relevance of different tick-borne diseases (TBDs) may vary in human vs. veterinary medicine, which is consequently reflected by the availability of human vs. veterinary diagnostic tests. Yet, as TBDs gain importance in both fields and rare zoonotic pathogens, such as Babesia spp., are increasingly identified as causes of human disease, a One Health approach regarding development of new diagnostic tools may lead to synergistic benefits. This review gives an overview on zoonotic protozoan, bacterial and viral tick-borne pathogens worldwide, discusses commonly used diagnostic techniques for TBDs, and compares commercial availability of diagnostic tests for humans vs. domestic animals, using Germany as an example, with the aim of highlighting existing gaps and opportunities for collaboration in a One Health framework.

scholarly journals Prioritization of zoonotic diseases of public health significance in Nigeria using the one-health approach

One Health ◽  
2021 ◽  
pp. 100257
Author(s):  
Chikwe Ihekweazu ◽  
Charles Akataobi Michael ◽  
Patrick M. Nguku ◽  
Ndadilnasiya Endie Waziri ◽  
Abdulrazaq Garba Habib ◽  
...  
Keyword(s):  
Public Health ◽  
One Health ◽  
Zoonotic Diseases ◽  
Public Health Significance ◽  
Health Significance ◽  
The One

scholarly journals Assessing Environmental Factors within the One Health Approach

Medicina ◽  
2021 ◽  
Vol 57 (3) ◽  
pp. 240
Author(s):  
Sarah Humboldt-Dachroeden ◽  
Alberto Mantovani
Keyword(s):  
Case Studies ◽  
One Health ◽  
Animal Health ◽  
Grey Literature ◽  
Aflatoxin M1 ◽  
First Case ◽  
Italian Regions ◽  
Environmental Component ◽  
Environmental Considerations ◽  
The One

Background: One Health is a comprehensive and multisectoral approach to assess and examine the health of animals, humans and the environment. However, while the One Health approach gains increasing momentum, its practical application meets hindrances. This paper investigates the environmental pillar of the One Health approach, using two case studies to highlight the integration of environmental considerations. The first case study pertains to the Danish monitoring and surveillance programme for antimicrobial resistance, DANMAP. The second case illustrates the occurrence of aflatoxin M1 (AFM1) in milk in dairy-producing ruminants in Italian regions. Method: A scientific literature search was conducted in PubMed and Web of Science to locate articles informing the two cases. Grey literature was gathered to describe the cases as well as their contexts. Results: 19 articles and 10 reports were reviewed and informed the two cases. The cases show how the environmental component influences the apparent impacts for human and animal health. The DANMAP highlights the two approaches One Health and farm to fork. The literature provides information on the comprehensiveness of the DANMAP, but highlights some shortcomings in terms of environmental considerations. The AFM1 case, the milk metabolite of the carcinogenic mycotoxin aflatoxin B1, shows that dairy products are heavily impacted by changes of the climate as well as by economic drivers. Conclusions: The two cases show that environmental conditions directly influence the onset and diffusion of hazardous factors. Climate change, treatment of soils, water and standards in slaughterhouses as well as farms can have a great impact on the health of animals, humans and the environment. Hence, it is important to include environmental considerations, for example, via engaging environmental experts and sharing data. Further case studies will help to better define the roles of environment in One Health scenarios.

Leptospirosis prevalence and risk factors in India: Evidence gap maps

2021 ◽  
pp. 004947552110052
Author(s):  
Sandeep Moola ◽  
Deepti Beri ◽  
Abdul Salam ◽  
Jagnoor Jagnoor ◽  
Arun Teja ◽  
...  
Keyword(s):  
Risk Factors ◽  
One Health ◽  
Data Extraction ◽  
Research Priorities ◽  
Risk Groups ◽  
Public Health Importance ◽  
Country Level ◽  
Disease Condition ◽  
Extraction Parameters ◽  
The One

Leptospirosis is a zoonotic disease of public health importance in India. A country-level evidence gap map was developed to identify gaps on epidemiology of leptospirosis. It is the first such on leptospirosis globally and on any single disease condition in India. The steps for development of evidence gap map were development of a framework to map evidence, retrieval of evidence, data extraction parameters and mapping of available evidence in evidence gap map framework. The prevalence evidence gap map consisted of 157 studies (102 in humans, 55 in animals, and 12 in both). The evidence gap map on risk factors had 120 studies (102 in humans, 11 in animals and 7 in both). There were inter-state differences in availability of research and disparity between animal and human research. Research on high-risk groups was limited and studies did not use the One Health approach to identify epidemiology, which can help understand the issue more comprehensively. The study demonstrates the potential of evidence gap maps to inform research priorities.

scholarly journals The outstanding relevance of the One Health approach

Public Health ◽  
2021 ◽  
Author(s):  
S. Bellizzi ◽  
G. Pichierri ◽  
G. Canu ◽  
D. Dessi' ◽  
C.M. Panu Napodano
Keyword(s):  
One Health ◽  
The One

scholarly journals How has Covid‐19 changed our views of the One Health agenda?

2021 ◽  
Vol 188 (9) ◽  
pp. 361-361
Author(s):  
Michael James Francis
Keyword(s):  
One Health ◽  
The One ◽  
Health Agenda

scholarly journals Finding What Is Inaccessible: Antimicrobial Resistance Language Use among the One Health Domains

Antibiotics ◽  
2021 ◽  
Vol 10 (4) ◽  
pp. 385
Author(s):  
Lauren L. Wind ◽  
Jonathan S. Briganti ◽  
Anne M. Brown ◽  
Timothy P. Neher ◽  
Meghan F. Davis ◽  
...  
Keyword(s):  
Antibiotic Resistance ◽  
Open Access ◽  
Antimicrobial Resistance ◽  
Language Processing ◽  
One Health ◽  
Language Use ◽  
Language Usage ◽  
Health Domains ◽  
Accessibility Issues ◽  
The One

The success of a One Health approach to combating antimicrobial resistance (AMR) requires effective data sharing across the three One Health domains (human, animal, and environment). To investigate if there are differences in language use across the One Health domains, we examined the peer-reviewed literature using a combination of text data mining and natural language processing techniques on 20,000 open-access articles related to AMR and One Health. Evaluating AMR key term frequency from the European PubMed Collection published between 1990 and 2019 showed distinct AMR language usage within each domain and incongruent language usage across domains, with significant differences in key term usage frequencies when articles were grouped by the One Health sub-specialties (2-way ANOVA; p < 0.001). Over the 29-year period, “antibiotic resistance” and “AR” were used 18 times more than “antimicrobial resistance” and “AMR”. The discord of language use across One Health potentially weakens the effectiveness of interdisciplinary research by creating accessibility issues for researchers using search engines. This research was the first to quantify this disparate language use within One Health, which inhibits collaboration and crosstalk between domains. We suggest the following for authors publishing AMR-related research within the One Health context: (1) increase title/abstract searchability by including both antimicrobial and antibiotic resistance related search terms; (2) include “One Health” in the title/abstract; and (3) prioritize open-access publication.

scholarly journals State of the art on lung organoids in mammals

2021 ◽  
Vol 52 (1) ◽  
Author(s):  
Fabienne Archer ◽  
Alexandra Bobet-Erny ◽  
Maryline Gomes
Keyword(s):  
Lung Development ◽  
One Health ◽  
State Of The Art ◽  
Animal Health ◽  
In Vitro Models ◽  
Cancer Genetic ◽  
3 Dimensional ◽  
The One ◽  
Species Specific

AbstractThe number and severity of diseases affecting lung development and adult respiratory function have stimulated great interest in developing new in vitro models to study lung in different species. Recent breakthroughs in 3-dimensional (3D) organoid cultures have led to new physiological in vitro models that better mimic the lung than conventional 2D cultures. Lung organoids simulate multiple aspects of the real organ, making them promising and useful models for studying organ development, function and disease (infection, cancer, genetic disease). Due to their dynamics in culture, they can serve as a sustainable source of functional cells (biobanking) and be manipulated genetically. Given the differences between species regarding developmental kinetics, the maturation of the lung at birth, the distribution of the different cell populations along the respiratory tract and species barriers for infectious diseases, there is a need for species-specific lung models capable of mimicking mammal lungs as they are of great interest for animal health and production, following the One Health approach. This paper reviews the latest developments in the growing field of lung organoids.

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