Evidence map›Paper›PMID 39763738›Full record

ArticlebioRxiv : the preprint server for biology2024

Tiled Amplicon Sequencing Enables Culture-free Whole-Genome Sequencing of Pathogenic Bacteria From Clinical Specimens.

Chaney C Kalinich, Freddy L Gonzalez, Alice Osmaston, Mallery I Breban, Isabel Distefano, Candy Leon, Patricia Sheen, Mirko Zimic, Jorge Coronel, Grace Tan and 15 more

Abstract readPreprint
PubMed Full text at PMC Publisher
In one paragraph

Article in bioRxiv : the preprint server for biology, 2024. 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

25 authors.

Chaney C KalinichDepartment of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, Connecticut, USA.ORCID 0000-0001-9675-0065
Freddy L GonzalezDepartment of Ecology and Evolutionary Biology, Yale University, New Haven, Connecticut, USA.
Alice OsmastonDepartment of Infection, Immunity, and Inflammation, Institute of Child Health, University College Longon, London, England.
Mallery I BrebanDepartment of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, Connecticut, USA.
Isabel DistefanoDepartment of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, Connecticut, USA.
Candy LeonUniversidad Peruana Cayetano Heredia, Lima, Peru.
Patricia SheenUniversidad Peruana Cayetano Heredia, Lima, Peru.
Mirko ZimicUniversidad Peruana Cayetano Heredia, Lima, Peru.
Jorge CoronelUniversidad Peruana Cayetano Heredia, Lima, Peru.
Grace TanDepartment of Infection, Immunity, and Inflammation, Institute of Child Health, University College Longon, London, England.
Valeriu CruduInstitute of Phthisiopneumology, Chisinau, Moldova.
Nelly CiobanuInstitute of Phthisiopneumology, Chisinau, Moldova.
Alexandru CodreanuInstitute of Phthisiopneumology, Chisinau, Moldova.
Walter SolanoUniversidad Peruana Cayetano Heredia, Lima, Peru.
Jimena RáezUniversidad Peruana Cayetano Heredia, Lima, Peru.
Orchid M AllicockDepartment of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, Connecticut, USA.
Chrispin ChaguzaDepartment of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, Connecticut, USA.
Anne L WyllieDepartment of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, Connecticut, USA.
Matthew BrandtDepartment of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, Connecticut, USA.
Daniel M WeinbergerDepartment of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, Connecticut, USA.
Benjamin SobkowiakDepartment of Infection, Immunity, and Inflammation, Institute of Child Health, University College Longon, London, England.ORCID 0000-0002-1382-1137
Ted CohenDepartment of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, Connecticut, USA.
Louis GrandjeanDepartment of Infection, Immunity, and Inflammation, Institute of Child Health, University College Longon, London, England.
Nathan D GrubaughDepartment of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, Connecticut, USA.
Seth N RedmondDepartment of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, Connecticut, USA.

Funding

Using the Mycobacterium tuberculosis Genome to Predict Tuberculosis Pathology, Drug Resistance Acquisition and Identify Community Transmission SitesR01AI146338 · NIAID · JOHNS HOPKINS UNIVERSITY · PI GILMAN, ROBERT H · 2020 to 2024
$3.3M
NCEZID CDC HHS NU50CK000629NIAID NIH HHS R01 AI146338Wellcome Trust
6 · The paper itself

Abstract

Pathogen sequencing is an important tool for disease surveillance and demonstrated its high value during the COVID-19 pandemic. Viral sequencing during the pandemic allowed us to track disease spread, quickly identify new variants, and guide the development of vaccines. Tiled amplicon sequencing, in which a panel of primers is used for multiplex amplification of fragments across an entire genome, was the cornerstone of SARS-CoV-2 sequencing. The speed, reliability, and cost-effectiveness of this method led to its implementation in academic and public health laboratories across the world and adaptation to a broad range of viral pathogens. However, similar methods are not available for larger bacterial genomes, for which whole-genome sequencing typically requires

Identifiers

PMID39763738
PMCPMC11702625

What OpenQuestion holds

Textmetadata
LicenceCC BY-NC-ND
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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.