Azithromycin MDA and gut resistome in Malawi children
181 faecal samples from children in a Malawi trachoma MDA site, studying azithromycin's effect on gut macrolide resistance and microbiome composition, in a randomized controlled trial (azithromycin vs placebo). machine-written summary
181 samples · 181 runs · ZA, MW · Infant / toddler · 2021 · 2.65 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ○ Sequence archive | records read; no usable sample values |
| ✓ Abstract / description | 185 sample values (country, location site) |
| ○ Full text | read; no usable statement or table · PMC10269646, PMC12769767 |
| ✓ Supplementary tables | 708 sample values (country, feeding mode, subject id, timepoint) |
| – External resources | not covered by the external resources we ingest |
| – User contribution | nothing uploaded yet · share metadata |
| – Human verified | not yet checked by a person · I checked this project — verify it |
intervention — arms not resolved
Antibiotic given as the study intervention (incl. eradication therapy design randomized_controlled_trial · population healthy_control · Azithromycin mass drug administration vs placebo in children, 4 rounds
“half receiving azithromycin and half placebo” — bioproject.description (study level; per-sample arms are in the intervention column below)
longitudinal — not resolvedcommunity — not resolved
4 of 173 people sampled more than once (8 samples; median 2, up to 2 per person).
Children from 30 MORDOR Malawi communities (40 per community per visit); no per-sample community id in archive.
Genera, mean relative abundance over 160 profiled gut samples of this project (Sandpiper SingleM profiles, GTDB R232; low-depth and non-metagenome profiles left out).
| field | samples | coverage | R1 | R2 | R3 | R4 |
|---|---|---|---|---|---|---|
| age_category | 0 | 0% | ||||
| country | 181 | 100% | 177 | 4 | ||
| health_condition | 0 | 0% | ||||
| subject_id | 177 | 98% | 177 | |||
| detailed_location | 181 | 100% | ||||
| location_site | 181 | 100% | 181 | |||
| feeding_mode | 177 | 98% | 177 | |||
| timepoint_label | 177 | 98% | 177 |
- Exploring Molecular Interactions between Human Milk Hormone Insulin and Bifidobacteria. PMID 37191543 PMC10269646 curated
- Compiling an early life human gut microbiome atlas and identification of key microbial drivers. PMID 41350579 PMC12769767 curated
Archive description
Mass drug administration (MDA) with azithromycin is the primary strategy for global trachoma control efforts. Numerous studies have reported secondary effects of MDA with azithromycin, including reductions in childhood mortality, diarrhoeal disease and malaria. Most recently, the MORDOR clinical trial demonstrated that treatment led to an overall reduction in all-cause childhood mortality in targeted communities. There is however considerable concern about the potential of increased antimicrobial resistance in treated communities.This study evaluated the impact of azithromycin MDA on prevalence of gastrointestinal carriage of macrolide-resistant bacteria in communities within the MORDOR Malawi study site, while additionally profiling changes in the gut microbiome after treatment. For faecal metagenomics, 60 children were sampled prior to treatment and 122 children after four rounds of MDA, half receiving azithromycin and half placebo.The proportion of bacteria carrying macrolide resistance increased after azithromycin treatment the effect was enhanced in children treated within six months of sampling. Diversity and global community structure of the gut was minimally impacted by treatment, however abundance of several individual species was altered by treatment. Notably, the putative human enteropathogen Escherichia albertii was more abundant after treatment.The impacts of MDA with azithromycin, including increased carriage of macrolide resistant bacteria, were enhanced in children treated more recently, suggesting effects may be transient. Increased abundance of enteropathogenic Escherichia species after treatment requires further, higher resolution investigation. Future studies should focus on the number of treatments and administration schedule to ensure clinical benefits continue to outweigh costs in antimicrobial resistance carriage.
How this project entered the registry
Classified as human gut / stool shotgun DNA metagenome of infant / toddler and child by deterministic_prior with confidence 0.90. Assay shotgun_dna.
- host external_curation.infant_catalog · “infant triage verdict include”
- body site study.title · “the antibiotic resistant gut microbiome: a randomized,”
- body site study.description · “on prevalence of gastrointestinal carriage of macrolide-resistant”
- life stage external_curation.infant_catalog · “infant triage verdict include (0-3 y scope)”
- life stage study.description · “including reductions in childhood mortality, diarrhoeal disease”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMEA7766609 | country | ZA | R2 | 0.75 | paper.supp.table | Geography=Africa |
| SAMEA7766647 | country | MW | R4 | 0.45 | study.description | MORDOR Malawi study site |
| SAMEA7766609 | feeding_mode | exclusive_breast | R2 | 0.75 | paper.supp.table | Feeding type=Breast Milk |
| SAMEA7766609 | location_site | MORDOR Malawi study site | R4 | 0.45 | ena.study_description | communities within the MORDOR Malawi study site |
| SAMEA7766609 | subject_id | FE498542-8F63-40D6-8B7B-FDEC33678F3F | R2 | 0.85 | paper.supp.13099_2021_478_MOESM1_ESM.xlsx[species!ParticipantID] | SampleID 147529; ParticipantID FE498542-8F63-40D6-8B7B-FDEC33678F3F |
| SAMEA7766609 | timepoint_label | pre-weaning | R2 | 0.75 | paper.supp.table | Time Group=pre-weaning |
Sequencing
181 runs over 181 samples · mean 2.76 Gbp per run (median 2.65 Gbp, total 499.41 Gbp; 181 runs with a base count) · layout PAIRED 181 · platform ILLUMINA 181 · models NextSeq 500 (181) · 88% of runs with a Sandpiper profile · first public 2021-04-01
Authors (18)
Rizzo SM first · Alessandri G · Lugli GA · Fontana F · Tarracchini C · Mancabelli L · Viappiani A · Bianchi MG · Bussolati O · van Sinderen D · Ventura M · Turroni F last · Longhi G · Gennaioli E · Muscò A · Vitale SG · Angioni S · Milani C
Help complete this project
2 of the 4 core fields are below 50% coverage: age_category, health_condition. Share metadata
Downloads
PRJEB42363.csv.gz (10.1 KB) · parquet (89.2 KB) — all 181 samples, every field with route and confidence · PRJEB42363_determinations.csv.gz (12.2 KB) — 893 evidence rows