Detection of mixed-strain infections by FACS and ultra-low input genome sequencing
The epidemiological tracking of a bacterial outbreak may be jeopardized by the presence of multiple pathogenic strains in one patient. Nevertheless, this fact is not considered in most of the epidemiological studies and only one colony per patient is sequenced. On the other hand, the routine whole g...
| Main Authors: | , , , , |
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| Format: | Article |
| Language: | English |
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Taylor & Francis Group
2020-05-01
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| Series: | Gut Microbes |
| Subjects: | |
| Online Access: | http://dx.doi.org/10.1080/19490976.2018.1526578 |
| _version_ | 1811270891548442624 |
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| author | Mária Džunková Andrés Moya Xinhua Chen Ciaran Kelly Giuseppe D’Auria |
| author_facet | Mária Džunková Andrés Moya Xinhua Chen Ciaran Kelly Giuseppe D’Auria |
| author_sort | Mária Džunková |
| collection | DOAJ |
| description | The epidemiological tracking of a bacterial outbreak may be jeopardized by the presence of multiple pathogenic strains in one patient. Nevertheless, this fact is not considered in most of the epidemiological studies and only one colony per patient is sequenced. On the other hand, the routine whole genome sequencing of many isolates from each patient would be costly and unnecessary, because the number of strains in a patient is never known a priori. In addition, the result would be biased by microbial culture conditions. Herein we propose an approach for detecting mixed-strain infection, providing C. difficile infection as an example. The cells of the target pathogenic species are collected from the bacterial suspension by the fluorescence activated cell sorting (FACS) and a shallow genome sequencing is performed. A modified sequencing library preparation protocol for low-input DNA samples can be used for low prevalence gut pathogens (< 0.1% of the total microbiome). This FACS-seq approach reduces diagnostics time (no culture is needed) and may promote discoveries of novel strains. Methodological details, possible issues and future directions for the sequencing of these natural pan-genomes are herein discussed. |
| first_indexed | 2024-04-12T22:11:20Z |
| format | Article |
| id | doaj.art-d759c2d6c75f467bad59947b6efa3c04 |
| institution | Directory Open Access Journal |
| issn | 1949-0976 1949-0984 |
| language | English |
| last_indexed | 2024-04-12T22:11:20Z |
| publishDate | 2020-05-01 |
| publisher | Taylor & Francis Group |
| record_format | Article |
| series | Gut Microbes |
| spelling | doaj.art-d759c2d6c75f467bad59947b6efa3c042022-12-22T03:14:46ZengTaylor & Francis GroupGut Microbes1949-09761949-09842020-05-0111330530910.1080/19490976.2018.15265781526578Detection of mixed-strain infections by FACS and ultra-low input genome sequencingMária Džunková0Andrés Moya1Xinhua Chen2Ciaran Kelly3Giuseppe D’Auria4Foundation for the Promotion of Health and Biomedical Research of Valencia Region (FISABIO-Public Health)Foundation for the Promotion of Health and Biomedical Research of Valencia Region (FISABIO-Public Health)Beth Israel Deaconess Medical Center, Harvard Medical SchoolBeth Israel Deaconess Medical Center, Harvard Medical SchoolFoundation for the Promotion of Health and Biomedical Research of Valencia Region (FISABIO-Public Health)The epidemiological tracking of a bacterial outbreak may be jeopardized by the presence of multiple pathogenic strains in one patient. Nevertheless, this fact is not considered in most of the epidemiological studies and only one colony per patient is sequenced. On the other hand, the routine whole genome sequencing of many isolates from each patient would be costly and unnecessary, because the number of strains in a patient is never known a priori. In addition, the result would be biased by microbial culture conditions. Herein we propose an approach for detecting mixed-strain infection, providing C. difficile infection as an example. The cells of the target pathogenic species are collected from the bacterial suspension by the fluorescence activated cell sorting (FACS) and a shallow genome sequencing is performed. A modified sequencing library preparation protocol for low-input DNA samples can be used for low prevalence gut pathogens (< 0.1% of the total microbiome). This FACS-seq approach reduces diagnostics time (no culture is needed) and may promote discoveries of novel strains. Methodological details, possible issues and future directions for the sequencing of these natural pan-genomes are herein discussed.http://dx.doi.org/10.1080/19490976.2018.1526578facs-seqc. difficilemixed-strain infectionlow-input dna sequencingepidemiology |
| spellingShingle | Mária Džunková Andrés Moya Xinhua Chen Ciaran Kelly Giuseppe D’Auria Detection of mixed-strain infections by FACS and ultra-low input genome sequencing Gut Microbes facs-seq c. difficile mixed-strain infection low-input dna sequencing epidemiology |
| title | Detection of mixed-strain infections by FACS and ultra-low input genome sequencing |
| title_full | Detection of mixed-strain infections by FACS and ultra-low input genome sequencing |
| title_fullStr | Detection of mixed-strain infections by FACS and ultra-low input genome sequencing |
| title_full_unstemmed | Detection of mixed-strain infections by FACS and ultra-low input genome sequencing |
| title_short | Detection of mixed-strain infections by FACS and ultra-low input genome sequencing |
| title_sort | detection of mixed strain infections by facs and ultra low input genome sequencing |
| topic | facs-seq c. difficile mixed-strain infection low-input dna sequencing epidemiology |
| url | http://dx.doi.org/10.1080/19490976.2018.1526578 |
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