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”

Last Webinar for the Spring

Today, the last EMBARK webinar for the spring will take place, at 13:00 CEST (11:00 UTC). Today’s invited speaker is Kimberly Kline  who will give a talk entitled “Pathogenesis and persistence during Enterococcus faecalis biofilm-associated infection”.

She will be followed by our EMBARK speaker Sofia Forslund, who will give a talk on “High-throughput measurement of host and microbiota”

Register here

Note that this webinar does take place at another time than the previous webinars!

EMBARK Webinars on Youtube

The first two spring webinars have now been posted on the new EMBARK YouTube channel! Tune in to watch Gerry Wright talk about approaches to measure and monitor AMR in various environments, and Heike Schmitt preset the international efforts for one-health surveillance of AMR within WHO Tricycle.

The remaining two EMBARK Webinars from the spring will also be posted online later this summer.

AMR June, 2021

prepared by Ioannis Kampouris

This week, the @EMBARK_JPIAMR team is at the World Microbe Forum:
Svetlana Ugarcina Perovic and Luis Pedro Coelho with their work on ARGs at global scale,
Anna Abramova, Thomas Berendonk and Johan Bengtsson-Palme on ARGs across environments,
Saba Yasmin and Rabaab Zahra on E. coli in sewage water.

We would like to invite you for the 4th #EMBARK2021 webinar with Kimberly Kline and Sofia Forslund!


There is no market for new antibiotics: this allows an open approach to research and development – Dana M. Klug, Fahima I. M. Idiris – Welcome Open Research
*This opinion paper suggests that there is a necessity for a new open source model for antibiotic discovery, which should be independent from whether a market for new antibiotics exist or not.

Destination shapes antibiotic resistance gene acquisitions, abundance increases, and diversity changes in Dutch travelers – Alaric W. D’Souza, Manish Boolchandani – Genome Medicine
*The authors claim that travel shapes the architecture of the human gut resistome and results in AMR gene acquisition against a variety of antimicrobial drug classes.

Soil environment

Modeling the vertical transport of antibiotic resistance genes in agricultural soils following manure application – Renys E. Barrios – Environmental Pollution
*The authors claim that detachment and decay coefficients for ARGs in soil were not affected by manure, while the load of ARGs in leachate was not significantly affected by manure.

Wastewater Treatment

Antibiotic transformation in an anaerobic membrane bioreactor linked to membrane biofilm microbial activity – Moustapha Harb – Environmental Research

Wastewater Based Epidemiology Enabled Surveillance of Antibiotic Resistance – M.V. Riquelme – MedRxiv
*The Wastewater Based Epidemiology approach helped to identify geographic hot-spots where attention towards curbing the spread of antibiotic resistance may be particularly warranted.

Hospital environment

A species-wide genetic atlas of antimicrobial resistance in Clostridioides difficile – Korakrit Imwattana – BioRxiv
*This review provides insights in the global C. difficile population, which may help in the early detection of drug-resistant C. difficile strains.

Human experiments

The infant gut resistome associates with E. coli, environmental exposures, gut microbiome maturity, and asthma-associated bacterial composition – Xuanji Li – Cell Host & Microbiome
*The study reveals a clear bimodal distribution of ARG richness that is driven by the composition of the gut microbiome, especially E. coli.

Agricultural applications

Chitosan as additive affects the bacterial community, accelerates the removals of antibiotics and related resistance genes during chicken manure composting – Hongdou Liu – Science of Total Environment
*The use of chitosan can enhance the remove of antibiotics and antibiotic resistance genes during manure composting.

Animal experiments

Chironomidae larvae: A neglected enricher of antibiotic resistance genes in the food chain of freshwater environments – Chengshi Ding – Environmental Pollution
*Feeding experiments further confirmed that ARGs from Chironomidae larvae can be transferred to the fish gut.


A Peek into the Plasmidome of Global Sewage – Philipp Kirstahler – mSystems
*The authors describe a laboratory and bioinformatics workflow for the recovery of plasmids and other potential extrachromosomal DNA elements from complex microbiomes.

Validation of selective agars for detection and quantification of Escherichia coli resistant to critically important antimicrobials – Zheng Z Lee – bioRxiv


Predicting Antimicrobial Resistance Using Partial Genome Alignments – D. Aytan-Aktug – mSystems

Review: Antibiotic resistance: Time of synthesis in a post-genomic age – Teresa Gil-Gil – Computational and Structural Biotechnology Journal

Horizontal Gene Transfer

Quantitative analysis of horizontal gene transfer in complex systems – Jenifer Moralez – Current Opinion in Microbiology


Comprehensive Scanning of Prophages in Lactobacillus: Distribution, Diversity, Antibiotic Resistance Genes, and Linkages with CRISPR-Cas Systems – Zhangming Pei – mSystems
*Uneven prophage distribution, with highly diverse genome features and distinct clusters based on host species along with detection of ARGs in Lactobacillus prophages.

L-form switching confers antibiotic, phage and stress tolerance in pathogenic Escherichia coli – Aleksandra Petrovic Fabijan – bioRxiv


Superbugs and You – True Stories from Scientists and Patients around the World – The Antimicrobial Resistance Fighter Coalition

The @EMBARK_JPIAMR team wishes you happy Summer holidays!

EMBARK Webinar today

Today we will have the third webinar of the EMBARK Webinar Series!

The invited speaker today is Dearbháile Morris who will give a talk entitled “What lurks beneath: the role of water in the transmission and persistence of AMR”. She will be complemented by our own Rabaab Zahra who will talk about “E. coli STs and Resistance Mechanisms in Sewage from Islamabad”.

This will be followed by a short Q&A, including discussion between the two presenters and the moderator

Register here for the webinar, which will begin at 12:00 UTC (14:00 CEST).