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

Maud Billaud (1, 2) , Quentin Lamy-Besnier (1) , Julien Lossouarn (1) , Elisabeth Moncaut (1) , Moira Dion (3) , Sylvain S. Moineau (3) , Fatoumata Traoré (4) , Emmanuelle Le Chatelier (4) , Catherine Denis (5) , Jordi Estellé (6) , Caroline Achard (6) , Olivier Zemb (7) , Marie-Agnès Petit (1)

1 MICALIS - MICrobiologie de l'ALImentation au Service de la Santé
2 Pherecydes Pharma
3 FSG - Faculté des sciences et de génie [Laval-Québec]
4 MGP (US 1367) - MetaGenoPolis
5 GABI - Génétique Animale et Biologie Intégrative
6 GenPhySE - Génétique Physiologie et Systèmes d'Elevage
7 ENVT - Ecole Nationale Vétérinaire de Toulouse

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.

Mots clés: viromes; microbiomes; antibiotic resistance genes; viromes

Domaines: Sciences du Vivant [q-bio]

Maud Billaud, Quentin Lamy-Besnier, Julien Lossouarn, Elisabeth Moncaut, Moira Dion, et al.. Analysis of viromes and microbiomes from pig fecal sample reveals that phages and prophages rarely carry antibiotic resistance genes. The International Society of Microbiologial Ecology Journal, 2021, 1 (55), ⟨10.1038/s43705-021-00054-8⟩. ⟨hal-03299373⟩