Evidence map›Paper›PMID 37425917›Full record

ArticlebioRxiv : the preprint server for biology2023

Nanopore Adaptive Sampling Enriches for Antimicrobial Resistance Genes in Microbial Communities.

Danielle C Wrenn, Devin M Drown

Open access · greenAbstract readPreprint
PubMed Full text at PMC Publisher
In one paragraph

Article in bioRxiv : the preprint server for biology, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.

0numbers the graph read from it
0cells of the map it votes in
0citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

0 citing papers in PubMed, 6 citations in OpenAlex.

No citing paper in PubMed yet.

4 · The record

Corrections and comments

5 · Who and what money

Authors and funding

2 authors at 1 institution in 1 country.

Danielle C WrennDepartment of Biology and Wildlife, University of Alaska Fairbanks, Fairbanks, Alaska, USA.
Devin M DrownDepartment of Biology and Wildlife, University of Alaska Fairbanks, Fairbanks, Alaska, USA.
University of Alaska Fairbanks · US

Funding

The Administrative CoreP20GM103395 · NIGMS · UNIVERSITY OF ALASKA FAIRBANKS · PI BRIAN M BARNES · 2012 to 2026
$66.1M
Biomedical Learning and Student Training (BLaST) ProgramUL1GM118991 · NIGMS · UNIVERSITY OF ALASKA FAIRBANKS · PI HUEFFER, KARSTEN · 2015 to 2023
$19.0M
Biomedical Learning and Student Training (BLaST) ProgramRL5GM118990 · NIGMS · UNIVERSITY OF ALASKA FAIRBANKS · PI HUEFFER, KARSTEN, REYNOLDS, ARLEIGH JAMES · 2015 to 2023
$10.5M
Biomedical Learning and Student Training (BLaST) ProgramTL4GM118992 · NIGMS · UNIVERSITY OF ALASKA FAIRBANKS · PI HUEFFER, KARSTEN, REYNOLDS, ARLEIGH JAMES · 2015 to 2023
$7.1M
NIGMS NIH HHS P20 GM103395NIGMS NIH HHS RL5 GM118990NIGMS NIH HHS TL4 GM118992NIGMS NIH HHS UL1 GM118991
6 · The paper itself

Abstract

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 to encourage their persistence. Genomic surveillance could provide insight into how these reservoirs are changing and their impact on public health. The ability to enrich for AMR genomic signatures in complex microbial communities would strengthen surveillance efforts and reduce time-to-answer. Here, we test 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. We observed consistent enrichment by composition when using adaptive sampling. On average, adaptive sampling resulted in a target composition that was 4x higher than a treatment without adaptive sampling. Despite a decrease in total sequencing output, the use of adaptive sampling increased target yield in most replicates.

Indexed as

antibiotic resistanceenvironmental microbial communities

Identifiers

PMID37425917
PMCPMC10327016
OpenAlexW4382646025

What OpenQuestion holds

Textmetadata
LicenceCC BY-NC-ND
Read underepoch 390

Registered trials

None linked

Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.