Next Generation and Other Sequencing Technologies in Diagnostic Microbiology and Infectious Diseases
Next-generation sequencing (NGS) technologies have become increasingly available for use in the clinical microbiology diagnostic environment. There are three main applications of these technologies in the clinical microbiology laboratory: whole genome sequencing (WGS), targeted metagenomics sequenci...
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| Format: | Article |
| Language: | English |
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MDPI AG
2022-08-01
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| Series: | Genes |
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| Online Access: | https://www.mdpi.com/2073-4425/13/9/1566 |
| _version_ | 1797488055974625280 |
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| author | Evann E. Hilt Patricia Ferrieri |
| author_facet | Evann E. Hilt Patricia Ferrieri |
| author_sort | Evann E. Hilt |
| collection | DOAJ |
| description | Next-generation sequencing (NGS) technologies have become increasingly available for use in the clinical microbiology diagnostic environment. There are three main applications of these technologies in the clinical microbiology laboratory: whole genome sequencing (WGS), targeted metagenomics sequencing and shotgun metagenomics sequencing. These applications are being utilized for initial identification of pathogenic organisms, the detection of antimicrobial resistance mechanisms and for epidemiologic tracking of organisms within and outside hospital systems. In this review, we analyze these three applications and provide a comprehensive summary of how these applications are currently being used in public health, basic research, and clinical microbiology laboratory environments. In the public health arena, WGS is being used to identify and epidemiologically track food borne outbreaks and disease surveillance. In clinical hospital systems, WGS is used to identify multi-drug-resistant nosocomial infections and track the transmission of these organisms. In addition, we examine how metagenomics sequencing approaches (targeted and shotgun) are being used to circumvent the traditional and biased microbiology culture methods to identify potential pathogens directly from specimens. We also expand on the important factors to consider when implementing these technologies, and what is possible for these technologies in infectious disease diagnosis in the next 5 years. |
| first_indexed | 2024-03-09T23:56:39Z |
| format | Article |
| id | doaj.art-9fc6671d0e0542158ab93ecf3ef6deb3 |
| institution | Directory Open Access Journal |
| issn | 2073-4425 |
| language | English |
| last_indexed | 2024-03-09T23:56:39Z |
| publishDate | 2022-08-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Genes |
| spelling | doaj.art-9fc6671d0e0542158ab93ecf3ef6deb32023-11-23T16:24:15ZengMDPI AGGenes2073-44252022-08-01139156610.3390/genes13091566Next Generation and Other Sequencing Technologies in Diagnostic Microbiology and Infectious DiseasesEvann E. Hilt0Patricia Ferrieri1Department of Laboratory Medicine and Pathology, University of Minnesota, Minneapolis, MN 55455, USADepartment of Laboratory Medicine and Pathology, University of Minnesota, Minneapolis, MN 55455, USANext-generation sequencing (NGS) technologies have become increasingly available for use in the clinical microbiology diagnostic environment. There are three main applications of these technologies in the clinical microbiology laboratory: whole genome sequencing (WGS), targeted metagenomics sequencing and shotgun metagenomics sequencing. These applications are being utilized for initial identification of pathogenic organisms, the detection of antimicrobial resistance mechanisms and for epidemiologic tracking of organisms within and outside hospital systems. In this review, we analyze these three applications and provide a comprehensive summary of how these applications are currently being used in public health, basic research, and clinical microbiology laboratory environments. In the public health arena, WGS is being used to identify and epidemiologically track food borne outbreaks and disease surveillance. In clinical hospital systems, WGS is used to identify multi-drug-resistant nosocomial infections and track the transmission of these organisms. In addition, we examine how metagenomics sequencing approaches (targeted and shotgun) are being used to circumvent the traditional and biased microbiology culture methods to identify potential pathogens directly from specimens. We also expand on the important factors to consider when implementing these technologies, and what is possible for these technologies in infectious disease diagnosis in the next 5 years.https://www.mdpi.com/2073-4425/13/9/1566next-generation sequencingmicrobiologydiagnostics |
| spellingShingle | Evann E. Hilt Patricia Ferrieri Next Generation and Other Sequencing Technologies in Diagnostic Microbiology and Infectious Diseases Genes next-generation sequencing microbiology diagnostics |
| title | Next Generation and Other Sequencing Technologies in Diagnostic Microbiology and Infectious Diseases |
| title_full | Next Generation and Other Sequencing Technologies in Diagnostic Microbiology and Infectious Diseases |
| title_fullStr | Next Generation and Other Sequencing Technologies in Diagnostic Microbiology and Infectious Diseases |
| title_full_unstemmed | Next Generation and Other Sequencing Technologies in Diagnostic Microbiology and Infectious Diseases |
| title_short | Next Generation and Other Sequencing Technologies in Diagnostic Microbiology and Infectious Diseases |
| title_sort | next generation and other sequencing technologies in diagnostic microbiology and infectious diseases |
| topic | next-generation sequencing microbiology diagnostics |
| url | https://www.mdpi.com/2073-4425/13/9/1566 |
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