Manure as a Potential Hotspot for Antibiotic Resistance Dissemination by Horizontal Gene Transfer Events

Abstract

The increasing demand for animal-derived foods has led to intensive and large-scale livestock production with the consequent formation of large amounts of manure. Livestock manure is widely used in agricultural practices as soil fertilizer worldwide. However, several antibiotic residues, antibiotic resistance genes (ARGs) and antibiotic-resistant bacteria are frequently detected in manure and manure-amended soils. This review explores the role of manure in the persistence and dissemination of ARGs in the environment, analyzes the procedures used to decrease antimicrobial resistance in manure and the potential impact of manure application in public health. We highlight that manure shows unique features as a hotspot for antimicrobial gene dissemination by horizontal transfer events: richness in nutrients, a high abundance and diversity of bacteria populations and antibiotic residues that may exert a selective pressure on bacteria and trigger gene mobilization; reduction methodologies are able to reduce the concentrations of some, but not all, antimicrobials and microorganisms. Conjugation events are often seen in the manure environment, even after composting. Antibiotic resistance is considered a growing threat to human, animal and environmental health. Therefore, it is crucial to reduce the amount of antimicrobials and the load of antimicrobial resistant bacteria that end up in soil.

The Role of Aquatic Ecosystems (River Tua, Portugal) as Reservoirs of Multidrug-Resistant Aeromonas spp.

“…Antibiotics and resistant bacteria are entering our local waterways and have the potential to influence biotic processes. Another important point is associated with the transfer of resistant genes from not-pathogenic bacteria to pathogenic bacteria, and on to humans interacting with the aquatic environment [69][70][71].…”

Role played by the environment in the emergence and spread of antimicrobial resistance (AMR) through the food chain

“…The impact of the measures mentioned above on the reduction of ARB transmission or ARG transfer within source environments cannot be fully assessed, as there are very few available studies on ARB and ARG transmission in the environment (Lima et al., 2020), particularly in the EU. However, a number of measures have been shown to be effective for the reduction of pathogens, which will also have an impact on the occurrence and level of ARB.…”

“…More structured, standardised, repeatable and targeted studies and more efficient methodologies to investigate the ecology of ARB and ARGs in the microbiome of food animals and sources of AMR for the food production environment are required (Cao et al., 2020; Feye et al., 2020; Johansson et al., 2020; Lee et al., 2020; Lima et al., 2020), including the relevance of biofilms (Trampari et al., 2021). Scientific approaches need to move beyond surveys that simply identify ARB in the environment towards systematic and harmonised hypothesis‐driven investigations that definitively identify sources of AMR and selective agents for food‐producing environments, providing data that can be used to assess the risk to the food chain and public health.…”

Developing a one health approach by using a multi-dimensional matrix

“…Improperly processed manure can contaminate food, water, and spread antimicrobial resistant genes to soil microbes. Animal manure has been found to be a potential hot spot, a perfect breeding ground, for antimicrobial resistance gene dissemination via horizontal gene transfer mechanisms [ 34 ]. Manure microbes mix with soil microbes, altering microbial biomes, and potentially changing the ‘Global Resistome,’ the total amount of resistance genes in the world's microbial ecosystems [ 35 ].…”