Prepared by Marcus Wenne (

The October AMR Digest brings a variety of discussions to the table, covering the realm of AMR through different scopes. It sheds light on the role of genomic surveillance, the interactions between humans and their environment in the context of AMR, and presents potential alternative therapeutic avenues against drug-resistant pathogens. The digest also touches on the importance of accurate antimicrobial use, intriguing findings from wastewater treatment plant studies, and the potential of leveraging technology to combat AMR. Through a blend of clinical, environmental, and technological perspectives, the digest offers a broad view on the current strides in the AMR landscape.

Our monthly EMBARK Webinar for November is titled Ecology and evolution of ARGs: From surveillance to intervention strategies with Prof. Craig MacLean & Prof. Sofia K. Forslund, moderated by Ulrike Löber .

November 15, 1400: CEST – Registration Link

Global picture

The uncertain role of substandard and falsified medicines in the emergence and spread of antimicrobial resistance – Sean Cavany – Nature Communications


Systematic analysis of drug combinations against Gram-positive bacteria – Elisabetta Cacace et al. – Nature Microbiology

What is the appropriate antimicrobial use surveillance tool at the health facility level for Uganda and other low- and middle-income countries? – John Paul Waswa et al. – Journal of Global Antimicrobial Resistance

Changes in community structure and microbiological risks in a small stream after receiving treated shale gas wastewater for two years – Shuchan Penn et al. – Environmental Pollution

A critical role of outer membrane vesicles in antibiotic resistance in carbapenem-resistant Klebsiella pneumoniae – Lifeng Yao – Annals of Clinical Microbiology and Antimicrobials

Insights from a Cross-Sectional Study on Knowledge, Attitudes and Behaviors Concerning Antibiotic Use in a Large Metropolitan Area: Implications for Public Health and Policy Interventions – Francesca Pennino et al. – Antibiotics


Genomic surveillance for antimicrobial resistance – a One Health perspective – Steven P. Djordjevic et al. – Nature Reviews Genetics

*The authors of this paper underscores the importance of an integrated ‘One Health’ approach for monitoring and managing AMR. They point out the potential of genomic technologies in understanding and tracing the dynamics of AMR ecology. The text highlights recent advancements in genomic AMR surveillance, discusses the strengths of various technologies, and contemplates the challenges in broader adoption.

Culturing the Plastisphere: comparing methods to isolate culturable bacteria colonising microplastics – Emily Stevenson et al. – Frontiers in Microbiology

Evolution of Resistance

Di-berberine conjugates as chemical probes of Pseudomonas aeruginosa MexXY-OprM efflux function and inhibition – Logan G. Kavanaugh et al. – npj Antimicrobials and Resistance

RecA levels modulate biofilm development in Acinetobacter baumannii – Carly Ching et al. – Molecular Microbiology

Coupled environmental and demographic fluctuations shape the evolution of cooperative antimicrobial resistance – Lluís Hernández-Navarro et al. – Journal of The Royal Society Interface

Gene Transfer/Plasmids

Metagenomic investigation reveals bacteriophage-mediated horizontal transfer of antibiotic resistance genes in microbial communities of an organic agricultural ecosystem – Yujie Zhang et al. – Microbiology Spectrum 

Role of natural transformation in the evolution of small cryptic plasmids in Synechocystis sp. PCC 6803 – Fabian Nies et al. – Environmental Microbiology 


Pet cats may shape the antibiotic resistome of their owner’s gut and living environment – Yiwen Yang et al. – Microbiome

The resistome and microbiome of wastewater treatment plant workers–The AWARE Study

– Fanny Berglund et al. – Environmental international

*The study explored antibiotic ARGs in wastewater treatment plant workers, hypothesizing they’d have more diverse resistant bacteria. Analyzing fecal microbiomes and resistomes of 87 wastewater treatment plant workers and 87 controls via shotgun metagenomics, no significant difference in ARG abundance or microbiome composition was found between groups. Interestingly, women had higher disinfectant resistance genes, hinting at cosmetics or cleaning products use as possible contributors. The study concludes that wastewater treatment plant employment doesn’t increase ARG abundance/diversity, and other factors like country of residence, recent antibiotic intake, and gender have more significant impacts.

AMR removal

CRISPR-Cas inhibits plasmid transfer and immunizes bacteria against antibiotic resistance acquisition in manure – Chahat Upreti et al. – bioRxiv preprint 

Aquatic environments

Anthropogenic Contributions to Antibiotic Resistance Gene Pollution in Household Drinking Water Revealed by Machine-learning-based Source-Tracking – Chen Wang et al. – Water Research

Antimicrobial resistance in aquaculture: Occurrence and strategies in Southeast Asia – Bongkotrat Suyamud et al. – Science of The Total Environment

Occurrence of sulfonamides and tetracyclines in the coastal areas of the Yangtze River (China) Estuary – Shuguang Liu et al. – Environmental Science and Pollution Research 


Investigation of 29 Antimicrobial Compounds in Soil Using Newly Developed UHPLC-MS/MS Method – Małgorzata Gbylik-Sikorska – Molecules


Acquisition of a novel conjugative multidrug‐resistant hypervirulent plasmid leads to hypervirulence in clinical carbapenem‐resistant Klebsiella pneumoniae strains – Gong Li et al. – mLife

Effects of a multimodal intervention in primary care to reduce second line antibiotic prescriptions for urinary tract infections in women: parallel, cluster randomised, controlled trial – Guido Schmiemann et al. – BMJ

Antibiotic prescribing practices and perceptions on antimicrobial resistance among healthcare practitioners in Russia – M.M. Fedotova et al. – Public Health

Discovery of highly neutralizing human antibodies targeting Pseudomonas aeruginosa – Alexander Simonis – Cell

*The authors of this paper explore alternative treatments for infections caused by drug-resistant Pseudomonas aeruginosa, a growing health threat. They study the immune response in chronically infected patients, discovering a potential therapeutic pathway involving certain neutralizing antibodies. These antibodies are identified as effective against drug-resistant strains, showing promise as an alternative treatment option. Through this work, the authors propose exploiting the immune responses from chronically infected patients as a potential resource for developing new therapeutics against Pseudomonas aeruginosa infections.


From tide to table: A whole-year, coastal-wide surveillance of antimicrobial resistance in Escherichia coli from marine bivalves – Cecilie Smith Svanevik – International Journal of Food Microbiology

Animals / Wildlife

Oxytetracycline-resistant Paenibacillus larvae identified in commercial beekeeping operations in Saskatchewan using pooled honey sampling – Oleksii Obshta et al. – Journal of Veterinary Diagnostic Investigation

Interventions to change antimicrobial use in livestock: A scoping review and an impact pathway analysis of what works, how, for whom and why – Marie-Jeanne Guenin et al. – Preventive Veterinary Medicine


Beyond antibiotics: phage-encoded lysins against Gram-negative pathogens – Sanket Shah – Frontiers in Microbiology


Bayesian modeling of the impact of antibiotic resistance on the efficiency of MRSA decolonization – Fanni Ojala et al. – Plos Computational Biology

Machine learning to predict ceftriaxone resistance using single nucleotide polymorphisms within a global database of Neisseria gonorrhoeae genomes – Sung Min Ha –  Microbiology Spectrum

New Antibiotics

An antibiotic from an uncultured bacterium binds to an immutable target – Rhythm Shukla

et al. – Cell

The novel bacteriocin romsacin from Staphylococcus haemolyticus inhibits Gram-positive WHO priority pathogens – Runa Wolden – Microbiology Spectrum