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Rimoldi SG, Tamoni A, Rizzo A, Longobardi C, Pagani C, Salari F, Matinato C, Vismara C, Gagliardi G, Cutrera M, Gismondo MR. Evaluation of 16S-Based Metagenomic NGS as Diagnostic Tool in Different Types of Culture-Negative Infections. Pathogens 2024; 13:743. [PMID: 39338934 PMCID: PMC11434932 DOI: 10.3390/pathogens13090743] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2024] [Revised: 08/28/2024] [Accepted: 08/29/2024] [Indexed: 09/30/2024] Open
Abstract
Bacterial infections pose significant global health challenges, often underestimated due to difficulties in accurate diagnosis, especially when culture-based diagnostics fail. This study assesses the effectiveness of 16S-based metagenomic next generation sequencing (NGS) for identifying pathogens in culture-negative clinical samples across various medical settings. Overall, 48% of samples were collected from orthopedics, 15% from neurosurgery, and 12% in cardiac surgery, among others. The detection rate of monomicrobial infections was 68.6%, and 5.7% for polymicrobial infections. In addition, NGS detected bacteria in all samples from the lungs, head and neck, and eye specimens. Cutibacterium acnes (11%, 12/105) was the most frequent microorganism, followed by Staphylococcus epidermidis (10.4%, 11/105), and Staphylococcus aureus (9.5%, 10/105). In conclusion, 16S-targeted metagenomic sequencing enhances pathogen detection capabilities, particularly in instances where traditional cultures fail. By the combination of NGS and bacterial cultures, microbiologists might provide a more accurate diagnosis, guiding more effective treatments and potentially reducing healthcare costs associated with empirical treatments.
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Affiliation(s)
- Sara Giordana Rimoldi
- Laboratory of Clinical Microbiology, Virology and Bioemergencies, ASST Fatebenefratelli Sacco, Luigi Sacco Hospital, 20157 Milan, Italy; (S.G.R.); (A.T.); (C.L.); (C.P.); (F.S.); (G.G.); (M.C.); (M.R.G.)
| | - Alessandro Tamoni
- Laboratory of Clinical Microbiology, Virology and Bioemergencies, ASST Fatebenefratelli Sacco, Luigi Sacco Hospital, 20157 Milan, Italy; (S.G.R.); (A.T.); (C.L.); (C.P.); (F.S.); (G.G.); (M.C.); (M.R.G.)
| | - Alberto Rizzo
- Laboratory of Clinical Microbiology, Virology and Bioemergencies, ASST Fatebenefratelli Sacco, Luigi Sacco Hospital, 20157 Milan, Italy; (S.G.R.); (A.T.); (C.L.); (C.P.); (F.S.); (G.G.); (M.C.); (M.R.G.)
| | - Concetta Longobardi
- Laboratory of Clinical Microbiology, Virology and Bioemergencies, ASST Fatebenefratelli Sacco, Luigi Sacco Hospital, 20157 Milan, Italy; (S.G.R.); (A.T.); (C.L.); (C.P.); (F.S.); (G.G.); (M.C.); (M.R.G.)
| | - Cristina Pagani
- Laboratory of Clinical Microbiology, Virology and Bioemergencies, ASST Fatebenefratelli Sacco, Luigi Sacco Hospital, 20157 Milan, Italy; (S.G.R.); (A.T.); (C.L.); (C.P.); (F.S.); (G.G.); (M.C.); (M.R.G.)
| | - Federica Salari
- Laboratory of Clinical Microbiology, Virology and Bioemergencies, ASST Fatebenefratelli Sacco, Luigi Sacco Hospital, 20157 Milan, Italy; (S.G.R.); (A.T.); (C.L.); (C.P.); (F.S.); (G.G.); (M.C.); (M.R.G.)
| | - Caterina Matinato
- Microbiology and Virology Laboratory, Fondazione IRCCS Ca’ Granda Ospedale Maggiore Policlinico, 20122 Milan, Italy;
| | - Chiara Vismara
- Clinical Microbiology Laboratory, ASST Grande Ospedale Metropolitano Niguarda, 20162 Milan, Italy;
| | - Gloria Gagliardi
- Laboratory of Clinical Microbiology, Virology and Bioemergencies, ASST Fatebenefratelli Sacco, Luigi Sacco Hospital, 20157 Milan, Italy; (S.G.R.); (A.T.); (C.L.); (C.P.); (F.S.); (G.G.); (M.C.); (M.R.G.)
| | - Miriam Cutrera
- Laboratory of Clinical Microbiology, Virology and Bioemergencies, ASST Fatebenefratelli Sacco, Luigi Sacco Hospital, 20157 Milan, Italy; (S.G.R.); (A.T.); (C.L.); (C.P.); (F.S.); (G.G.); (M.C.); (M.R.G.)
| | - Maria Rita Gismondo
- Laboratory of Clinical Microbiology, Virology and Bioemergencies, ASST Fatebenefratelli Sacco, Luigi Sacco Hospital, 20157 Milan, Italy; (S.G.R.); (A.T.); (C.L.); (C.P.); (F.S.); (G.G.); (M.C.); (M.R.G.)
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Russo AE, Memon A, Ahmed S. Bladder Cancer and the Urinary Microbiome-New Insights and Future Directions: A Review. Clin Genitourin Cancer 2024; 22:434-444. [PMID: 38220540 DOI: 10.1016/j.clgc.2023.12.015] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Revised: 12/26/2023] [Accepted: 12/28/2023] [Indexed: 01/16/2024]
Abstract
The presence of a microbiome in the urinary system has been established through recent advancements in technology and investigation of microbial communities in the human body. The study of the taxonomic and genomic ecology of microbial communities has been greatly improved by the use of metagenomics. The research in this area has expanded our understanding of microbial ecosystems and shows that the urinary tract contains over 100 species from over 50 genera, with Lactobacillus, Gardnerella, and Streptococcus being the most common. Previous studies have suggested that the microbiota in the urinary tract may play a role in carcinogenesis by causing chronic inflammation and genotoxicity, but more research is needed to reach a definite conclusion. This is a narrative review. We conducted a search for relevant publications by using the databases Medline/PubMed and Google Scholar. The search was based on keywords such as "urinary microbiome," "bladder cancer," "carcinogenesis," "urothelial carcinoma," and "next-generation sequencing." The retrieved publications were then reviewed to study the contribution of the urinary microbiome in the development of bladder cancer. The results have been categorized into four sections to enhance understanding of the urinary microbiome and to highlight its role in the emergence of bladder cancer through alterations in the immune response that involve T-cells and antibodies. The immune system and microbiome play crucial roles in maintaining health and preventing disease. Manipulating the immune system is a key aspect of various cancer treatments, and certain gut bacteria have been linked to positive responses to immunotherapies. However, the impact of these treatments on the urinary microbiome, and how diet and lifestyle affect it, are not well understood. Research in this area could have significant implications for improving bladder cancer treatment and patient outcomes.
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Affiliation(s)
- Angela E Russo
- Larner College of Medicine, University of Vermont, Burlington, VT.
| | - Areeba Memon
- Medical College, Aga Khan University, Karachi, Sindh, Pakistan
| | - Shahid Ahmed
- Department of Hematology and Oncology, University of Vermont, Burlington, VT
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Song Y, Song F, Liu S, Chen S, Song Z. Rapid diagnosis of a complex oral mucosal infection using metagenomic next-generation sequencing: a case report. J Int Med Res 2022; 50:3000605221136679. [DOI: 10.1177/03000605221136679] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
The most commonly used methods for pathogen detection and identification in oral mucosal infectious diseases are DNA or RNA quantitative polymerase chain reaction detection, bacterial or fungal cultures, and immunohistochemical analysis. These traditional methods are time-consuming and can only detect one specific targeted pathogen at a time. An efficient and sensitive method with higher species richness is urgently needed. Metagenomic next-generation sequencing (mNGS) is a new method of pathogen detection with high efficiency and sensitivity. In this case report, mNGS was used to identify the pathogens in oral mucosal tissues of a patient with complex oral mucosal infections and oral leukoplakia. Candida albicans, human gamma herpesvirus 4, and many other pathogens were identified using this method. For complex oral mucosal infections, mNGS is a more efficient and sensitive approach that can replace conventional detection methods.
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Affiliation(s)
- Yuhan Song
- Department of Oral Mucosa, Shanghai Stomatological Hospital, Fudan University, Shanghai, P. R. China
- Shanghai Key Laboratory of Craniomaxillofacial Development and Diseases, Shanghai Stomatological Hospital, Fudan University, Shanghai, P. R. China
| | - Fujie Song
- Department of First Dental Clinic, Shanghai Ninth People’s Hospital, Shanghai Jiao Tong University School of Medicine; College of Stomatology, Shanghai Jiao Tong University; National Center for Stomatology; National Clinical Research Center for Oral Diseases; Shanghai Key Laboratory of Stomatology, Shanghai, P. R. China
| | - Shangfeng Liu
- Shanghai Key Laboratory of Craniomaxillofacial Development and Diseases, Shanghai Stomatological Hospital, Fudan University, Shanghai, P. R. China
| | - Shuang Chen
- Shanghai Key Laboratory of Craniomaxillofacial Development and Diseases, Shanghai Stomatological Hospital, Fudan University, Shanghai, P. R. China
| | - Zhifeng Song
- Department of Oral Mucosa, Shanghai Stomatological Hospital, Fudan University, Shanghai, P. R. China
- Shanghai Key Laboratory of Craniomaxillofacial Development and Diseases, Shanghai Stomatological Hospital, Fudan University, Shanghai, P. R. China
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Zhang M, Wang W, Li X, Zhang X, Yang D. Fast and precise pathogen detection and identification of overlapping infection in patients with CUTI based on metagenomic next-generation sequencing: A case report. Medicine (Baltimore) 2021; 100:e27902. [PMID: 34889238 PMCID: PMC8663832 DOI: 10.1097/md.0000000000027902] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Accepted: 11/03/2021] [Indexed: 01/05/2023] Open
Abstract
RATIONALE The gold standard for pathogen detection and identification of complicated urinary tract infection (CUTI) remains quantitative urine culture, however, the diagnostic value of urine culture remains limited due to the time-consuming procedure and low detection rate. Here we report a case of successfully using Metagenomic next-generation sequencing (mNGS) provided fast and precise detection and identification of overlapping infection in patients with CUTI with no similar reports or studies published before to the best of our knowledge. PATIENT CONCERNS A 70-year-old male was admitted to hospital due to elevated serum creatinine for 2 weeks. DIAGNOSES Acute exacerbation of chronic renal failure and CUTI were the most critical diagnosis on admission. INTERVENTIONS Blood purification, bladder irrigation and aggressive anti-infective therapy were administered. But the empirical anti-infection therapy and the adjustment of treatment according to the evidence of urine culture drug sensitivity had no obvious effect. We further carried out urinary PMseq-DNA detection and the results showed overlapping infection with Enterococcus faecium, Enterococcus hirae, Pseudomonas aeruginosa, Pseudomonas denitrificans and Candida albicans. According to the genetic test results, linezolid, meropenem and fluconazole triple anti-infection treatment was given. OUTCOMES After adjusting the treatment, the infection was basically controlled in 10 days, and even the renal function was significantly improved, dialysis independence was achieved after 3 months. LESSONS Our case illustrated the potential application of mNGS in detecting pathogenic microorganisms in patients with CUTI especially when overlapping infections are present.
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