Tag Archives: Infection control/infectious disease

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.

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.

August 2023—Analyzing the nasal epigenome can shed light on viral infections, strain differences, and potentially infection severity, and for influenza B in particular the results are striking.

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.

July 2023—Though it’s been suggested that newer drugs have made cytomegalovirus less relevant in patients with inflammatory bowel disease, CMV remains an important opportunistic infection in patients with IBD. Knowing where to biopsy and how many are needed is one of the histologic challenges, said Joseph Misdraji, MD, associate professor of pathology, Yale School of Medicine, in a CAP22 session.

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).

August 2022—The atypia in Epstein-Barr virus-positive mucocutaneous ulcers can mimic diffuse large B-cell lymphoma or classical Hodgkin lymphoma, a diagnostic pitfall that can result in overtreatment. And esophageal ulcers in immunocompromised patients should trigger cytomegalovirus immunohistochemistry in addition to GMS and herpes simplex virus-1 and -2 stains.

May 2022—Among the countless interruptions COVID-19 has inflicted on the medical community, one of the most obvious has been conversational. In the face of a global pandemic, other topics can seem unworthy of discussion. But as some post-pandemic normalcy creeps back in, so does the focus on topics of equal, if less dramatic, importance.

May 2022—Studies show promise for new approaches to biomarkers for myocarditis diagnosis, one of which is circulating micro­RNA mmu-miR-721. Another biomarker, sera soluble ST2 (sST2), which has been found to be clinically useful in predicting heart failure, could be added to existing biomarkers used to diagnose patients with myocarditis, interpreted according to sex and age. And serial high-sensitivity troponin measurements might be another approach to diagnosing and monitoring myocarditis.

May 2022—Infectious disease diagnosis sometimes requires a surgical pathologist, often in unexpected situations. In a CAP21 session, “Uncultured: Infectious Diseases in Surgical Pathology,” Sarah D. Hackman, MD, assistant professor, Department of Pathology and Laboratory Medicine, University of Texas Health San Antonio, presented a sampling of such cases, two of which follow.

April 2022—A study published last fall examined antimicrobial prescribing in gram-negative bloodstream infections based on three rapid diagnostic panels and using what’s known as the DOOR-MAT framework. The study’s findings were explained in a CAP TODAY webinar on stewardship interventions to optimize the management of gram-negative bacteremia. It was presented last December and made possible by a special educational grant from BioFire.

June 2021—Testing for viral infections post-transplant is an important part of care for transplant patients because of the risk for infections during immunosuppression. But viral load monitoring suffers from interlaboratory variability for several reasons, and while the problem is greater at higher viral loads, the interlaboratory variability is also present at lower viral loads. Steve Miller, MD, PhD, of the University of California San Francisco, and Joseph Yao, MD, of Mayo Clinic in Rochester, reported the monitoring difficulties, solutions, and new directions last fall in a CAP TODAY webinar made possible by a special educational grant from Roche.

March 2021—Fresh from its Dec. 27, 2020 FDA clearance, the Bruker MALDI Sepsityper Kit US IVD promises to provide microbiology laboratories with a universal, rapid sepsis identification solution. With the Bruker MALDI Biotyper platform’s reference library covering 491 organisms, the Sepsityper’s ability to identify pathogens directly from positive blood cultures in suspected bacterial or fungal sepsis cases delivers an “order of magnitude increase” in the number of microorganisms that can be identified through PCR detection, said Wolfgang Pusch, Bruker Daltonics executive vice president of microbiology and diagnostics, in a company statement.

January 2021—Susan Butler-Wu, PhD, D(ABMM), is clear about who she is and what she does. “I’m just a microbiologist,” she says. But in a viral pandemic, a microbiologist—and everyone else associated with clinical laboratory testing—becomes so much more than the job title. (For the record, Dr. Butler-Wu is director of the clinical microbiology laboratory, LAC+USC Medical Center, Los Angeles, and associate professor of clinical pathology, Keck School of Medicine of USC.) Likewise, a test becomes more than a lab value. The very fact that testing has become the focus of national discourse is a testament to the upending nature of the pandemic, she says. “The public are having conversations about Ct values. It’s mind-blowing.”

January 2021—The use of molecular assays at the point of care is exciting but a bit scary. That’s how Raquel Martinez, PhD, D(ABMM), described the state of the science for molecular infectious disease POC testing when she spoke in a virtual AMP session in November with Omai Garner, PhD, D(ABMM), of UCLA Health.

January 2021—Wrestling with rapid test shortfalls and with open laboratory positions. Expecting the post-holiday surge, frustrated by federal level disconnect. That is what Compass Group members were doing and feeling on Dec. 1 last year, when they gathered on Zoom for another conversation about COVID-19.

December 2020—By its very nature, the global pandemic has forced laboratories to look far and wide, to bring binoculars, in essence, to their views of supply chains, testing platforms, personnel, and the like. As COVID-19 churns on, some labs are looking through a tinier lens as well. These labs aren’t trading their binoculars for a jeweler’s loupe, exactly, but they have found small and significant success stories closer to home. Like so many others, Erin Graf, PhD, D(ABMM), has confronted a spinning roulette wheel since the pandemic’s start. In a talk she gave in an AMP webinar in October, Dr. Graf posted a vibrantly colored wheel titled, “Which supply chain issue will impact us this week?” Each segment contained a phrase familiar to everyone in 2020, ranging from “swabs” and “sheep blood agar” to “pipette tips” and “chlamydia and gonorrhea tests.” As she surveys these continuous claims on her attention, Dr. Graf says, “I think none of us could have ever thought that COVID would have an impact on all these arms of the testing that we do.”

December 2020—In Colorado, Joan Coleman, MBA, MT(ASCP), and her UCHealth colleagues launched an expansive pooled testing program this summer that, after much work, worked well—until it didn’t, thanks to rising positivity rates in October.

November 2020—Adam Barker, PhD, D(ABMM), was ready to call it quits. For weeks, he had been working to bring saliva-based SARS-CoV-2 testing to ARUP Laboratories and the University of Utah. Dr. Barker, director of ARUP’s COVID-19 rapid response lab, and his colleagues had done studies comparing saliva with nasopharyngeal swabs, which seemed to be following the flight of the passenger pigeon out of existence. They had wrestled with the FDA over emergency use authorization. They’d developed their own transport media, since that supply was also becoming extinct. He had begun building kits for saliva collection and figured out what sample size worked best. Kits had been delivered to collection sites on campus, and staff were being trained in their use. He was, in other words, creating a laboratory success story, one of the many that have been written since March. He was not basking in this fact. “I have to tell you: I lost so much sleep because of saliva,” says Dr. Barker, who is also director, ARUP Institute for Clinical and Experimental Pathology.

October 2020—Barely a half year into the pandemic’s presence in the United States, history has already begun pressing down on SARS-CoV-2 testing. Like an actor playing Hamlet, it’s been difficult not to feel the burden of past performances when preparing for the months ahead. Now, at the start of fall, that also means readying for the return of influenza. Here, even longer experience has shown that each new season is, indeed, a new season. As in the theater world itself these days, planning for what lies ahead feels tempest-tossed. Plans are being laid. Discussions continue. Creativity abounds, and hard work persists. The season shall unfold. But no one knows how it will look until the curtain—or whatever is passing for one this year—goes up. Poor Hamlet is troubled enough to fill the stage for hours—it is, in fact, Shakespeare’s longest play. Yet he’s just one man. Laboratories this fall are absorbing the slings and arrows of two roles simultaneously. Can they prepare for both parts (think Richard II and III sparring on the same stage) with confidence?

October 2020—Planning for respiratory season is always tricky but never more so than this year. “Uncharted territory for influenza” is how Frederick Nolte, PhD, D(ABMM), of the Medical University of South Carolina, describes the prospect of testing for influenza at the scale labs have been testing for SARS-CoV-2.

September 2020—Between a rock and a hard place. Trying to stay ahead, trying to build inventory. Chasing multiple new testing requests. Anticipating influenza. That’s where laboratory leaders said their labs were in early August when CAP TODAY publisher Bob McGonnagle convened members of the Compass Group on Zoom to share their pandemic experiences. They shared surprise, too, that the situation is what it is: “Not a clue in my mind that this would go past the springtime,” said Stan Schofield, president of NorDx and senior VP, MaineHealth. McGonnagle asked them about the diversion of supplies, the coming flu season, IT support, lessons and long-term changes, and more.

See current issue below for additional COVID-19 coverage or access all COVID-19 articles here.

September 2020—The twinned challenge of testing for SARS-CoV-2 and the upcoming influenza season has a bit of The Cat in the Hat energy running through it. How does one manage to keep Thing One and Thing Two from creating unmitigated chaos? Maybe one doesn’t, not completely. A pandemic-based flu season will by its very nature be protean.

August 2020—In March, the COVID-19 pandemic came in like a lion—and has yet to leave, like a lamb or anything else. Instead, it roared through April and May in early hot spots like New York City and New Orleans. As lockdowns took hold, the cautious hope was that by summer the virus would be tamed (if not simply go away “like a miracle” or “as the heat comes in,” per several infamous predictions), giving health care providers a chance to exhale before a likely second wave in the fall. Instead, June and July saw other cities and states hit hard in turn, while many places that appeared to have flattened the curve were starting to see concerning upticks in cases.

August 2020—If there’s one thing scarier to experience than COVID-19, it’s Ebola. Or so you might think. “Ebola was easier,” says Beverly Dickson, MD, medical director of the clinical laboratory at Texas Health Presbyterian Hospital Dallas.

August 2020—The CAP treats emergency use authorization assays similar to FDA-cleared assays and thus requires full verification. In a June 4 CAP webinar, Neil Anderson, MD, D(ABMM), assistant director of clinical microbiology, Washington University School of Medicine in St. Louis, walked through how to approach verification for SARS-CoV-2 assays. Co-presenter Elitza Theel, PhD, D(ABMM), director of the infectious diseases serology laboratory at Mayo Clinic, reported what’s known about protective immunity against SARS-CoV-2.

August 2020—As the need for COVID-19 testing grows well beyond that for hospital patients, clinical laboratories in mid-summer were again overwhelmed by demand while at the same time bracing for flu season. That was the gist of a July 10 webinar that brought together Gyorgy Abel, MD, PhD, medical director of clinical chemistry, molecular diagnostics, immunology, and point-of-care testing at Lahey Hospital and Medical Center, Burlington, Mass.; Bob McGonnagle, CAP TODAY publisher; and moderator Steve Beuchaw, director of life science and medical device research, Wolfe Research.

July 2020—A machine learning algorithm, used in conjunction with BioFire’s Syndromic Trends, demonstrated a mechanism for near real-time outbreak detection of enterovirus D68, says a study reported in the Journal of Clinical Virology.

July—When COVID-19 set in, much of residency education in the U.S. moved online. At the University of Washington School of Medicine, anatomic pathology faculty took online learning a step further by creating a virtual two-week anatomic pathology rotation for medical students. The faculty is aiming for a four-week virtual rotation inclusive of more laboratory medicine, to be used even after the pandemic has passed.

June 2020—The arrival of a pandemic has shown—among many, many other things—that anyone who talks about it typically starts by saying, “This is a pandemic.” The next sentence tends to be, “It’s a completely different situation,” whether the focus is grocery shopping, exercising (or not), voting, or practicing medicine. Pointing to the pandemic is a polite way of saying, “All bets are off.” For many, it’s been a springboard to innovation and breakthroughs, even in the midst of considerable anguish. For clinical laboratories, however, much has felt unsettling, especially when the conversation turns to serology testing for SARS-CoV-2. It’s a topic stuffed to overflowing with interest, enthusiasm—and, early on, antibody tests themselves.

Published in June: Autopsies show many faces of COVID-19 Sudden” and “global” are descriptors that seldom appear in tandem, especially in relation to disease epidemiology. But they both fit the COVID-19 pandemic, which has left the health care world reeling. “COVID-19 has infected the entire planet pretty much all at once,” says Alex K. Williamson, MD. Read more.

June 2020—At NYU Langone Health, pathologists and others typically not seen out front in the fight against COVID-19 became the bridge between families and the floors. When Katherine A. Hochman, MD, associate chair for quality in the Department of Medicine at NYU Langone, contracted a mild case of COVID-19, she finally had a chance to take a step back and think. Before going into quarantine to recover, Dr. Hochman had been on the floors day in and day out attending to COVID-19 patients.

June 2020—The key lesson for policymakers and hospital administrators stemming from the pandemic is that continuing to cut human and economic resources will create large organizational issues when the entire system of care, including laboratory diagnostics, is challenged by “an enormously amplified volume of tests to manage emergent situations,” write Giuseppe Lippi, MD, of the University of Verona, and Mario Plebani, MD, of University Hospital of Padova, Italy, in an opinion paper published online March 19.

Published in July: Reading COVID-19’s signature: lung tissue injury Alain Charles Borczuk, MD, began his practice of pathology as a resident 28 years ago and has spent quite a bit of his career doing autopsies. But it is this year, during the pandemic, that he’s finding some of the best applications of his autopsy work as he seeks to understand the lung injury patterns in SARS CoV-2, or COVID-19 patients. Read more.

May 2020—Along with SARS-CoV-2, clinical laboratory testing has been hiding in plain sight far longer than many people realize. But it took the novel coronavirus (which, frankly, hardly feels novel anymore) to make that clear to the rest of the world. As the COVID-19 pandemic spread across the globe, laboratory testing crashed the news cycle. National leaders sought to reassure citizens by promising millions of test kits.

May 2020—To combat the spread of COVID-19, Louisiana’s governor in late March issued an order directing state residents to limit their excursions outside.

May 2020—But as the prevalence of tick-borne infections in the United States rises steadily and widens geographically, the number of novel pathogens carried by ticks—including non-Lyme bacteria, protozoa, and viruses—has been climbing as well.

May 2020—Christine C. Ginocchio, PhD, MT(ASCP), in an April 8 CAP TODAY webinar, reported findings on the analytical efficiencies and sensitivities of four of the original and most common of the SARS-CoV-2 assays. Read more.

April 2020—When Romney Humphries, PhD, D(ABMM), was section chief for clinical microbiology at UCLA Medical Center, it wasn’t unusual for her to take calls from worried clinicians who were concerned about patients who’d been transferred to the hospital for a higher level of care. The accompanying laboratory reports would indicate the presence of an isolate that was susceptible to a particular drug. But when Dr. Humphries’ lab did its own testing, the results were strikingly different: The isolate was drug resistant. When Dr. Humphries would call the first lab, the reason for the discrepancy became clear. “Sure enough, they were using old breakpoints,” says Dr. Humphries, who is now chief scientific officer, Accelerate Diagnostics, and professor of pathology, University of Arizona. Unlike Bordeaux, antimicrobial susceptibility test breakpoints do not age well. Over time, they might no longer be clinically useful, even as they continue to be used clinically. Dr. Humphries’ anecdote is, of course, just that—an anecdote.

High rates of positivity but glimmers of hope. That’s what Gregory Sossaman, MD, was seeing in southeast Louisiana on April 14 when writer Meredith Salisbury spoke to him for CAP TODAY. Dr. Sossaman is system chairman of the Department of Pathology and Laboratory Medicine, Ochsner Health, New Orleans. Ochsner is an integrated delivery network located primarily in southeast Louisiana, though it has formed partnerships in recent years with other systems and hospitals in the state. Here is what Dr. Sossaman had to say.

March 2020—Where should molecular infectious disease testing be performed? That was the question at the center of a point-counterpoint session at last year’s AMP annual meeting.

September 2018—The advantages of moving from stool culture to a molecular platform are many: faster time to results, more accurate pathogen identification, a savings of space and staff time. For Jose Alexander, MD, D(ABMM), SM, MB(ASCP), and colleagues at Florida Hospital Orlando, another plus is being able to adhere to the Infectious Diseases Society of America guideline suggestion that labs use a diagnostic approach that can distinguish O157 from non-O157 E. coli and Shiga toxin 1 from Shiga toxin 2 E. coli.

August 2018—If you were casting about for the severest test of a laboratory’s capabilities, day in and day out, sepsis admissions at a pediatric hospital might fit the bill. At Children’s Hospital of Philadelphia, and at other hospitals, waging war on sepsis requires battles on multiple fronts and clinical pathways that rely on an agile and highly equipped microbiology laboratory. Three main categories of patients ensure there is no shortage of sepsis cases at CHOP, says Erin H. Graf, PhD, D(ABMM), director of the infectious disease diagnostics laboratory.

May 2018—If a seismic shift were to happen in microbiology, the technology behind the Accelerate Pheno system and PhenoTest BC test kit, which won FDA approval last year as a rapid pathogen identification and antimicrobial susceptibility testing (AST) system for blood cultures, could well be the cause.

April 2018—Scratch the surface of TB testing, and things quickly get interesting. The standard skin reaction test, widely adopted by the early 1940s, is still in use today. The goal has remained steady as well: break the transmission cycle. “From the clinician perspective and the laboratory perspective, because of its infectious nature, we want to identify people with latent tuberculosis,” says Elitza Theel, PhD, lab director for the infectious disease serology laboratory, Mayo Clinic and Mayo Medical Laboratories.

April 2018—If you were asked to pick a place on the map where problems with detecting a mutant strain of an infectious disease would likely come to light, the capital of Nebraska might not be your first guess.

March 2018—In a severe flu season that started early, laboratories faced unprecedented test volumes, used new testing platforms, and negotiated vendor supply shortages. When laboratory staff at Arkansas Children’s Hospital in Little Rock began seeing a rising number of requests for respiratory tests, and five positive flu results,

March 2018—New from CAP Press this month is the Atlas of Fundamental Infectious Diseases Histopathology: A Guide for Daily Practice, edited by Bobbi S. Pritt, MD, MSc, DTM&H. It covers bacterial, viral, fungal, and parasitic infections and contains more than 800 images.

November 2016—Raquel M. Martinez, PhD, D(ABMM), is very happy in her role as director of clinical and molecular microbiology at Geisinger Health System, Danville, Pa.

October 2016—Take a bar graph, any bar graph, and compare it to the natural landscape of the United States. If most of it resembles the Great Plains but the right-hand side starts looking more like Rocky Mountain territory . . . well, something interesting is going on.

January 2016—There is a reason why rigorous studies are done to prove even the seemingly apparent benefits of advanced techniques. Sometimes comparisons turn up unexpected findings, as demonstrated by two selected infectious disease abstracts about real-time PCR presented at the Nov. 5–7, 2015 meeting of the Association for Molecular Pathology. Even so, both abstracts show the value of PCR testing.

September 2015—Emerging and re-emerging viruses are well and alive, says Sherif Zaki, MD, PhD, chief of the Infectious Diseases Pathology Branch, Centers for Disease Control and Prevention. At the Clinical Virology Symposium in April, he spoke on viral etiology in unexpected deaths, presenting a list of outbreaks of unexplained illnesses in which his branch took part in the past two decades and which turned out to be caused by viruses.

August 2015—The problem of carbapenem resistance first made its way to Detroit’s Henry Ford Hospital in 2007, when a multidrug-resistant organism appeared in a sputum sample from the intensive care unit. Within weeks, several other cases emerged.

April 2015—If you ask average patients what infectious diseases they worry about contracting during a hospital stay, Ebola may top the list, perhaps followed by MRSA and HIV. But ask clinical microbiologists what has been keeping them up at night lately, and those pathogens aren’t the ones they cite.

December 2014—Elevated vancomycin minimum inhibitory concentrations do not increase the risk of death in patients with Staphylococcus aureus bacteremia, according to the findings of a comprehensive meta-analysis published in the Oct. 9 issue of JAMA. Despite widespread speculation about rising vancomycin resistance, or “MIC creep,” the authors find little evidence to challenge the current CLSI susceptibility breakpoint of ≤ 2 µg/mL for vancomycin.

December 2014—Clinical laboratories have made impressive headway in their Ebola preparedness, though their plans are shaping up in different ways. That’s due, in part, to varying opinions about how to manage a dangerous and unpredictable virus. “We are really learning as we go along with this,” says D. Jane Hata, PhD, D(ABMM), director of microbiology and serology at Mayo Clinic in Jacksonville, Fla. For years there has been talk of the possibility of an airplane passenger bringing Ebola into the U.S., she says. “But we are on the ground now and we’re all actively planning to deal with this.”

August 2014—A race for prevention may lack the drama of a race for the cure. But to fight methicillin-resistant Staphylococcus aureus and other multidrug- resistant organisms, hospitals really have no choice. A disease with a higher number of annual U.S. deaths than for salmonella, tuberculosis, influenza, and HIV put together, MRSA can only be tamed with prevention.

October 2013—Since 1942, when penicillin was first used to treat infections caused by gram-positive bacteria, many improved and potent beta-lactam antimicrobials have been developed. Yet today, if a patient in an intensive care unit develops a bloodstream infection with Staphylococcus aureus, that person has a one in three chance of dying. High mortality rates apply to many other pathogens that cause bloodstream infections in ICU patients—from one in five for coagulase-negative staphylococci and Escherichia coli to almost 40 percent for Pseudomonas aeruginosa and Candida spp. Enterobacter spp and Enterococcus spp have intermediate mortality rates: one in four and one in three, respectively. Even among patients on a non-ICU ward, bloodstream infections are associated with mortality rates between 20 percent and 30 percent.

April 2013—When 19th-century Hungarian obstetrician Ignaz Semmelweis found that doctors could dramatically decrease puerperal infections by washing their hands with a chlorinated lime solution before delivering babies, his colleagues thought he was nuts. Why, everyone knew that infections were caused by noxious air!