prepared by Víctor Hugo Jarquín-Díaz

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!

Join us for the autumn #EMBARK2021 webinars!


A non-profit drug development model is part of the AMR solution – Laura J. V. Piddock, Jean-Pierre Paccaud, Seamus O’Brien, Michelle Childs, Rohit Malpani, and Manica Balasegaram – Clinical Infectious Diseases, ciab887.

Enterococcus spp. as a Producer and Target of Bacteriocins: A Double-Edged Sword in the Antimicrobial Resistance Crisis Context – Ana C. Almeida-Santos, Carla Novais, Luísa Peixe, and Ana R. Freitas – Antibiotics, 10(10), 1215.

Biological Mitigation of Antibiotic Resistance Gene Dissemination by Antioxidant-Producing Microorganisms in Activated Sludge Systems – Chong-Yang Ren, En-Ling Wu, Erica M. Hartmann, and He-Ping Zhao – Environmental Science & Technology.

*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.

“Our historically pathogen-based view of host-microbe interactions may be limiting the scope of new and alternative strategies for engineering microbiomes”

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.

Proportions of antibiotic resistance (ABR) genes identified in healthy, male ring-tailed lemurs (Lemur catta) that received no treatment (CON), antibiotics only (ABX), or antibiotics plus fecal transfaunation (ABXFT). Shown are color-coded resistance gene families at four time points during the study, during which antibiotic treatment was administered on days 0–6 and fecal transfaunation was administered on day 7. MDR = Multi-Drug Resistant

Ecological impact of antibiotics on bioremediation performance of constructed wetlands: Microbial and plant dynamics, and potential antibiotic resistance genes hotspots – Okugbe Ebiotubo Ohore, Zhirui Qin, Edmond Sanganyado, Yuwen Wang, Xiaoyang Jiao, Wenhua Liu, and Zhen Wang – Journal of Hazardous Materials, 127495.

Host age increased conjugal plasmid transfer in gut microbiota of the soil invertebrate Caenorhabditis elegans – Guo-Wei Zhou, Fei Zheng, Xiao-Ting Fan, Ming-JunLi, Qing-Ye Sun, Yong-Guan Zhu, and Xiao-Ru Yang- Journal of Hazardous Materials, 127525.

Antibiotic resistance genes in bacteria: Occurrence, spread, and control – Zonghui Jian, Li Zeng, Taojie Xu, Shuai Sun, Shixiong Yan, Lan Yang, Ying Huang, Junjing Jia, and Tengfei Dou – Journal of Basic Microbiology.

Grassland ecology system: A critical reservoir and dissemination medium of antibiotic resistance in Xilingol Pasture, Inner Mongolia – Jinmei Li, Irfan Ali Phulpoto, Lizheng Guo, Jie Zeng, and Zhisheng Yu – Science of The Total Environment, 150985.

Mobile genetic elements-mediated Enterobacterales-associated carbapenemase antibiotic resistance genes propagation between the environment and humans: A One Health South African study – Yogandree Ramsamy, Koleka P. Mlisana, Daniel G. Amoako, Akebe Luther King Abia, Arshad Ismail, Mushal Allam, Joshua Mbanga, Ravesh Singh, and Sabiha Y. Essack – Science of The Total Environment, 150641.

Antibiotics and microbial ecology

*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.

Modelling the exposure protection as a combined function of antibiotic effect and inactivation rate.

Water environment and waste water treatment

Seizing the moment: now is the time for integrated global surveillance of antimicrobial resistance in wastewater environments – Amy Pruden, Peter J. Vikesland, Benjamin C. Davis, Ana Mariade Roda Husman – Current Opinion in Microbiology, 64, 91-99.

Dynamics of integron structures across a wastewater network–Implications to resistance gene transfer – Marcos Quintela-Balujaab, Dominic Frigon, M.Abouelnaga, Kelly Jobling, Jesús L.Romalde, Mariano Gomez Lopez, and David W.Graham – Water Research, 117720.

Microbiome and antibiotic resistance profiling in submarine effluent-receiving coastal waters in Croatia – Marija Kvesić, Hrvoje Kalinić, Mia Dželalija, Ivica Šamanić, Roko Andričević, and Ana Maravić – Environmental Pollution, 118282.

Monitoring antibiotic resistance genes in wastewater environments: The challenges of filling a gap in the One-Health cycle – Aleksandra Miłobedzka, Catarina Ferreira, Ivone Vaz-Moreira, David Calderón-Franco, Adrian Gorecki, Sabina Purkrtova, Jan Bartacek, Lukasz Dziewit, Caitlin M. Singleton, Per Halkjær Nielsen, David Gregory Weissbrodt, and Célia M. Manaia – Journal of Hazardous Materials, 127407.

The Microplastic-Antibiotic Resistance Connection – Nachiket P. Marathe and Michael S. Bank – In Microplastic in the Environment: Pattern and Process (pp. 311-322). Springer, Cham.

Enhanced propagation of intracellular and extracellular antibiotic resistance genes in municipal wastewater by microplastics – Yuan Chenga, Jiarui Lub, Shusen Fua, Shangjie Wanga, Naomi Senehic, and Qingbin Yuan – Environmental Pollution, 118284.

Seasonal distribution of antibiotic resistance genes in the Yellow River water and tap water, and their potential transmission from water to human – Qiaoling Yu, Tianshu Feng, Jiawei Yang, Wanghong Su, Rui Zhou, Yijie Wang, Hong Zhang, and Huan Li – Environmental Pollution, 118304.

Metagenomic exploration reveals a differential patterning of antibiotic resistance genes in urban and peri-urban stretches of a riverine system – Vinay Rajput, Rakeshkumar Yadav, and Mahesh S. Dharne – Environmental Science and Pollution Research, 1-8.

Towards risk assessment for antibiotic resistant pathogens in recycled water: A systematic review and summary of research needs – Emily Garner, Marisa Organiscak, Lucien Dieter, Carley Shingleton, Madison Haddix, Sayalee Joshi, Amy Pruden, Nicholas Ashbolt, Gertjan Medema, and Kerry A. Hamilton – Environmental Microbiology.

Metagenomic assembly deciphered the type-dependent effects of surfactants on the fates of antibiotics resistance genes during sludge fermentation and the underlying mechanisms – Jingyang Luo, Xiaoshi Cheng, Yinglong Su, Le Zhang, Wei Du, Xingchen Bao, Wenxuan Huang, Qian Feng, Jiashun Cao, and Yang Wu – Science of The Total Environment, 150822.

How anammox process resists the multi-antibiotic stress: Resistance gene accumulation and microbial community evolution – Jin-Jin Fu, Dong-Qi Huang, Yu-Hui Bai, Yang-Yang Shen, Xia-Zhen Lin, Yong Huang, Yi-Rong Ling, Nian-Si Fan, and Ren-Cun Jin – Science of The Total Environment, 150784.

Soil and sediment environment

Influence of soil characteristics and metal (loid) s on antibiotic resistance genes in green stormwater infrastructure in Southern California – Wei-Cheng Hung, Megyn Rugh, Marina Feraud, Sumant Avasarala, Jessica Kurylo, Mathew Gutierrez, Karina Jimenez, Nhi Truong, Patricia A.Holden, Stanley B.Grant, Haizhou Liu, Richard F. Ambrose, and Jennifer A. Jay – Journal of Hazardous Materials, 127469.

Influence of Legacy Mercury on Antibiotic Resistomes: Evidence from Agricultural Soils with Different Cropping Systems – Yi Zhao, Hang-Wei Hu, Jian-Qiang Su, Xiuli Hao, Huaming Guo, Yu-Rong Liu, and Yong-Guan Zhu – Environmental Science & Technology.

Zero valent iron improved methane production and specifically reduced aminoglycoside and tetracycline resistance genes in anaerobic digestion – Junya Zhang, Tiedong Lu, Hui Zhong, Peihong Shen, and Yuansong Wei – Waste Management, 136, 122-131.

Fate of land-based antibiotic resistance genes in marginal-sea sediment: Territorial differentiation and corresponding drivers – Jian Lu, Yuxuan Zhang, Jun Wu, Jianhua Wang, Cui Zhang, and Jie Wu – Chemosphere, 132540.

Attenuation of antibiotic resistance genes in livestock manure through vermicomposting via Protaetia brevitarsis and its fate in a soil-vegetable system – Xiang Zhao, Ju-Pei Shen, Chang-Long Shu, Sheng-Sheng Jin, Hong J.Die, Li-Mei Zhang, and Ji-Zheng He – Science of The Total Environment, 150781.


Viral Community and Virus-Associated Antibiotic Resistance Genes in Soils Amended with Organic Fertilizers – Mo-Lian Chen, Xin-Li An, Hu Liao, Kai Yang, Jian-Qiang Su, and Yong-Guan Zhu – Environmental Science & Technology.

Performance and mechanism in degradation of typical antibiotics and antibiotic resistance genes by magnetic resin-mediated UV-Fenton process – Jie Zhong, Bin Yang, Fang-Zhou Gao, Qian Xiong, Yong Feng, Yu Li, Jin-Na Zhang, and Guang-Guo Ying – Ecotoxicology and Environmental Safety, 227, 112908.

Farm and domestic animals

Aerobic composting and anaerobic digestion decrease the copy numbers of antibiotic-resistant genes and the levels of lactose-degrading Enterobacteriaceae in dairy farms in Hokkaido, Japan – Satoshi Katada, Akira Fukuda, Chie Nakajima, Yasuhiko Suzuki, Takashi Azuma, Ayaka Takei, Hideshige Takada, Eiryu Okamoto, Toshihide Kato, Yutaka Tamura, and Masaru Usui – Frontiers in Microbiology, 12.

*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.

Effect of cattle farm exposure on oropharyngeal and gut microbial communities and antibiotic resistance genes in workers – Dong Ding, Jingyuan Zhu, Yanling Gao, Fan Yang, Yan Ma, Xuemin Cheng, Jinlei Li, Peng Dong, Haiyan Yang, and Shuaiyin Chen – Science of The Total Environment, 150685.

Spread of airborne antibiotic resistance from animal farms to the environment: Dispersal pattern and exposure risk – Hong Bai, Liang-Ying He, Dai-Ling Wu, Fang-Zhou Gao, Min Zhang, Hai-Yan Zou, Mao-Sheng Yao, and Guang-Guo Ying – Environment International, 158- 106927

“Farm-to-fork” ARG transmission

Antibiotic resistance in the pathogenic foodborne bacteria isolated from raw kebab and hamburger: phenotypic and genotypic study – Maryam Rajaei, Mir‑Hassan Moosavy, Sahar Nouri Gharajalar, and Seyed Amin Khatibi – BMC microbiology, 21(1), 1-16.

Microbial colonization and resistome dynamics in food processing environments of a newly opened pork cutting industry during 1.5 years of activity – José F. Cobo-Díaz, Adrián Alvarez-Molina, Elena A. Alexa, Calum J. Walsh, Oscar Mencía-Ares, Paula Puente-Gómez, Eleni Likotrafiti, Paula Fernández-Gómez, Bernardo Prieto, Fiona Crispie, Lorena Ruiz, Montserrat González-Raurich, Mercedes López, Miguel Prieto, Paul Cotter, and Avelino Alvarez-Ordóñez – Microbiome, 9(1), 1-19.


Prediction of antimicrobial resistance based on whole-genome sequencing and machine learning – Yunxiao Ren, Trinad Chakraborty, Swapnil Doijad, Linda Falgenhauer, Jane Falgenhauer, Alexander Goesmann, Anne-Christin Hauschild, Oliver Schwengers, and Dominik Heide – Bioinformatics.


Long-term evolution of antibiotic persistence in P. aeruginosa lung infections – Melanie Ghoul, Sandra B Andersen, Helle Krogh Johansen, Lars Jelsbak, Søren Molin, Gabriel Perron, and Ashleigh S. Griffin – bioRxiv

The membrane-proximal domain of the periplasmic adapter protein plays a role in vetting substrates utilising channels 1 and 2 of RND efflux transporters – Ilyas Alav, Vassiliy N. Bavro, and Jessica M. A. Blair – bioRxiv

Webinars & conferences

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