This February issue presents studies on the presence of antibiotic resistance genes, as usual, in various environments according to the One Health concept. Human microbiome is considered as a reservoir of antibiotic resistance genes and in this digest we have a special highlight on the effect of antibiotics on newborns microbiome. Hospital environment is also discussed with methods for prediction of resistance and resistance prevalence in several context. Finally, studies focusing on antibiotic resistance in a more environmental perspective are also presented to complete this One Health circle.
Effects of early-life antibiotics on the developing infant gut microbiome and resistome: a randomized trial – Marta Reyman – Nature Communications In addition to the undeniable beneficial effects of antibiotics on newborns life span, antibiotics also have deleterious side effects such as microbiome species richness depletion and antibiotic resistant bacteria selection. Side effects could be even more deleterious if we take into account side effects that might have detrimental effects later in life according to the developmental origin of health and disease concept. Reyman et al. conducted the ZEBRA study enrolling 147 infants born at term either by natural delivery or cesarean section, for whom broad spectrum antibiotics were used. Reduced gut microbial diversity and prolonged ecological perturbations were detected compared with healthy term-born controls (still measurable after 12 months). Also, shifts in AMR gene profile were evidenced using qPCR and confirmed by metagenomic shotgun sequencing of a subset of samples. Those effects were different depending on the antimicrobial use (penicillin+gentamicin being the least deleterious) highlighting antibiotics choice importance.
The evolution of colistin resistance increases bacterial resistance to host antimicrobial peptides and virulence – Pramod K. Jangir – bioRxiv Colistin is an efficient antimicrobial peptide (AMP) used at a large scale in agriculture in the 1980s. Today, it is being used as “last-resort” antimicrobial to treat infections. One serious concern lies in the potential cross resistance between colistin resistance and host AMP resistance (since they have common physicochemical properties and mechanisms) which could increase pathogen transmission and virulence. Colistin resistance is mainly due to MCR-1 which became widely distributed across all niches because of bacterial migration and horizontal transfer. Here, Jangir et al. tested the hypothesis that evolving colistin resistance via MCR genes acquisition promotes resistance in bacteria against host AMPs. The presence of MCR indeed increased resistance against several AMPs coming from different sources. It highlights the importance of assessing the impact of evolved resistance to future therapeutic AMPs.
In December’s AMR digest we ask a wide range of questions. Why do antibiotics exist? What effect do they have on our own microbiota? Can they increase the colonizing capability of plasmid carrying bacteria? And what methods can we use to measure resistance against them? This is a small sample of the wide range of topics in this month’s digest.
Combinatorial, additive and dose-dependent drug–microbiome associations – Sofia K Forslund – Nature *This study used a multi-omics approach to investigate drug-microbiome interactions in patients suffering from cardiometabolic disease. The authors found that multiple antibiotic exposures had cumulative effects on the patients microbiome. Leading to reduced richness and increased resistance, which are hallmarks of microbiota in patients suffering from obesity, insulin resistance and low-grade inflammation.
Rapid absolute quantification of pathogens and ARGs by nanopore sequencing – Yu Yang – The Science of the Total Environment *Sequencing has become cheaper, faster and more accessible these last few decades. With the use of third generation sequencing these authors test a method where they can quantify the absolute abundance of both pathogens and resistance genes in 4 hours using third generation nanopore sequencing. Taking advantage of the nanopore technologies long reads, the authors were able to link resistance genes to individual taxa.
Make sure not to miss the last EMBARK Webinar of the fall! This time we have two very exciting speakers:
December 15:Willem van Schaik – “Metagenomic approaches to understand the spread of antibiotic resistance genes in microbial ecosystems” Svetlana Ugarcina Perovic – “Exploring the global resistome using the global microbial gene catalog” [Register]
The AMR digest from November features studies on antibiotic perception, consumption and also how the environment can influence AMR diffusion. Fundamental microbiology linked to AMR is also part of this month digest including subjects such as bacterial cell wall or biofilm. Different environments are also discussed within the papers on natural habitat and animals or water environments. Finally, there’s a special highlight on antibiotic resistance in cancer patient in this “movember” month.
Global antibiotic consumption and usage in humans, 2000-18: a spatial modelling study – Annie J Browne – The Lancet *This article describes how antibiotic is consumed globally. Thanks to individual level data and geostatistical model they could estimate antibiotic usage and consumption in 204 countries from 2000 to 2018. Beside large increases in the consumption of different classes of antibiotics in several regions, lack of access to antibiotics still seems to be a problem in other regions. Having those estimation, strategies can be thought to adapt the combat against antibiotic resistance increase.
Antibiotic resistance in the patient with cancer: Escalating challenges and paths forward – Amila K Nanayakkara – CA: a cancer journal for clinicians *In this interesting review, Nanayakkara and colleagues are discussing the impact of antimicrobial resistance on patient with cancer lifespan. Infection is one of the leading complications in patient with cancer and antimicrobial resistance is related to unfavorable outcomes. Several strategies are discussed to prevent antimicrobial resistant strain outbreak in patient with cancer.
The AMR digest from this month is full of “spooktacular” stories about resistant bacterial monsters that might scare you… The EMBARK team invites you to a free broom ride through many works on AMR in soil, water, domestic and wild animals, microbial ecology linked to antibiotics usage, microplastics and more… Boo!
*Cultivating Healthy Connections: Exploring and Engineering the Microbial Flow That Shapes Microbiomes – Wiles, Travis J. – mSystems, 6(5), e00863-21. In this commentary, Travis J. Wiles invites us to change our focus towards a more systems-level view of the host-microbe interactions framework. He suggests describing how microbial communities assemble or disperse into new hosts and environments. Focusing on understanding the evolution of communities, which includes not only pathogens, but also commensal bacteria, viruses, and mobile genetic elements. Exploring these topics could inspire new strategies of therapeutic intervention for individual health and control microbiome interactions.
Natural habitats and wildlife
*Antibiotics and fecal transfaunation differentially affect microbiota recovery, associations, and antibiotic resistance in lemur guts – Sally L. Bornbusch, Rachel L. Harris, Nicholas M. Grebe, Kimberly Roche, Kristin Dimac‑Stohl, and Christine M. Drea – Animal microbiome, 3(1), 1-15. Like other papers in this AMR digest, Sally L. Bornbusch and collaborators address the effect of antibiotics on the structure and composition of gut microbiomes. Unlike the others, this work focuses on a nonhuman primate wildlife species (ring‑tailed lemurs – Lemur catta) as a model. They found that the treatment of healthy lemurs with broad spectrum antibiotics leads to a decline in bacterial diversity and composition and a long-term instability of the community, nevertheless treatment with fecal transfaunation reduces the impact. They found potential keystone species in the lemur gut microbiota and described ARGs in them despite the lack of previous exposure to antibiotics.
*Unravelling the collateral damage of antibiotics on gut bacteria – Lisa Maier, Camille V. Goemans, Jakob Wirbel, Michael Kuhn, Claudia Eberl, Mihaela Pruteanu, Patrick Müller, Sarela Garcia-Santamarina, Elisabetta Cacace, Boyao Zhang, Cordula Gekeler, Tisya Banerjee, Exene Erin Anderson, Alessio Milanese, Ulrike Löber, Sofia K. Forslund, Kiran Raosaheb Patil, Michael Zimmermann, Bärbel Stecher, Georg Zeller, Peer Bork and Athanasios Typas – Nature, 1-5. The work of Lisa Maier and collaborators drives our attention to a topic that recently has received more attention which is the collateral damage of antibiotics on the gut microbiota. They characterized over 140 antibiotics on 38 representative bacterial species from the human gut microbiome. One of the most striking results indicates that macrolides and tetracyclines not only inhibited all tested commensal bacteria but killed commensal E. coli strains among the others. Moreover, the use of drug antagonists selectively protects certain species. Overall, their findings reflect the different effects of antibiotics on the commensal microbiome and suggest strategies to diminish those adverse effects.
*Inter-species interactions alter antibiotic efficacy in bacterial communities – Michael J. Bottery, Jessica L. Matthews, A. Jamie Wood, Helle Krogh Johansen, Jon W. Pitchford and Ville-Petri Friman – The ISME Journal, 1-10. Michael J. Bottery and collaborators evaluate how interactions among bacterial community members alter susceptibility to antibiotics. They quantify and identify these mechanisms for community-modulated efficacy using a clinically relevant pathogen, Pseudomonas aeruginosa, and cystic fibrosis lung communities. Multidrug-resistant Stenotrophomonas maltophilia protect sensitive P. aeruginosa against imipenem but not to meropenem. They model the level of exposure protection provided against different carbapenems explained by differences in antibiotic efficacy and inactivation rate.
*Abundance, diversity and diffusion of antibiotic resistance genes in cat feces and dog feces – Yiwen Yang, Xinwen Hu, Wenjie Li, Linfei Li, Xindi Liao, and Sicheng Xing – Environmental Pollution, 118364. What could be the role of our pets in antimicrobial resistance transmission?… Well, the work from Yiwen Yang and collaborators explores ARGs in the understudied environment of cat and dog feces. They aimed to provide some answers about the potential threat of ARG in pet feces to environmental safety. They found higher abundance of ARGs in dogs when compared to cats and linked the difference to a higher abundance of Proteobacteria in dogs. They also confirmed that ARGs from pets feces might diffuse into the air, however they could not find any evidence that these could be seen as a threat to environmental safety or human health.
Bilateral AMR Symposium – Imperial College London, A*STAR ID Labs, and ID TRP – Nov 18 – 19, 2021 04:00 PM (Singapore time) Clinical perspectives, epidemiology, infection control strategies, the biology of resistance and transmission, to novel treatment strategies. Register here!
EMBARK Fall Webinars continue in November and December with amazing speakers! Register and don’t miss them!
November 10: Michael Baym – “Exploring non-anthropic selective pressures on antibiotic resistance” Register here!
November 24: Nikolina Udikovic Kolic – “Pharmaceutical waste and antimicrobial resistance” Register here!
December 15: Willem van Schaik – “Metagenomic approaches to understand the spread of antibiotic resistance genes in microbial ecosystems” Svetlana Ugarcina Perovic – TBA Register here!
Superbugs and You: True Stories from Scientists and Patients Around the Globe – Co-created by CIDRAP-ASP and the Antimicrobial Resistance Fighter Coalition (ARFC). First episode was released on October 20!
AMR Studio Podcast Ep 33: Manica Balasegaram & the work of GARDP. AMR & patients with cancer. CRISPR-Cas antimicrobials – Uppsala Antibiotic Center