Prepared by Anna Abramova

The final AMR Digest of 2023 features microbial wars and weaponry evolution, “plastisphere” as a new home for bacterial communities, inter-phylum ARGs exchange, peculiarities of honeybee and stray cats microbiota, and how the distance that your steak travels before ending-up on your plate is related to MDR contamination. And much more!


The evolution of short- and long-range weapons for bacterial competition – Sean C. Booth et al. – Nature Ecology & Evolution

A database of glacier microbiomes for the Three Poles – Yongqin Liu et al. – Earth System Science Data

Review: Selection for antimicrobial resistance in the plastisphere – Emily M. Stevenson et al. – Science of The Total Environment



Global pathogenomic analysis identifies known and candidate genetic antimicrobial resistance determinants in twelve species – Jason C. Hyun et al. – Nature Communications

Development of a portable on-site applicable metagenomic data generation workflow for enhanced pathogen and antimicrobial resistance surveillance – Bram Bloemen et al. – Scientific Reports

Evolution of Resistance

Evolution and transmission of antibiotic resistance is driven by Beijing lineage Mycobacterium tuberculosis in Vietnam – Matthew Silcocks et al. – Antimicrobial Chemotherapy

Rapid evolution bacteria reveal pathogenic mechanisms and clinical risk – Toyotaka Sato et al. – under review in Nature Portfolio 

Gene Transfer/Plasmids

Inter-phylum circulation of a beta-lactamase – encoding gene: a rare but observable event Rémi Gschwind, Marie Petitjean, Claudine Fournier, Julie Lao, Olivier Clermont, Patrice Nordmann, Alexander Mellmann, Erick Denamur, Laurent Poirel, Etienne Ruppé – bioRxiv preprint
*While transfer of beta-lactamase encoding genes typically occurs between closely-related bacteria, the research documents a unique case of inter-phylum transfer between the Peudomonadota and Bacteroidota phyla. The investigation focuses on an extended-spectrum beta-lactamase (ESBL)-encoding gene, blaMUN-1, from an Escherichia coli strain. This study marks the first reported instance of inter-phylum transfer of an ESBL-encoding gene, indicating that while inter-phylum barriers are generally robust, they are not insurmountable.

Evolutionary “Crowdsourcing”: Alignment of Fitness Landscapes Allows for Cross-species Adaptation of a Horizontally Transferred Gene – Olivia Kosterlitz et al. – Molecular Biology and Evolution

Is ICE hot? A genomic comparative study reveals integrative and conjugative elements as “hot” vectors for the dissemination of antibiotic resistance genes – Qi Zheng et al. – Msystems

Characterization of a mobilizable megaplasmid carrying multiple resistance genes from a clinical isolate of Pseudomonas aeruginosa – Li Mei et al. – Frontiers in Microbiology


Monitoring longitudinal antimicrobial resistance trends of Staphylococcus aureus strains worldwide over the past 100 years to decipher its evolution and transmission – Guan-Yu Fang et al. – Journal of Hazardous Materials


Swine farming shifted the gut antibiotic resistome of local people – Fang-Zhou Gao et al. – Journal of Hazardous Materials

Impact of contrasting poultry exposures on human, poultry, and wastewater antibiotic resistomes in Bangladesh – Alexander D. Williams et al. – Environmental Microbiology

One health transmission of fluoroquinolone-resistant Escherichia coli and risk factors for their excretion by dogs living in urban and nearby rural settings – Jordan E. Sealey et al. – One Health

AMR removal

Degradation of chromosomal and plasmid encoded extracellular and intracellular resistance genes across different types and sizes in water matrices during ozone-based oxidation process – Dabojani Das et al. – Journal of Water Process Engineering

Aquatic environments

The diversity of the antimicrobial resistome of lake Tanganyika increases with the water depth – Raffaella Sabatino et al. – Environmental Pollution

Impacts of net cages on pollutant accumulation and its consequence on antibiotic resistance genes (ARGs) dissemination in freshwater ecosystems: Insights for sustainable urban water management – Min Wang et al. – Environment International


Soil-specific responses in the antibiotic resistome of culturable Acinetobacter spp. and other non-fermentative Gram-negative bacteria following experimental manure application – Puspendu Sarda et al. – FEMS Microbiology Ecology

Unveiling antimicrobial resistance in Chilean fertilized soils: a One Health perspective on environmental AMR surveillance – Marcela Fresno et al. – Frontiers in Microbiology


Emergency of the plasmid co-carrying blaKPC-2 and blaNDM-1 genes in carbapenem-resistant hypervirulent Klebsiella pneumoniae – Shijun Sun et al. – Journal of Global Antimicrobial Resistance


Distance and destination of retail meat alter multidrug resistant contamination in the United States food system – Gabriel Innes et al. – Scientific Reports

Genomic characterization of Salmonella isolated from retail chicken and humans with diarrhea in Qingdao, China – Wei Wang et al. – Frontiers in Microbiology

Animals / Wildlife
Review: The honeybee microbiota and its impact on health and disease – Erick Motta & Nancy Moran – Nature Reviews Microbiology


Figure 1: Microbial dynamics and spatial organization in the honeybee gut. Honeybees are key pollinators and have a long history of domestication for wax and honey production. Recently, they have emerged as models for studying gut microbial communities.

Antibiotic Resistance Genes Carried by Commensal Escherichia colifrom Shelter Cats in Italy – Delia Gambino et al. – Veterinary Sciences


Multimodal learning in clinical proteomics: enhancing antimicrobial resistance prediction models with chemical information – Giovanni Visonà et al. – Bioinformatics
Sarand: Exploring Antimicrobial Resistance Gene Neighborhoods in Complex Metagenomic Assembly Graphs – Somayeh Kafaie et al. – bioRxiv preprint