Uli Klümper
@ulikluemper.bsky.social
Microbial Ecologist @ TU Dresden
Focusing on Evolution, Ecology and Environmental dimensions of AMR & plasmids
Formerly @ DTU & UoExeter
He/him
Focusing on Evolution, Ecology and Environmental dimensions of AMR & plasmids
Formerly @ DTU & UoExeter
He/him
Reposted by Uli Klümper
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!!!!!
🧬 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
"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
Cefiderocol resistance genes identified in environmental samples using functional metagenomics
Abstract. Antibiotic resistance poses a global public health threat, which can originate from the transfer of environmental antibiotic resistance genes to
academic.oup.com
January 30, 2026 at 9:17 PM
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
SEARCHER – Surveillance for Emerging Antimicrobial Resistance through Characterization of the uncharted Environmental Resistome
antimicrobialresistance.eu
January 30, 2026 at 1:26 PM
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
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
January 30, 2026 at 1:26 PM
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
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
4/5
January 30, 2026 at 1:26 PM
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
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
3/5
January 30, 2026 at 1:26 PM
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
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
2/5
January 30, 2026 at 1:26 PM
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
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
"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
Cefiderocol resistance genes identified in environmental samples using functional metagenomics
Abstract. Antibiotic resistance poses a global public health threat, which can originate from the transfer of environmental antibiotic resistance genes to
academic.oup.com
January 30, 2026 at 1:26 PM
🧬 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
"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
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
Client Challenge
doi.org
January 12, 2026 at 9:32 AM
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
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
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
Combined exposure of enrofloxacin and disinfection byproducts under environmentally relevant concentrations enhances antibiotic resistance risks in livestock wastewater
Livestock wastewater is a crucial source of antibiotic resistance. However, the impact of disinfection byproducts (DBPs), stemming from disinfectants …
www.sciencedirect.com
December 16, 2025 at 4:04 PM
👥 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
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
2/3
December 16, 2025 at 4:04 PM
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
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
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
Combined exposure of enrofloxacin and disinfection byproducts under environmentally relevant concentrations enhances antibiotic resistance risks in livestock wastewater
Livestock wastewater is a crucial source of antibiotic resistance. However, the impact of disinfection byproducts (DBPs), stemming from disinfectants …
www.sciencedirect.com
December 16, 2025 at 4:04 PM
💊 🌊 🐷 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
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.
The study provides one of the most comprehensive comparisons between acquired ARGs and latent ones identified through functional metagenomics.
November 23, 2025 at 11:18 AM
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.
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
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
Geographics and bacterial networks differently shape the acquired and latent global sewage resistomes - Nature Communications
Antimicrobial resistance genes that have been mobilized between bacterial species represent a subset of the naturally occurring resistome. Here, the authors compare the abundance, diversity and geogra...
doi.org
November 23, 2025 at 11:18 AM
📢 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
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.
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.
October 19, 2025 at 2:47 AM
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...
CFD and OCT-Based Optimisation of Impeller-Induced Shear Stress on Membrane Surfaces in a Circular Test Cell
www.sciencedirect.com/science/arti...
CFD and OCT-Based Optimisation of Impeller-Induced Shear Stress on Membrane Surfaces in a Circular Test Cell
This study investigates the distribution of shear stress in a lab-scale membrane bioreactor consisting of a 56 mm-diameter cylindrical test cell, a 0.…
www.sciencedirect.com
September 29, 2025 at 12:49 PM
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...
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
3/3
September 21, 2025 at 12:49 PM
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
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
2/3
September 21, 2025 at 12:49 PM
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
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
“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
ONE-Bridge project | Conference | Workshops
Fostering collaboration and addressing the interconnected challenges at the interface of human, animal, and environmental health.
one-bridge.iwaterfood.gr
September 21, 2025 at 12:49 PM
🚨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
“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...
Check the full study led by Jin Huang (Central South University) & Bing Li (Tsinghua Uni Shenzhen Graduate School) here:
www.nature.com/articles/s44...
Microbial risks triggered by oral administration of antibiotics in fish aquaculture persist long after the legally mandated antibiotic withdrawal time - Nature Water
Florfenicol treatment substantially increased the abundance and mobility of antibiotic resistance genes (ARGs) in the common carp gut microbiome. The resistome and mobilome profiles failed to return t...
www.nature.com
September 21, 2025 at 11:11 AM
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...
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
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
September 21, 2025 at 11:11 AM
🚨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
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
6/8
September 21, 2025 at 11:11 AM
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
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
5/8
September 21, 2025 at 11:11 AM
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
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
4/8
September 21, 2025 at 11:11 AM
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
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
3/8
September 21, 2025 at 11:11 AM
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
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
2/8
September 21, 2025 at 11:11 AM
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
2/8