Clinical Pathogen Genomics

Cameron, R. Andrew; Bohrhunter, Jessica L; Taffner, Samantha M.; Malek, Adel; Pecora, Nicole

doi:10.1016/j.cll.2020.08.003

Cited by 14 publications

(9 citation statements)

References 63 publications

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“…Genomics can be used to identify the infectious agents of disease with more confidence and precision than ever before, and at increasing speed, allowing treatments that can quickly resolve infections 78 – 80 as well as identifying the evolution of new species that may evade antibiotics, antivirals, and vaccines. The main challenges to deployment of genomics in infectious disease care are managing cost and logistics, tracking disease progression and its characterization, achieving precise phenotypic prediction (e.g., antibiotic resistance), and harmonizing historical knowledge bases from non-genomic-based assays to integrate with contemporary genomic tests.…”

Section: Genomics In Healthcarementioning

confidence: 99%

GA4GH: International policies and standards for data sharing across genomic research and healthcare

Rehm¹,

Page²,

Smith³

et al. 2021

Cell Genomics

137

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Section: Genomics In Healthcarementioning

confidence: 99%

GA4GH: International policies and standards for data sharing across genomic research and healthcare

Rehm¹,

Page²,

Smith³

et al. 2021

Cell Genomics

137

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“…The emergence of pathogen genomics as a disruptive technology has led to major changes in clinical and public health microbiology, particularly over the last decade, as the technology has moved from use primarily in research settings, towards routine use in public health [1]. Genomic surveillance and outbreak investigations of pathogens of public health importance, such as foodborne pathogens, have been revolutionized, offering superior resolution, depth and breadth of data from a single laboratory test compared to previous methods [1, 2] ().…”

Section: Pathogen Genomics: From Research To a Routine Public Health ...mentioning

confidence: 99%

Public health implementation of pathogen genomics: the role for accreditation and application of ISO standards

Ballard,

Sherry,

Howden

2023

Microbial Genomics

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Pathogen genomics has transitioned rapidly from the research setting into a powerful tool now routinely used in public health microbiology, for surveillance, outbreak investigations and disease control. As these investigations can have significant public health, treatment and legal impacts, we must ensure the accuracy of these results through validation of testing processes. For laboratories working in this space, it is important to approach this work with a quality and accreditation framework in mind, working towards implementation of quality systems and test validation that meet international regulatory standards. Here we outline the key international standards and processes that lead toward accreditation for pathogen genomics.

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“…Clinical laboratories are increasingly pursuing pathogen genomics for infectious disease diagnosis and characterizing whole genome sequences of cultured isolates to help with infection prevention and control practices (IPAC) regarding outbreaks and surveillance (Cameron et al 2020). For example, the presence of plasmid-mediated antimicrobial resistance (AMR) genes is an important concern because plasmid-mediated AMR genes can easily spread to other bacterial pathogens (Das 2023).…”

Section: Introductionmentioning

confidence: 99%

“…Consider a scenario where there will soon be standardized and routine pathogen genomic investigations within the hospitals. This would mean real-time clinical decision support (CDS) where bioinformatics computation can draw from massive genomic information as well as both broader curated knowledge database systems (Cameron et al 2020) . Logic (for electronic clinical quality measurement and clinical decision support) and FHIR operations are two relevant areas that provide foundations for clinical decision support based on genomic data.…”

Section: Introductionmentioning

confidence: 99%

Applying Fast Healthcare Interoperability Resources (FHIR) for Pathogen Genomics at the Point of Care

Kim,

Ritchie,

Mobini

et al. 2024

Preprint

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Modern-day microbial diagnostics and genomics have the potential to revolutionize individual and population-level infectious disease prevention, patient care, and treatment. To realize the potential, we need new approaches to standardizing testing and genomic data so that complex data and knowledge can be integrated at the point of care reliably and without ambiguity. We provide a series of approaches to pathogen genomic information standardization and guides to improve data interoperability which is key to harnessing the power of modern testing and genomics data.We develop generalizable knowledge and guidance to integrate the systems of terminology management, data modeling and inference that can provide flexibility for collaborative development across multiple domains (i.e. public health, clinical, academic research and open source communities) in order to significantly speed up the applications of pathogen genomic knowledge.We observed numerous advantages to using healthcare-specific standards such as Fast Healthcare Interoperability Resources (FHIR) and Clinical Quality Language (CQL). Advantages include convenient information models, mechanisms for verification, and the availability of tools, documentation and expertise to provide assistance during development. We also found the critical role of community-driven domain-specific ontologies which provide a source of terminologies thereby addressing content coverage gaps in the common clinical terminologies.Strengths and limitations of this studyTo our knowledge, this is the first work of its kind to provide structured guidance on pathogen genomic data interoperability using HL7 FHIR resources for a clinical scenario involving whole genome sequencing. We believe this provides a clear path for broader stakeholders including implementors and knowledge curators on how to collaborate and facilitate automation in support of speedy exchange of complex knowledge for genomic epidemiology.We believe the tools and documentation provided can be a resource for clinical informatics, researchers, and public health organizations who want to collaborate, grow and exchange pathogen genomic knowledge for critical public health applications.We acknowledge the limitations of this work.First, the tools developed here are limited in scope and not yet validated among the broader FHIR community. Therefore the ability to generalize for a broad set of pathogens is limited. Standardization of external ontology will require approval from the HL7 terminology authority. This approval process will require the demonstration of quality processes and measures and licensing and legal processes as well as community buy-ins.The information model here is developed based on scenario modelling. Additional validation using real clinical scenarios and patient data will be required for future developments. As the whole genome sequencing process is only beginning to emerge in clinical practices, more patient-derived whole genome sequence result data from multiple facilities will be needed to create generalized clinically valid pathogen genomic tools.The privacy issues surrounding the utilization of social determinants of health data (SDOH), while taking into account the relational and structural aspects of infectious disease outbreaks that impact vulnerable communities, will further require careful consideration prior to standardizing the discovery and access of SDOH data.PreambleModern-day medical diagnostics using microbial genomics have the potential to revolutionize individual and population-level disease prevention, patient care, and treatment. Clinical laboratories are increasingly pursuing pathogen genomics for infectious disease diagnosis and characterizing whole genome sequences of cultured isolates to help with infection prevention and control practices (IPAC) regarding outbreaks and surveillanceHowever, to achieve that goal, we need to consider the speed, complexity, and ability to integrate the point-of-care data with genomic data. We provide a series of approaches to pathogen genomic information standardization and guides to improve data interoperability, which is key to harnessing the power of modern testing and genomics data.

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Clinical Pathogen Genomics

Cited by 14 publications

References 63 publications

GA4GH: International policies and standards for data sharing across genomic research and healthcare

GA4GH: International policies and standards for data sharing across genomic research and healthcare

Public health implementation of pathogen genomics: the role for accreditation and application of ISO standards

Applying Fast Healthcare Interoperability Resources (FHIR) for Pathogen Genomics at the Point of Care

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