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Hizlisoy H, Dishan A, Bekdik IK, Barel M, Koskeroglu K, Ozkaya Y, Aslan O, Yilmaz OT. Candida albicans in the oral cavities of pets: biofilm formation, putative virulence, antifungal resistance profiles and classification of the isolates. Int Microbiol 2024:10.1007/s10123-024-00552-4. [PMID: 38955904 DOI: 10.1007/s10123-024-00552-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2024] [Revised: 06/20/2024] [Accepted: 06/25/2024] [Indexed: 07/04/2024]
Abstract
The study aimed to investigate Candida albicans presence, antifungal resistance, biofilm formation, putative virulence genes, and molecular characterization in oral samples of dogs and cats. A total of 239 oral samples were collected from cats and dogs of various breeds and ages at Erciyes University, Faculty of Veterinary Medicine Clinics, between May 2017 and April 2018. Among 216 isolates obtained, 15 (6.95%) were identified as C. albicans, while 8 (3.7%) were non-albicans Candida species. Antifungal susceptibility testing revealed sensitivities to caspofungin, fluconazole, and flucytosine in varying proportions. Molecular analysis indicated the presence of fluconazole and caspofungin resistance genes in all C. albicans isolates. Additionally, virulence genes ALS1, HWP1, and HSP90 showed variable presence. Biofilm formation varied among isolates, with 46.7% strong, 33.3% moderate, and 20% weak producers. PCA analysis categorized isolates into two main clusters, with some dog isolates grouped separately. The findings underscore the significance of oral care and protective measures in pets due to C. albicans prevalence, biofilm formation, virulence factors, and antifungal resistance in their oral cavity, thereby aiding clinical diagnosis and treatment in veterinary medicine.
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Affiliation(s)
- Harun Hizlisoy
- Faculty of Veterinary Medicine, Department of Veterinary Public Health, Erciye University, Kayseri, Türkiye.
| | - Adalet Dishan
- Faculty of Veterinary Medicine, Department of Food Hygiene and Technology, Bozok University, Yozgat, Türkiye
| | - Ilknur Karaca Bekdik
- Faculty of Veterinary Medicine, Department of Internal Medicine, Erciyes University, Kayseri, Türkiye
| | - Mukaddes Barel
- Faculty of Veterinary Medicine, Department of Veterinary Public Health, Erciye University, Kayseri, Türkiye
| | | | - Yasin Ozkaya
- Health Sciences Institute, Erciyes University, Kayseri, Türkiye
| | - Oznur Aslan
- Faculty of Veterinary Medicine, Department of Internal Medicine, Erciyes University, Kayseri, Türkiye
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Sumlu E, Aydin M, Korucu EN, Alyar S, Nsangou AM. Artemisinin May Disrupt Hyphae Formation by Suppressing Biofilm-Related Genes of Candida albicans: In Vitro and In Silico Approaches. Antibiotics (Basel) 2024; 13:310. [PMID: 38666986 PMCID: PMC11047306 DOI: 10.3390/antibiotics13040310] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2024] [Revised: 03/26/2024] [Accepted: 03/27/2024] [Indexed: 04/29/2024] Open
Abstract
This study aimed to assess the antifungal and antibiofilm efficacy of artemisinin against Candida (C.) species, analyze its impact on gene expression levels within C. albicans biofilms, and investigate the molecular interactions through molecular docking. The antifungal efficacy of artemisinin on a variety of Candida species, including fluconazole-resistant and -susceptible species, was evaluated by the microdilution method. The effect of artemisinin on C. albicans biofilm formation was investigated by MTT and FESEM. The mRNA expression of the genes related to biofilm was analyzed by qRT-PCR. In addition, molecular docking analysis was used to understand the interaction between artemisinin and C. albicans at the molecular level with RAS1-cAMP-EFG1 and EFG1-regulated genes. Artemisinin showed higher sensitivity against non-albicans Candida strains. Furthermore, artemisinin was strongly inhibitory against C. albicans biofilms at 640 µg/mL. Artemisinin downregulated adhesion-related genes ALS3, HWP1, and ECE1, hyphal development genes UME6 and HGC1, and hyphal CAMP-dependent protein kinase regulators CYR1, RAS1, and EFG1. Furthermore, molecular docking analysis revealed that artemisinin and EFG1 had the highest affinity, followed by UME6. FESEM analysis showed that the fluconazole- and artemisinin-treated groups exhibited a reduced hyphal network, unusual surface bulges, and the formation of pores on the cell surfaces. Our study suggests that artemisinin may have antifungal potential and showed a remarkable antibiofilm activity by significantly suppressing adhesion and hyphal development through interaction with key proteins involved in biofilm formation, such as EFG1.
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Affiliation(s)
- Esra Sumlu
- Department of Medical Pharmacology, Faculty of Medicine, KTO Karatay University, 42020 Konya, Turkey;
| | - Merve Aydin
- Department of Medical Microbiology, Faculty of Medicine, KTO Karatay University, 42020 Konya, Turkey
| | - Emine Nedime Korucu
- Department of Molecular Biology and Genetics, Faculty of Science, Necmettin Erbakan University, 42090 Konya, Turkey;
| | - Saliha Alyar
- Department of Chemistry, Faculty of Science, Karatekin University, 18100 Çankırı, Turkey;
| | - Ahmed Moustapha Nsangou
- Department of Medical Microbiology, Faculty of Medicine, Selçuk University, 42130 Konya, Turkey;
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Battah B, Shbibe L, Ahmad O, Soukkarieh C, Al Okla SM, Chianese T, Rosati L, Vora LK, Zhao L, Marrazzo A, Ferrari M, Li L, Donnelly RF, Zanetti S, Mazzarello V, Donadu MG. Juniperus oxycedrus L. ssp. Essential Oil Microneedles: A Promising Antimicrobial and Wound Healing Activity. Pharmaceuticals (Basel) 2023; 17:40. [PMID: 38256874 PMCID: PMC10821373 DOI: 10.3390/ph17010040] [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: 11/20/2023] [Revised: 12/22/2023] [Accepted: 12/24/2023] [Indexed: 01/24/2024] Open
Abstract
The use of essential oil (EO) in treating infected wounds is still challenging. A lot of effort has been made to make such an application more convenient. Recently, microneedles (MNDs) have been considered as a smart dermal delivery system to overcome the poor absorption and distribution, low bioavailability, and skin penetration of some drugs. The aim of our study is to evaluate the wound healing activity of juniper-EO-loaded MNDs (EO MNDs) against wounds with bacterial and fungal infection. The Polyvinylpyrrolidone (PVP) MNDs were prepared using the gel-filled mold technique and loaded with juniper EO. In vivo models were created and wounds on rats were infected with two clinically isolated bacterial strains Pseudomonas aeruginosa and Staphylococcus aureus. Furthermore, Candida albicans was used to mimic fungal infection and juniper EO MNDs were tested. The obtained results showed an improvement in wound healing which started from the third day after application of the juniper EO MNDs, and at the sixth day post-infection, the treated wounds were significantly smaller than untreated wounds. A complete healing was shown by the 12th day after infection. Furthermore, our cytotoxicity results showed a cytotoxic effect of juniper EO MNDs on epithelial cells, which explained the faster wound healing in rats. Our study showed that juniper EO MNDs represent a novel strategy in EO delivery with minimal invasion. Juniper EO MNDs demonstrated significant antimicrobial activity against both the bacterial strains Pseudomonas aeruginosa and Staphylococcus aureus and against one fungal strain, Candida albicans. Finally, application of juniper EO MNDs exerted promising activity in the treatment and healing of wound infection.
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Affiliation(s)
- Basem Battah
- Department of Biochemistry and Microbiology, Faculty of Pharmacy, Antioch Syrian Private University, Maaret Saidnaya 22734, Syria
| | - Lama Shbibe
- Faculty of Science, Damascus University, Damascus P.O. Box 30621, Syria; (L.S.); (C.S.)
| | - Osama Ahmad
- Faculty of Medicine, Syrian Private University (SPU), Daraa International Highway, Damascus 36822, Syria;
- Faculty of Medicine, Kalamoon University, Damascus 222, Syria
| | - Chadi Soukkarieh
- Faculty of Science, Damascus University, Damascus P.O. Box 30621, Syria; (L.S.); (C.S.)
| | - Souad Mahmoud Al Okla
- College of Medicine and Health Sciences, National University of Science, Sohar 321, Oman;
| | - Teresa Chianese
- Department of Biology, University Federico II, Via Cintia 21, 80126 Napoli, Italy; (T.C.); (L.R.)
| | - Luigi Rosati
- Department of Biology, University Federico II, Via Cintia 21, 80126 Napoli, Italy; (T.C.); (L.R.)
| | - Lalitkumar K. Vora
- Medical Biology Centre, School of Pharmacy, Queen’s University Belfast, 97 Lisburn Road, Belfast BT9 7BL, UK; (L.K.V.); (L.Z.); (L.L.); (R.F.D.)
| | - Li Zhao
- Medical Biology Centre, School of Pharmacy, Queen’s University Belfast, 97 Lisburn Road, Belfast BT9 7BL, UK; (L.K.V.); (L.Z.); (L.L.); (R.F.D.)
| | - Alessandra Marrazzo
- Hospital Pharmacy, Azienda Ospedaliero Universitaria di Sassari, 07100 Sassari, Italy;
| | - Marco Ferrari
- Institute for Maternal and Child Health—IRCCS Burlo Garofolo, Via dell’Istria, 65, 34137 Trieste, Italy;
| | - Linlin Li
- Medical Biology Centre, School of Pharmacy, Queen’s University Belfast, 97 Lisburn Road, Belfast BT9 7BL, UK; (L.K.V.); (L.Z.); (L.L.); (R.F.D.)
| | - Ryan F. Donnelly
- Medical Biology Centre, School of Pharmacy, Queen’s University Belfast, 97 Lisburn Road, Belfast BT9 7BL, UK; (L.K.V.); (L.Z.); (L.L.); (R.F.D.)
| | - Stefania Zanetti
- Department of Biomedical Sciences, University of Sassari, 07100 Sassari, Italy; (S.Z.); (V.M.)
| | - Vittorio Mazzarello
- Department of Biomedical Sciences, University of Sassari, 07100 Sassari, Italy; (S.Z.); (V.M.)
| | - Matthew Gavino Donadu
- Scuola di Specializzazione in Farmacia Ospedaliera, Department of Medicine, Surgery and Pharmacy, University of Sassari, 07100 Sassari, Italy;
- Hospital Pharmacy, Giovanni Paolo II Hospital, ASL Gallura, 07026 Olbia, Italy
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Atiencia-Carrera MB, Cabezas-Mera FS, Tejera E, Machado A. Prevalence of biofilms in Candida spp. bloodstream infections: A meta-analysis. PLoS One 2022; 17:e0263522. [PMID: 35113972 PMCID: PMC8812928 DOI: 10.1371/journal.pone.0263522] [Citation(s) in RCA: 37] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Accepted: 01/20/2022] [Indexed: 01/10/2023] Open
Abstract
CONTEXT Candida-related infections are nowadays a serious Public Health Problem emerging multidrug-resistant strains. Candida biofilm also leads bloodstream infections to invasive systemic infections. OBJECTIVE The present meta-analysis aimed to analyze Candida biofilm rate, type, and antifungal resistance among hospitalized patients between 1995 and 2020. DATA SOURCES Web of Science, Scopus, PubMed, and Google Scholar databases were searched for English papers using the following medical subject heading terms (MESH): "invasive candidiasis"; "bloodstream infections"; "biofilm formation"; "biofilm-related infections"; "mortality"; and "prevalence". STUDY SELECTION The major inclusion criteria included reporting the rate of biofilm formation and the prevalence of biofilm-related to Candida species, including observational studies (more exactly, cohort, retrospective, and case-control studies). Furthermore, data regarding the mortality rate, the geographical location of the study set, and the use of anti-fungal agents in clinical isolates were also extracted from the studies. DATA EXTRACTION Independent extraction of articles by 2 authors using predefined data fields, including study quality indicators. DATA SYNTHESIS A total of 31 studies from publicly available databases met our inclusion criteria. The biofilm formation in the data set varied greatly from 16 to 100% in blood samples. Most of the studies belonged to Europe (17/31) and Asia (9/31). Forest plot showed a pooled rate of biofilm formation of 80.0% (CI: 67-90), with high heterogeneity (Q = 2567.45, I2 = 98.83, τ2 = 0.150) in random effects model (p < 0.001). The funnel plot and Egger's linear regression test failed to find publication bias (p = 0.896). The mortality rate in Candida-related bloodstream infections was 37.9% of which 70.0% were from biofilm-associated infections. Furthermore, Candida isolates were also characterized in low, intermediate, or high biofilm formers through their level of biofilm mass (crystal violet staining or XTT assays) after a 24h growth. When comparing between countries, statistical differences were obtained (p = 0.0074), showing the lower and higher biofilm prevalence values in Italy and Spain, respectively. The prevalence of low, intermediate, and high biofilms were 36.2, 18.9, and 35.0% (p < 0.0001), respectively. C. tropicalis was the prevalent species in high biofilm formation (67.5%) showing statistically significant differences when compared to other Candida species, except for C. krusei and C. glabrata. Finally, the rates of antifungal resistance to fluconazole, voriconazole, and caspofungin related to biofilm were 70.5, 67.9 and 72.8% (p < 0.001), respectively. CONCLUSIONS Early detection of biofilms and a better characterization of Candida spp. bloodstream infections should be considered, which eventually will help preserve public health resources and ultimately diminish mortality among patients.
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Affiliation(s)
- María Belén Atiencia-Carrera
- Instituto de Microbiología, Colegio de Ciencias Biológicas y Ambientales (COCIBA), Universidad San Francisco de Quito (USFQ), Diego de Robles y Vía Interoceánica, Campus Cumbayá, Quito, Pichincha, Ecuador
| | - Fausto Sebastián Cabezas-Mera
- Instituto de Microbiología, Colegio de Ciencias Biológicas y Ambientales (COCIBA), Universidad San Francisco de Quito (USFQ), Diego de Robles y Vía Interoceánica, Campus Cumbayá, Quito, Pichincha, Ecuador
| | - Eduardo Tejera
- Facultad de Ingeniería y Ciencias Agropecuarias Aplicadas, Grupo de Bioquimioinformática, Universidad de Las Américas, Quito, Pichincha, Ecuador
- * E-mail: (ET); (AM)
| | - António Machado
- Instituto de Microbiología, Colegio de Ciencias Biológicas y Ambientales (COCIBA), Universidad San Francisco de Quito (USFQ), Diego de Robles y Vía Interoceánica, Campus Cumbayá, Quito, Pichincha, Ecuador
- * E-mail: (ET); (AM)
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Hoang MTV, Irinyi L, Hu Y, Schwessinger B, Meyer W. Long-Reads-Based Metagenomics in Clinical Diagnosis With a Special Focus on Fungal Infections. Front Microbiol 2022; 12:708550. [PMID: 35069461 PMCID: PMC8770865 DOI: 10.3389/fmicb.2021.708550] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Accepted: 12/03/2021] [Indexed: 12/12/2022] Open
Abstract
Identification of the causative infectious agent is essential in the management of infectious diseases, with the ideal diagnostic method being rapid, accurate, and informative, while remaining cost-effective. Traditional diagnostic techniques rely on culturing and cell propagation to isolate and identify the causative pathogen. These techniques are limited by the ability and the time required to grow or propagate an agent in vitro and the facts that identification based on morphological traits are non-specific, insensitive, and reliant on technical expertise. The evolution of next-generation sequencing has revolutionized genomic studies to generate more data at a cheaper cost. These are divided into short- and long-read sequencing technologies, depending on the length of reads generated during sequencing runs. Long-read sequencing also called third-generation sequencing emerged commercially through the instruments released by Pacific Biosciences and Oxford Nanopore Technologies, although relying on different sequencing chemistries, with the first one being more accurate both platforms can generate ultra-long sequence reads. Long-read sequencing is capable of entirely spanning previously established genomic identification regions or potentially small whole genomes, drastically improving the accuracy of the identification of pathogens directly from clinical samples. Long-read sequencing may also provide additional important clinical information, such as antimicrobial resistance profiles and epidemiological data from a single sequencing run. While initial applications of long-read sequencing in clinical diagnosis showed that it could be a promising diagnostic technique, it also has highlighted the need for further optimization. In this review, we show the potential long-read sequencing has in clinical diagnosis of fungal infections and discuss the pros and cons of its implementation.
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Affiliation(s)
- Minh Thuy Vi Hoang
- Molecular Mycology Research Laboratory, Centre for Infectious Diseases and Microbiology, Faculty of Medicine and Health, Sydney Medical School, Westmead Clinical School, The University of Sydney, Sydney, NSW, Australia
- Westmead Institute for Medical Research, Westmead, NSW, Australia
| | - Laszlo Irinyi
- Molecular Mycology Research Laboratory, Centre for Infectious Diseases and Microbiology, Faculty of Medicine and Health, Sydney Medical School, Westmead Clinical School, The University of Sydney, Sydney, NSW, Australia
- Westmead Institute for Medical Research, Westmead, NSW, Australia
- Sydney Infectious Disease Institute, The University of Sydney, Sydney, NSW, Australia
| | - Yiheng Hu
- Research School of Biology, Australia National University, Canberra, ACT, Australia
| | | | - Wieland Meyer
- Molecular Mycology Research Laboratory, Centre for Infectious Diseases and Microbiology, Faculty of Medicine and Health, Sydney Medical School, Westmead Clinical School, The University of Sydney, Sydney, NSW, Australia
- Westmead Institute for Medical Research, Westmead, NSW, Australia
- Sydney Infectious Disease Institute, The University of Sydney, Sydney, NSW, Australia
- Westmead Hospital (Research and Education Network), Westmead, NSW, Australia
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M El-Ganiny A, E Yossef N, A Kamel H. Prevalence and antifungal drug resistance of nosocomial Candida species isolated from two university hospitals in Egypt. Curr Med Mycol 2021; 7:31-37. [PMID: 34553095 PMCID: PMC8443875 DOI: 10.18502/cmm.7.1.6181] [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] [Received: 12/04/2020] [Revised: 02/17/2021] [Accepted: 04/07/2021] [Indexed: 11/24/2022] Open
Abstract
Background and Purpose: There is a significant rise in morbidity and mortality of infections caused by Candida. Candida spp. infections are currently ranked fourth among nosocomial infections which are difficult
to diagnose and refractory to therapy. Given the differences in susceptibility among various spp., identification of Candida spp. is an important step that leads to the selection of a suitable antifungal. Materials and Methods: A prevalence study was conducted on 122 Candida isolates. The Candida spp. were identified using Chromogenic agar and polymerase chain reaction (PCR).
The antifungal susceptibility (AFS) of Candida spp. to amphotericin B, fluconazole, voriconazole, and caspofungin was determined by the disc diffusion method. Results: In total, 122 Candida clinical isolates were investigated in this study. Candida albicans with 57.4% (70 isolates) had the highest prevalence rate,
while 52 isolates (42.6%) were non-albicansCandida species (NAC). The NAC include Candida krusei (20.4%), Candida tropicalis (6.5%), Candida parapsilolsis (5.7%),
Candida dubliniensis (4.9%), and Candida glabrata (4.9%). The AFS showed that the resistance rates of Candida spp. to fluconazole and voriconazole were 13.1% (16 isolates)
and 9.8% (12 isolates), respectively. Moreover, only five isolates (4.1%) were resistant to caspofungin. Furthermore, there was no resistance against amphotericin B. The spp.
that showed the highest resistance were C. glabrata and C. tropicalis, while the lowest resistance was observed in C. albicans and C. dubliniensis. Conclusion: In conclusion, rapid identification of clinical Candida isolates and standard AFS are essential procedures for controlling the rise of resistant NAC spp. in clinical settings.
Usage of fluconazole should be restricted, especially in patients with recurrent Candida infections.
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Affiliation(s)
- Amira M El-Ganiny
- Microbiology and Immunology Department, Faculty of Pharmacy, Zagazig University, Zagazig, Egypt
| | - Nehal E Yossef
- Microbiology and Immunology Department, Faculty of Pharmacy, Zagazig University, Zagazig, Egypt
| | - Hend A Kamel
- Microbiology and Immunology Department, Faculty of Pharmacy, Zagazig University, Zagazig, Egypt.,Microbiology Department, Faculty of Pharmacy and Pharmaceutical Industries, Sinai University, Kantara, Egypt
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Fakhruddin KS, Perera Samaranayake L, Egusa H, Ngo HC, Pesee S. Profuse diversity and acidogenicity of the candida-biome of deep carious lesions of Severe Early Childhood Caries (S-ECC). J Oral Microbiol 2021; 13:1964277. [PMID: 34447489 PMCID: PMC8386706 DOI: 10.1080/20002297.2021.1964277] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Introduction: The retentive niches of deep caries lesions have a distinct biome. Methods: We evaluated the site-specific (occlusal and proximal) Candida-biome of Severe-Early Childhood Caries (S-ECC) in 66- children (132 lesions). Asymptomatic primary molars fitting the definition of the International Caries Detection and Assessment-(ICDAS)-caries-code 5/6 were analyzed. Deep-dentinal sampling and simultaneous assessment of pH were performed. Clinical isolates were speciated using multiplex-PCR and evaluated for their acidogenic and aciduric potential.Results: Surprisingly, a high prevalence of Candida species (72.7%), either singly or in combination, was noted from both the proximal and occlusal cavities. C. tropicalis was the most prevalent species (47%; 34/72), followed by C. krusei (43.1%; 31/72) and C. albicans (40.3%; 29/72), with C. glabrata being the least (9.7%; 7/72). Over 45% low-pH niches (pH <7) of both sites yielded either dual or triple species of Candida. Genotyping revealed three distinct C. albicans genotypes (A, B, and C) with (14/29; 48.3%) of strains belonging to Genotype A. All four evaluated Candida species exhibited acidogenic and aciduric potential, C. tropicalis being the most potent.Conclusion: This, the first report of the high-density, multispecies, yeast colonization of deep-dentinal lesions in S-ECC, suggests that the Candida-biome plays a significant etiologic role in the condition, possibly due to their profound acidogenicity in milieus rich in dietary carbohydrates.
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Affiliation(s)
| | | | - Hiroshi Egusa
- Division of Molecular and Regenerative Prosthodontics, Tohoku University Graduate School of Dentistry, Sendai, Miyagi, Japan
| | - Hien Chi Ngo
- University of Western Australia, Perth, Australia
| | - Siripen Pesee
- Faculty of Dentistry, Department of Oral Diagnostic Science, Faculty of Dentistry, Thammasat University, Pathum Thani, Thailand
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Boutin RCT, Petersen C, Woodward SE, Serapio-Palacios A, Bozorgmehr T, Loo R, Chalanuchpong A, Cirstea M, Lo B, Huus KE, Barcik W, Azad MB, Becker AB, Mandhane PJ, Moraes TJ, Sears MR, Subbarao P, McNagny KM, Turvey SE, Finlay BB. Bacterial-fungal interactions in the neonatal gut influence asthma outcomes later in life. eLife 2021; 10:e67740. [PMID: 33876729 PMCID: PMC8075585 DOI: 10.7554/elife.67740] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2021] [Accepted: 04/07/2021] [Indexed: 12/13/2022] Open
Abstract
Bacterial members of the infant gut microbiota and bacterial-derived short-chain fatty acids (SCFAs) have been shown to be protective against childhood asthma, but a role for the fungal microbiota in asthma etiology remains poorly defined. We recently reported an association between overgrowth of the yeast Pichia kudriavzevii in the gut microbiota of Ecuadorian infants and increased asthma risk. In the present study, we replicated these findings in Canadian infants and investigated a causal association between early life gut fungal dysbiosis and later allergic airway disease (AAD). In a mouse model, we demonstrate that overgrowth of P. kudriavzevii within the neonatal gut exacerbates features of type-2 and -17 inflammation during AAD later in life. We further show that P. kudriavzevii growth and adherence to gut epithelial cells are altered by SCFAs. Collectively, our results underscore the potential for leveraging inter-kingdom interactions when designing putative microbiota-based asthma therapeutics.
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Affiliation(s)
- Rozlyn CT Boutin
- Department of Microbiology and Immunology, University of British ColumbiaVancouverCanada
- Michael Smith Laboratories, University of British ColumbiaVancouverCanada
| | - Charisse Petersen
- Michael Smith Laboratories, University of British ColumbiaVancouverCanada
| | - Sarah E Woodward
- Department of Microbiology and Immunology, University of British ColumbiaVancouverCanada
- Michael Smith Laboratories, University of British ColumbiaVancouverCanada
| | | | - Tahereh Bozorgmehr
- Michael Smith Laboratories, University of British ColumbiaVancouverCanada
| | - Rachelle Loo
- Department of Microbiology and Immunology, University of British ColumbiaVancouverCanada
- Michael Smith Laboratories, University of British ColumbiaVancouverCanada
| | - Alina Chalanuchpong
- Department of Microbiology and Immunology, University of British ColumbiaVancouverCanada
- Michael Smith Laboratories, University of British ColumbiaVancouverCanada
| | - Mihai Cirstea
- Department of Microbiology and Immunology, University of British ColumbiaVancouverCanada
- Michael Smith Laboratories, University of British ColumbiaVancouverCanada
| | - Bernard Lo
- Department of Microbiology and Immunology, University of British ColumbiaVancouverCanada
| | - Kelsey E Huus
- Department of Microbiology and Immunology, University of British ColumbiaVancouverCanada
- Michael Smith Laboratories, University of British ColumbiaVancouverCanada
| | - Weronika Barcik
- Michael Smith Laboratories, University of British ColumbiaVancouverCanada
| | - Meghan B Azad
- Children’s Hospital Research Institute of Manitoba and Department of Pediatrics and Child Health, University of ManitobaWinnipegMBCanada
| | - Allan B Becker
- Children’s Hospital Research Institute of Manitoba and Department of Pediatrics and Child Health, University of ManitobaWinnipegMBCanada
| | - Piush J Mandhane
- Department of Pediatrics, University of AlbertaEdmontonCanada
- School of Public Health, University of AlbertaEdmontonCanada
| | | | | | - Padmaja Subbarao
- The Hospital for Sick ChildrenTorontoCanada
- Department of Pediatrics, University of TorontoTorontoCanada
| | - Kelly M McNagny
- Department of Biomedical Engineering, University of British ColumbiaVancouverCanada
- Department of Medical Genetics University of British ColumbiaVancouverCanada
| | - Stuart E Turvey
- Department of Microbiology and Immunology, University of British ColumbiaVancouverCanada
- Department of Pediatrics, University of British ColumbiaVancouverCanada
| | - B Brett Finlay
- Department of Microbiology and Immunology, University of British ColumbiaVancouverCanada
- Michael Smith Laboratories, University of British ColumbiaVancouverCanada
- Department of Biochemistry and Molecular Biology, University of British ColumbiaVancouverCanada
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9
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Fakhruddin KS, Egusa H, Ngo HC, Panduwawala C, Pesee S, Venkatachalam T, Samaranayake LP. Silver diamine fluoride (SDF) used in childhood caries management has potent antifungal activity against oral Candida species. BMC Microbiol 2020; 20:95. [PMID: 32295517 PMCID: PMC7161255 DOI: 10.1186/s12866-020-01776-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2019] [Accepted: 03/30/2020] [Indexed: 12/24/2022] Open
Abstract
Background The microbiome of Severe-Early Childhood Caries (S-ECC), is characterized by an ecosystem comprising bacterial and fungal species, with a predominance of Candida species. Hence, an anti-cariogen effective against both bacteria and fungi would be valuable in the management of S-ECC. Here we evaluate the antifungal effect of silver diamine fluoride (SDF) against 35-clinical yeast isolates (Ten-each of C. albicans, C. krusei, C. tropicalis and five C. glabrata strains) from dentinal caries-lesions from S-ECC. Results Disc-diffusion and time-kill assays as well as MIC50 and MIC90 evaluations against therapeutic concentrations confirmed the broad-spectrum anti-candidal potency of SDF. Ultrastructural images revealed morphologic aberrations of yeast-cell walls on exposure to SDF. All C. krusei and C. glabrata isolates were significantly more sensitive to SDF, relative to the standard antifungal fluconazole. Further, SDF appears to effectively abrogate filamentation of C. albicans even at very low concentrations. Conclusions Our data, for the first time, elucidate the antifungal potency of SDF, in addition to its known antibacterial activity, in the management of S-ECC.
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Affiliation(s)
- Kausar Sadia Fakhruddin
- Department of Preventive and Restorative Dentistry, University City- Sharjah, University of Sharjah, 27272, United Arab Emirates.,Division of Molecular and Regenerative Prosthodontics, Tohoku University Graduate School of Dentistry, 4-1 Seiryo-machi, Aoba-ku, Sendai-city, Miyagi, 980-8575, Japan
| | - Hiroshi Egusa
- Division of Molecular and Regenerative Prosthodontics, Tohoku University Graduate School of Dentistry, 4-1 Seiryo-machi, Aoba-ku, Sendai-city, Miyagi, 980-8575, Japan.
| | - Hien Chi Ngo
- Department of Preventive and Restorative Dentistry, University City- Sharjah, University of Sharjah, 27272, United Arab Emirates
| | - Chamila Panduwawala
- Department of Preventive and Restorative Dentistry, University City- Sharjah, University of Sharjah, 27272, United Arab Emirates
| | - Siripen Pesee
- Faculty of Dentistry, Department of Oral Diagnostic Science, Faculty of Dentistry, Thammasat University, Pathum Thani, Thailand
| | - Thenmozhi Venkatachalam
- Sharjah Institute of Medical Research, University City- Sharjah, University of Sharjah, 27272, United Arab Emirates
| | - Lakshman Perera Samaranayake
- Department of Preventive and Restorative Dentistry, University City- Sharjah, University of Sharjah, 27272, United Arab Emirates. .,The University of Hong Kong, Hong Kong, Special Administrative Region, China.
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10
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Fakhruddin KS, Perera Samaranayake L, Egusa H, Chi Ngo H, Panduwawala C, Venkatachalam T, Kumarappan A, Pesee S. Candida biome of severe early childhood caries (S-ECC) and its cariogenic virulence traits. J Oral Microbiol 2020; 12:1724484. [PMID: 32128040 PMCID: PMC7034489 DOI: 10.1080/20002297.2020.1724484] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2019] [Revised: 12/18/2019] [Accepted: 12/19/2019] [Indexed: 01/04/2023] Open
Abstract
The protected niche of deep-caries lesions is a distinctive ecosystem. We assessed the Candida biome and its cariogenic traits from dentin samples of 50 children with severe-early childhood caries (S-ECC). Asymptomatic, primary molars belonging to International Caries Detection and Assessment-ICDAS caries-code 5 and 6 were analyzed, and C. albicans (10-isolates), C. tropicalis (10), C. krusei (10), and C. glabrata (5) isolated from the lesions were then evaluated for their biofilm formation, acidogenicity, and the production of secreted hydrolases: hemolysins, phospholipase, proteinase and DNase. Candida were isolated from 14/43 ICDAS-5 lesions (32.5%) and 44/57 ICDAS-6 lesions (77.2%). Compared to, ICDAS-5, a significantly higher frequency of multi-species infestation was observed in ICDAS-6 lesions (p=0.001). All four candidal species (above) showed prolific biofilm growth, and an equal potency for tooth demineralization. A significant interspecies difference in the mean phospholipase, as well as proteinase activity was noted (p < 0.05), with C. albicans being the predominant hydrolase producer. Further, a positive correlation between phospholipase and proteinase activity of Candida-isolates was noted (r = 0.818, p < 0.001). Our data suggest that candidal mycobiota with their potent cariogenic traits may significantly contribute to the development and progression of S-ECC.
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Affiliation(s)
| | - Lakshman Perera Samaranayake
- Department of Preventive and Restorative Dentistry, University of Sharjah, Sharjah, UAE.,Faculty of Dentistry, The University of Hong Kong, Hong Kong Special Administrative Region, China
| | - Hiroshi Egusa
- Division of Molecular and Regenerative Prosthodontics, Tohoku University Graduate School of Dentistry, Sendai, Japan
| | - Hien Chi Ngo
- Department of Preventive and Restorative Dentistry, University of Sharjah, Sharjah, UAE
| | - Chamila Panduwawala
- Department of Preventive and Restorative Dentistry, University of Sharjah, Sharjah, UAE
| | | | - Allagappan Kumarappan
- Research Institute of Medical and Health Sciences, University of Sharjah, Sharjah, UAE
| | - Siripen Pesee
- Faculty of Dentistry, Thammasat University, Pathum Thani, Thailand
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11
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Arastehfar A, Wickes BL, Ilkit M, Pincus DH, Daneshnia F, Pan W, Fang W, Boekhout T. Identification of Mycoses in Developing Countries. J Fungi (Basel) 2019; 5:E90. [PMID: 31569472 PMCID: PMC6958481 DOI: 10.3390/jof5040090] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2019] [Revised: 09/22/2019] [Accepted: 09/26/2019] [Indexed: 12/12/2022] Open
Abstract
Extensive advances in technology offer a vast variety of diagnostic methods that save time and costs, but identification of fungal species causing human infections remains challenging in developing countries. Since the echinocandins, antifungals widely used to treat invasive mycoses, are still unavailable in developing countries where a considerable number of problematic fungal species are present, rapid and reliable identification is of paramount importance. Unaffordability, large footprints, lack of skilled personnel, and high costs associated with maintenance and infrastructure are the main factors precluding the establishment of high-precision technologies that can replace inexpensive yet time-consuming and inaccurate phenotypic methods. In addition, point-of-care lateral flow assay tests are available for the diagnosis of Aspergillus and Cryptococcus and are highly relevant for developing countries. An Aspergillus galactomannan lateral flow assay is also now available. Real-time PCR remains difficult to standardize and is not widespread in countries with limited resources. Isothermal and conventional PCR-based amplification assays may be alternative solutions. The combination of real-time PCR and serological assays can significantly increase diagnostic efficiency. However, this approach is too expensive for medical institutions in developing countries. Further advances in next-generation sequencing and other innovative technologies such as clustered regularly interspaced short palindromic repeats (CRISPR)-based diagnostic tools may lead to efficient, alternate methods that can be used in point-of-care assays, which may supplement or replace some of the current technologies and improve the diagnostics of fungal infections in developing countries.
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Affiliation(s)
- Amir Arastehfar
- Westerdijk Fungal Biodiversity Institute, 3584 CT Utrecht, The Netherlands.
| | - Brian L Wickes
- The Department of Microbiology, Immunology, and Molecular Genetics, The University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA.
| | - Macit Ilkit
- Division of Mycology, Department of Microbiology, Faculty of Medicine, University of Çukurova, Adana 01330, Turkey.
| | | | - Farnaz Daneshnia
- Westerdijk Fungal Biodiversity Institute, 3584 CT Utrecht, The Netherlands.
| | - Weihua Pan
- Department of Dermatology, Shanghai Key Laboratory of Molecular Medical Mycology, Shanghai Institute of Medical Mycology, Second Military Medical University, Shanghai 200003, China.
| | - Wenjie Fang
- Department of Dermatology, Shanghai Key Laboratory of Molecular Medical Mycology, Shanghai Institute of Medical Mycology, Second Military Medical University, Shanghai 200003, China.
| | - Teun Boekhout
- Westerdijk Fungal Biodiversity Institute, 3584 CT Utrecht, The Netherlands.
- Department of Dermatology, Shanghai Key Laboratory of Molecular Medical Mycology, Shanghai Institute of Medical Mycology, Second Military Medical University, Shanghai 200003, China.
- Institute of Biodiversity and Ecosystem Dynamics, University of Amsterdam, 1012 WX Amsterdam, The Netherlands.
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12
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Franco-Duarte R, Černáková L, Kadam S, Kaushik KS, Salehi B, Bevilacqua A, Corbo MR, Antolak H, Dybka-Stępień K, Leszczewicz M, Relison Tintino S, Alexandrino de Souza VC, Sharifi-Rad J, Coutinho HDM, Martins N, Rodrigues CF. Advances in Chemical and Biological Methods to Identify Microorganisms-From Past to Present. Microorganisms 2019; 7:E130. [PMID: 31086084 PMCID: PMC6560418 DOI: 10.3390/microorganisms7050130] [Citation(s) in RCA: 168] [Impact Index Per Article: 33.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2019] [Revised: 04/30/2019] [Accepted: 05/08/2019] [Indexed: 12/12/2022] Open
Abstract
Fast detection and identification of microorganisms is a challenging and significant feature from industry to medicine. Standard approaches are known to be very time-consuming and labor-intensive (e.g., culture media and biochemical tests). Conversely, screening techniques demand a quick and low-cost grouping of bacterial/fungal isolates and current analysis call for broad reports of microorganisms, involving the application of molecular techniques (e.g., 16S ribosomal RNA gene sequencing based on polymerase chain reaction). The goal of this review is to present the past and the present methods of detection and identification of microorganisms, and to discuss their advantages and their limitations.
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Affiliation(s)
- Ricardo Franco-Duarte
- CBMA (Centre of Molecular and Environmental Biology), Department of Biology, University of Minho, 4710-057 Braga, Portugal.
- Institute of Science and Innovation for Bio-Sustainability (IB-S), University of Minho, 4710-057 Braga, Portugal.
| | - Lucia Černáková
- Department of Microbiology and Virology, Faculty of Natural Sciences, Comenius University in Bratislava, Ilkovičova 6, 842 15 Bratislava, Slovakia.
| | - Snehal Kadam
- Ramalingaswami Re-entry Fellowship, Department of Biotechnology, Government of India, India.
| | - Karishma S Kaushik
- Ramalingaswami Re-entry Fellowship, Department of Biotechnology, Government of India, India.
| | - Bahare Salehi
- Student Research Committee, School of Medicine, Bam University of Medical Sciences, Bam 14665-354, Iran.
| | - Antonio Bevilacqua
- Department of the Science of Agriculture, Food and Environment, University of Foggia, 71121 Foggia, Italy.
| | - Maria Rosaria Corbo
- Department of the Science of Agriculture, Food and Environment, University of Foggia, 71121 Foggia, Italy.
| | - Hubert Antolak
- Institute of Fermentation Technology and Microbiology, Department of Biotechnology and Food Science, Lodz University of Technology, Wolczanska 171/173, 90-924 Lodz, Poland.
| | - Katarzyna Dybka-Stępień
- Institute of Fermentation Technology and Microbiology, Department of Biotechnology and Food Science, Lodz University of Technology, Wolczanska 171/173, 90-924 Lodz, Poland.
| | - Martyna Leszczewicz
- Laboratory of Industrial Biotechnology, Bionanopark Ltd, Dubois 114/116, 93-465 Lodz, Poland.
| | - Saulo Relison Tintino
- Laboratory of Microbiology and Molecular Biology (LMBM), Department of Biological Chemistry/CCBS/URCA, 63105-000 Crato, Brazil.
| | | | - Javad Sharifi-Rad
- Zabol Medicinal Plants Research Center, Zabol University of Medical Sciences, Zabol 61615-585, Iran.
| | - Henrique Douglas Melo Coutinho
- Laboratory of Microbiology and Molecular Biology (LMBM), Department of Biological Chemistry/CCBS/URCA, 63105-000 Crato, Brazil.
| | - Natália Martins
- Faculty of Medicine, University of Porto, Alameda Professor Hernâni Monteiro, 4200-319 Porto, Portugal.
- Institute for Research and Innovation in Health (i3S), University of Porto, 4200-135 Porto, Portugal.
| | - Célia F Rodrigues
- LEPABE⁻Dep. of Chemical Engineering, Faculty of Engineering, University of Porto, Rua Dr. Roberto Frias, s/n, 4200-465 Porto, Portugal.
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Reagent-Free Identification of Clinical Yeasts by Use of Attenuated Total Reflectance Fourier Transform Infrared Spectroscopy. J Clin Microbiol 2019; 57:JCM.01739-18. [PMID: 30787141 DOI: 10.1128/jcm.01739-18] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2018] [Accepted: 02/06/2019] [Indexed: 12/23/2022] Open
Abstract
Invasive fungal infections by opportunistic yeasts have increased concomitantly with the growth of an immunocompromised patient population. Misidentification of yeasts can lead to inappropriate antifungal treatment and complications. Attenuated total reflectance Fourier transform infrared (ATR-FTIR) spectroscopy is a promising method for rapid and accurate identification of microorganisms. ATR-FTIR spectroscopy is a standalone, inexpensive, reagent-free technique that provides results within minutes after initial culture. In this study, a comprehensive spectral reference database of 65 clinically relevant yeast species was constructed and tested prospectively on spectra recorded (from colonies taken from culture plates) for 318 routine yeasts isolated from various body fluids and specimens received from 38 microbiology laboratories over a 4-month period in our clinical laboratory. ATR-FTIR spectroscopy attained comparable identification performance with matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS). In a preliminary validation of the ATR-FTIR method, correct identification rates of 100% and 95.6% at the genus and species levels, respectively, were achieved, with 3.5% unidentified and 0.9% misidentified. By expanding the number of spectra in the spectral reference database for species for which isolates could not be identified or had been misidentified, we were able to improve identification at the species level to 99.7%. Thus, ATR-FTIR spectroscopy provides a new standalone method that can rival MALDI-TOF MS for the accurate identification of a broad range of medically important yeasts. The simplicity of the ATR-FTIR spectroscopy workflow favors its use in clinical laboratories for timely and low-cost identification of life-threatening yeast strains for appropriate treatment.
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Barbosa AH, Damasceno JL, Casemiro LA, Martins CHG, Pires RH, Candido RC. Susceptibility to Oral Antiseptics and Virulence Factors Ex Vivo Associated with Candida spp. Isolated from Dental Prostheses. J Prosthodont 2019; 28:398-408. [PMID: 30768738 DOI: 10.1111/jopr.13037] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/03/2019] [Indexed: 12/16/2022] Open
Abstract
PURPOSE To isolate Candida spp. from dental prosthesis users' saliva and to evaluate the isolates for the presence of several virulence factors. This research also aimed to investigate the antifungal activity of 3 commercial mouthwashes/oral antiseptic formulations containing 0.12% chlorhexidine, 0.07% cetylpyridinium, or 0.075% cetylpyridinium against planktonic and sessile (biofilm mode) yeast cells. MATERIALS AND METHODS Forty-three Candida yeasts were isolated from 32 of 70 selected patients, and the virulence factors of C. albicans, C. krusei, C. glabrata, C. tropicalis, and C. parapsilosis species were investigated by polymerase chain reaction (PCR) and proteinase in plates. Minimum inhibitory concentration (MIC), and in vitro biofilm assay evaluated the antifungal activity of antiseptics. RESULTS C. albicans, C. krusei, C. glabrata, C. tropicalis, and C. parapsilosis were detected in mono and mixed cultures. Only C. albicans displayed genes related to adhesion and proteinases (ALS2, ALS3, SAP1, and SAP3). The aspartate proteinase activity was found in 60.46% of isolates. The tested antiseptic formulations exhibited a MIC less than 1.25% toward yeasts in the planktonic mode. According to XTT ((2,3-bis(2-methoxy-4-nitro-5-sulfophenyl)-2H-tetrazolium-5-carboxanilide) assay results, most Candida isolates and all mixed cultures formed biofilms within 24 hours. The evaluated antiseptic formulations were also active against biofilms. CONCLUSION Most virulence factors investigated here (ALS2, ALS3, SAP1, and SAP3) occurred in the majority of the Candida spp. isolates, especially in C. albicans. The tested mouthwash formulations were effective against all the yeast isolates in both the planktonic and sessile growth modes. Developing alternative therapies that can avoid or control biofilm formation is necessary to prevent oral candidiasis and other Candida spp. infections.
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Affiliation(s)
| | | | | | | | - Regina Helena Pires
- Laboratory of Research in Applied Microbiology (LAPEMA), University of Franca, São Paulo, Brazil
| | - Regina Célia Candido
- School of Pharmaceutical Sciences, University of São Paulo, Ribeirão Preto, Brazil
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15
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Fidler G, Leiter E, Kocsube S, Biro S, Paholcsek M. Validation of a simplex PCR assay enabling reliable identification of clinically relevant Candida species. BMC Infect Dis 2018; 18:393. [PMID: 30103686 PMCID: PMC6090785 DOI: 10.1186/s12879-018-3283-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2017] [Accepted: 07/31/2018] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Fungal bloodstream infections (BSI) may be serious and are associated with drastic rise in mortality and health care costs. Candida spp. are the predominant etiological agent of fungal sepsis. The prompt and species-level identification of Candida may influence patient outcome and survival. The aim of this study was to develop and evaluate the CanTub-simplex PCR assay coupled with Tm calling and subsequent high resolution melting (HRM) analysis to barcode seven clinically relevant Candida species. METHODS Efficiency, coefficient of correlation and the limit of reliable detection were estimated on purified Candida EDTA-whole blood (WB) reference panels seeded with Candida albicans, Candida glabrata, Candida parapsilosis, Candida tropicalis, Candida krusei, Candida guilliermondii, Candida dubliniensis cells in a 6-log range. Discriminatory power was measured on EDTA-WB clinical panels on three different PCR platforms; LightCycler®96, LightCycler® Nano, LightCycler® 2.0. Inter- and intra assay consistencies were also calculated. RESULTS The limit of reliable detection proved to be 0.2-2 genomic equivalent and the method was reliable on broad concentration ranges (106-10 CFU) providing distinctive melting peaks and characteristic HRM curves. The diagnostic accuracy of the discrimination proved to be the best on Roche LightCycler®2.0 platform. Repeatability was tested and proved to be % C.V.: 0.14 ± 0.06 on reference- and % C.V.: 0.14 ± 0.02 on clinical-plates accounting for a very high accuracy. Reproducibility was % C.V.: 0.11 between reference- and % C.V.: 0.12between clinical-panels which is highly acceptable. CONCLUSION Our assay demonstrates recent advances on Tm calling and HRM analysis for the molecular identification of relevant Candida species. This unique, simplex PCR assay may be capable to outperform conventional phenotypic methods by reducing time and providing accurate and reliable results directly from blood (2 h) or from whole blood culture bottles (12-24 h).
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Affiliation(s)
- Gabor Fidler
- Faculty of Medicine, Department of Human Genetics, University of Debrecen, Nagyerdei krt. 98, Debrecen, H-4032, Hungary
| | - Eva Leiter
- Faculty of Science and Technology, Department of Biotechnology and Microbiology, University of Debrecen, Debrecen, Hungary
| | - Sandor Kocsube
- Faculty of Science and Informatics, Department of Microbiology, University of Szeged, Szeged, Hungary
| | - Sandor Biro
- Faculty of Medicine, Department of Human Genetics, University of Debrecen, Nagyerdei krt. 98, Debrecen, H-4032, Hungary
| | - Melinda Paholcsek
- Faculty of Medicine, Department of Human Genetics, University of Debrecen, Nagyerdei krt. 98, Debrecen, H-4032, Hungary.
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16
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[new multiplex PCR for species-specific diagnosis of human candidiasis]. BIOMEDICA 2017; 37:200-208. [PMID: 28527284 DOI: 10.7705/biomedica.v37i2.3202] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 12/22/2015] [Revised: 06/01/2016] [Indexed: 11/21/2022]
Abstract
INTRODUCTION Candidiases is a group of opportunistic infections caused by yeasts belonging to the genus Candida. Candida albicans is the most prevalent species in both superficial and deep infections, however, the clinical importance of non-albicans Candida has increased during the last decade, driving an urgent need for diagnostic tests that allow for species-level resolution and selection of the optimum therapeutic approach. OBJECTIVE To design and to optimize a new multiplex PCR assay for the simultaneous identification of the five most relevant species of Candida involved in human candidiasis etiology. MATERIALS AND METHODS For primers design, the physical and thermodynamic restrictions that affect multiplex PCR performance were analyzed using Gene Runner and Mult-PSOS. As templates, the internal transcribed region 2 (ITR2) was selected for C. albicans (AJ249486.1), and topoisomerase II (TOPII) for C. parasilopsis (AB049144.1), C. krusei (AB049139.1), C. tropicalis (AB049141.1), and C. guillermondii (AB049145.1). We used ATCC strains of all these five species and clinical isolates as templates. RESULTS We designed ten oligonucleotides for the simultaneous amplification of the Candida species. The electrophoresis band profile was: C. albicans (206 bp), C. guillermondii (244 bp), C. tropicalis (474 bp), C. parasilopsis (558 bp), and C. krusei (419 bp). CONCLUSION The new multiplex PCR assay designed in this study allowed a simultaneous and efficient amplification of the amplicons corresponding to the five species of Candida under study, with an adequate resolution in standard agarose gel.
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17
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Sampath A, Weerasekera M, Gunasekara C, Dilhari A, Bulugahapitiya U, Fernando N. A sensitive and a rapid multiplex polymerase chain reaction for the identification of Candida species in concentrated oral rinse specimens in patients with diabetes. Acta Odontol Scand 2017; 75:113-122. [PMID: 27960572 DOI: 10.1080/00016357.2016.1265146] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
OBJECTIVES Oral candidiasis is being frequently recognized in patients with diabetes, and is associated with multiple pathogens including Candida albicans, Candida parapsilosis, Candida glabrata and Candida tropicalis. The aim of this study was to evaluate a usefulness of a Multiplex Polymerase Chain Reaction as a rapid diagnostic tool for identification of four oral Candida pathogens in patients with diabetes. MATERIALS AND METHODS A multiplex PCR was optimized to identify four Candida species in concentrated oral rinse samples. Common reverse primer, ITS4 and four species-specific forward primers targeting ITS1 and ITS2 regions of yeast genome were used. Species-specific single amplicon were detected by agarose gel electrophoresis. Performance efficacy of multiplex PCR was compared with phenotypic identification. RESULTS Out of 100 oral rinse samples, 72 were culture positive and of these 43 were at risk of oral Candida infection (>600cfu/ml). Multiple Candida species including C. albicans, C. parapsilosis and C. tropicalis were identified in 22 samples which had risk of oral Candida infection. In total, 85 patients were positive for Candida by multiplex PCR and of them 49 had multiple Candida species. All 43 colonized specimens were also positive by multiplex PCR. C. albicans was the most predominant organism (75/85) followed by C. parapsilosis (47/85), C. tropicalis (17/85) and C. glabrata (6/85). In specimens with multiple species, the two most common organisms were C. albicans and C. parapsilosis. Multiplex PCR yielded a sensitivity of 10 Candida cells/ml of oral rinse sample. CONCLUSIONS Multiplex PCR is found to be rapid, sensitive and specific than phenotypic identification methods in discriminating multiple Candida species in oral rinse specimens.
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Affiliation(s)
- Asanga Sampath
- Department of Microbiology, Faculty of Medical Sciences, University of Sri Jayewardenepura, Nugegoda, Sri Lanka
| | - Manjula Weerasekera
- Department of Microbiology, Faculty of Medical Sciences, University of Sri Jayewardenepura, Nugegoda, Sri Lanka
| | - Chinthika Gunasekara
- Department of Microbiology, Faculty of Medical Sciences, University of Sri Jayewardenepura, Nugegoda, Sri Lanka
| | - Ayomi Dilhari
- Department of Microbiology, Faculty of Medical Sciences, University of Sri Jayewardenepura, Nugegoda, Sri Lanka
| | - Uditha Bulugahapitiya
- Diabetes and Endocrinology Unit, Colombo South Teaching Hospital, Dehiwala, Sri Lanka
| | - Neluka Fernando
- Department of Microbiology, Faculty of Medical Sciences, University of Sri Jayewardenepura, Nugegoda, Sri Lanka
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Heisel T, Podgorski H, Staley CM, Knights D, Sadowsky MJ, Gale CA. Complementary amplicon-based genomic approaches for the study of fungal communities in humans. PLoS One 2015; 10:e0116705. [PMID: 25706290 PMCID: PMC4338280 DOI: 10.1371/journal.pone.0116705] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2014] [Accepted: 12/14/2014] [Indexed: 12/12/2022] Open
Abstract
Recent studies highlight the importance of intestinal fungal microbiota in the development of human disease. Infants, in particular, are an important population in which to study intestinal microbiomes because microbial community structure and dynamics during this formative window of life have the potential to influence host immunity and metabolism. When compared to bacteria, much less is known about the early development of human fungal communities, owing partly to their lower abundance and the relative lack of established molecular and taxonomic tools for their study. Herein, we describe the development, validation, and use of complementary amplicon-based genomic strategies to characterize infant fungal communities and provide quantitative information about Candida, an important fungal genus with respect to intestinal colonization and human disease. Fungal communities were characterized from 11 infant fecal samples using primers that target the internal transcribed spacer (ITS) 2 locus, a region that provides taxonomic discrimination of medically relevant fungi. Each sample yielded an average of 27,553 fungal sequences and Candida albicans was the most abundant species identified by sequencing and quantitative PCR (qPCR). Low numbers of Candida krusei and Candida parapsilosis sequences were observed in several samples, but their presence was detected by species-specific qPCR in only one sample, highlighting a challenge inherent in the study of low-abundance organisms. Overall, the sequencing results revealed that infant fecal samples had fungal diversity comparable to that of bacterial communities in similar-aged infants, which correlated with the relative abundance of C. albicans. We conclude that targeted sequencing of fungal ITS2 amplicons in conjunction with qPCR analyses of specific fungi provides an informative picture of fungal community structure in the human intestinal tract. Our data suggests that the infant intestine harbors diverse fungal species and is consistent with prior culture-based analyses showing that the predominant fungus in the infant intestine is C. albicans.
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Affiliation(s)
- Timothy Heisel
- Department of Pediatrics, University of Minnesota, Minneapolis, MN, 55454, United States of America
| | - Heather Podgorski
- Department of Pediatrics, University of Minnesota, Minneapolis, MN, 55454, United States of America
| | - Christopher M. Staley
- Biotechnology Institute, University of Minnesota, St. Paul, MN, 55108, United States of America
| | - Dan Knights
- Biotechnology Institute, University of Minnesota, St. Paul, MN, 55108, United States of America
- Department of Computer Science and Engineering, University of Minnesota, Minneapolis, MN, 55455, United States of America
| | - Michael J. Sadowsky
- Biotechnology Institute, University of Minnesota, St. Paul, MN, 55108, United States of America
- Department of Soil, Water, and Climate, University of Minnesota, St. Paul, MN, 55108, United States of America
| | - Cheryl A. Gale
- Department of Pediatrics, University of Minnesota, Minneapolis, MN, 55454, United States of America
- Department of Genetics, Cell Biology and Development, University of Minnesota, Minneapolis, MN, 55455, United States of America
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Taira CL, Okay TS, Delgado AF, Ceccon MEJR, de Almeida MTG, Del Negro GMB. A multiplex nested PCR for the detection and identification of Candida species in blood samples of critically ill paediatric patients. BMC Infect Dis 2014; 14:406. [PMID: 25047415 PMCID: PMC4223582 DOI: 10.1186/1471-2334-14-406] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2014] [Accepted: 07/10/2014] [Indexed: 01/30/2023] Open
Abstract
BACKGROUND Nosocomial candidaemia is associated with high mortality rates in critically ill paediatric patients; thus, the early detection and identification of the infectious agent is crucial for successful medical intervention. The PCR-based techniques have significantly increased the detection of Candida species in bloodstream infections. In this study, a multiplex nested PCR approach was developed for candidaemia detection in neonatal and paediatric intensive care patients. METHODS DNA samples from the blood of 54 neonates and children hospitalised in intensive care units with suspected candidaemia were evaluated by multiplex nested PCR with specific primers designed to identify seven Candida species, and the results were compared with those obtained from blood cultures. RESULTS The multiplex nested PCR had a detection limit of four Candida genomes/mL of blood for all Candida species. Blood cultures were positive in 14.8% of patients, whereas the multiplex nested PCR was positive in 24.0% of patients, including all culture-positive patients. The results obtained with the molecular technique were available within 24 hours, and the assay was able to identify Candida species with 100% of concordance with blood cultures. Additionally, the multiplex nested PCR detected dual candidaemia in three patients. CONCLUSIONS Our proposed PCR method may represent an effective tool for the detection and identification of Candida species in the context of candidaemia diagnosis in children, showing highly sensitive detection and the ability to identify the major species involved in this infection.
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Affiliation(s)
| | | | | | | | | | - Gilda Maria Barbaro Del Negro
- Laboratory of Medical Mycology (LIM-53), Clinical Dermartology Division, Hospital das Clínicas da Faculdade de Medicina da Universidade de São Paulo (HCFMUSP) and Instituto de Medicina Tropical da Universidade de São Paulo (IMT-USP), Av, Dr, Enéas Carvalho de Aguiar, 500, Andar térreo, Predio 2, CEP, 05403-900 São Paulo, SP, Brazil.
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Alnuaimi A, Wiesenfeld D, O'Brien-Simpson N, Reynolds E, Peng B, McCullough M. The development and validation of a rapid genetic method for species identification and genotyping of medically important fungal pathogens using high-resolution melting curve analysis. Mol Oral Microbiol 2014; 29:117-30. [DOI: 10.1111/omi.12050] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/12/2014] [Indexed: 11/26/2022]
Affiliation(s)
- A.D. Alnuaimi
- Melbourne Dental School; Oral Health CRC; The University of Melbourne; Melbourne Vic. Australia
| | - D. Wiesenfeld
- Melbourne Dental School; Oral Health CRC; The University of Melbourne; Melbourne Vic. Australia
- Head and Neck Oncology; The Royal Melbourne Hospital; Melbourne Vic. Australia
| | - N.M. O'Brien-Simpson
- Melbourne Dental School; Oral Health CRC; The University of Melbourne; Melbourne Vic. Australia
| | - E.C. Reynolds
- Melbourne Dental School; Oral Health CRC; The University of Melbourne; Melbourne Vic. Australia
| | - B. Peng
- Melbourne Dental School; Oral Health CRC; The University of Melbourne; Melbourne Vic. Australia
| | - M.J. McCullough
- Melbourne Dental School; Oral Health CRC; The University of Melbourne; Melbourne Vic. Australia
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21
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Neppelenbroek KH, Seó RS, Urban VM, Silva S, Dovigo LN, Jorge JH, Campanha NH. Identification of
Candida
species in the clinical laboratory: a review of conventional, commercial, and molecular techniques. Oral Dis 2013; 20:329-44. [DOI: 10.1111/odi.12123] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2013] [Revised: 03/25/2013] [Accepted: 04/15/2013] [Indexed: 01/24/2023]
Affiliation(s)
- KH Neppelenbroek
- Department of Prosthodontics Bauru Dental School University of São Paulo‐USP Bauru São PauloBrazil
| | - RS Seó
- Department of Prosthodontics Varzea Grande School of Dentistry Varzea Grande Mato GrossoBrazil
| | - VM Urban
- Department of Dentistry Ponta Grossa State University‐UEPG Ponta Grossa Paraná Brazil
| | - S Silva
- Department of Biological Engineering Institute for Biotechnology and Bioengineering University of Minho Braga Portugal
| | - LN Dovigo
- Department of Social Dentistry Araraquara Dental School UNESP – Univ. Estadual Paulista Araraquara São PauloBrazil
| | - JH Jorge
- Department of Dental Materials and Prosthodontics Araraquara Dental School UNESP – Univ. Estadual Paulista Araraquara São Paulo Brazil
| | - NH Campanha
- Department of Dentistry Ponta Grossa State University‐UEPG Ponta Grossa Paraná Brazil
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22
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Weerasekera MM, Sissons CH, Wong L, Anderson S, Holmes AR, Cannon RD. Use of denaturing gradient gel electrophoresis for the identification of mixed oral yeasts in human saliva. J Med Microbiol 2012; 62:319-330. [PMID: 23065546 DOI: 10.1099/jmm.0.050237-0] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A PCR-denaturing gradient gel electrophoresis (DGGE) method was established for the simultaneous presumptive identification of multiple yeast species commonly present in the oral cavity. Published primer sets targeting different regions of the Saccharomyces cerevisiae 26-28S rRNA gene (denoted primer sets N and U) and the 18S rRNA gene (primer set E) were evaluated with ten Candida and four non-Candida yeast species, and twenty Candida albicans isolates. Optimized PCR-DGGE conditions using primer set N were applied to presumptively identify, by band matching, yeasts in the saliva of 25 individuals. Identities were confirmed by DNA sequencing and compared with those using CHROMagar Candida culture. All primer sets yielded detectable DGGE bands for all species tested. Primer set N yielded mainly single bands and could distinguish all species examined, including differentiating Candida dubliniensis from C. albicans. Primer set U was less discriminatory among species but yielded multiple bands that distinguished subspecies groups within C. albicans. Primer set E gave poor yeast discrimination. DGGE analysis identified yeasts in 17 of the 25 saliva samples. Six saliva samples contained two yeast species: three contained C. albicans and three C. dubliniensis. C. dubliniensis was present alone in one saliva sample (total prevalence 16 %). CHROMagar culture detected yeasts in 16 of the yeast-containing saliva samples and did not enable identification of 7 yeast species identified by DGGE. In conclusion, DGGE identification of oral yeast species with primer set N is a relatively fast and reliable method for the simultaneous presumptive identification of mixed yeasts in oral saliva samples.
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Affiliation(s)
- Manjula M Weerasekera
- Department of Microbiology, Faculty of Medical Sciences, University of Sri Jayewardenepura, Nugegoda 10250, Sri Lanka.,Dental Research Group, School of Medicine and Health Sciences, University of Otago, Wellington 6242, New Zealand
| | - Chris H Sissons
- Dental Research Group, School of Medicine and Health Sciences, University of Otago, Wellington 6242, New Zealand
| | - Lisa Wong
- Dental Research Group, School of Medicine and Health Sciences, University of Otago, Wellington 6242, New Zealand
| | - Sally Anderson
- Dental Research Group, School of Medicine and Health Sciences, University of Otago, Wellington 6242, New Zealand
| | - Ann R Holmes
- Department of Oral Sciences, Faculty of Dentistry, University of Otago, Dunedin 9016, New Zealand
| | - Richard D Cannon
- Department of Oral Sciences, Faculty of Dentistry, University of Otago, Dunedin 9016, New Zealand
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23
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Prevalence of Dermatomycosis in a Brazilian Tertiary Care Hospital. Mycopathologia 2012; 174:489-97. [DOI: 10.1007/s11046-012-9576-1] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2012] [Accepted: 08/14/2012] [Indexed: 10/28/2022]
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24
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Ahmad S, Khan Z. Invasive candidiasis: A review of nonculture-based laboratory diagnostic methods. Indian J Med Microbiol 2012; 30:264-9. [DOI: 10.4103/0255-0857.99482] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
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25
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Silva S, Negri M, Henriques M, Oliveira R, Williams DW, Azeredo J. Candida glabrata, Candida parapsilosisandCandida tropicalis: biology, epidemiology, pathogenicity and antifungal resistance. FEMS Microbiol Rev 2012; 36:288-305. [DOI: 10.1111/j.1574-6976.2011.00278.x] [Citation(s) in RCA: 578] [Impact Index Per Article: 48.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
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26
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Schell WA, Benton JL, Smith PB, Poore M, Rouse JL, Boles DJ, Johnson MD, Alexander BD, Pamula VK, Eckhardt AE, Pollack MG, Benjamin DK, Perfect JR, Mitchell TG. Evaluation of a digital microfluidic real-time PCR platform to detect DNA of Candida albicans in blood. Eur J Clin Microbiol Infect Dis 2012; 31:2237-45. [PMID: 22327343 DOI: 10.1007/s10096-012-1561-6] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2011] [Accepted: 01/18/2012] [Indexed: 11/24/2022]
Abstract
Species of Candida frequently cause life-threatening infections in neonates, transplant and intensive care unit (ICU) patients, and others with compromised host defenses. The successful management of systemic candidiasis depends upon early, rapid diagnosis. Blood cultures are the standard diagnostic method, but identification requires days and less than half of the patients are positive. These limitations may be eliminated by using real-time polymerase chain reaction (PCR) to detect Candida DNA in the blood specimens of patients at risk. Here, we optimized a PCR protocol to detect 5-10 yeasts in low volumes of simulated and clinical specimens. We also used a mouse model of systemic candidiasis and determined that candidemia is optimally detectable during the first few days after infection. However, PCR tests are often costly, labor-intensive, and inconvenient for routine use. To address these obstacles, we evaluated the innovative microfluidic real-time PCR platform (Advanced Liquid Logic, Inc.), which has the potential for full automation and rapid turnaround. Eleven and nine of 16 specimens from individual patients with culture-proven candidemia tested positive for C. albicans DNA by conventional and microfluidic real-time PCR, respectively, for a combined sensitivity of 94%. The microfluidic platform offers a significant technical advance in the detection of microbial DNA in clinical specimens.
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Affiliation(s)
- W A Schell
- Division of Infectious Diseases, Department of Medicine, Duke University Medical Center, Durham, NC, USA
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27
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Ruhnke M, Rickerts V, Cornely OA, Buchheidt D, Glöckner A, Heinz W, Höhl R, Horré R, Karthaus M, Kujath P, Willinger B, Presterl E, Rath P, Ritter J, Glasmacher A, Lass-Flörl C, Groll AH. Diagnosis and therapy of Candida infections: joint recommendations of the German Speaking Mycological Society and the Paul-Ehrlich-Society for Chemotherapy. Mycoses 2011; 54:279-310. [PMID: 21672038 DOI: 10.1111/j.1439-0507.2011.02040.x] [Citation(s) in RCA: 106] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Invasive Candida infections are important causes of morbidity and mortality in immunocompromised and hospitalised patients. This article provides the joint recommendations of the German-speaking Mycological Society (Deutschsprachige Mykologische Gesellschaft, DMyKG) and the Paul-Ehrlich-Society for Chemotherapy (PEG) for diagnosis and treatment of invasive and superficial Candida infections. The recommendations are based on published results of clinical trials, case-series and expert opinion using the evidence criteria set forth by the Infectious Diseases Society of America (IDSA). Key recommendations are summarised here: The cornerstone of diagnosis remains the detection of the organism by culture with identification of the isolate at the species level; in vitro susceptibility testing is mandatory for invasive isolates. Options for initial therapy of candidaemia and other invasive Candida infections in non-granulocytopenic patients include fluconazole or one of the three approved echinocandin compounds; liposomal amphotericin B and voriconazole are secondary alternatives because of their less favourable pharmacological properties. In granulocytopenic patients, an echinocandin or liposomal amphotericin B is recommended as initial therapy based on the fungicidal mode of action. Indwelling central venous catheters serve as a main source of infection independent of the pathogenesis of candidaemia in the individual patients and should be removed whenever feasible. Pre-existing immunosuppressive treatment, particularly by glucocorticosteroids, ought to be discontinued, if feasible, or reduced. The duration of treatment for uncomplicated candidaemia is 14 days following the first negative blood culture and resolution of all associated symptoms and findings. Ophthalmoscopy is recommended prior to the discontinuation of antifungal chemotherapy to rule out endophthalmitis or chorioretinitis. Beyond these key recommendations, this article provides detailed recommendations for specific disease entities, for antifungal treatment in paediatric patients as well as a comprehensive discussion of epidemiology, clinical presentation and emerging diagnostic options of invasive and superficial Candida infections.
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Affiliation(s)
- Markus Ruhnke
- Medizinische Klinik m S Onkologie u Hämatologie, Charité Universitätsmedizin, Charité, Campus Mitte, Berlin, Germany.
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28
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Muir A, Harrison E, Wheals A. A multiplex set of species-specific primers for rapid identification of members of the genus Saccharomyces. FEMS Yeast Res 2011; 11:552-63. [PMID: 22093682 DOI: 10.1111/j.1567-1364.2011.00745.x] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2010] [Revised: 07/16/2011] [Accepted: 07/21/2011] [Indexed: 11/30/2022] Open
Abstract
The Saccharomyces genus (previously Saccharomyces sensu stricto) formally comprises Saccharomyces arboricola, Saccharomyces bayanus, Saccharomyces cariocanus, Saccharomyces cerevisiae, Saccharomyces kudriavzevii, Saccharomyces mikatae, Saccharomyces paradoxus and Saccharomyces pastorianus. Species-specific primer pairs that produce a single band of known and different product size have been developed for each member of the clade with the exception of S. pastorianus, which is a polyphyletic allopolyploid hybrid only found in lager breweries, and for which signature sequences could not be reliably created. Saccharomyces cariocanus is now regarded as an American variant of S. paradoxus, and accordingly a single primer pair that recognizes both species was developed. A different orthologous and essential housekeeping gene was used to detect each species, potentially avoiding competition between PCR primers and overlap between amplicons. In multiplex format, two or more different species could be identified in a single reaction; double and triple hybrids could not always be correctly identified. Forty-two unidentified yeasts from sugar cane juice fermentations were correctly identified as S. cerevisiae. A colony PCR method was developed that is rapid, robust, inexpensive and capable of automation, requires no mycological expertise on the part of the user and is thus useful for large-scale preliminary screens.
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Affiliation(s)
- Alastair Muir
- Department of Biology and Biochemistry, University of Bath, Bath, UK
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30
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High rate of Exophiala dermatitidis recovery in the airways of patients with cystic fibrosis is associated with pancreatic insufficiency. J Clin Microbiol 2011; 49:1004-9. [PMID: 21209163 DOI: 10.1128/jcm.01899-10] [Citation(s) in RCA: 81] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The black-pigmented fungus Exophiala dermatitidis is considered to be a harmless colonizer of the airways of cystic fibrosis (CF) patients. The aim of this study was to establish the recovery rate of E. dermatitidis in respiratory specimens from CF patients, transplant recipients, and subjects with other respiratory disorders in Sweden. Second, we wished to determine if particular clinical traits were associated with E. dermatitidis colonization of the airways and the antifungal susceptibility profiles of Exophiala strains. Sputum and bronchoalveolar lavage samples (n = 492) derived from 275 patients were investigated. E. dermatitidis was isolated in respiratory specimens from 19% (18/97) of the CF patients but in none of the other patient categories. All isolates were recovered after 6 to 25 days of incubation on erythritol-chloramphenicol agar (ECA) medium. Morphological and genetic analyses confirmed species identity. Pancreatic insufficiency was positively associated with the presence of E. dermatitidis in sputum samples (P = 0.0198). Antifungal susceptibility tests demonstrated that voriconazole and posaconazole had the lowest MICs against E. dermatitidis. In conclusion, E. dermatitidis is a frequent colonizer of the respiratory tract in CF patients in Sweden and appears to be associated with more advanced disease. Whether E. dermatitidis is pathogenic remains to be elucidated.
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31
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Vieira C, De Carvalho M, De Resende M, De Menezes Cussiol N, Alvarez-Leite M, Dos Santos S, De Oliveira M, De Magalhães T, Silva M, Nicoli J, De Macêdo Farias L. Isolation of clinically relevant fungal species from solid waste and environment of dental health services. Lett Appl Microbiol 2010; 51:370-6. [DOI: 10.1111/j.1472-765x.2010.02907.x] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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32
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Mandviwala T, Shinde R, Kalra A, Sobel JD, Akins RA. High-throughput identification and quantification of Candida species using high resolution derivative melt analysis of panfungal amplicons. J Mol Diagn 2009; 12:91-101. [PMID: 20007848 DOI: 10.2353/jmoldx.2010.090085] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Fungal infections pose unique challenges to molecular diagnostics; fungal molecular diagnostics consequently lags behind bacterial and viral counterparts. Nevertheless, fungal infections are often life-threatening, and early detection and identification of species is crucial to successful intervention. A high throughput PCR-based method is needed that is independent of culture, is sensitive to the level of one fungal cell per milliliter of blood or other tissue types, and is capable of detecting species and resistance mutations. We introduce the use of high resolution melt analysis, in combination with more sensitive, inclusive, and appropriately positioned panfungal primers, to address these needs. PCR-based amplification of the variable internal transcribed regions of the rDNA genes generates an amplicon whose sequence melts with a shape that is characteristic and therefore diagnostic of the species. Simple analysis of the differences between test and reference melt curves generates a single number that calls the species. Early indications suggest that high resolution melt analysis can distinguish all eight major species of Candida of clinical significance without interference from excess human DNA. Candida species, including mixed and novel species, can be identified directly in vaginal samples. This tool can potentially detect, count, and identify fungi in hundreds of samples per day without further manipulation, costs, or delays, offering a major step forward in fungal molecular diagnostics.
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Affiliation(s)
- Tasneem Mandviwala
- Department of Biochemistry and Molecular Biology, Wayne State University School of Medicine, Detroit, Michigan, USA
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33
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Lau A, Chen S, Sleiman S, Sorrell T. Current status and future perspectives on molecular and serological methods in diagnostic mycology. Future Microbiol 2009; 4:1185-222. [DOI: 10.2217/fmb.09.70] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Invasive fungal infections are an important cause of infectious morbidity. Nonculture-based methods are increasingly used for rapid, accurate diagnosis to improve patient outcomes. New and existing DNA amplification platforms have high sensitivity and specificity for direct detection and identification of fungi in clinical specimens. Since laboratories are increasingly reliant on DNA sequencing for fungal identification, measures to improve sequence interpretation should support validation of reference isolates and quality control in public gene repositories. Novel technologies (e.g., isothermal and PNA FISH methods), platforms enabling high-throughput analyses (e.g., DNA microarrays and Luminex® xMAP™) and/or commercial PCR assays warrant further evaluation for routine diagnostic use. Notwithstanding the advantages of molecular tests, serological assays remain clinically useful for patient management. The serum Aspergillus galactomannan test has been incorporated into diagnostic algorithms of invasive aspergillosis. Both the galactomannan and the serum β-D-glucan test have value for diagnosing infection and monitoring therapeutic response.
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Affiliation(s)
- Anna Lau
- Centre for Infectious Diseases & Microbiology, University of Sydney, Sydney, Australia
| | - Sharon Chen
- Centre for Infectious Diseases & Microbiology, University of Sydney, Sydney, Australia and Centre for Infectious Diseases & Microbiology Laboratory Services, Institute of Clinical Pathology & Medical Research, Westmead Hospital, Westmead, NSW 2145, Australia
| | - Sue Sleiman
- Centre for Infectious Diseases & Microbiology Laboratory Services, Institute of Clinical Pathology & Medical Research, Westmead Hospital, Westmead, NSW 2145, Australia
| | - Tania Sorrell
- Centre for Infectious Diseases & Microbiology, Westmead Hospital, Darcy and Hawkesbury Roads, Westmead, NSW 2145, Australia
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Yamamura M, Makimura K, Fujisaki R, Satoh K, Kawakami S, Nishiya H, Ota Y. Polymerase chain reaction assay for specific identification of Candida guilliermondii (Pichia guilliermondii). J Infect Chemother 2009; 15:214-8. [PMID: 19688239 DOI: 10.1007/s10156-009-0701-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2008] [Accepted: 05/01/2009] [Indexed: 11/27/2022]
Abstract
The incidence rates of fungemia caused by Candida guilliermondii have been increasing over the past several years. Although still relatively rare (1.3% of all cases of fungemia in Japan), most cases of C. guilliermondii fungemia occur in patients with cancer or hematological malignancy and their mortality rate is high. As C. guilliermondii tends to be resistant to various antifungal agents, early identification of this pathogen and treatment with an appropriate antifungal agent are required to improve survival rates in these patients. However, it is extremely difficult to differentiate C. guilliermondii (Pichia guilliermondii) from members of the C. famata complex. To date, identification based on DNA sequencing has been the only reliable method for the identification of fungal groups. Here, we used a polymerase chain reaction (PCR)-based method that we developed for the simple and reliable identification of C. guilliermondii (P. guilliermondii). A pair of specific primers was designed corresponding to the 18S rDNA sequence. The PCR system was applied to isolates from fungemia patients. These yeasts could not be identified with CHROMagar Candida, but were successfully identified using this PCR-based system.
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Affiliation(s)
- Mariko Yamamura
- Department of Internal Medicine, Teikyo University School of Medicine, 2-11-1 Kaga, Itabashi-ku, Tokyo, Japan.
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Arancia S, Sandini S, Cassone A, De Bernardis F. Use of 65kDa mannoprotein gene primers in PCR methods for the identification of five medically important Candida species. Mol Cell Probes 2009; 23:218-26. [PMID: 19393314 DOI: 10.1016/j.mcp.2009.04.003] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2008] [Revised: 04/01/2009] [Accepted: 04/06/2009] [Indexed: 11/30/2022]
Abstract
We have developed PCR and Multiplex PCR assays for the detection of medically important Candida spp. using different species and genus-specific PCR primers selected within the MP65 gene, a recently cloned gene encoding a mannoprotein adhesin. The genus-specific PCR primers were able to amplify Candida species DNA (100% positivity) whereas DNA from all other isolates tested, belonging to other fungal genera, was not amplified. The species-specific PCR primers allowed differentiation of each of five Candida species by the amplicon length produced. No amplicons were detected using species- or genus-specific primers in several bacterial or human DNA templates. The methods described in this study are reproducible, simple and specific. The total time required for each PCR method was less than 4 h from the extraction to the visualized amplicons after PCR. In conclusion, we developed PCR methods to differentiate the five most medically important Candida species using primers directed to the MP65 gene.
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Affiliation(s)
- S Arancia
- Department of Infectious, Parasitic and Immune-mediated Diseases, Istituto Superiore di Sanità, Rome, Italy
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36
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Haas B, Nathens AB. Future diagnostic and therapeutic approaches in surgical infections. Surg Clin North Am 2009; 89:539-54, xi. [PMID: 19281899 DOI: 10.1016/j.suc.2008.09.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
Despite ongoing efforts to standardize therapy and improve management, the morbidity and mortality associated with surgical infections remain high. Continued innovation is required to improve outcomes further, particularly in the face of the increasing prevalence of multidrug resistant organisms. Although they remain in the experimental stages, a number of recent advances have the potential to have significant impact on the management and outcomes of surgical infections. These include novel diagnostic strategies, antimicrobials targeting microbial virulence factors, novel vaccines, and risk stratification based on genetic profiling.
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Affiliation(s)
- Barbara Haas
- Department of Surgery, University of Toronto, Toronto, Ontario, M5G 1L5, Canada.
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37
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Colony multiplex-tandem PCR for rapid, accurate identification of fungal cultures. J Clin Microbiol 2008; 46:4058-60. [PMID: 18945844 DOI: 10.1128/jcm.01411-08] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
We developed a multiplex tandem PCR (MT-PCR) assay for the rapid identification of 16 fungi directly from culture. MT-PCR results were concordant with phenotypic identification for all cultures studied (n = 183). The colony MT-PCR assay was rapid (<2 h), sensitive, and specific in identifying fungal pathogens directly from primary isolation plates.
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38
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39
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Multiplex tandem PCR: a novel platform for rapid detection and identification of fungal pathogens from blood culture specimens. J Clin Microbiol 2008; 46:3021-7. [PMID: 18632914 DOI: 10.1128/jcm.00689-08] [Citation(s) in RCA: 72] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
We describe the first development and evaluation of a rapid multiplex tandem PCR (MT-PCR) assay for the detection and identification of fungi directly from blood culture specimens that have been flagged as positive. The assay uses a short-cycle multiplex amplification, followed by 12 simultaneous PCRs which target the fungal internal transcribed spacer 1 (ITS1) and ITS2 region, elongation factor 1-alpha (EF1-alpha), and beta-tubulin genes to identify 11 fungal pathogens: Candida albicans, Candida dubliniensis, Candida glabrata, Candida guilliermondii, Candida krusei, Candida parapsilosis complex, Candida tropicalis, Cryptococcus neoformans complex, Fusarium solani, Fusarium species, and Scedosporium prolificans. The presence or absence of a fungal target was confirmed by melting curve analysis. Identification by MT-PCR correlated with culture-based identification for 44 (100%) patients. No cross-reactivity was detected in 200 blood culture specimens that contained bacteria or in 30 blood cultures without microorganisms. Fungi were correctly identified in five specimens with bacterial coinfection and in blood culture samples that were seeded with a mixture of yeast cells. The MT-PCR assay was able to provide rapid (<2 h), sensitive, and specific simultaneous detection and identification of fungal pathogens directly from blood culture specimens.
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