Serotype-specific evolutionary patterns of antimicrobial-resistant Salmonella enterica

Area of Science:

• Genomics
• Evolutionary Biology
• Microbiology

Background:

• Antimicrobial-resistant (AMR) Salmonella enterica strains threaten public health in humans and animals.
• Studied genome-wide evolution of 90 AMR S. enterica isolates from three serotypes: S. Dublin, S. Newport, and S. Typhimurium.

Purpose of the Study:

• To investigate the genome-wide evolutionary patterns of AMR Salmonella enterica.
• To understand the association between serotype and genome content in AMR Salmonella.
• To explore the role of positive selection in AMR, host adaptation, and serotype diversification.

Main Methods:

• Genome-wide analysis of 90 Salmonella enterica AMR isolates.
• Comparative genomics across three serotypes (S. Dublin, S. Newport, S. Typhimurium).
• Phylogenetic analysis and identification of selection pressures.

Main Results:

• S. Typhimurium showed high diversity, large population size, and frequent positive selection/recombination.
• S. Newport exhibited a clonal structure with low diversity.
• S. Dublin displayed evidence of a population bottleneck, genome decay, and increased pseudogenes.
• Accessory genes, including AMR and prophage genes, were serotype-specifically over/under-represented.
• Core genes clustered phylogenetically by serotype, including the AMR gene aac(6')-Iaa.
• Positive selection targeted cell surface proteins and proteins involved in AMR and virulence.

Conclusions:

• Strong association exists between S. enterica genome content and serotype.
• Evolutionary patterns suggest multiple AMR emergence events for S. Typhimurium.
• AMR in S. Newport likely emerged from a single lineage (Lineage IIC).
• S. Dublin's bottleneck and genome decay align with its narrow host range.
• Positive selection plays a significant role in AMR evolution, host adaptation, and serotype diversification in Salmonella.