AMR November, 2022

prepared by Faina Tskhay

The EMBARK team is happy and proud to announce that Dr Johan Bengtsson-Palme, coordinator of the EMBARK project, became a laureate of the Einhorn SIGHT award. Congratulations!

The November AMR Digest delivers some fresh and crisp publications from the world of antibiotic resistance. This time we collected publications featuring the AMR evolution, AMR in water and soil, advances of metagenomics in tracking AMR and much more! Enjoy your reading!

Global

Special issue of Environmental Science and Technology Journal – AMR in the Environment: Informing Policy and Practice to Prevent the Spread

The synthesis report “Routes and reservoirs of AMR-determinants & One Health AMR-surveillance” of the Swiss National Research Program 72 “Antimicrobial Resistance”
This report summarizes the research of 18 projects in the field of antibiotic resistance over a 5-year period. Based on the findings and observations, the authors suggest key recommendations for action to restrict the spread of AMR.

Reviews

Molecular mechanisms of antibiotic resistance revisited – Elizabeth M. Darby – Natural Reviews Microbiology
In this article, the authors provide an overview of molecular mechanisms and strategies that bacteria apply to develop resistance to antimicrobials. They give insights into the role of efflux systems in decreased antibiotic susceptibility and their synergetic interaction with other resistance mechanisms. Understanding of molecular mechanisms is essential to overcome antimicrobial resistance and can be used, for example, for developing so-called antibiotic resistance breakers (ARBs) – compounds that can restore antibiotic activity by disrupting or inhibiting a specific resistance mechanism.

Does Environmental Exposure to Pharmaceutical and Personal Care Product Residues Result in the Selection of Antimicrobial-Resistant Microorganisms, and is this Important in Terms of Human Health Outcomes? – Isobel C. Stanton, Holly J. Tipper, Kevin Chau, Uli Klümper, Jessica Subirats, Aimee K. Murray – Environmental Toxicology and Chemistry
This review comprehensively compiles laboratory studies, and field based research evidence regarding the effects of pharmaceutical and personal care products on selection and horizontal gene transfer of antimicrobial resistance in multiple environments. It summarizes these studies and points out under which scenarios the promotion of AMR by PPCPs in the environment is and will be relevant to human health.

Clinical

Nearly Complete Genome Sequence of Raoultella ornithinolytica Strain MQB_Silv_108, Carrying an Uncommon Extended-Spectrum-β-Lactamase-like blaBEL Gene – Marcos Quintela-Baluja – Microbiology Resource Announcements

Report and Comparative Genomics of an NDM-5-Producing Escherichia coli in a Portuguese Hospital: Complex Class 1 Integrons as Important Players in blaNDM Spread – Rafael D. S. Tavares – Microorganisms

Gut microbiota

Noise reduction strategies in metagenomic chromosome confirmation capture to link antibiotic resistance genes to microbial hosts – Gregory E. McCallum – bioRxiv

Enterotoxin tilimycin from gut-resident Klebsiella promotes mutational evolution and antibiotic resistance in mice – Sabine Kienesberger – Nature Microbiology

Sharing Antimicrobial Resistance Genes between Humans and Food Animals – Huiluo Cao – mSystems

Gut microbiome dysbiosis in antibiotic-treated COVID-19 patients is associated with microbial translocation and bacteremia – Lucie Bernard-Raichon – Nature Communications

Characterization of antibiotic-resistance traits in Akkermansia muciniphila strains of human origin – Rossella Filardi – Scientific Reports

AMR evolution

Within-patient evolution of plasmid-mediated antimicrobial resistance – Javier DelaFuente – Nature Ecology and Evolution
This five-year study aimed at tracking AMR evolution in vivo in patients. By analyzing 224 poxA-48-carrying Enterobacteria isolated from 9000 patients, DelaFuente et al. were able to identify 35 variants of a poxA-48 plasmid. They monitored 121 patients for a potential case of within-patient AMR evolution and identified three instances in which the same bacterial host carried different plasmid variants over the treatment period. The authors compared plasmid fitness, susceptibility to antibiotics, plasmid copy number and HGT rates of the new plasmids and ancestral plasmids. According to their findings, the authors concluded that within-patient plasmid-mediated AMR requires an interplay between resistance levels and bacterial fitness.

Plasmid evolution in the clinic – Rosanna C. T. Wright & Michael A. Brockhurst – Nature Ecology and Evolution

Exposure to environmental stress decreases the resistance of river microbial communities towards invasion by antimicrobial-resistant bacteria – Kenyum Bagra, Xavier Bellanger, Christophe Merlin, Gargi Singh, Thomas Ulrich Berendonk, Uli Klümper – bioRxiv
In this preprint the authors utilize artificial river flume systems to explore the invasion dynamics of a model resistant strain (E. coli) into river microbial communities in the presence and absence of a co-introduced environmental stressor. Despite an initially successful introduction of E. coli into all the biofilms, independent of the imposed stress, over time the invader perished in absence of stress. However, under stress conditions the invading strain successfully established and proliferated in the biofilms. Noteworthy, the increased establishment success of the invader coincided with a loss in microbial community diversity under stress conditions, likely due to additional niche space becoming available for the invader.

Mobile genetic elements in Acinetobacter antibiotic-resistance acquisition and dissemination – Hannah R. Noel – Annals of the New York Academy of Science

Electrochemical disinfection may increase the spread of antibiotic resistance genes by promoting conjugal plasmid transfer – Hua Li – Science of The Total Environment

IncP-type plasmids carrying genes for antibiotic resistance or for aromatic compound degradation are prevalent in sequenced Aromatoleum and Thauera strains – Hao-Yu Lo – Environmental Microbiology

Reductive Stress Boosts the Horizontal Transfer of Plasmid-Borne Antibiotic Resistance Genes: The Neglected Side of the Intracellular Redox Spectrum – Haining Huang – Environmental Science & Technology

Novel Plasmid Carrying Mobile Colistin Resistance Gene mcr-4.3 and Mercury Resistance Genes in Shewanella baltica: Insights into Mobilization of mcr-4.3 in Shewanella Species – Nachiket P. Marathe – Microbiology Spectrum

Defense systems are pervasive across chromosomally integrated mobile genetic elements and are inversely correlated to virulence and antimicrobial resistance – João Botelho – bioRxiv

Animals

Concordance between Antimicrobial Resistance Phenotype and Genotype of Staphylococcus pseudintermedius from Healthy Dogs – Joaquim Viñes – Antibiotics

Genomic Insights into the Mobilome and Resistome of Sentinel Microorganisms Originating from Farms of Two Different Swine Production System – Oscar Mencía-Ares – Microbiology Spectrum

More than an anthropogenic phenomenon: Antimicrobial resistance in ungulates from natural and agricultural environments – Lee J. Pinnell – Science of the Total Environment

Viruses and phages

Quantification and fate of plasmid-specific bacteriophages in wastewater: Beyond the F-coliphages – Zhiming He – Water Research

Water

Dissemination of antibiotic resistance in antibiotic-free recirculating aquaculture systemsIoannis Kampouris, Uli Klümper, Lena Kramer, Henning Sorum, Helmut Wedekind, Thomas U. Berendonk – Journal of Hazardous Materials Advances

Explaining the resistomes in a megacity’s water supply catchment: Roles of microbial assembly-dominant taxa, niched environments and pathogenic bacteria – Dong Wu – Water Research

The global groundwater resistome: core ARGs and their dynamics – an in silico re-analysis of publicly available groundwater metagenomesIoannis D. Kampouris, Thomas U. Berendonk, Johan Bengtsson-Palme, Uli Klümper – bioRxiv

Wastewater Surveillance of Antibiotic-Resistant bacterial pathogens: a Systematic Review – Ananda Tiwari – Frontiers in Microbiology

Nanopore-based long-read metagenomics uncover the resistome intrusion by antibiotic-resistant bacteria from treated wastewater in receiving water body – Ziqi Wu – Water Research

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

Soil

Plants select antibiotic resistome in rhizosphere in early stage – Yitian Yua – Science of the Total Environment

Global biogeography and projection of soil antibiotic resistance genes – Dongsheng Zheng – Science Advances

Metagenomics, Bioinformatics

Functional and Sequence-Specific Screening Protocols for the Detection of Novel Antimicrobial Resistance Genes in Metagenomic DNA – Supathep Tansirichaiya – Methods in Molecular Biology

In Silico Characterization of blaNDM-Harboring Conjugative Plasmids in Acinetobacter Species – Biao Tang – Antimicrobial Chemotherapy

Target-enriched long-read sequencing (TELSeq) contextualizes antimicrobial resistance genes in metagenomes – Ilya B. Slizovskiy – Microbiome

Multiomics Characterization of the Canada Goose Fecal Microbiome Reveals Selective Efficacy of Simulated Metagenomes – Joshua C. Gil, Sarah M. Hird – Microbiology Spectrum

MEGARes and AMR++, v3.0: an updated comprehensive database of antimicrobial resistance determinants and an improved software pipeline for classification using high-throughput sequencing – Nathalie Bonin – Nucleic Acids Research

Three Distinct Annotation Platforms Differ in Detection of Antimicrobial Resistance Genes in Long-Read, Short-Read, and Hybrid Sequences Derived from Total Genomic DNA or from Purified Plasmid DNA – Grazieli Maboni – Antibiotics

Webinars

“Antimicrobial Resistance in the Environment” – UNFAO, UNEP, WHO, WOAH – Webinar Series.

AMR OCTOBER, 2022

prepared by Marcus Wenne

In September, the EMBARK team got together to:
1. discuss current and future AMR research efforts and
2. have fun!!

If you live in the Northern Hemisphere every day is becoming darker and colder when we are steadily approaching winter. It is therefore extra important to illuminate your mind with interesting research and get that warm feeling in your body when reading a well written and structured paper. This is hopefully the feeling you will get when reading our October AMR digest. It touches the topics of evolution, the release of new databases, biofilms, wastewater and so much more. If you are from the Southern Hemisphere, you are of course equally welcome to take part of this interesting collection of papers!

Wastewater
Predicting selection for antimicrobial resistance in UK wastewater and aquatic environments: Ciprofloxacin poses a significant risk – April Hayes – Environment International

Microbiome and resistome dynamics along a sewage-effluent-reservoir continuum underline the role of natural attenuation in effluent receiving reservoirs – Inês Leão, Leron Khalifa, Nicolas Gallois, Ivone Vaz-Moreira, Uli Klümper, Daniel Youdkes, Shaked Palmony, Lotan Dagai, Thomas U. Berendonk, Christophe Merlin, Célia M. Manaia, Eddie Cytryn – bioRxiv

New methods, tools or approaches
Evaluation of FEAST for metagenomics-based source tracking of antibiotic resistance genes – Jinping Chen – Journal of Hazardous Materials

Determination and quantification of microbial communities and antimicrobial resistance on food through host DNA-depleted metagenomics – Samuel J Bloomfield – Food Microbiology

Quantification of the mobility potential of antibiotic resistance genes through multiplexed ddPCR linkage analysis – Magali de la Cruz Barron, David Kneis, Alan Xavier Elena, Kenyum Bagra, Thomas U. Berendonk, Uli Klümper – bioRxiv

Biofilm
Metagenomic insights into taxonomic, functional diversity and inhibitors of microbial biofilms – Madangchanok Imchen – Microbiological Research

Biofilm antimicrobial susceptibility through an experimental evolutionary lens – Tom Coenye – Biofilms and Microbes

Databases & resources

*ResFinderFG v2.0: a database of antibiotic resistance genes obtained by functional metagenomics – Rémi Gschwind – bioRxiv
A bioinformatic analysis is not better than the database and tools you base it on. Here Rémi
Gschwind et al. describes a new and updated version of ResFinderFG, version 2.0. According
to the authors most genes in antibiotic resistance gene databases mostly originate from
culturable and pathogenic bacteria. ResfinderFG 2.0 is instead a database based on a
literature search on studies identifying resistance genes using functional metagenomics.
This means that there is a reduced bias in the ResFinderFG v.2.0 database towards
culturable pathogens.


Ab-AMR: A Comprehensive Repository of Acinetobacter baumannii to Understand the Molecular Landscape of Antimicrobial Resistance – Tina Sharma – bioRxiv

CARD 2023: expanded curation, support for machine learning, and resistome prediction at the Comprehensive Antibiotic Resistance Database – Brian P Alcock – Nucleic Acids Research

*A curated data resource of 214K metagenomes for characterization of the global antimicrobial resistome – Hannah-Marie Martiny – PLOS BIOLOGY
Large scale metagenomic screenings of the worlds entire catalogue of metagenomic data
could potentially reveal interesting global and local patterns of antibiotic resistance.
Undertaking such a task is however way to computer intensive for most research groups to
undertake. Luckily, Hannah-Marie Martiny et al. have already undertaken this task. In this
paper they present a publicly available resource of antibiotic resistance gene abundance
based on 442 Tbp of sequencing reads from 214,095 metagenomic samples from the
European Nucleotide Archive.

Fig 4. Composition of reads assigned to ARGs from different resistance classes grouped by sampling origin.

Reviews

Time for Some Group Therapy: Update on Identification, Antimicrobial Resistance, Taxonomy, and Clinical Significance of the Bacteroides fragilis Group – Sophonie Jean – Journal of Clinical Microbiology

Tackling AMR from a multidisciplinary perspective: a primer from education and psychology – Alicia Calvo‑Villamañán – International Microbiology

Machine learning in predicting antimicrobial resistance: a systematic review and meta-analysis – Rui Tang – International Journal of Antimicrobial Agents

A bottom-up view of antimicrobial resistance transmission in developing countries – Odion O. Ikhimiukor – Nature Microbiology

Plasmids
Phage-Plasmids Spread Antibiotic Resistance Genes through Infection and Lysogenic Conversion – Eugen Pfeifer – mBio

New antibiotics
Small Molecule Antibiotics Inhibit Distinct Stages of Bacterial Outer Membrane Protein Assembly – Janine H Peterson – mBio

Ring-fused 2-pyridones effective against multidrug-resistant Gram-positive pathogens and synergistic with standard-of-care antibiotics – Taylor M Nye – PNAS

Clinical studies

Oropharyngeal and intestinal concentrations of opportunistic pathogens are independently associated with death of SARS‑CoV‑2 critically ill adults – Juliette Patrier, Khanh Villageois‑Tran, Piotr Szychowiak, Stéphane Ruckly, Rémi Gschwind, Paul‑Henri Wicky, Signara Gueye, Laurence Armand‑Lefevre, Mehdi Marzouk, Romain Sonneville, Lila Bouadma, Marie Petitjean, Fariza Lamara, Etienne de Montmollin, Jean‑Francois Timsit, Etienne Ruppé and The French COVID Cohort Study Group – Critical Care

Genomic characterisation of multidrug-resistant Escherichia coli, Klebsiella pneumoniae, and Acinetobacter baumannii in two intensive care units in Hanoi, Viet Nam: a prospective observational cohort study – Leah W Roberts – Lancet Microbe

Evolution
*The evolution of spectrum in antibiotics and bacteriocins – Jacob D Palmer and Kevin R
Foster – PNAS
An important weapon in microbial competition is the production of antibiotics. But when is
it preferential for a microbial population to produce wide or narrow spectrum antibiotics?
In this paper Jacob D Palmer and Kevin R Foster have used an evolutionary model approach
in an attempt to shed light on this question.

Antibiotics in the environment
Deciphering chloramphenicol biotransformation mechanisms and microbial interactions via integrated multi‑omics and cultivation‑dependent approaches – Jiayu Zhang, Xiaoyan Li, Uli Klümper, Huaxin Lei, Thomas U. Berendonk, Fangliang Guo, Ke Yu, Chao Yang & Bing Li – Microbiome

Antibiotic resistance mechanisms
L-Form Switching in Escherichia coli as a Common b-Lactam Resistance Mechanism – Aleksandra P Fabijan – Microbiology Spectrum

Antibiotic usage
Factors influencing usage of antimicrobial drugs among pastoralists in Kenya – Dennis N Makau – Tropical Animal Health and Production

Soil
Active antibiotic resistome in soils unraveled by single-cell isotope probing and targeted metagenomics – Hong-Zhe Li – PNAS

Anthropogenic impact
Leave No Trace? Ecological and anthropogenic determinants of antibiotic resistant bacteria in a recreational alpine environment – Laura C Scott – Environmental Research

Podcasts
Microbiology Lab Pod September 2022 Pod: Environmental Antibiotic Resistance – Johan Bengtsson-Palme lab

Webinars
Vaccination as a strategy to combat antimicrobial resistance – Organised by the (CSA) DESIGN One Health AMR, together with MRC, BactiVac


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.