AMR APRIL, 2021

prepared by Saba Yasmin


Our April AMR digest features recent studies on antibiotics resistance in gut microbiota, prediction and quick diagnosis models as well as the role of birds and sewage water in AMR dissemination.


Join the SPRING AMR WEBINARS to discuss the latest AMR insights with us and our invited speakers. You can register HERE for the next webinar on May 19 with Heike Schmitt and Etienne Ruppé.


Global

Commentary: COVID-19: The therapeutic landscape – Catherine I. Paules and Anthony S. Fauci – Cell Press

Bioinformatics

ResistoXplorer: a web-based tool for visual, statistical, and exploratory data analysis of resistome data – Achal Dhariwal – NAR Genomics and Bioinformatics
*ResistoXplorer is a user-friendly tool that enables high-throughput analysis of common outputs generated from metagenomic resistome studies.

Forecasting the dissemination of antibiotic resistance genes across bacterial genomes – Mostafa M. H. Ellabaan – Nature Communications
*The authors predict the potential future dissemination of known ARGs by using statistical framework to identify putative horizontally transferred ARGs and the groups of bacteria that disseminate them. Analysis of ARG-surrounding sequences identify genes encoding putative mobilisation elements such as transposases and integrases that may be involved in gene transfer between genomes.

Rapid nanopore-based DNA sequencing protocol of antibiotic-resistant bacteria for use in surveillance and outbreak investigation – Fabienne Antunes Ferreira – Microbial Genomics
*This study developed and validated a complete analysis protocol for faster and more accurate surveillance and outbreak investigations of antibiotic-resistant microbes based on Oxford Nanopore Technologies (ONT) DNA whole-genome sequencing. The suggested protocol includes: (1) a 20 h sequencing run; (2) identification of the sequence type (ST); (3) de novo genome assembly; (4) polishing of the draft genomes; and (5) phylogenetic analysis based on SNPs.

Human associated microbiome

Signal vs. noise: how to analyze the microbiome and make progress on antimicrobial resistance – Jonathan L Golob and Krishna Rao – The Journal of Infectious Diseases

Dynamic Changes in Microbiome Composition Following Mare’s Milk Intake for Prevention of Collateral Antibiotic Effect – Almagul Kushugulova – Frontier in Cellular and Infectious Microbiology
*This study on the impact of mare’s milk consumption reveals it to be well tolerated in children concurrently receiving antibiotic treatment and suggests positive effects on recovery of the gut microbiome following such perturbation.

Resistome and microbial profiling of pediatric patient’s gut infected with multidrug-resistant diarrhoeagenic Enterobacteriaceae using next-generation sequencing; the first study from Pakistan – Ome Kalsoom Afridi – The Libyan Journal of Medicine
*The findings of the this study were an increased abundance of several pathogenic gram-negative bacteria namely E. coli, Enterobacter cloacae, and Salmonella enterica was observed in the gut microbiota of children infected with MDR bacterial infections than that of the healthy controls. This work indicates that children with MDR infections have reduced microbial diversity and enriched ARGs than healthy controls.

The infant gut resistome is associated with E. coli, environmental exposures, gut microbiome maturity, and asthma-associated bacterial composition – Xuanji Li – Cell Host and Microbe
*Distribution of infant gut resistome is bimodal, mainly driven by E. coli. The infant gut resistome is significantly affected by environmental factors. Low maturity of microbiome associates with high ARG load. A similar asthma-associated gut bacterial composition associates with high ARG load.

Animal associated microbiome

Faecal microbiota and antibiotic resistance genes in migratory waterbirds with contrasting habitat use – Dayana Jarma – Science of the Total Environment
*The authors summarized that storks and gulls carry more antibiotic resistance genes than cranes and geese. Gulls carrying more pathogenic bacteria and resistance to last resort antibiotics.

Review: Epidemiology and Molecular Basis of Multidrug Resistance in Rhodococcus equi – Sonsiray Álvarez Narváez – Microbiology and Molecular Biology Reviews
*This review summarizes the factors that contributed to the development and spread of MDR R. equi, the molecular epidemiology of the emergence of MDR R. equi, the repercussions of MDR R. equi for veterinary and human medicine, and measures that might mitigate antimicrobial resistance at horse-breeding farms, such as alternative treatments to traditional antibiotics.

Deposition of resistant bacteria and resistome through FMT in germ-free piglets – Jing Sun – Letters in Applied Microbiology

Resistance to widely used disinfectants and heavy metals and cross resistance to antibiotics in Escherichia coli isolated from pigs, pork and pig carcass – Jiratchaya Puangseree – Food Control
*The authors concluded that MDR was predominant among the E. coli isolates (89%) from pig, pig carcass and pork. TCS MICs for E. coli in 2011–2014 were significantly higher than those in 2008–2010. MICs of biocides and heavy metals were weak correlated with antibiotic resistance. Exposure to biocides TCS, BKC and CHX contributes to antibiotic resistance.

Microbial genetics

Genetic determinants facilitating the evolution of resistance to carbapenem antibiotics – Peijun Ma – eLife
*In clinical isolates, the authors found that high-level transposon insertional mutagenesis plays an important role in contributing to high-level resistance frequencies in several major and emerging carbapenem-resistant lineages.

CRISPR-Cas is associated with fewer antibiotic resistance genes in bacterial pathogens – Elizabeth Pursey – BioRxiv
*The authors modelled the association between CRISPR-Cas and indicators of horizontal gene transfer and found that pathogens with a CRISPR-Cas system were less likely to carry antibiotic resistance genes than those lacking this defence system.

Environmental microbiology

Review: Monitoring antibiotic resistance genes in wastewater treatment: Current strategies and future challenges – Anh Q. Nguyen – Science of the Total Environment
*Wastewater treatment is a double-edged sword that can act as either a pathway for AMR spread or as a barrier to reduce the environmental release of anthropogenic AMR. This review highlights significant knowledge gaps including inconsistencies in ARG reporting units, lack of ARG/ARB monitoring surrogates, lack of a standardised protocol for determining ARG removal via wastewater treatments, and the inability to support appropriate risk assessment.

Spread of antibiotic resistance genes and microbiota in airborne particulate matter, dust, and human airways in the urban hospital – Zhen-Chao Zhou – Environment International
*The authors found that dust contained diverse antibiotic resistance genes (ARGs) and microbes. Airborne particulate matter contained high total relative abundance of ARGs. Microbes and ARGs in particulate matter posed high risks to patient airways.

Extended-Spectrum β-Lactamase and Carbapenemase Genes are Substantially and Sequentially Reduced during Conveyance and Treatment of Urban Sewage – Liguan Li – Environmental Science & Technology

Podcast

Episode X7 with Otto Cars, Eldar Shafir and Vanessa Carter: How do we change behaviors around antimicrobial resistance? – Uppsala Antibiotic Center – The AMR Studio

Webinar

The Natural History of Antibiotic Resistance – Gerry Wright – CARe, June 7

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.

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”
    [Register]
  • June 30 **13:00 CEST*: Kimberly Kline – “Pathogenesis and persistence during Enterococcus faecalis biofilm-associated infection”
    [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.