Microbiome reservoirs of antimicrobial resistance

Antimicrobial resistance (AMR) presents a global threat to public health due to the inability to comprehensively treat bacterial infections. Emerging resistant bacteria residing within human, animal and environmental reservoirs may spread from one to the other, at both local and global levels. Consequently, AMR has the potential to rapidly become pandemic whereby it is no longer constrained by either geographical or human-animal borders. Therefore, to enhance our understanding on the dissemination of AMR we systematically resolved different reservoirs of antimicrobial resistance, leveraging animal, environmental and human samples, to provide a One Health perspective. To identify antimicrobial resistance genes (ARGs) and compare their identity and prevalence across different microbial reservoirs, we developed the PathoFact pipeline which also contextualizes ARG localization on mobile genetic elements (MGEs). This methodology was applied to several metagenomic datasets covering microbiomes of infants, laboratory mice, a wastewater treatment plant (WWTP) and biofilms from glacier-fed streams (GFS). Investigating the infant gut resistome we found that the abundance of ARGs against (semi)-synthetic agents were increased in infants born via caesarian section compared to those born via vaginal delivery. Additionally, we identified mobile genetic elements (MGEs) encoding ARGs such as glycopeptide, diaminopyrimidine and multidrug resistance at an early age. MGEs are often pivotal in the accumulation and dissemination of AMR within a microbial population. Therefore, we assessed the effect of selective pressure on the evolution and consecutive dissemination of AMR within the commensal gut microbiome, utilizing a mouse model. While plasmids and phages were found to contribute to the spread of AMR, we found that integrons represented the primary factors mediating AMR in the antibiotic-treated mice. In addition to the above-described studies, we investigated the environmental resistome, comprising both the urban environment, i.e., the WWTP, and a natural environment, GFS biofilms. Utilizing a multi-omics approach we investigated the WWTP resistome over a 1.5 years timeseries and found that a core group of fifteen AMR categories were always present. Additionally, we found a significant difference in AMR categories encoded on phages versus plasmids indicating that the MGEs contributed differentially to the dissemination of AMR. On the other hand, the GFS biofilms represent pristine environments with limited anthropogenic influences. Therein, we found that eukaryotes, as well as prokaryotes, may serve as AMR reservoirs owing to their potential for encoding ARGs. In addition to our identification of biosynthetic gene clusters encoding antibacterial secondary metabolites, our findings highlight the constant intra- and inter-domain competition and the underlying mechanisms influencing microbial survival in GFS epilithic biofilms. In general, we observed that the overall AMR abundances were highest in human and animal microbial reservoirs whilst environmental reservoirs demonstrated a higher diversity of ARG subtypes. Additionally, we identified human-associated, MGE-derived ARGs in all three components of the One Health triad, indicating possible transmission routes for AMR dissemination. In summary, this work provides a comprehensive assessment of the prevalence of antimicrobial resistance and its dissemination mechanisms in human, animal, and environmental mechanisms