AMR SEPTEMBER, 2021

prepared by Ulrike Löber

September digest features how artificial sweeteners stimulate horizontal gene transfer of extracellular antibiotic resistance genes; soil plastispheres as hotpots of antibiotic resistance genes and potential pathogens; a novel vancomycin resistance gene cluster in Enterococcus faecium; elevated levels of AMR in groundwater during treated wastewater irrigation associated with infiltration and accumulation of antibiotic residues, and many more. Enjoy!


EMBARK annual meeting

We had our 3rd annual EMBARK meeting on September 28/29. We had some fruitful discussions. We took a look back to the last two years, which were productive, but even under compulsion of the COVID pandemic. We were looking forward to continuing our teamwork. We found people with fantastic expertise, synergizing exceptionally well, and having a great team spirit. Social online activities rounded up this event, while we look forward to seeing each other again in person next year.


Global

From the soil to the clinic: the impact of microbial secondary metabolites on antibiotic tolerance and resistance – Elena K. Perry, Lucas A. Meirelles, Dianne K. Newman – Nature Reviews Microbiology

ARGuing the case for (or against) probiotics – Sondra Turjeman & Omry Koren – Trends in Microbiology

Design principles of collateral sensitivity-based dosing strategies – Linda B. S. Aulin, Apostolos Liakopoulos, Piet H. van der Graaf, Daniel E. Rozen, J. G. Coen van Hasselt – Nature Communications

*Artificial sweeteners stimulate horizontal transfer of extracellular antibiotic resistance genes through natural transformation – Zhigang Yu, Yue Wang, Ian R. Henderson & Jianhua Guo – The ISME Journal
Interesting paper about artificial sweeteners (saccharin, sucralose, aspartame, and acesulfame potassium) promoting transfer of ARGs via natural transformation in Acinetobacter baylyi. The phenomenon were validated by an in vitro transformation model (Model V) using mice faecal bacteria as the recipient.

Water environment

*Elevated levels of antibiotic resistance in groundwater during treated wastewater irrigation associated with infiltration and accumulation of antibiotic residuesIoannis D. Kampouris, Nikiforos Alygizakisb, Uli Klümper, Shelesh Agrawal, Susanne Lackner, Damiano Cacace, Steffen Kunze, Nikolaos S.Thomaidis, Jaroslav Slobdonik, Thomas U. Berendonk – Journal of Hazardous Materials
Our team members from Dresden published an article about bacterial abundances and antibiotics residues in ground water. The team around Thomas U. Berendonk could show that bacterial abundance did not increase due to treated wastewater irrigation. At each time-point, three samples each were taken from three groundwater wells (n = 9) located in the field at a depth of 10 m. Samples were collected from the facilities of Braunschweig Wastewater Association (Wendeburg, Lower Saxony, Germany).

Impact of biosolids amendment and wastewater effluent irrigation on enteric antibiotic-resistant bacteria – a greenhouse study – Catherine Maysa, Gabriel L.Garza, Joy Waite-Cusic, Tyler S. Radniecki, Tala Nava-Daneshmand – Water Research

Tracing Antibiotic Resistance Genes along the Irrigation Water Chain to Chive: Does Tap or Surface Water Make a Difference? – Maria-Theresia Gekenidis, Fiona Walsh and David Drissner – MDPI

Quantifying and predicting antimicrobials and antimicrobial resistance genes in waterbodies through a holistic approach: a study in Minnesota, United States – Irene Bueno, Amanda Beaudoin, William A. Arnold, Taegyu Kim, Lara E. Frankson, Timothy M. LaPara, Kaushi Kanankege, Kristine H. Wammer, Randall S. Singer – Scientific Reports

Soil environment

*Soil plastispheres as hotpots of antibiotic resistance genes and potential pathogens – Dong Zhu, Jun Ma, Gang Li, Matthias C. Rillig, Yong-Guan Zhu – The ISME Journal

Case reports

Novel vancomycin resistance gene cluster in Enterococcus faecium ST1486, Belgium, June 2021 – Basil Britto Xavier, Jasmine Coppens, Sien De Koster, Sahaya Glingston Rajakani, Sam Van Goethem, Samy Mzougui, Ahalieyah Anantharajah, Christine Lammens, Katherine Loens, Youri Glupczynski, Herman Goossens, Veerle Matheeussen – Eurosurveillance

Animal experiments

Dynamics of the fecal microbiome and antimicrobial resistome in commercial piglets during the weaning period – Prapat Suriyaphol, Jimmy Ka Ho Chiu, Nathamon Yimpring, Paiboon Tunsagool, Wuttichai Mhuantong, Rungtip Chuanchuen, Irina Bessarab, Rohan B. H. Williams, Rick Twee-Hee Ong, Gunnaporn Suriyaphol – Scientific Reports

Inappropriate use of antibiotics exacerbates inflammation through OMV-induced pyroptosis in MDR Klebsiella pneumoniae infection – Chao Ye, Weiran Li, Ying Yang, Qingwen Liu, Sijing Li, Peng Zheng, Xiao Zheng, Ye Zhang, Jinrong He, Yongjun Chen, Liangqun Hua, Zhongqian Yang, Duo Li, Zhaoling Ren, Ying Yang, Jialong Qi, Weiwei Huang, Yanbing Ma – Cell Reports

High-risk environments for transmission

Multidrug-Resistant Lineage of Enterotoxigenic Escherichia coli ST182 With Serotype O169:H41 in Airline Waste – Veronica M. Jarocki, Stefanie Heß, Kay Anantanawat, Thomas U. Berendonk, Steven P. Djordjevic – Frontiers in Microbiology

Bioinformatics

BiG-MAP: an Automated Pipeline To Profile Metabolic Gene Cluster Abundance and Expression in Microbiomes – Victória Pascal Andreu, Hannah E. Augustijn, Koen van den Berg, Justin J. J. van der Hooft, Michael A. Fischbach, Marnix H. Medema – mSystems

PlasmidHostFinder: Prediction of plasmid hosts using random forest – Derya Aytan-Aktug, Philip T.L.C. Clausen, Judit Szarvas, Patrick Munk, Saria Otani, Marcus Nguyen, James J. Davis, Ole Lund , Frank M. Aarestrup – bioRxiv

Courses

Podcast

The AMR Studio – Ep 32: Anna Dumitriu & bioart. Access to antibiotics in high-income countries – Uppsala Antibiotic Center

Webinars & conferences

Autumn Resistomap webinars: The science and application of antibiotic resistance monitoring (recordings available here)

Autumn EMBARK webinars: We would like to invite you for the 6th #EMBARK2021 webinar with Monika Dolejska and Victor Hugo Jarquin Diaz!

AMR June, 2021

prepared by Ioannis Kampouris

This week, the @EMBARK_JPIAMR team is at the World Microbe Forum:
Svetlana Ugarcina Perovic and Luis Pedro Coelho with their work on ARGs at global scale,
Anna Abramova, Thomas Berendonk and Johan Bengtsson-Palme on ARGs across environments,
Saba Yasmin and Rabaab Zahra on E. coli in sewage water.


We would like to invite you for the 4th #EMBARK2021 webinar with Kimberly Kline and Sofia Forslund!

Global

There is no market for new antibiotics: this allows an open approach to research and development – Dana M. Klug, Fahima I. M. Idiris – Welcome Open Research
*This opinion paper suggests that there is a necessity for a new open source model for antibiotic discovery, which should be independent from whether a market for new antibiotics exist or not.

Destination shapes antibiotic resistance gene acquisitions, abundance increases, and diversity changes in Dutch travelers – Alaric W. D’Souza, Manish Boolchandani – Genome Medicine
*The authors claim that travel shapes the architecture of the human gut resistome and results in AMR gene acquisition against a variety of antimicrobial drug classes.

Soil environment

Modeling the vertical transport of antibiotic resistance genes in agricultural soils following manure application – Renys E. Barrios – Environmental Pollution
*The authors claim that detachment and decay coefficients for ARGs in soil were not affected by manure, while the load of ARGs in leachate was not significantly affected by manure.

Wastewater Treatment

Antibiotic transformation in an anaerobic membrane bioreactor linked to membrane biofilm microbial activity – Moustapha Harb – Environmental Research

Wastewater Based Epidemiology Enabled Surveillance of Antibiotic Resistance – M.V. Riquelme – MedRxiv
*The Wastewater Based Epidemiology approach helped to identify geographic hot-spots where attention towards curbing the spread of antibiotic resistance may be particularly warranted.

Hospital environment

A species-wide genetic atlas of antimicrobial resistance in Clostridioides difficile – Korakrit Imwattana – BioRxiv
*This review provides insights in the global C. difficile population, which may help in the early detection of drug-resistant C. difficile strains.

Human experiments

The infant gut resistome associates with E. coli, environmental exposures, gut microbiome maturity, and asthma-associated bacterial composition – Xuanji Li – Cell Host & Microbiome
*The study reveals a clear bimodal distribution of ARG richness that is driven by the composition of the gut microbiome, especially E. coli.

Agricultural applications

Chitosan as additive affects the bacterial community, accelerates the removals of antibiotics and related resistance genes during chicken manure composting – Hongdou Liu – Science of Total Environment
*The use of chitosan can enhance the remove of antibiotics and antibiotic resistance genes during manure composting.

Animal experiments

Chironomidae larvae: A neglected enricher of antibiotic resistance genes in the food chain of freshwater environments – Chengshi Ding – Environmental Pollution
*Feeding experiments further confirmed that ARGs from Chironomidae larvae can be transferred to the fish gut.

Techniques

A Peek into the Plasmidome of Global Sewage – Philipp Kirstahler – mSystems
*The authors describe a laboratory and bioinformatics workflow for the recovery of plasmids and other potential extrachromosomal DNA elements from complex microbiomes.

Validation of selective agars for detection and quantification of Escherichia coli resistant to critically important antimicrobials – Zheng Z Lee – bioRxiv

Bioinformatics

Predicting Antimicrobial Resistance Using Partial Genome Alignments – D. Aytan-Aktug – mSystems

Review: Antibiotic resistance: Time of synthesis in a post-genomic age – Teresa Gil-Gil – Computational and Structural Biotechnology Journal

Horizontal Gene Transfer

Quantitative analysis of horizontal gene transfer in complex systems – Jenifer Moralez – Current Opinion in Microbiology

Phages

Comprehensive Scanning of Prophages in Lactobacillus: Distribution, Diversity, Antibiotic Resistance Genes, and Linkages with CRISPR-Cas Systems – Zhangming Pei – mSystems
*Uneven prophage distribution, with highly diverse genome features and distinct clusters based on host species along with detection of ARGs in Lactobacillus prophages.

L-form switching confers antibiotic, phage and stress tolerance in pathogenic Escherichia coli – Aleksandra Petrovic Fabijan – bioRxiv

Podcast

Superbugs and You – True Stories from Scientists and Patients around the World – The Antimicrobial Resistance Fighter Coalition


The @EMBARK_JPIAMR team wishes you happy Summer holidays!

AMR MAY, 2021

prepared by Fouzia Nahid


Our May digest features recent research and review articles relating to AMR, screening of ARGs in various environments and metagenomics.


Join the JUNE AMR WEBINARS to discuss the latest AMR insights with us and our invited speakers!

You can register for the next webinars

* on June 9 with Dearbháile Morris and Rabaab Zahra, and

* on June 30 with Kimberly Kline and Sofia Forslund.


On June 25, Big Data Biology Lab is doing an NGLess tutorial for processing metagenomes.

Read more about the tool HERE
Time: Noon UTC
Registration HERE


Global

🇵🇰 Review: Progress on the national action plan of Pakistan on antimicrobial resistance (AMR): a scoping review and the implications – Zikria Saleem – Expert Review of Anti-infective Therapy

The social dilemmas of climate change and antibiotic resistance: an analytic comparison and discussion of policy implications – Niklas Harring – Humanities and Social Sciences Communications
*This article analyses climate change and antimicrobial resistance within the context of game theory. Previous literature has identified these problems as common tragedies, where inherent incentive structures encourage selfish overuse of existing resources. While the game theoretical models provide a helpful conceptual basis, the present analysis suggests discrepancies between some of the theoretical assumptions and the practical realities of climate change and antimicrobial resistance.

Review: Antibiotic resistance: time of synthesis in a post-genomic age – Teresa Gil-Gil – Computational and Structural Biotechnology Journal
*The authors analyzed the capacities and drawbacks of the tools that are currently in use for the global analysis of AR, aiming to identify the more useful targets for effective corrective interventions.

Diversity of metal and antibiotic resistance genes in Enterococcus spp. from the last century reflects multiple pollution and genetic exchange among phyla from overlapping ecosystems – Andreia Rebelo – Science of The Total Environment
*The authors explored occurrence, diversity, and phenotypes associated with known acquired genes/operons conferring tolerance to As, Hg or Cu among Enterococcus and identified their genetic context.

Human-associated microbiome and resistome

Emergence and dissemination of antimicrobial resistance in Escherichia coli causing bloodstream infections in Norway in 2002–17: a nationwide, longitudinal, microbial population genomic study – Rebecca A Gladstone – THE LANCET Microbe
*The authors aimed to evaluate the clonal diversity underpinning trends in multidrug resistant Escherichia coli causing bloodstream infections which usually remains uncertain. They determined the contribution of individual clones to resistance over time, using large-scale genomics-based molecular epidemiology.

Review: The innate resistome of “recalcitrant” Acinetobacter baumannii and the role of nanoparticles in combating these MDR pathogens – Vasudevan Aparna – Applied Nanoscience
*The authors emphasize the role of intrinsic resistome involved in the antibiotic resistance of A. baumannii, the understanding of which will be very helpful in combating this opportunistic pathogen.

Trade-Offs Between Antibacterial Resistance and Fitness Cost in the Production of Metallo-β-Lactamases by Enteric Bacteria Manifest as Sporadic Emergence of Carbapenem Resistance in a Clinical Setting – Ching Hei Phoebe Cheung – Antimicrobial Agent and Chemotherapy

Reconstruction of ancient microbial genomes from the human gut – Marsha C. Wibowo – Nature

Fig. 4
Palaeofaeces exhibit a distinct functional genomic repertoire compared to present-day industrial stool samples

Mobile antimicrobial resistance genes in probiotics – Adrienn Gréta Tóth – bioRxiv
*The authors raised clinical and public health concerns as the consumption of probiotic products may lead to the transfer of ARGs to human gut bacteria.

Review Article: Antimicrobial resistance in nephrology – Tina Z. Wang – Nature Reviews Nephrology

Soil environment

Novel Soil-Derived Beta-Lactam, Chloramphenicol, Fosfomycin and Trimethoprim Resistance Genes Revealed by Functional Metagenomics – Inka Marie Willms – Antibiotics (Basel)
*The authors screened metagenomic libraries comprising of genes of cultivated microorganisms and uncultured microbial for novel ARGs from forest and grassland soils. Three new beta-lactam, a so far unknown chloramphenicol, a novel fosfomycin, as well as three previously undiscovered trimethoprim resistance genes are described in this study.

Manure Microbial Communities and Resistance Profiles Reconfigure after Transition to Manure Pits and Differ from Those in Fertilized Field Soil – Kimberley V. Sukhum – mBio
*The authors evaluated that on dairy farms, the storage of cow manure in manure pits and subsequent application to field soil as a fertilizer may facilitate the spread of the mammalian gut microbiome and its associated ARGs to the environment. To determine the extent of both taxonomic and resistance similarity during these transitions, they collected fresh manure, manure from pits, and field soil across 15 different dairy farms for three consecutive seasons and used a combination of shotgun metagenomic sequencing and functional metagenomics to quantitatively interrogate taxonomic and ARG compositional variation on farms.

Dissipation of antibiotic resistance genes in manure-amended agricultural soil – Liang-Ying He – Science of The Total Environment
*This study provides insight into the dissipation of antibiotic resistance genes in manure-applied agricultural soil. The continuous application of manure results in accumulation of ARGs which persists in soil for at least two years.

Metagenomics analysis reveals the distribution and communication of antibiotic resistance genes within two different red swamp crayfish Procambarus clarkii cultivation ecosystems – Limin Fan – Environmental Pollution
*This study showed that MacB and BcrA are two dominant ARGs, and macrolide is the dominant antibiotic not only in the water, but also in the sediment and gut of crayfish, in both the crayfish monoculture and the rice-crayfish cultivation ecosystems.

Distribution of the microbial community and antibiotic resistance genes in farmland surrounding gold tailings: A metagenomics approach – Longkai Qiao – Science of The Total Environment
*The authors studied microbes and antibiotic resistance genes in farmland near gold tailings. The main ARGs exhibited macrolide, lincosaminide, and streptogramin B resistance. Actinobacteria, Proteobacteria, and Acidobacteria were the main carriers of ARGs. The microbial community was the most important driver of soil ARG distribution.

Environmental fate of tetracycline antibiotics: degradation pathway mechanisms, challenges, and perspectives – Ahmad Fiaz – Environmental Sciences Europe
*The authors collected data on the available degradation strategies, mechanisms involved in biodegradable and non-biodegradable routes, the main factor affecting degradation strategies, compiled novel detection techniques of tetracycline antibiotics in the environment, and discussed antibiotic resistance genes and their potential role in degradation.

Water environment

Wastewater treatment plants as a reservoir of integrase and antibiotic resistance genes – An epidemiological threat to workers and environment – Wiktor Zieliński – Environmental International
*The authors found a significant increase in the quantities of ARGs and concentrations of antibiotics in the river following the discharge of treated wastewater in comparison to their amounts in the river water upstream from the point of discharge. A higher concentration of ARGs was detected in the DNA from swabs obtained from the wastewater treatment plant employees than from ones collected from the control group.

Built environment

Characterization of the public transit air microbiome and resistome reveals geographical specificity – M. H. Y. Leung – Microbiome

Geographical specificity in public transit air resistome.
Heatmap of the top 30 AR protein families based on average reads per kilobase per million (RPKM) reads across metagenomes. Core AR protein families (those detected in ≥ 75% of the entire dataset) are indicated in red and asterisks

A global metagenomic map of urban microbiomes and antimicrobial resistance – David Danko – Cell

Phages

Aminoglycoside antibiotics inhibit phage infection by blocking an early step of the phage infection cycle – Larissa Kever – bioRxiv
*The authors have described how aminoglycosides, a well-known class of antibiotics produced by Streptomyces, act as potent inhibitors of phage infection in widely divergent bacterial hosts.

COVID-19

Antibody-dependent enhancement and SARS-CoV-2 vaccines and therapies – Wen Shi Lee – Nature Microbiology
*The authors described the key ADE mechanisms and discussed mitigation strategies for SARS-CoV-2 vaccines and therapies in development and about the risk of ADE in SARS-CoV-2. They outline recently published data to evaluate the risks and opportunities for antibody-based protection against SARS-CoV-2.

Sample storage

Standard Sample Storage Conditions Impact on Inferred Microbiome Composition and Antimicrobial Resistance Patterns – Casper S. Poulsen –bioRxiv
*The authors examined the effect of common sample storage conditions on metagenomics-based microbiome composition and found significant and, in part, systematic effects.

Bioinformatics

A machine learning framework to predict antibiotic resistance traits and yet unknown genes underlying resistance to specific antibiotics in bacterial strains – Janak Sunuwar – Briefing in Bioinformatics
*There are several strains of bacteria lacking known resistance genes; however, they demonstrate resistance phenotype to drugs of that family. In this study, authors present a machine learning framework to predict novel AMR factors that are potentially responsible for resistance to specific antimicrobial drugs which may help proactive interventions.

Podcast

Listen to the AMS case studies illustrating the importance of antimicrobial stewardship and how it works in practice.

Rachel Irwin & the visual culture of AMR. WHO report on the antibacterial pipeline. Neonatal sepsis in LMICs. – The AMR Studio – Uppsala Antibiotic Center

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.