Stefan Riedel

Background: Lomentospora prolificans is an opportunistic fungal pathogen associated with significant morbidity and mortality in immunocompromised individuals. Its intrinsic resistance to most antifungal agents poses challenges in clinical management, particularly in patients with hematological malignancies. Case Summary: Herein, we report the case of a 60-year-old male with recently diagnosed acute monocytic leukemia who developed a disseminated L. prolificans infection during induction chemotherapy. Despite standard prophylactic antimicrobials, the patient experienced febrile neutropenia, progressive pulmonary findings, and neurological complications, culminating in disseminated fungal infection. Blood cultures confirmed the diagnosis, and antifungal therapy was promptly expanded. However, the infection progressed rapidly, and the patient died despite aggressive therapeutic interventions. Conclusion: This case highlights the complexities of diagnosing and treating L. prolificans infections in profoundly immunosuppressed patients. It underscores the importance of heightened clinical suspicion, early recognition, aggressive management, and the need for continued development of novel antifungal agents and diagnostic techniques.

Bloodstream infections frequently cause sepsis, a condition that can lead to organ dysfunction and death. Rapid antimicrobial susceptibility testing (AST) results are critical for appropriate medical intervention and to either de-escalate or escalate antibiotics to appropriate therapy. We describe the results from a multicenter clinical study evaluating the performance of the eQUANT system (Avails Medical, Inc., Menlo Park, CA). The eQUANT system generates a 0.5 McFarland equivalent suspension, the eMcFarland, directly from a positive blood culture bottle for use with downstream disk diffusion AST, thereby saving up to 24 hours compared to traditional AST workflow. A combination of fresh, prospectively collected clinical (42) and contrived (525) blood cultures were tested, and results for disk diffusion using the Avails eQUANT eMcFarland suspension as the inoculum were compared to disk diffusion results the next day using the standard 0.5 McFarland suspension prepared from plate subculture. Thirteen species of gram-negative rods were evaluated against 12 antibiotics. From the 2,679 pairs of AST results, overall categorical agreement was 95.0%. Overall very major errors, major errors, and minor errors were 0.15%, 0.60%, and 4.48%, respectively. The Avails eQUANT system has the potential to significantly accelerate the standard of care by eliminating the need for subculture. IMPORTANCE: Rapid reporting of antimicrobial susceptibility test results for bacterial isolates from blood cultures is critical for timely implementation of optimal antimicrobial therapy and improves outcomes of sepsis patients. In this study, we demonstrate the accuracy and performance characteristics of the eQUANT system, which generates a 0.5 McFarland equivalent suspension, the eMcFarland, directly from a positive blood culture bottle for use with downstream disk diffusion antimicrobial susceptibility testing (AST). Using the eMcFarland suspension allows for accurate and standardized reporting of disk diffusion AST results from positive blood cultures.

Universal PCR for bacteria, mycobacteria, and fungi can aid in the diagnosis of occult infections, especially in the case of fastidious organisms or when prior antimicrobial treatment compromises culture growth. However, the limitations of this technology, including lack of specificity, high cost, long turnaround time, and lack of susceptibility data, may limit its effect on clinical outcomes. We performed a retrospective analysis of all specimens sent for universal PCR over a 10-year period from 2013 to 2022, focusing on clinical indications for test utilization and patient outcomes. All specimens required approval by a microbiology laboratory director prior to testing. A total of 708 specimens were sent from 638 patients. Of these specimens, 163 were positive, with an overall positivity rate of 23%. Pre-analytic factors associated with a positive universal PCR result were the presence of organisms on Gram stain or histology, the presence of neutrophils on Gram stain, and growth on culture. Positivity rates varied significantly by specimen type. A total of 20% of all organisms detected were deemed clinically irrelevant by the clinical services. A positive universal PCR led to a change in antibiotic management in 29% of cases. Positive fungal universal PCR results sent from hospitalized patients were associated with worse outcomes, including increased hospital mortality. Our findings suggest that factors such as the presence of organisms or neutrophils on Gram stain, specimen source/clinical context, and anticipated changes in management based on results should be strongly considered when making stewardship decisions regarding the appropriateness of this testing modality. IMPORTANCE: Our work provides a retrospective analysis of universal PCR orders for bacteria, mycobacteria, and fungi across our institution across a 10-year period. We assessed the positivity rates for this diagnostic tool by test type and specimen type and, critically, studied whether and how the results influenced the outcomes from treatment change, to readmission, to death.

The rapid pace of name changes of medically important fungi is creating challenges for clinical laboratories and clinicians involved in patient care. We describe two sources of name change which have different drivers, at the species versus the genus level. Some suggestions are made here to reduce the number of name changes. We urge taxonomists to provide diagnostic markers of taxonomic novelties. Given the instability of phylogenetic trees due to variable taxon sampling, we advocate to maintain genera at the largest possible size. Reporting of identified species in complexes or series should where possible comprise both the name of the overarching species and that of the molecular sibling, often cryptic species. Because the use of different names for the same species will be unavoidable for many years to come, an open access online database of the names of all medically important fungi, with proper nomenclatural designation and synonymy, is essential. We further recommend that while taxonomic discovery continues, the adaptation of new name changes by clinical laboratories and clinicians be reviewed routinely by a standing committee for validation and stability over time, with reference to an open access database, wherein reasons for changes are listed in a transparent way.

Universal PCR for bacteria, mycobacteria, and fungi can aid in the diagnosis of occult infections, especially in the case of fastidious organisms or when prior antimicrobial treatment compromises culture growth. However, the limitations of this technology, including lack of specificity, high cost, long turnaround time, and lack of susceptibility data, may limit its effect on clinical outcomes. We performed a retrospective analysis of all specimens sent for universal PCR over a 10-year period from 2013-2022, focusing on clinical indications for test utilization and patient outcomes. A total of 708 specimens were sent from 638 patients. Of those specimens, 163 were positive, for an overall positivity rate of 23%. Pre-analytic factors associated with a positive universal PCR result were the presence of organisms on Gram stain or histology, the presence of neutrophils on Gram stain, and growth on culture. Positivity rates varied significantly by specimen type. 20% of all organisms detected were deemed contaminants by the clinical services. A positive universal PCR led to a change in antibiotic management in 29% of cases. Positive fungal universal PCR results sent from hospitalized patients were associated with worse outcomes, including increased hospital mortality. Our findings suggest that factors such as the presence of organisms or neutrophils on Gram stain, specimen source/clinical context, and anticipated changes in management based on results should be strongly considered when making stewardship decisions regarding the appropriateness of this testing modality.

Despite the initially reported high efficacy of vaccines directed against ancestral SARS-CoV-2, repeated infections in both unvaccinated and vaccinated populations remain a major global health challenge. Because of mutation-mediated immune escape by variants-of-concern (VOC), approved neutralizing antibodies (neutAbs) effective against the original strains have been rendered non-protective. Identification and characterization of mutation-independent pan-neutralizing antibody responses are therefore essential for controlling the pandemic. Here, we characterize and discuss the origins of SARS-CoV-2 neutAbs, arising from either natural infection or following vaccination. In our study, neutAbs in COVID-19 patients were detected using the combination of two lateral flow immunoassay (LFIA) tests, corroborated by plaque reduction neutralization testing (PRNT). A point-of-care neutAb LFIA, NeutraXpress™, was validated using serum samples from historical pre-COVID-19 negative controls, patients infected with other respiratory pathogens, and PCR-confirmed COVID-19 patients. Surprisingly, potent neutAb activity was mainly noted in patients generating both IgM and IgG against the Spike receptor-binding domain (RBD), in contrast to samples possessing anti-RBD IgG alone. We propose that low-affinity, high-avidity, germline-encoded natural IgM and subsequent generation of class-switched IgG may have an underappreciated role in cross-protection, potentially offsetting immune escape by SARS-CoV-2 variants. We suggest Reverse Vaccinology 3.0 to further exploit this innate-like defense mechanism. Our proposition has potential implications for immunogen design, and provides strategies to elicit pan-neutAbs from natural B1-like cells. Refinements in future immunization protocols might further boost long-term cross-protection, even at the mucosal level, against clinical manifestations of COVID-19.

There has been debate in the literature about the ability of antigen tests to detect the SARS-CoV-2 Omicron variant including indication on the US Food and Drug administration website that antigen tests may have lower sensitivity for the Omicron variant without provision of data or the potential scale of the issue (see https://www.fda.gov/medical-devices/coronavirus-covid-19-and-medical-devices/sars-cov-2-viral-mutations-impact-covid-19-tests-omicronvariantimpact , accessed 1/27/2022). Here we determined the limit of detection (LoD) for the Omicron variant compared with the WA1 strain used for LoD studies described in the Instructions for Use for all Emergency Use Authorization (EUA)-approved antigen tests. Using live virus (to avoid artifactual findings potentially obtained with gamma-irradiated or heat-killed virus) quantified by plaque forming units (PFU), we examined the analytical sensitivity of three antigen tests widely used in the United States: the Abbott Binax Now, the AccessBio CareStart, and LumiraDx antigen tests. We found that the 95% detection threshold (LoD) for antigen tests was at least as good for Omicron as for the WA1 strain. Furthermore, the relationship of genome copies to plaque forming units for Omicron and WA1 overlap. Therefore, the LoD equivalency also applies if the quantitative comparator is genome copies determined from live virus preparations. Taken together, our data support the continued ability of the antigen tests examined to detect the Omicron variant.