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Abdulsalam RA, Ijabadeniyi OA, Cason ED, Sabiu S. Characterization of Microbial Diversity of Two Tomato Cultivars through Targeted Next-Generation Sequencing 16S rRNA and ITS Techniques. Microorganisms 2023; 11:2337. [PMID: 37764180 PMCID: PMC10534366 DOI: 10.3390/microorganisms11092337] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Revised: 09/14/2023] [Accepted: 09/15/2023] [Indexed: 09/29/2023] Open
Abstract
Even though the nutritional and economic values of Solanum lycopersicum (tomato) are substantially impacted by microbial spoilage, the available data on its microbial community, particularly during spoilage, are limited and have primarily been characterized using conventional culture-dependent methods. This study employed a targeted high-throughput next-generation sequencing method to longitudinally characterize the microbial diversity of two South African tomato cultivars (jam and round) at varied storage intervals (1, 6, and 12 days). Throughout the storage period, the bacterial communities of the two cultivars were more diverse than the fungal communities. The microbial diversity of both bacteria and fungi was greater and comparable between the cultivars on day 1, but becomes distinct as the storage period increases, with round tomatoes being more diverse than jam tomato, though, on day 12, jam tomato develops greater diversity than round tomato. Overall, the most abundant phyla (though Proteobacteria was most dominant) were Proteobacteria, Firmicutes, and Bacteriodota in the bacterial communities, while Ascomycota and Basidiomycota formed most fungal communities with Ascomycota being dominant. At the genus level, Pantoea and Klebsiella (bacteria), Hanseniaspora, Stemphylium, and Alternaria (fungi) were prevalent. Taken together, this study casts light on a broad microbial diversity profile thus, confirms the cultivars' diversity and abundance differences.
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Affiliation(s)
- Rukayat Abiola Abdulsalam
- Department of Biotechnology and Food Science, Durban University of Technology, Durban 4000, South Africa
| | | | - Errol D. Cason
- Department of Animal Science, University of the Free State, Bloemfontein 9300, South Africa
| | - Saheed Sabiu
- Department of Biotechnology and Food Science, Durban University of Technology, Durban 4000, South Africa
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2
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Huang TS, Wang K, Ye XY, Chen CS, Chang FC. Attention-Guided Transfer Learning for Identification of Filamentous Fungi Encountered in the Clinical Laboratory. Microbiol Spectr 2023; 11:e0461122. [PMID: 37154722 PMCID: PMC10269873 DOI: 10.1128/spectrum.04611-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Accepted: 04/12/2023] [Indexed: 05/10/2023] Open
Abstract
This study addresses the challenge of accurately identifying filamentous fungi in medical laboratories using transfer learning with convolutional neural networks (CNNs). The study uses microscopic images from touch-tape slides with lactophenol cotton blue staining, the most common method in clinical settings, to classify fungal genera and identify Aspergillus species. The training and test data sets included 4,108 images with representative microscopic morphology for each genus, and a soft attention mechanism was incorporated to enhance classification accuracy. As a result, the study achieved an overall classification accuracy of 94.9% for four frequently encountered genera and 84.5% for Aspergillus species. One of the distinct features is the involvement of medical technologists in developing a model that seamlessly integrates into routine workflows. In addition, the study highlights the potential of merging advanced technology with medical laboratory practices to diagnose filamentous fungi accurately and efficiently. IMPORTANCE This study utilizes transfer learning with CNNs to classify fungal genera and identify Aspergillus species using microscopic images from touch-tape preparation and lactophenol cotton blue staining. The training and test data sets included 4,108 images with representative microscopic morphology for each genus, and a soft attention mechanism was incorporated to enhance classification accuracy. As a result, the study achieved an overall classification accuracy of 94.9% for four frequently encountered genera and 84.5% for Aspergillus species. One of the distinct features is the involvement of medical technologists in developing a model that seamlessly integrates into routine workflows. In addition, the study highlights the potential of merging advanced technology with medical laboratory practices to diagnose filamentous fungi accurately and efficiently.
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Affiliation(s)
- Tsi-Shu Huang
- Division of Microbiology, Department of Pathology and Laboratory Medicine, Kaohsiung Veterans General Hospital, Kaohsiung, Taiwan
| | - Kevin Wang
- Department of Applied Mathematics, National Sun Yat-sen University, Kaohsiung, Taiwan
| | - Xiu-Yuan Ye
- Division of Microbiology, Department of Pathology and Laboratory Medicine, Kaohsiung Veterans General Hospital, Kaohsiung, Taiwan
| | - Chii-Shiang Chen
- Division of Microbiology, Department of Pathology and Laboratory Medicine, Kaohsiung Veterans General Hospital, Kaohsiung, Taiwan
| | - Fu-Chuen Chang
- Department of Applied Mathematics, National Sun Yat-sen University, Kaohsiung, Taiwan
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3
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Du X, Li H, Qi J, Chen C, Lu Y, Wang Y. Genome mining of secondary metabolites from a marine-derived Aspergillus terreus B12. Arch Microbiol 2021; 203:5621-5633. [PMID: 34459930 DOI: 10.1007/s00203-021-02548-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Revised: 08/15/2021] [Accepted: 08/19/2021] [Indexed: 12/29/2022]
Abstract
Owing to the prominent capabilities of bioconversion and biosynthesis, A. terreus has become attractive in biotechnical and pharmaceutical industry. In this work, an Aspergillus strain with potential antibacterial activities, was isolated from sponge in South China Sea. Based on the morphological and phylogenetic analysis, the strain was identified as A. terreus B12. Via the Illumina MiSeq sequencing platform, the complete genome was obtained, showing a genetic richness of biosynthetic gene clusters (BGCs), which might underpin the metabolic plasticity and adaptive resilience for the strain. Genome mining identified 67 BGCs, among which, 6 gene clusters could allocate to known BGCs (100% identity), corresponding to diverse metabolites like clavaric acid, dihydroisoflavipucine/isoflavipucine, dimethylcoprogen, alternariol, aspterric acid, and pyranonigrin E. Moreover, a range of compounds was isolated from B12 fermentation, e.g., terrein, butyrolactone I, terretonin A&E, acoapetaline B, and epi-aszonalenins A. Of note, acoapetaline B and epi-aszonalenins A, which had been respectively reported in plants and A. novofumigatus but with scarce information, was unexpectedly obtained from this species for the first time. The genomic and metabolic heterogeneity observed in strain B12, should be at least partially attributed to the genetic variability and biochemical diversity of A. terreus, which could be an interesting issue open to future efforts.
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Affiliation(s)
- Xinyang Du
- School of Life Science and Technology, China Pharmaceutical University, Nanjing, 211198, China
| | - Huanhuan Li
- School of Life Science and Technology, China Pharmaceutical University, Nanjing, 211198, China
| | - Jiangfeng Qi
- School of Life Science and Technology, China Pharmaceutical University, Nanjing, 211198, China
| | - Chaoyi Chen
- School of Life Science and Technology, China Pharmaceutical University, Nanjing, 211198, China
| | - Yuanyuan Lu
- School of Life Science and Technology, China Pharmaceutical University, Nanjing, 211198, China
| | - Ying Wang
- School of Life Science and Technology, China Pharmaceutical University, Nanjing, 211198, China.
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4
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Culture Cell Block Controls as a Tool to the Biomolecular Diagnosis of Infectious Diseases. Appl Immunohistochem Mol Morphol 2021; 28:484-487. [PMID: 31633490 DOI: 10.1097/pai.0000000000000811] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
The cell block (CB) technique has allowed easy obtainment of samples such as cellular and culture suspensions, to perform specific molecular tests such as immunohistochemistry and in situ hybridization. It has been improved along time, accuracy, and quality of the diagnoses, however, the cost of a commercial gel matrix for the preparation of CB is high and not suitable depending on the situation. The objective of this study is to test agarose as an alternative to the commercial gel matrix in the preparation of Aspergillus fumigatus' CB.
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A new lineage of mazaediate fungi in the Eurotiomycetes: Cryptocaliciomycetidae subclass. nov., based on the new species Cryptocalicium blascoi and the revision of the ascoma evolution. Mycol Prog 2021. [DOI: 10.1007/s11557-021-01710-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
AbstractThe class Eurotiomycetes (Ascomycota, Pezizomycotina) comprises important fungi used for medical, agricultural, industrial and scientific purposes. Eurotiomycetes is a morphologically and ecologically diverse monophyletic group. Within the Eurotiomycetes, different ascoma morphologies are found including cleistothecia and perithecia but also apothecia or stromatic forms. Mazaediate representatives (with a distinct structure in which loose masses of ascospores accumulate to be passively disseminated) have evolved independently several times. Here we describe a new mazaediate species belonging to the Eurotiomycetes. The multigene phylogeny produced (7 gene regions: nuLSU, nuSSU, 5.8S nuITS, mtSSU, RPB1, RPB2 and MCM7) placed the new species in a lineage sister to Eurotiomycetidae. Based on the evolutionary relationships and morphology, a new subclass, a new order, family and genus are described to place the new species: Cryptocalicium blascoi. This calicioid species occurs on the inner side of loose bark strips of Cupressaceae (Cupressus, Juniperus). Morphologically, C. blascoi is characterized by having minute apothecioid stalked ascomata producing mazaedia, clavate bitunicate asci with hemiamyloid reaction, presence of hamathecium and an apothecial external surface with dark violet granules that becomes turquoise green in KOH. The ancestral state reconstruction analyses support a common ancestor with open ascomata for all deep nodes in Eurotiomycetes and the evolution of closed ascomata (cleistothecioid in Eurotiomycetidae and perithecioid in Chaetothyriomycetidae) from apothecioid ancestors. The appropriateness of the description of a new subclass for this fungus is also discussed.
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Watanabe R, Huruta H, Ueno Y, Nukada T, Niwa H, Shinyashiki N, Kano R. Antifungal susceptibility of dermatophytes from racehorses in Japan. Vet Dermatol 2021; 32:474-e129. [PMID: 34189781 DOI: 10.1111/vde.12993] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2020] [Revised: 04/05/2021] [Accepted: 05/05/2021] [Indexed: 11/27/2022]
Abstract
BACKGROUND Luliconazole (LCZ) is an imidazole antifungal medication that exhibits excellent activity against dermatophytes. As a topical cream and lotion (approved for human use), LCZ has demonstrated a broad spectrum of activity against human dermatophytoses. OBJECTIVES This is the first study to investigate the in vitro susceptibility of clinical isolates from horse dermatophytoses to LCZ. ANIMALS No animals were used in this study. METHODS AND MATERIALS In the present study, the in vitro susceptibilities of clinical isolates of dermatophytes to LCZ, clotrimazole (CTZ), miconazole (MCZ) and terbinafine (TRF) were investigated using the Clinical & Laboratory Standards Institute M38-A2 test. RESULTS The minimum inhibitory concentrations (MICs) for all 16 clinical isolates of Trichophyton equinum, Microsporum equinum/canis and M. gypseum for LCZ were <0.03 mg/L. The MICs of all isolates were <0.03-0.5 mg/L for CTZ, 0.03-16 mg/L for MCZ and <0.03-1 mg/L for TRF. CONCLUSIONS LCZ demonstrated a broad spectrum of activity against clinical isolates from horse dermatophytoses. We consider that LCZ will become the primary antifungal agent for treating horse dermatophytosis.
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Affiliation(s)
- Ryousuke Watanabe
- Department of Veterinary Dermatology, Nihon University College of Bioresource Sciences, Fujisawa, Kanagawa, Japan
| | - Hikaru Huruta
- Department of Veterinary Dermatology, Nihon University College of Bioresource Sciences, Fujisawa, Kanagawa, Japan
| | - Yuji Ueno
- Racehorse Hospital, Miho Training Center, Japan Racing Association, Inashiki, Ibaraki, Japan
| | - Toshio Nukada
- Microbiology Division, Equine Research Institute, Japan Racing Association, Shimotsuke, Tochigi, Japan
| | - Hidekazu Niwa
- Microbiology Division, Equine Research Institute, Japan Racing Association, Shimotsuke, Tochigi, Japan
| | - Naoki Shinyashiki
- Racehorse Hospital, Miho Training Center, Japan Racing Association, Inashiki, Ibaraki, Japan
| | - Rui Kano
- Department of Veterinary Dermatology, Nihon University College of Bioresource Sciences, Fujisawa, Kanagawa, Japan
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Miyake R, Ito T, Kamata H, Kano R. Isolation of antifungal-resistant yeasts from bulk milk in Japan. J Vet Med Sci 2021; 83:1090-1092. [PMID: 34108335 PMCID: PMC8349809 DOI: 10.1292/jvms.21-0023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
We isolated ascomycetous yeasts including Candida species, that originally belonged to the genus Candida, from bulk milk in
the Aichi area of Japan, and determined the minimum inhibitory concentrations (MICs) of antifungal drugs on these isolates by conducting E-tests. We isolated 7
human pathogenic species (14 isolates) from 14 bulk milk samples: 5 Candida species of yeasts, and 2 Candida-related species.
Two isolates of C. albicans and C. inconspicua were resistant to fluconazole (MIC >32 mg/l). One isolate of C.
krusei was resistant to both azoles (fluconazole: >256 mg/ml and itraconazole: 4 mg/l). One isolate of C. catenulata might be
resistant to amphotericin B (>32 mg/l).
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Affiliation(s)
- Ryoka Miyake
- Veterinary Dermatology, Nihon University College of Bioresource Sciences, 1866 Kameino, Fusisawa, Kanagawa 252-0880, Japan
| | - Takakaki Ito
- Veterinary Hospital Aichi P.F.A.M.A.A., 91-1 Oike, Hane-cho, Okazaki, Aichi 444-0816, Japan
| | - Hiroshi Kamata
- Veterinary Pathobiology, Nihon University College of Bioresource Sciences, 1866 Kameino, Fusisawa, Kanagawa 252-0880, Japan
| | - Rui Kano
- Veterinary Dermatology, Nihon University College of Bioresource Sciences, 1866 Kameino, Fusisawa, Kanagawa 252-0880, Japan
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8
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Watanabe R, Furuta H, Ueno Y, Nukada T, Niwa H, Shinyashiki N, Kano R. First isolation of Trichophyton bullosum from a horse with dermatophytosis in Japan. Med Mycol Case Rep 2021; 32:81-83. [PMID: 34012768 PMCID: PMC8113804 DOI: 10.1016/j.mmcr.2021.04.004] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Revised: 04/23/2021] [Accepted: 04/24/2021] [Indexed: 11/30/2022] Open
Abstract
Trichophyton bullosum is a zoophilic dermatophyte that has been rarely isolated from horses and humans in Africa and Europe. This is the first reported isolation of T. bullosum from a horse with dermatophytosis in Japan. The isolate from a skin lesion formed a cream-colored and waxy colony that was slightly elevated in the center. Sequencing of the internal transcribe spacer region of the isolate revealed that it was 100% identical to that of T. bullosum.
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Affiliation(s)
- Ryosuke Watanabe
- Department of Veterinary Dermatology, Nihon University College of Bioresource, 1866 Kameino, Fujisawa, Kanagawa, 252-0880, Japan
| | - Hikaru Furuta
- Department of Veterinary Dermatology, Nihon University College of Bioresource, 1866 Kameino, Fujisawa, Kanagawa, 252-0880, Japan
| | - Yuji Ueno
- Racehorse Hospital, Miho Training Center, Japan Racing Association, Inashiki, Ibaraki, Japan
| | - Toshio Nukada
- Microbiology Division, Equine Research Institute, Japan Racing Association, Shimotsuke, Tochigi, Japan
| | - Hidekazu Niwa
- Microbiology Division, Equine Research Institute, Japan Racing Association, Shimotsuke, Tochigi, Japan
| | - Naoki Shinyashiki
- Racehorse Hospital, Miho Training Center, Japan Racing Association, Inashiki, Ibaraki, Japan
| | - Rui Kano
- Department of Veterinary Dermatology, Nihon University College of Bioresource, 1866 Kameino, Fujisawa, Kanagawa, 252-0880, Japan
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9
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Dehghani Bidgoli R. Chemical composition of essential oil and antifungal activity of Artemisia persica Boiss. from Iran. Journal of Food Science and Technology 2021; 58:1313-1318. [PMID: 33746259 DOI: 10.1007/s13197-020-04640-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Revised: 06/22/2020] [Accepted: 07/08/2020] [Indexed: 10/23/2022]
Abstract
Artemisia is the largest and most diverse genus from the Asteraceae family that named locally "Dermaneh" in Iran. This study was conducted to determine, the chemical compounds of Artemisia persica Boiss essential oil and its antifungal effect, toward six toxigenic fungal strains in vitro. The yield of essential oil from the aerial parts of this plant species, using hydrodistillation method obtained 0.18% (v/w). The results of GC/MS analysis identified 31 components in the essential oil that laciniata furanone E (17.1%), artedouglasia oxide C (13.2%), Trans-pinocarveol (10.2%), pinocarvone (8.5%), and α-pinene (5.8%) were the major compounds. The results of the antifungal activity showed that the most sensitive fungal strains to A. persica Boiss. essential oil were Aspergillus ochraceus and Aspergillus parasiticus with lower minimal fungicidal concentration (MFC) of 1.25 μl/ml (v/v). Also the strong fungicidal effect was observed against Aspergillus flavus and Aspergillus nidulans at a MFC value of 2.5 μl/ml, while the fungicidal activity against Aspergillus fumigatus and Aspergillus niger observed in the 10 μl/ml oil concentration. According to the results A. persica Boiss essential oil has a acceptable antifungal activity against Aspergillus strains and can be used to prevent food crops from fungal contaminations.
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Affiliation(s)
- Reza Dehghani Bidgoli
- Department of Rangeland and Watershed Management, Faculty of Natural Resources and Earth Sciences, University of Kashan, 87317-53153 Kashan, Iran
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10
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Kano R, Tsunoi M, Nakaya Y, Nagamine T, Ono K. Antifungal drugs-low-susceptibility in Aspergillus flavus isolated from a captively reared Okinawa rail (Hypotaenidia okinawae). J Vet Med Sci 2020; 83:28-30. [PMID: 33191334 PMCID: PMC7870398 DOI: 10.1292/jvms.20-0380] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
A four-month old female Okinawa rail (Hypotaenidia okinawae) presented with respiratory distress. Despite antifungal treatment with voriconazole (VRZ), micafungin (MCF), and itraconazole (ITZ), respiratory distress did not improve and the bird died 167 days after initiating treatment. Necropsy revealed multifocal pyogranulomatous necrotic nodular lesions with numerous whitish-green fungal hyphae in the left air sac. Aspergillus flavus was isolated from the left air sac lesion. Antifungal susceptibility tests indicated that the isolate showed low susceptibility to amphotericin B (AMB), fluconazole (FLZ), VRZ and MCF.
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Affiliation(s)
- Rui Kano
- Department of Veterinary Dermatology, Nihon University College of Bioresource, 1866 Kameino, Fujisawa, Kanagawa 252-0880, Japan
| | - Meika Tsunoi
- Department of Veterinary Dermatology, Nihon University College of Bioresource, 1866 Kameino, Fujisawa, Kanagawa 252-0880, Japan
| | - Yumiko Nakaya
- Okinawa Wildlife Federation, 308 Maehara, Uruma, Okinawa 904-2235, Japan
| | - Takashi Nagamine
- Okinawa Wildlife Federation, 308 Maehara, Uruma, Okinawa 904-2235, Japan
| | - Koji Ono
- Yambaru Wildlife Conservation Center, Ministry of the Environment, 1-15-15 Higawa, Naha, Okinawa 900-0022, Japan
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11
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Okada K, Kano R, Hasegawa T, Kagawa Y. Granulomatous polyarthritis caused by Talaromyces georgiensis in a dog. J Vet Diagn Invest 2020; 32:912-917. [PMID: 33000702 DOI: 10.1177/1040638720957964] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
A 6-y-old, 3.5-kg, spayed female Toy Poodle was presented with left forelimb lameness of 2-d duration. Two months before the initial presentation, radiography showed osteolysis of the medial epicondyle of the left humerus, and the left forelimb was amputated. Grossly, the articular villi of the elbow joint were markedly thickened, and the articular cartilage surfaces of the distal humerus and proximal radius had partial erosion. Histologically, granulomatous arthritis and osteomyelitis characterized by the presence of abundant macrophages containing numerous fungi were observed. ITS and β-tubulin sequences amplified from the isolate from the specimen were 100% and 99% identical to type strain UTHSC D16-145T of Talaromyces georgiensis, respectively. Canine osteoarthritis caused by T. georgiensis has not been reported previously, to our knowledge.
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Affiliation(s)
| | - Rui Kano
- Department of Veterinary Pathobiology, College of Bioresource Sciences, Nihon University, Fujisawa, Kanagawa, Japan
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12
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Ortiz-Lemus JF, Campoy S, Martín JF. Biological control of mites by xerophile Eurotium species isolated from the surface of dry cured ham and dry beef cecina. J Appl Microbiol 2020; 130:665-676. [PMID: 32869458 DOI: 10.1111/jam.14839] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2020] [Revised: 07/28/2020] [Accepted: 08/20/2020] [Indexed: 11/29/2022]
Abstract
Some meat dry products, including dry cured ham and dry beef cecina, are cured in cellars at moderately cold temperature allowing the growth of a lawn of fungi on their surface. During the curing process, frequently these products became contaminated with fungivore mites of the Acaridae family that feed on fungal mycelium and spores. AIMS The aim of this article is to study the possible biological control of mites by fungi that form part of the normal microbiota of these meat products. METHODS AND RESULTS Some yellow/orange pigmented fungi growing on the ham surface decreased the proliferation of mites; therefore, we isolated from ham and cecina xerophilic yellow/orange coloured fungal strains that were identified as members of the genus Eurotium (recently reclassified as Aspergillus section Aspergillus). Using molecular genetic tools, we have identified 158 strains as Eurotium rubrum (Aspergillus ruber), Eurotium repens (Aspergillus pseudoglaucus) and Eurotium chevalieri (Aspergillus chevalieri). Two strains, E. rubrum C47 and E. rubrum C49, showed strong miticidal activity. The toxic compound(s) are associated with the formation of cleistothecia. In synchronized mite development experiments, we observed that all stages of the mite lifecycle were inhibited by the E. rubrum C47 strain. In addition, we searched for miticidal activity in 13 culture collection Eurotium strains isolated from different habitats, and found that only one, Eurotium cristatum NRRL 4222 (Aspergillus cristatus) has a strong miticidal activity. CONCLUSIONS These fungal strains have proliferated on the surface of ham and cecina for decades, and possibly have acquired miticidal activity as a resistance mechanism against fungivores. SIGNIFICANCE AND IMPACT OF THE STUDY Biological control of infecting mites by favouring growth of E. rubrun C47, in place of the normal mixed population of Aspergillus and Penicillium, is an attractive approach to control mite infestations.
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Affiliation(s)
- J F Ortiz-Lemus
- Área de Microbiología, Departmento de Biología Molecular, Universidad de León, León, Spain.,Instituto de Biotecnología de León, INBIOTEC, León, Spain.,Departamento de Microbiología, Universidad de Pamplona, Pamplona, Colombia
| | - S Campoy
- Área de Microbiología, Departmento de Biología Molecular, Universidad de León, León, Spain.,Instituto de Biotecnología de León, INBIOTEC, León, Spain
| | - J F Martín
- Área de Microbiología, Departmento de Biología Molecular, Universidad de León, León, Spain.,Instituto de Biotecnología de León, INBIOTEC, León, Spain
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13
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Larkin PMK, Lawson KL, Contreras DA, Le CQ, Trejo M, Realegeno S, Hilt EE, Chandrasekaran S, Garner OB, Fishbein GA, Yang S. Amplicon-Based Next-Generation Sequencing for Detection of Fungi in Formalin-Fixed, Paraffin-Embedded Tissues: Correlation with Histopathology and Clinical Applications. J Mol Diagn 2020; 22:1287-1293. [PMID: 32738297 DOI: 10.1016/j.jmoldx.2020.06.017] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Accepted: 06/26/2020] [Indexed: 01/13/2023] Open
Abstract
Invasive fungal infections are increasing in prevalence because of an expanding population of immunocompromised individuals. To reduce morbidity and mortality, it is critical to accurately identify fungal pathogens to guide treatment. Current methods rely on histopathology, fungal culture, and serology, which are often insufficient for diagnosis. Herein, we describe the use of a laboratory-developed internal transcribed spacer-targeted amplicon-based next-generation sequencing (NGS) assay for the identification of fungal etiology in fungal stain-positive formalin-fixed, paraffin-embedded tissues by using Illumina MiSeq. A total of 44 specimens from 35 patients were included in this study, with varying degrees of fungal burden from multiple anatomic sites. NGS identified 20 unique species across the 54 total organisms detected, including 40 molds, 10 yeasts, and 4 dimorphic fungi. The histopathologic morphology and the organisms suspected by surgical pathologist were compared with the organisms identified by NGS, with 100% (44/44) and 93.2% (41/44) concordance, respectively. In contrast, fungal culture only provided an identification in 27.3% (12/44) of specimens. We demonstrated that NGS is a powerful method for accurate and unbiased fungal identification in formalin-fixed, paraffin-embedded tissues. A retrospective evaluation of the clinical utility of the NGS results also suggests this technology can potentially improve both the speed and the accuracy of diagnosis for invasive fungal infections.
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Affiliation(s)
- Paige M K Larkin
- Department of Pathology and Laboratory Medicine, University of California, Los Angeles, Los Angeles, California
| | - Katy L Lawson
- Department of Pathology and Laboratory Medicine, University of California, Los Angeles, Los Angeles, California
| | - Deisy A Contreras
- Department of Pathology and Laboratory Medicine, University of California, Los Angeles, Los Angeles, California
| | - Catherine Q Le
- Department of Pathology and Laboratory Medicine, University of California, Los Angeles, Los Angeles, California
| | - Marisol Trejo
- Department of Pathology and Laboratory Medicine, University of California, Los Angeles, Los Angeles, California
| | - Susan Realegeno
- Department of Pathology and Laboratory Medicine, University of California, Los Angeles, Los Angeles, California
| | - Evann E Hilt
- Department of Pathology and Laboratory Medicine, University of California, Los Angeles, Los Angeles, California
| | - Sukantha Chandrasekaran
- Department of Pathology and Laboratory Medicine, University of California, Los Angeles, Los Angeles, California
| | - Omai B Garner
- Department of Pathology and Laboratory Medicine, University of California, Los Angeles, Los Angeles, California
| | - Gregory A Fishbein
- Department of Pathology and Laboratory Medicine, University of California, Los Angeles, Los Angeles, California
| | - Shangxin Yang
- Department of Pathology and Laboratory Medicine, University of California, Los Angeles, Los Angeles, California.
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Larkin PMK, Multani A, Beaird OE, Dayo AJ, Fishbein GA, Yang S. A Collaborative Tale of Diagnosing and Treating Chronic Pulmonary Aspergillosis, from the Perspectives of Clinical Microbiologists, Surgical Pathologists, and Infectious Disease Clinicians. J Fungi (Basel) 2020; 6:E106. [PMID: 32664547 PMCID: PMC7558816 DOI: 10.3390/jof6030106] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2020] [Revised: 07/08/2020] [Accepted: 07/09/2020] [Indexed: 02/06/2023] Open
Abstract
Chronic pulmonary aspergillosis (CPA) refers to a spectrum of Aspergillus-mediated disease that is associated with high morbidity and mortality, with its true prevalence vastly underestimated. The diagnosis of CPA includes characteristic radiographical findings in conjunction with persistent and systemic symptoms present for at least three months, and evidence of Aspergillus infection. Traditionally, Aspergillus infection has been confirmed through histopathology and microbiological studies, including fungal culture and serology, but these methodologies have limitations that are discussed in this review. The treatment of CPA requires an individualized approach and consideration of both medical and surgical options. Most Aspergillus species are considered susceptible to mold-active triazoles, echinocandins, and amphotericin B; however, antifungal resistance is emerging and well documented, demonstrating the need for novel therapies and antifungal susceptibility testing that correlates with clinical response. Here, we describe the clinical presentation, diagnosis, and treatment of CPA, with an emphasis on the strengths and pitfalls of diagnostic and treatment approaches, as well as future directions, including whole genome sequencing and metagenomic sequencing. The advancement of molecular technology enables rapid and precise species level identification, and the determination of molecular mechanisms of resistance, bridging the clinical infectious disease, anatomical pathology, microbiology, and molecular biology disciplines.
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Affiliation(s)
- Paige M. K. Larkin
- Department of Pathology and Laboratory Medicine, University of California Los Angeles, Los Angeles, CA 90095, USA; (P.M.K.L.); (A.J.D.); (G.A.F.)
- Department of Pathology, NorthShore University HealthSystem, Evanston, IL 60201, USA
| | - Ashrit Multani
- Department of Medicine, Division of Infectious Diseases, University of California Los Angeles, Los Angeles, CA 90095, USA; (A.M.); (O.E.B.)
| | - Omer E. Beaird
- Department of Medicine, Division of Infectious Diseases, University of California Los Angeles, Los Angeles, CA 90095, USA; (A.M.); (O.E.B.)
| | - Ayrton J. Dayo
- Department of Pathology and Laboratory Medicine, University of California Los Angeles, Los Angeles, CA 90095, USA; (P.M.K.L.); (A.J.D.); (G.A.F.)
| | - Gregory A. Fishbein
- Department of Pathology and Laboratory Medicine, University of California Los Angeles, Los Angeles, CA 90095, USA; (P.M.K.L.); (A.J.D.); (G.A.F.)
| | - Shangxin Yang
- Department of Pathology and Laboratory Medicine, University of California Los Angeles, Los Angeles, CA 90095, USA; (P.M.K.L.); (A.J.D.); (G.A.F.)
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Sulaiman IM, Jacobs E, Simpson S. Application of Ribosomal Internal Transcribed Spacer 1, Internal Transcribed Spacer 2, and Large-Subunit D1-D2 Regions as the Genetic Markers to Identify Fungi Isolated from Different Environmental Samples: A Molecular Surveillance Study of Public Health Importance. J AOAC Int 2020; 103:843-850. [PMID: 33241369 DOI: 10.1093/jaocint/qsz012] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2019] [Revised: 10/08/2019] [Accepted: 12/20/2019] [Indexed: 01/12/2023]
Abstract
BACKGROUND In September 2012, a multistate fungal meningitis outbreak started across 20 states in the United States. It affected 753 individuals and caused 64 deaths who received contaminated spinal injections. In a previous study, we analyzed 26 environmental samples collected from the manufacturing premises of a compounding company to determine the possible cause of an outbreak and identified 14 distinct fungal species. OBJECTIVES In this follow-up study, we have analyzed 198 environmental samples collected from three additional compounding company premises located in the United States for the presence of pathogenic fungi. METHODS Environmental swab samples were initially examined by standard microbiological methods. Subsequently, DNA sequencing was performed on all of the 25 recovered fungal isolates at the D1-D2 domain of the large subunit (LSU) ribosomal RNA (rRNA) and the internal transcribed spacer (ITS) regions. RESULTS Sequence analysis of the ITS1, ITS2, and LSU rRNA regions confirmed the presence of the following fungal species in the environmental samples analyzed: (i) Pestalotiopsis cocculi from the region Ia; (ii) Epicoccum nigrum and Trichaptum biforme from the region Ib; (iii) Nigrospora sphaerica and Fusarium sp. from the region II; and (iv) Curvularia sp., Fusarium sp., Penicillium sp., and Preussia sp. from the region III. Species identification of 25 recovered fungal isolates matched, in most cases, at 3 sequenced loci (ITS1, ITS2, and LSU). HIGHLIGHTS DNA sequencing of ITS1, ITS2, and LSU D1-D2 regions can be used to perform fungal typing and in implementing effective environmental monitoring programs of public health importance.
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Affiliation(s)
- Irshad M Sulaiman
- Microbiological Sciences Branch, Southeast Food and Feed Laboratory, Office of Regulatory Affairs, U. S. Food and Drug Administration, 60, Eighth Street NE, Atlanta, GA 30309, USA
| | - Emily Jacobs
- Microbiological Sciences Branch, Southeast Food and Feed Laboratory, Office of Regulatory Affairs, U. S. Food and Drug Administration, 60, Eighth Street NE, Atlanta, GA 30309, USA
| | - Steven Simpson
- Microbiological Sciences Branch, Southeast Food and Feed Laboratory, Office of Regulatory Affairs, U. S. Food and Drug Administration, 60, Eighth Street NE, Atlanta, GA 30309, USA
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Kano R, Kimura U, Kakurai M, Hiruma J, Kamata H, Suga Y, Harada K. Trichophyton indotineae sp. nov.: A New Highly Terbinafine-Resistant Anthropophilic Dermatophyte Species. Mycopathologia 2020; 185:947-958. [PMID: 32449054 DOI: 10.1007/s11046-020-00455-8] [Citation(s) in RCA: 105] [Impact Index Per Article: 26.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2019] [Accepted: 05/12/2020] [Indexed: 12/14/2022]
Abstract
In this report, we describe the first isolation of two highly terbinafine (TRF)-resistant Trichophyton interdigitale-like strains from a Nepali patient and an Indian patient with tinea corporis in Japan. These strains (designated NUBS19006 and NUBS19007) exhibited a TRF minimal inhibitory concentration (MIC) of > 32 mg/L and contained a missense mutation (Phe397Leu) in squalene epoxidase (SQLE) gene. The internal transcribed spacer (ITS) region sequences amplified from the isolates (NUBS19006 and NUBS19007) were 99.5% identical to Japanese isolates of T. interdigitale and T. interdigitale strain CBS 428.63. The homology of region sequences were also 97.6% identical to T. mentagrophytes strain CBS 318.56. Moreover, the ITS sequences amplified from the isolates were 100% identical to highly TRF-resistant strains of T. interdigitale, which were isolated in Delhi, India, and harbored mutations in SQLE. The urease test on Christensen's urease agar was positive for T. mentagrophytes and T. interdigitale after 7 days of incubation. On the other hand, the type strain of T. rubrum CBS 100081 T and highly TRF-resistant strains (NUBS19006 and NUBS19007) were negative on Christensen urease agar after 7 and 14 days of incubation. Moreover, NUBS19006 and NUBS19007 were also negative reaction on the hair perforation test. To avoid confusion in the taxonomy of the T. mentagrophytes/T. interdigitale complex, we suggest that the highly TRF-resistant Indian strains be considered a new species independent of T. interdigitale, according to clinical and mycological features.
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Affiliation(s)
- Rui Kano
- Department of Veterinary Dermatology, Nihon University College of Bioresource Sciences, 1866 Kameino, Fujisawa, Kanagawa, 252-0880, Japan.
| | - Utako Kimura
- Department of Dermatology, Juntendo University Urayasu Hospital, 2-1-1 Tomioka, Urayasu, Chiba, 279-0021, Japan
| | - Maki Kakurai
- Kakurai Dermatology Clinic, 905-1, Ojima, Shimotsuma, Ibaraki, 304-0051, Japan
| | - Junichiro Hiruma
- Department of Dermatology, Tokyo Medical University, 6-1-1 Nishishinjuku, Shinjuku-ku, Tokyo, 160-0023, Japan
| | - Hiroshi Kamata
- Department of Veterinary Dermatology, Nihon University College of Bioresource Sciences, 1866 Kameino, Fujisawa, Kanagawa, 252-0880, Japan
| | - Yasushi Suga
- Department of Dermatology, Juntendo University Urayasu Hospital, 2-1-1 Tomioka, Urayasu, Chiba, 279-0021, Japan
| | - Kazutoshi Harada
- Department of Dermatology, Tokyo Medical University, 6-1-1 Nishishinjuku, Shinjuku-ku, Tokyo, 160-0023, Japan
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Kamali Kakhki R, Najafzadeh MJ, Kachuei R, Ghazvini K. Targeting novel genes for simultaneous detection of five fungal and bacterial agents from BAL samples using multiplex PCR assay. Eur J Clin Microbiol Infect Dis 2020; 39:1535-1542. [PMID: 32253622 DOI: 10.1007/s10096-020-03879-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Accepted: 03/24/2020] [Indexed: 12/26/2022]
Abstract
The main purpose of our study was to evaluate multiplex PCR assay targeting novel genes for detection of five fungal and bacterial agents in BAL samples; because many fungi and bacteria that cause respiratory infections have similar clinical symptoms, diagnosing and differentiating them are therefore essential to controlling and treating them. A total of 100 BAL specimens from a mycobacterium and mycology laboratory were collected from patients suspected of having TB or other respiratory diseases. Novel DNA targets for Aspergillus, Nocardia, Cryptococcus, and Streptomyces were found using modified comparative genomic analysis. Afterward, the primers were designed based on novel targets, and the sensitivity and specificity of the newly designed primers were evaluated. These primers, along with specific primers for M. tuberculosis (SDR), were used in a multiplex PCR assay. The results showed the culture test to be more sensitive than the PCR assay in detecting M. tuberculosis. However, in the detection of Aspergillus, the PCR assay was more sensitive than the culture test. We also found one positive culture and two positive PCR assays for Nocardiosis. Cryptococcal infections and Streptomyces associated with lung diseases were not identified by the culture test nor by the PCR assay. The multiplex PCR is one of the cheapest molecular diagnostic tests readily available for BAL samples in clinical laboratories. This assay can be used for early reports of the causative agents and for treating patients with appropriate drugs at an early stage.
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Affiliation(s)
- Reza Kamali Kakhki
- Antimicrobial Resistance Research Center, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Mohammad Javad Najafzadeh
- Department of Parasitology and Mycology, School of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Reza Kachuei
- Molecular Biology Research Center, Systems Biology and Poisonings Institute, Baqiyatallah University of Medical Sciences, Tehran, Iran.
| | - Kiarash Ghazvini
- Antimicrobial Resistance Research Center, Mashhad University of Medical Sciences, Mashhad, Iran
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The Yeast Atlas of Appalachia: Species and Phenotypic Diversity of Herbicide Resistance in Wild Yeast. DIVERSITY 2020. [DOI: 10.3390/d12040139] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Glyphosate and copper-based herbicides/fungicides affect non-target organisms, and these incidental exposures can impact microbial populations. In this study, glyphosate resistance was found in the historical collection of S. cerevisiae, which was collected over the last century, but only in yeast isolated after the introduction of glyphosate. Although herbicide application was not recorded, the highest glyphosate-resistant S. cerevisiae were isolated from agricultural sites. In an effort to assess glyphosate resistance and impact on non-target microorganisms, different yeast species were harvested from 15 areas with known herbicidal histories, including an organic farm, conventional farm, remediated coal mine, suburban locations, state park, and a national forest. Yeast representing 23 genera were isolated from 237 samples of plant, soil, spontaneous fermentation, nut, flower, fruit, feces, and tree material samples. Saccharomyces, Candida, Metschnikowia, Kluyveromyces, Hanseniaspora, and Pichia were other genera commonly found across our sampled environments. Managed areas had less species diversity, and at the brewery only Saccharomyces and Pichia were isolated. A conventional farm growing RoundUp Ready™ corn had the lowest phylogenetic diversity and the highest glyphosate resistance. The mine was sprayed with multiple herbicides including a commercial formulation of glyphosate; however, the S. cerevisiae did not have elevated glyphosate resistance. In contrast to the conventional farm, the mine was exposed to glyphosate only one year prior to sample isolation. Glyphosate resistance is an example of the anthropogenic selection of nontarget organisms.
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Kimura U, Hiruma M, Kano R, Matsumoto T, Noguchi H, Takamori K, Suga Y. Caution and warning: Arrival of terbinafine‐resistant
Trichophyton interdigitale
of the Indian genotype, isolated from extensive dermatophytosis, in Japan. J Dermatol 2020; 47:e192-e193. [DOI: 10.1111/1346-8138.15300] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Affiliation(s)
- Utako Kimura
- Department of Dermatology Juntendo University Urayasu Hospital Urayasu Japan
- Ochanomizu Institute for Medical Mycology and Allergology Toshima Japan
| | - Masataro Hiruma
- Ochanomizu Institute for Medical Mycology and Allergology Toshima Japan
| | - Rui Kano
- Department of Veterinary Pathobiology Nihon University College of Bioresource Sciences Fujisawa Japan
| | - Tadahiko Matsumoto
- Ochanomizu Institute for Medical Mycology and Allergology Toshima Japan
- Noguchi Dermatology Clinic Kumamoto Japan
| | - Hiromitsu Noguchi
- Ochanomizu Institute for Medical Mycology and Allergology Toshima Japan
- Noguchi Dermatology Clinic Kumamoto Japan
| | - Kenji Takamori
- Department of Dermatology Juntendo University Urayasu Hospital Urayasu Japan
| | - Yasushi Suga
- Department of Dermatology Juntendo University Urayasu Hospital Urayasu Japan
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20
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Vanegas J, Muñoz-García A, Pérez-Parra KA, Figueroa-Galvis I, Mestanza O, Polanía J. Effect of salinity on fungal diversity in the rhizosphere of the halophyte Avicennia germinans from a semi-arid mangrove. FUNGAL ECOL 2019. [DOI: 10.1016/j.funeco.2019.07.009] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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21
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Kano R, Huruta H, Kamata H. Antifungal susceptibility of dermatophyte isolates from companion animals to ravuconazole. Vet Dermatol 2019; 31:175-176. [PMID: 31769120 DOI: 10.1111/vde.12815] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/06/2019] [Indexed: 11/30/2022]
Affiliation(s)
- Rui Kano
- Department of Veterinary Pathobiology, Nihon University College of Bioresource Sciences, 1866 Kameino, Fujisawa, Kanagawa, 252-0880, Japan
| | - Hikaru Huruta
- Department of Veterinary Pathobiology, Nihon University College of Bioresource Sciences, 1866 Kameino, Fujisawa, Kanagawa, 252-0880, Japan
| | - Hiroshi Kamata
- Department of Veterinary Pathobiology, Nihon University College of Bioresource Sciences, 1866 Kameino, Fujisawa, Kanagawa, 252-0880, Japan
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22
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Ohno Y, Akune Y, Inoshima Y, Kano R. First isolation of voriconazole-resistant Candida albicans, C. tropicalis, and Aspergillus niger from the blowholes of bottlenose dolphins (Tursiops truncatus). J Vet Med Sci 2019; 81:1628-1631. [PMID: 31611481 PMCID: PMC6895615 DOI: 10.1292/jvms.18-0749] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
Pulmonary mycosis is a fungal disease that commonly affects bottlenose dolphins (Tursiops truncatus) and is generally treated by the oral administration of azoles, such as itraconazole (ITZ) and voriconazole (VRZ). However, antifungal susceptibility testing of clinical isolates has not been well performed as a routine clinical examination in aquaria. In this study, we collected fungal species from the blowholes of 14 bottlenose dolphins, of which 12 were treated with ITZ or VRZ. All dolphins were housed in the Port of Nagoya Public Aquarium. The fungal species Candida albicans, C. tropicalis, C. glabrata, Aspergillus fumigatus, and A. niger were isolated. E-tests were performed to determine the minimum inhibitory concentrations (MICs) of ITZ and VRZ on these isolates. VRZ-resistant C. tropicalis (MIC: >32 µg/ml) and A. niger (MIC: >32 µg/ml) were isolated from three dolphins treated with ITZ or VRZ. Additionally, azole-resistant isolates of C. albicans and C. glabrata were collected from two dolphins that had never received azole therapy. To the best of our knowledge, our study is the first to report the isolation of VRZ-resistant C. albicans, C. tropicalis, and A. niger from the blowholes of bottlenose dolphins. Thus, antifungal susceptibility testing is a crucial strategy for selecting antifungal agents to treat respiratory fungal infections in bottlenose dolphins in aquaria.
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Affiliation(s)
- Yoshito Ohno
- Port of Nagoya Public Aquarium, 1-3 Minato-machi, Minato-ku, Nagoya, Aichi 455-0033, Japan
| | - Yuichiro Akune
- Port of Nagoya Public Aquarium, 1-3 Minato-machi, Minato-ku, Nagoya, Aichi 455-0033, Japan
| | - Yasuo Inoshima
- Cooperative Department of Veterinary Medicine, Gifu University, 1-1 Yanagido, Gifu, Gifu 501-1193, Japan
| | - Rui Kano
- Department of Veterinary Pathobiology, Nihon University College of Bioresource Sciences, 1866 Kameino, Fujisawa, Kanagawa 252-0880, Japan
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Meyers TR, Ferguson J, Bentz C, Burton T. Opportunistic phaeohyphomycoses in wild saffron cod Eleginus gracilis from waterways of Norton Sound and Toksook Bay, Alaska, USA. DISEASES OF AQUATIC ORGANISMS 2019; 135:211-226. [PMID: 31486413 DOI: 10.3354/dao03393] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
These case reports describe locally invasive black pigmented mycotic infections of the skin and gills of saffron cod Eleginus gracilis associated with 8 different opportunistic ascomycete fungi: Alternaria sp., Cladosporium herbarum, Chaetomium globosum, Cadophora luteo-olivacea, Penicillium sp., Phoma herbarum, Pseudophacidium ledi and Valsa sordida. These fungi were isolated on conventional media, identified according to morphological structures and confirmed by genetic sequencing. Several of these fungi are primary plant pathogens as well as opportunistic human pathogens in immunocompromised individuals. Several have also been described as causing opportunistic infections of fish. This case material represents the first report of C. luteo-olivacea, C. globosum, P. ledi and V. sordida as likely opportunistic fish pathogens in Alaskan watersheds of Norton Sound and south in Toksook Bay and possibly elsewhere.
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Affiliation(s)
- Theodore R Meyers
- Department of Fish and Game, Commercial Fisheries Division, Juneau Fish Pathology Laboratory, PO Box 115526, Juneau, Alaska 99811-5526, USA
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Hiruma J, Kitagawa H, Noguchi H, Kano R, Hiruma M, Kamata H, Harada K. Terbinafine‐resistant strain of
Trichophyton interdigitale
strain isolated from a tinea pedis patient. J Dermatol 2019; 46:351-353. [DOI: 10.1111/1346-8138.14809] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2018] [Accepted: 01/15/2019] [Indexed: 11/28/2022]
Affiliation(s)
| | - Hiroyuki Kitagawa
- Department of Veterinary Pathobiology Nihon University College of Bioresource Sciences Kanagawa Japan
| | - Hiromitsu Noguchi
- Noguchi Dermatology Clinic Kumamoto Japan
- Ochanomizu Institute for Medical Mycology and Allergology Tokyo Japan
| | - Rui Kano
- Department of Veterinary Pathobiology Nihon University College of Bioresource Sciences Kanagawa Japan
| | - Masataro Hiruma
- Ochanomizu Institute for Medical Mycology and Allergology Tokyo Japan
| | - Hiroshi Kamata
- Department of Veterinary Pathobiology Nihon University College of Bioresource Sciences Kanagawa Japan
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Kano R, Sakai M, Hiyama M, Tani K. Isolation of Aspergillus caninus (Synonym: Phialosimplex caninus) from a Canine Iliac Lymph node. Mycopathologia 2019; 184:335-339. [DOI: 10.1007/s11046-018-0312-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2018] [Accepted: 12/03/2018] [Indexed: 10/27/2022]
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Impacts and Challenges of Advanced Diagnostic Assays for Transplant Infectious Diseases. PRINCIPLES AND PRACTICE OF TRANSPLANT INFECTIOUS DISEASES 2019. [PMCID: PMC7121269 DOI: 10.1007/978-1-4939-9034-4_47] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The advanced technologies described in this chapter should allow for full inventories to be made of bacterial genes, their time- and place-dependent expression, and the resulting proteins as well as their outcome metabolites. The evolution of these molecular technologies will continue, not only in the microbial pathogens but also in the context of host-pathogen interactions targeting human genomics and transcriptomics. Their performance characteristics and limitations must be clearly understood by both laboratory personnel and clinicians to ensure proper utilization and interpretation.
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Ejmal MA, Holland DJ, MacDiarmid RM, Pearson MN. A novel chrysovirus from a clinical isolate of Aspergillus thermomutatus affects sporulation. PLoS One 2018; 13:e0209443. [PMID: 30571748 PMCID: PMC6301774 DOI: 10.1371/journal.pone.0209443] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2018] [Accepted: 12/05/2018] [Indexed: 12/15/2022] Open
Abstract
A clinical isolate of Aspergillus thermomutatus (Teleomorph: Neosartorya pseudofischeri) was found to contain ~35 nm isometric virus-like particles associated with four double-stranded (ds) RNA segments, each of which coded for a single open reading frame. The longest dsRNA element (3589 nt) encodes a putative RNA-dependent RNA polymerase (1114 aa), the second longest dsRNA element (2772 nt) encodes a coat protein (825 aa), and the other two dsRNAs (2676 nt, 2514 nt) encode hypothetical proteins of 768 aa and 711 aa, respectively. Phylogenetic analysis of the amino acid sequences showed 41-60% similarity to the proteins coded by the dsRNAs of the most closely related virus, Penicillium janczewskii chrysovirus 2, indicating that it is a new species based on the International Committee on Taxonomy of Viruses criteria for the genus Chrysovirus. This is the first virus reported from A. thermomutatus and was tentatively named Aspergillus thermomutatus chrysovirus 1. A virus free line of the fungal isolate, cured by cycloheximide treatment, produced large numbers of conidia but no ascospores at both 20°C and 37°C, whereas the virus infected line produced ten-fold fewer conidia at 20°C and a large number of ascospores at both temperatures. The effects of the virus on fungal sporulation have interesting implications for the spread of the fungus and possible use of the virus as a biological control agent.
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Affiliation(s)
- Mahjoub A. Ejmal
- School of Biological Sciences, the University of Auckland, Auckland, New Zealand
| | - David J. Holland
- Infectious Diseases Unit, Division of Medicine, Staff Centre, Middlemore Hospital, Auckland, New Zealand
| | - Robin M. MacDiarmid
- School of Biological Sciences, the University of Auckland, Auckland, New Zealand
- The New Zealand Institute for Plant and Food Research Limited, Auckland, New Zealand
| | - Michael N. Pearson
- School of Biological Sciences, the University of Auckland, Auckland, New Zealand
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28
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Durigan M, Cardoso-Silva CB, Ciampi-Guillardi M, Toledo-Silva G, Mori GM, Franco RMB, Souza AP. Molecular genotyping, diversity studies and high-resolution molecular markers unveiled by microsatellites in Giardia duodenalis. PLoS Negl Trop Dis 2018; 12:e0006928. [PMID: 30500829 PMCID: PMC6291164 DOI: 10.1371/journal.pntd.0006928] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2017] [Revised: 12/12/2018] [Accepted: 10/16/2018] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND Giardia duodenalis (synonyms G. lamblia and G. intestinalis) is an enteric protozoan parasite of a wide range of mammalian hosts, including humans and various domestic and wild animals. There is considerable genetic variability in G. duodenalis and isolates of this parasite have been divided into eight genetic assemblages. Microsatellites markers can be used to discriminate isolates with a high level of sensitivity. This study was conducted to identify and characterize genomic microsatellites (simple sequence repeats-SSRs), sequences of one- to six-nucleotide motifs repeated in tandem, present in the available genomes of G. duodenalis and to develop new markers that can serve as a tool for detection and for characterizing the genetic diversity of this parasite. METHODOLOGY/ PRINCIPAL FINDINGS For each genetic assemblage, polymorphism levels for the microsatellite markers were evaluated. After performing the analysis using the MISA and SciRoKo software, 1,853 simple sequence repeats (SSRs) were identified. In all the genomes, trinucleotide repeats were the most common class followed by tetranucleotide. Many of the SSR loci are assemblage-specific, and 36 SSR loci shared among all the genomes were identified. Together with hypothetical proteins, variant-specific surface proteins represented nearly half of the annotated SSR loci. The results regarding the most common repeat among the SSRs led us to infer that positive selection occurred to avoid frameshift mutations. Additionally, based on inter- and intra-genetic assemblages polymorphism analyses, we unveiled previously undetected genetic variation, indicating that the microsatellite markers we developed are useful molecular tools for epidemiological inferences based on population genetics patterns and processes. CONCLUSIONS There is increasing demand for the development of new molecular markers and for the characterization of pathogens at a higher resolution level. In this study, we present 60 G. duodenalis microsatellites markers that exhibited high polymerase chain reaction (PCR) amplification efficiency among the different genetic assemblages. Twenty of these markers presented nucleotide sequence polymorphisms and may be used as a genotyping tool. The monomorphic markers can be used for the detection of the parasite at the species and genetic assemblage level. These polymorphic markers revealed a genetic diversity that was previously undetectable, thus they can be considered valuable molecular tools for high resolution markers in future studies investigating Giardia and may also be used for epidemiological inferences based on populations genetics patterns and processes.
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Affiliation(s)
- Maurício Durigan
- Centro de Biologia Molecular e Engenharia Genética (CBMEG), Universidade Estadual de Campinas (UNICAMP), Campinas, São Paulo, Brazil
| | - Claudio Benício Cardoso-Silva
- Centro de Biologia Molecular e Engenharia Genética (CBMEG), Universidade Estadual de Campinas (UNICAMP), Campinas, São Paulo, Brazil
| | - Maísa Ciampi-Guillardi
- Centro de Biologia Molecular e Engenharia Genética (CBMEG), Universidade Estadual de Campinas (UNICAMP), Campinas, São Paulo, Brazil
- Departamento de Fitopatologia–ESALQ–Universidade de São Paulo, Piracicaba, São Paulo, Brazil
| | - Guilherme Toledo-Silva
- Centro de Biologia Molecular e Engenharia Genética (CBMEG), Universidade Estadual de Campinas (UNICAMP), Campinas, São Paulo, Brazil
| | - Gustavo M. Mori
- Instituto de Biociências, Campus do Litoral Paulista, Universidade Estadual Paulista (Unesp), São Vicente, Sao Paulo, Brazil
| | - Regina M. B. Franco
- Departamento de Biologia Animal, Instituto de Biologia, Universidade Estadual de Campinas (UNICAMP), Campinas, São Paulo, Brazil
| | - Anete P. Souza
- Centro de Biologia Molecular e Engenharia Genética (CBMEG), Universidade Estadual de Campinas (UNICAMP), Campinas, São Paulo, Brazil
- Departamento de Biologia Vegetal, Instituto de Biologia, Universidade Estadual de Campinas (UNICAMP), Campinas, São Paulo, Brazil
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Aghaei-Gharehbolagh S, Shams-Ghahfarokhi M, Amanloo S, Razzaghi-Abyaneh M. Molecular characterization of Aspergilli isolated from outdoor air. J Mycol Med 2018; 28:606-611. [PMID: 30292392 DOI: 10.1016/j.mycmed.2018.09.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2018] [Revised: 06/30/2018] [Accepted: 09/11/2018] [Indexed: 11/30/2022]
Abstract
Ubiquitous airborne conidia of the genus Aspergillus are responsible for a diverse group of human disorders from allergy to life treating invasive aspergillosis and mycotoxicoses. The aim of this study was to determine the population structure of Aspergillus isolated from outdoor air in Tehran by comparing the nucleotide sequences of ITS region and the PCR-RFLP molecular method. Internal transcribed spacer domains of 47 Aspergillus spp. were amplified and sequenced and PCR products were digested individually with restriction enzymes TaqI and EcoRI. For all species the PCR reaction produced a fragment of approximately 600bp in length. All of the nucleotide sequences were highly similar with the corresponding reference sequences registered at the gene bank. The all isolates displayed same banding pattern on the basis EcoR1 cleavage. While Taq1 enzyme profiling provided 5 different banding pattern. The results show that the A. niger section has the highest frequency with 27 isolates (57.4%). Of these, 23 isolates (48.9%) belonged to the A. niger complex and 4 isolates (8.5%) to the A. aculeatus complex. The A. flavus complex was also placed in the next ranking with 9 isolates (19.1%). These results strongly support the need for using molecular markers as an auxiliary tool in differentiating Aspergillus species.
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Affiliation(s)
- S Aghaei-Gharehbolagh
- Department of Mycology, Faculty of Medical Sciences, Tarbiat Modares University, Tehran 14115-331, Iran
| | - M Shams-Ghahfarokhi
- Department of Mycology, Faculty of Medical Sciences, Tarbiat Modares University, Tehran 14115-331, Iran.
| | - S Amanloo
- Department of Parasitology and Mycology, School of Medicine, Zanjan University of Medical Sciences, Zanjan 4513956111, Iran
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30
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Chen J, Leng L, Ye C, Lu Q, Addy M, Wang J, Liu J, Chen P, Ruan R, Zhou W. A comparative study between fungal pellet- and spore-assisted microalgae harvesting methods for algae bioflocculation. BIORESOURCE TECHNOLOGY 2018; 259:181-190. [PMID: 29554598 DOI: 10.1016/j.biortech.2018.03.040] [Citation(s) in RCA: 66] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/01/2018] [Revised: 03/06/2018] [Accepted: 03/07/2018] [Indexed: 06/08/2023]
Abstract
Fungi assisted microalgae bioflocculation is an emerging, efficient and cost-effective microalgal harvesting method, but no study has systematically evaluated and compared fungal spore-assisted (FSA) and fungal pellet-assisted (FPA) microalgal harvesting methods. In this study, harvesting Chlorella sp. cells by co-culture with Penicillium sp. spores or pellets was compared. Temperature, glucose concentration, pH and fungi:algae ratio were the critical parameters for harvesting efficiency. The highest flocculation efficiency (99%) of FSA method was achieved in 28 h at 40 °C, 160 rpm, 5 g glucose/L and 1.1 × 104 cells/mL (spore). FPA method can harvest 98.26% algae cells in 2.5 h at 34 °C, 160 rpm, pH 4.0 with the fungi:algae ratio of 1:2. The carbon input for FPA is only half of that for FSA. FPA takes less time and needs less glucose input compared with FSA and may be more promising to be further developed as an effective microalgae bioflocculation method.
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Affiliation(s)
- Jie Chen
- School of Resources, Environmental & Chemical Engineering and Key Laboratory of Poyang Lake Environment and Resource Utilization, Nanchang University, Nanchang, China
| | - Lijian Leng
- School of Resources, Environmental & Chemical Engineering and Key Laboratory of Poyang Lake Environment and Resource Utilization, Nanchang University, Nanchang, China
| | - Chensong Ye
- School of Resources, Environmental & Chemical Engineering and Key Laboratory of Poyang Lake Environment and Resource Utilization, Nanchang University, Nanchang, China
| | - Qian Lu
- School of Resources, Environmental & Chemical Engineering and Key Laboratory of Poyang Lake Environment and Resource Utilization, Nanchang University, Nanchang, China
| | - Min Addy
- Bioproducts and Biosystems Engineering Department, University of Minnesota, Saint Paul, MN 55108, United States
| | - Jinghan Wang
- Environmental Simulation and Pollution Control State Key Joint Laboratory, State Environmental Protection Key Laboratory of Microorganism Application and Risk Control (SMARC), School of Environment, Tsinghua University, Beijing 100084, China
| | - Jin Liu
- Institute for Food and Bioresource Engineering, Department of Energy and Resources Engineering and BIC-ESAT, College of Engineering, Peking University, Beijing 100871, China
| | - Paul Chen
- Bioproducts and Biosystems Engineering Department, University of Minnesota, Saint Paul, MN 55108, United States
| | - Roger Ruan
- School of Resources, Environmental & Chemical Engineering and Key Laboratory of Poyang Lake Environment and Resource Utilization, Nanchang University, Nanchang, China; Bioproducts and Biosystems Engineering Department, University of Minnesota, Saint Paul, MN 55108, United States.
| | - Wenguang Zhou
- School of Resources, Environmental & Chemical Engineering and Key Laboratory of Poyang Lake Environment and Resource Utilization, Nanchang University, Nanchang, China; Bioproducts and Biosystems Engineering Department, University of Minnesota, Saint Paul, MN 55108, United States.
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Rodriguez-Palacios A, Aladyshkina N, Ezeji JC, Erkkila HL, Conger M, Ward J, Webster J, Cominelli F. 'Cyclical Bias' in Microbiome Research Revealed by A Portable Germ-Free Housing System Using Nested Isolation. Sci Rep 2018; 8:3801. [PMID: 29491439 PMCID: PMC5830500 DOI: 10.1038/s41598-018-20742-1] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2017] [Accepted: 01/12/2018] [Indexed: 12/24/2022] Open
Abstract
Germ-Free (GF) research has required highly technical pressurized HEPA-ventilation anchored systems for decades. Herein, we validated a GF system that can be easily implemented and portable using Nested Isolation (NesTiso). GF-standards can be achieved housing mice in non-HEPA-static cages, which only need to be nested 'one-cage-inside-another' resembling 'Russian dolls'. After 2 years of monitoring ~100,000 GF-mouse-days, NesTiso showed mice can be maintained GF for life (>1.3 years), with low animal daily-contamination-probability risk (1 every 867 days), allowing the expansion of GF research with unprecedented freedom and mobility. At the cage level, with 23,360 GF cage-days, the probability of having a cage contamination in NesTiso cages opened in biosafety hoods was statistically identical to that of opening cages inside (the 'gold standard') multi-cage pressurized GF isolators. When validating the benefits of using NesTiso in mouse microbiome research, our experiments unexpectedly revealed that the mouse fecal microbiota composition within the 'bedding material' of conventional SPF-cages suffers cyclical selection bias as moist/feces/diet/organic content ('soiledness') increases over time (e.g., favoring microbiome abundances of Bacillales, Burkholderiales, Pseudomonadales; and cultivable Enterococcus faecalis over Lactobacillus murinus and Escherichia coli), which in turn cyclically influences the gut microbiome dynamics of caged mice. Culture 'co-streaking' assays showed that cohoused mice exhibiting different fecal microbiota/hemolytic profiles in clean bedding (high-within-cage individual diversity) 'cyclically and transiently appear identical' (less diverse) as bedding soiledness increases, and recurs. Strategies are proposed to minimize this novel functional form of cyclical bedding-dependent microbiome selection bias.
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Affiliation(s)
- Alexander Rodriguez-Palacios
- Digestive Health Research Institute, Case Western Reserve University School of Medicine, Cleveland, OH, 44106, USA.
- Division of Gastroenterology and Liver Diseases, Case Western Reserve University School of Medicine, Cleveland, OH, 44106, USA.
| | - Natalia Aladyshkina
- Digestive Health Research Institute, Case Western Reserve University School of Medicine, Cleveland, OH, 44106, USA
- Division of Gastroenterology and Liver Diseases, Case Western Reserve University School of Medicine, Cleveland, OH, 44106, USA
| | - Jessica C Ezeji
- Division of Gastroenterology and Liver Diseases, Case Western Reserve University School of Medicine, Cleveland, OH, 44106, USA
| | - Hailey L Erkkila
- Division of Gastroenterology and Liver Diseases, Case Western Reserve University School of Medicine, Cleveland, OH, 44106, USA
| | - Mathew Conger
- Digestive Health Research Institute, Case Western Reserve University School of Medicine, Cleveland, OH, 44106, USA
- Division of Gastroenterology and Liver Diseases, Case Western Reserve University School of Medicine, Cleveland, OH, 44106, USA
| | - John Ward
- Digestive Health Research Institute, Case Western Reserve University School of Medicine, Cleveland, OH, 44106, USA
- Division of Gastroenterology and Liver Diseases, Case Western Reserve University School of Medicine, Cleveland, OH, 44106, USA
| | - Joshua Webster
- Digestive Health Research Institute, Case Western Reserve University School of Medicine, Cleveland, OH, 44106, USA
- Division of Gastroenterology and Liver Diseases, Case Western Reserve University School of Medicine, Cleveland, OH, 44106, USA
| | - Fabio Cominelli
- Digestive Health Research Institute, Case Western Reserve University School of Medicine, Cleveland, OH, 44106, USA
- Division of Gastroenterology and Liver Diseases, Case Western Reserve University School of Medicine, Cleveland, OH, 44106, USA
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Gade L, Hurst S, Balajee SA, Lockhart SR, Litvintseva AP. Detection of mucormycetes and other pathogenic fungi in formalin fixed paraffin embedded and fresh tissues using the extended region of 28S rDNA. Med Mycol 2018; 55:385-395. [PMID: 27630252 DOI: 10.1093/mmy/myw083] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2015] [Accepted: 04/11/2016] [Indexed: 01/04/2023] Open
Abstract
Molecular methods of detection based on DNA-sequencing of the internal transcribed spacer 1 and 2 (ITS1 and ITS2) or 5΄ end region of 28S (D1-D2 region) of ribosomal RNA gene (rDNA) have been used extensively for molecular identification and detection of fungal infections. However, these regions are not always informative for identification of mucormycetes and other rare fungal pathogens as they often contain large introns, heterogenic regions, and/or cannot be PCR-amplified using broad range fungal PCR primers. In addition, because of the difficulties of recovering intact fungal DNA from human specimens, smaller regions of DNA are more useful for the direct detection of fungal DNA in tissues and fluids. In this study, we investigated the utility of 12F/13R PCR primers targeting a 200-230 bp region of the extended 28S region of rDNA for molecular identification of fungal DNA in formalin fixed paraffin embedded tissues and other clinical specimens. We demonstrated that this region can be successfully used for identification of all genera and some species of clinically relevant mucormycetes, as well as other medically important fungi, such as Aspergillus, Fusarium, Coccidioides, and Cryptococcus. We also demonstrated that PCR amplification and direct sequencing of the extended 28S region of rDNA was more sensitive compared to targeting the ITS2 region, as we were able to detect and identify mucormycetes and other fungal pathogens in tissues from patients with histopathological and/or culture evidence of fungal infections that were negative with PCR using ITS-specific primers.
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Affiliation(s)
- Lalitha Gade
- Mycotic Diseases Branch, Centers for Disease Control and Prevention, Atlanta, GA
| | - Steven Hurst
- Mycotic Diseases Branch, Centers for Disease Control and Prevention, Atlanta, GA
| | - S Arunmozhi Balajee
- Division of Viral Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, GA
| | - Shawn R Lockhart
- Mycotic Diseases Branch, Centers for Disease Control and Prevention, Atlanta, GA
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Agha Kuchak Afshari S, Rahimi H, Hashemi SJ, Daie Ghazvini R, Badali H, Aghaei Gharehbolagh S, Rezaie S. Evaluation of PCR-reverse line blot hybridization assay for simultaneous identification of medically important saprophytic fungi. J Mycol Med 2017; 28:173-179. [PMID: 29100947 DOI: 10.1016/j.mycmed.2017.09.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2017] [Revised: 09/05/2017] [Accepted: 09/11/2017] [Indexed: 11/29/2022]
Abstract
BACKGROUND In immunocompromised patients suffering from invasive fungal infections, rapid identification of fungal species is important since the appropriate treatment is usually related to the responsible species. We describe here, an assay based on combination of PCR and reverse line blot hybridization (PCR/RLB) for differentiation causative agent of fungal infections. MATERIALS AND METHODS We performed PCR/RLB assay on 10 reference strains, which include Aspergillus species (A. fumigatus, A. flavus, A. niger, A. terreus, and A. clavatus), Mucor circnelloides, Rhizopus oryzae, Alternaria alternata, Cladosporium herbarum, and Fusarium solani. Besides, twenty-two clinical specimens from patients with proven fungal infections were analyzed for the identification of species. The obtained results were then compared with the results of culture and sequence analysis. RESULTS The fungal species-specific oligonucleotide probes were able to distinguish between all species represented in this study with the exception of cross-reactivity between A. niger and A. fumigatus species. Two specimens, which were represented as mixed fungi in culture, were identified properly by this method. Results of the RLB assay were concordant with the culture and ITS sequencing results. CONCLUSION Our result demonstrate that the RLB assay potentially is suitable for rapid and simultaneous identification of variety fungal pathogens directly from culture as well as from clinical specimens.
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Affiliation(s)
- S Agha Kuchak Afshari
- Department of Medical Mycology and Parasitology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
| | - H Rahimi
- Molecular Medicine Department, Biotechnology Research Center, Pasteur Institute of Iran, Tehran, Iran
| | - S J Hashemi
- Department of Medical Mycology and Parasitology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
| | - R Daie Ghazvini
- Department of Medical Mycology and Parasitology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
| | - H Badali
- Department of Medical Mycology and Parasitology, Antimicrobial Resistance Research Center (ARRC), Mazandaran University of Medical Science, Sari, Iran
| | - S Aghaei Gharehbolagh
- Department of Medical Mycology and Parasitology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
| | - S Rezaie
- Department of Medical Mycology and Parasitology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran.
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Evans DE, Kawabata A, Wilson LD, Kim K, Dehghanpir SD, Gaunt SD, Welborn M, Grasperge B, Gill MS. Entomophthoromycosis and mucormycosis as causes of pneumonia in Vietnamese potbellied pigs. J Vet Diagn Invest 2017; 30:161-164. [PMID: 29034814 DOI: 10.1177/1040638717729860] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Two Vietnamese potbellied pigs ( Sus scrofa) had respiratory disease and, on autopsy, both pigs had large masses in the lungs and thoracic cavity. Microscopically, pulmonary and pleural masses contained large areas with hyphae surrounded by hypereosinophilic cellular debris rimmed by abundant eosinophils, lymphocytes, plasma cells, and histiocytes with occasional multinucleate giant cells. The hypereosinophilic debris usually formed tight cuffs, or "sleeves" around the hyphae, compatible with Splendore-Hoeppli-like material. The fungal organisms were determined by PCR to be Conidiobolus incongruus in one pig and Mucor circinelloides in the other. Entomophthoromycosis and mucormycosis should be included in the differential diagnoses for swine pneumonia, particularly when there is evidence of granulomatous pulmonary masses and pleural effusion with eosinophilic inflammation.
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Affiliation(s)
- Dawn E Evans
- Department of Pathobiological Sciences (Evans, Kawabata, Wilson, Kim, Dehghanpir, Gaunt, Grasperge), School of Veterinary Medicine, Louisiana State University, Baton Rouge, LA
- Veterinary Teaching Hospital and Clinics, Food Animal Medicine (Welborn, Gill), School of Veterinary Medicine, Louisiana State University, Baton Rouge, LA
| | - Atsushi Kawabata
- Department of Pathobiological Sciences (Evans, Kawabata, Wilson, Kim, Dehghanpir, Gaunt, Grasperge), School of Veterinary Medicine, Louisiana State University, Baton Rouge, LA
- Veterinary Teaching Hospital and Clinics, Food Animal Medicine (Welborn, Gill), School of Veterinary Medicine, Louisiana State University, Baton Rouge, LA
| | - Leslie D Wilson
- Department of Pathobiological Sciences (Evans, Kawabata, Wilson, Kim, Dehghanpir, Gaunt, Grasperge), School of Veterinary Medicine, Louisiana State University, Baton Rouge, LA
- Veterinary Teaching Hospital and Clinics, Food Animal Medicine (Welborn, Gill), School of Veterinary Medicine, Louisiana State University, Baton Rouge, LA
| | - Kenneth Kim
- Department of Pathobiological Sciences (Evans, Kawabata, Wilson, Kim, Dehghanpir, Gaunt, Grasperge), School of Veterinary Medicine, Louisiana State University, Baton Rouge, LA
- Veterinary Teaching Hospital and Clinics, Food Animal Medicine (Welborn, Gill), School of Veterinary Medicine, Louisiana State University, Baton Rouge, LA
| | - Shannon D Dehghanpir
- Department of Pathobiological Sciences (Evans, Kawabata, Wilson, Kim, Dehghanpir, Gaunt, Grasperge), School of Veterinary Medicine, Louisiana State University, Baton Rouge, LA
- Veterinary Teaching Hospital and Clinics, Food Animal Medicine (Welborn, Gill), School of Veterinary Medicine, Louisiana State University, Baton Rouge, LA
| | - Steve D Gaunt
- Department of Pathobiological Sciences (Evans, Kawabata, Wilson, Kim, Dehghanpir, Gaunt, Grasperge), School of Veterinary Medicine, Louisiana State University, Baton Rouge, LA
- Veterinary Teaching Hospital and Clinics, Food Animal Medicine (Welborn, Gill), School of Veterinary Medicine, Louisiana State University, Baton Rouge, LA
| | - Matt Welborn
- Department of Pathobiological Sciences (Evans, Kawabata, Wilson, Kim, Dehghanpir, Gaunt, Grasperge), School of Veterinary Medicine, Louisiana State University, Baton Rouge, LA
- Veterinary Teaching Hospital and Clinics, Food Animal Medicine (Welborn, Gill), School of Veterinary Medicine, Louisiana State University, Baton Rouge, LA
| | - Britton Grasperge
- Department of Pathobiological Sciences (Evans, Kawabata, Wilson, Kim, Dehghanpir, Gaunt, Grasperge), School of Veterinary Medicine, Louisiana State University, Baton Rouge, LA
- Veterinary Teaching Hospital and Clinics, Food Animal Medicine (Welborn, Gill), School of Veterinary Medicine, Louisiana State University, Baton Rouge, LA
| | - Marjorie S Gill
- Department of Pathobiological Sciences (Evans, Kawabata, Wilson, Kim, Dehghanpir, Gaunt, Grasperge), School of Veterinary Medicine, Louisiana State University, Baton Rouge, LA
- Veterinary Teaching Hospital and Clinics, Food Animal Medicine (Welborn, Gill), School of Veterinary Medicine, Louisiana State University, Baton Rouge, LA
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Abstract
Morphology and molecular characteristics of Microsporum gypseum clinical isolates obtained from the fur of a normal rabbit (n=1) and the soil from 10 different rabbit hutches in six elementary schools (n=10) were examined. Isolates were also identified by sequence analysis of the internal transcribed spacer (ITS) region. All 11 isolates demonstrated homology with the Arthroderma fulvum ITS sequence. Furthermore, PCR analysis for the presence of mating type genes detected positivity for MAT1-1 (n=10) and MAT1-2 (n=1). However, no mating reaction was detected between A. fulvum reference strains and the clinical isolates.
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Affiliation(s)
- Teru Fukutomi
- Department of Veterinary Pathobiology, Nihon University College of Bioresource Sciences, School of Veterinary Medicine.,Bright Pet Clinic
| | - Rui Kano
- Department of Veterinary Pathobiology, Nihon University College of Bioresource Sciences, School of Veterinary Medicine
| | - Hiroshi Kamata
- Department of Veterinary Pathobiology, Nihon University College of Bioresource Sciences, School of Veterinary Medicine
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Han HS, Kano R, Chen C, Noli C. Comparison of two in vitro antifungal sensitivity tests and monitoring during therapy of Sporothrix schenckii sensu stricto in Malaysian cats. Vet Dermatol 2017; 28:156-e32. [PMID: 28133872 DOI: 10.1111/vde.12417] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/01/2016] [Indexed: 01/21/2023]
Abstract
BACKGROUND Feline sporotrichosis is common in Malaysia. Thermosensitivity and effects of azole treatment on fungal susceptibility are unknown. OBJECTIVES To evaluate thermotolerance and antifungal susceptibility of feline Malaysian Sporothrix isolates, compare microdilution (MD) and E-test results, and investigate changes in susceptibility during azole therapy. METHODS Sporothrix schenckii sensu stricto was isolated from 44 cats. Thermotolerance was determined via culture at 37°C for 7 days. Susceptibility to itraconazole (ITZ), ketoconazole (KTZ) and terbinafine (TRB) was assessed in 40 isolates by MD; to amphotericin B (AMB), KTZ, ITZ, fluconazole (FLC) and posaconazole (POS) by E-test. Results were statistically compared by Pearson's Product Moment. In eight ketoconazole treated cats, susceptibility testing to itraconazole and ketoconazole was repeated every two months for six months. RESULTS Thermotolerance was observed in 36 of 44 (82%) isolates. Assuming that isolates growing at antifungal concentrations ≥4 mg/mL were resistant, all were resistant on E-test to FLC and AMB, 11 (28%) to POS, 6 (15%) to ITZ and 1 (3%) to KTZ. On MD, 27 of 40 (68%) were resistant to TRB, 2 (5%) to ITZ and 3 (8%) to KTZ. There was no correlation between E-test and MD results (KTZ r = 0.10, P = 0.54, and ITZ r = 0.11, P = 0.48). MD values for ITZ and KTZ did not exceed 4 mg/L during KTZ therapy. CONCLUSION The majority of feline isolates in Malaysia are thermosensitive. Lack of correlation between E-test and MD suggests that the E-test is unreliable to test antifungal susceptibility for Sporothrix spp. compared to MD. KTZ was the antifungal drug with the lowest MIC. Prolonged KTZ administration may not induce changes in antifungal susceptibility.
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Affiliation(s)
- Hock Siew Han
- Han Veterinary Surgery, 50 JLN Molek 2/2, TMN Molek, 81100, Johor Bahru, Johor, Malaysia
| | - Rui Kano
- Department of Pathobiology, Nihon University College of Bioresource Sciences, 1866, Kameino, Fujisawa, Kanagawa, 252-0880, Japan
| | - Charles Chen
- Asian Veterinary Specialist Referral Center, 109 Section 4, XinYi Road, Taipei, Taiwan
| | - Chiara Noli
- Servizi Dermatologici Veterinari, Strada Bedale della Ressia 2, 12016, Peveragno (CN), Italy
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Arbefeville S, Harris A, Ferrieri P. Comparison of sequencing the D2 region of the large subunit ribosomal RNA gene (MicroSEQ®) versus the internal transcribed spacer (ITS) regions using two public databases for identification of common and uncommon clinically relevant fungal species. J Microbiol Methods 2017. [PMID: 28647582 DOI: 10.1016/j.mimet.2017.06.015] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
CONTEXT Fungal infections cause considerable morbidity and mortality in immunocompromised patients. Rapid and accurate identification of fungi is essential to guide accurately targeted antifungal therapy. With the advent of molecular methods, clinical laboratories can use new technologies to supplement traditional phenotypic identification of fungi. OBJECTIVE The aims of the study were to evaluate the sole commercially available MicroSEQ® D2 LSU rDNA Fungal Identification Kit compared to the in-house developed internal transcribed spacer (ITS) regions assay in identifying moulds, using two well-known online public databases to analyze sequenced data. DESIGN 85 common and uncommon clinically relevant fungi isolated from clinical specimens were sequenced for the D2 region of the large subunit (LSU) of ribosomal RNA (rRNA) gene with the MicroSEQ® Kit and the ITS regions with the in house developed assay. The generated sequenced data were analyzed with the online GenBank and MycoBank public databases. RESULTS The D2 region of the LSU rRNA gene identified 89.4% or 92.9% of the 85 isolates to the genus level and the full ITS region (f-ITS) 96.5% or 100%, using GenBank or MycoBank, respectively, when compared to the consensus ID. When comparing species-level designations to the consensus ID, D2 region of the LSU rRNA gene aligned with 44.7% (38/85) or 52.9% (45/85) of these isolates in GenBank or MycoBank, respectively. By comparison, f-ITS possessed greater specificity, followed by ITS1, then ITS2 regions using GenBank or MycoBank. Using GenBank or MycoBank, D2 region of the LSU rRNA gene outperformed phenotypic based ID at the genus level. Comparing rates of ID between D2 region of the LSU rRNA gene and the ITS regions in GenBank or MycoBank at the species level against the consensus ID, f-ITS and ITS2 exceeded performance of the D2 region of the LSU rRNA gene, but ITS1 had similar performance to the D2 region of the LSU rRNA gene using MycoBank. CONCLUSION Our results indicated that the MicroSEQ® D2 LSU rDNA Fungal Identification Kit was equivalent to the in-house developed ITS regions assay to identify fungi at the genus level. The MycoBank database gave a better curated database and thus allowed a better genus and species identification for both D2 region of the LSU rRNA gene and ITS regions.
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Affiliation(s)
- S Arbefeville
- Department of Laboratory Medicine and Pathology, University of Minnesota Medical School, MMC 609 Mayo, 420 Delaware St. S.E., Minneapolis, MN 55455, USA.
| | - A Harris
- Department of Laboratory Medicine and Pathology, University of Minnesota Medical School, MMC 609 Mayo, 420 Delaware St. S.E., Minneapolis, MN 55455, USA
| | - P Ferrieri
- Department of Laboratory Medicine and Pathology, University of Minnesota Medical School, MMC 609 Mayo, 420 Delaware St. S.E., Minneapolis, MN 55455, USA
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Nouripour-Sisakht S, Ahmadi B, Makimura K, Hoog SD, Umeda Y, Alshahni MM, Mirhendi H. Characterization of the translation elongation factor 1-α gene in a wide range of pathogenic Aspergillus species. J Med Microbiol 2017; 66:419-429. [PMID: 28425876 DOI: 10.1099/jmm.0.000450] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
PURPOSE We aimed to evaluate the resolving power of the translation elongation factor (TEF)-1α gene for phylogenetic analysis of Aspergillus species. METHODOLOGY Sequences of 526 bp representing the coding region of the TEF-1α gene were used for the assessment of levels of intra- and inter-specific nucleotide polymorphism in 33 species of Aspergillus, including 57 reference, clinical and environmental strains. RESULTS Analysis of TEF-1α sequences indicated a mean similarity of 92.6 % between the species, with inter-species diversity ranging from 0 to 70 nucleotides. The species with the closest resemblance were A. candidus/A. carneus, and A. flavus/A. oryzae/A. ochraceus, with 100 and 99.8 % identification, respectively. These species are phylogenetically very close and the TEF-1α gene appears not to have sufficient discriminatory power to differentiate them. Meanwhile, intra-species differences were found within strains of A. clavatus, A. clavatonanicus, A. candidus, A. fumigatus, A. terreus, A. alliaceus, A. flavus, Eurotium amstelodami and E. chevalieri. The tree topology with strongly supported clades (≥70 % bootstrap values) was almost compatible with the phylogeny inferred from analysis of the DNA sequences of the beta tubulin gene (BT2). However, the backbone of the tree exhibited low bootstrap values, and inter-species correlations were not obvious in some clades; for example, tree topologies based on BT2 and TEF-1α genes were incompatible for some species, such as A. deflectus, A. janus and A. penicillioides. CONCLUSION The gene was not phylogenetically more informative than other known molecular markers. It will be necessary to test other genes or larger genomic regions to better understand the taxonomy of this important group of fungi.
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Affiliation(s)
- Sadegh Nouripour-Sisakht
- Cellular and Molecular Research Center, Yasuj University of Medical Sciences, Yasuj, Iran.,Departments of Medical Parasitology & Mycology, School of Public Health; National Institute of Health Research, Tehran University of Medical Sciences, Tehran, Iran
| | - Bahram Ahmadi
- Department of Microbiology and Parasitology, School of Para-Medicine, Bushehr University of Medical Sciences, Bushehr, Iran
| | - Koichi Makimura
- Laboratory of Space and Environmental Medicine, Graduate School of Medicine, Teikyo University, Tokyo, Japan
| | - Sybren de Hoog
- Fungal Biodiversity Center, Institute of the Royal Netherlands, Academy of Arts and Sciences, Centraalbureau voor Schimmelcultures-KNAW, Utrecht, Netherlands
| | - Yoshiko Umeda
- Laboratory of Space and Environmental Medicine, Graduate School of Medicine, Teikyo University, Tokyo, Japan
| | - Mohamed Mahdi Alshahni
- Laboratory of Space and Environmental Medicine, Graduate School of Medicine, Teikyo University, Tokyo, Japan
| | - Hossein Mirhendi
- Departments of Medical Parasitology and Mycology, School of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran
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Nakamura S, Sato H, Tanaka R, Kusuya Y, Takahashi H, Yaguchi T. Ribosomal subunit protein typing using matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS) for the identification and discrimination of Aspergillus species. BMC Microbiol 2017; 17:100. [PMID: 28441930 PMCID: PMC5405522 DOI: 10.1186/s12866-017-1009-3] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2017] [Accepted: 04/12/2017] [Indexed: 11/10/2022] Open
Abstract
Background Accurate identification of Aspergillus species is a very important subject. Mass spectral fingerprinting using matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS) is generally employed for the rapid identification of fungal isolates. However, the results are based on simple mass spectral pattern-matching, with no peak assignment and no taxonomic input. We propose here a ribosomal subunit protein (RSP) typing technique using MALDI-TOF MS for the identification and discrimination of Aspergillus species. The results are concluded to be phylogenetic in that they reflect the molecular evolution of housekeeping RSPs. Results The amino acid sequences of RSPs of genome-sequenced strains of Aspergillus species were first verified and compared to compile a reliable biomarker list for the identification of Aspergillus species. In this process, we revealed that many amino acid sequences of RSPs (about 10–60%, depending on strain) registered in the public protein databases needed to be corrected or newly added. The verified RSPs were allocated to RSP types based on their mass. Peak assignments of RSPs of each sample strain as observed by MALDI-TOF MS were then performed to set RSP type profiles, which were then further processed by means of cluster analysis. The resulting dendrogram based on RSP types showed a relatively good concordance with the tree based on β-tubulin gene sequences. RSP typing was able to further discriminate the strains belonging to Aspergillus section Fumigati. Conclusions The RSP typing method could be applied to identify Aspergillus species, even for species within section Fumigati. The discrimination power of RSP typing appears to be comparable to conventional β-tubulin gene analysis. This method would therefore be suitable for species identification and discrimination at the strain to species level. Because RSP typing can characterize the strains within section Fumigati, this method has potential as a powerful and reliable tool in the field of clinical microbiology. Electronic supplementary material The online version of this article (doi:10.1186/s12866-017-1009-3) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Sayaka Nakamura
- Research Institute for Sustainable Chemistry, National Institute of Advanced Industrial Science and Technology (AIST), Higashi 1-1-1, Tsukuba, Ibaraki, 305-8565, Japan
| | - Hiroaki Sato
- Research Institute for Sustainable Chemistry, National Institute of Advanced Industrial Science and Technology (AIST), Higashi 1-1-1, Tsukuba, Ibaraki, 305-8565, Japan.
| | - Reiko Tanaka
- Medical Mycology Research Center, Chiba University, 1-8-1 Inohana, Chuo-ku, Chiba, 260-8673, Japan
| | - Yoko Kusuya
- Medical Mycology Research Center, Chiba University, 1-8-1 Inohana, Chuo-ku, Chiba, 260-8673, Japan
| | - Hiroki Takahashi
- Medical Mycology Research Center, Chiba University, 1-8-1 Inohana, Chuo-ku, Chiba, 260-8673, Japan
| | - Takashi Yaguchi
- Medical Mycology Research Center, Chiba University, 1-8-1 Inohana, Chuo-ku, Chiba, 260-8673, Japan
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Batista-García RA, Sutton T, Jackson SA, Tovar-Herrera OE, Balcázar-López E, Sánchez-Carbente MDR, Sánchez-Reyes A, Dobson ADW, Folch-Mallol JL. Characterization of lignocellulolytic activities from fungi isolated from the deep-sea sponge Stelletta normani. PLoS One 2017; 12:e0173750. [PMID: 28339473 PMCID: PMC5365110 DOI: 10.1371/journal.pone.0173750] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2015] [Accepted: 02/24/2017] [Indexed: 12/03/2022] Open
Abstract
Extreme habitats have usually been regarded as a source of microorganisms that possess robust proteins that help enable them to survive in such harsh conditions. The deep sea can be considered an extreme habitat due to low temperatures (<5°C) and high pressure, however marine sponges survive in these habitats. While bacteria derived from deep-sea marine sponges have been studied, much less information is available on fungal biodiversity associated with these sponges. Following screening of fourteen fungi isolated from the deep-sea sponge Stelletta normani sampled at a depth of 751 metres, three halotolerant strains (TS2, TS11 and TS12) were identified which displayed high CMCase and xylanase activities. Molecular based taxonomic approaches identified these strains as Cadophora sp. TS2, Emericellopsis sp. TS11 and Pseudogymnoascus sp. TS 12. These three fungi displayed psychrotolerance and halotolerant growth on CMC and xylan as sole carbon sources, with optimal growth rates at 20°C. They produced CMCase and xylanase activities, which displayed optimal temperature and pH values of between 50-70°C and pH 5-8 respectively, together with good thermostability and halotolerance. In solid-state fermentations TS2, TS11 and TS12 produced CMCases, xylanases and peroxidase/phenol oxidases when grown on corn stover and wheat straw. This is the first time that CMCase, xylanase and peroxidase/phenol oxidase activities have been reported in these three fungal genera isolated from a marine sponge. Given the biochemical characteristics of these ligninolytic enzymes it is likely that they may prove useful in future biomass conversion strategies involving lignocellulosic materials.
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Affiliation(s)
- Ramón Alberto Batista-García
- Centro de Investigación en Dinámica Celular, Universidad Autónoma del Estado de Morelos, Cuernavaca, Morelos, Mexico
- Centro de Investigación en Biotecnología, Universidad Autónoma del Estado de Morelos, Cuernavaca, Morelos, Mexico
| | - Thomas Sutton
- School of Microbiology, University College Cork, Cork, Ireland
| | - Stephen A. Jackson
- School of Microbiology, University College Cork, Cork, Ireland
- Marine Biotechnology Centre, Environmental Research Institute, University College Cork, Cork, Ireland
| | - Omar Eduardo Tovar-Herrera
- Instituto de Biotecnología, Facultad de Ciencias Biológicas, Universidad Autónoma de Nuevo León, San Nicolás de los Garza, Nuevo León, Mexico
| | - Edgar Balcázar-López
- Centro de Investigación en Dinámica Celular, Universidad Autónoma del Estado de Morelos, Cuernavaca, Morelos, Mexico
- Centro de Investigación en Biotecnología, Universidad Autónoma del Estado de Morelos, Cuernavaca, Morelos, Mexico
| | | | - Ayixon Sánchez-Reyes
- Centro de Investigación en Dinámica Celular, Universidad Autónoma del Estado de Morelos, Cuernavaca, Morelos, Mexico
- Centro de Investigación en Biotecnología, Universidad Autónoma del Estado de Morelos, Cuernavaca, Morelos, Mexico
| | - Alan D. W. Dobson
- School of Microbiology, University College Cork, Cork, Ireland
- Marine Biotechnology Centre, Environmental Research Institute, University College Cork, Cork, Ireland
| | - Jorge Luis Folch-Mallol
- Centro de Investigación en Biotecnología, Universidad Autónoma del Estado de Morelos, Cuernavaca, Morelos, Mexico
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41
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Affiliation(s)
- Stephen W. Peterson
- Microbial Genomics and Bioprocessing Research Unit, National Center for Agricultural Utilization Research, Agricultural Research Service, U.S. Department of Agriculture, 1815 North University Street, Peoria, Illinois 61604
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42
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Current Approaches Towards Development of Molecular Markers in Diagnostics of Invasive Aspergillosis. Fungal Biol 2017. [DOI: 10.1007/978-3-319-34106-4_13] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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43
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de Gannes V, Bekele I, Dipchansingh D, Wuddivira MN, De Cairies S, Boman M, Hickey WJ. Microbial Community Structure and Function of Soil Following Ecosystem Conversion from Native Forests to Teak Plantation Forests. Front Microbiol 2016; 7:1976. [PMID: 28018311 PMCID: PMC5145857 DOI: 10.3389/fmicb.2016.01976] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2016] [Accepted: 11/25/2016] [Indexed: 11/28/2022] Open
Abstract
Soil microbial communities can form links between forest trees and functioning of forest soils, yet the impacts of converting diverse native forests to monoculture plantations on soil microbial communities are limited. This study tested the hypothesis that conversion from a diverse native to monoculture ecosystem would be paralleled by a reduction in the diversity of the soil microbial communities. Soils from Teak (Tectona grandis) plantations and adjacent native forest were examined at two locations in Trinidad. Microbial community structure was determined via Illumina sequencing of bacterial 16S rRNA genes and fungal internal transcribed spacer (ITS) regions, and by phospholipid fatty acid (PLFA) analysis. Functional characteristics of microbial communities were assessed by extracellular enzyme activity (EEA). Conversion to Teak plantation had no effect on species richness or evenness of bacterial or fungal communities, and no significant effect on EEA. However, multivariate analyses (nested and two-way crossed analysis of similarity) revealed significant effects (p < 0.05) of forest type (Teak vs. native) upon the composition of the microbial communities as reflected in all three assays of community structure. Univariate analysis of variance identified two bacterial phyla that were significantly more abundant in the native forest soils than in Teak soils (Cyanobacteria, p = 0.0180; Nitrospirae, p = 0.0100) and two more abundant in Teak soils than in native forest (candidate phyla TM7, p = 0.0004; WS6, p = 0.044). Abundance of an unidentified class of arbuscular mycorrhizal fungi (AMF) was significantly greater in Teak soils, notable because Teak is colonized by AMF rather than by ectomycorrihzal fungi that are symbionts of the native forest tree species. In conclusion, microbial diversity indices were not affected in the conversion of native forest to teak plantation, but examination of specific bacterial taxa showed that there were significant differences in community composition.
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Affiliation(s)
- Vidya de Gannes
- Faculty of Food and Agriculture, The University of the West Indies at St. Augustine Trinidad and Tobago
| | - Isaac Bekele
- Faculty of Food and Agriculture, The University of the West Indies at St. Augustine Trinidad and Tobago
| | - Denny Dipchansingh
- Ministry of Agriculture, Land and Fisheries, The University of the West Indies at St. Augustine Trinidad and Tobago
| | - Mark N Wuddivira
- Faculty of Food and Agriculture, The University of the West Indies at St. Augustine Trinidad and Tobago
| | - Sunshine De Cairies
- Faculty of Food and Agriculture, The University of the West Indies at St. Augustine Trinidad and Tobago
| | - Mattias Boman
- Faculty of Food and Agriculture, The University of the West Indies at St. Augustine Trinidad and Tobago
| | - William J Hickey
- O. N. Allen Laboratory for Soil Microbiology, Department Soil Science, University of Wisconsin-Madison Madison, WI, USA
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Lim SY, Kano R, Ooya K, Kimura S, Yanai T, Hasegawa A, Kamata H. The First Isolation of Aspergillus allahabadii from a Cormorant with Pulmonary Aspergillosis. Med Mycol J 2016; 57:E77-E79. [PMID: 27904055 DOI: 10.3314/mmj.16-00016] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
In this study, we report the first isolation of Aspergillus allahabadii from a Japanese cormorant with pulmonary aspergillosis. We performed molecular identification and antifungal susceptibility testing with the E-test. A 7-month-old male cormorant died because of uric acid deposition secondary to dehydration. Whitish nodular lesions were present on the caudal thoracic air sac in the right thoracic cavity. Histopathology revealed multifocal pyogranulomatous necrotic lesions with numerous fungal hyphae in the thoracic air sac. Identification of the etiologic agent was confirmed by comparative analyses of the sequences of the internal transcribed spacer (ITS) region and β-tubulin-encoding genes. According to the E-test, the minimum inhibitory concentrations of the isolate to amphotericin B, fluconazole, itraconazole, and voriconazole were 0.75 μg/ml, >256 μg/ml, 0.38 μg/ml, and 0.38 μg/ml, respectively.
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Affiliation(s)
- Sue Yee Lim
- Veterinary Pathobiology, Nihon University College of Bioresource Sciences
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45
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Nakamura S, Sato H, Tanaka R, Yaguchi T. Verification of Ribosomal Proteins of Aspergillus fumigatus for Use as Biomarkers in MALDI-TOF MS Identification. ACTA ACUST UNITED AC 2016; 5:A0049. [PMID: 27843740 DOI: 10.5702/massspectrometry.a0049] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2016] [Accepted: 09/26/2016] [Indexed: 11/23/2022]
Abstract
We have previously proposed a rapid identification method for bacterial strains based on the profiles of their ribosomal subunit proteins (RSPs), observed using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS). This method can perform phylogenetic characterization based on the mass of housekeeping RSP biomarkers, ideally calculated from amino acid sequence information registered in public protein databases. With the aim of extending its field of application to medical mycology, this study investigates the actual state of information of RSPs of eukaryotic fungi registered in public protein databases through the characterization of ribosomal protein fractions extracted from genome-sequenced Aspergillus fumigatus strains Af293 and A1163 as a model. In this process, we have found that the public protein databases harbor problems. The RSP names are in confusion, so we have provisionally unified them using the yeast naming system. The most serious problem is that many incorrect sequences are registered in the public protein databases. Surprisingly, more than half of the sequences are incorrect, due chiefly to mis-annotation of exon/intron structures. These errors could be corrected by a combination of in silico inspection by sequence homology analysis and MALDI-TOF MS measurements. We were also able to confirm conserved post-translational modifications in eleven RSPs. After these verifications, the masses of 31 expressed RSPs under 20,000 Da could be accurately confirmed. These RSPs have a potential to be useful biomarkers for identifying clinical isolates of A. fumigatus.
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Affiliation(s)
- Sayaka Nakamura
- Environmental Management Research Institute, National Institute of Advanced Industrial Science and Technology (AIST)
| | - Hiroaki Sato
- Environmental Management Research Institute, National Institute of Advanced Industrial Science and Technology (AIST); Environmental Management Research Institute, National Institute of Advanced Industrial Science and Technology (AIST)
| | - Reiko Tanaka
- Medical Mycology Research Center, Chiba University
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Clinical Effects of Gamma-Radiation-Resistant Aspergillus sydowii on Germ-Free Mice Immunologically Prone to Inflammatory Bowel Disease. J Pathog 2016; 2016:5748745. [PMID: 27630775 PMCID: PMC5007358 DOI: 10.1155/2016/5748745] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2016] [Accepted: 07/18/2016] [Indexed: 11/17/2022] Open
Abstract
We report and investigated a case of inadvertent contamination of 125 mice (housed in two germ-free positive-pressurized isolators) with emerging human and coral pathogen Aspergillus sydowii. The infected mice correspond to genetic line SAMP1/YitFc, which have 100% immune predisposition to develop Crohn's disease-like spontaneous pathologies, namely, inflammatory bowel disease (IBD). Pathogen update based on a scoping review of the literature and our clinical observations and experimentation are discussed. The unwanted infection of germ-free mice (immunologically prone to suffer chronic inflammation) with human pathogen A. sydowii resulted in no overt signs of clinical disease over 3-week exposure period, or during DSS-induced colitis experiments. Results and observations suggest that A. sydowii alone has limited clinical effect in immunocompromised germ-free mice or that other commensal microbial flora is required for Aspergillus-associated disease to occur.
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47
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Biodegradative Activities of Selected Environmental Fungi on a Polyester Polyurethane Varnish and Polyether Polyurethane Foams. Appl Environ Microbiol 2016; 82:5225-35. [PMID: 27316963 DOI: 10.1128/aem.01344-16] [Citation(s) in RCA: 101] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2016] [Accepted: 06/10/2016] [Indexed: 11/20/2022] Open
Abstract
UNLABELLED Polyurethane (PU) is widely used in many aspects of modern life because of its versatility and resistance. However, PU waste disposal generates large problems, since it is slowly degraded, there are limited recycling processes, and its destruction may generate toxic compounds. In this work, we isolated fungal strains able to grow in mineral medium with a polyester PU (PS-PU; Impranil DLN) or a polyether PU (PE-PU; Poly Lack) varnish as the only carbon source. Of the eight best Impranil-degrading strains, the six best degraders belonged to the Cladosporium cladosporioides complex, including the species C. pseudocladosporioides, C. tenuissimum, C. asperulatum, and C. montecillanum, and the two others were identified as Aspergillus fumigatus and Penicillium chrysogenum The best Impranil degrader, C. pseudocladosporioides strain T1.PL.1, degraded up to 87% after 14 days of incubation. Fourier transform infrared (FTIR) spectroscopy analysis of Impranil degradation by this strain showed a loss of carbonyl groups (1,729 cm(-1)) and N-H bonds (1,540 and 1,261 cm(-1)), and gas chromatography-mass spectrometry (GC-MS) analysis showed a decrease in ester compounds and increase in alcohols and hexane diisocyanate, indicating the hydrolysis of ester and urethane bonds. Extracellular esterase and low urease, but not protease activities were detected at 7 and 14 days of culture in Impranil. The best eight Impranil-degrading fungi were also able to degrade solid foams of the highly recalcitrant PE-PU type to different extents, with the highest levels generating up to 65% of dry-weight losses not previously reported. Scanning electron microscopy (SEM) analysis of fungus-treated foams showed melted and thinner cell wall structures than the non-fungus-treated ones, demonstrating fungal biodegradative action on PE-PU. IMPORTANCE Polyurethane waste disposal has become a serious problem. In this work, fungal strains able to efficiently degrade different types of polyurethanes are reported, and their biodegradative activity was studied by different experimental approaches. Varnish biodegradation analyses showed that fungi were able to break down the polymer in some of their precursors, offering the possibility that they may be recovered and used for new polyurethane synthesis. Also, the levels of degradation of solid polyether polyurethane foams reported in this work have never been observed previously. Isolation of efficient polyurethane-degrading microorganisms and delving into the mechanisms they used to degrade the polymer provide the basis for the development of biotechnological processes for polyurethane biodegradation and recycling.
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Delgado-Serrano L, Restrepo S, Bustos JR, Zambrano MM, Anzola JM. Mycofier: a new machine learning-based classifier for fungal ITS sequences. BMC Res Notes 2016; 9:402. [PMID: 27516337 PMCID: PMC4982325 DOI: 10.1186/s13104-016-2203-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2016] [Accepted: 08/03/2016] [Indexed: 01/05/2023] Open
Abstract
BACKGROUND The taxonomic and phylogenetic classification based on sequence analysis of the ITS1 genomic region has become a crucial component of fungal ecology and diversity studies. Nowadays, there is no accurate alignment-free classification tool for fungal ITS1 sequences for large environmental surveys. This study describes the development of a machine learning-based classifier for the taxonomical assignment of fungal ITS1 sequences at the genus level. RESULTS A fungal ITS1 sequence database was built using curated data. Training and test sets were generated from it. A Naïve Bayesian classifier was built using features from the primary sequence with an accuracy of 87 % in the classification at the genus level. CONCLUSIONS The final model was based on a Naïve Bayes algorithm using ITS1 sequences from 510 fungal genera. This classifier, denoted as Mycofier, provides similar classification accuracy compared to BLASTN, but the database used for the classification contains curated data and the tool, independent of alignment, is more efficient and contributes to the field, given the lack of an accurate classification tool for large data from fungal ITS1 sequences. The software and source code for Mycofier are freely available at https://github.com/ldelgado-serrano/mycofier.git .
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Affiliation(s)
- Luisa Delgado-Serrano
- Bioinformatics & Computational Biology, Corporación CorpoGen, Bogotá, DC, Colombia.,Department of Biological Sciences, Universidad de Los Andes, Bogotá, DC, Colombia
| | - Silvia Restrepo
- Department of Biological Sciences, Universidad de Los Andes, Bogotá, DC, Colombia
| | - Jose Ricardo Bustos
- Bioinformatics & Computational Biology, Corporación CorpoGen, Bogotá, DC, Colombia
| | | | - Juan Manuel Anzola
- Bioinformatics & Computational Biology, Corporación CorpoGen, Bogotá, DC, Colombia.
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49
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Anti-biofouling property studies on carboxyl-modified multi-walled carbon nanotubes filled PDMS nanocomposites. World J Microbiol Biotechnol 2016; 32:148. [DOI: 10.1007/s11274-016-2094-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2016] [Accepted: 06/03/2016] [Indexed: 12/14/2022]
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50
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Hiruma J, Okubo M, Kano R, Kumagawa M, Hiruma M, Hasegawa A, Kamata H, Tsuboi R. Mating Type Gene (MAT) and Itraconazole Susceptibility of Trichophyton tonsurans Strains Isolated in Japan. Mycopathologia 2016; 181:441-4. [PMID: 26762628 DOI: 10.1007/s11046-015-9980-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2015] [Accepted: 12/20/2015] [Indexed: 11/25/2022]
Abstract
Infection by Trichophyton tonsurans is an emerging fungal epidemic in Japan. Itraconazole (ITZ) and terbinafine have been used for the treatment of this infection for 15 years. However, patients with T. tonsurans infections have been shown to remain uncured or to become reinfected, suggesting that subclinical infection or polyphyletic strains and/or antifungal drug-resistant strains might be occurring in Japan. In this study, PCR analysis was performed to confirm the presence of the mating type locus MAT in genomic DNA from 60 Japanese clinical isolates of T. tonsurans, and to assess the previously postulated clonal origin of clinical isolates of this species. Antifungal susceptibility testing on isolates also was performed to confirm the absence of strains resistant to ITZ. PCR analysis proved that all 60 strains contained the MAT1-1 allele, while none contained the MAT1-2 allele. As determined by E-test, the mean MIC of ITZ in the 60 strains was 0.023 mg/L (range 0.002-0.125 mg/L). All strains of T. tonsurans isolated in Japan were clonal and were not resistant to ITZ. Therefore, dermatophytosis due to T. tonsurans is expected to respond to ITZ, since clinical isolates of T. tonsurans tested to date have been susceptible to this antifungal. This infection is proliferating as a subclinical infection in Japan.
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Affiliation(s)
- Junichiro Hiruma
- Department of Dermatology, Tokyo Medical University, 6-1-1 Nishishinjuku, Shinjuku-ku, Tokyo, 160-0023, Japan
| | - Miki Okubo
- Department of Pathobiology, Nihon University School of Veterinary Medicine, 1866, Fujisawa, Kanagawa, 252-0880, Japan
| | - Rui Kano
- Department of Pathobiology, Nihon University School of Veterinary Medicine, 1866, Fujisawa, Kanagawa, 252-0880, Japan. .,Department of Veterinary Pathobiology, Nihon University College of Bioresource Sciences, 1866 Kameino, Fujisawa, Kanagawa, 252-0880, Japan.
| | - Mai Kumagawa
- Department of Pathobiology, Nihon University School of Veterinary Medicine, 1866, Fujisawa, Kanagawa, 252-0880, Japan
| | - Masataro Hiruma
- Ochanomizu Institute for Medical Mycology and Allergology, Nakamura Bldg. 2F, 2-12-4 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan
| | - Atsuhiko Hasegawa
- Teikyo University Institute of Medical Mycology, 359 Otsuka, Hachioji, Tokyo, 192-0395, Japan
| | - Hiroshi Kamata
- Department of Pathobiology, Nihon University School of Veterinary Medicine, 1866, Fujisawa, Kanagawa, 252-0880, Japan
| | - Ryoji Tsuboi
- Department of Dermatology, Tokyo Medical University, 6-1-1 Nishishinjuku, Shinjuku-ku, Tokyo, 160-0023, Japan
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