AMR DIGEST – End of the year 2023

Prepared by Anna Abramova

The final AMR Digest of 2023 features microbial wars and weaponry evolution, “plastisphere” as a new home for bacterial communities, inter-phylum ARGs exchange, peculiarities of honeybee and stray cats microbiota, and how the distance that your steak travels before ending-up on your plate is related to MDR contamination. And much more!


The evolution of short- and long-range weapons for bacterial competition – Sean C. Booth et al. – Nature Ecology & Evolution

A database of glacier microbiomes for the Three Poles – Yongqin Liu et al. – Earth System Science Data

Review: Selection for antimicrobial resistance in the plastisphere – Emily M. Stevenson et al. – Science of The Total Environment



Global pathogenomic analysis identifies known and candidate genetic antimicrobial resistance determinants in twelve species – Jason C. Hyun et al. – Nature Communications

Development of a portable on-site applicable metagenomic data generation workflow for enhanced pathogen and antimicrobial resistance surveillance – Bram Bloemen et al. – Scientific Reports

Evolution of Resistance

Evolution and transmission of antibiotic resistance is driven by Beijing lineage Mycobacterium tuberculosis in Vietnam – Matthew Silcocks et al. – Antimicrobial Chemotherapy

Rapid evolution bacteria reveal pathogenic mechanisms and clinical risk – Toyotaka Sato et al. – under review in Nature Portfolio 

Gene Transfer/Plasmids

Inter-phylum circulation of a beta-lactamase – encoding gene: a rare but observable event Rémi Gschwind, Marie Petitjean, Claudine Fournier, Julie Lao, Olivier Clermont, Patrice Nordmann, Alexander Mellmann, Erick Denamur, Laurent Poirel, Etienne Ruppé – bioRxiv preprint
*While transfer of beta-lactamase encoding genes typically occurs between closely-related bacteria, the research documents a unique case of inter-phylum transfer between the Peudomonadota and Bacteroidota phyla. The investigation focuses on an extended-spectrum beta-lactamase (ESBL)-encoding gene, blaMUN-1, from an Escherichia coli strain. This study marks the first reported instance of inter-phylum transfer of an ESBL-encoding gene, indicating that while inter-phylum barriers are generally robust, they are not insurmountable.

Evolutionary “Crowdsourcing”: Alignment of Fitness Landscapes Allows for Cross-species Adaptation of a Horizontally Transferred Gene – Olivia Kosterlitz et al. – Molecular Biology and Evolution

Is ICE hot? A genomic comparative study reveals integrative and conjugative elements as “hot” vectors for the dissemination of antibiotic resistance genes – Qi Zheng et al. – Msystems

Characterization of a mobilizable megaplasmid carrying multiple resistance genes from a clinical isolate of Pseudomonas aeruginosa – Li Mei et al. – Frontiers in Microbiology


Monitoring longitudinal antimicrobial resistance trends of Staphylococcus aureus strains worldwide over the past 100 years to decipher its evolution and transmission – Guan-Yu Fang et al. – Journal of Hazardous Materials


Swine farming shifted the gut antibiotic resistome of local people – Fang-Zhou Gao et al. – Journal of Hazardous Materials

Impact of contrasting poultry exposures on human, poultry, and wastewater antibiotic resistomes in Bangladesh – Alexander D. Williams et al. – Environmental Microbiology

One health transmission of fluoroquinolone-resistant Escherichia coli and risk factors for their excretion by dogs living in urban and nearby rural settings – Jordan E. Sealey et al. – One Health

AMR removal

Degradation of chromosomal and plasmid encoded extracellular and intracellular resistance genes across different types and sizes in water matrices during ozone-based oxidation process – Dabojani Das et al. – Journal of Water Process Engineering

Aquatic environments

The diversity of the antimicrobial resistome of lake Tanganyika increases with the water depth – Raffaella Sabatino et al. – Environmental Pollution

Impacts of net cages on pollutant accumulation and its consequence on antibiotic resistance genes (ARGs) dissemination in freshwater ecosystems: Insights for sustainable urban water management – Min Wang et al. – Environment International


Soil-specific responses in the antibiotic resistome of culturable Acinetobacter spp. and other non-fermentative Gram-negative bacteria following experimental manure application – Puspendu Sarda et al. – FEMS Microbiology Ecology

Unveiling antimicrobial resistance in Chilean fertilized soils: a One Health perspective on environmental AMR surveillance – Marcela Fresno et al. – Frontiers in Microbiology


Emergency of the plasmid co-carrying blaKPC-2 and blaNDM-1 genes in carbapenem-resistant hypervirulent Klebsiella pneumoniae – Shijun Sun et al. – Journal of Global Antimicrobial Resistance


Distance and destination of retail meat alter multidrug resistant contamination in the United States food system – Gabriel Innes et al. – Scientific Reports

Genomic characterization of Salmonella isolated from retail chicken and humans with diarrhea in Qingdao, China – Wei Wang et al. – Frontiers in Microbiology

Animals / Wildlife
Review: The honeybee microbiota and its impact on health and disease – Erick Motta & Nancy Moran – Nature Reviews Microbiology


Figure 1: Microbial dynamics and spatial organization in the honeybee gut. Honeybees are key pollinators and have a long history of domestication for wax and honey production. Recently, they have emerged as models for studying gut microbial communities.

Antibiotic Resistance Genes Carried by Commensal Escherichia colifrom Shelter Cats in Italy – Delia Gambino et al. – Veterinary Sciences


Multimodal learning in clinical proteomics: enhancing antimicrobial resistance prediction models with chemical information – Giovanni Visonà et al. – Bioinformatics
Sarand: Exploring Antimicrobial Resistance Gene Neighborhoods in Complex Metagenomic Assembly Graphs – Somayeh Kafaie et al. – bioRxiv preprint

AMR DIGEST – October 2023

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

AMR DIGEST – September 2023

Prepared by Rémi GSCHWIND (

The September AMR Digest features general issues about AMR and more specific topics about policy, surveillance, AMR removal/transmission and about several specific environments.  It encompasses as well from the EMBARK consortium: a study on antibiotic discovery including Luis Pedro Coelho. Enjoy your reading but first “Race against AMR” from BBC StoryWorks.

Race Against Resistance: The Life And Death Struggle To Save Antibiotics | BBC StoryWorks

Our monthly EMBARK Webinar for October is titled “AMR: a link between clinical settings and other environments” with Prof. Adam P. Roberts & Prof. Etienne Ruppe, moderated by Remi Gschwind.

October 11th, 14:00 CEST – Register here

Global picture

Computational exploration of the global microbiome for antibiotic discovery – Célio Dias Santos-Júnior, Marcelo D. T. Torres, Yiqian Duan, Álvaro Rodríguez del Río, Thomas S.B. Schmidt, Hui Chong, Anthony Fullam, Kuhn Michael, Chengkai Zhu, Amy Houseman, Jelena Somborski, Anna Vines, Xing-Ming Zhao, Peer Bork, Jaime Huerta-Cepas, Cesar de la Fuente-Nunez, Luis Pedro Coelho – bioRxiv preprint

Global patterns and correlates in the emergence of antimicrobial resistance in humans – E. Mendelsohn et al. – Proceedings of the Royal Society B


Repurposing sunscreen as an antibiotic: zinc-activated avobenzone inhibits methicillin-resistant Staphylococcus aureus. – Andrews RM et al. – Metallomics.

Gut microbiome perturbation, antibiotic resistance, and Escherichia coli strain dynamics associated with international travel: a metagenomic analysis. – Worby C et al. – Lancet Microbe.

Based on analysis of pre- and post-travel fecal microbiomes using metagenomics and culture dependent methods a significant proportion of travelers acquired ARGs and ARBs.

Regulation Transcriptional of Antibiotic Resistance Genes (ARGs) in Bacteria Isolated from WWTP. – Díaz-Palafox G et al. – Curr Microbiol.

Household environment and animal fecal contamination are critical modifiers of the gut microbiome and resistome in young children from rural Nicaragua. – Mills M et al. – Microbiome.

Dynamic human exposure to airborne bacteria-associated antibiotic resistomes revealed by longitudinal personal monitoring data. – Zhang RM et al. – Sci Total Environ.

Pangenome analysis of Corynebacterium striatum: insights into a neglected multidrug-resistant pathogen. – Nageeb WM et al. – BMC Microbiol.

Synergistic Role of Biofilm-Associated Genes and Efflux Pump Genes in Tigecycline Resistance of Acinetobacter baumannii. – Luo B et al. – Med Sci Monit.

Exploiting the aggregation propensity of beta-lactamases to design inhibitors that induce enzyme misfolding. – Khodaparast L et al. – Nat Commun.

Beta-lactamases are the main resistance mechanism against beta-lactam antibiotics. They represent a threat for infectious diseases treatment as their resistance spectrum includes all the beta-lactam antibiotics and even beta-lactam associated with beta-lactamases inhibitors. This study reports the test of a new strategy targeting the beta-lactamase itself rather than its active site on beta-lactam antibiotics with inhibitors. It lays on targeting aggregation-prone regions of the enzyme which cause inactivation of the enzyme. TEM and SHV beta-lactamases were investigated regarding their tendency to aggregate. The aggregation of TEM, SHV, and NDM was not bactericidal but it allowed to restore sensitivity to beta-lactam antibiotics.


Reducing antimicrobial use in chicken production in Vietnam: Exploring the systemic dimension of change. – Bâtie C et al. – PLoS One.


Metagenome meta-analysis reveals an increase in the abundance of some multidrug efflux pumps and mobile genetic elements in chemically polluted environments – J. Subirats et al. – Applied and Environmental Microbiology

Quantifying health risks of plastisphere antibiotic resistome and deciphering driving mechanisms in an urbanizing watershed. – Zhu L et al. – Water Res.

Evolution of Resistance

Parallel evolution of linezolid-resistant Staphylococcus aureus in patients with cystic fibrosis. – Pitcher NJ et al. – Microbiol Spectr. 

Bacterial motility can govern the dynamics of antibiotic resistance evolution. Piskovski V et al. Nat Commun.

Fitness Costs of Antibiotic Resistance Impede the Evolution of Resistance to Other Antibiotics. Chowdury FR et al. ACS Infect Dis. 

Regulatory fine-tuning of mcr-1 increases bacterial fitness and stabilises antibiotic resistance in agricultural settings – L. Ogunlana et al. – The ISME Journal

Gene Transfer/Plasmids

Oxytetracycline and heavy metals promote the migration of resistance genes in the intestinal microbiome by plasmid transferXiaojun Lin et al. – The ISME Journal

Integrons, transposons and IS elements promote diversification of multidrug resistance plasmids and adaptation of their hosts to antibiotic pollutants from pharmaceutical companies. – Shintani M et al. – Environ Microbiol.

The extensively antibiotic resistant ST111 Acinetobacter baumannii isolate RBH2 carries an extensive mobile element complement of plasmids, transposons and insertion sequences. – Ambrose SJ et al. – Plasmid.


Phylogenomic analysis of a global collection of Escherichia coli ST38: evidence of interspecies and environmental transmission? – Roy Chowdhury P et al. – mSystems.

Circulation of enterotoxigenic Escherichia coli (ETEC) isolates expressing CS23 from the environment to clinical settings. – Calderon Toledo C et al. – mSystems.

AMR removal

Engineering conjugative CRISPR-Cas9 systems for the targeted control of enteric pathogens and antibiotic resistance – H. Sheng et al. – PLOS One

Recent advances in sulfidized nanoscale zero-valent iron materials for environmental remediation and challenges. – Xue W et al. – Environ Sci Pollut Res Int.

Antibiotics resistance removal from piggery wastewater by an integrated anaerobic-aerobic biofilm reactor: Efficiency and mechanism. – Tang L et al. – Sci Total Environ.

Aquatic environments

Impact of corrosion inhibitors on antibiotic resistance, metal resistance, and microbial communities in drinking water – LK Kimbell et al. – mSphere 

Free-floating extracellular DNA (exDNA) in different wastewaters: Status quo on exDNA-associated antimicrobial resistance genes. – Savin M et al. – Environ Pollut. 

Wastewater treatment plants (WWTPs) are hotspots for ARGs. Studies on ARG in WWTP environments mainly focus on intracellular DNA while a significant proportion of the total DNA is extracellular DNA due to wastewater decontamination. Extracellular DNA has to be taken into account as transformation of naturally competent bacteria can occur with extracellular DNA containing ARGs. The study shows how wastewater is a source of ARGs associated with free-floating exDNA.

Antibiotic resistance genes and the association with bacterial community in biofilms occurring during the drinking water granular activated carbon (GAC) sandwich biofiltration. – Xu L et al. – J Hazard Mater.

Microbial diversity characterizations, associated pathogenesis and antimicrobial resistance profiling of Najafgarh drain. – Tyagi I et al. – Environ Res. 

Combined effects of microplastics and antibiotic-resistant bacteria on Daphnia magna growth and expression of functional genes. – Chen X et al. – Sci Total Environ.

Comparison of antibiotic-resistant Escherichia coli and extra-intestinal pathogenic E. coli from main river basins under different levels of the sewer system development. – Chen JS et al. – Ecotoxicol Environ Saf.

Comparative bacteriome and antibiotic resistome analysis of water and sediment of the Ganga River of India. – Srivastava A et al. – World J Microbiol Biotechnol.

Metagenomic analysis reveals the dissemination mechanisms and risks of resistance genes in plateau lakes. – Mao C et al. – iScience.

Simultaneous stream assessment of antibiotics, bacteria, antibiotic resistant bacteria, and antibiotic resistance genes in an agricultural region of the United States. – Givens CE et al. – Sci Total Environ.

Wastewater treatment plant effluents exert different impacts on antibiotic resistome in water and sediment of the receiving river: Metagenomic analysis and risk assessment. – Wu Y et al. – J Hazard Mater.

Antibiotics and their associations with antibiotic resistance genes and microbial communities in estuarine and coastal sediment of Quanzhou Bay, Southeast China. – Chen Y et al. – Mar Pollut Bull.


Uncovering the prevalence and drivers of antibiotic resistance genes in soils across different land-use types. – Wu J et al. – J Environ Manage.

Antibiotic resistome and associated bacterial communities in agricultural soil following the amendments of swine manure-derived fermentation bed waste. – Pan Z et al. – Environ Sci Pollut Res Int. 


Antibiotics promote intestinal growth of carbapenem-resistant Enterobacteriaceae by enriching nutrients and depleting microbial metabolites – A. Yip et al. – Nature Communications

Effect on the resistome of dual- vs monotherapy for the treatment of Neisseria gonorrhoeae: results from a randomized controlled trial (ResistAZM Trial) – Thibaut Vanbaelen et al. – Open Forum Infectious Diseases

Co-administration of amoxicillin-loaded chitosan nanoparticles and inulin: A novel strategy for mitigating antibiotic resistance and preserving microbiota balance in Helicobacter pylori treatment. – Fayed B et al. – Int J Biol Macromol.

Characterization of Pseudomonas aeruginosa resistance to ceftolozane-tazobactam due to ampC and/or ampD mutations observed during treatment using semi-mechanistic PKPD modeling. – Deroche L et al. – Antimicrob Agents Chemother.

Within-Host Dynamics and Duration of Colonization of Travel-Acquired Multidrug-Resistant Enterobacterales in Untreated Individuals. – Olivier Cotto et al. – Clin Infect Dis.


Large-scale genomic survey and characterization of mcr genes carried by foodborne Cronobacter isolates. – Zhu Q et al. – mSystems.

Comparative proteomics reveals the antibiotic resistance and virulence of Cronobacter isolated from powdered infant formula and its processing environment. – Song D et al. – Int J Food Microbiol.

Advanced strategies to overcome the challenges of bacteriophage-based antimicrobial treatments in food and agricultural systems. Liu S et al. Crit Rev Food Sci Nutr.

Extended-spectrum β-lactamase-producing Enterobacteriaceae from ready-to-eat foods: Genetic diversity and antibiotic susceptibility. – Liu Y et al. – Food Sci Nutr.

Postbiotic as Novel Alternative Agent or Adjuvant for the Common Antibiotic Utilized in the Food Industry. – Sepordeh et al. – Curr Pharm Biotechnol.

Animals / Wildlife

Effects of the coexistence of antibiotics and heavy metals on the fate of antibiotic resistance genes in chicken manure and surrounding soils. – Shen C et al. – Ecotoxicol Environ

Prevalence of neonatal calf diarrhea caused by Escherichia coli and investigation of virulence factors, serotypes, and antibiotic susceptibility. – Coşkun M R et al. – Pol J Vet Sci.

Complete genome sequences of bacteria isolated from cockroaches collected in a Bangladeshi hospital. – Workman SD et al. – Microbiol Resour Announc

Bacterial community succession and the enrichment of antibiotic resistance genes on microplastics in an oyster farm. – Xiao S et al. – Marine Pollution Bulletin

Assessing the mechanisms of multi-drug resistant non-typhoidal Salmonella (NTS) serovars isolated from layer chicken farms in Nigeria. – Fagbamila IO et al. – PLoS One

Whole genome sequencing-based cataloguing of antibiotic resistant genes in piggery waste borne samples. – Niharika J et al. – Gene

Anthropic Impact on the Critically Endangered Melanophryniscus admirabilis (Admirable Redbelly Toad): Evidence from the Presence of Multiresistant Enterobacteriaceae. – Ienes-Lima J et al. – Current Microbiology

Presence and Resistance Profile of Staphylococcus spp. Isolated from Slaughtered Pigs. Santos ICD et al. Vector borne Zoonotic Diseases

Antibiotic Resistance Profiles and Molecular Characteristics of bla(CMY-2)-Carrying Salmonella enterica Serovar Albany Isolated from Chickens During 2013-2020 in South Korea. – Ali MS et al. – Foodborn Pathogen Dissemination 

Integrative conjugative elements mediate the high prevalence of tmexCD3-toprJ1b in Proteus spp. of animal source. – Peng K et al. – mSystems

Fate of high-risk antibiotic resistance genes in large-scale aquaculture sediments: geographical differentiation and corresponding drivers. – Wanyan R et al. – Science of the Total Environment 


Bacteriophages limitedly contribute to the antimicrobial resistome of microbial communities in wastewater treatment plants – R. Sabbatino et al. – Microbiology Spectrum


Identification of mobile genetic elements with geNomad. – Camargo AP et al. – Nature Biotechnology

AMR digest – Summer 2023

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

AMR DIGEST – May 2023

Prepared by Víctor Hugo Jarquín Díaz ( on behalf of the EMBARK consortium (

The weather is getting warm and the AMR digest of May features a lot of hot-topics on gene transfer and plasmid research, AMR in aquatic environments, food, wildlife, and more!

Have a look at the podcast section and don’t miss the upcoming EMBARK seminar! 


Deep learning-guided discovery of an antibiotic targeting Acinetobacter baumannii – Gary Liu et al. – Nature Chemical Biology 

* In times of ChatGPT and artificial intelligence (AI) as part of our daily-life, Gary Lui and colleagues present a deep-learning approach to discover new antibacterial molecules. They screened ~7,500 molecules that inhibited the growth of A. baumannii in vitro and then trained a neural network to make predictions in silico for new molecules which could have antimicrobial activity against A. baumannii. Their work led to the discovery of a new narrow-spectrum antibacterial compound called abaucin against A. baumannii. This work highlights the promising use of AI algorithms for a rapid discovery of new and more specific antimicrobial compounds. 

Wastewater monitoring can anchor global disease surveillance systems – Aparna Keshaviah et al. – The Lancet Global Health

Endemicity and diversification of carbapenem-resistant Acinetobacter baumannii in an intensive care unit – Emma Doughty et al. – The Lancet Regional Health – Western Pacific

Mechanisms of antibiotic resistance in Pseudomonas aeruginosa biofilms. – María Fernández-Billón et al. –  Biofilm

Translating eco-evolutionary biology into therapy to tackle antibiotic resistance – Fernando Sanz-García et al. – Nature Reviews Microbiology

* This review by Fernando Sanz-García and cols., discusses the trade-offs in antibiotic resistance evolution to design eco-evolutionary based treatment approaches. Understanding the evolution of antimicrobial resistance is key to tackling this worldwide relevant problem. 


ANTIBIOTIC RESISTANCE: Federal Agencies Have Taken Steps to Combat the Threat, But Additional Actions Needed – United States Government Accountability Office (US-GAO) Report

Report of the Global Leaders Group AMR Reception at WHA 76: The Road to the UNGA High-level Meeting on AMR in 2024 – 76th World Health Assembly in Geneva, Switzerland on May 22, 2023

Evolution of Resistance

Functionally distinct mutations within AcrB underpin antibiotic resistance in different lifestyles – Eleftheria Trampari et al. – npj Antimicrobials and Resistance

Role of bacterial efflux pumps in antibiotic resistance, virulence, and strategies to discover novel efflux pump inhibitor – Amit Gaurav et al. – Microbiology

Removal of Resistance

Removal of AMR plasmids using a mobile, broad host-range CRISPR-Cas9 delivery tool – David Walker-Sünderhauf, Uli Klümper, Elizabeth Pursey, Edze Westra, William H. Gaze, Stineke van Houte – Microbiology

* The researchers harnessed the CRISPR-Cas gene editing system, which can target specific sequences of DNA, and cut through them when they are encountered. The researchers engineered a self-transmissible plasmid which can specifically target the resistance gene for Gentamicin – a commonly used antibiotic. In laboratory experiments, they found that the plasmid protected its host cell from developing resistance. Furthermore, researchers found that the plasmid effectively targeted antimicrobial resistant genes in hosts to which it transferred at high frequencies, reversing their resistance and resensitising them to antibiotic treatment

Climate change

Enhanced freeze-thaw cycles facilitate the antibiotic resistance proliferation and dissemination risk under global climate change – Zhengang Lou et al. – Process Safety and Environmental Protection

Gene Transfer/Plasmids

Catch me if you can: capturing microbial community transformation by extracellular DNA using Hi-C sequencing – David Calderon-Franco et al. – Antonie van Leeuwenhoek

Plasmid-mediated antibiotic resistance gene transfer under environmental stresses: Insights from laboratory-based studies – Li-Guan Li & Tong Zhang – Science of the Total Environment

Low concentration quaternary ammonium compounds promoted antibiotic resistance gene transfer via plasmid conjugation – Congcong Liu et al. – Science of the Total Environment

A novel bidirectional regulation mechanism of mancozeb on the dissemination of antibiotic resistance – Jiajin Song et al. – Journal of Hazardous Materials

DNA modifications impact natural transformation of Acinetobacter baumannii – Vesel et al. – Nucleic acid research 

A scalable framework for high-throughput identification of functional origins of replication in non-model bacteria – Charlie Gilbert et al. – bioRxiv preprint

Complete sequence of a new conjugative multidrug-resistance encoding IncFII/IncFIA/IncFIB plasmid carrying NDM-6 metallo-β-lactamase from pathogenic Escherichia coli sequence type 167 isolated from sewage in Norway – Didrik H. Grevskott et al. – Journal of Global Antimicrobial Resistance


Discrepancy in the transmissibility of multidrug-resistant mycobacterium tuberculosis in urban and rural areas in China – Li Meng et al. – Emerging Microbes and Infection

Aquatic environments/Wastewater

Microbiome and Resistome Profiles along a Sewage-Effluent-Reservoir Trajectory Underline the Role of Natural Attenuation in Wastewater Stabilization Reservoirs – I. Leão, L. Khalifa, N. Gallois, I. Vaz-Moreira, Uli Klümper, D. Youdkes, S. Palmony, L. Dagai, Thomas U. Berendonk, C. Merlin, C.M. Manaia, E. Cytryn – Applied and Environmental Microbiology

Anthropogenic pollution drives the bacterial resistome in a complex freshwater ecosystem – Andrea di Cesare et al. – Chemosphere

* This research highlights the role of anthropogenic pressure in promoting the spread of antimicrobial resistance genes and pathogenic bacteria and the relationship between ARGs and metal resistance genes (MRGs). The authors studied the fate of ARGs in a continuum system of two lakes connected by a river in the Northern of Italy. The authors suggest that under high levels of pollutant in aquatic environments, the ARGs and MRGs could be under co-selection.

An extensive assessment of seasonal rainfall on intracellular and extracellular antibiotic resistance genes in Urban River systems – Wenchao Yu et al. – Journal of Hazardous Materials

Transfer route and driving forces of antibiotic resistance genes from reclaimed water to groundwater – Xiangyu Guan et al. – Environmental Pollution 

Synergistic removal of pharmaceuticals and antibiotic resistance from ultrafiltered WWTP effluent: Free-floating ARGs exceptionally susceptible to degradation – Stanislav Gajdoš et al., – Journal of Environmental Management

Microbial niches and dynamics of antibiotic resistance genes in a bio-enhanced granular-activated carbon biofilm treating greywater – Ting Wei et al. – Chemosphere 

Land-derived wastewater facilitates antibiotic resistance contamination in marine sediment of semi-closed bay: A case study in Jiaozhou Bay, China. – Quian Wang et al. – Journal of Environmental Management

Carbapenemase-producing Gram-negative bacteria in hospital wastewater, wastewater treatment plants and surface waters in a metropolitan area in Germany, 2020 – Markus Hoffman et al. – Science of the total environment 

Metagenomic analysis to determine the characteristics of antibiotic resistance genes in typical antibiotic-contaminated sediments – Han Yang et al. – Journal of Environmental Sciences


Reforestation substantially changed the soil antibiotic resistome and its relationships with metal resistance genes, mobile genetic elements, and pathogens – Song Zhang et al. – Journal of Environmental Management


A snapshot survey of antimicrobial resistance in food-animals in low and middle-income countries – Odion O. Ikhimiukor & Iruka N. Okeke – One Health 

* Large screening of bacterial isolates in food animals from low and middle-income countries (LMICs) in Africa, Middle East and Central America. Iruka Okeke and Odion Ikhimiukor analyzed over 150 studies and observed that despite wide variation between countries, food animals are important reservoirs of AMR in LMICs and highlight the necessity of surveillance and monitoring.

Molecular characterization of extended-spectrum β-lactamases-producing Enterobacteriaceae species in ground beef and chicken meat – Gökhan İnat et al. – International Journal of Food Microbiology

Contribution of different class 2 integron elements to fitness costs in multi-drug resistant Escherichia coli and evaluation of their adaptability in “farm-to-table” environments – Han Jiang et al. – Food Microbiology

Farmed Animals / Wildlife

Effects of different laying periods on airborne bacterial diversity and antibiotic resistance genes in layer hen houses – Huan Cui et al. – The International Journal of Hygiene and Environmental Health

Limited impacts of high doses of dietary copper on the gut bacterial metal resistome explain negligible co-selection of antibiotic resistance – Asal Forouzandeh et al. – Science of the Total Environment

Genome-resolving metagenomics reveals wild western capercaillies (Tetrao urogallus) as avian hosts for antibiotic-resistance bacteria and their interactions with the gut-virome community – 

Jacob A. Rasmussen & Pysilia Y. S. Chua- Microbiological Research 

Acinetobacter Metabolism in Infection and Antimicrobial Resistance – Xiaomei Ren et al. – Infection and Immunity


Lysogenic bacteriophages encoding arsenic resistance determinants promote bacterial community adaptation to arsenic toxicity – Xiang Tang et al. – The ISME Journal


ResFinderFG v2.0: a database of antibiotic resistance genes obtained by functional metagenomicsRémi Gschwind, Svetlana Ugarcina Perovic, Maja Weiss, Marie Petitjean, Julie Lao, Luis Pedro Coelho, Etienne Ruppé – Nucleic Acids Research

* The second version of ResFinderFG is published and available! Check it at the portal of the Center of Genomic Epidemiology ( This new version contains over 3900 ARGs identified by functional metagenomics. 


LongDat: an R package for covariate-sensitive longitudinal analysis of high-dimensional data – Chia-Yu Chen, Ulrike Lӧber, Sofia K Forslund – Bioinformatics Advances

* LongDat R package is a computationally efficient and low-memory-cost tool for longitudinal data with multiple covariates and facilitates robust biomarker searches in high-dimensional datasets. 


Our monthly EMBARK Webinar on Strategies for AMR surveillance with an One Health approach with Prof. Frank van Leth & Ass. Prof.  Johan Bengtsson-Palme. Moderated by Anna Abramova. June 14, 14:00 CEST. Register here


FAO – knowledge dissemination dialogues on AMR – Jun 8, 2023 12:30 PM  – Online 


Know Something About Antimicrobial Resistance by the Students against superbugs – Africa

Microbe Talk: A Deep Dive Into Wastewater Monitoring – Microbiology Society – Posted on May 24, 2023  by Clare Baker