Population Gene Introgression and High Genome Plasticity for the Zoonotic Pathogen Streptococcus agalactiae

Area of Science:

• Microbiology
• Genomics
• Evolutionary Biology

Background:

• Bacterial adaptation and gene flow between niches are crucial for pathogen evolution but not fully understood.
• Streptococcus agalactiae, a pathogen with diverse hosts, serves as an ideal model for studying these dynamics.

Purpose of the Study:

• To investigate how bacterial adaptation within species influences gene spillover and transmission across different host niches.
• To analyze genomic data from Streptococcus agalactiae across multiple host species to understand adaptation and gene exchange.

Main Methods:

• Analysis of 901 global genome sequences from Streptococcus agalactiae across nine host species.
• Bayesian clustering for population delineation and comparative genomics for gene gain/loss.
• Phylogenomic and Bayesian migration analyses to detect gene spillover and transmission patterns.

Main Results:

• Twelve bacterial populations were identified, largely corresponding to host niches, with extensive gene gain/loss and a large, partitioned pan-genome.
• Biochemical characteristics were highly distinctive among populations, with enriched dispensable genes under positive selection.
• Gene spillover was detected, notably tetracycline resistance transmission from human-associated to other hosts, with biased human-to-bovine transmission confirmed.

Conclusions:

• High bacterial genome plasticity, driven by niche-specific selection pressures, facilitates adaptation.
• A partitioned dispensable genome supports extensive and ongoing bacterial adaptation across diverse hosts.
• Gene spillover, exemplified by antibiotic resistance, demonstrates a mechanism for rapid adaptation and spread between bacterial populations in different niches.