Gut metagenomes in premature infants with BSIs, Singapore
Gut microbiome and bloodstream infections among premature infants in Singapore
Longitudinal cohort study of 606 gut metagenome samples from premature infants (neonates and infants) in Singapore, investigating the gut as a source of bloodstream infection organisms using shotgun metagenomic sequencing and blood isolate whole-genome sequencing. machine-written summary
Sequencing depth per sample · this project all projects
Sampling design and relatedness
longitudinal
75 of 76 people sampled more than once (605 samples; median 8, up to 12 per person) · follow-up median 53 d (max 2 mo) · median interval between samples 7 d(time from age at collection).
Schedule stated by the source: “Weekly stool samples from birth through 65 days of age in premature infants in a NICU” (time origin: birth); stated follow-up 2 mo.
Each row is one person (36 shown of 75); dots are samples at days since that person's first sample.
Bifidobacterium 34.3%Klebsiella 20.6%Escherichia 13.7%Clostridium 5.4%Enterococcus 5.0%Staphylococcus 4.3%Enterobacter 3.5%Streptococcus 1.1%Veillonella 1.0%Serratia 0.9%Cutibacterium 0.9%Enterococcus_A 0.7%not assigned to a genus 2.5%other genera 6.0%
Genera, mean relative abundance over 474 profiled gut samples of this project (Sandpiper SingleM profiles, GTDB R232; low-depth and non-metagenome profiles left out).
Strain-resolved metagenomic analysis of the gut as a reservoir for bloodstream infection pathogens among premature infants in Singapore. PMID 37974294PMC10652614curated
Strain-resolved metagenomic analysis of the gut as a reservoir for bloodstream infection pathogens among premature infants in Singapore. 2023PMID 37974294PMC10652614own_data
Details
Archive description
This study explored the role of the gut as a source of organisms causing bloodstream infection among premature infants in Singapore. Shotgun metagenomic sequencing was used to characterize the gut metagenomes of infants. Whole-genome sequencing was performed to assemble genomes of blood culture isolates.
How this project entered the registry
Classified as human gut / stool / blood / tissue / internal fluids shotgun DNA metagenome of infant / toddler and neonate by deterministic_prior with confidence 0.90. Assay shotgun_dna.
body sitestudy.title · “Gut microbiome and bloodstream”
body sitestudy.description · “role of the gut as a source”
body sitestudy.description · “assemble genomes of blood culture isolates.”
life stageexternal_curation.infant_catalog · “infant triage verdict include (0-3 y scope)”
life stagestudy.title · “infections among premature infants in Singapore”
life stagestudy.title · “bloodstream infections among premature infants in Singapore”
life stagestudy.description · “bloodstream infection among premature infants in Singapore.”
Evidence examples (one per field × route)
sample
field
value
route
conf.
source
quote
SAMN33952825
age_at_collection_days
14
R1
0.90
biosample_attr
14
SAMN33952825
collection_date
2019-06/2021-05
R3
0.70
paper.fulltext.methods
between June 2019 and May 2021
SAMN33952825
country
SG
R1
0.90
biosample_attr
Singapore
SAMN33952825
location_site
KK Women's and Children's Hospital (KKH) NICU
R3
0.70
paper.fulltext.methods
admitted to the KKH NICU between June 2019 and May 2021
SAMN33952825
preterm_status
preterm
R4
0.50
study.description
premature infants in Singapore
SAMN33952825
subject_id
AD8134
R1
0.85
biosample_attr
AD8134
SAMN33952825
timepoint_label
14
R1
0.85
biosample.attribute:day_of_life
14
Sequencing
622 runs over 606 samples · mean 6.09 Gbp per run (median 2.31 Gbp, total 3,786.54 Gbp; 622 runs with a base count) · layout PAIRED 622 · platform ILLUMINA 622 · models Illumina NovaSeq 6000 (622) · 79% of runs with a Sandpiper profile · first public 2023-07-01 – 2023-07-30