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!

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

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.


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

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

*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

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

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

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 ^^


*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


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


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!


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


*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


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


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


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


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


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


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


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


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


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


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


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


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


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


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


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.


prepared by Svetlana Ugarcina Perovic

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

Join us for the spring #EMBARK2022 webinars!


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

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

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

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

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

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


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

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

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

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

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

Human microbiome

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

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

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


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

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

Animal experiments

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


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


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

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


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

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


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

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


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

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


Recordings of the EDAR6 count down webinars available here.

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