AMR February, 2023

prepared by Svetlana Ugarcina Perovic

This very first 2023 AMR digest features global AMR use trends in food-producing animals, antibiotic resistance in the commensal human gut microbiota, functional metagenomics in clinical strains, and more!

Antibiotic development

Deep mutational scanning of essential bacterial proteins can guide antibiotic development – Liselot Dewachter – Nature Communications

Global resistome

Global trends in antimicrobial use in food-producing animals: 2020 to 2030 – Ranya Mulchandani – Plos Global Public Health
*The global usage of veterinary antimicrobials in 2020 at 99,502 tonnes, and -on current trends- project an 8% increase by 2030 (~107,500 tonnes). In 2020, China, Brazil, India, and United States remain in the top 5 countries for absolute antimicrobial use in tonnes. There is still no publicly available country-level reports of veterinary antimicrobial use in the majority of countries of the world!

Human gut

Antibiotic resistance in the commensal human gut microbiota – Lisa E Lamberte, Willem van Schaik – Current Opinion in Microbiology

Longitudinal fluctuations of common antimicrobial resistance genes in the gut microbiomes of healthy Dutch individuals – Jakob J. Malin – International Journal of Antimicrobial Agents

Vaginal microbiome

Microdiversity of the Vaginal Microbiome is Associated with Preterm Birth – Jingqiu Liao – bioRxiv

Urinary tract

Phenotypic and genomic characterization of Pseudomonas aeruginosa isolates recovered from catheter-associated urinary tract infections in an Egyptian hospital – Mohamed Eladawy – bioRxiv

Wastewater resistome

A proposed framework for the identification of indicator genes for monitoring antibiotic resistance in wastewater: Insights from metagenomic sequencing – Mehedi Hasan Tarek, Emily Garner – Science of The Total Environment
*Based on public data from 191 wastewater samples originating from 64 countries, this framework revealed 56 candidate indicator ARGs distributed across four modules of strongly correlated ARGs, with one ARG from each module (oqxA, ermB, sul1, and mexE) proposed as a minimally redundant monitoring target.

Metagenomic Insight into Microbiome and Antibiotic Resistance Genes of High Clinical Concern in Urban and Rural Hospital Wastewater of Northern India Origin: a Major Reservoir of Antimicrobial Resistance – Absar Talat – Microbiology Spectrum

Metagenomic Analysis of the Abundance and Composition of Antibiotic Resistance Genes in Hospital Wastewater in Benin, Burkina Faso, and Finland – Melina A. Markkanen – mSphere

Hospital and urban wastewaters shape the structure and active resistome of environmental biofilms – Elena Buelow – bioRxiv

The @UK_WIR CIP3 AMR in wastewater report is now available online here


Evolutionary Responses to Acquiring a Multidrug Resistance Plasmid Are Dominated by Metabolic Functions across Diverse Escherichia coli Lineages – Laura Carrilero – mSystems


Comparative metagenomics reveals poultry and swine farming are hotspots for multidrug and tetracycline resistance – Victoria Osorio – Environmental Pollution

Deciphering risks of resistomes and pathogens in intensive laying hen production chain – Yixiao Zhu – Science of The Total Environments

Expanded catalogue of metagenome-assembled genomes reveals resistome characteristics and athletic performance-associated microbes in horse – Cunyuan Li – Microbiome


Characterization of antibiotic resistomes by reprogrammed bacteriophage-enabled functional metagenomics in clinical strains – Gábor Apjok – Nature Microbiology
*A functional metagenomics pipeline called Reprogrammed Bacteriophage Particle Assisted Multi-species Functional Metagenomics (DEEPMINE). The authors use of T7 bacteriophage with exchanged tail fibres and targeted mutagenesis to expand phage host-specificity and efficiency for functional metagenomics. By screening for ARGs in soil and gut microbiomes and clinical genomes against 13 antibiotics, the authors demonstrate that this approach substantially expands the list of identified ARGs.

An optogenetic toolkit for light-inducible antibiotic resistance – Michael B. Sheets – Nature Communications


A global Corynebacterium diphtheriae genomic framework sheds light on current diphtheria reemergence – Melanie Hennart – bioRxiv
*The authors developed the bioinformatics pipeline DIPHTOSCAN (available at to extract from genomes, medically relevant features including the toxin gene presence and disruption.

Comparison of long- and short-read metagenomic assembly for low-abundance species and resistance genes – Sosie Yorki – Briefings in Bioinformatics

Education & Courses

MicroMundo: experimental project fostering contribution to knowledge on antimicrobial resistance in secondary school – Beatriz Robredo – FEMS Microbiology Letters

Course: Antibiotic Resistance – The Silent Tsunami by ReAct

AMR December, 2022

prepared by Anna Abramova

This AMR digest features overview of sewage resistomes from most countries on Earth and importance of sewage surveillance of antibiotic resistance, latest news on inner secrets of Asgard archaea and microbiomes of Galapagos marine iguanas… and lots of Santas hats here and there. Happy #AMR reading!

EMBARK team wishes you happy holidays!


Genomic analysis of sewage from 101 countries reveals global landscape of antimicrobial resistance – Patrick Munk – Nature Communications
* The authors analyzed 757 sewage samples from 243 cities in 101 countries. This study provides a comprehensive sewage-based overview of global ARG abundance, diversity, and genomic backgrounds from most countries on Earth.

Review: Sewage surveillance of antibiotic resistance holds both opportunities and challenges – Joakim Larsson – Nature Reviews Microbiology
* In this brief commentary, the authors discuss recent European Union-directive that requests that member states monitor antibiotic resistance at all sewage treatment plants serving >100,000.

Review: Bacterial survivors: evaluating the mechanisms of antibiotic persistence – Xiaoyi Shi and Ashraf Zarkan – Microbiology

Defining the Benefits of Antibiotic Resistance in Commensals and the Scope for Resistance Optimization – Kristofer Wollein Waldetoft – Microbial Ecology
* Antibiotic resistance is commonly viewed as universally costly, regardless of which bacterial cells express resistance. In this paper, the authors derive an opposing logic, where resistance in commensal bacteria can lead to reductions in pathogen density and improved outcomes on both the patient and public health scales (Figure 1).

Figure 1. Potential costs and benefits of antibiotic resistance in commensal organisms.

Review: The role of bacterial transport systems in the removal of host antimicrobial peptides in Gram-negative bacteria – Jessica M A Blair – FEMS Microbiology Reviews

Mysterious Asgard archaea microbes reveal their inner secrets – Jan Löwe – Nature News and Views
* Asgard archaeal cells have been grown successfully in the laboratory and their internal architecture offers clues to the early evolution of eukaryotic cells. Have a look inside a proposed relative of our cellular ancestors!


Extended-spectrum β-lactamase genes traverse the Escherichia coli populations of ICU patients, staff and environment – Robert A. Moran – bioRxiv

A Clinical Study Provides the First Direct Evidence That Interindividual Variations in Fecal β-Lactamase Activity Affect the Gut Mycobiota Dynamics in Response to β-Lactam Antibiotics – Margot Delavy – Human Microbiome

Meta-analysis of sputum microbiome studies identifies airway disease-specific taxonomic and functional signatures – Abhirupa Ghosh and Sudipto Saha – Journal of Medical Microbiology

Human microbiome

Human microbiota drives hospital-associated antimicrobial resistance dissemination in the urban environment and mirrors patient case rates – Cecilia Salazar – Microbiome

Characterization and Spatial Mapping of the Human Gut Metasecretome – Florencia Velez-Cortes and Harris Wang – Computational Biology


Characterization of the gut microbiome and resistome of Galapagos marine iguanas (Amblyrhynchus cristatus) from uninhabited islands – Karla Vasco – BMC Animal Microbiome
* This study shows a diverse resistome composition in the Galapagos marine iguanas from remote islands raising concerns about the dispersion of microbial-resistant threats in pristine areas.

Guts within guts: the microbiome of the intestinal helminth parasite Ascaris suum is derived but distinct from its host – Ankur Midha, Víctor Hugo Jarquín-Díaz, Friederike Ebner, Ulrike Löber, Rima Hayani, Arkadi Kundik, Alessio Cardilli, Emanuel Heitlinger, Sofia Kirke Forslund & Susanne Hartmann – Microbiome
* Intestinal helminths are extremely prevalent among humans and animals, and live in intimate contact with the host gut microbiota and harbor bacteria within their own intestines. This study shows that a nematode infection reduces the microbiome diversity of the host gut, and that the nematode gut represents a selective bacterial niche harboring bacteria that are derived but distinct from the host gut.

Gut microbiota of homing pigeons shows summer–winter variation under constant diet indicating a substantial effect of temperature – Maurine W. Dietz – Animal Microbiome

The skin microbiota of the axolotl Ambystoma altamirani is highly influenced by metamorphosis and seasonality but not by pathogen infection – Emanuel Martínez-Ugalde – Animal Microbiome


Biophysical basis of phage liquid crystalline droplet-mediated antibiotic tolerance in pathogenic bacteria – Jan Böhning – bioRxiv
* In this work the authors investigate how phage liquid crystalline droplets in P. aeruginosa biofilms protect bacteria from antibiotics (Figure 2).

Figure 2 Schematic depicting biophysical nature of phage liquid crystalline droplet-mediated antibiotic tolerance of bacteria.


Microbiome, resistome and mobilome of chlorine-free drinking water treatment systems – David Calderón-Franco – bioRxiv

The antibiotic resistance and risk heterogeneity between urban and rural rivers in a pharmaceutical industry dominated city in China: The importance of social-economic factors – Lulu Zhang – Science of The Total Environment

Genome-resolved insight into the reservoir of antibiotic resistance genes in aquatic microbial community – Zahra Goodarzi – Scientific Reports
* This study shows the distribution of ARGs in the Caspian Sea ecosystem (Figure 3). To this end, the authors performed genome-resolved metagenomic analyses of deeply sequenced depth profile metagenomes of the Caspian Sea and applied Hidden Markov models. They further investigated how ecological strategies of resistance bacteria affect the ARGs they contain. Comparative analysis revealed that Acidimicrobiia and Actinobacteria characterized by streamlined genomes modify the antibiotic target via mutation to develop antibiotic resistance rather than carrying extra resistance genes.

Figure 3 Antibiotic resistance gene profile of the Caspian Sea Bacteria


Early season soil microbiome best predicts wheat grain quality – Numan Ibne Asad – FEMS Microbiology Ecology


Validation and Application of Long-Read Whole-Genome Sequencing for Antimicrobial Resistance Gene Detection and Antimicrobial Susceptibility Testing – Thomas Weinmaier – Computational Biology


Ten simple rules for investigating (meta)genomic data from environmental ecosystems – Paton Vuong – PLoS Computational Biology

Events, Podcasts and more

10th Congress of European Microbiologists: 9 – 13 July 2023, Hamburg, Germany

Remember to wash your hands and stay healthy! ☺️

Last EMBARK webinar this year

Time flies and it is time for the last EMBARK webinar of 2022. This month, we are pleased to have Joakim Larsson talk about the environment’s role antibiotic resistance and Antti Karkman present hosts of antibiotic resistance genes in urban sewage. Welcome on Thursday December 15! Registration link below.

Dec 15, 14:00 UTC+2
Joakim Larsson – On the environment’s role in evolution, transmission and surveillance of antibiotic resistance
Antti V. Karkman – Host and vehicles of antibiotic resistance genes in urban sewage
[Register here]

AMR November, 2022

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.

EMBARK coordinator receives Global Health award

EMBARK coordinator Johan Bengtsson-Palme has been selected as the 2022 recipient of the Einhorn SIGHT awardThe award, which is granted by the Swedish Institute for Global Health Transformation and the Einhorn Family Foundation, recognizes outstanding global health research work by young researchers in the context of low- and middle-income countries. Johan was selected motivated by “outstanding research and development of tools to limit the global challenge of infectious diseases and antibiotic resistance”. Largely, these results have come out of the work performed in the EMBARK program.