This AMR digest features overview of sewage resistomes from most countries on Earth and importance of sewage surveillance of antibiotic resistance, latest news on inner secrets of Asgard archaea and microbiomes of Galapagos marine iguanas… and lots of Santas hats here and there. Happy #AMR reading!
Defining the Benefits of Antibiotic Resistance in Commensals and the Scope for Resistance Optimization – Kristofer Wollein Waldetoft – Microbial Ecology * Antibiotic resistance is commonly viewed as universally costly, regardless of which bacterial cells express resistance. In this paper, the authors derive an opposing logic, where resistance in commensal bacteria can lead to reductions in pathogen density and improved outcomes on both the patient and public health scales (Figure 1).
Figure 1. Potential costs and benefits of antibiotic resistance in commensal organisms.
Mysterious Asgard archaea microbes reveal their inner secrets – Jan Löwe – Nature News and Views * Asgard archaeal cells have been grown successfully in the laboratory and their internal architecture offers clues to the early evolution of eukaryotic cells. Have a look inside a proposed relative of our cellular ancestors!
Guts within guts: the microbiome of the intestinal helminth parasite Ascaris suum is derived but distinct from its host – Ankur Midha, Víctor Hugo Jarquín-Díaz, Friederike Ebner, Ulrike Löber, Rima Hayani, Arkadi Kundik, Alessio Cardilli, Emanuel Heitlinger, Sofia Kirke Forslund & Susanne Hartmann – Microbiome * Intestinal helminths are extremely prevalent among humans and animals, and live in intimate contact with the host gut microbiota and harbor bacteria within their own intestines. This study shows that a nematode infection reduces the microbiome diversity of the host gut, and that the nematode gut represents a selective bacterial niche harboring bacteria that are derived but distinct from the host gut.
Genome-resolved insight into the reservoir of antibiotic resistance genes in aquatic microbial community – Zahra Goodarzi – Scientific Reports * This study shows the distribution of ARGs in the Caspian Sea ecosystem (Figure 3). To this end, the authors performed genome-resolved metagenomic analyses of deeply sequenced depth profile metagenomes of the Caspian Sea and applied Hidden Markov models. They further investigated how ecological strategies of resistance bacteria affect the ARGs they contain. Comparative analysis revealed that Acidimicrobiia and Actinobacteria characterized by streamlined genomes modify the antibiotic target via mutation to develop antibiotic resistance rather than carrying extra resistance genes.
Figure 3 Antibiotic resistance gene profile of the Caspian Sea Bacteria
The bacterial hand print of my 5yo son, after he finished playing outside 🙂 We had a group activity at daycare to prove how washing your hands **with soap** actually makes a difference 💪🧫👩🔬 pic.twitter.com/qok7nYlDle
Very happy to share that I am the recipient of the 2022 Einhorn SIGHT award for our work on #AMR. I am honoured and very grateful!https://t.co/soqtz8xYAG
The November AMR Digest delivers some fresh and crisp publications from the world of antibiotic resistance. This time we collected publications featuring the AMR evolution, AMR in water and soil, advances of metagenomics in tracking AMR and much more! Enjoy your reading!
The synthesis report “Routes and reservoirs of AMR-determinants & One Health AMR-surveillance” of the Swiss National Research Program 72 “Antimicrobial Resistance” This report summarizes the research of 18 projects in the field of antibiotic resistance over a 5-year period. Based on the findings and observations, the authors suggest key recommendations for action to restrict the spread of AMR.
Reviews
Molecular mechanisms of antibiotic resistance revisited – Elizabeth M. Darby – Natural Reviews Microbiology In this article, the authors provide an overview of molecular mechanisms and strategies that bacteria apply to develop resistance to antimicrobials. They give insights into the role of efflux systems in decreased antibiotic susceptibility and their synergetic interaction with other resistance mechanisms. Understanding of molecular mechanisms is essential to overcome antimicrobial resistance and can be used, for example, for developing so-called antibiotic resistance breakers (ARBs) – compounds that can restore antibiotic activity by disrupting or inhibiting a specific resistance mechanism.
Within-patient evolution of plasmid-mediated antimicrobial resistance – Javier DelaFuente – Nature Ecology and Evolution This five-year study aimed at tracking AMR evolution in vivo in patients. By analyzing 224 poxA-48-carrying Enterobacteria isolated from 9000 patients, DelaFuente et al. were able to identify 35 variants of a poxA-48 plasmid. They monitored 121 patients for a potential case of within-patient AMR evolution and identified three instances in which the same bacterial host carried different plasmid variants over the treatment period. The authors compared plasmid fitness, susceptibility to antibiotics, plasmid copy number and HGT rates of the new plasmids and ancestral plasmids. According to their findings, the authors concluded that within-patient plasmid-mediated AMR requires an interplay between resistance levels and bacterial fitness.
Very happy to see this work finally published! Many thanks to all authors, my lab mates and special thanks to @AlvSanMillan !
Exposure to environmental stress decreases the resistance of river microbial communities towards invasion by antimicrobial-resistant bacteria – Kenyum Bagra, Xavier Bellanger, Christophe Merlin, Gargi Singh, Thomas Ulrich Berendonk, Uli Klümper – bioRxiv In this preprint the authors utilize artificial river flume systems to explore the invasion dynamics of a model resistant strain (E. coli) into river microbial communities in the presence and absence of a co-introduced environmental stressor. Despite an initially successful introduction of E. coli into all the biofilms, independent of the imposed stress, over time the invader perished in absence of stress. However, under stress conditions the invading strain successfully established and proliferated in the biofilms. Noteworthy, the increased establishment success of the invader coincided with a loss in microbial community diversity under stress conditions, likely due to additional niche space becoming available for the invader.
If you live in the Northern Hemisphere every day is becoming darker and colder when we are steadily approaching winter. It is therefore extra important to illuminate your mind with interesting research and get that warm feeling in your body when reading a well written and structured paper. This is hopefully the feeling you will get when reading our October AMR digest. It touches the topics of evolution, the release of new databases, biofilms, wastewater and so much more. If you are from the Southern Hemisphere, you are of course equally welcome to take part of this interesting collection of papers!
*ResFinderFG v2.0: a database of antibiotic resistance genes obtained by functional metagenomics – Rémi Gschwind – bioRxiv A bioinformatic analysis is not better than the database and tools you base it on. Here Rémi Gschwind et al. describes a new and updated version of ResFinderFG, version 2.0. According to the authors most genes in antibiotic resistance gene databases mostly originate from culturable and pathogenic bacteria. ResfinderFG 2.0 is instead a database based on a literature search on studies identifying resistance genes using functional metagenomics. This means that there is a reduced bias in the ResFinderFG v.2.0 database towards culturable pathogens.
*ResFinderFG version 2.0 is out*https://t.co/l88RXjxPr6 If you do antibiotic resistance genes (ARGs) annotation you should use it, and here is why : (1/4)
*A curated data resource of 214K metagenomes for characterization of the global antimicrobial resistome – Hannah-Marie Martiny – PLOS BIOLOGY Large scale metagenomic screenings of the worlds entire catalogue of metagenomic data could potentially reveal interesting global and local patterns of antibiotic resistance. Undertaking such a task is however way to computer intensive for most research groups to undertake. Luckily, Hannah-Marie Martiny et al. have already undertaken this task. In this paper they present a publicly available resource of antibiotic resistance gene abundance based on 442 Tbp of sequencing reads from 214,095 metagenomic samples from the European Nucleotide Archive.
Fig 4. Composition of reads assigned to ARGs from different resistance classes grouped by sampling origin.
Evolution *The evolution of spectrum in antibiotics and bacteriocins – Jacob D Palmer and Kevin R Foster – PNAS An important weapon in microbial competition is the production of antibiotics. But when is it preferential for a microbial population to produce wide or narrow spectrum antibiotics? In this paper Jacob D Palmer and Kevin R Foster have used an evolutionary model approach in an attempt to shed light on this question.
For those in the northern hemisphere… Summer is here ⛱️! With it, the EMBARK team brings a refreshing AMR digest with many sunshiny papers. Put your 🕶️ on and swim deep into many works that we have compiled for you: AMR in soil, water, clinical or livestock settings, antibiotic resistance gene ecology and evolution and more … for those in the southern hemisphere, we also wish you a happy reading despite the cold winter ^^
*Addressing a future pandemic: how can non-biological complex drugs prepare us for antimicrobial resistance threats? – Blackman, L. D., Sutherland, T. D., De Barro, P. J., Thissen, H., & Locock, K. E. – Materials Horizons Lewis D. Blackman et al. review the different ways in which bacteria develop resistance against antibiotics and alternative agents that could be employed. They focused on non-biological complex drugs (NBCDs) as the next generation antimicrobial agents. They outline the advancements in antimicrobial polymer materials, carbon nanomaterials, and inorganic nanomaterials and highlight the remaining challenges for their clinical translation.
*Environmental Dimensions of “One Health” to Combat Antimicrobial Resistance: Essential Research Needs – Jin, L., Pruden, A., Boehm, A. B., Alvarez, P. J., Raskin, L., Kohn, T., & Li, X. – Integrating Environmental Science & Technology In this viewpoint article, Jin et al. critically address the lack of relevance and impact on health outcomes in environmental AMR research. They invite to “better define impactful contributions from the environmental dimension of AMR as part of a broader “One Health” vision” by implementing and developing models in line with an anthropocentric context of bacterial transfer within the interface between environment and humans. The authors promote multidisciplinary cross-national participation and coordination to establish analytical approaches to interpret ARG in the environment comprehensively. Approaches to identify responsible agents or conditions that select for AMR evolution and fit-for-purpose treatment technologies for mitigating high-risk ARGs and ARB at crucial sources.
*A bottom-up view of antimicrobial resistance transmission in developing countries – Ikhimiukor, O.O., Odih, E.E., Donado-Godoy, P. and Iruka N. Okeke – Nature Microbiology This review from Odion O. Ikhimiukor et al. focuses on AMR transmission in low- and middle-income countries, emphasizing high-risk transmission points such as urban settings and food-animal handling. The authors describe the integration of top-down and bottom-up strategies as AMR-containment approaches. They suggest that technological innovations are required to control AMR in low- and middle-income settings.
*Globally distributed mining-impacted environments are underexplored hotspots of multidrug resistance genes – Yi, X., Liang, J. L., Su, J. Q., Jia, P., Lu, J. L., Zheng, J. & Zhu, Y. G. – The ISME Journal Yi et al. focused their work on giving further insight into antimicrobial resistance in mining-impacted environments. They suggest developing constant monitoring strategies as the mining sites represent an underexplored hotspot for multidrug resistance genes. Overall, they described around 54 high-quality ARG-carrying MAGs from the phylum Proteobacteria, Acidobacteria, Actinobacteria, Bacteroidota, Firmicutes, Nitrospira, Planctomycetes and Thermoplasmatota and confirmed high mobility of ARGs, mainly trough transposons and plasmid.
Very proud to share our publication "Metagenomic DNA sequencing for semi-quantitative pathogen detection from urine: a prospective, laboratory-based, proof-of-concept study", published in @LancetMicrobe today! https://t.co/cyLS5TSeRJ
🧵on the latest @DETECTIVE_AMR manuscript, which might be my favourite so far. It's about a quirky group of plasmids that accumulate and disseminate all sorts of accessory genes in Acinetobacter… 1/20 https://t.co/Yzid2Q5Y5z
Check out our newest work on phage-plasmids: https://t.co/7s2bRIE1xn Unlike other phages, they often encode #AMR genes and, of concern, also contribute to their spread (by infection and lysogenic conversion). !Thanks a lot! for great support and help @epcrocha & RemyBonnin!
Latest lab publication led by @amito@FinlayM – Datasets for benchmarking antimicrobial resistance genes in bacterial metagenomic and whole genome sequencing https://t.co/93GQg9FpCl
1/14 A fun 🙂 thread on our latest paper, which touches on how bacteria such as Strep pneumo process antibiotics, how this can be exploited for new antimicrobial therapies and how tolerance is just a simple genetic change away. https://t.co/WjnQPN8ikW
Join CIDRAP-ASP on June 21, 6:00 – 7:15 pm CDT for a webinar discussing the importance of effective, data-driven infection prevention strategies (IPC) and antibiotic stewardship (AS) initiatives. It has been shown that IPC and AS reduce drug-resistant infections and diminish the burden of antimicrobial resistance (AMR) within healthcare systems. More information here.
AMR Studio Podcast Ep 39: Vanessa Carter & patient advocacy. A stewardship game. Evolution of antibiotic tolerance – Uppsala Antibiotic Center
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!
Join us for the last #EMBARK2022 before summer break ⛱️
Using competition, we found that Couchioplanes bacteria make a family of new antibiotics called dynaplanins! These small molecules act as metabolic inhibitors. Check out our latest publication by @DynaCockusRose to learn more:https://t.co/j6UmySL9QN
Ep. 39: the AMR STUDIO podcast – Carl-Fredrik Flach & sewage surveillance. Water chlorination & microbiome. C. difficile spread between humans & animals.
