Editorial Board Members' Collection Series: Antimicrobial Resistance in the Environment

A special issue of Microorganisms (ISSN 2076-2607). This special issue belongs to the section "Antimicrobial Agents and Resistance".

Deadline for manuscript submissions: closed (31 July 2025) | Viewed by 329

Special Issue Editors


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Guest Editor
Microbiology Department, Institut Pasteur, 75015 Paris, France
Interests: antibiotic resistance; bacteriology; molecular microbiology; protein purification; genomics; protein-protein Interaction
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Guest Editor
Faculty of Pharmacy, University of Coimbra, 3000-548 Coimbra, Portugal
Interests: molecular epidemiology; antimicrobial resistance; horizontal gene transfer; Gram-negative bacteria; One Health
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Special Issue Information

Dear Colleagues,

Antimicrobial resistance (AMR) is a global health crisis that extends beyond human medicine, affecting agriculture, veterinary medicine, and environmental health. The environment plays a critical role in the spread and evolution of antimicrobial resistance, serving as both a reservoir and a vector for resistant pathogens and genes. Understanding the dynamics of AMR in environmental contexts is essential for developing comprehensive strategies to combat its spread.

This collection aims to highlight the latest research and advances in our understanding of how antimicrobial resistance emerges, persists, and spreads in different environments. We invite contributions from leading experts and researchers covering a wide range of topics, including but not limited to the following:

  • Environmental reservoirs of AMR: studies of natural and anthropogenic environments that harbor antimicrobial-resistant bacteria and genes, including soil, water, wildlife habitats, and agricultural land;
  • Pathways of transmission: studies of the mechanisms and pathways by which antimicrobial resistance is transferred between the environment, animals, and humans, including the role of vectors, wildlife, and direct human activities;
  • Impact of agricultural practices: research that examines the influence of agricultural practices, such as the use of antibiotics in livestock and crop production, on the development and spread of AMR in the environment;
  • Waste management and treatment: assessing how waste management, including treatment of sewage, industrial effluent, and agricultural runoff, affects the prevalence and spread of antimicrobial resistance in the environment;
  • Detection and surveillance: development and application of advanced methods for detection and monitoring antimicrobial-resistant bacteria and genes in various environments, including molecular and genomic approaches;
  • Mitigation strategies: exploring innovative strategies to reduce the spread of antimicrobial resistance in the environment, such as the development of alternative antimicrobial agents and bioremediation techniques;
  • Intertwining between AMR and climate changes: how warmer climates affect heavy metal or biocide concentrations in soil and water, creating conditions for hotspots either with co-resistance and co-selection mechanisms or when sharp variations in river flows increase the risk of floodwater pollution and resuspension of sediments;
  • AMR in aquaculture: studies on how productive industrial activities, particularly aquaculture, contribute to the development and dissemination of AMR.

Dr. Olivier Chesneau
Dr. Gabriela Jorge Da Silva
Guest Editors

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Keywords

  • antimicrobial resistance (AMR)
  • environmental microbiology
  • soil microbiota
  • water contamination
  • antibiotic residues
  • wastewater treatment
  • horizontal gene transfer
  • resistance genes
  • ecotoxicology

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Published Papers (1 paper)

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Research

25 pages, 2009 KB  
Article
Molecular Epidemiology, Antimicrobial Resistance, and Virulence Profiles of Staphylococcus aureus from Fish, Aquatic Environments, and Fish Handlers in Southeast Nigeria
by Uju Catherine Okafor, Onyinye Josephine Okorie-Kanu, Akwoba Joseph Ogugua, Chika Florence Ikeogu, Simeon Chibuko Okafor, Madubuike Umunna Anyanwu, Obichukwu Chisom Nwobi, Chidiebere Ohazuruike Anyaoha, Anthony Christian Mgbeahuruike, Lynda Onyinyechi Majesty-Alukagberie, Innocent Okwundu Nwankwo, Chukwunonso Francis Obi, Ejike Ekene Ugwuijem, Nkechi Harriet Ikenna-Ezeh, Ifeyinwa Riona Okosi, Onyemaechi Ugboh, George Okey Ezeifeka, Ekene Vivienne Ezenduka, Charles Odilichukwu R. Okpala and Edet Ekpenyong Udo
Microorganisms 2025, 13(9), 2059; https://doi.org/10.3390/microorganisms13092059 - 4 Sep 2025
Abstract
Background: Staphylococcus aureus is a major zoonotic and foodborne pathogen with substantial One Health implications, yet its prevalence, resistance, and virulence potential within the aquaculture sector in Nigeria remains poorly characterized. Objectives: To supplement existing information, this current study investigated the [...] Read more.
Background: Staphylococcus aureus is a major zoonotic and foodborne pathogen with substantial One Health implications, yet its prevalence, resistance, and virulence potential within the aquaculture sector in Nigeria remains poorly characterized. Objectives: To supplement existing information, this current study investigated the prevalence, clonal distribution, antimicrobial resistance, and virulence gene profiles of S. aureus isolates from fish, fish water, and occupationally exposed fish handlers in Anambra State, Southeast Nigeria. Methods: A total of 607 samples—comprising 465 surface swabs from raw and processed fish, 36 fish water samples, and 106 nasal swabs from fish handlers—were processed using selective culture, biochemical tests, antimicrobial susceptibility testing, DNA microarray analysis, spa typing, and SCCmec typing. Results: S. aureus was recovered from 16.5% (100/607) of the samples. Fourteen (14%) isolates were methicillin-resistant (MRSA), harboring mecA and SCCmec types IV and V, with a combined MRSA prevalence of 2.3%. Multidrug resistance was observed in 52.2% of isolates (mean Multiple Antimicrobial Resistance index: 0.23), with 19 resistance genes spanning nine antimicrobial classes—including heavy metal and biocide resistance. Twenty-eight spa types across 13 clonal complexes (CCs) were identified, with CC1, CC5, and CC8 predominating. The detection of shared spa types between fish and handlers indicates potential cross-contamination. Detected virulence genes included those for accessory gene regulators (agrI-IV), Pantone–Valentine leucocidin (lukFS-PV), toxic shock syndrome (tsst-1), hemolysins (hla, hlb, hld/hlIII, hlgA), biofilm formation (icaA, icaD), immune evasion (chp, scn, sak), enterotoxins (sea, seb, sec, sed, egc, and others), exfoliative toxins (etA, etB), epidermal cells differentiation (edinA, edinB), and capsular types (cap5, cap8). Conclusions: This study reveals that the aquaculture sector in Southeast Nigeria serves as a significant reservoir of genetically diverse, multidrug-resistant S. aureus strains with robust virulence profiles. These findings highlight the necessity of integrated One Health surveillance and targeted interventions addressing antimicrobial use and hygiene practices within aquatic food systems. Full article
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