Quantitative PCR (qPCR) Detection of Mucorales DNA in Bronchoalveolar Lavage Fluid To Diagnose Pulmonary Mucormycosis

Invasive Fungal Disease, Isavuconazole Treatment Failure, and Death in Acute Myeloid Leukemia Patients

We present 2 fatal cases of invasive fungal disease with isavuconazole treatment failure in immunocompromised patients: one with a TR34-L98H azole–resistant Aspergillus fumigatus isolate and the other a Rhizomucor–A. fumigatus co-infection. Such patients probably require surveillance by galactomannan antigen detection and quantitative PCRs for A. fumigatus and Mucorales fungi.

A New Age in Molecular Diagnostics for Invasive Fungal Disease: Are We Ready?

Invasive fungal diseases (IFDs) present an increasing global burden in immunocompromised and other seriously ill populations, including those caused by pathogens which are inherently resistant or less susceptible to antifungal drugs. Early diagnosis encompassing accurate detection and identification of the causative agent and of antifungal resistance is critical for optimum patient outcomes. Many molecular-based diagnostic approaches have good clinical utility although interpretation of results should be according to clinical context. Where an IFD is in the differential diagnosis, panfungal PCR assays allow the rapid detection/identification of fungal species directly from clinical specimens with good specificity; sensitivity is also high when hyphae are seen in the specimen including in paraffin-embedded tissue. Aspergillus PCR assays on blood fractions have good utility in the screening of high risk hematology patients with high negative predictive value (NPV) and positive predictive value (PPV) of 94 and 70%, respectively, when two positive PCR results are obtained. The standardization, and commercialization of Aspergillus PCR assays has now enabled direct comparison of results between laboratories with commercial assays also offering the simultaneous detection of common azole resistance mutations. Candida PCR assays are not as well standardized with the only FDA-approved commercial system (T2Candida) detecting only the five most common species; while the T2Candida outperforms blood culture in patients with candidemia, its role in routine Candida diagnostics is not well defined. There is growing use of Mucorales-specific PCR assays to detect selected genera in blood fractions. Quantitative real-time Pneumocystis jirovecii PCRs have replaced microscopy and immunofluorescent stains in many diagnostic laboratories although distinguishing infection may be problematic in non-HIV-infected patients. For species identification of isolates, DNA barcoding with dual loci (ITS and TEF1α) offer optimal accuracy while next generation sequencing (NGS) technologies offer highly discriminatory analysis of genetic diversity including for outbreak investigation and for drug resistance characterization. Advances in molecular technologies will further enhance routine fungal diagnostics.

Clinical characteristics and prognoses of pulmonary mucormycosis in four children

IMPORTANCE

Pulmonary mucormycosis is life threatening and carries a poor prognosis. Identification of factors that improve prognosis is urgently necessary.

OBJECTIVE

To analyze the clinical features and outcomes of pulmonary mucormycosis in children.

METHODS

A retrospective analysis of clinical data of four cases with pulmonary mucormycosis was conducted in Beijing Children's Hospital from January 2017 to December 2018.

RESULTS

Underlying diseases were identified in all four cases (diabetes in three individuals and a hematological malignancy in one individual). The predominant clinical manifestations were fever, cough, chest pain and hemoptysis. Imaging features included consolidation or nodules with cavities. All four cases were treated with liposomal amphotericin B, one case underwent lobectomy, and three cases received a full course of posaconazole. All four cases were cured.

INTERPRETATION

Patients with pulmonary mucormycosis often have underlying diseases. Imaging features are relatively characteristic. Treatment with liposomal amphotericin B at an early stage and a sufficient course of posaconazole for maintenance significantly improves prognosis.

Molecular Diagnostics of Mucormycosis in Hematological Patients: A Literature Review

OBJECTIVES

to analyze the results of molecular methods applying for the diagnosis of mucormycosis in hematologic patients based on a literature review.

DATA SOURCES

A systematic search in databases PubMed, Google Scholar for August 2019. Review eligibility criteria: original articles published in English, studies of molecular methods for the diagnosis of mucormycosis in hematologic patients.

RESULTS

We analyzed the research data from 116 hematological patients with mucormycosis, including children (6%). Patients with localized forms of mucormycosis prevailed (72%), and lung involvement was diagnosed in 58% of these cases. For molecular verification of the causative agent of mucormycosis, blood serum was most often used, less commonly postoperative and autopsy material, biopsy specimens, formalin-fixed paraffin-embedded samples and bronchoalveolar lavage, pleural fluid and sputum. The sensitivity of molecular diagnostics of mucormycosis in a cohort of hematological patients was 88.2%.

CONCLUSION

The use of molecular techniques along with standard mycological methods will improve the diagnostics of mucormycosis in hematologic patients. However, prospective studies of the effectiveness of molecular methods for the diagnosis of mucormycosis of various etiologies in hematological patients, including children, using bronchoalveolar lavage (BAL) and cerebrospinal fluid (CSF) are needed.

Molecular Diagnostic Advances in Transplant Infectious Diseases

PURPOSE OF REVIEW

The infectious complications of transplantation can have devastating consequences for patients. Early and accurate diagnosis is essential to good outcomes. This review describes recent advances in pathogen-directed diagnostic testing and discusses the role of new methods for transplant infectious diseases.

RECENT FINDINGS

Several molecular assays have been introduced into clinical practice in recent years. When the results of rapid testing are linked to patient-specific interventions, improved outcomes can be realized. Syndromic testing along with metagenomic next-generation sequencing (mNGS) represents novel approaches to infection diagnosis. However, the optimal use of these tests for transplant patients along with an overall assessment of cost-effectiveness demands further study. Molecular diagnostics are revolutionizing transplant care. Clinicians need to be aware of the current diagnostic landscape and have a working knowledge of the nuances related to test performance, result interpretation, and cost.

Updates on the Taxonomy of Mucorales with an Emphasis on Clinically Important Taxa

Fungi of the order Mucorales colonize all kinds of wet, organic materials and represent a permanent part of the human environment. They are economically important as fermenting agents of soybean products and producers of enzymes, but also as plant parasites and spoilage organisms. Several taxa cause life-threatening infections, predominantly in patients with impaired immunity. The order Mucorales has now been assigned to the phylum Mucoromycota and is comprised of 261 species in 55 genera. Of these accepted species, 38 have been reported to cause infections in humans, as a clinical entity known as mucormycosis. Due to molecular phylogenetic studies, the taxonomy of the order has changed widely during the last years. Characteristics such as homothallism, the shape of the suspensors, or the formation of sporangiola are shown to be not taxonomically relevant. Several genera including Absidia, Backusella, Circinella, Mucor, and Rhizomucor have been amended and their revisions are summarized in this review. Medically important species that have been affected by recent changes include Lichtheimia corymbifera, Mucor circinelloides, and Rhizopus microsporus. The species concept of Rhizopus arrhizus (syn. R. oryzae) is still a matter of debate. Currently, species identification of the Mucorales is best performed by sequencing of the internal transcribed spacer (ITS) region. Ecologically, the Mucorales represent a diverse group but for the majority of taxa, the ecological role and the geographic distribution remain unknown. Understanding the biology of these opportunistic fungal pathogens is a prerequisite for the prevention of infections, and, consequently, studies on the ecology of the Mucorales are urgently needed.

Pathogenicity patterns of mucormycosis: epidemiology, interaction with immune cells and virulence factors

Fungi of the basal lineage order Mucorales are able to cause infections in animals and humans. Mucormycosis is a well-known, life-threatening disease especially in patients with a compromised immune system. The rate of mortality and morbidity caused by mucormycosis has increased rapidly during the last decades, especially in developing countries. The systematic, phylogenetic, and epidemiological distributions of mucoralean fungi are addressed in relation to infection in immunocompromised patients. The review highlights the current achievements in (i) diagnostics and management of mucormycosis, (ii) the study of the interaction of Mucorales with cells of the innate immune system, (iii) the assessment of the virulence of Mucorales in vertebrate and invertebrate infection models, and (iv) the determination of virulence factors that are key players in the infection process, for example, high-affinity iron permease (FTR1), spore coat protein (CotH), alkaline Rhizopus protease enzyme (ARP), ADP-ribosylation factor (ARF), dihydrolipoyl dehydrogenase, calcineurin (CaN), serine and aspartate proteases (SAPs). The present mini-review attempts to increase the awareness of these difficult-to-manage fungal infections and to encourage research in the detection of ligands and receptors as potential diagnostic parameters and drug targets.

Mucormycosis as the Elusive Cause of an Aortic Thrombus and Tissue-Obliterating Abscess

Invasive mucormycosis is an increasingly common cause of morbidity and mortality in hematologic malignancy patients. Early consideration of the diagnosis is essential in at-risk patients, exhibiting suggestive signs and symptoms. A 56-year-old female with acute myeloid leukemia initially presented with neutropenic fever before subsequently developing dense hemiplegia due to septic emboli to the spine and multifocal abscesses. These findings were later determined to be a result of a disseminated mucor infection and represented a rare manifestation of the disease. Despite the disseminated nature of the infection, identification of the causative organism was initially impeded by limitations in obtaining a tissue sample in a severely thrombocytopenic patient, as is common among hematologic malignancy patients. As a result of this limitation, diagnosis was ultimately made via PCR on bronchiolar lavage fluid. Early consideration of the diagnosis with prompt initiation of treatment is of utmost importance in this invasive infection. Further research is needed to identify and validate rapid, minimally invasive strategies for early diagnosis of mucormycosis.

Molecular Strategies to Diagnose Mucormycosis

Molecular techniques have provided a new understanding of the epidemiology of mucormycosis and improved the diagnosis and therapeutic management of this life-threatening disease. PCR amplification and sequencing were first applied to better identify isolates that were grown from cultures of biopsies or bronchalveolar lavage samples that were collected in patients with Mucorales infection. Subsequently, molecular techniques were used to identify the fungus directly from the infected tissues or from bronchalveolar lavage, and they helped to accurately identify Mucorales fungi in tissue samples when the cultures were negative. However, these tools require invasive sampling (biospsy, bronchalveolar lavage), which is not feasible in patients in poor condition in Hematology or Intensive Care units. Very recently, PCR-based procedures to detect Mucorales DNA in non-invasive samples, such as plasma or serum, have proved successful in diagnosing mucormycosis early in all patients, whatever the clinical status, and these procedures are becoming essential to improving patient outcome.

New Concepts in Diagnostics for Invasive Mycoses: Non-Culture-Based Methodologies

Non-culture-based diagnostics have been developed to help establish an early diagnosis of invasive fungal infection. Studies have shown that these tests can significantly impact the diagnosis of infection in high risk patients. Aspergillus galactomannan EIA testing is well-recognized as an important adjunct to the diagnosis of invasive aspergillosis and can be detected in serum, bronchoalveolar lavage and other fluids. Galactomannan testing used along with PCR testing has been shown to be effective when integrated into care paths for high risk patients for both diagnoses and as a surrogate marker for outcome when used in serial testing. Beta-d-glucan assays are non-specific for several fungal genera including Aspergillus and Candida and in high risk patients have been an important tool to augment the diagnosis. Lateral flow technology using monoclonal antibodies to Aspergillus are available that allow rapid testing of clinical samples. While standard PCR for Candida remains investigational, T2 magnetic resonance allows for the rapid diagnosis of Candida species from blood cultures. Aspergillus PCR has been extensively validated with standardized approaches established for these methods and will be included in the diagnostic criteria in the revised European Organization for Research and Treatment of Cancer/Mycoses Study Group (EORTC-MSG) definitions. Finally, these non-culture-based tests can be used in combination to significantly increase the detection of invasive mycoses with the ultimate aim of establishing an early diagnosis of infection.