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: https://gu-se.zoom.us/webinar/register/WN_h8-CkMMeQpixgDQ8Jtz7Dg

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: https://gu-se.zoom.us/webinar/register/WN_L7QmrDM5Rn2sWRnC7FnhVQ

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: https://gu-se.zoom.us/webinar/register/WN_-XjYy26RTlWyWLWMFagyOw


prepared by Ulrike Löber

March digest features a review of novel methods to quantifying the physical linkage between specific antimicrobial resistance genes and mobile genetic elements, how traveling affects AMR, and more.

We are looking for speakers for our EMBARK webinars in 2023. If you want to share your groundbreaking research on antimicrobial resistance, please get in touch with us!


Latent antibiotic resistance genes are abundant, diverse, and mobile in human, animal, and environmental microbiomes – Juan Salvador Inda-Díaz, Marcos Parras-Moltó, Anna Johnning, Johan Bengtsson-Palme & Erik Kristiansson – Microbiome

Prevalence of Plasmid-Associated Tetracycline Resistance Genes in Multidrug-Resistant Escherichia coli Strains Isolated from Environmental, Animal and Human Samples in Panama – I. E. Ramírez-Bayard – Antibiotics

Perspective: Challenges in Forecasting Antimicrobial Resistance – Sen Pei – Emerging Infectious Diseases

Determination and quantification of microbial communities and antimicrobial resistance on food through host DNA-depleted metagenomics – Samuel J. Bloomfield – Food Microbiology

Editorial: Antimicrobial resistance and antimicrobial alternatives – Marwan Osman – Frontiers in Medicine

Review: Reframing antimicrobial resistance as a continuous spectrum of manifestations – Sarah M Schrader – Current Opinion in Microbiology

Intermittent antibiotic treatment of bacterial biofilms favors the rapid evolution of resistance – Masaru Usui – Communications Biology

Heavy Metal Pollution Impacts Soil Bacterial Community Structure and Antimicrobial Resistance at the Birmingham 35th Avenue Superfund Site – Anuradha Goswami – Microbiology Spectrum

Horizontal gene transfer
Review: How do interactions between mobile genetic elements affect horizontal gene transfer? – Tanya Horne – Current Opinion in Microbiology

Antimicrobial peptides

Development of novel broad-spectrum antimicrobial lipopeptides derived from plantaricin NC8 β – Emanuel Wiman – Scientific Reports

Global health

*Preprint: Within-host density and duration of colonization of multidrug-resistant Enterobacterales acquired during travel to the tropics – Olivier Cotto, Laurence Armand-Lefèvre, Sophie Matheron, Etienne Ruppé, François Blanquart the VOYAG-R study group – bioRxiv

Review: Reservoirs of antimicrobial resistance in the context of One Health – Milena Despotovic – Current Opinion in Microbiology

Alterations in faecal microbiome and resistome in Chinese international travellers: a metagenomic analysis – Man Kit Cheung – Journal of Travel Medicine

Human-associated AMR

Functional metagenomic libraries generated from anthropogenically impacted environments reveal importance of metabolic genes in biocide and antibiotic resistance – Aimee K. Murray – Current Research in Microbial Sciences

Population-level impacts of antibiotic usage on the human gut microbiome – Kihyun Lee – Nature Communications

Genomic diversity of non-diarrheagenic fecal Escherichia coli from children in sub-Saharan Africa and south Asia and their relatedness to diarrheagenic E. coli – Tracy H. Hazen – Nature Communications

Integrative omics identifies conserved and pathogen-specific responses of sepsis-causing bacteria – Andre Mu – Nature Communications

Development of the oral resistome during the first decade of life – Smitha Sukumar – Nature Communications

Mutations Related to Antibiotics Resistance in Helicobacter pylori Clinical Isolates from Bangladesh – Kartika Afrida Fauzia – Antibiotics


Extended-Spectrum β-Lactamase Genes Traverse the Escherichia coli Populations of Intensive Care Unit Patients, Staff, and Environment – Robert A. Moran – Microbiology Spectrum

Rectal carriage of extended-spectrum β-lactamase-producing Enterobacteriales among neonates admitted into a special care baby unit, southwest Nigeria – Temitope O Obadare – Transactions of The Royal Society of Tropical Medicine and Hygiene

Virulence analysis and antibiotic resistance of Klebsiella pneumoniae isolates from hospitalised patients in Poland – Barbara Kot – Scientific Reports


Plasmid-Mediated Colistin Resistance Genes mcr-1 and mcr-4 in Multidrug-Resistant Escherichia coli Strains Isolated from a Healthy Pig in Portugal – Ana Amaro – Microbial Drug Resistance

Phenotypic and genotypic characterization of antibiotic resistance of Salmonella Heidelberg in the south of Brazil – Luana Sielski Galvão Soares – International Journal of Food Microbiology

Trophic level and proteobacteria abundance drive antibiotic resistance levels in fish from coastal New England – Benjamin J. Korry – Animal Microbiome

Longitudinal study of the short- and long-term effects of hospitalisation and oral trimethoprim-sulfadiazine administration on the equine faecal microbiome and resistome – Mathijs J. P. Theelen – Microbiome

In vitro digestion of ESC-resistant Escherichia coli from poultry meat and evaluation of human health risk – May Linn Buberg – Frontiers in Microbiology

Identification and characterization of the causative agents of Focal Ulcerative Dermatitis in commercial laying hens – Diana I. Ayala – Frontiers in Veterinary Science


Microbiome, resistome and mobilome of chlorine-free drinking water treatment systems – David Calderón-Franco – Water Research

Review: Sewage surveillance of antibiotic resistance holds both opportunities and challenges – D. G. Joakim Larsson – Nature Reviews Microbiology

Preprint: Antibiotic Resistance Gene Variant Sequencing is Necessary to Reveal the Complex Dynamics of Immigration from Sewers to Activated Sludge – Claire Gibson – bioRxiv

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

Viruses and phages

The persistence and stabilization of auxiliary genes in the human skin virome – Ema H. Graham – Virology Journal

Altered infective competence of the human gut microbiome in COVID-19 – Laura de Nies – Microbiome

Review: Antimicrobial resistance in patients with COVID-19: a systematic review and meta-analysis – Bradley J Langford – The Lancet Microbe

Characterization of antibiotic resistomes by reprogrammed bacteriophage-enabled functional metagenomics in clinical strains – Gábor Apjok – Nature Microbiology


AMR for R package v2.0

Prediction of vancomycin initial dosage using artificial intelligence models applying ensemble strategy – Wen-Hsien Ho – BMC Bioinformatics


Nanopore Sequencing Discloses Compositional Quality of Commercial Probiotic Feed Supplements – Worarat Kruasuwan – Scientific Reports

*Quantification of the mobility potential of antibiotic resistance genes through multiplexed ddPCR linkage analysis – Magali de la Cruz Barron, David Kneis, Alan Xavier Elena, Kenyum Bagra, Thomas U Berendonk, Uli Klümper – FEMS Microbiology Ecology

News and Views

European Science-Media Hub – Interview with Prof. Francesco Imperi on new strategies to fight antimicrobial resistance

Antibiotic Resistance: A mobile target – Carolina Oliveira de Santana – eLife


The AMR Studio Episode 46 – Alison Prendiville & service design. Antimicrobials in food animals. Bacteriuria & ICU stays.

EDITORS IN CONVERSATION Episode 63 – Antimicrobial Resistance in Neisseria gonorrhoeae


WHO costing & budgeting tool for national action plans on AMR – A review and country experiences

AMR February, 2023

prepared by Svetlana Ugarcina Perovic

This very first 2023 AMR digest features global AMR use trends in food-producing animals, antibiotic resistance in the commensal human gut microbiota, functional metagenomics in clinical strains, and more!

Antibiotic development

Deep mutational scanning of essential bacterial proteins can guide antibiotic development – Liselot Dewachter – Nature Communications

Global resistome

Global trends in antimicrobial use in food-producing animals: 2020 to 2030 – Ranya Mulchandani – Plos Global Public Health
*The global usage of veterinary antimicrobials in 2020 at 99,502 tonnes, and -on current trends- project an 8% increase by 2030 (~107,500 tonnes). In 2020, China, Brazil, India, and United States remain in the top 5 countries for absolute antimicrobial use in tonnes. There is still no publicly available country-level reports of veterinary antimicrobial use in the majority of countries of the world!

Human gut

Antibiotic resistance in the commensal human gut microbiota – Lisa E Lamberte, Willem van Schaik – Current Opinion in Microbiology

Longitudinal fluctuations of common antimicrobial resistance genes in the gut microbiomes of healthy Dutch individuals – Jakob J. Malin – International Journal of Antimicrobial Agents

Vaginal microbiome

Microdiversity of the Vaginal Microbiome is Associated with Preterm Birth – Jingqiu Liao – bioRxiv

Urinary tract

Phenotypic and genomic characterization of Pseudomonas aeruginosa isolates recovered from catheter-associated urinary tract infections in an Egyptian hospital – Mohamed Eladawy – bioRxiv

Wastewater resistome

A proposed framework for the identification of indicator genes for monitoring antibiotic resistance in wastewater: Insights from metagenomic sequencing – Mehedi Hasan Tarek, Emily Garner – Science of The Total Environment
*Based on public data from 191 wastewater samples originating from 64 countries, this framework revealed 56 candidate indicator ARGs distributed across four modules of strongly correlated ARGs, with one ARG from each module (oqxA, ermB, sul1, and mexE) proposed as a minimally redundant monitoring target.

Metagenomic Insight into Microbiome and Antibiotic Resistance Genes of High Clinical Concern in Urban and Rural Hospital Wastewater of Northern India Origin: a Major Reservoir of Antimicrobial Resistance – Absar Talat – Microbiology Spectrum

Metagenomic Analysis of the Abundance and Composition of Antibiotic Resistance Genes in Hospital Wastewater in Benin, Burkina Faso, and Finland – Melina A. Markkanen – mSphere

Hospital and urban wastewaters shape the structure and active resistome of environmental biofilms – Elena Buelow – bioRxiv

The @UK_WIR CIP3 AMR in wastewater report is now available online here


Evolutionary Responses to Acquiring a Multidrug Resistance Plasmid Are Dominated by Metabolic Functions across Diverse Escherichia coli Lineages – Laura Carrilero – mSystems


Comparative metagenomics reveals poultry and swine farming are hotspots for multidrug and tetracycline resistance – Victoria Osorio – Environmental Pollution

Deciphering risks of resistomes and pathogens in intensive laying hen production chain – Yixiao Zhu – Science of The Total Environments

Expanded catalogue of metagenome-assembled genomes reveals resistome characteristics and athletic performance-associated microbes in horse – Cunyuan Li – Microbiome


Characterization of antibiotic resistomes by reprogrammed bacteriophage-enabled functional metagenomics in clinical strains – Gábor Apjok – Nature Microbiology
*A functional metagenomics pipeline called Reprogrammed Bacteriophage Particle Assisted Multi-species Functional Metagenomics (DEEPMINE). The authors use of T7 bacteriophage with exchanged tail fibres and targeted mutagenesis to expand phage host-specificity and efficiency for functional metagenomics. By screening for ARGs in soil and gut microbiomes and clinical genomes against 13 antibiotics, the authors demonstrate that this approach substantially expands the list of identified ARGs.

An optogenetic toolkit for light-inducible antibiotic resistance – Michael B. Sheets – Nature Communications


A global Corynebacterium diphtheriae genomic framework sheds light on current diphtheria reemergence – Melanie Hennart – bioRxiv
*The authors developed the bioinformatics pipeline DIPHTOSCAN (available at https://gitlab.pasteur.fr/BEBP/diphtoscan) to extract from genomes, medically relevant features including the toxin gene presence and disruption.

Comparison of long- and short-read metagenomic assembly for low-abundance species and resistance genes – Sosie Yorki – Briefings in Bioinformatics

Education & Courses

MicroMundo: experimental project fostering contribution to knowledge on antimicrobial resistance in secondary school – Beatriz Robredo – FEMS Microbiology Letters

Course: Antibiotic Resistance – The Silent Tsunami by ReAct

AMR December, 2022

prepared by Anna Abramova

This AMR digest features overview of sewage resistomes from most countries on Earth and importance of sewage surveillance of antibiotic resistance, latest news on inner secrets of Asgard archaea and microbiomes of Galapagos marine iguanas… and lots of Santas hats here and there. Happy #AMR reading!

EMBARK team wishes you happy holidays!


Genomic analysis of sewage from 101 countries reveals global landscape of antimicrobial resistance – Patrick Munk – Nature Communications
* The authors analyzed 757 sewage samples from 243 cities in 101 countries. This study provides a comprehensive sewage-based overview of global ARG abundance, diversity, and genomic backgrounds from most countries on Earth.

Review: Sewage surveillance of antibiotic resistance holds both opportunities and challenges – Joakim Larsson – Nature Reviews Microbiology
* In this brief commentary, the authors discuss recent European Union-directive that requests that member states monitor antibiotic resistance at all sewage treatment plants serving >100,000.

Review: Bacterial survivors: evaluating the mechanisms of antibiotic persistence – Xiaoyi Shi and Ashraf Zarkan – Microbiology

Defining the Benefits of Antibiotic Resistance in Commensals and the Scope for Resistance Optimization – Kristofer Wollein Waldetoft – Microbial Ecology
* Antibiotic resistance is commonly viewed as universally costly, regardless of which bacterial cells express resistance. In this paper, the authors derive an opposing logic, where resistance in commensal bacteria can lead to reductions in pathogen density and improved outcomes on both the patient and public health scales (Figure 1).

Figure 1. Potential costs and benefits of antibiotic resistance in commensal organisms.

Review: The role of bacterial transport systems in the removal of host antimicrobial peptides in Gram-negative bacteria – Jessica M A Blair – FEMS Microbiology Reviews

Mysterious Asgard archaea microbes reveal their inner secrets – Jan Löwe – Nature News and Views
* Asgard archaeal cells have been grown successfully in the laboratory and their internal architecture offers clues to the early evolution of eukaryotic cells. Have a look inside a proposed relative of our cellular ancestors!


Extended-spectrum β-lactamase genes traverse the Escherichia coli populations of ICU patients, staff and environment – Robert A. Moran – bioRxiv

A Clinical Study Provides the First Direct Evidence That Interindividual Variations in Fecal β-Lactamase Activity Affect the Gut Mycobiota Dynamics in Response to β-Lactam Antibiotics – Margot Delavy – Human Microbiome

Meta-analysis of sputum microbiome studies identifies airway disease-specific taxonomic and functional signatures – Abhirupa Ghosh and Sudipto Saha – Journal of Medical Microbiology

Human microbiome

Human microbiota drives hospital-associated antimicrobial resistance dissemination in the urban environment and mirrors patient case rates – Cecilia Salazar – Microbiome

Characterization and Spatial Mapping of the Human Gut Metasecretome – Florencia Velez-Cortes and Harris Wang – Computational Biology


Characterization of the gut microbiome and resistome of Galapagos marine iguanas (Amblyrhynchus cristatus) from uninhabited islands – Karla Vasco – BMC Animal Microbiome
* This study shows a diverse resistome composition in the Galapagos marine iguanas from remote islands raising concerns about the dispersion of microbial-resistant threats in pristine areas.

Guts within guts: the microbiome of the intestinal helminth parasite Ascaris suum is derived but distinct from its host – Ankur Midha, Víctor Hugo Jarquín-Díaz, Friederike Ebner, Ulrike Löber, Rima Hayani, Arkadi Kundik, Alessio Cardilli, Emanuel Heitlinger, Sofia Kirke Forslund & Susanne Hartmann – Microbiome
* Intestinal helminths are extremely prevalent among humans and animals, and live in intimate contact with the host gut microbiota and harbor bacteria within their own intestines. This study shows that a nematode infection reduces the microbiome diversity of the host gut, and that the nematode gut represents a selective bacterial niche harboring bacteria that are derived but distinct from the host gut.

Gut microbiota of homing pigeons shows summer–winter variation under constant diet indicating a substantial effect of temperature – Maurine W. Dietz – Animal Microbiome

The skin microbiota of the axolotl Ambystoma altamirani is highly influenced by metamorphosis and seasonality but not by pathogen infection – Emanuel Martínez-Ugalde – Animal Microbiome


Biophysical basis of phage liquid crystalline droplet-mediated antibiotic tolerance in pathogenic bacteria – Jan Böhning – bioRxiv
* In this work the authors investigate how phage liquid crystalline droplets in P. aeruginosa biofilms protect bacteria from antibiotics (Figure 2).

Figure 2 Schematic depicting biophysical nature of phage liquid crystalline droplet-mediated antibiotic tolerance of bacteria.


Microbiome, resistome and mobilome of chlorine-free drinking water treatment systems – David Calderón-Franco – bioRxiv

The antibiotic resistance and risk heterogeneity between urban and rural rivers in a pharmaceutical industry dominated city in China: The importance of social-economic factors – Lulu Zhang – Science of The Total Environment

Genome-resolved insight into the reservoir of antibiotic resistance genes in aquatic microbial community – Zahra Goodarzi – Scientific Reports
* This study shows the distribution of ARGs in the Caspian Sea ecosystem (Figure 3). To this end, the authors performed genome-resolved metagenomic analyses of deeply sequenced depth profile metagenomes of the Caspian Sea and applied Hidden Markov models. They further investigated how ecological strategies of resistance bacteria affect the ARGs they contain. Comparative analysis revealed that Acidimicrobiia and Actinobacteria characterized by streamlined genomes modify the antibiotic target via mutation to develop antibiotic resistance rather than carrying extra resistance genes.

Figure 3 Antibiotic resistance gene profile of the Caspian Sea Bacteria


Early season soil microbiome best predicts wheat grain quality – Numan Ibne Asad – FEMS Microbiology Ecology


Validation and Application of Long-Read Whole-Genome Sequencing for Antimicrobial Resistance Gene Detection and Antimicrobial Susceptibility Testing – Thomas Weinmaier – Computational Biology


Ten simple rules for investigating (meta)genomic data from environmental ecosystems – Paton Vuong – PLoS Computational Biology

Events, Podcasts and more

10th Congress of European Microbiologists: 9 – 13 July 2023, Hamburg, Germany

Remember to wash your hands and stay healthy! ☺️

Last EMBARK webinar this year

Time flies and it is time for the last EMBARK webinar of 2022. This month, we are pleased to have Joakim Larsson talk about the environment’s role antibiotic resistance and Antti Karkman present hosts of antibiotic resistance genes in urban sewage. Welcome on Thursday December 15! Registration link below.

Dec 15, 14:00 UTC+2
Joakim Larsson – On the environment’s role in evolution, transmission and surveillance of antibiotic resistance
Antti V. Karkman – Host and vehicles of antibiotic resistance genes in urban sewage
[Register here]