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