Transmission and persistence of IncF conjugative plasmids in the gut microbiota of full-term infants

Abstract

Conjugative plasmids represent major reservoirs for horizontal transmission of antibiotic resistance (AR) and virulence genes. Our knowledge about the ecology and persistence of these plasmids in the gut microbiota remains limited. The IncF plasmids are the most widespread in clinical samples and in healthy humans. Therefore, the main aim is to study their ecology and association with the developing gut microbiota. Using a longitudinal (2, 10, 30 and 90 days) cohort of full-term infants, we investigated the transmission and persistence of IncFIA and IncFIB plasmids. The prevalence of IncFIB plasmids was higher than IncFIA in the cohort, while IncFIA always co-occurred with IncFIB. However, the relative gene abundance of IncFIA was significantly higher than IncFIB for all time periods, indicating that IncFIA may be a higher copy-number plasmid. Through LEfSe and OTU-level associations, we observed major differences in the abundance of Enterobacteriaceae in samples positive and negative to IncFIB. This association was significant at 2, 10 and 30 days and showed an association with vaginal delivery. From the shot-gun analyses, we de novo assembled multi-replicon shared (IncFIA/IncFIB) and integrated (IncFIA/IB) plasmids that were persistent through the dataset. Overall, the study demonstrates the nature of IncF plasmids in complex microbial communities.

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