Laboratory diagnostics of invasive fungal infections: an overview with emphasis on molecular approach

A Single-Center Study of the Utility of Bronchoalveolar Lavage in Critically Ill Patients With Haematological Malignancy or Stem Cell Transplants

INTRODUCTION

The aim of this study was to evaluate the yield of bronchoscopy-guided bronchoalveolar lavage (BAL) and decisions on management of antimicrobials in critically ill patients with hematological malignancy and/or hematological stem cell transplant (HSCT). The safety and tolerance of bronchoscopy were also reported.

METHODS

A retrospective cohort study was conducted by reviewing health charts of all adult patients with a hematological malignancy and/or an HSCT who were admitted to the intensive care unit and underwent bronchoscopy and BAL over four years from April 2016 to April 2020 at King Abdulaziz Medical City, Riyadh.  Results: The cohort included 75 critically ill patients. Of these 75 patients, 53 (70.7%) had HSCT (allogenic 66%, autologous 32.1%, haplogenic 3.8%). Computed tomography of the chest was abnormal in all patients. Predominant findings included airspace abnormalities, ground glass opacities, and others. The positive yield was found to be 20% for bacterial, 22% for viral, 21% for fungal, and other organisms were identified in 2%. Although cytology was not performed in 18 patients, malignant cells were identified on BAL in two patients. While the overall mortality of the cohort was high (46.7%), the vast majority (94.7%) tolerated bronchoscopy and BAL without any complications. However, three patients (4%) developed a pneumothorax and one patient bled and developed the acute respiratory distress syndrome post bronchoscopy.

CONCLUSIONS

BAL can identify and detect microorganisms directly influencing the clinical care of patients who have received non-invasive diagnostic tests that yielded negative culture results. Bronchoscopy and BAL are generally safe and well tolerated by critically ill patients with hematological malignancy or HSCT.

Deep fungal infections diagnosed by histology in Uganda: a 70-year retrospective study

Fungal infections cause substantial morbidity and mortality. However, the burden of deep fungal infections is not well described in Uganda. We aimed to estimate the burden and etiology of histologically diagnosed deep fungal infections in Uganda. We retrospectively reviewed histology reports at the Pathology Reference Laboratory, Department of Pathology, Makerere University, Kampala, Uganda from January 1950 to September 2019 to identify any reports that had a fungal infection as the diagnosis. Over the study period, 697 cases of deep fungal infections were identified with an average incidence of 0.73/100,000 persons per decade. There was a general decline in the number of cases detected. Median age of the cases was 28 years (IQR: 11-40) and majority (59%) were male. The age group of 0-10 years were the most affected. The foot was the most affected part of the body (26%). Deep mycoses identified include eumycetoma (32%), subcutaneous phycomycosis (26%), histoplasmosis (9.2%), chromoblastomycosis (4.6%), aspergillosis (3.3%), cryptococcosis (3.3%), blastomycosis (1.6%), subcutaneous mycosis (1.4%), dermatomycosis (1.3%), coccidioidomycosis (0.6%), mucormycosis (0.6%), and sporotrichosis (0.1%). Histoplasma was the commonest causative agent (9.2%) followed by Aspergillus (3.4%) and Cryptococcus (3.3%), while 81% of the fungal pathogens were not identified to genus/species level. Only 31% of the cases were diagnosed clinically as deep fungal infections. There is a substantial burden of deep fungal infections caused by multiple fungal pathogens in Uganda. There is need to build local capacity for mycology so as to improve on the index of clinical suspicion and diagnostic capabilities.

Identification of pathogens causing invasive fungal rhinosinusitis in surgical biopsies using polymerase chain reaction

BACKGROUND

Invasive fungal rhinosinusitis is associated with high morbidity and mortality. Rapid pathogen identification is mandatory, but fresh tissue is not always available. A polymerase chain reaction method was designed in order to detect fungi in formalin-fixed paraffin-embedded samples. This was applied to a retrospective series of tissue biopsies from Thai patients with invasive fungal rhinosinusitis.

METHODS

Tissue blocks from 64 cases yielded adequate DNA. Three sequential polymerase chain reaction were performed: ZP3 (housekeeping gene) and panfungal polymerase chain reactions, and a differentiating polymerase chain reaction based on the 5.8s ribosomal RNA and internal transcribed spacer 2 regions. The polymerase chain reaction products were then sequenced.

RESULTS

Polymerase chain reaction identified a fungal pathogen in 20 of 64 cases (31 per cent). Aspergillus species was the most common cause of invasive fungal rhinosinusitis (nine cases). Other causes included candida (n = 4), cladosporium (n = 4), mucor (n = 1), alternaria (n = 1) and dendryphiella (n = 1) species.

CONCLUSION

Polymerase chain reaction can provide rapid identification of fungal pathogens in paraffin-embedded tissue, enabling prompt treatment of invasive fungal rhinosinusitis.

Visible DNA Microarray System as an Adjunctive Molecular Test in Identification of Pathogenic Fungi Directly from a Blood Culture Bottle

A DNA microarray platform, based on the nucleotide sequences of the internal transcribed spacer regions (ITS1 and ITS2) of the rRNA gene, was developed to identify 32 fungal pathogens at the species level. The probe sequences were spotted onto polycarbonate slides with a mini-microarray printer, and after the hybridization, the results were visible with the naked eye. The performance of the microarray platform was evaluated against the commercial automated systems (Vitek 2 and BD Phoenix systems) and DNA sequencing (gold standard). A total of 461 blood culture bottles were tested: 127 positive for fungi, 302 positive for bacteria, and 32 that were negative. Once the microorganisms were identified by automated systems, fungal DNA was extracted directly from the blood culture bottles. The DNA products were tested using the microarray platform, and DNA sequencing was performed. The results of the microarray and DNA sequencing were concordant in 96.7% of cases, and the results from the automated systems and DNA sequencing were concordant in 98.4%. Of all the nucleotide sequences contained in the microarray platform, the microarray failed to identify four fungal isolates (one Candida parapsilosis, two Candida tropicalis, and one Cryptococcus neoformans). Of note, the microarray detected Candida krusei DNA in two blood cultures from the same patient, whereas the automated system was only positive for Enterococcus faecium Our microarray system provided reliable and fast fungal identification compared to that from DNA sequencing and the automated systems. The simplicity of reading the results by the naked eye made this DNA platform a suitable method for fungal molecular diagnosis.

Utility of bronchoalveolar lavage in diagnosing respiratory tract infections in patients with hematological malignancies: are invasive diagnostics still needed?

BACKGROUND

Patients treated for hematological malignancies have an increased risk of serious infections. Diagnosis and prompt initiation of therapy are essential. Bronchoalveolar lavage (BAL) is a well-established investigation for identifying the cause of pulmonary infiltrates in immunocompromised patients. The aim of the study was to determine the diagnostic yield of BAL in patients treated for hematological malignancies and how often it contributed to a modification of the anti-infectious therapy.

METHODS

We reviewed records from 151 consecutive BAL procedures in 133 adult patients with hematological malignancies, treated at a tertiary hematology unit from 2004 to 2013. Extensive microbiological work-ups on BAL samples had been performed according to a standardized protocol.

RESULTS

A microbiological finding causing the infectious episode could be identified in 59 (39%) cases. In 44 (29%) of the cases, results from BAL had an impact on clinical management either by contributing to a specific diagnosis (25%) or by leading to cessation of ongoing microbiological therapy. The most common diagnoses were invasive pulmonary aspergillosis (IPA) and Pneumocystis jirovecii pneumonia (PJP). Diagnoses of IPA and PJP were based on results from BAL in 65% and 93% of cases, respectively. Several microbiological tests on BAL samples rendered no positive results. Complications were few and mainly mild.

CONCLUSION

BAL is still important for either verifying or excluding some of the most important respiratory tract pathogens in patients with hematological malignancies, particularly IPA and PJP. Standardized procedures for BAL sampling should be continually revised to exclude unnecessary microbiological tests.

Fungal skull base osteomyelitis: Emerging microbial identification techniques

Culture-based pathogen identification in skull base osteomyelitis, particularly for fungi, is often inaccurate. We report the case of patient with fungal skull base osteomyelitis cured by sustained antifungal therapy after 16 months of debilitating illness. Due to medical complications, a strong clinical rationale was needed to justify long-term antifungal therapy. The offending fungus was identified by experimental molecular technology (Ibis T5000 universal biosensor); invasive fungal disease was corroborated by biochemical assays. Our discussion will help familiarize the otolaryngologist with existing biochemical and molecular diagnostics for invasive fungal disease. We encourage future investigators to study their application in cases of skull base osteomyelitis. Laryngoscope, 127:E5-E7, 2017.

Comparison of galactomannan, beta-D-glucan, and Aspergillus DNA in sera of high-risk adult patients with hematological malignancies for the diagnosis of invasive aspergillosis

BACKGROUND/AIM

Invasive aspergillosis (IA) is a fatal infection that is difficult to diagnose in immunocompromised patients. In this study, Aspergillus-specific DNA was searched using real-time PCR (RT-PCR) in serum samples. Galactomannan (GM) and/or beta-D-glucan (BDG) tests were previously performed on these samples for 70 neutropenic patients with hematological malignancy.

MATERIALS AND METHODS

The patients were categorized according to the criteria of the European Organization for Research and Treatment of Cancer/Mycoses Study Group (EORTC/MSG). Among the patient serum samples, the first positive GM or BDG test sample and the median sample of GM or BDG test for negative patients were used to detect DNA levels by RT-PCR method (Light Cycler 480, Roche Molecular Biochemicals, Meylan, France) using a commercial kit (Way2Gene Fungi; Genmar, İzmir, Turkey).

RESULTS

When the proven and probable IA group were considered as real patients, sensitivity of Aspergillus-specific DNA test was 90%, specificity was 73.3%, positive predictive value was 81.8%, and negative predictive value was 84.6%.

CONCLUSION

This study found that searching for specific DNA by RT-PCR method has a sensitivity as high as the GM test. Although specificity was rather low, it was concluded that it can be used jointly with GM and BDG tests after decreasing contamination by severe laboratory applications.

Uncommon opportunistic fungal infections of oral cavity: A review

The majority of opportunistic oral mucosal fungal infections are due to Candida albicans and Aspergillus fumigatus species. Mucor and Cryptococcus also have a major role in causing oral infections, whereas Geotrichum, Fusarium, Rhodotorula, Saccharomyces and Penicillium marneffei are uncommon pathogens in the oral cavity. The broad spectrum of clinical presentation includes pseudo-membranes, abscesses, ulcers, pustules and extensive tissue necrosis involving bone. This review discusses various uncommon opportunistic fungal infections affecting the oral cavity including their morphology, clinical features and diagnostic methods.

Establishment and application of real-time quantitative PCR for diagnosing invasive aspergillosis via the blood in hematological patients: targeting a specific sequence of Aspergillus 28S-ITS2

BACKGROUND

Invasive aspergillosis (IA) is an important cause of morbidity and mortality in immunocompromised individuals. This study was conducted to identify a desirable target DNA sequence for the diagnosis of aspergillosis using real-time quantitative polymerase chain reaction (qPCR).

METHODS

Genomic DNA was extracted from Aspergillus, Candida, and bacteria species, and qPCR was applied to validate a partial ribosomal DNA 28S-ITS2 sequence. Ethylenediaminetetraacetic acid-anticoagulated blood samples were collected from 72 febrile hematological patients, while total DNA was isolated from plasma and whole blood for the Aspergillus qPCR. The results were analyzed using a receiver operating characteristic curve. All cases were evaluated using the revised European Organization for Research and Treatment of Cancer/Invasive Fungal Infections Cooperative Group and the National Institute of Allergy and Infectious Diseases Mycoses Study Group (EORTC/MSG) diagnostic criteria.

RESULTS

Use of qPCR yielded positive results for 15 Aspergillus species but negative results for Candida species, bacterial strains, and human DNA. The limit of detection was one copy per microliter of DNA. Analytical sensitivity and specificity were six copies of DNA and 100%, respectively. The standard curve showed that qPCR was reliable for Aspergillus detection and that significantly more DNA copies were obtained from whole blood than from plasma (P < 0.001). At a cut-off value ≥ 25 copies/μL, the diagnostic sensitivity and specificity for IA using 28S-ITS2 qPCR were 90.9% and 73.4%, respectively.

CONCLUSIONS

The use of qPCR with whole blood to detect and verify the 28S-ITS2 sequence is a specific and useful way to diagnose IA.