AMR MARCH, 2021

March digest features review on nonlytic antimicrobial functions of complement, metabolic fitness models, BActeriophage SElection for your Laboratory (a collection of representative E. coli phages), Dr Dirt game, and more. Check out our list of AMR focused podcasts. Enjoy!


And, we are exciting to share with you EMBARK NEWS – the SPRING AMR WEBINARS! Join us and our invited speakers to discuss the latest AMR insights. Register for the first webinar on April 28 with Gerry Wright and Luis Pedro Coelho HERE.


General

Review: More than a Pore: Nonlytic Antimicrobial Functions of Complement and Bacterial Strategies for Evasion – Elisabet Bjanes and Victor Nizet – Microbiology and Molecular Biology Reviews
*This review covers lytic and nonlytic roles of complement in the context of antimicrobial immunity and detail bacterial evasion mechanisms with a particular emphasis on clinically relevant Gram-positive pathogens.

Bacterial defenses against a natural antibiotic promote collateral resilience to clinical antibiotics – Lucas A. Meirelles – PlosOne
*Study on how natural toxins can promote tolerance and resistance to clinical antibiotics.

Review: Ancient Antibiotics, Ancient Resistance – Nicholas Waglechner – EcoSalPlus

Metabolism

Metabolic fitness landscapes predict the evolution of antibiotic resistance – Fernanda Pinheiro – Nature Ecology & Evolution
*Pinheiro et al. developed a metabolic model of antibiotic resistance that predicts the dosage-response of common resistance mutants and prevalent resistance mechanisms depending on drug levels and nutrient conditions. These predictions are confirmed by empirical growth inhibition curves and genomic data of Escherichia coli populations exposed to streptomycin challenge.

News & Views: Metabolic models predict evolutionary dynamics – Matthew Scott – Nature Ecology & Evolution

Horizontal gene transfer

Adaptive evolution of hybrid bacteria by horizontal gene transfer – Jeffrey J. Power – PNAS

A mobile genetic element increases bacterial host fitness by manipulating development – Joshua M Jones – eLife

Plasmids facilitate pathogenicity, not cooperation, in bacteria – Anna E. Dewar – ResearchSquare

Piggybacking on niche-adaptation improves the maintenance of multidrug resistance plasmids – Julia Kloos – Molecular Biology and Evolution
*The findings represent a new solution to the “plasmid paradox” and may contribute to an increased understanding of successful associations between specific E. coli lineages and MDR plasmids.

Antimicrobial peptides

Review: Chemically modified and conjugated antimicrobial peptides against superbugs – Wenyi Li – Chemical Society Reviews

Accelerated antimicrobial discovery via deep generative models and molecular dynamics simulations – Payel Das – Nature Biomedical Engineering

Novel antibiotics

Looking for Solutions to the Pitfalls of Developing Novel Antibacterials in an Economically Challenging System – Gilles Courtemanche – Microbiology Research

Enhancement of antibiotic production by co-cultivation of two antibiotic producing marine Vibrionaceae strains – Yannick Buijs – FEMS Microbiology Ecology

Low-cost drug discovery with engineered E. coli reveals an anti-mycobacterial activity of benazepril – Nadine Bongaerts – bioRxiv

Global health

Community-based antibiotic access and use in six low-income and middle-income countries: a mixed-method approach – Nga T T Do – Lancet Glob Health

Antibiotic resistance: Global health crisis and metagenomics – Shailendra Yadav and Atya Kapley – Biotechnology Reports

Human-associated microbiome

Human-associated microbiota suppress invading bacteria even under disruption by antibiotics – Andrew D. Letten – The ISME Journal
*Letten et al. found strong evidence of community-level suppression of the resistant strain in the absence of antibiotics and, despite large changes in community composition and abundance following rifampicin exposure, suppression of the invading resistant strain was maintained in both antibiotic treatments.

Persistence of birth mode-dependent effects on gut microbiome composition, immune system stimulation and antimicrobial resistance during the first year of life – Susheel Bhanu Busi, Laura de Nies – ISME Communications
*The study follows the babies from 5 days after birth through one year of age. Caesarean-section babies had an over-abundance of “synthetic” antibiotic resistance genes.

Review: Association between antibiotics and gut microbiome dysbiosis in children: systematic review and meta-analysis – Lucy McDonnell – Gut Microbes

Review: Early life antibiotics and childhood gastrointestinal disorders: a systematic review – Kim Kamphorst – BMJ Paediatrics Open

Whole-genome analysis of probiotic product isolates reveals the presence of genes related to antimicrobial resistance, virulence factors, and toxic metabolites, posing potential health risks – Ying Wang – BMC Genomics

Clinical environment

Characterization of antimicrobial-resistant Gram-negative bacteria that cause neonatal sepsis in seven low- and middle-income countries – Kirsty Sands – Nature Microbiology

Pervasive transmission of a carbapenem resistance plasmid in the gut microbiota of hospitalized patients – Ricardo León-Sampedro – Nature Microbiology

Investigating potential transmission of antimicrobial resistance in an open-plan hospital ward: a cross-sectional metagenomic study of resistome dispersion in a lower middle-income setting – Anushia Ashokan– Antimicrobial Resistance & Infection Control

Economic Evaluation: Economic Burden of Urinary Tract Infections From Antibiotic-Resistant Escherichia coli Among Hospitalized Adult Patients in Lebanon: A Prospective Cohort Study – Katia Iskandar – Value in Health Regional Issues

Apparent nosocomial adaptation of Enterococcus faecalis predates the modern hospital era – Anna K. Pöntinen – Nature Communications

Antibiotic intervention redisposes bacterial interspecific interacting dynamics in competitive environments – Jing Li – Environmental Microbiology

The evolutionary trade‐offs in phage‐resistant Klebsiella pneumoniae entail cross‐phage sensitization and loss of multidrug resistance – Grazyna Majkowska‐Skrobek – Environmental Microbiology

Resistance to aztreonam in combination with non-β-lactam β-lactamase inhibitors due to the layering of mechanisms in Escherichia coli identified following mixed culture selection – Ching Hei Phoebe Cheung – bioRxiv

Multiple classes of bactericidal antibiotics cause DNA double strand breaks in Staphylococcus aureus – Rebecca S Clarke and Andrew M Edwards – bioRxiv

Comparing treatment strategies to reduce antibiotic resistance in an in vitro epidemiological setting – Daniel C. Angst – PNAS

Discontinuing β-lactam treatment after 3 days for patients with community-acquired pneumonia in non-critical care wards (PTC): a double-blind, randomised, placebo-controlled, non-inferiority trial – Aurélien Dinh – The Lancet

Animal microbiome

Differences in the gut microbiomes of dogs and wolves: roles of antibiotics and starch – Yuting Liu – BMC Veterinary Research

Transmission of Similar Mcr-1 Carrying Plasmids among Different Escherichia coli Lineages Isolated from Livestock and the Farmer – Joaquim Viñes – Antibiotics
*This work highlights the role of livestock as a reservoir of pathotypes with zoonotic potential.

Soil and plant microbiome

Vertical distribution of antibiotic resistance genes in an urban green facade – Shu-Yi-Dan Zhou – Environment International
*Study suggests that microorganisms may move from soil to plant, potentially through an endophytic mechanism and thus, there is a clear potential for movement of ARGs and human pathogens from the outdoor environment.

Targeted metagenomics reveals inferior resilience of farm soil resistome compared to soil microbiome after manure application – Gonçalo Macedo – Science of The Total Environment

Water environment

Unraveling the riverine antibiotic resistome: the downstream fate of anthropogenic inputs – Jangwoo Lee – Water Research
*Great work on drivers of riverine resistomes, pinpointing monitoring targets to identify where human sources and exposures are likely to be most acute. The authors observed the increase of certain gene markers downstream, without obvious sources of anthropogenic contamination.

Review: A systematic review of antibiotics and antibiotic resistance genes in estuarine and coastal environments – Dongsheng Zheng – Science of The Total Environment

Responses of bacterial and bacteriophage communities to long-term exposure to antimicrobial agents in wastewater treatment systems – Bingbing Du – Journal of Hazardous Materials

A Peek into the Plasmidome of Global Sewage – Philipp Kirstahler – bioRxiv

Biotransformation of lincomycin and fluoroquinolone antibiotics by the ammonia oxidizers AOA, AOB and comammox: A comparison of removal, pathways, and mechanisms – Li-Jun Zhou – Water Research

Selective enrichment of comammox from activated sludge using antibiotics – Yulin Wang – Water Research

Viruses and phages

Systematic exploration of Escherichia coli phage-host interactions with the BASEL phage collection – Enea Maffei – bioRxiv
*The BASEL (BActeriophage SElection for your Laboratory) is a collection of representative E. coli phages from all major families with their systematic phenotypic and genomic characterization.

The evolutionary trade‐offs in phage‐resistant Klebsiella pneumoniae entail cross‐phage sensitization and loss of multidrug resistance – Grazyna Majkowska‐Skrobek – Environmental Microbiology

Rapid evolutionary turnover of mobile genetic elements drives microbial resistance to viruses – Fatima Aysha Hussain – bioRxiv

Bioinformatics

The extent of carbapenemase-encoding genes in public genome sequences – Ingmar Janse – PeerJ

Origin Sample Prediction and Spatial Modeling of Antimicrobial Resistance in Metagenomic Sequencing Data – Maya Zhelyazkova – Frontiers in Genetics

Machine-learning prediction of resistance to sub-inhibitory antimicrobial concentrations from Escherichia coli genomes – Sam Benkwitz-Bedford – bioRxiv

Protocols

Protocol for an interdisciplinary cross-sectional study investigating the social, biological and community-level drivers of antimicrobial resistance (AMR): Holistic Approach to Unravel Antibacterial Resistance in East Africa (HATUA) – Benon B Asiimwe – BMJ

Podcast

February 2021 Pod: Global Chang‪e‬ – Bengtsson-Palme Lab – Microbiology Lab Pod

Ep 26. Mirko Ancillotti & bioethics. Resistance to antibiotics vs. vaccines. – Uppsala Antibiotic Center – The AMR Studio

Ep 84. The Dangers of Antibiotic Resistance – Sean Allen and Nathan Allen – Petri Dish

Webinars

University of Nottingham Sutton Bonington AMR Webinar Series 2021

UAC Seminar: The visual culture of antimicrobial resistance by Rachel Irwin – Uppsala Antibiotic Center – April 9

Fun

Dr Dirt – a simulation game from Hoskisson Lab and Game Doctor team on antibiotic discovery

And the Microbes – a comic by Edward Ross and Jamie Hall: Join Luna and her sulky brother Simon on a journey into the weird and wonderful world of microbes.

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!