Performance of the Aspergillus galactomannan lateral flow assay with a digital reader for the diagnosis of invasive aspergillosis: a multicenter study.

PURPOSE: The objective of this multicenter study was to compare the diagnostic performance of lateral flow assay (LFA) and enzyme-linked immunosorbent assay (ELISA) to detect the Dynamiker Aspergillus Galactomannan levels in serum and bronchoalveolar lavage fluid (BALF) samples for I. METHODS: We registered 310 clinically suspected Aspergillus infection patients from December 2021 to February 2023 and classified them into subgroups as the "IA group" and "non-IA group" based on the latest EORTC/MSG guidelines. The immunoassays were analyzed by LFA and ELISA respectively. RESULTS: Galactomannan was examined using LFA, and serum and BALF samples demonstrated sensitivities of 82.57% and 89.47%, specificities of 90.76% and 92.00%, PPVs of 89.11% and 96.23%, and NPVs of 85.04% and 79.31%, respectively. Galactomannan was observed using two assays in serum and BALF samples and showed PPAs of 95.11% and 93.33%, NPAs of 89.19% and 96.30%, and TPAs of 92.47% and 94.25%, respectively. The ROC curve demonstrated that LFA had optimum diagnostic value when the index value (I value) = 0.5, the sensitivity was 84.94%, and the specificity was 90.97%. CONCLUSION: Compared to the ELISA method, the LFA has shown excellent performance for the diagnosis of IA in serum and BALF sample and can be used as an assay for the early diagnosis of patients with IA. The dynamic change in galactomannan levels may be useful for assessing treatment response.

In vitro antifungal susceptibility profile and genotypic characterization of clinical Aspergillus isolates in Eastern China on behalf of Eastern China Invasive Fungi Infection Group.

Aspergillus species is a widespread environmental mould that can cause aspergillosis. The purpose of this study was to investigate the antifungal susceptibility profile and genotypic characterization of clinical Aspergillus isolates from different provinces in Eastern China. The data included the antifungal susceptibility distributions with eight common antifungal drugs, cyp51A gene mutations of triazole-resistant Aspergillus fumigatus sensu stricto, and the genotypic relationships among the A. fumigatus sensu stricto isolates based on microsatellite typing. A. fumigatus sensu lato was the most common clinical Aspergillus species (n = 252), followed by A. flavus (n = 169), A. terreus (n = 37), A. niger (n = 29), and A. nidulans (n = 4). The modal minimum effective concentration values of micafungin and anidulafungin were lower than those of caspofungin for all Aspergillus species. The in vitro efficacy of isavuconazole was similar to that of voriconazole against most Aspergillus species. Sequencing revealed cyp51A gene mutations TR34/L98H, TR34/L98H/S297T/F495I, and TR46/Y121F/T289A in four triazole-resistant A. fumigatus sensu stricto. Phylogenetic analyses using microsatellite markers of A. fumigatus sensu stricto revealed that 211 unique genotypes clustered into two clades. The data demonstrate the diversity of clinically relevant Aspergillus species in Eastern China. Routine antifungal susceptibility testing should be performed to monitor the antifungal resistance and guide clinical therapy.

The 6-year multicenter study collected a total of 491 Aspergillus isolates from Eastern China to investigate the in vitro antifungal susceptibility to eight antifungal drugs, the cyp51A gene mutations of triazole-resistant A. fumigatus sensu stricto, and the genetic relatedness through microsatellite typing.

MALDI-TOF MS Identification of some Clinically-Relevant Filamentous Fungi with the Direct Smear Method, a Simple Sample Preparation Method.

BACKGROUND: Matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS) is a powerful technique for the identification of microorganisms. The technique normally requires a sample preparation procedure before instrumental analysis, which can be somewhat labor-intensive when numbers of samples are large. The direct smear method, in which samples are directly smeared on the sample plates and subsequently subjected to instrumental analyses, can save time and is less labor-intensive. However, the method has rarely been tested on filamentous fungi, although it has been successfully used in the identification of bacteria and yeasts. In the present study, we examined the method using clinically-collected filamentous fungi. METHODS: Three hundred forty-eight isolates of filamentous fungi representing 9 species collected from body fluids of patients were analyzed on the VITEK MS version 3.0 system, a popular commercial MALDI-TOF MS system, using the direct smear method. For those misidentified or unidentified, the samples were retested. All fungal species were determined through DNA sequencing. RESULTS: Among 334 isolates that were included in the database of the VITEK system, 286 (85.6%) samples were correctly identified. After retesting, the rate of correct identification increased to 91.0%. Aspergillus fumigatus exhibited a 95.2% rate of correct identification before retesting, whereas Aspergillus niger showed the rate at only 46.5% (58.1% even with retesting). CONCLUSIONS: The direct smear method could be used in the identification of filamentous fungi found in body fluids of patients by MALDI-TOF MS at good rates of correct identification. The method is simple and time-saving, and deserves further evaluation.

Prevalence and molecular characteristics of polymyxin-resistant Enterobacterales in a Chinese tertiary teaching hospital.

Introduction: Polymyxin-resistant Enterobacterales poses a significant threat to public health globally, but its prevalence and genomic diversity within a sole hospital is less well known. In this study, the prevalence of polymyxin-resistant Enterobacterales in a Chinese teaching hospital was investigated with deciphering of their genetic determinants of drug resistance. Methods: Polymyxin-resistant Enterobacterales isolates identified by matrix-assisted laser desorption were collected in Ruijin Hospital from May to December in 2021. Both the VITEK 2 Compact and broth dilution methods were used to determine polymyxin B (PMB) susceptibility. Polymyxin-resistant isolates were further characterized by molecular typing using PCR, multi-locus sequence typing, and sequencing of the whole genome. Results: Of the 1,216 isolates collected, 32 (2.6%) across 12 wards were polymyxin-resistant (minimum inhibitory concentration (MIC) range, PMB 4-256 mg/ml, and colistin 4 ≥ 16 mg/ ml). A total of 28 (87.5%) of the polymyxin-resistant isolates had reduced susceptibility to imipenem and meropenem (MIC ≥ 16 mg/ml). Of the 32 patients, 15 patients received PMB treatment and 20 survived before discharge. The phylogenetic tree of these isolates showed they belonged to different clones and had multiple origins. The polymyxin-resistant Klebsiella pneumoniae isolates belonged to ST-11 (85.72%), ST-15 (10.71%), and ST-65 (3.57%), and the polymyxin-resistant Escherichia coli belonged to four different sequence types, namely, ST-69 (25.00%), ST-38 (25.00%), ST-648 (25.00%), and ST-1193 (25.00%). In addition, six mgrB specific mutations (snp_ALT c.323T>C and amino acid change p.Val8Ala) were identified in 15.6% (5/32) of the isolates. mcr-1, a plasmid-mediated polymyxin-resistant gene, was found in three isolates, and non-synonymous mutations including T157P, A246T, G53V, and I44L were also observed. Discussion: In our study, a low prevalence of polymyxin-resistant Enterobacterales was observed, but these isolates were also identified as multidrug resistant. Therefore, efficient infection control measures should be implemented to prevent the further spread of resistance to last-line polymyxin therapy.

Clinical and Microbiological Characteristics of Aspergillosis at a Chinese Tertiary Teaching Hospital.

Background: Aspergillus spp. infection in immunocompromised patients results in increasing morbidity and mortality. This study investigated clinical and microbiological characteristics of aspergillosis in a Chinese tertiary teaching hospital. Methods: A total of 114 patients with aspergillosis were included over a 5-year period at Ruijin Hospital. In sum, 114 Aspergillus strains were isolated and identified at species level using matrix-assisted laser desorption ionization time-of-flight mass spectrometry, confirmed by ITS gene region and ß-tubulin (BenA) gene sequencing. Sensititre YeastOne was used in vitro to test susceptibility to antifungal drugs: amphotericin B, itraconazole, voriconazole, posaconazole, isavuconazole, micafungin, anidulafungin, and caspofungin. Results: The median age of the patients was 61 (19) years, men accounted for 53.5% (n=61) of the sample, about 64% were immunocompromised, and 36% had underlying diseases. Pulmonary diseases accounted for 27.2%. Aspergillus isolates were mainly isolated from sputum (n=42, 36.8%). Antifungal therapy was administered to 106 (93.0%) patients and voriconazole (n=76, 66.7%) was the most frequently used as empirical therapy. Aspergillus fumigatus (n=69, 60.5%) was the most common species. There was a 73.7% concordance between MALDI-TOF MS and molecular identification. All Aspergillus isolates showed good susceptibility to anidulafungin and caspofungin. Conclusion: Immunocompromised patients are an at-risk population for aspergillosis, and voriconazole was used as empirical therapy in Ruijin Hospital, China. A. fumigatus was the predominant Aspergillus species causing aspergillosis, and A. flavus - as non-A. fumigatus species are increasing - the second-leading cause of aspergillosis. Anidulafungin and caspofungin were the most active in vitro against the Aspergillus isolates tested. The MALDI-TOF MS method showed good accuracy for identification of common Aspergillus spp. In vitro antifungal-susceptibility testing is crucially important for decisions on effective therapy with aspergillosis.

Prevalence and Molecular Characteristics of Polymyxin-Resistant Pseudomonas aeruginosa in a Chinese Tertiary Teaching Hospital.

Polymyxin-resistant Pseudomonas aeruginosa is a major threat to public health globally. We investigated the prevalence of polymyxin-resistant P. aeruginosa in a Chinese teaching hospital and determined the genetic and drug-resistant phenotypes of the resistant isolates. P. aeruginosa isolates identified by MALDI-TOF MS were collected across a 3-month period in Ruijin Hospital. Antimicrobial susceptibility was determined by a Vitek-2 Compact system with broth dilution used to determine polymyxin B (PMB) susceptibility. Polymyxin-resistant isolates were further characterized by molecular typing using PCR, multi-locus sequence typing (MLST) and whole-genome sequencing. Phylogenetic relationships were analyzed using single nucleotide polymorphism (SNP) from the whole-genome sequencing. Of 362 P. aeruginosa isolates collected, 8 (2.2%) isolates from separate patients across six wards were polymyxin-resistant (MIC range, PMB 4-16 µg/mL and colistin 4-≥16 µg/mL). Four patients received PMB treatments (intravenous, aerosolized and/or topical) and all patients survived to discharge. All polymyxin-resistant isolates were genetically related and were assigned to five different clades (Isolate 150 and Isolate 211 being the same ST823 type). Genetic variations V51I, Y345H, G68S and R155H in pmrB and L71R in pmrA were identified, which might confer polymyxin resistance in these isolates. Six of the polymyxin-resistant isolates showed reduced susceptibility to imipenem and meropenem (MIC range ≥ 16 µg/mL), while two of the eight isolates were resistant to ceftazidime. We revealed a low prevalence of polymyxin-resistant P. aeruginosa in a Chinese teaching hospital with most polymyxin-resistant isolates being multidrug-resistant. Therefore, effective infection control measures are urgently needed to prevent further spread of resistance to the last-line polymyxins.

Integrated analysis of gut microbiome and host immune responses in COVID-19.

Emerging evidence indicates that the gut microbiome contributes to the host immune response to infectious diseases. Here, to explore the role of the gut microbiome in the host immune responses in COVID-19, we conducted shotgun metagenomic sequencing and immune profiling of 14 severe/critical and 24 mild/moderate COVID-19 cases as well as 31 healthy control samples. We found that the diversity of the gut microbiome was reduced in severe/critical COVID-19 cases compared to mild/moderate ones. We identified the abundance of some gut microbes altered post-SARS-CoV-2 infection and related to disease severity, such as Enterococcus faecium, Coprococcus comes, Roseburia intestinalis, Akkermansia muciniphila, Bacteroides cellulosilyticus and Blautia obeum. We further analyzed the correlation between the abundance of gut microbes and host responses, and obtained a correlation map between clinical features of COVID-19 and 16 severity-related gut microbe, including Coprococcus comes that was positively correlated with CD3+/CD4+/CD8+ lymphocyte counts. In addition, an integrative analysis of gut microbiome and the transcriptome of peripheral blood mononuclear cells (PBMCs) showed that genes related to viral transcription and apoptosis were up-regulated in Coprococcus comes low samples. Moreover, a number of metabolic pathways in gut microbes were also found to be differentially enriched in severe/critical or mild/moderate COVID-19 cases, including the superpathways of polyamine biosynthesis II and sulfur oxidation that were suppressed in severe/critical COVID-19. Together, our study highlighted a potential regulatory role of severity related gut microbes in the immune response of host.

Integrating longitudinal clinical laboratory tests with targeted proteomic and transcriptomic analyses reveal the landscape of host responses in COVID-19.

The pathophysiology of coronavirus disease 19 (COVID-19) involves a multitude of host responses, yet how they unfold during the course of disease progression remains unclear. Here, through integrative analysis of clinical laboratory tests, targeted proteomes, and transcriptomes of 963 patients in Shanghai, we delineate the dynamics of multiple circulatory factors within the first 30 days post-illness onset and during convalescence. We show that hypercortisolemia represents one of the probable causes of acute lymphocytopenia at the onset of severe/critical conditions. Comparison of the transcriptomes of the bronchoalveolar microenvironment and peripheral blood indicates alveolar macrophages, alveolar epithelial cells, and monocytes in lungs as the potential main sources of elevated cytokines mediating systemic immune responses and organ damages. In addition, the transcriptomes of patient blood cells are characterized by distinct gene regulatory networks and alternative splicing events. Our study provides a panorama of the host responses in COVID-19, which may serve as the basis for developing further diagnostics and therapy.

Rare/cryptic Aspergillus species infections and importance of antifungal susceptibility testing.

BACKGROUND: The number of patients infected with Aspergillus rose dramatically in recent years. However, studies on the clinical spectrum and antifungal susceptibilities of non-classical (non-fumigatus, non-flavus, non-niger and non-terreus) pathogenic Aspergillus species are very limited. OBJECTIVES: We examined the clinical spectrum and antifungal susceptibilities of 34 non-duplicated, non-classical Aspergillus isolates collected from Hong Kong, Shenzhen and Shanghai. METHODS: The Aspergillus isolates were identified by internal transcribed spacer, partial BenA and partial CaM sequencing and phylogenetic analyses. Susceptibility testing against eight antifungals was performed following the European Committee for Antimicrobial Susceptibility Testing's methodology. RESULTS: The 34 Aspergillus isolates were identified as 14 different rare/cryptic species of four sections (Flavi [n = 8], Nidulantes [n = 8], Nigri [n = 17] and Restricti [n = 1]). Except for one patient whose clinical history could not be retrieved, 72.7% of the remaining patients had underlying conditions predisposing them to Aspergillus infections. The most common diseases were pulmonary infections (n = 15), followed by skin/nail infections (n = 6), chronic otitis externa and/or media (n = 5), wound infections (n = 2) and mastoiditis/radionecrosis (n = 1), while three were colonisations. Five patients succumbed due to the infections during the admission, and another two died 5 years later because of chronic pulmonary aspergillosis. Antifungal susceptibility testing showed that they possessed different susceptibility profiles compared to the classical Aspergillus species. The majority of isolates characterised were sensitive or wild-type to amphotericin B. The minimum effective concentrations for all the three echinocandins were also low. CONCLUSION: Susceptibility testing should be performed for infections due to these rare/cryptic Aspergillus species to guide proper patient management.

A 10-year study reveals clinical and laboratory evidence for the 'semi-invasive' properties of chronic pulmonary aspergillosis.

In recent years, infections caused by Aspergillus sp. have become an emerging focus of clinical microbiology and infectious disease, as the number of patients infected with Aspergillus sp. has increased markedly. Although chronic pulmonary aspergillosis (CPA) is considered a 'semi-invasive' or 'intermediate' disease, little data are available for the direct comparison of CPA with invasive pulmonary aspergillosis (IPA) and pulmonary aspergilloma (PA) to quantify invasiveness. In this study, we compared the characteristics of CPA with those of IPA and PA among hospitalized patients over a 10-year period. A total of 29, 51 and 31 cases of CPA, IPA and PA, respectively, were included. An increasing trend in galactomannan antigen seropositivity rate from PA (24.1%) to CPA (35.7%) to IPA (54.9%) and an opposite trend for anti-Aspergillus antibody (PA (71.0%) to CPA (45.8%) to IPA (7.1%)) were observed. Eight percent of CPA patients were infected with more than one Aspergillus sp. The survival rate of the CPA group also fell between the survival rate of PA and IPA, confirming the intermediate severity of CPA. The survival rate of the CPA group became significantly higher than that of the IPA group from day 180 onwards until 2 years after admission (P<0.05). The survival rate of the CPA group remained lower than that of the PA group from day 30 onwards until 2 years after admission. Poor prognostic factors for CPA included older age (P=0.019), higher total leukocyte count (P=0.011) and higher neutrophil count (P=0.012) on admission. This study provided clinical and laboratory evidence for the semi-invasive properties of CPA.

[The retrospective study of serum aspergillus galactomannan (GM) antigen assay in invasive aspergillosis on hematological diseases].

OBJECTIVE: To explore the relationship between the optical density index of serum aspergillus galactomannan (GM) assay and invasive aspergillosis (IA). METHODS: From Jan 2008 to Dec 2011, 825 hematological diseases patients with neutrophil count <0.5×109/L9 by continuous blood count tests were admitted into our hospital. The optical density index of GM assay was ≥0.5 at least once. Of 825 patients, 247 cases were manifested as fever during hospitalization. The optical density index of GM antigen was detected by enzyme-linked immunosorbent assay, and the sensitivity and specificity of optical density ranged in 0.5-1.5. RESULTS: In this study, the sensitivity and specificity of GM assay with continuous twice samples (73% and 93%, respectively) were higher than single sample (66% and 80%, respectively) when optical density index ≥1.0. 69 cases were diagnosed as proven IA with the incidence rate of 8.36%. CONCLUSION: The cut-off level for serum GM antigen assay should be decided as optical density index in two continuous samples of ≥1.0.