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Date:Posted By:Category:AMR Digest

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

Date:Posted By:Category:EMBARK NEWS, WebinarsTag:

EMBARK Spring Webinars

We have a very exciting lineup of speakers for the 2022 EMBARK Webinars! Let’s begin with the speakers for the spring. Registration opens today!

March 16: Windi Muziasari – “Global database of ARGs in the environment”
Anna Abramova – “Meta-analysis reveals the global picture of antibiotic resistance gene prevalence across environments”
[Register]

April 13: Ramanan Laxminarayan – “State of the World’s Antibiotics 2022”
Cheng Zhao – “Optimizing antimicrobial resistance surveillance in farm animals”
[Register]

May 18: Nichole Broderick – “Tiny Earth”
Filipa Grosso – “Implementing citizen-based projects on Antimicrobial Resistance Awareness in Southern Europe: the experience from MicroMundo”
[Register]

June 15: Marisa Haenni – “From AMR surveillance to research in the French veterinary sector”
Reshma Silvester – “AMR in aquaculture- Averting the crisis and the way forward”
[Register]

And for the fall, we have preliminary confirmation for the following speakers:
Jon Hobman
Stineke van Houte
Iruka Okeke
Joakim Larsson

Date:Posted By:Category:AMR Digest

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

Date:Posted By:Category:AMR Digest

AMR DECEMBER, 2021

prepared by Marcus Wenne

In December’s AMR digest we ask a wide range of questions. Why do antibiotics exist? What effect do they have on our own microbiota? Can they increase the colonizing capability of plasmid carrying bacteria? And what methods can we use to measure resistance against them? This is a small sample of the wide range of topics in this month’s digest.

Antibiotic research and development

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

Why Do Antibiotics Exist? – Fabrizio Spagnolo – mBio

Global

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

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

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

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

Clinical

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

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

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

Human Microbiome

Combinatorial, additive and dose-dependent drug–microbiome associations – Sofia K Forslund – Nature
*This study used a multi-omics approach to investigate drug-microbiome interactions in patients suffering from cardiometabolic disease. The authors found that multiple antibiotic exposures had cumulative effects on the patients microbiome. Leading to reduced richness and increased resistance, which are hallmarks of microbiota in patients suffering from obesity, insulin resistance and low-grade inflammation.

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

Agriculture

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

AMR detection methods

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

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

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

Rapid absolute quantification of pathogens and ARGs by nanopore sequencing – Yu Yang – The Science of the Total Environment
*Sequencing has become cheaper, faster and more accessible these last few decades. With the use of third generation sequencing these authors test a method where they can quantify the absolute abundance of both pathogens and resistance genes in 4 hours using third generation nanopore sequencing. Taking advantage of the nanopore technologies long reads, the authors were able to link resistance genes to individual taxa.

Sewage treatment

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

Water environment

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

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

Animal experiment

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

Courses

Webinars

Future conferences

Podcasts

Date:Posted By:Category:WebinarsTag:

Last Fall Webinar

Make sure not to miss the last EMBARK Webinar of the fall! This time we have two very exciting speakers:

  • December 15: Willem van Schaik – “Metagenomic approaches to understand the spread of antibiotic resistance genes in microbial ecosystems”
    Svetlana Ugarcina Perovic – “Exploring the global resistome using the global microbial gene catalog”
    [Register]

Register today!