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Authors
Lu, Dan
Kalantar, Katrina L.
Glascock, Abigail L.
Chu, Victoria T.
Guerrero, Estella S.
Bernick, Nina
Butcher, Xochitl
Ewing, Kirsty
Fahsbender, Elizabeth
Holmes, Olivia
Hoops, Erin
Jones, Ann E.
Lim, Ryan
McCanny, Suzette
Reynoso, Lucia
Rosario, Karyna
Tang, Jennifer
Valenzuela, Omar
Mourani, Peter M.
Pickering, Amy J.
Raphenya, Amogelang R.
Alcock, Brian P.
McArthur, Andrew G.
Langelier, Charles R.
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Funding
Funding for this research was provided by:
Chan Zuckerberg Initiative
Chan Zuckerberg Biohub
NIH/NHLBI (5R01HL155418, 5R01HL155418, 5R01HL155418)
Canadian Institutes of Health Research (PJT-156214, PJT-156214, PJT-156214)
McMaster University (David Braley Chair in Computational Biology)
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Article History
Received: 10 June 2024
Accepted: 23 April 2025
First Online: 6 May 2025
Declarations
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: This research conformed to the principles of the Helsinki Declaration.Skin swabs and cultured isolates analyzed for Application 2 (hospital outbreak) were collected under the University of California San Francisco (UCSF) Institutional Review Board (IRB) protocol no. 17–24056. A waiver of consent was granted for swab collection given that the primary purpose was for monitoring and preventing transmission of healthcare-associated pathogens in the hospital, in coordination with the UCSF Department of Hospital Epidemiology and Infection Prevention.Samples analyzed for Application 4 (longitudinal profiling) were collected from patients enrolled in a prospective cohort study of mechanically ventilated children admitted to eight intensive care units in the National Institute of Child Health and Human Development’s Collaborative Pediatric Critical Care Research Network (CPCCRN) from February 2015 to December 2017. The original cohort study was approved by the Collaborative Pediatric Critical Care Research IRB at the University of Utah (protocol no. 00088656). Details regarding enrollment and consent have previously been described [, ]. Briefly, children aged 31 days to 18 years who were expected to require mechanical ventilation via endotracheal tube for at least 72 h were enrolled. Parents or other legal guardians of eligible patients were approached for consent by study-trained staff as soon as possible after intubation. To permit sample collection as early as possible following intensive care unit admission, the IRB granted an initial waiver of consent for the collection of endotracheal aspirate by standard-of-care suctioning. Parents or guardians were then approached for informed consent, and samples were only retained and analyzed if written informed consent for participation in the study was provided.For all other applications and analyses, previously published datasets were used as described in the data and code availability section.
: Not applicable.
: The authors declare no competing interests.
