We have two more EMBARK Webinars to go before the end of the year. For the second one with Joakim Larsson we have updated the date to December 14. Make a note in your calendars!
Nov 9, 14:00 UTC+2 Iruka Okeke – Genomic surveillance of human-invasive Salmonella in Nigeria Miranda Wallace – Understanding and predicting resistance in Bacteroides fragilis group bacteria using clinical and modern genomics tools [Register here]
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.
Time again for a new round of EMBARK Webinars. This fall we will have four fantastic main speakers, together with a group of excellent junior speakers. Sign up for the webinars today!
Sep 14, 14:00 UTC+2 Jon Hobman – Antimicrobial resistance in a UK dairy farm Kenyum Bagra – Invasion dynamics of AMR bacteria into microbiomes under stress [Register here]
Oct 5, 14:00 UTC+2 Stineke van Houte – Towards the development of CRISPR-Cas based tools to remove AMR from microbial communities Ruben Vazquez-Uribe – CRISPR-Cas antimicrobials: Resistance mechanisms [Register here]
Nov 9, 14:00 UTC+2 Iruka Okeke – Genomic surveillance of human-invasive Salmonella in Nigeria Miranda Wallace – Understanding and predicting resistance in Bacteroides fragilis group bacteria using clinical and modern genomics tools [Register here]
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.
