Building resources to expand genomic epidemiology on the frontline
Healthcare-associated infections (HAIs) are secondary infections that may result after a patient receives medical care or undergoes a medical procedure (e.g., surgery or catheterization). Millions of patients are diagnosed with HAIs every year in the United States. Methicillin-Resistant Staphylococcus aureus (MRSA), Clostridium difficile, and Candida auris are examples of the many HAIs commonly seen in healthcare facilities. Genomic epidemiology is a way to investigate HAI outbreaks and clusters by using pathogen genetic data to determine the spread and distribution within a specific population. One key component of genomic epidemiology is whole genome sequencing, which allows epidemiologists to determine transmission patterns and relatedness.
At TGen, we utilize genomic epidemiology as a tool to characterize and investigate infectious disease outbreaks and want to enhance our ability to support our public health partners, healthcare, and infection control partners in Arizona. To do this, we deployed an anonymous survey to over 350 infection control and healthcare partners in Arizona to gauge their interest in and capacity to incorporate genomic epidemiology as a complementary tool for the investigation of HAI outbreaks and clusters. The survey asked about respondent demographics, current practice and perceptions, as well as engagement in genomic epidemiology. The survey responses helped guide the creation of internal genomic investigation workflow documents and development of guidance resources for partners.
We received 10 responses; 80% of respondents stated their facility had previously engaged in an epidemiology investigation (e.g., sending samples for genomic sequencing). The most common HAIs of outbreak concern listed by the respondents were C. auris, Carbapenem-resistant Enterobacteriaceae (CRE), C. difficile, and MRSA. Cost and general availability of resources were identified as barriers to applying genomic epidemiology in the healthcare setting. Respondents also commented that more information about TGen’s sample-processing workflow would be helpful to their own investigations.
In order to successfully expand the use of genomic epidemiology and better support our partners in Arizona, we developed an internal intake form and workflow document on which to base a more organized system for conduction of genomic epidemiology investigations. We also developed an external guidance document, outlining the general workflow and guidelines for sample submission, and provided responses for frequently asked questions. This document will be shared with infection control and healthcare partners in Arizona; we hope it will support continued relationship building and enhanced genomic epidemiology capacity in these settings.