Clinical metagenomics for infection diagnosis

Salais, Robert; Filkins, Laura

doi:10.1016/b978-0-12-801496-7.00004-6

Cited by 4 publications

(3 citation statements)

References 127 publications

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“…This issue can be particularly pronounced in specimens with low pathogen loads or when analysing complex microbial communities [76]. This challenge can be especially concerning in specimens such as tissues or respiratory secretions, or when the pathogen load is exceptionally low [77]. Addressing this requires robust bioinformatics pipelines capable of accurately distinguishing relevant microbial sequences from noise.…”

Section: Metagenomicsmentioning

confidence: 99%

Current Uses and Future Perspectives of Genomic Technologies in Clinical Microbiology

Bianconi,

Aschbacher,

Pagani

2023

Antibiotics

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Recent advancements in sequencing technology and data analytics have led to a transformative era in pathogen detection and typing. These developments not only expedite the process, but also render it more cost-effective. Genomic analyses of infectious diseases are swiftly becoming the standard for pathogen analysis and control. Additionally, national surveillance systems can derive substantial benefits from genomic data, as they offer profound insights into pathogen epidemiology and the emergence of antimicrobial-resistant strains. Antimicrobial resistance (AMR) is a pressing global public health issue. While clinical laboratories have traditionally relied on culture-based antimicrobial susceptibility testing, the integration of genomic data into AMR analysis holds immense promise. Genomic-based AMR data can furnish swift, consistent, and highly accurate predictions of resistance phenotypes for specific strains or populations, all while contributing invaluable insights for surveillance. Moreover, genome sequencing assumes a pivotal role in the investigation of hospital outbreaks. It aids in the identification of infection sources, unveils genetic connections among isolates, and informs strategies for infection control. The One Health initiative, with its focus on the intricate interconnectedness of humans, animals, and the environment, seeks to develop comprehensive approaches for disease surveillance, control, and prevention. When integrated with epidemiological data from surveillance systems, genomic data can forecast the expansion of bacterial populations and species transmissions. Consequently, this provides profound insights into the evolution and genetic relationships of AMR in pathogens, hosts, and the environment.

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Section: Metagenomicsmentioning

confidence: 99%

Current Uses and Future Perspectives of Genomic Technologies in Clinical Microbiology

Bianconi,

Aschbacher,

Pagani

2023

Antibiotics

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“…In a recent perspective, Segata (2018) emphasized the importance of accurately elucidating human-associated microbial communities at strain level through developing new computational tools, which can link strain variants to host phenotypes and holds the potential of understanding the personalized host-microbiome interactions. In fact, with the fast development of metagenomic techniques, this culture-independent approach has been applied in detecting microbial pathogens in public health (Miller et al, 2013;Chiu and Miller, 2019), identifying genes or genetic mutations conferring resistance to antimicrobial drugs (De, 2019;De Abreu et al, 2021), and enabling genotyping analysis for molecular epidemiology and so on (Robert and Filkins, 2019), which makes the method gradually transiting from research fields to clinical laboratories (Chiu and Miller, 2019) and slowly integrating into clinician's toolbox to identify infectious diseases (De Vries, 2021), though it functions as a diagnostic tool yet to be widely established due to a variety of issues such as costs, turnaround time, sensitivity, specificity, validation, and reproducibility, etc. in clinical microbiology laboratories.…”

Section: Potential Applications Of Metaomics In Clinical Diagnosis Me...mentioning

confidence: 99%

Metaomics in Clinical Laboratory: Potential Driving Force for Innovative Disease Diagnosis

Wang

Li²,

et al. 2022

Front. Microbiol.

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Currently, more and more studies suggested that reductionism was lack of holistic and integrative view of biological processes, leading to limited understanding of complex systems like microbiota and the associated diseases. In fact, microbes are rarely present in individuals but normally live in complex multispecies communities. With the recent development of a variety of metaomics techniques, microbes could be dissected dynamically in both temporal and spatial scales. Therefore, in-depth understanding of human microbiome from different aspects such as genomes, transcriptomes, proteomes, and metabolomes could provide novel insights into their functional roles, which also holds the potential in making them diagnostic biomarkers in many human diseases, though there is still a huge gap to fill for the purpose. In this mini-review, we went through the frontlines of the metaomics techniques and explored their potential applications in clinical diagnoses of human diseases, e.g., infectious diseases, through which we concluded that novel diagnostic methods based on human microbiomes shall be achieved in the near future, while the limitations of these techniques such as standard procedures and computational challenges for rapid and accurate analysis of metaomics data in clinical settings were also examined.

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“…Metagenomics also provides a hypothesis-independent approach to profiling microbial communities' taxonomy and function, eliminating the need for cultivating microorganisms in controlled laboratory settings [6]. Clinical metagenomics enables comprehensive pathogen identification and characterization of indigenous microbiota associated with different diseases [7], thus enhancing our understanding of sample microbiomes and their role in disease management. This study delves into how the constituents of basic viral transport media can affect NGS outcomes.…”

Section: Introductionmentioning

confidence: 99%

Emerging Importance of Viral Transport Media in High-Throughput Sequencing Fidelity for Genomic Analysis

Beniwal,

Saharan

2023

JSRR

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The impact of Viral Transport Media (VTM) components on the efficacy and accuracy of high-throughput Next-Generation Sequencing (NGS) techniques is a subject of paramount importance in the field of viral genomics and diagnostics. VTMs play a pivotal role in preserving viral samples, and their composition can profoundly influence the quality and reliability of NGS results. This study explores the intricate relationship between VTM components and NGS outcomes, with a focus on optimizing diagnostic precision and the efficiency of NGS in viral genomics. Through comprehensive investigation, this research sheds light on the critical implications of VTM composition for enhancing viral genomic analysis, streamlining diagnostic processes, and bolstering public health responses. The findings have far-reaching consequences, including the potential for personalized medicine, rapid detection of emerging viral threats, and the improvement of public health surveillance. Standardized protocols and ongoing technological advancements are essential in harnessing the full potential of NGS for genomics and metagenomics, marking a significant step toward more effective viral disease management and outbreak response.

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Clinical metagenomics for infection diagnosis

Cited by 4 publications

References 127 publications

Current Uses and Future Perspectives of Genomic Technologies in Clinical Microbiology

Current Uses and Future Perspectives of Genomic Technologies in Clinical Microbiology

Metaomics in Clinical Laboratory: Potential Driving Force for Innovative Disease Diagnosis

Emerging Importance of Viral Transport Media in High-Throughput Sequencing Fidelity for Genomic Analysis

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