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

EMBARK Spring Webinars

The EMBARK webinars are back for the spring season. This year we have an exciting lineup with representatives from other JPIAMR programs joining forces with speakers from this program. For the spring, we welcome Sabrina Giebner, Andrew Stubbs and Frank van Leth who will share the stage with Thomas Berendonk, Luis Pedro Coelho and Johan Bengtsson-Palme from EMBARK. The first webinar is already next week!

April 19, 14:00 CEST
Topic: AMR Surveillance in aquatic environments
Sabrina Giebner (AquaticPollutantsTransNet)
EMBARK speaker: Thomas Berendonk
Moderator: Uli Klümper
Aim of AquaticPollutantsTransNet: Improve stakeholders’ & citizens’ perception through active involvement in the reduction of aquatic pollutants in the water cycle
Registration link:

May 17, 14:00 CEST
Topic: ARG annotation
Andrew Stubbs (Seq4AMR)
EMBARK speaker: Luis Pedro Coelho
Moderator: Svetlana Ugarčina Perović
Aim of Seq4AMR: Establish a strategy to link AMR NGS stakeholders and individual fields of NGS technologies, algorithms, quality standards, teaching/training and sequence databanks
Registration link:

June 14, 14:00 CEST
Topic: Strategies for AMR surveillance with an One Health approach
Frank van Leth (OASIS)
EMBARK speaker: Johan Bengtsson-Palme
Moderator: Anna Abramova
Aim of OASIS: Optimise the Lot Quality Assurance Sampling (LQAS) approach as a rapid, domain-, and setting-appropriate AMR surveillance strategy, within a One Health context
Registration link:

Updated webinar times

We have two more EMBARK Webinars to go before the end of the year. For the second one with Joakim Larsson we have updated the date to December 14. Make a note in your calendars!

Nov 9, 14:00 UTC+2
Iruka Okeke – Genomic surveillance of human-invasive Salmonella in Nigeria
Miranda Wallace – Understanding and predicting resistance in Bacteroides fragilis group bacteria using clinical and modern genomics tools
[Register here]

Dec 14, 14:00 UTC+2
Joakim Larsson – TBA
[Register here]

EMBARK Fall Webinars

The EMBARK webinar series continues in the fall, starting September 1. We already have three confirmed invited speakers who will present their research and be contrasted to EMBARK members presenting the work performed in the project. This will be followed by a discussion and Q&A. All the webinars, except for one, will take place at 14:00 CEST (12:00 UTC).

These are the three already scheduled webinars:

  • September 1: Amy Pruden – “Towards coordinated local and global surveillance of antibiotic resistance at wastewater treatment plants”
    Thomas Berendonk – “AMR in WWTPs – the European perspective”
  • September 22: Gautam Dantas – “Predicting and Combating Biotic and Abiotic Perturbations to Diverse Microbiomes”
    Johan Bengtsson-Palme – “Antibiotic perturbations to interactions in microbial communities”
  • October 13: Monika Dolejska – “Antibiotic resistance is going wild”
    Victor Hugo Jarquin Diaz – “AMR spread in rodents”
  • November 10: Michael Baym – “Exploring non-anthropic selective pressures on antibiotic resistance”
    Uli Klümper – TBA
  • November 24: Nikolina Udikovic Kolic – “Pharmaceutical waste and antimicrobial resistance”
    Ulrike Löber – “Drugs as antidotes – How drugs affect the damage on gut commensals under antibiotics course
  • December 15: Willem van Schaik – “Metagenomic approaches to understand the spread of antibiotic resistance genes in microbial ecosystems”
    Svetlana Ugarcina Perovic – “Exploring the global resistome using the global microbial gene catalog”

EMBARK Spring Webinars

EMBARK is starting a webinar series where invited speakers will be presenting their research and be contrasted to EMBARK members presenting the work performed in the project. This will be followed by a discussion and Q&A. All the webinars, except for one, will take place at 14:00 CEST.

Four webinars will take place before the summer break:

  • April 28: Gerry Wright – “Approaches to measure and monitor AMR in various environments”
    Luis Pedro Coelho – “Quantifying AMR at very large scales”
  • May 19: Heike Schmitt – “International efforts for One Health surveillance of AMR (WHO Tricycle)”
    Etienne Ruppé – “On the use of Tricycle in EMBARK”
  • June 9: Dearbháile Morris – “What lurks beneath: the role of water in the transmission and persistence of AMR”
    Rabaab Zahra – “E. coli STs and Resistance Mechanisms in Sewage from Islamabad”
  • June 30 **13:00 CEST*: Kimberly Kline – “Pathogenesis and persistence during Enterococcus faecalis biofilm-associated infection”
    Sofia Forslund – High-throughput measurement of host and microbiota

Here is also a sneak peek at the first webinars of the fall:

  • September 1: Amy Pruden – “Towards coordinated local and global surveillance of antibiotic resistance at wastewater treatment plants”
    Thomas Berendonk – “AMR in WWTPs – the European perspective”
  • September 22: Gautam Dantas – “Predicting and Combating Biotic and Abiotic Perturbations to Diverse Microbiomes”
    Johan Bengtsson-Palme – “Antibiotic perturbations to interactions in microbial communities”
  • October 13: Barry McMahon – “How AMR in wildlife can inform zoonoses research”
    Victor Hugo Jarquin Diaz – “AMR spread in rodents”