AMR NOVEMBER, 2021

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

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.

AMR OCTOBER, 2021

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!


Global

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.

Virome

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.

Bioinformatics

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.

Pre-prints

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!

Podcast

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

AMR SEPTEMBER, 2021

prepared by Ulrike Löber

September digest features how artificial sweeteners stimulate horizontal gene transfer of extracellular antibiotic resistance genes; soil plastispheres as hotpots of antibiotic resistance genes and potential pathogens; a novel vancomycin resistance gene cluster in Enterococcus faecium; elevated levels of AMR in groundwater during treated wastewater irrigation associated with infiltration and accumulation of antibiotic residues, and many more. Enjoy!


EMBARK annual meeting

We had our 3rd annual EMBARK meeting on September 28/29. We had some fruitful discussions. We took a look back to the last two years, which were productive, but even under compulsion of the COVID pandemic. We were looking forward to continuing our teamwork. We found people with fantastic expertise, synergizing exceptionally well, and having a great team spirit. Social online activities rounded up this event, while we look forward to seeing each other again in person next year.


Global

From the soil to the clinic: the impact of microbial secondary metabolites on antibiotic tolerance and resistance – Elena K. Perry, Lucas A. Meirelles, Dianne K. Newman – Nature Reviews Microbiology

ARGuing the case for (or against) probiotics – Sondra Turjeman & Omry Koren – Trends in Microbiology

Design principles of collateral sensitivity-based dosing strategies – Linda B. S. Aulin, Apostolos Liakopoulos, Piet H. van der Graaf, Daniel E. Rozen, J. G. Coen van Hasselt – Nature Communications

*Artificial sweeteners stimulate horizontal transfer of extracellular antibiotic resistance genes through natural transformation – Zhigang Yu, Yue Wang, Ian R. Henderson & Jianhua Guo – The ISME Journal
Interesting paper about artificial sweeteners (saccharin, sucralose, aspartame, and acesulfame potassium) promoting transfer of ARGs via natural transformation in Acinetobacter baylyi. The phenomenon were validated by an in vitro transformation model (Model V) using mice faecal bacteria as the recipient.

Water environment

*Elevated levels of antibiotic resistance in groundwater during treated wastewater irrigation associated with infiltration and accumulation of antibiotic residuesIoannis D. Kampouris, Nikiforos Alygizakisb, Uli Klümper, Shelesh Agrawal, Susanne Lackner, Damiano Cacace, Steffen Kunze, Nikolaos S.Thomaidis, Jaroslav Slobdonik, Thomas U. Berendonk – Journal of Hazardous Materials
Our team members from Dresden published an article about bacterial abundances and antibiotics residues in ground water. The team around Thomas U. Berendonk could show that bacterial abundance did not increase due to treated wastewater irrigation. At each time-point, three samples each were taken from three groundwater wells (n = 9) located in the field at a depth of 10 m. Samples were collected from the facilities of Braunschweig Wastewater Association (Wendeburg, Lower Saxony, Germany).

Impact of biosolids amendment and wastewater effluent irrigation on enteric antibiotic-resistant bacteria – a greenhouse study – Catherine Maysa, Gabriel L.Garza, Joy Waite-Cusic, Tyler S. Radniecki, Tala Nava-Daneshmand – Water Research

Tracing Antibiotic Resistance Genes along the Irrigation Water Chain to Chive: Does Tap or Surface Water Make a Difference? – Maria-Theresia Gekenidis, Fiona Walsh and David Drissner – MDPI

Quantifying and predicting antimicrobials and antimicrobial resistance genes in waterbodies through a holistic approach: a study in Minnesota, United States – Irene Bueno, Amanda Beaudoin, William A. Arnold, Taegyu Kim, Lara E. Frankson, Timothy M. LaPara, Kaushi Kanankege, Kristine H. Wammer, Randall S. Singer – Scientific Reports

Soil environment

*Soil plastispheres as hotpots of antibiotic resistance genes and potential pathogens – Dong Zhu, Jun Ma, Gang Li, Matthias C. Rillig, Yong-Guan Zhu – The ISME Journal

Case reports

Novel vancomycin resistance gene cluster in Enterococcus faecium ST1486, Belgium, June 2021 – Basil Britto Xavier, Jasmine Coppens, Sien De Koster, Sahaya Glingston Rajakani, Sam Van Goethem, Samy Mzougui, Ahalieyah Anantharajah, Christine Lammens, Katherine Loens, Youri Glupczynski, Herman Goossens, Veerle Matheeussen – Eurosurveillance

Animal experiments

Dynamics of the fecal microbiome and antimicrobial resistome in commercial piglets during the weaning period – Prapat Suriyaphol, Jimmy Ka Ho Chiu, Nathamon Yimpring, Paiboon Tunsagool, Wuttichai Mhuantong, Rungtip Chuanchuen, Irina Bessarab, Rohan B. H. Williams, Rick Twee-Hee Ong, Gunnaporn Suriyaphol – Scientific Reports

Inappropriate use of antibiotics exacerbates inflammation through OMV-induced pyroptosis in MDR Klebsiella pneumoniae infection – Chao Ye, Weiran Li, Ying Yang, Qingwen Liu, Sijing Li, Peng Zheng, Xiao Zheng, Ye Zhang, Jinrong He, Yongjun Chen, Liangqun Hua, Zhongqian Yang, Duo Li, Zhaoling Ren, Ying Yang, Jialong Qi, Weiwei Huang, Yanbing Ma – Cell Reports

High-risk environments for transmission

Multidrug-Resistant Lineage of Enterotoxigenic Escherichia coli ST182 With Serotype O169:H41 in Airline Waste – Veronica M. Jarocki, Stefanie Heß, Kay Anantanawat, Thomas U. Berendonk, Steven P. Djordjevic – Frontiers in Microbiology

Bioinformatics

BiG-MAP: an Automated Pipeline To Profile Metabolic Gene Cluster Abundance and Expression in Microbiomes – Victória Pascal Andreu, Hannah E. Augustijn, Koen van den Berg, Justin J. J. van der Hooft, Michael A. Fischbach, Marnix H. Medema – mSystems

PlasmidHostFinder: Prediction of plasmid hosts using random forest – Derya Aytan-Aktug, Philip T.L.C. Clausen, Judit Szarvas, Patrick Munk, Saria Otani, Marcus Nguyen, James J. Davis, Ole Lund , Frank M. Aarestrup – bioRxiv

Courses

Podcast

The AMR Studio – Ep 32: Anna Dumitriu & bioart. Access to antibiotics in high-income countries – Uppsala Antibiotic Center

Webinars & conferences

Autumn Resistomap webinars: The science and application of antibiotic resistance monitoring (recordings available here)

Autumn EMBARK webinars: We would like to invite you for the 6th #EMBARK2021 webinar with Monika Dolejska and Victor Hugo Jarquin Diaz!

AMR June, 2021

prepared by Ioannis Kampouris

This week, the @EMBARK_JPIAMR team is at the World Microbe Forum:
Svetlana Ugarcina Perovic and Luis Pedro Coelho with their work on ARGs at global scale,
Anna Abramova, Thomas Berendonk and Johan Bengtsson-Palme on ARGs across environments,
Saba Yasmin and Rabaab Zahra on E. coli in sewage water.


We would like to invite you for the 4th #EMBARK2021 webinar with Kimberly Kline and Sofia Forslund!

Global

There is no market for new antibiotics: this allows an open approach to research and development – Dana M. Klug, Fahima I. M. Idiris – Welcome Open Research
*This opinion paper suggests that there is a necessity for a new open source model for antibiotic discovery, which should be independent from whether a market for new antibiotics exist or not.

Destination shapes antibiotic resistance gene acquisitions, abundance increases, and diversity changes in Dutch travelers – Alaric W. D’Souza, Manish Boolchandani – Genome Medicine
*The authors claim that travel shapes the architecture of the human gut resistome and results in AMR gene acquisition against a variety of antimicrobial drug classes.

Soil environment

Modeling the vertical transport of antibiotic resistance genes in agricultural soils following manure application – Renys E. Barrios – Environmental Pollution
*The authors claim that detachment and decay coefficients for ARGs in soil were not affected by manure, while the load of ARGs in leachate was not significantly affected by manure.

Wastewater Treatment

Antibiotic transformation in an anaerobic membrane bioreactor linked to membrane biofilm microbial activity – Moustapha Harb – Environmental Research

Wastewater Based Epidemiology Enabled Surveillance of Antibiotic Resistance – M.V. Riquelme – MedRxiv
*The Wastewater Based Epidemiology approach helped to identify geographic hot-spots where attention towards curbing the spread of antibiotic resistance may be particularly warranted.

Hospital environment

A species-wide genetic atlas of antimicrobial resistance in Clostridioides difficile – Korakrit Imwattana – BioRxiv
*This review provides insights in the global C. difficile population, which may help in the early detection of drug-resistant C. difficile strains.

Human experiments

The infant gut resistome associates with E. coli, environmental exposures, gut microbiome maturity, and asthma-associated bacterial composition – Xuanji Li – Cell Host & Microbiome
*The study reveals a clear bimodal distribution of ARG richness that is driven by the composition of the gut microbiome, especially E. coli.

Agricultural applications

Chitosan as additive affects the bacterial community, accelerates the removals of antibiotics and related resistance genes during chicken manure composting – Hongdou Liu – Science of Total Environment
*The use of chitosan can enhance the remove of antibiotics and antibiotic resistance genes during manure composting.

Animal experiments

Chironomidae larvae: A neglected enricher of antibiotic resistance genes in the food chain of freshwater environments – Chengshi Ding – Environmental Pollution
*Feeding experiments further confirmed that ARGs from Chironomidae larvae can be transferred to the fish gut.

Techniques

A Peek into the Plasmidome of Global Sewage – Philipp Kirstahler – mSystems
*The authors describe a laboratory and bioinformatics workflow for the recovery of plasmids and other potential extrachromosomal DNA elements from complex microbiomes.

Validation of selective agars for detection and quantification of Escherichia coli resistant to critically important antimicrobials – Zheng Z Lee – bioRxiv

Bioinformatics

Predicting Antimicrobial Resistance Using Partial Genome Alignments – D. Aytan-Aktug – mSystems

Review: Antibiotic resistance: Time of synthesis in a post-genomic age – Teresa Gil-Gil – Computational and Structural Biotechnology Journal

Horizontal Gene Transfer

Quantitative analysis of horizontal gene transfer in complex systems – Jenifer Moralez – Current Opinion in Microbiology

Phages

Comprehensive Scanning of Prophages in Lactobacillus: Distribution, Diversity, Antibiotic Resistance Genes, and Linkages with CRISPR-Cas Systems – Zhangming Pei – mSystems
*Uneven prophage distribution, with highly diverse genome features and distinct clusters based on host species along with detection of ARGs in Lactobacillus prophages.

L-form switching confers antibiotic, phage and stress tolerance in pathogenic Escherichia coli – Aleksandra Petrovic Fabijan – bioRxiv

Podcast

Superbugs and You – True Stories from Scientists and Patients around the World – The Antimicrobial Resistance Fighter Coalition


The @EMBARK_JPIAMR team wishes you happy Summer holidays!

AMR MAY, 2021

prepared by Fouzia Nahid


Our May digest features recent research and review articles relating to AMR, screening of ARGs in various environments and metagenomics.


Join the JUNE AMR WEBINARS to discuss the latest AMR insights with us and our invited speakers!

You can register for the next webinars

* on June 9 with Dearbháile Morris and Rabaab Zahra, and

* on June 30 with Kimberly Kline and Sofia Forslund.


On June 25, Big Data Biology Lab is doing an NGLess tutorial for processing metagenomes.

Read more about the tool HERE
Time: Noon UTC
Registration HERE


Global

🇵🇰 Review: Progress on the national action plan of Pakistan on antimicrobial resistance (AMR): a scoping review and the implications – Zikria Saleem – Expert Review of Anti-infective Therapy

The social dilemmas of climate change and antibiotic resistance: an analytic comparison and discussion of policy implications – Niklas Harring – Humanities and Social Sciences Communications
*This article analyses climate change and antimicrobial resistance within the context of game theory. Previous literature has identified these problems as common tragedies, where inherent incentive structures encourage selfish overuse of existing resources. While the game theoretical models provide a helpful conceptual basis, the present analysis suggests discrepancies between some of the theoretical assumptions and the practical realities of climate change and antimicrobial resistance.

Review: Antibiotic resistance: time of synthesis in a post-genomic age – Teresa Gil-Gil – Computational and Structural Biotechnology Journal
*The authors analyzed the capacities and drawbacks of the tools that are currently in use for the global analysis of AR, aiming to identify the more useful targets for effective corrective interventions.

Diversity of metal and antibiotic resistance genes in Enterococcus spp. from the last century reflects multiple pollution and genetic exchange among phyla from overlapping ecosystems – Andreia Rebelo – Science of The Total Environment
*The authors explored occurrence, diversity, and phenotypes associated with known acquired genes/operons conferring tolerance to As, Hg or Cu among Enterococcus and identified their genetic context.

Human-associated microbiome and resistome

Emergence and dissemination of antimicrobial resistance in Escherichia coli causing bloodstream infections in Norway in 2002–17: a nationwide, longitudinal, microbial population genomic study – Rebecca A Gladstone – THE LANCET Microbe
*The authors aimed to evaluate the clonal diversity underpinning trends in multidrug resistant Escherichia coli causing bloodstream infections which usually remains uncertain. They determined the contribution of individual clones to resistance over time, using large-scale genomics-based molecular epidemiology.

Review: The innate resistome of “recalcitrant” Acinetobacter baumannii and the role of nanoparticles in combating these MDR pathogens – Vasudevan Aparna – Applied Nanoscience
*The authors emphasize the role of intrinsic resistome involved in the antibiotic resistance of A. baumannii, the understanding of which will be very helpful in combating this opportunistic pathogen.

Trade-Offs Between Antibacterial Resistance and Fitness Cost in the Production of Metallo-β-Lactamases by Enteric Bacteria Manifest as Sporadic Emergence of Carbapenem Resistance in a Clinical Setting – Ching Hei Phoebe Cheung – Antimicrobial Agent and Chemotherapy

Reconstruction of ancient microbial genomes from the human gut – Marsha C. Wibowo – Nature

Fig. 4
Palaeofaeces exhibit a distinct functional genomic repertoire compared to present-day industrial stool samples

Mobile antimicrobial resistance genes in probiotics – Adrienn Gréta Tóth – bioRxiv
*The authors raised clinical and public health concerns as the consumption of probiotic products may lead to the transfer of ARGs to human gut bacteria.

Review Article: Antimicrobial resistance in nephrology – Tina Z. Wang – Nature Reviews Nephrology

Soil environment

Novel Soil-Derived Beta-Lactam, Chloramphenicol, Fosfomycin and Trimethoprim Resistance Genes Revealed by Functional Metagenomics – Inka Marie Willms – Antibiotics (Basel)
*The authors screened metagenomic libraries comprising of genes of cultivated microorganisms and uncultured microbial for novel ARGs from forest and grassland soils. Three new beta-lactam, a so far unknown chloramphenicol, a novel fosfomycin, as well as three previously undiscovered trimethoprim resistance genes are described in this study.

Manure Microbial Communities and Resistance Profiles Reconfigure after Transition to Manure Pits and Differ from Those in Fertilized Field Soil – Kimberley V. Sukhum – mBio
*The authors evaluated that on dairy farms, the storage of cow manure in manure pits and subsequent application to field soil as a fertilizer may facilitate the spread of the mammalian gut microbiome and its associated ARGs to the environment. To determine the extent of both taxonomic and resistance similarity during these transitions, they collected fresh manure, manure from pits, and field soil across 15 different dairy farms for three consecutive seasons and used a combination of shotgun metagenomic sequencing and functional metagenomics to quantitatively interrogate taxonomic and ARG compositional variation on farms.

Dissipation of antibiotic resistance genes in manure-amended agricultural soil – Liang-Ying He – Science of The Total Environment
*This study provides insight into the dissipation of antibiotic resistance genes in manure-applied agricultural soil. The continuous application of manure results in accumulation of ARGs which persists in soil for at least two years.

Metagenomics analysis reveals the distribution and communication of antibiotic resistance genes within two different red swamp crayfish Procambarus clarkii cultivation ecosystems – Limin Fan – Environmental Pollution
*This study showed that MacB and BcrA are two dominant ARGs, and macrolide is the dominant antibiotic not only in the water, but also in the sediment and gut of crayfish, in both the crayfish monoculture and the rice-crayfish cultivation ecosystems.

Distribution of the microbial community and antibiotic resistance genes in farmland surrounding gold tailings: A metagenomics approach – Longkai Qiao – Science of The Total Environment
*The authors studied microbes and antibiotic resistance genes in farmland near gold tailings. The main ARGs exhibited macrolide, lincosaminide, and streptogramin B resistance. Actinobacteria, Proteobacteria, and Acidobacteria were the main carriers of ARGs. The microbial community was the most important driver of soil ARG distribution.

Environmental fate of tetracycline antibiotics: degradation pathway mechanisms, challenges, and perspectives – Ahmad Fiaz – Environmental Sciences Europe
*The authors collected data on the available degradation strategies, mechanisms involved in biodegradable and non-biodegradable routes, the main factor affecting degradation strategies, compiled novel detection techniques of tetracycline antibiotics in the environment, and discussed antibiotic resistance genes and their potential role in degradation.

Water environment

Wastewater treatment plants as a reservoir of integrase and antibiotic resistance genes – An epidemiological threat to workers and environment – Wiktor Zieliński – Environmental International
*The authors found a significant increase in the quantities of ARGs and concentrations of antibiotics in the river following the discharge of treated wastewater in comparison to their amounts in the river water upstream from the point of discharge. A higher concentration of ARGs was detected in the DNA from swabs obtained from the wastewater treatment plant employees than from ones collected from the control group.

Built environment

Characterization of the public transit air microbiome and resistome reveals geographical specificity – M. H. Y. Leung – Microbiome

Geographical specificity in public transit air resistome.
Heatmap of the top 30 AR protein families based on average reads per kilobase per million (RPKM) reads across metagenomes. Core AR protein families (those detected in ≥ 75% of the entire dataset) are indicated in red and asterisks

A global metagenomic map of urban microbiomes and antimicrobial resistance – David Danko – Cell

Phages

Aminoglycoside antibiotics inhibit phage infection by blocking an early step of the phage infection cycle – Larissa Kever – bioRxiv
*The authors have described how aminoglycosides, a well-known class of antibiotics produced by Streptomyces, act as potent inhibitors of phage infection in widely divergent bacterial hosts.

COVID-19

Antibody-dependent enhancement and SARS-CoV-2 vaccines and therapies – Wen Shi Lee – Nature Microbiology
*The authors described the key ADE mechanisms and discussed mitigation strategies for SARS-CoV-2 vaccines and therapies in development and about the risk of ADE in SARS-CoV-2. They outline recently published data to evaluate the risks and opportunities for antibody-based protection against SARS-CoV-2.

Sample storage

Standard Sample Storage Conditions Impact on Inferred Microbiome Composition and Antimicrobial Resistance Patterns – Casper S. Poulsen –bioRxiv
*The authors examined the effect of common sample storage conditions on metagenomics-based microbiome composition and found significant and, in part, systematic effects.

Bioinformatics

A machine learning framework to predict antibiotic resistance traits and yet unknown genes underlying resistance to specific antibiotics in bacterial strains – Janak Sunuwar – Briefing in Bioinformatics
*There are several strains of bacteria lacking known resistance genes; however, they demonstrate resistance phenotype to drugs of that family. In this study, authors present a machine learning framework to predict novel AMR factors that are potentially responsible for resistance to specific antimicrobial drugs which may help proactive interventions.

Podcast

Listen to the AMS case studies illustrating the importance of antimicrobial stewardship and how it works in practice.

Rachel Irwin & the visual culture of AMR. WHO report on the antibacterial pipeline. Neonatal sepsis in LMICs. – The AMR Studio – Uppsala Antibiotic Center