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Gerrits van den Ende B, Rodrigues AM, Hahn RC, Hagen F. A surprising finding: The curious case of a tongue lesion misdiagnosed as paracoccidioidomycosis. Rev Iberoam Micol 2023; 40:10-14. [PMID: 36690509 DOI: 10.1016/j.riam.2022.11.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Revised: 11/08/2022] [Accepted: 11/23/2022] [Indexed: 01/22/2023] Open
Abstract
BACKGROUND Paracoccidioidomycosis is an endemic mycosis caused by members of the Paracoccidioides genus. Brazil remains the focus area and, to a lesser extent, the disease has been reported from Argentina, Colombia and Venezuela. AIMS A Venezuelan Paracoccidioides brasiliensis strain, isolated from a patient diagnosed with chronic multifocal paracoccidioidomycosis, was subjected to whole genome sequencing to provide more insight about Paracoccidioides outside the endemic focus area. METHODS P. brasiliensis strain CBS 118890 was whole genome sequenced using nanopore; library preparation with the 'native barcoding genomic DNA kit' was followed by sequencing on Flongle and MinION flowcells. Batches of strain CBS 118890 were re-identified by sequencing the internal transcribed spacer (ITS) region, and final identification was made based on phylogenetic analysis. RESULTS Surprisingly, the Venezuelan P. brasiliensis strain CBS 118890 turned out to be a Nannizziopsis species. The batches of this strain were ITS sequenced followed by phylogenetic analysis and resulted in the final identification of Nannizziopsis arthrosporioides. CONCLUSIONS Nannizziopsis infections are commonly seen in a wide variety of reptiles, but are particularly rare in human infections. This case underlines the need for molecular characterization of cases that clinically mimic paracoccidioidomycosis but that are serologically negative for Paracoccidioides.
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Affiliation(s)
| | - Anderson Messias Rodrigues
- Laboratory of Emerging Fungal Pathogens, Department of Microbiology, Immunology, and Parasitology, Discipline of Cellular Biology, Federal University of São Paulo (UNIFESP), São Paulo, Brazil; Department of Medicine, Discipline of Infectious Diseases, Federal University of São Paulo (UNIFESP), São Paulo, Brazil
| | - Rosane Christine Hahn
- Laboratory of Mycology/Research, Faculty of Medicine, Federal University of Mato Grosso, Cuiabá, Mato Grosso, Brazil; Júlio Muller University Hospital - Ebserh, Federal University of Mato Grosso, Cuiabá, Mato Grosso, Brazil
| | - Ferry Hagen
- Westerdijk Fungal Biodiversity Institute, Utrecht, The Netherlands; Institute for Biodiversity and Ecosystem Dynamics (IBED), University of Amsterdam, Amsterdam, The Netherlands; Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, The Netherlands.
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Michaelson-Cohen R, Murik O, Zeligson S, Lobel O, Weiss O, Picard E, Mann T, Mor-Shaked H, Zeevi DA, Segel R. Combining cytogenetic and genomic technologies for deciphering challenging complex chromosomal rearrangements. Mol Genet Genomics 2022; 297:925-933. [PMID: 35488049 DOI: 10.1007/s00438-022-01898-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2021] [Accepted: 04/13/2022] [Indexed: 11/28/2022]
Abstract
Complex chromosomal rearrangements (CCRs), a class of structural variants (SVs) involving more than two chromosome breaks, were classically thought to be extremely rare. As advanced technologies become more available, it has become apparent that CCRs are more common than formerly thought, and are a substantial cause of genetic disorders. We attempted a novel approach for solving the mechanism of challenging CCRs, which involve repetitive sequences, by precisely identifying sequence-level changes and their order. Chromosomal microarray (CMA) and FISH analyses were used for interpretation of SVs detected by whole exome sequencing (WES). Breakpoint junctions were analyzed by Nanopore sequencing, a novel long-read whole genome sequencing tool. A large deletion identified by WES, encompassing the FOXF1 enhancer, was the cause of alveolar capillary dysplasia and respiratory insufficiency, resulting in perinatal death. CMA analysis of the newborn's mother revealed two duplications encompassing the deleted region in the proband, raising our hypothesis that the deletion resulted from the mother's CCR. Breakpoint junctions of complex SVs were determined at the nucleotide level using Nanopore long-read sequencing. According to sequencing results of breakpoint junctions, the CCR in the newborn was considered the consequence of at least one double-strand break during meiosis, and reassembly of DNA fragments by intra-chromosomal homologous recombination. Our comprehensive approach, combining cytogenetics and long-read sequencing, enabled delineation of the exact breakpoints in a challenging CCR, and proposal of a mechanism in which it arises. We suggest applying our integrative approach combining technologies for deciphering future challenging CCRs, enabling risk assessment in families.
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Affiliation(s)
- Rachel Michaelson-Cohen
- Medical Genetics Institute, Shaare Zedek Medical Center, Jerusalem, Israel. .,Department of Obstetrics and Gynecology, Shaare Zedek Medical Center, Jerusalem, Israel. .,Faculty of Medicine, Hebrew University, Jerusalem, Israel.
| | - Omer Murik
- Translational Genomics Laboratory, Medical Genetics Institute, Shaare Zedek Medical Center, Jerusalem, Israel
| | - Sharon Zeligson
- Cytogenomics Laboratory, Medical Genetics Institute, Shaare Zedek Medical Center, Jerusalem, Israel
| | - Orit Lobel
- Cytogenomics Laboratory, Medical Genetics Institute, Shaare Zedek Medical Center, Jerusalem, Israel
| | - Omri Weiss
- Medical Genetics Institute, Shaare Zedek Medical Center, Jerusalem, Israel.,Cytogenomics Laboratory, Medical Genetics Institute, Shaare Zedek Medical Center, Jerusalem, Israel
| | - Elie Picard
- Faculty of Medicine, Hebrew University, Jerusalem, Israel.,Pediatric Pulmonary Institute, Shaare Zedek Medical Center, Jerusalem, Israel
| | - Tzvia Mann
- Translational Genomics Laboratory, Medical Genetics Institute, Shaare Zedek Medical Center, Jerusalem, Israel
| | - Hagar Mor-Shaked
- Faculty of Medicine, Hebrew University, Jerusalem, Israel.,Department of Genetics, Hadassah Medical Organization, Jerusalem, Israel
| | - David A Zeevi
- Translational Genomics Laboratory, Medical Genetics Institute, Shaare Zedek Medical Center, Jerusalem, Israel
| | - Reeval Segel
- Medical Genetics Institute, Shaare Zedek Medical Center, Jerusalem, Israel.,Faculty of Medicine, Hebrew University, Jerusalem, Israel.,Cytogenomics Laboratory, Medical Genetics Institute, Shaare Zedek Medical Center, Jerusalem, Israel
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