Evidence map›Paper›PMID 41994130›Full record

ArticleResearch square2026

Shotgun metagenomic profiling of bacterial microbiomes, metagenome-assembled genomes and antimicrobial resistance in respiratory and blood samples from Gambian children with pneumonia.

Dam Khan, Josh L Espinoza, Peggy-Estelle Tientcheu, Isaac Darko Otchere, Nuredin Ibrahim Mohammed, Archibald Worwui, Mark P Nicol, Brenda Kwambana-Adams, Martin Antonio, Chris L Dupont

Abstract readPreprint
PubMed Full text at PMC Publisher
In one paragraph

Article in Research square, 2026. 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

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

10 authors.

Dam KhanMedical Research Council Unit The Gambia at the London School of Hygiene & Tropical Medicine.
Josh L EspinozaJ. Craig Venter Institute.
Peggy-Estelle TientcheuMedical Research Council Unit The Gambia at the London School of Hygiene & Tropical Medicine.
Isaac Darko OtchereNoguchi Memorial Institute for Medical Research.
Nuredin Ibrahim MohammedMedical Research Council Unit The Gambia at the London School of Hygiene & Tropical Medicine.
Archibald WorwuiMedical Research Council Unit The Gambia at the London School of Hygiene & Tropical Medicine.
Mark P NicolUniversity of Western Australia.
Brenda Kwambana-AdamsLiverpool School of Tropical Medicine.
Martin AntonioMedical Research Council Unit The Gambia at the London School of Hygiene & Tropical Medicine.
Chris L DupontJ. Craig Venter Institute.

Funding

Identifying Influenza Virus Infection Severity and Outcome Signatures Through Artificial Intelligence-driven AnalysesR01AI170111 · NIAID · J. CRAIG VENTER INSTITUTE, INC. · PI Christopher L. Dupont · 2022 to 2026
$3.0M
The nasopharyngeal microbiota of African children and lower respiratory tract infectionU54HG009824 · NHGRI · UNIVERSITY OF CAPE TOWN · PI NICOL, MARK PATRICK, ZAR, HEATHER JOY · 2017 to 2021
$2.9M
NHGRI NIH HHS U54 HG009824NIAID NIH HHS R01 AI170111
6 · The paper itself

Abstract

Pneumonia is a leading cause of morbidity and mortality in children, with bacterial pathogens being important etiologic agents. Most microbiome studies in pneumonia use technologies with limited taxonomical resolution and few include lung aspirate or blood samples. In this study, we assessed the microbial communities of the nasopharynx, nasopharynx/oropharynx, induced sputum, lung aspirate and blood, and recovered metagenome-assembled genomes from the same sites using shotgun metagenomics sequencing of samples from children with severe and very severe pneumonia in The Gambia. Our data show that Proteobacteria and Firmicutes were the most common phyla across the body sites, and this was largely driven by

Indexed as

antimicrobial resistanceHaemophilus strainsmetagenome-assembled genomesmicrobiomeStreptococcus pneumoniae

Identifiers

PMID41994130
PMCPMC13082154

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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.