Genome-wide approaches to bacterial strain typing: a history and review of recent methodological advances

PURPOSE OF REVIEW: Whole genome sequencing (WGS) has transformed bacterial strain typing, an essential tool for outbreak detection, antimicrobial resistance surveillance, and tracking clonal emergence across clinical, research, and public health settings. Herein, we will review recent advances in WGS-based bacterial strain typing methods for purposes of comparison and classification with a focus on improvements in variant identification, strain classification, and transmission assessment. RECENT FINDINGS: Advances in sequencing technologies as well as variant calling methodologies and parameter optimization have enhanced the precision and accuracy of single nucleotide variant identification. Hierarchical clustering of gene-by-gene strain typing, combined with novel data management and classification strategies, has improved standardized pathogen typing schemes in an effort to streamline inter-laboratory comparison. Additionally, novel approaches to defining transmission thresholds now better account for species-specific traits, while progress in metagenomic sequencing enables strain identification and tracking within mixed microbial communities. SUMMARY: Recent developments have enhanced the accuracy, portability, scalability, and standardization of bacterial typing methods, integrating variant calling and gene-by-gene approaches into unified genotyping systems. However, challenges still remain in nomenclature consistency, inter-laboratory variant calling compatibility, and capturing bacterial heterogeneity. Future work should focus on refining genotyping frameworks to enhance surveillance and optimize detection of pathogen transmission while accounting for microbial diversity across various environments.