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Zhang H, Zhou F, Liu X, Huang J. Clinical application of metagenomic next-generation sequencing in patients with different organ system infection: A retrospective observational study. Medicine (Baltimore) 2024; 103:e36745. [PMID: 38277518 PMCID: PMC10817116 DOI: 10.1097/md.0000000000036745] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Accepted: 11/30/2023] [Indexed: 01/28/2024] Open
Abstract
Microbiological identification is essential for appropriate treatment, but conventional methods are time-consuming and have a low sensitivity. In contrast, metagenomic next-generation sequencing (mNGS) is a culture-free and hypothesis-free technique that can detect a wide array of potential pathogens. This study aimed to reveal the overall diagnostic value of mNGS for infectious diseases of different organ systems and compare the sensitivity and specificity of mNGS with conventional methods. In a retrospective cohort study, 94 patients with mNGS results were enrolled, and clinical data were recorded and analyzed to compare the positive rate of mNGS with traditional methods including as smears, serological tests, and traditional PCR, etc. In this study, mNGS and culture were both positive in 12.77% cases and were both negative in 23.4% cases. There were positive results in 56 cases (54.26%) only by mNGS and 4 cases (4.26%) were positive only by culture. There were significant differences in sensitivity of pathogen detection between of ID and NID group for mNGS (χ2 = 10.461, P = .001)and conventional methods(χ2 = 7.963, P = .005). The positive predictive values and negative predictive values of diagnosing infectious disease by mNGS were 94.12% and 30.77%, respectively. mNGS increased the sensitivity rate by approximately 53.66% compared with that of culture (78.05% vs24.39%; χ2 = 47.248, P < .001) and decreased the specificity rate by 12.5% compared with that of culture (66.67% vs 100.0%; χ2 = 4.8, P = .028). mNGS can identify emerging or rare pathogen and further guide treatment regimens. mNGS has advantages in identifying overall pathogens and bacteria, however, there was no obvious advantage in identifying fungi, virus and tuberculosis. mNGS has higher specificity than conventional methods in identifying pathogens and advantages in detecting emerging or rare pathogens.
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Affiliation(s)
- Haiyan Zhang
- Department of General Practice, The Third Affiliated Hospital of Sun Yat-Sen University Lingnan Hospital, Guangzhou, Guangdong Province, People’s Republic of China
| | - Fengli Zhou
- Department of General Practice, The Third Affiliated Hospital of Sun Yat-Sen University Lingnan Hospital, Guangzhou, Guangdong Province, People’s Republic of China
| | - Xiaoyun Liu
- Department of General Practice, The Third Affiliated Hospital of Sun Yat-Sen University Lingnan Hospital, Guangzhou, Guangdong Province, People’s Republic of China
| | - Jiabao Huang
- Department of General Practice, The Third Affiliated Hospital of Sun Yat-Sen University Lingnan Hospital, Guangzhou, Guangdong Province, People’s Republic of China
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Rapti V, Iliopoulou K, Poulakou G. The Gordian Knot of C. auris: If You Cannot Cut It, Prevent It. Pathogens 2023; 12:1444. [PMID: 38133327 PMCID: PMC10747958 DOI: 10.3390/pathogens12121444] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2023] [Revised: 11/30/2023] [Accepted: 12/11/2023] [Indexed: 12/23/2023] Open
Abstract
Since its first description in 2009, Candida auris has, so far, resulted in large hospital outbreaks worldwide and is considered an emerging global public health threat. Exceptionally for yeast, it is gifted with a profoundly worrying invasive potential and high inter-patient transmissibility. At the same time, it is capable of colonizing and persisting in both patients and hospital settings for prolonged periods of time, thus creating a vicious cycle of acquisition, spreading, and infection. It exhibits various virulence qualities and thermotolerance, osmotolerance, filamentation, biofilm formation and hydrolytic enzyme production, which are mainly implicated in its pathogenesis. Owing to its unfavorable profile of resistance to diverse antifungal agents and the lack of effective treatment options, the implementation of robust infection prevention and control (IPC) practices is crucial for controlling and minimizing intra-hospital transmission of C. auris. Rapid and accurate microbiological identification, adherence to hand hygiene, use of adequate personal protective equipment (PPE), proper handling of catheters and implantable devices, contact isolation, periodical environmental decontamination, targeted screening, implementation of antimicrobial stewardship (AMS) programs and communication between healthcare facilities about residents' C. auris colonization status are recognized as coherent strategies for preventing its spread. Current knowledge on C. auris epidemiology, clinical characteristics, and its mechanisms of pathogenicity are summarized in the present review and a comprehensive overview of IPC practices ensuring yeast prevention is also provided.
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Affiliation(s)
- Vasiliki Rapti
- Third Department of Internal Medicine, School of Medicine, National & Kapodistrian University of Athens, Sotiria General Hospital, 115 27 Athens, Greece;
| | | | - Garyfallia Poulakou
- Third Department of Internal Medicine, School of Medicine, National & Kapodistrian University of Athens, Sotiria General Hospital, 115 27 Athens, Greece;
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Friedrich B, Tietze R, Dümig M, Sover A, Boca MA, Schreiber E, Band J, Janko C, Krappmann S, Alexiou C, Lyer S. Magnetic Removal of Candida albicans Using Salivary Peptide-Functionalized SPIONs. Int J Nanomedicine 2023; 18:3231-3246. [PMID: 37337577 PMCID: PMC10276999 DOI: 10.2147/ijn.s409559] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Accepted: 05/07/2023] [Indexed: 06/21/2023] Open
Abstract
Purpose Magnetic separation of microbes can be an effective tool for pathogen identification and diagnostic applications to reduce the time needed for sample preparation. After peptide functionalization of superparamagnetic iron oxide nanoparticles (SPIONs) with an appropriate interface, they can be used for the separation of sepsis-associated yeasts like Candida albicans. Due to their magnetic properties, the magnetic extraction of the particles in the presence of an external magnetic field ensures the accumulation of the targeted yeast. Materials and Methods In this study, we used SPIONs coated with 3-aminopropyltriethoxysilane (APTES) and functionalized with a peptide originating from GP340 (SPION-APTES-Pep). For the first time, we investigate whether this system is suitable for the separation and enrichment of Candida albicans, we investigated its physicochemical properties and by thermogravimetric analysis we determined the amount of peptide on the SPIONs. Further, the toxicological profile was evaluated by recording cell cycle and DNA degradation. The separation efficiency was investigated using Candida albicans in different experimental settings, and regrowth experiments were carried out to show the use of SPION-APTES-Pep as a sample preparation method for the identification of fungal infections. Conclusion SPION-APTES-Pep can magnetically remove more than 80% of the microorganism and with a high selective host-pathogen distinction Candida albicans from water-based media and about 55% in blood after 8 minutes processing without compromising effects on the cell cycle of human blood cells. Moreover, the separated fungal cells could be regrown without any restrictions.
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Affiliation(s)
- Bernhard Friedrich
- Department of Otorhinolaryngology, Head and Neck Surgery, Section of Experimental Oncology and Nanomedicine (SEON), Else Kröner-Fresenius-Stiftung Professorship, Universitätsklinikum Erlangen, Erlangen, Germany
| | - Rainer Tietze
- Department of Otorhinolaryngology, Head and Neck Surgery, Section of Experimental Oncology and Nanomedicine (SEON), Else Kröner-Fresenius-Stiftung Professorship, Universitätsklinikum Erlangen, Erlangen, Germany
| | - Michaela Dümig
- Mikrobiologisches Institut – Klinische Mikrobiologie, Immunologie und Hygiene, Universitätsklinikum Erlangen, Friedrich-Alexander-Universität (FAU) Erlangen-Nürnberg, Erlangen, Germany
| | - Alexandru Sover
- Faculty of Engineering, Ansbach University of Applied Sciences, Ansbach, Germany
| | - Marius-Andrei Boca
- Faculty of Engineering, Ansbach University of Applied Sciences, Ansbach, Germany
| | - Eveline Schreiber
- Department of Otorhinolaryngology, Head and Neck Surgery, Section of Experimental Oncology and Nanomedicine (SEON), Else Kröner-Fresenius-Stiftung Professorship, Universitätsklinikum Erlangen, Erlangen, Germany
| | - Julia Band
- Department of Otorhinolaryngology, Head and Neck Surgery, Section of Experimental Oncology and Nanomedicine (SEON), Else Kröner-Fresenius-Stiftung Professorship, Universitätsklinikum Erlangen, Erlangen, Germany
| | - Christina Janko
- Department of Otorhinolaryngology, Head and Neck Surgery, Section of Experimental Oncology and Nanomedicine (SEON), Else Kröner-Fresenius-Stiftung Professorship, Universitätsklinikum Erlangen, Erlangen, Germany
| | - Sven Krappmann
- Mikrobiologisches Institut – Klinische Mikrobiologie, Immunologie und Hygiene, Universitätsklinikum Erlangen, Friedrich-Alexander-Universität (FAU) Erlangen-Nürnberg, Erlangen, Germany
| | - Christoph Alexiou
- Department of Otorhinolaryngology, Head and Neck Surgery, Section of Experimental Oncology and Nanomedicine (SEON), Else Kröner-Fresenius-Stiftung Professorship, Universitätsklinikum Erlangen, Erlangen, Germany
| | - Stefan Lyer
- Department of Otorhinolaryngology, Head and Neck Surgery, Section of Experimental Oncology and Nanomedicine (SEON), Else Kröner-Fresenius-Stiftung Professorship, Universitätsklinikum Erlangen, Erlangen, Germany
- Department of Otorhinolaryngology, Head and Neck Surgery, Section of Experimental Oncology and Nanomedicine (SEON), Professorship for AI-Controlled Nanomaterials, Universitätsklinikum Erlangen, Erlangen, Germany
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LIU R, CHEN C, HUANG Y, CHENG L, LU R, FU G, SHI S, CHEN H, WAN C, FU Q, LIN J. Microbiological identification and analysis of waterfowl livers collected from backyard farms in southern China. J Vet Med Sci 2018; 80:667-671. [PMID: 29398671 PMCID: PMC5938198 DOI: 10.1292/jvms.17-0452] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2017] [Accepted: 01/14/2018] [Indexed: 11/22/2022] Open
Abstract
In total, 985 livers were collected from 275 backyard waterfowl farms distributed in seven provinces of southern China. The virus that was most commonly isolated was avian influenza virus, with a 12.1% positivity rate. Of the other positive samples, 10.6% tested positive for avian Tembusu virus, 6.8% for duck hepatitis A virus, 3.8% for duck plague virus, 3.4% for Muscovy duck parvovirus, 3.1% for goose parvovirus, 1.0% for mycoplasma and 0.9% for respiratory enteric orphan virus. The bacterium that was most commonly isolated was Escherichia coli, with a 47.1% positivity rate. This survey suggests that backyard waterfowl in southern China could be an important vector for the storage, variation, and transmission of various pathogens.
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Affiliation(s)
- Rongchang LIU
- Institute of Animal Husbandry and Veterinary Medicine,
Fujian Academy of Agricultural Sciences, Fujian Animal Diseases Control Technology Center,
Fujian Provincial Key Laboratory for Avian Diseases Control and Prevention, Fuzhou 350013,
China
| | - Cuiteng CHEN
- Institute of Animal Husbandry and Veterinary Medicine,
Fujian Academy of Agricultural Sciences, Fujian Animal Diseases Control Technology Center,
Fujian Provincial Key Laboratory for Avian Diseases Control and Prevention, Fuzhou 350013,
China
| | - Yu HUANG
- Institute of Animal Husbandry and Veterinary Medicine,
Fujian Academy of Agricultural Sciences, Fujian Animal Diseases Control Technology Center,
Fujian Provincial Key Laboratory for Avian Diseases Control and Prevention, Fuzhou 350013,
China
| | - Longfei CHENG
- Institute of Animal Husbandry and Veterinary Medicine,
Fujian Academy of Agricultural Sciences, Fujian Animal Diseases Control Technology Center,
Fujian Provincial Key Laboratory for Avian Diseases Control and Prevention, Fuzhou 350013,
China
| | - Ronghui LU
- Institute of Animal Husbandry and Veterinary Medicine,
Fujian Academy of Agricultural Sciences, Fujian Animal Diseases Control Technology Center,
Fujian Provincial Key Laboratory for Avian Diseases Control and Prevention, Fuzhou 350013,
China
| | - Guanghua FU
- Institute of Animal Husbandry and Veterinary Medicine,
Fujian Academy of Agricultural Sciences, Fujian Animal Diseases Control Technology Center,
Fujian Provincial Key Laboratory for Avian Diseases Control and Prevention, Fuzhou 350013,
China
| | - Shaohua SHI
- Institute of Animal Husbandry and Veterinary Medicine,
Fujian Academy of Agricultural Sciences, Fujian Animal Diseases Control Technology Center,
Fujian Provincial Key Laboratory for Avian Diseases Control and Prevention, Fuzhou 350013,
China
| | - Hongmei CHEN
- Institute of Animal Husbandry and Veterinary Medicine,
Fujian Academy of Agricultural Sciences, Fujian Animal Diseases Control Technology Center,
Fujian Provincial Key Laboratory for Avian Diseases Control and Prevention, Fuzhou 350013,
China
| | - Chunhe WAN
- Institute of Animal Husbandry and Veterinary Medicine,
Fujian Academy of Agricultural Sciences, Fujian Animal Diseases Control Technology Center,
Fujian Provincial Key Laboratory for Avian Diseases Control and Prevention, Fuzhou 350013,
China
| | - Qiuling FU
- Institute of Animal Husbandry and Veterinary Medicine,
Fujian Academy of Agricultural Sciences, Fujian Animal Diseases Control Technology Center,
Fujian Provincial Key Laboratory for Avian Diseases Control and Prevention, Fuzhou 350013,
China
| | - Jiansheng LIN
- Institute of Animal Husbandry and Veterinary Medicine,
Fujian Academy of Agricultural Sciences, Fujian Animal Diseases Control Technology Center,
Fujian Provincial Key Laboratory for Avian Diseases Control and Prevention, Fuzhou 350013,
China
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