The morbidity and mortality associated with chronic and acute infections are substantial, and antimicrobial-resistant pathogens are a global threat. Although there are numerous methods that can be used to identify a pathogen and its resistance profile, these methods are often time-consuming, may be inaccurate, and/or fail to provide sufficient information for the clinical management of individual patients or to reduce the public health impact of an outbreak. Next-generation sequencing (NGS) methods may provide an accurate identification of the causative agent(s) of an infection more rapidly than conventional methods, and may direct treatment based on antimicrobial resistance genes of the pathogens. This report evaluates the clinical utility of NGS methods for microbial outbreak investigation.

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