Mission

The aims and goals of the SEARCHER program

Read More

Protocols

Find the protocol proposals made by the EMBARK and SEARCHER programs

Read More

The Team

Read more about the people involved in SEARCHER

Read More

Date:Posted By:Category:AMR Digest

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!

Date:Posted By:Category:EMBARK NEWSTag:

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!

Date:Posted By:Category:EMBARK NEWSTag:, , ,

Coronavirus-related setbacks

Unfortunately, the novel coronavirus disease (COVID-19) is impacting some of the EMBARK communications and outreach as well, and I regret to inform you that today’s meeting with on NordicMappingAMR arranged by the Swedish Medical Products Agency where we would have presented and discussed EMBARK has been cancelled and postponed until after the summer.

Similarly, the workshop and seminar on monitoring of antibiotic resistance in the environment organized by Resistomap and others that was to take place in late April in Helsinki, and where EMBARK was going to be presented, has also been postponed until August.

Finally, the team is discussing how to best proceed with e.g. sampling strategies in the time of lockdowns and travel restrictions. We are still working on this, but at this point this only looks like it will delay portions of the program, and not have major impacts on the research activities. This analysis may of course change depending on how the COVID-19 outbreak develops.

Date:Posted By:Category:EMBARK NEWSTag:, ,

Open Postdoc Position Coelho Lab

The Coelho lab is hiring a postdoc to work with understand antimicrobial resistance trends in public metagenome databases directly connected to the EMBARK program. The work is mostly computational, but there can also be some field and lab work (collecting samples).

As all EMBARK positions, this postdoc project will be performed n collaboration with the rest of the EMBARK team, so if your current skill set doesn’t include all of this, but you are interested in the position, then do apply! This position is open until being filled, so send your application as soon as possible.

The lab looks for a candidate with a strong background (including graduate work) in either computational biology or microbiology. If you feel that you are the right person for this position, you can apply here. To apply: send an email to luispedro@big-data-biology.org with your CV (preferably without a photo) and one representative publication. Later in the process, you will be asked for two reference letters, but they are not necessary for the initial application.

More information is available here: http://big-data-biology.org/positions/pd-embark/