Prepared by Uli Klümper (http://www.twitter.com/UliKluemper)
The April AMR digest features global drivers of AMR, environmental barriers to AMR, a number of papers on the ecology underlying plasmid-based spread of AMR, wastewater as a major source for ARG mobility, and more!
General
Bacterial defences: mechanisms, evolution and antimicrobial resistance – William P.J. Smith – Nature Reviews Microbiology
Global picture
Global antimicrobial-resistance drivers: an ecological country-level study at the human–animal interface – Kasim Allel et al. – The Lancet Planetary Health
Global trends in antimicrobial use in food-producing animals: 2020 to 2030 – Ranya Mulchandani et al. – PLOS Glob Public Health
Global trends in antimicrobial resistance on organic and conventional farms – Eldon Ager et al. – bioRxiv preprint
Policy
Environmental surveillance of antimicrobial resistance (AMR), perspectives from a national environmental regulator in 2023. – Alwyn Hart et al. – Euro Surveillance
International manufacturing and trade in colistin, its implications in colistin resistance and One Health global policies: a microbiological, economic, and anthropological study – Muhammad Umair et al. – The Lancet Microbe
Commission proposal for a Council Recommendation on stepping up EU actions to combat antimicrobial resistance in a One Health approach – European Commission
Environment
Microbiome diversity: A barrier to the environmental spread of antimicrobial resistance? – Uli Klümper, G. Gionchetta, E. C. P. Catao, X. Bellanger, I. Dielacher, P. Fang, S. Galazka, A. Goryluk-Salmonowicz, David Kneis, U. Okafor, E. Radu, M. Szadziul, E. Szekeres, A. Teban-Man, C. Coman, N. Kreuzinger, M. Popowska, J. Vierheilig, F. Walsh, M. Woegerbauer, H. Bürgmann, C. Merlin, Thomas U. Berendonk – bioRxiv preprint
*The study is based on ~200 samples of forest soils and riverbed material of low anthropogenic impact in 7 European countries In stationary soils with established niches the number of and the relative abundance of these ARGs is inversely correlated with microbial diversity. Contrary, in dynamic riverbeds, where ecological niches are constantly disturbed, no such effects can be observed. The study hence proposes that microbiome diversity can serve as a barrier to the spread of AMR, but only in ecosystems with “stable” niche structures.
Gene Transfer/Plasmids
Tradeoff between lag time and growth rate drives the plasmid acquisition cost – Mehrose Ahmad et al. – Nature Communications
*Plasmid acquisition costs are primarily driven by changes in lag time, rather than growth rate, for nearly 60 conditions covering diverse plasmids, selection environments, and clinical strains/species. Surprisingly, for a costly plasmid, clones exhibiting longer lag times also achieve faster recovery growth rates, suggesting an evolutionary tradeoff.
Preceding Host History of Conjugative Resistance Plasmids Affects Intra- and Interspecific Transfer Potential from Biofilm – Ilmur Jonsdottir et al. – mSPhere
Antagonistic Mobile Genetic Elements Can Counteract Each Other’s Effects on Microbial Community Composition – Meaghan Castledine et al. – mBio
* In-silico simulations predict increasing antagonist diversity diminishes individual antagonist effects on community composition as conflicting effects cancel out. This is proven experimentally as a conjugative plasmid and bacteriophages have effects on community composition when they’re the only antagonist. But when together, the community reverts back to its antagonist-free state.
Differences in vertical and horizontal transmission dynamics shape plasmid distribution in clinical enterobacteria – Aida Alonso-del Valle et al. – bioRxiv preprint
Insertion Sequences Determine Plasmid Adaptation to New Bacterial Hosts – Emelia Wedel et al. – mBio
Comprehensive analysis of disinfectants on the horizontal transfer of antibiotic resistance genes – Shuyao Zhu et al. – Journal of Hazardous Materials
Phthalates Promote Dissemination of Antibiotic Resistance Genes: An Overlooked Environmental Risk – Jing Wu et al. – Environmental Science & Technology
Simulated Gastric Acid Promotes the Horizontal Transfer of Multidrug Resistance Genes across Bacteria in the Gastrointestinal Tract at Elevated pH Levels – Hai-yan Wu et al. – Microbiology Spectrum
Wastewater
Evidence for wastewaters as environments where mobile antibiotic resistance genes emerge – Fanny Berglund et al. – Communications Biology
*The majority of previously identified mobile ARG hosts did not carry the mobilizing elements that likely enabled their original intracellular mobility, suggesting a necessary interplay between different bacteria resulting in their spread in human pathogens. Analyses of a broad range of metagenomes revealed that wastewaters and wastewater-impacted environments had by far the highest abundance of both origin species and corresponding mobilizing elements.
Simultaneous removal of antibiotics and antibiotic resistance genes in wastewater by a novel nonthermal plasma/peracetic acid combination system: Synergistic performance and mechanism – Ai Zhang et al. – Journal of Hazardous Materials
Metagenomic insights into the distribution, mobility, and hosts of extracellular antibiotic resistance genes in activated sludge under starvation stress – Shuai Zhou et al. – Water Research
Soil
Identification of diverse antibiotic resistant bacteria in agricultural soil with H218O stable isotope probing combined with high-throughput sequencing – Marcela Hernández Et al. – Environmental Microbiome
Partitioning and migration of antibiotic resistance genes at soil-water-air interface mediated by plasmids – Yang Zhu et al. – Environmental Pollution
Food
Exploiting a targeted resistome sequencing approach in assessing antimicrobial resistance in retail foods – Julia A. Shay et al. – Environmental Microbiome
Zoonotic infections
Using source-associated mobile genetic elements to identify zoonotic extraintestinal E. coli infections – Cindy M. Liu et al. – One Health
Wildlife
White stork movements reveal the ecological connectivity between landfills and different habitats – Cosme López-Calderón et al. – Movement Ecology
Bioinformatics
HOTSPOT: Hierarchical hOst predicTion for aSsembled Plasmid cOntigs with Transformer – Yongxin Ji et al. – Bioinformatics
Addressing antibiotic resistance: computational answers to a biological problem? – Anna H Behling et al. – Current Opinion in Microbiology
Messages from the seventh international conference on clinical metagenomics (ICCMg7) – Mikael de Lorenzi-Tognon, Etienne Ruppe, J. Schrenzel – Microbes and Infection
Tools
A Streamlined Approach for Fluorescence Labelling of Low-Copy-Number Plasmids for Determination of Conjugation Frequency by Flow Cytometry – Qin Qi et al. – Microorganisms
Webinars
Our monthly EMBARK Webinar on ARG annotation
with Prof. Andrew Stubbs & Prof. Luis Pedro Coelho, moderated by Svetlana Ugarčina Perović
May 17th, 14:00 CEST – Register here
NCBI Webinar: Accessing NCBI AMR Pathogen Data in the Cloud – Now available as a recording on Youtube
Courses/Workshops
EMBO Workshop: Plasmids as vehicles of AMR spread, in Triest, Italy – 18. – 22. September 2023 | Trieste, Italy
Molecular Approaches to Clinical Microbiology in Africa, hosted by the Kenya Medical Research Institute (KEMRI) – 2. – 8. September 2023
Artificial Intelligence & Antibiotic Resistance – Health Talks – Free hybrid event by The Global Antibiotics Resistance Foundation in Helsinki Finland – 22. May 2023
Podcast
EFSA Europe podcast: Episode 6 – Antibiotics: handle with care by Ernesto Liebana