Nanopore adaptive sampling enriches for antimicrobial resistance genes in microbial communities
Antimicrobial resistance (AMR) is a global public health threat. Environmental microbial communities act as reservoirs for AMR, containing genes associated with resistance, their precursors, and the selective pressures promoting their persistence. Genomic surveillance could provide insi...
| Main Authors: | , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
GigaScience Press
2023-12-01
|
| Series: | GigaByte |
| Online Access: | https://gigabytejournal.com/articles/103 |
| _version_ | 1797397462319628288 |
|---|---|
| author | Danielle C. Wrenn Devin M. Drown |
| author_facet | Danielle C. Wrenn Devin M. Drown |
| author_sort | Danielle C. Wrenn |
| collection | DOAJ |
| description |
Antimicrobial resistance (AMR) is a global public health threat. Environmental microbial communities act as reservoirs for AMR, containing genes associated with resistance, their precursors, and the selective pressures promoting their persistence. Genomic surveillance could provide insights into how these reservoirs change and impact public health. Enriching for AMR genomic signatures in complex microbial communities would strengthen surveillance efforts and reduce time-to-answer. Here, we tested the ability of nanopore sequencing and adaptive sampling to enrich for AMR genes in a mock community of environmental origin. Our setup implemented the MinION mk1B, an NVIDIA Jetson Xavier GPU, and Flongle flow cells. Using adaptive sampling, we observed consistent enrichment by composition. On average, adaptive sampling resulted in a target composition 4× higher than without adaptive sampling. Despite a decrease in total sequencing output, adaptive sampling increased target yield in most replicates. We also demonstrate enrichment in a diverse community using an environmental sample. This method enables rapid and flexible genomic surveillance.
|
| first_indexed | 2024-03-09T01:10:22Z |
| format | Article |
| id | doaj.art-21a341dad9464af5b554a62e3a3ac97f |
| institution | Directory Open Access Journal |
| issn | 2709-4715 |
| language | English |
| last_indexed | 2024-03-09T01:10:22Z |
| publishDate | 2023-12-01 |
| publisher | GigaScience Press |
| record_format | Article |
| series | GigaByte |
| spelling | doaj.art-21a341dad9464af5b554a62e3a3ac97f2023-12-11T06:18:41ZengGigaScience PressGigaByte2709-47152023-12-0110.46471/gigabyte.103Nanopore adaptive sampling enriches for antimicrobial resistance genes in microbial communitiesDanielle C. Wrenn 0https://orcid.org/0000-0001-5081-2232Devin M. Drown 1https://orcid.org/0000-0002-2437-7019Department of Biology and Wildlife, University of Alaska Fairbanks, Fairbanks, Alaska, USADepartment of Biology and Wildlife, University of Alaska Fairbanks, Fairbanks, Alaska, USA, Institute of Arctic Biology, University of Alaska Fairbanks, Fairbanks, Alaska, USA Antimicrobial resistance (AMR) is a global public health threat. Environmental microbial communities act as reservoirs for AMR, containing genes associated with resistance, their precursors, and the selective pressures promoting their persistence. Genomic surveillance could provide insights into how these reservoirs change and impact public health. Enriching for AMR genomic signatures in complex microbial communities would strengthen surveillance efforts and reduce time-to-answer. Here, we tested the ability of nanopore sequencing and adaptive sampling to enrich for AMR genes in a mock community of environmental origin. Our setup implemented the MinION mk1B, an NVIDIA Jetson Xavier GPU, and Flongle flow cells. Using adaptive sampling, we observed consistent enrichment by composition. On average, adaptive sampling resulted in a target composition 4× higher than without adaptive sampling. Despite a decrease in total sequencing output, adaptive sampling increased target yield in most replicates. We also demonstrate enrichment in a diverse community using an environmental sample. This method enables rapid and flexible genomic surveillance. https://gigabytejournal.com/articles/103 |
| spellingShingle | Danielle C. Wrenn Devin M. Drown Nanopore adaptive sampling enriches for antimicrobial resistance genes in microbial communities GigaByte |
| title | Nanopore adaptive sampling enriches for antimicrobial resistance genes in microbial communities |
| title_full | Nanopore adaptive sampling enriches for antimicrobial resistance genes in microbial communities |
| title_fullStr | Nanopore adaptive sampling enriches for antimicrobial resistance genes in microbial communities |
| title_full_unstemmed | Nanopore adaptive sampling enriches for antimicrobial resistance genes in microbial communities |
| title_short | Nanopore adaptive sampling enriches for antimicrobial resistance genes in microbial communities |
| title_sort | nanopore adaptive sampling enriches for antimicrobial resistance genes in microbial communities |
| url | https://gigabytejournal.com/articles/103 |
| work_keys_str_mv | AT daniellecwrenn nanoporeadaptivesamplingenrichesforantimicrobialresistancegenesinmicrobialcommunities AT devinmdrown nanoporeadaptivesamplingenrichesforantimicrobialresistancegenesinmicrobialcommunities |