Hospitals in 38 states confirmed patient infections of the dangerous, drug-resistant fungus
Rapidly spreading Candida auris fungus is once again showing up in hospitals throughout the United States, with multiple cases confirmed in Georgia and Florida. Hospital laboratories and pathology departments are encouraged to take advantage of CDC resources to help in the diagnosis of this deadly pathogen.
Candida auris (C. auris) spreads between patients in hospital settings, is resistant to anti-fungal medications, and can cause severe illness, according to the Centers for Disease Control and Prevention (CDC). Tracking data from CDC’s National Notifiable Diseases Surveillance System found 4,514 new clinical cases of C. auris in the US in 2023.
“The number of clinical cases has continued to increase since the first US case was reported in 2016,” said the CDC of past outbreaks of C. auris. “Based on information from a limited number of patients, 30–60% of people with C. auris infections have died. However, many of these people had other serious illnesses that also increased their risk of death.” The fungus has been spreading at a high rate from 2016-2023 with several cases cropping up recently in Georgia.
According to representatives from the Georgia Department of Public Health, “the state has seen over 1,300 cases as of the end of February,” WJCL reported.
The Hill reports a significant recent increase in the spread of the fungus in all but 12 states. Though the number of cases in each state remains small, the overall percentage of increased cases is large and growing.
And a study conducted at Jackson Health System in Miami, Fla., and published in the American Journal of Infection Control, found that “The volumes of clinical cultures with C. auris have rapidly increased, accompanied by an expansion in the sources of infection.”
“If you get infected with this pathogen that’s resistant to any treatment, there’s no treatment we can give you to help combat it. You’re all on your own,” Melissa Nolan, PhD, associate professor of epidemiology and biostatistics at the Arnold School of Public Health, University of South Carolina, told Nexstar. (Photo copyright: University of South Carolina.)
CDC Recommendations
The deadly fungus was first detected in 2016 in US hospitals, and the number of cases in hospital patients has grown every year based on CDC data from 2023. Invasive medical procedures can provide a gateway for C. auris to infect patients, and the immunosuppressed nature of these patients can lead to further complications.
Invasive procedures that could expose a patient to C. auris include the placing of breathing and feeding tubes, and the insertion of vein or urinary catheters.
“We’ve had four people at one time on and off over the past few months, and in years past, it was unusual to have one or even two people with Candida auris in our hospital,” Timothy Connelly, MD, told WJCL about the spread of the fungus at Memorial Health in Savannah, Ga.
Cases have also rapidly increased in Miami according to the Jackson Health System study. The researchers found that, “The volumes of clinical cultures increased every year and infection sources expanded.”
The CDC considers C. auris “an urgent antimicrobial resistance threat” based on the severe risk an infected patient can face. “The rapid rise and geographic spread of cases is concerning and emphasizes the need for continued surveillance, expanded lab capacity, quicker diagnostic tests, and adherence to proven infection prevention and control,” said Meghan Lyman, MD, in a CDC news release.
Fungal Infection is Difficult to Treat and Diagnose
C. auris has been shown to be resistant to antifungal medications, making it an acute threat to ill patients. And since it tends to infect already sick patients, it can be difficult to detect because symptoms of infection can be generic, such as fever or chills.
The fungus is also adept at surviving on hospital surfaces.
“It’s really good at just being, generally speaking, in the environment,” Melissa Nolan, PhD, associate professor of epidemiology and biostatistics at the Arnold School of Public Health, University of South Carolina, told Nexstar. “So, if you have it on a patient’s bed for example, on the railing, and you go to wipe everything down, if in whatever way maybe a couple of pathogens didn’t get cleared, then they’re becoming resistant. And so over time, they can kind of grow and populate in that hospital environment.”
CDC Resources to Help Identify C. auris
C. auris also can be misidentified with other candida species fungi. The CDC recommends identification using a diagnostic device “based on matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF).” The CDC also recommends using supplemental MALDI-TOF databases and molecular methods to help distinguish C. auris from other candida.
Prompt clinical laboratory diagnosis is extremely important to stem outbreaks as they become more frequent in hospital settings. The CDC offers resources for hospital pathology departments to aid in screening and detection.
“I think we need to do a better job of predicting,” Nolan told Nexstar. “Moving forward [we need] more funding to support quality surveillance of these potential infectious strains so that we can know in advance, and we can do a better job of stopping disease spread before it becomes a problem.”
According to the CDC, the fungus typically spreads in hospital settings and is not known to affect healthy people.
While working to increase turn-around-times for STAT tests, Florida’s first coronavirus patient arrived, requiring SMH’s clinical laboratory team to adapt its plans
Despite the COVID-19 pandemic, the clinical laboratory team at 839-bed Sarasota Memorial Hospital, part of the Sarasota Memorial Health Care System (SMH) in Sarasota, Fla., not only implemented a new automated microbiology system, it also installed a new mass spectrometry analyzer, along with new instruments to support large volumes of SARS-CoV-2 testing.
How SMH’s microbiology laboratory team accomplished this while shelter-in-place directives in Florida caused many patients to stop visiting emergency departments and physicians’ offices—and as hospitals and medical laboratory facilities restricted access to staff and essential personnel—provides useful lessons for pathologists and clinical laboratory managers.
“Florida reported its first positive SARS-CoV-2 infection on March 2, marking the beginning of an outbreak that continues today,” he noted, adding, “This created the need to support the hospital in identifying infected patients in Sarasota County by having the microbiology lab acquire and set up more instruments. Also, the micro lab needed space for a new mass spectrometry analyzer to speed up pathogen identification this year.
In the same TDR interview, Olevia Fulkert, Microbiology Technical Supervisor at SMH said the microbiology lab had to reconfigure its layout to be prepared for the new COPAN system. “Our team had to arrange space for these new instruments, while protecting the space needed for the microbiology automation.”
“The WASPLab (above) literally went right into the middle of the busiest area of our lab,” said SMH’s Director of Laboratory Services, Harold Vore, MS, MT. “That’s the room we call COVID central, because that’s where we process all SARS-CoV-2 specimens.” SMH’s medical laboratory team began this implementation in the early months of the COVID-19 pandemic and relied on Lean processes to accomplish its goals. (Photo copyright: Sarasota Memorial Health Care System.)
Return of the ‘Snowbirds’
In August, SMH’s microbiology laboratory staff was busy validating the WASPLab instruments so the lab would be ready to process patient specimens when Florida’s snowbirds—out-of-state residents who arrive for the winter—return to Sarasota.
Vore knew several elements would be required for SMH’s microbiology automation project to succeed:
He had to assure the microbiology lab’s staff that adding automation would not cause any loss of jobs.
Timing of the implementation was critical, because lab test volume rises in the winter when tourists and part-time residents return.
Lean methods would be important because lab staff was familiar with them and they would help the vendor to arrange the physical layout and workflow to optimize productivity, reduce errors, and decrease turnaround times.
Vore needed documentation that showed automating the microbiology lab met and exceeded the return-on-investment projections he and his lab team used to persuade health system administrators of its value.
According to Vore, to date the installation has gone smoothly. “The staff in the microbiology lab has been phenomenal,” he commented. “They have continued to do what they always do, while at the same time we’re installing this large new system right in their midst.
“And they did not complain. In fact, they were eager to make progress in improving production,” he continued. “That attitude is common among our laboratory staff, because we saw the same thing happen when we automated our core lab.”
Increasing Microbiology Lab Capacity without Increasing Staff
Vore estimates automation will expand SMH’s microbiology laboratory capacity by up to 40%. “We measure that 40% in terms of the number of plates our techs can read per day with the WASPLab versus how we did it manually with our existing staff,” he explained. “We may still need to increase some staff. But even without adding staff, we thought we could move the peg further down the road in terms of throughput and improve our turnaround time too.
“We cannot make bacteria grow any faster and yet our specimen volume continues to increase,” he noted. “That makes automating microbiology the right strategy. Also, if we hadn’t automated the core lab starting in 2015, we might not have been able to handle the increased volume that we saw last year and this year’s additional surge in COVID-19 tests.”
How Lean Helped with the Implementation
Workflow in microbiology has traditionally been mostly manual. Therefore, combining Lean and automation can generate substantial benefits for a lab. “By definition, the design of the WASPLab is Lean,” Vore explained. “By that I mean the person who touches each specimen the least wins. That’s why the WASPLab is designed the way it is. Once we load a specimen in the front end, theoretically, no one needs to touch those plates until the testing is complete.”
“That’s the ideal we’re trying to reach,” he added. “At the moment, we still need to pull the plates to, as we say, ‘pick them.’ But we just introduced a way to improve that part of the process.
Adding Mass Spectrometry
“Along with the microbiology automation, we now read specimens digitally and we tell the machine to take a certain plate off so we can spot it,” Vore continued. “To speed up that process, we got some additional funding and bought a mass spec analyzer that uses MALDI-TOF to identify pathogens. Now we get the boost from the WASPLab, and we also use mass spec to cut six hours off our first read,” Vore added.
“The WASPLab and the mass spec give us higher quality incubation and better harvest of pathogens. Once we spot the plate, the mass spec can identify the pathogen in about two minutes,” he said.
“After going live with the mass spectrometry in August, we’ve made huge progress versus the normal process, where we would plate the specimen manually under a hood and then put the specimen in the incubator and pull it out to read 24 hours later,” he said.
“That whole step-by-step process to identify the pathogen could take 48 hours,” he continued. “But now we can move to a 24-hour, seven-day-a-week operation, where we can do first-in-first-out of pathogens in about 18 hours. That cuts six hours off the time to do the first plate read. Then we can spot it and get a result from the mass spec in two minutes. The impact for patient care can be tremendous.
“In a recent case, for example, we had to identify a specimen from an infant and used the mass spec to identify salmonella in two minutes,” Vore noted. “Normally that would take at least a day or more. That’s what I mean about making tremendous impact on patient care by using automation in microbiology.”
Clearly, this would be a challenging project for any medical laboratory to complete during the best of times, let alone during the early months of the COVID-19 pandemic. But through determination, the use of Lean, and a positive approach, SMH’s microbiology lab team implemented the first WASPLab in the state of Florida. And it will improve SMH’s ability to care for patients for years to come.
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