1
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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.
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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
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2
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Rocchi S, Sewell TR, Valot B, Godeau C, Laboissiere A, Millon L, Fisher MC. Molecular Epidemiology of Azole-Resistant Aspergillus fumigatus in France Shows Patient and Healthcare Links to Environmentally Occurring Genotypes. Front Cell Infect Microbiol 2021; 11:729476. [PMID: 34660341 PMCID: PMC8512841 DOI: 10.3389/fcimb.2021.729476] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2021] [Accepted: 09/09/2021] [Indexed: 01/14/2023] Open
Abstract
Resistance of the human pathogenic fungus Aspergillus fumigatus to antifungal agents is on the rise. However, links between patient infections, their potential acquisition from local environmental sources, and links to global diversity remain cryptic. Here, we used genotyping analyses using nine microsatellites in A. fumigatus, in order to study patterns of diversity in France. In this study, we genotyped 225 local A. fumigatus isolates, 112 azole susceptible and 113 azole resistant, collected from the Bourgogne-Franche-Comté region (Eastern France) and sampled from both clinical (n = 34) and environmental (n = 191) sources. Azole-resistant clinical isolates (n = 29) were recovered mainly from cystic fibrosis patients and environmental isolates (n = 84) from market gardens and sawmills. In common with previous studies, the TR34/L98H allele predominated and comprised 80% of resistant isolates. The genotypes obtained for these local TR34/L98H isolates were integrated into a broader analysis including all genotypes for which data are available worldwide. We found that dominant local TR34/L98H genotypes were isolated in different sample types at different dates (different patients and types of environments) with hospital air and patient's isolates linked. Therefore, we are not able to rule out the possibility of some nosocomial transmission. We also found genotypes in these same environments to be highly diverse, emphasizing the highly mixed nature of A. fumigatus populations. Identical clonal genotypes were found to occur both in the French Eastern region and in the rest of the world (notably Australia), while others have not yet been observed and could be specific to our region. Our study demonstrates the need to integrate patient, healthcare, and environmental sampling with global databases in order to contextualize the local-scale epidemiology of antifungal resistant aspergillosis.
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Affiliation(s)
- Steffi Rocchi
- Department of Parasitology and Mycology, Centre Hospitalier Universitaire, Besançon, France.,Chrono-Environnement Research Team UMR/CNRS-6249, Bourgogne-Franche-Comté University, Besançon, France
| | - Thomas R Sewell
- Medical Research Council (MRC) Centre for Global Infectious Disease Analysis, Department of Infectious Disease Epidemiology, Imperial School of Public Health, Imperial College London, London, United Kingdom
| | - Benoit Valot
- Chrono-Environnement Research Team UMR/CNRS-6249, Bourgogne-Franche-Comté University, Besançon, France
| | - Chloé Godeau
- Chrono-Environnement Research Team UMR/CNRS-6249, Bourgogne-Franche-Comté University, Besançon, France
| | - Audrey Laboissiere
- Chrono-Environnement Research Team UMR/CNRS-6249, Bourgogne-Franche-Comté University, Besançon, France
| | - Laurence Millon
- Department of Parasitology and Mycology, Centre Hospitalier Universitaire, Besançon, France.,Chrono-Environnement Research Team UMR/CNRS-6249, Bourgogne-Franche-Comté University, Besançon, France
| | - Matthew C Fisher
- Medical Research Council (MRC) Centre for Global Infectious Disease Analysis, Department of Infectious Disease Epidemiology, Imperial School of Public Health, Imperial College London, London, United Kingdom
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3
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Arastehfar A, Carvalho A, Houbraken J, Lombardi L, Garcia-Rubio R, Jenks J, Rivero-Menendez O, Aljohani R, Jacobsen I, Berman J, Osherov N, Hedayati M, Ilkit M, Armstrong-James D, Gabaldón T, Meletiadis J, Kostrzewa M, Pan W, Lass-Flörl C, Perlin D, Hoenigl M. Aspergillus fumigatus and aspergillosis: From basics to clinics. Stud Mycol 2021; 100:100115. [PMID: 34035866 PMCID: PMC8131930 DOI: 10.1016/j.simyco.2021.100115] [Citation(s) in RCA: 106] [Impact Index Per Article: 35.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
The airborne fungus Aspergillus fumigatus poses a serious health threat to humans by causing numerous invasive infections and a notable mortality in humans, especially in immunocompromised patients. Mould-active azoles are the frontline therapeutics employed to treat aspergillosis. The global emergence of azole-resistant A. fumigatus isolates in clinic and environment, however, notoriously limits the therapeutic options of mould-active antifungals and potentially can be attributed to a mortality rate reaching up to 100 %. Although specific mutations in CYP 51A are the main cause of azole resistance, there is a new wave of azole-resistant isolates with wild-type CYP 51A genotype challenging the efficacy of the current diagnostic tools. Therefore, applications of whole-genome sequencing are increasingly gaining popularity to overcome such challenges. Prominent echinocandin tolerance, as well as liver and kidney toxicity posed by amphotericin B, necessitate a continuous quest for novel antifungal drugs to combat emerging azole-resistant A. fumigatus isolates. Animal models and the tools used for genetic engineering require further refinement to facilitate a better understanding about the resistance mechanisms, virulence, and immune reactions orchestrated against A. fumigatus. This review paper comprehensively discusses the current clinical challenges caused by A. fumigatus and provides insights on how to address them.
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Affiliation(s)
- A. Arastehfar
- Center for Discovery and Innovation, Hackensack Meridian Health, Nutley, NJ, 07110, USA
| | - A. Carvalho
- Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho, Braga, Portugal
- ICVS/3B's - PT Government Associate Laboratory, Guimarães/Braga, Portugal
| | - J. Houbraken
- Westerdijk Fungal Biodiversity Institute, Utrecht, the Netherlands
| | - L. Lombardi
- UCD Conway Institute and School of Medicine, University College Dublin, Dublin 4, Ireland
| | - R. Garcia-Rubio
- Center for Discovery and Innovation, Hackensack Meridian Health, Nutley, NJ, 07110, USA
| | - J.D. Jenks
- Department of Medicine, University of California San Diego, San Diego, CA, 92103, USA
- Clinical and Translational Fungal-Working Group, University of California San Diego, La Jolla, CA, 92093, USA
| | - O. Rivero-Menendez
- Medical Mycology Reference Laboratory, National Center for Microbiology, Instituto de Salud Carlos III, Madrid, 28222, Spain
| | - R. Aljohani
- Department of Infectious Diseases, Imperial College London, London, UK
| | - I.D. Jacobsen
- Department of Microbial Pathogenicity Mechanisms, Leibniz Institute for Natural Product Research and Infection Biology—Hans Knöll Institute, Jena, Germany
- Institute for Microbiology, Friedrich Schiller University, Jena, Germany
| | - J. Berman
- Research Group Microbial Immunology, Leibniz Institute for Natural Product Research and Infection Biology—Hans Knöll Institute, Jena, Germany
| | - N. Osherov
- Department of Clinical Microbiology and Immunology, Sackler School of Medicine Ramat-Aviv, Tel-Aviv, 69978, Israel
| | - M.T. Hedayati
- Invasive Fungi Research Center/Department of Medical Mycology, School of Medicine, Mazandaran University of Medical Sciences, Sari, Iran
| | - M. Ilkit
- Division of Mycology, Department of Microbiology, Faculty of Medicine, Çukurova University, 01330, Adana, Turkey
| | | | - T. Gabaldón
- Life Sciences Programme, Supercomputing Center (BSC-CNS), Jordi Girona, Barcelona, 08034, Spain
- Mechanisms of Disease Programme, Institute for Research in Biomedicine (IRB), Barcelona, Spain
- ICREA, Pg. Lluís Companys 23, Barcelona, Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Pg. Lluís Companys 23, 08010, Barcelona, Spain
| | - J. Meletiadis
- Clinical Microbiology Laboratory, Attikon University Hospital, Medical School, National and Kapodistrian University of Athens, Athens, Greece
| | | | - W. Pan
- Medical Mycology, Shanghai Changzheng Hospital, Second Military Medical University, Shanghai, 200003, China
| | - C. Lass-Flörl
- Institute of Hygiene and Medical Microbiology, Medical University of Innsbruck, Innsbruck, Austria
| | - D.S. Perlin
- Center for Discovery and Innovation, Hackensack Meridian Health, Nutley, NJ, 07110, USA
| | - M. Hoenigl
- Department of Medicine, University of California San Diego, San Diego, CA, 92103, USA
- Section of Infectious Diseases and Tropical Medicine, Department of Internal Medicine, Medical University of Graz, 8036, Graz, Austria
- Division of Infectious Diseases and Global Public Health, Department of Medicine, University of California San Diego, San Diego, CA 92093, USA
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4
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van der Torre MH, Shen H, Rautemaa-Richardson R, Richardson MD, Novak-Frazer L. Molecular Epidemiology of Aspergillus fumigatus in Chronic Pulmonary Aspergillosis Patients. J Fungi (Basel) 2021; 7:jof7020152. [PMID: 33672698 PMCID: PMC7924367 DOI: 10.3390/jof7020152] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2021] [Revised: 02/15/2021] [Accepted: 02/17/2021] [Indexed: 12/17/2022] Open
Abstract
Molecular fungal genotyping techniques developed and employed for epidemiological studies have understandably concentrated on establishing the genetic diversity of Aspergillus fumigatus in invasive aspergillosis due to its severity, the urgency for treatment, and the need to demonstrate possible sources. Some early studies suggested that these strains were phenotypically, if not genotypically, different from others. However, with improved discrimination and evaluations, incorporating environmental as well as clinical isolates from other Aspergillus conditions (e.g., chronic pulmonary aspergillosis and cystic fibrosis), this premise is no longer upheld. Moreover, with the onset of increased global triazole resistance, there has been a concerted effort to incorporate resistance profiling into genotyping studies and the realisation that the wider population of non-immunocompromised aspergillosis patients are at risk. This review summarises the developments in molecular genotyping studies that incorporate resistance profiling with attention to chronic pulmonary aspergillosis and an example of our UK experience.
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Affiliation(s)
- Mireille H. van der Torre
- Mycology Reference Centre Manchester, ECMM Centre of Excellence in Clinical and Laboratory Mycology and Clinical Studies, Manchester University NHS Foundation Trust, Wythenshawe Hospital, Manchester M23 9LT, UK; (M.H.v.d.T.); (R.R.-R.); (M.D.R.)
- Division of Infection, Inflammation and Respiratory Medicine, Faculty of Biology, Medicine and Health, University of Manchester, Manchester M13 9PL, UK;
| | - Hongwei Shen
- Division of Infection, Inflammation and Respiratory Medicine, Faculty of Biology, Medicine and Health, University of Manchester, Manchester M13 9PL, UK;
| | - Riina Rautemaa-Richardson
- Mycology Reference Centre Manchester, ECMM Centre of Excellence in Clinical and Laboratory Mycology and Clinical Studies, Manchester University NHS Foundation Trust, Wythenshawe Hospital, Manchester M23 9LT, UK; (M.H.v.d.T.); (R.R.-R.); (M.D.R.)
- Division of Infection, Inflammation and Respiratory Medicine, Faculty of Biology, Medicine and Health, University of Manchester, Manchester M13 9PL, UK;
- Department of Infectious Diseases, Manchester University NHS Foundation Trust, Wythenshawe Hospital, Manchester M23 9LT, UK
| | - Malcolm D. Richardson
- Mycology Reference Centre Manchester, ECMM Centre of Excellence in Clinical and Laboratory Mycology and Clinical Studies, Manchester University NHS Foundation Trust, Wythenshawe Hospital, Manchester M23 9LT, UK; (M.H.v.d.T.); (R.R.-R.); (M.D.R.)
- Division of Infection, Inflammation and Respiratory Medicine, Faculty of Biology, Medicine and Health, University of Manchester, Manchester M13 9PL, UK;
| | - Lilyann Novak-Frazer
- Mycology Reference Centre Manchester, ECMM Centre of Excellence in Clinical and Laboratory Mycology and Clinical Studies, Manchester University NHS Foundation Trust, Wythenshawe Hospital, Manchester M23 9LT, UK; (M.H.v.d.T.); (R.R.-R.); (M.D.R.)
- Division of Infection, Inflammation and Respiratory Medicine, Faculty of Biology, Medicine and Health, University of Manchester, Manchester M13 9PL, UK;
- Correspondence: ; Tel.: +44-161-2915856
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5
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Puértolas-Balint F, Rossen JWA, Oliveira Dos Santos C, Chlebowicz MMA, Raangs EC, van Putten ML, Sola-Campoy PJ, Han L, Schmidt M, García-Cobos S. Revealing the Virulence Potential of Clinical and Environmental Aspergillus fumigatus Isolates Using Whole-Genome Sequencing. Front Microbiol 2019; 10:1970. [PMID: 31551947 PMCID: PMC6737835 DOI: 10.3389/fmicb.2019.01970] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2019] [Accepted: 08/12/2019] [Indexed: 01/09/2023] Open
Abstract
Aspergillus fumigatus is considered a common causative agent of human fungal infections. A restricted number of virulence factors have been described, and none of them lead to a differentiation in the virulence level among different strains. Variations in the virulence phenotype depending on the isolate origin, measured as survival percentage in animal infection models, have been previously reported. In this study, we analyzed the whole-genome sequence of A. fumigatus isolates from clinical and environmental origins to determine their virulence genetic content. The sample included four isolates sequenced at the University Medical Center Groningen (UMCG), three clinical (two of them isolated from the same patient) and the experimental strain B5233, and the draft genomes of one reference strain, two environmental and two clinical isolates obtained from a public database. The fungal genomes were screened for the presence of virulence-related genes (VRGs) using an in-house database of 244 genes related to thermotolerance, resistance to immune responses, cell wall formation, nutrient uptake, signaling and regulation, and production of toxins and secondary metabolites and allergens. In addition, we performed a variant calling analysis to compare the isolates sequenced at the UMCG and investigated their genetic relatedness using the TRESP (Tandem Repeats located within Exons of Surface Protein coding genes) genotyping method. We neither observed a difference in the virulence genetic content between the clinical isolates causing an invasive infection and a colonizing clinical isolate nor between isolates from the clinical and environmental origin. The four novel A. fumigatus sequences had a different TRESP genotype and a total number of genetic variants ranging from 48,590 to 68,352. In addition, a comparative genomics analysis showed the presence of single nucleotide polymorphisms in VRGs and repetitive genetic elements located next to VRG groups, which could influence the regulation of these genes. In conclusion, our genomic analysis revealed a high genetic diversity between environmental and clinical A. fumigatus isolates, as well as between clinical isolates from the same patient, indicating an infection with a mixed-population in the latter case. However, all isolates had a similar virulence genetic content, demonstrating their pathogenic potential at least at the genomic level.
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Affiliation(s)
- Fabiola Puértolas-Balint
- University of Groningen, University Medical Center Groningen, Department of Medical Microbiology and Infection Prevention, Groningen, Netherlands.,University of Groningen, Department of Molecular Pharmacology, Groningen, Netherlands
| | - John W A Rossen
- University of Groningen, University Medical Center Groningen, Department of Medical Microbiology and Infection Prevention, Groningen, Netherlands
| | - Claudy Oliveira Dos Santos
- University of Groningen, University Medical Center Groningen, Department of Medical Microbiology and Infection Prevention, Groningen, Netherlands
| | - Monika M A Chlebowicz
- University of Groningen, University Medical Center Groningen, Department of Medical Microbiology and Infection Prevention, Groningen, Netherlands
| | - Erwin C Raangs
- University of Groningen, University Medical Center Groningen, Department of Medical Microbiology and Infection Prevention, Groningen, Netherlands
| | - Maarten L van Putten
- University of Groningen, University Medical Center Groningen, Department of Medical Microbiology and Infection Prevention, Groningen, Netherlands
| | - Pedro J Sola-Campoy
- Reference and Research Laboratory on Antimicrobial Resistance and Healthcare Infections, National Microbiology Centre, Institute of Health Carlos III, Madrid, Spain
| | - Li Han
- Institute of Disease Control and Prevention, Academy of Military Medical Sciences, Beijing, China
| | - Martina Schmidt
- University of Groningen, Department of Molecular Pharmacology, Groningen, Netherlands.,University Medical Center Groningen, Groningen Research Institute for Asthma and COPD, Groningen, Netherlands
| | - Silvia García-Cobos
- University of Groningen, University Medical Center Groningen, Department of Medical Microbiology and Infection Prevention, Groningen, Netherlands
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6
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Garcia-Rubio R, Escribano P, Gomez A, Guinea J, Mellado E. Comparison of Two Highly Discriminatory Typing Methods to Analyze Aspergillus fumigatus Azole Resistance. Front Microbiol 2018; 9:1626. [PMID: 30079058 PMCID: PMC6062602 DOI: 10.3389/fmicb.2018.01626] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2018] [Accepted: 06/28/2018] [Indexed: 11/24/2022] Open
Abstract
Aspergillus fumigatus molecular typing has become increasingly more important for detecting outbreaks as well as for local and global epidemiological investigations and surveillance. Over the years, many different molecular methods have been described for genotyping this species. Some outstanding approaches are based on microsatellite markers (STRAf assay, which is the current gold standard), or based on sequencing data (TRESP typing improved in this work with a new marker and was renamed TRESPERG). Both methodologies were used to type a collection of 212 A. fumigatus isolates that included 70 azole resistant strains with diverse resistance mechanisms from different geographic locations. Our results showed that both methods are totally reliable for epidemiological investigations showing similar stratification of the A. fumigatus population. STRAf assay offered higher discriminatory power (D = 0.9993) than the TRESPERG typing method (D = 0.9972), but the latter does not require specific equipment or skilled personnel, allowing for a prompt integration into any clinical microbiology laboratory. Among azole resistant isolates, two groups were differentiated considering their resistance mechanisms: cyp51A single point mutations (G54, M220, or G448), and promoter tandem repeat integrations with or without cyp51A modifications (TR34/L98H, TR46/Y121F/A289T, or TR53). The genotypic differences were assessed to explore the population structure as well as the genetic relationship between strains and their azole resistance profile. Genetic cluster analyses suggested that our A. fumigatus population was formed by 6–7 clusters, depending on the methodology. Also, the azole susceptible and resistance population showed different structure and organization. The combination of both methodologies resolved the population structure in a similar way to what has been described in whole-genome sequencing works.
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Affiliation(s)
- Rocio Garcia-Rubio
- Mycology Reference Laboratory, National Centre for Microbiology, Instituto de Salud Carlos III, Madrid, Spain
| | - Pilar Escribano
- Department of Clinical Microbiology and Infectious Diseases, Hospital General Universitario Gregorio Marañón, Madrid, Spain.,Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain
| | - Ana Gomez
- Department of Clinical Microbiology and Infectious Diseases, Hospital General Universitario Gregorio Marañón, Madrid, Spain.,Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain
| | - Jesus Guinea
- Department of Clinical Microbiology and Infectious Diseases, Hospital General Universitario Gregorio Marañón, Madrid, Spain.,Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain.,Department of Medicine, School of Medicine, Complutense University of Madrid, Madrid, Spain
| | - Emilia Mellado
- Mycology Reference Laboratory, National Centre for Microbiology, Instituto de Salud Carlos III, Madrid, Spain
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7
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Rico-Munoz E, Samson RA, Houbraken J. Mould spoilage of foods and beverages: Using the right methodology. Food Microbiol 2018; 81:51-62. [PMID: 30910088 DOI: 10.1016/j.fm.2018.03.016] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2017] [Revised: 03/16/2018] [Accepted: 03/29/2018] [Indexed: 11/19/2022]
Abstract
Fungal spoilage of products manufactured by the food and beverage industry imposes significant annual global revenue losses. Mould spoilage can also be a food safety issue due to the production of mycotoxins by these moulds. To prevent mould spoilage, it is essential that the associated mycobiota be adequately isolated and accurately identified. The main fungal groups associated with spoilage are the xerophilic, heat-resistant, preservative-resistant, anaerobic and psychrophilic fungi. To assess mould spoilage, the appropriate methodology and media must be used. While classic mycological detection methods can detect a broad range of fungi using well validated protocols, they are time consuming and results can take days or even weeks. New molecular detection methods are faster but require good DNA isolation techniques, expensive equipment and may detect viable and non-viable fungi that probably will not spoil a specific product. Although there is no complete and easy method for the detection of fungi in food it is important to be aware of the limitation of the methodology. More research is needed on the development of methods of detection and identification that are both faster and highly sensitive.
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Affiliation(s)
- Emilia Rico-Munoz
- BCN Research Laboratories, Inc., 2491 Stock Creek Blvd., Rockford, TN 37853, USA.
| | - Robert A Samson
- Westerdijk Fungal Biodiversity Institute, Dept. Applied and Industrial Mycology, Uppsalalaan 8, Utrecht, CT 3584, The Netherlands
| | - Jos Houbraken
- Westerdijk Fungal Biodiversity Institute, Dept. Applied and Industrial Mycology, Uppsalalaan 8, Utrecht, CT 3584, The Netherlands
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8
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A New Aspergillus fumigatus Typing Method Based on Hypervariable Tandem Repeats Located within Exons of Surface Protein Coding Genes (TRESP). PLoS One 2016; 11:e0163869. [PMID: 27701437 PMCID: PMC5049851 DOI: 10.1371/journal.pone.0163869] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2016] [Accepted: 09/15/2016] [Indexed: 11/19/2022] Open
Abstract
Aspergillus fumigatus is a saprotrophic mold fungus ubiquitously found in the environment and is the most common species causing invasive aspergillosis in immunocompromised individuals. For A. fumigatus genotyping, the short tandem repeat method (STRAf) is widely accepted as the first choice. However, difficulties associated with PCR product size and required technology have encouraged the development of novel typing techniques. In this study, a new genotyping method based on hypervariable tandem repeats within exons of surface protein coding genes (TRESP) was designed. A. fumigatus isolates were characterized by PCR amplification and sequencing with a panel of three TRESP encoding genes: cell surface protein A; MP-2 antigenic galactomannan protein; and hypothetical protein with a CFEM domain. The allele sequence repeats of each of the three targets were combined to assign a specific genotype. For the evaluation of this method, 126 unrelated A. fumigatus strains were analyzed and 96 different genotypes were identified, showing a high level of discrimination [Simpson’s index of diversity (D) 0.994]. In addition, 49 azole resistant strains were analyzed identifying 26 genotypes and showing a lower D value (0.890) among them. This value could indicate that these resistant strains are closely related and share a common origin, although more studies are needed to confirm this hypothesis. In summary, a novel genotyping method for A. fumigatus has been developed which is reproducible, easy to perform, highly discriminatory and could be especially useful for studying outbreaks.
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9
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Malassezia arunalokei sp. nov., a Novel Yeast Species Isolated from Seborrheic Dermatitis Patients and Healthy Individuals from India. J Clin Microbiol 2016; 54:1826-1834. [PMID: 27147721 DOI: 10.1128/jcm.00683-16] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2016] [Accepted: 04/27/2016] [Indexed: 11/20/2022] Open
Abstract
The majority of species within the genus Malassezia are lipophilic yeasts that colonize the skin of warm-blooded animals. Two species, Malassezia globosa and Malassezia restricta, are implicated in the causation of seborrheic dermatitis/dandruff (SD/D). During our survey of SD/D cases, we isolated several species of Malassezia and noticed vast variations within a few lipid-dependent species. Variations observed in the phenotypic characteristics (colony morphology, absence of catalase activity, growth at 37°C, and precipitation surrounding wells containing Tween 20 or Cremophor EL) suggested the possible presence of a novel species. Sequence divergence observed in the internal transcribed spacer (ITS) region, the D1/D2 domain, and the intergenic spacer 1 (IGS1) region of rDNA and the TEF1 gene, PCR-restriction fragment length polymorphism (RFLP) analysis of the ITS2 region, and fluorescent amplified fragment length polymorphism analysis support the existence of a novel species. Based on phenotypic and molecular characterization of these strains, we propose a new species, namely, M. arunalokei sp. nov., and we designate NCCPF 127130 (= MTCC 12054 = CBS 13387) as the type strain.
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Gibbons JG, Rokas A. The function and evolution of the Aspergillus genome. Trends Microbiol 2012; 21:14-22. [PMID: 23084572 DOI: 10.1016/j.tim.2012.09.005] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2012] [Revised: 09/20/2012] [Accepted: 09/24/2012] [Indexed: 10/27/2022]
Abstract
Species in the filamentous fungal genus Aspergillus display a wide diversity of lifestyles and are of great importance to humans. The decoding of genome sequences from a dozen species that vary widely in their degree of evolutionary affinity has galvanized studies of the function and evolution of the Aspergillus genome in clinical, industrial, and agricultural environments. Here, we synthesize recent key findings that shed light on the architecture of the Aspergillus genome, on the molecular foundations of the genus' astounding dexterity and diversity in secondary metabolism, and on the genetic underpinnings of virulence in Aspergillus fumigatus, one of the most lethal fungal pathogens. Many of these insights dramatically expand our knowledge of fungal and microbial eukaryote genome evolution and function and argue that Aspergillus constitutes a superb model clade for the study of functional and comparative genomics.
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Affiliation(s)
- John G Gibbons
- Department of Biological Sciences, Vanderbilt University, Nashville, TN 37235, USA
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Illnait-Zaragozí MT, Martínez-Machín GF, Fernández-Andreu CM, Perurena-Lancha MR, Theelen B, Boekhout T, Meis JF, Klaassen CH. Environmental isolation and characterisation of Cryptococcus species from living trees in Havana city, Cuba. Mycoses 2012; 55:e138-44. [DOI: 10.1111/j.1439-0507.2012.02168.x] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
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Lackner M, Rezusta A, Villuendas MC, Palacian MP, Meis JF, Klaassen CH. Infection and colonisation due to Scedosporium in Northern Spain. An in vitro antifungal susceptibility and molecular epidemiology study of 60 isolates. Mycoses 2012; 54 Suppl 3:12-21. [PMID: 21995658 DOI: 10.1111/j.1439-0507.2011.02110.x] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Since the latest taxonomical changes in the genus Scedosporium by Gilgado et al. in 2010, no species-specific studies on epidemiology and antifungal susceptibility patterns (AFSP) have so far been published. This study aimed to provide qualitative epidemiological data of Scedosporium spp. isolated from cystic fibrosis (CF) patients and immunocompromised patients from Northern Spain. Isolates were identified by using amplified fragment length polymorphism (AFLP), and species-specific AFSP were generated for all currently available antifungal compounds. AFLP was a useful tool for identification to species-level and for the discrimination of inter- and intra-patient isolates. Scedosporium prolificans represents the most prevalent species in the respiratory tract of CF patients and immunocompromised patients in Northern-Spain, followed by Pseudallescheria boydii, P. apiosperma, and P. ellipsoidea. CF patients were exclusively colonised with either P. boydii or S. prolificans. Patients were colonised over years exclusively with isolates affiliated to one species, but some patients were colonised with multiple strains with different AFSP. The sum of those co-colonising strains in one patient, may appear in vitro and in vivo as a multi-resistant S. prolificans isolate, as strains are morphologically identical and might therefore be regarded as only one strain. A majority of Scedosporium strains (with exception of S. prolificans) were found susceptible for voriconazole and micafungin.
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Affiliation(s)
- M Lackner
- Department of Medical Microbiology and Infectious Diseases, Canisius Wilhelmina Hospital, Nijmegen, The Netherlands.
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Najafzadeh MJ, Sun J, Vicente VA, Klaassen CHW, Bonifaz A, Gerrits van den Ende AHG, Menken SBJ, de Hoog GS. Molecular epidemiology of Fonsecaea species. Emerg Infect Dis 2011; 17:464-9. [PMID: 21392438 DOI: 10.3201/eid1703.100555] [Citation(s) in RCA: 60] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
To assess population diversities among 81 strains of fungi in the genus Fonsecaea that had been identified down to species level, we applied amplified fragment-length polymorphism (AFLP) technology and sequenced the internal transcribed spacer regions and the partial cell division cycle, beta-tubulin, and actin genes. Many species of the genus Fonsecaea cause human chromoblastomycosis. Strains originated from a global sampling of clinical and environmental sources in the Western Hemisphere, Asia, Africa, and Europe. According to AFLP fingerprinting, Fonsecaea isolates clustered in 5 groups corresponding with F. pedrosoi, F. monophora, and F. nubica: the latter 2 species each comprised 2 groups, and F. pedrosoi appeared to be of monophyletic origin. F. pedrosoi was found nearly exclusively in Central and South America. F. monophora and F. nubica were distributed worldwide, but both showed substantial geographic structuring. Clinical cases outside areas where Fonsecaea is endemic were probably distributed by human migration.
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Rudramurthy SM, de Valk HA, Chakrabarti A, Meis JFGM, Klaassen CHW. High resolution genotyping of clinical Aspergillus flavus isolates from India using microsatellites. PLoS One 2011; 6:e16086. [PMID: 21264229 PMCID: PMC3022034 DOI: 10.1371/journal.pone.0016086] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2010] [Accepted: 12/06/2010] [Indexed: 11/30/2022] Open
Abstract
BACKGROUND Worldwide, Aspergillus flavus is the second leading cause of allergic, invasive and colonizing fungal diseases in humans. However, it is the most common species causing fungal rhinosinusitis and eye infections in tropical countries. Despite the growing challenges due to A. flavus, the molecular epidemiology of this fungus has not been well studied. We evaluated the use of microsatellites for high resolution genotyping of A. flavus from India and a possible connection between clinical presentation and genotype of the involved isolate. METHODOLOGY/PRINCIPAL FINDINGS A panel of nine microsatellite markers were selected from the genome of A. flavus NRRL 3357. These markers were used to type 162 clinical isolates of A. flavus. All nine markers proved to be polymorphic displaying up to 33 alleles per marker. Thirteen isolates proved to be a mixture of different genotypes. Among the 149 pure isolates, 124 different genotypes could be recognized. The discriminatory power (D) for the individual markers ranged from 0.657 to 0.954. The D value of the panel of nine markers combined was 0.997. The multiplex multicolor approach was instrumental in rapid typing of a large number of isolates. There was no correlation between genotype and the clinical presentation of the infection. CONCLUSIONS/SIGNIFICANCE There is a large genotypic diversity in clinical A. flavus isolates from India. The presence of more than one genotype in clinical samples illustrates the possibility that persons may be colonized by multiple genotypes and that any isolate from a clinical specimen is not necessarily the one actually causing infection. Microsatellites are excellent typing targets for discriminating between A. flavus isolates from various origins.
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Affiliation(s)
- Shivaprakash M. Rudramurthy
- Mycology Division, Department of Medical Microbiology, Post Graduate Institute of Medical Education and Research, Chandigarh, India
| | - Hanneke A. de Valk
- Department of Medical Microbiology and Infectious Diseases, Canisius Wilhelmina Hospital, Nijmegen, The Netherlands
| | - Arunaloke Chakrabarti
- Mycology Division, Department of Medical Microbiology, Post Graduate Institute of Medical Education and Research, Chandigarh, India
| | - Jacques F. G. M. Meis
- Department of Medical Microbiology and Infectious Diseases, Canisius Wilhelmina Hospital, Nijmegen, The Netherlands
| | - Corné H. W. Klaassen
- Department of Medical Microbiology and Infectious Diseases, Canisius Wilhelmina Hospital, Nijmegen, The Netherlands
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Vanhee LME, Nelis HJ, Coenye T. What can be learned from genotyping of fungi? Med Mycol 2010; 48 Suppl 1:S60-9. [DOI: 10.3109/13693786.2010.484816] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
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Apophysomyces elegans: epidemiology, amplified fragment length polymorphism typing, and in vitro antifungal susceptibility pattern. J Clin Microbiol 2010; 48:4580-5. [PMID: 20881165 DOI: 10.1128/jcm.01420-10] [Citation(s) in RCA: 61] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Abstract
Apophysomyces elegans is an emerging pathogen in India. We planned the present study to analyze the clinical pattern of the disease, to perform molecular strain typing, and to determine the in vitro activities of eight antifungal drugs against A. elegans. A total of 16 clinical and two environmental A. elegans isolates were included in the study. The clinical histories of the patients were noted. MICs or minimum effective concentrations (MECs) were determined for antifungal drugs by microdilution testing in accordance with CLSI standard M38-A2 guidelines. Of 16 patients, seven had rhino-cerebral, five had cutaneous, and three had renal zygomycosis. One patient had osteomyelitis. Uncontrolled diabetes was observed in 63% of the patients. Amplified fragment length polymorphism (AFLP) analysis divided the strains into two clearly different clades. The fingerprints of the environmental strains (including the type strain) were clearly different from those of the clinical strains. The MIC50s and MIC90s for amphotericin B, itraconazole, posaconazole, and isavuconazole were 2 and 4, 1 and 2, 0.5 and 1, and 2 and 4 μg/ml, respectively. The strains had high MICs for fluconazole, voriconazole, and echinocandins. The study indicates a possible change in the clinical pattern of zygomycosis due to A. elegans in India. The fungus caused not only cutaneous or subcutaneous infection but also other deep-seated infections, and the disease is commonly associated with uncontrolled diabetes. The AFLP patterns show a clear difference between environmental and clinical strains. Posaconazole is the most active drug against the isolates, followed by itraconazole. The MICs of amphotericin B against A. elegans were higher than those of the other drugs.
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Use of amplified fragment length polymorphism to identify 42 Cladophialophora strains related to cerebral phaeohyphomycosis with in vitro antifungal susceptibility. J Clin Microbiol 2010; 48:2350-6. [PMID: 20421439 DOI: 10.1128/jcm.00653-10] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The amplified fragment length polymorphism technique has been applied to identify neurotropic chaetothyrialean black yeasts and relatives from clinical sources. Cladophialophora bantiana, C. emmonsii, C. arxii, C. devriesii, and C. modesta, previously identified on the basis of sequencing and phenotypic and physiological criteria, were confirmed by cluster analysis, demonstrating the clear separation of C. bantiana as a rather homogeneous group from the other species. C. bantiana is a neurotropic fungus causing cerebral abscesses with a mortality of up to 70%. Successful therapy consists of neurosurgical intervention and optimal antifungal therapy. Since the latter is not clearly defined in a large series, we tested the in vitro activities of eight antifungal drugs against clinical isolates of C. bantiana (n = 37), C. modesta (n = 2), C. arxii (n = 1), C. emmonsii (n = 1), and C. devriesii (n = 1), all of which had caused invasive infections. The resulting MIC(90)s for all neurotropic C. bantiana strains were as follows, in increasing order: posaconazole, 0.125 microg/ml; itraconazole, 0.125 microg/ml; isavuconazole, 0.5 microg/ml; amphotericin B, 1 microg/ml; voriconazole, 2 microg/ml; anidulafungin, 2 microg/ml; caspofungin, 4 microg/ml; and fluconazole, 64 microg/ml. On the basis of these in vitro results and the findings of previous clinical and animal studies, posaconazole seems to be a good alternative to the standard treatment, amphotericin B, for C. bantiana cerebral infections. The new agent isavuconazole, which is also available as an intravenous preparation, has adequate activity against C. bantiana.
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Advances in molecular detection of Aspergillus: an update. Arch Microbiol 2010; 192:409-25. [DOI: 10.1007/s00203-010-0563-y] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2009] [Revised: 11/01/2009] [Accepted: 03/10/2010] [Indexed: 10/19/2022]
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Klaassen CHW. MLST versus microsatellites for typing Aspergillus fumigatus isolates. Med Mycol 2009; 47 Suppl 1:S27-33. [PMID: 19255901 DOI: 10.1080/13693780802382244] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022] Open
Abstract
In recent years, there has been a clear and growing tendency to use exact typing methods for discrimination between microbial isolates. Exact typing methods that yield an unambiguous typing result offer a number of advantages over conventional methods in the generation of typing data that is reproducible, portable and exchangeable. Two such methods are multi-locus sequence typing (MLST) and microsatellite-based typing. Here I will discuss the basic principles of both methods and compare them from a practical and performance point of view with respect to typing Aspergillus fumigatus isolates. Microsatellites offer the best available typing option by outperforming MLST in terms of speed, throughput, costs and discriminatory power. This latter advantage of microsatellites is a direct consequence of their inherent instability. This (in)stability of individual microsatellite markers and alleles should be taken into account in the interpretation of microsatellite-based typing data.
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Affiliation(s)
- C H W Klaassen
- Department of Medical Microbiology and Infectious Diseases, Canisius Wilhelmina Hospital, Nijmegen, The Netherlands.
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Abstract
Aspergillus species are widely distributed fungi that release large amounts of airborne conidia, which are dispersed in the environment. Several Aspergillus species have been described as human pathogens. Molecular techniques have been developed to investigate the epidemiological relation between environmental and clinical isolates. Several typing methods have been described for Aspergillus species, most of them with reference to Aspergillus fumigatus. Here, we summarise all the different available molecular typing techniques for Aspergillus. The performance of these techniques is evaluated with respect to their practical feasibility, and their interpretation and discriminatory power assessed. For A. fumigatus isolates, a large extent of genetic variability is demonstrated and therefore fingerprinting techniques with high discriminatory power and high reproducibility are required for this species. Afut1-restriction fragment length polymorphism and microsatellite typing showed the highest discriminatory power. In addition, the microsatellites show excellent reproducibility. Other typing techniques are still useful for smaller epidemiological problems and for less well-equipped laboratories.
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Affiliation(s)
- H A de Valk
- Department of Medical Microbiology and Infectious Diseases, Canisius Wilhelmina Hospital, Nijmegen, The Netherlands.
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