Fungal Biomarkers Research Articles

Microbiological Non-Culture-Based Methods for Diagnosing Invasive Pulmonary Aspergillosis in ICU Patients.

The diagnosis of invasive pulmonary aspergillosis (IPA) in intensive care unit (ICU) patients is crucial since most clinical signs are not specific to invasive fungal infections. To detect an IPA, different criteria should be considered. Next to host factors and radiological signs, microbiological criteria should be fulfilled. For microbiological diagnostics, different methods are available. Next to the conventional culture-based approaches like staining and culture, non-culture-based methods can increase sensitivity and improve time-to-result. Besides fungal biomarkers, like galactomannan and (1→3)-β-D-glucan as nonspecific tools, molecular-based methods can also offer detection of resistance determinants. The detection of novel biomarkers or targets is promising. In this review, we evaluate and discuss the value of non-culture-based microbiological methods (galactomannan, (1→3)-β-D-glucan, Aspergillus PCR, new biomarker/targets) for diagnosing IPA in ICU patients.

Life-stage and geographic location determine the microbial assemblage in Eurasian spruce bark beetle, Ips typographus L. (Coleoptera: Curculionidae)

Ips typographusL. (Coleoptera: Curculionidae) is one of the serious pests causing mass destruction of European spruce forests, with a substantial economic impact. Symbiotic microbes associated with bark beetles often play a definitive role in accomplishing their physiological and ecological functions by detoxifying chemicals, inhibiting pathogens, and offering nutrients. Although a few research works explored the microbes associated withI. typographus, much is yet to be studied to understand their adaptive ecology as holobionts comprehensively. The present study examined bacterial and fungal communities of larvae, adults, and feeding galleries from Austria and Czech Republic using high-throughput sequencing that elucidated the influence of geographic location, host, and life stage on the microbial assemblage in Eurasian spruce bark beetle,I. typographus. The most abundant bacterial genera inI. typographusincludedPseudoxanthomonas,Spiroplasma,Pseudomonas,Cellulomonas,Tyzzerella,Bacillus, andMycobacterium. Alternatively,Wickerhamomyces,Nakazawaea,Aspergillus,Ophiostoma,Cryptococcus,Rhexographium,Yamadazyma,Talaromyces, andKuraishiawere highly dominant fungal genera. Significant differences in bacterial and fungal community richness and diversity were detected among the tested samples. LEfSe analysis revealed species-specific bacterial and fungal biomarkers from different locations in the larvae, adults, and feeding gallery samples. PICRUSt2 and FUNGuild analysis documented putative roles of the bacterial and fungal communities in beetle holobiont and provided a foundation for downstream functional analyses. The current findings further enhanced our understanding of bark beetles as holobionts.

Fungal plasma biomarkers in patients admitted for inpatient treatment of alcohol use disorder.

Fungal plasma biomarkers have not been studied in patients with unhealthy alcohol use and no apparent end-stage liver disease. We examined the prevalence of fungal plasma biomarkers, assessed by the presence of anti-Saccharomyces cerevisiae antibodies (ASCA; IgA and IgM), and its disease correlates in patients with alcohol use disorder (AUD). We performed logistic regression analyses to detect the association between clinical and laboratory characteristics and the presence of fungal plasma biomarkers. We included 395 patients (75.9% male, median age of 49 years, and median body mass index of 25.6) who drank a median of 150 g of alcohol daily and had a median duration of AUD of 20 years. ASCA IgA and IgG were present in 34.4% and 14.9%, respectively, and 9.9% had both ASCA IgA and ASCA IgG. The presence of ASCA IgA was associated with male sex (p < 0.01); values of serum aspartate transferase (AST) (p = 0.02), gamma-glutamyl transferase (GGT) (p < 0.01), alkaline phosphatase (ALP) (p < 0.01), and bilirubin in the highest quartile (p < 0.01); Fibrosis-4 Index (FIB-4) values suggestive of advanced liver fibrosis (p < 0.01); and values of the macrophage activation factors sCD163 (p < 0.01) and sCD14 (p < 0.01), the cytokine IL-6 (p = 0.01), and lipopolysaccharide-binding protein in the highest quartile (p < 0.01). The presence of ASCA IgG was associated with omeprazole use (p = 0.04); values of AST (p = 0.04) and GGT (p = 0.04) in the highest quartile; FIB-4 values suggestive of advanced liver fibrosis (p < 0.01); and values of sCD163 (p < 0.01) in the highest quartile. The variables associated with the presence of both ASCA IgA and IgG were male sex (p = 0.04) and values of GGT (p = 0.04) and sCD163 in the highest quartile (p < 0.01). In AUD patients, the presence of fungal biomarkers in plasma was common and associated with FIB-4 values suggestive of advanced liver fibrosis and with markers of liver damage, monocyte activation, and microbial translocation, male gender, and omeprazole use. These findings suggest that the presence of plasma anti-Saccharomyces cerevisiae antibodies could be used as a biomarker for an elevated risk of progressive liver disease in patients with AUD.

Shifts in the diversity of root endophytic microorganisms across the life cycle of the ratooning rice Jiafuzhan.

The diversity of root endophytic microorganisms, which is closely related to plant life activities, is known to vary with the plant growth stage. This study on the ratooning rice Jiafuzhan explored the diversity of the root endophytic bacteria and fungi and their dynamics during the plant life cycle. By sequencing the 16S ribosomal ribonucleic acid (16S rRNA) and internal transcribed spacer (ITS) genes, 12,154 operational taxonomic units (OTUs) and 497 amplicon sequence variants (ASVs) were obtained, respectively. The root endophytic microorganisms of rice in the seedling, tillering, jointing, heading, and mature stages of the first crop and at 13, 25, and 60 days after regeneration (at the heading, full heading, and mature stages of the second crop, respectively) were analyzed using diversity and correlation analyses. There were significant differences in the α-diversity and β-diversity of root endophytic bacteria and fungi in the growth stage. Additionally, linear discriminant analysis (LDA) effect size (LEfSe) analysis revealed biomarker bacteria for each growth stage, but biomarker fungi did not exist in every stage. Moreover, the correlation analysis showed that the bacterial and fungal biomarkers interacted with each other. Furthermore, the nitrogen-fixing genus Bradyrhizobium existed in all growth stages. These findings indicate the pattern of root endophytic microorganisms of ratooning rice at different growth stages, and they provide new insights into the high yield of the second crop of ratooning rice (in light of the abundance of various bacteria and fungi).

Changes in assembly processes and differential responses of soil microbial communities during mining disturbance in mining reclamation and surrounding grassland

Soil microbes play critical roles in regulating ecosystem-level functioning and responding to environmental changes after disturbance events. However, a systematic understanding of soil microbial community assembly processes and responses in the context of severe anthropogenic disturbance remains lacking. Here, microbial communities collected from the soil in the mining reclamation and surrounding grassland of the Baiyinhua #1 open-pit coal mine were profiled and compared by three-generation PacBio sequencing to identify the response characteristics of the soil microbial communities to mining-induced disturbance, microbial community assembly and their relevance to environmental variables. The results suggested that the five locations surveyed had heterogeneous microbial community structures, distribution patterns and network topological characteristics, especially exhibiting contrasting differences between the mining reclamation and the grassland surrounding the mine, and different survey sites supported the enrichment of different and adaptative bacterial and fungal taxa and biomarkers. In comparison to the bacterial community, the fungal community was more susceptible to the current mining disturbances, and the stability of the core fungal interaction network, fungal diversity and resistance index were relatively low. Redundancy analysis showed that the differences in microbial communities were driven by the joint impacts of soil alkaline phosphatase and total nitrogen, and differences in bacterial communities were also driven by pH. Stochastic processes dominated the microbial assemblies at the entire site across the mining reclamation and grasslands around the coal mine, and dispersal limitation and drift were the dominant processes of the bacterial and fungal assemblies, respectively, at most individual sites. The relative influences of deterministic and stochastic processes in terms of shaping microbial community assemblies shifted with soil enzyme activity and nutrients. These findings provide critical insights into the prediction of soil ecosystem recovery after disturbance and deepen our understanding of the responses and assembly rules associated with severe anthropogenic disturbance.

Spectroscopic investigations of fungal biomarkers after exposure to heavy ion irradiation

The main objective of the ongoing and future space exploration missions is the search for traces of extant or extinct life (biomarkers) on Mars. One of the main limiting factors on the survival of Earth-like life is the presence of harmful space radiation, that could damage or modify also biomolecules, therefore understanding the effects of radiation on terrestrial biomolecules stability and detectability is of utmost importance. Which terrestrial molecules could be preserved in a Martian radiation scenario? Here, we investigated the potential endurance of fungal biomolecules, by exposing de-hydrated colonies of the Antarctic cryptoendolithic black fungus Cryomyces antarcticus mixed with Antarctic sandstone and with two Martian regolith analogues to increasing doses (0, 250 and 1000 Gy) of accelerated ions, namely iron (Fe), argon (Ar) and helium (He) ions. We analyzed the feasibility to detect fungal compounds with Raman and Infrared spectroscopies after exposure to these space-relevant radiations.

Effect of Irrigation Water Salinity on Soil Characteristics and Microbial Communities in Cotton Fields in Southern Xinjiang, China

Irrigation with saline water is a possible solution to alleviate freshwater shortages. The long-term use of saline water for irrigation requires consideration of the influence of salt on the environmental conditions of the soil. The objective of this field study was to determine the effects of three continuous years of saline water irrigation on physiochemical properties and microbial communities in drip-irrigated cotton fields. The three total dissolved solid (TDS) levels of irrigation water treatments were (i) 1 g L−1 (fresh water, FWI), (ii) 3 g L−1 (brackish water, BWI), and (iii) 7 g L−1 (salt water, SWI). After three years, the electrical conductivity (EC), sodium adsorption ratio (SAR), and contents of K+, Na+, Mg2+, Cl−, and SO42− in the SWI treatment were significantly higher than those in the FWI and BWI treatments, but there were no significant differences in EC and K+ between the FWI and BWI treatments. BWI treatment significantly increased microbial biomass carbon (MBC), microbial biomass nitrogen (MBN), urease, and sucrase contents. The diversity and abundance of bacteria and fungi were not affected by saline water irrigation, but the microbial community structure was altered. Saline water irrigation resulted in an elevation in the bacterial abundance of the phylum Chloroflexi and a decline in Proteobacteria and Actinobacteria. For fungi, the abundance of the phylum Ascomycota in the BWI treatment was greater than that in the FWI and SWI treatments. Linear discriminant analysis effect size (NMDS) results indicated clear variation in the microbiota profiles between the FWI, BWI, and SWI treatments for bacteria. Regarding the fungal microbiota profiles, the BWI and SWI treatments had similar microbiota profiles but were different from the FWI treatment. The number of bacterial biomarkers gradually increased with increasing total dissolved solids of irrigation water, while the number of fungal biomarkers gradually decreased. Additionally, cotton yield was significantly and positively correlated with the observed species of fungi, while it was significantly and negatively correlated with EC. Redundancy analysis (RDA) showed that bacterial community structure was regulated by SAR and fungal community structure was regulated by soil salinity and bulk density (BD). Future research will need to look into how the structure of the microbial community and the associated functional microorganisms are gradually changing with increased irrigation frequency under saline irrigation, as well as explore and screen for advantageous functional microorganisms.

Effect of two broad-spectrum fungicides on the microbial communities of a soil subjected to different degrees of water erosion

The impact of both fungicide and water erosion on soil microbial communities has been little studied, and far less in subhumid-dry climates. To help fill this knowledge gap, we evaluated the influence of two broad-spectrum fungicides applied to soil subjected to different degrees of water erosion on microbial population and function. Soil samples were taken from an experimental site under three water erosion levels: an agricultural land subjected to minimum water erosion by terrace farming (MIN), an agricultural land subjected to moderate water erosion without terrace farming (MOD), and a land with no water erosion control treatment (non-eroded, NON). Three dosages of both carbendazim and iprodione were applied to microcosms, and the responses of microbial community and function were examined after 30-day exposure. Phospholipid fatty acid (PLFA) analysis, soil enzyme activities, and microbial abundances estimated by quantitative real-time PCR (qPCR) were used to evaluate the impact of carbendazim and iprodione fungicides applied at three dosages on microbial community structure and enzyme activities. The lowest values of fluorescein diacetate hydrolase (FDA), dehydrogenase, urease, and glucosidase activities were registered in soil under moderate erosion, while the highest ones were observed in non-eroded soils. Both carbendazim and iprodione decreased C- and P-related activities, even when those fungicides were applied at field rate doses. Thus, phosphomonoesterase, glucosidase, and xylosidase in soil treated with fungicides applied at recommended field rate decreased by 46 %, 61 %, and 34 % compared to soil without fungicide application. The lowest values of PLFA biomarkers for Gram-positive bacteria, Gram-negative bacteria, and arbuscular mycorrhizal fungi were registered in soils treated with the highest dose of both carbendazim and iprodione. Thus, Gram-positive bacteria, Gram-negative bacteria, arbuscular mycorrhizal fungi, and fungal PLFA biomarkers in soils without fungicide application were about 36 %, 3 %, 47 %, and 82 % higher than those soils treated with the highest doses of fungicides, respectively. In addition, the highest doses of fungicide application tended to greater decrease total PLFAs in both non-eroded and minimum eroded compared to moderate eroded soils. Similarly, the response of bacterial and fungal populations to fungicide treatment was more pronounced in non-eroded soils than in eroded soils. This study illustrates how the interactions between fungicides and water erosion levels affect soil enzyme activities, microbial abundances, and microbial community structure in agroecosystems.

Which trial do we need? Combination treatment of Pneumocystis jirovecii pneumonia in non-HIV infected patients

Global cure will be evaluated at various time points and consists of clinical cure, radiological response, and mycological resolution. Clinical evaluation will be accompanied by fungal biomarker monitoring, and by TMP-SMX and caspofungin therapeutic drug monitoring.

Oral Fungal Alterations in Patients with COVID-19 and Recovered Patients.

The oral bacteriome, gut bacteriome, and gut mycobiome are associated with coronavirus disease 2019 (COVID-19). However, the oral fungal microbiota in COVID-19 remains unclear. This article aims to characterize the oral mycobiome in COVID-19 and recovered patients. Tongue coating specimens of 71 COVID-19 patients, 36 suspected cases (SCs), 22 recovered COVID-19 patients, 36 SCs who recovered, and 132 controls from Henan are collected and analyzed using internal transcribed spacer sequencing. The richness of oral fungi is increased in COVID-19 versus controls, and beta diversity analysis reveals separate fungal communities for COVID-19 and control. The ratio of Ascomycota and Basidiomycota is higher in COVID-19, and the opportunistic pathogens, including the genera Candida, Saccharomyces, and Simplicillium, are increased in COVID-19. The classifier based on two fungal biomarkers is constructed and can distinguish COVID-19 patients from controls in the training, testing, and independent cohorts. Importantly, the classifier successfully diagnoses SCs with positive specific severe acute respiratory syndrome coronavirus 2 immunoglobulin G antibodies as COVID-19 patients. The correlation between distinct fungi and bacteria in COVID-19 and control groups is depicted. These data suggest that the oral mycobiome may play a role in COVID-19.

Dual Disseminated Aspergillosis and Mucormycosis Diagnosed at Autopsy: A Report of Two Cases of Coinfection and a Review of the Literature.

Coinfection with invasive aspergillosis and mucormycosis in immunocompromised patients has been reported but is rarely confirmed by tissue histology or autopsy. Serum fungal biomarkers and culture are the primary diagnostic tools but are suboptimal for detecting fungal coinfection. Here, we present the cases of two patients who were immunocompromised due to hematologic malignancy where disseminated aspergillosis and mucormycosis coinfection was only diagnosed upon autopsy despite extensive fungal diagnostic workup, and also review recent literature of such instances of coinfection.

Fungal Biomarkers in Traditional Starter Determine the Chemical Characteristics of Turbid Rice Wine from the Rim of the Sichuan Basin, China.

The fungal community in Qu plays a key role in the formation of turbid rice wine (TRW) style. The Sichuan Basin and its surrounding areas have become one of the main TRW production regions in China; however, the fungal community in Qu and how they affect the characteristics of TRW remain unknown. Therefore, this study provided insight into the fungal biomarkers in Qu from Guang'an (GQ), Dazhou (DQ), Aba (AQ), and Liangshan (LQ), as well as their relationships with compounds in TRW. The main biomarkers in GQ were Rhizopus arrhizus, Candida glabrata, Rhizomucor pusillus, Thermomyces lanuginosus and Wallemia sebi. However, they changed to Saccharomycopsis fibuligera and Mucor indicus in DQ, Lichtheimia ramose in AQ, and Rhizopus microsporus and Saccharomyces cerevisiae in LQ. As a response to fungal biomarkers, the reducing sugar, ethanol, organic acids, and volatile compounds were also changed markedly in TRWs. Among important volatile compounds (VIP > 1.00), phenethyl alcohol (14.1-29.4%) was dominant in TRWs. Meanwhile, 3-methyl-1-butanol (20.6-56.5%) was dominant in all TRWs except that fermented by GQ (GW). Acetic acid (29.4%) and ethyl palmitate (10.1%) were dominant in GW and LW, respectively. Moreover, GQ biomarkers were positively correlated with acetic acid and all unique important volatile compounds in GW. DQ biomarkers had positive correlations with unique compounds of acetoin and ethyl 5-chloro-1,3,4-thiadiazole-2-carboxylate in DW. Meanwhile, the AQ biomarkers were positively correlated with all AW unique, important, and volatile compounds. Although there were not any unique volatile compounds in LW, 16 important volatile compounds in LW were positively related to LQ biomarkers. Obviously, biomarkers in different geographic Qu played vital roles in the formation of important volatile compounds, which could contribute specific flavor to TRWs. This study provided a scientific understanding for future efforts to promote the excellent characteristics of TRW by regulating beneficial fungal communities.

Average Daily Gain in Lambs Weaned at 60 Days of Age Is Correlated with Rumen and Rectum Microbiota.

Colonization of gastrointestinal microbiota in mammals during early life is vital to host health. The objective of this study was to investigate whether lambs with high and low ADG have a different rumen and rectum microbial community. Thus, we investigated potential relationships between rumen and rectum microbiota and average daily gain (ADG) in weaned lambs. Sixteen lambs with similar body weights (7.63 ± 1.18 kg) were selected at 30 days of age. At 60 days of age, lambs were weaned, and ADG was calculated from 60 to 90 days. Then, two groups were generated: higher ADG (HG, 134.17 ± 13.48 g/day) and lower ADG (LG, 47.50 ± 19.51 g/day). Microbiota was evaluated at 30, 60, and 90 days of age. The final live weight and ADG at 90 days of age was higher (p < 0.05) in the HG group compared to the LG group. The maturity of bacterial and fungal communities was increased (p < 0.05) in the HG group for the 30 days vs. 90 days comparison and 60 days vs. 90 days comparison. Linear discriminant analysis effect size (LEfSe) analysis revealed a total of 18 bacterial biomarkers that are ADG-specific in the rumen and 35 bacterial biomarkers in the rectum. Meanwhile, 15 fungal biomarkers were found in the rumen and 8 biomarkers were found in the rectum. Our findings indicated that ADG is related to the rumen and rectum microbiota in lambs.

Effect of disease severity on the structure and diversity of the phyllosphere microbial community in tobacco.

Tobacco target spot is a serious fungal disease and it is important to study the similarities and differences between fungal and bacterial community under different disease severities to provide guidance for the biological control of tobacco target spot. In this study, tobacco leaves at disease severity level of 1, 5, 7 and 9 (S1, S5, S7, and S9) were collected, both healthy and diseased leaf tissues for each level were sampled. The community structure and diversity of fungi and bacteria in tobacco leaves with different disease severities were compared using high-throughput sequencing technology. The results indicated that there was a significant differences in the community structure of fungi and bacteria for both healthy and diseased samples depending on the disease severity. In both healthy and diseased tobacco leaves for all four different disease severities, the most dominant fungal phylum was Basidiomycota with a high prevalence of genus Thanatephorus. The relative abundance of Thanatephorus was most found at S9 diseased samples. Proteobacteria represent the most prominent bacterial phylum, with Pseudomonas as predominant genus, followed by Pantoea. The relative abundance of Pseudomonas was most found at S7 healthy samples. In fungal community, the Alpha-diversity of healthy samples was higher than that of diseased samples. In contrast, in bacterial community, the Alpha-diversity of healthy samples was lower than that of diseased samples. LEfSe analysis showed that the most enrich fungal biomarker was Thanatephorus cucumeris in diseased samples. Clostridium disporicum and Ralstonia pickettii were the most enrich bacterial biomarker in healthy samples. FUNGuild analysis showed that the pathotroph mode was the most abundant trophic modes. The relative abundance of pathotroph mode in diseased samples changes insignificantly, but a peak at S5 was observed for healthy samples. PICRUSt analysis showed that most bacterial gene sequences seem to be independent of the disease severity. The results of this study provide scientific references for future studies on tobacco phyllosphere microecology aiming at prevention and control of tobacco target spot.

Disseminated Cryptococcosis and Pulmonary Mucormycosis: Dealing with Dual Mycoses in a Renal Transplant Patient.

We describe a 36-year-old post-renal transplant patient diagnosed with a rare dual infection by Cryptococcus neoformans and Lichtheimia ramosa. The case highlights the significance of invasive samples and accurate interpretation of fungal biomarkers in the diagnosis of fungal infections in immunosuppressed patients. The mortality in such cases is high owing to delay in diagnosis, inability to perform surgical management or antifungal resistance.

Improving lung cancer diagnosis with cancer, fungal, and imaging biomarkers

ObjectiveIndeterminate pulmonary nodules (IPNs) represent a significant diagnostic burden in health care. We aimed to compare a combination clinical prediction model (Mayo Clinic model), fungal (histoplasmosis serology), imaging (computed tomography [CT] radiomics), and cancer (high-sensitivity cytokeratin fraction 21; hsCYFRA 21-1) biomarker approach to a validated prediction model in diagnosing lung cancer. MethodsA prospective specimen collection, retrospective blinded evaluation study was performed in 3 independent cohorts with 6- to 30-mm IPNs (n = 281). Serum histoplasmosis immunoglobulin G and immunoglobulin M antibodies and hsCYFRA 21-1 levels were measured and a validated CT radiomic score was calculated. Multivariable logistic regression models were estimated with Mayo Clinic model variables, histoplasmosis antibody levels, CT radiomic score, and hsCYFRA 21-1. Diagnostic performance of the combination model was compared with that of the Mayo Clinic model. Bias-corrected clinical net reclassification index (cNRI) was used to estimate the clinical utility of a combination biomarker approach. ResultsA total of 281 patients were included (111 from a histoplasmosis-endemic region). The combination biomarker model including the Mayo Clinic model score, histoplasmosis antibody levels, radiomics, and hsCYFRA 21-1 level showed improved diagnostic accuracy for IPNs compared with the Mayo Clinic model alone with an area under the receiver operating characteristics curve of 0.80 (95% CI, 0.76-0.84) versus 0.72 (95% CI, 0.66-0.78). Use of this combination model correctly reclassified intermediate risk IPNs into low- or high-risk category (cNRI benign = 0.11 and cNRI malignant = 0.16). ConclusionsThe addition of cancer, fungal, and imaging biomarkers improves the diagnostic accuracy for IPNs. Integrating a combination biomarker approach into the diagnostic algorithm of IPNs might decrease unnecessary invasive testing of benign nodules and reduce time to diagnosis for cancer.

The Comparative Evaluation of the Fujifilm Wako β-Glucan Assay and Fungitell Assay for Diagnosing Invasive Fungal Disease.

Serum 1,3-β-d-glucan(BDG) is a broad fungal biomarker for invasive fungal disease (IFD). More data is still required to support the Fujifilm Wako assay as a valuable alternative to the widely used Fungitell assay. We included archived serum samples from 157 individuals (97 cases; 33-IA, 64-IC, and 60 controls) for the comparative performance evaluation of the Fungitell assay and the Fujifilm Wako assay for IFD diagnosis. The BDG value was significantly higher in patients with IFD vs. controls (70.79 pg/mL vs. 3.03 pg/mL, p: 0.0002). An area under the curve (AUC) for the IFD, IC, and IA diagnosis was 0.895, 0.910, and 0.866, respectively, for the Fujifilm Wako assay. Based on the highest Youden's index (0.667), a cutoff of 5 pg/mL was selected as the optimum for the Fujifilm Wako assay with good sensitivity (79.4%), specificity (88.3%) and agreement (84.7%, Cohen's k:0.691) with the Fungitell assay. The mean run-time of the Fujifilm Wako assay was 70.12 min, and real-time observation allowed earlier time to result in Fujifilm Wako vs. Fungitell assay (37 vs. 120 min, p: &lt; 0.0001). Thus, our findings support the diagnostic value of the Fujifilm Wako assay for the diagnosis of IFD. However, there is still a need to validate diagnostic protocols to optimize their use in multi-centre studies with different patient groups.

The Use of Host Biomarkers for the Management of Invasive Fungal Disease.

Invasive fungal disease (IFD) causes severe morbidity and mortality, and the number of IFD cases is increasing. Exposure to opportunistic fungal pathogens is inevitable, but not all patients with underlying diseases increasing susceptibility to IFD, develop it. IFD diagnosis currently uses fungal biomarkers and clinical risk/presentation to stratify high-risk patients and classifies them into possible, probable, and proven IFD. However, the fungal species responsible for IFD are highly diverse and present numerous diagnostic challenges, which culminates in the empirical anti-fungal treatment of patients at risk of IFD. Recent studies have focussed on host-derived biomarkers that may mediate IFD risk and can be used to predict, and even identify IFD. The identification of novel host genetic variants, host gene expression changes, and host protein expression (cytokines and chemokines) associated with increased risk of IFD has enhanced our understanding of why only some patients at risk of IFD actually develop disease. Furthermore, these host biomarkers when incorporated into predictive models alongside conventional diagnostic techniques enhance predictive and diagnostic results. Once validated in larger studies, host biomarkers associated with IFD may optimize the clinical management of populations at risk of IFD. This review will summarise the latest developments in the identification of host biomarkers for IFD, their use in predictive modelling and their potential application/usefulness for informing clinical decisions.

Improving Lung Cancer Diagnosis with CT Radiomics and Serum Histoplasmosis Testing.

Indeterminate pulmonary nodules (IPN) are a diagnostic challenge in regions where pulmonary fungal disease and smoking prevalence are high. We aimed to determine the impact of a combined fungal and imaging biomarker approach compared with a validated prediction model (Mayo) to rule out benign disease and diagnose lung cancer. Adults ages 40 to 90 years with 6-30 mm IPNs were included from four sites. Serum samples were tested for histoplasmosis IgG and IgM antibodies by enzyme immunoassay and a CT-based risk score was estimated from a validated radiomic model. Multivariable logistic regression models including Mayo score, radiomics score, and IgG and IgM histoplasmosis antibody levels were estimated. The areas under the ROC curves (AUC) of the models were compared among themselves and to Mayo. Bias-corrected clinical net reclassification index (cNRI) was estimated to assess clinical reclassification using a combined biomarker model. We included 327 patients; 157 from histoplasmosis-endemic regions. The combined biomarker model including radiomics, histoplasmosis serology, and Mayo score demonstrated improved diagnostic accuracy when endemic histoplasmosis was accounted for [AUC, 0.84; 95% confidence interval (CI), 0.79-0.88; P < 0.0001 compared with 0.73; 95% CI, 0.67-0.78 for Mayo]. The combined model demonstrated improved reclassification with cNRI of 0.18 among malignant nodules. Fungal and imaging biomarkers may improve diagnostic accuracy and meaningfully reclassify IPNs. The endemic prevalence of histoplasmosis and cancer impact model performance when using disease related biomarkers. Integrating a combined biomarker approach into the diagnostic algorithm of IPNs could decrease time to diagnosis.

348. Cell-free plasma next-generation sequencing assists in the evaluation of invasive mold infection in patients with COVID-19: a case series

Abstract Background Distinguishing COVID-19 Associated Pulmonary Aspergillosis (CAPA) and invasive mold infections (IMIs) from other causes of secondary pneumonia in COVID-19 can be challenging. 1,3-β-D-Glucan and galactomannan are commonly utilized biomarkers for the workup of IMIs but are limited by a lack of specificity and sensitivity respectively. Cell-free plasma next-generation sequencing (cfNGS) is a promising non-invasive approach that can provide direct detection of pathogens in patient's serum. This study explored its potential role in the evaluation of secondary pneumonia in patients with COVID-19. Methods We performed a retrospective single-center observational study from March 2020 to December 2021 at Virginia Commonwealth University Medical Center, a 811-bed tertiary care center, to evaluate patients with laboratory confirmed SARS-CoV-2 virus infection who underwent cfNGS for the evaluation of CAPA. CfNGS (Karius, Inc., Redwood City, CA) was performed at the discretion of the clinical provider and we evaluated the test indication, patient history, clinical impact, correlation with serum biomarkers, and 30 day all-cause mortality. Results Thirteen patients were evaluated and none had Aspergillus species detected. One patient had Pneumocystis jirovecii on cfNGS. There was a 76.9% (10/13) concordance rate with patients’ serum fungal biomarkers. CfNGS also detected concomitant organisms in 53.8% (7/13) of our cohort. These data assisted in changes of clinical management for 84.6% (11/13) of patients and lead to the change in antifungal usage in 69.2% (9/13). Conclusion In this study, both negative and positive cfNGS test results assisted in important clinical decision making. cfNGS may have a role in the evaluation of CAPA or other IMIs in patients with COVID-19. Disclosures Megan M. Morales, MD, Karius: Paid speaker.