prepared by Svetlana Ugarcina Perovic

The AMR March digest features the latest publications on global health risk of antibiotic resistance genes, bacterial responses to antibiotic combinations, Hi-C assisted metagenomics for AMR resistance tracking and more. Happy #AMR reading!

Join us for the spring #EMBARK2022 webinars!


Assessment of global health risk of antibiotic resistance genes – Zhenyan Zhang – Nature Communications
*Authors developed a novel method for quantitatively surveilling the health risk of ARGs, by integrating human accessibility, mobility, pathogenicity and clinical availability. Antibiotic resistance risk was detected all around the world, even in the polar region. Human-associated habitats posed the highest risk of antibiotic resistance than other habitats.

ARGs shared between the human-associated and three main habitats.
Number in the circles represents the number of shared ARGs.

Existing evidence on antibiotic resistance exposure and transmission to humans from the environment: a systematic map – Isobel Catherine Stanton – Environmental Evidence

Landscape of mobile genetic elements and their antibiotic resistance cargo in prokaryotic genomes – Supriya Khedkar, Georgy Smyshlyaev, Ivica Letunic, Oleksandr M Maistrenko, Luis Pedro Coelho, Askarbek Orakov, Sofia K Forslund, Falk Hildebrand, Mechthild Luetge, Thomas S B Schmidt, Orsolya Barabas, Peer Bork – Nucleic Acids Research

Intra- and interpopulation transposition of mobile genetic elements driven by antibiotic selection – Yi Yao – Nature Ecology & Evolution

Role of mobile genetic elements in the global dissemination of the carbapenem resistance gene blaNDM – Mislav Acman – Nature Communications


Phenotypic and Genotypic Characterization of a Hypervirulent Carbapenem-Resistant Klebsiella pneumoniae ST17-KL38 Clinical Isolate Harboring the Carbapenemase IMP-4 – Jintao He – Antimicrobial Chemotherapy

The repurposing of Tebipenem pivoxil as alternative therapy for severe gastrointestinal infections caused by extensively drug resistant Shigella spp. – Elena Fernández Alvaro – eLife

Urinary culture sensitivity after a single empirical antibiotic dose for upper or febrile urinary tract infection: a prospective multicenter observational study – John Gregor – Clinical Microbiology and Infection

Review: The physiology and genetics of bacterial responses to antibiotic combinations – Roderich Roemhild – Nature Reviews Microbiology
*Authors discuss the effects of antibiotic combinations, previous treatments and the role of stress-response systems as well as resistance mutation–drug interactions.

Decreased efficacy of antimicrobial agents in a polymicrobial environment – Thomas James O’Brien – The ISME Journal

Human microbiome

Strain-level characterization of broad host range mobile genetic elements transferring antibiotic resistance from the human microbiome – Samuel C. Forster – Nature Communications

Review: Good microbes, bad genes? The dissemination of antimicrobial resistance in the human microbiome – Alexander Crits-Christoph – Gut Microbe

Inflammatory Endotype-Associated Airway Resistome in Chronic Obstructive Pulmonary Disease – Xinzhu Yi – Microbiology Spectrum


Extensive metagenomic analysis of the porcine gut resistome to identify indicators reflecting antimicrobial resistance – Yunyan Zhou – Microbiome

Novel canine high-quality metagenome-assembled genomes, prophages and host-associated plasmids provided by long-read metagenomics together with Hi-C proximity ligation – Anna Cuscó – Microbial Genomics

Animal experiments

Antibiotics cause metabolic changes in mice primarily through microbiome modulation rather than behavioral changes – Kale S. Bongers – PlosOne


A Phage Foundry framework to systematically develop viral countermeasures to combat antibiotic resistant bacterial pathogens – Vivek K. Mutalik and Adam P. Arkin – iScience


Characteristics of Antibiotic Resistance Genes and Antibiotic-Resistant Bacteria in Full-Scale Drinking Water Treatment System Using Metagenomics and Culturing – Qihui Gu – Frontiers in Microbiology

Municipal Wastewaters Carry Important Carbapenemase Genes Independent of Hospital Input and Can Mirror Clinical Resistance Patterns – Adela Teban-Man, Edina Szekeres, Peiju Fang, Uli Klümper, Adriana Hegedus, Andreea Baricz, Thomas Ulrich Berendonk, Marcel Pârvu, Cristian Coman – Environmental Microbiology


Cross-biome antibiotic resistance decays after millions of years of soil development – Qing-Lin Chen – The ISME Journal

Metagenomic strategies identify diverse integron-integrase and antibiotic resistance genes in the Antarctic environment – Verónica Antelo – MicrobiologyOpen


HAM-ART: An optimised culture-free Hi-C metagenomics pipeline for tracking antimicrobial resistance genes in complex microbial communities – Lajos Kalmar – Plos Genetics
*A comprehensive laboratory and bioinformatics pipeline HAM-ART (Hi-C Assisted Metagenomics for Antimicrobial Resistance Tracking) optimised for the generation of metagenome-assembled genomes including both chromosomal and extrachromosomal AMR genes. Authors found significant differences in the distribution of AMR genes between low- and high-antimicrobial use farms including a plasmid-borne lincosamide resistance gene exclusive to high-antimicrobial use farms in three species of Lactobacilli.

Comparing Long-Read Assemblers to Explore the Potential of a Sustainable Low-Cost, Low-Infrastructure Approach to Sequence Antimicrobial Resistant Bacteria With Oxford Nanopore Sequencing – Ian Boostrom – Frontiers in Microbiology


IntegronFinder 2.0: identification and analysis of integrons across Bacteria, with a focus on antibiotic resistance in Klebsiella – Bertrand Néron – bioRxiv

Whole genome sequencing and gene sharing network analysis powered by machine learning identifies antibiotic resistance sharing between animals, humans and environment in livestock farming – Zixin Peng – Plos Computational Biology
*Authors developed a computational framework identifying known AMR genes as well as yet unknown genetic determinants underlying AMR in E. coli from complex anthropogenic environments.


Recordings of the EDAR6 count down webinars available here.

Antimicrobial Resistance – Genomes, Big Data and Emerging Technologies (Virtual Conference): 27–29 April 2022, Wellcome Genome Campus, UK