Enterococcus faecalis prophage dynamics and contributions to pathogenic traits

Polylysogeny is frequently considered to be the result of an adaptive evolutionary process in which prophages confer fitness and/or virulence factors, thus making them important for evolution of both bacterial populations and infectious diseases. The Enterococcus faecalis V583 isolate belongs to the high-risk clonal complex 2 that is particularly well adapted to the hospital environment. Its genome carries 7 prophage-like elements (V583-pp1 to -pp7), one of which is ubiquitous in the species. In this study, we investigated the activity of the V583 prophages and their contribution to E. faecalis biological traits. We systematically analyzed the ability of each prophage to excise from the bacterial chromosome, to replicate and to package its DNA. We also created a set of E. faecalis isogenic strains that lack from one to all six non-ubiquitous prophages by mimicking natural excision. Our work reveals that prophages of E. faecalis V583 excise from the bacterial chromosome in the presence of a fluoroquinolone, and are able to produce active phage progeny. Intricate interactions between V583 prophages were also unveiled: i) pp7, coined EfCIV583 for E. faecalis chromosomal island of V583, hijacks capsids from helper phage 1, leading to the formation of distinct virions, and ii) pp1, pp3 and pp5 inhibit excision of pp4 and pp6. The hijacking exerted by EfCIV583 on helper phage 1 capsids is the first example of molecular piracy in Gram positive bacteria other than staphylococci. Furthermore, prophages encoding platelet-binding-like proteins were found to be involved in adhesion to human platelets, considered as a first step towards the development of infective endocarditis. Our findings reveal not only a role of E. faecalis V583 prophages in pathogenicity, but also provide an explanation for the correlation between antibiotic usage and E. faecalis success as a nosocomial pathogen, as fluoriquinolone may provoke release of prophages and promote gene dissemination among isolates.

Dynamics and diversity of Escherichia coli in animals and system management of the manure on a commercial farrow-to-finish pig farm

The objective of this study was to determine the dynamics and diversity of Escherichia coli populations in animal and environmental lines of a commercial farrow-to-finish pig farm in Spain along a full production cycle (July 2008 to July 2009), with special attention to antimicrobial resistance and the presence of integrons. In the animal line, a total of 256 isolates were collected from pregnant sows (10 samples and 20 isolates), 1-week-old piglets (20 samples and 40 isolates), unweaned piglets (20 samples and 38 isolates), growers (20 samples and 40 isolates), and the finishers' floor pen (6 samples and 118 isolates); from the underfloor pits and farm slurry tank environmental lines, 100 and 119 isolates, respectively, were collected. Our results showed that E. coli populations in the pig fecal microbiota and in the farm environment are highly dynamic and show high levels of diversity. These issues have been proven through DNA-based typing data (repetitive extragenic palindromic PCR [REP-PCR]) and phenotypic typing data (antimicrobial resistance profile comprising 19 antimicrobials). Clustering of the sampling groups based on their REP-PCR typing results showed that the spatial features (the line) had a stronger weight than the temporal features (sampling week) for the clustering of E. coli populations; this weight was less significant when clustering was performed based on resistotypes. Among animals, finishers harbored an E. coli population different from those of the remaining animal populations studied, considering REP-PCR fingerprints and resistotypes. This population, the most important from a public health perspective, demonstrated the lowest levels of antimicrobial resistance and integron presence.