The clinical and epidemiological impacts of whole genomic sequencing on bacterial and virological agents

Timsit, Sarah; Armand-Lefèvre, Laurence; Le Goff, Jérôme; Salmona, Maud

doi:10.1016/j.idnow.2023.104844

Infectious Diseases Now

2024

DOI: 10.1016/j.idnow.2023.104844

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The clinical and epidemiological impacts of whole genomic sequencing on bacterial and virological agents

Sarah Timsit,

Laurence Armand-Lefèvre,

Jérôme Le Goff

et al.

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Bridging Classical Methodologies in Salmonella Investigation with Modern Technologies: A Comprehensive Review

Kitchens,

Wang,

Price

2024

Microorganisms

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Advancements in genomics and machine learning have significantly enhanced the study of Salmonella epidemiology. Whole-genome sequencing has revolutionized bacterial genomics, allowing for detailed analysis of genetic variation and aiding in outbreak investigations and source tracking. Short-read sequencing technologies, such as those provided by Illumina, have been instrumental in generating draft genomes that facilitate serotyping and the detection of antimicrobial resistance. Long-read sequencing technologies, including those from Pacific Biosciences and Oxford Nanopore Technologies, offer the potential for more complete genome assemblies and better insights into genetic diversity. In addition to these sequencing approaches, machine learning techniques like decision trees and random forests provide powerful tools for pattern recognition and predictive modeling. Importantly, the study of bacteriophages, which interact with Salmonella, offers additional layers of understanding. Phages can impact Salmonella population dynamics and evolution, and their integration into Salmonella genomics research holds promise for novel insights into pathogen control and epidemiology. This review revisits the history of Salmonella and its pathogenesis and highlights the integration of these modern methodologies in advancing our understanding of Salmonella.

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Bridging Classical Methodologies in Salmonella Investigation with Modern Technologies: A Comprehensive Review

Kitchens,

Wang,

Price

2024

Microorganisms

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The clinical and epidemiological impacts of whole genomic sequencing on bacterial and virological agents

Cited by 1 publication

References 85 publications

Bridging Classical Methodologies in Salmonella Investigation with Modern Technologies: A Comprehensive Review

Bridging Classical Methodologies in Salmonella Investigation with Modern Technologies: A Comprehensive Review

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