Prepared by Rémi GSCHWIND (

The September AMR Digest features general issues about AMR and more specific topics about policy, surveillance, AMR removal/transmission and about several specific environments.  It encompasses as well from the EMBARK consortium: a study on antibiotic discovery including Luis Pedro Coelho. Enjoy your reading but first “Race against AMR” from BBC StoryWorks.

Race Against Resistance: The Life And Death Struggle To Save Antibiotics | BBC StoryWorks

Our monthly EMBARK Webinar for October is titled “AMR: a link between clinical settings and other environments” with Prof. Adam P. Roberts & Prof. Etienne Ruppe, moderated by Remi Gschwind.

October 11th, 14:00 CEST – Register here

Global picture

Computational exploration of the global microbiome for antibiotic discovery – Célio Dias Santos-Júnior, Marcelo D. T. Torres, Yiqian Duan, Álvaro Rodríguez del Río, Thomas S.B. Schmidt, Hui Chong, Anthony Fullam, Kuhn Michael, Chengkai Zhu, Amy Houseman, Jelena Somborski, Anna Vines, Xing-Ming Zhao, Peer Bork, Jaime Huerta-Cepas, Cesar de la Fuente-Nunez, Luis Pedro Coelho – bioRxiv preprint

Global patterns and correlates in the emergence of antimicrobial resistance in humans – E. Mendelsohn et al. – Proceedings of the Royal Society B


Repurposing sunscreen as an antibiotic: zinc-activated avobenzone inhibits methicillin-resistant Staphylococcus aureus. – Andrews RM et al. – Metallomics.

Gut microbiome perturbation, antibiotic resistance, and Escherichia coli strain dynamics associated with international travel: a metagenomic analysis. – Worby C et al. – Lancet Microbe.

Based on analysis of pre- and post-travel fecal microbiomes using metagenomics and culture dependent methods a significant proportion of travelers acquired ARGs and ARBs.

Regulation Transcriptional of Antibiotic Resistance Genes (ARGs) in Bacteria Isolated from WWTP. – Díaz-Palafox G et al. – Curr Microbiol.

Household environment and animal fecal contamination are critical modifiers of the gut microbiome and resistome in young children from rural Nicaragua. – Mills M et al. – Microbiome.

Dynamic human exposure to airborne bacteria-associated antibiotic resistomes revealed by longitudinal personal monitoring data. – Zhang RM et al. – Sci Total Environ.

Pangenome analysis of Corynebacterium striatum: insights into a neglected multidrug-resistant pathogen. – Nageeb WM et al. – BMC Microbiol.

Synergistic Role of Biofilm-Associated Genes and Efflux Pump Genes in Tigecycline Resistance of Acinetobacter baumannii. – Luo B et al. – Med Sci Monit.

Exploiting the aggregation propensity of beta-lactamases to design inhibitors that induce enzyme misfolding. – Khodaparast L et al. – Nat Commun.

Beta-lactamases are the main resistance mechanism against beta-lactam antibiotics. They represent a threat for infectious diseases treatment as their resistance spectrum includes all the beta-lactam antibiotics and even beta-lactam associated with beta-lactamases inhibitors. This study reports the test of a new strategy targeting the beta-lactamase itself rather than its active site on beta-lactam antibiotics with inhibitors. It lays on targeting aggregation-prone regions of the enzyme which cause inactivation of the enzyme. TEM and SHV beta-lactamases were investigated regarding their tendency to aggregate. The aggregation of TEM, SHV, and NDM was not bactericidal but it allowed to restore sensitivity to beta-lactam antibiotics.


Reducing antimicrobial use in chicken production in Vietnam: Exploring the systemic dimension of change. – Bâtie C et al. – PLoS One.


Metagenome meta-analysis reveals an increase in the abundance of some multidrug efflux pumps and mobile genetic elements in chemically polluted environments – J. Subirats et al. – Applied and Environmental Microbiology

Quantifying health risks of plastisphere antibiotic resistome and deciphering driving mechanisms in an urbanizing watershed. – Zhu L et al. – Water Res.

Evolution of Resistance

Parallel evolution of linezolid-resistant Staphylococcus aureus in patients with cystic fibrosis. – Pitcher NJ et al. – Microbiol Spectr. 

Bacterial motility can govern the dynamics of antibiotic resistance evolution. Piskovski V et al. Nat Commun.

Fitness Costs of Antibiotic Resistance Impede the Evolution of Resistance to Other Antibiotics. Chowdury FR et al. ACS Infect Dis. 

Regulatory fine-tuning of mcr-1 increases bacterial fitness and stabilises antibiotic resistance in agricultural settings – L. Ogunlana et al. – The ISME Journal

Gene Transfer/Plasmids

Oxytetracycline and heavy metals promote the migration of resistance genes in the intestinal microbiome by plasmid transferXiaojun Lin et al. – The ISME Journal

Integrons, transposons and IS elements promote diversification of multidrug resistance plasmids and adaptation of their hosts to antibiotic pollutants from pharmaceutical companies. – Shintani M et al. – Environ Microbiol.

The extensively antibiotic resistant ST111 Acinetobacter baumannii isolate RBH2 carries an extensive mobile element complement of plasmids, transposons and insertion sequences. – Ambrose SJ et al. – Plasmid.


Phylogenomic analysis of a global collection of Escherichia coli ST38: evidence of interspecies and environmental transmission? – Roy Chowdhury P et al. – mSystems.

Circulation of enterotoxigenic Escherichia coli (ETEC) isolates expressing CS23 from the environment to clinical settings. – Calderon Toledo C et al. – mSystems.

AMR removal

Engineering conjugative CRISPR-Cas9 systems for the targeted control of enteric pathogens and antibiotic resistance – H. Sheng et al. – PLOS One

Recent advances in sulfidized nanoscale zero-valent iron materials for environmental remediation and challenges. – Xue W et al. – Environ Sci Pollut Res Int.

Antibiotics resistance removal from piggery wastewater by an integrated anaerobic-aerobic biofilm reactor: Efficiency and mechanism. – Tang L et al. – Sci Total Environ.

Aquatic environments

Impact of corrosion inhibitors on antibiotic resistance, metal resistance, and microbial communities in drinking water – LK Kimbell et al. – mSphere 

Free-floating extracellular DNA (exDNA) in different wastewaters: Status quo on exDNA-associated antimicrobial resistance genes. – Savin M et al. – Environ Pollut. 

Wastewater treatment plants (WWTPs) are hotspots for ARGs. Studies on ARG in WWTP environments mainly focus on intracellular DNA while a significant proportion of the total DNA is extracellular DNA due to wastewater decontamination. Extracellular DNA has to be taken into account as transformation of naturally competent bacteria can occur with extracellular DNA containing ARGs. The study shows how wastewater is a source of ARGs associated with free-floating exDNA.

Antibiotic resistance genes and the association with bacterial community in biofilms occurring during the drinking water granular activated carbon (GAC) sandwich biofiltration. – Xu L et al. – J Hazard Mater.

Microbial diversity characterizations, associated pathogenesis and antimicrobial resistance profiling of Najafgarh drain. – Tyagi I et al. – Environ Res. 

Combined effects of microplastics and antibiotic-resistant bacteria on Daphnia magna growth and expression of functional genes. – Chen X et al. – Sci Total Environ.

Comparison of antibiotic-resistant Escherichia coli and extra-intestinal pathogenic E. coli from main river basins under different levels of the sewer system development. – Chen JS et al. – Ecotoxicol Environ Saf.

Comparative bacteriome and antibiotic resistome analysis of water and sediment of the Ganga River of India. – Srivastava A et al. – World J Microbiol Biotechnol.

Metagenomic analysis reveals the dissemination mechanisms and risks of resistance genes in plateau lakes. – Mao C et al. – iScience.

Simultaneous stream assessment of antibiotics, bacteria, antibiotic resistant bacteria, and antibiotic resistance genes in an agricultural region of the United States. – Givens CE et al. – Sci Total Environ.

Wastewater treatment plant effluents exert different impacts on antibiotic resistome in water and sediment of the receiving river: Metagenomic analysis and risk assessment. – Wu Y et al. – J Hazard Mater.

Antibiotics and their associations with antibiotic resistance genes and microbial communities in estuarine and coastal sediment of Quanzhou Bay, Southeast China. – Chen Y et al. – Mar Pollut Bull.


Uncovering the prevalence and drivers of antibiotic resistance genes in soils across different land-use types. – Wu J et al. – J Environ Manage.

Antibiotic resistome and associated bacterial communities in agricultural soil following the amendments of swine manure-derived fermentation bed waste. – Pan Z et al. – Environ Sci Pollut Res Int. 


Antibiotics promote intestinal growth of carbapenem-resistant Enterobacteriaceae by enriching nutrients and depleting microbial metabolites – A. Yip et al. – Nature Communications

Effect on the resistome of dual- vs monotherapy for the treatment of Neisseria gonorrhoeae: results from a randomized controlled trial (ResistAZM Trial) – Thibaut Vanbaelen et al. – Open Forum Infectious Diseases

Co-administration of amoxicillin-loaded chitosan nanoparticles and inulin: A novel strategy for mitigating antibiotic resistance and preserving microbiota balance in Helicobacter pylori treatment. – Fayed B et al. – Int J Biol Macromol.

Characterization of Pseudomonas aeruginosa resistance to ceftolozane-tazobactam due to ampC and/or ampD mutations observed during treatment using semi-mechanistic PKPD modeling. – Deroche L et al. – Antimicrob Agents Chemother.

Within-Host Dynamics and Duration of Colonization of Travel-Acquired Multidrug-Resistant Enterobacterales in Untreated Individuals. – Olivier Cotto et al. – Clin Infect Dis.


Large-scale genomic survey and characterization of mcr genes carried by foodborne Cronobacter isolates. – Zhu Q et al. – mSystems.

Comparative proteomics reveals the antibiotic resistance and virulence of Cronobacter isolated from powdered infant formula and its processing environment. – Song D et al. – Int J Food Microbiol.

Advanced strategies to overcome the challenges of bacteriophage-based antimicrobial treatments in food and agricultural systems. Liu S et al. Crit Rev Food Sci Nutr.

Extended-spectrum β-lactamase-producing Enterobacteriaceae from ready-to-eat foods: Genetic diversity and antibiotic susceptibility. – Liu Y et al. – Food Sci Nutr.

Postbiotic as Novel Alternative Agent or Adjuvant for the Common Antibiotic Utilized in the Food Industry. – Sepordeh et al. – Curr Pharm Biotechnol.

Animals / Wildlife

Effects of the coexistence of antibiotics and heavy metals on the fate of antibiotic resistance genes in chicken manure and surrounding soils. – Shen C et al. – Ecotoxicol Environ

Prevalence of neonatal calf diarrhea caused by Escherichia coli and investigation of virulence factors, serotypes, and antibiotic susceptibility. – Coşkun M R et al. – Pol J Vet Sci.

Complete genome sequences of bacteria isolated from cockroaches collected in a Bangladeshi hospital. – Workman SD et al. – Microbiol Resour Announc

Bacterial community succession and the enrichment of antibiotic resistance genes on microplastics in an oyster farm. – Xiao S et al. – Marine Pollution Bulletin

Assessing the mechanisms of multi-drug resistant non-typhoidal Salmonella (NTS) serovars isolated from layer chicken farms in Nigeria. – Fagbamila IO et al. – PLoS One

Whole genome sequencing-based cataloguing of antibiotic resistant genes in piggery waste borne samples. – Niharika J et al. – Gene

Anthropic Impact on the Critically Endangered Melanophryniscus admirabilis (Admirable Redbelly Toad): Evidence from the Presence of Multiresistant Enterobacteriaceae. – Ienes-Lima J et al. – Current Microbiology

Presence and Resistance Profile of Staphylococcus spp. Isolated from Slaughtered Pigs. Santos ICD et al. Vector borne Zoonotic Diseases

Antibiotic Resistance Profiles and Molecular Characteristics of bla(CMY-2)-Carrying Salmonella enterica Serovar Albany Isolated from Chickens During 2013-2020 in South Korea. – Ali MS et al. – Foodborn Pathogen Dissemination 

Integrative conjugative elements mediate the high prevalence of tmexCD3-toprJ1b in Proteus spp. of animal source. – Peng K et al. – mSystems

Fate of high-risk antibiotic resistance genes in large-scale aquaculture sediments: geographical differentiation and corresponding drivers. – Wanyan R et al. – Science of the Total Environment 


Bacteriophages limitedly contribute to the antimicrobial resistome of microbial communities in wastewater treatment plants – R. Sabbatino et al. – Microbiology Spectrum


Identification of mobile genetic elements with geNomad. – Camargo AP et al. – Nature Biotechnology