Bridging Classical Methodologies in <i>Salmonella</i> Investigation with Modern Technologies: A Comprehensive Review
Advancements in genomics and machine learning have significantly enhanced the study of <i>Salmonella</i> epidemiology. Whole-genome sequencing has revolutionized bacterial genomics, allowing for detailed analysis of genetic variation and aiding in outbreak investigations and source track...
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MDPI AG
2024-11-01
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| Series: | Microorganisms |
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| Online Access: | https://www.mdpi.com/2076-2607/12/11/2249 |
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| author | Steven Ray Kitchens Chengming Wang Stuart B. Price |
| author_facet | Steven Ray Kitchens Chengming Wang Stuart B. Price |
| author_sort | Steven Ray Kitchens |
| collection | DOAJ |
| description | Advancements in genomics and machine learning have significantly enhanced the study of <i>Salmonella</i> 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 <i>Salmonella</i>, offers additional layers of understanding. Phages can impact <i>Salmonella</i> population dynamics and evolution, and their integration into <i>Salmonella</i> genomics research holds promise for novel insights into pathogen control and epidemiology. This review revisits the history of <i>Salmonella</i> and its pathogenesis and highlights the integration of these modern methodologies in advancing our understanding of <i>Salmonella</i>. |
| format | Article |
| id | doaj-art-c4b0fbb5f9c145ffa979f215a48c64cd |
| institution | OA Journals |
| issn | 2076-2607 |
| language | English |
| publishDate | 2024-11-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Microorganisms |
| spelling | doaj-art-c4b0fbb5f9c145ffa979f215a48c64cd2025-08-20T02:04:55ZengMDPI AGMicroorganisms2076-26072024-11-011211224910.3390/microorganisms12112249Bridging Classical Methodologies in <i>Salmonella</i> Investigation with Modern Technologies: A Comprehensive ReviewSteven Ray Kitchens0Chengming Wang1Stuart B. Price2Department of Pathobiology, College of Veterinary Medicine, Auburn University, 1130 Wire Road, Auburn, AL 36849-5519, USADepartment of Pathobiology, College of Veterinary Medicine, Auburn University, 1130 Wire Road, Auburn, AL 36849-5519, USADepartment of Pathobiology, College of Veterinary Medicine, Auburn University, 1130 Wire Road, Auburn, AL 36849-5519, USAAdvancements in genomics and machine learning have significantly enhanced the study of <i>Salmonella</i> 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 <i>Salmonella</i>, offers additional layers of understanding. Phages can impact <i>Salmonella</i> population dynamics and evolution, and their integration into <i>Salmonella</i> genomics research holds promise for novel insights into pathogen control and epidemiology. This review revisits the history of <i>Salmonella</i> and its pathogenesis and highlights the integration of these modern methodologies in advancing our understanding of <i>Salmonella</i>.https://www.mdpi.com/2076-2607/12/11/2249<i>Salmonella</i>virulenceenvironmentbacteriophageepidemiologycomputational biology |
| spellingShingle | Steven Ray Kitchens Chengming Wang Stuart B. Price Bridging Classical Methodologies in <i>Salmonella</i> Investigation with Modern Technologies: A Comprehensive Review Microorganisms <i>Salmonella</i> virulence environment bacteriophage epidemiology computational biology |
| title | Bridging Classical Methodologies in <i>Salmonella</i> Investigation with Modern Technologies: A Comprehensive Review |
| title_full | Bridging Classical Methodologies in <i>Salmonella</i> Investigation with Modern Technologies: A Comprehensive Review |
| title_fullStr | Bridging Classical Methodologies in <i>Salmonella</i> Investigation with Modern Technologies: A Comprehensive Review |
| title_full_unstemmed | Bridging Classical Methodologies in <i>Salmonella</i> Investigation with Modern Technologies: A Comprehensive Review |
| title_short | Bridging Classical Methodologies in <i>Salmonella</i> Investigation with Modern Technologies: A Comprehensive Review |
| title_sort | bridging classical methodologies in i salmonella i investigation with modern technologies a comprehensive review |
| topic | <i>Salmonella</i> virulence environment bacteriophage epidemiology computational biology |
| url | https://www.mdpi.com/2076-2607/12/11/2249 |
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