EMBARK Webinar April 28

The first instance of our webinar series will take place on April 28, at 2PM CEST. Our invited speaker is Gerry Wright who will talk about Approaches to measure and monitor AMR in various environments. There will also be a speaker from the EMBARK program matched to each invited speaker in this webinar series, and this time Luis Pedro Coelho will talk about their work on quantifying AMR at very large scales.

This will be followed by a short Q&A, including a discussion between the two presenters and the moderator. We look forward to seeing you there!

Register for the webinar here!

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”
    [Register]
  • May 19: Heike Schmitt – “International efforts for One Health surveillance of AMR (WHO Tricycle)”
    Etienne Ruppé – “On the use of Tricycle in EMBARK”
    [Register]
  • 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”
    [Register]
  • 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
    [Register]

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”

AMR FEBRUARY, 2021

February digest highlights the current state of vaccines against resistant bacterial pathogens and novel ways by which they can evolve resistance, effects of common sweeteners on conjugation rate and how international travel contributes to spread of multidrug-resistant bacteria, and much more. Check out our selection of AMR focused podcast episodes and webinars. Happy reading!

Global

Newsletter: WHO Antimicrobial Resistance Newsletter 2021 – WHO

Review: Antimicrobial resistance and COVID-19: Intersections and implications – Gwenan M. Knight – eLife

Review: The role of vaccines in combatting antimicrobial resistance – Francesca Micoli – Nature Reviews Microbiology

Vaccines against AMR pathogens

Review: Beyond Antimicrobial Use: A Framework for Prioritizing Antimicrobial Resistance Interventions – Noelle R. Noyes – Annual Review of Animal Biosciences

Clinically relevant mutations in core metabolic genes confer antibiotic resistance – Allison J. Lopatkin – Science

mutations in core metabolic genes confer antibiotic resistance *Mutations targeting central carbon and energy metabolism arise in response to antibiotic treatment. These mutations confer resistance and are highly prevalent in clinical pathogens, expanding the known means by which pathogenic microbes can evolve resistance.

Nonnutritive sweeteners can promote the dissemination of antibiotic resistance through conjugative gene transfer – Zhigang Yu – ISME Journal
*Exposure to nonnutritive sweeteners (saccharine, sucralose, aspartame) enhances conjugation in bacteria.

Using ecological coexistence theory to understand antibiotic resistance and microbial competition – Andrew D. Letten – Nature Ecology & Evolution

Human resistome

Characterization of the human skin resistome and identification of two microbiota cutotypes – Zhiming Li – Microbiome

Dynamics of intestinal multidrug-resistant bacteria colonisation contracted by visitors to a high-endemic setting: a prospective, daily, real-time sampling study – Anu Kantele – Lancet Microbe
*International travel contributes substantially to the global spread of intestinal multidrug-resistant Gram-negative bacteria. Real-time sampling study of 20 European visitors to Laos volunteered to provide daily stool samples.

Quantifying the effects of antibiotic treatment on the extracellular polymer network of antimicrobial resistant and sensitive biofilms using multiple particle tracking – Lydia C. Powell – npj Biofilms Microbiomes

Soil

Bacterial communities regulate temporal variations of the antibiotic resistome in soil following manure amendment – Jianhua Cheng – Environmental Science and Pollution Research

Water environment

Microbiota analysis of rural and urban surface waters and sediments in Bangladesh identifies human waste as driver of antibiotic resistance – Ross Stuart McInnes – bioRxiv

Antibiotic Resistance in Wastewater Treatment Plants and Transmission Risks for Employees and Residents: The Concept of the AWARE Study – Laura Wengenroth – medRxiv

Animal studies

Metagenomics of antimicrobial and heavy metal resistance in the cecal microbiome of fattening pigs raised without antibiotics – Paiboon Tunsagool – Applied and Environmental Microbiology

Bioinformatics

A roadmap for the generation of benchmarking resources for antimicrobial resistance detection using next generation sequencing – Mauro Petrillo – F1000Research

HMD-ARG: hierarchical multi-task deep learning for annotating antibiotic resistance genes – Yu Li – Microbiome

Critical evaluation of short, long, and hybrid assembly for contextual analysis of antibiotic resistance genes in complex environmental metagenomes – Connor L. Brown – Scientific Reports
Critical evaluation of the impact of assembly leveraging short reads, nanopore MinION long-reads, and a combination of the two (hybrid) on ARG contextualization using seven prominent assemblers.

PathoFact: a pipeline for the prediction of virulence factors and antimicrobial resistance genes in metagenomic data – Laura de Nies – Microbiome

Techniques

Creation of Universal Primers Targeting Nonconserved, Horizontally Mobile Genes: Lessons and Considerations – Damon C. Brown and Raymond J. Turner – Applied and Environmental Microbiology

Robustness in quantifying the abundance of antimicrobial resistance genes in pooled faeces samples from batches of slaughter pigs using metagenomics analysis – Vibe Dalhoff Andersen – Journal of Global Antimicrobial Resistance

Webinars and conferences

Resistomap Webinar Series: Monitoring ARGs in LMICs –  Resistomap – 30 March 2021

CAMDA 2021 Conference – ISMB ECCB – 26-27 July 2021
Data analysis contest challenges: The Metagenomic Phage Forensics of Anti-Microbial Resistance

The Initiative Seminar Engineering Health: Joining forces in healthcare solutions – Chalmers University of Technology in Gothenburg – 13-14 April 2021
*Johan Bengtsson-Palme will talk about Antibiotic resistance as a health and research challenge.

Learning from COVID-19 to tackle the silent pandemic of antibiotic resistance – GARDP – 4 March 2021

AMR Innovation Mission UK 2021 – AMR Insights – 10-12 May 2021

The One Health EJP Annual Scientific Meeting – One Health EJP – 9-11 June 2021

Podcast

The AMR studio:  Ep 25. Linus Sandegren & mobile genetic elements. Identifying resistance origins. Reimbursing ABs. – Uppsala Antibiotic Center – 1 February 2021 

Dr. Heer Mehta: Antibiotic Resistance and Experimental Evolution – The Bioinformatics and Beyond Podcast – 6 February 2021

Courses

Tackling Antibiotic Resistance: What Should Dental Teams Do? – British Society for Antimicrobial Chemotherapy and FDI World Dental Federation
Discover the danger posed by antibiotic resistance, and how dental teams can meet the challenge to protect patients.

AMR January, 2021

January digest features a novel type of colistin resistance genes, effect of exogenic antimicrobials on natural microbiota, in silico prediction of antimicrobial resistance, Micro-combat game, and more. Check out our selection of free web-based AMR seminars &c. Enjoy!

Global

Global Antibiotic Consumption in Humans, 2000 to 2018: A Spatial Modelling Study – Annie J. Browne – SSRN preprint
*GRAMProject study estimating global antibiotic consumption in 204 countries from 2000-2018
Both high rates of antibiotic consumption and a lack of access to antibiotics identified!

Polarization of microbial communities between competitive and cooperative metabolism – Daniel Machado – Nature Ecology & Evolution
*Global microbiome analysis revealed stark polarisation between competitive and cooperative communities. Competitive groups harbour more antimicrobial potential, but cooperative ones are more abundant and occupy diverse habitats.

Perspective: Proximate and ultimate causes of the bactericidal action of antibiotics – Fernando Baquero and Bruce R. Levin – Nature Reviews Microbiology

Carbapenem and Colistin Resistance in Enterobacter: Determinants and Clones – Zhiyong Zong – Trends in Microbiology

Natural habitats

Antimicrobial-specific response from resistance gene carriers studied in a natural, highly diverse microbiome – Wisnu Adi Wicaksono – Microbiome
*After exposure of lichen to a range of antimicrobials, antimicrobial-specific shifts in the lichen bacterial community structure observed! 

Water environment

Review: Antimicrobial Resistance and Bacteriophages: An Overlooked Intersection in Water Disinfection – Ana Carolina Maganha de Almeida Kumlien – Trends in Microbiology

The microbiome of a polluted urban lake harbors pathogens with diverse antimicrobial resistance and virulence genes – Jorge Quillaguamán – Environmental Pollution

Microbial retention and resistances in stormwater quality improvement devices treating road runoff – Renato Liguori – bioRxiv

Annual dynamics of antimicrobials and resistance determinants in flocculent and aerobic granular sludge treatment systems – Rebeca Pallares-Vega – Water Research

Metagenomics analysis of bacteriophages and antimicrobial resistance from global urban sewage – Josephine E. S. Strange – Scientific Reports

Antibiotic resistance gene load and irrigation intensity determine the impact of wastewater irrigation on antimicrobial resistance in the soil microbiome – Ioannis D.Kampouris – Water Research
*Antibiotic resistance gene load and irrigation intensity determine the impact of wastewater irrigation on AMR in the soil microbiome.

wastewater irrigation on AMR

Soil environment

Cross-comparison of methods for quantifying antibiotic resistance in agricultural soils amended with dairy manure and compost – Lauren Wind – Science of The Total Environment

Hospital environment

Antimicrobial resistance determinants are associated with Staphylococcus aureus bacteraemia and adaptation to the hospital environment: a bacterial genome-wide association study – Bernadette C Young – medRxiv

Mode and dynamics of vanA-type vancomycin resistance dissemination in Dutch hospitals – Sergio Arredondo-Alonso – Genome Medicine

Animal experiments

Vancomycin-Induced Changes in Host Immunity and Behavior: Comparative Genomic and Metagenomic Analysis in C57BL/6 and BALB/c Mice – Pratikshya Ray – Digestive Diseases and Sciences

Techniques

Antibiotic Efficacy Testing in an Ex vivo Model of Pseudomonas aeruginosa and Staphylococcus aureus Biofilms in the Cystic Fibrosis Lung – Niamh E. Harrington – Immunology and Infection

Bioinformatics

A novel type of colistin resistance genes selected from random sequence space – Michael Knopp – Plos Genetics
*Random sequences can encode proteins with beneficial functions. Encoded peptides are highly hydrophobic. Dcr are a novel class of resistance genes for last resort antibiotic Colistin.
Read more: Perspective: Harder, better, faster, stronger: Colistin resistance mechanisms in Escherichia coli – Axel B. Janssen and Willem van Schaik – Plos Genetics

Identifying novel β-lactamase substrate activity through in silico prediction of antimicrobial resistance – Kara K. Tsang – Microbial Genomics
*Even simple machine learning (in combination with follow-up experiments) can be used to identify previously undiscovered antimicrobial resistance gene activity!

Mobilization of antibiotic resistance genes differ by resistance mechanism – Tue Kjaergaard Nielsen – bioRxiv

A framework for identifying the recent origins of mobile antibiotic resistance genes – Stefan Ebmeyer – Communications Biology
Read more: Behind the paper 

Webinars &c

13th JPIAMR joint call – live Q&A and presentations: One Health interventions to prevent or reduce the development and transmission of AMR – JPIAMR – 28 January 2021/
Recorded webinar will be available here

Antimicrobial Chemotherapy Virtual Conference 2021 – GARDP and the British Society for Antimicrobial Chemotherapy  –  2- 3 February 2021

If patients had antibiotic treatment options, how would they choose? A trade-off between antibiotic resistance and cost – Uppsala Antibiotic Center & Mirko Ancillotti – 5 February 2021

EU-JAMRAI Final Conference – EU-JAMRAI – 11-12 February 2021

The 2nd International Symposium on Anti-microbial resistance “Man vs Microbe: AMR—The Race of the Century”  – Amrita School of Biotechnology & CHARM UC San Diego – 24-26 February 2021

Managing Antimicrobial Resistance through Behaviour Change – The Uppsala Health Summit –  15-18 March 2021

What’s up with MALDI—TOF mass spectrometry in microbiology? – Luxembourg Institute of Science & Technology – 15-16 April 2021

Courses

TARGET Antibiotics – Prescribing in Primary Care –  British Society for Antimicrobial Chemotherapy & TARGET
Helping primary care professionals to target the use of antibiotics to reduce antimicrobial resistance

Podcast

December 2020 Pod: Christmas theme – Bengtsson-Palme Lab – Microbiology Lab Pod

Fun

Micro-combat – European Joint Action on Antimicrobial Resistance and Healthcare-Associated Infections & Barcelona Institute for Global Health
*A card game where viruses, bacteria, fungi and parasites threaten the health of citizens and you can only save them working as a team!

Luis Pedro Coelho on building a research group in China

EMBARK PI Luis Pedro Coelho recently wrote a perspective piece in Nature Reviews Molecular Cell Biology on starting up a research group in China and the specific and general problems he and other young PIs are facing. Well worth a read if you are curious on scientific diversity, and it also highlights a few of the challenges with large international collaborations, just in terms of sheer administration!