Low zoonotic potential but multi-drug resistance in Streptococcus suis isolates from healthy and diseased birds

Streptococcus suis is a respiratory commensal of pigs, with some lineages causing serious swine disease and zoonotic disease in humans. In recent years, S. suis has also been isolated from cats, dogs, cattle, sheep, wild boars, and different bird species, including chicken. It is generally assumed that, as in humans, these infections are due to "spillovers" from pigs, but no genomic investigation of respective isolates has yet been performed. This project aimed at investigating the zoonotic potential of these isolates by employing bioinformatics analyses with a special emphasis on host adaptation, virulence, and antimicrobial resistance.

Over the last six years, we collected and whole-genome sequenced S. suis samples from birds in the veterinary diagnostics department of the Freie Universität Berlin. Most of these birds were diseased, and S. suis was isolated among other pathogens. We combined these samples with published genomes of Vietnamese healthy chicken isolates and compared them to S. suis lineages isolated from pigs, wild boars, and human. In addition, to examine potential survival advantages of bird isolates in birds, we performed growth experiments in chicken vs. pig blood.

All the bird isolates clustered phylogenetically within a group of largely commensal isolates of pigs, and distinct from the lineages responsible for most zoonoses, lacking most known virulence genes. Using genome-wide association studies, we detected several unique mobile genetic elements specific to bird isolates, suggestive of S. suis adaptation to birds. Concordantly, S. suis bird isolates showed a better survival in chicken than in porcine blood, although this effect was not significant. Furthermore, bird isolates had a larger genome size than closely related pig isolates. Finally, our analyses revealed that bird isolates were often multi-drug resistant.

In summary, our results imply that S. suis could be persisting in bird populations independently of pigs, at least for short periods of time, but that birds are unlikely to be a source of zoonotic infection in humans. Our study also suggests a potential role for antibiotic resistance in host switching.