@inbook{645f6efcdf424cd9a44f7f61070c0e70,
title = "Application of Pathogen Genomics to Outbreak Investigation",
abstract = "Outbreaks are a risk to public health particularly when pathogenic, hypervirulent, and/or multidrug-resistant organisms (MDROs) are involved. In a hospital setting, vulnerable populations such as the immunosuppressed, intensive care patients, and neonates are most at risk. Rapid and accurate outbreak detection is essential to implement effective interventions in clinical areas to control and stop further transmission. Advances in the field of whole genome sequencing (WGS) have resulted in lowered costs, increased capacity, and improved reproducibility of results. WGS now has the potential to revolutionize the investigation and management of outbreaks replacing conventional genotyping and other discrimination systems. Here, we outline specific procedures and protocols to implement WGS into investigation of outbreaks in healthcare settings.",
keywords = "Bacterial pathogens, Outbreak, Short-read sequencing, Typing, Whole-genome sequencing",
author = "Parcell, {Benjamin J.} and Pettigrew, {Kerry A.} and Katarina Oravcova",
note = "Publisher Copyright: {\textcopyright} The Author(s), under exclusive license to Springer Science+Business Media, LLC, part of Springer Nature 2024.",
year = "2024",
month = jul,
day = "2",
doi = "10.1007/978-1-0716-3981-8_16",
language = "English",
isbn = "9781071639801",
series = "Methods in Molecular Biology",
publisher = "Humana Press",
pages = "161--183",
editor = "Gillespie, {Stephen H.}",
booktitle = "Antibiotic Resistance Protocols",
address = "United States",
edition = "4",
}
