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Rutgers Developing PCR Assays to Detect Superbug in Hospitals


NEW YORK (360Dx) – Under a recent Centers for Disease Control and Prevention contract, Rutgers University is validating PCR and real-time PCR assays that could one day be used by hospitals to quickly identify Candida auris, an emerging multidrug-resistant fungal pathogen.

The pathogen is difficult to identity, often does not respond to antifungal drugs, and causes invasive infections that are often acquired in hospitals and are associated with high mortality in patients.

In October, the CDC awarded Rutgers a $300,000 contract over two years as part of its Antibiotic Resistance Solutions Initiative. David Perlin, executive director of the Public Health Research Institute at Rutgers New Jersey Medical School, said in an interview that the university will leverage the CDC funding to conduct clinical testing of its C. Auris test currently in development.  

Perlin, along with a CDC researcher and an international team of investigators consisting of researchers from Delhi, India, and Medellin, Colombia, recently published the results of a study in the Journal of Clinical Microbiology, demonstrating the utility of their tests.

The group demonstrated two types of assays, a PCR test and real-time PCR test, that identified C. auris and related species — including Candida duobushaemulonii, Candida haemulonii, and Candida lusitaniae — and they are now progressing to testing the assays in hospital settings.

The results from the assays were 100 percent concordant with DNA sequencing results, the researchers noted, adding that the molecular assays overcome the deficiencies of existing phenotypic tests to identify C. auris and related species.

"Our tests look directly at DNA sequences that define and are unique to Candida auris," Perlin said. They have "extreme specificity" and can be completed within two hours, he added.

The PCR assay is a low-tech version of the real-time PCR assay, which can be used with real-time devices present in most clinical labs to detect bacteria and viruses, Perlin said. "In principle, the PCR assay can be used in low-resource environments," such as developing countries and rural centers, he added.

Quick and early detection of the pathogen is vital to positive patient outcomes.

“It is essential to rapidly and accurately identify Candida auris in patients, because choosing the right therapy for this mostly drug-resistant pathogenic organism will dictate the probability for a successful clinical outcome," Perlin said, adding that "as C. auris can spread in healthcare facilities, it is essential to detect it accurately to implement infection control measures.”

Perlin noted that "what makes Candida auris so unique is its ability to develop drug resistance and then to be transmitted much more readily than we would normally see."

This is significant for a couple of reasons, he said, adding that there are few antifungal drugs available to treat these infections, and "what we found with this organism is that it is highly virulent and produces a high mortality. It has another unique property for a yeast-type infection in that it can be transmitted from patient to patient and into the environment."

Globally, nearly 1.4 million deaths a year are attributed to invasive fungal infections, which is on par with deadly diseases like tuberculosis. In 2016, the CDC released an alert advising that C. auris is an emerging pathogen causing invasive infections due to the challenging identification, common multidrug resistance, and outbreaks in healthcare settings.

Earlier, in 2009, the pathogen was first isolated from the external ear discharge of a patient in Japan. That same year, several other countries, including South Korea, India, Pakistan, Kuwait, Israel, South Africa, the UK, Spain, the US, Colombia, and Venezuela, also reported infections.

In the US, most infections have been observed in New York and New Jersey hospitals, Perlin said.

The CDC reported that as of Oct. 20, there were 166 confirmed and probable infections due to the yeast in the US, and infections have been observed in 10 states. It is prevalent in patients who have been in a hospital for an extended duration, who have lines or tubes entering their bodies, or who have previously received antibiotics or antifungal medications. And the pathogen is frequently observed in patients who are immunosuppressed, Perlin noted.

"Typically, what we see with Candida infections, which are particularly invasive, is that they are associated with colonization in, for example, the gastrointestinal tract, the oral cavity, or the vaginal tract, and if you become immunosuppressed, as these patients tend to be, you see a blood-stream infection," he added.

The infection presents a challenge for in vitro diagnostic test makers. "One of the outstanding issues with this organism, and one of the reasons it flew under the radar for a while, is that it just did not show up in commercial tests that we use to detect fungal infections, whether they are growth-based assays, or they use molecular or MALDI-TOF rapid detection methodologies," Perlin said.

T2 Biosystems Chief Scientific Officer Tom Lowery said in an interview that presently "a patient is not known to be colonized or infected until weeks after samples are obtained." He added that "a high sensitivity, direct-from-specimen test" is necessary to being able to intervene with an outbreak and make treatment decisions for patients known to be infected or colonized with the superbug.

Lowery told 360Dx that the firm has plans to soon make available a research-use-only swab sample test. "This should enable laboratories to validate the swab test internally and then use it to detect the pathogen in hospitals," he said.

Perlin noted that there are two key factors in containing a C. auris epidemic —  developing molecular tools to identify the pathogen reliably and rapidly, and developing a better understanding of its genetic profile to understand why it facilitates transmission within hospital environments.

As part of the CDC contract, he is working with Rutgers postdoctoral fellow Milena Kordalewska to develop their PCR-based tests to detect C. auris in swabs from patients in hospitals.

They will also analyze transmission patterns in New Jersey healthcare facilities using genetic fingerprint technology, in collaboration with Thomas Kirn, medical director of the Public Health Laboratory Service at the New Jersey Department of Health.

Other than validating molecular tools, looking at some of the underlying genetic properties of C. Auris is an important part of the research being done as part of the CDC-funded project. "We know that there are different clades of the infection, including North American and Asia clades, and we are trying to understand if there are differences in the genetic background that are important for transmission of these organisms," Perlin said.

He said that the team is using molecular-fingerprint tools to do this. "We'll look at the genetic and genomic structure of infecting and transmitting organisms to see if they are different," he said. That work involves "the use of genetic tests, including sequencing and random amplified polymorphic detection, to see if it's the same organism or variants that are being transmitted," he said.

Perlin and his team also have an objective to deploy their PCR-based diagnostic tests in hospitals to implement infection control measures and management of patients.

He noted that he has spoken to the US Food and Drug Administration about the development of the test and what could be required for its clearance. "The studies we are conducting now will dictate how we implement the assay and the best path forward for regulatory approval," Perlin said.

He noted that the BioFire business of BioMérieux and T2 Biosystems are among several in vitro diagnostic companies with whom he has had discussions. "We would like to put together a commercial product with a partner who can take this forward, whether it is exactly what we have or a modified form," he added.

He noted that standard laboratory tests are being refined to try to pick up this pathogen. "As of today, the best types of tests for this are molecular tests — either our tests or related types of tests that other groups have developed in-house to detect this organism," he said.

In September, T2 Biosystems announced that it agreed with the CDC to utilize its T2Dx instrument in its laboratory for testing and monitoring the emergence and outbreaks of Candida auris in hospitals around the US.

The use of the T2Dx Instrument for the detection of Candida auris represents multiple, new applications of the T2MR platform, the firm said, including for testing patient skin and blood samples and for environmental surveillance to monitor outbreaks and the spread of the superbug. These applications are now available as research tools for investigational purposes in the US and Europe, T2 said.

In August, the CDC announced that it had awarded $201 million to programs to help state and local governments address infectious disease threats using genomics and other technologies.

Of the total funding, $77 million has been set aside to help state health departments combat antibiotic-resistance threats by increasing nationwide testing for Candida auris; improving national tuberculosis surveillance through the establishment of a new national laboratory — dubbed the National TB Molecular Surveillance Center — that will be equipped to perform DNA sequencing of Mycobacterium tuberculosis bacteria from newly diagnosed patients; and enhancing the detection of drug-resistant gonorrhea using whole-genome sequencing.

The CDC has awarded more than $9 million to 25 investigators to pilot innovative solutions and explore knowledge gaps about antibiotic resistance related to the human microbiome, healthcare settings, and surface water and soil.

The awards are part of the CDC's Antibiotic Resistance Solutions Initiative and are intended to grow the agency’s approaches to combat antibiotic resistance. In fiscal years 2016 and 2017, the initiative awarded more than $24 million to investigators to fight antibiotic resistance.