8 - AMR & the Environment Flashcards
ARGs
Antimicrobial resistance genes
Where are ARGs detected
- Soil
- Marine sediments
- Wildlife
- Areas with high human contact
- Remote areas
How did ARGs become so widespread
Most were there already (“native” or endogenous)
Endogenous ARGs
- ARGs that have developed in situ
- e.g. in response to selection pressure exerted by microbial secondary compounds
- de novo random mutations that confer a benefit and provide competitive advantage
Exogenous ARGs
- Result of human activity (pollution)
- In livestock waste, treated sewage, agricultural antibiotics
- Spread by wildlife
Intrinsic antibiotic resistance
- Encoded on bacterial chromosome
- E.g. permeability barrier, efflux
Acquired antibiotic resistance
- Present on mobile genetic elements (plasmids, integrons, bacteriophage)
- E.g. Target modification, antibiotic degradation, efflux
Horizontal gene transfer
- Novel DNA acquired via horizontal gene transfer in natural communities
- Transformation, transduction, conjugation
Transformation
Uptake of naked DNA from lysed cells in environment
Transduction
Genetic material is introduced from a phage into bacterial genomes
Conjugation
DNA transferred through conjugative pili and is the predominant mechanism by which DNA is transferred between bacteria
Role of the environment in the emergence of ARGS
- Chromosomal, immobile ARG
- ARG mobilisation within the genome by integrons
- Relocation to an element that can move autonomously between cells
- HGT of such a mobile element, either directly to a pathogen or via intermediary hosts
Resistome
- Encompassess all ARGs
- Includes both cryptic, embedded resistance genes and expressed resistance genes
- Includes chromosomal and mobile genes
Cryptic, embedded resistance genes
- Not necessarily expressed
- Present on chromosome
Expressed resistance genes
Present in pathogens and antibiotic resistant organisms
Sources of ARGs
- Agriculture
- Human medicine
- Soil
Sinks of ARGs
Soil
Reservoirs
- Soil
- Water
Soil resistome
- Both endogenous and exogenous
- Primary reservoir for clinically relevant ARGs (diverse range of ARGs can be detected in pristine soil)
- Human pathogens have acquired ARGs from environment by HGT
- Exogenous sources include spreading of manure, wastewater treatment, agricultural antibiotics and pollutants
Water resistome
- Exogenous sources are treated sewage wastewater, agricultural runoff
- Wastewater may contain ARGs and/or antibiotics
- Antibiotics excreted by humans in unaltered state
Resistome of freshwater
- ARGs found in rivers, streams, lakes
- Water itself not reservoir but rather sediments
- Another issue is uptake of ARB by food animals (e.g. fish)
Why is water itself unlikely to be major reservoir
- Low nutrient availability
- Human pathogens not suited to freshwater
- Biodegradation
Resistome of air and atmosphere
- ARB detected in air samples
- Sources include: fine particulate matter or dust carried in air and bioaerosols from range of facilities (e.g. agriculture, wastewater treatment plants)
- May explain how ARGs can travel over large distances (animal vectors more likely)
Resistome of production animals
- Cows, pigs, chicken, sheep (pigs and chicken have most)
- Large volumes of antimicrobials used typically for non-therapeutic purposes (prevention of disease and growth promotion)
- Exerts selective pressure for de novo ARGs
- Aids in spread of ARGs as easily disseminated via faeces and run off
- FIsh farms big issue
Wildlife resistome
- ARGs detected in wild animals
- Higher levels closer to human contact (e.g. Galapagos tortoises levels of ARGs were higher in tortoises nearer human activity than those on remote islands)
- Birds problematic as migratory binds disseminate ARB ober migratory range
Human activity and ARGs
- Levels of ARGs higher in modern times, beyond natural baseline
- ARGs detected in antibiotic free ancient samples (examination of DNA from pathogens Yersinia pestis and Vibrio cholerae showed ONLY resistance genes belonging to that intrinsic resistome of each organism - no additional ARGs)
Factors that influence fate of resistance genes in the environment
- Specific environment
- Conditions
- Type of ARG
Fate of resistance genes in soil
- May be degraded
- May absorb onto soil minerals
- May move via HGT into other organisms
Strategies to mitigate spread of ARGs
- Reduce antibiotic use (especially in livestock)
- Improve wastewater treatment (modify disinfection step and use coagulation)
- Uee of constructed wetlands (artificial lakes, shown to remove ARGs from water BUT sediment may serve as a reservoir)
