AMR JUNE, 2022

prepared by Víctor Hugo Jarquín-Díaz

For those in the northern hemisphere… Summer is here ⛱️! With it, the EMBARK team brings a refreshing AMR digest with many sunshiny papers. Put your 🕶️ on and swim deep into many works that we have compiled for you: AMR in soil, water, clinical or livestock settings, antibiotic resistance gene ecology and evolution and more … for those in the southern hemisphere, we also wish you a happy reading despite the cold winter ^^

Global

*Addressing a future pandemic: how can non-biological complex drugs prepare us for antimicrobial resistance threats? – Blackman, L. D., Sutherland, T. D., De Barro, P. J., Thissen, H., & Locock, K. E. – Materials Horizons
Lewis D. Blackman et al. review the different ways in which bacteria develop resistance against antibiotics and alternative agents that could be employed. They focused on non-biological complex drugs (NBCDs) as the next generation antimicrobial agents. They outline the advancements in antimicrobial polymer materials, carbon nanomaterials, and inorganic nanomaterials and highlight the remaining challenges for their clinical translation.

*Environmental Dimensions of “One Health” to Combat Antimicrobial Resistance: Essential Research Needs – Jin, L., Pruden, A., Boehm, A. B., Alvarez, P. J., Raskin, L., Kohn, T., & Li, X. – Integrating Environmental Science & Technology
In this viewpoint article, Jin et al. critically address the lack of relevance and impact on health outcomes in environmental AMR research. They invite to “better define impactful contributions from the environmental dimension of AMR as part of a broader “One Health” vision” by implementing and developing models in line with an anthropocentric context of bacterial transfer within the interface between environment and humans. The authors promote multidisciplinary cross-national participation and coordination to establish analytical approaches to interpret ARG in the environment comprehensively. Approaches to identify responsible agents or conditions that select for AMR evolution and fit-for-purpose treatment technologies for mitigating high-risk ARGs and ARB at crucial sources.

*A bottom-up view of antimicrobial resistance transmission in developing countries – Ikhimiukor, O.O., Odih, E.E., Donado-Godoy, P. and Iruka N. Okeke – Nature Microbiology
This review from Odion O. Ikhimiukor et al. focuses on AMR transmission in low- and middle-income countries, emphasizing high-risk transmission points such as urban settings and food-animal handling. The authors describe the integration of top-down and bottom-up strategies as AMR-containment approaches. They suggest that technological innovations are required to control AMR in low- and middle-income settings.

Editorial: Antimicrobial resistance – da Silva Dantas, A. – Molecular Microbiology

Global burden of antimicrobial resistance: essential pieces of a global puzzle – Charani, E., McKee, M., Balasegaram, M., Mendelson, M., Singh, S., & Holmes, A. – The Lancet

Soil antimicrobial resistance

*Globally distributed mining-impacted environments are underexplored hotspots of multidrug resistance genes – Yi, X., Liang, J. L., Su, J. Q., Jia, P., Lu, J. L., Zheng, J. & Zhu, Y. G. – The ISME Journal
Yi et al. focused their work on giving further insight into antimicrobial resistance in mining-impacted environments. They suggest developing constant monitoring strategies as the mining sites represent an underexplored hotspot for multidrug resistance genes. Overall, they described around 54 high-quality ARG-carrying MAGs from the phylum Proteobacteria, Acidobacteria, Actinobacteria, Bacteroidota, Firmicutes, Nitrospira, Planctomycetes and Thermoplasmatota and confirmed high mobility of ARGs, mainly trough transposons and plasmid.

Deciphering environmental resistome and mobilome risks on the stone monument: A reservoir of antimicrobial resistance genes – He, J., Zhang, N., Shen, X., Muhammad, A., & Shao, Y. – Science of The Total Environment

Plant cultivar determined bacterial community and potential risk of antibiotic resistance gene spread in the phyllosphere – Fan, X., Su, J., Zhou, S., An, X., & Li, H. – Journal of Environmental Sciences

β-lactamase genes transmission influenced by tetracycline, sulfonamide and β-lactams antibiotics contamination in the on-site farm soil – Qi, Z., Le, Z., Han, F., Qi, Y., & Liu, R. – Ecotoxicology and Environmental Safety

Effect of pesticides on nitrification activity and its interaction with chemical fertilizer and manure in long-term paddy soils – Mukhles, M. B., Rahman, M. M., Rana, M. R., Huda, N., Ferdous, J., Rahman, F., & Biswas, S. K. – Chemosphere

Insights into microbial contamination in multi-type manure-amended soils: the profile of human bacterial pathogens, virulence factor genes and antibiotic resistance genes – Zhu, L., Lian, Y., Lin, D., Huang, D., Yao, Y., Ju, F., & Wang, M. – Journal of Hazardous Materials

Water environment and waste water treatment

Exploring the microbiome, antibiotic resistance genes, mobile genetic element, and potential resistant pathogens in municipal wastewater treatment plants in Brazil – Leroy-Freitas, D., Machado, E. C., Torres-Franco, A. F., Dias, M. F., Leal, C. D., & Araújo, J. C . – Science of The Total Environment

Genomic Analysis of Carbapenem-Resistant Comamonas in Water Matrices: Implications for Public Health and Wastewater Treatments – Hem, S., Wyrsch, E. R., Drigo, B., Baker, D. J., Charles, I. G., Donner, E., & Djordjevic, S. P. – Applied and Environmental Microbiology

Metagenomic assembly and binning analyses the prevalence and spread of antibiotic resistome in water and fish gut microbiomes along an environmental gradient – Guan, Y., Xue, X., Jia, J., Li, X., Xing, H., & Wang, Z. – Journal of Environmental Management

Wastewater plastisphere enhances antibiotic resistant elements, bacterial pathogens, and toxicological impacts in the environment – Junaid, M., Liu, S., Liao, H., Liu, X., Wu, Y., & Wang, J. – Science of The Total Environment

Antimicrobial Resistance Monitoring of Water Environments: A Framework for Standardized Methods and Quality Control – Liguori, K., Keenum, I., Davis, B. C., Calarco, J., Milligan, E., Harwood, V. J., & Pruden, A. – Environmental Science & Technology

Air environment and airborne ARGs

A review of the emergence of antibiotic resistance in bioaerosols and its monitoring methods – Lee, G., & Yoo, K. – Reviews in Environmental Science and Bio/Technology

Effects of antibiotics consumption on the behavior of airborne antibiotic resistance genes in chicken farms – Song, L., Jiang, G., Wang, C., Ma, J., & Chen, H. – Journal of Hazardous Materials

Phages and antimicrobial resistance

Antibiotic Exposure Leads to Reduced Phage Susceptibility in Vancomycin Intermediate Staphylococcus aureus (VISA) – McCallin, S., Menzi, C., Lassen, S., Daraspe, J., Oechslin, F., & Moreillon, P. – Antimicrobial Agents and Chemotherapy

Isolation of a lytic bacteriophage against extensively drug‐resistant Acinetobacter baumannii infections and its dramatic effect in rat model of burn infection – Ghaznavi-Rad, E., Komijani, M., Moradabadi, A., Rezaei, M., & Shaykh-Baygloo, N. – Journal of Clinical Laboratory Analysis

Domestic animals, “Farm-to-fork” ARG transmission and wildlife

Multiresistant Enterobacteriaceae in yellow-legged gull chicks in their first weeks of life – Vittecoq, M., Brazier, L., Elguero, E., Bravo, I. G., Renaud, N., Manzano‐Marín, A., & Thomas, F. – Ecology and Evolution

Effect of antimicrobial administration on fecal microbiota of critically ill dogs: dynamics of antimicrobial resistance over time – Menard, J., Goggs, R., Mitchell, P., Yang, Y., Robbins, S., Franklin-Guild, R. J., & Goodman, L. B. – Animal Microbiome

Expressions of resistome is linked to the key functions and stability of active rumen microbiome – Ma, T., Zaheer, R., McAllister, T. A., Guo, W., Li, F., Tu, Y., & Guan, L. L. – Animal Microbiome

Role of Horizontal Gene Transfer in the Dissemination of Antimicrobial Resistance in Food Animal Production – Vinayamohan, P. G., Pellissery, A. J., & Venkitanarayanan, K. – Current Opinion in Food Science

High Throughput Screening of Antimicrobial Resistance Genes in Gram-Negative Seafood Bacteria – Delannoy, S., Hoffer, C., Youf, R., Dauvergne, E., Webb, H. E., Brauge, T., & Brisabois, A. – Microorganisms

Bacillus licheniformis–fermented products and enramycin differentially modulate microbiota and antibiotic resistome in the cecal digesta of broilers – Chen, Y. C., & Yu, Y. H. – Poultry Science

Metagenomic analysis of the gut microbiota in piglets either challenged or not with enterotoxigenic Escherichia coli reveals beneficial effects of probiotics on microbiome composition, resistome, digestive function and oxidative stress responses – Apiwatsiri P, Pupa P, Sirichokchatchawan W, Sawaswong V, Nimsamer P, Payungporn S, et al. – PLoS ONE

Antibiotic resistance in clinical settings

Metagenomic DNA sequencing for semi-quantitative pathogen detection from urine: a prospective, laboratory-based, proof-of-concept study – Janes, V. A., Matamoros, S., Munk, P., Clausen, P. T., Koekkoek, S. M., Koster, L. A., & Schultsz, C. – The Lancet Microbe

A resistome roadmap: from the human body to pristine environments – Maestre-Carballa, L., Navarro-López, V., & Martinez-Garcia, M. – Frontiers in Microbiology

Antibiotic-resistant organisms establish reservoirs in new hospital built environments and are related to patient blood infection isolates – Sukhum, K. V., Newcomer, E. P., Cass, C., Wallace, M. A., Johnson, C., Fine, J., & Kwon, J. H. – Communications Medicine

Economic burden of antibiotic-not-susceptible isolates in uncomplicated urinary tract infection: Analysis of a US integrated delivery network database – Shafrin, J., Marijam, A., Joshi, A.V. – Antimicrobial Resistance & Infection Control

Fusion plasmid carrying the colistin resistance gene mcr of Escherichia coli isolated from healthy residents – Hoa, H. T. T., Higashi, A., Yamaguchi, T., Kawahara, R., Calvopina, M., Bastidas-Caldés, A., & Yamamoto, Y. – Journal of Global Antimicrobial Resistance

An Optogenetic Toolkit for Light-Inducible Antibiotic Resistance – Sheets, M. B., & Dunlop, M. J – bioRxiv

Attributable mortality of vancomycin resistance in ampicillin-resistant Enterococcus faecium bacteremia in Denmark and the Netherlands: A matched cohort study – Rottier, W. C., Pinholt, M., van der Bij, A. K., Arpi, M., Blank, S. N., Nabuurs-Franssen, M. H., & Danish Collaborative Bacteraemia Network (DACOBAN) – Infection Control & Hospital Epidemiology

ARG ecology and evolution

GR13-type plasmids in Acinetobacter potentiate the accumulation and horizontal transfer of diverse accessory genes – Moran, R. A., Liu, H., Doughty, E. L., Hua, X., Cummins, E. A., Liveikis, T., McNally, A., Zhou, Z., van Schaik, W., Yu, Y. – Microbial Genomics

Exploring the Ecological Effects of Naturally Antibiotic-Insensitive Bifidobacteria in the Recovery of the Resilience of the Gut Microbiota during and after Antibiotic Treatment – Argentini, C., Mancabelli, L., Alessandri, G., Tarracchini, C., Barbetti, M., Carnevali, L., & Turroni, F. – Applied and Environmental Microbiology

Evolved resistance to a novel cationic peptide antibiotic requires high mutation supply – Santos-Lopez, A., Fritz, M. J., Lombardo, J. B., Burr, A. H., Heinrich, V. A., Marshall, C. W., & Cooper, V. S. – Evolution, Medicine, and Public Health

Localized pmrB hypermutation drives the evolution of colistin heteroresistance – Kapel, N., Caballero, J. D., & MacLean, R. C. – Cell Reports

Within-patient evolution of plasmid-mediated antimicrobial resistance – DelaFuente, J., Toribio-Celestino, L., Santos-Lopez, A., Leon-Sampedro, R., Alonso-del Valle, A. A., Costas, C., & San Millan, A. – bioRxiv

Effect of sulfamethazine on the horizontal transfer of plasmid-mediated antibiotic resistance genes and its mechanism of action – Yan, X., Liu, W., Wen, S., Wang, L., Zhu, L., Wang, J., & Wang, J. – Journal of Environmental Sciences

Phage-plasmids spread antibiotic resistance genes through infection and lysogenic conversion – Eugen Pfeifer, Remy Bonnin, Eduardo P. C. Rocha – bioRxiv

Bioinformatics

Datasets for benchmarking antimicrobial resistance genes in bacterial metagenomic and whole genome sequencing – Raphenya, A. R., Robertson, J., Jamin, C., de Oliveira Martins, L., Maguire, F., McArthur, A. G., & Hays, J. P. – Scientific Data

A genome-wide atlas of antibiotic susceptibility targets and pathways to tolerance – Leshchiner, D., Rosconi, F., Sundaresh, B., Rudmann, E., Ramirez, L. M. N., Nishimoto, A. T., & van Opijnen, T. – Nature Communications

Unraveling antimicrobial resistance using metabolomics – Kok, M., Maton, L., van der Peet, M., Hankemeier, T., & van Hasselt, J. C. – Drug Discovery Today

Webinar/Podcast

Join CIDRAP-ASP on June 21, 6:00 – 7:15 pm CDT for a webinar discussing the importance of effective, data-driven infection prevention strategies (IPC) and antibiotic stewardship (AS) initiatives. It has been shown that IPC and AS reduce drug-resistant infections and diminish the burden of antimicrobial resistance (AMR) within healthcare systems. More information here.

AMR Studio Podcast Ep 39: Vanessa Carter & patient advocacy. A stewardship game. Evolution of antibiotic tolerance – Uppsala Antibiotic Center

AMR MAY, 2022

prepared by Ulrike Löber

May digest features review on the gut microbiota – urinary tract infections axis, novel antimicrobial compounds detected – the dynaplanins -, phage therapy tackling antibiotic-resistant bacteria and more.

We are excited to share with you EMBARK NEWS – after the SPRING #AMR WEBINARS we are already planning the fall #EMBARK2022:
Join us and our invited speakers to discuss the latest AMR insights!

General

Perspective: Bacterial species rarely work together – Jacob D. Palmer – Science

Intermittent antibiotic treatment of bacterial biofilms favors the rapid evolution of resistance – Masaru Usui – bioRxiv

Long-term ecological and evolutionary dynamics in the gut microbiomes of carbapenemase-producing Enterobacteriaceae colonized subjects – Jonathan T. L. Kang – bioRxiv

Evaluation of metagenomic, 16S rRNA gene and ultra-plexed PCR-based sequencing approaches for profiling antimicrobial resistance gene and bacterial taxonomic composition of polymicrobial samples – KK Chau – bioRxiv

Review: Unbiased antimicrobial resistance prevalence estimates through population-based surveillance – Frank van Leth, Constance Schultsz – Clinical Microbiology Infection

Fitness effects of plasmids shape the structure of bacteria–plasmid interaction networks – Arthur Newbury, Beth Dawson, Uli Klümper, Elze Hesse, Meaghan Castledine, Colin Fontaine, Angus Buckling, and Dirk Sanders – PNAS

Metabolism

*Harnessing Rare Actinomycete Interactions and Intrinsic Antimicrobial Resistance Enables Discovery of an Unusual Metabolic Inhibitor – Dylan J. McClung – mBio

Horizontal gene transfer

Persisting uropathogenic Escherichia coli lineages show signatures of niche-specific within-host adaptation mediated by mobile genetic elements – Robert Thänert – Cell Host & Microbe

Antimicrobial peptides

News and Views: Antibiotic discovery with machine learning – Cesar de la Fuente-Nunez – Nature Biotechnology

Global health
Human-associated AMR

Dosing a synbiotic of human milk oligosaccharides and B. infantis leads to reversible engraftment in healthy adult microbiomes without antibiotics – Julie E. Button – Cell Host & Microbe

*Longitudinal multi-omics analyses link gut microbiome dysbiosis with recurrent urinary tract infections in women – Colin J. Worby – nature microbiology

Review: Antimicrobial resistance in Antarctica: is it still a pristine environment? – Kudzai Hwengwere – BMC Microbiome

News & Views: Antibiotic resistance in the commensal human gut microbiota – Lisa E Lamberte, Willem van Schaik – Current Opinion in Microbiology

Review: The resistance within: Antibiotic disruption of the gut microbiome and resistome dynamics in infancy – Robert Thänert – Cell Host & Microbe

Association of Diet and Antimicrobial Resistance in Healthy U.S. Adults – Andrew Oliver – mBio

Long-term antibiotic exposure promotes mortality after systemic fungal infection by driving lymphocyte dysfunction and systemic escape of commensal bacteria – Rebecca A. Drummond – Cell Host & Microbe

Editorial: The problem of antimicrobial resistance in chronic liver disease – The Lancet Gastroenterology & Hepatology

Hospital

Carbapenem heteroresistance of KPC-producing Klebsiella pneumoniae results from tolerance, persistence and resistance – Adriana Chiarelli – bioRxiv

Clinical implementation of routine whole-genome sequencing for hospital infection control of multi-drug resistant pathogens – Brian M Forde – medRxiv

Animal

Metagenomic assembly reveals the circadian oscillations of the microbiome and antibiotic resistance genes in a model of laying hens – Yu Zhang – Science of The Total Environment

Taking metagenomics under the wings – Physilia Ying Shi Chua, Jacob Agerbo Rasmussen – Nature Reviews Microbiology

Biological units of antimicrobial resistance and strategies for their containment in animal production – Johanna Muurinen – FEMS Microbiology Ecology

A Qualitative Study of Antibiotic Use Practices in Intensive Small-Scale Farming in Urban and Peri-Urban Blantyre, Malawi: Implications for Antimicrobial Resistance – John Mankhomwa – Frontiers in Veterinary Science

Water

Metagenomic profiling and transfer dynamics of antibiotic resistance determinants in a full-scale granular sludge wastewater treatment plant – David Calderón-Franco – Water Research

Antimicrobial resistance genes predict plasmid generalism and network structure in wastewater – Alice Risely – bioRxiv

Viruses and phages

Phage-antibiotic combination is a superior treatment against Acinetobacter baumannii in a preclinical study – Fernando L. Gordillo Altamirano – eBioMedicine

Review: Biological foundations of successful bacteriophage therapy – Carola Venturini – EMBO Molecular Medicine

*Bacteriophage treatment of disseminated cutaneous Mycobacterium chelonae infection – Jessica S. Little – Nature Communications

Bioinformatics

A curated data resource of 214K metagenomes for characterization of the global resistome – Hannah-Marie Martiny – bioRxiv

VRprofile2: detection of antibiotic resistance-associated mobilome in bacterial pathogens – Meng Wang – Nucleic Acids Research

PlasmidMaker is a versatile, automated, and high throughput end-to-end platform for plasmid construction – Behnam Enghiad – Nature Communications

Protocols

Prediction of Antibiotic Resistance Evolution by Growth Measurement of All Proximal Mutants of Beta-Lactamase – Siyuan Feng – Molecular Biology and Evolution

Podcast

Ep. 39: the AMR STUDIO podcast – Carl-Fredrik Flach & sewage surveillance. Water chlorination & microbiome. C. difficile spread between humans & animals.

Webinars

DRIAMS: a database for antimicrobial resistance prediction based on MALDI-TOF mass spectrometry – Caroline Weis – in silico talks

AMR APRIL, 2022

prepared by Ayaz Ali Khan

Join us for the next #EMBARK2022 with Nichole Broderick, on 18th of May!

AMR terminology

Consensus on β-Lactamase Nomenclature – Patricia A. Bradford – Antimicrobial Chemotherapy

Human health

Neonatal sepsis and mortality in low-income and middle-income countries from a facility-based birth cohort: an international multisite prospective observational study – Rebecca Milton et al. Rabaab Zahra, et al. BARNARDS Group, Grace J Chan – The Lancet Global Health

Exploring the economic impact of inappropriate antibiotic use: the case of upper respiratory tract infections in Ghana – Jip Janssen – Antimicrobial Resistance & Infection Control

High prevalence of multidrug-resistant Gram-negative bacteria carriage in children screened prospectively for multidrug resistant organisms at admission to a paediatric hospital, Hamburg, Germany, September 2018 to May 2019 – Safiullah Najem – Euro Surveillance

Genomic insights into the mechanism of carbapenem resistance dissemination in Enterobacterales from a tertiary public heath setting in South Asia – Refath Farzana – Clinical Infectious Diseases

Carbapenem-resistant Gram-negative pathogens associated with septic shock: a review of 120 cases – Ugur Onal – Journal of Chemotherapy

Human gut microbiome

Gut colonisation by extended-spectrum fl-lactamase-producing Escherichia coli and its association with the gut microbiome and metabolome in Dutch adults: a matched case-control study – Quinten R Ducarmon – The Lancet Microbe

Catestatin selects for colonization of antimicrobial-resistant gut bacterial communities – Pamela González-Dávila – The ISME Journal

Enterobacteriaceae and Bacteroidaceae provide resistance to travel-associated intestinal colonization by multi-drug resistant Escherichia coli – Matthew Daviesa – Gut Microbes

Drinking water chlorination has minor effects on the intestinal flora and resistomes of Bangladeshi children – Maya L. Nadimpalli – Nature Microbiology

Animals

Extensive metagenomic analysis of the porcine gut resistome to identify indicators reflecting antimicrobial resistance – Yunyan Zhou – Microbiome
*The diversity and distribution of antimicrobial resistance genes (ARGs) were studied using metagenomic sequencing data of gut microbiome samples from pigs. The AMR level was significantly higher in pigs at commercial farms. The ARGs diversity and 41 drug resistance classes were significantly different between cecum, lumen, and feces in pigs at commercial farms.

Genotyping, antibiotic resistance and prevalence of Arcobacter species in milk and dairy products – Abazar Lameei – Veterinary Medicine and Science

Modelling the impact of antimicrobial use and external introductions on commensal E. coli colistin resistance in small-scale chicken farms of the Mekong delta of Vietnam – Jonathan Bastard – Transboundry and Emerging Diseases

Genome and virulome characterization of Escherichia coli encoding multiple antimicrobial resistance genes isolated from commercial dairy operations – Seon Woo Kim – Journal of Global Antimicrobial Resistance

Presence and antimicrobial resistance profiles of Escherichia coli, Enterococcus spp. and Salmonella sp. in 12 species of Australian shorebirds and terns – Hannah G Smith – Zoonoses and Public Health

Antimicrobial resistance in Escherichia coli isolated from on-farm and conventional hatching broiler farms in Ireland – Noelle Byrne – Irish Veterinary Journal

Antimicrobial resistance genes aph(3′)-III, erm(B), sul2 and tet(W) abundance in animal faeces, meat, production environments and human faeces in Europe – Dongsheng Yang – The Journal of Antimicrobial Chemotherapy
*Antimicrobial resistance genes (ARGs) can be quantified using real-time quantitative PCR (qPCR), allowing comparisons across animal production chains. The authors have examined the abundance of ARGs in various animal species, production environments, and humans in Europe in this study. The sources of AMR variation have been identified. Data from qPCR and previously published metagenomic studies were compared to determine the strength of the correlation between the ARGs abundances.

Animal experiments

An engineered live biotherapeutic for the prevention of antibiotic-induced dysbiosis – Andrés Cubillos-Ruiz – Nature Biomedical Engineering

Synergistic efficacy of colistin and silver nanoparticles impregnated human amniotic membrane in a burn wound infected rat model – Nadia Wali – Scientific Reports

Soil

Identifying the spatiotemporal vulnerability of soils to antimicrobial contamination through land application of animal manure in Minnesota, United States – Irene Bueno – The Science of the Total Environment

Carbendazim shapes microbiome and enhances resistome in the earthworm gut – Jiajin Song – Microbiome

Review: An Overview of Antibiotic Resistance and Abiotic Stresses Affecting Antimicrobial Resistance in Agricultural Soils – Abdullah Kaviani Rad – International Journal of Environmental Research and Public Health

Water environment

Multiwalled Carbon Nanotubes Promote Bacterial Conjugative Plasmid Transfer – Katrin Weise, Lena Winter, Emily Fischer, David Kneis, Magali de la Cruz Barron, Steffen Kunze, Thomas U. Berendonk, Dirk Jungmann, Uli Klümper – Microbiology Spectrum
*In this paper, the authors have highlighted the importance of multi-walled carbon nanotubes (MWCNTs) used in various products related to bacterial plasmid transfer in aquatic environments. MWCNTs form bigger agglomerates and provide novel surfaces for bacterial interactions, promoting the spread of antimicrobial resistance genes in microbial communities.

Tidal flat aquaculture pollution governs sedimentary antibiotic resistance gene profiles but not bacterial community based on metagenomic data – Linqiong Wang – The Science of the Total Environment

Impact of surface-applied liquid manure on the drainage resistance profile of an agricultural tile-drained clay till field – Tina B Bech – Journal of Environmental Quality

Antibiotic Resistance Genes in River Biofilms: A Metagenomic Approach toward the Identification of Sources and Candidate Hosts – David Kneis, Thomas U. Berendonk, Sofia K. Forslund, and Stefanie Hess – Environmental Science & Technology

Ecology

Minireview: Elucidating the Mechanisms of Action of Antimicrobial Agents – M. Ashley Hudson, Steve W. Lockless – Antimicrobial Chemotherapy

Mutational background influences P. aeruginosa ciprofloxacin resistance evolution but preserves collateral sensitivity robustness – Sara Hernando-Amado – Proceedings of the National Academy of Sciences

Decreased thermal niche breadth as a trade-off of antibiotic resistance – Cristina M. Herren – The ISME Journal

Phage

Phage-mediated horizontal gene transfer and its implications for the human gut microbiome – Tatiana Borodovich – Gastroenterology Report

Technique

Targeted Elimination of bla NDM-5 Gene in Escherichia coli by Conjugative CRISPR-Cas9 System – Peisi Li – Infection and Drug Resistance

A high-efficiency scar-free genome editing toolkit for Acinetobacter baumannii – Rubén de Dios – bioRxiv

The AMR-ARRAY: A modular bead array detecting fl-lactam, (fluoro) quinolone, colistin, aminoglycoside and macrolide resistance determinants in Gram-negative bacteria – Michaël Timmermans – Journal of Microbiological Methods

Bioinformatics

Review: Bioinformatics tools used for whole-genome sequencing analysis of Neisseria gonorrhoeae: a literature review – Reema Singh – Briefings in Functional Genomics

Enhancing predictions of antimicrobial resistance of pathogens by expanding the potential resistance gene repertoire using a pan-genome-based feature selection approach – Ming-Ren Yang & Yu-Wei Wu – BMC Bioinformatics

Events

The HOH Helsinki One Health Monthly Research Seminar Series “Current Research in One Health”: Marko Virta – Antimicrobial resistance and human activities – April 6 (Recordings will be available)

Workshop on Development Considerations of Antimicrobial Drugs for the Treatment of Uncomplicated Urinary Tract Infections (UTI) (Virtual) – June 3

Podcast

ASM podcast, Editors in Conversation: Consensus on B-lactamases – Patricia Bradford, Karen Bush, Robert Bonomo.

The AMR Studio podcast, Ep 37: Celia Souque & evolution + outreach. Colistin and silver. Qualitative research on AMS.

AMR MARCH, 2022

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!

Global

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

Clinical

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

Animal

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

Phages

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

Water

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

Soil

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

Techniques

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

Bioinformatics

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.

Events

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

Podcast

AMR FEBRUARY, 2022

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.

Courses

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