1
|
Wu C, Ao K, Zheng Y, Jin Y, Liu Y, Chen Z, Li D. Formic acid sandwich method is well-suited for filamentous fungi identification and improves turn around time using Zybio EXS2600 mass spectrometry. BMC Microbiol 2024; 24:238. [PMID: 38961393 PMCID: PMC11220970 DOI: 10.1186/s12866-024-03394-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2024] [Accepted: 06/20/2024] [Indexed: 07/05/2024] Open
Abstract
OBJECTIVES Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) is extensively employed for the identification of filamentous fungi on MALDI Biotyper (Bruker Daltonics) and Vitek MS (biomerieux), but the performance of fungi identification on new EXS2600 (Zybio) is still unknow. Our study aims to evaluate the new EXS2600 system's (Zybio) ability to rapidly identify filamentous fungi and determine its effect on turnaround time (TAT) in our laboratory. METHODS We tested 117 filamentous fungi using two pretreatment methods: the formic acid sandwich (FA-sandwich) and a commercial mold extraction kit (MEK, Zybio). All isolates were confirmed via sequence analysis. Laboratory data were extracted from our laboratory information system over two 9-month periods: pre-EXS (April to December 2022) and post-EXS (April to December 2023), respectively. RESULTS The total correct identification (at the species, genus, or complex/group level) rate of fungi was high, FA-sandwich (95.73%, 112/117), followed by MEK (94.02%, 110/117). Excluding 6 isolates not in the database, species-level identification accuracy was 92.79% (103/111) for FA-sandwich and 91.89% (102/111) for MEK; genus-level accuracy was 97.29% (108/111) and 96.39% (107/111), respectively. Both methods attained a 100% correct identification rate for Aspergillus, Lichtheimia, Rhizopus Mucor and Talaromyces species, and were able to differentiate between Fusarium verticillioides and Fusarium proliferatum within the Fusarium fujikuroi species complex. Notably, high confidence was observed in the species-level identification of uncommon fungi such as Trichothecium roseum and Geotrichum candidum. The TAT for all positive cultures decreased from pre EXS2600 to post (108.379 VS 102.438, P < 0.05), and the TAT for tissue decreased most (451.538 VS 222.304, P < 0.001). CONCLUSIONS The FA-sandwich method is more efficient and accurate for identifying filamentous fungi with EXS2600 than the MEK. Our study firstly evaluated the performance of fungi identification on EXS2600 and showed it is suitable for clinical microbiology laboratories use.
Collapse
Affiliation(s)
- Chongyang Wu
- Department of Laboratory Medicine, West China Hospital of Sichuan University, Sichuan Province, Chengdu, 610041, P.R. China
| | - Keping Ao
- Department of Laboratory Medicine, West China Hospital of Sichuan University, Sichuan Province, Chengdu, 610041, P.R. China
| | - Yue Zheng
- Department of Laboratory Medicine, Yaan People's Hospital, Yaan, 625000, China
| | - Ying Jin
- Department of Laboratory Medicine, LuZhou Longmatan TCM Hospital, LuZhou, 646000, China
| | - Ya Liu
- Department of Laboratory Medicine, West China Hospital of Sichuan University, Sichuan Province, Chengdu, 610041, P.R. China
| | - Zhixing Chen
- Department of Laboratory Medicine, West China Hospital of Sichuan University, Sichuan Province, Chengdu, 610041, P.R. China
| | - Dongdong Li
- Department of Laboratory Medicine, West China Hospital of Sichuan University, Sichuan Province, Chengdu, 610041, P.R. China.
| |
Collapse
|
2
|
Rolland N, Girard V, Monnin V, Arend S, Perrin G, Ballan D, Beau R, Collin V, D’Arbaumont M, Weill A, Deniel F, Tréguer S, Pawtowski A, Jany JL, Mounier J. Identification of Food Spoilage Fungi Using MALDI-TOF MS: Spectral Database Development and Application to Species Complex. J Fungi (Basel) 2024; 10:456. [PMID: 39057341 PMCID: PMC11277938 DOI: 10.3390/jof10070456] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2024] [Revised: 06/20/2024] [Accepted: 06/20/2024] [Indexed: 07/28/2024] Open
Abstract
Fungi, including filamentous fungi and yeasts, are major contributors to global food losses and waste due to their ability to colonize a very large diversity of food raw materials and processed foods throughout the food chain. In addition, numerous fungal species are mycotoxin producers and can also be responsible for opportunistic infections. In recent years, MALDI-TOF MS has emerged as a valuable, rapid and reliable asset for fungal identification in order to ensure food safety and quality. In this context, this study aimed at expanding the VITEK® MS database with food-relevant fungal species and evaluate its performance, with a specific emphasis on species differentiation within species complexes. To this end, a total of 380 yeast and mold strains belonging to 51 genera and 133 species were added into the spectral database including species from five species complexes corresponding to Colletotrichum acutatum, Colletotrichum gloeosporioides, Fusarium dimerum, Mucor circinelloides complexes and Aspergillus series nigri. Database performances were evaluated by cross-validation and external validation using 78 fungal isolates with 96.55% and 90.48% correct identification, respectively. This study also showed the capacity of MALDI-TOF MS to differentiate closely related species within species complexes and further demonstrated the potential of this technique for the routine identification of fungi in an industrial context.
Collapse
Affiliation(s)
- Nolwenn Rolland
- bioMérieux, R&D Microbiologie, Route de Port Michaud, F-38390 La Balme les Grottes, France; (N.R.); (V.G.); (V.M.); (S.A.); (G.P.); (R.B.); (V.C.); (M.D.)
- Univ Brest, INRAE, Laboratoire Universitaire de Biodiversité et Écologie Microbienne, F-29280 Plouzané, France; (D.B.); (A.W.); (F.D.); (S.T.); (A.P.); (J.-L.J.)
| | - Victoria Girard
- bioMérieux, R&D Microbiologie, Route de Port Michaud, F-38390 La Balme les Grottes, France; (N.R.); (V.G.); (V.M.); (S.A.); (G.P.); (R.B.); (V.C.); (M.D.)
| | - Valérie Monnin
- bioMérieux, R&D Microbiologie, Route de Port Michaud, F-38390 La Balme les Grottes, France; (N.R.); (V.G.); (V.M.); (S.A.); (G.P.); (R.B.); (V.C.); (M.D.)
| | - Sandrine Arend
- bioMérieux, R&D Microbiologie, Route de Port Michaud, F-38390 La Balme les Grottes, France; (N.R.); (V.G.); (V.M.); (S.A.); (G.P.); (R.B.); (V.C.); (M.D.)
| | - Guillaume Perrin
- bioMérieux, R&D Microbiologie, Route de Port Michaud, F-38390 La Balme les Grottes, France; (N.R.); (V.G.); (V.M.); (S.A.); (G.P.); (R.B.); (V.C.); (M.D.)
| | - Damien Ballan
- Univ Brest, INRAE, Laboratoire Universitaire de Biodiversité et Écologie Microbienne, F-29280 Plouzané, France; (D.B.); (A.W.); (F.D.); (S.T.); (A.P.); (J.-L.J.)
| | - Rachel Beau
- bioMérieux, R&D Microbiologie, Route de Port Michaud, F-38390 La Balme les Grottes, France; (N.R.); (V.G.); (V.M.); (S.A.); (G.P.); (R.B.); (V.C.); (M.D.)
| | - Valérie Collin
- bioMérieux, R&D Microbiologie, Route de Port Michaud, F-38390 La Balme les Grottes, France; (N.R.); (V.G.); (V.M.); (S.A.); (G.P.); (R.B.); (V.C.); (M.D.)
| | - Maëlle D’Arbaumont
- bioMérieux, R&D Microbiologie, Route de Port Michaud, F-38390 La Balme les Grottes, France; (N.R.); (V.G.); (V.M.); (S.A.); (G.P.); (R.B.); (V.C.); (M.D.)
| | - Amélie Weill
- Univ Brest, INRAE, Laboratoire Universitaire de Biodiversité et Écologie Microbienne, F-29280 Plouzané, France; (D.B.); (A.W.); (F.D.); (S.T.); (A.P.); (J.-L.J.)
- Univ Brest, UBO Culture Collection, F-29280 Plouzané, France
| | - Franck Deniel
- Univ Brest, INRAE, Laboratoire Universitaire de Biodiversité et Écologie Microbienne, F-29280 Plouzané, France; (D.B.); (A.W.); (F.D.); (S.T.); (A.P.); (J.-L.J.)
| | - Sylvie Tréguer
- Univ Brest, INRAE, Laboratoire Universitaire de Biodiversité et Écologie Microbienne, F-29280 Plouzané, France; (D.B.); (A.W.); (F.D.); (S.T.); (A.P.); (J.-L.J.)
| | - Audrey Pawtowski
- Univ Brest, INRAE, Laboratoire Universitaire de Biodiversité et Écologie Microbienne, F-29280 Plouzané, France; (D.B.); (A.W.); (F.D.); (S.T.); (A.P.); (J.-L.J.)
| | - Jean-Luc Jany
- Univ Brest, INRAE, Laboratoire Universitaire de Biodiversité et Écologie Microbienne, F-29280 Plouzané, France; (D.B.); (A.W.); (F.D.); (S.T.); (A.P.); (J.-L.J.)
| | - Jérôme Mounier
- Univ Brest, INRAE, Laboratoire Universitaire de Biodiversité et Écologie Microbienne, F-29280 Plouzané, France; (D.B.); (A.W.); (F.D.); (S.T.); (A.P.); (J.-L.J.)
| |
Collapse
|
3
|
Djenontin E, Costa JM, Mousavi B, Nguyen LDN, Guillot J, Delhaes L, Botterel F, Dannaoui E. The Molecular Identification and Antifungal Susceptibility of Clinical Isolates of Aspergillus Section Flavi from Three French Hospitals. Microorganisms 2023; 11:2429. [PMID: 37894087 PMCID: PMC10609271 DOI: 10.3390/microorganisms11102429] [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: 09/07/2023] [Revised: 09/20/2023] [Accepted: 09/22/2023] [Indexed: 10/29/2023] Open
Abstract
(1) Background: Aspergillus flavus is a cosmopolitan mold with medical, veterinary, and agronomic concerns. Its morphological similarity to other cryptic species of the Flavi section requires molecular identification techniques that are not routinely performed. For clinical isolates of Aspergillus section Flavi, we present the molecular identification, susceptibility to six antifungal agents, and clinical context of source patients. (2) Methods: One hundred forty fungal clinical isolates were included in the study. These isolates, recovered over a 15-year period (2001-2015), were identified based on their morphological characteristics as belonging to section Flavi. After the subculture, sequencing of a part of the β-tubulin and calmodulin genes was performed, and resistance to azole antifungals was screened on agar plates containing itraconazole and voriconazole. Minimum inhibitory concentrations were determined for 120 isolates by the European Committee on Antimicrobial Susceptibility Testing (EUCAST) broth microdilution method. (3) Results: Partial β-tubulin and calmodulin sequences analysis showed that 138/140 isolates were A. flavus sensu stricto, 1 isolate was A. parasiticus/sojae, and 1 was A. nomiae. Many of the isolates came from samples collected in the context of respiratory tract colonization. Among probable or proven aspergillosis, respiratory infections were the most frequent, followed by ENT infections. Antifungal susceptibility testing was available for isolates (n = 120, all A. flavus ss) from one hospital. The MIC range (geometric mean MIC) in mg/L was 0.5-8 (0.77), 0.5-8 (1.03), 0.125-2 (0.25), 0.03-2 (0.22), 0.25-8 (1.91), and 0.03-0.125 (0.061) for voriconazole, isavuconazole, itraconazole, posaconazole, amphotericin B, and caspofungin, respectively. Two (1.67%) isolates showed resistance to isavuconazole according to current EUCAST breakpoints with MICs at 8 mg/L for isavuconazole and voriconazole. One of these two isolates was also resistant to itraconazole with MIC at 2 mg/L. (4) Conclusions: The present characterization of a large collection of Aspergillus belonging to the Flavi section confirmed that A. flavus ss is the predominant species. It is mainly implicated in respiratory and ENT infections. The emergence of resistance highlights the need to perform susceptibility tests on section Flavi isolates.
Collapse
Affiliation(s)
- Elie Djenontin
- Dynamyc UPEC, EnvA, USC Anses, Faculté de Médecine de Créteil, 94010 Créteil, France; (E.D.); (B.M.); (F.B.)
- Service de Parasitologie-Mycologie, Hôpital Universitaire Mondor, AP-HP, 8 Rue du Général Sarrail, 94010 Créteil, France
| | - Jean-Marc Costa
- Laboratoire CERBA, 11 Rue de l’Équerre, 95310 Saint-Ouen-l’Aumône, France;
| | - Bita Mousavi
- Dynamyc UPEC, EnvA, USC Anses, Faculté de Médecine de Créteil, 94010 Créteil, France; (E.D.); (B.M.); (F.B.)
| | | | - Jacques Guillot
- Unité pédagogique de Dermatologie, Parasitologie, Mycologie, Ecole Nationale Vétérinaire Agroalimentaire et de l’Alimentation Nantes Atlantique, Oniris, 44300 Nantes, France;
| | - Laurence Delhaes
- Laboratoire de Parasitologie-Mycologie, CNR des Aspergilloses Chroniques—CHU de Bordeaux, INSERM U1045—Univ. Bordeaux, 33000 Bordeaux, France;
| | - Françoise Botterel
- Dynamyc UPEC, EnvA, USC Anses, Faculté de Médecine de Créteil, 94010 Créteil, France; (E.D.); (B.M.); (F.B.)
- Service de Parasitologie-Mycologie, Hôpital Universitaire Mondor, AP-HP, 8 Rue du Général Sarrail, 94010 Créteil, France
| | - Eric Dannaoui
- Dynamyc UPEC, EnvA, USC Anses, Faculté de Médecine de Créteil, 94010 Créteil, France; (E.D.); (B.M.); (F.B.)
- Faculté de Médecine, Université Paris Cité, 75006 Paris, France
- Unité de Parasitologie-Mycologie, Hôpital Necker Enfants Malades, AP-HP, 149 Rue de Sèvres, 75015 Paris, France
| |
Collapse
|
4
|
Moura-Mendes J, Cazal-Martínez CC, Rojas C, Ferreira F, Pérez-Estigarribia P, Dias N, Godoy P, Costa J, Santos C, Arrua A. Species Identification and Mycotoxigenic Potential of Aspergillus Section Flavi Isolated from Maize Marketed in the Metropolitan Region of Asunción, Paraguay. Microorganisms 2023; 11:1879. [PMID: 37630439 PMCID: PMC10458825 DOI: 10.3390/microorganisms11081879] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2023] [Revised: 07/13/2023] [Accepted: 07/18/2023] [Indexed: 08/27/2023] Open
Abstract
Zea mays var. amylacea and Zea mays var. indurata are maize ecotypes from Paraguay. Aspergillus section Flavi is the main spoilage fungus of maize under storage conditions. Due to its large intraspecific genetic variability, the accurate identification of this fungal taxonomic group is difficult. In the present study, potential mycotoxigenic strains of Aspergillus section Flavi isolated from Z. mays var. indurata and Z. mays var. amylacea that are marketed in the metropolitan region of Asunción were identified by a polyphasic approach. Based on morphological characters, 211 isolates were confirmed to belong to Aspergillus section Flavi. A subset of 92 strains was identified as Aspergillus flavus by mass spectrometry MALDI-TOF and the strains were classified by MALDI-TOF MS into chemotypes based on their aflatoxins and cyclopiazonic acid production. According to the partial sequencing of ITS and CaM genes, a representative subset of 38 A. flavus strains was confirmed. Overall, 75 A. flavus strains (86%) were characterized as producers of aflatoxins. The co-occurrence of at least two mycotoxins (AF/ZEA, FUM/ZEA, and AF/ZEA/FUM) was detected for five of the Z. mays samples (63%). Considering the high mycological bioburden and mycotoxin contamination, maize marketed in the metropolitan region of Asunción constitutes a potential risk to food safety and public health and requires control measures.
Collapse
Affiliation(s)
- Juliana Moura-Mendes
- Centro Multidisciplinario de Investigaciones Tecnológicas, Universidad Nacional de Asunción, San Lorenzo 111421, Paraguay; (J.M.-M.)
| | - Cinthia C. Cazal-Martínez
- Centro Multidisciplinario de Investigaciones Tecnológicas, Universidad Nacional de Asunción, San Lorenzo 111421, Paraguay; (J.M.-M.)
- Facultad de Ciencias Exactas y Naturales, Universidad Nacional de Asunción, San Lorenzo 111421, Paraguay
| | - Cinthia Rojas
- Centro Multidisciplinario de Investigaciones Tecnológicas, Universidad Nacional de Asunción, San Lorenzo 111421, Paraguay; (J.M.-M.)
- Facultad de Ciencias Exactas y Naturales, Universidad Nacional de Asunción, San Lorenzo 111421, Paraguay
| | - Francisco Ferreira
- Facultad de Ciencias Exactas y Naturales, Universidad Nacional de Asunción, San Lorenzo 111421, Paraguay
| | - Pastor Pérez-Estigarribia
- Facultad Politécnica, Universidad Nacional de Asunción, San Lorenzo 111421, Paraguay
- Facultad de Medicina, Universidad Sudamericana, Pedro Juan Caballero 130112, Paraguay
| | - Nathalia Dias
- BIOREN-UFRO Scientific and Technological Bioresource Nucleus, Universidad de La Frontera, Temuco 4811230, Chile
| | - Patrício Godoy
- Instituto de Microbiología Clínica, Facultad de Medicina, Universidad Austral de Chile, Valdivia 5090000, Chile
| | - Jéssica Costa
- Departamento de Biologia, Instituto de Ciências Biológicas-ICB, Universidade Federal do Amazonas, Av. Rodrigo Otávio Jordão Ramos 3000, Bloco 01, Manaus 69077-000, Brazil;
| | - Cledir Santos
- Department of Chemical Science and Natural Resources, Universidad de La Frontera, Temuco 4811230, Chile
| | - Andrea Arrua
- Centro Multidisciplinario de Investigaciones Tecnológicas, Universidad Nacional de Asunción, San Lorenzo 111421, Paraguay; (J.M.-M.)
- Facultad de Ciencias Exactas y Naturales, Universidad Nacional de Asunción, San Lorenzo 111421, Paraguay
| |
Collapse
|
5
|
Proteomics as a New-Generation Tool for Studying Moulds Related to Food Safety and Quality. Int J Mol Sci 2023; 24:ijms24054709. [PMID: 36902140 PMCID: PMC10003330 DOI: 10.3390/ijms24054709] [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: 01/31/2023] [Revised: 02/24/2023] [Accepted: 02/26/2023] [Indexed: 03/06/2023] Open
Abstract
Mould development in foodstuffs is linked to both spoilage and the production of mycotoxins, provoking food quality and food safety concerns, respectively. The high-throughput technology proteomics applied to foodborne moulds is of great interest to address such issues. This review presents proteomics approaches useful for boosting strategies to minimise the mould spoilage and the hazard related to mycotoxins in food. Metaproteomics seems to be the most effective method for mould identification despite the current problems related to the bioinformatics tool. More interestingly, different high resolution mass spectrometry tools are suitable for evaluating the proteome of foodborne moulds able to unveil the mould's response under certain environmental conditions and the presence of biocontrol agents or antifungals, being sometimes combined with a method with limited ability to separate proteins, the two-dimensional gel electrophoresis. However, the matrix complexity, the high ranges of protein concentrations needed and the performing of multiple steps are some of the proteomics limitations for the application to foodborne moulds. To overcome some of these limitations, model systems have been developed and proteomics applied to other scientific fields, such as library-free data independent acquisition analyses, the implementation of ion mobility, and the evaluation of post-translational modifications, are expected to be gradually implemented in this field for avoiding undesirable moulds in foodstuffs.
Collapse
|
6
|
Silva JJ, Fungaro MHP, Soto TS, Taniwaki MH, Iamanaka BT. Low-cost, specific PCR assays to identify the main aflatoxigenic species of Aspergillus section Flavi. METHODS IN MICROBIOLOGY 2022; 196:106470. [PMID: 35447279 DOI: 10.1016/j.mimet.2022.106470] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Revised: 03/26/2022] [Accepted: 04/12/2022] [Indexed: 01/10/2023]
Abstract
Aflatoxins are fungal metabolites that are present as contaminants in food globally. Most aflatoxigenic species belong to Aspergillus section Flavi, and the main ones are grouped in the A. flavus clade, where many cryptic species that are difficult to discriminate are found. In this study, we investigated inter- and intraspecific diversity of the A. flavus clade to develop low-cost, species-specific PCR assays for identifying aflatoxigenic species. A total of 269 sequences of the second largest subunit of RNA polymerase II (RPB2) locus were retrieved from GenBank, and primer pairs were designed using data mining to identify A. flavus, A. parasiticus, and A. novoparasiticus. Species-specific amplicons of approximately 620, 350, and 860 bp enabled identification of target species as A. flavus, A. parasiticus, and A. novoparasiticus, respectively.
Collapse
Affiliation(s)
- Josué J Silva
- Institute of Food Technology - ITAL, Campinas, SP, Brazil.
| | | | | | | | | |
Collapse
|
7
|
Peng D, Zhu X, Liu Y, Li X, Chen G, Li Y, Xiao X. Evaluation of Formic Acid Sandwich (FA-sandwich), A Pretreatment method for Filamentous Fungi, for the Identification of Clinically Relevant Filamentous Fungi by Two MALDI-TOF MS systems. Med Mycol 2022; 60:6535568. [PMID: 35199840 DOI: 10.1093/mmy/myac018] [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: 10/29/2021] [Revised: 02/05/2022] [Accepted: 02/22/2022] [Indexed: 11/14/2022] Open
Abstract
Matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS) has been successfully applied to identify microorganisms. However, unlike bacteria and yeast where identification results can be obtained rapidly and accurately by using a simple direct-coating pretreatment method, the traditional pretreatment methods for filamentous fungi are more complex, involving ethanol, formic acid, acetonitrile, and a protein extraction process by centrifugation, i.e., the EtOH-FA full extraction. This cumbersome pretreatment for filamentous fungi is a major reason for the lack of widespread use of MALDI-TOF MS for the identification of filamentous fungi in clinical settings. The present study describes an alternative method, the FA-sandwich, and demonstrates that the approach is efficient and effective. 148 clinical filamentous fungal isolates collected from three large general hospitals in Hubei Province, China, were processed by the FA-sandwich method and identified by two MALDI-TOF MS platforms, Autof ms and Vitek MS. The FA-sandwich allowed a 93.9% species-level identification with Autof ms, and 97.3% species-level identification rates were found for Vitek MS when the IVD, the RUO and in-house databases are used in combination. Further comparison of the ease of FA-sandwich with the EtOH-FA full extraction showed that the FA-sandwich is a more convenient, time- and reagent-saving, and sensitive pretreatment method. These findings indicate that the FA-sandwich method is suitable for pretreating filamentous fungi followed by MALDI-TOF MS identification in clinical microbiology laboratories.
Collapse
Affiliation(s)
- Dan Peng
- Department of Clinical Laboratory, Huanggang Central Hospital, Huanggang, Hubei Province, China
| | - Xiaobin Zhu
- Department of Spine Surgery and Musculoskeletal Tumor, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Yanhua Liu
- Department of clinical laboratory, Hospital of China University of Geosciences, Wuhan, China
| | - Xiaoning Li
- Department of Nephrology, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Guoqiang Chen
- Department of Clinical Laboratory, Huanggang Central Hospital, Huanggang, Hubei Province, China
| | - Yirong Li
- Department of Laboratory Medicine, Zhongnan Hospital of Wuhan University, Wuhan, China.,Hubei Engineering Center for Infectious Disease Prevention, Control and Treatment
| | - Xiao Xiao
- Department of Laboratory Medicine, Zhongnan Hospital of Wuhan University, Wuhan, China.,Hubei Engineering Center for Infectious Disease Prevention, Control and Treatment
| |
Collapse
|
8
|
Salah H, Kolecka A, Rozaliyani A, Wahyuningsih R, Taj-Aldeen SJ, Boekhout T, Houbraken J. A New Filter Based Cultivation Approach for Improving Aspergillus Identification using Matrix-Assisted Laser Desorption/Ionization Time-of-Flight Mass Spectrometry (MALDI-TOF MS). Mycopathologia 2022; 187:39-52. [PMID: 35006478 PMCID: PMC8807449 DOI: 10.1007/s11046-021-00603-8] [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: 05/12/2021] [Accepted: 10/27/2021] [Indexed: 11/30/2022]
Abstract
Matrix-Assisted Laser Desorption/Ionization Time-of-Flight Mass Spectrometry (MALDI-TOF MS) is widely used in clinical laboratories for routine identification of bacteria and yeasts. However, methodological difficulties are still apparent when applied to filamentous fungi. The liquid cultivation method recommended by Bruker Daltonics GmbH for identification of filamentous fungi by MALDI-TOF MS is labour intensive and time-consuming. In this study, growth of Aspergillus species on different (porous) surfaces was investigated with the aim to develop a more reliable, quicker and less laborious identification method using MALDI-TOF MS. Mycelial growth without sporulation mimicking liquid cultivation and reliable MALDI-TOF MS spectra were obtained when A. fumigatus strains were grown on and in between a polycarbonate membrane filter on Sabouraud dextrose agar. A database of in-house reference spectra was created by growing Aspergillus reference strains (mainly focusing on sections Fumigati and Flavi) under these selected conditions. A test set of 50 molecularly identified strains grown under different conditions was used to select the best growth condition for identification and to perform an initial validation of the in-house database. Based on these results, the cultivation method on top of a polycarbonate filter proved to be most successful for species identification. This method was therefore selected for the identification of two sets of clinical isolates that mainly consisted of Aspergilli (100 strains originating from Indonesia, 70 isolates from Qatar). The results showed that this cultivation method is reliable for identification of clinically relevant Aspergillus species, with 67% and 76% correct identification of strains from Indonesia and Qatar, respectively. In conclusion, cultivation of Aspergilli on top of a polycarbonate filter showed improved results compared to the liquid cultivation protocol recommended by Bruker in terms of percentage of correct identification, ease of MSP creation, time consumption, cost and labour intensity. This method can be reliably applied for identification of clinically important Aspergilli and has potential for identification of other filamentous fungi.
Collapse
Affiliation(s)
- Husam Salah
- Division of Microbiology, Department of Laboratory Medicine and Pathology, Hamad Medical Corporation, Doha, Qatar.,Westerdijk Fungal Biodiversity Institute, Utrecht, The Netherlands
| | - Anna Kolecka
- Westerdijk Fungal Biodiversity Institute, Utrecht, The Netherlands
| | - Anna Rozaliyani
- Department of Parasitology Faculty of Medicine, Universitas Indonesia, Jakarta, Indonesia
| | - Retno Wahyuningsih
- Department of Parasitology Faculty of Medicine, Universitas Indonesia, Jakarta, Indonesia.,Department of Parasitology Faculty of Medicine, Universitas Kristen Indonesia, Jakarta, Indonesia
| | - Saad J Taj-Aldeen
- Division of Microbiology, Department of Laboratory Medicine and Pathology, Hamad Medical Corporation, Doha, Qatar.,University of Babylon, Hilla, Iraq
| | - Teun Boekhout
- Westerdijk Fungal Biodiversity Institute, Utrecht, The Netherlands.,Institute of Biodiversity and Ecosystem Dynamics (IBED), University of Amsterdam, Amsterdam, The Netherlands
| | - Jos Houbraken
- Westerdijk Fungal Biodiversity Institute, Utrecht, The Netherlands.
| |
Collapse
|
9
|
Xu L, Ntakatsane M, Wang L, Meng X, Sun W, Bi Y, Chen P, Ren D. Improved sensitive fluorescent/visible dual detection count plate for mold and yeast in food. Food Control 2021. [DOI: 10.1016/j.foodcont.2021.108174] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
|
10
|
de Souza T, Evangelista S, Passamani F, Bertechini R, de Abreu L, Batista L. Mycobiota of Minas artisanal cheese: Safety and quality. Int Dairy J 2021. [DOI: 10.1016/j.idairyj.2021.105085] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
|
11
|
Zhao L, Jia L, Ma B, Zhong W, Huang Y, Duan F. Heat-resistant bacteria contamination investigation in Chinese soybean curd industrial processing using high-throughput gene sequencing and MALDI-TOF-MS. Lebensm Wiss Technol 2021. [DOI: 10.1016/j.lwt.2021.111618] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
|
12
|
Kim E, Yang SM, Kim HY. Analysis of Cultivable Microbial Community during Kimchi Fermentation Using MALDI-TOF MS. Foods 2021; 10:foods10051068. [PMID: 34066045 PMCID: PMC8151656 DOI: 10.3390/foods10051068] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2021] [Revised: 04/28/2021] [Accepted: 05/08/2021] [Indexed: 12/31/2022] Open
Abstract
Kimchi, a traditional Korean fermented vegetable, has received considerable attention for its health-promoting effects. This study analyzes the cultivable microbial community in kimchi fermented at different temperatures using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) to comprehensively understand the factors affecting the quality of kimchi. Of the 5204 strains isolated from kimchi, aligned with the in-house database, 4467 (85.8%) were correctly identified at the species level. The fermentation temperature affected the microbial community by varying the pH and acidity, which was mainly caused by temperature-dependent competition between the different lactic acid bacteria (LAB) species in kimchi. LAB, such as Levilactobacillus (Lb.) brevis and Lactiplantibacillus (Lpb.) plantarum associated with rancidity and tissue softening, proliferated faster at higher temperatures than at low temperature. In addition, LAB, such as Latilactobacillus (Lat.) sakei and Leuconostoc (Leu.) mesenteroides, which produce beneficial substances and flavor, were mainly distributed in kimchi fermented at 4 °C. This study shows as a novelty that MALDI-TOF MS is a robust and economically affordable method for investigating viable microbial communities in kimchi.
Collapse
Affiliation(s)
| | | | - Hae-Yeong Kim
- Correspondence: ; Tel.: +82-31-201-2600; Fax: +82-31-204-8116
| |
Collapse
|
13
|
Lau AF. Matrix-Assisted Laser Desorption Ionization Time-of-Flight for Fungal Identification. Clin Lab Med 2021; 41:267-283. [PMID: 34020763 DOI: 10.1016/j.cll.2021.03.006] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Many studies have shown successful performance of matrix-assisted laser desorption ionization time-of-flight mass spectrometry for rapid yeast and mold identification, yet few laboratories have chosen to apply this technology into their routine clinical mycology workflow. This review provides an overview of the current status of matrix-assisted laser desorption ionization time-of-flight mass spectrometry for fungal identification, including key findings in the literature, processing and database considerations, updates in technology, and exciting future prospects. Significant advances toward standardization have taken place recently; thus, accurate species-level identification of yeasts and molds should be highly attainable, achievable, and practical in most clinical laboratories.
Collapse
Affiliation(s)
- Anna F Lau
- Sterility Testing Service, Department of Laboratory Medicine, Clinical Center, National Institutes of Health, 10 Center Drive, Room 2C306, Bethesda, MD 20892, USA.
| |
Collapse
|
14
|
MALDI-TOF mass spectrometry–based identification of Eurotiales from different substrates and locations in Brazil. Mycol Prog 2021. [DOI: 10.1007/s11557-021-01691-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
|
15
|
Meng Y, Liu W, Liu X, Zhang J, Peng M, Zhang T. A review on analytical methods for pharmaceutical and personal care products and their transformation products. J Environ Sci (China) 2021; 101:260-281. [PMID: 33334521 DOI: 10.1016/j.jes.2020.08.025] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Revised: 08/11/2020] [Accepted: 08/21/2020] [Indexed: 05/18/2023]
Abstract
Pharmaceutical and personal care products (PPCPs) and corresponding transformation products have caused widespread concern due to their persistent emissions and potential toxicity. They have wide octanol-water partition coefficients (Kow) and different ionization constants (pKa) resulting in a poor analysis accuracy and efficiency. A suitable analytical method is the first prerequisite for further research on their environmental behavior to prioritize the substances. This study reviewed a full-scale analytical protocol for environmental samples in the recent ten years: from sampling to instrumental methods. Passive sampling techniques were compared and recommended for long-term continuous and scientific observation. A quick and effective sample extraction and clean-up method are highly required. Chromatographic methods coupled to mass spectrometry for determining PPCPs with a wide range of logKow (-7.53 to 10.80) were summed up. High-resolution mass spectrometry was confirmed to be a promising strategy for screening unknown transformation products, which would provide a nanogram level of detection limits and more accurate mass resolution. Screening strategies and mass change principles were summarized in detail. The recovery rate was important in multiple contaminants analysis identification and factors affecting the recovery rate of PPCPs were also discussed in this review, including sample matrix, target compounds characteristics, extraction method and solid-phase adsorbent. This review provides useful information for the selection of appropriate analytical methods and future development directions.
Collapse
Affiliation(s)
- Yuan Meng
- Department of Environmental Science and Engineering, Beijing Environmental Pollution Control and Resource Engineering Research Center, Beijing University of Chemical Technology, Beijing 100029, China
| | - Weiyi Liu
- Department of Environmental Science and Engineering, Beijing Environmental Pollution Control and Resource Engineering Research Center, Beijing University of Chemical Technology, Beijing 100029, China
| | - Xiaohui Liu
- National Engineering Laboratory for Lake Pollution Control and Ecological Restoration, State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing 100012, China
| | - Jinlan Zhang
- Department of Environmental Science and Engineering, Beijing Environmental Pollution Control and Resource Engineering Research Center, Beijing University of Chemical Technology, Beijing 100029, China
| | - Meng Peng
- School of Environment, Tsinghua University, Beijing 100084, China
| | - Tingting Zhang
- Department of Environmental Science and Engineering, Beijing Environmental Pollution Control and Resource Engineering Research Center, Beijing University of Chemical Technology, Beijing 100029, China.
| |
Collapse
|
16
|
Levy Y, Miltgen G, Rousseau A, Lugagne N, Teysseyre L, Traversier N, Desnos-Ollivier M, Allou N, Allyn J. Case Report: Emergence of Candida auris in the Indian Ocean Region. Am J Trop Med Hyg 2020; 104:739-743. [PMID: 33319729 PMCID: PMC7866352 DOI: 10.4269/ajtmh.20-0758] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2020] [Accepted: 09/27/2020] [Indexed: 12/28/2022] Open
Abstract
Candida auris is an emerging multidrug-resistant yeast that can cause severe infections and spread easily between hospitalized patients, leading to outbreaks in hospital. Here, we report the first four cases of colonization and invasive infection with C. auris reported in the Indian Ocean region. All cases were observed in the French overseas Reunion Island, a very popular destination for European travelers. Three patients had urinary tract or skin colonization, and one had a fatal invasive infection. In three cases, including that of the infected patient, the yeast was not initially identified as C. auris, preventing specific hygiene measures to be implemented as suggested in the December 2016 clinical alert to European healthcare facilities. The infected patient likely acquired C. auris in the intensive care unit from the first colonized patient. This is the first case of C. auris infection and the first potential case of nosocomial transmission of the pathogen to be reported in the French overseas Reunion Island.
Collapse
Affiliation(s)
- Yaël Levy
- Réanimation Polyvalente, Centre Hospitalier Universitaire La Réunion, Saint-Denis, France
| | - Guillaume Miltgen
- Laboratoire de Bactériologie, Centre Hospitalier Universitaire La Réunion, Saint-Denis, France
- UMR Processus Infectieux en Milieu Insulaire Tropical (PIMIT), CNRS 9192, INSERM U1187, IRD 249, Université de La Réunion, Saint-Denis, France
| | | | - Nathalie Lugagne
- CLIN, Centre Hospitalier Universitaire La Réunion, Saint-Denis, France
| | - Laura Teysseyre
- Réanimation Polyvalente, Centre Hospitalier Universitaire La Réunion, Saint-Denis, France
| | - Nicolas Traversier
- Laboratoire de Bactériologie, Centre Hospitalier Universitaire La Réunion, Saint-Denis, France
| | - Marie Desnos-Ollivier
- Molecular Mycology Unit, National Reference Center for Invasive Mycoses and Antifungals, Institut Pasteur, CNRS, UMR2000, Paris, France
| | - Nicolas Allou
- Réanimation Polyvalente, Centre Hospitalier Universitaire La Réunion, Saint-Denis, France
- Département d’informatique Clinique, Centre Hospitalier Universitaire La Réunion, Saint-Denis Cedex, France
| | - Jérôme Allyn
- Réanimation Polyvalente, Centre Hospitalier Universitaire La Réunion, Saint-Denis, France
- Département d’informatique Clinique, Centre Hospitalier Universitaire La Réunion, Saint-Denis Cedex, France
| |
Collapse
|
17
|
Penicillium roqueforti: an overview of its genetics, physiology, metabolism and biotechnological applications. FUNGAL BIOL REV 2020. [DOI: 10.1016/j.fbr.2020.03.001] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
|