Rapid Microbial Typing Technologies for Outbreak Control and Public Health

Timely and accurate microbial typing is a cornerstone of infectious disease surveillance, outbreak investigation, and public health response. Conventional typing methods, although robust, are often limited by long turnaround times and limited scalability, which can delay interventions during rapidly evolving outbreaks. In the context of emerging pathogens, antimicrobial resistance (AMR), and increasing global interconnectedness, there is an urgent need for rapid, portable, high-throughput and high-resolution microbial typing technologies that can support real-time decision-making. To address this need, recent advances in genomics, spectroscopic and spectrometry methods, and bioinformatics have revolutionized microbial typing. Moving beyond traditional centralized laboratories, these fields are driving the deployment of portable sequencing platforms, microfluidic systems, and automated analytical pipelines. This technological shift is pivotal for enabling real-time analysis and is particularly critical for implementation in resource-limited settings. Despite rapid advances, challenges remain in validating accuracy and cost-effectiveness, defining standards across outbreak scenarios, and harmonizing data across infrastructures, and resource settings. Bridging the gap between high-tech innovation and practical implementation in resource-limited settings is essential to democratize outbreak control. Machine-learning approaches are increasingly supporting real-time analysis, but their effective use depends on smooth integration with epidemiological and surveillance systems. Linking rapid typing data with clinical and environmental metadata under a One Health framework is essential for timely outbreak detection and control. Persistent barriers in standardization, interoperability, and equitable access highlight the need for multidisciplinary collaboration to translate innovation into public health impact. This Research Topic aims to showcase cutting-edge developments and applications of rapid microbial typing technologies for outbreak control and public health, promoting the shift from retrospective to prospective, real-time surveillance studies, including: • Genomic and metagenomic sequencing approaches (e.g., short- and long-read sequencing)• Spectroscopic, spectrometric and other phenotypic methods (e.g., FT-IR, MALDI-TOF MS, Raman)• Rapid antimicrobial resistance (AMR) typing and profiling (e.g., NG-STAR, MALDI-TOF mass spectra) for timely treatment optimization• Targeted molecular assays for rapid, scalable and cost-effective screening• Advances in bioinformatics pipelines for rapid typing and nomenclature standardization (e.g., LIN codes)• Artificial intelligence, machine-learning and algorithms for real-time analysis• Benchmarking accuracy and comparative studies between rapid and reference methods• Integration of rapid typing data into outbreak investigation and real-time surveillance. By bringing together methodological innovations and applied studies, this collection provides the evidence base needed to guide integration of rapid microbial typing into routine clinical and public health practice.This Research Topic welcomes the following article types: FAIR² DATA Direct Submission, FAIR² Data, Hypothesis and Theory, Methods, Mini Review, Opinion, Original Research, Perspective, Review, Systematic Review, and Technology and Code. Topic editors: Ana R. Freitas, Angela Novais, Natacha Couto Source: https://www.frontiersin.org/research-topics/78285/rapid-microbial-typing-technologies-for-outbreak-control-and-public-health