Waggle, Kady D
(2024)
Methods and Analysis of a Whole Genome Sequencing Surveillance Approach for Enhanced Detection of Outbreaks in a Hospital Setting.
Master's Thesis, University of Pittsburgh.
(Unpublished)
Abstract
Background: Outbreaks of healthcare-associated infections (HAI) result in substantial patient morbidity and mortality. Mitigation efforts by infection prevention teams have the potential to curb outbreaks and prevent transmission to additional patients. The incorporation of whole genome sequencing (WGS) surveillance of suspected high-risk pathogens often identifies outbreaks that are not detected by traditional infection prevention methods and provides evidence for transmission. Our approach to real-time WGS surveillance, the Enhanced Detection System for Healthcare-Associated Transmission (EDS-HAT), has both identified serious outbreaks that were otherwise undetected and shown the potential to be cost saving because HAIs are expensive to treat and WGS has become relatively inexpensive.
Aims: This thesis aims to describe the weekly laboratory and bioinformatics methods of EDS-HAT as well as characterize antibiotic profiles of isolates within a subset of significant clusters detected by EDS-HAT. A genotype and phenotype concordance analysis was conducted to further characterize the antibiotic resistance profiles of the isolates. Finally, this thesis provides a cost analysis for the associated supplies, reagents, and staff salaries for performing the weekly WGS surveillance workflow.
Results: In an average week at our tertiary healthcare system, we sequenced 48 samples at a cost of less than $100 per sample, inclusive of laboratory reagents and staff salaries. The turnaround time from sample collection to data reporting to the infection prevention and control team was approximately ten days. Of three clusters explored, all clusters had a 100% phenotypic concordance rate, and two of three clusters had a 100% genotypic concordance rate.
Conclusions: Our findings demonstrate that performing EDS-HAT WGS surveillance in real-time can be both affordable and time-efficient. Providing timely information to aid in outbreak investigations can identify transmission events sooner with the goal to improve patient outcomes.
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Details
| Item Type: |
University of Pittsburgh ETD
|
| Status: |
Unpublished |
| Creators/Authors: |
|
| ETD Committee: |
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| Date: |
27 June 2024 |
| Date Type: |
Publication |
| Defense Date: |
18 June 2024 |
| Approval Date: |
27 June 2024 |
| Submission Date: |
21 June 2024 |
| Access Restriction: |
2 year -- Restrict access to University of Pittsburgh for a period of 2 years. |
| Number of Pages: |
53 |
| Institution: |
University of Pittsburgh |
| Schools and Programs: |
School of Public Health > Infectious Diseases and Microbiology |
| Degree: |
MS - Master of Science |
| Thesis Type: |
Master's Thesis |
| Refereed: |
Yes |
| Uncontrolled Keywords: |
Healthcare-Associated Transmission; Bacteria, Antimicrobial Resistance, Whole Genome Sequencing; Laboratory Methods; Cost Analysis |
| Date Deposited: |
27 Jun 2024 18:40 |
| Last Modified: |
27 Jun 2024 18:40 |
| URI: |
http://d-scholarship.pitt.edu/id/eprint/46611 |
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