Doxy-PEP trial gut resistome in MSM/trans women, San Francisco
127 rectal swab metagenomic samples from men who have sex with men and transgender women in San Francisco, USA, comparing doxycycline post-exposure prophylaxis to standard of care in a randomized clinical trial of gut antimicrobial resistance genes. machine-written summary
127 samples · 127 runs · US · Adult · 2025 · 0.76 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 762 sample values (collection date, country, latitude, location locality, location region, longitude) |
| ○ Abstract / description | read; no usable statement |
| ✓ Full text | 254 sample values (location site, sex) · PMC11750720 |
| ○ Supplementary tables | files read; no table could be matched to the samples |
| – 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 other_infection · Doxycycline 200mg post-exposure prophylaxis vs standard of care
“randomized clinical trial comparing doxy-PEP use” — abstract:39363100 (study level; per-sample arms are in the intervention column below)
longitudinal — not resolved
Schedule stated by the source: “Rectal swabs self-collected at enrollment (day-0) and at a 6-month visit (month-6)” (time origin: enrolment); stated follow-up 6 mo.
Genera, mean relative abundance over 120 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 | 127 | 100% | ||||
| country | 127 | 100% | 127 | |||
| health_condition | 0 | 0% | ||||
| subject_id | 0 | 0% | ||||
| collection_date | 127 | 100% | 127 | |||
| detailed_location | 127 | 100% | ||||
| latitude | 127 | 100% | 127 | |||
| location_locality | 127 | 100% | 127 | |||
| location_region | 127 | 100% | 127 | |||
| location_site | 127 | 100% | 127 | |||
| longitude | 127 | 100% | 127 | |||
| sex | 127 | 100% | 127 |
- Impact of doxycycline post-exposure prophylaxis for sexually transmitted infections on the gut microbiome and antimicrobial resistome. 2025 PMID 39363100 PMC11750720 own_data
Archive description
Doxycycline post-exposure prophylaxis (doxy-PEP) reduces bacterial sexually transmitted infections (STIs) among men who have sex with men and transgender women. While poised for widespread clinical implementation, the impact of doxy-PEP on antimicrobial resistance remains a primary concern as its effects on the gut microbiome and resistome, or the antimicrobial resistance genes (ARGs) present in the gut microbiome, are unknown. To investigate these effects, we studied participants from a randomized clinical trial who either received doxy-PEP as a one-time doxycycline 200 mg taken after condomless sex (DP arm, n = 100) or standard of care treatment (SOC arm, n = 50). From self-collected rectal swabs at enrollment (day-0) and after 6 months (month-6), we performed metagenomic DNA sequencing (DNA-seq) or metatranscriptomic RNA sequencing (RNA-seq). DNA-seq data was analyzable from 127 samples derived from 89 participants, and RNA-seq data from 86 samples derived from 70 participants. We compared the bacterial microbiome and resistome between the two study arms and over time.
How this project entered the registry
Classified as human gut / stool mixed assays of adult by sonnet_x2 with confidence 0.70. Assay mixed.
- host run.host_tax_id · “9606”
- body site study.description · “self-collected rectal swabs”
- life stage study.description · “men who have sex with men”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMN48325089 | collection_date | 2020-03-01 | R1 | 0.90 | biosample.attribute:collection_date | 2020-03-01 |
| SAMN48325089 | country | US | R1 | 0.90 | sample.attr.geo_loc_name | USA: San Francisco |
| SAMN48325089 | latitude | 37.7700 | R1 | 0.90 | biosample.attribute:lat_lon | 37.77 N 122.42 W |
| SAMN48325089 | location_locality | San Francisco | R1 | 0.85 | biosample.attribute:geo_loc_name | USA: San Francisco |
| SAMN48325089 | location_region | California | R1 | 0.60 | biosample.attribute:lat_lon | 37.77 N 122.42 W |
| SAMN48325089 | location_site | two HIV clinics and two sexual health clinics | R3 | 0.70 | paper.fulltext.methods | conducted at two HIV clinics and two sexual health clinics |
| SAMN48325089 | longitude | -122.4200 | R1 | 0.90 | biosample.attribute:lat_lon | 37.77 N 122.42 W |
| SAMN48325089 | sex | male | R3 | 0.70 | paper.fulltext.methods | had male sex assigned at birth |
Sequencing
127 runs over 127 samples · mean 0.83 Gbp per run (median 0.76 Gbp, total 105.31 Gbp; 127 runs with a base count) · layout PAIRED 127 · platform ILLUMINA 127 · models Illumina NovaSeq 6000 (127) · 94% of runs with a Sandpiper profile · first public 2025-05-08 – 2025-05-11
Authors (15)
Chu VT first · Glascock A · Donnell D · Grabow C · Brown CE · Ward R · Love C · Kalantar KL · Cohen SE · Cannon C · Woodworth MH · Kelley CF · Celum C · Luetkemeyer AF · Langelier CR last
Help complete this project
2 of the 4 core fields are below 50% coverage: health_condition, subject_id. Share metadata
Downloads
PRJNA1099775.csv.gz (3.8 KB) · parquet (75.2 KB) — all 127 samples, every field with route and confidence · PRJNA1099775_determinations.csv.gz (6.1 KB) — 1,016 evidence rows