Advances in Clinical Sample Preparation for Identification and Characterization of Bacterial Pathogens Using Metagenomics
Whole genome sequencing (WGS) plays an increasing role in communicable disease control through high-resolution outbreak tracing, laboratory surveillance and diagnostics. However, WGS has traditionally relied on microbial culture in order to obtain pathogen specific DNA for sequencing. This has sever...
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| Format: | Article |
| Language: | English |
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Frontiers Media S.A.
2018-12-01
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| Series: | Frontiers in Public Health |
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| Online Access: | https://www.frontiersin.org/article/10.3389/fpubh.2018.00363/full |
| _version_ | 1818929564078833664 |
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| author | Nathan L. Bachmann Nathan L. Bachmann Rebecca J. Rockett Rebecca J. Rockett Verlaine Joy Timms Vitali Sintchenko Vitali Sintchenko |
| author_facet | Nathan L. Bachmann Nathan L. Bachmann Rebecca J. Rockett Rebecca J. Rockett Verlaine Joy Timms Vitali Sintchenko Vitali Sintchenko |
| author_sort | Nathan L. Bachmann |
| collection | DOAJ |
| description | Whole genome sequencing (WGS) plays an increasing role in communicable disease control through high-resolution outbreak tracing, laboratory surveillance and diagnostics. However, WGS has traditionally relied on microbial culture in order to obtain pathogen specific DNA for sequencing. This has severely limited the application of whole genome sequencing on pathogens with fastidious culturing requirements. In addition, the widespread adoption of culture-independent diagnostic tests has reduced availability of cultured isolates for confirmatory testing and surveillance. These recent developments have created demand for the implementation of techniques enabling direct sequencing of microbial genomes in clinical samples without having to culture an isolate. However, sequencing of specific organisms from clinical samples can be affected by high levels of contaminating DNA from the host and other commensal microorganisms. Several methods have been introduced for selective lysis of host cells and/or separate specific organisms from a clinical sample. This review examines the different approaches for sample preparation that have been used in diagnostic and public health laboratories for metagenomic sequencing. |
| first_indexed | 2024-12-20T03:46:48Z |
| format | Article |
| id | doaj.art-b79f464395cc4b71bf78010ceffe76a6 |
| institution | Directory Open Access Journal |
| issn | 2296-2565 |
| language | English |
| last_indexed | 2024-12-20T03:46:48Z |
| publishDate | 2018-12-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Public Health |
| spelling | doaj.art-b79f464395cc4b71bf78010ceffe76a62022-12-21T19:54:35ZengFrontiers Media S.A.Frontiers in Public Health2296-25652018-12-01610.3389/fpubh.2018.00363420029Advances in Clinical Sample Preparation for Identification and Characterization of Bacterial Pathogens Using MetagenomicsNathan L. Bachmann0Nathan L. Bachmann1Rebecca J. Rockett2Rebecca J. Rockett3Verlaine Joy Timms4Vitali Sintchenko5Vitali Sintchenko6Sydney Medical School, University of Sydney, Camperdown, NSW, AustraliaCentenary Institute, University of Sydney, Camperdown, NSW, AustraliaSydney Medical School, University of Sydney, Camperdown, NSW, AustraliaCentre for Infectious Diseases and Microbiology–Public Health, Westmead Hospital, Sydney, NSW, AustraliaCentre for Infectious Diseases and Microbiology–Public Health, Westmead Hospital, Sydney, NSW, AustraliaSydney Medical School, University of Sydney, Camperdown, NSW, AustraliaCentre for Infectious Diseases and Microbiology–Public Health, Westmead Hospital, Sydney, NSW, AustraliaWhole genome sequencing (WGS) plays an increasing role in communicable disease control through high-resolution outbreak tracing, laboratory surveillance and diagnostics. However, WGS has traditionally relied on microbial culture in order to obtain pathogen specific DNA for sequencing. This has severely limited the application of whole genome sequencing on pathogens with fastidious culturing requirements. In addition, the widespread adoption of culture-independent diagnostic tests has reduced availability of cultured isolates for confirmatory testing and surveillance. These recent developments have created demand for the implementation of techniques enabling direct sequencing of microbial genomes in clinical samples without having to culture an isolate. However, sequencing of specific organisms from clinical samples can be affected by high levels of contaminating DNA from the host and other commensal microorganisms. Several methods have been introduced for selective lysis of host cells and/or separate specific organisms from a clinical sample. This review examines the different approaches for sample preparation that have been used in diagnostic and public health laboratories for metagenomic sequencing.https://www.frontiersin.org/article/10.3389/fpubh.2018.00363/fullmetagenomicculture-independent genome sequencingbacterial pathogensMycobacterium tuberculosispublic health |
| spellingShingle | Nathan L. Bachmann Nathan L. Bachmann Rebecca J. Rockett Rebecca J. Rockett Verlaine Joy Timms Vitali Sintchenko Vitali Sintchenko Advances in Clinical Sample Preparation for Identification and Characterization of Bacterial Pathogens Using Metagenomics Frontiers in Public Health metagenomic culture-independent genome sequencing bacterial pathogens Mycobacterium tuberculosis public health |
| title | Advances in Clinical Sample Preparation for Identification and Characterization of Bacterial Pathogens Using Metagenomics |
| title_full | Advances in Clinical Sample Preparation for Identification and Characterization of Bacterial Pathogens Using Metagenomics |
| title_fullStr | Advances in Clinical Sample Preparation for Identification and Characterization of Bacterial Pathogens Using Metagenomics |
| title_full_unstemmed | Advances in Clinical Sample Preparation for Identification and Characterization of Bacterial Pathogens Using Metagenomics |
| title_short | Advances in Clinical Sample Preparation for Identification and Characterization of Bacterial Pathogens Using Metagenomics |
| title_sort | advances in clinical sample preparation for identification and characterization of bacterial pathogens using metagenomics |
| topic | metagenomic culture-independent genome sequencing bacterial pathogens Mycobacterium tuberculosis public health |
| url | https://www.frontiersin.org/article/10.3389/fpubh.2018.00363/full |
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