Prepared by Faina Tskhay ( and Uli Klümper (

The summer 2023 AMR Digest features antibiotic resistance in the aquatic environment, global trends in AMR, the evolution of resistance, new bioinformatics tools, novel approaches to addressing antibiotic resistance, and more, including a number of new publications from the EMBARK consortium. 


Our monthly EMBARK Webinar on AMR survillance in aquatic environments and animals 

with Prof. Jonas Bonnedahl & Prof. Rabaab Zahra, moderated by Víctor Hugo Jarquín-Díaz

September 13th, 14:00 CEST – Register here


Toward a Universal Unit for Quantification of Antibiotic Resistance Genes in Environmental Samples – Xiaole Yin, Xi Chen, Xiao-Tao Jiang, Ying Yang, Bing Li, Marcus Ho-Hin Shum, Tommy T. Y. Lam, Gabriel M. Leung, Joan Rose, Concepcion Sanchez-Cid, Timothy M. Vogel, Fiona Walsh, Thomas U. Berendonk,Janet Midega, Chibuzor Uchea, Dominic Frigon, Gerard D. Wright, Carlos Bezuidenhout, Renata C. Picão, Shaikh Z. Ahammad, Per Halkjær Nielsen, Philip Hugenholtz, Nicholas J. Ashbolt, Gianluca Corno, Despo Fatta-Kassinos, Helmut Bürgmann, Heike Schmitt, Chang-Jun Cha, Amy Pruden, Kornelia Smalla, Eddie Cytryn, Yu Zhang, Min Yang, Yong-Guan Zhu, Arnaud Dechesne, Barth F. Smets, David W. Graham, Michael R. Gillings, William H. Gaze, Célia M. Manaia, Mark C. M. van Loosdrecht, Pedro J. J. Alvarez, Martin J. Blaser, James M. Tiedje, Edward Topp, and Tong Zhang – Environmental Science & Technology Article

*Comparison and standardization of numerous studies on ARGs dissimination are hampered by the lack of a universal unit for ARG quantification. Considering the advantages and disadvantages of the various methods currently used to normalize ARGs quantities, the authors propose “ARG copy per cell” as the most comprehensive universal unit for ARGs quantification.

Towards Monitoring of Antimicrobial Resistance in the Environment: For what Reasons, How to Implement It, and What Are the Data Needs?Johan Bengtsson-Palme, Anna Abramova, Thomas U. Berendonk, Luis Pedro Coelho, Sofia K. Forslund, Rémi Gschwind, Annamari Heikinheimo, Víctor Hugo Jarquín-Díaz, Ayaz Ali Khan, Uli Klümper, Ulrike Löber, Marmar Nekoro, Adriana D. Osińska, Svetlana Ugarcina Perovic, Tarja Pitkänen, Ernst Kristian Rødland, Etienne Ruppé, Yngvild Wasteson, Astrid Louise Wester, Rabaab Zahra – Environment International

Emerging Antimicrobial Resistance – Cynthia E. Flynn and  Jeannette Guarner – Modern Pathology

Global picture

A global baseline for qPCR-determined antimicrobial resistance gene prevalence across environmentsAnna Abramova, Thomas U. Berendonk, Johan Bengstson-Palme – Environment International

Determinants of worldwide antibiotic resistance dynamics across drug-bacterium pairs: a multivariable spatialtemporal analysis using ATLAS – Eve Rahbe et al. – The Lancet Planetary Health

Antimicrobial Resistance: Addressing a Global Threat to Humanity – Timothy R. Walsh et al. – PLOS Medicine

Global knowledge gaps on antimicrobial resistance in the human health sector: a scoping review – Raph L Hamers et al. – International Journal of Infectious Diseases

Global incidence in hospital-associated infections resistant to antibiotics: An analysis of point prevalence surveys from 99 countries – Ruchita Balasubramanian et al. – PLOS Medicine

Global Self-Medication with Antibiotics Among the Public and its Associated Factors: A Mixed-Methods Systematic ReviewTenghao Wang et al. – The Lancet Preprint


Changes in the prevalence of hospital-acquired pneumonia-causing bacterial pathogens and the impact of their antimicrobial resistance patterns on clinical outcomes: A propensity score-matched study – Min Hyuk Choi et al. – Interantional Journal of Antimicrobial Agents

A three-level model for therapeutic drug monitoring of antimicrobials at the site of infection – Noé Brasier et al. – The Lancet Infectious Diseases

Quantifying the Economic and Clinical Value of Reducing Antimicrobial Resistance in Gram-negative Pathogens Causing Hospital-Acquired Infections in Australia – Jason P. Gordon et al.- Infectious Disease and Therapy


Global research agenda for antimicrobial resistance in human health – World Health Organization

*In this agenda, WHO prioritizes forty research objectives in five different themes:

  • Prevention which can be achieved through proper sanitation, water and waste management, hygiene, and immunization.
  • Diagnosis. Requirement of proper diagnosis including implementation of rapid point-of-care diagnostic tests, reduction of inappropriate antibiotic prescription and consumption.
  • Treatment and care. Need for proper antimicrobial stewardship, especially for low- and middle-income countries. Optimization of antimicrobial usage and control of prescriptions.
  • Cross-cutting. Attention to the socioeconomic aspects of AMR, including evaluation of inappropriate antibiotic consumption in healthcare and financial systems. 
  • Drug-resistant TB. Preventing the incidence of drug-resistant TB by developing effective TB vaccines, implementation of molecular methods for the detection of TB, improvement of treatment methods by determinating optimal dosage and combination regimens.

Tackling antimicrobial resistance: European Council adopts recommendation

Pharmaceutical pollution from human use and the Polluter Pays Principle – Erik Malmqvist et al. –  Public Health Ethics 


Evaluation of the One Health-Ness of 20 Years of Antimicrobial Resistance Surveillance in NorwayMadelaine Norström et al. – Antibiotics

Evolution of Resistance

Restriction-modification systems have shaped the evolution and distribution of plasmids across bacteria – Liam P Shaw et al. – Nucleic Acid Research

Reduced selection for antibiotic resistance in community context is maintained despite pressure by additional antibiotics– Peiju Fang, Alan X Elena, Maxi A Kunath, Thomas U Berendonk & Uli Klümper – ISME Communications

Differential dose-response patterns of intracellular and extracellular antibiotic resistance genes under sub-lethal antibiotic exposure – Lele Liu et al. – Ecotoxicology and Environmental Safety. 

Nothing makes sense in drug resistance except in the light of evolution –  Toni Gabaldón – Current Opinions in Microbiology

Antibiotic-degrading resistance changes bacterial community structure via species-specific responsesAyush Pathak et al.- ISME Journal

Mixed strain pathogen populations accelerate the evolution of antibiotic resistance in patients – Julio Diaz Caballero et al. – Nature Communications

Chance favors the prepared genomes: horizontal transfer shapes the emergence of antibiotic resistance mutations in core genes – Charles Coluzzi et al. – bioRxiv preprint

Removal of Resistance

Type IV-A3 CRISPR-Cas systems drive inter-plasmid conflicts by acquiring spacers in trans – Fabienne Benz et al. – bioRxiv preprint

Low-Generation Cationic Phosphorus Dendrimers: Novel Approach to Tackle Drug-Resistant S. aureus In Vitro and In Vivo  – Evgeny Apartsin et al. – Biomacromolecules

Synthetic Star Nanoengineered Antimicrobial Polymers as Antibiofilm Agents: Bacterial Membrane Disruption and Cell Aggregation – Sophie Laroque et al. – Biomacromolecules

Gene Transfer/Plasmids

Plasmids, a molecular cornerstone of antimicrobial resistance in the One Health era – Salvador Castañeda-Barba et al. – Nature Reviews Microbiology 

*Castañeda-Barba et al. compiled a comprehensive review of the role of plasmids in the global and local spread of AMR. The authors outline the effects of various factors such as degree of selection, spatial organization, temporal variation, and community context on the fate of plasmids.

Interspecific competition can drive plasmid loss from a focal species in a microbial community – David Sünderhauf, Uli Klümper, William H Gaze, Edze R Westra, Stineke van Houte – The ISME Journal

Lociq provides a loci-seeking approach for enhanced plasmid subtyping and structural characterization – Lucas Harrison et al. – Communications biology

An overview of plasmid transfer in the plant microbiome – Angela M. Sánchez-Salazar et al. – Plasmid

Characterizing conjugative plasmids from an antibiotic-resistant dataset for use as broad-host delivery vectorsHéctor G. Loyola Irizarry et al. – Frontiers in Microbiology

Evaporation-induced hydrodynamics control plasmid transfer during surface-associated microbial growth – Chujin Ruan et al. – npj Biofilms and Microbiomes


Zoonotic sources and the spread of antimicrobial resistance from the perspective of low and middle-income countries Ioana D. Olaru et al. – Infectious Diseases of poverty

Cigarette smoking promotes the spread of antimicrobial resistance in the human lung and the environment – Peiju Fang, Diala Konyali, Emily Fischer, Robin Pascal Mayer, Jin Huang, Alan Xavier Elena, Gerit Hartmut Orzechowski, Andrew Tony-Odigie, David Kneis, Alexander Dalpke, Peter Krebs, Bing Li, Thomas U. Berendonk, Uli Klümper – bioRxiv preprint

Aquatic environments/Wastewater

Trimethoprim resistance in surface and wastewater is mediated by contrasting variants of the dfrB geneDavid Kneis, Claudèle Lemay-St-Denis, Stella Cellier-Goetghebeur, Alan X. Elena, Thomas U. Berendonk, Joelle N. Pelletier & Stefanie Heß – ISME Journal

Environmental stress increases the invasion success of antimicrobial resistant bacteria in river microbial communities – Kenyum Bagra, Xavier Bellanger, Christophe Merlin, Gargi Singh, Thomas U Berendonk, Uli Klümper – Science of the Total Environment

Tradeoffs of increasing temperatures for the spread of antimicrobial resistance in river biofilms – Kenyum Bagra, David Kneis, Daniel Padfield, Edina Szekeres, Adela Teban-Man, Cristian Coman, Gargi Singh, Thomas U Berendonk, Uli Klümper – bioRxiv preprint

The knock-on effects of different wastewater feeding modes: Change in microbial communities versus resistance genes in pilot-scale aerobic sludge granulation reactors – Yi Guo et al. – Science of the Total Environment

Persistence of antibiotic resistance from animal agricultural effluents to surface water revealed by genome-centric metagenomics – Jin Ju Kim et al. – Journal of Hazardous Materials

Subsidized veterinary extension services may reduce antimicrobial resistance in aquaculture Sophie St-Hilaire et al. – Scientific Reports 

Metagenomic insights into the distribution, mobility, and hosts of extracellular antibiotic resistance genes in activated sludge under starvation stress – Shuai Zhou et al. – Water Research

Dynamics of antibiotic resistance markers and Escherichia coli invasion in riverine heterotrophic biofilms facing increasing heat and flow stagnation  – Giulia Gionchetta et al.- Science of the total environment

Antimicrobial Transformation Products in the Aquatic Environment: Global Occurrence, Ecotoxicological Risks, and Potential of Antibiotic Resistance – Paul Löffler et al. – Environmental Science & Technology Article

High-resolution characterization of short-term temporal variability in the taxonomic and resistome composition of wastewater influent – Kevin K. Chau et al. – Microbial genomics

Metagenomic survey of antimicrobial resistance (AMR) in Maryland surface waters differentiated by high and low human impact – Brandon Kocurek et al. – bioRxiv preprint

Antimicrobial resistance in southeast Asian water environments: A systematic review of current evidence and future research directions  -Yadpiroon Siri et al. – Science of the Total Environment

Persistence of Antibiotic Resistance Genes Varies with Particle Size and Substrate Conditions in Recirculating Streams – Olivia Ginn et al. – Environmental Science & Technology Article 

iDfferential effects of wastewater treatment plant effluents on the antibiotic resistomes of diverse river habitats – Jangwoo Lee et al. – The ISME Journal

Hospital and urban wastewaters shape the matrix and active resistome of environmental biofilms – Elena Bülow et al. – Water Research


Soil minerals and organic matters affect ARGs transformation by changing the morphology of plasmid and bacterial responses – Hongyu Shi et al. – Journal of Hazardous Materials


Antibiotic resistance genes in food production systems support One Health opinions – James M. Tiedje et al. – Current Opiniins in Environmental Science and Health 

Animals / Wildlife

In vitro and in vivo susceptibility to cefalexin and amoxicillin/clavulanate in canine low-level methicillin-resistant Staphylococcus pseudintermedius – Mattia Pirolo et al. – Journal of Antimicrobial Chemotherapy

Antimicrobial susceptibility among respiratory tract pathogens isolated from diseased cattle and pigs from different parts of Europe – Anno de Jong et al.- Journal of Applied Microbiology


Developing Phage Therapy That Overcomes the Evolution of Bacterial Resistance – Agnès Oromí-Bosch et al. – Annual Review of Virology


Plasmid permissiveness of wastewater microbiomes can be predicted from 16S rRNA sequences by machine learning – Moradigaravand et al. – Bioinformatics

A comparison of single-coverage and multi-coverage metagenomic binning reveals extensive hidden contamination – Jennifer Mattock and Mick Watson – Nature Methods


SemiBin2: self-supervised contrastive learning leads to better MAGs for short- and long-read sequencing – Shaojun Pan, Xing-Ming Zhao and Luis Pedro Coelho – Bioinformatics 

QurvE: user-friendly software for the analysis of biological growth and fluorescence dataNicolas T. Wirth et al. – Nature Protocols

Plassembler: an automated bacterial plasmid assembly tool – George Bouras et al.- Bioinformatics
ARGem: A New Metagenomics Pipeline for Antibiotic Resistance Genes: Metadata, Analysis, and Visualization – Xiao Liang et al. – Frontiers in Genetics