prepared by Svetlana Ugarcina Perovic

The AMR March digest features the latest publications on global health risk of antibiotic resistance genes, bacterial responses to antibiotic combinations, Hi-C assisted metagenomics for AMR resistance tracking and more. Happy #AMR reading!

Join us for the spring #EMBARK2022 webinars!


Assessment of global health risk of antibiotic resistance genes – Zhenyan Zhang – Nature Communications
*Authors developed a novel method for quantitatively surveilling the health risk of ARGs, by integrating human accessibility, mobility, pathogenicity and clinical availability. Antibiotic resistance risk was detected all around the world, even in the polar region. Human-associated habitats posed the highest risk of antibiotic resistance than other habitats.

ARGs shared between the human-associated and three main habitats.
Number in the circles represents the number of shared ARGs.

Existing evidence on antibiotic resistance exposure and transmission to humans from the environment: a systematic map – Isobel Catherine Stanton – Environmental Evidence

Landscape of mobile genetic elements and their antibiotic resistance cargo in prokaryotic genomes – Supriya Khedkar, Georgy Smyshlyaev, Ivica Letunic, Oleksandr M Maistrenko, Luis Pedro Coelho, Askarbek Orakov, Sofia K Forslund, Falk Hildebrand, Mechthild Luetge, Thomas S B Schmidt, Orsolya Barabas, Peer Bork – Nucleic Acids Research

Intra- and interpopulation transposition of mobile genetic elements driven by antibiotic selection – Yi Yao – Nature Ecology & Evolution

Role of mobile genetic elements in the global dissemination of the carbapenem resistance gene blaNDM – Mislav Acman – Nature Communications


Phenotypic and Genotypic Characterization of a Hypervirulent Carbapenem-Resistant Klebsiella pneumoniae ST17-KL38 Clinical Isolate Harboring the Carbapenemase IMP-4 – Jintao He – Antimicrobial Chemotherapy

The repurposing of Tebipenem pivoxil as alternative therapy for severe gastrointestinal infections caused by extensively drug resistant Shigella spp. – Elena Fernández Alvaro – eLife

Urinary culture sensitivity after a single empirical antibiotic dose for upper or febrile urinary tract infection: a prospective multicenter observational study – John Gregor – Clinical Microbiology and Infection

Review: The physiology and genetics of bacterial responses to antibiotic combinations – Roderich Roemhild – Nature Reviews Microbiology
*Authors discuss the effects of antibiotic combinations, previous treatments and the role of stress-response systems as well as resistance mutation–drug interactions.

Decreased efficacy of antimicrobial agents in a polymicrobial environment – Thomas James O’Brien – The ISME Journal

Human microbiome

Strain-level characterization of broad host range mobile genetic elements transferring antibiotic resistance from the human microbiome – Samuel C. Forster – Nature Communications

Review: Good microbes, bad genes? The dissemination of antimicrobial resistance in the human microbiome – Alexander Crits-Christoph – Gut Microbe

Inflammatory Endotype-Associated Airway Resistome in Chronic Obstructive Pulmonary Disease – Xinzhu Yi – Microbiology Spectrum


Extensive metagenomic analysis of the porcine gut resistome to identify indicators reflecting antimicrobial resistance – Yunyan Zhou – Microbiome

Novel canine high-quality metagenome-assembled genomes, prophages and host-associated plasmids provided by long-read metagenomics together with Hi-C proximity ligation – Anna Cuscó – Microbial Genomics

Animal experiments

Antibiotics cause metabolic changes in mice primarily through microbiome modulation rather than behavioral changes – Kale S. Bongers – PlosOne


A Phage Foundry framework to systematically develop viral countermeasures to combat antibiotic resistant bacterial pathogens – Vivek K. Mutalik and Adam P. Arkin – iScience


Characteristics of Antibiotic Resistance Genes and Antibiotic-Resistant Bacteria in Full-Scale Drinking Water Treatment System Using Metagenomics and Culturing – Qihui Gu – Frontiers in Microbiology

Municipal Wastewaters Carry Important Carbapenemase Genes Independent of Hospital Input and Can Mirror Clinical Resistance Patterns – Adela Teban-Man, Edina Szekeres, Peiju Fang, Uli Klümper, Adriana Hegedus, Andreea Baricz, Thomas Ulrich Berendonk, Marcel Pârvu, Cristian Coman – Environmental Microbiology


Cross-biome antibiotic resistance decays after millions of years of soil development – Qing-Lin Chen – The ISME Journal

Metagenomic strategies identify diverse integron-integrase and antibiotic resistance genes in the Antarctic environment – Verónica Antelo – MicrobiologyOpen


HAM-ART: An optimised culture-free Hi-C metagenomics pipeline for tracking antimicrobial resistance genes in complex microbial communities – Lajos Kalmar – Plos Genetics
*A comprehensive laboratory and bioinformatics pipeline HAM-ART (Hi-C Assisted Metagenomics for Antimicrobial Resistance Tracking) optimised for the generation of metagenome-assembled genomes including both chromosomal and extrachromosomal AMR genes. Authors found significant differences in the distribution of AMR genes between low- and high-antimicrobial use farms including a plasmid-borne lincosamide resistance gene exclusive to high-antimicrobial use farms in three species of Lactobacilli.

Comparing Long-Read Assemblers to Explore the Potential of a Sustainable Low-Cost, Low-Infrastructure Approach to Sequence Antimicrobial Resistant Bacteria With Oxford Nanopore Sequencing – Ian Boostrom – Frontiers in Microbiology


IntegronFinder 2.0: identification and analysis of integrons across Bacteria, with a focus on antibiotic resistance in Klebsiella – Bertrand Néron – bioRxiv

Whole genome sequencing and gene sharing network analysis powered by machine learning identifies antibiotic resistance sharing between animals, humans and environment in livestock farming – Zixin Peng – Plos Computational Biology
*Authors developed a computational framework identifying known AMR genes as well as yet unknown genetic determinants underlying AMR in E. coli from complex anthropogenic environments.


Recordings of the EDAR6 count down webinars available here.

Antimicrobial Resistance – Genomes, Big Data and Emerging Technologies (Virtual Conference): 27–29 April 2022, Wellcome Genome Campus, UK



prepared by Rémi Gschwind

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.

Human microbiome

Impact of long-term dietary habits on the human gut resistome in the Dutch population – Paul B. Stege – Scientific Reports

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.

Gut microbiome signatures and host colonization with multidrug-resistant bacteria – Nicole S.Isles – Trends in Microbiology

Hospital environment

Extended-Spectrum Beta-Lactamase and Carbapenemase-Producing prediction in Klebsiella pneumoniae based on MALDI-TOF mass spectra – Alejandro Guerrero-López – bioRxiv

Genomic diversity and antimicrobial resistance of Prevotella species isolated from chronic lung disease airways – Kasey A. Webb –Microbial Genomics

Long read sequencing reveals genomic diversity and associated plasmid movement of carbapenemase-producing bacteria in a UK hospital over six years – Leah Roberts – OSF Preprints

Environmental antibiotic resistance

Deciphering the extracellular and intracellular antibiotic resistance genes in multiple environments reveals the persistence of extracellular ones – Yina Zou – Journal of Hazardous Materials

Long-read metagenomic sequencing reveals shifts in associations of antibiotic resistance genes with mobile genetic elements from sewage to activated sludge – Dongjuan Dai – Microbiome

Carriage of antibiotic resistant bacteria in endangered and declining Australian pinniped pups – Mariel Fulham – PlosOne

A new insight into the ARG association with antibiotics and non-antibiotic agents—antibiotic resistance and toxicity – Shaojing Sun – Environmental Pollution

Impact of fertilization with pig or calf slurry on antibiotic residues and resistance genes in the soil – Huygens Judith – Science of The Total Environment

Monitoring and evaluation of antibiotic resistance genes in three rivers in northeast China – Chen Zao – Environmental Science and Pollution Research

Meta-analysis reveals the global picture of antibiotic resistance gene prevalence across environments – Anna Abramova – bioRxiv

Fundamental microbiology

Evolution of ColE1-like plasmids across γ-Proteobacteria: From bacteriocin production to antimicrobial resistance – Manuel Ares-Arroyo – PLOS Genetics

Tolerance and resistance of microbial biofilms – Oana Ciofu – Nature Reviews – Microbiology

Gradients in gene essentiality reshape antibacterial research – Andrew M Hogan – FEMS Microbiology Reviews

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.


Emerging laboratory and point-of-care technologies for detection of AMR and bacterial infection in veterinary medicine – ESCMID, 9 March 2022

Workshops, Seminars &c

Risk assessment of biocide and antibiotic resistance – BIOCIDE consortium, 9 March 2022

Plasmids as vehicles of AMR spread – The Abdus Salam International Centre for Theoretical Physics, 21-25 March 2022

CHARM Virtual Seminar Series 2022, Bi-weekly Tuesdays 9:00-10-00 am


prepared by Marcus Wenne

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.

Antibiotic research and development

Review: Prospects for Antibacterial Discovery and Development – Thomas M Privalsky – Journal of the American Chemical Society

Why Do Antibiotics Exist? – Fabrizio Spagnolo – mBio


Increase in antimicrobial resistance in Escherichia coli in food animals between 1980 and 2018 assessed using genomes from public databases – João Pires – Journal of Antimicrobial Chemotherapy
*This study utilized public databases to infer the level of multi drug resistance in E .coli on a global scale from 1980 to 2018. The authors detected an increase in the number of antibiotics E. coli tended to carry resistance against (MDR score) by 1.6 times during this time frame.

Evolution of ColE1-like plasmids across γ-Proteobacteria: From bacteriocin production to antimicrobial resistance – Manuel Ares-Arroyo – Plos Genetics

Global protein responses of multi-drug resistant plasmid containing Escherichia coli to ampicillin, cefotaxime, imipenem and ciprofloxacin – Anatte Margalit – Journal of Global Antimicrobial Resistance

Towards the biogeography of prokaryotic genes – Luis Pedro Coelho – Nature


Correlation between phenotypic virulence traits and antibiotic resistance in Pseudomonas aeruginosa clinical isolates – Osama Nassar – Microbial Pathogenesis

Antimicrobial resistance in commensal opportunistic pathogens isolated from non-sterile sites can be an effective proxy for surveillance in bloodstream infections – Karina-Doris Vihta – Scientific Reports

Identification of antibiotic collateral sensitivity and resistance interactions in population surveillance data – Laura B Zwep – JAC-Antimicrobial Resistance

Human Microbiome

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.

Influence of timing of maternal antibiotic administration during caesarean section on infant microbial colonisation: a randomised controlled trial – Thomas Dierikx – Gut Microbiota


Implications of the use of organic fertilizers for antibiotic resistance gene distribution in agricultural soils and fresh food products. A plot-scale study – Claudia Sanz – Science of The Total Environment

AMR detection methods

Review: Progressing Antimicrobial Resistance Sensing Technologies across Human, Animal, and Environmental Health Domains – Kira J Fitzpatrick – Journal of the American Chemical Society

Integrating Scalable Genome Sequencing Into Microbiology Laboratories for Routine Antimicrobial Resistance Surveillance – Mihir Kekre – Clinical Infectious Diseases

Review: Engineered CRISPR-Cas systems for the detection and control of antibiotic-resistant infections – Yuye Wu – Journal of Nanobiotechnology

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.

Sewage treatment

The physiological and ecological properties of bacterial persisters discovered from municipal sewage sludge and the potential risk – Xiang Liu – Environmental Research

Water environment

Metagenomic profiles of the resistome in subtropical estuaries: Co-occurrence patterns, indicative genes, and driving factors – Lei Zhou – Science of The Total Environment

Assessment on impact of sewage in coastal pollution and distribution of fecal pathogenic bacteria with reference to antibiotic resistance in the coastal area of Cape Comorin, India – Nanthini S Victoria – Marine Pollution Bulletin

Animal experiment

Colonization of gut microbiota by plasmid-carrying bacteria is facilitated by evolutionary adaptation to antibiotic treatment – Peng Zhang – The ISME Journal



Future conferences



prepared by Rémi Gschwind

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.

‘They eat it like sweets’: A mixed methods study of antibiotic perceptions and their use among patients, prescribers and pharmacists in a district hospital in Kabul, Afghanistan – Doris Burtscher – PlosOne

What Is the Role of the Environment in the Emergence of Novel Antibiotic Resistance Genes? A Modeling Approach – Johan Bengtsson-Palme -Environmental Science and Technology

Trends, relationships and case attribution of antibiotic resistance between children and environmental sources in rural India – Joseph Mitchell – Scientific Reports

Fundamental microbiology

Colistin resistance in Escherichia coli confers protection of the cytoplasmic but not outer membrane from the polymixin antibiotic – Madeleine Humphrey – Microbiology Society

Microniches in biofilm depth are hot-spots fro antibiotic resistance acquisition in response to in situ stress – Linda Tlili – bioRxiv

The vulnerable versatility of Salmonella antibiotic persisters during infection – Peter W.S. Hill – Cell Host & Microbe

The role of potentiating mutations in the evolution of pandemic Escherichia coli clones – Elizabeth A. Cummins – European Journal of Clinical Microbiology & Infectious Diseases

Phase separation in the outer membrane of Escherichia coli Georgina Benn – PNAS

Human associated resistome

Metagenomic analysis of microbial communities and antibiotic resistance genes in spoiled household chemicals – Gang Zhou – Chemosphere

Risks of antibiotic resistance genes and antimicrobial resistance under chlorination disinfection with public health concerns – Liping Ma – Environment International

Multidrug resistance dynamics in Salmonella in food animals in the United States: An analysis of genomes from public databases – João Pires – Microbiology Spectrum

Natural Habitat & Animals

Antibiotic resistance in the environment – D. G. Joakim Larsson and Carl-Fredrik Flack – Nature Reviews Microbiology

The myth of antibiotic spider silk – Simon Fruergaard – iScience

Metagenomic strategies identify diverse integron-integrase and antibiotic resistance genes in the Antartic environment – Verónica Antelo – Microbiology Open

Gacier-fed stream biofilmsz harbour diverse resistomes and biosynthetic gene clusters – Sussheel Bhanu Busi – bioRxiv

Water environment & Waste water

Mobilome-driven segregation of the resistome in biological wastewater treatment – Laura de Nies – bioRxiv

Wastewater bypass is a major temporary point-source of antibiotic resistance genes and multi-resistance risk factors in a Swiss river – Jangwoo Lee – Water Research

AMR & diseases

Antibiotic inhibition of the Plasmodium apicoplast decreases haemoglobin degradation and antagonises dihydroartemisinin action – Emily M. Crisafulli – bioRxiv

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.


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