Microbiology

April 2024—The rise in fungal infections in recent years troubles Sean Zhang, MD, PhD, for reasons near and far. It’s readily apparent in the patient populations at Johns Hopkins Hospital, where he is director of the mycology laboratory. Especially concerning is the increase in Candida auris following the height of the COVID-19 pandemic, both in terms of colonization and infection cases, says Dr. Zhang, who is also associate professor of pathology, Division of Medical Microbiology, Department of Pathology, Johns Hopkins University School of Medicine. “Since 2022, we suddenly saw an uptick in Candida auris cases across the Johns Hopkins Health System.” But the situation isn’t unique to Johns Hopkins. Pointing to CDC figures, he notes that the tide is rising more broadly as well. The agency reports that in 2020, there were 757 clinical cases and 1,310 screening cases of C. auris in the United States. In 2022, there were 2,377 clinical cases and 5,754 screening cases.

October 2023—With respiratory virus season near, those with a close eye on it in August gave the lay of the land for test algorithms, technologies, and forecasts, even as SARS-CoV-2 and RSV cases were rising in parts of the country.

October 2023—A CAP accreditation program requirement that microbiology laboratories use current antimicrobial susceptibility testing breakpoints, which was added to the checklist in 2021, will go into effect Jan. 1, 2024.

September 2023—For the tickborne and mosquito-borne arboviruses, which are frequently more transient in blood and tissue than other pathogens, both molecular and serologic testing have a place in the diagnostic toolkit.

September 2023—A casual comment made in a routine exchange in an Avera McKennan Hospital laboratory sparked a five-year campaign to bring down the urine culture contamination rate. “I feel like all I do is report contaminated cultures,” a microbiology technologist said in 2016.

July 2023—As the COVID-19 federal public health emergency drew to a close in mid-May, industry experts explained what will and won’t change for the laboratory and weighed the fallout from the drop-off in SARS-CoV-2 testing.

July 2023—When Butler Health System in early 2020 installed the Beckman Coulter DxA 5000 automation line, its hospitals were among the first in the country to do so. At the same time, Butler went live with the DxH 900 hematology analyzer.

June 2023—A bad-news, good-news, bad-news, good-news bass line thrums through the ongoing story of Candida auris as it continues to spread in the United States. Initially identified in Japan, in 2009, in an ear specimen—hence the auris—the yeast was first reported in the United States in 2016. Like certain other pathogens, C. auris’ domestic presence appeared to be linked to travel-related cases, then quickly spread, first to the metropolitan regions of Chicago and New York City and now to more than half the states. That’s worrisome. Yet the spread hasn’t been unbridled. Early fears that it would sweep indiscriminately through all patient populations have not been realized. “It’s not as virulent as albicans,” says Sixto M. Leal Jr., MD, PhD, director of the clinical microbiology laboratory and of the fungal reference laboratory, University of Alabama at Birmingham, and a member of the CAP Microbiology Committee. “It’s about as virulent as Candida glabrata. It’s not too much of a significant threat if you’re healthy.”

June 2023—For Lyme disease testing, immuno­blots became optional in 2019 when the FDA cleared enzyme immunoassays for use as part of a modified two-tiered testing algorithm. “It was a historic event in the world of Lyme diagnostics,” says Elitza Theel, PhD, D(ABMM).

June 2023—For HIV and HCV algorithmic testing, the workflow options have risks to consider. Molecular testing performed as an automatic reflex on the same sample used for the serologic testing risks carryover contamination, and requiring a dedicated sample for the molecular assay risks incomplete testing.

March 2023—When it comes to molecular syndromic panels for pneumonia, there’s both upside and downside, says Neil W. Anderson, MD, D(ABMM), associate professor, Department of Pathology and Laboratory Medicine, Washington University School of Medicine in St. Louis.

March 2023—Urinalysis was at the heart of a Feb. 7 discussion between CAP TODAY publisher Bob McGonnagle; Ron Jackups Jr., MD, PhD, of Washington University School of Medicine; and Jason Anderson of Sysmex America. “There’s a lot of room to explore what the optimal parameters are to use with the best specificity and sensitivity for a reflex to the sediment analysis or the culture,” Anderson said. Here’s what he and Dr. Jackups said about reflex testing, automation, and middleware.

February 2023—Traditional algorithm? Or reverse? Elitza Theel, PhD, D(ABMM), of Mayo Clinic, in an AACC session last year walked through the two primary diagnostic algorithms for syphilis, explaining where the complexities lie and how her laboratory uncovered inappropriate testing for neurosyphilis.

January 2023—For the central microbiology laboratory serving Barnes-Jewish and four other hospitals in the St. Louis area, validating and implementing a new blood culture system and moving to a shorter incubation time came at a perfect time: right before the pandemic.

December 2022—Reflex urine culture algorithms have become common and have been shown to reduce urine culture utilization, but efforts to sharpen clinical decision support continue.

November 2022—In mid-October, flu was picking up, with high levels of activity in Texas, Georgia, the District of Columbia, South Carolina, Tennessee, and New York. Elsewhere, it was still on the lower side, with less known about what was to come but plans in place. And questions, too, about laboratory testing as it relates to SARS-CoV-2, “which is going to be a challenge,” says David Peaper, MD, PhD, D(ABMM), a member of the CAP Microbiology Committee.

October 2022—It might be possible to tot up, using only the number of toes on an ordinary foot, how many labs are feeling full of vim and vigor these days, open to concepts like creative destruction and get those creative juices flowing and have fun with it—slogans once easily uttered but now tiring to enact. Nevertheless, Margie Morgan, PhD, D(ABMM), would like her colleagues to at least consider the possibility of inspiration in the microbiology laboratory. In particular, Dr. Morgan, medical director of microbiology and professor of pathology and laboratory medicine, Cedars-Sinai Medical Center, Los Angeles, has some thoughts about using a new automated system to facilitate rapid microbial identification from positive blood cultures. The Arc system, from Accelerate Diagnostics, is composed of the Arc module and blood culture kit and concentrates organisms recovered in positive blood cultures for direct testing on MALDI-TOF mass spectrometry. Dr. Morgan and colleagues have been using the system since February.

October 2022—Influenza incidence and what it will mean for testing in this respiratory virus season is a wild card, as is how SARS-CoV-2 will evolve. In early September, SARS-CoV-2 prevalence was declining in parts of the United States. “And if you believe in the theory of viral interference,” says Michelle Tabb, PhD, chief scientific officer at DiaSorin Molecular, “it’s leaving the door wide open right now for something else to step in. We’ll see if that’s RSV, or flu A, or if it’s a new COVID variant.”

July 2022—Thanks to more than two years’ experience with SARS-CoV-2, perhaps at no point in U.S. history has the general public been as aware of antigen and PCR testing, and the difference between them, as it is now.