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

AMR DIGEST April, 2023

Prepared by Uli Klümper (

The April AMR digest features global drivers of AMR, environmental barriers to AMR, a number of papers on the ecology underlying plasmid-based spread of AMR,  wastewater as a major source for ARG mobility, and more!


Bacterial defences: mechanisms, evolution and antimicrobial resistance – William P.J. Smith – Nature Reviews Microbiology

Global picture

Global antimicrobial-resistance drivers: an ecological country-level study at the human–animal interface – Kasim Allel et al. – The Lancet Planetary Health 

Global trends in antimicrobial use in food-producing animals: 2020 to 2030 – Ranya Mulchandani et al. – PLOS Glob Public Health

Global trends in antimicrobial resistance on organic and conventional farms – Eldon Ager et al. – bioRxiv preprint


Environmental surveillance of antimicrobial resistance (AMR), perspectives from a national environmental regulator in 2023. – Alwyn Hart et al. –  Euro Surveillance

International manufacturing and trade in colistin, its implications in colistin resistance and One Health global policies: a microbiological, economic, and anthropological study – Muhammad Umair et al. – The Lancet Microbe

Commission proposal for a Council Recommendation on stepping up EU actions to combat antimicrobial resistance in a One Health approach – European Commission


Microbiome diversity: A barrier to the environmental spread of antimicrobial resistance?Uli Klümper, G. Gionchetta, E. C. P. Catao, X. Bellanger, I. Dielacher, P. Fang, S. Galazka, A. Goryluk-Salmonowicz, David Kneis, U. Okafor, E. Radu, M. Szadziul, E. Szekeres, A. Teban-Man, C. Coman, N. Kreuzinger, M. Popowska, J. Vierheilig, F. Walsh, M. Woegerbauer, H. Bürgmann, C. Merlin, Thomas U. Berendonk – bioRxiv preprint

*The study is based on ~200 samples of forest soils and riverbed material of low anthropogenic impact in 7 European countries In stationary soils with established niches the number of and the relative abundance of these ARGs is inversely correlated with microbial diversity. Contrary, in dynamic riverbeds, where ecological niches are constantly disturbed, no such effects can be observed. The study hence proposes that microbiome diversity can serve as a barrier to the spread of AMR, but only in ecosystems with “stable” niche structures.

Gene Transfer/Plasmids

Tradeoff between lag time and growth rate drives the plasmid acquisition cost – Mehrose Ahmad et al. – Nature Communications

*Plasmid acquisition costs are primarily driven by changes in lag time, rather than growth rate, for nearly 60 conditions covering diverse plasmids, selection environments, and clinical strains/species. Surprisingly, for a costly plasmid, clones exhibiting longer lag times also achieve faster recovery growth rates, suggesting an evolutionary tradeoff. 

Preceding Host History of Conjugative Resistance Plasmids Affects Intra- and Interspecific Transfer Potential from Biofilm – Ilmur Jonsdottir et al. – mSPhere

Antagonistic Mobile Genetic Elements Can Counteract Each Other’s Effects on Microbial Community Composition – Meaghan Castledine et al. – mBio

* In-silico simulations predict increasing antagonist diversity diminishes individual antagonist effects on community composition as conflicting effects cancel out. This is proven experimentally as a conjugative plasmid and bacteriophages have effects on community composition when they’re the only antagonist. But when together, the community reverts back to its antagonist-free state.

Differences in vertical and horizontal transmission dynamics shape plasmid distribution in clinical enterobacteria – Aida Alonso-del Valle et al. – bioRxiv preprint

Insertion Sequences Determine Plasmid Adaptation to New Bacterial Hosts – Emelia Wedel et al. – mBio

Comprehensive analysis of disinfectants on the horizontal transfer of antibiotic resistance genes – Shuyao Zhu et al. – Journal of Hazardous Materials

Phthalates Promote Dissemination of Antibiotic Resistance Genes: An Overlooked Environmental Risk – Jing Wu et al. – Environmental Science & Technology

Simulated Gastric Acid Promotes the Horizontal Transfer of Multidrug Resistance Genes across Bacteria in the Gastrointestinal Tract at Elevated pH Levels – Hai-yan Wu et al. – Microbiology Spectrum


Evidence for wastewaters as environments where mobile antibiotic resistance genes emerge – Fanny Berglund et al. – Communications Biology

*The majority of previously identified mobile ARG hosts did not carry the mobilizing elements that likely enabled their original intracellular mobility, suggesting a necessary interplay between different bacteria resulting in their spread in human pathogens. Analyses of a broad range of metagenomes revealed that wastewaters and wastewater-impacted environments had by far the highest abundance of both origin species and corresponding mobilizing elements. 

Simultaneous removal of antibiotics and antibiotic resistance genes in wastewater by a novel nonthermal plasma/peracetic acid combination system: Synergistic performance and mechanism – Ai Zhang et al. – Journal of Hazardous Materials

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


Identification of diverse antibiotic resistant bacteria in agricultural soil with H218O stable isotope probing combined with high-throughput sequencing – Marcela Hernández Et al. – Environmental Microbiome

Partitioning and migration of antibiotic resistance genes at soil-water-air interface mediated by plasmids – Yang Zhu et al. – Environmental Pollution


Exploiting a targeted resistome sequencing approach in assessing antimicrobial resistance in retail foods – Julia A. Shay et al. – Environmental Microbiome

Zoonotic infections

Using source-associated mobile genetic elements to identify zoonotic extraintestinal E. coli infections – Cindy M. Liu et al. – One Health


White stork movements reveal the ecological connectivity between landfills and different habitats – Cosme López-Calderón et al. – Movement Ecology


HOTSPOT: Hierarchical hOst predicTion for aSsembled Plasmid cOntigs with Transformer – Yongxin Ji et al. – Bioinformatics

Addressing antibiotic resistance: computational answers to a biological problem? – Anna H Behling et al. – Current Opinion in Microbiology

Messages from the seventh international conference on clinical metagenomics (ICCMg7) – Mikael de Lorenzi-Tognon, Etienne Ruppe, J. Schrenzel – Microbes and Infection


A Streamlined Approach for Fluorescence Labelling of Low-Copy-Number Plasmids for Determination of Conjugation Frequency by Flow Cytometry – Qin Qi et al. – Microorganisms


Our monthly EMBARK Webinar on ARG annotation 

with Prof. Andrew Stubbs & Prof. Luis Pedro Coelho, moderated by Svetlana Ugarčina Perović
May 17th, 14:00 CEST – Register here

NCBI Webinar: Accessing NCBI AMR Pathogen Data in the Cloud – Now available as a recording on Youtube


EMBO Workshop: Plasmids as vehicles of AMR spread, in Triest, Italy – 18. – 22. September 2023 | Trieste, Italy

Molecular Approaches to Clinical Microbiology in Africa, hosted by the Kenya Medical Research Institute (KEMRI) – 2. – 8. September 2023

Artificial Intelligence & Antibiotic Resistance – Health Talks – Free hybrid event by The Global Antibiotics Resistance Foundation in Helsinki Finland – 22. May 2023


EFSA Europe podcast: Episode 6 – Antibiotics: handle with care by Ernesto Liebana