Faculty, Staff and Student Publications
Language
English
Publication Date
8-1-2025
Journal
Current Opinion in Infectious Diseases
DOI
10.1097/QCO.0000000000001118
PMID
40464921
PMCID
New NIH Public Access Policy Effective as of July 1 - MLA,PMC12237114
PubMedCentral® Posted Date
6-12-2025
PubMedCentral® Full Text Version
Post-print
Abstract
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.
Keywords
Humans, Bacteria, Whole Genome Sequencing, Genome, Bacterial, Bacterial Typing Techniques, Bacterial Infections, gene-by-gene strain typing, hierarchical clustering, metagenomics, transmission threshold, variant calling
Published Open-Access
yes
Recommended Citation
, "Genome-Wide Approaches to Bacterial Strain Typing: A History and Review of Recent Methodological Advances" (2025). Faculty, Staff and Student Publications. 1091.
https://digitalcommons.library.tmc.edu/uthsph_docs/1091