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Shankarnarayan SA, Charlebois DA. Machine learning to identify clinically relevant Candida yeast species. Med Mycol 2024; 62:myad134. [PMID: 38130236 DOI: 10.1093/mmy/myad134] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2023] [Revised: 12/06/2023] [Accepted: 12/19/2023] [Indexed: 12/23/2023] Open
Abstract
Fungal infections, especially due to Candida species, are on the rise. Multi-drug resistant organisms such as Candida auris are difficult and time consuming to identify accurately. Machine learning is increasingly being used in health care, especially in medical imaging. In this study, we evaluated the effectiveness of six convolutional neural networks (CNNs) to identify four clinically important Candida species. Wet-mounted images were captured using bright field live-cell microscopy followed by separating single-cells, budding-cells, and cell-group images which were then subjected to different machine learning algorithms (custom CNN, VGG16, ResNet50, InceptionV3, EfficientNetB0, and EfficientNetB7) to learn and predict Candida species. Among the six algorithms tested, the InceptionV3 model performed best in predicting Candida species from microscopy images. All models performed poorly on raw images obtained directly from the microscope. The performance of all models increased when trained on single and budding cell images. The InceptionV3 model identified budding cells of C. albicans, C. auris, C. glabrata (Nakaseomyces glabrata), and C. haemulonii in 97.0%, 74.0%, 68.0%, and 66.0% cases, respectively. For single cells of C. albicans, C. auris, C. glabrata, and C. haemulonii InceptionV3 identified 97.0%, 73.0%, 69.0%, and 73.0% cases, respectively. The sensitivity and specificity of InceptionV3 were 77.1% and 92.4%, respectively. Overall, this study provides proof of the concept that microscopy images from wet-mounted slides can be used to identify Candida yeast species using machine learning quickly and accurately.
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Affiliation(s)
| | - Daniel A Charlebois
- Department of Physics, University of Alberta, Edmonton, Alberta, T6G-2E1, Canada
- Department of Physics, Department of Biological Sciences, University of Alberta, Edmonton, Alberta, T6G-2E9, Canada
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Nouroloyouni A, Moghaddam N, Nuroloyuni S, Milani AS, Yavari HR, Majidi AR. Molecular Identification of Candida albicans in Endodontic Retreatment Cases by SYBR Green I Real-time Polymerase Chain Reaction and its Association with Endodontic Symptoms. JOURNAL OF DENTISTRY (SHIRAZ, IRAN) 2023; 24:429-437. [PMID: 38149236 PMCID: PMC10749437 DOI: 10.30476/dentjods.2023.91706.1786] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Figures] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Revised: 03/25/2023] [Accepted: 04/11/2023] [Indexed: 12/28/2023]
Abstract
Statement of the Problem Recent microbiological studies have expressed ever-increasing concerns about Candida albicans as a causal factor in the failure of endodontic treatments. Real-time quantitative polymerase chain reaction (qPCR), including the SYBR Green I system, is a technique in which a fluorescent dye is incorporated into the double-stranded DNA that is produced during DNA polymerase activity. Purpose This study aimed to determine the relative prevalence of Candida albicans in root canals of retreatment cases and its association with endodontic symptoms. Materials and Method In the present cross-sectional/analytical study fifty subjects were selected. Clinical features and radiographic status of the teeth were also evaluated. After access cavity preparation, the retrieved material and dentinal chips removed from the root canal were transferred into 1.5-mL microtubes, followed by storage at -20ºC until used for DNA extraction. A DNeasy Tissue Kit was used to extract DNA using the DNeasy protocol for animal tissues. Master Plus SYBR Green I (Jena Bioscience, Germany) was used in a Rotor-gene Real-time PCR System for real-time PCR. The relationship between the presence of Candida albicans and the clinical and radiographic features were analyzed using McNemar's test. Results There was a significant relationship between the radiographic findings in endodontically treated teeth and the presence of Candida albicans. However, there was no significant relationship between the presence of Candida albicans and any of the clinical symptoms. Conclusion In spite of the limitations of this study, we concluded that Candida albicans was associated with root canal infections in endodontic retreatment cases, but there was no relationship between root canal infections and the clinical symptoms.
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Affiliation(s)
- Ahmad Nouroloyouni
- Dept. of Endodontics, Faculty of Dentistry, Ardabil University of Medical Sciences, Ardabil, Iran
| | - Negar Moghaddam
- Dept. of Endodontics, Faculty of Dentistry, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Sarah Nuroloyuni
- Dept. of Pediatric Dentistry, Faculty of Dentistry, Ardabil University of Medical Sciences, Ardabil, Iran
| | - Amin Salem Milani
- Dept. of Endodontics, Faculty of Dentistry, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Hamid Reza Yavari
- Dept. of Endodontics, Faculty of Dentistry, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Ali Reza Majidi
- Dept. of Endodontics, Faculty of Dentistry, Qom University of Medical Sciences, Qom, Iran
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Lorenzo-Villegas DL, Gohil NV, Lamo P, Gurajala S, Bagiu IC, Vulcanescu DD, Horhat FG, Sorop VB, Diaconu M, Sorop MI, Oprisoni A, Horhat RM, Susan M, MohanaSundaram A. Innovative Biosensing Approaches for Swift Identification of Candida Species, Intrusive Pathogenic Organisms. Life (Basel) 2023; 13:2099. [PMID: 37895480 PMCID: PMC10608220 DOI: 10.3390/life13102099] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2023] [Revised: 10/17/2023] [Accepted: 10/20/2023] [Indexed: 10/29/2023] Open
Abstract
Candida is the largest genus of medically significant fungi. Although most of its members are commensals, residing harmlessly in human bodies, some are opportunistic and dangerously invasive. These have the ability to cause severe nosocomial candidiasis and candidemia that affect the viscera and bloodstream. A prompt diagnosis will lead to a successful treatment modality. The smart solution of biosensing technologies for rapid and precise detection of Candida species has made remarkable progress. The development of point-of-care (POC) biosensor devices involves sensor precision down to pico-/femtogram level, cost-effectiveness, portability, rapidity, and user-friendliness. However, futuristic diagnostics will depend on exploiting technologies such as multiplexing for high-throughput screening, CRISPR, artificial intelligence (AI), neural networks, the Internet of Things (IoT), and cloud computing of medical databases. This review gives an insight into different biosensor technologies designed for the detection of medically significant Candida species, especially Candida albicans and C. auris, and their applications in the medical setting.
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Affiliation(s)
| | - Namra Vinay Gohil
- Department of Internal Medicne, Medical College Baroda, Vadodara 390001, India;
- Department of Internal Medicne, SSG Hospital Vadodara, Gotri, Vadodara 390021, India
| | - Paula Lamo
- Escuela Superior de Ingeniería y Tecnología, Universidad Internacional de La Rioja, 26006 Logroño, Spain;
| | - Swathi Gurajala
- College of Applied Medical Sciences in Jubail, Imam Abdulrahman bin Faisal University, Dammam 31441, Saudi Arabia;
| | - Iulia Cristina Bagiu
- Department of Microbiology, “Victor Babes” University of Medicine and Pharmacy, Eftimie Murgu Square 2, 300041 Timisoara, Romania; (D.D.V.); (F.G.H.)
- Multidisciplinary Research Center on Antimicrobial Resistance (MULTI-REZ), Microbiology Department, “Victor Babes” University of Medicine and Pharmacy, Eftimie Murgu Square 2, 300041 Timisoara, Romania
| | - Dan Dumitru Vulcanescu
- Department of Microbiology, “Victor Babes” University of Medicine and Pharmacy, Eftimie Murgu Square 2, 300041 Timisoara, Romania; (D.D.V.); (F.G.H.)
- Multidisciplinary Research Center on Antimicrobial Resistance (MULTI-REZ), Microbiology Department, “Victor Babes” University of Medicine and Pharmacy, Eftimie Murgu Square 2, 300041 Timisoara, Romania
| | - Florin George Horhat
- Department of Microbiology, “Victor Babes” University of Medicine and Pharmacy, Eftimie Murgu Square 2, 300041 Timisoara, Romania; (D.D.V.); (F.G.H.)
- Multidisciplinary Research Center on Antimicrobial Resistance (MULTI-REZ), Microbiology Department, “Victor Babes” University of Medicine and Pharmacy, Eftimie Murgu Square 2, 300041 Timisoara, Romania
| | - Virgiliu Bogdan Sorop
- Department of Obstetrics and Gynecology, “Victor Babes” University of Medicine and Pharmacy, Eftimie Murgu Square, No. 2, 300041 Timisoara, Romania; (V.B.S.); (M.D.)
| | - Mircea Diaconu
- Department of Obstetrics and Gynecology, “Victor Babes” University of Medicine and Pharmacy, Eftimie Murgu Square, No. 2, 300041 Timisoara, Romania; (V.B.S.); (M.D.)
| | - Madalina Ioana Sorop
- Doctoral School, “Victor Babes” University of Medicine and Pharmacy, 300041 Timisoara, Romania;
| | - Andrada Oprisoni
- Department of Pediatrics, Discipline of Pediatric Oncology and Hematology, “Victor Babes” University of Medicine and Pharmacy, Eftimie Murgu Square, No. 2, 300041 Timisoara, Romania;
| | - Razvan Mihai Horhat
- Department of Conservative Dentistry and Endodontics, Faculty of Dental Medicine, “Victor Babes” University of Medicine and Pharmacy Timisoara, Eftimie Murgu Square 2, 300041 Timisoara, Romania;
| | - Monica Susan
- Centre for Preventive Medicine, Department of Internal Medicine, “Victor Babes” University of Medicine and Pharmacy, Eftimie Murgu Square, No. 2, 300041 Timisoara, Romania;
| | - ArunSundar MohanaSundaram
- School of Pharmacy, Sathyabama Institute of Science and Technology, Jeppiaar Nagar, Rajiv Gandhi Salai, Chennai 600119, India;
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Dubois VA, Salgado PA, Gliosca LA, Molgatini SL. gDNA extraction from Candida albicans and Candida dubliniensis in subgingival samples in Argentina. Evaluation of different methods. ACTA ODONTOLOGICA LATINOAMERICANA : AOL 2023; 36:78-85. [PMID: 37776504 PMCID: PMC10557081 DOI: 10.54589/aol.36/2/78] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/01/2022] [Accepted: 02/01/2022] [Indexed: 10/02/2023]
Abstract
The oral cavity constitutes a unique ecosystem with highly variable ecological niches that harbor a great variety of microorganisms, including yeasts. Molecular methods are currently considered the gold standard for identifying species, although they involve limitations associated with the disruption of yeast cell walls to release the genomic DNA (gDNA) for amplification. AIM The aim of this study was to compare the performance of different methods for extracting gDNA from Candida albicans and Candida dubliniensis, subsequently amplifying DNA by PCR. MATERIALS AND METHOD Fifty-two isolates (16 C. albicans and 36 C. dubliniensis) were obtained from subgingival biofilm of HIV+ patients with clinical signs of periodontal disease. The study evaluated 6 gDNA extraction methods and two PCR amplification methods. Furthermore, the presence of alleles of HWP1 gene was determined in C. albicans. RESULTS Comparisons of six methods show statistically significant differences (p <0.001) except for C. albicans in two of them. For C. dubliniensis, statistical differences were observed in all comparisons. Commercial methods were more efficient for concentrating gDNA than in-house methods, and both PCRs were effective. Ten heterozygous C. albicans isolates for this allele were positive for the HWP1-1 / HWP1-2 allele, one was homozygous for Wild Type HWP1-1 allele, and 5 were homozygous for novel/rare HWP1-2 allele. CONCLUSIONS This study aims to provide simple, inexpensive strategies for phenotypic identification and molecular confirmation of Candida albicans and Candida dubliniensis for non-reference laboratories with low complexity and/or low budgets.
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Affiliation(s)
- Verónica A Dubois
- Universidad de Buenos Aires. Facultad de Odontología. Hospital Odontológico Universitario. Cátedra de Microbiología y Parasitología, Buenos Aires, Argentina
- Universidad de Buenos Aires, Facultad de Odontología, Instituto de Investigaciones en Salud Pública, Buenos Aires, Argentina
| | - Pablo A Salgado
- Universidad de Buenos Aires. Facultad de Odontología. Hospital Odontológico Universitario. Cátedra de Microbiología y Parasitología, Buenos Aires, Argentina
- Universidad de Buenos Aires, Facultad de Odontología, Instituto de Investigaciones en Salud Pública, Buenos Aires, Argentina
- Universidad de Buenos Aires, Facultad de Odontología, Hospital Odontológico Universitario, Cátedra de Odontología Preventiva y Comunitaria, Buenos Aires, Argentina
| | - Laura A Gliosca
- Universidad de Buenos Aires. Facultad de Odontología. Hospital Odontológico Universitario. Cátedra de Microbiología y Parasitología, Buenos Aires, Argentina.
- Universidad de Buenos Aires, Facultad de Odontología, Instituto de Investigaciones en Salud Pública, Buenos Aires, Argentina
| | - Susana L Molgatini
- Universidad de Buenos Aires. Facultad de Odontología. Hospital Odontológico Universitario. Cátedra de Microbiología y Parasitología, Buenos Aires, Argentina
- Universidad de Buenos Aires, Facultad de Odontología, Instituto de Investigaciones en Salud Pública, Buenos Aires, Argentina
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Feng J, Cui X, Du B, Zhao H, Feng Y, Cui J, Yan C, Gan L, Fan Z, Fu T, Xu Z, Yu Z, Zhang R, Du S, Tian Z, Zhang Q, Xue G, Yuan J. Detection and Quantification of Klebsiella pneumoniae in Fecal Samples Using Digital Droplet PCR in Comparison with Real-Time PCR. Microbiol Spectr 2023; 11:e0424922. [PMID: 37306605 PMCID: PMC10433836 DOI: 10.1128/spectrum.04249-22] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Accepted: 05/18/2023] [Indexed: 06/13/2023] Open
Abstract
This study aimed to develop a rapid and sensitive droplet digital PCR (ddPCR) assay for the specific detection of Klebsiella pneumoniae in fecal samples, and to evaluate its application in the clinic by comparison with real-time PCR assay and conventional microbial culture. Specific primers and a probe targeting the K. pneumoniae hemolysin (khe) gene were designed. Thirteen other pathogens were used to evaluate the specificity of the primers and probe. A recombinant plasmid containing the khe gene was constructed and used to assess the sensitivity, repeatability, and reproducibility of the ddPCR. Clinical fecal samples (n = 103) were collected and tested by the ddPCR, real-time PCR, and conventional microbial culture methods. The detection limit of ddPCR for K. pneumoniae was 1.1 copies/μL, about a 10-fold increase in sensitivity compared with real-time PCR. The ddPCR was negative for the 13 pathogens other than K. pneumoniae, confirming its high specificity. Clinical fecal samples gave a higher rate of positivity in the K. pneumoniae ddPCR assay than in analysis by real-time PCR or conventional culture. ddPCR also showed less inhibition by the inhibitor in fecal sample than real-time PCR. Thus, we established a sensitive and effective ddPCR-based assay method for K. pneumoniae. It could be a useful tool for K. pneumoniae detection in feces and may serve as a reliable method to identify causal pathogens and help guide treatment decisions. IMPORTANCE Klebsiella pneumoniae can cause a range of illnesses and has a high colonization rate in the human gut, making it crucial to develop an efficient method for detecting K. pneumoniae in fecal samples.
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Affiliation(s)
- Junxia Feng
- Department of Bacteriology, Capital Institute of Pediatrics, Beijing, China
| | - Xiaohu Cui
- Department of Bacteriology, Capital Institute of Pediatrics, Beijing, China
| | - Bing Du
- Department of Bacteriology, Capital Institute of Pediatrics, Beijing, China
- School of Biological Sciences, University of Edinburgh, Edinburgh, United Kingdom
| | - Hanqing Zhao
- Department of Bacteriology, Capital Institute of Pediatrics, Beijing, China
| | - Yanling Feng
- Department of Bacteriology, Capital Institute of Pediatrics, Beijing, China
| | - Jinghua Cui
- Department of Bacteriology, Capital Institute of Pediatrics, Beijing, China
| | - Chao Yan
- Department of Bacteriology, Capital Institute of Pediatrics, Beijing, China
| | - Lin Gan
- Department of Bacteriology, Capital Institute of Pediatrics, Beijing, China
| | - Zheng Fan
- Department of Bacteriology, Capital Institute of Pediatrics, Beijing, China
| | - Tongtong Fu
- Department of Bacteriology, Capital Institute of Pediatrics, Beijing, China
| | - Ziying Xu
- Department of Bacteriology, Capital Institute of Pediatrics, Beijing, China
| | - Zihui Yu
- Department of Bacteriology, Capital Institute of Pediatrics, Beijing, China
| | - Rui Zhang
- Department of Bacteriology, Capital Institute of Pediatrics, Beijing, China
| | - Shuheng Du
- Department of Bacteriology, Capital Institute of Pediatrics, Beijing, China
| | - Ziyan Tian
- Department of Bacteriology, Capital Institute of Pediatrics, Beijing, China
| | - Qun Zhang
- Department of Bacteriology, Capital Institute of Pediatrics, Beijing, China
| | - Guanhua Xue
- Department of Bacteriology, Capital Institute of Pediatrics, Beijing, China
| | - Jing Yuan
- Department of Bacteriology, Capital Institute of Pediatrics, Beijing, China
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Taqi Al-Khazali M, Mousa Hassan B, Ahmed AbedIbrahim S. Molecular Identification of Candida albicans and C. dubliniensis Using Small Subunit rRNA Gene Sequence in Kerbala, Iraq. ARCHIVES OF RAZI INSTITUTE 2023; 78:1035-1040. [PMID: 38028831 PMCID: PMC10657961 DOI: 10.22092/ari.2022.360086.2546] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Accepted: 11/26/2022] [Indexed: 12/01/2023]
Abstract
This study was conducted to confirm the phenotypic diagnosis of two Candida species, including Candida albicans (C. albicans) and Candida dubliniensis (C. dubliniensis). They were previously isolated in another study from cases of oral candidiasis using polymerase chain reaction and determining the nitrogenous base sequences of the 18 SrRNA product duplication using the NS1 and NS8 primers. The sequences of the multiple bases were analyzed using the Basic Local Alignment Search Tool program (BLAST), which proved that the two diagnosed Candida strains belong to two species, including C. albicans and C. dubliniensis, respectively. Additionally, the comparison of these sequences to the data available in the National Center for Biotechnology Information (NCBI) database showed that C. albicans strains in this study were 99% similar to the universal strains of C. albicans from Japan, Brazil, the United States, Germany, India, China, Pakistan, and Egypt. The C. dubliniensis strains in this study also had the highest genetic similarity rate of 99% to the C. dubliniensis strains isolated from the United States, Netherlands, France, and Germany. The study strains were recorded in the GenBank database with the sequence codes MZ574137 and MZ574410.1 for C. albicans and C. dubliniensis, respectively. The results of the 18 SrRNA region's duplication also showed variations between C. albicans and C. dubliniensis, represented by the presence of three mutations of the first type and two mutations in the second type at different sequence sites.
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Affiliation(s)
- M Taqi Al-Khazali
- Department of Biology, College of Science, University of Kerbala, Kerbala, Iraq
| | - B Mousa Hassan
- Department of Biology, College of Education, University of Kerbala, Kerbala, Iraq
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Yang Z, Zhang F, Li D, Wang S, Pang Z, Chen L, Li R, Shi D. Correlation Between Drug Resistance and Virulence of Candida Isolates from Patients with Candidiasis. Infect Drug Resist 2022; 15:7459-7473. [PMID: 36544991 PMCID: PMC9762413 DOI: 10.2147/idr.s387675] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2022] [Accepted: 11/23/2022] [Indexed: 12/23/2022] Open
Abstract
Purpose This article aims to provide a theoretical basis for new or adjuvant strategies to facilitate the early diagnosis and treatment of candidiasis and to determine if drug-resistant Candida would affect virulence. Patients and Methods Our strains were collected from patients diagnosed with candidiasis in our hospital. The strains were identified by MALDI-TOF system and ITS sequencing. Antifungal sensitivity testing in vitro was performed to evaluate susceptibility of these isolates to current widely used antifungal drugs. The Galleria mellonella larvae model infected by Candida spp. was used to compare the virulence of drug-resistant and susceptible Candida spp. Results A total of 206 Candida strains were collected from clinical specimens. Candida albicans was the most common species among them, and was predominantly isolated from male patients aged over 40 years in ICU environments suffering from pulmonary and/or cerebral conditions. The accuracy rate of MALDI TOF-MS identification was 92.72% when compared with ITS sequencing as the standard method. Most Candida species, except for C. tropicalis which showed high resistance to micafungin, showed high susceptibilities to voriconazole, itraconazole, amphotericin B and micafungin but were highly resistant to terbinafine. For each specific Candida species, the G. mellonella larvae model revealed that the virulence of drug-resistant Candida isolates did not markedly differ from that of the drug-susceptible isolates, however, the virulence was dose-dependent on inoculated fungal cells in this model. Conclusion The possibility of Candida infection should not be neglected in patients at critical care hospital settings and C. albicans is the most common causative agent. MALDI-TOF MS has the advantages of rapidity and high accuracy, and should be a preferred method for identification of Candida spp. in a clinical laboratory. Voriconazole, itraconazole, amphotericin B and micafungin can still be recommended as the first line antifungals to treat candidiasis.
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Affiliation(s)
- Zhiya Yang
- The Laboratory of Medical Mycology, Jining No.1 People’s Hospital, Jining, Shandong, 272111, People’s Republic of China
| | - Fangfang Zhang
- Department of Dermatology, Jining Dermatosis Prevention and Treatment Hospital, Jining, Shandong, 272000, People’s Republic of China
| | - Dongmei Li
- Department of Microbiology & Immunology, Georgetown University Medical Center, Washington, DC, 20057USA
| | - Sisi Wang
- The Laboratory of Medical Mycology, Jining No.1 People’s Hospital, Jining, Shandong, 272111, People’s Republic of China
| | - Zhiping Pang
- The Laboratory of Medical Mycology, Jining No.1 People’s Hospital, Jining, Shandong, 272111, People’s Republic of China
| | - Liu Chen
- The Laboratory of Medical Mycology, Jining No.1 People’s Hospital, Jining, Shandong, 272111, People’s Republic of China
| | - Renzhe Li
- The Laboratory of Clinical Medicine, Jining No.1 People’s Hospital, Jining, Shandong, 272111, People’s Republic of China,Renzhe Li, Clinical Laboratory of Jining No.1 People’s Hospital, 272111, People’s Republic of China, Tel +86 13563704987, Email
| | - Dongmei Shi
- The Laboratory of Medical Mycology, Jining No.1 People’s Hospital, Jining, Shandong, 272111, People’s Republic of China,Department of Dermatology, Jining No.1 People’s Hospital, Jining, Shandong, 272001, People’s Republic of China,Correspondence: Dongmei Shi, The Laboratory of Medical Mycology and Dermatology Department of Jining No.1 People’s Hospital, Shandong, 272011, China, Tel +86 537-6051008, Email
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Wang Y, Zhao X, Zhou Y, Lu J, Yu H, Li S. Establishment and application of loop-mediated isothermal amplification coupled with nanoparticle-based lateral flow biosensor (LAMP-LFB) for visual and rapid diagnosis of Candida albicans in clinical samples. Front Bioeng Biotechnol 2022; 10:1025083. [PMID: 36420441 PMCID: PMC9676452 DOI: 10.3389/fbioe.2022.1025083] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Accepted: 10/24/2022] [Indexed: 10/29/2023] Open
Abstract
Candida albicans is an opportunistic pathogenic yeast that predominantly causes invasive candidiasis. Conventional methods for detecting Candida species are costly, take 3-5 days, and require skilled technicians. Rapid pathogen identification is important in managing invasive candidiasis infection. Here, a novel molecular diagnostic assay termed loop-mediated isothermal amplification combined with nanoparticles-based lateral flow biosensor (LAMP-LFB) was developed for C. albicans rapid detection. A set of six primers was designed based on the C. albicans species-specific internal transcribed spacer 2 (ITS2) gene. The C. albicans-LAMP results were visually reported by LFB within 2 min. Various fungal strains representing Candida species, as well as several Gram-negative and Gram-positive bacterial species, were used to determine the analytical sensitivity and specificity of the assay. The optimal LAMP conditions were 64 °C for 40 min, with a sensitivity of 1 fg of genomic DNA template from C. albicans pure cultures. No cross-reactions were obtained with non-albicans strains. Thus, the analytical specificity of the LAMP-LFB assay was 100%. The entire procedure could be completed within 85 min, including specimen processing (40 min), isothermal reaction (40 min), and result reporting (within 2 min). In 330 clinical samples (including 30 whole blood, 100 middle segment urine, and 200 sputum samples), all C. albicans-positive (62/330) samples were identified by LAMP-LFB assay, and the diagnostic accuracy was 100% when compared to the traditional clinical cultural-based methods. Thus, this assay can be used as a diagnostic tool for the rapid, accurate, sensitive, low-cost and specific detection of C. albicans strains, especially in resource-limited settings.
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Affiliation(s)
- Yu Wang
- Department of Clinical Laboratory, The First People’s Hospital of Guiyang, Guiyang, China
| | - Xue Zhao
- Department of Clinical Laboratory, The First People’s Hospital of Guiyang, Guiyang, China
| | - Yuhong Zhou
- School of Public Health, The Key Laboratory of Environmental Pollution Monitoring and Disease Control, Ministry of Education, Guizhou Medical University, Guiyang, China
| | - Jingrun Lu
- Department of Clinical Laboratory, The First People’s Hospital of Guiyang, Guiyang, China
| | - Honglan Yu
- Department of Clinical Laboratory, The First People’s Hospital of Guiyang, Guiyang, China
| | - Shijun Li
- Laboratory of Bacterial Infectious Disease of Experimental Center, Guizhou Provincial Centre for Disease Control and Prevention, Guiyang, China
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Parker A, James SA, Purse C, Brion A, Goldson A, Telatin A, Baker D, Carding SR. Absence of Bacteria Permits Fungal Gut-To-Brain Translocation and Invasion in Germfree Mice but Ageing Alone Does Not Drive Pathobiont Expansion in Conventionally Raised Mice. Front Aging Neurosci 2022; 14:828429. [PMID: 35923548 PMCID: PMC9339909 DOI: 10.3389/fnagi.2022.828429] [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: 12/03/2021] [Accepted: 06/20/2022] [Indexed: 11/13/2022] Open
Abstract
Age-associated changes in the structure of the intestinal microbiome and in its interaction with the brain via the gut-brain axis are increasingly being implicated in neurological and neurodegenerative diseases. Intestinal microbial dysbiosis and translocation of microbes and microbial products including fungal species into the brain have been implicated in the development of dementias such as Alzheimer's disease. Using germ-free mice, we investigated if the fungal gut commensal, Candida albicans, an opportunistic pathogen in humans, can traverse the gastrointestinal barrier and disseminate to brain tissue and whether ageing impacts on the gut mycobiome as a pre-disposing factor in fungal brain infection. C. albicans was detected in different regions of the brain of colonised germ-free mice in both yeast and hyphal cell forms, often in close association with activated (Iba-1+) microglial cells. Using high-throughput ITS1 amplicon sequencing to characterise the faecal gut fungal composition of aged and young SPF mice, we identified several putative gut commensal fungal species with pathobiont potential although their abundance was not significantly different between young and aged mice. Collectively, these results suggest that although some fungal species can travel from the gut to brain where they can induce an inflammatory response, ageing alone is not correlated with significant changes in gut mycobiota composition which could predispose to these events. These results are consistent with a scenario in which significant disruptions to the gut microbiota or intestinal barrier, beyond those which occur with natural ageing, are required to allow fungal escape and brain infection.
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Affiliation(s)
- Aimée Parker
- Gut Microbes and Health Research Programme, Quadram Institute, Norwich, United Kingdom
| | - Steve A. James
- Gut Microbes and Health Research Programme, Quadram Institute, Norwich, United Kingdom
| | - Catherine Purse
- Gut Microbes and Health Research Programme, Quadram Institute, Norwich, United Kingdom
| | - Arlaine Brion
- Gut Microbes and Health Research Programme, Quadram Institute, Norwich, United Kingdom
| | - Andrew Goldson
- Gut Microbes and Health Research Programme, Quadram Institute, Norwich, United Kingdom
| | - Andrea Telatin
- Gut Microbes and Health Research Programme, Quadram Institute, Norwich, United Kingdom
| | - David Baker
- Gut Microbes and Health Research Programme, Quadram Institute, Norwich, United Kingdom
| | - Simon R. Carding
- Norwich Medical School, University of East Anglia, Norwich, United Kingdom
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10
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Wang F, Ge D, Wang L, Li N, Chen H, Zhang Z, Zhu W, Wang S, Liang W. Rapid and sensitive recombinase polymerase amplification combined with lateral flow strips for detecting Candida albicans. Anal Biochem 2021; 633:114428. [PMID: 34678249 DOI: 10.1016/j.ab.2021.114428] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2021] [Revised: 10/13/2021] [Accepted: 10/16/2021] [Indexed: 12/30/2022]
Abstract
Owing to modern lifestyles and increasing amounts of medical intervention, clinical infections caused by conditionally pathogenic fungi are becoming increasingly serious. Among these, Candida albicans is the most common. Therefore, the rapid and accurate detection of this pathogenic fungus is important to guiding the selection of clinical therapeutic agents. Recombinase polymerase amplification (RPA) combined with lateral flow strips (LFS) is a promising molecular detection method with the advantages of rapidity, simplicity of operation and high sensitivity. However, this simplicity brings with it the inherent and non-negligible risk of false-positive signals from primer-dimers. In this study, primer-dependent artifacts were eliminated by using probes in the RPA reaction, introducing specific base substitutions to the primer and probe sequences and analyzing and screening the formation of primer-probe complexes. These measures were rigorously tested for efficacy, leading to the creation of an improved RPA-LFS system. The standardized method enabled the specific detection of C. albicans within 25 min at 37 °C without interference. The system had a detection limit of 1 CFU per reaction without DNA purification or 102 fg genomic DNA/50 μL. The detection sensitivity was not affected by the presence of other fungal DNA. The RPA-LFS method can therefore be used to detect clinical samples, and the results are accurate and consistent in comparison with those obtained using quantitative PCR. This study provides a paradigm for eliminating the risk of false-positive primer dimers in isothermal amplification assays and establishes a simple and easy method for the detection of C. albicans.
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Affiliation(s)
- Fang Wang
- Department of Central Laboratory, the Second People's Hospital of Lianyungang City (Cancer Hospital of Lianyungang), Affiliated to Bengbu Medical College, Lianyungang, 222000, Jiangsu, China
| | - Duobao Ge
- Department of Central Laboratory, the Second People's Hospital of Lianyungang City (Cancer Hospital of Lianyungang), Affiliated to Bengbu Medical College, Lianyungang, 222000, Jiangsu, China
| | - Lei Wang
- Department of Central Laboratory, the Second People's Hospital of Lianyungang City (Cancer Hospital of Lianyungang), Affiliated to Bengbu Medical College, Lianyungang, 222000, Jiangsu, China; School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, 212018, Jiangsu, China
| | - Na Li
- Department of Central Laboratory, the Second People's Hospital of Lianyungang City (Cancer Hospital of Lianyungang), Affiliated to Bengbu Medical College, Lianyungang, 222000, Jiangsu, China
| | - Huimin Chen
- Department of Central Laboratory, the Second People's Hospital of Lianyungang City (Cancer Hospital of Lianyungang), Affiliated to Bengbu Medical College, Lianyungang, 222000, Jiangsu, China
| | - Zhexiong Zhang
- Department of Central Laboratory, the Second People's Hospital of Lianyungang City (Cancer Hospital of Lianyungang), Affiliated to Bengbu Medical College, Lianyungang, 222000, Jiangsu, China
| | - Wenjun Zhu
- Department of Central Laboratory, the Second People's Hospital of Lianyungang City (Cancer Hospital of Lianyungang), Affiliated to Bengbu Medical College, Lianyungang, 222000, Jiangsu, China
| | - Siming Wang
- Department of Central Laboratory, the Second People's Hospital of Lianyungang City (Cancer Hospital of Lianyungang), Affiliated to Bengbu Medical College, Lianyungang, 222000, Jiangsu, China.
| | - Wei Liang
- Department of Central Laboratory, the Second People's Hospital of Lianyungang City (Cancer Hospital of Lianyungang), Affiliated to Bengbu Medical College, Lianyungang, 222000, Jiangsu, China.
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11
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Van Genechten W, Van Dijck P, Demuyser L. Fluorescent toys 'n' tools lighting the way in fungal research. FEMS Microbiol Rev 2021; 45:fuab013. [PMID: 33595628 PMCID: PMC8498796 DOI: 10.1093/femsre/fuab013] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2020] [Accepted: 02/14/2021] [Indexed: 12/13/2022] Open
Abstract
Although largely overlooked compared to bacterial infections, fungal infections pose a significant threat to the health of humans and other organisms. Many pathogenic fungi, especially Candida species, are extremely versatile and flexible in adapting to various host niches and stressful situations. This leads to high pathogenicity and increasing resistance to existing drugs. Due to the high level of conservation between fungi and mammalian cells, it is hard to find fungus-specific drug targets for novel therapy development. In this respect, it is vital to understand how these fungi function on a molecular, cellular as well as organismal level. Fluorescence imaging allows for detailed analysis of molecular mechanisms, cellular structures and interactions on different levels. In this manuscript, we provide researchers with an elaborate and contemporary overview of fluorescence techniques that can be used to study fungal pathogens. We focus on the available fluorescent labelling techniques and guide our readers through the different relevant applications of fluorescent imaging, from subcellular events to multispecies interactions and diagnostics. As well as cautioning researchers for potential challenges and obstacles, we offer hands-on tips and tricks for efficient experimentation and share our expert-view on future developments and possible improvements.
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Affiliation(s)
- Wouter Van Genechten
- VIB-KU Leuven Center for Microbiology, Kasteelpark Arenberg 31, 3001 Leuven-heverlee, Belgium
- Laboratory of Molecular Cell Biology, Institute of Botany and Microbiology, KU Leuven, Kasteelpark Arenberg 31, 3001 Leuven-Heverlee, Belgium
- Laboratory for Nanobiology, Department of Chemistry, KU Leuven, Celestijnenlaan 200g, 3001 Leuven-Heverlee, Belgium
| | - Patrick Van Dijck
- VIB-KU Leuven Center for Microbiology, Kasteelpark Arenberg 31, 3001 Leuven-heverlee, Belgium
- Laboratory of Molecular Cell Biology, Institute of Botany and Microbiology, KU Leuven, Kasteelpark Arenberg 31, 3001 Leuven-Heverlee, Belgium
| | - Liesbeth Demuyser
- VIB-KU Leuven Center for Microbiology, Kasteelpark Arenberg 31, 3001 Leuven-heverlee, Belgium
- Laboratory of Molecular Cell Biology, Institute of Botany and Microbiology, KU Leuven, Kasteelpark Arenberg 31, 3001 Leuven-Heverlee, Belgium
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12
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Pawlak Z, Andrusiów S, Pajączkowska M, Janczura A. Identification of Fungi Isolated from Oral Cavity of Patients with HIV Using MALDI-TOF MS. J Clin Med 2021; 10:jcm10081570. [PMID: 33917925 PMCID: PMC8068364 DOI: 10.3390/jcm10081570] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Revised: 04/02/2021] [Accepted: 04/06/2021] [Indexed: 01/16/2023] Open
Abstract
BACKGROUND A growing incidence of invasive fungal infections, especially among immunocompromised patients, has given increased significance to microbiological diagnostics of yeast-like fungi. More accurate and faster fungi identification methods that can compete with classical methods are being searched for. In this paper, classical microbiological methods are compared to MALDI-TOF MS (matrix-assisted laser desorption/ionization time-of-flight mass spectrometry). METHODS The diagnostic material was collected from buccal mucosa from 98 adults, including 69 with HIV. Only positive cultures were included in the study. RESULTS Matching results were obtained in 45 samples, and there were nonmatching results in 35 samples, with the majority of these in the study group, constituting 50% of identifications within this group. A particularly common mistake resulting from the use of classical methods is the false identification of C. dubliniensis as C. albicans. Additionally, C. tropicalis proves to be difficult to identify. CONCLUSIONS Our results and literature data suggest that MALDI-TOF MS should be considered an effective alternative to classical methods in terms of fungi identification, especially among HIV-positive patients, due to the different morphology of fungal colonies.
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Affiliation(s)
- Zuzanna Pawlak
- Students Scientific Society of Infectious Diseases, Liver Diseases and Acquired Immune Deficiencies, Faculty of Medicine, Wroclaw Medical University, 51-149 Wroclaw, Poland; (Z.P.); (S.A.)
| | - Szymon Andrusiów
- Students Scientific Society of Infectious Diseases, Liver Diseases and Acquired Immune Deficiencies, Faculty of Medicine, Wroclaw Medical University, 51-149 Wroclaw, Poland; (Z.P.); (S.A.)
| | - Magdalena Pajączkowska
- Department of Microbiology, Faculty of Medicine, Wroclaw Medical University, 50-368 Wroclaw, Poland;
| | - Adriana Janczura
- Department of Microbiology, Faculty of Medicine, Wroclaw Medical University, 50-368 Wroclaw, Poland;
- Correspondence:
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13
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Eghtedar Nejad E, Ghasemi Nejad Almani P, Mohammadi MA, Salari S. Molecular identification of Candida isolates by Real-time PCR-high-resolution melting analysis and investigation of the genetic diversity of Candida species. J Clin Lab Anal 2020; 34:e23444. [PMID: 32656934 PMCID: PMC7595915 DOI: 10.1002/jcla.23444] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2020] [Revised: 06/01/2020] [Accepted: 06/03/2020] [Indexed: 01/03/2023] Open
Abstract
BACKGROUND Candida species are considered as the cause of one of the most important opportunistic fungal diseases. Accurate identification of Candida species is important because of antifungal susceptibility patterns are different among these species, so proper identification helps in the selection of antifungal drugs for the prevention and treatment. Phenotypic methods for identification of Candida species, which are widely used in clinical microbiology laboratories, have some limitations. Real-time PCR followed by the high-resolution melting analysis (HRMA) is a novel approach for the rapid recognition of pathogenic fungi. Molecular phylogeny is essential for obtaining a better understanding of the evolution of the genus Candida and the identification of the relative degree of the Candida species. The purpose of this study was molecular identification of Candida isolates by Real-time PCR-high-resolution melting analysis and investigation of the genetic diversity of Candida species. METHODS Two hundred and thirty-two Candida isolates including 111 Candida isolates obtained from 96 HIV/AIDS patients and 121 Candida isolates obtained from 98 non-HIV persons were identified by real-time PCR and high-resolution melting curve analysis. To evaluate genetic diversity and relationships among Candida species, PCR products of nine clinical Candida isolates, as a representative of each kind of species, were randomly selected for DNA sequence analysis. RESULTS In HIV/AIDS patients, six species of Candida spp. were identified as follows: C albicans (n = 64; 57.7%), C glabrata (n = 31; 27.92%), C parapsilosis (n = 9; 8.1%), C tropicalis (n = 4; 3.6%), C krusei (n = 2; 1.8%), and C kefyr (n = 1; 0.90%). In non-HIV persons, we identified eight species of Candida including C albicans (n = 46; 38.33%) followed by C glabrata and C krusei (each one, n = 18; 15%), C tropicalis (n = 13; 10.83%), C lusitaniae (n = 12; 5.17%), C parapsilosis (n = 10; 4.31%), and C kefyr and C guillermondii (each one, n = 2; 1.66%). Also, the phylogenetic analysis showed the presence of two main clades and six separate subclades. Accordingly, about 88.9% of the isolates were located in clade I and 11.10% of the studied isolates were in clade II. CONCLUSIONS Real-time PCR followed by high-resolution melting analysis (HRMA) is known as a reliable, fast, and simple approach for detection and accurate identification of Candida species, especially in clinical samples.
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Affiliation(s)
- Esmaeel Eghtedar Nejad
- Pathobiology and Medical Diagnosis Laboratory, Mehregan Hospital, Kerman, Iran.,Department of Medical Parasitology and Mycology, Kerman University of Medical Sciences, Kerman, Iran
| | - Pooya Ghasemi Nejad Almani
- HIV/STI Surveillance Research Center, and WHO Collaborating Center for HIV Surveillance, Institute for Futures Studies in Health, Kerman University of Medical Sciences, Kerman, Iran.,Students Research Committee, Kerman University of Medical Sciences, Kerman, Iran.,Leishmaniasis Research Center, Kerman University of Medical Sciences, Kerman, Iran
| | - Mohammad Ali Mohammadi
- Research Center for Hydatid Disease in Iran, Kerman University of Medical Sciences, Kerman, Iran
| | - Samira Salari
- Department of Medical Parasitology and Mycology, Kerman University of Medical Sciences, Kerman, Iran.,HIV/STI Surveillance Research Center, and WHO Collaborating Center for HIV Surveillance, Institute for Futures Studies in Health, Kerman University of Medical Sciences, Kerman, Iran.,Medical Mycology and Bacteriology Research Center, Kerman University of Medical Sciences, Kerman, Iran
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14
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Franco-Duarte R, Černáková L, Kadam S, Kaushik KS, Salehi B, Bevilacqua A, Corbo MR, Antolak H, Dybka-Stępień K, Leszczewicz M, Relison Tintino S, Alexandrino de Souza VC, Sharifi-Rad J, Coutinho HDM, Martins N, Rodrigues CF. Advances in Chemical and Biological Methods to Identify Microorganisms-From Past to Present. Microorganisms 2019; 7:E130. [PMID: 31086084 PMCID: PMC6560418 DOI: 10.3390/microorganisms7050130] [Citation(s) in RCA: 168] [Impact Index Per Article: 33.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2019] [Revised: 04/30/2019] [Accepted: 05/08/2019] [Indexed: 12/12/2022] Open
Abstract
Fast detection and identification of microorganisms is a challenging and significant feature from industry to medicine. Standard approaches are known to be very time-consuming and labor-intensive (e.g., culture media and biochemical tests). Conversely, screening techniques demand a quick and low-cost grouping of bacterial/fungal isolates and current analysis call for broad reports of microorganisms, involving the application of molecular techniques (e.g., 16S ribosomal RNA gene sequencing based on polymerase chain reaction). The goal of this review is to present the past and the present methods of detection and identification of microorganisms, and to discuss their advantages and their limitations.
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Affiliation(s)
- Ricardo Franco-Duarte
- CBMA (Centre of Molecular and Environmental Biology), Department of Biology, University of Minho, 4710-057 Braga, Portugal.
- Institute of Science and Innovation for Bio-Sustainability (IB-S), University of Minho, 4710-057 Braga, Portugal.
| | - Lucia Černáková
- Department of Microbiology and Virology, Faculty of Natural Sciences, Comenius University in Bratislava, Ilkovičova 6, 842 15 Bratislava, Slovakia.
| | - Snehal Kadam
- Ramalingaswami Re-entry Fellowship, Department of Biotechnology, Government of India, India.
| | - Karishma S Kaushik
- Ramalingaswami Re-entry Fellowship, Department of Biotechnology, Government of India, India.
| | - Bahare Salehi
- Student Research Committee, School of Medicine, Bam University of Medical Sciences, Bam 14665-354, Iran.
| | - Antonio Bevilacqua
- Department of the Science of Agriculture, Food and Environment, University of Foggia, 71121 Foggia, Italy.
| | - Maria Rosaria Corbo
- Department of the Science of Agriculture, Food and Environment, University of Foggia, 71121 Foggia, Italy.
| | - Hubert Antolak
- Institute of Fermentation Technology and Microbiology, Department of Biotechnology and Food Science, Lodz University of Technology, Wolczanska 171/173, 90-924 Lodz, Poland.
| | - Katarzyna Dybka-Stępień
- Institute of Fermentation Technology and Microbiology, Department of Biotechnology and Food Science, Lodz University of Technology, Wolczanska 171/173, 90-924 Lodz, Poland.
| | - Martyna Leszczewicz
- Laboratory of Industrial Biotechnology, Bionanopark Ltd, Dubois 114/116, 93-465 Lodz, Poland.
| | - Saulo Relison Tintino
- Laboratory of Microbiology and Molecular Biology (LMBM), Department of Biological Chemistry/CCBS/URCA, 63105-000 Crato, Brazil.
| | | | - Javad Sharifi-Rad
- Zabol Medicinal Plants Research Center, Zabol University of Medical Sciences, Zabol 61615-585, Iran.
| | - Henrique Douglas Melo Coutinho
- Laboratory of Microbiology and Molecular Biology (LMBM), Department of Biological Chemistry/CCBS/URCA, 63105-000 Crato, Brazil.
| | - Natália Martins
- Faculty of Medicine, University of Porto, Alameda Professor Hernâni Monteiro, 4200-319 Porto, Portugal.
- Institute for Research and Innovation in Health (i3S), University of Porto, 4200-135 Porto, Portugal.
| | - Célia F Rodrigues
- LEPABE⁻Dep. of Chemical Engineering, Faculty of Engineering, University of Porto, Rua Dr. Roberto Frias, s/n, 4200-465 Porto, Portugal.
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