1
|
Hiel SJP, Hendriks ACA, Eijkenboom JJA, Bosch T, Coolen JPM, Melchers WJG, Anröchte P, Camps SMT, Verweij PE, Zhang J, van Dommelen L. Aspergillus Outbreak in an Intensive Care Unit: Source Analysis with Whole Genome Sequencing and Short Tandem Repeats. J Fungi (Basel) 2024; 10:51. [PMID: 38248960 PMCID: PMC10817286 DOI: 10.3390/jof10010051] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2023] [Revised: 12/17/2023] [Accepted: 12/29/2023] [Indexed: 01/23/2024] Open
Abstract
Whole genome sequencing (WGS) is widely used for outbreak analysis of bacteriology and virology but is scarcely used in mycology. Here, we used WGS for genotyping Aspergillus fumigatus isolates from a potential Aspergillus outbreak in an intensive care unit (ICU) during construction work. After detecting the outbreak, fungal cultures were performed on all surveillance and/or patient respiratory samples. Environmental samples were obtained throughout the ICU. WGS was performed on 30 isolates, of which six patient samples and four environmental samples were related to the outbreak, and twenty samples were unrelated, using the Illumina NextSeq 550. A SNP-based phylogenetic tree was created from outbreak samples and unrelated samples. Comparative analysis (WGS and short tandem repeats (STRs), microsatellite loci analysis) showed that none of the strains were related to each other. The lack of genetic similarity suggests the accumulation of Aspergillus spores in the hospital environment, rather than a single source that supported growth and reproduction of Aspergillus fumigatus. This supports the hypothesis that the Aspergillus outbreak was likely caused by release of Aspergillus fumigatus spores during construction work. Indeed, no new Aspergillus cases were observed in the ICU after cessation of construction. This study demonstrates that WGS is a suitable technique for examining inter-strain relatedness of Aspergillus fumigatus in the setting of an outbreak investigation.
Collapse
Affiliation(s)
- Stephan J. P. Hiel
- Department of Intensive Care, Máxima Medical Centre, De Run 4600, 5504 DB Veldhoven, The Netherlands
| | - Amber C. A. Hendriks
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment, Antonie van Leeuwenhoeklaan 9, 3721 MA Bilthoven, The Netherlands
- Department of Medical Microbiology, Radboud University Medical Centre, Geert Grooteplein Zuid 10, 6525 GA Nijmegen, The Netherlands
| | - Jos J. A. Eijkenboom
- Department of Intensive Care, Máxima Medical Centre, De Run 4600, 5504 DB Veldhoven, The Netherlands
| | - Thijs Bosch
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment, Antonie van Leeuwenhoeklaan 9, 3721 MA Bilthoven, The Netherlands
| | - Jordy P. M. Coolen
- Department of Medical Microbiology, Radboud University Medical Centre, Geert Grooteplein Zuid 10, 6525 GA Nijmegen, The Netherlands
| | - Willem J. G. Melchers
- Department of Medical Microbiology, Radboud University Medical Centre, Geert Grooteplein Zuid 10, 6525 GA Nijmegen, The Netherlands
| | - Paul Anröchte
- Department of Infection Prevention and Control, Máxima Medical Centre, De Run 4600, 5504 DB Veldhoven, The Netherlands
| | - Simone M. T. Camps
- Department of Infection Prevention and Control, Máxima Medical Centre, De Run 4600, 5504 DB Veldhoven, The Netherlands
| | - Paul E. Verweij
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment, Antonie van Leeuwenhoeklaan 9, 3721 MA Bilthoven, The Netherlands
- Department of Medical Microbiology, Radboud University Medical Centre, Geert Grooteplein Zuid 10, 6525 GA Nijmegen, The Netherlands
| | - Jianhua Zhang
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment, Antonie van Leeuwenhoeklaan 9, 3721 MA Bilthoven, The Netherlands
| | - Laura van Dommelen
- Stichting PAMM, Laboratory of Medical Microbiology, De Run 6250, 5504 DL Veldhoven, The Netherlands
| |
Collapse
|
2
|
Srivastava AK, Ghosh I, Sonawane S. Clinical profile and microbiological spectrum of patients with continuous ambulatory peritoneal dialysis-associated peritonitis at a tertiary care center. Med J Armed Forces India 2023; 79:S175-S180. [PMID: 38144612 PMCID: PMC10746806 DOI: 10.1016/j.mjafi.2022.05.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Accepted: 05/02/2022] [Indexed: 10/17/2022] Open
Abstract
Background We present risk factors, clinical profile, and microbiological spectrum of patients with continuous ambulatory peritoneal dialysis (CAPD)-associated peritonitis who were managed at our center. Methods All consecutive patients with CAPD-associated peritonitis who presented to our center between July 2018 and December 2019 were included in the study. Risk factors, microbiological spectrum, clinical profile, and outcome of patients were studied. Results Eighty-five patients with CAPD-associated peritonitis and 50 patients who never had peritonitis during the study period were included. Diabetes Mellitus (OR 0.058, 95% CI0.007-0.493, p < 0.05), residence in rural area (OR 3.376, 95% CI 1.084-10.516, p < 0.05), duration of peritoneal dialysis (OR 0.935, 95% CI 0.886-0.987, p < 0.05), mean serum hemoglobin (OR 1.674, 95% CI 1.119-2.502, p < 0.05) and serum albumin (OR 0.148, 95% CI 0.066-0.333, p < 0.05) were associated with higher risk of peritonitis in CAPD patients. Eight-three patients (98.8%) had turbid CAPD fluid and 52 (61.2%) had fever at the time of presentation to the hospital. The mean CAPD fluid TLC on day 1, 3, and 5 were 2034.3 ± 3330.1 cells/cumm, 1049.0 ± 1210.9 cells/cumm, and 605.2 ± 950.5 cells/cumm, respectively. The organisms isolated were two Escherichia coli (2.4%), one Staphylococcus aureus (1.2%), one Klebsiella (1.2%), two Acinetobacter (2.4%), 10 Fungal organisms (11.7%), and in two (2.4%) cases, Mycobacterium tuberculosis (MTB) was detected by polymerase chain reaction (PCR) of CAPD fluid. Thirty-seven (43.5%) patients had a complete cure and 48 (56.5%) patients were refractory to treatment; hence catheter was removed in them (catheter loss). Six (7.0%) patients died during the study period. Conclusion CAPD-associated peritonitis is an important risk factor for technique failure. The majority of episodes are culture-negative, and PCR can help in detecting fungal and tubercular peritonitis early in the course.
Collapse
Affiliation(s)
| | - Indranil Ghosh
- Senior Adviser (Medicine & Nephrology), Command Hospital (Central Command), Lucknow, India
| | | |
Collapse
|
3
|
Wilmes D, Hagen F, Verissimo C, Alanio A, Rickerts V, Buitrago MJ. A multicentre external quality assessment: A first step to standardise PCR protocols for the diagnosis of histoplasmosis and coccidioidomycosis. Mycoses 2023. [PMID: 37169736 DOI: 10.1111/myc.13603] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Revised: 04/25/2023] [Accepted: 04/27/2023] [Indexed: 05/13/2023]
Abstract
BACKGROUND In-house real-time PCR (qPCR) is increasingly used to diagnose the so-called endemic mycoses as commercial assays are not widely available. OBJECTIVES To compare the performance of different molecular diagnostic assays for detecting Histoplasma capsulatum and Coccidioides spp. in five European reference laboratories. METHODS Two blinded external quality assessment (EQA) panels were sent to each laboratory that performed the analysis with their in-house assays. Both panels included a range of concentrations of H. capsulatum (n = 7) and Coccidioides spp. (n = 6), negative control and DNA from other fungi. Four laboratories used specific qPCRs, and one laboratory a broad-range fungal conventional PCR (cPCR) and a specific cPCR for H. capsulatum with subsequent sequencing. RESULTS qPCR assays were the most sensitive for the detection of H. capsulatum DNA. The lowest amount of H. capsulatum DNA detected was 1-4 fg, 0.1 pg and 10 pg for qPCRs, specific cPCR and broad-range cPCR, respectively. False positive results occurred with high concentrations of Blastomyces dermatitidis DNA in two laboratories and with Emergomyces spp. in one laboratory. For the Coccidioides panel, the lowest amount of DNA detected was 1-16 fg by qPCRs and 10 pg with the broad-range cPCR. One laboratory reported a false positive result by qPCR with high load of Uncinocarpus DNA. CONCLUSION All five laboratories were able to correctly detect H. capsulatum and Coccidioides spp. DNA and qPCRs had a better performance than specific cPCR and broad-range cPCR. EQAs may help standardise in-house molecular tests for the so-called endemic mycoses improving patient management.
Collapse
Affiliation(s)
- Dunja Wilmes
- FG16, Unit for Mycotic and Parasitic Agents and Mycobacteria, Robert Koch Institute, Berlin, Germany
| | - Ferry Hagen
- Westerdijk Fungal Biodiversity Institute (WI-KNAW), Utrecht, The Netherlands
- Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, Amsterdam, The Netherlands
- Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Cristina Verissimo
- Department of Infectious Diseases, Reference Laboratory for Parasites and Fungal infections, Instituto Nacional de Saúde Dr. Ricardo Jorge, Lisbon, Portugal
| | - Alexandre Alanio
- Mycology Department, Translational Mycology Research Group, National Reference Center for Invasive Mycoses and Antifungals, Institut Pasteur, Université Paris Cité, Paris, France
- Laboratoire de Parasitologie-Mycologie, AP-HP, Hôpital Saint-Louis, Paris, France
| | - Volker Rickerts
- FG16, Unit for Mycotic and Parasitic Agents and Mycobacteria, Robert Koch Institute, Berlin, Germany
- Konsiliarlabor für Kryptokokkose und Seltene Systemmykosen, Robert Koch Institute, Berlin, Germany
| | - Maria José Buitrago
- Reference Mycology Laboratory, National Centre for Microbiology, Instituto de Salud Carlos III, Madrid, Spain
- CIBERINFEC, ISCIII-CIBER de Enfermedades Infecciosas, Instituto de Salud Carlos III, Madrid, Spain
| |
Collapse
|
4
|
Oliveira M, Pinto M, Simões H, Gomes JP, Veríssimo C, Sabino R. Molecular detection of Aspergillus in respiratory samples collected from patients at higher risk of chronic pulmonary aspergillosis. Infect Dis Now 2023; 53:104633. [PMID: 36375764 DOI: 10.1016/j.idnow.2022.11.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2022] [Revised: 10/12/2022] [Accepted: 11/04/2022] [Indexed: 11/13/2022]
Abstract
OBJECTIVE Aspergillosis diagnosis depends on the detection of Aspergillus in biological samples ─ usually using cultural and immunoenzyme techniques ─ but their sensitivity and specificity varies. We aimed to study the prevalence of Aspergillus in patients at higher risk of chronic pulmonary aspergillosis (i.e., HIV-infected patients and individuals with active or previous tuberculosis), and to determine the potential role of molecular approaches to increase detection of Aspergillus in respiratory samples. METHODS The DNA extracted from 43 respiratory samples that had been previously analyzed by immunoenzyme and/or cultural techniques was amplified by real-time multiplex PCR, and the results of these methods were compared. We also sequenced the ITS1 region and the calmodulin gene in 10 respiratory samples to perform a pilot metagenomic study to understand the ability of this methodology to detect potential pathogenic fungi in the lung mycobiome. RESULTS Real-time Aspergillus PCR test exhibited a higher positivity rate than the conventional techniques used for aspergillosis diagnosis, particularly in individuals at risk for chronic pulmonary aspergillosis. The metagenomic analysis allowed for the detection of various potentially pathogenic fungi. CONCLUSIONS Molecular techniques, including metagenomics, have great ability to detect potentially pathogenic fungi rapidly and efficiently in human biological samples.
Collapse
Affiliation(s)
- M Oliveira
- Animal Biology Department, Faculty of Sciences of the University of Lisbon, 1749-016 Lisbon, Portugal; Reference Unit for Parasitic and Fungal Infections, Department of Infectious Diseases, National Institute of Health, Dr. Ricardo Jorge, 1649-016 Lisbon, Portugal.
| | - M Pinto
- Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health, Dr. Ricardo Jorge, 1649-016 Lisbon, Portugal.
| | - H Simões
- Reference Unit for Parasitic and Fungal Infections, Department of Infectious Diseases, National Institute of Health, Dr. Ricardo Jorge, 1649-016 Lisbon, Portugal.
| | - J P Gomes
- Reference Unit for Parasitic and Fungal Infections, Department of Infectious Diseases, National Institute of Health, Dr. Ricardo Jorge, 1649-016 Lisbon, Portugal.
| | - C Veríssimo
- Reference Unit for Parasitic and Fungal Infections, Department of Infectious Diseases, National Institute of Health, Dr. Ricardo Jorge, 1649-016 Lisbon, Portugal.
| | - R Sabino
- Reference Unit for Parasitic and Fungal Infections, Department of Infectious Diseases, National Institute of Health, Dr. Ricardo Jorge, 1649-016 Lisbon, Portugal; Instituto de Saúde Ambiental, Faculdade de Medicina, Universidade de Lisboa, 1649-028 Lisboa, Portugal.
| |
Collapse
|
5
|
Molecular Diagnosis of Endemic Mycoses. J Fungi (Basel) 2022; 9:jof9010059. [PMID: 36675880 PMCID: PMC9866865 DOI: 10.3390/jof9010059] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Revised: 12/22/2022] [Accepted: 12/24/2022] [Indexed: 01/03/2023] Open
Abstract
Diagnosis of endemic mycoses is still challenging. The moderated availability of reliable diagnostic methods, the lack of clinical suspicion out of endemic areas and the limitations of conventional techniques result in a late diagnosis that, in turn, delays the implementation of the correct antifungal therapy. In recent years, molecular methods have emerged as promising tools for the rapid diagnosis of endemic mycoses. However, the absence of a consensus among laboratories and the reduced availability of commercial tests compromises the diagnostic effectiveness of these methods. In this review, we summarize the advantages and limitations of molecular methods for the diagnosis of endemic mycoses.
Collapse
|
6
|
Xie Y, Zhou X, Zhang J, Yu H, Song Z. Immunomodulatory responses of differentially polarized macrophages to fungal infections. Int Immunopharmacol 2022; 111:109089. [PMID: 35964406 DOI: 10.1016/j.intimp.2022.109089] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2022] [Revised: 07/16/2022] [Accepted: 07/22/2022] [Indexed: 11/05/2022]
Abstract
Macrophages, the first line of defense against invasive fungi in the innate immune system, are widely distributed in the blood and tissues of the body. In response to various internal and external stimulators, macrophages can polarize into classically activated macrophages (M1) and alternatively activated macrophages (M2). These two types of polarized macrophages play different roles in antifungal activity and in maintaining the steady-state balance between inflammation and tissue repair. However, the antifungal mechanisms of M1- and M2-type macrophages have not been fully described. In this review, the immune regulatory mechanisms against pathogenic fungi of these two classical types of macrophages in various tissues are summarized. The effects of antifungal factors on macrophage differentiation are also highlighted. The description of these data, on the one hand provides valuable insight for future investigations and also highlights new strategies for the treatment of pathogenic fungal infections.
Collapse
Affiliation(s)
- Yuxin Xie
- School of Basic Medical Sciences, Southwest Medical University, Luzhou 646000, PR China.
| | - Xue Zhou
- School of Basic Medical Sciences, Southwest Medical University, Luzhou 646000, PR China.
| | - Jinping Zhang
- School of Basic Medical Sciences, Southwest Medical University, Luzhou 646000, PR China; The Public Platform of Molecular Biotechnology, Public Center of Experimental Technology, Southwest Medical University, Luzhou 646000, People's Republic of China.
| | - Hong Yu
- School of Basic Medical Sciences, Southwest Medical University, Luzhou 646000, PR China; The Public Platform of Cell Biotechnology, Public Center of Experimental Technology, Southwest Medical University, Luzhou 646000, PR China.
| | - Zhangyong Song
- School of Basic Medical Sciences, Southwest Medical University, Luzhou 646000, PR China; The Public Platform of Molecular Biotechnology, Public Center of Experimental Technology, Southwest Medical University, Luzhou 646000, People's Republic of China.
| |
Collapse
|
7
|
Invasive and Subcutaneous Infections Caused by Filamentous Fungi: Report from a Portuguese Multicentric Surveillance Program. Microorganisms 2022; 10:microorganisms10051010. [PMID: 35630453 PMCID: PMC9145964 DOI: 10.3390/microorganisms10051010] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Revised: 05/06/2022] [Accepted: 05/09/2022] [Indexed: 12/03/2022] Open
Abstract
Invasive fungal infections (IFI) have significantly increased over the past years due to advances in medical care for the at-risk immunocompromised population. IFI are often difficult to diagnose and manage, and can be associated with substantial morbidity and mortality. This study aims to contribute to understanding the etiology of invasive and subcutaneous fungal infections, their associated risk factors, and to perceive the outcome of patients who developed invasive disease, raising awareness of these infections at a local level but also in a global context. A laboratory surveillance approach was conducted over a seven-year period and included: (i) cases of invasive and subcutaneous fungal infections caused by filamentous/dimorphic fungi, confirmed by either microscopy or positive culture from sterile samples, (ii) cases diagnosed as probable IFI according to the criteria established by EORTC/MSG when duly substantiated. Fourteen Portuguese laboratories were enrolled. Cases included in this study were classified according to the new consensus definitions of invasive fungal diseases (IFD) published in 2020 as follows: proven IFI (N = 31), subcutaneous fungal infection (N = 23). Those proven deep fungal infections (N = 54) totalized 71.1% of the total cases, whereas 28.9% were classified as probable IFI (N = 22). It was possible to identify the etiological fungal agent in 73 cases (96%). Aspergillus was the most frequent genera detected, but endemic dimorphic fungi represented 14.47% (N = 11) of the total cases. Despite the small number of cases, a high diversity of species were involved in deep fungal infections. This fact has implications for clinical and laboratory diagnosis, and on the therapeutic management of these infections, since different species, even within the same genus, can present diverse patterns of susceptibility to antifungals.
Collapse
|
8
|
Chen SCA, Halliday CL, Hoenigl M, Cornely OA, Meyer W. Scedosporium and Lomentospora Infections: Contemporary Microbiological Tools for the Diagnosis of Invasive Disease. J Fungi (Basel) 2021; 7:23. [PMID: 33406673 PMCID: PMC7823285 DOI: 10.3390/jof7010023] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2020] [Revised: 12/25/2020] [Accepted: 12/28/2020] [Indexed: 12/19/2022] Open
Abstract
Scedosporium/Lomentospora fungi are increasingly recognized pathogens. As these fungi are resistant to many antifungal agents, early diagnosis is essential for initiating targeted drug therapy. Here, we review the microbiological tools for the detection and diagnosis of invasive scedosporiosis and lomentosporiosis. Of over 10 species, Lomentospora prolificans, Scedosporium apiospermum, S. boydii and S. aurantiacum cause the majority of infections. Definitive diagnosis relies on one or more of visualization, isolation or detection of the fungus from clinical specimens by microscopy techniques, culture and molecular methods such as panfungal PCR or genus-/species-specific multiplex PCR. For isolation from respiratory tract specimens, selective media have shown improved isolation rates. Species identification is achieved by macroscopic and microscopic examination of colonies, but species should be confirmed by ITS with or without β-tubulin gene sequencing or other molecular methods. Matrix-assisted laser desorption ionization-time of flight mass spectrometry databases are improving but may need supplementation by in-house spectra for species identification. Reference broth microdilution methods is preferred for antifungal susceptibility testing. Next-generation sequencing technologies have good potential for characterization of these pathogens. Diagnosis of Scedosporium/Lomentospora infections relies on multiple approaches encompassing both phenotypic- and molecular-based methods.
Collapse
Affiliation(s)
- Sharon C.-A. Chen
- Centre for Infectious Diseases and Microbiology Laboratory Services, Institute of Clinical Pathology and Medical Research, New South Wales Health Pathology, Westmead Hospital, Westmead, Sydney, NSW 2145, Australia;
- Marie Bashir Institute for Infectious Diseases & Biosecurity, The University of Sydney, Sydney, NSW 2006, Australia;
| | - Catriona L. Halliday
- Centre for Infectious Diseases and Microbiology Laboratory Services, Institute of Clinical Pathology and Medical Research, New South Wales Health Pathology, Westmead Hospital, Westmead, Sydney, NSW 2145, Australia;
- Marie Bashir Institute for Infectious Diseases & Biosecurity, The University of Sydney, Sydney, NSW 2006, Australia;
| | - Martin Hoenigl
- Division of Infectious Diseases and Global Health, University of California San Diego, San Diego, CA 92103, USA;
- Clinical and Translational Fungal-Working Group, University of California San Diego, San Diego, CA 92103, USA
- Section of Infectious Diseases and Tropical Medicine, Medical University of Graz, 8036 Graz, Austria
| | - Oliver A. Cornely
- Department of Internal Medicine, Excellence Centre for Medical Mycology (ECMM), Faculty of Medicine and University Hospital Cologne, University of Cologne, 50923 Cologne, Germany;
- Translational Research Cologne Excellence Cluster on Cellular Responses in Aging-associated Diseases (CECAD), 50923 Cologne, Germany
- Clinical Trials Centre Cologne (ZKS Koln), 50923 Cologne, Germany
| | - Wieland Meyer
- Marie Bashir Institute for Infectious Diseases & Biosecurity, The University of Sydney, Sydney, NSW 2006, Australia;
- Molecular Mycology Research Laboratory, Centre for Infectious Diseases and Microbiology, Clinical School, Sydney Medical School, Faculty of Medicine and Health, The University of Sydney, Westmead, Sydney, NSW 2006, Australia
- Westmead Hospital (Research and Education Network), Westmead, NSW 2145, Australia
- Westmead Institute for Medical Research, Westmead, NSW 2145, Australia
| |
Collapse
|
9
|
Kidd SE, Chen SCA, Meyer W, Halliday CL. A New Age in Molecular Diagnostics for Invasive Fungal Disease: Are We Ready? Front Microbiol 2020; 10:2903. [PMID: 31993022 PMCID: PMC6971168 DOI: 10.3389/fmicb.2019.02903] [Citation(s) in RCA: 91] [Impact Index Per Article: 22.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2019] [Accepted: 12/02/2019] [Indexed: 12/18/2022] Open
Abstract
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.
Collapse
Affiliation(s)
- Sarah E. Kidd
- National Mycology Reference Centre, Microbiology and Infectious Diseases, South Australia Pathology, Adelaide, SA, Australia
| | - Sharon C.-A. Chen
- Centre for Infectious Diseases and Microbiology Laboratory Services, ICPMR, New South Wales Health Pathology, Westmead Hospital, Westmead, NSW, Australia
- Marie Bashir Institute for Infectious Diseases and Biosecurity, The University of Sydney, Sydney, NSW, Australia
| | - Wieland Meyer
- Marie Bashir Institute for Infectious Diseases and Biosecurity, The University of Sydney, Sydney, NSW, Australia
- Molecular Mycology Research Laboratory, Centre for Infectious Diseases and Microbiology, Faculty of Medicine and Health, Westmead Clinical School, The University of Sydney, Sydney, NSW, Australia
- The Westmead Institute for Medical Research, Westmead, NSW, Australia
- Research and Education Network, Westmead Hospital, Westmead, NSW, Australia
| | - Catriona L. Halliday
- Centre for Infectious Diseases and Microbiology Laboratory Services, ICPMR, New South Wales Health Pathology, Westmead Hospital, Westmead, NSW, Australia
| |
Collapse
|