Advancing pathogen genomics in resource-limited settings

Pronyk, Paul Michael; de Alwis, Ruklanthi; Rockett, Rebecca; Basile, Kerri; Boucher, Yann Felix; Pang, Vincent; Sessions, October; Getchell, Marya; Golubchik, Tanya; Lam, Connie; Lin, Raymond; Mak, Tze-Minn; Marais, Ben; Twee-Hee Ong, Rick; Clapham, Hannah Eleanor; Wang, Linfa; Cahyorini, Yorin; Polotan, Francisco Gerardo M.; Rukminiati, Yuni; Sim, Eby; Suster, Carl; Smith, Gavin J.D.; Sintchenko, Vitali

doi:10.1016/j.xgen.2023.100443

Cited by 14 publications

(5 citation statements)

References 73 publications

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“…However, timing is key when monitoring diseases as infectious pathogens can mutate and be rapidly transmitted between wildlife, humans, and domestic animals, with potentially devastating impacts on human health and animal welfare. Therefore, novel and rapid genetic techniques, such as culture-free pathogen genetic sequencing [ 82 ], can greatly benefit disease surveillance by decreasing the time needed to sequence pathogens and, consequently, the time needed to make essential ecological management decisions and activate public health responses. In addition, these new sequencing technologies can be very useful during wildlife field studies in isolated areas since they can be rapidly deployed and need limited laboratory equipment for processing [ 82 ].…”

Section: Discussionmentioning

confidence: 99%

“…Therefore, novel and rapid genetic techniques, such as culture-free pathogen genetic sequencing [ 82 ], can greatly benefit disease surveillance by decreasing the time needed to sequence pathogens and, consequently, the time needed to make essential ecological management decisions and activate public health responses. In addition, these new sequencing technologies can be very useful during wildlife field studies in isolated areas since they can be rapidly deployed and need limited laboratory equipment for processing [ 82 ]. In addition, when monitoring zoonosis such as bTB and collecting related data (invasively or not) it is important to recall the characteristics of the bacterium itself, Mycobacterium bovis .…”

Section: Discussionmentioning

confidence: 99%

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A scoping review on bovine tuberculosis highlights the need for novel data streams and analytical approaches to curb zoonotic diseases

Conteddu,

English,

Byrne

et al. 2024

Vet Res

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Zoonotic diseases represent a significant societal challenge in terms of their health and economic impacts. One Health approaches to managing zoonotic diseases are becoming more prevalent, but require novel thinking, tools and cross-disciplinary collaboration. Bovine tuberculosis (bTB) is one example of a costly One Health challenge with a complex epidemiology involving humans, domestic animals, wildlife and environmental factors, which require sophisticated collaborative approaches. We undertook a scoping review of multi-host bTB epidemiology to identify trends in species publication focus, methodologies, and One Health approaches. We aimed to identify knowledge gaps where novel research could provide insights to inform control policy, for bTB and other zoonoses. The review included 532 articles. We found different levels of research attention across episystems, with a significant proportion of the literature focusing on the badger-cattle-TB episystem, with far less attention given to tropical multi-host episystems. We found a limited number of studies focusing on management solutions and their efficacy, with very few studies looking at modelling exit strategies. Only a small number of studies looked at the effect of human disturbances on the spread of bTB involving wildlife hosts. Most of the studies we reviewed focused on the effect of badger vaccination and culling on bTB dynamics with few looking at how roads, human perturbations and habitat change may affect wildlife movement and disease spread. Finally, we observed a lack of studies considering the effect of weather variables on bTB spread, which is particularly relevant when studying zoonoses under climate change scenarios. Significant technological and methodological advances have been applied to bTB episystems, providing explicit insights into its spread and maintenance across populations. We identified a prominent bias towards certain species and locations. Generating more high-quality empirical data on wildlife host distribution and abundance, high-resolution individual behaviours and greater use of mathematical models and simulations are key areas for future research. Integrating data sources across disciplines, and a “virtuous cycle” of well-designed empirical data collection linked with mathematical and simulation modelling could provide additional gains for policy-makers and managers, enabling optimised bTB management with broader insights for other zoonoses.

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Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

A scoping review on bovine tuberculosis highlights the need for novel data streams and analytical approaches to curb zoonotic diseases

Conteddu,

English,

Byrne

et al. 2024

Vet Res

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“…It is estimated that the cost per pathogen sequence ranges from US $20-$200, with poor countries paying up to 10-fold more than high-income countries. 19 Pathogen genomics in public health in Africa requires continuous engagement among different stakeholders including NGS platform manufacturers/distributors, program/project funders, sequencing facilities, research/academic institutions, the national ministries of health, and policymakers. Each of these has a unique contribution, therefore planning and supporting multi-pathogen activities is a multi-sectoral endeavor that requires continued engagement to ensure an impactful genomic ecosystem.…”

Section: Major Emerging Challengesmentioning

confidence: 99%

The rise of pathogen genomics in Africa

Mboowa,

Kakooza,

Egesa

et al. 2024

F1000Res

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The routine genomic surveillance of pathogens in diverse geographical settings and equitable data sharing are critical to inform effective infection control and therapeutic development. The coronavirus disease 2019 (COVID-19) pandemic highlighted the importance of routine genomic surveillance of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) to detect emerging variants of concern. However, the majority of high-income countries sequenced >0.5% of their COVID-19 cases, unlike low- and middle-income countries. By the end of 2022, many countries around the world had managed to establish capacity for pathogen genomic surveillance. Notably, Beta and Omicron; 2 of the 5 current SARS-CoV-2 variants of concern were first discovered in Africa through an aggressive sequencing campaign led by African scientists. To sustain such infrastructure and expertise beyond this pandemic, other endemic pathogens should leverage this investment. Therefore, countries are establishing multi-pathogen genomic surveillance strategies. Here we provide a catalog of the current landscape of sequenced and publicly shared pathogens in different countries in Africa. Drawing upon our collective knowledge and expertise, we review the ever-evolving challenges and propose innovative recommendations.

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“…Specifically, genomics involves the study of an organism's entire genome, including its genes and non-coding sequences. Sequencing the genomes of infectious agents (e.g., bacteria, viruses, parasites) helped us to understand their genetic diversity, transmission pathways, evolution, and disease dynamics [25]. More importantly, genome sequencing of aquaculture species helped us to understand the genetic factors in the host that influence susceptibility, resistance, and immune response to infectious diseases.…”

Section: Introductionmentioning

confidence: 99%

Genetics and Genomics of Infectious Diseases in Key Aquaculture Species

Nguyen

2024

Biology

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Diseases pose a significant and pressing concern for the sustainable development of the aquaculture sector, particularly as their impact continues to grow due to climatic shifts such as rising water temperatures. While various approaches, ranging from biosecurity measures to vaccines, have been devised to combat infectious diseases, their efficacy is disease and species specific and contingent upon a multitude of factors. The fields of genetics and genomics offer effective tools to control and prevent disease outbreaks in aquatic animal species. In this study, we present the key findings from our recent research, focusing on the genetic resistance to three specific diseases: White Spot Syndrome Virus (WSSV) in white shrimp, Bacterial Necrotic Pancreatitis (BNP) in striped catfish, and skin fluke (a parasitic ailment) in yellowtail kingfish. Our investigations reveal that all three species possess substantial heritable genetic components for disease-resistant traits, indicating their potential responsiveness to artificial selection in genetic improvement programs tailored to combat these diseases. Also, we observed a high genetic association between disease traits and survival rates. Through selective breeding aimed at enhancing resistance to these pathogens, we achieved substantial genetic gains, averaging 10% per generation. These selection programs also contributed positively to the overall production performance and productivity of these species. Although the effects of selection on immunological traits or immune responses were not significant in white shrimp, they yielded favorable results in striped catfish. Furthermore, our genomic analyses, including shallow genome sequencing of pedigreed populations, enriched our understanding of the genomic architecture underlying disease resistance traits. These traits are primarily governed by a polygenic nature, with numerous genes or genetic variants, each with small effects. Leveraging a range of advanced statistical methods, from mixed models to machine and deep learning, we developed prediction models that demonstrated moderate-to-high levels of accuracy in forecasting these disease-related traits. In addition to genomics, our RNA-seq experiments identified several genes that undergo upregulation in response to infection or viral loads within the populations. Preliminary microbiome data, while offering limited predictive accuracy for disease traits in one of our studied species, underscore the potential for combining such data with genome sequence information to enhance predictive power for disease traits in our populations. Lastly, this paper briefly discusses the roles of precision agriculture systems and AI algorithms and outlines the path for future research to expedite the development of disease-resistant genetic lines tailored to our target species. In conclusion, our study underscores the critical role of genetics and genomics in fortifying the aquaculture sector against the threats posed by diseases, paving the way for more sustainable and resilient aquaculture development.

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Advancing pathogen genomics in resource-limited settings

Cited by 14 publications

References 73 publications

A scoping review on bovine tuberculosis highlights the need for novel data streams and analytical approaches to curb zoonotic diseases

A scoping review on bovine tuberculosis highlights the need for novel data streams and analytical approaches to curb zoonotic diseases

The rise of pathogen genomics in Africa

Genetics and Genomics of Infectious Diseases in Key Aquaculture Species

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