Viromes As Genetic Reservoir for the Microbial Communities in Aquatic Environments: A Focus on Antimicrobial-Resistance Genes

Abstract

Despite studies of viromes isolated from aquatic environments are becoming increasingly frequent, most of them are limited to the characterization of viral taxonomy. Bacterial reads in viromes are abundant but the extent to which this genetic material is playing a role in the ecology of aquatic microbiology remains unclear. To this aim, we developed of a useful approach for the characterization of viral and microbial communities of aquatic environments with a particular focus on the identification of microbial genes harbored in the viromes. Virus-like particles were isolated from water samples collected across the Lambro River, from the spring to the high urbanized Milan area. The derived viromes were analyzed by shotgun metagenomic sequencing looking for the presence, relative abundance of bacterial genes with particular focus on those genes involved in antimicrobial resistance mechanisms. Antibiotic and heavy metal resistance genes have been identified in all virome samples together with a high abundance of reads assigned to cellular processes and signaling. Virome data compared to those identified in the microbiome isolated from the same sample revealed differences in terms of functional categories and their relative abundance. To verify the role of aquatic viral population in bacterial gene transfer, water-based mesocosms were perturbed or not perturbed with a low dose of tetracycline. The results obtained by qPCR assays revealed variation in abundance of tet genes in the virome and microbiome highlighting a relevant role of viral populations in microbial gene mobilization.

Freshwater Viral Metagenome Reveals Novel and Functional Phage-borne Antibiotic Resistance Genes

“…However, we observed no significant differences in ARG levels among the six samples from diverse areas (Table 1). Similar trends were observed in the Lambro River, Italy [19]. Virome samples collected from a pristine area on the Lambro River appeared to have the highest level of ARGs (1.92%), while that collected from an urbanized site showed the lowest level of ARGs (0.48%).…”

“…Multidrug transport proteins were largely composed of ABCtype multidrug efflux pump components. Both types of ARGs were relatively frequently found in diverse viromes while less was reported in isolated phage genomes [19], indicating that the majority of phages harboring these ARGs are not cultured yet. Genes for lactamases and vancomycin resistance proteins were also detected in the Han River virome at relatively lower frequencies.…”

“…The rapid development of viral metagenomics over the last decade has led to several viral metagenome (virome) analyses of various environments, including oceans, freshwater, and clinical samples [10][11][12][13][14], revealing a great number of novel viral sequences, including ARGs [15]. Phageassociated ARGs were found in clinical viromes [16,17] where both bacteria and phages are heavily exposed to antibiotics, and in marine and river viromes [18][19][20], indicating that ARGs are commonly carried by phages in natural environments. Although a high proportion of virome reads were found to be encoding ARGs, those genes remain uncertain whether they were collected from phage genomes or bacterial genome remnants [21].…”

Occurrence, identification and antibiogram signatures of selected Enterobacteriaceae from Tsomo and Tyhume rivers in the Eastern Cape Province, Republic of South Africa

“…Surface waters have been reported to be "hotspots" of antimicrobial resistance contamination owing to being a recipient of discharges from diverse sources which include contaminants from industrial, agricultural and domestic settings of varying chemical and microbial concerns (5,18,26,27). Furthermore, the surface water being a reservoir of ARB and ARGs could serve as a dissemination port for the proliferation of new resistant strains which can be enhanced by the acquisition bacteriophages or integrons through horizontal gene transfer mechanisms (28,29).…”

Antimicrobial Resistance in the Environment

“…With the large amount of data being generated due to the advent of low-cost next generation sequencing approaches, the collection, curation, and classification of this reference data is of critical importance. ARG data is no exception and the development and utilization of databases and tools that process this data into digestible forms is being which have been reported to harbor crucial ARGs that can be disseminated in the environment (Colombo et al, 2017).…”