• ARGs were increasingly associated with mobilizable plasmids, integrons, and composite transposons, indicating elevated HGT potential.
• Microbial community restructuring under antibiotic stress was marked by Enterococcus dominance and resistome host shifts.
Key findings:
• Sulfonamide exposure selectively enriched sulfonamide resistance genes without broad co-selection of other ARG classes.
• Distinct temporal dynamics: short-term stress amplified sul2/sul3, whereas long-term exposure favored sul1.
🐷 💊 Happy to share our latest paper in Journal of Hazardous Materials 🐷 💊
“Impact of sulfonamides on microbial community and antibiotic resistome profiles in anaerobic digestion of swine wastewater.”
doi.org/10.1016/j.jh...
led by Qinmao 'Brook' Zhou and Bing Li
#AMR #microsky
📄 New paper out in Water Research:
Impact of human activities on groundwater biogeochemical cycles and microbial communities: Insights from metagenomic analysis
Led by @pennyhan.bsky.social & Zhengxing Chen
🔗 doi.org/10.1016/j.wa...
Before leaving Dresden to increase my knowledge and independence as a researcher, I participated in a large-scale sampling campaign for the EMBARK project... some years later, this new and amazing study (which included these samples as well) came out!!!!!
Part of the JPIAMR SEARCHER project (antimicrobialresistance.eu) funded in Germany by the @BMFTR_bund
Why this matters:
Environmental resistomes are not just background noise. They contain functionally active genes with future clinical relevance. This work shows why functional discovery approaches are essential if AMR surveillance is to be proactive rather than reactive.
5/5
A personal highlight🍻: 3 of the newly identified resistance genes originated from a sampling campaign by Ioannis Kampouris and myself in Dresden, a nice reminder that my rare hands-on field sampling at human–environment interfaces can directly inform global #AMR risk assessment.
4/5
One gene (blaVEB-3) is mobile and already widespread in wastewater across multiple countries & several genes have closest homologs in known pathogens, highlighting realistic pathways by which environmental ARGs could mobilize into clinical bacteria in the future
3/5
Using functional metagenomics on environmental samples, we identified 4 yet unrecognized ARGs increasing cefiderocol MICs to clinically relevant levels. These include novel class A & D beta-lactamases (VEB-3, OXA-372-like, YbxI-like) & a truncated penicillin-binding protein
2/5
🧬 Our new paper in @ISMEJournal
"Cefiderocol resistance genes identified in environmental samples using functional metagenomics"
Led by Remi Gschwind and Etienne Ruppe as part of JPIAMR SEARCHER.
academic.oup.com/ismej/advanc...
#AMR #microsky
1/5
New paper accepted in Microbiome 🎉
Weiss A, Elena AX, Klümper U, Dumack K
We show that viruses and microeukaryotes strongly shape bacterial and ARG diversity in wastewater, highlighting the role of multi-trophic ecology.
doi.org/10.1186/s401...
#AMR #Microbiome #Wastewater #MicrobialEcology
👥 expertedly led by Jin Huang & Bing Li (Tsinghua University)
with Jingjia Zhang, @ulikluemper.bsky.social, @jianhuaguo.bsky.social, Thomas Berendonk, Ryo Honda, Hebin Liang, Lin Lin, & Xiaoyan Li
www.sciencedirect.com/science/arti...
3/3
In this study, we show that environmentally relevant co-exposure to antibiotics and disinfection byproducts can substantially enhance antibiotic resistance risks at the microbial community level, with important implications for livestock wastewater management and #OneHealth risk assessment.
2/3
💊 🌊 🐷 Our new paper in Water Research💊 🌊 🐷
Combined exposure of enrofloxacin and disinfection byproducts under environmentally relevant concentrations enhances antibiotic resistance risks in livestock wastewater
www.sciencedirect.com/science/arti...
1/3
#AMR #microsky
I’m grateful that our group could contribute German wastewater samples to this truly collaborative dataset of 1240 sewage metagenomes from 111 countries.
The study provides one of the most comprehensive comparisons between acquired ARGs and latent ones identified through functional metagenomics.
📢 New paper in @natcomms.nature.com
Geographics and bacterial networks differently shape the acquired and latent global sewage resistomes
doi.org/10.1038/s414...
Thrilled to share this massive global effort led by H.M. Martiny, @patrickmunk.bsky.social, F. Aarestrup & the Global Sewage Consortium
Having a great time at the 6th Meeting of Bergey’s Society for Microbial Systematics #BISMiS in Qingdao, China.
Thanks to the organizers for inviting me to give a talk on how we can infer pathogenicity and #AMR in environmental microbial communities based on their taxonomic makeup.
Our first manuscript from the TARGIM project led by Masoud Haghshenasfard:
CFD and OCT-Based Optimisation of Impeller-Induced Shear Stress on Membrane Surfaces in a Circular Test Cell
www.sciencedirect.com/science/arti...
In-person participation for the workshop (free of charge) is limited to 40 places and will be allocated on a first-come, first-served basis. To register, send an email to uli.kluemper@tu-dresden.de indicating your interest in attending.
3/3
As part of our new EU Project “One Bridge”, led by the University of Patras, we are organizing an 'AMR & #OneHealth Workshop in Dresden, Germany on the 6th of October 2025. The workshop will take place at BUSINESSPARK DRESDEN, Bertolt-Brecht-Allee 22-24, 01309 Dresden from 8:30 – 17:00.
2/3
🚨WORKSHOP announcement 🚨
“Making environmental #AMR Surveillance Fit for Purpose: Data Integration and the Ecology of Resistance”
6th of October
Dresden, Germany
Free of charge
one-bridge.iwaterfood.gr/workshops/wo...
Register now!
Details below:
1/3
Our findings urge a #OneHealth rethink of antibiotic use in aquaculture.
Check the full study led by Jin Huang (Central South University) & Bing Li (Tsinghua Uni Shenzhen Graduate School) here:
www.nature.com/articles/s44...
🚨Key message🚨
Regulations based solely on chemical residues overlook microbial risks. Withdrawal times must also consider ARG abundance, mobility, and pathogen enrichment to protect food safety & the environment.
7/8
Nearly half of the enriched potential pathogens (e.g., Aeromonas, Vibrio, Citrobacter) carried ARGs identical to those on plasmids, showing strong plasmid–chromosome links for resistance spread.
6/8
Resistance genes weren’t just more abundant, they were also more mobile! Integrons, transposons (carrying floR), and diverse plasmids persisted after withdrawal, keeping ARGs ready for transfer.
5/8
ARG abundance spiked up to 17× during treatment. It dropped after stopping antibiotics but stayed significantly above control levels even long past the 15-day withdrawal time required for residue compliance.
4/8
We simulated standard (5 & 10 days) and prolonged (30 & 90 days) florfenicol treatments in common carp and tracked gut microbiota, ARGs, and mobile genetic elements (MGEs) before, during, and after treatment.
3/8
We reveal that antibiotic resistance #AMR risks in fish farming don’t stop after the legal withdrawal time. Our study shows that oral florfenicol in carp leaves a lasting “resistome” footprint even after fish are deemed market-ready.
2/8
🐟💊🦠Our new study in @natwater.nature.com 🐟💊🦠
"Microbial risks triggered by oral administration of antibiotics in fish aquaculture persist long after the legally mandated antibiotic withdrawal time"
www.nature.com/articles/s44...
#microsky #amr
1/8
