prepared by Faina Tskhay

The EMBARK team is happy and proud to announce that Dr Johan Bengtsson-Palme, coordinator of the EMBARK project, became a laureate of the Einhorn SIGHT award. Congratulations!

The November AMR Digest delivers some fresh and crisp publications from the world of antibiotic resistance. This time we collected publications featuring the AMR evolution, AMR in water and soil, advances of metagenomics in tracking AMR and much more! Enjoy your reading!


Special issue of Environmental Science and Technology Journal – AMR in the Environment: Informing Policy and Practice to Prevent the Spread

The synthesis report “Routes and reservoirs of AMR-determinants & One Health AMR-surveillance” of the Swiss National Research Program 72 “Antimicrobial Resistance”
This report summarizes the research of 18 projects in the field of antibiotic resistance over a 5-year period. Based on the findings and observations, the authors suggest key recommendations for action to restrict the spread of AMR.


Molecular mechanisms of antibiotic resistance revisited – Elizabeth M. Darby – Natural Reviews Microbiology
In this article, the authors provide an overview of molecular mechanisms and strategies that bacteria apply to develop resistance to antimicrobials. They give insights into the role of efflux systems in decreased antibiotic susceptibility and their synergetic interaction with other resistance mechanisms. Understanding of molecular mechanisms is essential to overcome antimicrobial resistance and can be used, for example, for developing so-called antibiotic resistance breakers (ARBs) – compounds that can restore antibiotic activity by disrupting or inhibiting a specific resistance mechanism.

Does Environmental Exposure to Pharmaceutical and Personal Care Product Residues Result in the Selection of Antimicrobial-Resistant Microorganisms, and is this Important in Terms of Human Health Outcomes? – Isobel C. Stanton, Holly J. Tipper, Kevin Chau, Uli Klümper, Jessica Subirats, Aimee K. Murray – Environmental Toxicology and Chemistry
This review comprehensively compiles laboratory studies, and field based research evidence regarding the effects of pharmaceutical and personal care products on selection and horizontal gene transfer of antimicrobial resistance in multiple environments. It summarizes these studies and points out under which scenarios the promotion of AMR by PPCPs in the environment is and will be relevant to human health.


Nearly Complete Genome Sequence of Raoultella ornithinolytica Strain MQB_Silv_108, Carrying an Uncommon Extended-Spectrum-β-Lactamase-like blaBEL Gene – Marcos Quintela-Baluja – Microbiology Resource Announcements

Report and Comparative Genomics of an NDM-5-Producing Escherichia coli in a Portuguese Hospital: Complex Class 1 Integrons as Important Players in blaNDM Spread – Rafael D. S. Tavares – Microorganisms

Gut microbiota

Noise reduction strategies in metagenomic chromosome confirmation capture to link antibiotic resistance genes to microbial hosts – Gregory E. McCallum – bioRxiv

Enterotoxin tilimycin from gut-resident Klebsiella promotes mutational evolution and antibiotic resistance in mice – Sabine Kienesberger – Nature Microbiology

Sharing Antimicrobial Resistance Genes between Humans and Food Animals – Huiluo Cao – mSystems

Gut microbiome dysbiosis in antibiotic-treated COVID-19 patients is associated with microbial translocation and bacteremia – Lucie Bernard-Raichon – Nature Communications

Characterization of antibiotic-resistance traits in Akkermansia muciniphila strains of human origin – Rossella Filardi – Scientific Reports

AMR evolution

Within-patient evolution of plasmid-mediated antimicrobial resistance – Javier DelaFuente – Nature Ecology and Evolution
This five-year study aimed at tracking AMR evolution in vivo in patients. By analyzing 224 poxA-48-carrying Enterobacteria isolated from 9000 patients, DelaFuente et al. were able to identify 35 variants of a poxA-48 plasmid. They monitored 121 patients for a potential case of within-patient AMR evolution and identified three instances in which the same bacterial host carried different plasmid variants over the treatment period. The authors compared plasmid fitness, susceptibility to antibiotics, plasmid copy number and HGT rates of the new plasmids and ancestral plasmids. According to their findings, the authors concluded that within-patient plasmid-mediated AMR requires an interplay between resistance levels and bacterial fitness.

Plasmid evolution in the clinic – Rosanna C. T. Wright & Michael A. Brockhurst – Nature Ecology and Evolution

Exposure to environmental stress decreases the resistance of river microbial communities towards invasion by antimicrobial-resistant bacteria – Kenyum Bagra, Xavier Bellanger, Christophe Merlin, Gargi Singh, Thomas Ulrich Berendonk, Uli Klümper – bioRxiv
In this preprint the authors utilize artificial river flume systems to explore the invasion dynamics of a model resistant strain (E. coli) into river microbial communities in the presence and absence of a co-introduced environmental stressor. Despite an initially successful introduction of E. coli into all the biofilms, independent of the imposed stress, over time the invader perished in absence of stress. However, under stress conditions the invading strain successfully established and proliferated in the biofilms. Noteworthy, the increased establishment success of the invader coincided with a loss in microbial community diversity under stress conditions, likely due to additional niche space becoming available for the invader.

Mobile genetic elements in Acinetobacter antibiotic-resistance acquisition and dissemination – Hannah R. Noel – Annals of the New York Academy of Science

Electrochemical disinfection may increase the spread of antibiotic resistance genes by promoting conjugal plasmid transfer – Hua Li – Science of The Total Environment

IncP-type plasmids carrying genes for antibiotic resistance or for aromatic compound degradation are prevalent in sequenced Aromatoleum and Thauera strains – Hao-Yu Lo – Environmental Microbiology

Reductive Stress Boosts the Horizontal Transfer of Plasmid-Borne Antibiotic Resistance Genes: The Neglected Side of the Intracellular Redox Spectrum – Haining Huang – Environmental Science & Technology

Novel Plasmid Carrying Mobile Colistin Resistance Gene mcr-4.3 and Mercury Resistance Genes in Shewanella baltica: Insights into Mobilization of mcr-4.3 in Shewanella Species – Nachiket P. Marathe – Microbiology Spectrum

Defense systems are pervasive across chromosomally integrated mobile genetic elements and are inversely correlated to virulence and antimicrobial resistance – João Botelho – bioRxiv


Concordance between Antimicrobial Resistance Phenotype and Genotype of Staphylococcus pseudintermedius from Healthy Dogs – Joaquim Viñes – Antibiotics

Genomic Insights into the Mobilome and Resistome of Sentinel Microorganisms Originating from Farms of Two Different Swine Production System – Oscar Mencía-Ares – Microbiology Spectrum

More than an anthropogenic phenomenon: Antimicrobial resistance in ungulates from natural and agricultural environments – Lee J. Pinnell – Science of the Total Environment

Viruses and phages

Quantification and fate of plasmid-specific bacteriophages in wastewater: Beyond the F-coliphages – Zhiming He – Water Research


Dissemination of antibiotic resistance in antibiotic-free recirculating aquaculture systemsIoannis Kampouris, Uli Klümper, Lena Kramer, Henning Sorum, Helmut Wedekind, Thomas U. Berendonk – Journal of Hazardous Materials Advances

Explaining the resistomes in a megacity’s water supply catchment: Roles of microbial assembly-dominant taxa, niched environments and pathogenic bacteria – Dong Wu – Water Research

The global groundwater resistome: core ARGs and their dynamics – an in silico re-analysis of publicly available groundwater metagenomesIoannis D. Kampouris, Thomas U. Berendonk, Johan Bengtsson-Palme, Uli Klümper – bioRxiv

Wastewater Surveillance of Antibiotic-Resistant bacterial pathogens: a Systematic Review – Ananda Tiwari – Frontiers in Microbiology

Nanopore-based long-read metagenomics uncover the resistome intrusion by antibiotic-resistant bacteria from treated wastewater in receiving water body – Ziqi Wu – Water Research

Mobilome-driven segregation of the resistome in biological wastewater treatment – Laura de Nies – eLife


Plants select antibiotic resistome in rhizosphere in early stage – Yitian Yua – Science of the Total Environment

Global biogeography and projection of soil antibiotic resistance genes – Dongsheng Zheng – Science Advances

Metagenomics, Bioinformatics

Functional and Sequence-Specific Screening Protocols for the Detection of Novel Antimicrobial Resistance Genes in Metagenomic DNA – Supathep Tansirichaiya – Methods in Molecular Biology

In Silico Characterization of blaNDM-Harboring Conjugative Plasmids in Acinetobacter Species – Biao Tang – Antimicrobial Chemotherapy

Target-enriched long-read sequencing (TELSeq) contextualizes antimicrobial resistance genes in metagenomes – Ilya B. Slizovskiy – Microbiome

Multiomics Characterization of the Canada Goose Fecal Microbiome Reveals Selective Efficacy of Simulated Metagenomes – Joshua C. Gil, Sarah M. Hird – Microbiology Spectrum

MEGARes and AMR++, v3.0: an updated comprehensive database of antimicrobial resistance determinants and an improved software pipeline for classification using high-throughput sequencing – Nathalie Bonin – Nucleic Acids Research

Three Distinct Annotation Platforms Differ in Detection of Antimicrobial Resistance Genes in Long-Read, Short-Read, and Hybrid Sequences Derived from Total Genomic DNA or from Purified Plasmid DNA – Grazieli Maboni – Antibiotics


“Antimicrobial Resistance in the Environment” – UNFAO, UNEP, WHO, WOAH – Webinar Series.