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Zacharias M, Thüringer A, Krause R, Kashofer K, Gorkiewicz G. The mutual value of histopathology and ITS sequencing in the diagnosis of mucormycosis. Histopathology 2024; 84:702-706. [PMID: 38192085 DOI: 10.1111/his.15131] [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] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2023] [Revised: 11/29/2023] [Accepted: 12/13/2023] [Indexed: 01/10/2024]
Abstract
AIMS Mucormycosis is a fast-progressing disease with a high mortality rate. The most important factor determining survival of patients is early and accurate diagnosis. Although histopathology often recognises invasive mould infections at first, histomorphology alone is insufficient in providing an accurate diagnosis. Unbiased molecular methods to detect and identify fungi are promising, yet their role in complementing routine histopathological workflows has not been studied sufficiently. METHODS AND RESULTS We performed a retrospective single-centre study examining the clinical value of complementing histopathology with internal transcribed spacer (ITS) sequencing of fungal DNA in the routine diagnosis of mucormycosis. At our academic centre, we identified 14 consecutive mucormycosis cases diagnosed by histopathology and subsequent ITS sequencing. Using histomorphological examination, fungal hyphae could be detected in all cases; however, morphological features were unreliable regarding specifying the taxa. Subsequent ITS sequencing identified a remarkable phylogenetic diversity among Mucorales: the most common species was Rhizopus microsporus (six of 14; 42.9%), followed by Lichtheimia corymbifera (three of 14, 21.4%) and single detections of Rhizopus oryzae, Actinomucor elegans, Mucor circinelloides, Rhizomucor pusillus and Rhizomucor miehei (one of 14; 7.1%, respectively). In one case, we additionally detected Pneumocystis jirovecii in the same lung tissue specimen, suggesting a clinically relevant co-infection. Fungal culture was performed in 10 cases but yielded positive results in only two of 10 (20%), revealing its limited value in the diagnosis of mucormycosis. CONCLUSIONS Our study demonstrates that a combination of histopathology and ITS sequencing is a practically feasible approach that outperforms fungal culture in detecting Mucorales in tissue-associated infections. Therefore, pathologists might adapt diagnostic workflows accordingly when mucormycosis is suspected.
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Affiliation(s)
- Martin Zacharias
- Diagnostic and Research Institute of Pathology, Medical University of Graz, Graz, Austria
| | - Andrea Thüringer
- Diagnostic and Research Institute of Pathology, Medical University of Graz, Graz, Austria
| | - Robert Krause
- Division of Infectious Diseases, Medical University of Graz, Graz, Austria
| | - Karl Kashofer
- Diagnostic and Research Institute of Pathology, Medical University of Graz, Graz, Austria
| | - Gregor Gorkiewicz
- Diagnostic and Research Institute of Pathology, Medical University of Graz, Graz, Austria
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2
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Ferreira MS, Katchborian-Neto A, Nicácio KDJ, Santos MFC, Dias DF, Chagas-Paula DA, Soares MG. Phytochemical investigation of Nigrospora zimmermanii isolated from Poincianella pluviosa (Sibipiruna): metabolites characterisation and screening for anti-inflammatory activity. Nat Prod Res 2024:1-7. [PMID: 38384115 DOI: 10.1080/14786419.2024.2320733] [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: 10/03/2023] [Accepted: 02/11/2024] [Indexed: 02/23/2024]
Abstract
Endophytic fungi residing symbiotically in plant tissues are promising sources of bioactive natural products. This study explored the anti-inflammatory potential of an endophytic fungus isolated from the Brazilian medicinal plant Poincianella pluviosa (Sibipiruna). The extract from the endophyte FPD13 exhibited potential ex vivo anti-inflammatory effects by inhibiting prostaglandin E2 (PGE2) release by 75.22%. Phytochemical analysis using High-Performance Liquid Chromatography (HPLC), Nuclear Magnetic Resonance (NMR), and Liquid Chromatography-High Resolution Mass Spectrometry (LC-HRMS) enabled the isolation and identification of three compounds, including the macrolide Nigrosporolide, the phenyl-propanol Tyrosol, and the terpene Decarestrictine A. Morphological characteristics and Internal Transcribed Spacers region (ITS) sequencing classified fungus FPD13 as Nigrospora zimmermanii. The results reveal the anti-inflammatory potential and chemical diversity of P. pluviosa endophytes, warranting further investigation into the bioactivity and structure elucidation of their bioactive metabolites.
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Affiliation(s)
| | | | | | - Mario F C Santos
- Department of Chemistry and Physics, Federal University of Espírito Santo, Alegre, Espírito Santo, Brazil
| | - Danielle F Dias
- Institute of Chemistry, Federal University of Alfenas, Alfenas, Minas Gerais, Brazil
| | | | - Marisi G Soares
- Institute of Chemistry, Federal University of Alfenas, Alfenas, Minas Gerais, Brazil
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3
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Fernández Vecilla D, López-Plandolit Antolín S, Blasco Palacio PB, Unzaga Barañano MJ, Díaz de Tuesta Del Arco JL. Corneal abscess caused by Filobasidium uniguttulatum. Case report and literature review on cryptococcal keratitis. Rev Esp Quimioter 2024; 37:112-115. [PMID: 38083838 PMCID: PMC10874669 DOI: 10.37201/req/097.2023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Revised: 10/06/2023] [Accepted: 10/31/2023] [Indexed: 01/28/2024]
Affiliation(s)
- D Fernández Vecilla
- Domingo Fernández Vecilla, Clinical microbiology service. Basurto University Hospital. Bilbao (Biscay). Spain.
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Wang R, He S, Huang D, He S, Guo T, Chen T, Peng H, Jiaka L, He M, Chen C, Song D, Huang X, Wu D, Mao H. Differences in composition and diversity of rumen fungi in buffalo fed different diets. Anim Biotechnol 2023; 34:5075-5086. [PMID: 37946542 DOI: 10.1080/10495398.2023.2276974] [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] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2023]
Abstract
The rumen is a complex ecosystem containing a variety of fungi, which are crucial for the digestive activities of ruminants. Previous research on rumen fungi has mainly focused on anaerobic fungi, given the rumen's reputation as a mainly anaerobic environment. The objective of this study was to investigate rumen fungal diversity and the presence of aerobic fungi in buffalo fed on different diets. Three adult buffaloes were used as experimental animals. Alfalfa hay, oat hay, whole corn silage, sugarcane shoot silage, fresh king grass, dried rice straw, and five kinds of mixed diets with concentrate to roughage ratios of 20:80, 35:65, 50:50, 65:35, and 80:20 were used as the experimental diets. The experimental animals were fed different diets for 22 days. Rumen fluid was collected from the rumen fistula for ITS (Internal Transcribed Spacer) sequencing 2 h after feeding on the morning of day 22. The results indicate the presence of large quantities of aerobic fungi in the rumen of the buffaloes 2 h after feeding and suggest that Ascomycota and Basidiomycota are the dominant fungal groups under different feeding conditions. The study also identified 62 different fungal types, which showed significant differences among the 11 experimental diets.
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Affiliation(s)
- Rongjiao Wang
- Panzhihua Academy of Agricultural and Forestry Sciences, Panzhihua, China
| | - Shichun He
- Yunnan Provincial Key Laboratory of Animal Nutrition and Feed Science, Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming, China
| | - Dan Huang
- Panzhihua Academy of Agricultural and Forestry Sciences, Panzhihua, China
| | - Shaoying He
- Yunnan Provincial Key Laboratory of Animal Nutrition and Feed Science, Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming, China
| | - Taiqing Guo
- Yunnan Provincial Key Laboratory of Animal Nutrition and Feed Science, Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming, China
| | - Tao Chen
- Animal Husbandry Station, Mangshi, Yunnan, China
| | - Hongen Peng
- Panzhihua Academy of Agricultural and Forestry Sciences, Panzhihua, China
| | - Latie Jiaka
- Panzhihua Academy of Agricultural and Forestry Sciences, Panzhihua, China
| | - Min He
- Panzhihua Academy of Agricultural and Forestry Sciences, Panzhihua, China
| | - Changguo Chen
- Panzhihua Academy of Agricultural and Forestry Sciences, Panzhihua, China
| | - Dingzhou Song
- Panzhihua Academy of Agricultural and Forestry Sciences, Panzhihua, China
| | - Xiujun Huang
- Panzhihua Academy of Agricultural and Forestry Sciences, Panzhihua, China
| | - Dongwang Wu
- Yunnan Provincial Key Laboratory of Animal Nutrition and Feed Science, Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming, China
| | - Huaming Mao
- Yunnan Provincial Key Laboratory of Animal Nutrition and Feed Science, Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming, China
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5
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Chen Y, Li W, Chang ET, Debelius JW, Manoharan L, Zheng Y, Li Y, Huang G, Adami HO, Knight R, Cai Y, Zhang Z, Ye W. Oral fungal profiling and risk of nasopharyngeal carcinoma: a population-based case-control study. EBioMedicine 2023; 96:104813. [PMID: 37776725 PMCID: PMC10550808 DOI: 10.1016/j.ebiom.2023.104813] [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] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2023] [Revised: 08/06/2023] [Accepted: 09/15/2023] [Indexed: 10/02/2023] Open
Abstract
BACKGROUND Dysbiosis of the oral mycobiome has been linked to some diseases, including cancers. However, the role of oral fungal communities in nasopharyngeal carcinoma (NPC) carcinogenesis has not previously been investigated. METHODS We characterized the oral salivary fungal mycobiome in 476 untreated incident NPC patients and 537 population-based controls using fungal internal transcribed spacer (ITS)-2 sequencing. The relationship between oral fungal mycobiome and the risk of NPC was assessed through bioinformatic and biostatistical analyses. FINDINGS We found that lower fungal alpha diversity was associated with an increased odds of NPC [lower vs. higher: observed features (adjusted odds ratio [OR] = 5.81, 95% confidence interval [CI] = 3.60-9.38); Simpson diversity (1.53, 1.03-2.29); Shannon diversity (2.03, 1.35-3.04)]. We also observed a significant difference in global fungal community patterns between cases and controls based on Bray-Curtis dissimilarity (P < 0.001). Carriage of oral fungal species, specifically, Saccharomyces cerevisiae, Candida tropicalis, Lodderomyces elongisporus, Candida albicans, and Fusarium poae, was associated with significantly higher odds of NPC, with ORs ranging from 1.56 to 4.66. Individuals with both low fungal and low bacterial alpha diversity had a profoundly elevated risk of NPC. INTERPRETATION Our results suggest that dysbiosis in the oral mycobiome, characterized by a loss of fungal community diversity and overgrowth of several fungal organisms, is associated with a substantially increased risk of NPC. FUNDING This work was funded by the US National Institutes of Health, the Swedish Research Council, the High-level Talents Research Start-up Project of Fujian Medical University, and the China Scholarship Council.
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Affiliation(s)
- Yufeng Chen
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, 17177, Sweden
| | - Wanxin Li
- Department of Epidemiology and Health Statistics & Key Laboratory of Ministry of Education for Gastrointestinal Cancer, Fujian Medical University, Fuzhou, 350000, China
| | - Ellen T Chang
- Department of Epidemiology and Biostatistics, University of California, San Francisco, CA, 94143, USA
| | - Justine W Debelius
- Center for Translational Microbiome Research, Department of Microbiology, Tumor and Cancer Biology, Karolinska Institutet, Stockholm, 17177, Sweden; Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, 21205, USA
| | - Lokeshwaran Manoharan
- National Bioinformatics Infrastructure Sweden (NBIS), Lund University, Lund, 22100, Sweden
| | - Yuming Zheng
- Guangxi Health Commission Key Laboratory of Molecular Epidemiology of Nasopharyngeal Carcinoma, Wuzhou Red Cross Hospital, Wuzhou, 543002, China; Department of Preventive Medicine, Wuzhou Cancer Center, Wuzhou, 543002, China
| | - Yancheng Li
- Guangxi Health Commission Key Laboratory of Molecular Epidemiology of Nasopharyngeal Carcinoma, Wuzhou Red Cross Hospital, Wuzhou, 543002, China; Cangwu Institute for Nasopharyngeal Carcinoma Control and Prevention, Wuzhou, 543002, China
| | - Guangwu Huang
- Department of Otolaryngology-Head & Neck Surgery, First Affiliated Hospital of Guangxi Medical University, Nanning, 530021, China; Key Laboratory of High-Incidence-Tumor Prevention & Treatment (Guangxi Medical University), Ministry of Education, Nanning, 530021, China
| | - Hans-Olov Adami
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, 17177, Sweden; Clinical Effectiveness Group, Institute of Health and Society, University of Oslo, Oslo, NO-0316, Norway
| | - Rob Knight
- Department of Pediatrics, University of California San Diego, CA, 92093, USA
| | - Yonglin Cai
- Guangxi Health Commission Key Laboratory of Molecular Epidemiology of Nasopharyngeal Carcinoma, Wuzhou Red Cross Hospital, Wuzhou, 543002, China; Department of Preventive Medicine, Wuzhou Cancer Center, Wuzhou, 543002, China.
| | - Zhe Zhang
- Department of Otolaryngology-Head & Neck Surgery, First Affiliated Hospital of Guangxi Medical University, Nanning, 530021, China; Key Laboratory of High-Incidence-Tumor Prevention & Treatment (Guangxi Medical University), Ministry of Education, Nanning, 530021, China.
| | - Weimin Ye
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, 17177, Sweden; Department of Epidemiology and Health Statistics & Key Laboratory of Ministry of Education for Gastrointestinal Cancer, Fujian Medical University, Fuzhou, 350000, China.
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Nafis MMH, Quach ZM, Al-Shaarani AAQA, Muafa MHM, Pecoraro L. Pathogenicity of Aspergillus Airborne Fungal Species Collected from Indoor and Outdoor Public Areas in Tianjin, China. Pathogens 2023; 12:1154. [PMID: 37764962 PMCID: PMC10534727 DOI: 10.3390/pathogens12091154] [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: 08/01/2023] [Revised: 08/29/2023] [Accepted: 09/06/2023] [Indexed: 09/29/2023] Open
Abstract
Airborne fungi play an important role in air pollution and may have various negative effects on human health. In particular, Aspergillus fungi are pathogenic to humans and several domestic animals. In this work, Aspergillus strains isolated from airborne fungal communities sampled from different indoor and outdoor environments in Tianjin University were tested for pathogenicity on Drosophila melanogaster. Airborne fungi were sampled using an HAS-100B air sampler, over a one-year sampling period. Isolated fungal strains were identified based on morphological and molecular analysis. The Aspergillus-centered study was conducted as part of a larger work focusing on the total airborne fungal community in the analyzed environments, which yielded 173 fungal species. In this context, the genus Aspergillus showed the second-highest species richness, with 14 isolated species. Pathogenicity tests performed on male adults of Drosophila melanogaster through a bodily contact bioassay showed that all analyzed airborne Aspergillus species were pathogenic to fruit flies, with high insect mortality rates and shortened lifespan. All the studied fungi induced 100% mortality of fruit flies within 30 culture days, with one exception constituted by A. creber (39 days), while the shortest lifespan (17 days) was observed in fruit flies treated with A. tubingensis. Our results allow us to hypothesize that the studied airborne fungal species may have a pathogenic effect on humans, given the affinity between fruit flies and the human immune system, and may help to explain the health risk linked with Aspergillus fungi exposure in densely populated environments.
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Affiliation(s)
| | | | | | | | - Lorenzo Pecoraro
- School of Pharmaceutical Science and Technology, Tianjin University, 92 Weijin Road, Tianjin 300072, China
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Sun A, Gou X, Zhu Y, Lv H, Ge Y. Identification of Talaromyces marneffei Infection in an HIV-Negative Patient by ITS Sequencing. Infect Drug Resist 2023; 16:5275-5282. [PMID: 37601563 PMCID: PMC10438431 DOI: 10.2147/idr.s418174] [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: 05/08/2023] [Accepted: 08/02/2023] [Indexed: 08/22/2023] Open
Abstract
Disseminated ankle mycosis is a life-threatening systemic infection caused by the emerging opportunistic and lethal fungal pathogen Talaromyces marneffei which is more common in HIV-positive patients. However, an increasing number of infections are occurring in HIV-negative patients. Here, we report a case of Talaromyces marneffei infection in HIV-negative patient. A 50s HIV-negative male patient with fever, cough, bloody sputum expectoration, pulmonary sarcoidosis and body rashes was hospitalized at Zhejiang Provincial People's Hospital. CT scanning showed pulmonary multiple nodules with apical bronchial occlusion, patchy infiltration and pathological biopsy demonstrated bronchiolitis obliterans with organized pneumonia and chronic active inflammation of lung tissue with infiltration of numerous lymphocytes, plasma cells, phagocytes and neutrophils. Laboratory tests revealed significantly increased white blood cells count 18.3 ×109/L, neutrophil count 15.34 ×109/L, monocyte count 0.66 ×109/L, platelet count 517 ×109/L, C-reactive protein 116 mg/L, erythrocyte sedimentation rate 112mm/h. The β-D-glucan test was negative (33.06 pg/mL) while fungal culture of broncho alveolar lavage fluid revealed colonies with temperature-dependent dimorphic growth character and Talaromyces marneffei was confirmed by ITS sequencing of the colonies. The patient exhibited radiological improvement and clinical recuperation after intravenously guttae of voriconazole. Talaromycosis in immunocompetent and HIV-negative individuals is relatively rare and is characterized by an insidious onset, various clinical manifestations, and is clinically challenging. Fungal culture and ITS sequencing are warranted for diagnosis Talaromyces marneffei infection. This is the first report on identification of Talaromyces marneffei infection in an HIV-negative patient with skin involvement by ITS sequencing in Zhejiang.
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Affiliation(s)
- Aihua Sun
- Laboratory Medicine Center, Department of Clinical Laboratory, Zhejiang Provincial People’s Hospital (Affiliated People’s Hospital), Hangzhou Medical College, Hangzhou, Zhejiang, 310014, People’s Republic of China
- School of Basic Medical Sciences and Forensic Medicine, Hangzhou Medical College, Hangzhou, Zhejiang, 310059, People’s Republic of China
| | - Xiaoyu Gou
- Laboratory Medicine Center, Department of Clinical Laboratory, Zhejiang Provincial People’s Hospital (Affiliated People’s Hospital), Hangzhou Medical College, Hangzhou, Zhejiang, 310014, People’s Republic of China
- School of Basic Medical Sciences and Forensic Medicine, Hangzhou Medical College, Hangzhou, Zhejiang, 310059, People’s Republic of China
| | - Yongze Zhu
- Laboratory Medicine Center, Department of Clinical Laboratory, Zhejiang Provincial People’s Hospital (Affiliated People’s Hospital), Hangzhou Medical College, Hangzhou, Zhejiang, 310014, People’s Republic of China
| | - Huoyang Lv
- Laboratory Medicine Center, Department of Clinical Laboratory, Zhejiang Provincial People’s Hospital (Affiliated People’s Hospital), Hangzhou Medical College, Hangzhou, Zhejiang, 310014, People’s Republic of China
| | - Yumei Ge
- Laboratory Medicine Center, Department of Clinical Laboratory, Zhejiang Provincial People’s Hospital (Affiliated People’s Hospital), Hangzhou Medical College, Hangzhou, Zhejiang, 310014, People’s Republic of China
- School of Basic Medical Sciences and Forensic Medicine, Hangzhou Medical College, Hangzhou, Zhejiang, 310059, People’s Republic of China
- Key Laboratory of Biomarkers and in vitro Diagnosis Translation of Zhejiang Province, Hangzhou, Zhejiang, 310053, People’s Republic of China
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8
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Gibson E, Zimmerman NB. Urban biogeography of fungal endophytes across San Francisco. PeerJ 2023; 11:e15454. [PMID: 37547726 PMCID: PMC10399560 DOI: 10.7717/peerj.15454] [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] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Accepted: 05/03/2023] [Indexed: 08/08/2023] Open
Abstract
In natural and agricultural systems, the plant microbiome-the microbial organisms associated with plant tissues and rhizosphere soils-has been shown to have important effects on host physiology and ecology, yet we know little about how these plant-microbe relationships play out in urban environments. Here we characterize the composition of fungal communities associated with living leaves of one of the most common sidewalk trees in the city of San Francisco, California. We focus our efforts on endophytic fungi (asymptomatic microfungi that live inside healthy leaves), which have been shown in other systems to have large ecological effects on the health of their plant hosts. Specifically, we characterized the foliar fungal microbiome of Metrosideros excelsa (Myrtaceae) trees growing in a variety of urban environmental conditions. We used high-throughput culturing, PCR, and Sanger sequencing of the internal transcribed spacer nuclear ribosomal DNA (ITS nrDNA) region to quantify the composition and structure of fungal communities growing within healthy leaves of 30 M. excelsa trees from six distinct sites, which were selected to capture the range of environmental conditions found within city limits. Sequencing resulted in 854 high-quality ITS sequences. These sequences clustered into 85 Operational Taxonomic Units (97% OTUs). We found that these communities encompass relatively high alpha (within) and beta (between-site) diversity. Because the communities are all from the same host tree species, and located in relatively close geographical proximity to one another, these analyses suggest that urban environmental factors such as heat islands or differences in vegetation or traffic density (and associated air quality) may potentially be influencing the composition of these fungal communities. These biogeographic patterns provide evidence that plant microbiomes in urban environments can be as dynamic and complex as their natural counterparts. As human populations continue to transition out of rural areas and into cities, understanding the factors that shape environmental microbial communities in urban ecosystems stands to become increasingly important.
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Affiliation(s)
- Emma Gibson
- Department of Biology, University of San Francisco, San Francisco, CA, United States of America
| | - Naupaka B. Zimmerman
- Department of Biology, University of San Francisco, San Francisco, CA, United States of America
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Dawadi P, Odari R, Poudel RC, Pokhrel LR, Bhatt LR. Isolation of Lactococcus garvieae NEP21 from raw cow (Bos indicus) milk in Nepal. Sci Total Environ 2023; 861:160641. [PMID: 36470377 DOI: 10.1016/j.scitotenv.2022.160641] [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] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Revised: 11/27/2022] [Accepted: 11/28/2022] [Indexed: 06/17/2023]
Abstract
Lactococcus garvieae is an emerging zoonotic pathogen impacting both humans and animals. Infection of this bacterium is known to cause mastitis in cattle, and endocarditis, osteomyelitis, liver abscess, and gastrointestinal problems are reported in immunocompromised and elderly people that regularly consume or handle raw meat, milk, dairy products, and seafood. This study aimed at investigating and detecting lactic acid bacteria in raw cow (Bos indicus) milk samples from a smallholder farm in Nepal. Based on the plate culture, biochemical tests, and molecular sequencing of 16 s ribosomal RNA coding nuclear DNA region followed by phenotypic and genotypic analyses, L. garvieae NEP21 was detected and identified for the first time in Nepal in raw cow milk samples. This finding suggests the prevalence of L. garvieae NEP21 in raw cow milk and recommends further research and surveillance for understanding the extent of its presence in Nepal and globally for informed management of its infection in cattle and humans.
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Affiliation(s)
- Prabin Dawadi
- Biological Resource Unit, Nepal Academy of Science and Technology, Khumaltar, Lalitpur, Nepal
| | - Ranjeeta Odari
- Molecular Biotechnology Unit, Nepal Academy of Science and Technology, Khumaltar, Lalitpur, Nepal
| | - Ram Chandra Poudel
- Molecular Biotechnology Unit, Nepal Academy of Science and Technology, Khumaltar, Lalitpur, Nepal
| | - Lok R Pokhrel
- Department of Public Health, The Brody School of Medicine, East Carolina University, Greenville, NC 27834, USA.
| | - Lok Ranjan Bhatt
- Biological Resource Unit, Nepal Academy of Science and Technology, Khumaltar, Lalitpur, Nepal.
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10
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Li BZ, Wang H, Li XB, Zhang QR, Huang RG, Wu H, Wang YY, Li KD, Chu XJ, Cao NW, Zhou HY, Fang XY, Leng RX, Fan YG, Tao JH, Shuai ZW, Ye DQ. Altered gut fungi in systemic lupus erythematosus - A pilot study. Front Microbiol 2022; 13:1031079. [PMID: 36545195 PMCID: PMC9760866 DOI: 10.3389/fmicb.2022.1031079] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Accepted: 11/18/2022] [Indexed: 12/12/2022] Open
Abstract
Objective Gut fungi, as symbiosis with the human gastrointestinal tract, may regulate physiology via multiple interactions with host cells. The plausible role of fungi in systemic lupus erythematosus (SLE) is far from clear and need to be explored. Methods A total of 64 subjects were recruited, including SLE, rheumatoid arthritis (RA), undifferentiated connective tissue diseases (UCTDs) patients and healthy controls (HCs). Fecal samples of subjects were collected. Gut fungi and bacteria were detected by ITS sequencing and 16S rRNA gene sequencing, respectively. Alpha and beta diversities of microbiota were analyzed. Linear discriminant analysis effect size analysis was performed to identify abundance of microbiota in different groups. The correlation network between bacterial and fungal microbiota was analyzed based on Spearman correlation. Results Gut fungal diversity and community composition exhibited significant shifts in SLE compared with UCTDs, RA and HCs. Compared with HCs, the alpha and beta diversities of fungal microbiota decreased in SLE patients. According to principal coordinates analysis results, the constitution of fungal microbiota from SLE, RA, UCTDs patients and HCs exhibited distinct differences with a clear separation between fungal microbiota. There was dysbiosis in the compositions of fungal and bacterial microbiota in the SLE patients, compared to HCs. Pezizales, Cantharellales and Pseudaleuria were enriched in SLE compared with HCs, RA and UCTDs. There was a complex relationship network between bacterial and fungal microbiota, especially Candida which was related to a variety of bacteria. Conclusion This study presents a pilot analysis of fungal microbiota with diversity and composition in SLE, and identifies several gut fungi with different abundance patterns taxa among SLE, RA, UCTDs and HCs. Furthermore, the gut bacterial-fungal association network in SLE patients was altered compared with HCs.
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Affiliation(s)
- Bao-Zhu Li
- Department of Epidemiology and Biostatistics, School of Public Health, Anhui Medical University, Hefei, Anhui, China,Inflammatory and Immune Diseases Laboratory of Anhui Province, Hefei, Anhui, China
| | - Hua Wang
- Department of Epidemiology and Biostatistics, School of Public Health, Anhui Medical University, Hefei, Anhui, China,Inflammatory and Immune Diseases Laboratory of Anhui Province, Hefei, Anhui, China
| | - Xian-Bao Li
- Department of Epidemiology and Biostatistics, School of Public Health, Anhui Medical University, Hefei, Anhui, China,Inflammatory and Immune Diseases Laboratory of Anhui Province, Hefei, Anhui, China
| | - Qian-Ru Zhang
- Department of Epidemiology and Biostatistics, School of Public Health, Anhui Medical University, Hefei, Anhui, China,Inflammatory and Immune Diseases Laboratory of Anhui Province, Hefei, Anhui, China
| | - Rong-Gui Huang
- Department of Epidemiology and Biostatistics, School of Public Health, Anhui Medical University, Hefei, Anhui, China,Inflammatory and Immune Diseases Laboratory of Anhui Province, Hefei, Anhui, China
| | - Hong Wu
- Department of Epidemiology and Biostatistics, School of Public Health, Anhui Medical University, Hefei, Anhui, China,Inflammatory and Immune Diseases Laboratory of Anhui Province, Hefei, Anhui, China
| | - Yi-Yu Wang
- Department of Epidemiology and Biostatistics, School of Public Health, Anhui Medical University, Hefei, Anhui, China,Inflammatory and Immune Diseases Laboratory of Anhui Province, Hefei, Anhui, China
| | - Kai-Di Li
- Department of Epidemiology and Biostatistics, School of Public Health, Anhui Medical University, Hefei, Anhui, China,Inflammatory and Immune Diseases Laboratory of Anhui Province, Hefei, Anhui, China
| | - Xiu-Jie Chu
- Department of Epidemiology and Biostatistics, School of Public Health, Anhui Medical University, Hefei, Anhui, China,Inflammatory and Immune Diseases Laboratory of Anhui Province, Hefei, Anhui, China
| | - Nv-Wei Cao
- Department of Epidemiology and Biostatistics, School of Public Health, Anhui Medical University, Hefei, Anhui, China,Inflammatory and Immune Diseases Laboratory of Anhui Province, Hefei, Anhui, China
| | - Hao-Yue Zhou
- Department of Epidemiology and Biostatistics, School of Public Health, Anhui Medical University, Hefei, Anhui, China,Inflammatory and Immune Diseases Laboratory of Anhui Province, Hefei, Anhui, China,The First Hospital of Jiaxing, Jiaxing, Zhejiang, China
| | - Xin-Yu Fang
- Department of Epidemiology and Biostatistics, School of Public Health, Anhui Medical University, Hefei, Anhui, China,Inflammatory and Immune Diseases Laboratory of Anhui Province, Hefei, Anhui, China
| | - Rui-Xue Leng
- Department of Epidemiology and Biostatistics, School of Public Health, Anhui Medical University, Hefei, Anhui, China,Inflammatory and Immune Diseases Laboratory of Anhui Province, Hefei, Anhui, China
| | - Yin-Guang Fan
- Department of Epidemiology and Biostatistics, School of Public Health, Anhui Medical University, Hefei, Anhui, China,Inflammatory and Immune Diseases Laboratory of Anhui Province, Hefei, Anhui, China
| | - Jin-Hui Tao
- Department of Rheumatology and Immunology, The First Affiliated Hospital of University of Science and Technology of China, Hefei, Anhui, China
| | - Zong-Wen Shuai
- Department of Rheumatology and Immunology, The First Affiliated Hospital of Anhui Medical University, Hefei, Anhui, China
| | - Dong-Qing Ye
- Department of Epidemiology and Biostatistics, School of Public Health, Anhui Medical University, Hefei, Anhui, China,Inflammatory and Immune Diseases Laboratory of Anhui Province, Hefei, Anhui, China,*Correspondence: Dong-Qing Ye,
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11
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Wang J, Zhao H, Guo Q, Ding H. Identification and antibacterial activity of Thamnolia vermicularis and Thamnolia subuliformis. J Microbiol Methods 2022; 203:106628. [PMID: 36442696 DOI: 10.1016/j.mimet.2022.106628] [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: 08/05/2022] [Revised: 11/14/2022] [Accepted: 11/23/2022] [Indexed: 11/27/2022]
Abstract
Thamnolia vermicularis (Tv) and Thamnolia subuliformis (Ts) are two species from the same habitat with such similar external morphological characteristics that researchers often confuse the two in their scientific work and do not distinguish between them. This study applies three different methods to distinguish them. The diversity of endophytic fungi was also compared and their antibacterial activity in vitro was evaluated. The results show that all three methods can distinguish Tv and Ts, and can be used to cross-validate each other. The ultraviolet fluorescence method and the chemical colour change method are simpler strategies, while thin-layer chromatography is relatively complicated but can more clearly distinguish the chemical composition of the two species. In the analysis of the endophytic fungi community structure of Tv and Ts, it was found that the diversity of endophytic fungi in Tv was more abundant and had wider antibacterial activity and better inhibitory activity against gram-positive bacteria in vitro.
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Affiliation(s)
- Jing Wang
- School of Public Health, Dali University, Dali 671000, China
| | - Haojun Zhao
- Dali Quality and Technical Comprehensive Supervision Testing Center, Dali 671000, China
| | - Qixin Guo
- Dali Quality and Technical Comprehensive Supervision Testing Center, Dali 671000, China
| | - Haiyan Ding
- School of Public Health, Dali University, Dali 671000, China; Yunnan Key Laboratory of Screening and Research on Anti-pathogenic Plant Resources from West Yunnan (Cultivation), Dali 671000, China.
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12
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Liu B, Yao J, Ma B, Li S, Duran R. Disentangling biogeographic and underlying assembly patterns of fungal communities in metalliferous mining and smelting soils. Sci Total Environ 2022; 845:157151. [PMID: 35798111 DOI: 10.1016/j.scitotenv.2022.157151] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Revised: 06/29/2022] [Accepted: 06/30/2022] [Indexed: 06/15/2023]
Abstract
Elucidating community assembly and their relevance to environmental variables are fundamental for understanding microbial diversity and functioning in terrestrial ecosystems, yet the geographical diversity and assembly patterns of the fungal community in metalliferous ecospheres associated with mining and smelting activities have received penurious understandings. Here, the fungal communities collected from three groups of soils around the mining and smelting sites were profiled by Internal Transcribed Spacer (ITS) sequencing, in order to understand the geographical distributions of fungal community diversities, structures, compositions, assembly processes and the occurrence patterns. The results suggested obvious biogeographic distribution patterns of fungal compositions among the three groups of soils. Among them, 15 fungal phyla including Ascomycota, Basidiomycota and Mortierellomycota were recognized across the samples. 12 abundant classes showing significantly different in relative abundances among the three groups of soils. Total metal(loid)s and level significantly decreased the fungal abundances and diversities. The community similarity demonstrated distance-decay pattern among the three sites. Metal(loid)s explained relatively higher fungal community variations (4.16 %) relative to other factors (1.89 %) and geography (1.21 %), though 83.32 % of the variations could not be explained. Stochastic dispersal limitation and undominated fraction were dominated relative to deterministic heterogeneous selection in total and individual site, respectively. These results highlighted the stochastic processes in governing the biogeography of fungal communities in mining and smelting ecospheres.
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Affiliation(s)
- Bang Liu
- School of Water Resource and Environment, Research Center of Environmental Science and Engineering, MOE Key Laboratory of Groundwater Circulation and Environmental Evolution, China University of Geosciences (Beijing), 29 Xueyuan Road, Haidian District, Beijing 100083, People's Republic of China
| | - Jun Yao
- School of Water Resource and Environment, Research Center of Environmental Science and Engineering, MOE Key Laboratory of Groundwater Circulation and Environmental Evolution, China University of Geosciences (Beijing), 29 Xueyuan Road, Haidian District, Beijing 100083, People's Republic of China.
| | - Bo Ma
- School of Water Resource and Environment, Research Center of Environmental Science and Engineering, MOE Key Laboratory of Groundwater Circulation and Environmental Evolution, China University of Geosciences (Beijing), 29 Xueyuan Road, Haidian District, Beijing 100083, People's Republic of China
| | - Shuzhen Li
- School of Minerals Processing and Bioengineering, Central South University, Changsha 410083, People's Republic of China
| | - Robert Duran
- School of Water Resource and Environment, Research Center of Environmental Science and Engineering, MOE Key Laboratory of Groundwater Circulation and Environmental Evolution, China University of Geosciences (Beijing), 29 Xueyuan Road, Haidian District, Beijing 100083, People's Republic of China; Equipe Environnement et Microbiologie, MELODY group, Université de Pau et des Pays de l'Adour, E2S-UPPA, IPREM UMR CNRS 5254, BP 1155, 64013 Pau Cedex, France
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13
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Chen A, Najeeb S, Wang Y, Khan RAA, Ping X, Ling J. First Report of Colletotrichum circinans Causing Anthracnose in Allium fistulosum var. giganteum in Gansu Province, China. Plant Dis 2022; 106:PDIS09212011PDN. [PMID: 34931896 DOI: 10.1094/pdis-09-21-2011-pdn] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Affiliation(s)
- A Chen
- Dingxi Station of Plant Protection and Quarantine, Dingxi 74300, China
| | - S Najeeb
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Y Wang
- Dingxi Station of Agroecology Resource Protection Technology Promotion, Dingxi 74300, China
| | - R A A Khan
- Department of Plant Pathology, The University of Agriculture Peshawar, Peshawar 25130, Pakistan
- Key Laboratory of Green Prevention and Control of Tropical Diseases and Pests (College of Plant Protection, Hainan University), Ministry of Education, Haikou, Hainan 570228, China
| | - X Ping
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - J Ling
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
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14
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Gréau L, Blaudez D, Heintz D, Zumsteg J, Billet D, Cébron A. Response of Poplar and Associated Fungal Endophytic Communities to a PAH Contamination Gradient. Int J Mol Sci 2022; 23:ijms23115909. [PMID: 35682588 PMCID: PMC9180295 DOI: 10.3390/ijms23115909] [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] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Revised: 05/19/2022] [Accepted: 05/20/2022] [Indexed: 01/27/2023] Open
Abstract
Microbial populations associated to poplar are well described in non-contaminated and metal-contaminated environments but more poorly in the context of polycyclic aromatic hydrocarbon (PAH) contamination. This study aimed to understand how a gradient of phenanthrene (PHE) contamination affects poplar growth and the fungal microbiome in both soil and plant endosphere (roots, stems and leaves). Plant growth and fitness parameters indicated that the growth of Populus canadensis was impaired when PHE concentration increased above 400 mg kg-1. Values of alpha-diversity indicators of fungal diversity and richness were not affected by the PHE gradient. The PHE contamination had a stronger impact on the fungal community composition in the soil and root compartments compared to that of the aboveground organs. Most of the indicator species whose relative abundance was correlated with PHE contamination decreased along the gradient indicating a toxic effect of PHE on these fungal OTUs (Operational Taxonomic Units). However, the relative abundance of some OTUs such as Cadophora, Alternaria and Aspergillus, potentially linked to PHE degradation or being plant-beneficial taxa, increased along the gradient. Finally, this study allowed a deeper understanding of the dual response of plant and fungal communities in the case of a soil PAH contamination gradient leading to new perspectives on fungal assisted phytoremediation.
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Affiliation(s)
- Lilian Gréau
- Université de Lorraine, CNRS, LIEC, 54000 Nancy, France; (L.G.); (D.B.); (D.B.)
| | - Damien Blaudez
- Université de Lorraine, CNRS, LIEC, 54000 Nancy, France; (L.G.); (D.B.); (D.B.)
| | - Dimitri Heintz
- Institut de Biologie Moléculaire des Plantes, CNRS, Université de Strasbourg, 67000 Strasbourg, France; (D.H.); (J.Z.)
| | - Julie Zumsteg
- Institut de Biologie Moléculaire des Plantes, CNRS, Université de Strasbourg, 67000 Strasbourg, France; (D.H.); (J.Z.)
| | - David Billet
- Université de Lorraine, CNRS, LIEC, 54000 Nancy, France; (L.G.); (D.B.); (D.B.)
- Pôle de Compétences en Biologie Environnementale, Université de Lorraine, CNRS, LIEC, 54000 Nancy, France
| | - Aurélie Cébron
- Université de Lorraine, CNRS, LIEC, 54000 Nancy, France; (L.G.); (D.B.); (D.B.)
- Correspondence:
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15
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Ahirwar LK, Sheba E, Jakati S, Jayasudha R, Padakandla SR, Bagga B, Sharma S. Elucidating the clinical, microbiological and molecular diagnostic aspects of Macrophomina phaseolina keratitis. Med Mycol 2022; 60:myac024. [PMID: 35472145 DOI: 10.1093/mmy/myac024] [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] [Indexed: 02/21/2024] Open
Abstract
This study reports the clinico-microbiological features of Macrophomina phaseolina keratitis. Clinically diagnosed as microbial keratitis, six patients underwent microbiological evaluation. Fungal culture isolates from cornea were subjected to DNA sequencing of the ITS region, phylogenetic analysis and reconfirmation by polymerase chain reaction (PCR). Minimum inhibitory concentrations (MICs) of six antifungal drugs were determined by microbroth dilution method against the six isolates. All patients were treated with antifungals. Failed medical therapy necessitated therapeutic penetrating keratoplasty (TPK). Corneal buttons were processed for histopathology. In all patients, the corneal scraping showed septate hyaline fungal filaments. The BLAST analysis for ITS sequences of all six fungal isolates suggested M. phaseolina, however, when limited to sequences from type material, they matched M. pseudophaseolina. Phylogenetic analysis could not differentiate between these two species and clustered in a single clade. PCR assay of specific gene sequence [MpCal (calmodulin)] reconfirmed all isolates as M. phaseolina. The MICs of voriconazole and posaconazole were lowest (0.03 to 2 and 0.1 to 2µg/mL respectively) and all isolates were susceptible to natamycin. Except for case 1, which healed with a scar on treatment, all other cases worsened, despite medical treatment, necessitating TPK. Histopathology of 3 out of 4 buttons showed the presence of fungal filaments. While direct microscopic examination of corneal scrapings is helpful in diagnosis, identification of M. phaseolina in culture is challenging. Although MICs of commonly used antifungals are low response to medical therapy is not encouraging; patients may require TPK for resolution of infection in M. phaseolina keratitis.
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Affiliation(s)
- Lalit Kishore Ahirwar
- Jhaveri Microbiology Centre, Brien Holden Eye Research Centre, L. V. Prasad Eye Institute, Kallam Anji Reddy Campus, L. V. Prasad Marg, Banjara Hills, Hyderabad-500034, India
| | - Esther Sheba
- Jhaveri Microbiology Centre, Brien Holden Eye Research Centre, L. V. Prasad Eye Institute, Kallam Anji Reddy Campus, L. V. Prasad Marg, Banjara Hills, Hyderabad-500034, India
| | - Saumya Jakati
- Ophthalmic Pathology Laboratory, Kallam Anji Reddy Campus, L. V. Prasad Marg, Banjara Hills, Hyderabad-500034, India
| | - Rajagopalaboopathi Jayasudha
- Jhaveri Microbiology Centre, Brien Holden Eye Research Centre, L. V. Prasad Eye Institute, Kallam Anji Reddy Campus, L. V. Prasad Marg, Banjara Hills, Hyderabad-500034, India
| | - Shalem Raj Padakandla
- Jhaveri Microbiology Centre, Brien Holden Eye Research Centre, L. V. Prasad Eye Institute, Kallam Anji Reddy Campus, L. V. Prasad Marg, Banjara Hills, Hyderabad-500034, India
| | - Bhupesh Bagga
- The Cornea Institute, Kallam Anji Reddy Campus, L. V. Prasad Marg, Banjara Hills, Hyderabad-500034, India
| | - Savitri Sharma
- Jhaveri Microbiology Centre, Brien Holden Eye Research Centre, L. V. Prasad Eye Institute, Kallam Anji Reddy Campus, L. V. Prasad Marg, Banjara Hills, Hyderabad-500034, India
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16
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Gu X, Cheng X, Zhang J, She W. Identification of the Fungal Community in Otomycosis by Internal Transcribed Spacer Sequencing. Front Microbiol 2022; 13:820423. [PMID: 35369424 PMCID: PMC8965282 DOI: 10.3389/fmicb.2022.820423] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Accepted: 01/26/2022] [Indexed: 11/25/2022] Open
Abstract
We used internal transcribed spacer (ITS) sequencing to identify the fungal community in otomycosis patients and to evaluate the treatment effects of bifonazole. Ten patients who visited the Department of Otolaryngology of Jiangsu Provincial Hospital on Integration of Chinese and Western Medicine from May 2020 to April 2021 were recruited. Otomycosis patients were treated with bifonazole solution once a day for 14 days. Samples collected from the external auditory canal before and after treatment (Pre-treatment, n = 14 ears; Post-treatment, n = 14 ears) were used for microscopic examination, fungal culture, and ITS sequencing. Samples collected from 10 volunteers (Control, n = 20 ears) were used as controls. The symptoms, including ear itching, aural fullness, otalgia, hearing loss, and physical signs were recorded before treatment as well as on the 7th and 14th days after treatment. Aspergillus was identified as a main pathogenic fungus by microscopic examination, fungal culture, and ITS sequencing. At the genus level, Aspergillus was more abundant in the pre-treatment group than the control and post-treatment groups, and Malassezia was more abundant in the control and post-treatment groups than the pre-treatment group. The fungal species richness and diversity reduced significantly in the pre-treatment group compared with the control and post-treatment groups. The effective rate of bifonazole was 64.29% and 100% on the 7th and 14th days after treatment, respectively. In conclusion, the results obtained from morphologic studies and ITS sequencing indicate that Aspergillus is the main pathogenic fungus of otomycosis patients in Nanjing, Jiangsu Province, China. Malassezia is the dominant resident fungi in healthy individuals. ITS sequencing provides comprehensive information about fungal community in otomycosis and is helpful in evaluating the efficacy of antifungal agents.
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Affiliation(s)
- Xiaona Gu
- Nanjing Drum Tower Hospital Clinical College of Traditional Chinese and Western Medicine, Nanjing University of Chinese Medicine, Nanjing, China.,Department of Otolaryngology, Affiliated Hospital of Integrated Traditional Chinese and Western Medicine, Nanjing University of Chinese Medicine, Nanjing, China
| | - Xiangrong Cheng
- Department of Otolaryngology, Affiliated Hospital of Integrated Traditional Chinese and Western Medicine, Nanjing University of Chinese Medicine, Nanjing, China
| | - Jinhua Zhang
- Department of Laboratory Medicine, Affiliated Hospital of Integrated Traditional Chinese and Western Medicine, Nanjing University of Chinese Medicine, Nanjing, China
| | - Wandong She
- Nanjing Drum Tower Hospital Clinical College of Traditional Chinese and Western Medicine, Nanjing University of Chinese Medicine, Nanjing, China.,Department of Otolaryngology-Head and Neck Surgery, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Nanjing, China
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17
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Abstract
Identification of Candida auris by conventional identification methodologies can be challenging. While whole genome sequencing is seen as the golden standard to genotype C. auris at an inter- and intraspecies level, it is costly and time-consuming. Sequencing the transcribed spacer (ITS) region and microsatellite typing provide simple, fast, and inexpensive alternatives for identification and genotyping of C. auris. Here we will describe both molecular approaches.
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Affiliation(s)
- Auke W de Jong
- Westerdijk Fungal Biodiversity Institute, Utrecht, The Netherlands
- Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, The Netherlands
| | | | - Ferry Hagen
- Westerdijk Fungal Biodiversity Institute, Utrecht, The Netherlands.
- Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, The Netherlands.
- Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, Amsterdam, The Netherlands.
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18
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T S S, Ninan MM, Premanand A, Chacko A, Sahni RD, Michael JS. Candida utilis: a rare cause of septicemia in children. Access Microbiol 2021; 3:000281. [PMID: 34816095 PMCID: PMC8604182 DOI: 10.1099/acmi.0.000281] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2021] [Accepted: 09/17/2021] [Indexed: 11/20/2022] Open
Abstract
Candida utilis is an emerging fungal pathogen in blood. The main aim of this study was to describe the prevalence, methods of speciation and antifungal susceptibility of Candida utilis at a tertiary care centre.
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Affiliation(s)
- Sreelekshmi T S
- Department of Clinical Microbiology, Christian Medical College, Vellore - 632004, India
| | - Marilyn M Ninan
- Department of Clinical Microbiology, Christian Medical College, Vellore - 632004, India
| | - Arul Premanand
- Department of Child Health, Christian Medical College, Vellore - 632004, India
| | - Anila Chacko
- Department of Child Health, Christian Medical College, Vellore - 632004, India
| | - Rani Diana Sahni
- Department of Clinical Microbiology, Christian Medical College, Vellore - 632004, India
| | - Joy S Michael
- Department of Clinical Microbiology, Christian Medical College, Vellore - 632004, India
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19
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Yang Q, Liu J, Robinson KJ, Whitmore MA, Stewart SN, Zhang G. Perturbations of the ileal mycobiota by necrotic enteritis in broiler chickens. J Anim Sci Biotechnol 2021; 12:107. [PMID: 34625122 PMCID: PMC8501549 DOI: 10.1186/s40104-021-00628-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2021] [Accepted: 08/05/2021] [Indexed: 02/02/2023] Open
Abstract
Background Intestinal microbiota is critical for maintaining animal health and homeostasis. However, involvement of the fungal community, also known as the mycobiota, in animal health and disease is poorly understood. This study was aimed to examine the association between the intestinal mycobiota and the severity of necrotic enteritis (NE), an economically significant poultry disease. Methods A total of 90 day-of-hatch Cobb broilers were infected with Eimeria maxima on d 10, followed by an oral challenge with C. perfringens on d 14 to induce NE, while another 10 broilers were served as mock-infected controls. On d 17, the lesions in the jejunum were scored, and the ileal digesta were subjected to DNA isolation and real-time PCR quantification of total bacterial and fungi populations. Internal transcribed spacer 2 (ITS2) amplicon sequencing was also performed to profile the ileal mycobiota composition. Changes in the ileal mycobiota in response to NE were investigated. Spearman correlation analysis was further conducted to identify the correlations between relative abundances of individual ileal fungi and the severity of NE. Results While the total bacterial population in the ileum was increased by 2- to 3-fold in NE chickens, the total fungal population was progressively declined in more exacerbated NE, with the most severely infected chickens showing a nearly 50-fold reduction relative to mock-infected controls. Richness of the ileal mycobiota also tended to reduce in chickens with NE (P = 0.06). Compositionally, among 30 most abundant fungal amplicon sequence variants (ASVs), 11 were diminished and 7 were enriched (P < 0.05), while 12 remained largely unchanged in NE-afflicted chickens (P > 0.05). Multiple Wallemia and Aspergillus species were markedly diminished in NE (P < 0.05) and also showed a significant negative correlation with NE severity (P < 0.05). Conclusions Dysbiosis of the ileal mycobiota is induced evidently by NE and the extent of the dysbiosis is positively correlated with disease severity. These findings suggest a possible role of the intestinal mycobiota in NE pathogenesis and highlight the mycobiota as a new potential target for NE mitigation in poultry. Supplementary Information The online version contains supplementary material available at 10.1186/s40104-021-00628-5.
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Affiliation(s)
- Qing Yang
- Department of Animal and Food Sciences, Oklahoma State University, Stillwater, OK, USA
| | - Jing Liu
- Department of Animal and Food Sciences, Oklahoma State University, Stillwater, OK, USA
| | - Kelsy J Robinson
- Department of Animal and Food Sciences, Oklahoma State University, Stillwater, OK, USA.,Present address: Poultry Production and Product Safety Research Unit, USDA-Agricultural Research Service, Fayetteville, AR, USA
| | - Melanie A Whitmore
- Department of Animal and Food Sciences, Oklahoma State University, Stillwater, OK, USA
| | - Sydney N Stewart
- Department of Animal and Food Sciences, Oklahoma State University, Stillwater, OK, USA.,Present address: Safety and Security Division, Institute for Public Research, CNA, Arlington, VA, USA
| | - Guolong Zhang
- Department of Animal and Food Sciences, Oklahoma State University, Stillwater, OK, USA.
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20
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Dear T, Joe Yu Y, Pandey S, Fuller J, Devlin MK. The first described case of Lodderomyces elongisporus meningitis. J Assoc Med Microbiol Infect Dis Can 2021; 6:221-228. [PMID: 36337753 PMCID: PMC9615464 DOI: 10.3138/jammi-2021-0006] [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] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Accepted: 05/12/2021] [Indexed: 06/16/2023]
Abstract
We describe the first documented case of meningitis caused by Lodderomyces elongisporus. Identification of L. elongisporus was made on the basis of an arachnoid biopsy with pathology samples sent for fungal internal transcribed spacer sequencing after multiple central nervous system (CNS) fungal culture specimens were negative. After final diagnosis, treatment was transitioned from amphotericin to fluconazole, which, combined with insertion of lumbar drain followed by a permanent ventriculopleural shunt, resulted in significant clinical improvement. Our report reviews the literature of (1) cases of L. elongisporus, which almost exclusively describe fungemia or endocarditis; (2) CNS infections caused by Candida parapsilosis, an organism with which L. elongisporus was previously conflated; and (3) management of fungal meningitis-associated hydrocephalus.
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Affiliation(s)
- Taylor Dear
- Department of Medicine, Western University, London, Ontario, Canada
- London Health Sciences Centre, London, Ontario, Canada
| | - Yeyao Joe Yu
- London Health Sciences Centre, London, Ontario, Canada
- Department of Clinical Neurological Sciences, Western University, London, Ontario, Canada
| | - Sachin Pandey
- London Health Sciences Centre, London, Ontario, Canada
- Department of Medicine Imaging, Western University, London, Ontario, Canada
| | - Jeff Fuller
- London Health Sciences Centre, London, Ontario, Canada
- Department of Pathology and Laboratory Medicine, Western University, London, Ontario, Canada
| | - Megan K Devlin
- Department of Medicine, Western University, London, Ontario, Canada
- Division of Infectious Diseases, Western University, London, Ontario, Canada
- St. Joseph’s Health Centre, London, Ontario, Canada
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21
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Taghipour S, Abastabar M, Piri F, Aboualigalehdari E, Jabbari MR, Zarrinfar H, Nouripour-Sisakht S, Mohammadi R, Ahmadi B, Ansari S, Katiraee F, Niknejad F, Didehdar M, Nazeri M, Makimura K, Rezaei-Matehkolaei A. Diversity of Geophilic Dermatophytes Species in the Soils of Iran; The Significant Preponderance of Nannizzia fulva. J Fungi (Basel) 2021; 7:345. [PMID: 33925095 DOI: 10.3390/jof7050345] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2021] [Revised: 04/18/2021] [Accepted: 04/26/2021] [Indexed: 12/02/2022] Open
Abstract
A molecular epidemiology study was conducted between 2016 and 2017 by a network of collaborators from 12 provinces in the Islamic Republic of Iran. A total of 1484 soil samples from different habitats were screened for the presence of dermatophytes by using the hair baiting technique. The primary identification of isolates was carried out by amplification and MvaI restriction fragment length polymorphism (RFLP) of the internal transcribed spacers regions of ribosomal DNA (ITS-rDNA). The identifications, especially in the cases of isolates with unknown RFLP patterns, were confirmed by sequencing of the ITS-rDNA region. As a result, 256 isolates were recovered. The isolation rate was higher in soils with pH range 7.1–8.0, collected from animal habitats (n = 78; 34%) and parks and gardens (n = 75; 32%), geographically from Mazandaran Province (n = 115; 49.5%) and seasonally in the spring (n = 129; 50.4%), all of which were statistically significant (p < 0.05). The dermatophytes comprising five species of the two genera, viz., Nannizzia fulva (n = 214), N. gypsea (n = 34), Arthroderma quadrifidum (n = 5), A. gertleri (n = 2) and A. tuberculatum (n = 1), were isolated. The geophilic dermatophytes occurred in various soils from different parts of Iran; however, surprisingly, N. fulva emerged as the dominant species, outnumbering the common geophilic species of N. gypsea. For the definitive identification of soil inhabitant dermatophytes, DNA-based identification is strongly recommended.
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22
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Tiew PY, Mac Aogáin M, Ter SK, Aliberti S, Chalmers JD, Chotirmall SH. Respiratory Mycoses in COPD and Bronchiectasis. Mycopathologia 2021. [PMID: 33709335 DOI: 10.1007/s11046-021-00539-z] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Accepted: 02/22/2021] [Indexed: 02/07/2023]
Abstract
Chronic obstructive pulmonary disease (COPD) and bronchiectasis represent chronic airway diseases associated with significant morbidity and mortality. Bacteria and viruses are commonly implicated in acute exacerbations; however the significance of fungi in these airways remains poorly defined. While COPD and bronchiectasis remain recognized risk factors for the occurrence of Aspergillus-associated disease including chronic and invasive aspergillosis, underlying mechanisms that lead to the progression from colonization to invasive disease remain uncertain. Nonetheless, advances in molecular technologies have improved our detection, identification and understanding of resident fungi characterizing these airways. Mycobiome sequencing has revealed the complex varied and myriad profile of airway fungi in COPD and bronchiectasis, including their association with disease presentation, progression, and mortality. In this review, we outline the emerging evidence for the clinical importance of fungi in COPD and bronchiectasis, available diagnostic modalities, mycobiome sequencing approaches and association with clinical outcomes.
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Gao B, Zhang X, Schnabl B. Fungi-Bacteria Correlation in Alcoholic Hepatitis Patients. Toxins (Basel) 2021; 13:toxins13020143. [PMID: 33672887 PMCID: PMC7917833 DOI: 10.3390/toxins13020143] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Revised: 01/27/2021] [Accepted: 02/10/2021] [Indexed: 12/13/2022] Open
Abstract
Alcohol-related liver disease is one of the most prevalent types of chronic liver diseases globally. Alcohol-related liver disease begins with fatty liver, which further develops into hepatic inflammation, hepatocyte injury, and progresses to fibrosis and cirrhosis. Compositional changes of gut bacteria and fungi were found in patients with alcohol-related liver disease. However, the functional changes of fungi and correlations between fungi and bacteria have not been investigated. In this study, we first examined the functional capacity of fungi in patients with alcohol-related liver disease using shotgun metagenomics. Among 24 MetaCyc pathways contributed by fungi, superpathway of allantoin degradation in yeast was enriched in patients with alcoholic hepatitis. Furthermore, we compared the predictive power of bacteria versus fungi and found that bacteria performed better than fungi to separate patients with alcoholic hepatitis from non-alcoholic controls and patients with alcohol use disorder. Finally, we investigated the associations between the intestinal fungi and bacteria in alcoholic hepatitis patients. Positive association between fungi and bacteria was found between Cladosporium and Gemmiger, meanwhile negative association was found between Cryptococcus and Pseudomonas in alcoholic hepatitis patients.
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Affiliation(s)
- Bei Gao
- School of Marine Sciences, Nanjing University of Information Science and Technology, Nanjing 210044, China;
- Department of Medicine, University of California San Diego, La Jolla, CA 92093, USA
| | - Xinlian Zhang
- Division of Biostatistics and Bioinformatics, Department of Family Medicine and Public Health, University of California San Diego, San Diego, CA 92093, USA;
| | - Bernd Schnabl
- Department of Medicine, University of California San Diego, La Jolla, CA 92093, USA
- Department of Medicine, VA San Diego Healthcare System, San Diego, CA 92161, USA
- Correspondence: ; Tel.: +1-858-822-5311
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Kusstatscher P, Adam E, Wicaksono WA, Bernhart M, Olimi E, Müller H, Berg G. Microbiome-Assisted Breeding to Understand Cultivar-Dependent Assembly in Cucurbita pepo. Front Plant Sci 2021; 12:642027. [PMID: 33897731 PMCID: PMC8063107 DOI: 10.3389/fpls.2021.642027] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Accepted: 03/08/2021] [Indexed: 05/14/2023]
Abstract
Recently, it was shown that long-term plant breeding does not only shape plant characteristics but also impacts plant-associated microbiota substantially. This requires a microbiome-integrative breeding approach, which was not yet shown. Here we investigate this for the Styrian oil pumpkin (Cucurbita pepo L. subsp. pepo var. styriaca Greb.) by analyzing the microbiome of six genotypes (the complete pedigree of a three-way cross-hybrid, consisting of three inbred lines and one open pollinating cultivar) in the seed and rhizosphere as well as the progeny seeds. Using high-throughput amplicon sequencing targeting the 16S rRNA and the ITS1 genes, the bacterial and fungal microbiomes were accessed. Seeds were found to generally carry a significantly lower microbial diversity compared to the rhizosphere and soil as well as a different microbial composition, with an especially high fraction of Enterobacteriaceae (40-83%). Additionally, potential plant-beneficial bacterial taxa, including Bacillaceae, Burkholderiaceae, and Pseudomonadaceae, were found to be enriched in progeny seeds. Between genotypes, more substantial changes can be observed for seed microbiomes compared to the rhizosphere. Moreover, rhizosphere communities were assembled for the most part from soil. Interestingly, bacterial signatures are mainly linked from seed to seed, while fungal communities are shaped by the soil and rhizosphere. Our findings provide a deep look into the rhizosphere and seed microbiome assembly of pumpkin-associated communities and represent the first steps into microbiome-driven breeding for plant-beneficial microbes.
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Affiliation(s)
- Peter Kusstatscher
- Institute of Environmental Biotechnology, Graz University of Technology, Graz, Austria
- *Correspondence: Peter Kusstatscher,
| | - Eveline Adam
- Institute of Environmental Biotechnology, Graz University of Technology, Graz, Austria
- Saatzucht Gleisdorf GmbH, Gleisdorf, Austria
| | - Wisnu Adi Wicaksono
- Institute of Environmental Biotechnology, Graz University of Technology, Graz, Austria
| | | | - Expedito Olimi
- Institute of Environmental Biotechnology, Graz University of Technology, Graz, Austria
| | - Henry Müller
- Institute of Environmental Biotechnology, Graz University of Technology, Graz, Austria
| | - Gabriele Berg
- Institute of Environmental Biotechnology, Graz University of Technology, Graz, Austria
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Huang YS, Wang FD, Chen YC, Huang YT, Hsieh MH, Hii IM, Lee YL, Ho MW, Liu CE, Chen YH, Liu WL. High rates of misidentification of uncommon Candida species causing bloodstream infections using conventional phenotypic methods. J Formos Med Assoc 2020; 120:1179-1187. [PMID: 33250336 DOI: 10.1016/j.jfma.2020.11.002] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [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: 05/14/2020] [Revised: 10/02/2020] [Accepted: 11/09/2020] [Indexed: 01/25/2023] Open
Abstract
BACKGROUND Candidemia caused by uncommon Candida species is increasing and misidentification may compromise optimal antifungal therapy. This multicenter study aimed to evaluate the accuracy of species-level identification of uncommon Candida. METHODS Uncommon causative species of candidemia identified in routine laboratories using CHROMagar, API-32C and VITEK-2 Yeast ID system were collected from July 2011 to June 2014. These isolates were further identified using matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) system and sequencing of the internal transcribed spacer and 28S rRNA gene. Susceptibility of the isolates was determined. RESULTS Of 85 isolates evaluated, Candida guilliermondii (n = 36) was the most common, followed by Candid sake (n = 7) and Candida famata (n = 4). Using DNA-sequencing analysis as standard, none of C. sake and C. famata was correct, while VITEK MS correctly identified 10 of the 11 isolates. With the exclusion of one unspecified Candida by DNA-sequencing methods, the accuracy of conventional methods and VITEK MS was 64.3% and 86.9%, respectively (p = 0.001). Eight isolates were confirmed to be yeasts other than Candida. Compared with other Candida species, C. guilliermondii showed elevated minimal inhibitory concentration of echinocandins. CONCLUSION Misidentification of uncommon Candida species was common using the conventional methods, especially for C. sake and C. famata. MALDI-TOF MS assisted by DNA-sequencing methods should be considered.
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Affiliation(s)
- Yu-Shan Huang
- Department of Internal Medicine, National Taiwan University Hospital, Taipei, Taiwan
| | - Fu-Der Wang
- Division of Infectious Diseases, Department of Medicine, Taipei Veterans General Hospital, Taipei, Taiwan; School of Medicine, National Yang-Ming University, Taipei, Taiwan
| | - Yee-Chun Chen
- Department of Internal Medicine, National Taiwan University Hospital, Taipei, Taiwan
| | - Yu-Tsung Huang
- Department of Laboratory Medicine, National Taiwan University Hospital, Taipei, Taiwan
| | - Min-Han Hsieh
- Division of Infectious Diseases, Department of Internal Medicine, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung, Taiwan
| | - Ing-Moi Hii
- Division of Infectious Diseases, Department of Internal Medicine, Changhua Christian Hospital, Changhua, Taiwan
| | - Yu-Lin Lee
- Division of Infectious Diseases, Department of Internal Medicine, Changhua Christian Hospital, Changhua, Taiwan
| | - Mao-Wang Ho
- Division of Infectious Diseases, Department of Internal Medicine, China Medical University Hospital, Taichung, Taiwan
| | - Chun-Eng Liu
- Division of Infectious Diseases, Department of Internal Medicine, Changhua Christian Hospital, Changhua, Taiwan
| | - Yen-Hsu Chen
- Division of Infectious Diseases, Department of Internal Medicine, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung, Taiwan
| | - Wei-Lun Liu
- School of Medicine, College of Medicine, Fu Jen Catholic University, New Taipei, Taiwan; Division of Critical Care Medicine, Department of Emergency and Critical Care Medicine, Fu Jen Catholic University Hospital, Fu Jen Catholic University, New Taipei City, Taiwan.
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Vanam HP, Ather M, Madhura KS, Rudramurthy SM. First report of Lasiodiplodia pseudotheobromae keratitis susceptible to voriconazole in an Indian mango grower. Access Microbiol 2020; 1:e000055. [PMID: 32974536 PMCID: PMC7470297 DOI: 10.1099/acmi.0.000055] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2019] [Accepted: 08/07/2019] [Indexed: 11/18/2022] Open
Abstract
The family Botriosphaeriacea comprises cosmopolitan endophytic fungi and many of the genera have frequently been implicated in causing human infections, including subcutaneous infection, sinusitis, invasive mycoses and keratitis. Among them, the genus Lasiodiplodia, which contains >30 species, is grouped as coelomycetous fungi with prototype species Lasiodiplodia theobromae as an important cause of keratitis. Several cryptic species morphologically resembling L. theobromae exist, one of which is Lasiodiplodia pseudotheobromae. We present a rare case of mycotic keratitis in an Indian mango grower following penetrating trauma to the left eye. Direct microscopy revealed retractile hyphal elements, and fungal cultures yielded a dematiaceous mould which was confirmed by sequencing as L. pseudotheobromae. Antifungal susceptibility testing revealed low MICs to amphotericin B and voriconazole and increased MICs to itraconazole and posaconazole. This is the first report of phytopathogenic L. pseudotheobromae keratitis, successfully treated with 2 % voriconazole without keratoplasty.
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Affiliation(s)
- Hari Pankaj Vanam
- Mycology Division, Department of Microbiology, Bhaskar Medical College and General Hospital, Bhaskar Nagar, Yenkapally, Moinabad, R.R. District, Telangana 500 075, India
- *Correspondence: Hari Pankaj Vanam,
| | - Mohammed Ather
- Department of Ophthalmology, Bhaskar Medical College and General Hospital, Bhaskar Nagar, Yenkapally, Moinabad, R.R. District, Telangana 500 075, India
| | - K. S. Madhura
- Department of Ophthalmology, Bhaskar Medical College and General Hospital, Bhaskar Nagar, Yenkapally, Moinabad, R.R. District, Telangana 500 075, India
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Dutra VR, Silva LF, Oliveira ANM, Beirigo EF, Arthur VM, Bernardes da Silva R, Ferreira TB, Andrade-Silva L, Silva MV, Fonseca FM, Silva-Vergara ML, Ferreira-Paim K. Fatal Case of Fungemia by Wickerhamomyces anomalus in a Pediatric Patient Diagnosed in a Teaching Hospital from Brazil. J Fungi (Basel) 2020; 6:jof6030147. [PMID: 32854208 PMCID: PMC7558373 DOI: 10.3390/jof6030147] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Revised: 08/20/2020] [Accepted: 08/21/2020] [Indexed: 02/07/2023] Open
Abstract
In recent decades, emerging fungal infections have changed the clinical mycology scenario as a consequence of the advances in medical diagnostics and therapeutic procedures, long hospitalization times, and the growing number of individuals with debilitating chronic diseases and impaired immune systems. This report presents a 19 months old Brazilian female patient who developed a severe fungal sepsis by an uncommon yeast. She was admitted at the intensive care unit with severe pneumonia, bronchopulmonary dysplasia, and weight-for-age z score of less than −2. She remained more than 30 days in the intensive care unit where she had a femoral venous catheter placement, enteral nutrition, broad-spectrum antibiotic therapy, and prophylaxis with fluconazole. Moreover, pericardiocentesis was performed due to cardiac tamponade. She had a previous history of prematurity, cardiac surgery due to patent ductus arteriosus, and a long period of hospital stay. Despite the antifungal prophylaxis, two yeast isolates were recovered from blood and then identified by classical mycological methods and internal transcribed spacer (ITS) sequencing as Wickerhamomyces anomalus. Both isolates exhibited susceptibility to amphotericin B, ketoconazole, itraconazole, voriconazole, and fluconazole. Her clinical state worsened, presenting anasarca, epistaxis, and hemorrhagic suffusions in the mouth, sclera, oliguria, and bradycardia. Two days after the first positive culture, she presented a gradual reduction of the white blood cells count, with severe leukopenia and neutropenia. She died five days after.
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Affiliation(s)
- Vitor Rodrigues Dutra
- Department of Microbiology, Immunology and Parasitology, Federal University of Triangulo Mineiro, Uberaba 38015-050, Brazil; (V.R.D.); (L.F.S.); (E.F.B.); (V.M.A.); (R.B.d.S.); (M.V.S.)
| | - Leonardo Francisco Silva
- Department of Microbiology, Immunology and Parasitology, Federal University of Triangulo Mineiro, Uberaba 38015-050, Brazil; (V.R.D.); (L.F.S.); (E.F.B.); (V.M.A.); (R.B.d.S.); (M.V.S.)
| | | | - Emília Freitas Beirigo
- Department of Microbiology, Immunology and Parasitology, Federal University of Triangulo Mineiro, Uberaba 38015-050, Brazil; (V.R.D.); (L.F.S.); (E.F.B.); (V.M.A.); (R.B.d.S.); (M.V.S.)
| | - Vanessa Mello Arthur
- Department of Microbiology, Immunology and Parasitology, Federal University of Triangulo Mineiro, Uberaba 38015-050, Brazil; (V.R.D.); (L.F.S.); (E.F.B.); (V.M.A.); (R.B.d.S.); (M.V.S.)
| | - Raíssa Bernardes da Silva
- Department of Microbiology, Immunology and Parasitology, Federal University of Triangulo Mineiro, Uberaba 38015-050, Brazil; (V.R.D.); (L.F.S.); (E.F.B.); (V.M.A.); (R.B.d.S.); (M.V.S.)
| | - Thatiana Bragine Ferreira
- Department of Infectious Diseases, Federal University of Triangulo Mineiro, Uberaba 38025-440, Brazil; (T.B.F.); (L.A.-S.); (M.L.S.-V.)
| | - Leonardo Andrade-Silva
- Department of Infectious Diseases, Federal University of Triangulo Mineiro, Uberaba 38025-440, Brazil; (T.B.F.); (L.A.-S.); (M.L.S.-V.)
| | - Marcos Vinícius Silva
- Department of Microbiology, Immunology and Parasitology, Federal University of Triangulo Mineiro, Uberaba 38015-050, Brazil; (V.R.D.); (L.F.S.); (E.F.B.); (V.M.A.); (R.B.d.S.); (M.V.S.)
| | | | - Mario León Silva-Vergara
- Department of Infectious Diseases, Federal University of Triangulo Mineiro, Uberaba 38025-440, Brazil; (T.B.F.); (L.A.-S.); (M.L.S.-V.)
| | - Kennio Ferreira-Paim
- Department of Microbiology, Immunology and Parasitology, Federal University of Triangulo Mineiro, Uberaba 38015-050, Brazil; (V.R.D.); (L.F.S.); (E.F.B.); (V.M.A.); (R.B.d.S.); (M.V.S.)
- Department of Infectious Diseases, Federal University of Triangulo Mineiro, Uberaba 38025-440, Brazil; (T.B.F.); (L.A.-S.); (M.L.S.-V.)
- Correspondence: ; Tel.: +55-34-3700-6480
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Vanam HP, Karumuri SR, Poojari SS, Rudramurthy SM. Mycosis of the Plantar Surface of Foot Owing to Nondermatophyte Mold Nodulisporium griseobrunneum Mimicking a Tinea Pedis. Mycopathologia 2020; 185:1033-40. [PMID: 32816251 DOI: 10.1007/s11046-020-00483-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2020] [Accepted: 08/06/2020] [Indexed: 10/20/2022]
Abstract
Nondermatophyte molds (NDM) and dematiaceous molds are less frequently implicated as the etiological agents of tinea-like infections of the foot. Among the etiological agents, Hendersonula toruloidea (now, Nattrassia mangiferae), Scytalidium hyalinum, Alternaria species (spp.), and Fusarium spp. are infrequently associated with foot mycoses. Nodulisporium (N.) spp. is a mitosporic NDM, which has been implicated in human infections like cerebral phaeohyphomycosis and allergic fungal sinusitis. Here, we report N. griseobrunneum in a 9-year-old female with mycosis of the plantar surface of foot mimicking a tinea pedis. Potassium hydroxide mount of skin specimen demonstrated dichotomous branching septate hyphae. Fungal culture and molecular sequencing established N. griseobrunneum as the etiological agent. Antifungal susceptibility testing revealed lower MICs to all seven drugs tested including itraconazole (ITR). The patient was treated with ITR and topical terbinafine. To the best of our knowledge, this is the first communication depicting molecular confirmation of the etiologic agent and antifungal susceptibility data of the mycosis of the plantar surface of foot owing to N. griseobrunneum from India.
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Tiew PY, Mac Aogain M, Ali NABM, Thng KX, Goh K, Lau KJX, Chotirmall SH. The Mycobiome in Health and Disease: Emerging Concepts, Methodologies and Challenges. Mycopathologia 2020; 185:207-231. [PMID: 31894501 PMCID: PMC7223441 DOI: 10.1007/s11046-019-00413-z] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2019] [Accepted: 12/02/2019] [Indexed: 02/07/2023]
Abstract
Fungal disease is an increasingly recognised global clinical challenge associated with high mortality. Early diagnosis of fungal infection remains problematic due to the poor sensitivity and specificity of current diagnostic modalities. Advances in sequencing technologies hold promise in addressing these shortcomings and for improved fungal detection and identification. To translate such emerging approaches into mainstream clinical care will require refinement of current sequencing and analytical platforms, ensuring standardisation and consistency through robust clinical benchmarking and its validation across a range of patient populations. In this state-of-the-art review, we discuss current diagnostic and therapeutic challenges associated with fungal disease and provide key examples where the application of sequencing technologies has potential diagnostic application in assessing the human ‘mycobiome’. We assess how ready access to fungal sequencing may be exploited in broadening our insight into host–fungal interaction, providing scope for clinical diagnostics and the translation of emerging mycobiome research into clinical practice.
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Affiliation(s)
- Pei Yee Tiew
- Lee Kong Chian School of Medicine, Nanyang Technological University, 11 Mandalay Road, Singapore, 308232, Singapore
- Department of Respiratory and Critical Care Medicine, Singapore General Hospital, Singapore, Singapore
| | - Micheál Mac Aogain
- Lee Kong Chian School of Medicine, Nanyang Technological University, 11 Mandalay Road, Singapore, 308232, Singapore
| | | | - Kai Xian Thng
- Lee Kong Chian School of Medicine, Nanyang Technological University, 11 Mandalay Road, Singapore, 308232, Singapore
| | - Karlyn Goh
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Kenny J X Lau
- Lee Kong Chian School of Medicine, Nanyang Technological University, 11 Mandalay Road, Singapore, 308232, Singapore
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, Singapore
| | - Sanjay H Chotirmall
- Lee Kong Chian School of Medicine, Nanyang Technological University, 11 Mandalay Road, Singapore, 308232, Singapore.
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Brito-Santos F, Figueiredo-Carvalho MHG, Coelho RA, de Oliveira JCA, Monteiro RV, da Silva Chaves AL, Almeida-Paes R. Molecular identification and antifungal susceptibility testing of Pucciniomycotina red yeast clinical isolates from Rio de Janeiro, Brazil. Braz J Microbiol 2019; 51:95-98. [PMID: 31776863 DOI: 10.1007/s42770-019-00191-2] [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: 05/22/2019] [Accepted: 11/13/2019] [Indexed: 11/30/2022] Open
Abstract
Infections caused by Rhodotorula spp. are increasing worldwide. This study identified, through the light of the new taxonomic advances on the subphylum Pucciniomycotina, 16 isolates from blood cultures and compared their antifungal susceptibility on microdilution and gradient diffusion methods. Internal transcriber spacer sequencing identified Rhodotorula mucilaginosa (n = 12), Rhodotorula toruloides (n = 2), Rhodotorula dairenensis (n = 1), and Cystobasidium minutum (n = 1). Amphotericin B was the most effective drug. A good essential agreement was observed on MIC values of amphotericin B and voriconazole determined by the two methods. Therefore, the gradient method is useful for susceptibility tests of R. mucilaginosa against these drugs.
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Affiliation(s)
- Fabio Brito-Santos
- Mycology Laboratory, Evandro Chagas National Institute of Infectious Diseases, Oswaldo Cruz Foundation, FIOCRUZ, Av. Brazil 4365, Manguinhos, Rio de Janeiro, RJ, 21045-900, Brazil.
| | - Maria Helena Galdino Figueiredo-Carvalho
- Mycology Laboratory, Evandro Chagas National Institute of Infectious Diseases, Oswaldo Cruz Foundation, FIOCRUZ, Av. Brazil 4365, Manguinhos, Rio de Janeiro, RJ, 21045-900, Brazil
| | - Rowena Alves Coelho
- Mycology Laboratory, Evandro Chagas National Institute of Infectious Diseases, Oswaldo Cruz Foundation, FIOCRUZ, Av. Brazil 4365, Manguinhos, Rio de Janeiro, RJ, 21045-900, Brazil
| | - Jean Carlos Almeida de Oliveira
- Mycology Laboratory, Evandro Chagas National Institute of Infectious Diseases, Oswaldo Cruz Foundation, FIOCRUZ, Av. Brazil 4365, Manguinhos, Rio de Janeiro, RJ, 21045-900, Brazil
| | - Raissa Vieira Monteiro
- Mycology Laboratory, Evandro Chagas National Institute of Infectious Diseases, Oswaldo Cruz Foundation, FIOCRUZ, Av. Brazil 4365, Manguinhos, Rio de Janeiro, RJ, 21045-900, Brazil
| | | | - Rodrigo Almeida-Paes
- Mycology Laboratory, Evandro Chagas National Institute of Infectious Diseases, Oswaldo Cruz Foundation, FIOCRUZ, Av. Brazil 4365, Manguinhos, Rio de Janeiro, RJ, 21045-900, Brazil
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de Freitas RS, de Freitas THP, Siqueira LPM, Gimenes VMF, Benard G. First report of tinea corporis caused by Arthroderma benhamiae in Brazil. Braz J Microbiol 2019; 50:985-987. [PMID: 31463867 DOI: 10.1007/s42770-019-00141-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2019] [Accepted: 08/12/2019] [Indexed: 11/30/2022] Open
Abstract
Arthroderma benhamiae is a zoophilic dermathophyte that can cause highly inflammatory tinea corporis and tinea capitis in humans. This is the first report of a patient with dermatophytosis caused by A. benhamiae in Brazil. The lesion was an erythematous, annular plaque on the lumbar region that appeared few weeks after playing with a street cat in a 19-month-old girl. Initial presumed diagnosis was tinea corporis caused by Microsporum canis. Topical treatments were ineffective and the patient required systemic treatment with griseofulvin. Mycological diagnosis was inconclusive: morphological differentiation between M. canis and Trichophyton benhamiae may be difficult, especially when the latter present yellow colonies. The etiological agent was identified only by ITS sequencing of the isolates aligned with reference strains to A. benhamiae. This report highlights the importance of ITS sequencing in the identification of isolates from some cases of dermatophytosis, because conventional morphological diagnosis may result in misdiagnosis of the agent and delay proper treatment.
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Affiliation(s)
- Roseli Santos de Freitas
- Laboratório de Micologia Medica (LIM 53), Instituto de Medicina Tropical and Hospital das Clínicas, Faculdade de Medicina, Universidade de São Paulo, LIM 53 - Av Dr Eneas de, Carvalho Aguiar, 470, São Paulo, São Paulo, CEP 0504-000, Brazil.
| | | | - Lumena Pereira Machado Siqueira
- Laboratório de Micologia Medica (LIM 53), Instituto de Medicina Tropical and Hospital das Clínicas, Faculdade de Medicina, Universidade de São Paulo, LIM 53 - Av Dr Eneas de, Carvalho Aguiar, 470, São Paulo, São Paulo, CEP 0504-000, Brazil
| | - Viviane Mazo Fávero Gimenes
- Laboratório de Micologia Medica (LIM 53), Instituto de Medicina Tropical and Hospital das Clínicas, Faculdade de Medicina, Universidade de São Paulo, LIM 53 - Av Dr Eneas de, Carvalho Aguiar, 470, São Paulo, São Paulo, CEP 0504-000, Brazil
| | - Gil Benard
- Laboratório de Micologia Medica (LIM 53), Instituto de Medicina Tropical and Hospital das Clínicas, Faculdade de Medicina, Universidade de São Paulo, LIM 53 - Av Dr Eneas de, Carvalho Aguiar, 470, São Paulo, São Paulo, CEP 0504-000, Brazil
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Rothman JA, Andrikopoulos C, Cox-Foster D, McFrederick QS. Floral and Foliar Source Affect the Bee Nest Microbial Community. Microb Ecol 2019; 78:506-516. [PMID: 30552443 DOI: 10.1007/s00248-018-1300-3] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/23/2018] [Accepted: 11/22/2018] [Indexed: 06/09/2023]
Abstract
Managed pollinators such as the alfalfa leafcutting bee, Megachile rotundata, are essential to the production of a wide variety of agricultural crops. These pollinators encounter a diverse array of microbes when foraging for food and nest-building materials on various plants. To test the hypothesis that food and nest-building source affects the composition of the bee-nest microbiome, we exposed M. rotundata adults to treatments that varied both floral and foliar source in a 2 × 2 factorial design. We used 16S rRNA gene and internal transcribed spacer (ITS) sequencing to capture the bacterial and fungal diversity of the bee nests. We found that nest microbial communities were significantly different between treatments, indicating that bee nests become inoculated with environmentally derived microbes. We did not find evidence of interactions between the fungi and bacteria within our samples. Furthermore, both the bacterial and fungal communities were quite diverse and contained numerous exact sequence variants (ESVs) of known plant and bee pathogens that differed based on treatment. Our research indicates that bees deposit plant-associated microbes into their nests, including multiple plant pathogens such as smut fungi and bacteria that cause blight and wilt. The presence of plant pathogens in larval pollen provisions highlights the potential for bee nests to act as disease reservoirs across seasons. We therefore suggest that future research should investigate the ability of bees to transmit pathogens from nest to host plant.
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Affiliation(s)
- Jason A Rothman
- Graduate Program in Microbiology, University of California, 900 University Ave., Riverside, CA, 92521, USA
- Department of Entomology, University of California, 900 University Ave., Riverside, CA, 92521, USA
| | - Corey Andrikopoulos
- Department of Biology, Utah State University, UMC5310, Logan, UT, 84322, USA
- USDA-ARS Pollinating Insect-Biology, Management, and Systematics Research, Logan, UT, 84322, USA
| | - Diana Cox-Foster
- Department of Biology, Utah State University, UMC5310, Logan, UT, 84322, USA.
- USDA-ARS Pollinating Insect-Biology, Management, and Systematics Research, Logan, UT, 84322, USA.
| | - Quinn S McFrederick
- Graduate Program in Microbiology, University of California, 900 University Ave., Riverside, CA, 92521, USA.
- Department of Entomology, University of California, 900 University Ave., Riverside, CA, 92521, USA.
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Miller EC, Perron GG, Collins CD. Plant-driven changes in soil microbial communities influence seed germination through negative feedbacks. Ecol Evol 2019; 9:9298-9311. [PMID: 31463022 PMCID: PMC6706191 DOI: 10.1002/ece3.5476] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2018] [Revised: 06/24/2019] [Accepted: 06/28/2019] [Indexed: 01/25/2023] Open
Abstract
Plant-soil feedbacks (PSFs) drive plant community diversity via interactions between plants and soil microbes. However, we know little about how frequently PSFs affect plants at the seed stage, and the compositional shifts in fungi that accompany PSFs on germination.We conducted a pairwise PSF experiment to test whether seed germination was differentially impacted by conspecific versus heterospecific soils for seven grassland species. We used metagenomics to characterize shifts in fungal community composition in soils conditioned by each plant species. To investigate whether changes in the abundance of certain fungal taxa were associated with multiple PSFs, we assigned taxonomy to soil fungi and identified putative pathogens that were significantly more abundant in soils conditioned by plant species that experienced negative or positive PSFs.We observed negative, positive, and neutral PSFs on seed germination. Although conspecific and heterospecific soils for pairs with significant PSFs contained host-specialized soil fungal communities, soils with specialized microbial communities did not always lead to PSFs. The identity of host-specialized pathogens, that is, taxa uniquely present or significantly more abundant in soils conditioned by plant species experiencing negative PSFs, overlapped among plant species, while putative pathogens within a single host plant species differed depending on the identity of the heterospecific plant partner. Finally, the magnitude of feedback on germination was not related to the degree of fungal community differentiation between species pairs involved in negative PSFs. Synthesis. Our findings reveal the potential importance of PSFs at the seed stage. Although plant species developed specialized fungal communities in rhizosphere soil, pathogens were not strictly host-specific and varied not just between plant species, but according to the identity of plant partner. These results illustrate the complexity of microbe-mediated interactions between plants at different life stages that next-generation sequencing can begin to unravel.
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Vanam HP, Mohanram K, Reddy KSR, Rengasamy M, Rudramurthy SM. Naive tinea corporis et cruris in an Immunocompetent adult caused by a geophile Nannizzia gypsea susceptible to Terbinafine -Rarity in the current scenario of Dermatophytosis in India. Access Microbiol 2019; 1:e000022. [PMID: 32974531 PMCID: PMC7470300 DOI: 10.1099/acmi.0.000022] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2019] [Accepted: 03/12/2019] [Indexed: 12/23/2022] Open
Abstract
Introduction Dermatophytosis caused by Nannizzia gypsea formerly Microsporum gypse um is rare in occurrence due to its geophilic adaptation and weak pathogenic potential in establishing infection in humans. The taxonomical status of N. gypsea has been controversial over the years and has now reached a concordance among mycologists. Innumerable reports of N. gypsea causing widespread infection in human immunodeficiency virus patients trails them as an important agent of consideration in an immunocompromised host. There have been sporadic reports of N. gypsea causing glabrous skin tinea and onychomycosis in healthy patients and the prevalence reports gravitate around 1-6.5 %. A variety of non-anthropophilic dermatophytes including novel species have now been implicated in causing dermatophytosis reflecting the era of crux changes in the epidemiology. Case report We present a case of chronic dermatophytosis in a 22-year-old healthy Indian with a history of contact with a dog and soil and other factors favouring dermatophytosis. Conventional and molecular sequencing established the isolate as N. gypsea. Antifungal susceptibility test revealed a higher MIC of griseofulvin and lower MIC to azoles and terbinafine. The patient had complete clinical resolution following administration of oral terbinafine. Conclusion Amidst the hyper-endemic-like scenario of tinea in India, this case report stands as a unique example of a patient infected with N. gypsea showing complete clinical resolution using terbinafine. Studies implicating N. gypsea in an immunocompetent host are rare and there is a need for more studies on geophilic dermatophytes causing tinea in the man for laying down effective preventive measures.
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Affiliation(s)
- Hari Pankaj Vanam
- Mycology Division, Department of Microbiology, Bhaskar Medical College and General hospital, Bhaskar Nagar, Yenkapally, Moinabad, R.R. District, Telangana 500 075, India
| | - Kalyani Mohanram
- Department of Microbiology, Saveetha Medical College, Thandalam, Chennai, Tamilnadu 602 105, India
| | - K Siva Rami Reddy
- Dermatology, Department of DVL, Bhaskar Medical College and General hospital, Bhaskar Nagar, Yenkapally, Moinabad, R.R. District, Telangana 500 075, India
| | - Madhu Rengasamy
- Dermatology (Mycology), Madras Medical College, Chennai 600 003, India
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Cornut J, De Respinis S, Tonolla M, Petrini O, Bärlocher F, Chauvet E, Bruder A. Rapid characterization of aquatic hyphomycetes by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry. Mycologia 2019; 111:177-189. [PMID: 30640580 DOI: 10.1080/00275514.2018.1528129] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
Protein fingerprinting using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI--TOF MS) is a rapid, reliable, and economical method to characterize isolates of terrestrial fungi and other microorganisms. The objective of our study was to evaluate the suitability of MALDI-TOF MS for the identification of aquatic hyphomycetes, a polyphyletic group of fungi that play crucial roles in stream ecosystems. To this end, we used 34 isolates of 21 aquatic hyphomycete species whose identity was confirmed by spore morphology and internal transcribed spacer (ITS1-5.8S-ITS2 = ITS) nuc rDNA sequencing. We tested the efficiency of three protein extraction methods, including chemical and mechanical treatments using 13 different protocols, with the objective of producing high-quality MALDI-TOF mass spectra. In addition to extraction protocols, mycelium age was identified as a key parameter affecting protein extraction efficiency. The dendrogram based on mass-spectrum similarity indicated good and relevant taxonomic discrimination; the tree structure was comparable to that of the phylogram based on ITS sequences. Consequently, MALDI-TOF MS could reliably identify the isolates studied and provided greater taxonomic accuracy than classical morphological methods. MALDI-TOF MS seems suited for rapid characterization and identification of aquatic hyphomycete species.
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Affiliation(s)
- Julien Cornut
- a Laboratory of Applied Microbiology, University of Applied Sciences and Arts of Southern Switzerland , Via Mirasole 22A, 6501 Bellinzona , Switzerland.,b Institute of Earth Sciences, University of Applied Sciences and Arts of Southern Switzerland, Trevano Campus , 6952 Canobbio , Switzerland
| | - Sophie De Respinis
- a Laboratory of Applied Microbiology, University of Applied Sciences and Arts of Southern Switzerland , Via Mirasole 22A, 6501 Bellinzona , Switzerland
| | - Mauro Tonolla
- a Laboratory of Applied Microbiology, University of Applied Sciences and Arts of Southern Switzerland , Via Mirasole 22A, 6501 Bellinzona , Switzerland.,c Microbial Ecology Laboratory, Microbiology Unit, Department of Botany and Plant Biology , University of Geneva , Switzerland
| | | | - Felix Bärlocher
- e Department of Biology , Mount Allison University , Sackville , News Brunswick E4L1G7, Canada
| | - Eric Chauvet
- f EcoLab, Université de Toulouse , CNRS, UPS, INPT, 31062 Toulouse , France
| | - Andreas Bruder
- a Laboratory of Applied Microbiology, University of Applied Sciences and Arts of Southern Switzerland , Via Mirasole 22A, 6501 Bellinzona , Switzerland.,b Institute of Earth Sciences, University of Applied Sciences and Arts of Southern Switzerland, Trevano Campus , 6952 Canobbio , Switzerland
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Murali A, Bhargava A, Wright ES. IDTAXA: a novel approach for accurate taxonomic classification of microbiome sequences. Microbiome 2018; 6:140. [PMID: 30092815 PMCID: PMC6085705 DOI: 10.1186/s40168-018-0521-5] [Citation(s) in RCA: 239] [Impact Index Per Article: 39.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/21/2018] [Accepted: 07/25/2018] [Indexed: 05/11/2023]
Abstract
BACKGROUND Microbiome studies often involve sequencing a marker gene to identify the microorganisms in samples of interest. Sequence classification is a critical component of this process, whereby sequences are assigned to a reference taxonomy containing known sequence representatives of many microbial groups. Previous studies have shown that existing classification programs often assign sequences to reference groups even if they belong to novel taxonomic groups that are absent from the reference taxonomy. This high rate of "over classification" is particularly detrimental in microbiome studies because reference taxonomies are far from comprehensive. RESULTS Here, we introduce IDTAXA, a novel approach to taxonomic classification that employs principles from machine learning to reduce over classification errors. Using multiple reference taxonomies, we demonstrate that IDTAXA has higher accuracy than popular classifiers such as BLAST, MAPSeq, QIIME, SINTAX, SPINGO, and the RDP Classifier. Similarly, IDTAXA yields far fewer over classifications on Illumina mock microbial community data when the expected taxa are absent from the training set. Furthermore, IDTAXA offers many practical advantages over other classifiers, such as maintaining low error rates across varying input sequence lengths and withholding classifications from input sequences composed of random nucleotides or repeats. CONCLUSIONS IDTAXA's classifications may lead to different conclusions in microbiome studies because of the substantially reduced number of taxa that are incorrectly identified through over classification. Although misclassification error is relatively minor, we believe that many remaining misclassifications are likely caused by errors in the reference taxonomy. We describe how IDTAXA is able to identify many putative mislabeling errors in reference taxonomies, enabling training sets to be automatically corrected by eliminating spurious sequences. IDTAXA is part of the DECIPHER package for the R programming language, available through the Bioconductor repository or accessible online ( http://DECIPHER.codes ).
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Affiliation(s)
- Adithya Murali
- Department of Computer Sciences, University of Wisconsin-Madison, Madison, WI 53715 USA
| | - Aniruddha Bhargava
- Department of Electrical and Computer Engineering, University of Wisconsin-Madison, Madison, WI 53715 USA
| | - Erik S. Wright
- Department of Biomedical Informatics, Pittsburgh Center for Evolutionary Biology and Medicine, School of Medicine, University of Pittsburgh, 426 Bridgeside Point II, 450 Technology Dr, Pittsburgh, PA 15219 USA
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Zimudzi J, van der Waals JE, Coutinho TA, Cowan DA, Valverde A. Temporal shifts of fungal communities in the rhizosphere and on tubers in potato fields. Fungal Biol 2018; 122:928-934. [PMID: 30115327 DOI: 10.1016/j.funbio.2018.05.008] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [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: 11/17/2017] [Revised: 05/24/2018] [Accepted: 05/29/2018] [Indexed: 10/14/2022]
Abstract
Soil fungal communities perform important ecological roles determining, at least in part, agricultural productivity. This study aimed at examining the fungal community dynamics in the potato rhizosphere across different development stages in two consecutive growing seasons (winter and summer). Microbial fingerprinting of rhizosphere soil samples collected at pre-planting, tuber initiation, flowering and at senescence was performed using ARISA in conjunction with Next Generation Sequencing (Illumina MiSeq). The epiphytic fungal communities on tubers at harvest were also investigated. Alpha-diversity was stable over time within and across the two seasons. In contrast, rhizospheric fungal community structure and composition were different between the two seasons and in the different plant growth stages within a given season, indicating the significance of the rhizosphere in shaping microbial communities. The phylum Ascomycota was dominant in the potato fungal rhizosphere, with Operational Taxonomic Units (OTUs) belonging to the genus Peyronellaea being the most abundant in all samples. Important fungal pathogens of potato, together with potential biological control agents and saprophytic species, were identified as indicator OTUs at different plant growth stages. These findings indicate that potato rhizosphere fungal communities are functionally diverse, which may contribute to soil health.
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Affiliation(s)
- Josephine Zimudzi
- Department of Plant and Soil Sciences, University of Pretoria, Pretoria, South Africa
| | | | - Teresa A Coutinho
- Department of Biochemistry, Genetics and Microbiology, Centre for Microbial Ecology and Genomics, University of Pretoria, Pretoria, South Africa
| | - Don A Cowan
- Department of Biochemistry, Genetics and Microbiology, Centre for Microbial Ecology and Genomics, University of Pretoria, Pretoria, South Africa
| | - Angel Valverde
- Department of Biochemistry, Genetics and Microbiology, Centre for Microbial Ecology and Genomics, University of Pretoria, Pretoria, South Africa; Department of Microbial, Biochemical and Food Biotechnology, University of the Free State, Bloemfontein, South Africa
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Yang H, Ye W, Ma J, Zeng D, Rong Z, Xu M, Wang Y, Zheng X. Endophytic fungal communities associated with field-grown soybean roots and seeds in the Huang-Huai region of China. PeerJ 2018; 6:e4713. [PMID: 29736345 PMCID: PMC5933319 DOI: 10.7717/peerj.4713] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2018] [Accepted: 04/16/2018] [Indexed: 12/03/2022] Open
Abstract
Plants depend on beneficial interactions between roots and fungal endophytes for growth, disease suppression, and stress tolerance. In this study, we characterized the endophytic fungal communities associated with the roots and corresponding seeds of soybeans grown in the Huang-Huai region of China. For the roots, we identified 105 and 50 genera by culture-independent and culture-dependent (CD) methods, respectively, and isolated 136 fungal strains (20 genera) from the CD samples. Compared with the 52 soybean endophytic fungal genera reported in other countries, 28 of the genera we found were reported, and 90 were newly discovered. Even though Fusarium was the most abundant genus of fungal endophyte in every sample, soybean root samples from three cities exhibited diverse endophytic fungal communities, and the results between samples of roots and seeds were also significantly different. Together, we identified the major endophytic fungal genera in soybean roots and seeds, and revealed that the diversity of soybean endophytic fungal communities was influenced by geographical effects and tissues. The results will facilitate a better understanding of soybean–endophytic fungi interaction systems and will assist in the screening and utilization of beneficial microorganisms to promote healthy of plants such as soybean.
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Affiliation(s)
- Hongjun Yang
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing, Jiangsu Province, China.,The Key Laboratory of Integrated Management of Crop Diseases and Pests (Ministry of Education), Nanjing, Jiangsu Province, China
| | - Wenwu Ye
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing, Jiangsu Province, China.,The Key Laboratory of Integrated Management of Crop Diseases and Pests (Ministry of Education), Nanjing, Jiangsu Province, China
| | - Jiaxin Ma
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing, Jiangsu Province, China.,The Key Laboratory of Integrated Management of Crop Diseases and Pests (Ministry of Education), Nanjing, Jiangsu Province, China
| | - Dandan Zeng
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing, Jiangsu Province, China.,The Key Laboratory of Integrated Management of Crop Diseases and Pests (Ministry of Education), Nanjing, Jiangsu Province, China
| | - Zhenyang Rong
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing, Jiangsu Province, China.,The Key Laboratory of Integrated Management of Crop Diseases and Pests (Ministry of Education), Nanjing, Jiangsu Province, China
| | - Miao Xu
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing, Jiangsu Province, China.,The Key Laboratory of Integrated Management of Crop Diseases and Pests (Ministry of Education), Nanjing, Jiangsu Province, China
| | - Yuanchao Wang
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing, Jiangsu Province, China.,The Key Laboratory of Integrated Management of Crop Diseases and Pests (Ministry of Education), Nanjing, Jiangsu Province, China
| | - Xiaobo Zheng
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing, Jiangsu Province, China.,The Key Laboratory of Integrated Management of Crop Diseases and Pests (Ministry of Education), Nanjing, Jiangsu Province, China
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Sadeghi G, Ebrahimi-Rad M, Mousavi SF, Shams-Ghahfarokhi M, Razzaghi-Abyaneh M. Emergence of non-Candida albicans species: Epidemiology, phylogeny and fluconazole susceptibility profile. J Mycol Med 2018; 28:51-58. [PMID: 29366545 DOI: 10.1016/j.mycmed.2017.12.008] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [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: 05/17/2017] [Revised: 12/05/2017] [Accepted: 12/15/2017] [Indexed: 01/19/2023]
Abstract
OBJECTIVE Non-Candida albicans (NCA) species now account for a significant part of clinical candidiasis worldwide. In the present study, epidemiology and antifungal susceptibility profile of NCA isolated from various forms of candidiasis were studied with special focus on their phylogenetic relationship by ITS sequencing. PATIENTS AND METHODS Seventy-nine NCA isolates were isolated from skin and nail scrapings (67.0%), vaginal discharges (8.8%), blood (8.8%), sputa (5.0%), urine (5.0%), oral swabs (2.6%), biopsy and eye tumor, each (1.4%). These isolates were identified by morphological, biochemical and molecular (ITS sequencing) techniques. In vitro antifungal susceptibility of the isolates to fluconazole (FCZ) was tested according to the CLSI method (M27-S4). RESULTS Among a total number of 79 cases of proven NCA infections, C. parapsilosis (36.8%) was the most prevalent species followed by C. glabrata (32.9%), C. orthopsilosis (11.4%), C. tropicalis (8.9%), C. krusei (5.0%) and C. guilliermondii (5.0%). The susceptibility to FCZ was assessed for C. parapsilosis (96.5%), C. orthopsilosis (88.9%), C. tropicalis (85.7%) and C. guilliermondii (50.0%). C. glabrata and C. krusei isolates were not susceptible to FCZ. NCA species were distributed in various phylogenetic clades including C. glabrata (1), C. tropicalis (3), C. parapsilosis (6) and C. orthopsilosis, C. krusei and C. guilliermondii (each 2). CONCLUSION C. parapsilosis and C. glabrata were the most predominant NCA species involve in the etiology of candidiasis. C. orthopsilosis was reported from superficial candidiasis. Taken together, our results further substantiate the increasing importance of the involvement of NCA species in the etiology of candidiasis.
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Affiliation(s)
- G Sadeghi
- Department of Medical Mycology, Pasteur Institute of Iran, 1316943551 Tehran, Iran
| | - M Ebrahimi-Rad
- Department of Biochemistry, Pasteur Institute of Iran, 1316943551 Tehran, Iran
| | - S F Mousavi
- Department of Microbiology, Pasteur Institute of Iran, 1316943551 Tehran, Iran
| | - M Shams-Ghahfarokhi
- Department of Medical Mycology, Faculty of Medical Sciences, Tarbiat Modares University, 14115-331 Tehran, Iran
| | - M Razzaghi-Abyaneh
- Department of Medical Mycology, Pasteur Institute of Iran, 1316943551 Tehran, Iran.
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Trablesi H, Hadrich I, Neji S, Fendri N, Ghorbel D, Makni F, Ayadi H, Kammoun S, Ayadi A. Environmental and molecular study of fungal flora in asthmatic patients. J Mycol Med 2017; 28:180-185. [PMID: 29102311 DOI: 10.1016/j.mycmed.2017.09.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2017] [Revised: 09/17/2017] [Accepted: 09/18/2017] [Indexed: 11/29/2022]
Abstract
The aim of the present study was to investigate the epidemiological and fungal environmental profile in asthmatic patients. We conducted a prospective study involving 49 patients with allergic asthma. One hundred and forty-five clinical samples and 289 environmental samples were performed. Only 30 patients accepted to participate to the environmental study at their home. For specific IgE antibodies, ELISA assay was conducted for 21 patients. Molecular ITS sequencing was performed for 37 isolates. The frequency of attacks was significantly associated with the seasonality, which was closely related to climate (P=0.024), exposure to animals (cats, P=0.025), plants (olive, P=0.018), physical effort (P=0.04) and the number of permanent occupants in house (>6) (P=0.026). Fungal contaminants were detected from 78.6% of biological samples and 97.8% of environmental samples. Antibodies corresponding to the studied allergens were detected in 10 patients (10/21). PCR sequencing allowed as rectified morphological identification for 27.02% (10/37) strains of Aspergillus. The allergy in molds is an indisputable reality that is necessary to look for in front of any severe asthma. So, it is important to establish clearly a relationship between exposure to fungi and health disorders in order to set up specific and effective preventive measures.
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Affiliation(s)
- H Trablesi
- Laboratory of Fungal and Parasitic Molecular Biology, School of Medicine, University of Sfax, Sfax, Tunisia
| | - I Hadrich
- Laboratory of Fungal and Parasitic Molecular Biology, School of Medicine, University of Sfax, Sfax, Tunisia
| | - S Neji
- Laboratory of Fungal and Parasitic Molecular Biology, School of Medicine, University of Sfax, Sfax, Tunisia
| | - N Fendri
- Laboratory of Fungal and Parasitic Molecular Biology, School of Medicine, University of Sfax, Sfax, Tunisia
| | - D Ghorbel
- Laboratory of Fungal and Parasitic Molecular Biology, School of Medicine, University of Sfax, Sfax, Tunisia
| | - F Makni
- Laboratory of Fungal and Parasitic Molecular Biology, School of Medicine, University of Sfax, Sfax, Tunisia
| | - H Ayadi
- Department of Pneumology, UH Hedi Chaker, University of Sfax, Sfax, Tunisia.
| | - S Kammoun
- Department of Pneumology, UH Hedi Chaker, University of Sfax, Sfax, Tunisia
| | - A Ayadi
- Laboratory of Fungal and Parasitic Molecular Biology, School of Medicine, University of Sfax, Sfax, Tunisia
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Schuermans W, Hoet K, Stessens L, Meeuwissen J, Vandepitte A, Van Mieghem A, Vandebroek K, Oris E, Coppens G. Molecular Identification of Cutaneous Alternariosis in a Renal Transplant Patient. Mycopathologia 2017; 182:873-877. [PMID: 28656553 DOI: 10.1007/s11046-017-0166-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [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: 03/30/2017] [Accepted: 06/17/2017] [Indexed: 01/15/2023]
Abstract
Cutaneous alternariosis is a rare condition, caused by an uncommon opportunistic pathogen. The most frequently affected individuals are immunosuppressed patients, e.g., organ transplant patients on immunosuppressive therapy. Clinical manifestations range from local skin lesions to disseminated disease. We present a case report of cutaneous alternariosis in a renal transplant recipient, confirmed by histological examination and molecular means. In addition, a review of the literature was performed.
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Affiliation(s)
- W Schuermans
- Department of Laboratory Medicine, Clinical Microbiology, Ziekenhuis Oost-Limburg, Genk, Belgium.
| | - K Hoet
- Department of Laboratory Medicine, Clinical Microbiology, Ziekenhuis Oost-Limburg, Genk, Belgium
| | - L Stessens
- Department of Pathology, Ziekenhuis Oost-Limburg, Genk, Belgium
| | - J Meeuwissen
- Department of General Internal Medicine, Infectious Diseases and Geriatric Medicine, Ziekenhuis Oost-Limburg, Genk, Belgium
| | - A Vandepitte
- Department of Dermatology, Ziekenhuis Oost-Limburg, Genk, Belgium
| | - A Van Mieghem
- Department of Nephrology, Ziekenhuis Oost-Limburg, Genk, Belgium
| | - K Vandebroek
- Department of Laboratory Medicine, Clinical Microbiology, Ziekenhuis Oost-Limburg, Genk, Belgium
| | - E Oris
- Department of Laboratory Medicine, Clinical Microbiology, Ziekenhuis Oost-Limburg, Genk, Belgium
| | - G Coppens
- Department of Laboratory Medicine, Clinical Microbiology, Ziekenhuis Oost-Limburg, Genk, Belgium
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Hazirolan G, Altun HU, Gumral R, Gursoy NC, Otlu B, Sancak B. Prevalence of Candida africana and Candida dubliniensis, in vulvovaginal candidiasis: First Turkish Candida africana isolates from vulvovaginal candidiasis. J Mycol Med 2017. [PMID: 28641919 DOI: 10.1016/j.mycmed.2017.04.106] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
INTRODUCTION Candida africana and C. dubliniensis are closely related species of C. albicans. Current phenotypic methods are not suitable to accurately distinguish all the species belonging to the C. albicans complex. Several molecular-based methods have recently been designed for discriminating among closely related Candida species. The aim of this study was to establish the prevalence of C. dubliniensis and C. africana in vulvovaginal samples with phenotypic and genotypic methods. MATERIALS AND METHODS We re-examined 376 vulvovaginal C. albicans complex isolates. All the isolates were identified with morphological features and HWP1 gene polymorphisms. ITS and D1/D2 sequencing, carbohydrate assimilation, MALDI-TOF MS profiles and antifungal susceptibilities were evaluated for C. africana and C. dubliniensis isolates. RESULTS Of the 376 isolates, three C. africana and three C. dubliniensis isolates (0.8% and 0.8% prevalence, respectively) were identified by molecular methods (HPW1, ITS and D1/D2) Phenotypically, C. africana differed from C. albicans and C. dubliniensis by formation of no/rare pseudohyphae, absence of chlamydospores and, the development of turquoise green colonies on CHROMagar. MALDI-TOF MS and API ID 32C could not revealed C. africana isolates. C. africana and C. dubliniensis isolates showed very low MIC values for all the tested antifungals. DISCUSSION This first report of C. africana from Turkey provides additional data for epidemiological, phenotypic features and antimicrobial susceptibility profiles. This study also highlights the importance of using genotypic methods in combination with phenotypic methods.
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Affiliation(s)
- G Hazirolan
- Department of microbiology, Ankara Numune training and research hospital, Ulku Mahallesi Talatpasa Bulvari No:5 Altindag, 06100 Ankara, Turkey.
| | - H U Altun
- Department of medical microbiology, Turgut Ozal university faculty of medicine, Ayvalı Mah.,Gazze Cad No:7, 06010 Etlik-Keçiören-Ankara, Turkey
| | - R Gumral
- Department of microbiology, Gulhane military medical academy, GATA, 06010 Keçiören-Ankara, Turkey
| | - N C Gursoy
- Department of microbiology, faculty of medicine, university of Inönü, 44000 Üzümlü-Malatya Merkez-Malatya, Turkey
| | - B Otlu
- Department of microbiology, faculty of medicine, university of Inönü, 44000 Üzümlü-Malatya Merkez-Malatya, Turkey
| | - B Sancak
- Department of microbiology, faculty of medicine, university of Hacettepe, Hacettepe university medicine, faculty Sıhhiye, 06100, Ankara, Turkey
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Kamari A, Sepahvand A, Mohammadi R. Isolation and molecular characterization of Cryptococcus species isolated from pigeon nests and Eucalyptus trees. Curr Med Mycol 2017; 3:20-25. [PMID: 29354777 PMCID: PMC5763894 DOI: 10.29252/cmm.3.2.20] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Background and Purpose: Cryptococcus species are pathogenic and non-pathogenic basidiomycete yeasts that are found widely in the environment. Based on phenotypic methods, this genus has many species; however, its taxonomy is presently being re-evaluated by modern techniques. The Cryptococcus species complex includes two sibling taxa of Cryptococcus neoformans and Cryptococcus gattii. We aimed to investigate the possible distribution of Cryptococcus species in pigeon nests and Eucalyptus trees in Ilam, Iran, using molecular techniques. Materials and Methods: Two hundred and seventy-four specimens were collected from pigeon nests and Eucalyptus trees during 2016-2017. All the specimens were sub-cultured on Sabouraud Glucose Agar with chloramphenicol and bird seed agar. For molecular identification, the ITS15.8SITS2 rDNA region was amplified using the first and fourth internal transcribed spacer (ITS1 and ITS4, respectively) primers. The purified products were applied for cycle sequencing reactions in forward direction with ITS1 primer. The obtained results were analyzed with Chromas 2.3. Results: Thirty-three out of 186 cultures (17.7%) and 11 out of 88 cultures (12.5%) were positive among pigeon nest and Eucalyptus tree specimens, respectively. Cryptococcus albidus (17.2%), C. albidus var. kuetzingii (3.4%), C. adeliensis (3.4%), C. uzbekistanensis (3.4%), and C. neoformans var. grubii (3.4%) were isolated from pigeon nests, and Cryptococcusadeliensis (25%) was the only Cryptococcus species isolated from Eucalyptus trees. Conclusion: The presence of pigeons and Eucalyptus trees in the vicinity of some particular places such as rest homes and hospitals should be considered as a risk factor for the immunocompromised population.
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Affiliation(s)
- A Kamari
- Department of Medical Parasitology and Mycology, School of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran
| | - A Sepahvand
- Razi Herbal Medicines Research Center, Lorestan University of Medical Sciences, Khorramabad, Iran
| | - R Mohammadi
- Department of Medical Parasitology and Mycology, School of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran.,Infectious Diseases and Tropical Medicine Research Center, Isfahan University of Medical Sciences, Isfahan, Iran
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Sun L, Cao X, Li M, Zhang X, Li X, Cui Z. Enhanced bioremediation of lead-contaminated soil by Solanum nigrum L. with Mucor circinelloides. Environ Sci Pollut Res Int 2017; 24:9681-9689. [PMID: 28251531 DOI: 10.1007/s11356-017-8637-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/11/2016] [Accepted: 02/13/2017] [Indexed: 06/06/2023]
Abstract
Strain selected from mine tailings in Anshan for Pb bioremediation was characterized at the genetic level by internal transcribed spacer (ITS) sequencing. Results revealed that the strain belongs to Mucor circinelloides. Bioremediation of lead-contaminated soil was conducted using Solanum nigrum L. combined with M. circinelloides. The removal efficacy was in the order microbial/phytoremediation > phytoremediation > microbial remediation > control. The bioremediation rates were 58.6, 47.2, and 40.2% in microbial/phytoremediation, microbial remediation, and phytoremediation groups, respectively. Inoculating soil with M. circinelloides enhanced Pb removal and S. nigrum L. growth. The bioaccumulation factor (BF, 1.43), enrichment factor (EF, 1.56), and translocation factor (TF, 1.35) were higher than unit, suggesting an efficient ability of S. nigrum L. in Pb bioremediation. Soil fertility was increased after bioremediation according to change in enzyme activities. The results indicated that inoculating S. nigrum L. with M. circinelloides enhanced its efficiency for phytoremediation of soil contaminated with Pb.
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Affiliation(s)
- Liqun Sun
- School of Environmental Science and Engineering, Shandong University, Ji'nan, 250100, China
| | - Xiufeng Cao
- Weifang University of Science and Technology, Shouguang, 262700, China
| | - Min Li
- School of Environmental Science and Engineering, Shandong University, Ji'nan, 250100, China
| | - Xu Zhang
- School of Environmental Science and Engineering, Shandong University, Ji'nan, 250100, China
| | - Xinxin Li
- School of Environmental Science and Engineering, Shandong University, Ji'nan, 250100, China
| | - Zhaojie Cui
- School of Environmental Science and Engineering, Shandong University, Ji'nan, 250100, China.
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45
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Linde CC, May TW, Phillips RD, Ruibal M, Smith LM, Peakall R. New species of Tulasnella associated with terrestrial orchids in Australia. IMA Fungus 2017; 8:27-47. [PMID: 28824838 PMCID: PMC5493536 DOI: 10.5598/imafungus.2017.08.01.03] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2016] [Accepted: 02/06/2017] [Indexed: 10/26/2022] Open
Abstract
Recent studies using sequence data from eight sequence loci and coalescent-based species delimitation methods have revealed several species-level lineages of Tulasnella associated with the orchid genera Arthrochilus, Caleana, Chiloglottis, and Drakaea in Australia. Here we formally describe three of those species, Tulasnella prima, T. secunda, and T. warcupii spp. nov., as well as an additional Tulasnella species associated with Chiloglottis growing in Sphagnum, T. sphagneti sp. nov. Species were identified by phylogenetic analyses of the ITS with up to 1.3 % sequence divergence within taxa and a minimum of 7.6 % intraspecific divergence. These new Tulasnella (Tulasnellaceae, Cantharellales) species are currently only known from orchid hosts, with each fungal species showing a strong relationship with an orchid genus. In this study, T. prima and T. sphagneti associate with Chiloglottis, while T. secunda associates with Drakaea and Caleana, and T. warcupii associates with Arthrochilus oreophilus.
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Affiliation(s)
- Celeste C Linde
- Ecology and Evolution, Research School of Biology, The Australian National University, Canberra, ACT 2601, Australia
| | - Tom W May
- Royal Botanic Gardens Victoria, Birdwood Ave, South Yarra VIC 3141, Australia
| | - Ryan D Phillips
- Ecology and Evolution, Research School of Biology, The Australian National University, Canberra, ACT 2601, Australia
| | - Monica Ruibal
- Ecology and Evolution, Research School of Biology, The Australian National University, Canberra, ACT 2601, Australia
| | - Leon M Smith
- Ecology and Evolution, Research School of Biology, The Australian National University, Canberra, ACT 2601, Australia
| | - Rod Peakall
- Ecology and Evolution, Research School of Biology, The Australian National University, Canberra, ACT 2601, Australia
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Hou X, Xiao M, Chen SCA, Wang H, Yu SY, Fan X, Kong F, Xu YC. Identification and Antifungal Susceptibility Profiles of Candida nivariensis and Candida bracarensis in a Multi-Center Chinese Collection of Yeasts. Front Microbiol 2017; 8:5. [PMID: 28154553 PMCID: PMC5243801 DOI: 10.3389/fmicb.2017.00005] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2016] [Accepted: 01/03/2017] [Indexed: 12/18/2022] Open
Abstract
Candida nivariensis and C. bracarensis are two emerging cryptic species within the C. glabrata complex. Thirteen of these isolates from 10 hospitals in China were studied for their species identification and antifungal susceptibilities. Phenotypic and molecular [rDNA ITS sequencing, D1/D2 sequencing and ITS sequencer-based capillary gel electrophoresis (SCGE)] and matrix-assisted laser desorption ionization-time of flight (MALDI-TOF) MS identification methods were compared for their performance in species identification. Twelve of 13 (92.3%) isolates were identified as C. nivariensis and one as C. bracarensis using ITS sequencing as the reference method. Results obtained by D1/D2 sequencing and ITS SCGE were concordant with ITS sequencing results for all (100%) isolates. SCGE was able to subtype 12 C. nivariensis into four ITS SCGE length types. All isolates failed to be identified by the Vitek MALDI-TOF MS system (bioMérieux), whilst the Bruker MS system (Bruker Daltoniks) correctly identified all C. nivariensis isolates but using a lowered (≥1.700) cut-off score for species assignment; the C. bracarensis isolate was identified but with score <1.700. The Vitek 2 Compact system could not identify 11 C. nivariensis and one C. bracarensis isolate and misidentified the remaining C. nivarensis strain as “C. glabrata.” All isolates were susceptible-dose dependent to fluconazole [minimum inhibitory concentration (MIC) range 0.5–4 μg/mL] and were classed as susceptible to echinocandins (MICs ≤ 0.06 μg/mL). All 13 isolates had low MICs for other azoles (MICs ≤ 0.5 μg/mL), amphotericin B (MICs ≤ 2 μg/mL) and 5-flucytosine (MICs ≤ 0.25 μg/mL). Our results reinforce the need for molecular differentiation of species of C. nivarensis and C. bracarensis. The performance of MALDI-TOF may be improved by adding mass spectral profiles (MSPs) into the current databases. The antifungal susceptibility profile of isolates should be monitored.
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Affiliation(s)
- Xin Hou
- Department of Clinical Laboratory, Peking Union Medical College Hospital, Chinese Academy of Medical SciencesBeijing, China; Graduate School, Peking Union Medical College, Chinese Academy of Medical SciencesBeijing, China
| | - Meng Xiao
- Department of Clinical Laboratory, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences Beijing, China
| | - Sharon C-A Chen
- Centre for Infectious Diseases and Microbiology Laboratory Services, Institute of Clinical Pathology and Medical Research-Pathology West, Westmead Hospital, University of Sydney, Sydney NSW, Australia
| | - He Wang
- Department of Clinical Laboratory, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences Beijing, China
| | - Shu-Ying Yu
- Department of Clinical Laboratory, Peking Union Medical College Hospital, Chinese Academy of Medical SciencesBeijing, China; Graduate School, Peking Union Medical College, Chinese Academy of Medical SciencesBeijing, China
| | - Xin Fan
- Department of Clinical Laboratory, Peking Union Medical College Hospital, Chinese Academy of Medical SciencesBeijing, China; Graduate School, Peking Union Medical College, Chinese Academy of Medical SciencesBeijing, China
| | - Fanrong Kong
- Centre for Infectious Diseases and Microbiology Laboratory Services, Institute of Clinical Pathology and Medical Research-Pathology West, Westmead Hospital, University of Sydney, Sydney NSW, Australia
| | - Ying-Chun Xu
- Department of Clinical Laboratory, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences Beijing, China
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Coombs K, Vesper S, Green BJ, Yermakov M, Reponen T. Fungal Microbiomes Associated with Green and Non-Green Building Materials. Int Biodeterior Biodegradation 2017; 125:251-257. [PMID: 29681691 PMCID: PMC5906815 DOI: 10.1016/j.ibiod.2017.07.018] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Water-damaged buildings can lead to fungal growth and occupant health problems. Green building materials, derived from renewable sources, are increasingly utilized in construction and renovations. However, the question as to what fungi will grow on these green compared to non-green materials, after they get wet, has not been adequately studied. By determining what fungi grow on each type of material, the potential health risks can be more adequately assessed. In this study, we inoculated green and non-green pieces of ceiling tile, composite board, drywall, and flooring with indoor dust containing a complex mixture of naturally occurring fungi. The materials were saturated with water and incubated for two months in a controlled environment. The resulting fungal microbiomes were evaluated using ITS amplicon sequencing. Overall, the richness and diversity of the mycobiomes on each pair of green and non-green pieces were not significantly different. However, different genera dominated on each type of material. For example, Aspergillus spp. had the highest relative abundance on green and non-green ceiling tiles and green composite boards, but Peniophora spp. dominated the non-green composite board. In contrast, Penicillium spp. dominated green and non-green flooring samples. Green gypsum board was dominated by Phialophora spp. and Stachybotrys spp., but non-green gypsum board by Myrothecium spp. These data suggest that water-damaged green and non-green building materials can result in mycobiomes that are dominated by fungal genera whose member species pose different potentials for health risks.
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Affiliation(s)
- Kanistha Coombs
- Department of Environmental Health, University of Cincinnati, P.O. Box 670056, Cincinnati, OH 45267-0056
| | - Stephen Vesper
- United States Environmental Protection Agency, 26 W. M. L. King Drive, Mail Stop 314, Cincinnati, OH 45268
| | - Brett J Green
- Centers for Disease Control and Prevention, National Institute for Occupational Safety and Health, 1095 Willowdale Road, Morgantown, WV 26505
| | - Mikhail Yermakov
- Department of Environmental Health, University of Cincinnati, P.O. Box 670056, Cincinnati, OH 45267-0056
| | - Tiina Reponen
- Department of Environmental Health, University of Cincinnati, P.O. Box 670056, Cincinnati, OH 45267-0056
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Denis J, Machouart M, Morio F, Sabou M, Kauffmann-LaCroix C, Contet-Audonneau N, Candolfi E, Letscher-Bru V. Performance of Matrix-Assisted Laser Desorption Ionization-Time of Flight Mass Spectrometry for Identifying Clinical Malassezia Isolates. J Clin Microbiol 2017; 55:90-6. [PMID: 27795342 DOI: 10.1128/JCM.01763-16] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2016] [Accepted: 10/07/2016] [Indexed: 11/20/2022] Open
Abstract
The genus Malassezia comprises commensal yeasts on human skin. These yeasts are involved in superficial infections but are also isolated in deeper infections, such as fungemia, particularly in certain at-risk patients, such as neonates or patients with parenteral nutrition catheters. Very little is known about Malassezia epidemiology and virulence. This is due mainly to the difficulty of distinguishing species. Currently, species identification is based on morphological and biochemical characteristics. Only molecular biology techniques identify species with certainty, but they are time-consuming and expensive. The aim of this study was to develop and evaluate a matrix-assisted laser desorption ionization-time of flight (MALDI-TOF) database for identifying Malassezia species by mass spectrometry. Eighty-five Malassezia isolates from patients in three French university hospitals were investigated. Each strain was identified by internal transcribed spacer sequencing. Forty-five strains of the six species Malassezia furfur, M. sympodialis, M. slooffiae, M. globosa, M. restricta, and M. pachydermatis allowed the creation of a MALDI-TOF database. Forty other strains were used to test this database. All strains were identified by our Malassezia database with log scores of >2.0, according to the manufacturer's criteria. Repeatability and reproducibility tests showed a coefficient of variation of the log score values of <10%. In conclusion, our new Malassezia database allows easy, fast, and reliable identification of Malassezia species. Implementation of this database will contribute to a better, more rapid identification of Malassezia species and will be helpful in gaining a better understanding of their epidemiology.
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Neji S, Trabelsi H, Hadrich I, Cheikhrouhou F, Sellami H, Makni F, Ayadi A. Molecular study of the Candida parapsilosis complex in Sfax, Tunisia. Med Mycol 2016; 55:137-144. [PMID: 27555560 DOI: 10.1093/mmy/myw063] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [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: 06/22/2016] [Revised: 03/04/2016] [Accepted: 06/25/2016] [Indexed: 11/14/2022] Open
Abstract
Candida parapsilosis, which was previously considered to be a complex of three genetically distinct groups, has emerged as a significant agent of nosocomial infections. Recently, this complex was separated into three species: C. parapsilosis sensu stricto, C. orthopsilosis, and C. metapsilosis In Tunisia, data pertaining to these fungi are limited. Thus, the purpose of our study was to determine by BanI PCR-RFLP and ITS sequencing, the occurrence of Candida parapsilosis complex among 182 isolates identified as C. parapsilosis by phenotypical methods. C. parapsilosis sensu stricto represented 94.5% of all isolates, while C. metapsilosis and. C. orthopsilosis were identified in 3.3% and 2.2%, respectively. Sequence analysis of internal transcribed spacer region confirmed and revealed only one genotype among the C. parapsilosis sensu stricto strains, three genotypes among six C. metapsilosis strains and two genotypes among four C. orthopsilosis strains.
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Affiliation(s)
- Sourour Neji
- Laboratory of Parasitology-Mycology, Habib Bourguiba, University Hospital, Sfax, Tunisia.,Laboratory of Fungal and Parasitic Molecular Biology, School of Medicine, University of Sfax, Tunisia
| | - Houaida Trabelsi
- Laboratory of Parasitology-Mycology, Habib Bourguiba, University Hospital, Sfax, Tunisia.,Laboratory of Fungal and Parasitic Molecular Biology, School of Medicine, University of Sfax, Tunisia
| | - Ines Hadrich
- Laboratory of Fungal and Parasitic Molecular Biology, School of Medicine, University of Sfax, Tunisia
| | - Fatma Cheikhrouhou
- Laboratory of Parasitology-Mycology, Habib Bourguiba, University Hospital, Sfax, Tunisia.,Laboratory of Fungal and Parasitic Molecular Biology, School of Medicine, University of Sfax, Tunisia
| | - Hayet Sellami
- Laboratory of Parasitology-Mycology, Habib Bourguiba, University Hospital, Sfax, Tunisia.,Laboratory of Fungal and Parasitic Molecular Biology, School of Medicine, University of Sfax, Tunisia
| | - Fattouma Makni
- Laboratory of Parasitology-Mycology, Habib Bourguiba, University Hospital, Sfax, Tunisia.,Laboratory of Fungal and Parasitic Molecular Biology, School of Medicine, University of Sfax, Tunisia
| | - Ali Ayadi
- Laboratory of Parasitology-Mycology, Habib Bourguiba, University Hospital, Sfax, Tunisia .,Laboratory of Fungal and Parasitic Molecular Biology, School of Medicine, University of Sfax, Tunisia
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50
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Ahmed A. Analysis of Metagenomics Next Generation Sequence Data for Fungal ITS Barcoding: Do You Need Advance Bioinformatics Experience? Front Microbiol 2016; 7:1061. [PMID: 27507959 PMCID: PMC4960088 DOI: 10.3389/fmicb.2016.01061] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2016] [Accepted: 06/23/2016] [Indexed: 11/13/2022] Open
Abstract
During the last few decades, most of microbiology laboratories have become familiar in analyzing Sanger sequence data for ITS barcoding. However, with the availability of next-generation sequencing platforms in many centers, it has become important for medical mycologists to know how to make sense of the massive sequence data generated by these new sequencing technologies. In many reference laboratories, the analysis of such data is not a big deal, since suitable IT infrastructure and well-trained bioinformatics scientists are always available. However, in small research laboratories and clinical microbiology laboratories the availability of such resources are always lacking. In this report, simple and user-friendly bioinformatics work-flow is suggested for fast and reproducible ITS barcoding of fungi.
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Affiliation(s)
- Abdalla Ahmed
- College of Medicine, Umm Al-Qura University Makkah, Saudi Arabia
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