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Sun WW, Dong ZW, Zhou YM, Jin F, Liu HC, Fan L. Improving the identification and diagnostic efficiency of Metagenomic Next-Generation Sequencing for mycobacterial granuloma on postoperative formalin-fixed paraffin-embedded specimens. Microbes Infect 2023; 25:105185. [PMID: 37453490 DOI: 10.1016/j.micinf.2023.105185] [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: 01/22/2023] [Revised: 07/05/2023] [Accepted: 07/10/2023] [Indexed: 07/18/2023]
Abstract
OBJECTIVE Metagenomic Next-Generation Sequencing (mNGS) has been validated to have an important role in the diagnosis of mycobacterium infection. The study aimed to further explore the mycobacteria identification ability of mNGS on formalin-fixed paraffin-embedded(FFPE)tissues from postoperative specimens. METHODS Patients who underwent surgical biopsy or resection for clarifying the diagnosis and whose initial postoperative pathology indicated granulomatous lesions were included. Fresh tissues were sent for mycobacterium culture and Xpert MTB/RIF (Xpert) to establish the diagnosis. FFPE specimens were sent for mNGS and molecular pathology,the diagnostic values were compared between the two methods. RESULTS A total of 65 cases with definite diagnoses were finally included in the study. 31 cases were confirmed as mycobacterium granuloma using the fresh specimen etiology as diagnostic criteria. The overall sensitivity and specificity of mNGS on FFPE specimens in the diagnosis of mycobacterium granuloma were 100% and 88.24%, respectively. In 19 cases diagnosed as tuberculous granulomas, the sensitivity (100% vs47.37%) and negative predictive value (NPV, 100%vs 82.14%) of mNGS were both significantly higher than that of molecular pathology on the FFPE section(both p 0.00)while the positive predictive value (PPV) and specificity were not significantly different. In 12 cases diagnosed as Non-tuberculous mycobacterium (NTM)granuloma, the sensitivity of mNGS was also significantly higher than that of molecular pathology on FFPE section (100% vs 66.67%, p 0.00) while the specificity, PPV and NPV were all not significantly different. CONCLUSIONS The mNGS could be used for one-time detection of pathogens on FFPE sections with high sensitivity. It could be recommended as a supplementary method for the identification of pathogenic bacteria in the diagnosis of postoperative granuloma lesions.
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Affiliation(s)
- Wen-Wen Sun
- Shanghai Clinic and Research Center of Tuberculosis, Department of Tuberculosis, Shanghai Key Laboratory of Tuberculosis, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, China
| | - Zheng-Wei Dong
- Department of Pathology, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, China
| | - Yi-Ming Zhou
- Department of Thoracic Surgery, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, China
| | - Feng Jin
- Department of Thoracic Surgery, Shandong Key Laboratory of Infectious Respiratory Diseases, Shandong Public Health Clinical Center Affiliated to Shandong University, Jinan, China.
| | - Hong-Cheng Liu
- Department of Thoracic Surgery, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, China.
| | - Lin Fan
- Shanghai Clinic and Research Center of Tuberculosis, Department of Tuberculosis, Shanghai Key Laboratory of Tuberculosis, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, China.
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Wang Y, Chen T, Zhang S, Zhang L, Li Q, Lv Q, Kong D, Jiang H, Ren Y, Jiang Y, Li Y, Huang W, Liu P. Clinical evaluation of metagenomic next-generation sequencing in unbiased pathogen diagnosis of urinary tract infection. J Transl Med 2023; 21:762. [PMID: 37891586 PMCID: PMC10612365 DOI: 10.1186/s12967-023-04562-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Accepted: 09/22/2023] [Indexed: 10/29/2023] Open
Abstract
BACKGROUND Early availability of pathogen identification in urinary tract infections (UTIs) has critical importance in disease management. Metagenomic next-generation sequencing (mNGS) has the potential to transform how acute and serious infections are diagnosed by offering unbiased and culture-free pathogen detection. However, clinical experience with application of the mNGS test is relatively limited. METHODS We therefore established a MinION-based mNGS pathogens diagnostic platform and evaluated its potential for clinical implementation in UTIs with clinical samples. 213 urine samples from patients with suspected UTIs were included and subjected to mNGS testing using the MinION platform. mNGS results were compared to the gold standard of clinical culture and composite standard of combining clinical testing, confirmatory qPCR testing, and clinical adjudication by doctors. RESULTS The mNGS exhibited a sensitivity of 81.4% and a specificity of 92.3%, along with a positive predictive value of 96.6%, a negative predictive value of 64.9%, and an overall accuracy of 84.4%, all of which were determined based on the gold standard of routine culture results. When assessed against the composite standard, the sensitivity and specificity both increased to 89.9% and 100%, respectively, while the accuracy rose to 92.4%. Notably, the positive predictive value and negative predictive value also saw improvements, reaching 100% and 76.8%, respectively. Moreover, this diagnostic platform successfully identified dsDNA viruses. Among the 65 culture-negative samples, the viral detection rate reached 33.8% (22/65) and was subsequently validated through qPCR. Furthermore, the automatic bioinformatics pipeline we developed enabled one-click analysis from data to results, leading to a significant reduction in diagnosis time. CONCLUSION These results demonstrate that the pathogen detection performance of mNGS is sufficient for diagnostic testing in clinical settings. As the method is generally unbiased, it can improve diagnostic testing of UTIs and other microbial infections.
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Affiliation(s)
- Ye Wang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences, Beijing, China
| | - Ting Chen
- Department of Critical Care Medicine, The Fifth Medical Center of PLA General Hospital, Beijing, China
| | - Shengwei Zhang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences, Beijing, China
| | - Lei Zhang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences, Beijing, China
| | - Qian Li
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences, Beijing, China
| | - Qingyu Lv
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences, Beijing, China
| | - Decong Kong
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences, Beijing, China
| | - Hua Jiang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences, Beijing, China
| | - Yuhao Ren
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences, Beijing, China
| | - Yongqiang Jiang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences, Beijing, China
| | - Yan Li
- Department of Critical Care Medicine, The Fifth Medical Center of PLA General Hospital, Beijing, China.
| | - Wenhua Huang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences, Beijing, China.
| | - Peng Liu
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences, Beijing, China.
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3
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Trecourt A, Rabodonirina M, Mauduit C, Traverse-Glehen A, Devouassoux-Shisheboran M, Meyronet D, Dijoud F, Ginevra C, Chapey-Picq E, Josse E, Martins-Simoes P, Bentaher A, Dupont D, Miossec C, Persat F, Wallon M, Ferry T, Pham F, Simon B, Menotti J. Fungal Integrated Histomolecular Diagnosis Using Targeted Next-Generation Sequencing on Formalin-Fixed Paraffin-Embedded Tissues. J Clin Microbiol 2023; 61:e0152022. [PMID: 36809009 PMCID: PMC10035294 DOI: 10.1128/jcm.01520-22] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Accepted: 01/30/2023] [Indexed: 02/23/2023] Open
Abstract
Histopathology is the gold standard for fungal infection (FI) diagnosis, but it does not provide a genus and/or species identification. The objective of the present study was to develop targeted next-generation sequencing (NGS) on formalin-fixed tissue samples (FTs) to achieve a fungal integrated histomolecular diagnosis. Nucleic acid extraction was optimized on a first group of 30 FTs with Aspergillus fumigatus or Mucorales infection by macrodissecting the microscopically identified fungal-rich area and comparing Qiagen and Promega extraction methods through DNA amplification by A. fumigatus and Mucorales primers. Targeted NGS was developed on a second group of 74 FTs using three primer pairs (ITS-3/ITS-4, MITS-2A/MITS-2B, and 28S-12-F/28S-13-R) and two databases (UNITE and RefSeq). A prior fungal identification of this group was established on fresh tissues. Targeted NGS and Sanger sequencing results on FTs were compared. To be valid, the molecular identifications had to be compatible with the histopathological analysis. In the first group, the Qiagen method yielded a better extraction efficiency than the Promega method (100% and 86.7% of positive PCRs, respectively). In the second group, targeted NGS allowed fungal identification in 82.4% (61/74) of FTs using all primer pairs, in 73% (54/74) using ITS-3/ITS-4, in 68.9% (51/74) using MITS-2A/MITS-2B, and in 23% (17/74) using 28S-12-F/28S-13-R. The sensitivity varied according to the database used (81% [60/74] using UNITE compared to 50% [37/74] using RefSeq [P = 0.000002]). The sensitivity of targeted NGS (82.4%) was higher than that of Sanger sequencing (45.9%; P < 0.00001). To conclude, fungal integrated histomolecular diagnosis using targeted NGS is suitable on FTs and improves fungal detection and identification.
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Affiliation(s)
- Alexis Trecourt
- Service de Pathologie Multi-Site—Site Sud, Hospices Civils de Lyon, Centre Hospitalier Lyon Sud, Lyon, France
- Faculté de Médecine Lyon-Sud Charles Mérieux, UR 3738–CICLY–Equipe Inflammation et Immunité de L’épithélium Respiratoire, Université Claude Bernard Lyon 1, Lyon, France
| | - Meja Rabodonirina
- Institut des Agents Infectieux, Service de Parasitologie et Mycologie Médicale, Hospices Civils de Lyon, Hôpital Croix-Rousse, Lyon, France
- Faculté de Médecine Lyon Sud Charles Mérieux, Université Claude Bernard Lyon 1, Lyon, France
| | - Claire Mauduit
- Service de Pathologie Multi-Site—Site Sud, Hospices Civils de Lyon, Centre Hospitalier Lyon Sud, Lyon, France
- Faculté de Médecine Lyon Sud Charles Mérieux, Université Claude Bernard Lyon 1, Lyon, France
- Centre Méditerranéen de Médecine Moléculaire (C3M), Unité 1065, Institut National de la Santé et de la Recherche Médicale, Nice, France
| | - Alexandra Traverse-Glehen
- Service de Pathologie Multi-Site—Site Sud, Hospices Civils de Lyon, Centre Hospitalier Lyon Sud, Lyon, France
- Faculté de Médecine Lyon Sud Charles Mérieux, Université Claude Bernard Lyon 1, Lyon, France
- Faculté de Médecine Lyon Sud Charles Mérieux, Centre de Recherche en Cancérologie de Lyon, INSERM U1052-CNRS UMR5286, Université Claude Bernard Lyon 1, Lyon, France
| | - Mojgan Devouassoux-Shisheboran
- Service de Pathologie Multi-Site—Site Sud, Hospices Civils de Lyon, Centre Hospitalier Lyon Sud, Lyon, France
- Faculté de Médecine Lyon Est, Université Claude Bernard Lyon 1, Lyon, France
| | - David Meyronet
- Faculté de Médecine Lyon Est, Université Claude Bernard Lyon 1, Lyon, France
- Service de Pathologie Multi-site—Site Est, Hospices Civils de Lyon, Centre Hospitalier Lyon Est, Lyon, France
| | - Frédérique Dijoud
- Faculté de Médecine Lyon Est, Université Claude Bernard Lyon 1, Lyon, France
- Service de Pathologie Multi-site—Site Est, Hospices Civils de Lyon, Centre Hospitalier Lyon Est, Lyon, France
| | - Christophe Ginevra
- Institut des Agents Infectieux, Génomique Épidémiologique des Maladies Infectieuses (GENEPII), Hospices Civils de Lyon, Hôpital Croix-Rousse, Lyon, France
- Institut des Agents Infectieux, Centre National de Référence des Légionelles, Hospices Civils de Lyon, Hôpital Croix-Rousse, Lyon, France
| | - Emmanuelle Chapey-Picq
- Institut des Agents Infectieux, Service de Parasitologie et Mycologie Médicale, Hospices Civils de Lyon, Hôpital Croix-Rousse, Lyon, France
- Faculté de Médecine Lyon Sud Charles Mérieux, Université Claude Bernard Lyon 1, Lyon, France
| | - Emilie Josse
- Institut des Agents Infectieux, Service de Parasitologie et Mycologie Médicale, Hospices Civils de Lyon, Hôpital Croix-Rousse, Lyon, France
| | - Patricia Martins-Simoes
- Institut des Agents Infectieux, Génomique Épidémiologique des Maladies Infectieuses (GENEPII), Hospices Civils de Lyon, Hôpital Croix-Rousse, Lyon, France
- Institut des Agents Infectieux, Centre National de Référence des Staphyloccoques, Hospices Civils de Lyon, Hôpital Croix-Rousse, Lyon, France
| | - Abderrazzak Bentaher
- Faculté de Médecine Lyon-Sud Charles Mérieux, UR 3738–CICLY–Equipe Inflammation et Immunité de L’épithélium Respiratoire, Université Claude Bernard Lyon 1, Lyon, France
- Faculté de Médecine Lyon Sud Charles Mérieux, Université Claude Bernard Lyon 1, Lyon, France
| | - Damien Dupont
- Institut des Agents Infectieux, Service de Parasitologie et Mycologie Médicale, Hospices Civils de Lyon, Hôpital Croix-Rousse, Lyon, France
- Faculté de Médecine Lyon Est, Université Claude Bernard Lyon 1, Lyon, France
| | - Charline Miossec
- Institut des Agents Infectieux, Service de Parasitologie et Mycologie Médicale, Hospices Civils de Lyon, Hôpital Croix-Rousse, Lyon, France
| | - Florence Persat
- Faculté de Médecine Lyon-Sud Charles Mérieux, UR 3738–CICLY–Equipe Inflammation et Immunité de L’épithélium Respiratoire, Université Claude Bernard Lyon 1, Lyon, France
- Institut des Agents Infectieux, Service de Parasitologie et Mycologie Médicale, Hospices Civils de Lyon, Hôpital Croix-Rousse, Lyon, France
- Faculté de Médecine Lyon Est, Université Claude Bernard Lyon 1, Lyon, France
| | - Martine Wallon
- Institut des Agents Infectieux, Service de Parasitologie et Mycologie Médicale, Hospices Civils de Lyon, Hôpital Croix-Rousse, Lyon, France
- Faculté de Médecine Lyon Sud Charles Mérieux, Université Claude Bernard Lyon 1, Lyon, France
| | - Tristan Ferry
- Faculté de Médecine Lyon Est, Université Claude Bernard Lyon 1, Lyon, France
- Service de Maladies Infectieuses et Tropicales, Hospices Civils de Lyon, Hôpital Croix-Rousse, Lyon, France
| | - Félix Pham
- Service de Dermatologie, Hospices Civils de Lyon, Centre Hospitalier Lyon Sud, Lyon, France
| | - Bruno Simon
- Institut des Agents Infectieux, Génomique Épidémiologique des Maladies Infectieuses (GENEPII), Hospices Civils de Lyon, Hôpital Croix-Rousse, Lyon, France
- Institut des Agents Infectieux, Service de Virologie, Hospices Civils de Lyon, Hôpital Croix-Rousse, Lyon, France
| | - Jean Menotti
- Faculté de Médecine Lyon-Sud Charles Mérieux, UR 3738–CICLY–Equipe Inflammation et Immunité de L’épithélium Respiratoire, Université Claude Bernard Lyon 1, Lyon, France
- Institut des Agents Infectieux, Service de Parasitologie et Mycologie Médicale, Hospices Civils de Lyon, Hôpital Croix-Rousse, Lyon, France
- Faculté de Médecine Lyon Est, Université Claude Bernard Lyon 1, Lyon, France
- Institut des Agents Infectieux, Génomique Épidémiologique des Maladies Infectieuses (GENEPII), Hospices Civils de Lyon, Hôpital Croix-Rousse, Lyon, France
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Metagenomic Sequencing for the Diagnosis of Plasmodium spp. with Different Levels of Parasitemia in EDTA Blood of Malaria Patients—A Proof-of-Principle Assessment. Int J Mol Sci 2022; 23:ijms231911150. [PMID: 36232449 PMCID: PMC9569645 DOI: 10.3390/ijms231911150] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2022] [Revised: 09/17/2022] [Accepted: 09/20/2022] [Indexed: 11/17/2022] Open
Abstract
Molecular diagnostic approaches are increasingly included in the diagnostic workup and even in the primary diagnosis of malaria in non-endemic settings, where it is difficult to maintain skillful microscopic malaria detection due to the rarity of the disease. Pathogen-specific nucleic acid amplification, however, bears the risk of overlooking other pathogens associated with febrile illness in returnees from the tropics. Here, we assessed the discriminatory potential of metagenomic sequencing for the identification of different Plasmodium species with various parasitemia in EDTA blood of malaria patients. Overall, the proportion of Plasmodium spp.-specific sequence reads in the assessed samples showed a robust positive correlation with parasitemia (Spearman r = 0.7307, p = 0.0001) and a robust negative correlation with cycle threshold (Ct) values of genus-specific real-time PCR (Spearman r = −0.8626, p ≤ 0.0001). Depending on the applied bioinformatic algorithm, discrimination on species level was successful in 50% (11/22) to 63.6% (14/22) instances. Limiting factors for the discrimination on species level were very low parasitemia, species-depending lacking availability of reliable reference genomes, and mixed infections with high variance of the proportion of the infecting species. In summary, metagenomic sequencing as performed in this study is suitable for the detection of malaria in human blood samples, but the diagnostic detection limit for a reliable discrimination on species level remains higher than for competing diagnostic approaches like microscopy and PCR.
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5
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Ravegnini G, Fosso B, Ricci R, Gorini F, Turroni S, Serrano C, Pilco-Janeta DF, Zhang Q, Zanotti F, De Robertis M, Nannini M, Pantaleo MA, Hrelia P, Angelini S. Analysis of microbiome in GISTs: looking for different players in tumorigenesis and novel therapeutic options. Cancer Sci 2022; 113:2590-2599. [PMID: 35633186 PMCID: PMC9357631 DOI: 10.1111/cas.15441] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2022] [Revised: 04/20/2022] [Accepted: 05/23/2022] [Indexed: 12/02/2022] Open
Abstract
Preclinical forms of gastrointestinal stromal tumor (GIST), small asymptomatic lesions, called microGIST, are detected in approximately 30% of the general population. Gastrointestinal stromal tumor driver mutation can be already detected in microGISTs, even if they do not progress into malignant cancer; these mutations are necessary, but insufficient events to foster tumor progression. Here we profiled the tissue microbiota of 60 gastrointestinal specimens in three different patient cohorts—micro, low‐risk, and high‐risk or metastatic GIST—exploring the compositional structure, predicted function, and microbial networks, with the aim of providing a complete overview of microbial ecology in GIST and its preclinical form. Comparing microGISTs and GISTs, both weighted and unweighted UniFrac and Bray–Curtis dissimilarities showed significant community‐level separation between them and a pronounced difference in Proteobacteria, Firmicutes, and Bacteroidota was observed. Through the LEfSe tool, potential microbial biomarkers associated with a specific type of lesion were identified. In particular, GIST samples were significantly enriched in the phylum Proteobacteria compared to microGISTs. Several pathways involved in sugar metabolism were also highlighted in GISTs; this was expected as cancer usually displays high aerobic glycolysis in place of oxidative phosphorylation and rise of glucose flux to promote anabolic request. Our results highlight that specific differences do exist in the tissue microbiome community between GIST and benign lesions and that microbiome restructuration can drive the carcinogenesis process.
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Affiliation(s)
- Gloria Ravegnini
- Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy
| | - Bruno Fosso
- National Research Council, Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies (IBIOM), Bari, Italy.,Department of Biosciences, Biotechnology and Biopharmaceutics (DBBB), University of Bari "A. Moro", Bari, Italy
| | - Riccardo Ricci
- UOC di Anatomia Patologica, Fondazione Policlinico Universitario "A. Gemelli" IRCCS, Rome, Italy
| | - Francesca Gorini
- Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy
| | - Silvia Turroni
- Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy
| | - Cesar Serrano
- Department of Medical Oncology, Vall d'Hebron University Hospital, Barcelona, Spain
| | - Daniel F Pilco-Janeta
- Department of Medical Oncology, Vall d'Hebron University Hospital, Barcelona, Spain.,Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts, USA
| | - Qianqian Zhang
- UOC di Anatomia Patologica, Fondazione Policlinico Universitario "A. Gemelli" IRCCS, Rome, Italy
| | - Federica Zanotti
- Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy
| | - Mariangela De Robertis
- Department of Biosciences, Biotechnology and Biopharmaceutics (DBBB), University of Bari "A. Moro", Bari, Italy
| | - Margherita Nannini
- Department of Experimental, Diagnostic and Specialized Medicine (DIMES), Alma Mater Studiorum, University of Bologna, Bologna, Italy.,Medical Oncology Unit, IRCCS Azienda Ospedaliero-Universitaria di Bologna, Bologna, Italy
| | - Maria Abbondanza Pantaleo
- Department of Experimental, Diagnostic and Specialized Medicine (DIMES), Alma Mater Studiorum, University of Bologna, Bologna, Italy.,Medical Oncology Unit, IRCCS Azienda Ospedaliero-Universitaria di Bologna, Bologna, Italy
| | - Patrizia Hrelia
- Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy
| | - Sabrina Angelini
- Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy
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Sun W, Dong Z, Zhou Y, Xiong K, Liu H, Zhang Z, Fan L. Early Identification of Fungal and Mycobacterium Infections in Pulmonary Granulomas Using Metagenomic Next-Generation Sequencing on Formalin fixation and paraffin embedding tissue. Expert Rev Mol Diagn 2022; 22:461-468. [PMID: 35261303 DOI: 10.1080/14737159.2022.2052046] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Abstract
BACKGROUND The purpose of the study is to assess the etiology detection ability of Metagenomic Next-Generation Sequencing (mNGS) on formalin fixation and paraffin embedding (FFPE) tissue from postoperative biopsy specimen. METHODS We prospectively enrolled specimens from patients undergone surgery biopsy due to undefinite diagnosis and pathologically indicated granulomatous lesions. FFPE tissues were tested by mNGS and histopathology. The etiology detection rate of mNGS was calculated and compared with histopathology, using the clinical diagnosis as the reference criteria. RESULTS Among the 69 cases eventually included, 41 (59.42%) were diagnosed as infectious granuloma. The overall fungi and mycobacteria etiology detection rate of mNGS in granuloma lesions was 87.80 % (36/41) . The mNGS increased detection rate by 68.29 % (28/41) compared with histopathology, the difference was statistically significant (χ2= 28.97, P 0.00).The detection rates of mNGS in fungal infections (12/12,100%) and in mycobacterium infections (22/27, 81.48%) were significant higher than those of histopathology (8/12, 66.67% and 0/27,0.00 %;both P 0.00). 2 (2/2.100%) cases of co-infection were detected at one time by mNGS. All mNGS-based clinical decisions were made within 2 days. CONCLUSIONS The mNGS could accurately and quickly detect fungi and mycobacteria on FFPE specimens from postoperative granuloma specimens and identify the pathogens to the species level. CLINICAL TRIALS REGISTRATION China Clinical Trial Registry ChiCTR2000035464.
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Affiliation(s)
- Wenwen Sun
- Department of Tuberculosis and Shanghai Key Lab of Tuberculosis, Shanghai Pulmonary Hospital Affiliated to School of Medicine, Tongji University, Shanghai 200092, China
| | - Zhengwei Dong
- Department of Pathology, Shanghai Pulmonary Hospital Affiliated to School of Medicine, Tongji University, Shanghai, China
| | - Yiming Zhou
- Department of Thoracic Surgery, Shanghai Pulmonary Hospital Affiliated to School of Medicine, Tongji University, Shanghai, China
| | - Kunlong Xiong
- Department of Tuberculosis and Shanghai Key Lab of Tuberculosis, Shanghai Pulmonary Hospital Affiliated to School of Medicine, Tongji University, Shanghai 200092, China
| | - Hongcheng Liu
- Department of Thoracic Surgery, Shanghai Pulmonary Hospital Affiliated to School of Medicine, Tongji University, Shanghai, China
| | | | - Lin Fan
- Department of Tuberculosis and Shanghai Key Lab of Tuberculosis, Shanghai Pulmonary Hospital Affiliated to School of Medicine, Tongji University, Shanghai 200092, China
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7
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Hashizume H, Taga S, Sakata MK, Taha MHM, Siddig EE, Minamoto T, Fahal AH, Kaneko S. Detection of multiple mycetoma pathogens using fungal metabarcoding analysis of soil DNA in an endemic area of Sudan. PLoS Negl Trop Dis 2022; 16:e0010274. [PMID: 35275915 PMCID: PMC8942264 DOI: 10.1371/journal.pntd.0010274] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Revised: 03/23/2022] [Accepted: 02/23/2022] [Indexed: 01/14/2023] Open
Abstract
Mycetoma is a tropical disease caused by several fungi and bacteria present in the soil. Fungal mycetoma and eumycetoma are especially challenging to treat; therefore, prevention, early diagnosis, and early treatment are important, but it is also necessary to understand the geographic distribution of these pathogenic fungi. In this study, we used DNA metabarcoding methodology to identify fungal species from soil samples. Soil sampling was implemented at seven villages in an endemic area of Sennar State in Sudan in 2019, and ten sampling sites were selected in each village according to land-use conditions. In total, 70 soil samples were collected from ground surfaces, and DNA in the soil was extracted with a combined method of alkaline DNA extraction and a commercial soil DNA extraction kit. The region for universal primers was selected to be the ribosomal internal transcribed spacer one region for metabarcoding. After the second PCR for DNA library preparation, the amplicon-based DNA analysis was performed using next-generation sequencing with two sets of universal primers. A total of twelve mycetoma-causative fungal species were identified, including the prime agent, Madurella mycetomatis, and additional pathogens, Falciformispora senegalensis and Falciformispora tompkinsii, in 53 soil samples. This study demonstrated that soil DNA metabarcoding can elucidate the presence of multiple mycetoma-causative fungi, which may contribute to accurate diagnosis for patient treatment and geographical mapping. Mycetoma, a chronic subcutaneous and cutaneous disease, designated as a "neglected tropical disease," is prevalent in dry and hot climates. Fungal mycetoma is caused by more than 50 species of soil-dwelling pathogenic fungi, and its diagnosis and treatment can be challenging. The prevention of infection and early diagnosis and treatment are essential, and for this purpose, environmental assessment to understand the fungal habitat is necessary. In this study, we performed DNA metabarcoding analysis using next-generation sequencing (NGS) for mycetoma pathogens from environmental soil samples in Sudan. The results suggest that multiple causative agents of fungal mycetoma are widespread regardless of the environment and can be a source of infection anywhere in an endemic area. Based on the results of this study, we expect that the investigation of fungi in soil using NGS technology may help identify infection routes and create risk maps for the prevention of mycetoma.
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Affiliation(s)
- Hiroki Hashizume
- School of Tropical Medicine and Global Health, Nagasaki University, Nagasaki, Japan
- Department of Ecoepidemiology, Institute of Tropical Medicine (NEKKEN), Nagasaki University, Nagasaki, Japan
| | - Suguru Taga
- Department of Ecoepidemiology, Institute of Tropical Medicine (NEKKEN), Nagasaki University, Nagasaki, Japan
| | - Masayuki K. Sakata
- Graduate School of Human Development and Environment, Kobe University, Kobe, Japan
| | | | | | - Toshifumi Minamoto
- Graduate School of Human Development and Environment, Kobe University, Kobe, Japan
| | | | - Satoshi Kaneko
- School of Tropical Medicine and Global Health, Nagasaki University, Nagasaki, Japan
- Department of Ecoepidemiology, Institute of Tropical Medicine (NEKKEN), Nagasaki University, Nagasaki, Japan
- * E-mail:
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8
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Identification of Pneumocystis jirovecii with Fluorescence In-Situ Hybridization (FISH) in Patient Samples-A Proof-of-Principle. J Fungi (Basel) 2021; 8:jof8010013. [PMID: 35049953 PMCID: PMC8778293 DOI: 10.3390/jof8010013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Revised: 12/21/2021] [Accepted: 12/23/2021] [Indexed: 11/17/2022] Open
Abstract
In resource-limited settings, where pneumocystosis in immunocompromised patients is infrequently observed, cost-efficient, reliable, and sensitive approaches for the diagnostic identification of Pneumocystis jirovecii in human tissue samples are desirable. Here, an in-house fluorescence in situ hybridization assay was comparatively evaluated against Grocott’s staining as a reference standard with 30 paraffin-embedded tissue samples as well as against in-house real-time PCR with 30 respiratory secretions from immunocompromised patients with clinical suspicion of pneumocystosis. All pneumocystosis patients included in the study suffered from HIV/AIDS. Compared with Grocott’s staining as the reference standard, sensitivity of the FISH assay was 100% (13/13), specificity was 41% (7/17), and the overall concordance was 66.7% with tissue samples. With respiratory specimens, sensitivity was 83.3% (10/12), specificity was 100% (18/18), and the overall concordance was 93.3% as compared with real-time PCR. It remained unresolved to which proportions sensitivity limitations of Grocott’s staining or autofluorescence phenomena affecting the FISH assay accounted for the recorded reduced specificity with the tissue samples. The assessment confirmed Pneumocystis FISH in lung tissue as a highly sensitive screening approach; however, dissatisfying specificity in paraffin-embedded biopsies calls for confirmatory testing with other techniques in case of positive FISH screening results. In respiratory secretions, acceptable sensitivity and excellent specificity were demonstrated for the diagnostic application of the P. jirovecii-specific FISH assay.
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9
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Sunagawa K, Nakamura S, Sato Y, Iida S, Miyazaki Y, Suzuki T, Katano H. Morphological and genetic identification of fungal genus/species in formalin-fixed, paraffin-embedded specimens obtained from patients with histologically proven fungal infection. Mycoses 2021; 64:851-859. [PMID: 34028893 DOI: 10.1111/myc.13325] [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: 02/16/2021] [Revised: 05/18/2021] [Accepted: 05/18/2021] [Indexed: 11/29/2022]
Abstract
BACKGROUND Although fungi are found relatively easily by microscopic examination of pathological samples, identification of fungal genus and species in pathological samples is not easy because the morphological features of fungi are similar among genera and species. OBJECTIVES A multiple real-time PCR was developed for identification of fungal genus/species, and morphological characterizations of fungi were analysed in pathological samples. PATIENTS/METHODS Seventy-five formalin-fixed paraffin-embedded (FFPE) samples morphologically proven to contain any fungus were examined. A multiple real-time PCR system was developed to identify 25 fungal genus/species in pathological samples. Morphology of fungus in the specimens was re-reviewed retrospectively based on the results of real-time PCR. RESULTS Real-time PCR identified fungal genus/species in 56 of 75 (74.6%) specimens with histologically proven fungal infection. In 53 specimens of filamentous fungi, Aspergillus spp. (22 specimens), Cladosporium (8), Scedosporium apiospermum (4), Malassezia sympodialis (1) and Candida albicans (1) were identified. Pseudohyphae of Candida were confused with filamentous fungus in a case. Morphological observation suggested differences in the presence of septated or non-septated hyphae, the filament size, and the branch angle among genus/species of filamentous fungi; however, genus/species was not able to be determined by their morphological features. In 22 specimens of yeasts, real-time PCR allowed for the identification of Candida albicans (12 specimens), Candida glabrata (2), Cladosporium (2), Scedosporium apiospermum (2), Pichia kudriavzevii (1) and Aspergillus sydowii (1). CONCLUSIONS These data suggest that it is difficult to identify fungal genus/species by morphological features alone. Real-time PCR is useful to identify fungal genus/species in pathological samples.
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Affiliation(s)
- Keishin Sunagawa
- Department of Pathology, National Institute of Infectious Diseases, Tokyo, Japan.,Clinical Pathology and Laboratory Medicine, Anatomic Pathology, Saitama Cooperative Hospital, Saitama, Japan
| | - Shigeki Nakamura
- Department of Microbiology, Tokyo Medical University, Tokyo, Japan
| | - Yuko Sato
- Department of Pathology, National Institute of Infectious Diseases, Tokyo, Japan
| | - Shun Iida
- Department of Pathology, National Institute of Infectious Diseases, Tokyo, Japan.,Division of Infectious Diseases Pathology, Department of Global Infectious Diseases, Tohoku University Graduate School of Medicine, Miyagi, Japan
| | - Yoshitsugu Miyazaki
- Department of Chemotherapy and Mycoses, National Institute of Infectious Diseases, Tokyo, Japan
| | - Tadaki Suzuki
- Department of Pathology, National Institute of Infectious Diseases, Tokyo, Japan
| | - Harutaka Katano
- Department of Pathology, National Institute of Infectious Diseases, Tokyo, Japan
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10
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Loderstädt U, Hagen RM, Hahn A, Frickmann H. New Developments in PCR-Based Diagnostics for Bacterial Pathogens Causing Gastrointestinal Infections-A Narrative Mini-Review on Challenges in the Tropics. Trop Med Infect Dis 2021; 6:tropicalmed6020096. [PMID: 34199650 PMCID: PMC8293448 DOI: 10.3390/tropicalmed6020096] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Revised: 05/31/2021] [Accepted: 05/31/2021] [Indexed: 12/15/2022] Open
Abstract
The application of modern PCR approaches for the diagnosis of bacterial gastrointestinal pathogens is on the rise due to their rapidly available results combined with high sensitivity. While multiple studies describe the ongoing implementation of this technique for routine diagnostic purposes in laboratories in Western industrialized countries, reports on successful and also sustainable respective approaches in resource-poor tropical settings are still scarce. In order to shed light on potential reasons for this marked discrepancy, this narrative review summarizes identified challenges for the application of diagnostic PCR targeting bacterial gastrointestinal pathogens from stool samples in the tropics. The identified and discussed issues comprise the lack of generally accepted definitions for (1) minimum standards regarding sample acquisition, storage and transport time for diagnostic PCR analyses in the tropics, (2) nucleic acid extraction standards allowing an optimum detection of all types of pathogens which may be responsible for gastroenteritis in the tropics, (3) validation standards to ensure comparable quality of applied diagnostic assays, and (4) cut-offs for a reliable discrimination of infection and mere colonization in areas where semi-immunity due to repeated exposition associated with poor hygiene conditions has to be expected. Further implementation research is needed to solve those issues.
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Affiliation(s)
- Ulrike Loderstädt
- Institute for Infection Control and Infectious Diseases, University Medical Center Göttingen, 37075 Göttingen, Germany;
| | - Ralf Matthias Hagen
- Department of Microbiology and Hospital Hygiene, Bundeswehr Central Hospital Koblenz, Andernacher Str. 100, 56070 Koblenz, Germany;
| | - Andreas Hahn
- Institute for Medical Microbiology, Virology and Hygiene, University Medicine Rostock, 18057 Rostock, Germany;
| | - Hagen Frickmann
- Institute for Medical Microbiology, Virology and Hygiene, University Medicine Rostock, 18057 Rostock, Germany;
- Department of Microbiology and Hospital Hygiene, Bundeswehr Hospital Hamburg, 20359 Hamburg, Germany
- Correspondence: or or ; Tel.: +49-40-6947-28743
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11
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Kattner S, Herbstreit F, Schmidt K, Stevens P, Grumaz S, Dubler S, Rath PM, Brenner T. Next-Generation Sequencing-Based Decision Support for Intensivists in Difficult-to-Diagnose Disease States: A Case Report of Invasive Cerebral Aspergillosis. A A Pract 2021; 15:e01447. [PMID: 33955856 DOI: 10.1213/xaa.0000000000001447] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Aspergillus spp. are widespread environmental pathogens that can induce invasive aspergillosis, especially in immunocompromised patients. An 86-year-old female patient presented with a rare case of invasive cerebral aspergillosis. The aspergilloma invaded the intracranial region originating from the ethmoidal sinus and the orbital apex. In contrast to routine diagnostic procedures, next-generation sequencing (NGS) was able to identify the fungal pathogen in the cerebrospinal fluid as well as in plasma samples, supporting the biopsy-based diagnosis of invasive cerebral aspergillosis. Therefore, NGS-based diagnostics may be of particular importance for difficult-to-diagnose disease states, when conventional diagnostic procedures fail.
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Affiliation(s)
- Simone Kattner
- From the Department of Anesthesiology and Intensive Care Medicine, University Hospital Essen, University Duisburg-Essen, Essen, Germany
| | - Frank Herbstreit
- From the Department of Anesthesiology and Intensive Care Medicine, University Hospital Essen, University Duisburg-Essen, Essen, Germany
| | - Karsten Schmidt
- From the Department of Anesthesiology and Intensive Care Medicine, University Hospital Essen, University Duisburg-Essen, Essen, Germany
| | | | | | - Simon Dubler
- From the Department of Anesthesiology and Intensive Care Medicine, University Hospital Essen, University Duisburg-Essen, Essen, Germany
| | - Peter-Michael Rath
- Institute of Medical Microbiology, Essen Center of Excellence in Clinical and Laboratory Mycology and Clinical Studies, University Hospital Essen, University Duisburg-Essen, Essen, Germany
| | - Thorsten Brenner
- From the Department of Anesthesiology and Intensive Care Medicine, University Hospital Essen, University Duisburg-Essen, Essen, Germany
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12
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Hurdeal VG, Gentekaki E, Lee HB, Jeewon R, Hyde KD, Tibpromma S, Mortimer PE, Xu J. Mucoralean Fungi in Thailand: Novel Species of Absidia from Tropical Forest Soil. CRYPTOGAMIE MYCOL 2021. [DOI: 10.5252/cryptogamie-mycologie2021v42a4] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Vedprakash G. Hurdeal
- Center of Excellence in Fungal Research, Mae Fah Luang University, Chiang Rai, 57100 and School of Science, Mae Fah Luang University, Chiang Rai, 57100 (Thailand)
| | - Eleni Gentekaki
- School of Science, Mae Fah Luang University, Chiang Rai, 57100 (Thailand)
| | - Hyang B. Lee
- Environmental Microbiology Lab., Dept. of Agricultural Biological Chemistry, College of Agriculture and Life Sciences, Chonnam National University, Gwangju 61186 (Korea)
| | - Rajesh Jeewon
- Department of Health Sciences, Faculty of Medicine and Health Sciences, University of Mauritius, Reduit (Mauritius)
| | - Kevin D. Hyde
- Center of Excellence in Fungal Research, Mae Fah Luang University, Chiang Rai, 57100 (Thailand) and Institute of Plant Health, Zhongkai University of Agriculture and Engineering, Haizhu District, Guangzhou 510225 (China) and CAS Key Laboratory for Pl
| | - Saowaluck Tibpromma
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Science, Kunming, 650201, Yunnan and Mountain futures, Kunming Institute of Botany, Chinese Academy of Science, Kunming 650201, Yunn
| | - Peter E. Mortimer
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Science, Kunming, 650201, Yunnan and Mountain futures, Kunming Institute of Botany, Chinese Academy of Science, Kunming 650201, Yunn
| | - Jianchu Xu
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Science, Kunming, 650201, Yunnan and Mountain futures, Kunming Institute of Botany, Chinese Academy of Science, Kunming 650201, Yunn
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13
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Toscanini MA, Nusblat AD, Cuestas ML. Diagnosis of histoplasmosis: current status and perspectives. Appl Microbiol Biotechnol 2021; 105:1837-1859. [PMID: 33587157 DOI: 10.1007/s00253-021-11170-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2020] [Revised: 01/29/2021] [Accepted: 02/03/2021] [Indexed: 11/29/2022]
Abstract
Histoplasmosis is a worldwide-distributed systemic mycosis caused by the dimorphic fungus Histoplasma capsulatum. Its clinical manifestations range from subclinical or mild respiratory illness to progressive disseminated histoplasmosis (PDH), a life-threatening disease, whose accurate diagnosis is still challenging and limited in many countries, where this disease is highly endemic. In this regard, Histoplasma antigen testing is now included in the WHO Essential Diagnostics List. The final diagnosis of histoplasmosis is established by culture and/or visualization of the yeast cells by cytology or histopathology using specific stains. However, both procedures have limited sensitivity to detect the disease and cultures are time-consuming. Antibody detection assays are effective for the subacute and chronic clinical forms of histoplasmosis. However, their sensitivity is low in the immunocompromised host. Several molecular "in-house" tests were also developed and showed promising results, but none of these tests are commercially available and their standardization and validation are still pending. Antigen detection assays have high sensitivity in PDH cases and are of great value for the follow-up of patients with histoplasmosis; however, cross-reactivity with other related fungi are common. In addition, this assay is expensive and only performed in few laboratories. Novel protein antigen candidates have been recently identified and produced by DNA-recombinant techniques in order to obtain standardized and specific reagents for the diagnosis of histoplasmosis, as opposed to the unspecific antigens or crude extracts currently used. This review describes the currently available assays, highlighting their strengths and limitations and reports the latest approaches to achieve reliable and rapid diagnostic tests for histoplasmosis. KEY POINTS: • PDH causes thousands of deaths per year globally. • Rapid accurate diagnosis of PDH is unfeasible in many regions. • Fast, accurate, and low-cost diagnostic alternatives are currently under development.
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Affiliation(s)
- María Agustina Toscanini
- Facultad de Farmacia y Bioquímica, CONICET, Instituto de Nanobiotecnología (NANOBIOTEC), Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Alejandro David Nusblat
- Facultad de Farmacia y Bioquímica, CONICET, Instituto de Nanobiotecnología (NANOBIOTEC), Universidad de Buenos Aires, Buenos Aires, Argentina
| | - María Luján Cuestas
- CONICET, Instituto de Investigaciones en Microbiología y Parasitología Médica (IMPaM), Universidad de Buenos Aires, Buenos Aires, Argentina.
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14
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Sheka D, Alabi N, Gordon PMK. Oxford nanopore sequencing in clinical microbiology and infection diagnostics. Brief Bioinform 2021; 22:6109725. [PMID: 33483726 DOI: 10.1093/bib/bbaa403] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Revised: 10/26/2020] [Accepted: 12/09/2020] [Indexed: 12/16/2022] Open
Abstract
Extended turnaround times and large economic costs hinder the usage of currently applied screening methods for bacterial pathogen identification (ID) and antimicrobial susceptibility testing. This review provides an overview of current detection methods and their usage in a clinical setting. Issues of timeliness and cost could soon be circumvented, however, with the emergence of detection methods involving single molecule sequencing technology. In the context of bringing diagnostics closer to the point of care, we examine the current state of Oxford Nanopore Technologies (ONT) products and their interaction with third-party software/databases to assess their capabilities for ID and antimicrobial resistance (AMR) prediction. We outline and discuss a potential diagnostic workflow, enumerating (1) rapid sample prep kits, (2) ONT hardware/software and (3) third-party software and databases to improve the cost, accuracy and turnaround times for ID and AMR. Multiple studies across a range of infection types support that the speed and accuracy of ONT sequencing is now such that established ID and AMR prediction tools can be used on its outputs, and so it can be harnessed for near real time, close to the point-of-care diagnostics in common clinical circumstances.
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Affiliation(s)
- Dropen Sheka
- Department of Biochemistry & Molecular Biology, Faculty of Medicine, University of Calgary, Calgary, Alberta, Canada
| | - Nikolay Alabi
- Department of Biochemistry & Molecular Biology, Faculty of Medicine, University of Calgary, Calgary, Alberta, Canada
| | - Paul M K Gordon
- Cumming School of Medicine Centre for Health Genomics and Informatics, University of Calgary
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15
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Li N, Cai Q, Miao Q, Song Z, Fang Y, Hu B. High-Throughput Metagenomics for Identification of Pathogens in the Clinical Settings. SMALL METHODS 2021; 5:2000792. [PMID: 33614906 PMCID: PMC7883231 DOI: 10.1002/smtd.202000792] [Citation(s) in RCA: 88] [Impact Index Per Article: 29.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Revised: 10/24/2020] [Indexed: 05/25/2023]
Abstract
The application of sequencing technology is shifting from research to clinical laboratories owing to rapid technological developments and substantially reduced costs. However, although thousands of microorganisms are known to infect humans, identification of the etiological agents for many diseases remains challenging as only a small proportion of pathogens are identifiable by the current diagnostic methods. These challenges are compounded by the emergence of new pathogens. Hence, metagenomic next-generation sequencing (mNGS), an agnostic, unbiased, and comprehensive method for detection, and taxonomic characterization of microorganisms, has become an attractive strategy. Although many studies, and cases reports, have confirmed the success of mNGS in improving the diagnosis, treatment, and tracking of infectious diseases, several hurdles must still be overcome. It is, therefore, imperative that practitioners and clinicians understand both the benefits and limitations of mNGS when applying it to clinical practice. Interestingly, the emerging third-generation sequencing technologies may partially offset the disadvantages of mNGS. In this review, mainly: a) the history of sequencing technology; b) various NGS technologies, common platforms, and workflows for clinical applications; c) the application of NGS in pathogen identification; d) the global expert consensus on NGS-related methods in clinical applications; and e) challenges associated with diagnostic metagenomics are described.
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Affiliation(s)
- Na Li
- Department of Infectious DiseasesZhongshan HospitalFudan UniversityShanghai200032China
| | - Qingqing Cai
- Genoxor Medical Science and Technology Inc.Zhejiang317317China
| | - Qing Miao
- Department of Infectious DiseasesZhongshan HospitalFudan UniversityShanghai200032China
| | - Zeshi Song
- Genoxor Medical Science and Technology Inc.Zhejiang317317China
| | - Yuan Fang
- Genoxor Medical Science and Technology Inc.Zhejiang317317China
| | - Bijie Hu
- Department of Infectious DiseasesZhongshan HospitalFudan UniversityShanghai200032China
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16
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Krumkamp R, Oppong K, Hogan B, Strauss R, Frickmann H, Wiafe-Akenten C, Boahen KG, Rickerts V, McCormick Smith I, Groß U, Schulze M, Jaeger A, Loderstädt U, Sarpong N, Owusu-Dabo E, May J, Dekker D. Spectrum of antibiotic resistant bacteria and fungi isolated from chronically infected wounds in a rural district hospital in Ghana. PLoS One 2020; 15:e0237263. [PMID: 32764812 PMCID: PMC7413558 DOI: 10.1371/journal.pone.0237263] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2020] [Accepted: 07/22/2020] [Indexed: 01/26/2023] Open
Abstract
Background Chronic infected wounds are generally difficult to manage and treatment can be particularly challenging in resource-limited settings where diagnostic testing is not readily available. In this study, the epidemiology of microbial pathogens in chronically infected wounds in rural Ghana was assessed to support therapeutic choices for physicians. Methods Culture-based bacterial diagnostics including antimicrobial resistance testing were performed on samples collected from patients with chronic wounds at a hospital in Asante Akim North Municipality, Ghana. Fungal detection was performed by broad-range fungal PCR and sequencing of amplicons. Results In total, 105 patients were enrolled in the study, from which 207 potential bacterial pathogens were isolated. Enterobacteriaceae (n = 84, 41%) constituted the most frequently isolated group of pathogens. On species level, Pseudomonas aeruginosa (n = 50, 24%) and Staphylococcus aureus (n = 28, 14%) were predominant. High resistance rates were documented, comprising 29% methicillin resistance in S. aureus as well as resistance to 3rd generation cephalosporins and fluoroquinolones in 33% and 58% of Enterobacteriaceae, respectively. One P. aeruginosa strain with carbapenem resistance was identified. The most frequently detected fungi were Candida tropicalis. Conclusions The pathogen distribution in chronic wounds in rural Ghana matched the internationally observed patterns with a predominance of P. aeruginosa and S. aureus. Very high resistance rates discourage antibiotic therapy but suggest an urgent need for microbiological diagnostic approaches, including antimicrobial resistance testing to guide the management of patients with chronic wounds in Ghana.
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Affiliation(s)
- Ralf Krumkamp
- Department of Infectious Disease Epidemiology, Bernhard Nocht Institute for Tropical Medicine (BNITM), Hamburg, Germany
- German Centre for Infection Research (DZIF), Hamburg-Lübeck-Borstel-Riems, Germany
| | - Kwabena Oppong
- Kumasi Centre for Collaborative Research in Tropical Medicine (KCCR), Kumasi, Ghana
| | - Benedikt Hogan
- Department of Infectious Disease Epidemiology, Bernhard Nocht Institute for Tropical Medicine (BNITM), Hamburg, Germany
| | - Ricardo Strauss
- Department of Infectious Disease Epidemiology, Bernhard Nocht Institute for Tropical Medicine (BNITM), Hamburg, Germany
| | - Hagen Frickmann
- Department for Tropical Medicine at the Bernhard Nocht Institute, Bundeswehr Hospital Hamburg, Germany
| | | | - Kennedy G. Boahen
- Kumasi Centre for Collaborative Research in Tropical Medicine (KCCR), Kumasi, Ghana
| | - Volker Rickerts
- Department Mycotic and Parasitic Agents and Mycobacteria, Robert Koch Institute (RKI), Berlin, Germany
| | - Ilka McCormick Smith
- Department Mycotic and Parasitic Agents and Mycobacteria, Robert Koch Institute (RKI), Berlin, Germany
| | - Uwe Groß
- Institute for Medical Microbiology, University Medical Center Göttingen (UMG), Göttingen, Germany
| | - Marco Schulze
- Institute for Medical Microbiology, University Medical Center Göttingen (UMG), Göttingen, Germany
| | - Anna Jaeger
- Department of Infectious Disease Epidemiology, Bernhard Nocht Institute for Tropical Medicine (BNITM), Hamburg, Germany
| | - Ulrike Loderstädt
- Department of Infectious Disease Epidemiology, Bernhard Nocht Institute for Tropical Medicine (BNITM), Hamburg, Germany
| | - Nimako Sarpong
- Kumasi Centre for Collaborative Research in Tropical Medicine (KCCR), Kumasi, Ghana
| | - Ellis Owusu-Dabo
- Kumasi Centre for Collaborative Research in Tropical Medicine (KCCR), Kumasi, Ghana
| | - Jürgen May
- Department of Infectious Disease Epidemiology, Bernhard Nocht Institute for Tropical Medicine (BNITM), Hamburg, Germany
| | - Denise Dekker
- Department of Infectious Disease Epidemiology, Bernhard Nocht Institute for Tropical Medicine (BNITM), Hamburg, Germany
- German Centre for Infection Research (DZIF), Hamburg-Lübeck-Borstel-Riems, Germany
- * E-mail:
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17
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Larkin PMK, Lawson KL, Contreras DA, Le CQ, Trejo M, Realegeno S, Hilt EE, Chandrasekaran S, Garner OB, Fishbein GA, Yang S. Amplicon-Based Next-Generation Sequencing for Detection of Fungi in Formalin-Fixed, Paraffin-Embedded Tissues: Correlation with Histopathology and Clinical Applications. J Mol Diagn 2020; 22:1287-1293. [PMID: 32738297 DOI: 10.1016/j.jmoldx.2020.06.017] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Accepted: 06/26/2020] [Indexed: 01/13/2023] Open
Abstract
Invasive fungal infections are increasing in prevalence because of an expanding population of immunocompromised individuals. To reduce morbidity and mortality, it is critical to accurately identify fungal pathogens to guide treatment. Current methods rely on histopathology, fungal culture, and serology, which are often insufficient for diagnosis. Herein, we describe the use of a laboratory-developed internal transcribed spacer-targeted amplicon-based next-generation sequencing (NGS) assay for the identification of fungal etiology in fungal stain-positive formalin-fixed, paraffin-embedded tissues by using Illumina MiSeq. A total of 44 specimens from 35 patients were included in this study, with varying degrees of fungal burden from multiple anatomic sites. NGS identified 20 unique species across the 54 total organisms detected, including 40 molds, 10 yeasts, and 4 dimorphic fungi. The histopathologic morphology and the organisms suspected by surgical pathologist were compared with the organisms identified by NGS, with 100% (44/44) and 93.2% (41/44) concordance, respectively. In contrast, fungal culture only provided an identification in 27.3% (12/44) of specimens. We demonstrated that NGS is a powerful method for accurate and unbiased fungal identification in formalin-fixed, paraffin-embedded tissues. A retrospective evaluation of the clinical utility of the NGS results also suggests this technology can potentially improve both the speed and the accuracy of diagnosis for invasive fungal infections.
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Affiliation(s)
- Paige M K Larkin
- Department of Pathology and Laboratory Medicine, University of California, Los Angeles, Los Angeles, California
| | - Katy L Lawson
- Department of Pathology and Laboratory Medicine, University of California, Los Angeles, Los Angeles, California
| | - Deisy A Contreras
- Department of Pathology and Laboratory Medicine, University of California, Los Angeles, Los Angeles, California
| | - Catherine Q Le
- Department of Pathology and Laboratory Medicine, University of California, Los Angeles, Los Angeles, California
| | - Marisol Trejo
- Department of Pathology and Laboratory Medicine, University of California, Los Angeles, Los Angeles, California
| | - Susan Realegeno
- Department of Pathology and Laboratory Medicine, University of California, Los Angeles, Los Angeles, California
| | - Evann E Hilt
- Department of Pathology and Laboratory Medicine, University of California, Los Angeles, Los Angeles, California
| | - Sukantha Chandrasekaran
- Department of Pathology and Laboratory Medicine, University of California, Los Angeles, Los Angeles, California
| | - Omai B Garner
- Department of Pathology and Laboratory Medicine, University of California, Los Angeles, Los Angeles, California
| | - Gregory A Fishbein
- Department of Pathology and Laboratory Medicine, University of California, Los Angeles, Los Angeles, California
| | - Shangxin Yang
- Department of Pathology and Laboratory Medicine, University of California, Los Angeles, Los Angeles, California.
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18
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A Collaborative Tale of Diagnosing and Treating Chronic Pulmonary Aspergillosis, from the Perspectives of Clinical Microbiologists, Surgical Pathologists, and Infectious Disease Clinicians. J Fungi (Basel) 2020; 6:jof6030106. [PMID: 32664547 PMCID: PMC7558816 DOI: 10.3390/jof6030106] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2020] [Revised: 07/08/2020] [Accepted: 07/09/2020] [Indexed: 02/06/2023] Open
Abstract
Chronic pulmonary aspergillosis (CPA) refers to a spectrum of Aspergillus-mediated disease that is associated with high morbidity and mortality, with its true prevalence vastly underestimated. The diagnosis of CPA includes characteristic radiographical findings in conjunction with persistent and systemic symptoms present for at least three months, and evidence of Aspergillus infection. Traditionally, Aspergillus infection has been confirmed through histopathology and microbiological studies, including fungal culture and serology, but these methodologies have limitations that are discussed in this review. The treatment of CPA requires an individualized approach and consideration of both medical and surgical options. Most Aspergillus species are considered susceptible to mold-active triazoles, echinocandins, and amphotericin B; however, antifungal resistance is emerging and well documented, demonstrating the need for novel therapies and antifungal susceptibility testing that correlates with clinical response. Here, we describe the clinical presentation, diagnosis, and treatment of CPA, with an emphasis on the strengths and pitfalls of diagnostic and treatment approaches, as well as future directions, including whole genome sequencing and metagenomic sequencing. The advancement of molecular technology enables rapid and precise species level identification, and the determination of molecular mechanisms of resistance, bridging the clinical infectious disease, anatomical pathology, microbiology, and molecular biology disciplines.
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19
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Innovative Approaches for Histoplasma Detection. CURRENT FUNGAL INFECTION REPORTS 2020. [DOI: 10.1007/s12281-020-00393-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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20
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Hahn A, Podbielski A, Meyer T, Zautner AE, Loderstädt U, Schwarz NG, Krüger A, Cadar D, Frickmann H. On detection thresholds-a review on diagnostic approaches in the infectious disease laboratory and the interpretation of their results. Acta Trop 2020; 205:105377. [PMID: 32007448 DOI: 10.1016/j.actatropica.2020.105377] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2019] [Revised: 11/18/2019] [Accepted: 01/29/2020] [Indexed: 02/06/2023]
Abstract
Diagnostic testing in the infectious disease laboratory facilitates decision-making by physicians at the bedside as well as epidemiological assessments and surveillance at study level. Problems may arise if test results are uncritically considered as being the same as the unknown true value. To allow a better understanding, the influence of external factors on the interpretation of test results is introduced with the example of prevalence, followed by the presentation of strengths and weaknesses of important techniques in the infectious disease laboratory like microscopy, cultural diagnostics, serology, mass spectrometry, nucleic acid amplification and hypothesis-free metagenomic sequencing with focus on basic, high-technology and potential future approaches. Special problems like multiplex testing as well as uncertainty of test evaluations, if no gold standard is available, are also stressed with a final glimpse on emerging future technologies for the infectious disease laboratory. In the conclusions, suitability for point-of-care-testing and field laboratory applications is summarized. The aim is to illustrate the limitations of diagnostic accuracy to both clinicians and study planners and to stress the importance of close cooperation with experts in laboratory disciplines so as to avoid potentially critical misunderstandings due to inappropriate interpretation of diagnostic test results.
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Affiliation(s)
- Andreas Hahn
- Institute for Medical Microbiology, Virology and Hygiene, University Medicine Rostock, Rostock, Germany
| | - Andreas Podbielski
- Institute for Medical Microbiology, Virology and Hygiene, University Medicine Rostock, Rostock, Germany
| | - Thomas Meyer
- Department of Dermatology, St. Josef Hospital, Bochum, Germany
| | - Andreas Erich Zautner
- Institut für Medizinische Mikrobiologie, Universitätsmedizin Göttingen, Göttingen, Germany
| | - Ulrike Loderstädt
- Bernhard Nocht Institute for Tropical Medicine Hamburg, Hamburg, Germany
| | | | - Andreas Krüger
- Department of Microbiology and Hospital Hygiene, Bundeswehr Hospital Hamburg, Hamburg, Germany
| | - Daniel Cadar
- Bernhard Nocht Institute for Tropical Medicine Hamburg, Hamburg, Germany
| | - Hagen Frickmann
- Institute for Medical Microbiology, Virology and Hygiene, University Medicine Rostock, Rostock, Germany; Department of Microbiology and Hospital Hygiene, Bundeswehr Hospital Hamburg, Hamburg, Germany.
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Trabelsi H, Hadrich I, Neji S, Khemakhem N, Hammami B, Makni F, Sellami H, Ayadi A. Microsatellite analysis of the population structure in Rhizopus arrhizus. J Appl Microbiol 2020; 128:1793-1801. [PMID: 31965685 DOI: 10.1111/jam.14583] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2019] [Revised: 01/06/2020] [Accepted: 01/15/2020] [Indexed: 11/27/2022]
Abstract
OBJECTIVES Rhizopus arrhizus is recognized as an emergent agent of superficial and invasive mucormycosis. Despite an increasing number of these infections, the molecular epidemiology of Rhizopus species has not been well studied. MATERIALS AND METHODS In this study, 43 R. arrhizus strains (25 environmental and 18 clinical isolates) were genotyped using six novel panels of microsatellite markers. RESULTS Upon the analysis of 43 isolates, 4-8 distinct alleles were detected for each marker. The discriminatory power for the individual markers ranged from 0·522 to 0·830. The combination of all six markers yielded 33 different haplotypes with a high degree of discrimination (0·989 D value). A four-marker combination were selected as the most parsimonious panel achieving D > 0·95. One clinical isolate and one environmental isolate shared the same genotype suggesting the possible nosocomial outbreak of mucormycosis in hospitalized patients. We have noted that the strains isolated from cutaneous mucormycosis were different from the strains isolated from rhino-orbito-cerebral mucormycosis. Then, the hypothesis of particular tropism of infectious strains for a given site is not excluded. The standardized indices of association IA and rBarD were significantly different from zero (P < 0·01), suggesting a prevailing clonal reproduction. The environmental population was significantly differentiated from clinical populations (Fst = 0·2249). CONCLUSIONS Microsatellite typing method described in our study showed an excellent degree of discriminatory power. It is a promising tool for illuminating the molecular epidemiology of R. arrhizus species, including strain relatedness and transmission pathways.
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Affiliation(s)
- H Trabelsi
- Laboratory of Parasitology-Mycology, Habib Bourguiba Hospital, Sfax, Tunisia.,Fungi and Parasitic Molecular Biology Laboratory, School of Medicine, University of Sfax, Sfax, Tunisia
| | - I Hadrich
- Fungi and Parasitic Molecular Biology Laboratory, School of Medicine, University of Sfax, Sfax, Tunisia
| | - S Neji
- Laboratory of Parasitology-Mycology, Habib Bourguiba Hospital, Sfax, Tunisia.,Fungi and Parasitic Molecular Biology Laboratory, School of Medicine, University of Sfax, Sfax, Tunisia
| | - N Khemakhem
- Laboratory of Parasitology-Mycology, Habib Bourguiba Hospital, Sfax, Tunisia.,Fungi and Parasitic Molecular Biology Laboratory, School of Medicine, University of Sfax, Sfax, Tunisia
| | - B Hammami
- ENT Department, Habib Bourguiba Hospital, Sfax, Tunisia
| | - F Makni
- Laboratory of Parasitology-Mycology, Habib Bourguiba Hospital, Sfax, Tunisia.,Fungi and Parasitic Molecular Biology Laboratory, School of Medicine, University of Sfax, Sfax, Tunisia
| | - H Sellami
- Laboratory of Parasitology-Mycology, Habib Bourguiba Hospital, Sfax, Tunisia.,Fungi and Parasitic Molecular Biology Laboratory, School of Medicine, University of Sfax, Sfax, Tunisia
| | - A Ayadi
- Laboratory of Parasitology-Mycology, Habib Bourguiba Hospital, Sfax, Tunisia.,Fungi and Parasitic Molecular Biology Laboratory, School of Medicine, University of Sfax, Sfax, Tunisia
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Zhu ZZ, Zhu J, Zhu K, Wang H, Xu Q, Bai C. Next generation sequencing-guided anti-infective therapy of large liver abscess due to Edwardsiella tarda: a case report. J LAB MED 2019. [DOI: 10.1515/labmed-2019-0070] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
AbstractBackgroundLiver abscess is a potentially fatal disease, however identification of its causative pathogen remains challenging, which is crucial for guiding appropriate antibiotic therapy. To the best of our knowledge, the use of plasma next-generation sequencing (NGS) based pathogen analysis in patients with liver abscess has never been reported.Case presentationWe report a case with large liver abscess due toEdwardsiella tardathat was diagnosed by the plasma-based NGS assay within 24 h. After a 2-week single agent anti-infection therapy, the patient completely recovered. A second NGS assay following anti-infection therapy failed to detect the pathogenic DNA. Follow-up magnetic resonance imaging (MRI) of the abdomen on 1 month and 3 months showed a gradually decrease in size of the liver abscess, and the 6-month MRI showed that the abscess disappeared completely.ConclusionsOur data indicated that the plasma NGS test can sensitively and minimal-invasively detect pathogens within a clinically actionable timeframe, and antibiotic alone is an alternative to first-line treatment for large liver abscess with the aid of NGS for accurate detection of the pathogenic bacterial genome.
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