prepared by Ulrike Löber

May digest features review on the gut microbiota – urinary tract infections axis, novel antimicrobial compounds detected – the dynaplanins -, phage therapy tackling antibiotic-resistant bacteria and more.

We are excited to share with you EMBARK NEWS – after the SPRING #AMR WEBINARS we are already planning the fall #EMBARK2022:
Join us and our invited speakers to discuss the latest AMR insights!


Perspective: Bacterial species rarely work together – Jacob D. Palmer – Science

Intermittent antibiotic treatment of bacterial biofilms favors the rapid evolution of resistance – Masaru Usui – bioRxiv

Long-term ecological and evolutionary dynamics in the gut microbiomes of carbapenemase-producing Enterobacteriaceae colonized subjects – Jonathan T. L. Kang – bioRxiv

Evaluation of metagenomic, 16S rRNA gene and ultra-plexed PCR-based sequencing approaches for profiling antimicrobial resistance gene and bacterial taxonomic composition of polymicrobial samples – KK Chau – bioRxiv

Review: Unbiased antimicrobial resistance prevalence estimates through population-based surveillance – Frank van Leth, Constance Schultsz – Clinical Microbiology Infection

Fitness effects of plasmids shape the structure of bacteria–plasmid interaction networks – Arthur Newbury, Beth Dawson, Uli Klümper, Elze Hesse, Meaghan Castledine, Colin Fontaine, Angus Buckling, and Dirk Sanders – PNAS


*Harnessing Rare Actinomycete Interactions and Intrinsic Antimicrobial Resistance Enables Discovery of an Unusual Metabolic Inhibitor – Dylan J. McClung – mBio

Horizontal gene transfer

Persisting uropathogenic Escherichia coli lineages show signatures of niche-specific within-host adaptation mediated by mobile genetic elements – Robert Thänert – Cell Host & Microbe

Antimicrobial peptides

News and Views: Antibiotic discovery with machine learning – Cesar de la Fuente-Nunez – Nature Biotechnology

Global health
Human-associated AMR

Dosing a synbiotic of human milk oligosaccharides and B. infantis leads to reversible engraftment in healthy adult microbiomes without antibiotics – Julie E. Button – Cell Host & Microbe

*Longitudinal multi-omics analyses link gut microbiome dysbiosis with recurrent urinary tract infections in women – Colin J. Worby – nature microbiology

Review: Antimicrobial resistance in Antarctica: is it still a pristine environment? – Kudzai Hwengwere – BMC Microbiome

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

Review: The resistance within: Antibiotic disruption of the gut microbiome and resistome dynamics in infancy – Robert Thänert – Cell Host & Microbe

Association of Diet and Antimicrobial Resistance in Healthy U.S. Adults – Andrew Oliver – mBio

Long-term antibiotic exposure promotes mortality after systemic fungal infection by driving lymphocyte dysfunction and systemic escape of commensal bacteria – Rebecca A. Drummond – Cell Host & Microbe

Editorial: The problem of antimicrobial resistance in chronic liver disease – The Lancet Gastroenterology & Hepatology


Carbapenem heteroresistance of KPC-producing Klebsiella pneumoniae results from tolerance, persistence and resistance – Adriana Chiarelli – bioRxiv

Clinical implementation of routine whole-genome sequencing for hospital infection control of multi-drug resistant pathogens – Brian M Forde – medRxiv


Metagenomic assembly reveals the circadian oscillations of the microbiome and antibiotic resistance genes in a model of laying hens – Yu Zhang – Science of The Total Environment

Taking metagenomics under the wings – Physilia Ying Shi Chua, Jacob Agerbo Rasmussen – Nature Reviews Microbiology

Biological units of antimicrobial resistance and strategies for their containment in animal production – Johanna Muurinen – FEMS Microbiology Ecology

A Qualitative Study of Antibiotic Use Practices in Intensive Small-Scale Farming in Urban and Peri-Urban Blantyre, Malawi: Implications for Antimicrobial Resistance – John Mankhomwa – Frontiers in Veterinary Science


Metagenomic profiling and transfer dynamics of antibiotic resistance determinants in a full-scale granular sludge wastewater treatment plant – David Calderón-Franco – Water Research

Antimicrobial resistance genes predict plasmid generalism and network structure in wastewater – Alice Risely – bioRxiv

Viruses and phages

Phage-antibiotic combination is a superior treatment against Acinetobacter baumannii in a preclinical study – Fernando L. Gordillo Altamirano – eBioMedicine

Review: Biological foundations of successful bacteriophage therapy – Carola Venturini – EMBO Molecular Medicine

*Bacteriophage treatment of disseminated cutaneous Mycobacterium chelonae infection – Jessica S. Little – Nature Communications


A curated data resource of 214K metagenomes for characterization of the global resistome – Hannah-Marie Martiny – bioRxiv

VRprofile2: detection of antibiotic resistance-associated mobilome in bacterial pathogens – Meng Wang – Nucleic Acids Research

PlasmidMaker is a versatile, automated, and high throughput end-to-end platform for plasmid construction – Behnam Enghiad – Nature Communications


Prediction of Antibiotic Resistance Evolution by Growth Measurement of All Proximal Mutants of Beta-Lactamase – Siyuan Feng – Molecular Biology and Evolution


Ep. 39: the AMR STUDIO podcast – Carl-Fredrik Flach & sewage surveillance. Water chlorination & microbiome. C. difficile spread between humans & animals.


DRIAMS: a database for antimicrobial resistance prediction based on MALDI-TOF mass spectrometry – Caroline Weis – in silico talks