EMBARK Spring Webinars

We have a very exciting lineup of speakers for the 2022 EMBARK Webinars! Let’s begin with the speakers for the spring. Registration opens today!

March 16Windi Muziasari – “Global database of ARGs in the environment”
Anna Abramova – “Meta-analysis reveals the global picture of antibiotic resistance gene prevalence across environments”

April 13: Ramanan Laxminarayan – “State of the World’s Antibiotics 2022”
Cheng Zhao – “Optimizing antimicrobial resistance surveillance in farm animals”

May 18: Nichole Broderick – “Tiny Earth”
Filipa Grosso – “Implementing citizen-based projects on Antimicrobial Resistance Awareness in Southern Europe: the experience from MicroMundo”

June 15: Marisa Haenni – “From AMR surveillance to research in the French veterinary sector”
Reshma Silvester – “AMR in aquaculture- Averting the crisis and the way forward”

And for the fall, we have preliminary confirmation for the following speakers:
Jon Hobman
Stineke van Houte
Iruka Okeke
Joakim Larsson


prepared by Rémi Gschwind

This February issue presents studies on the presence of antibiotic resistance genes, as usual, in various environments according to the One Health concept. Human microbiome is considered as a reservoir of antibiotic resistance genes and in this digest we have a special highlight on the effect of antibiotics on newborns microbiome. Hospital environment is also discussed with methods for prediction of resistance and resistance prevalence in several context. Finally, studies focusing on antibiotic resistance in a more environmental perspective are also presented to complete this One Health circle.

Human microbiome

Impact of long-term dietary habits on the human gut resistome in the Dutch population – Paul B. Stege – Scientific Reports

Effects of early-life antibiotics on the developing infant gut microbiome and resistome: a randomized trial – Marta Reyman – Nature Communications
In addition to the undeniable beneficial effects of antibiotics on newborns life span, antibiotics also have deleterious side effects such as microbiome species richness depletion and antibiotic resistant bacteria selection. Side effects could be even more deleterious if we take into account side effects that might have detrimental effects later in life according to the developmental origin of health and disease concept. Reyman et al. conducted the ZEBRA study enrolling 147 infants born at term either by natural delivery or cesarean section, for whom broad spectrum antibiotics were used. Reduced gut microbial diversity and prolonged ecological perturbations were detected compared with healthy term-born controls (still measurable after 12 months). Also, shifts in AMR gene profile were evidenced using qPCR and confirmed by metagenomic shotgun sequencing of a subset of samples. Those effects were different depending on the antimicrobial use (penicillin+gentamicin being the least deleterious) highlighting antibiotics choice importance.

Gut microbiome signatures and host colonization with multidrug-resistant bacteria – Nicole S.Isles – Trends in Microbiology

Hospital environment

Extended-Spectrum Beta-Lactamase and Carbapenemase-Producing prediction in Klebsiella pneumoniae based on MALDI-TOF mass spectra – Alejandro Guerrero-López – bioRxiv

Genomic diversity and antimicrobial resistance of Prevotella species isolated from chronic lung disease airways – Kasey A. Webb –Microbial Genomics

Long read sequencing reveals genomic diversity and associated plasmid movement of carbapenemase-producing bacteria in a UK hospital over six years – Leah Roberts – OSF Preprints

Environmental antibiotic resistance

Deciphering the extracellular and intracellular antibiotic resistance genes in multiple environments reveals the persistence of extracellular ones – Yina Zou – Journal of Hazardous Materials

Long-read metagenomic sequencing reveals shifts in associations of antibiotic resistance genes with mobile genetic elements from sewage to activated sludge – Dongjuan Dai – Microbiome

Carriage of antibiotic resistant bacteria in endangered and declining Australian pinniped pups – Mariel Fulham – PlosOne

A new insight into the ARG association with antibiotics and non-antibiotic agents—antibiotic resistance and toxicity – Shaojing Sun – Environmental Pollution

Impact of fertilization with pig or calf slurry on antibiotic residues and resistance genes in the soil – Huygens Judith – Science of The Total Environment

Monitoring and evaluation of antibiotic resistance genes in three rivers in northeast China – Chen Zao – Environmental Science and Pollution Research

Meta-analysis reveals the global picture of antibiotic resistance gene prevalence across environments – Anna Abramova – bioRxiv

Fundamental microbiology

Evolution of ColE1-like plasmids across γ-Proteobacteria: From bacteriocin production to antimicrobial resistance – Manuel Ares-Arroyo – PLOS Genetics

Tolerance and resistance of microbial biofilms – Oana Ciofu – Nature Reviews – Microbiology

Gradients in gene essentiality reshape antibacterial research – Andrew M Hogan – FEMS Microbiology Reviews

The evolution of colistin resistance increases bacterial resistance to host antimicrobial peptides and virulence – Pramod K. Jangir – bioRxiv
Colistin is an efficient antimicrobial peptide (AMP) used at a large scale in agriculture in the 1980s. Today, it is being used as “last-resort” antimicrobial to treat infections. One serious concern lies in the potential cross resistance between colistin resistance and host AMP resistance (since they have common physicochemical properties and mechanisms) which could increase pathogen transmission and virulence. Colistin resistance is mainly due to MCR-1 which became widely distributed across all niches because of bacterial migration and horizontal transfer. Here, Jangir et al. tested the hypothesis that evolving colistin resistance via MCR genes acquisition promotes resistance in bacteria against host AMPs. The presence of MCR indeed increased resistance against several AMPs coming from different sources. It highlights the importance of assessing the impact of evolved resistance to future therapeutic AMPs.


Emerging laboratory and point-of-care technologies for detection of AMR and bacterial infection in veterinary medicine – ESCMID, 9 March 2022

Workshops, Seminars &c

Risk assessment of biocide and antibiotic resistance – BIOCIDE consortium, 9 March 2022

Plasmids as vehicles of AMR spread – The Abdus Salam International Centre for Theoretical Physics, 21-25 March 2022

CHARM Virtual Seminar Series 2022, Bi-weekly Tuesdays 9:00-10-00 am


prepared by Marcus Wenne

In December’s AMR digest we ask a wide range of questions. Why do antibiotics exist? What effect do they have on our own microbiota? Can they increase the colonizing capability of plasmid carrying bacteria? And what methods can we use to measure resistance against them? This is a small sample of the wide range of topics in this month’s digest.

Antibiotic research and development

Review: Prospects for Antibacterial Discovery and Development – Thomas M Privalsky – Journal of the American Chemical Society

Why Do Antibiotics Exist? – Fabrizio Spagnolo – mBio


Increase in antimicrobial resistance in Escherichia coli in food animals between 1980 and 2018 assessed using genomes from public databases – João Pires – Journal of Antimicrobial Chemotherapy
*This study utilized public databases to infer the level of multi drug resistance in E .coli on a global scale from 1980 to 2018. The authors detected an increase in the number of antibiotics E. coli tended to carry resistance against (MDR score) by 1.6 times during this time frame.

Evolution of ColE1-like plasmids across γ-Proteobacteria: From bacteriocin production to antimicrobial resistance – Manuel Ares-Arroyo – Plos Genetics

Global protein responses of multi-drug resistant plasmid containing Escherichia coli to ampicillin, cefotaxime, imipenem and ciprofloxacin – Anatte Margalit – Journal of Global Antimicrobial Resistance

Towards the biogeography of prokaryotic genes – Luis Pedro Coelho – Nature


Correlation between phenotypic virulence traits and antibiotic resistance in Pseudomonas aeruginosa clinical isolates – Osama Nassar – Microbial Pathogenesis

Antimicrobial resistance in commensal opportunistic pathogens isolated from non-sterile sites can be an effective proxy for surveillance in bloodstream infections – Karina-Doris Vihta – Scientific Reports

Identification of antibiotic collateral sensitivity and resistance interactions in population surveillance data – Laura B Zwep – JAC-Antimicrobial Resistance

Human Microbiome

Combinatorial, additive and dose-dependent drug–microbiome associations – Sofia K Forslund – Nature
*This study used a multi-omics approach to investigate drug-microbiome interactions in patients suffering from cardiometabolic disease. The authors found that multiple antibiotic exposures had cumulative effects on the patients microbiome. Leading to reduced richness and increased resistance, which are hallmarks of microbiota in patients suffering from obesity, insulin resistance and low-grade inflammation.

Influence of timing of maternal antibiotic administration during caesarean section on infant microbial colonisation: a randomised controlled trial – Thomas Dierikx – Gut Microbiota


Implications of the use of organic fertilizers for antibiotic resistance gene distribution in agricultural soils and fresh food products. A plot-scale study – Claudia Sanz – Science of The Total Environment

AMR detection methods

Review: Progressing Antimicrobial Resistance Sensing Technologies across Human, Animal, and Environmental Health Domains – Kira J Fitzpatrick – Journal of the American Chemical Society

Integrating Scalable Genome Sequencing Into Microbiology Laboratories for Routine Antimicrobial Resistance Surveillance – Mihir Kekre – Clinical Infectious Diseases

Review: Engineered CRISPR-Cas systems for the detection and control of antibiotic-resistant infections – Yuye Wu – Journal of Nanobiotechnology

Rapid absolute quantification of pathogens and ARGs by nanopore sequencing – Yu Yang – The Science of the Total Environment
*Sequencing has become cheaper, faster and more accessible these last few decades. With the use of third generation sequencing these authors test a method where they can quantify the absolute abundance of both pathogens and resistance genes in 4 hours using third generation nanopore sequencing. Taking advantage of the nanopore technologies long reads, the authors were able to link resistance genes to individual taxa.

Sewage treatment

The physiological and ecological properties of bacterial persisters discovered from municipal sewage sludge and the potential risk – Xiang Liu – Environmental Research

Water environment

Metagenomic profiles of the resistome in subtropical estuaries: Co-occurrence patterns, indicative genes, and driving factors – Lei Zhou – Science of The Total Environment

Assessment on impact of sewage in coastal pollution and distribution of fecal pathogenic bacteria with reference to antibiotic resistance in the coastal area of Cape Comorin, India – Nanthini S Victoria – Marine Pollution Bulletin

Animal experiment

Colonization of gut microbiota by plasmid-carrying bacteria is facilitated by evolutionary adaptation to antibiotic treatment – Peng Zhang – The ISME Journal



Future conferences


Last Fall Webinar

Make sure not to miss the last EMBARK Webinar of the fall! This time we have two very exciting speakers:

  • 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”

Register today!


prepared by Rémi Gschwind

The AMR digest from November features studies on antibiotic perception, consumption and also how the environment can influence AMR diffusion. Fundamental microbiology linked to AMR is also part of this month digest including subjects such as bacterial cell wall or biofilm. Different environments are also discussed within the papers on natural habitat and animals or water environments. Finally, there’s a special highlight on antibiotic resistance in cancer patient in this “movember” month.


Global antibiotic consumption and usage in humans, 2000-18: a spatial modelling study – Annie J Browne – The Lancet
*This article describes how antibiotic is consumed globally. Thanks to individual level data and geostatistical model they could estimate antibiotic usage and consumption in 204 countries from 2000 to 2018. Beside large increases in the consumption of different classes of antibiotics in several regions, lack of access to antibiotics still seems to be a problem in other regions. Having those estimation, strategies can be thought to adapt the combat against antibiotic resistance increase.

‘They eat it like sweets’: A mixed methods study of antibiotic perceptions and their use among patients, prescribers and pharmacists in a district hospital in Kabul, Afghanistan – Doris Burtscher – PlosOne

What Is the Role of the Environment in the Emergence of Novel Antibiotic Resistance Genes? A Modeling Approach – Johan Bengtsson-Palme -Environmental Science and Technology

Trends, relationships and case attribution of antibiotic resistance between children and environmental sources in rural India – Joseph Mitchell – Scientific Reports

Fundamental microbiology

Colistin resistance in Escherichia coli confers protection of the cytoplasmic but not outer membrane from the polymixin antibiotic – Madeleine Humphrey – Microbiology Society

Microniches in biofilm depth are hot-spots fro antibiotic resistance acquisition in response to in situ stress – Linda Tlili – bioRxiv

The vulnerable versatility of Salmonella antibiotic persisters during infection – Peter W.S. Hill – Cell Host & Microbe

The role of potentiating mutations in the evolution of pandemic Escherichia coli clones – Elizabeth A. Cummins – European Journal of Clinical Microbiology & Infectious Diseases

Phase separation in the outer membrane of Escherichia coli Georgina Benn – PNAS

Human associated resistome

Metagenomic analysis of microbial communities and antibiotic resistance genes in spoiled household chemicals – Gang Zhou – Chemosphere

Risks of antibiotic resistance genes and antimicrobial resistance under chlorination disinfection with public health concerns – Liping Ma – Environment International

Multidrug resistance dynamics in Salmonella in food animals in the United States: An analysis of genomes from public databases – João Pires – Microbiology Spectrum

Natural Habitat & Animals

Antibiotic resistance in the environment – D. G. Joakim Larsson and Carl-Fredrik Flack – Nature Reviews Microbiology

The myth of antibiotic spider silk – Simon Fruergaard – iScience

Metagenomic strategies identify diverse integron-integrase and antibiotic resistance genes in the Antartic environment – Verónica Antelo – Microbiology Open

Gacier-fed stream biofilmsz harbour diverse resistomes and biosynthetic gene clusters – Sussheel Bhanu Busi – bioRxiv

Water environment & Waste water

Mobilome-driven segregation of the resistome in biological wastewater treatment – Laura de Nies – bioRxiv

Wastewater bypass is a major temporary point-source of antibiotic resistance genes and multi-resistance risk factors in a Swiss river – Jangwoo Lee – Water Research

AMR & diseases

Antibiotic inhibition of the Plasmodium apicoplast decreases haemoglobin degradation and antagonises dihydroartemisinin action – Emily M. Crisafulli – bioRxiv

Antibiotic resistance in the patient with cancer: Escalating challenges and paths forward – Amila K Nanayakkara – CA: a cancer journal for clinicians
*In this interesting review, Nanayakkara and colleagues are discussing the impact of antimicrobial resistance on patient with cancer lifespan. Infection is one of the leading complications in patient with cancer and antimicrobial resistance is related to unfavorable outcomes. Several strategies are discussed to prevent antimicrobial resistant strain outbreak in patient with cancer.