Evidence map›Paper›PMID 39314343›Full record

ArticlebioRxiv : the preprint server for biology2025

Context-Seq: CRISPR-Cas9 Targeted Nanopore Sequencing for Transmission Dynamics of Antimicrobial Resistance.

Erica R Fuhrmeister, Sooyeol Kim, Shruteek A Mairal, Caroline McCormack, Benard Chieng, Jenna M Swarthout, Abigail Harvey Paulos, Sammy M Njenga, Amy J Pickering

Abstract readPreprint
PubMed Full text at PMC Publisher
In one paragraph

Article in bioRxiv : the preprint server for biology, 2025. 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.

No citing paper in PubMed yet.

4 · The record

Corrections and comments

5 · Who and what money

Authors and funding

9 authors.

Erica R FuhrmeisterDepartment of Environmental and Occupational Health Sciences, School of Public Health, University of Washington, Seattle, Washington, USA.ORCID 0000-0001-5264-7533
Sooyeol KimDepartment of Civil and Environmental Engineering, University of California, Berkeley, CA, USA.
Shruteek A MairalDepartment of Chemical and Biomolecular Engineering, University of California, Berkeley, CA, USA.
Caroline McCormackDepartment of Civil and Environmental Engineering, University of California, Berkeley, CA, USA.
Benard ChiengEastern and Southern Africa Centre of International Parasite Control, Kenya Medical Research Institute, Nairobi, Kenya.
Jenna M SwarthoutDepartment of Civil and Environmental Engineering, Tufts University, Medford, MA, USA.
Abigail Harvey PaulosDepartment of Civil and Environmental Engineering, University of California, Berkeley, CA, USA.
Sammy M NjengaEastern and Southern Africa Centre of International Parasite Control, Kenya Medical Research Institute, Nairobi, Kenya.
Amy J PickeringDepartment of Civil and Environmental Engineering, University of California, Berkeley, CA, USA.ORCID 0000-0001-6193-2221

Funding

Tufts Clinical and Translational Science Institute (Pilot Supplement)UL1TR002544 · NCATS · TUFTS UNIVERSITY BOSTON · PI SELKER, HARRY P. · 2018 to 2022
$50.2M
Natural infection of norovirus and sapovirus in a birth cohort in a Peruvian periurban communityR01AI108695 · NIAID · JOHNS HOPKINS UNIVERSITY · PI CHAKRABORTY, SUBHRA, GILMAN, ROBERT H · 2015 to 2019
$5.0M
NCATS NIH HHS UL1 TR002544NIAID NIH HHS R01 AI108695
6 · The paper itself

Abstract

Precisely understanding how and to what extent antimicrobial resistance (AMR) is exchanged between animals and humans is needed to inform control strategies. Metagenomic sequencing has low detection for rare targets such as antibiotic resistance genes, while whole genome sequencing of isolates misses exchange between uncultured bacterial species. We introduce Context-Seq, CRISPR-Cas9 targeted sequencing of ARGs and their genomic context with long-reads. Using Context-Seq, we investigate genetically similar AMR elements containing the ARGs

Identifiers

PMID39314343
PMCPMC11419053

What OpenQuestion holds

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Registered trials

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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.