Early Genomic Surveillance Leads to a Decrease in Candida Auris Cases

As Candida auris continues to emerge as a serious global health threat, one institution’s proactive approach to genomic surveillance is demonstrating how early intervention and real-time data can prevent hospital-based outbreaks. By combining advanced sequencing technologies with strict infection prevention strategies, clinicians and researchers are gaining critical insights into transmission patterns, drug resistance, and containment.

At the core of this effort is pathogen genomic surveillance, a process that uses next-generation sequencing to analyze the genetic makeup of high-risk organisms. This includes not only Candida auris, but also other concerning pathogens such as carbapenem-resistant Enterobacterales, extensively drug-resistant Shigella, and tuberculosis. According to the expert interviewed, this approach allows teams to “establish the genomic profile of these important pathogens” and use real-time data to detect trends, identify transmission links, and guide both infection control and treatment decisions.

Back in 2018, UCLA Health started utilizing genomic surveillance on C auris and published the first report on the west coast in 2019. They then summarized the clinical and genomic characteristics for more than 30 Cases of C auris in 2022.

“We are lucky that we started early,” said Shaun Yang, PhD, D(ABMM), associate clinical professor, UCLA Department of Pathology and Laboratory Medicine. “If you want to prevent anything, you want to do as early as possible—don’t wait until things get out of control.” By 2019, the team had implemented active screening protocols, including PCR testing of high-risk patients and collaboration with infection prevention specialists to identify those most likely to carry the organism.

They continue the screening and surveillance program. Due to their efforts their hospitals haven't had any large outbreaks except for a small cluster with only 2 patients involved in the last several years, highlighting the effectiveness of active genomic surveillance to prevent C auris outbreaks.

Patients meeting specific risk criteria, such as recent stays in long-term care facilities or travel from outbreak regions, are screened upon admission using skin swabs. If Candida auris is detected, isolation precautions are immediately implemented. In many cases, the organism is cultured and sequenced, enabling detailed phylogenetic analysis to determine how closely related different cases are and whether transmission has occurred.

This active surveillance is complemented by passive methods, in which all Candida species identified in the lab are further analyzed to detect unexpected cases. Together, these approaches have allowed the institution to identify more than 99% of colonized or infected patients.

Despite identifying over 200 cases since 2019—most of them colonization rather than active infection—the hospital system has avoided internal outbreaks.

“In the past six years until now, [we have] had no major outbreak,” Yang said.

Even when 2 genetically similar cases appeared in the same unit, whole genome sequencing enabled rapid identification of a potential link, prompting targeted infection control measures that prevented further spread.

The broader national picture, however, tells a different story. Following the COVID-19 pandemic, Candida auris cases surged across the United States, particularly in states like Nevada and Arizona. Increased healthcare strain, staffing shortages, and resource limitations contributed to widespread transmission. “That’s really the time Candida auris took off nationwide,” said Yang, highlighting the contrast with their institution’s preparedness.

Genomic surveillance has also revealed important shifts in the pathogen’s epidemiology. Initially dominated by a single clade, the local Candida auris population has become more diverse over time due to interstate patient movement.

“It really went from a more kind of a monoclonal local spread to now…a cross-state, nationwide spread,” he said. This evolution underscores the importance of continuous monitoring.

Equally critical is the role of genomic data in understanding drug resistance. While Candida auris is often resistant to older antifungals like fluconazole, the institution has found that first-line echinocandin therapies remain effective.

“We sequenced over 200 Candida auris isolates…and we haven’t found any mutations that can lead to resistance,” said Yang. This has allowed clinicians to confidently continue using standard treatments without widespread treatment failure.

Beyond guiding therapy, genomic surveillance enhances infection prevention efforts by improving efficiency and reducing unnecessary interventions. By quickly distinguishing between related and unrelated cases, teams can focus resources where they are most needed.

“Genomic surveillance is extremely powerful…it actually improves the efficiency and cost effectiveness for infection prevention,” Yang said.

Ultimately, this model demonstrates how integrating genomic data into routine clinical practice can transform how hospitals respond to emerging pathogens. With Candida auris continuing to spread in the community, sustained vigilance—and early action—remain essential to keeping healthcare settings safe.