Streptococcus suis adaptation to the host environment: genome-wide identification of fitness determinants using tn-seq and Nanopore sequencing

Streptococcus suis is a zoonotic agent capable of inducing sepsis and meningitis in both pigs and humans, causing substantial economic losses. Cross-protective vaccines are not available and antibiotics are commonly used to control the spread of S. suis on farms. This increases the development and spread of antimicrobial resistance drawing attention of the global health community [1]. Alternatives to the currently most often used antibiotics are crucial, requiring research on identifying new therapeutic targets. This is a challenging goal because a large proportion of S. suis genes and proteins only have predicted functions. A better understanding of the virulence factors required for survival and growth in the host environments during colonization and invasive disease would be valuable strategy to identify new therapeutic targets. Here, we present the construction of a highly saturated transposon library in S. suis P1/7 and high-throughput transposon sequencing screen (Tn-Seq) for fitness determinants in body fluids.

The mutant strain library was screened in porcine serum and cerebrospinal fluid extracted from choroid plexis organoids, representing early and late (meningitis-associated) stages of the infection, respectively. After growing the library, mutants were collected and sequenced using Nanopore, achieving fast in-house, accurate results. The Tn-Seq data analysis pipeline was updated to incorporate nanopore reads for the identification of gene disruptions that are significantly affecting growth in these conditions.

We characterized a nucleoside ABC transporter and a novel sensory system which are essential for proliferation in serum. Additionally, a small putatively exported protein played a crucial role in growth in both fluids. Our study highlights the relevance of functional characterization of genes mediating S. suis survival in diverse host body fluids. Further research into the roles that the conditionally essential genes play in S. suis pathogenicity and survival might eventually allow us to find novel ways to control or prevent S. suis disease.

[1] Dechêne-Tempier et al. (2021) Microorganisms. 18;9(8):1765.