PathoSPOT genomic epidemiology reveals under-the-radar nosocomial outbreaks
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RESEARCH
Open Access
PathoSPOT genomic epidemiology reveals under-the-radar nosocomial outbreaks Ana Berbel Caban1†, Theodore R. Pak2†, Ajay Obla2, Amy C. Dupper1, Kieran I. Chacko2, Lindsey Fox1, Alexandra Mills1, Brianne Ciferri2, Irina Oussenko2, Colleen Beckford2, Marilyn Chung2, Robert Sebra2,3,4,5, Melissa Smith2,3, Sarah Conolly6, Gopi Patel1,6, Andrew Kasarskis2,3,7, Mitchell J. Sullivan2, Deena R. Altman1,2† and Harm van Bakel2,3*†
Abstract Background: Whole-genome sequencing (WGS) is increasingly used to map the spread of bacterial and viral pathogens in nosocomial settings. A limiting factor for more widespread adoption of WGS for hospital infection prevention practices is the availability of standardized tools for genomic epidemiology. Methods: We developed the Pathogen Sequencing Phylogenomic Outbreak Toolkit (PathoSPOT) to automate integration of genomic and medical record data for rapid detection and tracing of nosocomial outbreaks. To demonstrate its capabilities, we applied PathoSPOT to complete genome surveillance data of 197 MRSA bacteremia cases from two hospitals during a 2-year period. Results: PathoSPOT identified 8 clonal clusters encompassing 33 patients (16.8% of cases), none of which had been recognized by standard practices. The largest cluster corresponded to a prolonged outbreak of a hospital-associated MRSA clone among 16 adults, spanning 9 wards over a period of 21 months. Analysis of precise timeline and location data with our toolkit suggested that an initial exposure event in a single ward led to infection and longterm colonization of multiple patients, followed by transmissions to other patients during recurrent hospitalizations. Conclusions: We demonstrate that PathoSPOT genomic surveillance enables the detection of complex transmission chains that are not readily apparent from epidemiological data and that contribute significantly to morbidity and mortality, enabling more effective intervention strategies. Keywords: PathoSPOT, Nosocomial outbreaks, Whole-genome sequencing, Visualization toolkits, MRSA bacteremia
* Correspondence: [email protected] † The authors Ana Berbel Caban and Theodore R. Pak contributed equally to this work. † The authors Deena R. Altman and Harm van Bakel are co-senior authors on this work. 2 Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York City, NY, USA 3 Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA Full list of author information is available at the end of the article © The Author(s). 2020 Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the arti
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