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Douglas AP, Stewart AG, Halliday CL, Chen SCA. Outbreaks of Fungal Infections in Hospitals: Epidemiology, Detection, and Management. J Fungi (Basel) 2023; 9:1059. [PMID: 37998865 PMCID: PMC10672668 DOI: 10.3390/jof9111059] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2023] [Revised: 10/17/2023] [Accepted: 10/26/2023] [Indexed: 11/25/2023] Open
Abstract
Nosocomial clusters of fungal infections, whilst uncommon, cannot be predicted and are associated with significant morbidity and mortality. Here, we review reports of nosocomial outbreaks of invasive fungal disease to glean insight into their epidemiology, risks for infection, methods employed in outbreak detection including genomic testing to confirm the outbreak, and approaches to clinical and infection control management. Both yeasts and filamentous fungi cause outbreaks, with each having general and specific risks. The early detection and confirmation of the outbreak are essential for diagnosis, treatment of affected patients, and termination of the outbreak. Environmental sampling, including the air in mould outbreaks, for the pathogen may be indicated. The genetic analysis of epidemiologically linked isolates is strongly recommended through a sufficiently discriminatory approach such as whole genome sequencing or a method that is acceptably discriminatory for that pathogen. An analysis of both linked isolates and epidemiologically unrelated strains is required to enable genetic similarity comparisons. The management of the outbreak encompasses input from a multi-disciplinary team with epidemiological investigation and infection control measures, including screening for additional cases, patient cohorting, and strict hygiene and cleaning procedures. Automated methods for fungal infection surveillance would greatly aid earlier outbreak detection and should be a focus of research.
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Affiliation(s)
- Abby P. Douglas
- National Centre for Infections in Cancer, Peter MacCallum Cancer Centre, Melbourne, VIC 3000, Australia
- Department of Infectious Diseases, Peter MacCallum Cancer Centre, Melbourne, VIC 3000, Australia
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, VIC 3000, Australia
- Department of Infectious Diseases, Austin Health, Heidelberg, VIC 3084, Australia
| | - Adam G. Stewart
- Centre for Clinical Research, Faculty of Medicine, Royal Brisbane and Women’s Hospital Campus, The University of Queensland, Herston, QLD 4006, Australia;
| | - Catriona L. Halliday
- Centre for Infectious Diseases and Microbiology Laboratory Services, Institute of Clinical Pathology and Medical Research, New South Wales Health Pathology, Westmead Hospital, Sydney, NSW 2145, Australia; (C.L.H.); (S.C.-A.C.)
| | - Sharon C.-A. Chen
- Centre for Infectious Diseases and Microbiology Laboratory Services, Institute of Clinical Pathology and Medical Research, New South Wales Health Pathology, Westmead Hospital, Sydney, NSW 2145, Australia; (C.L.H.); (S.C.-A.C.)
- Sydney Medical School, Faculty of Medicine and Health, The University of Sydney, Sydney, NSW 2050, Australia
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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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3
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Use of Metagenomic Next-Generation Sequencing in the Clinical Microbiology Laboratory: A Step Forward, but Not an End-All. J Mol Diagn 2021; 23:1415-1421. [PMID: 34756275 DOI: 10.1016/j.jmoldx.2021.09.003] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2021] [Accepted: 09/16/2021] [Indexed: 12/13/2022] Open
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Chowdhary A, Sharada K, Singh PK, Bhagwani DK, Kumar N, de Groot T, Meis JF. Outbreak of Dirkmeia churashimaensis Fungemia in a Neonatal Intensive Care Unit, India. Emerg Infect Dis 2021; 26:764-768. [PMID: 32186501 PMCID: PMC7101094 DOI: 10.3201/eid2604.190847] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
Bloodstream infections caused by uncommon or novel fungal species are challenging to identify and treat. We report a series of cases of fungemia due to a rare basidiomycete yeast, Dirkmeia churashimaensis, in neonatal patients in India. Whole-genome sequence typing demonstrated that the patient isolates were genetically indistinguishable, indicating a single-source infection.
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Sharma B, Nonzom S. Superficial mycoses, a matter of concern: Global and Indian scenario-an updated analysis. Mycoses 2021; 64:890-908. [PMID: 33665915 DOI: 10.1111/myc.13264] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2020] [Revised: 02/25/2021] [Accepted: 02/26/2021] [Indexed: 01/19/2023]
Abstract
Superficial mycoses of skin, nails and hair are among the common fungal infections. They are caused by dermatophytes, non-dermatophyte moulds, yeasts and yeast-like fungi. Such fungal infections are widespread all over the world and are predominant in tropical as well as subtropical regions. Environmental factors, such as warm, humid and pitiable hygienic conditions, are conducive for their growth and proliferation. Although it does not cause mortality, it is known to be associated with excessive morbidity which may be psychological or physical. This affects the quality of life of the infected individuals which leads to a negative impact on their occupational, emotional and social status. Such infections are increasing on a global scale and, therefore, are of serious concern worldwide. This review article covers the global and Indian scenario of superficial mycoses taking into account the historical background, aetiological agents, prevalence, cultural and environmental factors, risk factors, pathogenesis and hygienic practices for the prevention of superficial mycoses.
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Affiliation(s)
- Bharti Sharma
- Department of Botany, University of Jammu, Jammu, Jammu and Kashmir, India
| | - Skarma Nonzom
- Department of Botany, University of Jammu, Jammu, Jammu and Kashmir, India
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Puf4 Mediates Post-transcriptional Regulation of Cell Wall Biosynthesis and Caspofungin Resistance in Cryptococcus neoformans. mBio 2021; 12:mBio.03225-20. [PMID: 33436441 PMCID: PMC7844544 DOI: 10.1128/mbio.03225-20] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
The human fungal pathogen Cryptococcus neoformans is intrinsically resistant to the echinocandin antifungal drug caspofungin, which targets the β-1,3-glucan synthase encoded by FKS1 Echinocandins have been on the market for 20 years, yet they are the newest class of antifungal drugs. Analysis of a C. neoformans puf4Δ mutant, lacking the pumilio/FBF RNA binding protein family member Puf4, revealed exacerbated caspofungin resistance. In contrast, overexpression of PUF4 resulted in caspofungin sensitivity. The FKS1 mRNA contains three Puf4-binding elements (PBEs) in its 5' untranslated region. Puf4 binds with specificity to this region of FKS1 The FKS1 mRNA was destabilized in the puf4Δ mutant, and the abundance of the FKS1 mRNA was reduced compared to wild type, suggesting that Puf4 is a positive regulator of FKS1 mRNA stability. In addition to FKS1, the abundance of additional cell wall biosynthesis genes, including chitin synthases (CHS3, CHS4, and CHS6) and deacetylases (CDA1, CDA2, and CDA3) as well as a β-1,6-glucan synthase gene (SKN1), was regulated by Puf4. The use of fluorescent dyes to quantify cell wall components revealed that the puf4Δ mutant had increased chitin content, suggesting a cell wall composition that is less reliant on β-1,3-glucan. Overall, our findings suggest a mechanism by which caspofungin resistance, and more broadly, cell wall biogenesis, is regulated post-transcriptionally by Puf4.IMPORTANCE Cryptococcus neoformans is an environmental fungus that causes pulmonary and central nervous system infections. It is also responsible for 15% of AIDS-related deaths. A significant contributor to the high morbidity and mortality statistics is the lack of safe and effective antifungal therapies, especially in resource-poor settings. Yet, antifungal drug development has stalled in the pharmaceutical industry. Therefore, it is essential to understand the mechanism by which C. neoformans is resistant to caspofungin to design adjunctive therapies to potentiate the drug's activity toward this important pathogen.
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8
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Rizzo J, Stanchev LD, da Silva VK, Nimrichter L, Pomorski TG, Rodrigues ML. Role of lipid transporters in fungal physiology and pathogenicity. Comput Struct Biotechnol J 2019; 17:1278-1289. [PMID: 31921394 PMCID: PMC6944739 DOI: 10.1016/j.csbj.2019.09.001] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2019] [Revised: 08/20/2019] [Accepted: 09/02/2019] [Indexed: 02/08/2023] Open
Abstract
The fungal cell wall and membrane are the most common targets of antifungal agents, but the potential of membrane lipid organization in regulating drug-target interactions has yet to be investigated. Energy-dependent lipid transporters have been recently associated with virulence and drug resistance in many pathogenic fungi. To illustrate this view, we discuss (i) the structural and biological aspects of ATP-driven lipid transporters, comprising P-type ATPases and ATP-binding cassette transporters, (ii) the role of these transporters in fungal physiology and virulence, and (iii) the potential of lipid transporters as targets for the development of novel antifungals. These recent observations indicate that the lipid-trafficking machinery in fungi is a promising target for studies on physiology, pathogenesis and drug development.
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Affiliation(s)
- Juliana Rizzo
- Instituto de Microbiologia Paulo de Góes (IMPG), Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
| | - Lyubomir Dimitrov Stanchev
- Department of Molecular Biochemistry, Ruhr University Bochum, Faculty of Chemistry and Biochemistry, 44780 Bochum, Germany
- Department of Plant Biology and Biotechnology, University of Copenhagen, Thorvaldsensvej 40, 1871 Frederiksberg C,Denmark
| | - Vanessa K.A. da Silva
- Programa de Pós-Graduação em Biologia Parasitária do Instituto Oswaldo Cruz (IOC), Fundação Oswaldo Cruz (Fiocruz), Rio de Janeiro, Brazil
| | - Leonardo Nimrichter
- Instituto de Microbiologia Paulo de Góes (IMPG), Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
| | - Thomas Günther Pomorski
- Department of Molecular Biochemistry, Ruhr University Bochum, Faculty of Chemistry and Biochemistry, 44780 Bochum, Germany
- Department of Plant Biology and Biotechnology, University of Copenhagen, Thorvaldsensvej 40, 1871 Frederiksberg C,Denmark
| | - Marcio L. Rodrigues
- Instituto de Microbiologia Paulo de Góes (IMPG), Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
- Instituto Carlos Chagas, Fundação Oswaldo Cruz (Fiocruz), Curitiba, Brazil
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9
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Gómez LF, Arango M, McEwen JG, Gómez OM, Zuluaga A, Peláez CA, Acevedo JM, Taylor ML, Jiménez MDP. Molecular epidemiology of Colombian Histoplasma capsulatum isolates obtained from human and chicken manure samples. Heliyon 2019; 5:e02084. [PMID: 31372546 PMCID: PMC6660563 DOI: 10.1016/j.heliyon.2019.e02084] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2019] [Revised: 06/11/2019] [Accepted: 07/09/2019] [Indexed: 12/12/2022] Open
Abstract
The thermally dimorphic fungus Histoplasma capsulatum is the causative agent of histoplasmosis, one of the most prevalent endemic mycosis in the Americas. In tropical regions, agro-ecosystems require organic matter replacement, therefore, the use of organic fertilizers has increased disregarding the fact that certain number of such fertilizers might be contaminated with the fungus, and with their handling resulting in human cases and even outbreaks of histoplasmosis. Additionally, in Colombia, chicken manure is the most common raw material used in the production of organic fertilizers. In this work, we reported the isolation of this fungus from chicken manure, and genetically compared with 42 clinical isolates. The genetically compared environmental isolates grouped together with the clinical ones. Our result suggests that chicken manure may be one of H. capsulatum infection sources. Also, the phylogenetic analyses done with other H. capsulatum isolates indicate that the Colombian isolates are widely distributed in the relational tree thus reveling towards the great genetic diversity among the H. capsulatum Colombian isolates.
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Affiliation(s)
- Luisa F Gómez
- Grupo de Micología Médica, Departamento de Microbiología y Parasitología, Facultad de Medicina, Universidad de Antioquia, Medellín, Antioquia, Colombia.,Posgrado de Biología, Instituto de Biología, Facultad de Ciencias Exactas y Naturales, Universidad de Antioquia, Medellín, Antioquia, Colombia
| | - Myrtha Arango
- Grupo de Micología Médica, Departamento de Microbiología y Parasitología, Facultad de Medicina, Universidad de Antioquia, Medellín, Antioquia, Colombia
| | - Juan G McEwen
- Grupo de Micología Médica, Departamento de Microbiología y Parasitología, Facultad de Medicina, Universidad de Antioquia, Medellín, Antioquia, Colombia.,Grupo de Biología Celular y Molecular, Corporación para Investigaciones Biológicas (CIB), Universidad de Antioquia, Medellín, Antioquia, Colombia
| | - Oscar M Gómez
- Posgrado de Biología, Instituto de Biología, Facultad de Ciencias Exactas y Naturales, Universidad de Antioquia, Medellín, Antioquia, Colombia.,Grupo de Biología Celular y Molecular, Corporación para Investigaciones Biológicas (CIB), Universidad de Antioquia, Medellín, Antioquia, Colombia
| | - Alejandra Zuluaga
- Grupo de Micología Médica y Experimental, Corporación para Investigaciones Biológicas (CIB). Universidad de Antioquia, Medellín, Antioquia, Colombia
| | - Carlos A Peláez
- Grupo Interdisciplinario de Estudios Moleculares, (GIEM), Instituto de Química, Facultad de Ciencias Exactas y Naturales, Universidad de Antioquia, Medellín, Antioquia, Colombia
| | - Jose M Acevedo
- Grupo Interdisciplinario de Estudios Moleculares, (GIEM), Instituto de Química, Facultad de Ciencias Exactas y Naturales, Universidad de Antioquia, Medellín, Antioquia, Colombia
| | - María L Taylor
- Laboratorio de Inmunología de Hongos, Departamento de Microbiología y Parasitología, Facultad de Medicina, Universidad Nacional Autónoma de México, Ciudad de México, México
| | - María Del P Jiménez
- Grupo de Micología Médica, Departamento de Microbiología y Parasitología, Facultad de Medicina, Universidad de Antioquia, Medellín, Antioquia, Colombia
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10
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Barker BM, Litvintseva AP, Riquelme M, Vargas-Gastélum L. Coccidioides ecology and genomics. Med Mycol 2019; 57:S21-S29. [PMID: 30690605 DOI: 10.1093/mmy/myy051] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2018] [Indexed: 11/13/2022] Open
Abstract
Although the natural history and ecology of Coccidioides spp. have been studied for over 100 years, many fundamental questions about this fungus remain unanswered. Two of the most challenging aspects of the study of Coccidioides have been the undefined ecological niche and the outdated geographic distribution maps dating from midcentury. This review details the history of Coccidioides ecological research, and discusses current strategies and advances in understanding Coccidioides genetics and ecology.
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Affiliation(s)
- Bridget M Barker
- Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, USA
| | | | - Meritxell Riquelme
- Department of Microbiology, Centro de Investigación Científica y Educación Superior de Ensenada (CICESE), Ctra. Ensenada-Tijuana No. 3918, Ensenada, Baja California, 22860, Mexico
| | - Lluvia Vargas-Gastélum
- Department of Microbiology, Centro de Investigación Científica y Educación Superior de Ensenada (CICESE), Ctra. Ensenada-Tijuana No. 3918, Ensenada, Baja California, 22860, Mexico
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11
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Teixeira MM, Barker BM. Use of Population Genetics to Assess the Ecology, Evolution, and Population Structure of Coccidioides. Emerg Infect Dis 2018; 22:1022-30. [PMID: 27191589 PMCID: PMC4880095 DOI: 10.3201/eid2206.151565] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Although Coccidioides genotypes are highly genetically variable,
they cluster into discrete populations, which has implications for human
infections. During the past 20 years, a general picture of the genetic diversity and population
structure of Coccidioides, the causal agent of coccidioidomycosis
(Valley fever), has emerged. The genus consists of 2 genetically diverse species,
C. immitis and C. posadasii, each of which
contains 1 or more distinct populations with limited gene flow. Genotypic data
indicate that C. immitis is divided into 2 subpopulations (central
and southern California populations) and C. posadasii is divided
into 3 subpopulations (Arizona, Mexico, and Texas/South America populations).
However, admixture within and among these populations and the current paucity of
environmental isolates limit our understanding of the population genetics of
Coccidioides. We assessed population structure of
Coccidioides in Arizona by analyzing 495 clinical and
environmental isolates. Our findings confirm the population structure as previously
described and indicate a finer scale population structure in Arizona. Environmental
isolates appear to have higher genetic diversity than isolates from human
patients.
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Investigating Clinical Issues by Genotyping of Medically Important Fungi: Why and How? Clin Microbiol Rev 2017; 30:671-707. [PMID: 28490578 DOI: 10.1128/cmr.00043-16] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Genotyping studies of medically important fungi have addressed elucidation of outbreaks, nosocomial transmissions, infection routes, and genotype-phenotype correlations, of which secondary resistance has been most intensively investigated. Two methods have emerged because of their high discriminatory power and reproducibility: multilocus sequence typing (MLST) and microsatellite length polymorphism (MLP) using short tandem repeat (STR) markers. MLST relies on single-nucleotide polymorphisms within the coding regions of housekeeping genes. STR polymorphisms are based on the number of repeats of short DNA fragments, mostly outside coding regions, and thus are expected to be more polymorphic and more rapidly evolving than MLST markers. There is no consensus on a universal typing system. Either one or both of these approaches are now available for Candida spp., Aspergillus spp., Fusarium spp., Scedosporium spp., Cryptococcus neoformans, Pneumocystis jirovecii, and endemic mycoses. The choice of the method and the number of loci to be tested depend on the clinical question being addressed. Next-generation sequencing is becoming the most appropriate method for fungi with no MLP or MLST typing available. Whatever the molecular tool used, collection of clinical data (e.g., time of hospitalization and sharing of similar rooms) is mandatory for investigating outbreaks and nosocomial transmission.
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Benedict K, Richardson M, Vallabhaneni S, Jackson BR, Chiller T. Emerging issues, challenges, and changing epidemiology of fungal disease outbreaks. THE LANCET. INFECTIOUS DISEASES 2017; 17:e403-e411. [PMID: 28774697 DOI: 10.1016/s1473-3099(17)30443-7] [Citation(s) in RCA: 71] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/29/2016] [Revised: 10/12/2016] [Accepted: 02/09/2017] [Indexed: 12/14/2022]
Abstract
Several high-profile outbreaks have drawn attention to invasive fungal infections (IFIs) as an increasingly important public health problem. IFI outbreaks are caused by many different fungal pathogens and are associated with numerous settings and sources. In the community, IFI outbreaks often occur among people without predisposing medical conditions and are frequently precipitated by environmental disruption. Health-care-associated IFI outbreaks have been linked to suboptimal hospital environmental conditions, transmission via health-care workers' hands, contaminated medical products, and transplantation of infected organs. Outbreak investigations provide important insights into the epidemiology of IFIs, uncover risk factors for infection, and identify opportunities for preventing similar events in the future. Well recognised challenges with IFI outbreak recognition, response, and prevention include the need for improved rapid diagnostic methods, the absence of routine surveillance for most IFIs, adherence to infection control practices, and health-care provider awareness. Additionally, IFI outbreak investigations have revealed several emerging issues, including new populations at risk because of travel or relocation, occupation, or immunosuppression; fungal pathogens appearing in geographical areas in which they have not been previously recognised; and contaminated compounded medications. This report highlights notable IFI outbreaks in the past decade, with an emphasis on these emerging challenges in the USA.
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Affiliation(s)
- Kaitlin Benedict
- Mycotic Diseases Branch, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Malcolm Richardson
- Mycology Reference Centre, University Hospital of South Manchester and University of Manchester, Manchester, UK
| | - Snigdha Vallabhaneni
- Mycotic Diseases Branch, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Brendan R Jackson
- Mycotic Diseases Branch, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Tom Chiller
- Mycotic Diseases Branch, Centers for Disease Control and Prevention, Atlanta, GA, USA.
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14
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Etienne KA, Roe CC, Smith RM, Vallabhaneni S, Duarte C, Escadon P, Castaneda E, Gomez BL, de Bedout C, López LF, Salas V, Hederra LM, Fernandez J, Pidal P, Hormazabel JC, Otaiza F, Vannberg FO, Gillece J, Lemmer D, Driebe EM, Englethaler DM, Litvintseva AP. Whole-Genome Sequencing to Determine Origin of Multinational Outbreak of Sarocladium kiliense Bloodstream Infections. Emerg Infect Dis 2016; 22:476-81. [PMID: 26891230 PMCID: PMC4766898 DOI: 10.3201/eid2203.151193] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Next-generation technologies and bioinformatics enabled source attribution and implementation of effective control strategies. We used whole-genome sequence typing (WGST) to investigate an outbreak of Sarocladium kiliense bloodstream infections (BSI) associated with receipt of contaminated antinausea medication among oncology patients in Colombia and Chile during 2013–2014. Twenty-five outbreak isolates (18 from patients and 7 from medication vials) and 11 control isolates unrelated to this outbreak were subjected to WGST to elucidate a source of infection. All outbreak isolates were nearly indistinguishable (<5 single-nucleotide polymorphisms), and >21,000 single-nucleotide polymorphisms were identified from unrelated control isolates, suggesting a point source for this outbreak. S. kiliense has been previously implicated in healthcare-related infections; however, the lack of available typing methods has precluded the ability to substantiate point sources. WGST for outbreak investigation caused by eukaryotic pathogens without reference genomes or existing genotyping methods enables accurate source identification to guide implementation of appropriate control and prevention measures.
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15
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Pasquali M, Beyer M, Logrieco A, Audenaert K, Balmas V, Basler R, Boutigny AL, Chrpová J, Czembor E, Gagkaeva T, González-Jaén MT, Hofgaard IS, Köycü ND, Hoffmann L, Lević J, Marin P, Miedaner T, Migheli Q, Moretti A, Müller MEH, Munaut F, Parikka P, Pallez-Barthel M, Piec J, Scauflaire J, Scherm B, Stanković S, Thrane U, Uhlig S, Vanheule A, Yli-Mattila T, Vogelgsang S. A European Database of Fusarium graminearum and F. culmorum Trichothecene Genotypes. Front Microbiol 2016; 7:406. [PMID: 27092107 PMCID: PMC4821861 DOI: 10.3389/fmicb.2016.00406] [Citation(s) in RCA: 79] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2015] [Accepted: 03/14/2016] [Indexed: 12/15/2022] Open
Abstract
Fusarium species, particularly Fusarium graminearum and F. culmorum, are the main cause of trichothecene type B contamination in cereals. Data on the distribution of Fusarium trichothecene genotypes in cereals in Europe are scattered in time and space. Furthermore, a common core set of related variables (sampling method, host cultivar, previous crop, etc.) that would allow more effective analysis of factors influencing the spatial and temporal population distribution, is lacking. Consequently, based on the available data, it is difficult to identify factors influencing chemotype distribution and spread at the European level. Here we describe the results of a collaborative integrated work which aims (1) to characterize the trichothecene genotypes of strains from three Fusarium species, collected over the period 2000-2013 and (2) to enhance the standardization of epidemiological data collection. Information on host plant, country of origin, sampling location, year of sampling and previous crop of 1147 F. graminearum, 479 F. culmorum, and 3 F. cortaderiae strains obtained from 17 European countries was compiled and a map of trichothecene type B genotype distribution was plotted for each species. All information on the strains was collected in a freely accessible and updatable database (www.catalogueeu.luxmcc.lu), which will serve as a starting point for epidemiological analysis of potential spatial and temporal trichothecene genotype shifts in Europe. The analysis of the currently available European dataset showed that in F. graminearum, the predominant genotype was 15-acetyldeoxynivalenol (15-ADON) (82.9%), followed by 3-acetyldeoxynivalenol (3-ADON) (13.6%), and nivalenol (NIV) (3.5%). In F. culmorum, the prevalent genotype was 3-ADON (59.9%), while the NIV genotype accounted for the remaining 40.1%. Both, geographical and temporal patterns of trichothecene genotypes distribution were identified.
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Affiliation(s)
- Matias Pasquali
- Department of Environmental Research and Innovation, Luxembourg Institute of Science and TechnologyBelvaux, Luxembourg
| | - Marco Beyer
- Department of Environmental Research and Innovation, Luxembourg Institute of Science and TechnologyBelvaux, Luxembourg
| | - Antonio Logrieco
- Institute of Sciences of Food Production, National Research CouncilBari, Italy
| | - Kris Audenaert
- Department of Applied Biosciences, Faculty of Bioscience Engineering, Ghent UniversityGhent, Belgium
| | - Virgilio Balmas
- Department of Agriculture, University of SassariSassari, Italy
| | | | | | - Jana Chrpová
- Division of Crop Genetics and Breeding, Crop Research InstitutePrague, Czech Republic
| | - Elżbieta Czembor
- Department of Grasses, Legumes and Energy Plants, Plant Breeding and Acclimatization Institute-National Research InstituteRadzikow, Poland
| | - Tatiana Gagkaeva
- Laboratory of Mycology and Phytopathology, All-Russian Institute of Plant ProtectionSt. Petersburg, Russia
| | - María T. González-Jaén
- Department of Genetics, Faculty of Biology, Complutense University of MadridMadrid, Spain
| | | | - Nagehan D. Köycü
- Department of Plant Protection, Agriculture Faculty, Namık Kemal UniversityTekirdag, Turkey
| | - Lucien Hoffmann
- Department of Environmental Research and Innovation, Luxembourg Institute of Science and TechnologyBelvaux, Luxembourg
| | - Jelena Lević
- Laboratory of Phytopathology and Entomology, Maize Research Institute Zemun PoljeBelgrade, Serbia
| | - Patricia Marin
- Department of Genetics, Faculty of Biology, Complutense University of MadridMadrid, Spain
| | - Thomas Miedaner
- Plant Breeding Institute, University of HohenheimStuttgart, Germany
| | - Quirico Migheli
- Department of Agriculture, University of SassariSassari, Italy
| | - Antonio Moretti
- Institute of Sciences of Food Production, National Research CouncilBari, Italy
| | - Marina E. H. Müller
- Leibniz Centre for Agricultural Landscape Research, Institute for Landscape BiogeochemistryMüncheberg, Germany
| | - Françoise Munaut
- Applied Microbiology, Earth and Life Institute, Université Catholique de LouvainLouvain-la-Neuve, Belgium
| | - Päivi Parikka
- Department Natural Resources and Bioproduction, Natural Resources Institute Finland (Luke)Jokioinen, Finland
| | - Marine Pallez-Barthel
- Department of Environmental Research and Innovation, Luxembourg Institute of Science and TechnologyBelvaux, Luxembourg
| | - Jonathan Piec
- Department of Environmental Research and Innovation, Luxembourg Institute of Science and TechnologyBelvaux, Luxembourg
| | - Jonathan Scauflaire
- Applied Microbiology, Earth and Life Institute, Université Catholique de LouvainLouvain-la-Neuve, Belgium
| | - Barbara Scherm
- Department of Agriculture, University of SassariSassari, Italy
| | - Slavica Stanković
- Laboratory of Phytopathology and Entomology, Maize Research Institute Zemun PoljeBelgrade, Serbia
| | - Ulf Thrane
- Section for Eukaryotic Biotechnology, DTU Systems Biology, Technical University of DenmarkKongens Lyngby, Denmark
| | - Silvio Uhlig
- Section for Chemistry and Toxicology, Norwegian Veterinary InstituteOslo, Norway
| | - Adriaan Vanheule
- Department of Applied Biosciences, Faculty of Bioscience Engineering, Ghent UniversityGhent, Belgium
| | - Tapani Yli-Mattila
- Molecular Plant Biology, Department of Biochemistry, University of TurkuTurku, Finland
| | - Susanne Vogelgsang
- Research Division Grassland Sciences and Agro-Ecosystems, Institute for Sustainability Sciences, AgroscopeZürich, Switzerland
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16
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Vallabhaneni S, Purfield AE, Benedict K, Luvsansharav U, Lockhart SR, Pham CD, Pascoe N, Heseltine G, Chung W, Hall E, Brust KB, Wheeler CF, Halpin AL, Park BJ. Cardiothoracic surgical site phaeohyphomycosis caused by Bipolaris mould, multiple US states, 2008-2013: a clinical description. Med Mycol 2015; 54:318-21. [PMID: 26705838 DOI: 10.1093/mmy/myv101] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2015] [Accepted: 11/10/2015] [Indexed: 11/13/2022] Open
Abstract
Bipolaris mould surgical site infections (SSIs) are exceedingly rare. We describe 21 cases of Bipolaris SSIs in pediatric and adult cardiothoracic surgery patients at ten hospitals in Texas, Arkansas, and Florida during 2008-2013. Median case-patient age was 55 years (range: 3 days-82 years), and 19 (90%) were male. Ten (48%) had coronary artery bypass or valve surgery, and seven (33%) had heart transplantation. Fifteen (71%) had more than one cardiothoracic procedure (median: 3, range: 1-11). Thirteen (62%) case-patients (all 5 pediatric patients, and 8 (50%) of 16 adult patients) had delayed sternal closure (chest closed >1 day [median = 8 days; range: 2-22] following the initial cardiothoracic procedure). Thirteen (62%) had mediastinitis. Median time from initial surgery to positive Bipolaris culture was 20 days (range: 6-497). Sixteen (76%) case-patients died.
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Affiliation(s)
- Snigdha Vallabhaneni
- Epidemic Intelligence Service, Centers for Disease Control and Prevention, Atlanta, Georgia Division of Foodborne, Waterborne and Environmental Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia
| | - Anne E Purfield
- Epidemic Intelligence Service, Centers for Disease Control and Prevention, Atlanta, Georgia Division of Foodborne, Waterborne and Environmental Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia
| | - Kaitlin Benedict
- Division of Foodborne, Waterborne and Environmental Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia
| | - Ulzii Luvsansharav
- Epidemic Intelligence Service, Centers for Disease Control and Prevention, Atlanta, Georgia Division of Foodborne, Waterborne and Environmental Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia
| | - Shawn R Lockhart
- Division of Foodborne, Waterborne and Environmental Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia
| | - Cau D Pham
- Division of Foodborne, Waterborne and Environmental Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia
| | - Neil Pascoe
- Texas Department of State Health Services, Austin, Texas
| | - Gary Heseltine
- Texas Department of State Health Services, Austin, Texas
| | - Wendy Chung
- Dallas County Health and Human Services, Dallas, Texas
| | - Emily Hall
- Dallas County Health and Human Services, Dallas, Texas
| | | | | | - Alison Laufer Halpin
- Division of Healthcare Quality Promotion, Centers for Disease Control and Prevention, Atlanta, Georgia
| | - Benjamin J Park
- Division of Foodborne, Waterborne and Environmental Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia
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17
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Development of a Multilocus Sequence Typing System for Medically Relevant Bipolaris Species. J Clin Microbiol 2015. [PMID: 26202112 DOI: 10.1128/jcm.01546-15] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Multilocus sequence typing (MLST) is the gold standard genotyping technique for many microorganisms. This classification approach satisfies the requirements for a high-resolution, standardized, and archivable taxonomic system. Here, we describe the development of a novel MLST system to assist with the investigation of an unusual cluster of surgical site infections caused by Bipolaris spp. in postoperative cardiothoracic surgery (POCS) patients during January 2008 to December 2013 in the southeastern United States. We also used the same MLST system to perform a retrospective analysis on isolates from a 2012 Bipolaris endophthalmitis outbreak caused by a contaminated product. This MLST system showed high intraspecies discriminatory power for Bipolaris spicifera, B. hawaiiensis, and B. australiensis. Based on the relatedness of the isolates, the MLST data supported the hypothesis that infections in the POCS cluster were from different environmental sources while confirming that the endophthalmitis outbreak resulted from a point source, which was a contaminated medication.
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