Geographic spillover of antimicrobial resistance from mass distribution of azithromycin
630 rectal swab samples from children in 30 monitoring villages in Niger, examining geographic spillover of antimicrobial (macrolide) resistance after azithromycin mass drug administration, using an intervention (azithromycin vs placebo) design. machine-written summary
Antibiotic given as the study intervention (incl. eradication therapydesignrandomized_controlled_trial · populationhealthy_control · Mass drug administration of azithromycin vs placebo, twice-annual, children 1-59 months
“mass distribution of azithromycin” — study.title (study level; per-sample arms are in the intervention column below)
Samples at a glance
1 sampling locations · 1 country
Age
child630
Country
NE630
Body site
primary630
Sequencing depth per sample · this project all projects
Sampling design and relatedness
community
630 rectal swabs of children from 30 monitoring villages (whg_code), 15 azithromycin / 15 placebo villages; village-level AMR spillover30 shared settings.
member · circles are people (pale = no sequenced sample), arrows run donor → recipient and parent → child, curved lines join twins, partners and siblings, squares are shared settings or families without recorded roles. Shown: 8 of 30 shared settings.
Prevotella 29.2%Bacteroides 3.8%Bifidobacterium 3.7%Faecalibacterium 3.1%Fenollaria 2.7%Escherichia 2.5%Porphyromonas_A 2.2%Roseburia 2.2%Alloprevotella 2.1%Brachyspira 2.0%Campylobacter_D 1.9%Porphyromonas 1.8%not assigned to a genus 17.8%other genera 25.1%
Genera, mean relative abundance over 604 profiled gut samples of this project (Sandpiper SingleM profiles, GTDB R232; low-depth and non-metagenome profiles left out).
Geographic spillover of antimicrobial resistance from mass distribution of azithromycin. 2026PMID 41611691PMC12957345own_data
Details
Archive description
The study assessed between-village geographic spillover effects of genotypic resistance to macrolides and other antibiotic classes in rectal swabs collected from 1200 children in 30 monitoring villages in Niger after two years of MDA. Sequencing reads represent the gut microbiome containing multiple species, comparing Azithromycin and Placebo treated children. Human, other Chordata, plant, and arthropod reads removed.
How this project entered the registry
Classified as human gut / stool shotgun DNA metagenome of child by sonnet_x2 with confidence 0.85. Assay shotgun_dna.
hoststudy.description · “rectal swabs collected from 1200 children”
body sitestudy.description · “rectal swabs collected from 1200 children”
body sitestudy.description · “reads represent the gut microbiome”
life stagestudy.description · “rectal swabs collected from 1200 children”
Evidence examples (one per field × route)
sample
field
value
route
conf.
source
quote
SAMN53069759
collection_date
2015/2017
R1
0.90
biosample.attribute:collection_date
2015/2017
SAMN53069759
country
NE
R1
0.90
sample.attr.geo_loc_name
Niger
SAMN53069760
intervention
no_intervention
R1
0.80
biosample.attribute:Phase.Id.MEP
Phase.Id.MEP: 0
SAMN53069760
intervention_detail
baseline, before mass drug administration
R1
0.80
biosample.attribute:Phase.Id.MEP
Phase.Id.MEP: 0
SAMN53069759
latitude
13.5127
R1
0.90
biosample.attribute:lat_lon
13.5127 N 1.52812 E
SAMN53069759
location_region
Dosso Region
R3
0.70
paper.fulltext.methods
conducted in Niger's Dosso region
SAMN53069759
longitude
1.5281
R1
0.90
biosample.attribute:lat_lon
13.5127 N 1.52812 E
SAMN53069759
shared_setting_id
village 5
R1
0.60
biosample.attribute:whg_code
whg_code=5
SAMN53069759
shared_setting_type
village_or_community
R1
0.60
biosample.attribute:whg_code
whg_code=5
SAMN53069759
timepoint_label
24
R1
0.85
biosample.attribute:phase_id_mep
24
Sequencing
630 runs over 630 samples · mean 0.84 Gbp per run (median 0.56 Gbp, total 526.09 Gbp; 630 runs with a base count) · layout PAIRED 630 · platform ILLUMINA 630 · models Illumina HiSeq 4000 (630) · 96% of runs with a Sandpiper profile · first public 2026-01-13 – 2026-01-20