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Birhanu AG. Mass spectrometry-based proteomics as an emerging tool in clinical laboratories. Clin Proteomics 2023; 20:32. [PMID: 37633929 PMCID: PMC10464495 DOI: 10.1186/s12014-023-09424-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Accepted: 08/03/2023] [Indexed: 08/28/2023] Open
Abstract
Mass spectrometry (MS)-based proteomics have been increasingly implemented in various disciplines of laboratory medicine to identify and quantify biomolecules in a variety of biological specimens. MS-based proteomics is continuously expanding and widely applied in biomarker discovery for early detection, prognosis and markers for treatment response prediction and monitoring. Furthermore, making these advanced tests more accessible and affordable will have the greatest healthcare benefit.This review article highlights the new paradigms MS-based clinical proteomics has created in microbiology laboratories, cancer research and diagnosis of metabolic disorders. The technique is preferred over conventional methods in disease detection and therapy monitoring for its combined advantages in multiplexing capacity, remarkable analytical specificity and sensitivity and low turnaround time.Despite the achievements in the development and adoption of a number of MS-based clinical proteomics practices, more are expected to undergo transition from bench to bedside in the near future. The review provides insights from early trials and recent progresses (mainly covering literature from the NCBI database) in the application of proteomics in clinical laboratories.
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Fan X, Dai RC, Kudinha T, Gu L. A pseudo-outbreak of Cyberlindnera fabianii funguria: Implication from whole genome sequencing assay. Front Cell Infect Microbiol 2023; 13:1130645. [PMID: 36960046 PMCID: PMC10030058 DOI: 10.3389/fcimb.2023.1130645] [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: 12/23/2022] [Accepted: 02/21/2023] [Indexed: 03/09/2023] Open
Abstract
Background Although the yeast Cyberlindnera fabianii (C. fabianii) has been rarely reported in human infections, nosocomial outbreaks caused by this organism have been documented. Here we report a pseudo-outbreak of C. fabianii in a urology department of a Chinese hospital over a two-week period. Methods Three patients were admitted to the urology department of a tertiary teaching hospital in Beijing, China, from Nov to Dec 2018, for different medical intervention demands. During the period Nov 28 to Dec 5, funguria occurred in these three patients, and two of them had positive urine cultures multiple times. Sequencing of rDNA internal transcribed spacer (ITS) region and MALDI-TOF MS were applied for strain identification. Further, sequencing of rDNA non-transcribed spacer (NTS) region and whole genome sequencing approaches were used for outbreak investigation purpose. Results All the cultured yeast strains were identified as C. fabianii by sequencing of ITS region, and were 100% identical to the C. fabianii type strain CBS 5640T. However, the MALDI-TOF MS system failed to correctly identify this yeast pathogen. Moreover, isolates from these three clustered cases shared 99.91%-100% identical NTS region sequences, which could not rule out the possibility of an outbreak. However, whole genome sequencing results revealed that only two of the C. fabianii cases were genetically-related with a pairwise SNP of 192 nt, whilst the third case had over 26,000 SNPs on its genome, suggesting a different origin. Furthermore, the genomes of the first three case strains were phylogenetically even more diverged when compared to a C. fabianii strain identified from another patient, who was admitted to a general surgical department of the same hospital 7 months later. One of the first three patients eventually passed away due to poor general conditions, one was asymptomatic, and other clinically improved. Conclusion In conclusion, nosocomial outbreaks caused by emerging and uncommon fungal species are increasingly being reported, hence awareness must be raised. Genotyping with commonly used universal gene targets may have limited discriminatory power in tracing the sources of infection for these organisms, requiring use of whole genome sequencing to confirm outbreak events.
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Affiliation(s)
- Xin Fan
- Department of Infectious Diseases and Clinical Microbiology, Beijing Institute of Respiratory Medicine and Beijing Chao-Yang Hospital, Capital Medical University, Beijing, China
| | - Rong-Chen Dai
- School of Public Health, Zhejiang Chinese Medical University, Hangzhou, Zhejiang, China
| | - Timothy Kudinha
- School of Dentistry and Medical Sciences, Charles Sturt University, Leeds Parade, Oranges, NSW, Australia
- NSW Health Pathology, Regional and Rural, Orange hospital, Orange, NSW, Australia
| | - Li Gu
- Department of Infectious Diseases and Clinical Microbiology, Beijing Institute of Respiratory Medicine and Beijing Chao-Yang Hospital, Capital Medical University, Beijing, China
- *Correspondence: Li Gu,
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Genotypic Diversity of Candida parapsilosis Complex in Invasive Candidiasis at a Pediatric Tertiary Hospital: A 5-Year Retrospective Study. J Fungi (Basel) 2022; 8:jof8121280. [PMID: 36547613 PMCID: PMC9784890 DOI: 10.3390/jof8121280] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Revised: 12/01/2022] [Accepted: 12/03/2022] [Indexed: 12/12/2022] Open
Abstract
Invasive candidiasis (IC) contributes to the morbidity and mortality of hospitalized patients and represents a significant burden to the healthcare system. Previous Brazilian studies have reported the presence of endemic Candida parapsilosis sensu stricto genotypes causing candidemia and clonal transmission involving fluconazole-resistant isolates. We performed a 5-year retrospective analysis of IC cases in a Brazilian tertiary pediatric hospital and conducted a molecular investigation of C. parapsilosis sensu stricto. Non-duplicate C. parapsilosis sensu stricto genotyping was performed by microsatellite analysis. Antifungal susceptibility and biofilm formation were also evaluated. A total of 123 IC episodes were identified, with an IC incidence of 1.24 cases per 1000 hospital admissions and an overall mortality of 34%. The main species were the C. parapsilosis complex (35.8%), Candida albicans (29.2%), and Candida tropicalis (21.9%). All C. parapsilosis sensu stricto were recovered from blood cultures, and 97.5% were biofilm producers. Microsatellite typing identified high genotypic diversity among the isolates. We observed that all isolates were sensitive to amphotericin B, and although one isolate was non-sensitive to fluconazole, only a silent mutation on ERG11 gene was identified. No clear evidence of clonal outbreak or emergence of fluconazole-resistant isolates was found, suggesting that multiple sources may be involved in the epidemiology of IC in children.
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Daneshnia F, de Almeida Júnior JN, Arastehfar A, Lombardi L, Shor E, Moreno L, Mendes AV, Barberino MG, Yamamoto DT, Butler G, Perlin DS, Colombo AL. Determinants of fluconazole resistance and echinocandin tolerance in C. parapsilosis isolates causing a large clonal candidemia outbreak among COVID-19 patients in a Brazilian ICU. Emerg Microbes Infect 2022; 11:2264-2274. [PMID: 36066554 PMCID: PMC9542950 DOI: 10.1080/22221751.2022.2117093] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
Patients presenting with severe COVID-19 are predisposed to acquire secondary fungal infections such as COVID-19-associated candidemia (CAC), which are associated with poor clinical outcomes despite antifungal treatment. The extreme burden imposed on clinical facilities during the COVID-19 pandemic has provided a permissive environment for the emergence of clonal outbreaks of multiple Candida species, including C. auris and C. parapsilosis. Here we report the largest clonal CAC outbreak to date caused by fluconazole resistant (FLZR) and echinocandin tolerant (ECT) C. parapsilosis. Sixty C. parapsilosis strains were obtained from 57 patients at a tertiary care hospital in Brazil, 90% of them were FLZR and ECT. Although only 35.8% of FLZR isolates contained an ERG11 mutation, all of them contained the TAC1L518F mutation and significantly overexpressed CDR1. Introduction of TAC1L518F into a susceptible background increased the MIC of fluconazole and voriconazole 8-fold and resulted in significant basal overexpression of CDR1. Additionally, FLZR isolates exclusively harbored E1939G outside of Fks1 hotspot-2, which did not confer echinocandin resistance, but significantly increased ECT. Multilocus microsatellite typing showed that 51/60 (85%) of the FLZR isolates belonged to the same cluster, while the susceptible isolates each represented a distinct lineage. Finally, biofilm production in FLZR isolates was significantly lower than in susceptible counterparts Suggesting that it may not be an outbreak determinant. In summary, we show that TAC1L518F and FKS1E1393G confer FLZR and ECT, respectively, in CAC-associated C. parapsilosis. Our study underscores the importance of antifungal stewardship and effective infection control strategies to mitigate clonal C. parapsilosis outbreaks.
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Affiliation(s)
- Farnaz Daneshnia
- Center for Discovery and Innovation, Hackensack Meridian Health, Nutley, NJ 07110, USA
| | - João N de Almeida Júnior
- Special Mycology Laboratory, Federal University of São Paulo, Brazil.,Clinical Laboratory, Hospital Israelita Albert Einstein, São Paulo, Brazil
| | - Amir Arastehfar
- Center for Discovery and Innovation, Hackensack Meridian Health, Nutley, NJ 07110, USA
| | - Lisa Lombardi
- School of Biomolecular and Biomedical Science, Conway Institute, University College Dublin, Belfield, Dublin, Ireland
| | - Erika Shor
- Center for Discovery and Innovation, Hackensack Meridian Health, Nutley, NJ 07110, USA.,Hackensack Meridian School of Medicine, Nutley NJ 07710, USA
| | - Lis Moreno
- Hospital São Rafael, Salvador, Brazil.,Instituto D'OR de Pesquisa e Ensino (IDOR)
| | - Ana Verena Mendes
- Hospital São Rafael, Salvador, Brazil.,Instituto D'OR de Pesquisa e Ensino (IDOR)
| | | | | | - Geraldine Butler
- School of Biomolecular and Biomedical Science, Conway Institute, University College Dublin, Belfield, Dublin, Ireland
| | - David S Perlin
- Center for Discovery and Innovation, Hackensack Meridian Health, Nutley, NJ 07110, USA.,Hackensack Meridian School of Medicine, Nutley NJ 07710, USA.,Georgetown University Lombardi Comprehensive Cancer Center, Washington DC 20057, USA
| | - Arnaldo Lopes Colombo
- Special Mycology Laboratory, Federal University of São Paulo, Brazil.,Department of Medicine, Division of Infectious Diseases, Escola Paulista de Medicina, Universidade Federal de São Paulo, São Paulo, Brazil
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Thomaz DY, Del Negro GMB, Ribeiro LB, da Silva M, Carvalho GOMH, Camargo CH, de Almeida JN, Motta AL, Siciliano RF, Sejas ONE, Rossi F, Abdala E, Strabelli TMV, Benard G. A Brazilian Inter-Hospital Candidemia Outbreak Caused by Fluconazole-Resistant Candida parapsilosis in the COVID-19 Era. J Fungi (Basel) 2022; 8:jof8020100. [PMID: 35205855 PMCID: PMC8874954 DOI: 10.3390/jof8020100] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Revised: 01/09/2022] [Accepted: 01/10/2022] [Indexed: 02/06/2023] Open
Abstract
Horizontal transmission of fluconazole-resistant Candida parapsilosis (FRCP) through healthcare workers’ hands has contributed to the occurrence of candidemia outbreaks worldwide. Since the first COVID-19 case in Brazil was detected in early 2020, hospitals have reinforced hand hygiene and disinfection practices to minimize SARS-CoV-2 contamination. However, a Brazilian cardiology center, which shares ICU patients with a cancer center under a FRCP outbreak since 2019, reported an increased FRCP candidemia incidence in May 2020. Therefore, the purpose of this study was to investigate an inter-hospital candidemia outbreak caused by FRCP isolates during the first year of the COVID-19 pandemic in Brazil. C. parapsilosis bloodstream isolates obtained from the cancer (n = 35) and cardiology (n = 30) centers in 2020 were submitted to microsatellite genotyping and fluconazole susceptibility testing. The ERG11 gene of all isolates from the cardiology center was sequenced and compared to the corresponding sequences of the FRCP genotype responsible for the cancer center outbreak in 2019. Unprecedentedly, most of the FRCP isolates from the cardiology center presented the same genetic profile and Erg11-Y132F mutation detected in the strain that has been causing the persistent outbreak in the cancer center, highlighting the uninterrupted horizontal transmission of clonal isolates in our hospitals during the COVID-19 pandemic.
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Affiliation(s)
- Danilo Y. Thomaz
- Laboratory of Medical Mycology (LIM-53), Instituto de Medicina Tropical e Hospital das Clínicas da Faculdade de Medicina da Universidade de São Paulo, Sao Paulo 05403-000, Brazil; (D.Y.T.); (G.M.B.D.N.); (L.B.R.); (M.d.S.); (G.O.M.H.C.)
| | - Gilda M. B. Del Negro
- Laboratory of Medical Mycology (LIM-53), Instituto de Medicina Tropical e Hospital das Clínicas da Faculdade de Medicina da Universidade de São Paulo, Sao Paulo 05403-000, Brazil; (D.Y.T.); (G.M.B.D.N.); (L.B.R.); (M.d.S.); (G.O.M.H.C.)
| | - Leidiane B. Ribeiro
- Laboratory of Medical Mycology (LIM-53), Instituto de Medicina Tropical e Hospital das Clínicas da Faculdade de Medicina da Universidade de São Paulo, Sao Paulo 05403-000, Brazil; (D.Y.T.); (G.M.B.D.N.); (L.B.R.); (M.d.S.); (G.O.M.H.C.)
| | - Mirian da Silva
- Laboratory of Medical Mycology (LIM-53), Instituto de Medicina Tropical e Hospital das Clínicas da Faculdade de Medicina da Universidade de São Paulo, Sao Paulo 05403-000, Brazil; (D.Y.T.); (G.M.B.D.N.); (L.B.R.); (M.d.S.); (G.O.M.H.C.)
| | - Gabrielle O. M. H. Carvalho
- Laboratory of Medical Mycology (LIM-53), Instituto de Medicina Tropical e Hospital das Clínicas da Faculdade de Medicina da Universidade de São Paulo, Sao Paulo 05403-000, Brazil; (D.Y.T.); (G.M.B.D.N.); (L.B.R.); (M.d.S.); (G.O.M.H.C.)
| | - Carlos H. Camargo
- Bacteriology Center, Instituto Adolfo Lutz, Sao Paulo 01246-000, Brazil;
| | - João N. de Almeida
- Central Laboratory Division (LIM-03), Hospital das Clínicas da Faculdade de Medicina da Universidade de São Paulo, Sao Paulo 05403-010, Brazil; (J.N.d.A.J.); (A.L.M.); (F.R.)
| | - Adriana L. Motta
- Central Laboratory Division (LIM-03), Hospital das Clínicas da Faculdade de Medicina da Universidade de São Paulo, Sao Paulo 05403-010, Brazil; (J.N.d.A.J.); (A.L.M.); (F.R.)
| | - Rinaldo F. Siciliano
- Infection Control Team, Heart Institute (InCor), Hospital das Clínicas da Faculdade de Medicina da Universidade de São Paulo, Sao Paulo 05403-000, Brazil; (R.F.S.); (T.M.V.S.)
| | - Odeli N. E. Sejas
- Cancer Institute of São Paulo State, Hospital das Clínicas da Faculdade de Medicina da Universidade de São Paulo, Sao Paulo 01246-000, Brazil; (O.N.E.S.); (E.A.)
| | - Flávia Rossi
- Central Laboratory Division (LIM-03), Hospital das Clínicas da Faculdade de Medicina da Universidade de São Paulo, Sao Paulo 05403-010, Brazil; (J.N.d.A.J.); (A.L.M.); (F.R.)
| | - Edson Abdala
- Cancer Institute of São Paulo State, Hospital das Clínicas da Faculdade de Medicina da Universidade de São Paulo, Sao Paulo 01246-000, Brazil; (O.N.E.S.); (E.A.)
| | - Tânia M. V. Strabelli
- Infection Control Team, Heart Institute (InCor), Hospital das Clínicas da Faculdade de Medicina da Universidade de São Paulo, Sao Paulo 05403-000, Brazil; (R.F.S.); (T.M.V.S.)
| | - Gil Benard
- Laboratory of Medical Mycology (LIM-53), Instituto de Medicina Tropical e Hospital das Clínicas da Faculdade de Medicina da Universidade de São Paulo, Sao Paulo 05403-000, Brazil; (D.Y.T.); (G.M.B.D.N.); (L.B.R.); (M.d.S.); (G.O.M.H.C.)
- Correspondence:
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6
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Thomaz DY, de Almeida JN, Sejas ONE, Del Negro GMB, Carvalho GOMH, Gimenes VMF, de Souza MEB, Arastehfar A, Camargo CH, Motta AL, Rossi F, Perlin DS, Freire MP, Abdala E, Benard G. Environmental Clonal Spread of Azole-Resistant Candida parapsilosis with Erg11-Y132F Mutation Causing a Large Candidemia Outbreak in a Brazilian Cancer Referral Center. J Fungi (Basel) 2021; 7:259. [PMID: 33808442 PMCID: PMC8066986 DOI: 10.3390/jof7040259] [Citation(s) in RCA: 41] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Revised: 03/17/2021] [Accepted: 03/25/2021] [Indexed: 12/27/2022] Open
Abstract
Clonal outbreaks due to azole-resistant Candida parapsilosis (ARCP) isolates have been reported in numerous studies, but the environmental niche of such isolates has yet to be defined. Herein, we aimed to identify the environmental niche of ARCP isolates causing unremitting clonal outbreaks in an adult ICU from a Brazilian cancer referral center. C. parapsilosis sensu stricto isolates recovered from blood cultures, pericatheter skins, healthcare workers (HCW), and nosocomial surfaces were genotyped by multilocus microsatellite typing (MLMT). Antifungal susceptibility testing was performed by the EUCAST (European Committee for Antimicrobial Susceptibility Testing) broth microdilution reference method and ERG11 was sequenced to determine the azole resistance mechanism. Approximately 68% of isolates were fluconazole-resistant (76/112), including pericatheter skins (3/3, 100%), blood cultures (63/70, 90%), nosocomial surfaces (6/11, 54.5%), and HCW's hands (4/28, 14.2%). MLMT revealed five clusters: the major cluster contained 88.2% of ARCP isolates (67/76) collected from blood (57/70), bed (2/2), pericatheter skin (2/3), from carts (3/7), and HCW's hands (3/27). ARCP isolates were associated with a higher 30 day crude mortality rate (63.8%) than non-ARCP ones (20%, p = 0.008), and resisted two environmental decontamination attempts using quaternary ammonium. This study for the first time identified ARCP isolates harboring the Erg11-Y132F mutation from nosocomial surfaces and HCW's hands, which were genetically identical to ARCP blood isolates. Therefore, it is likely that persisting clonal outbreak due to ARCP isolates was fueled by environmental sources. The resistance of Y132F ARCP isolates to disinfectants, and their potential association with a high mortality rate, warrant vigilant source control using effective environmental decontamination.
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Affiliation(s)
- Danilo Y. Thomaz
- Laboratory of Medical Mycology (LIM-53), Instituto de Medicina Tropical e Hospital das Clínicas da Faculdade de Medicina da Universidade de São Paulo, São Paulo 05403-000, Brazil; (D.Y.T.); (G.M.B.D.N.); (G.O.M.H.C.); (V.M.F.G.)
| | - João N. de Almeida
- Laboratory of Medical Mycology (LIM-53), Instituto de Medicina Tropical e Hospital das Clínicas da Faculdade de Medicina da Universidade de São Paulo, São Paulo 05403-000, Brazil; (D.Y.T.); (G.M.B.D.N.); (G.O.M.H.C.); (V.M.F.G.)
- Central Laboratory Division (LIM-03), Hospital das Clínicas da Faculdade de Medicina da Universidade de São Paulo, São Paulo 05403-010, Brazil; (A.L.M.); (F.R.)
- Center for Discovery and Innovation, Hackensack Meridian Health, Nutley, NJ 07110, USA; (A.A.); (D.S.P.)
| | - Odeli N. E. Sejas
- Cancer Institute of São Paulo State, Hospital das Clínicas da Faculdade de Medicina da Universidade de São Paulo, São Paulo 01246-000, Brazil; (O.N.E.S.); (M.E.B.d.S.); (M.P.F.); (E.A.)
| | - Gilda M. B. Del Negro
- Laboratory of Medical Mycology (LIM-53), Instituto de Medicina Tropical e Hospital das Clínicas da Faculdade de Medicina da Universidade de São Paulo, São Paulo 05403-000, Brazil; (D.Y.T.); (G.M.B.D.N.); (G.O.M.H.C.); (V.M.F.G.)
| | - Gabrielle O. M. H. Carvalho
- Laboratory of Medical Mycology (LIM-53), Instituto de Medicina Tropical e Hospital das Clínicas da Faculdade de Medicina da Universidade de São Paulo, São Paulo 05403-000, Brazil; (D.Y.T.); (G.M.B.D.N.); (G.O.M.H.C.); (V.M.F.G.)
| | - Viviane M. F. Gimenes
- Laboratory of Medical Mycology (LIM-53), Instituto de Medicina Tropical e Hospital das Clínicas da Faculdade de Medicina da Universidade de São Paulo, São Paulo 05403-000, Brazil; (D.Y.T.); (G.M.B.D.N.); (G.O.M.H.C.); (V.M.F.G.)
| | - Maria Emilia B. de Souza
- Cancer Institute of São Paulo State, Hospital das Clínicas da Faculdade de Medicina da Universidade de São Paulo, São Paulo 01246-000, Brazil; (O.N.E.S.); (M.E.B.d.S.); (M.P.F.); (E.A.)
| | - Amir Arastehfar
- Center for Discovery and Innovation, Hackensack Meridian Health, Nutley, NJ 07110, USA; (A.A.); (D.S.P.)
| | - Carlos H. Camargo
- Bacteriology Center, Instituto Adolfo Lutz, São Paulo 01246-000, Brazil;
| | - Adriana L. Motta
- Central Laboratory Division (LIM-03), Hospital das Clínicas da Faculdade de Medicina da Universidade de São Paulo, São Paulo 05403-010, Brazil; (A.L.M.); (F.R.)
| | - Flávia Rossi
- Central Laboratory Division (LIM-03), Hospital das Clínicas da Faculdade de Medicina da Universidade de São Paulo, São Paulo 05403-010, Brazil; (A.L.M.); (F.R.)
| | - David S. Perlin
- Center for Discovery and Innovation, Hackensack Meridian Health, Nutley, NJ 07110, USA; (A.A.); (D.S.P.)
| | - Maristela P. Freire
- Cancer Institute of São Paulo State, Hospital das Clínicas da Faculdade de Medicina da Universidade de São Paulo, São Paulo 01246-000, Brazil; (O.N.E.S.); (M.E.B.d.S.); (M.P.F.); (E.A.)
| | - Edson Abdala
- Cancer Institute of São Paulo State, Hospital das Clínicas da Faculdade de Medicina da Universidade de São Paulo, São Paulo 01246-000, Brazil; (O.N.E.S.); (M.E.B.d.S.); (M.P.F.); (E.A.)
| | - Gil Benard
- Laboratory of Medical Mycology (LIM-53), Instituto de Medicina Tropical e Hospital das Clínicas da Faculdade de Medicina da Universidade de São Paulo, São Paulo 05403-000, Brazil; (D.Y.T.); (G.M.B.D.N.); (G.O.M.H.C.); (V.M.F.G.)
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Abstract
We analyzed 19 cases of breakthrough candidemia from a referral pediatric cancer center in Brazil. All patients had neutropenia and were under antifungal prophylactic regimens, mostly micafungin (68%). Most of the patients were treated with amphotericin B formulations and 30-day mortality was 21%. Candida parapsilosis was the main etiologic agent (63%), and horizontal transmission was not evidenced by microsatellite analysis.
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Vatanshenassan M, Boekhout T, Mauder N, Robert V, Maier T, Meis JF, Berman J, Then E, Kostrzewa M, Hagen F. Evaluation of Microsatellite Typing, ITS Sequencing, AFLP Fingerprinting, MALDI-TOF MS, and Fourier-Transform Infrared Spectroscopy Analysis of Candida auris. J Fungi (Basel) 2020; 6:jof6030146. [PMID: 32854308 PMCID: PMC7576496 DOI: 10.3390/jof6030146] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2020] [Revised: 08/13/2020] [Accepted: 08/18/2020] [Indexed: 12/19/2022] Open
Abstract
Candida auris is an emerging opportunistic yeast species causing nosocomial outbreaks at a global scale. A few studies have focused on the C. auris genotypic structure. Here, we compared five epidemiological typing tools using a set of 96 C. auris isolates from 14 geographical areas. Isolates were analyzed by microsatellite typing, ITS sequencing, amplified fragment length polymorphism (AFLP) fingerprint analysis, matrix-assisted laser desorption/ionization-time of flight mass spectrometry (MALDI-TOF MS), and Fourier-transform infrared (FTIR) spectroscopy methods. Microsatellite typing grouped the isolates into four main clusters, corresponding to the four known clades in concordance with whole genome sequencing studies. The other investigated typing tools showed poor performance compared with microsatellite typing. A comparison between the five methods showed the highest agreement between microsatellite typing and ITS sequencing with 45% similarity, followed by microsatellite typing and the FTIR method with 33% similarity. The lowest agreement was observed between FTIR spectroscopy, MALDI-TOF MS, and ITS sequencing. This study indicates that microsatellite typing is the tool of choice for C. auris outbreak investigations. Additionally, FTIR spectroscopy requires further optimization and evaluation before it can be used as an epidemiological typing method, comparable with microsatellite typing, as a rapid method for tracing nosocomial fungal outbreaks.
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Affiliation(s)
- Mansoureh Vatanshenassan
- Bruker Daltonik GmbH, 28359 Bremen, Germany; (M.V.); (N.M.); (T.M.)
- Westerdijk Fungal Biodiversity Institute, 3584 CT Utrecht, The Netherlands; (T.B.); (V.R.); (E.T.)
- Institute for Biodiversity and Ecosystem Dynamics (IBED), University of Amsterdam, 1012 WX Amsterdam, The Netherlands
| | - Teun Boekhout
- Westerdijk Fungal Biodiversity Institute, 3584 CT Utrecht, The Netherlands; (T.B.); (V.R.); (E.T.)
- Institute for Biodiversity and Ecosystem Dynamics (IBED), University of Amsterdam, 1012 WX Amsterdam, The Netherlands
| | - Norman Mauder
- Bruker Daltonik GmbH, 28359 Bremen, Germany; (M.V.); (N.M.); (T.M.)
| | - Vincent Robert
- Westerdijk Fungal Biodiversity Institute, 3584 CT Utrecht, The Netherlands; (T.B.); (V.R.); (E.T.)
- BioAware, B-4280 Hannut, Belgium
| | - Thomas Maier
- Bruker Daltonik GmbH, 28359 Bremen, Germany; (M.V.); (N.M.); (T.M.)
| | - Jacques F. Meis
- Department of Medical Microbiology and Infectious Diseases, Canisius Wilhelmina Hospital (CWZ), 6532 SZ Nijmegen, The Netherlands;
- Center of Expertise in Mycology Radboudumc, Canisius Wilhelmina Hospital (CWZ), 6532 SZ Nijmegen, The Netherlands
- Bioprocess Engineering and Biotechnology Graduate Program, Federal University of Paraná, 80060-000 Curitiba, Brazil
| | - Judith Berman
- Shmunis School of Biomedicine and Cancer Research, George S. Wise Faculty of Life Sciences, 6997801 Tel Aviv, Israel;
| | - Euníce Then
- Westerdijk Fungal Biodiversity Institute, 3584 CT Utrecht, The Netherlands; (T.B.); (V.R.); (E.T.)
| | - Markus Kostrzewa
- Bruker Daltonik GmbH, 28359 Bremen, Germany; (M.V.); (N.M.); (T.M.)
- Correspondence: (M.K.); (F.H.); Tel.: +49-421-2205-1258 (M.K.); +31-30-2122-600 (F.H.)
| | - Ferry Hagen
- Westerdijk Fungal Biodiversity Institute, 3584 CT Utrecht, The Netherlands; (T.B.); (V.R.); (E.T.)
- Department of Medical Microbiology, University Medical Center Utrecht, 3584 CX Utrecht, The Netherlands
- Correspondence: (M.K.); (F.H.); Tel.: +49-421-2205-1258 (M.K.); +31-30-2122-600 (F.H.)
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Li T, Huang Y, Chen X, Wang Z, Xu Y. Urinary Tract Infections Caused by Fluconazole-Resistant Trichosporon japonicum in 2 Kidney Transplant Patients and Analysis of Their Homology. Open Forum Infect Dis 2020; 7:ofaa365. [PMID: 33024792 PMCID: PMC7526867 DOI: 10.1093/ofid/ofaa365] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2020] [Accepted: 08/13/2020] [Indexed: 11/27/2022] Open
Abstract
Trichosporon spp. are emerging opportunistic agents that cause systemic diseases and life-threatening disseminated disease in immunocompromised hosts. Trichosporon japonicum is a highly rare cause of invasive trichosporonosis. In this study, we describe 2 cases of urinary tract infection caused by Trichosporon japonicum in kidney transplant patients. Culturing of urine samples yielded bluish-green colonies of T. japonicum on Candida chromogenic fungal medium. The isolates were identified as T. japonicum by matrix-assisted laser desorption ionization–time-of-flight mass spectrometry (MALDI TOF-MS; Autof MS 1000). The identification of T. japonicum was further confirmed by 18S rRNA gene sequencing. In vitro drug susceptibility testing showed that the 2 strains of T. japonicum were resistant to 5-flucytosine, fluconazole, and caspofungin, with dose-dependent sensitivity to itraconazole and voriconazole but sensitivity to amphotericin B. The homology of the 2 T. japonicum strains, as determined by cluster analysis and principal component analysis of MALDI-TOF MS, was ~85%, suggesting a common nosocomial origin. The first 2 case reports of fluconazole-resistant T. japonicum urinary infection in kidney transplant recipients are presented.
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Affiliation(s)
- Tingting Li
- Department of Clinical Laboratory, First Affiliated Hospital of Anhui Medical University, Hefei, Anhui, China
| | - Ying Huang
- Department of Clinical Laboratory, First Affiliated Hospital of Anhui Medical University, Hefei, Anhui, China
| | - Xianguo Chen
- Department of Urology, First Affiliated Hospital of Anhui Medical University, Hefei, Anhui, China
| | - Zhongxin Wang
- Department of Clinical Laboratory, First Affiliated Hospital of Anhui Medical University, Hefei, Anhui, China
| | - Yuanhong Xu
- Department of Clinical Laboratory, First Affiliated Hospital of Anhui Medical University, Hefei, Anhui, China
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10
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Zhang L, Yu SY, Chen SCA, Xiao M, Kong F, Wang H, Ning YT, Lu MY, Sun TS, Hou X, Zhou ML, Kang W, Zhang G, Duan SM, Xu YC. Molecular Characterization of Candida parapsilosis by Microsatellite Typing and Emergence of Clonal Antifungal Drug Resistant Strains in a Multicenter Surveillance in China. Front Microbiol 2020; 11:1320. [PMID: 32612597 PMCID: PMC7309193 DOI: 10.3389/fmicb.2020.01320] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2019] [Accepted: 05/25/2020] [Indexed: 12/22/2022] Open
Abstract
Candida parapsilosis is an important species causing invasive candidiasis (IC) in China. The present survey was a national multicenter study of the molecular epidemiology and antifungal susceptibility profiles of C. parapsilosis. Non-duplicate C. parapsilosis isolates were collected from 10 hospitals across China in the CHIF-NET program 2016–2017. Isolates were genotyped using four highly polymorphic microsatellite markers, and susceptibility profiles determined using Sensititre YeastOneTM YO10. A total of 319 C. parapsilosis from separate patients with IC were studied; 49.2, 17.9, and 10.3% isolates were from patients in surgical departments, general intensive care units (ICUs) and neonatal ICUs (NICU), respectively. C. parapsilosis showed good susceptibility to nine antifungal drugs. Microsatellite analysis identified 122 microsatellite (MT) types. Most MT types had sporadic distribution. However, we identified 32 clusters across 10 hospitals; seven clusters were caused by seven endemic genotypes involving five or more isolates in hospitals designated as H01, H02, H06, and H10. These clusters mainly affected surgical departments and ICUs, except for genotype MT42 which was seen in 22 patients from NICU (hospital H06). Of 16 fluconazole-resistant isolates, seven from hospital H02 shared the same genotype MT70, and three from hospital H04 were of genotype MT47. For 37 isolates with non-wild type MICs to 5-flucytosine, 29 were from hospital H01 (genotype MT48). Here we present the first nationwide molecular epidemiology study of C. parapsilosis in China, identified several previously unrecognized clusters, which included antifungal drug resistant isolates. These findings provide important data for control of IC in China.
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Affiliation(s)
- Li Zhang
- Department of Laboratory Medicine, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Beijing, China.,Beijing Key Laboratory for Mechanisms Research and Precision Diagnosis of Invasive Fungal Diseases (BZ0447), Beijing, China
| | - Shu-Ying Yu
- Department of Laboratory Medicine, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Beijing, China.,Beijing Key Laboratory for Mechanisms Research and Precision Diagnosis of Invasive Fungal Diseases (BZ0447), Beijing, China.,Graduate School, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China
| | - Sharon C-A Chen
- Centre for Infectious Diseases and Microbiology Laboratory Services, ICPMR - Pathology West, University of Sydney, Westmead, NSW, Australia
| | - Meng Xiao
- Department of Laboratory Medicine, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Beijing, China.,Beijing Key Laboratory for Mechanisms Research and Precision Diagnosis of Invasive Fungal Diseases (BZ0447), Beijing, China
| | - Fanrong Kong
- Centre for Infectious Diseases and Microbiology Laboratory Services, ICPMR - Pathology West, University of Sydney, Westmead, NSW, Australia
| | - He Wang
- Beijing Key Laboratory for Mechanisms Research and Precision Diagnosis of Invasive Fungal Diseases (BZ0447), Beijing, China
| | - Ya-Ting Ning
- Department of Laboratory Medicine, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Beijing, China.,Beijing Key Laboratory for Mechanisms Research and Precision Diagnosis of Invasive Fungal Diseases (BZ0447), Beijing, China.,Graduate School, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China
| | - Min-Ya Lu
- Department of Laboratory Medicine, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Beijing, China.,Beijing Key Laboratory for Mechanisms Research and Precision Diagnosis of Invasive Fungal Diseases (BZ0447), Beijing, China
| | - Tian-Shu Sun
- Beijing Key Laboratory for Mechanisms Research and Precision Diagnosis of Invasive Fungal Diseases (BZ0447), Beijing, China.,Medical Research Center, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Beijing, China
| | - Xin Hou
- Department of Laboratory Medicine, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Beijing, China.,Beijing Key Laboratory for Mechanisms Research and Precision Diagnosis of Invasive Fungal Diseases (BZ0447), Beijing, China
| | - Meng-Lan Zhou
- Department of Laboratory Medicine, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Beijing, China.,Beijing Key Laboratory for Mechanisms Research and Precision Diagnosis of Invasive Fungal Diseases (BZ0447), Beijing, China.,Graduate School, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China
| | - Wei Kang
- Department of Laboratory Medicine, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Beijing, China.,Beijing Key Laboratory for Mechanisms Research and Precision Diagnosis of Invasive Fungal Diseases (BZ0447), Beijing, China
| | - Ge Zhang
- Department of Laboratory Medicine, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Beijing, China.,Beijing Key Laboratory for Mechanisms Research and Precision Diagnosis of Invasive Fungal Diseases (BZ0447), Beijing, China
| | - Si-Meng Duan
- Department of Laboratory Medicine, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Beijing, China.,Beijing Key Laboratory for Mechanisms Research and Precision Diagnosis of Invasive Fungal Diseases (BZ0447), Beijing, China
| | - Ying-Chun Xu
- Department of Laboratory Medicine, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Beijing, China.,Beijing Key Laboratory for Mechanisms Research and Precision Diagnosis of Invasive Fungal Diseases (BZ0447), Beijing, China
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11
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Vita F, Giuntoli B, Bertolini E, Taiti C, Marone E, D'Ambrosio C, Trovato E, Sciarrone D, Zoccali M, Balestrini R, Scaloni A, Mondello L, Mancuso S, Alessio M, Alpi A. Tuberomics: a molecular profiling for the adaption of edible fungi (Tuber magnatum Pico) to different natural environments. BMC Genomics 2020; 21:90. [PMID: 31996138 PMCID: PMC6988325 DOI: 10.1186/s12864-020-6522-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2019] [Accepted: 01/21/2020] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Truffles are symbiotic fungi that develop underground in association with plant roots, forming ectomycorrhizae. They are primarily known for the organoleptic qualities of their hypogeous fruiting bodies. Primarily, Tuber magnatum Pico is a greatly appreciated truffle species mainly distributed in Italy and Balkans. Its price and features are mostly depending on its geographical origin. However, the genetic variation within T. magnatum has been only partially investigated as well as its adaptation to several environments. RESULTS Here, we applied an integrated omic strategy to T. magnatum fruiting bodies collected during several seasons from three different areas located in the North, Center and South of Italy, with the aim to distinguish them according to molecular and biochemical traits and to verify the impact of several environments on these properties. With the proteomic approach based on two-dimensional electrophoresis (2-DE) followed by mass spectrometry, we were able to identify proteins specifically linked to the sample origin. We further associated the proteomic results to an RNA-seq profiling, which confirmed the possibility to differentiate samples according to their source and provided a basis for the detailed analysis of genes involved in sulfur metabolism. Finally, geographical specificities were associated with the set of volatile compounds produced by the fruiting bodies, as quantitatively and qualitatively determined through proton transfer reaction-mass spectrometry (PTR-MS) and gas-chromatography-mass spectrometry (GC-MS). In particular, a partial least squares-discriminant analysis (PLS-DA) model built from the latter data was able to return high confidence predictions of sample source. CONCLUSIONS Results provide a characterization of white fruiting bodies by a wide range of different molecules, suggesting the role for specific compounds in the responses and adaptation to distinct environments.
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Affiliation(s)
- Federico Vita
- Dipartimento di Scienze e Tecnologie Agrarie, Alimentari, Ambientali e Forestali (DAGRI), University of Florence, Viale delle idee 30, 50019, Florence, Italy. .,A.R.E.A. Foundation, via Tavoleria 28, 56125, Pisa, Italy.
| | - Beatrice Giuntoli
- Department of Biology, Università di Pisa, via L. Ghini 13, 56126, Pisa, Italy.,Institute of Life Sciences, Scuola Superiore Sant'Anna, Piazza Martiri della Libertà 33, 56127, Pisa, Italy
| | - Edoardo Bertolini
- Institute of Life Sciences, Scuola Superiore Sant'Anna, Piazza Martiri della Libertà 33, 56127, Pisa, Italy.,Present address: Donald Danforth Plant Science Center, 975 North Warson Road, Saint Louis, MO, 63132, USA
| | - Cosimo Taiti
- Dipartimento di Scienze e Tecnologie Agrarie, Alimentari, Ambientali e Forestali (DAGRI), University of Florence, Viale delle idee 30, 50019, Florence, Italy
| | - Elettra Marone
- Faculty of Biosciences and Technologies for Agriculture Food and Environment, University of Teramo, Via R. Balzarini 1, 64100, Teramo, Italy
| | - Chiara D'Ambrosio
- Proteomics and Mass Spectrometry Laboratory, I.S.P.A.A.M., National Research Council, 80147, Napoli, Italy
| | - Emanuela Trovato
- Chromaleont Srl, c/o Department of Chemical, Biological, Pharmaceutical and Environmental Sciences Polo Annunziata, University of Messina, viale Annunziata, 98168, Messina, Italy
| | - Danilo Sciarrone
- Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, Polo Annunziata, University of Messina, viale Annunziata, 98168, Messina, Italy
| | - Mariosimone Zoccali
- Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, Polo Annunziata, University of Messina, viale Annunziata, 98168, Messina, Italy
| | - Raffaella Balestrini
- National Research Council of Italy, Institute for Sustainable Plant Protection (CNR-IPSP), Viale P.A. Mattioli 25, 10125, Torino, Italy
| | - Andrea Scaloni
- Proteomics and Mass Spectrometry Laboratory, I.S.P.A.A.M., National Research Council, 80147, Napoli, Italy
| | - Luigi Mondello
- Chromaleont Srl, c/o Department of Chemical, Biological, Pharmaceutical and Environmental Sciences Polo Annunziata, University of Messina, viale Annunziata, 98168, Messina, Italy
| | - Stefano Mancuso
- Dipartimento di Scienze e Tecnologie Agrarie, Alimentari, Ambientali e Forestali (DAGRI), University of Florence, Viale delle idee 30, 50019, Florence, Italy
| | - Massimo Alessio
- Division of Genetics and Cell Biology, IRCCS-Ospedale San Raffaele, Milan, Italy
| | - Amedeo Alpi
- A.R.E.A. Foundation, via Tavoleria 28, 56125, Pisa, Italy
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12
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Angeletti S, Ciccozzi M. Matrix-assisted laser desorption ionization time-of-flight mass spectrometry in clinical microbiology: An updating review. INFECTION GENETICS AND EVOLUTION 2019; 76:104063. [DOI: 10.1016/j.meegid.2019.104063] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/03/2019] [Revised: 09/29/2019] [Accepted: 10/05/2019] [Indexed: 12/17/2022]
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13
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Grenga L, Pible O, Armengaud J. Pathogen proteotyping: A rapidly developing application of mass spectrometry to address clinical concerns. CLINICAL MASS SPECTROMETRY 2019; 14 Pt A:9-17. [DOI: 10.1016/j.clinms.2019.04.004] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2018] [Revised: 04/25/2019] [Accepted: 04/27/2019] [Indexed: 12/13/2022]
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14
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Quéro L, Courault P, Cellière B, Lorber S, Jany JL, Puel O, Girard V, Vasseur V, Nodet P, Mounier J. Application of MALDI-TOF MS to species complex differentiation and strain typing of food related fungi: Case studies with Aspergillus section Flavi species and Penicillium roqueforti isolates. Food Microbiol 2019; 86:103311. [PMID: 31703856 DOI: 10.1016/j.fm.2019.103311] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2019] [Revised: 05/29/2019] [Accepted: 08/20/2019] [Indexed: 11/26/2022]
Abstract
Filamentous fungi are one of the main causes of food losses worldwide and their ability to produce mycotoxins represents a hazard for human health. Their correct and rapid identification is thus crucial to manage food safety. In recent years, MALDI-TOF emerged as a rapid and reliable tool for fungi identification and was applied to typing of bacteria and yeasts, but few studies focused on filamentous fungal species complex differentiation and typing. Therefore, the aim of this study was to evaluate the use of MALDI-TOF to identify species of the Aspergillus section Flavi, and to differentiate Penicillium roqueforti isolates from three distinct genetic populations. Spectra were acquired from 23 Aspergillus species and integrated into a database for which cross-validation led to more than 99% of correctly attributed spectra. For P. roqueforti, spectra were acquired from 63 strains and a two-step calibration procedure was applied before database construction. Cross-validation and external validation respectively led to 94% and 95% of spectra attributed to the right population. Results obtained here suggested very good agreement between spectral and genetic data analysis for both Aspergillus species and P. roqueforti, demonstrating MALDI-TOF applicability as a fast and easy alternative to molecular techniques for species complex differentiation and strain typing of filamentous fungi.
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Affiliation(s)
- Laura Quéro
- Univ Brest, Laboratoire Universitaire de Biodiversité et Ecologie Microbienne, F-29280, Plouzané, France; BioMérieux, R&D Microbiologie, Route de Port Michaud, 38390, La Balme les Grottes, France.
| | - Priscillia Courault
- BioMérieux, R&D Microbiologie, Route de Port Michaud, 38390, La Balme les Grottes, France.
| | - Beatrice Cellière
- BioMérieux, R&D Microbiologie, Route de Port Michaud, 38390, La Balme les Grottes, France.
| | - Sophie Lorber
- Toxalim (Research Center in Food Toxicology), Université de Toulouse, INRA, ENVT, INP-Purpan, UPS, 31027, Toulouse, France.
| | - Jean-Luc Jany
- Univ Brest, Laboratoire Universitaire de Biodiversité et Ecologie Microbienne, F-29280, Plouzané, France.
| | - Olivier Puel
- Toxalim (Research Center in Food Toxicology), Université de Toulouse, INRA, ENVT, INP-Purpan, UPS, 31027, Toulouse, France.
| | - Victoria Girard
- BioMérieux, R&D Microbiologie, Route de Port Michaud, 38390, La Balme les Grottes, France.
| | - Valérie Vasseur
- Univ Brest, Laboratoire Universitaire de Biodiversité et Ecologie Microbienne, F-29280, Plouzané, France.
| | - Patrice Nodet
- Univ Brest, Laboratoire Universitaire de Biodiversité et Ecologie Microbienne, F-29280, Plouzané, France.
| | - Jérôme Mounier
- Univ Brest, Laboratoire Universitaire de Biodiversité et Ecologie Microbienne, F-29280, Plouzané, France.
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15
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Asadzadeh M, Ahmad S, Al-Sweih N, Hagen F, Meis JF, Khan Z. High-resolution fingerprinting of Candida parapsilosis isolates suggests persistence and transmission of infections among neonatal intensive care unit patients in Kuwait. Sci Rep 2019; 9:1340. [PMID: 30718894 PMCID: PMC6361955 DOI: 10.1038/s41598-018-37855-2] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2018] [Accepted: 12/07/2018] [Indexed: 12/29/2022] Open
Abstract
Candida parapsilosis causes ~35% of all candidemia cases in neonates. High-resolution fingerprinting of C. parapsilosis isolates from neonatal intensive care unit (NICU) patients in Maternity Hospital (MH) was performed to identify epidemiologically related strains. Sixty-eight bloodstream/colonizing strains isolated from 59 NICU patients, two isolates from health care workers (HCWs) from MH and 18 bloodstream isolates from two other hospitals were used. Six microsatellite markers were employed, isolates were assigned a numerical microsatellite genotype (MSG), dendrogram was constructed and similarities between genotypes were visualized by minimum spanning tree. Fifty bloodstream isolates from MH yielded 37 MSGs with 20 isolates clustering in 7 MSGs. Duplicate isolates and colonizing strains yielded same/highly similar MSG as bloodstream isolates. Colonizing strains from two non-candidemia patients yielded unique MSGs while others belonged to a cluster. All isolates from HCWs and from two other hospitals belonged to unique MSGs. Cluster isolates came from patients in NICU-1 or from neonates in NICU-1 and other NICUs. Clonal complexes comprising closely related genotypes indicative of microevolution were also detected. Our data show that some C. parapsilosis strains have persisted in MH environment over several years and these endemic genotypes were transmitted to other patients in NICU-1 and/or other nearby NICUs.
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Affiliation(s)
- Mohammad Asadzadeh
- Department of Microbiology, Faculty of Medicine, Kuwait University, Jabriya, Kuwait
| | - Suhail Ahmad
- Department of Microbiology, Faculty of Medicine, Kuwait University, Jabriya, Kuwait
| | - Noura Al-Sweih
- Department of Microbiology, Faculty of Medicine, Kuwait University, Jabriya, Kuwait
| | - Ferry Hagen
- Department of Medical Mycology, Westerdijk Fungal Biodiversity Institute, Utrecht, Netherlands.,Department of Medical Microbiology and Infectious Diseases, Canisius Wilhelmina Hospital (CWZ), Nijmegen, Netherlands
| | - Jacques F Meis
- Department of Medical Microbiology and Infectious Diseases, Canisius Wilhelmina Hospital (CWZ), Nijmegen, Netherlands.,Centre of Expertise in Mycology, Radboudumc/CWZ, Nijmegen, Netherlands
| | - Ziauddin Khan
- Department of Microbiology, Faculty of Medicine, Kuwait University, Jabriya, Kuwait.
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16
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Thomaz DY, de Almeida JN, Lima GME, Nunes MDO, Camargo CH, Grenfell RDC, Benard G, Del Negro GMB. An Azole-Resistant Candida parapsilosis Outbreak: Clonal Persistence in the Intensive Care Unit of a Brazilian Teaching Hospital. Front Microbiol 2018; 9:2997. [PMID: 30568646 PMCID: PMC6290035 DOI: 10.3389/fmicb.2018.02997] [Citation(s) in RCA: 70] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2018] [Accepted: 11/20/2018] [Indexed: 01/12/2023] Open
Abstract
The incidence of candidemia by the Candida parapsilosis complex has increased considerably in recent decades, frequently related to use of indwelling intravascular catheters. The ability of this pathogen to colonize healthcare workers (HCW)' hands, and to form biofilm on medical devices has been associated with the occurrence of nosocomial outbreaks and high mortality rates. Fluconazole has been the leading antifungal drug for the treatment of invasive candidiasis in developing countries. However, azole-resistant C. parapsilosis isolates are emerging worldwide, including in Brazil. Few studies have correlated outbreak infections due to C. parapsilosis with virulence factors, such as biofilm production. We thus conducted a microbiological investigation of C. parapsilosis complex isolates from a Brazilian teaching hospital. Additionally, we identified a previously unrecognized outbreak caused by a persistent azole-resistant C. parapsilosis (sensu stricto) clone in the intensive care unit (ICU), correlating it with the main clinical data from the patients with invasive candidiasis. The molecular identification of the isolates was carried out by PCR-RFLP assay; antifungal susceptibility and biofilm formation were also evaluated. The genotyping of all C. parapsilosis (sensu stricto) was performed by microsatellite analysis and the presence of ERG11 mutations was assessed in the azole non-susceptible isolates. Fourteen C. parapsilosis (sensu stricto) isolates were recovered from patients with invasive candidiasis, eight being fluconazole and voriconazole-resistant, and two intermediate only to fluconazole (FLC). All non-susceptible isolates showed a similar pattern of biofilm formation with low biomass and metabolic activity. The A395T mutation in ERG11 was detected exclusively among the azole-resistant isolates. According to the microsatellite analysis, all azole non-susceptible isolates from the adult ICU were clustered together indicating the occurrence of an outbreak. Regarding clinical data, all patients infected by the clonal non-susceptible isolates and none of the patients infected by the susceptible isolates had been previously exposed to corticosteroids (p = 0.001), while the remaining characteristics showed no statistical significance. The current study revealed the persistence of an azole non-susceptible C. parapsilosis clone with low capacity to form biofilm over two years in the adult ICU. These results reinforce the need of epidemiological surveillance and monitoring antifungal susceptibility of C. parapsilosis isolates in hospital wards.
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Affiliation(s)
- Danilo Yamamoto Thomaz
- Laboratory of Medical Mycology-LIM-53, Clinical Dermatology Division, Hospital das Clínicas FMUSP and Instituto de Medicina Tropical de São Paulo, Universidade de São Paulo, São Paulo, Brazil
| | - João Nobrega de Almeida
- Laboratory of Medical Mycology-LIM-53, Clinical Dermatology Division, Hospital das Clínicas FMUSP and Instituto de Medicina Tropical de São Paulo, Universidade de São Paulo, São Paulo, Brazil.,Central Laboratory Division-LIM-03, Hospital das Clínicas da Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
| | - Glaucia Moreira Espindola Lima
- Laboratory of Clinical Analyzes, Hospital Universitário Maria Aparecida Pedrossian, Universidade Federal de Mato Grosso do Sul, Campo Grande, Brazil
| | - Maína de Oliveira Nunes
- Laboratory of Clinical Analyzes, Hospital Universitário Maria Aparecida Pedrossian, Universidade Federal de Mato Grosso do Sul, Campo Grande, Brazil
| | | | | | - Gil Benard
- Laboratory of Medical Mycology-LIM-53, Clinical Dermatology Division, Hospital das Clínicas FMUSP and Instituto de Medicina Tropical de São Paulo, Universidade de São Paulo, São Paulo, Brazil
| | - Gilda M B Del Negro
- Laboratory of Medical Mycology-LIM-53, Clinical Dermatology Division, Hospital das Clínicas FMUSP and Instituto de Medicina Tropical de São Paulo, Universidade de São Paulo, São Paulo, Brazil
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17
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Gamarra S, Chaves M, Cabeza M, Macedo D, Leonardelli F, Franco D, Boleas M, Garcia-Effron G. Mucormycosis outbreak due to Rhizopus microsporus after arthroscopic anterior cruciate ligament reconstruction surgery evaluated by RAPD and MALDI-TOF Mass spectrometry. J Mycol Med 2018; 28:617-622. [DOI: 10.1016/j.mycmed.2018.09.002] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2018] [Revised: 07/06/2018] [Accepted: 09/04/2018] [Indexed: 12/20/2022]
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18
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Trobajo-Sanmartín C, Ezpeleta G, Pais C, Eraso E, Quindós G. Design and validation of a multiplex PCR protocol for microsatellite typing of Candida parapsilosis sensu stricto isolates. BMC Genomics 2018; 19:718. [PMID: 30268088 PMCID: PMC6162959 DOI: 10.1186/s12864-018-5065-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2018] [Accepted: 09/11/2018] [Indexed: 02/08/2023] Open
Abstract
BACKGROUND Analysis of polymorphic microsatellite markers (STR) is a helpful genotyping technique to differentiate Candida parapsilosis sensu stricto isolates. The aim of this study is to develop and perform an initial validation of an alternative protocol for the reliable and accurate microsatellite genotyping of C. parapsilosis sensu stricto isolates using high-throughput multiplex PCR. To achieve this, the results obtained using the new protocol were compared to the ones obtained using a previously described reference method. To that end, diagnostic accuracy, informativeness and discrimination parameters were estimated. RESULTS Our results showed good concordance between both methods (Kappa index: 0.920), leading to a high sensitivity (1; CI(95%) (0.991-1)) and specificity (1; CI(95%) (0.772-1)) after the validation of the new protocol. Moreover, the electropherograms profiles obtained with the new PCR scheme showed a high signal to noise ratio (SNR). CONCLUSIONS The new multiplex protocol is valuable for the differentiation of C. parapsilosis sensu stricto, with direct clinical applications. Besides, the new protocol represents a shortening the hands-on time, reducing the sample manipulation (dismissing the possibility of cross-contamination), maintaining the quality of the results (when compared to the ones obtained with the reference method), and helping to the standardization and simplification of the genotyping scheme.
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Affiliation(s)
- Camino Trobajo-Sanmartín
- Laboratorio de Micología Médica, Departamento de Inmunología, Microbiología y Parasitología, UFI11/25 (Microbios y Salud), Facultad de Medicina y Enfermería, Universidad del País Vasco/Euskal Herriko Unibertsitatea (UPV/EHU), Apartado 699, E-48080 Bilbao, Spain
| | - Guillermo Ezpeleta
- Departamento de Medicina Preventiva y Salud Pública, Facultad de Medicina y Enfermería, Universidad del País Vasco/Euskal Herriko Unibertsitatea (UPV/EHU), Bilbao, Spain
- Servicio de Medicina Preventiva e Higiene Hospitalaria, Complejo Hospitalario de Navarra, Pamplona, Spain
| | - Célia Pais
- Centro de Biologia Molecular e Ambiental (CBMA), Departamento de Biologia, Universidade do Minho, Braga, Portugal
| | - Elena Eraso
- Laboratorio de Micología Médica, Departamento de Inmunología, Microbiología y Parasitología, UFI11/25 (Microbios y Salud), Facultad de Medicina y Enfermería, Universidad del País Vasco/Euskal Herriko Unibertsitatea (UPV/EHU), Apartado 699, E-48080 Bilbao, Spain
| | - Guillermo Quindós
- Laboratorio de Micología Médica, Departamento de Inmunología, Microbiología y Parasitología, UFI11/25 (Microbios y Salud), Facultad de Medicina y Enfermería, Universidad del País Vasco/Euskal Herriko Unibertsitatea (UPV/EHU), Apartado 699, E-48080 Bilbao, Spain
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19
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Yu SY, Guo LN, Xiao M, Kudinha T, Kong F, Wang H, Cheng JW, Zhou ML, Xu H, Xu YC. Trichosporon dohaense, a rare pathogen of human invasive infections, and literature review. Infect Drug Resist 2018; 11:1537-1547. [PMID: 30288064 PMCID: PMC6160283 DOI: 10.2147/idr.s174301] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Background Trichosporon dohaense is a rare fungal species that has not been described in human invasive infections. Patients and methods In this study, we investigated two T. dohaense isolates from patients with invasive infections in two hospitals in China, as part of the China Hospital Invasive Fungal Surveillance Net (CHIF-NET) program. Both patients were under immunocompromised conditions. Results On chromogenic agar, T. dohaense isolates were dark blue, similar to the color of Candida. tropicalis, but the characteristic moist colony appearance was quite different from that of T. asahii. The two isolates were misidentified as T. asahii and T. inkin by the VITEK 2 YST system. The rDNA internal transcribed spacer (ITS) region and the D1/D2 domain sequences of the two T. dohaense isolates were 100% identical to T. dohaense type strain CBS10761T. The sequence of the intergenic spacer region-1 also clearly distinguished the species. Of the three matrix-assisted laser desorption/ionization time-of-flight mass spectrometry systems, Bruker Biotyper and Autobio MS correctly identified the two isolates to species level, whereas Vitek MS systems misidentified them as T. ovoides or T. asteroides. Echinocandins exhibited no in vitro activities against the two T. dohaense isolates. In addition, the isolates exhibited intermediate susceptibility to fluconazole (with minimal inhibitory concentrations [MICs] of 8 and 16 µg/mL) and itraconazole, voriconazole, and posaconazole (MICs of 0.25-1 µg/mL). T. dohaense demonstrated susceptibility to amphotericin B with MIC of 1 µg/mL. The MICs of fluconazole and voriconazole in our study were higher than the MIC50 of 62 for T. asahii isolates (4 and 0.064 µg/mL) in the CHIF-NET program. Conclusion This case study points to a possible emergence of T. dohaense as an opportunistic human invasive fungal pathogen, and the reduced susceptibility should be noted.
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Affiliation(s)
- Shu-Ying Yu
- Department of Clinical Laboratory, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Beijing, China, .,Graduate School, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China, .,Beijing Key Laboratory for Mechanisms Research and Precision Diagnosis of Invasive Fungal Diseases, Beijing, China,
| | - Li-Na Guo
- Department of Clinical Laboratory, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Beijing, China, .,Beijing Key Laboratory for Mechanisms Research and Precision Diagnosis of Invasive Fungal Diseases, Beijing, China,
| | - Meng Xiao
- Department of Clinical Laboratory, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Beijing, China, .,Beijing Key Laboratory for Mechanisms Research and Precision Diagnosis of Invasive Fungal Diseases, Beijing, China,
| | - Timothy Kudinha
- Centre for Infectious Diseases and Microbiology Laboratory Services, ICPMR - Pathology West, University of Sydney, Westmead Hospital, Westmead, NSW, Australia.,Centre for Infectious Diseases and Microbiology Laboratory Services, Westmead Hospital, Westmead, NSW, Australia
| | - Fanrong Kong
- Centre for Infectious Diseases and Microbiology Laboratory Services, ICPMR - Pathology West, University of Sydney, Westmead Hospital, Westmead, NSW, Australia
| | - He Wang
- Department of Clinical Laboratory, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Beijing, China, .,Beijing Key Laboratory for Mechanisms Research and Precision Diagnosis of Invasive Fungal Diseases, Beijing, China,
| | - Jing-Wei Cheng
- Department of Clinical Laboratory, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Beijing, China, .,Graduate School, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China, .,Beijing Key Laboratory for Mechanisms Research and Precision Diagnosis of Invasive Fungal Diseases, Beijing, China,
| | - Meng-Lan Zhou
- Department of Clinical Laboratory, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Beijing, China, .,Graduate School, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China, .,Beijing Key Laboratory for Mechanisms Research and Precision Diagnosis of Invasive Fungal Diseases, Beijing, China,
| | - Hui Xu
- Department of Clinical Laboratory, First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China,
| | - Ying-Chun Xu
- Department of Clinical Laboratory, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Beijing, China, .,Graduate School, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China, .,Beijing Key Laboratory for Mechanisms Research and Precision Diagnosis of Invasive Fungal Diseases, Beijing, China,
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20
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Ghosh PN, Fisher MC, Bates KA. Diagnosing Emerging Fungal Threats: A One Health Perspective. Front Genet 2018; 9:376. [PMID: 30254662 PMCID: PMC6141620 DOI: 10.3389/fgene.2018.00376] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2018] [Accepted: 08/24/2018] [Indexed: 11/17/2022] Open
Abstract
Emerging fungal pathogens are a growing threat to global health, ecosystems, food security, and the world economy. Over the last century, environmental change and globalized transport, twinned with the increasing application of antifungal chemical drugs have led to increases in outbreaks of fungal diseases with sometimes catastrophic effects. In order to tackle contemporary epidemics and predemic threats, there is a pressing need for a unified approach in identification and monitoring of fungal pathogens. In this paper, we discuss current high throughput technologies, as well as new platforms capable of combining diverse data types to inform practical epidemiological strategies with a focus on emerging fungal pathogens of wildlife.
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Affiliation(s)
- Pria N. Ghosh
- Department of Infectious Disease Epidemiology, Imperial College London, London, United Kingdom
- Unit for Environmental Sciences and Management, North-West University, Potchefstroom, South Africa
| | - Matthew C. Fisher
- Department of Infectious Disease Epidemiology, Imperial College London, London, United Kingdom
| | - Kieran A. Bates
- Department of Infectious Disease Epidemiology, Imperial College London, London, United Kingdom
- Institute of Zoology, Zoological Society of London, London, United Kingdom
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21
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Neji S, Hadrich I, Ilahi A, Trabelsi H, Chelly H, Mahfoudh N, Cheikhrouhou F, Sellami H, Makni F, Ayadi A. Molecular Genotyping of Candida parapsilosis Species Complex. Mycopathologia 2018; 183:765-775. [DOI: 10.1007/s11046-018-0278-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2017] [Accepted: 10/10/2017] [Indexed: 11/30/2022]
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22
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Quainoo S, Coolen JPM, van Hijum SAFT, Huynen MA, Melchers WJG, van Schaik W, Wertheim HFL. Whole-Genome Sequencing of Bacterial Pathogens: the Future of Nosocomial Outbreak Analysis. Clin Microbiol Rev 2017; 30:1015-1063. [PMID: 28855266 PMCID: PMC5608882 DOI: 10.1128/cmr.00016-17] [Citation(s) in RCA: 226] [Impact Index Per Article: 32.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Outbreaks of multidrug-resistant bacteria present a frequent threat to vulnerable patient populations in hospitals around the world. Intensive care unit (ICU) patients are particularly susceptible to nosocomial infections due to indwelling devices such as intravascular catheters, drains, and intratracheal tubes for mechanical ventilation. The increased vulnerability of infected ICU patients demonstrates the importance of effective outbreak management protocols to be in place. Understanding the transmission of pathogens via genotyping methods is an important tool for outbreak management. Recently, whole-genome sequencing (WGS) of pathogens has become more accessible and affordable as a tool for genotyping. Analysis of the entire pathogen genome via WGS could provide unprecedented resolution in discriminating even highly related lineages of bacteria and revolutionize outbreak analysis in hospitals. Nevertheless, clinicians have long been hesitant to implement WGS in outbreak analyses due to the expensive and cumbersome nature of early sequencing platforms. Recent improvements in sequencing technologies and analysis tools have rapidly increased the output and analysis speed as well as reduced the overall costs of WGS. In this review, we assess the feasibility of WGS technologies and bioinformatics analysis tools for nosocomial outbreak analyses and provide a comparison to conventional outbreak analysis workflows. Moreover, we review advantages and limitations of sequencing technologies and analysis tools and present a real-world example of the implementation of WGS for antimicrobial resistance analysis. We aimed to provide health care professionals with a guide to WGS outbreak analysis that highlights its benefits for hospitals and assists in the transition from conventional to WGS-based outbreak analysis.
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Affiliation(s)
- Scott Quainoo
- Department of Microbiology, Radboud University, Nijmegen, The Netherlands
| | - Jordy P M Coolen
- Department of Medical Microbiology, Radboud University Medical Centre, Nijmegen, The Netherlands
| | - Sacha A F T van Hijum
- Centre for Molecular and Biomolecular Informatics, Radboud University Medical Centre, Nijmegen, The Netherlands
- NIZO, Ede, The Netherlands
| | - Martijn A Huynen
- Centre for Molecular and Biomolecular Informatics, Radboud University Medical Centre, Nijmegen, The Netherlands
| | - Willem J G Melchers
- Department of Medical Microbiology, Radboud University Medical Centre, Nijmegen, The Netherlands
| | - Willem van Schaik
- Institute of Microbiology and Infection, University of Birmingham, Birmingham, United Kingdom
| | - Heiman F L Wertheim
- Department of Medical Microbiology, Radboud University Medical Centre, Nijmegen, The Netherlands
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23
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Garzillo C, Bagattini M, Bogdanović L, Di Popolo A, Iula VD, Catania MR, Raimondi F, Triassi M, Zarrilli R. Risk factors for Candida parapsilosis bloodstream infection in a neonatal intensive care unit: a case-control study. Ital J Pediatr 2017; 43:10. [PMID: 28257640 PMCID: PMC5347820 DOI: 10.1186/s13052-017-0332-5] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/19/2016] [Accepted: 01/14/2017] [Indexed: 02/07/2023] Open
Abstract
Background Candida parapsilosis is increasingly responsible for invasive candidiasis in neonates. This study investigates phenotypic and genotypic features of C. parapsilosis microbial isolates and underlying clinical conditions associated with acquisition of C. parapsilosis in a neonatal intensive care unit (NICU) in Italy. Methods Identification of C. parapsilosis was performed by VITEK® 2 and MALDI TOF and confirmed by analysis of internal transcribed spacer ribosomal DNA sequences. Genotyping was performed by PCR fingerprinting. Antifungal susceptibility of strains was evaluated by microdilution. A case-control study was designed to identify risk factors for C. parapsilosis bloodstream infection. Results During the study period (April 2009- April 2012), C. parapsilosis was responsible for 6 umbilical catheter and 11 central catheter-associated bloodstream infection in 17 neonates in the NICU. Molecular typing identified identical fingerprinting profile in all C. parapsilosis isolates from neonates. Fifteen of 17 C. parapsilosis isolates were susceptible to all antifungal drugs, two isolates were resistant to fluconazole and intermediate susceptible to itraconazole. Low birthweight, gestational age and time to exposure to assisted ventilation were risk factors for C. parapsilosis infection in neonates in the NICU at univariate and multivariate analysis. Conclusion C. parapsilosis bloodstream infections in the NICU were caused by a single epidemic clone. Low birthweight, gestational age and time to exposure to invasive devices, with predominance of assisted ventilation, were the clinical conditions associated with C. parapsilosis bloodstream infection in the NICU. Electronic supplementary material The online version of this article (doi:10.1186/s13052-017-0332-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Carmine Garzillo
- Department of Public Health, University of Naples "Federico II", Via S. Pansini n.5, 80131, Naples, Italy
| | - Maria Bagattini
- Department of Public Health, University of Naples "Federico II", Via S. Pansini n.5, 80131, Naples, Italy
| | - Lidija Bogdanović
- Department of Public Health, University of Naples "Federico II", Via S. Pansini n.5, 80131, Naples, Italy
| | - Anna Di Popolo
- Department of Public Health, University of Naples "Federico II", Via S. Pansini n.5, 80131, Naples, Italy
| | - Vita Dora Iula
- Department of Molecular Medicine and Medical Biotechnologies, University of Naples "Federico II", Naples, Italy
| | - Maria Rosaria Catania
- Department of Molecular Medicine and Medical Biotechnologies, University of Naples "Federico II", Naples, Italy
| | - Francesco Raimondi
- Division of Neonatology, Department of Medical Translational Sciences, University of Naples "Federico II", Naples, Italy
| | - Maria Triassi
- Department of Public Health, University of Naples "Federico II", Via S. Pansini n.5, 80131, Naples, Italy
| | - Raffaele Zarrilli
- Department of Public Health, University of Naples "Federico II", Via S. Pansini n.5, 80131, Naples, Italy.
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24
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Dubourg G, Fournier PE. Advances in Diagnostic Microbiology. Infect Dis (Lond) 2017. [DOI: 10.1016/b978-0-7020-6285-8.00161-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
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25
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Cassagne C, Normand AC, L'Ollivier C, Ranque S, Piarroux R. Performance of MALDI-TOF MS platforms for fungal identification. Mycoses 2016; 59:678-690. [DOI: 10.1111/myc.12506] [Citation(s) in RCA: 103] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2015] [Revised: 03/04/2016] [Accepted: 03/12/2016] [Indexed: 01/03/2023]
Affiliation(s)
- Carole Cassagne
- Parasitology and Mycology; Assistance Publique-Hôpitaux de Marseille; CHU Timone-Adultes; Marseilles CEDEX 5 France
- Aix-Marseille University; UMR MD3 IP-TPT; Marseilles France
| | - Anne-Cécile Normand
- Parasitology and Mycology; Assistance Publique-Hôpitaux de Marseille; CHU Timone-Adultes; Marseilles CEDEX 5 France
| | - Coralie L'Ollivier
- Parasitology and Mycology; Assistance Publique-Hôpitaux de Marseille; CHU Timone-Adultes; Marseilles CEDEX 5 France
- Aix-Marseille University; UMR MD3 IP-TPT; Marseilles France
| | - Stéphane Ranque
- Parasitology and Mycology; Assistance Publique-Hôpitaux de Marseille; CHU Timone-Adultes; Marseilles CEDEX 5 France
- Aix-Marseille University; UMR MD3 IP-TPT; Marseilles France
| | - Renaud Piarroux
- Parasitology and Mycology; Assistance Publique-Hôpitaux de Marseille; CHU Timone-Adultes; Marseilles CEDEX 5 France
- Aix-Marseille University; UMR MD3 IP-TPT; Marseilles France
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26
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Sanguinetti M, Posteraro B. Mass spectrometry applications in microbiology beyond microbe identification: progress and potential. Expert Rev Proteomics 2016; 13:965-977. [DOI: 10.1080/14789450.2016.1231578] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Affiliation(s)
| | - Brunella Posteraro
- Institute of Public Health (Section of Hygiene), Università Cattolica del Sacro Cuore, Rome, Italy
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27
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Wang H, Zhang L, Kudinha T, Kong F, Ma XJ, Chu YZ, Kang M, Sun ZY, Li RY, Liao K, Lu J, Zou GL, Xiao M, Fan X, Xu YC. Investigation of an unrecognized large-scale outbreak of Candida parapsilosis sensu stricto fungaemia in a tertiary-care hospital in China. Sci Rep 2016; 6:27099. [PMID: 27251023 PMCID: PMC4890031 DOI: 10.1038/srep27099] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2016] [Accepted: 05/13/2016] [Indexed: 02/05/2023] Open
Abstract
A data analysis of yeast collections from the National China Hospital Invasive Fungal Surveillance Net (CHIF-NET) programme in 2013 revealed a sudden increase in the proportion of Candida parapsilosis complex isolates (n = 98) in one participating hospital (Hospital H). Out of 443 yeast isolates submitted to the CHIF-NET reference laboratory by Hospital H (2010–2014), 212 (47.9%) were identified as C. parapsilosis sensu stricto by sequencing analysis of the internal transcribed spacer region and D1/D2 domain of the 26S rRNA gene. Among the 212 C. parapsilosis sensu stricto isolates, 176 (83.0%) bloodstream-based isolates and 25 isolates from tip cultures of various vascular catheters from 25 patients with candidaemia, were subjected to microsatellite genotyping, and a phylogenetic relationship analysis was performed for 152 isolates. Among the 152 isolates, 45 genotypes (T01 to T45) were identified, and two prevalent genotypes (63.8%) were found: T15 (n = 74, 48.7%) and T16 (n = 23, 15.1%). These two main clones were confined mainly to three different wards of the hospital, and they persisted for 16–25 months and 12–13 months, respectively. The lack of proper coordination between the clinical microbiology laboratory and infection control staff as part of public health control resulted in the failure to timely identify an outbreak, which led to the wide and long-term dissemination of C. parapsilosis sensu stricto in Hospital H.
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Affiliation(s)
- He Wang
- Department of Clinical Laboratory, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Beijing, China.,Graduate School, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China
| | - Li Zhang
- Department of Clinical Laboratory, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Beijing, China
| | - Timothy Kudinha
- Charles Sturt University, Leeds Parade, Orange, New South Wales, Australia.,Centre for Infectious Diseases and Microbiology Laboratory Services, Westmead Hospital, Darcy Road, Westmead, New South Wales, Australia
| | - Fanrong Kong
- Centre for Infectious Diseases and Microbiology Laboratory Services, Westmead Hospital, Darcy Road, Westmead, New South Wales, Australia
| | - Xiao-Jun Ma
- Department of Infectious Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Beijing, China
| | - Yun-Zhuo Chu
- Department of Clinical Laboratory, the First Hospital of China Medical University, Shenyang, China
| | - Mei Kang
- Laboratory of Clinical Microbiology, West China Hospital, Sichuan University, Chengdu, China
| | - Zi-Yong Sun
- Department of Clinical Laboratory, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Ruo-Yu Li
- Department of Clinical Laboratory, Peking University First Hospital, Beijing, China
| | - Kang Liao
- Department of Clinical Laboratory, the First Affiliated Hospital of Sun Yat-Sen University, Guangzhou, China
| | - Juan Lu
- Department of Clinical Laboratory, the First Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Gui-Ling Zou
- Department of Clinical Laboratory, the Fourth Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Meng Xiao
- Department of Clinical Laboratory, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Beijing, China
| | - Xin Fan
- Department of Clinical Laboratory, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Beijing, China.,Graduate School, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China
| | - Ying-Chun Xu
- Department of Clinical Laboratory, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Beijing, China
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28
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Pushing the Limits of MALDI-TOF Mass Spectrometry: Beyond Fungal Species Identification. J Fungi (Basel) 2015; 1:367-383. [PMID: 29376916 PMCID: PMC5753130 DOI: 10.3390/jof1030367] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2015] [Revised: 10/05/2015] [Accepted: 10/07/2015] [Indexed: 12/12/2022] Open
Abstract
Matrix assisted laser desorption ionization time of flight (MALDI-TOF) is a powerful analytical tool that has revolutionized microbial identification. Routinely used for bacterial identification, MALDI-TOF has recently been applied to both yeast and filamentous fungi, confirming its pivotal role in the rapid and reliable diagnosis of infections. Subspecies-level identification holds an important role in epidemiological investigations aimed at tracing virulent or drug resistant clones. This review focuses on present and future applications of this versatile tool in the clinical mycology laboratory.
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29
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van Belkum A, Chatellier S, Girard V, Pincus D, Deol P, Dunne WM. Progress in proteomics for clinical microbiology: MALDI-TOF MS for microbial species identification and more. Expert Rev Proteomics 2015; 12:595-605. [DOI: 10.1586/14789450.2015.1091731] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
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30
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Singhal N, Kumar M, Kanaujia PK, Virdi JS. MALDI-TOF mass spectrometry: an emerging technology for microbial identification and diagnosis. Front Microbiol 2015; 6:791. [PMID: 26300860 PMCID: PMC4525378 DOI: 10.3389/fmicb.2015.00791] [Citation(s) in RCA: 748] [Impact Index Per Article: 83.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2015] [Accepted: 07/21/2015] [Indexed: 01/13/2023] Open
Abstract
Currently microorganisms are best identified using 16S rRNA and 18S rRNA gene sequencing. However, in recent years matrix assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) has emerged as a potential tool for microbial identification and diagnosis. During the MALDI-TOF MS process, microbes are identified using either intact cells or cell extracts. The process is rapid, sensitive, and economical in terms of both labor and costs involved. The technology has been readily imbibed by microbiologists who have reported usage of MALDI-TOF MS for a number of purposes like, microbial identification and strain typing, epidemiological studies, detection of biological warfare agents, detection of water- and food-borne pathogens, detection of antibiotic resistance and detection of blood and urinary tract pathogens etc. The limitation of the technology is that identification of new isolates is possible only if the spectral database contains peptide mass fingerprints of the type strains of specific genera/species/subspecies/strains. This review provides an overview of the status and recent applications of mass spectrometry for microbial identification. It also explores the usefulness of this exciting new technology for diagnosis of diseases caused by bacteria, viruses, and fungi.
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Affiliation(s)
- Neelja Singhal
- Department of Microbiology, University of Delhi New Delhi, India
| | - Manish Kumar
- Department of Biophysics, University of Delhi New Delhi, India
| | - Pawan K Kanaujia
- Department of Microbiology, University of Delhi New Delhi, India
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31
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Saracli M. MALDI-TOF MS: A Rapid and New Approach in Fungal Diagnosis and Susceptibility Testing. Med Mycol 2015. [DOI: 10.1201/b18707-20] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
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32
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Dhieb C, Normand AC, Al-Yasiri M, Chaker E, El Euch D, Vranckx K, Hendrickx M, Sadfi N, Piarroux R, Ranque S. MALDI-TOF typing highlights geographical and fluconazole resistance clusters in Candida glabrata. Med Mycol 2015; 53:462-9. [PMID: 25841053 DOI: 10.1093/mmy/myv013] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2014] [Accepted: 02/09/2015] [Indexed: 12/12/2022] Open
Abstract
Utilizing matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) mass spectra for Candida glabrata typing would be a cost-effective and easy-to-use alternative to classical DNA-based typing methods. This study aimed to use MALDI-TOF for the typing of C. glabrata clinical isolates from various geographical origins and test its capacity to differentiate between fluconazole-sensitive and -resistant strains.Both microsatellite length polymorphism (MLP) and MALDI-TOF mass spectra of 58 C. glabrata isolates originating from Marseilles (France) and Tunis (Tunisia) as well as collection strains from diverse geographic origins were analyzed. The same analysis was conducted on a subset of C. glabrata isolates that were either susceptible (MIC ≤ 8 mg/l) or resistant (MIC ≥ 64 mg/l) to fluconazole.According to the seminal results, both MALDI-TOF and MLP classifications could highlight C. glabrata population structures associated with either geographical dispersal barriers (p < 10(-5)) or the selection of antifungal drug resistance traits (<10(-5)).In conclusion, MALDI-TOF geographical clustering was congruent with MPL genotyping and highlighted a significant population genetic structure according to fluconazole susceptibility in C. glabrata. Furthermore, although MALDI-TOF and MLP resulted in distinct classifications, MALDI-TOF also classified the isolates with respect to their fluconazole susceptibility profile. Further prospective studies are required to evaluate the capacity of MALDI-TOF typing to investigate C. glabrata infection outbreaks and predict the antifungal susceptibility profile of clinical laboratory isolates.
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Affiliation(s)
- C Dhieb
- Laboratoire des Microorganismes et Biomolécules Actives, Faculté des Sciences de Tunis, 2092 Tunis, Tunisia
| | - A C Normand
- Parasitolgy-Mycology, APHM, CHU Timone, Marseille, France
| | - M Al-Yasiri
- Aix Marseille Université, IP-TPT UMR MD3, 13005, Marseille, France
| | - E Chaker
- Laboratoire de Parasitologie, Hôpital La Rabta, Tunis, Tunisia
| | - D El Euch
- Service de Dermatologie et de Vénéréologie, Hôpital La Rabta, Tunis, Tunisia
| | - K Vranckx
- Applied Maths NV, 9830, Sint-Martens-Latem, Belgium
| | - M Hendrickx
- BCCM/IHEM: Scientific Institute of Public Health, Mycology and Aerobiology Section, Brussels, Belgium
| | - N Sadfi
- Laboratoire des Microorganismes et Biomolécules Actives, Faculté des Sciences de Tunis, 2092 Tunis, Tunisia
| | - R Piarroux
- Parasitolgy-Mycology, APHM, CHU Timone, Marseille, France Aix Marseille Université, IP-TPT UMR MD3, 13005, Marseille, France
| | - S Ranque
- Parasitolgy-Mycology, APHM, CHU Timone, Marseille, France Aix Marseille Université, IP-TPT UMR MD3, 13005, Marseille, France
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33
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Abstract
Neonatal infections continue to cause morbidity and mortality in infants. Among approximately 400,000 infants followed nationally, the incidence rates of early-onset sepsis infection within 3 days of life are 0.98 cases per 1000 live births. Newborn infants are at increased risk for infections because they have relative immunodeficiency. This article provides evidence-based practical approaches to the diagnosis, management, and prevention of neonatal infections.
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Affiliation(s)
- Roberto Parulan Santos
- Pediatric Infectious Diseases, Bernard & Millie Duker Children's Hospital, Albany Medical Center, 47 New Scotland Avenue (MC88), Albany, NY 12208, USA.
| | - Debra Tristram
- Pediatric Infectious Disease, Department of Pediatrics, Albany Medical Center, 47 New Scotland Avenue (MC88), Albany, NY 12208, USA
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34
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Dhieb C, Normand AC, L'Ollivier C, Gautier M, Vranckx K, El Euch D, Chaker E, Hendrickx M, Dalle F, Sadfi N, Piarroux R, Ranque S. Comparison of MALDI-TOF mass spectra with microsatellite length polymorphisms in Candida albicans. JOURNAL OF MASS SPECTROMETRY : JMS 2015; 50:371-377. [PMID: 25800019 DOI: 10.1002/jms.3538] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2014] [Revised: 10/30/2014] [Accepted: 11/02/2014] [Indexed: 06/04/2023]
Abstract
Candida albicans is the most frequent yeast involved in human infections. Its population structure can be divided into several genetic clades, some of which have been associated with antifungal susceptibility. Therefore, detecting and monitoring fungal clones in a routine laboratory setting would be a major epidemiological advance. Matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) mass spectra results are now widely used as bar codes to identify microorganisms in clinical microbiology laboratories. This study aimed at testing MALDI-TOF mass spectra bar codes to identify clades among a set of C. albicans isolates. Accordingly, 102 clinical strains were genotyped using 10 microsatellite markers and analyzed via MALDI-TOF mass spectrometry. The mass spectra were compared with a reference spectral library including 33 well-characterized collection strains, using a Microflex(TM) system and Biotyper(TM) software, to test the capacity of the spectrum of a given isolate to match with the reference mass spectrum of an isolate from the same genetic clade. Despite high confidence species identification, the spectra failed to significantly match with the corresponding clade (p = 0.74). This was confirmed with the MALDI-TOF spectra similarity dendrogram, in which the strains were dispersed irrespective of their genetic clade. Various attempts to improve intra-clade spectra recognition were unsuccessful. In conclusion, MALDI-TOF mass spectra bar code analysis failed to reliably recognize genetically related C. albicans isolates. Further studies are warranted to develop alternative MALDI-TOF mass spectra analytical approaches to identify and monitor C. albicans clades in the routine clinical laboratory.
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Affiliation(s)
- C Dhieb
- Laboratoire de Microorganismes et Biomolécules Actives, Faculté des Sciences de Tunis, 2092, Tunis, Tunisia
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Genetic diversity among Candida albicans isolates associated with vertical transmission in preterm triplets. Mycopathologia 2014; 178:285-90. [PMID: 25151365 DOI: 10.1007/s11046-014-9803-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2014] [Accepted: 08/13/2014] [Indexed: 01/11/2023]
Abstract
We report a case of congenital candidiasis in triplets, in the context of premature labor at 25 weeks gestation, without symptomatic vaginitis or chorioamnionitis. All three infants died as a result of prematurity, aggravated by systemic candidiasis. Multi-locus sequence typing confirmed vertical transmission of Candida albicans from the mother to the triplets and revealed a slight diversity among the strains isolated from the neonates.
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MALDI-TOF mass spectrometry: any use for Aspergilli? Mycopathologia 2014; 178:417-26. [PMID: 25001870 DOI: 10.1007/s11046-014-9757-1] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2014] [Accepted: 05/06/2014] [Indexed: 12/11/2022]
Abstract
Recently, relentless efforts to develop rapid, cost-effective, and reliable laboratory methods for daily diagnosis of fungal diseases such as aspergillosis appear to be materialized in the relatively new, but revolutionary matrix-assisted laser desorption ionization-time-of-flight (MALDI-TOF) mass spectrometry (MS) technology. As for Aspergilli, MALDI-TOF MS profiling of isolates growing in culture--characteristic protein spectra are obtainable by means of simple and reproducible preanalytical and analytical procedures--ensures that single species within the different sections or complexes can be easily and accurately identified, including species that are morphologically and phylogenetically similar to each other. Thus, resort to longer and more onerous molecular biology techniques is restricted to those cases for which no spectra in the reference fungal database or library are available at the time of analysis. However, it is necessary to interrogate reference libraries composed of spectra that have been obtained using procedures similar to those used to obtain the test isolate's mass spectrum, as well as to continuously update these libraries for enriching them with fungal strains/species not (or not well) represented in their current versions. Compared to mold identification, very limited work was reported on the use of MALDI-TOF MS to perform strain typing or antifungal susceptibility testing for Aspergilli. If these complementing areas will be potentiated in the near future, MALDI-TOF MS could effectively support the clinical microbiology/mycology laboratory in its primary role of assisting either infection control specialists or physicians for the diagnosis and treatment of aspergillosis.
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The Genus Scedosporium and Pseudallescheria: Current Challenges in Laboratory Diagnosis. CURRENT CLINICAL MICROBIOLOGY REPORTS 2014. [DOI: 10.1007/s40588-014-0001-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
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Gago S, Alastruey-Izquierdo A, Marconi M, Buitrago MJ, Kerhornou A, Kersey PJ, Mellado E, Cuenca-Estrella M, Rodríguez-Tudela JL, Cuesta I. Ribosomic DNA intergenic spacer 1 region is useful when identifying Candida parapsilosis spp. complex based on high-resolution melting analysis. Med Mycol 2014; 52:472-81. [PMID: 24847037 DOI: 10.1093/mmy/myu009] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The epidemiology of Candida parapsilosis and the closely related species C. orthopsilosis and C. metapsilosis has changed in recent years, justify the need to identify this complex at the species level. In this study we investigate the intergenic spacer 1 (IGS1) of the ribosomal DNA (rDNA) to evaluate the utility of this gene region as a phylogenetic molecular marker and the suitability of a high-resolution melting (HRM) strategy based on this region for identification of members of the C. parapsilosis spp. complex. We sequenced the IGS1 and the internal transcribed spacer (ITS) regions of the rDNA from 33 C. parapsilosis sensu lato strains. Although both regions are useful in identifying species, comparative sequence analysis showed that the diversity in the IGS1 region was higher than in the ITS sequences. We also developed an HRM analysis that reliably identifies C. parapsilosis spp. complex based on the amplification of 70 bp in the IGS1 region. All isolates were correctly identified with a confidence interval >98%. Our results demonstrate that HRM analysis based on the IGS1 region is a powerful tool for distinguishing C. parapsilosis from cryptic species.
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Affiliation(s)
- Sara Gago
- Mycology Service, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Majadahonda, Madrid, Spain
| | - Ana Alastruey-Izquierdo
- Mycology Service, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Majadahonda, Madrid, Spain Spanish Network for Research on Infectious Diseases, Instituto de Salud Carlos III, Madrid, Spain
| | - Marco Marconi
- Bioinformatic Unit, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Majadahonda, Madrid, Spain
| | - María José Buitrago
- Mycology Service, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Majadahonda, Madrid, Spain
| | - Arnaud Kerhornou
- Protein and Nucleotide Database (PANDA) Group, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Paul J Kersey
- Protein and Nucleotide Database (PANDA) Group, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Emilia Mellado
- Mycology Service, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Majadahonda, Madrid, Spain
| | - Manuel Cuenca-Estrella
- Mycology Service, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Majadahonda, Madrid, Spain
| | - Juan Luis Rodríguez-Tudela
- Mycology Service, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Majadahonda, Madrid, Spain
| | - Isabel Cuesta
- Bioinformatic Unit, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Majadahonda, Madrid, Spain
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Affiliation(s)
- Oliver Bader
- Institute for Medical Microbiology; University Medical Center Göttingen; Göttingen, Germany
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Three clustered cases of candidemia caused by Candida quercitrusa and mycological characteristics of this novel species. J Clin Microbiol 2014; 52:3044-8. [PMID: 24696025 DOI: 10.1128/jcm.00246-14] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
We investigated three nosocomial Candida quercitrusa candidemia cases occurring within 2 months in a Chinese hospital. Isolates were identifiable only by DNA sequencing of the rRNA genes. Genetic (via random amplified polymorphic DNA [RAPD]) and protein mass spectral (via matrix-assisted laser desorption ionization-time of flight mass spectrometry [MALDI-TOF MS]) analyses yielded identical profiles suggesting an outbreak. The fluconazole MICs of all the strains were 16 to 32 μg/ml.
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Marcos-Zambrano LJ, Escribano P, Bouza E, Guinea J. Aplicación de las técnicas de tipificación molecular al estudio de brotes hospitalarios de candidemia. Rev Iberoam Micol 2014; 31:97-103. [DOI: 10.1016/j.riam.2013.06.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2013] [Revised: 04/08/2013] [Accepted: 06/05/2013] [Indexed: 01/08/2023] Open
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Paoletti I, Fusco A, Grimaldi E, Perillo L, Coretti L, Di Domenico M, Cozza V, Contaldo M, Serpico R, Guida A, Donnarumma G. Assessment of host defence mechanisms induced by Candida species. Int J Immunopathol Pharmacol 2014; 26:663-72. [PMID: 24067462 DOI: 10.1177/039463201302600309] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Some species of Candida are opportunistic pathogens that can cause disease in a host immunocompromised by underlying local or systemic pathological processes. C. albicans is the species most often associated with oral lesions, but other species of Candida, including C. glabrata, C. tropicalis and C. parapsilosis, have also been isolated in the saliva of subjects with and without candidiasis. In the present study we evaluated the host defence mechanisms induced by Candida albicans and other Candida species in monocytes and oral epithelial cells in order to establish the existence of a species-specific cellular response. Our results indicated that, during Candida species infection, the epithelial cells actively participate in the host defence by producing antimicrobial peptides and proinflammatory cytokines. Moreover, in infections caused by Candida tropicalis and Candida glabrata, the host defence may be strengthened by the release of perforin and granzyme by polymorphonuclear leukocytes recruited at the site of infection.
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Affiliation(s)
- I Paoletti
- Department of Experimental Medicine, Microbiology and Clinical Microbiology Section, Second University of Naples, Naples, Italy
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Quirino A, Pulcrano G, Rametti L, Puccio R, Marascio N, Catania MR, Matera G, Liberto MC, Focà A. Typing of Ochrobactrum anthropi clinical isolates using automated repetitive extragenic palindromic-polymerase chain reaction DNA fingerprinting and matrix-assisted laser desorption/ionization-time-of-flight mass spectrometry. BMC Microbiol 2014; 14:74. [PMID: 24655432 PMCID: PMC3977698 DOI: 10.1186/1471-2180-14-74] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2013] [Accepted: 03/18/2014] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND Ochrobactrum anthropi (O. anthropi), is a non-fermenting gram-negative bacillus usually found in the environment. Nevertheless, during the past decade it has been identified as pathogenic to immunocompromised patients. In this study, we assessed the usefulness of the automated repetitive extragenic palindromic-polymerase chain reaction (rep-PCR-based DiversiLab™ system, bioMèrieux, France) and of matrix-assisted laser desorption/ionization-time-of-flight (MALDI-TOF MS) for typing of twentythree O. anthropi clinical isolates that we found over a four-months period (from April 2011 to August 2011) in bacteriemic patients admitted in the same operative unit of our hospital. Pulsed-field gel electrophoresis (PFGE), commonly accepted as the gold standard technique for typing, was also used. Analysis was carried out using the Pearson correlation coefficient to determine the distance matrice and the unweighted pair group method with arithmetic mean (UPGMA) to generate dendogram. RESULTS Rep-PCR analysis identified four different patterns: three that clustered together with 97% or more pattern similarity, and one whose members showed < 95% pattern similarity. Interestingly, strains isolated later (from 11/06/2011 to 24/08/2011) displayed a pattern with 99% similarity. MALDI-TOF MS evaluation clustered the twentythree strains of O. anthropi into a single group containing four distinct subgroups, each comprising the majority of strains clustering below 5 distance levels, indicating a high similarity between the isolates. CONCLUSIONS Our results indicate that these isolates are clonally-related and the methods used afforded a valuable contribution to the epidemiology, prevention and control of the infections caused by this pathogen.
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Affiliation(s)
- Angela Quirino
- Institute of Microbiology, Department of Health Sciences, “Magna Graecia” University, Viale Europa, Catanzaro, Italy
| | - Giovanna Pulcrano
- Department of Molecular and Cellular Biology and Pathology L. Califano, Medicine School, University of Naples Federico II, Naples, Italy
| | - Linda Rametti
- Institute of Microbiology, Department of Health Sciences, “Magna Graecia” University, Viale Europa, Catanzaro, Italy
| | - Rossana Puccio
- Institute of Microbiology, Department of Health Sciences, “Magna Graecia” University, Viale Europa, Catanzaro, Italy
| | - Nadia Marascio
- Institute of Microbiology, Department of Health Sciences, “Magna Graecia” University, Viale Europa, Catanzaro, Italy
| | - Maria Rosaria Catania
- Department of Molecular and Cellular Biology and Pathology L. Califano, Medicine School, University of Naples Federico II, Naples, Italy
| | - Giovanni Matera
- Institute of Microbiology, Department of Health Sciences, “Magna Graecia” University, Viale Europa, Catanzaro, Italy
| | - Maria Carla Liberto
- Institute of Microbiology, Department of Health Sciences, “Magna Graecia” University, Viale Europa, Catanzaro, Italy
| | - Alfredo Focà
- Institute of Microbiology, Department of Health Sciences, “Magna Graecia” University, Viale Europa, Catanzaro, Italy
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Zimmerman KO, Smith PB. Current Epidemiology and Management of Invasive Candidiasis in Infants. CURRENT FUNGAL INFECTION REPORTS 2014. [DOI: 10.1007/s12281-013-0167-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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45
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Matrix-assisted laser desorption ionization-time of flight mass spectrometry: a fundamental shift in the routine practice of clinical microbiology. Clin Microbiol Rev 2014; 26:547-603. [PMID: 23824373 DOI: 10.1128/cmr.00072-12] [Citation(s) in RCA: 507] [Impact Index Per Article: 50.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Within the past decade, clinical microbiology laboratories experienced revolutionary changes in the way in which microorganisms are identified, moving away from slow, traditional microbial identification algorithms toward rapid molecular methods and mass spectrometry (MS). Historically, MS was clinically utilized as a high-complexity method adapted for protein-centered analysis of samples in chemistry and hematology laboratories. Today, matrix-assisted laser desorption ionization-time of flight (MALDI-TOF) MS is adapted for use in microbiology laboratories, where it serves as a paradigm-shifting, rapid, and robust method for accurate microbial identification. Multiple instrument platforms, marketed by well-established manufacturers, are beginning to displace automated phenotypic identification instruments and in some cases genetic sequence-based identification practices. This review summarizes the current position of MALDI-TOF MS in clinical research and in diagnostic clinical microbiology laboratories and serves as a primer to examine the "nuts and bolts" of MALDI-TOF MS, highlighting research associated with sample preparation, spectral analysis, and accuracy. Currently available MALDI-TOF MS hardware and software platforms that support the use of MALDI-TOF with direct and precultured specimens and integration of the technology into the laboratory workflow are also discussed. Finally, this review closes with a prospective view of the future of MALDI-TOF MS in the clinical microbiology laboratory to accelerate diagnosis and microbial identification to improve patient care.
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46
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Del Chierico F, Petrucca A, Vernocchi P, Bracaglia G, Fiscarelli E, Bernaschi P, Muraca M, Urbani A, Putignani L. Proteomics boosts translational and clinical microbiology. J Proteomics 2013; 97:69-87. [PMID: 24145144 DOI: 10.1016/j.jprot.2013.10.013] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2013] [Revised: 07/28/2013] [Accepted: 10/09/2013] [Indexed: 01/17/2023]
Abstract
The application of proteomics to translational and clinical microbiology is one of the most advanced frontiers in the management and control of infectious diseases and in the understanding of complex microbial systems within human fluids and districts. This new approach aims at providing, by dedicated bioinformatic pipelines, a thorough description of pathogen proteomes and their interactions within the context of human host ecosystems, revolutionizing the vision of infectious diseases in biomedicine and approaching new viewpoints in both diagnostic and clinical management of the patient. Indeed, in the last few years, many laboratories have matured a series of advanced proteomic applications, aiming at providing individual proteome charts of pathogens, with respect to their morph and/or cell life stages, antimicrobial or antimycotic resistance profiling, epidemiological dispersion. Herein, we aim at reviewing the current state-of-the-art on proteomic protocols designed and set-up for translational and diagnostic microbiological purposes, from axenic pathogens' characterization to microbiota ecosystems' full description. The final goal is to describe applications of the most common MALDI-TOF MS platforms to advanced diagnostic issues related to emerging infections, increasing of fastidious bacteria, and generation of patient-tailored phylotypes. This article is part of a Special Issue entitled: Trends in Microbial Proteomics.
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Affiliation(s)
- F Del Chierico
- Unit of Parasitology, Bambino Gesù Children's Hospital, IRCCS, Piazza Sant'Onofrio 4, 00165 Rome, Italy; Unit of Metagenomics, Bambino Gesù Children's Hospital, IRCCS, Piazza Sant'Onofrio 4, 00165 Rome, Italy
| | - A Petrucca
- Unit of Parasitology, Bambino Gesù Children's Hospital, IRCCS, Piazza Sant'Onofrio 4, 00165 Rome, Italy; Unit of Metagenomics, Bambino Gesù Children's Hospital, IRCCS, Piazza Sant'Onofrio 4, 00165 Rome, Italy; Department of Diagnostic Science, Sant'Andrea Hospital, Via di Grottarossa 1035, 00185 Rome, Italy
| | - P Vernocchi
- Unit of Parasitology, Bambino Gesù Children's Hospital, IRCCS, Piazza Sant'Onofrio 4, 00165 Rome, Italy; Unit of Metagenomics, Bambino Gesù Children's Hospital, IRCCS, Piazza Sant'Onofrio 4, 00165 Rome, Italy; Interdipartimental Centre for Industrial Research-CIRI-AGRIFOOD, Alma Mater Studiorum, University of Bologna, Bologna, Italy
| | - G Bracaglia
- Unit of Parasitology, Bambino Gesù Children's Hospital, IRCCS, Piazza Sant'Onofrio 4, 00165 Rome, Italy; Unit of Metagenomics, Bambino Gesù Children's Hospital, IRCCS, Piazza Sant'Onofrio 4, 00165 Rome, Italy
| | - E Fiscarelli
- Laboratory Medicine, Bambino Gesù Children's Hospital, IRCCS, Piazza Sant'Onofrio 4, 00165 Rome, Italy
| | - P Bernaschi
- Unit of Microbiology, Bambino Gesù Children's Hospital, IRCCS, Piazza Sant'Onofrio 4, 00165 Rome, Italy
| | - M Muraca
- Laboratory Medicine, Bambino Gesù Children's Hospital, IRCCS, Piazza Sant'Onofrio 4, 00165 Rome, Italy
| | - A Urbani
- Department of Experimental Medicine and Surgery, University "Tor Vergata", Rome, Italy; IRCCS-Santa Lucia Foundation, Rome, Italy
| | - L Putignani
- Unit of Parasitology, Bambino Gesù Children's Hospital, IRCCS, Piazza Sant'Onofrio 4, 00165 Rome, Italy; Unit of Metagenomics, Bambino Gesù Children's Hospital, IRCCS, Piazza Sant'Onofrio 4, 00165 Rome, Italy.
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Posteraro B, De Carolis E, Vella A, Sanguinetti M. MALDI-TOF mass spectrometry in the clinical mycology laboratory: identification of fungi and beyond. Expert Rev Proteomics 2013; 10:151-64. [PMID: 23573782 DOI: 10.1586/epr.13.8] [Citation(s) in RCA: 94] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
MALDI-TOF mass spectrometry (MS) is becoming essential in most clinical microbiology laboratories throughout the world. Its successful use is mainly attributable to the low operational costs, the universality and flexibility of detection, as well as the specificity and speed of analysis. Based on characteristic protein spectra obtained from intact cells - by means of simple, rapid and reproducible preanalytical and analytical protocols - MALDI-TOF MS allows a highly discriminatory identification of yeasts and filamentous fungi starting from colonies. Whenever used early, direct identification of yeasts from positive blood cultures has the potential to greatly shorten turnaround times and to improve laboratory diagnosis of fungemia. More recently, but still at an infancy stage, MALDI-TOF MS is used to perform strain typing and to determine antifungal drug susceptibility. In this article, the authors discuss how the MALDI-TOF MS technology is destined to become a powerful tool for routine mycological diagnostics.
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Fournier PE, Drancourt M, Colson P, Rolain JM, Scola BL, Raoult D. Modern clinical microbiology: new challenges and solutions. Nat Rev Microbiol 2013; 11:574-85. [PMID: 24020074 PMCID: PMC7097238 DOI: 10.1038/nrmicro3068] [Citation(s) in RCA: 208] [Impact Index Per Article: 18.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
In the twenty-first century, the clinical microbiology laboratory plays a central part in optimizing the management of infectious diseases and surveying local and global epidemiology. This pivotal role is made possible by the adoption of rational sampling, point-of-care tests, extended automation and new technologies, including mass spectrometry for colony identification, real-time genomics for isolate characterization, and versatile and permissive culture systems. When balanced with cost, these developments can improve the workflow and output of clinical microbiology laboratories and, by identifying and characterizing microbial pathogens, provide significant input to scientific discovery.
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Affiliation(s)
- Pierre-Edouard Fournier
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, UM63, CNRS7278, IRD198, INSERMU1095, Institut Hospitalo-Universitaire Méditerranée-Infection, Aix-Marseille Université, Faculté de Médecine, 27 Boulevard Jean Moulin, Marseille, 13385 France
| | - Michel Drancourt
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, UM63, CNRS7278, IRD198, INSERMU1095, Institut Hospitalo-Universitaire Méditerranée-Infection, Aix-Marseille Université, Faculté de Médecine, 27 Boulevard Jean Moulin, Marseille, 13385 France
| | - Philippe Colson
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, UM63, CNRS7278, IRD198, INSERMU1095, Institut Hospitalo-Universitaire Méditerranée-Infection, Aix-Marseille Université, Faculté de Médecine, 27 Boulevard Jean Moulin, Marseille, 13385 France
| | - Jean-Marc Rolain
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, UM63, CNRS7278, IRD198, INSERMU1095, Institut Hospitalo-Universitaire Méditerranée-Infection, Aix-Marseille Université, Faculté de Médecine, 27 Boulevard Jean Moulin, Marseille, 13385 France
| | - Bernard La Scola
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, UM63, CNRS7278, IRD198, INSERMU1095, Institut Hospitalo-Universitaire Méditerranée-Infection, Aix-Marseille Université, Faculté de Médecine, 27 Boulevard Jean Moulin, Marseille, 13385 France
| | - Didier Raoult
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, UM63, CNRS7278, IRD198, INSERMU1095, Institut Hospitalo-Universitaire Méditerranée-Infection, Aix-Marseille Université, Faculté de Médecine, 27 Boulevard Jean Moulin, Marseille, 13385 France
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Pulcrano G, Iula DV, Vollaro A, Tucci A, Cerullo M, Esposito M, Rossano F, Catania MR. Rapid and reliable MALDI-TOF mass spectrometry identification of Candida non-albicans isolates from bloodstream infections. J Microbiol Methods 2013; 94:262-6. [PMID: 23845229 DOI: 10.1016/j.mimet.2013.07.001] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2013] [Revised: 06/30/2013] [Accepted: 07/01/2013] [Indexed: 11/28/2022]
Abstract
Matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) mass spectrometry (MS) fingerprinting has recently become an effective instrument for rapid microbiological diagnostics and in particular for identification of micro-organisms directly in a positive blood culture. The aim of the study was to evaluate a collection of 82 stored yeast isolates from bloodstream infection, by MALDI-TOF MS; 21 isolates were identified also directly from positive blood cultures and in the presence of other co-infecting micro-organisms. Of the 82 isolates grown on plates, 64 (76%) were correctly identified by the Vitek II system and 82 (100%) by MALDI-TOF MS; when the two methods gave different results, the isolate was identified by PCR. MALDI-TOF MS was unreliable in identifying two isolates (Candida glabrata and Candida parapsilosis) directly from blood culture; however, direct analysis from positive blood culture samples was fast and effective for the identification of yeast, which is of great importance for early and adequate treatment.
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Affiliation(s)
- Giovanna Pulcrano
- Department of Molecular Medicine and Medical Biotechnology, Medicine School, University of Naples Federico II, via Pansini, 80131, Naples, Italy.
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50
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Bader O. MALDI-TOF-MS-based species identification and typing approaches in medical mycology. Proteomics 2013; 13:788-99. [DOI: 10.1002/pmic.201200468] [Citation(s) in RCA: 113] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2012] [Revised: 11/17/2012] [Accepted: 11/24/2012] [Indexed: 12/26/2022]
Affiliation(s)
- Oliver Bader
- Institute for Medical Microbiology and German National Reference Center for Systemic Mycoses; University Medical Center Göttingen; Göttingen Germany
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