Selective whole genome amplification and sequencing of Coxiella burnetii directly from environmental samples
| Autor: | J. M. Schupp, Tara N. Furstenau, Crystal M. Hepp, Albrecht I. Schulte-Hostedde, Kristin Wiggins, Claire M. Jardine, Ariel Porty, Michael Deberg, Talima Pearson, Viacheslav Y. Fofanov, Jill Hager Cocking, Heidie Hornstra, Jason W. Sahl |
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| Rok vydání: | 2020 |
| Předmět: |
0106 biological sciences
Population Computational biology Select agent Polymorphism Single Nucleotide 01 natural sciences Genome Article 03 medical and health sciences Genetics Animals education Phylogeny Organism 030304 developmental biology Whole Genome Amplification Whole genome sequencing 0303 health sciences education.field_of_study Whole Genome Sequencing biology Goats Coxiella burnetii biology.organism_classification Milk Metagenomics Metagenome Female Genome Bacterial 010606 plant biology & botany |
| Zdroj: | Genomics |
| ISSN: | 0888-7543 |
| DOI: | 10.1016/j.ygeno.2019.10.022 |
| Popis: | Whole genome sequencing (WGS) is a widely available, inexpensive means of providing a wealth of information about an organism’s diversity and evolution. However, WGS for many pathogenic bacteria remain limited because they are difficult, slow and/or dangerous to culture. To avoid culturing, metagenomic sequencing can be performed directly on samples, but the sequencing effort required to characterize low frequency organisms can be expensive. Recently developed methods for selective whole genome amplification (SWGA) can enrich target DNA to provide efficient sequencing. We amplified Coxiella burnetii (a bacterial select agent and human/livestock pathogen) from 3 three environmental samples that were overwhelmed with host DNA. The 68- to 147-fold enrichment of the bacterial sequences provided enough genome coverage for SNP analyses and phylogenetic placement. SWGA is a valuable tool for the study of difficult-to-culture organisms and has the potential to facilitate high-throughput population characterizations as well as targeted epidemiological or forensic investigations. |
| Databáze: | OpenAIRE |
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