Streptococcus suis infection on European farms is associated with an altered tonsil microbiome and resistome

Abstract

Introduction Streptoccocus suis is a Gram-positive opportunistic pathogen causing systemic disease in piglets around weaning age. Outbreaks of S. suis disease are controlled by metaphylactic use of antibiotics, leading to high levels of antimicrobial resistance in S. suis isolates. This is an issue for both animal and human health due to the zoonotic disease potential of S. suis. The mechanisms facilitating invasive disease are not known but may involve host and environmental factors. The palatine tonsils are considered a portal of entry for pathogenic strains to cause systemic disease. We hypothesised that tonsil colonization by pathogenic and commensal bacteria may impact on disease risk via colonization resistance and co-infections. We conducted a case-control study on 9 European farms, comparing the tonsil microbiome of piglets with S. suis systemic disease with asymptomatic controls. We also compared these to piglets on control farms and piglets reared naturally in a forest. Results We found a small but significant difference in the tonsil microbiota composition of case and control piglets. Case-control associations varied between amplicon sequence variants (ASVs) and metagenome assembled genomes (MAGs) within the same species. Variants of putatively commensal taxa including Rothia nasimurium were reduced in abundance in case piglets compared to asymptomatic controls. Case piglets had higher relative abundance of Fusobacterium gastrosuis, Bacteroides heparinolyticus, and uncultured Prevotella and Alloprevotella species. There was, however, no higher abundance of S. suis itself at the species-level or of clinical strain marker genes in case piglets. Piglets sampled prospectively weeks prior to developing clinical signs had reduced microbiota alpha diversity. Despite case-control pairs receiving equal antimicrobial treatment, case piglets had higher abundance of antimicrobial resistance genes (ARGs) conferring resistance to antimicrobial classes used to treat S. suis. Conclusions The tonsillar microbiota of S. suis case piglets had increased abundance of taxa not previously linked to S. suis disease. This coincided with increased ARG abundance in case piglets, possibly due to adaptation of the disease-associated microbiota to frequent antimicrobial treatment.

Transcriptomics in serum and culture medium reveal shared and differential gene regulation in pathogenic and commensalStreptococcus suis

“…We isolated DNA from overnight cultures using the PowerSoil DNA Isolation Kit (Qiagen). Generation of short-read sequencing data for the strains from Germany, Canada, and the UK has been previously reported [2, 3, 20]. Strains without available short-read sequencing data were 250 bp paired-end sequenced using an Illumina HiSeq 2500 instrument by MicrobesNG (Birmingham, UK).…”

“…Clinical and non-clinical strains are, however, found in all clades, showing that pathogenic lineages can colonize the oral cavity of asymptomatic pigs at low abundance and that commensal lineages can invade the host in certain circumstances. Recent microbiome studies have confirmed that commensal S. suis colonize the oral cavity of piglets at high abundance [3–5].…”

Environmental and maternal factors shaping tonsillar microbiota development in piglets

“…These studies used antimicrobial growth promoters, and the described microbiota development may vary from Europe where these are banned. Regardless, the increase in Streptococcaceae family abundance is of interest because correlations between S. suis, carbohydrate availability, and microbiota composition have been linked to S. suis virulence and disease risk [9,10,[14][15][16].…”

The piglet tonsillar microbiome and Streptococcus suis disease

“…These studies used antimicrobial growth promoters, and the described microbiota development may vary from Europe where these are banned. Regardless, the increase in Streptococcaceae family abundance is of interest because correlations between S. suis, carbohydrate availability, and microbiota composition have been linked to S. suis virulence and disease risk [8,78,102,149,150] .…”

“…These processes may lead to increased ARG abundance (resistome expansion) in disease-associated microbiomes. While some studies have theorised this mechanism to explain differences in ARG abundance between groups [150,[184][185][186][187] , a comprehensive overview of disease-associated resistomes is lacking. It is not known what resistome differences can be expected based on factors other than natural selection from antibiotic exposure.…”