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Bao J, Chen Y, Xing Y, Feng C, Hu Q, Li X, Jiang H. Development of a nested PCR assay for specific detection of Metschnikowia bicuspidata infecting Eriocheir sinensis. Front Cell Infect Microbiol 2022; 12:930585. [PMID: 35937694 PMCID: PMC9352885 DOI: 10.3389/fcimb.2022.930585] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Accepted: 06/30/2022] [Indexed: 11/15/2022] Open
Abstract
In recent years, the “milky disease” caused by Metschnikowia bicuspidata has seriously affected the Eriocheir sinensis culture industry. Discovering and blocking the transmission route has become the key to controlling this disease. The existing polymerase chain reaction (PCR) detection technology for M. bicuspidata uses the ribosomal DNA (rDNA) sequence, but low sensitivity and specificity lead to frequent false detections. We developed a highly specific and sensitive nested PCR method to detect M. bicuspidata, by targeting the hyphally regulated cell wall protein (HYR) gene. This nested HYR-PCR produced a single clear band, showed no cross-reaction with other pathogens, and was superior to rDNA-PCR in specificity and sensitivity. The sensitivity of nested HYR-PCR (6.10 × 101 copies/μL) was greater than those of the large subunit ribosomal RNA gene (LSU rRNA; 6.03 × 104 copies/μL) and internal transcribed spacer (ITS; 6.74 × 105 copies/μL) PCRs. The nested HYR-PCR also showed a higher positivity rate (71.1%) than those obtained with LSU rRNA (16.7%) and ITS rDNA (24.4%). In conclusion, we developed a new nested HYR-PCR method for the specific and sensitive detection of M. bicuspidata infection. This will help to elucidate the transmission route of M. bicuspidata and to design effective management and control measures for M. bicuspidata disease.
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Affiliation(s)
- Jie Bao
- Aquaculture Department, College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang, China
| | - Ye Chen
- Aquaculture Department, College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang, China
| | - Yuenan Xing
- Aquaculture Department, College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang, China
| | - Chengcheng Feng
- Aquaculture Department, College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang, China
| | - Qingbiao Hu
- Aquaculture Department, College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang, China
| | - Xiaodong Li
- Aquaculture Department, College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang, China
| | - Hongbo Jiang
- Aquaculture Department, College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang, China
- Key Laboratory of Livestock Infectious Diseases in Northeast China, Ministry of Education, Shenyang Agricultural University, Shenyang, China
- *Correspondence: Hongbo Jiang,
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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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Faria-Gonçalves P, Rolo J, Gaspar C, Palmeira-de-Oliveira R, Martinez-de-Oliveira J, Palmeira-de-Oliveira A. Virulence Factors as Promoters of Chronic Vulvovaginal Candidosis: A Review. Mycopathologia 2021; 186:755-773. [PMID: 34613569 DOI: 10.1007/s11046-021-00592-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Accepted: 09/09/2021] [Indexed: 01/09/2023]
Abstract
INTRODUCTION The vast majority of the species of the genus Candida spp. is commensal in humans; however, some are opportunistic pathogens that can cause infection, called candidosis. Among the different types of candidosis, we highlight the vulvovaginal (VVC) which can occur in two main clinical variants: chronic (cVVC) and episodic or sporadic. The incidence of cVVC has been worrying the scientific community, promoting the research on genotypic and phenotypic causes of its occurrence. We summarize important findings on factors that favor chronic vulvovaginal candidosis with respect to molecular epidemiology and the expression of various virulence factors, while clarifying the terminology involving these infections. AIM AND METHODOLOGY The aim of this review was to gather research that linked virulence factors to VVC and its persistence and recurrence, using two databases (Pubmed and Google Scholar). Predisposing factors in women for the occurrence of cVVC and some studies that refer new preventive and alternative therapies were also included, where appropriate. RESULTS AND DISCUSSION Several studies have been shedding light on the increasing number of persistence and recurrences of VVC. The expression of virulence factors has been related to both chronic forms of VVC and antifungal resistance. Other studies report mutations occurring in the genome of Candida spp. during the infection phase which may be important indications for new therapies. The introduction of preventive therapies and new therapies has revealed great importance and is also highlighted here.
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Affiliation(s)
- Paula Faria-Gonçalves
- Health Sciences Research Center, University of Beira Interior, Av. Infante D. Henrique, 6200-506, Covilhã, Portugal.,Faculty of Medicine, University Mandume Ya Ndemufayo, Lubango, Angola.,Faculty of Health Sciences, University of Beira Interior, Covilhã, Portugal
| | - Joana Rolo
- Health Sciences Research Center, University of Beira Interior, Av. Infante D. Henrique, 6200-506, Covilhã, Portugal.
| | - Carlos Gaspar
- Health Sciences Research Center, University of Beira Interior, Av. Infante D. Henrique, 6200-506, Covilhã, Portugal.,Faculty of Health Sciences, University of Beira Interior, Covilhã, Portugal.,Health Products Research and Development Lda, Covilhã, Portugal
| | - Rita Palmeira-de-Oliveira
- Health Sciences Research Center, University of Beira Interior, Av. Infante D. Henrique, 6200-506, Covilhã, Portugal.,Faculty of Health Sciences, University of Beira Interior, Covilhã, Portugal.,Health Products Research and Development Lda, Covilhã, Portugal.,Center for Neuroscience and Cell Biology, University of Coimbra, Rua Larga, 3004-504, Coimbra, Portugal
| | - José Martinez-de-Oliveira
- Health Sciences Research Center, University of Beira Interior, Av. Infante D. Henrique, 6200-506, Covilhã, Portugal
| | - Ana Palmeira-de-Oliveira
- Health Sciences Research Center, University of Beira Interior, Av. Infante D. Henrique, 6200-506, Covilhã, Portugal.,Faculty of Health Sciences, University of Beira Interior, Covilhã, Portugal.,Health Products Research and Development Lda, Covilhã, Portugal
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Sayed SA, Hassan EAB, Abdel Hameed MR, Agban MN, Mohammed Saleh MF, Mohammed HH, Abdel-Aal ABM, Elgendy SG. Ketorolac-fluconazole: A New Combination Reverting Resistance in Candida albicans from Acute Myeloid Leukemia Patients on Induction Chemotherapy: In vitro Study. J Blood Med 2021; 12:465-474. [PMID: 34163275 PMCID: PMC8214543 DOI: 10.2147/jbm.s302158] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2021] [Accepted: 05/20/2021] [Indexed: 11/23/2022] Open
Abstract
BACKGROUND AND OBJECTIVES Candida albicans is a significant source of morbidity and mortality for patients with acute myeloid leukemia (AML). Prolonged use of fluconazole as empirical antifungal prophylaxis in AML patients leads to overexpression of efflux pump genes that resulted in the emergence of azole-resistant species. Consequently, the introduction of a new strategy to improve the management of C. albicans infections is an urgent need. Nonsteroidal anti-inflammatory drug (NSAID) ketorolac is associated with a reduction in cancer relapses. The present study was performed to investigate the use of ketorolac-fluconazole combination to reverse fluconazole resistance in C. albicans isolated from AML patients on induction chemotherapy. PATIENTS AND METHODS One hundred and seventy AML patients were evaluated. Fifty C. albicans were isolated and subjected to disc diffusion assay and broth microdilution for fluconazole alone and combined with different concentrations of ketorolac. Efflux pump gene (CDR1, CDR2, and MDR1) expressions were quantified by real-time PCR. RESULTS The tested ketorolac acted synergistically with fluconazole against resistant C. albicans with the minimum inhibitory concentration (MIC) of fluconazole decreased from >160 μg/mL to 0.3-1.25 μg/mL in (93.8%) of resistant isolates with fractional inhibitory concentration index (FICI) value of 0.25. The majority of the resistant isolates overexpressed CDR1 (71.1%) and MDR1 (60%). CONCLUSION Ketorolac-fluconazole in vitro combination would be a promising strategy for further clinical in vivo trials to overcome fluconazole resistance in AML patients on induction chemotherapy.
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Affiliation(s)
- Shereen A Sayed
- Department of Microbiology and Immunology, Faculty of Veterinary Medicine, Assiut University, Assiut, Egypt
| | - Ehsan A B Hassan
- Department of Medical Microbiology and Immunology, Faculty of Medicine, Assiut University, Assiut, Egypt
| | - Muhamad R Abdel Hameed
- Department of Internal Medicine & Hematology Unit, Assiut University Hospitals and Bone Marrow Transplantation Unit, South Egypt Cancer Institute, Assiut University, Assiut, Egypt
| | - Michael N Agban
- Department of Medical Microbiology and Immunology, Faculty of Medicine, Assiut University, Assiut, Egypt
| | - Mostafa F Mohammed Saleh
- Department of Internal Medicine & Hematology Unit, Assiut University Hospitals and Bone Marrow Transplantation Unit, South Egypt Cancer Institute, Assiut University, Assiut, Egypt
| | - Hayam H Mohammed
- Department of Clinical Pathology, South Egypt Cancer Institute, Assiut University, Assiut, Egypt
| | - Abu-Baker M Abdel-Aal
- Department of Organic Chemistry, Faculty of Pharmacy, Assiut University, Assiut, Egypt
| | - Sherein G Elgendy
- Department of Medical Microbiology and Immunology, Faculty of Medicine, Assiut University, Assiut, Egypt
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Difference Between the Profiles Presented by Yeasts that Colonize the Vaginal Mucosa or Cause Primary or Recurrent Candidiasis. Mycopathologia 2021; 186:411-421. [PMID: 34120275 DOI: 10.1007/s11046-021-00556-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2020] [Accepted: 04/20/2021] [Indexed: 10/20/2022]
Abstract
Candida yeasts are the most frequent in the vaginal content. This yeast may be a normal microbiota but also causes candidiasis. In symptomatic cases, primary candidiasis (VVC) or recurrence (RVVC) can be considered. This study aims to compare the frequency and in vitro sensitivity profile of Candida species isolated in the vaginal content with the different stages of the presence of yeasts. A total of 258 non-pregnant patients with/without VVC were prospectively screened at a teaching Health Centre of the Faculty of Medicine, in the University of Sao Paulo. The vaginal isolates were identified by traditional and molecular methods. Yeasts were isolated in 160 women. 34% were asymptomatic, 34% with vulvovaginal candidiasis (VVC), and 32% recurrent vulvovaginal candidiasis (RVVC). C. albicans was the most frequent species with 50.1% (82/160), followed by C. parapsilosis 13.7%(22/160), C. glabrata 12.5% (20/160), and C. tropicalis (6.2%). Analysis by the group showed that, in the asymptomatic group, eight yeast species were isolated, C. albicans 44.5% (24/54), C. glabrata 20% (11/54), C. parapsilosis and Rhodotorula rubra being the most frequent. In the VVC group, 11 yeast species were identified. Most isolates were C. albicans 68.5% (37/54), C. tropicalis 7.5% (4/54), and C. parapsilosis 5.5% (3/54). In the RVVC group, ten species were identified, the most frequent being C. albicans 38.5% (20/52), C. parapsilosis 17% (9/52), C. glabrata 4% (8/52), and C. tropicalis 6% (3/52). Less frequent species, such as C. haemulonii and Trichosporon spp, were isolated in the VVC and RVVC groups, C. kefyr was isolated in the three groups studied, and Rhodotorula spp was isolated in the control and RVVC groups. Candida metapsilosis was present in two isolates from the RVVC group. Most isolates were considered sensitive to the tested antifungals. Less sensitivity was seen for caspofungin. In this study, we were able to verify that the most common species of yeasts found in vaginal secretion were isolated in the three groups studied; however, there was the diversity of species in VVC and RVVC. Cryptic species C. haemulonii and were isolated in symptomatic patients. High levels of MICs, some of the antifungals tested, in the control group, draw attention in the group of asymptomatic women. We would like to emphasize that this research aims to assist clinicians and gynecologists, as well as assist in the epidemiological studies of candidiasis, in our country, how to draw attention to the profile of sensitivity/resistance to antifungals.
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Hyposalivation, oral health, and Candida colonization in independent dentate elders. PLoS One 2020; 15:e0242832. [PMID: 33237956 PMCID: PMC7688165 DOI: 10.1371/journal.pone.0242832] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2020] [Accepted: 11/09/2020] [Indexed: 12/12/2022] Open
Abstract
Hyposalivation is an important problem in elders and could interfere with several oral functions and microbial ecology. While the number of independent elders who retain more natural teeth increases worldwide, few studies examined hyposalivation in this population. Thus, this study aims to examine relationships between hyposalivation, oral health conditions and oral Candida colonization in independent dentate elders and evaluate factors associated with salivary flow and Candida carriage. We conducted a cross-sectional study in fifty-three dentate elders (≥65 years old with at least 4 pairs of posterior occlusal contacts) with no, or well-controlled, systemic conditions. Participants were interviewed for medical history, subjective dry mouth symptoms, oral hygiene practices and denture information. Unstimulated and stimulated salivary flow rates, objective dry mouth signs, gingival, tongue-coating, and root-caries indices were recorded. Stimulated saliva was cultured on Sabouraud-dextrose agar for Candida counts. Candida species were identified using chromogenic Candida agar and polymerase chain reaction. Statistical significance level was set at p<0.05. The results showed that hyposalivation was associated with higher gingival and tongue-coating indices (p = 0.003 and 0.015, respectively), but not root-caries index. Hyposalivation was also associated with higher prevalence of oral Candida colonization (p = 0.010; adjusted OR = 4.36, 95% confidence interval = 1.29–14.72). These two indices and Candida load were negatively correlated with unstimulated and stimulated salivary flow rates. Interestingly, non-albicans Candida species were more prevalent in denture wearers (p = 0.017). Hence, hyposalivation is a risk factor for poorer oral health and oral Candida colonization in independent dentate elders. Because of its potential adverse effects on oral and systemic health, hyposalivation should be carefully monitored in elders.
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Lam-Ubol A, Matangkasombut O, Trachootham D, Tarapan S, Sattabanasuk V, Talungchit S, Paemuang W, Phonyiam T, Chokchaitam O, Mungkung OO. Efficacy of gel-based artificial saliva on Candida colonization and saliva properties in xerostomic post-radiotherapy head and neck cancer patients: a randomized controlled trial. Clin Oral Investig 2020; 25:1815-1827. [PMID: 32779011 PMCID: PMC7966128 DOI: 10.1007/s00784-020-03484-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Accepted: 07/29/2020] [Indexed: 11/28/2022]
Abstract
Objective To evaluate the efficacy of an edible artificial saliva gel, oral moisturizing jelly (OMJ), and a topical commercial gel (GC dry mouth gel) on Candida colonization and saliva properties. Materials and methods This study was a secondary analysis of a single-blinded randomized controlled trial conducted in xerostomic post-radiotherapy head and neck cancer patients. Candida colonization, stimulated salivary flow rate (SSFR), saliva pH, and buffering capacity (BC) were measured at 0, 1, and 2 months after each intervention. Candida colonization was quantified by colony counts and species identified by Candida Chromagar, polymerase chain reaction, and API 20C AUX system. Statistical significance level was 0.05. Results A total of 56 participants in OMJ (N = 30) and GC (N = 26) groups completed the study. OMJ significantly increased saliva pH (p = 0.042) and BC (p = 0.013) after 1-month use, while GC only improved saliva pH (p = 0.027). Both interventions tended to increase SSFR but only GC had a significant increase at 2 months (p = 0.015). GC and OMJ significantly decreased the number of Candida species at 1 and 2 months, respectively. Both groups tended to reduce Candida counts but not significant. Conclusions Both OMJ and GC saliva gels could improve saliva pH and decrease the number of Candida species. OMJ is superior to GC in its buffering capacity, while GC may better improve salivary flow rate. Long-term and large-scale study is warranted to test the efficacy of artificial saliva in oral health improvement. Clinical relevance OMJ and GC gel could decrease the number of Candida species and improve saliva properties in post-radiation xerostomic patients. Trial registration number Clinicaltrials.gov NCT03035825. Date of registration: 25th January 2017.
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Affiliation(s)
- Aroonwan Lam-Ubol
- Department of Oral Surgery and Oral Medicine, Faculty of Dentistry, Srinakharinwirot University, 114 Sukhumvit 23, Wattana, Bangkok, 10110, Thailand.
| | - Oranart Matangkasombut
- Department of Microbiology and Research Unit on Oral Microbiology and Immunology, Faculty of Dentistry, Chulalongkorn University, Bangkok, Thailand.,Laboratory of Biotechnology, Chulabhorn Research Institute, Bangkok, Thailand
| | | | - Supanat Tarapan
- Department of Oral Surgery and Oral Medicine, Faculty of Dentistry, Srinakharinwirot University, 114 Sukhumvit 23, Wattana, Bangkok, 10110, Thailand.,Langsuan Hospital, Chumphon, Thailand
| | | | - Sineepat Talungchit
- Department of Oral Surgery and Oral Medicine, Faculty of Dentistry, Srinakharinwirot University, 114 Sukhumvit 23, Wattana, Bangkok, 10110, Thailand
| | - Wannaporn Paemuang
- Department of Vascular Surgery, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Tawaree Phonyiam
- Institute of Nutrition, Mahidol University, Nakhon Pathom, Thailand
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Tarapan S, Matangkasombut O, Trachootham D, Sattabanasuk V, Talungchit S, Paemuang W, Phonyiam T, Chokchaitam O, Mungkung OO, Lam-Ubol A. Oral Candida colonization in xerostomic postradiotherapy head and neck cancer patients. Oral Dis 2019; 25:1798-1808. [PMID: 31257663 DOI: 10.1111/odi.13151] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2019] [Revised: 06/16/2019] [Accepted: 06/25/2019] [Indexed: 12/24/2022]
Abstract
OBJECTIVES To evaluate (a) oral colonization of Candida species, especially for non-albicans Candida species (NACS), in xerostomic postradiotherapy head and neck cancer patients and (b) risk factors affecting their colonization. MATERIALS AND METHODS Subjective and objective dry mouth scores, stimulated salivary flow rates, pH and buffering capacity were measured in 72 xerostomic postradiotherapy head and neck cancer patients. Candida counts and species identification were performed using oral rinse samples cultured in Candida Chromagar, followed by polymerase chain reaction and API 20C AUX system. RESULTS Candida colonization was observed in 87.5% of subjects, with 80.6% and 48.6% of study population colonized by C. albicans and NACS, respectively. NACS was associated with high objective dry mouth scores, denture use, and females (p = .006, .009, and .036, respectively). In addition, Candida glabrata was detected more in females (p = .018) and denture wearers (p = .026), while Candida tropicalis was associated with high objective dry mouth scores (p = .022) and females (p = .027). Quantity of Candida colonization correlated positively with objective dry mouth scores (r = 0.599, p < .001) and negatively with salivary flow rates (r = -0.258, p = .041) and pH (r = -0.290, p = .022). CONCLUSION NACS colonization was common in xerostomic head and neck cancer patients. Increased signs of dry mouth, female and dental prostheses may promote NACS colonization.
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Affiliation(s)
- Supanat Tarapan
- Faculty of Dentistry, Srinakharinwirot University, Bangkok, Thailand
| | - Oranart Matangkasombut
- Department of Microbiology and Research Unit on Oral Microbiology and Immunology, Faculty of Dentistry, Chulalongkorn University, Bangkok, Thailand.,Laboratory of Biotechnology, Chulabhorn Research Institute, Bangkok, Thailand
| | | | | | | | | | - Tawaree Phonyiam
- Institute of Nutrition, Mahidol University, Nakhon Pathom, Thailand
| | | | | | - Aroonwan Lam-Ubol
- Faculty of Dentistry, Srinakharinwirot University, Bangkok, Thailand
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9
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Gauch LMR, Pedrosa SS, Silveira-Gomes F, Esteves RA, Marques-da-Silva SH. Isolation of Candida spp. from denture-related stomatitis in Pará, Brazil. Braz J Microbiol 2017; 49:148-151. [PMID: 29054393 PMCID: PMC5790581 DOI: 10.1016/j.bjm.2017.07.001] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2013] [Accepted: 05/02/2016] [Indexed: 11/05/2022] Open
Abstract
The aim of this study was to isolate and identify Candida species from the oral cavity of denture wearers with denture-related stomatitis who were attended at the University Federal of Pará (Belém City, Pará State, Brazil). A total of 36 denture wearers with denture-related stomatitis were included, and type I (50%), type II (33%) and type III (17%) stomatitis were observed. Candida spp. were isolated from 89% of the cases and included five different Candida species. C. albicans was the most frequently recovered species (78% of the cases), followed by C. famata and C. tropicalis. We observed a significant association between Candida species isolation and unsatisfactory denture condition (p = 0.0017). Our results demonstrated the highly frequency of Candida species isolation in denture wearers with denture-related stomatitis and showed the relationship between these species and poor denture maintenance.
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Affiliation(s)
- Lurdete Maria Rocha Gauch
- Federal University of Pará, Science Health Institute Belém, Odontology College, Belém, PA, Brazil; Federal University of Pará, Science Biologic Institute, Postgraduate Program in Biology of Infectious and Parasitic Agents, Belém, PA, Brazil.
| | - Simone Soares Pedrosa
- Federal University of Pará, Science Health Institute Belém, Odontology College, Belém, PA, Brazil
| | - Fabíola Silveira-Gomes
- Federal University of Pará, Science Biologic Institute, Postgraduate Program in Biology of Infectious and Parasitic Agents, Belém, PA, Brazil
| | - Renata Antunes Esteves
- Federal University of Pará, Science Health Institute Belém, Odontology College, Belém, PA, Brazil
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Abastabar M, Hosseinpoor S, Hedayati MT, Shokohi T, Valadan R, Mirhendi H, Mohammadi R, Aghili SR, Rahimi N, Aslani N, Haghani I, Gholami S. Hyphal wall protein 1 gene: A potential marker for the identification of different Candida species and phylogenetic analysis. Curr Med Mycol 2016; 2:1-8. [PMID: 28959789 PMCID: PMC5611690 DOI: 10.18869/acadpub.cmm.2.4.1] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
BACKGROUND AND PURPOSE Hyphal wall protein 1 (HWP1) is an important adhesin which usually is expressed on the germ tube and hyphal surface produced by different Candida species. The hyphal wall protein-coding gene (HWP1) was evaluated as a novel identification and phylogenetic marker in Candida tropicalis, C. orthopsilosis, C. parapsilosis and C. glabrata. MATERIALS AND METHODS Initially, four specific primer pairs were designed, and the target was amplified and finally sequenced. A total of 77 Candida isolates from four different species were included in the study. Consensus sequences were used for the evaluation of phylogenetic tree using the CLC Genome Workbench, GENEIOUS, and MEGA softwares and the levels of nucleotide and amino acid polymorphism were assessed. RESULTS According to the results, the specific amplified fragments of HWP1 gene were useful for the differentiation of four species. Intra-species variation was observed only in C. tropicalis with two DNA types. The phylogenetic tree of Candida species based on the HWP1 gene showed consistency in topology with those inferred from other gene sequences. CONCLUSION We found that HWP1 gene was an excellent marker for the identification of non-albicansCandida species as well as the phylogenetic analysis of the most clinically significant Candida species.
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Affiliation(s)
- M Abastabar
- Invasive Fungi Research Center (IFRC), Mazandaran University of Medical Sciences, Sari, Iran.,Department of Medical Mycology and Parasitology, School of Medicine, Mazandaran University of Medical Sciences, Sari, Iran
| | - S Hosseinpoor
- Student Research Committee, Mazandaran University of Medical Sciences, Sari, Iran
| | - M T Hedayati
- Invasive Fungi Research Center (IFRC), Mazandaran University of Medical Sciences, Sari, Iran.,Department of Medical Mycology and Parasitology, School of Medicine, Mazandaran University of Medical Sciences, Sari, Iran
| | - T Shokohi
- Invasive Fungi Research Center (IFRC), Mazandaran University of Medical Sciences, Sari, Iran.,Department of Medical Mycology and Parasitology, School of Medicine, Mazandaran University of Medical Sciences, Sari, Iran
| | - R Valadan
- Molecular and Cell Biology Research Center (MCBRC), Mazandaran University of Medical Sciences, Sari, Mazandaran, Iran.,Department of Immunology, Faculty of Medicine, Mazandaran University of Medical Sciences, Sari, Mazandaran, Iran
| | - H Mirhendi
- Department of Medical Parasitology and Mycology, School of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran
| | - R Mohammadi
- Department of Medical Parasitology and Mycology, School of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran.,Infectious Diseases and Tropical Medicine Research Center, Isfahan University of Medical Sciences, Isfahan, Iran
| | - S R Aghili
- Invasive Fungi Research Center (IFRC), Mazandaran University of Medical Sciences, Sari, Iran.,Department of Medical Mycology and Parasitology, School of Medicine, Mazandaran University of Medical Sciences, Sari, Iran
| | - N Rahimi
- Department of Medical Mycology and Parasitology, School of Medicine, Mazandaran University of Medical Sciences, Sari, Iran
| | - N Aslani
- Department of Medical Mycology and Parasitology, School of Medicine, Mazandaran University of Medical Sciences, Sari, Iran
| | - I Haghani
- Department of Medical Mycology and Parasitology, School of Medicine, Mazandaran University of Medical Sciences, Sari, Iran
| | - S Gholami
- Department of Medical Mycology and Parasitology, School of Medicine, Mazandaran University of Medical Sciences, Sari, Iran
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11
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Application of high-resolution melting analysis for differentiation of spoilage yeasts. J Microbiol 2016; 54:618-625. [PMID: 27572511 DOI: 10.1007/s12275-016-6017-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2016] [Revised: 06/24/2016] [Accepted: 07/20/2016] [Indexed: 10/21/2022]
Abstract
A new method based on high resolution melting (HRM) analysis was developed for the differentiation and classification of the yeast species that cause food spoilage. A total 134 strains belonging to 21 different yeast species were examined to evaluate the discriminative power of HRM analysis. Two different highly variable DNA regions on the 26 rRNA gene were targeted to produce the HRM profiles of each strain. HRM-based grouping was compared and confirmed by (GTG)5 rep-PCR fingerprinting analysis. All of the yeast species belonging to the genera Pichia, Candida, Kazachstania, Kluyveromyces, Debaryomyces, Dekkera, Saccharomyces, Torulaspora, Ustilago, and Yarrowia, which were produced as species-specific HRM profiles, allowed discrimination at species and/or strain level. The HRM analysis of both target regions provided successful discrimination that correlated with rep-PCR fingerprinting analysis. Consequently, the HRM analysis has the potential for use in the rapid and accurate classification and typing of yeast species isolated from different foods to determine their sources and routes as well as to prevent contamination.
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12
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Identification of food and beverage spoilage yeasts from DNA sequence analyses. Int J Food Microbiol 2015; 213:71-8. [DOI: 10.1016/j.ijfoodmicro.2015.05.023] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2014] [Revised: 05/18/2015] [Accepted: 05/29/2015] [Indexed: 10/23/2022]
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13
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Kiraz N, Oz Y, Aslan H, Erturan Z, Ener B, Akdagli SA, Muslumanoglu H, Cetinkaya Z. Is the extraction by Whatman FTA filter matrix technology and sequencing of large ribosomal subunit D1-D2 region sufficient for identification of clinical fungi? Mycoses 2015; 58:588-97. [PMID: 26293550 DOI: 10.1111/myc.12365] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2015] [Revised: 07/05/2015] [Accepted: 07/07/2015] [Indexed: 11/30/2022]
Abstract
Although conventional identification of pathogenic fungi is based on the combination of tests evaluating their morphological and biochemical characteristics, they can fail to identify the less common species or the differentiation of closely related species. In addition these tests are time consuming, labour-intensive and require experienced personnel. We evaluated the feasibility and sufficiency of DNA extraction by Whatman FTA filter matrix technology and DNA sequencing of D1-D2 region of the large ribosomal subunit gene for identification of clinical isolates of 21 yeast and 160 moulds in our clinical mycology laboratory. While the yeast isolates were identified at species level with 100% homology, 102 (63.75%) clinically important mould isolates were identified at species level, 56 (35%) isolates at genus level against fungal sequences existing in DNA databases and two (1.25%) isolates could not be identified. Consequently, Whatman FTA filter matrix technology was a useful method for extraction of fungal DNA; extremely rapid, practical and successful. Sequence analysis strategy of D1-D2 region of the large ribosomal subunit gene was found considerably sufficient in identification to genus level for the most clinical fungi. However, the identification to species level and especially discrimination of closely related species may require additional analysis.
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Affiliation(s)
- Nuri Kiraz
- Cerrahpasa Medical Faculty, Department of Microbiology, Division of Mycology, Istanbul University, Istanbul, Turkey
| | - Yasemin Oz
- Faculty of Medicine, Department of Microbiology, Division of Mycology, Eskisehir Osmangazi University, Eskisehir, Turkey
| | - Huseyin Aslan
- Faculty of Medicine, Department of Medical Genetics, Eskisehir Osmangazi University, Eskisehir, Turkey
| | - Zayre Erturan
- Faculty of Medicine, Department of Microbiology, Division of Mycology, Istanbul University, Istanbul, Turkey
| | - Beyza Ener
- Faculty of Medicine, Department of Microbiology, Uludag University, Bursa, Turkey
| | - Sevtap Arikan Akdagli
- Faculty of Medicine, Department of Microbiology, Hacettepe University, Ankara, Turkey
| | - Hamza Muslumanoglu
- Faculty of Science and Arts, Department of Molecular Biology, Yildiz Technical University, Istanbul, Turkey
| | - Zafer Cetinkaya
- Department of Microbiology, Goztepe Research and Education Hospital, Istanbul, Turkey
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14
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Kurtzman CP, Mateo RQ, Kolecka A, Theelen B, Robert V, Boekhout T. Advances in yeast systematics and phylogeny and their use as predictors of biotechnologically important metabolic pathways. FEMS Yeast Res 2015; 15:fov050. [PMID: 26136514 DOI: 10.1093/femsyr/fov050] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/29/2015] [Indexed: 01/02/2023] Open
Abstract
Detection, identification and classification of yeasts have undergone a major transformation in the last decade and a half following application of gene sequence analyses and genome comparisons. Development of a database (barcode) of easily determined DNA sequences from domains 1 and 2 (D1/D2) of the nuclear large subunit rRNA gene and from ITS now permits many laboratories to identify species quickly and accurately, thus replacing the laborious and often inaccurate phenotypic tests previously used. Phylogenetic analysis of gene sequences is leading to a major revision of yeast systematics that will result in redefinition of nearly all genera. This new understanding of species relationships has prompted a change of rules for naming and classifying yeasts and other fungi, and these new rules are presented in the recently implemented International Code of Nomenclature for algae, fungi, and plants (Melbourne Code). The use of molecular methods for species identification and the impact of Code changes on classification will be discussed, as will use of phylogeny for prediction of biotechnological applications.
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Affiliation(s)
- Cletus P Kurtzman
- Bacterial Foodborne Pathogens and Mycology Research Unit, National Center for Agricultural Utilization Research, Agricultural Research Service, U.S. Department of Agriculture, Peoria, IL 61604, USA
| | - Raquel Quintilla Mateo
- CBS Fungal Biodiversity Centre (CBS-KNAW), 3584 CT Utrecht, the Netherlands Laboratory of Molecular Cell Biology, Institute of Botany and Microbiology, KU Leuven, B-3001 Leuven, Belgium Department of Molecular Microbiology, VIB, Kasteelpark Arenberg 31, B-3001 Leuven-Heverlee, Flanders, Belgium
| | - Anna Kolecka
- CBS Fungal Biodiversity Centre (CBS-KNAW), 3584 CT Utrecht, the Netherlands
| | - Bart Theelen
- CBS Fungal Biodiversity Centre (CBS-KNAW), 3584 CT Utrecht, the Netherlands
| | - Vincent Robert
- CBS Fungal Biodiversity Centre (CBS-KNAW), 3584 CT Utrecht, the Netherlands
| | - Teun Boekhout
- CBS Fungal Biodiversity Centre (CBS-KNAW), 3584 CT Utrecht, the Netherlands
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15
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Wang Q, Gong J, Chisti Y, Sirisansaneeyakul S. Fungal isolates from a Pu-erh type tea fermentation and their ability to convert tea polyphenols to theabrownins. J Food Sci 2015; 80:M809-17. [PMID: 25799937 DOI: 10.1111/1750-3841.12831] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2014] [Accepted: 02/03/2015] [Indexed: 01/16/2023]
Abstract
The natural microbiota involved in the fermentation influence the quality and taste of fully postfermented teas such as China's Pu-erh tea. Ten microbial isolates representing 6 species were recovered from a solid-state fermentation of a Pu-erh type tea. The isolates were Aspergillus tubingensis, Aspergillus marvanovae, Rhizomucor pusillus, Rhizomucor tauricus, Aspergillus fumigatus, and Candida mogii. With the exception of A. marvanovae and C. mogii, all these microorganisms have been previously reported in solid-state fermentations of native Pu-erh tea. The ability of the isolates for converting the tea polyphenols to bioactive theabrownins in infusions of sun-dried green tea leaves in a submerged fermentation process was subsequently investigated. All isolates except C. mogii TISTR 5938 effectively produced theabrownins in a 4-d fermentation in shake flasks at 40 °C, 250 rpm. A. tubingensis TISTR 3646, A. tubingensis TISTR 3647, A. marvanovae TISTR 3648, and A. fumigatus TISTR 3654 produced theabrownins at particularly high levels of 6.5, 12.4, 11.1, and 8.4 g/L, respectively.
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Affiliation(s)
- Qiuping Wang
- Dept. of Biotechnology, Faculty of Agro-Industry, Kasetsart Univ, 50 Ngam Wong Wan Road, Ladyao, Chatuchak, Bangkok, 10900, Thailand
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16
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Candida inconspicua and Candida norvegensis: new insights into identification in relation to sexual reproduction and genome organization. J Clin Microbiol 2015; 53:1655-61. [PMID: 25762773 DOI: 10.1128/jcm.02913-14] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2014] [Accepted: 03/05/2015] [Indexed: 01/22/2023] Open
Abstract
Candida inconspicua and Candida (Pichia) norvegensis are two emerging pathogenic species that exhibit reduced susceptibility to azole derivatives. Conventional (biochemical) approaches do not readily differentiate between the two species. The first aim of this work was to analyze the performance of biochemical, proteomic (matrix-assisted laser desorption ionization-time of flight [MALDI-TOF]), and molecular approaches in the precise identification of these species. These results then led us to sequence 3 genomic loci, i.e., the internal transcribed spacer (ITS) region of the ribosomal DNA (rDNA), the D1/D2 domain of the 28S rDNA, and the elongation factor 1α (EF-1α) gene, either directly or following cloning, of 13 clinical isolates and 9 reference strains belonging to the 5 species included in the Pichia cactophila clade, namely, Pichia cactophila, Pichia insulana, C. inconspicua, C. norvegensis, and P. pseudocactophila. Finally, isolates of C. inconspicua were challenged for sexual reproduction on the appropriate medium. Our results show that EF-1α sequencing and proteic profiling by MALDI-TOF are the two most efficient approaches to distinguish between C. norvegensis and C. inconspicua. As a characteristic of the P. cactophila clade, we found multiple alleles of the rDNA regions in certain strains belonging to the tested species, making ITS or D1/D2 sequencing not appropriate for identification. Whatever the method of identification, including MALDI-TOF and EF-1α sequencing, none could differentiate C. inconspicua from P. cactophila. The results of phylogenetic analysis and the generation of asci from pure cultures of all C. inconspicua strains both support the identification of P. cactophila as the teleomorph of C. inconspicua.
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17
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Ashrafi M, Nabili M, Shokohi T, Janbabaie G, Hedayati MT, Ali-Moghaddam K. A real time PCR assay on blood for diagnosis of invasive candidiasis in immunocompromised patient. Curr Med Mycol 2015; 1:35-41. [PMID: 28680979 PMCID: PMC5490320 DOI: 10.18869/acadpub.cmm.1.1.35] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
Background and Purpose: Invasive candidiasis (IC) is a significant cause of morbidity and mortality in patients with hematologic disorders and bone marrow transplant recipients. Rapid, specific and sensitive test for the timely accuracy in immunocompromised patients to reduce mortality rates and prevent IC progress is necessary. We established a real-time PCR assay on blood for the diagnosis and differentiation of the causative Candida species. Materials and Methods: Whole blood samples were collected twice, from 72 patients for Real Time PCR and blood culture assays. The primers and hybridization probes were designed to potentiate the specific sequence of 18S rRNA genes using Light Cycler system and Fluorescence Resonance Energy Transfer (FERT). The patients with hematologic malignancies and bone marrow transplant recipients were evaluated for IC based on the revised European Organization for Research and Treatment of Cancer/ Mycoses Study Group (EORTC/MSG) criteria. Results: From 2009 to 2011, 72 patients with hematologic malignancies and bone marrow transplant recipients were evaluated for IC. The female to male ratio was 27:45; the mean age was 32.1 years. The most common malignancy in this patient was acute myeloid leukemia (AML) (27.8%) and acute lymphoblastic leukemia (ALL) (26.4%). Out of 72 patients, 11 patients (15.3%) had positive real time PCR /probe results. Based on the melting temperature (Tm) analysis, 5 (45.4%) C. krusei, 3 (27.2%) C. tropicalis, 2 (18.1%) C. parapsilosis and 1 C. albicans (9%) were identified. According to the revised EORTC / MSG, 1 patient (9%) and 10 patients (91%) were defined as proven and possible groups of IC, respectively. The mortality rate in proven and possible IC patient was found 54.5%. Conclusion: The established Real-time PCR/FRET probe assay is an appropriate diagnostic tool for the detection of Candida species DNA and the management of patients suffering from hematologic malignancies and bone marrow recipient are at risk for IC
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Affiliation(s)
- M Ashrafi
- Student research committee, Mazandaran University of Medical Sciences, Sari, Iran
| | - M Nabili
- Student research committee, Mazandaran University of Medical Sciences, Sari, Iran.,Social Security Organization, Golestan, Iran
| | - T Shokohi
- Invasive Fungi Research Center (IFRC), and Department of Medical Parasitology and Mycology, Mazandaran University of Medical Sciences, Sari, Iran
| | - G Janbabaie
- Department of Internal Medicine, Cell and Molecular Biology Research Center, Mazandaran University of Medical Sciences, Sari, Iran
| | - M T Hedayati
- Invasive Fungi Research Center (IFRC), and Department of Medical Parasitology and Mycology, Mazandaran University of Medical Sciences, Sari, Iran
| | - K Ali-Moghaddam
- Hematology-Oncology Research Center and Stem Cell Transplantation Research Center (HORCSCT), Tehran University of Medical Sciences, Iran
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18
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Lee HP, Sheu TF. An algorithm of discovering signatures from DNA databases on a computer cluster. BMC Bioinformatics 2014; 15:339. [PMID: 25282047 PMCID: PMC4286918 DOI: 10.1186/1471-2105-15-339] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2014] [Accepted: 09/29/2014] [Indexed: 11/18/2022] Open
Abstract
Background Signatures are short sequences that are unique and not similar to any other sequence in a database that can be used as the basis to identify different species. Even though several signature discovery algorithms have been proposed in the past, these algorithms require the entirety of databases to be loaded in the memory, thus restricting the amount of data that they can process. It makes those algorithms unable to process databases with large amounts of data. Also, those algorithms use sequential models and have slower discovery speeds, meaning that the efficiency can be improved. Results In this research, we are debuting the utilization of a divide-and-conquer strategy in signature discovery and have proposed a parallel signature discovery algorithm on a computer cluster. The algorithm applies the divide-and-conquer strategy to solve the problem posed to the existing algorithms where they are unable to process large databases and uses a parallel computing mechanism to effectively improve the efficiency of signature discovery. Even when run with just the memory of regular personal computers, the algorithm can still process large databases such as the human whole-genome EST database which were previously unable to be processed by the existing algorithms. Conclusions The algorithm proposed in this research is not limited by the amount of usable memory and can rapidly find signatures in large databases, making it useful in applications such as Next Generation Sequencing and other large database analysis and processing. The implementation of the proposed algorithm is available athttp://www.cs.pu.edu.tw/~fang/DDCSDPrograms/DDCSD.htm.
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Affiliation(s)
| | - Tzu-Fang Sheu
- Department of Computer Science and Communication Engineering, Providence University, 200, Sec, 7, Taiwan Boulevard, 43301 Shalu Dist,, Taichung, Taiwan.
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19
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Oliveira VKP, Ruiz LDS, Oliveira NAJ, Moreira D, Hahn RC, Melo ASDA, Nishikaku AS, Paula CR. Fungemia caused by Candida species in a children's public hospital in the city of São Paulo, Brazil: study in the period 2007-2010. Rev Inst Med Trop Sao Paulo 2014; 56:301-5. [PMID: 25076430 PMCID: PMC4131815 DOI: 10.1590/s0036-46652014000400006] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2013] [Accepted: 01/10/2014] [Indexed: 11/21/2022] Open
Abstract
Candidemia remains a major cause of morbidity and mortality in the health care environment. The epidemiology of Candida infection is changing, mainly in relation to the number of episodes caused by species C. non-albicans. The overall objective of this study was to evaluate the frequency of yeasts of the genus Candida, in a four-year period, isolated from blood of pediatric patients hospitalized in a public hospital of the city of São Paulo, Brazil. In this period, yeasts from blood of 104 patients were isolated and, the identified species of Candida by phenotypic and genotypic methods were: C. albicans (39/104), C. tropicalis (25/104), C. parapsilosis (23/104), Pichia anomala (6/104), C. guilliermondii (5/104), C. krusei (3/104), C. glabrata (2/104) and C. pararugosa (1/104). During the period of the study, a higher frequency of isolates of C. non-albicans (63.55%) (p = 0.0286) was verified. In this study we verified the increase of the non-albicans species throughout the years (mainly in 2009 and 2010). Thus, considering the peculiarities presented by Candida species, a correct identification of species is recommended to lead to a faster diagnosis and an efficient treatment.
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Affiliation(s)
| | - Luciana da Silva Ruiz
- Department of Microbiology, Institute of Biomedical Science II, University of São Paulo, São Paulo, SP, Brazil
| | | | - Débora Moreira
- Department of Microbiology, Institute of Biomedical Science II, University of São Paulo, São Paulo, SP, Brazil
| | - Rosane Christine Hahn
- Division of Infectious and Tropical Diseases, Federal University of Mato Grosso, MT, Brazil
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20
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Wang Q, Gong J, Chisti Y, Sirisansaneeyakul S. Bioconversion of tea polyphenols to bioactive theabrownins by Aspergillus fumigatus. Biotechnol Lett 2014; 36:2515-22. [DOI: 10.1007/s10529-014-1632-0] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2014] [Accepted: 08/06/2014] [Indexed: 11/24/2022]
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21
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Bustamante B, Martins MA, Bonfietti LX, Szeszs MW, Jacobs J, Garcia C, Melhem MSC. Species distribution and antifungal susceptibility profile of Candida isolates from bloodstream infections in Lima, Peru. J Med Microbiol 2014; 63:855-860. [DOI: 10.1099/jmm.0.071167-0] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Yeast identification and in vitro susceptibility testing provide helpful information for appropriate administration of antifungal treatments; however, few reports from the Latin American region have been published. The aim of this study was to identify the species present in isolates from bloodstream infections diagnosed in nine hospitals in Lima, Peru and to determine their in vitro susceptibility to four antifungal drugs. We tested and identified 153 isolates collected between October 2009 and August 2011 using standard methods. PCR and PCR-RFLP assays were performed to distinguish Candida albicans from Candida dubliniensis and to identify species of the Candida parapsilosis and Candida glabrata complexes. Antifungal susceptibility testing for fluconazole, anidulafungin and voriconazole was performed using the CSLI M27-A3 method, and amphotericin B susceptibility was determined using the Etest method. The most frequently isolated species were: C. albicans (61; 39.9 %), C. parapsilosis (43; 28.1 %), C. tropicalis (36; 23.5%) and C. glabrata (8; 5.2 %). The overall susceptibility rates were 98.0 %, 98.7 %, 98.0 % and 97.4 % for amphotericin B, fluconazole, voriconazole and anidulafungin, respectively. No isolate was resistant to more than one drug. These results showed that the rate of resistance to four antifungal drugs was low among Candida bloodstream isolates in Lima, Peru.
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Affiliation(s)
- B. Bustamante
- Instituto de Medicina Tropical Alexander von Humboldt-Universidad Peruana Cayetano Heredia, Lima, Peru
| | | | | | | | - J. Jacobs
- Institute of Tropical Medicine, Antwerp, Belgium
| | - C. Garcia
- Instituto de Medicina Tropical Alexander von Humboldt-Universidad Peruana Cayetano Heredia, Lima, Peru
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22
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Thanyasrisung P, Kesakomol P, Pipattanagovit P, Youngnak-Piboonratanakit P, Pitiphat W, Matangkasombut O. Oral Candida carriage and immune status in Thai human immunodeficiency virus-infected individuals. J Med Microbiol 2014; 63:753-759. [PMID: 24591706 DOI: 10.1099/jmm.0.069773-0] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Oral candidiasis is a common opportunistic infection among human immunodeficiency virus (HIV)-infected individuals, with growing concerns about the emergence of non-albicans species with resistance to antifungal agents. This cross-sectional study determined the prevalence of oral Candida species in Thai HIV-infected adults and factors affecting their colonization. Candida species were identified from oral rinse samples of 60 HIV-infected participants of the MTCT-Plus initiative and 49 healthy controls by culture-based and molecular assays. The prevalence of oral Candida carriage was similar in HIV-infected patients (56.6 %) and in controls (55.1 %, P = 0.87). Candida albicans was the most predominant species in both groups (94.1 % of Candida carriers in HIV, 88.9 % in control). Interestingly, Candida dubliniensis was the second most common species in controls (29.6 %) and the third in HIV-infected patients (11.8 %, P = 0.08). Multivariate analysis showed that, amongst HIV-infected individuals, CD4 count <200 cells mm(-3) was associated with increased prevalence of oral carriage of both C. albicans (P = 0.03) and non-albicans species (P = 0.03). Moreover, patients with tuberculosis infection had a higher prevalence of the non-albicans species than those without (P = 0.03). Intriguingly, contraceptive use was also associated positively with non-albicans and multi-species carriage (P = 0.04 for both). However, use of antiretroviral drugs protected the patients from Candida carriage (P = 0.03), especially from C. albicans (P = 0.02). In conclusion, while HIV-infected individuals had a similar prevalence of oral Candida carriage to that of the control group, host immune status, tuberculosis infection, and contraceptive use may influence oral colonization of Candida, especially of the non-albicans species.
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Affiliation(s)
- Panida Thanyasrisung
- Department of Microbiology and DRU on Oral Microbiology, Faculty of Dentistry, Chulalongkorn University, Bangkok, Thailand
| | - Piyanate Kesakomol
- Interdepartmental Program in Medical Microbiology, Graduate School, Chulalongkorn University, Bangkok, Thailand
| | - Patchara Pipattanagovit
- Department of Microbiology and DRU on Oral Microbiology, Faculty of Dentistry, Chulalongkorn University, Bangkok, Thailand
| | | | - Waranuch Pitiphat
- Department of Community Dentistry, Faculty of Dentistry, Khon Kaen University, Khon Kaen, Thailand
| | - Oranart Matangkasombut
- Department of Microbiology and DRU on Oral Microbiology, Faculty of Dentistry, Chulalongkorn University, Bangkok, Thailand
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23
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Batista GCM, Krebs VLJ, Ruiz LS, Auler ME, Hahn RC, Paula CR. Oral colonization: a possible source for candidemia in low-weight neonates. J Mycol Med 2014; 24:81-6. [PMID: 24440610 DOI: 10.1016/j.mycmed.2013.11.004] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2013] [Revised: 11/07/2013] [Accepted: 11/21/2013] [Indexed: 11/16/2022]
Abstract
OBJECTIVE To check the oral colonization in neonates at high-risk and to associate these cases with candidemia. SUBJECTS AND METHODS This study was conducted in the NICU. For six months, 125 high-risk neonates were investigated for oral colonization and septicemia by yeasts. From this total, 19 neonates had yeasts on the oral mucosae and 12 neonates developed fungemia. All of the 12 neonates with fungemia were included in the amount of 19 who have presented oral colonization by yeasts. RESULTS There was a species concordance between the yeasts of the oral mucosae and the blood in 6 neonates (50%) among the 12 neonates with oral colonization and septicemia at the same time. The yeasts isolated in these 6 cases regarding the species concordance were Candida albicans (5 cases, 83.4%) and Candida parapsilosis (1 case, 16.6%). All of the cases involving an association were confirmed by PFGE. All of the strains of yeasts involved in oral colonization and also blood presented the same karyotype. A total of 66.6% of the patients with strains in agreement progressed to death. CONCLUSION The results indicate the relevance of monitoring the oral microbiota, as a possible source of fungal infection, and assisting to develop appropriate therapeutic strategy.
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Affiliation(s)
- G C M Batista
- Department of Microbiology, Institute of Biomedical Sciences II, University of São Paulo (USP), avenue Profesor Lineu Prestes, 1374, CEP 05508-900, São Paulo, Brazil
| | - V L J Krebs
- College of Medicine, University of São Paulo, São Paulo, Brazil
| | - L S Ruiz
- Department of Microbiology, Institute of Biomedical Sciences II, University of São Paulo (USP), avenue Profesor Lineu Prestes, 1374, CEP 05508-900, São Paulo, Brazil
| | - M E Auler
- Department of Pharmacy, Health Sciences, Universidade Estadual do Centro-Oeste (UNICENTRO), Guarapuava, Paraná, Brazil
| | - R C Hahn
- Division of Infections and Tropical Diseases, Federal University of Mato Grosso, Mato Grosso, MT, Brazil
| | - C R Paula
- Department of Microbiology, Institute of Biomedical Sciences II, University of São Paulo (USP), avenue Profesor Lineu Prestes, 1374, CEP 05508-900, São Paulo, Brazil.
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24
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Fadda M, Pisano M, Scaccabarozzi L, Mossa V, Deplano M, Moroni P, Liciardi M, Cosentino S. Use of PCR-restriction fragment length polymorphism analysis for identification of yeast species isolated from bovine intramammary infection. J Dairy Sci 2013; 96:7692-7. [DOI: 10.3168/jds.2013-6996] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2013] [Accepted: 08/16/2013] [Indexed: 11/19/2022]
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25
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Simitsopoulou M, Peshkova P, Tasina E, Katragkou A, Kyrpitzi D, Velegraki A, Walsh TJ, Roilides E. Species-specific and drug-specific differences in susceptibility of Candida biofilms to echinocandins: characterization of less common bloodstream isolates. Antimicrob Agents Chemother 2013; 57:2562-70. [PMID: 23529739 PMCID: PMC3716187 DOI: 10.1128/aac.02541-12] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2012] [Accepted: 03/15/2013] [Indexed: 11/20/2022] Open
Abstract
Candida species other than Candida albicans are increasingly recognized as causes of biofilm-associated infections. This is a comprehensive study that compared the in vitro activities of all three echinocandins against biofilms formed by different common and infrequently identified Candida isolates. We determined the activities of anidulafungin (ANID), caspofungin (CAS), and micafungin (MFG) against planktonic cells and biofilms of bloodstream isolates of C. albicans (15 strains), Candida parapsilosis (6 strains), Candida lusitaniae (16 strains), Candida guilliermondii (5 strains), and Candida krusei (12 strains) by XTT [2,3-bis(2-methoxy-4-nitro-5-sulfophenyl)-2H-tetrazolium-5-carboxanilide] assay. Planktonic and biofilm MICs were defined as ≥ 50% fungal damage. Planktonic cells of all Candida species were susceptible to the three echinocandins, with MICs of ≤ 1 mg/liter. By comparison, differences in the MIC profiles of biofilms in response to echinocandins existed among the Candida species. Thus, C. lusitaniae and C. guilliermondii biofilms were highly recalcitrant to all echinocandins, with MICs of ≥ 32 mg/liter. In contrast, the MICs of all three echinocandins for C. albicans and C. krusei biofilms were relatively low (MICs ≤ 1 mg/liter). While echinocandins exhibited generally high MICs against C. parapsilosis biofilms, MFG exhibited the lowest MICs against these isolates (4 mg/liter). A paradoxical growth effect was observed with CAS concentrations ranging from 8 to 64 mg/liter against C. albicans and C. parapsilosis biofilms but not against C. krusei, C. lusitaniae, or C. guilliermondii. While non-albicans Candida planktonic cells were susceptible to all echinocandins, there were drug- and species-specific differences in susceptibility among biofilms of the various Candida species, with C. lusitaniae and C. guilliermondii exhibiting profiles of high MICs of the three echinocandins.
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Affiliation(s)
- Maria Simitsopoulou
- Laboratory of Infectious Diseases, 3rd Department of Pediatrics, Aristotle University School of Medicine, Hippokration Hospital, Thessaloniki, Greece
| | - Pavla Peshkova
- Laboratory of Infectious Diseases, 3rd Department of Pediatrics, Aristotle University School of Medicine, Hippokration Hospital, Thessaloniki, Greece
| | - Efthymia Tasina
- Laboratory of Infectious Diseases, 3rd Department of Pediatrics, Aristotle University School of Medicine, Hippokration Hospital, Thessaloniki, Greece
| | - Aspasia Katragkou
- Laboratory of Infectious Diseases, 3rd Department of Pediatrics, Aristotle University School of Medicine, Hippokration Hospital, Thessaloniki, Greece
| | - Daniela Kyrpitzi
- Laboratory of Infectious Diseases, 3rd Department of Pediatrics, Aristotle University School of Medicine, Hippokration Hospital, Thessaloniki, Greece
| | - Aristea Velegraki
- Mycology Laboratory, Medical School, National & Kapodistrian University of Athens, Athens, Greece
| | - Thomas J. Walsh
- Transplantation-Oncology Infectious Diseases Program, Weill Cornell University Medical Center, New York, New York, USA
- Department of Pediatrics, Weill Cornell Medical Center, New York, New York, USA
- Department of Microbiology & Immunology, Weill Cornell Medical Center, New York, New York, USA
| | - Emmanuel Roilides
- Laboratory of Infectious Diseases, 3rd Department of Pediatrics, Aristotle University School of Medicine, Hippokration Hospital, Thessaloniki, Greece
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da Silva CM, de Carvalho Parahym AMR, Leão MPC, de Oliveira NT, de Jesus Machado Amorim R, Neves RP. Fungemia by Candida pelliculosa (Pichia anomala) in a neonatal intensive care unit: a possible clonal origin. Mycopathologia 2012; 175:175-9. [PMID: 23232762 DOI: 10.1007/s11046-012-9605-0] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2012] [Accepted: 11/27/2012] [Indexed: 10/27/2022]
Abstract
Neonatal candidemia can occur, however, infections caused by Candida pelliculosa are rare. Here, we describe an outbreak of candidemia caused by C. pelliculosa among babies hospitalized in a neonatal intensive care unit.
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Affiliation(s)
- Carolina Maria da Silva
- Departamento de Micologia, Centro de Ciências Biológicas, Universidade Federal de Pernambuco, Av. Prof. Nelson Chaves, s/nº, Cidade Universitária, Recife, PE, 50670-420, Brazil
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Ten-Year Study of Species Distribution and Antifungal Susceptibilities of Candida Bloodstream Isolates at a Brazilian Tertiary Hospital. Mycopathologia 2012; 174:389-96. [DOI: 10.1007/s11046-012-9566-3] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2011] [Accepted: 07/03/2012] [Indexed: 10/28/2022]
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Badiee P, Alborzi A. Susceptibility of clinical Candida species isolates to antifungal agents by E-test, Southern Iran: A five year study. IRANIAN JOURNAL OF MICROBIOLOGY 2011; 3:183-8. [PMID: 22530086 PMCID: PMC3330181] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
BACKGROUND AND OBJECTIVES The incidence of fungal infections in immunocompromised patients, especially by Candida species, has increased in recent years. This study was designed to identify Candida species and determine antifungal susceptibility patterns of 595 yeast strains isolated from various clinical specimens. MATERIAL AND METHODS Identification of the isolates were determined by the API 20 C AUX kit and antifungal susceptibilities of the species to fluconazole, amphotericin B, ketoconazole, itraconazole, voriconazole, and caspofungin were determined by the agar-based E-test method. RESULTS Candida albicans (48%) was the most frequently isolated species, followed by Candida kruzei (16.1%), Candida glabrata (13.5%), Candida kefyr (7.4%), Candida parapsilosis (4.8%), Candida tropicalis (1.7%) and other species (8.5%). Resistance varies depending on the species and the respective antifungal agents. Comparing the MIC90 for all the strains, the lower MIC90 was observed for caspofungin (0.5 µg/ml). The MIC90 for all Candida species were 64 µg/ml for fluconazole, 0.75 µg/ml for amphotericin B, 4 µg/ml for ketoconazole, 4 µg/ml for itraconazole, and 2 µg/ml for voriconazole. CONCLUSIONS Species definition and determination of antifungal susceptibility patterns are advised for the proper management and treatment of patients at risk for systemic candidiasis. Resistance to antifungal agents is an alarming sign for the emerging common nosocomial fungal infections.
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Affiliation(s)
- P Badiee
- Corresponding author: Parisa Badiee PhD Address: Prof. Alborzi Clinical Microbiology Research Center, Nemazi Hospital, Zand Ave, Shiraz, Iran. Tel: +98-711-6474292 Fax: +98-711-6474303. E-mail:
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Santiwongkarn P, Kachonboon S, Thanyasrisung P, Matangkasombut O. Prevalence of oral Candida carriage in Thai adolescents. ACTA ACUST UNITED AC 2011; 3:51-5. [DOI: 10.1111/j.2041-1626.2011.0089.x] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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Comparative evaluation of three commercial identification systems using common and rare bloodstream yeast isolates. J Clin Microbiol 2011; 49:2722-7. [PMID: 21543578 DOI: 10.1128/jcm.01253-10] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
The commercial yeast identification systems API ID32C, Auxacolor, and Vitek were evaluated using 251 molecularly identified bloodstream isolates and 2 reference strains, representing a total of 35 species (6 common and 29 rare). Correct identification rates were higher for common species (Auxacolor, 95%; API ID32C, 94%; Vitek, 92%) than for rare species (Auxacolor, 43%; API ID32C, 56%; Vitek, 64%). All systems performed equally among the former, and Vitek performed best among the latter.
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Abstract
Candida albicans is increasing as an opportunistic pathogen causing candidemia and candidiasis worldwide. In addition, other non-albicans Candida species are now also associated with pertinent infections. These include the closely related C. dubliniensis, which shares many phenotypic similarities with C. albicans. These similarities pose problems in the identification of isolates and have previously led to misidentification of these species. As a result, several identification techniques based on phenotypic and genotypic characteristics have been developed to differentiate between these Candida species. This review will focus on the similarities and differences between these two Candida species highlighting different identification methods and their advantages and disadvantages.
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Affiliation(s)
- Ruan Ells
- Department of Microbial, Biochemical and Food Biotechnology, University of the Free State, Bloemfontein, South Africa
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Favalessa OC, Martins MDA, Hahn RC. Aspectos micológicos e suscetibilidade in vitro de leveduras do gênero Candida em pacientes HIV-positivos provenientes do Estado de Mato Grosso. Rev Soc Bras Med Trop 2010; 43:673-7. [DOI: 10.1590/s0037-86822010000600014] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2010] [Accepted: 09/01/2010] [Indexed: 11/21/2022] Open
Abstract
INTRODUÇÃO: A candidíase é uma das infecções fúngicas mais frequentes entre os pacientes infectados pelo vírus da imunodeficiência humana. O presente estudo objetivou a caracterização das leveduras do gênero Candida de distintas amostras clínicas, provenientes de pacientes HIV - positivos, assim como a determinação do perfil de suscetibilidade in vitro a cinco drogas antifúngicas. MÉTODOS: A caracterização dos isolados de Candida sp foi realizada através da metodologia clássica, testes bioquímicos (zimograma e auxanograma) e morfológicos (prova do tubo germinativo e microcultivo em lâmina). Também, foram realizadas a técnica genotípica (PCR) e identificação pelo método comercial API 20C AUX (BioMeriéux). Para a determinação do perfil de suscetibilidade in vitro, foram utilizadas cinco drogas antifúngicas (cetoconazol, fluconazol, itraconazol, voriconazol e anfotericina B), através do método comercialmente disponível - Etest. RESULTADOS: Foram identificados 105 isolados de leveduras do gênero Candida provenientes de 102 pacientes infectados pelo vírus HIV. Destes, foram caracterizadas 82 (78,1%) Candida albicans, 8 (7,6%) Candida parapsilosis, 8 (7,6%) Candida tropicalis, 4 (3,8%) Candida krusei, 2 (1,9%) Candida glabrata e 1 (1%) Candida guilliermondii. CONCLUSÕES: Considerando o perfil geral de sensibilidade, 60% dos isolados foram suscetíveis a todos os antifúngicos testados, porém as espécies C. tropicalis e C. krusei demonstraram uma tendência a valores mais elevados de CIMs para os azóis do que os encontrados paraC. albicans, sugerindo resistência.
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Affiliation(s)
| | | | - Rosane Christine Hahn
- Universidade Federal de Mato Grosso; Universidade Federal de Mato Grosso, MT; Hospital Geral Universitário, MT
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Molecular typing of Candida albicans strains isolated from denture wearers by repetitive sequence-based PCR. Eur J Clin Microbiol Infect Dis 2010; 30:141-9. [DOI: 10.1007/s10096-010-1062-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2010] [Accepted: 08/28/2010] [Indexed: 11/28/2022]
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Auler ME, Morreira D, Rodrigues FFO, Abr Ao MS, Margarido PFR, Matsumoto FE, Silva EG, Silva BCM, Schneider RP, Paula CR. Biofilm formation on intrauterine devices in patients with recurrent vulvovaginal candidiasis. Med Mycol 2010; 48:211-6. [PMID: 20055746 DOI: 10.3109/13693780902856626] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
A biofilm is a complex community of surface-associated cells enclosed in a polymer matrix. They attach to solid surfaces and their formation can be affected by growth conditions and co-infection with other pathogens. The presence of biofilm may protect the microorganisms from host defenses, as well as significantly reduce their susceptibility to antifungal agents. Pathogenic microbes can form biofilms on the inert surfaces of implanted devices such as catheters, prosthetic cardiac valves and intrauterine devices (IUDs). The present study was carried out to analyze the presence of biofilm on the surface of intrauterine devices in patients with recurrent vulvovaginal candidiasis, and to determine the susceptibility profile of the isolated yeasts to amphotericin B and fluconazole. Candida albicans was recovered from the IUDs and it was found to be susceptible to the antifungal agents when tested under planktonic growing conditions. These findings indicate the presence of the biofilm on the surface of the IUD as an important risk factor for recurrent vulvovaginal candidiasis.
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Affiliation(s)
- Marcos E Auler
- Institute of Biomedical Science, Department Microbiology, University of São Paulo, Brazil
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Macêdo DPC, Oliveira NT, Farias AMA, Silva VKA, Wilheim AB, Couto FM, Neves RP. Esophagitis caused byCandida guilliermondiiin diabetes mellitus: first reported case. Med Mycol 2010; 48:862-5. [DOI: 10.3109/13693780903582614] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
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Marinho SA, Teixeira AB, Santos OS, Cazanova RF, Ferreira CAS, Cherubini K, de Oliveira SD. Identification of Candida spp. by phenotypic tests and PCR. Braz J Microbiol 2010; 41:286-94. [PMID: 24031493 PMCID: PMC3768677 DOI: 10.1590/s1517-83822010000200004] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2009] [Revised: 07/16/2009] [Accepted: 02/19/2010] [Indexed: 11/22/2022] Open
Abstract
The correct identification of Candida species is of great importance, as it presents prognostic and therapeutical significance, allowing an early and appropriate antifungical therapy. The purpose of this study was to identify isolates of Candida spp. from oral mucosa of 38 patients with oral candidosis evaluated in 2004 by phenotypic methods and PCR, discriminating C. albicans from the other Candida species. The tests used for phenotypic analysis were germ-tube and chlamydoconidia production, culture in CHROMAgar™ Candida, carbohydrate assimilation test, growth at 45ºC and culture in Tween 80 agar. Genotypic confirmation was performed by PCR. Phenotypic tests showed that 63.2% strains formed germ-tubes, 73.7% produced chlamydoconidia, and 63.2% showed green colonies in chromogenic medium, presumptively indicating C. albicans or C. dubliniensis. The carbohydrate assimilation test confirmed these results. A total of 21% strains were identified as C. krusei and 13.2% were indicative of C. tropicalis. Of these later strains, three produced chlamydoconidia. The association of other phenotypic tests with culture in Tween 80 agar identified 95.8% of strains as C. albicans and 4.2% as C. dubliniensis. All 24 strains indicative of C. albicans and C. dubliniensis were confirmed by PCR as C. albicans.
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Affiliation(s)
- Sandra Aparecida Marinho
- Laboratório de Imunologia e Microbiologia, Faculdade de Biociências, Pontifícia Universidade Católica do Rio Grande do Sul , Porto Alegre, RS , Brasil ; Serviço de Estomatologia, Hospital São Lucas, Pontifícia Universidade Católica do Rio Grande do Sul , Porto Alegre, RS , Brasil
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A parallel and incremental algorithm for efficient unique signature discovery on DNA databases. BMC Bioinformatics 2010; 11:132. [PMID: 20230647 PMCID: PMC2848650 DOI: 10.1186/1471-2105-11-132] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2009] [Accepted: 03/16/2010] [Indexed: 11/15/2022] Open
Abstract
Background DNA signatures are distinct short nucleotide sequences that provide valuable information that is used for various purposes, such as the design of Polymerase Chain Reaction primers and microarray experiments. Biologists usually use a discovery algorithm to find unique signatures from DNA databases, and then apply the signatures to microarray experiments. Such discovery algorithms require to set some input factors, such as signature length l and mismatch tolerance d, which affect the discovery results. However, suggestions about how to select proper factor values are rare, especially when an unfamiliar DNA database is used. In most cases, biologists typically select factor values based on experience, or even by guessing. If the discovered result is unsatisfactory, biologists change the input factors of the algorithm to obtain a new result. This process is repeated until a proper result is obtained. Implicit signatures under the discovery condition (l, d) are defined as the signatures of length ≤ l with mismatch tolerance ≥ d. A discovery algorithm that could discover all implicit signatures, such that those that meet the requirements concerning the results, would be more helpful than one that depends on trial and error. However, existing discovery algorithms do not address the need to discover all implicit signatures. Results This work proposes two discovery algorithms - the consecutive multiple discovery (CMD) algorithm and the parallel and incremental signature discovery (PISD) algorithm. The PISD algorithm is designed for efficiently discovering signatures under a certain discovery condition. The algorithm finds new results by using previously discovered results as candidates, rather than by using the whole database. The PISD algorithm further increases discovery efficiency by applying parallel computing. The CMD algorithm is designed to discover implicit signatures efficiently. It uses the PISD algorithm as a kernel routine to discover implicit signatures efficiently under every feasible discovery condition. Conclusions The proposed algorithms discover implicit signatures efficiently. The presented CMD algorithm has up to 97% less execution time than typical sequential discovery algorithms in the discovery of implicit signatures in experiments, when eight processing cores are used.
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Mycotic VulvoVaginitis: Epidemiology, Pathogenesis and Profile of Antifungal Agents. J Taibah Univ Med Sci 2009. [DOI: 10.1016/s1658-3612(09)70101-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
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Xavier PCN, Chang MR, Nunes MO, Palhares DB, Silva RAE, Bonfim GF, Almeida Júnior NF. Candidemia neonatal, em hospital público do Mato Grosso do Sul. Rev Soc Bras Med Trop 2008; 41:459-63. [DOI: 10.1590/s0037-86822008000500005] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2007] [Accepted: 08/27/2008] [Indexed: 11/22/2022] Open
Abstract
O objetivo de nosso estudo foi realizar tipagem molecular de 25 amostras clínicas de Candida spp, isoladas de crianças com candidemia, internadas na unidade de terapia intensiva neonatal de um Hospital Universitário entre 1998 a 2006. Dados demográficos e clínicos foram obtidos de prontuários para conhecimento dos aspectos clínicos e epidemiológicos. Identificação das leveduras foi feita por método convencional e a susceptibilidade antifúngica por método de microdiluição. O perfil genético foi determinado pela técnica de RAPD-PCR. Candida albicans (11; 44%) e Candida parapsilosis (10; 40%) foram as mais isoladas. Dezessete (68%) dos recém-nascidos tinham peso inferior a 1.500g. Prematuridade (92%), uso de cateter venoso central (100%), foram as condições de risco mais associados. Dezenove (76%) pacientes foram a óbito. Apenas uma cepa de Candida parapsilosis, mostrou ser sensível dose dependente ao fluconazol. Na análise molecular, foram observados 11 padrões genéticos distintos. Somente em dois casos foi observada relação epidemiológica, sugerindo mesma fonte de infecção.
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Huang CH, Lee FL, Tai CJ. A novel specific DNA marker in Saccharomyces bayanus for species identification of the Saccharomyces sensu stricto complex. J Microbiol Methods 2008; 75:531-4. [PMID: 18786577 DOI: 10.1016/j.mimet.2008.08.005] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2008] [Revised: 08/18/2008] [Accepted: 08/19/2008] [Indexed: 11/15/2022]
Abstract
This study was based on RAPD fingerprinting for species identification of the Saccharomyces sensu stricto complex. 40 random primers were used for RAPD analysis. The results showed that one of these primers, OPT-18, produced a 974 bp species-specific band, which was only found in the tested S. bayanus. Afterward this specific fragment was isolated from agarose gel and ligated into vector for DNA sequencing. A pair of primer SpeOPT18Sbay-F2 and SpeOPT18Sbay-R2 were designed according to the cloned species-specific sequence, which was employed for PCR with the template DNA of the S. sensu stricto strains, single 779 bp species-specific band was only found in S. bayanus. Therefore, we conclude that our novel species DNA marker could be used to rapidly and accurately identify the species of S. bayanus from S. sensu stricto complex by direct PCR.
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Affiliation(s)
- Chien-Hsun Huang
- Bioresource Collection and Research Center, Food Industry Research and Development Institute, Hsinchu, Taiwan
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Abaci Ö, Halki-Uztan A, Ates M. Specific identification ofCandida albicans andCandida dubliniensis by PCR using species-specific primers. ANN MICROBIOL 2008. [DOI: 10.1007/bf03175338] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
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Putignani L, Paglia MG, Bordi E, Nebuloso E, Pucillo LP, Visca P. Identification of clinically relevant yeast species by DNA sequence analysis of the D2 variable region of the 25–28S rRNA gene. Mycoses 2008; 51:209-27. [DOI: 10.1111/j.1439-0507.2007.01472.x] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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CHRYSSANTHOU E, FERNANDEZ V, PETRINI B. Performance of commercial latex agglutination tests for the differentiation ofCandida dubliniensisandCandida albicansin routine diagnostics. APMIS 2007; 115:1281-4. [DOI: 10.1111/j.1600-0643.2007.00801.x] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Linton CJ, Borman AM, Cheung G, Holmes AD, Szekely A, Palmer MD, Bridge PD, Campbell CK, Johnson EM. Molecular identification of unusual pathogenic yeast isolates by large ribosomal subunit gene sequencing: 2 years of experience at the United kingdom mycology reference laboratory. J Clin Microbiol 2007; 45:1152-8. [PMID: 17251397 PMCID: PMC1865856 DOI: 10.1128/jcm.02061-06] [Citation(s) in RCA: 82] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Rapid identification of yeast isolates from clinical samples is particularly important given their innately variable antifungal susceptibility profiles. We present here an analysis of the utility of PCR amplification and sequence analysis of the hypervariable D1/D2 region of the 26S rRNA gene for the identification of yeast species submitted to the United Kingdom Mycology Reference Laboratory over a 2-year period. A total of 3,033 clinical isolates were received from 2004 to 2006 encompassing 50 different yeast species. While more than 90% of the isolates, corresponding to the most common Candida species, could be identified by using the AUXACOLOR2 yeast identification kit, 153 isolates (5%), comprised of 47 species, could not be identified by using this system and were subjected to molecular identification via 26S rRNA gene sequencing. These isolates included some common species that exhibited atypical biochemical and phenotypic profiles and also many rarer yeast species that are infrequently encountered in the clinical setting. All 47 species requiring molecular identification were unambiguously identified on the basis of D1/D2 sequences, and the molecular identities correlated well with the observed biochemical profiles of the various organisms. Together, our data underscore the utility of molecular techniques as a reference adjunct to conventional methods of yeast identification. Further, we show that PCR amplification and sequencing of the D1/D2 region reliably identifies more than 45 species of clinically significant yeasts and can also potentially identify new pathogenic yeast species.
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Affiliation(s)
- Christopher J Linton
- Mycology Reference Laboratory, Health Protection Agency South-West Regional Laboratory, Myrtle Road, Bristol BS2 8EL, United Kingdom.
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Chavasco JK, Paula CR, Hirata MH, Aleva NA, Melo CED, Gambale W, Ruiz LDS, Franco MC. Molecular identification of Candida dubliniensis isolated from oral lesions of HIV-positive and HIV-negative patients in São Paulo, Brazil. Rev Inst Med Trop Sao Paulo 2006; 48:21-6. [PMID: 16547575 DOI: 10.1590/s0036-46652006000100005] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Candida dubliniensis is a new, recently described species of yeast. This emerging oral pathogen shares many phenotypic and biochemical characteristics with C. albicans, making it hard to differentiate between them, although they are genotypically distinct. In this study, PCR (Polymerase Chain Reaction) was used to investigate the presence of C. dubliniensis in samples in a culture collection, which had been isolated from HIV-positive and HIV-negative patients with oral erythematous candidiasis. From a total of 37 samples previously identified as C. albicans by the classical method, two samples of C. dubliniensis (5.4%) were found through the use of PCR. This study underscores the presence of C. dubliniensis, whose geographical and epidemiological distribution should be more fully investigated.
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Tekeli A, Akan OA, Koyuncu E, Dolapci I, Uysal S. Initial Candida dubliniensis isolate in Candida spp. positive haemocultures in Turkey between 2001 and 2004. Mycoses 2006; 49:60-4. [PMID: 16367821 DOI: 10.1111/j.1439-0507.2005.01181.x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
Candida dubliniensis which was first recognized in 1995 can be easily misidentified because of its phenotypic similarities with Candida albicans. In this study blood samples of patients from various departments of Ankara University Medical Faculty between January 2001-June 2004 were investigated for the distribution of Candida spp. and the presence of C. dubliniensis. Culture positive 67 fungi were included to the study. Phenotypic tests such as chlamydospore formation, colony morphology on Staib agar, growth at 45 degrees C, carbohydrate assimilation profiles were investigated for identification and differentiation of C. dubliniensis from C. albicans. To confirm the results polymerase chain reaction were used for suspected C. albicans and C. dubliniensis isolates. Among 38 germ tube and chlamydospore forming isolates, 37 of them were found as C. albicans and one as C. dubliniensis. The incidence of C. dubliniensis in our hospital is still low, this is the first C. dubliniensis isolate as an agent of candidaemia reported from Turkey.
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Affiliation(s)
- Alper Tekeli
- Department of Microbiology and Clinical Microbiology, Ibn-I Sina Hospital, Ankara University School of Medicine, Turkey.
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Beh AL, Fleet GH, Prakitchaiwattana C, Heard GM. Evaluation of molecular methods for the analysis of yeasts in foods and beverages. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2006; 571:69-106. [PMID: 16408594 DOI: 10.1007/0-387-28391-9_4] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Affiliation(s)
- Ai Lin Beh
- Food Science and Technology, School of Chemical Engineering and Industrial Chemistry, University of New South Wales, Sydney, Australia
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Ramos JP, Rosa CA, Carvalho EMM, Leoncini O, Valente P. Heteroduplex mobility assay of the 26S rDNA D1/D2 region for differentiation of clinically relevant Candida species. Antonie van Leeuwenhoek 2005; 89:39-44. [PMID: 16328861 DOI: 10.1007/s10482-005-9007-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/02/2005] [Accepted: 08/08/2005] [Indexed: 11/26/2022]
Abstract
The Heteroduplex Mobility Assay (HMA) method using the PCR amplified D1/D2 region of the 26S rDNA was tested for the differentiation of clinically relevant Candida species. Strains belonging to the same species are not expected to form heteroduplexes in this assay when their PCR products are mixed. D1/D2 HMA experiments between all Candida type strains tested showed heteroduplex formation, including Candida albicans and Candida dubliniensis. There was no heteroduplex formation when most clinical and non-type strains were tested against the type strain of their presumptive species, except when C. albicans WVE and C. dubliniensis TAI were analysed. Additional HMA experiments, phenotypic characterisation, and D1/D2 sequencing identified these isolates as Candida tropicalis and Candida parapsilosis, respectively. HMA provides a rapid and relatively simple molecular tool for the differentiation of potentially pathogenic Candida species.
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Affiliation(s)
- Jesus P Ramos
- Departamento de Genética, Instituto de Biologia, CCS, bloco A, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brasil
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