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Updated: Dec 16, 2025
Isolation and Identification of Waterborne Antibiotic-Resistant Bacteria and Molecular Characterization of their Antibiotic Resistance Genes
Published on: March 3, 2023
Risk assessment of antimicrobial resistance along the food chain through culture-independent methodologies
Abstract:
Antimicrobial resistance (AMR) represents a major challenge for Public Health and the scientific community, and requires immediate and drastic solutions. Acquired resistance to certain antimicrobials is already widespread to such an extent that their efficacy in the treatment of certain life-threatening infections is already compromised. To date, the emergence and spread of AMR has been attributed to the use, misuse or indiscriminate use of antibiotics as therapeutic drugs in human, animal and plant health, or as growth promoters in veterinary husbandry. In addition, there is growing concern over the possibility of AMR transmission via the food chain. Food processing environments could act as potential hotspots for AMR acquisition and spread. Indeed, biocide use and exposure to food-related stresses and food processing technologies could presumably act as selection pressures for increased microbial resistance against clinically relevant antibiotics. Global AMR surveillance is critical for providing the necessary information to form global strategies and to monitor the effectiveness of public health interventions as well as to detect new trends and emerging threats. Surveillance of AMR is currently based on the isolation of indicator microorganisms and the phenotypic characterisation of the strains isolated. However, this approach provides very limited information on the mechanisms driving AMR or on the presence and spread of AMR genes. Whole genome sequencing (WGS) of bacterial pathogens is a powerful tool that can be used for epidemiological surveillance, outbreak detection and infection control. In addition, whole metagenome sequencing (WMS) allows for the culture-independent analysis of complex microbial communities, providing useful information on the occurrence of AMR genes. Both approaches can be used to provide the information necessary for the implementation of quantitative risk assessment of AMR transmission routes along the food chain.
Insights
Antimicrobial resistance (AMR) is a global threat driven by antibiotic misuse. Advanced genomic surveillance methods like whole genome sequencing (WGS) and whole metagenome sequencing (WMS) are crucial for tracking AMR spread and informing public health strategies.
Area of Science:
- Public Health
- Microbiology
- Genomics
Background:
- Antimicrobial resistance (AMR) poses a significant global public health challenge, compromising the efficacy of life-saving treatments.
- The emergence and spread of AMR are linked to the extensive use and misuse of antibiotics in human, animal, and plant health, as well as in agriculture.
- Food processing environments are potential hotspots for AMR acquisition and dissemination, with factors like biocide use and food-related stresses acting as selection pressures.
Purpose of the Study:
- To highlight the critical need for global antimicrobial resistance (AMR) surveillance.
- To emphasize the limitations of traditional phenotypic methods in understanding AMR mechanisms and gene spread.
- To introduce advanced genomic sequencing techniques as powerful tools for AMR surveillance and risk assessment.
Main Methods:
- Review of current antimicrobial resistance (AMR) surveillance strategies.
- Discussion of the limitations of phenotypic characterization of indicator microorganisms.
- Introduction of whole genome sequencing (WGS) for bacterial pathogen surveillance and whole metagenome sequencing (WMS) for culture-independent analysis of microbial communities.
Main Results:
- Traditional AMR surveillance methods provide limited insights into the genetic basis and spread of resistance.
- Whole genome sequencing (WGS) offers powerful capabilities for epidemiological surveillance, outbreak detection, and infection control.
- Whole metagenome sequencing (WMS) enables the detection of AMR genes in complex microbial communities without culturing.
Conclusions:
- Genomic surveillance approaches, including WGS and WMS, are essential for comprehensive understanding and control of antimicrobial resistance (AMR).
- These advanced methods provide critical data for quantitative risk assessment of AMR transmission routes, particularly along the food chain.
- Implementing robust global AMR surveillance using genomic tools is vital for developing effective public health interventions and combating emerging threats.
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