Analysis of viromes and microbiomes from pig fecal samples reveals that phages and prophages rarely carry antibiotic resistance genes

Abstract

Understanding the transmission of antibiotic resistance genes (ARGs) is critical for human health. For this, it is necessary to identify which type of mobile genetic elements is able to spread them from animal reservoirs into human pathogens. Previous research suggests that in pig feces, ARGs may be encoded by bacteriophages. However, convincing proof for phage-encoded ARGs in pig viromes is still lacking, because of bacterial DNA contaminating issues. We collected 14 pig fecal samples and performed deep sequencing on both highly purified viral fractions and total microbiota, in order to investigate phage and prophage-encoded ARGs. We show that ARGs are absent from the genomes of active, virion-forming phages (below 0.02% of viral contigs from viromes), but present in three prophages, representing 0.02% of the viral contigs identified in the microbial dataset. However, the corresponding phages were not detected in the viromes, and their genetic maps suggest they might be defective. We conclude that among pig fecal samples, phages and prophages rarely carry ARG. Furthermore, our dataset allows for the first time a comprehensive view of the interplay between prophages and viral particles, and uncovers two large clades, inoviruses and Oengus-like phages.

Investigation of the Phageome and Prophages in French Cider, a Fermented Beverage

“…In the current study, it was not possible to determine if these prophages were active or not with this method of analysis and with the encountered difficulties to extract free lytic viral particles, as described above. In a study dealing with the virome of pigs, active and inactive prophages were distinguished with bioinformatic tools after the extraction of lytic viral particles [51]. Another possible method could be to induce prophages with mitomycine C as it has been performed on gut microbiota to study active prophages [52], bearing in mind a bias due to the fact that not all prophages are inducible.…”

The gut virome: A new microbiome component in health and disease

“… 54 , 55 The acquisition of ARG mediated by phage transduction has been observed in clinical bacterial pathogens, such as Enterococcus faecalis , 56 Staphylococcus aureus , 57 and C. difficile , 58 which partly accounts for the antibiotic resistance issues frequently observed in the clinical settings of bacterial infections. Of note, some recent studies showed contrasting results that human-associated and animal-associated phageomes rarely carried ARGs, 59 , 60 suggesting that bona fide ARG attributed to phages in viromes might be overestimated.…”

One or many? Multi-species livestock grazing influences soil microbiome community structure and antibiotic resistance potential

“…This may have implications for nutrient cycling and carbon sequestration, as dead microbial cells represent a large proportion of soil carbon stores (Kuzyakov and Mason-Jones, 2018), as well as bacterial community structure (Braga et al, 2020). Phages may also play a significant role in antibiotic resistance spread through horizontal gene transfer (Lekunberri et al, 2017;Debroas and Siguret, 2019), although conflicting studies suggest that exploratory prediction of ARGs from phage genomes has overestimated the importance of phages to antibiotic resistance spread (Enault et al, 2017;Billaud et al, 2021).…”