The deadly, drug-resistant infection is wreaking havoc in hospitals; what can laboratories do to identify it?

When most people think about yeasts, the smell of fresh-baked bread, or taste of a hoppy IPA or a bold Cabernet may come to mind. But yeasts can also be the source of life-threatening infections.

Yeasts are a type of fungi that are defined as eukaryotic single-celled microorganisms. There have been over 1,500 different species of yeasts discovered and are found everywhere in the environment: air, soil, skin, our gut, and food.

Figure 1. Electron microscope image of C. auris

There are a number of common illnesses caused by fungal infections, commonly referred to as mycosis. For example, ringworm and athlete’s foot are caused by filamentous fungi, whereas thrush and some vaginal infections are caused by yeast. These illnesses are treatable with over-the-counter or prescription medication.

However, yeast infections stemming from Candida auris, a germ putting many hospitals on high alert, can also lead to more serious illnesses due to its demonstrated multi-drug resistance. Over 600 cases of C. auris have been reported thus far in the US—mostly in New York, New Jersey, and Illinois—and nearly half who contract the infection die within 90 days, according to the US Centers for Disease Control and Prevention (CDC). Clinical laboratories that identify cases are required to report infections to state and local health departments and to the CDC.

C. auris was discovered in 2009 in Japan and has rapidly spread around the world. It can trigger a local ear or wound infection or cause a more dangerous systemic infection of the bloodstream. The population at greatest risk of acquiring C. auris is immunocompromised patients. The first clinical signs are fever and chills, which are easily masked by other medical conditions. Healthcare facilities are most often impacted, and special cleaning agents are required to adequately sanitize patient rooms and medical equipment.

What makes C. auris so dangerous is that it typically is resistant to major antifungal medications. There are three different classes of antifungal drugs: triazoles, polyenes, and echinocandins; about 90% of C. auris cases are resistant to at least one of the drugs, and some strains are resistant to all three. This resistance is why it’s been so difficult to control the outbreaks.

Another confounding factor is the difficulty in identifying Candida auris. There are three different methods for microbial identification: phenotypic, proteotypic, and genotypic. Phenotypic identifications are based off biochemical and metabolic analysis. The CDC states that “C. auris can be misidentified as a number of different organisms when using traditional phenotypic methods for yeast identification such as VITEK 2 YST, API 20C, BD Phoenix yeast identification system, and MicroScan.” These phenotypic methods were originally designed for clinical applications, but still can have difficulty resolving closely related species based on technical and reference database limitations.

Identification Method

Organism Name by Which C. auris Can Be Misidentified

VITEK 2 YST

Candida haemulonii
Candida duobushaemulonii

API 20C

Rhodotorula glutinis 
(characteristic red color not present)
Candida sake

BD Phoenix yeast identification system

Candida haemulonii
Candida catenulate

MicroScan

Candida famata
Candida guilliermondii
Candida lusitaniae

Candida parapsilosis

RapID Yeast Plus

Candida parapsilosis

 

The CDC thus recommends using proteotypic or genotypic methods for C. auris identification. Proteotypic IDs use MALDI-TOF technology to analyze the protein spectra of the microbial cell and compare it to a library of known organisms. Genotypic identifications consist of DNA sequencing, specifically the ITS2 DNA region for fungal identification, and is known as the “gold standard” for providing an identification. Due to the analytical and precise nature of these two technologies, both methods have higher accuracy and reproducibility than phenotypic methods, thus making them the preferred method for identifying such a dangerous bug that impacts patient health. However, caution still needs to be taken when using different systems, as not all the reference databases included with different MALDI-TOF instruments allow for identification.

Figure 2. Proteotypic identification of C. auris as per the CDC’s testing algorithm

Patient safety requires a fast diagnosis and strict adherence to contamination control procedures. This applies not only to healthcare facilities, but to medical and pharmaceutical product manufacturing facilities as well. Medical devices and sterile products need to be free of C. auris. Surveillance and environmental monitoring should be conducted to ensure a state of control is being maintained. Imperative to this is an accurate identification so risk to the product and patient can be appropriately assessed. How are you mitigating these risks, especially given the high possibility of misidentifying C. auris?

Charles River offers microbial identification services for medical device and pharmaceutical product manufacturing facilities using both MALDI-TOF and DNA sequencing technologies which contain a critical diversity of organisms, including C. auris, in the reference databases. Sample submission is easy through our secure online web portal. We offer fast turnaround times and complimentary tracking and trending to help with your operational decision-making. Our accurate and reproducible IDs can give you peace of mind. Read more about our services here.

 

References

https://www.cdc.gov/fungal/candida-auris/index.html

https://www.cdc.gov/fungal/candida-auris/recommendations.html

https://www.cdc.gov/fungal/diseases/candidiasis/pdf/Testing-algorithm-by-Method-temp.pdf

https://www.fda.gov/newsevents/newsroom/pressannouncements/ucm605336.htm

https://www.newscientist.com/article/2125283-deadly-drug-resistant-candida-yeast-infection-spreads-in-the-us/