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Moeckel C, Mareboina M, Konnaris MA, Chan CS, Mouratidis I, Montgomery A, Chantzi N, Pavlopoulos GA, Georgakopoulos-Soares I. A survey of k-mer methods and applications in bioinformatics. Comput Struct Biotechnol J 2024; 23:2289-2303. [PMID: 38840832 PMCID: PMC11152613 DOI: 10.1016/j.csbj.2024.05.025] [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: 03/13/2024] [Revised: 05/14/2024] [Accepted: 05/15/2024] [Indexed: 06/07/2024] Open
Abstract
The rapid progression of genomics and proteomics has been driven by the advent of advanced sequencing technologies, large, diverse, and readily available omics datasets, and the evolution of computational data processing capabilities. The vast amount of data generated by these advancements necessitates efficient algorithms to extract meaningful information. K-mers serve as a valuable tool when working with large sequencing datasets, offering several advantages in computational speed and memory efficiency and carrying the potential for intrinsic biological functionality. This review provides an overview of the methods, applications, and significance of k-mers in genomic and proteomic data analyses, as well as the utility of absent sequences, including nullomers and nullpeptides, in disease detection, vaccine development, therapeutics, and forensic science. Therefore, the review highlights the pivotal role of k-mers in addressing current genomic and proteomic problems and underscores their potential for future breakthroughs in research.
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Affiliation(s)
- Camille Moeckel
- Institute for Personalized Medicine, Department of Biochemistry and Molecular Biology, The Pennsylvania State University College of Medicine, Hershey, PA, USA
| | - Manvita Mareboina
- Institute for Personalized Medicine, Department of Biochemistry and Molecular Biology, The Pennsylvania State University College of Medicine, Hershey, PA, USA
| | - Maxwell A. Konnaris
- Institute for Personalized Medicine, Department of Biochemistry and Molecular Biology, The Pennsylvania State University College of Medicine, Hershey, PA, USA
| | - Candace S.Y. Chan
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA, USA
| | - Ioannis Mouratidis
- Institute for Personalized Medicine, Department of Biochemistry and Molecular Biology, The Pennsylvania State University College of Medicine, Hershey, PA, USA
- Huck Institute of the Life Sciences, Penn State University, University Park, Pennsylvania, USA
| | - Austin Montgomery
- Institute for Personalized Medicine, Department of Biochemistry and Molecular Biology, The Pennsylvania State University College of Medicine, Hershey, PA, USA
| | - Nikol Chantzi
- Institute for Personalized Medicine, Department of Biochemistry and Molecular Biology, The Pennsylvania State University College of Medicine, Hershey, PA, USA
| | | | - Ilias Georgakopoulos-Soares
- Institute for Personalized Medicine, Department of Biochemistry and Molecular Biology, The Pennsylvania State University College of Medicine, Hershey, PA, USA
- Huck Institute of the Life Sciences, Penn State University, University Park, Pennsylvania, USA
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2
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Murali H, Wang P, Liao EC, Wang K. Genetic variant classification by predicted protein structure: A case study on IRF6. Comput Struct Biotechnol J 2024; 23:892-904. [PMID: 38370976 PMCID: PMC10869248 DOI: 10.1016/j.csbj.2024.01.019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2023] [Revised: 01/24/2024] [Accepted: 01/25/2024] [Indexed: 02/20/2024] Open
Abstract
Next-generation genome sequencing has revolutionized genetic testing, identifying numerous rare disease-associated gene variants. However, to impute pathogenicity, computational approaches remain inadequate and functional testing of gene variant is required to provide the highest level of evidence. The emergence of AlphaFold2 has transformed the field of protein structure determination, and here we outline a strategy that leverages predicted protein structure to enhance genetic variant classification. We used the gene IRF6 as a case study due to its clinical relevance, its critical role in cleft lip/palate malformation, and the availability of experimental data on the pathogenicity of IRF6 gene variants through phenotype rescue experiments in irf6-/- zebrafish. We compared results from over 30 pathogenicity prediction tools on 37 IRF6 missense variants. IRF6 lacks an experimentally derived structure, so we used predicted structures to explore associations between mutational clustering and pathogenicity. We found that among these variants, 19 of 37 were unanimously predicted as deleterious by computational tools. Comparing in silico predictions with experimental findings, 12 variants predicted as pathogenic were experimentally determined as benign. Even with the recently published AlphaMissense model, 15/18 (83%) of the predicted pathogenic variants were experimentally determined as benign. In comparison, mapping variants to the protein revealed deleterious mutation clusters around the protein binding domain, whereas N-terminal variants tend to be benign, suggesting the importance of structural information in determining pathogenicity of mutations in this gene. In conclusion, incorporating gene-specific structural features of known pathogenic/benign mutations may provide meaningful insights into pathogenicity predictions in a gene-specific manner and facilitate the interpretation of variant pathogenicity.
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Affiliation(s)
- Hemma Murali
- Graduate Program in Biochemistry and Molecular Biophysics, University of Pennsylvania, Philadelphia, PA 19104, United States
- Center for Cellular and Molecular Therapeutics, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, United States
| | - Peng Wang
- Center for Cellular and Molecular Therapeutics, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, United States
- Master of Biotechnology Program, University of Pennsylvania, Philadelphia, PA 19104, United States
| | - Eric C. Liao
- Department of Surgery, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, United States
- Center for Craniofacial Innovation, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, United States
| | - Kai Wang
- Center for Cellular and Molecular Therapeutics, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, United States
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA 19104, United States
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3
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Fernández-Manteca MG, Ocampo-Sosa AA, Vecilla DF, Ruiz MS, Roiz MP, Madrazo F, Rodríguez-Grande J, Calvo-Montes J, Rodríguez-Cobo L, López-Higuera JM, Fariñas MC, Cobo A. Identification of hypermucoviscous Klebsiella pneumoniae K1, K2, K54 and K57 capsular serotypes by Raman spectroscopy. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2024; 319:124533. [PMID: 38820814 DOI: 10.1016/j.saa.2024.124533] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2024] [Revised: 05/17/2024] [Accepted: 05/24/2024] [Indexed: 06/02/2024]
Abstract
Antimicrobial resistance poses a significant challenge in modern medicine, affecting public health. Klebsiella pneumoniae infections compound this issue due to their broad range of infections and the emergence of multiple antibiotic resistance mechanisms. Efficient detection of its capsular serotypes is crucial for immediate patient treatment, epidemiological tracking and outbreak containment. Current methods have limitations that can delay interventions and increase the risk of morbidity and mortality. Raman spectroscopy is a promising alternative to identify capsular serotypes in hypermucoviscous K. pneumoniae isolates. It provides rapid and in situ measurements with minimal sample preparation. Moreover, its combination with machine learning tools demonstrates high accuracy and reproducibility. This study analyzed the viability of combining Raman spectroscopy with one-dimensional convolutional neural networks (1-D CNN) to classify four capsular serotypes of hypermucoviscous K. pneumoniae: K1, K2, K54 and K57. Our approach involved identifying the most relevant Raman features for classification to prevent overfitting in the training models. Simplifying the dataset to essential information maintains accuracy and reduces computational costs and training time. Capsular serotypes were classified with 96 % accuracy using less than 30 Raman features out of 2400 contained in each spectrum. To validate our methodology, we expanded the dataset to include both hypermucoviscous and non-mucoid isolates and distinguished between them. This resulted in an accuracy rate of 94 %. The results obtained have significant potential for practical healthcare applications, especially for enabling the prompt prescription of the appropriate antibiotic treatment against infections.
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Affiliation(s)
- María Gabriela Fernández-Manteca
- Instituto de Investigación Sanitaria Valdecilla (IDIVAL), Santander, Spain; Photonics Engineering Group, Universidad de Cantabria, Santander, Spain.
| | - Alain A Ocampo-Sosa
- Instituto de Investigación Sanitaria Valdecilla (IDIVAL), Santander, Spain; Servicio de Microbiología, Hospital Universitario Marqués de Valdecilla, Santander, Spain; CIBER de Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III, Madrid, Spain
| | - Domingo Fernandez Vecilla
- Clinical Microbiology and Parasitology Department, Basurto University Hospital, Bilbao, Vizcaya, Spain; Biocruces Bizkaia Health Research Institute, Barakaldo, Vizcaya, Spain
| | - María Siller Ruiz
- Instituto de Investigación Sanitaria Valdecilla (IDIVAL), Santander, Spain; Servicio de Microbiología, Hospital Universitario Marqués de Valdecilla, Santander, Spain
| | - María Pía Roiz
- Instituto de Investigación Sanitaria Valdecilla (IDIVAL), Santander, Spain; Servicio de Microbiología, Hospital Universitario Marqués de Valdecilla, Santander, Spain
| | - Fidel Madrazo
- Instituto de Investigación Sanitaria Valdecilla (IDIVAL), Santander, Spain
| | - Jorge Rodríguez-Grande
- Instituto de Investigación Sanitaria Valdecilla (IDIVAL), Santander, Spain; Servicio de Microbiología, Hospital Universitario Marqués de Valdecilla, Santander, Spain
| | - Jorge Calvo-Montes
- Instituto de Investigación Sanitaria Valdecilla (IDIVAL), Santander, Spain; Servicio de Microbiología, Hospital Universitario Marqués de Valdecilla, Santander, Spain; CIBER de Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III, Madrid, Spain
| | - Luis Rodríguez-Cobo
- Instituto de Investigación Sanitaria Valdecilla (IDIVAL), Santander, Spain; Photonics Engineering Group, Universidad de Cantabria, Santander, Spain; CIBER de Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN), Instituto de Salud Carlos III, Madrid, Spain
| | - José Miguel López-Higuera
- Instituto de Investigación Sanitaria Valdecilla (IDIVAL), Santander, Spain; Photonics Engineering Group, Universidad de Cantabria, Santander, Spain; CIBER de Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN), Instituto de Salud Carlos III, Madrid, Spain
| | - María Carmen Fariñas
- Instituto de Investigación Sanitaria Valdecilla (IDIVAL), Santander, Spain; CIBER de Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III, Madrid, Spain; Servicio de Enfermedades Infecciosas, Hospital Universitario Marqués de Valdecilla, Santander, Spain; Departamento de Medicina y Psiquiatría, Universidad de Cantabria, Santander, Spain
| | - Adolfo Cobo
- Instituto de Investigación Sanitaria Valdecilla (IDIVAL), Santander, Spain; Photonics Engineering Group, Universidad de Cantabria, Santander, Spain; CIBER de Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN), Instituto de Salud Carlos III, Madrid, Spain.
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Wang X, Guo X, Liu H, Wang B, Wu J, Chen S, Zhang W, Zhang X, Wang X. Augmented pathogen detection in brain abscess using metagenomic next-generation sequencing: a retrospective cohort study. Microbiol Spectr 2024; 12:e0032524. [PMID: 39264158 PMCID: PMC11448231 DOI: 10.1128/spectrum.00325-24] [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: 02/17/2024] [Accepted: 08/06/2024] [Indexed: 09/13/2024] Open
Abstract
Brain abscess is a severe infection characterized by the accumulation of pus within the brain parenchyma. Accurate identification of the causative pathogens is crucial for effective treatment and improved patient outcomes. This 10-year retrospective, single-center study aimed to compare the detection performance of conventional culture methods and metagenomic next-generation sequencing (mNGS) in brain abscess. We reviewed 612 patients diagnosed with brain abscess and identified 174 cases with confirmed etiology. The median age was 52 years, with 69.5% males. Culture tests predominately identified gram-positive bacteria, particularly Streptococcus spp. Gram-negative bacteria, including Klebsiella spp., were also detected. However, mNGS revealed a more diverse pathogen spectrum, focusing on anaerobes (e.g., Fusobacterium spp., Parvimonas spp., Porphyromonas spp., Prevotella spp., and Tannerella spp.). mNGS exhibited significantly higher overall pathogen-positive rates in pus samples (85.0% vs 50.0%, P = 0.0181) and CSF samples (84.2% vs 7.9%, P < 0.0001) compared to culture. Furthermore, the detection rates for anaerobes displayed a notable disparity, with mNGS yielding significantly higher positive detections in both pus samples (50.0% vs 10%, P = 0.0058) and CSF samples (18.4% vs 0%, P = 0.0115) when compared to culture methods. The assistance of mNGS in pathogen detection, particularly anaerobes in brain abscess, was evident in our findings. mNGS demonstrated the ability to identify rare and fastidious pathogens, even in culture-negative cases. These results emphasize the clinical value of mNGS as a supplement for brain abscess, enabling more comprehensive and accurate pathogen identification.IMPORTANCEThe accurate identification of pathogens causing brain abscess is crucial for effective treatment and improved patient outcomes. In this 10-year retrospective study, the detection performance of conventional culture methods and metagenomic next-generation sequencing (mNGS) was compared. The study analyzed 612 patients with brain abscess and confirmed etiology in 174 cases. The results showed that culture tests predominantly identified gram-positive bacteria, while mNGS unveiled a broader diverse pathogen spectrum, particularly anaerobes. The mNGS method exhibited significantly higher overall rates of pathogen positivity both in pus and cerebrospinal fluid (CSF) samples, surpassing the culture methods. Notably, mNGS detected a significantly higher number of anaerobes in both pus and CSF samples compared to culture methods. These findings underscore the clinical value of mNGS as a supplement for brain abscess diagnosis, enabling more comprehensive and accurate pathogen identification, particularly for rare and fastidious pathogens that evade detection by conventional culture methods.
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Affiliation(s)
- Xuyang Wang
- Department of Infectious Diseases, Shanghai Key Laboratory of Infectious Diseases and Biosafety Emergency Response, National Medical Center for Infectious Diseases, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai, China
| | - Xiaoxiao Guo
- Department of Infectious Diseases, Shanghai Key Laboratory of Infectious Diseases and Biosafety Emergency Response, National Medical Center for Infectious Diseases, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai, China
| | - Hong Liu
- Department of Laboratory Medicine, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai, China
| | - Bei Wang
- Department of Laboratory Medicine, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai, China
| | - Jing Wu
- Department of Infectious Diseases, Shanghai Key Laboratory of Infectious Diseases and Biosafety Emergency Response, National Medical Center for Infectious Diseases, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai, China
| | - Shengsen Chen
- Department of Endoscopy, Cancer Hospital of the University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), Institute of Cancer and Basic Medicine (IBMC), Chinese Academy of Sciences, Hangzhou, China
| | - Wenhong Zhang
- Department of Infectious Diseases, Shanghai Key Laboratory of Infectious Diseases and Biosafety Emergency Response, National Medical Center for Infectious Diseases, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai, China
- National Clinical Research Center for Aging and Medicine, Huashan Hospital, Fudan University, Shanghai, China
- Key Laboratory of Medical Molecular Virology (MOE/MOH) Shanghai Medical College, Fudan University, Shanghai, China
| | - Xinyun Zhang
- Department of Infectious Diseases, Shanghai Key Laboratory of Infectious Diseases and Biosafety Emergency Response, National Medical Center for Infectious Diseases, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai, China
| | - Xinyu Wang
- Department of Infectious Diseases, Shanghai Key Laboratory of Infectious Diseases and Biosafety Emergency Response, National Medical Center for Infectious Diseases, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai, China
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5
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Penzes JJ, Holm M, Yost SA, Kaelber JT. Cryo-EM-based discovery of a pathogenic parvovirus causing epidemic mortality by black wasting disease in farmed beetles. Cell 2024; 187:5604-5619.e14. [PMID: 39208798 DOI: 10.1016/j.cell.2024.07.053] [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: 06/29/2023] [Revised: 05/23/2024] [Accepted: 07/30/2024] [Indexed: 09/04/2024]
Abstract
We use cryoelectron microscopy (cryo-EM) as a sequence- and culture-independent diagnostic tool to identify the etiological agent of an agricultural pandemic. For the past 4 years, American insect-rearing facilities have experienced a distinctive larval pathology and colony collapse of farmed Zophobas morio (superworm). By means of cryo-EM, we discovered the causative agent: a densovirus that we named Zophobas morio black wasting virus (ZmBWV). We confirmed the etiology of disease by fulfilling Koch's postulates and characterizing strains from across the United States. ZmBWV is a member of the family Parvoviridae with a 5,542 nt genome, and we describe intersubunit interactions explaining its expanded internal volume relative to human parvoviruses. Cryo-EM structures at resolutions up to 2.1 Å revealed single-strand DNA (ssDNA) ordering at the capsid inner surface pinned by base-binding pockets in the capsid inner surface. Also, we demonstrated the prophylactic potential of non-pathogenic strains to provide cross-protection in vivo.
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Affiliation(s)
- Judit J Penzes
- Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, NJ, USA.
| | - Martin Holm
- Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, NJ, USA
| | - Samantha A Yost
- Research and Early Development, REGENXBIO Inc., Rockville, MD, USA
| | - Jason T Kaelber
- Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, NJ, USA.
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6
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Liu L, Hakhverdyan M, Wallgren P, Vanneste K, Fu Q, Lucas P, Blanchard Y, de Graaf M, Oude Munnink BB, van Boheemen S, Bossers A, Hulst M, Van Borm S. An interlaboratory proficiency test using metagenomic sequencing as a diagnostic tool for the detection of RNA viruses in swine fecal material. Microbiol Spectr 2024; 12:e0420823. [PMID: 39162509 PMCID: PMC11448438 DOI: 10.1128/spectrum.04208-23] [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: 12/18/2023] [Accepted: 07/19/2024] [Indexed: 08/21/2024] Open
Abstract
Metagenomic shotgun sequencing (mNGS) can serve as a generic molecular diagnostic tool. An mNGS proficiency test (PT) was performed in six European veterinary and public health laboratories to detect porcine astroviruses in fecal material and the extracted RNA. While different mNGS workflows for the generation of mNGS data were used in the different laboratories, the bioinformatic analysis was standardized using a metagenomic read classifier as well as read mapping to selected astroviral reference genomes to assess the semiquantitative representation of astrovirus species mixtures. All participants successfully identified and classified most of the viral reads to the two dominant species. The normalized read counts obtained by aligning reads to astrovirus reference genomes by Bowtie2 were in line with Kraken read classification counts. Moreover, participants performed well in terms of repeatability when the fecal sample was tested in duplicate. However, the normalized read counts per detected astrovirus species differed substantially between participants, which was related to the different laboratory methods used for data generation. Further modeling of the mNGS data indicated the importance of selecting appropriate reference data for mNGS read classification. As virus- or sample-specific biases may apply, caution is needed when extrapolating this swine feces-based PT for the detection of other RNA viruses or using different sample types. The suitability of experimental design to a given pathogen/sample matrix combination, quality assurance, interpretation, and follow-up investigation remain critical factors for the diagnostic interpretation of mNGS results. IMPORTANCE Metagenomic shotgun sequencing (mNGS) is a generic molecular diagnostic method, involving laboratory preparation of samples, sequencing, bioinformatic analysis of millions of short sequences, and interpretation of the results. In this paper, we investigated the performance of mNGS on the detection of porcine astroviruses, a model for RNA viruses in a pig fecal material, among six European veterinary and public health laboratories. We showed that different methods for data generation affect mNGS performance among participants and that the selection of reference genomes is crucial for read classification. Follow-up investigation remains a critical factor for the diagnostic interpretation of mNGS results. The paper contributes to potential improvements of mNGS as a diagnostic tool in clinical settings.
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Affiliation(s)
- Lihong Liu
- Department of Microbiology, Swedish Veterinary Agency, Uppsala, Sweden
| | | | - Per Wallgren
- Department of Animal Health and Antimicrobial Strategies, Swedish Veterinary Agency, Uppsala, Sweden
| | - Kevin Vanneste
- Department of Transversal activities in Applied Genomics, Sciensano, Brussels, Belgium
| | - Qiang Fu
- Department of Transversal activities in Applied Genomics, Sciensano, Brussels, Belgium
| | - Pierrick Lucas
- Ploufragan-Plouzané-Niort Laboratory, French Agency for Food, Environmental and Occupational Health Safety, Ploufragan, France
| | - Yannick Blanchard
- Ploufragan-Plouzané-Niort Laboratory, French Agency for Food, Environmental and Occupational Health Safety, Ploufragan, France
| | - Miranda de Graaf
- Department of Viroscience, Erasmus University Medical Center, Rotterdam, the Netherlands
| | - Bas B Oude Munnink
- Department of Viroscience, Erasmus University Medical Center, Rotterdam, the Netherlands
| | - Sander van Boheemen
- Department of Viroscience, Erasmus University Medical Center, Rotterdam, the Netherlands
| | - Alex Bossers
- Department of Epidemiology, Bioinformatics and Animal models, Wageningen BioVeterinary Research, Wageningen University & Research, Lelystad, the Netherlands
| | - Marcel Hulst
- Department of Epidemiology, Bioinformatics and Animal models, Wageningen BioVeterinary Research, Wageningen University & Research, Lelystad, the Netherlands
| | - Steven Van Borm
- Department of Avian Virology and Immunology, Sciensano, Ukkel, Belgium
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7
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Li S, Zhang Y, Han D. Severe community‑acquired pneumonia caused by Legionella gormanii in combination with influenza A subtype (H1N1) virus in an immunocompetent patient detected by metagenomic next‑generation sequencing: A case report. Biomed Rep 2024; 21:145. [PMID: 39170755 PMCID: PMC11337151 DOI: 10.3892/br.2024.1833] [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: 02/07/2024] [Accepted: 07/19/2024] [Indexed: 08/23/2024] Open
Abstract
Legionella pneumonia is an atypical form of pneumonia caused by Legionella gormanii that can also lead to multiple organ diseases, including acute respiratory distress syndrome and multiple organ dysfunction syndrome. Legionella gormanii requires a long incubation period for culture in clinical practice using BCYE medium. The specificity of serum for serological detection is low, resulting in a relatively high rate of missed Legionella diagnoses. Contracting the H1N1 virus can lead to the misdiagnosis of Legionella gormanii. Metagenomic next-generation sequencing (mNGS) is a novel tool that can rapidly and accurately identify potential Legionella gormanii strains. A severe case of community-acquired pneumonia in a 79-year-old patient was reported. The patient was diagnosed with Legionella gormanii and influenza A subtype (H1N1) virus using mNGS at The First Affiliated Hospital, Zhejiang University School of Medicine. After anti-Legionella and antiviral therapy, the number of reads identifying Legionella gormanii in bronchoalveolar lavage fluid using mNGS decreased from 665 to 112 as the patient's condition gradually improved. A search of PubMed revealed few reports of Legionella gormanii in association with the influenza A subtype (H1N1) virus. Patients with severe pneumonia caused by Legionella and influenza A subtype H1N1 virus infections should be screened early for infections using methods such as mNGS. This approach enables early and precise treatment, simplifying the administration of antibiotics and enhancing patient outcomes.
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Affiliation(s)
- Sujuan Li
- Department of Clinical Laboratory, Hangzhou Traditional Chinese Medicine Hospital Affiliated to Zhejiang Chinese Medical University, Hangzhou, Zhejiang 310005, P.R. China
| | - Yuanhang Zhang
- Department of Clinical Laboratory, Hangzhou Traditional Chinese Medicine Hospital Affiliated to Zhejiang Chinese Medical University, Hangzhou, Zhejiang 310005, P.R. China
| | - Dongsheng Han
- Department of Laboratory Medicine, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310003, P.R. China
- Key Laboratory of Clinical In Vitro Diagnostic Techniques of Zhejiang, Hangzhou, Zhejiang 310003, P.R. China
- Institute of Laboratory Medicine, Zhejiang University, Hangzhou, Zhejiang 310003, P.R. China
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8
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Wu X, Xu A, Tian F, Yang J, Lin L, Zhai M, Wu B, Zheng Y. A case report of acute Q fever with low-read detection of Coxiella burnetii genome by next-generation metagenomic sequencing. Diagn Microbiol Infect Dis 2024; 110:116434. [PMID: 39111107 DOI: 10.1016/j.diagmicrobio.2024.116434] [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: 04/10/2024] [Revised: 06/04/2024] [Accepted: 07/09/2024] [Indexed: 08/24/2024]
Abstract
The case presents a 47-year-old man with sudden abdominal pain and fever, but the cause was uncertain. Through metagenomic next-generation sequencing (mNGS) and detecting Q fever antibodies in serum, along with the patient's clinical and epidemiological history, a precise diagnosis was made, enabling timely and proper treatment.
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Affiliation(s)
- Xianglin Wu
- Department of Laboratory Medicine, Shenzhen Guangming District People's Hospital, Shenzhen, Guangdong, China
| | - Aohong Xu
- Center for Medical Experiments (CME), Shenzhen Guangming District People's Hospital, Shenzhen, 518106, Guangdong, China
| | - Feng Tian
- Department of Laboratory Medicine, Shenzhen Guangming District People's Hospital, Shenzhen, Guangdong, China
| | - Juhong Yang
- Center for Medical Experiments (CME), Shenzhen Guangming District People's Hospital, Shenzhen, 518106, Guangdong, China
| | - Liekun Lin
- Center for Medical Experiments (CME), Shenzhen Guangming District People's Hospital, Shenzhen, 518106, Guangdong, China
| | - Mingzhu Zhai
- Center for Medical Experiments (CME), Shenzhen Guangming District People's Hospital, Shenzhen, 518106, Guangdong, China
| | - Benqing Wu
- Center for Medical Experiments (CME), Shenzhen Guangming District People's Hospital, Shenzhen, 518106, Guangdong, China
| | - Yi Zheng
- Center for Medical Experiments (CME), Shenzhen Guangming District People's Hospital, Shenzhen, 518106, Guangdong, China.
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9
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Verhoeven JE, Wolkowitz OM, Barr Satz I, Conklin Q, Lamers F, Lavebratt C, Lin J, Lindqvist D, Mayer SE, Melas PA, Milaneschi Y, Picard M, Rampersaud R, Rasgon N, Ridout K, Söderberg Veibäck G, Trumpff C, Tyrka AR, Watson K, Wu GWY, Yang R, Zannas AS, Han LKM, Månsson KNT. The researcher's guide to selecting biomarkers in mental health studies. Bioessays 2024; 46:e2300246. [PMID: 39258367 DOI: 10.1002/bies.202300246] [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: 12/25/2023] [Revised: 07/01/2024] [Accepted: 07/03/2024] [Indexed: 09/12/2024]
Abstract
Clinical mental health researchers may understandably struggle with how to incorporate biological assessments in clinical research. The options are numerous and are described in a vast and complex body of literature. Here we provide guidelines to assist mental health researchers seeking to include biological measures in their studies. Apart from a focus on behavioral outcomes as measured via interviews or questionnaires, we advocate for a focus on biological pathways in clinical trials and epidemiological studies that may help clarify pathophysiology and mechanisms of action, delineate biological subgroups of participants, mediate treatment effects, and inform personalized treatment strategies. With this paper we aim to bridge the gap between clinical and biological mental health research by (1) discussing the clinical relevance, measurement reliability, and feasibility of relevant peripheral biomarkers; (2) addressing five types of biological tissues, namely blood, saliva, urine, stool and hair; and (3) providing information on how to control sources of measurement variability.
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Affiliation(s)
- Josine E Verhoeven
- Department of Psychiatry, Amsterdam UMC location Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
- Amsterdam Public Health, Mental Health program, Amsterdam, The Netherlands
| | - Owen M Wolkowitz
- Department of Psychiatry and Behavioral Sciences, and Weill Institute for Neurosciences, University of California San Francisco School of Medicine, San Francisco, California, USA
| | - Isaac Barr Satz
- Department of Psychiatry & Behavioral Sciences, Stanford University School of Medicine, Stanford, California, USA
| | - Quinn Conklin
- Center for Mind and Brain, University of California, Davis, California, USA
- Center for Health and Community, University of California, San Francisco, California, USA
| | - Femke Lamers
- Department of Psychiatry, Amsterdam UMC location Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
- Amsterdam Public Health, Mental Health program, Amsterdam, The Netherlands
| | - Catharina Lavebratt
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
- Center for Molecular Medicine, L8:00, Karolinska University Hospital, Stockholm, Sweden
| | - Jue Lin
- Department of Biochemistry and Biophysics, University of California, San Francisco, California, USA
| | - Daniel Lindqvist
- Unit for Biological and Precision Psychiatry, Department of Clinical Sciences Lund, Lund University, Lund, Sweden
- Office for Psychiatry and Habilitation, Psychiatry Research Skåne, Region Skåne, Lund, Sweden
| | - Stefanie E Mayer
- Department of Psychiatry and Behavioral Sciences, and Weill Institute for Neurosciences, University of California San Francisco School of Medicine, San Francisco, California, USA
| | - Philippe A Melas
- Center for Psychiatry Research, Department of Clinical Neuroscience, Karolinska Institutet, Stockholm, Sweden
| | - Yuri Milaneschi
- Department of Psychiatry, Amsterdam UMC location Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
- Amsterdam Public Health, Mental Health program, Amsterdam, The Netherlands
- Amsterdam Neuroscience, Complex Trait Genetics, Amsterdam, The Netherlands
| | - Martin Picard
- Department of Psychiatry, Division of Behavioral Medicine, College of Physicians and Surgeons, Columbia University Irving Medical Center, New York, USA
- Department of Neurology, H. Houston Merritt Center, Columbia Translational Neuroscience Initiative, College of Physicians and Surgeons, Columbia University Irving Medical Center, New York, USA
- New York State Psychiatric Institute, New York, USA
- Robert N Butler Columbia Aging Center, Columbia University Mailman School of Public Health, New York, New York, USA
| | - Ryan Rampersaud
- Department of Psychiatry and Behavioral Sciences, and Weill Institute for Neurosciences, University of California San Francisco School of Medicine, San Francisco, California, USA
| | - Natalie Rasgon
- Department of Psychiatry & Behavioral Sciences, Stanford University School of Medicine, Stanford, California, USA
| | - Kathryn Ridout
- Division of Research, Kaiser Permanente Northern California, Oakland, California, USA
- Department of Psychiatry, Kaiser Permanente, Santa Rosa Medical Center, Santa Rosa, California, USA
| | - Gustav Söderberg Veibäck
- Unit for Biological and Precision Psychiatry, Department of Clinical Sciences Lund, Lund University, Lund, Sweden
- Office for Psychiatry and Habilitation, Psychiatry Research Skåne, Region Skåne, Lund, Sweden
| | - Caroline Trumpff
- Department of Psychiatry, Division of Behavioral Medicine, College of Physicians and Surgeons, Columbia University Irving Medical Center, New York, USA
| | - Audrey R Tyrka
- Department of Psychiatry and Human Behavior, Alpert Medical School of Brown University, Providence, Rhode Island, USA
| | - Kathleen Watson
- Department of Psychiatry & Behavioral Sciences, Stanford University School of Medicine, Stanford, California, USA
| | - Gwyneth Winnie Y Wu
- Department of Psychiatry and Behavioral Sciences, and Weill Institute for Neurosciences, University of California San Francisco School of Medicine, San Francisco, California, USA
| | - Ruoting Yang
- Medical Readiness Systems Biology, Walter Reed Army Institute of Research, Silver Spring, Maryland, USA
| | - Anthony S Zannas
- Department of Psychiatry, University of North Carolina, Chapel Hill, North Carolina, USA
- Department of Genetics, University of North Carolina, Chapel Hill, North Carolina, USA
| | - Laura K M Han
- Department of Psychiatry, Amsterdam UMC location Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
- Centre for Youth Mental Health, The University of Melbourne, Parkville, Victoria, Australia
- Orygen, Parkville, Victoria, Australia
| | - Kristoffer N T Månsson
- Center for Psychiatry Research, Department of Clinical Neuroscience, Karolinska Institutet, Stockholm, Sweden
- Department of Clinical Psychology and Psychotherapy, Babeș-Bolyai University, Cluj-Napoca, Romania
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Gong H, Cai G, Chen C, Chen F, Cai C. Construction of a monoclonal molecular imprinted sensor with high affinity for specific recognition of influenza a virus subtype. Talanta 2024; 278:126568. [PMID: 39018763 DOI: 10.1016/j.talanta.2024.126568] [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: 04/13/2024] [Revised: 06/26/2024] [Accepted: 07/12/2024] [Indexed: 07/19/2024]
Abstract
Although molecular imprinting technology has been widely used in the construction of virus sensors, it is still a great challenge to identify subtypes viruses specifically because of their high similarity in morphology, size and structure. Here, a monoclonal molecular imprinted polymers (MIPs) sensor for recognition of H5N1 is constructed to permit the accurate distinguishing of H5N1 from other influenza A virus (IAV) subtypes. Firstly, H5N1 are immobilized on magnetic microspheres to produce H5N1-MagNPs, then the high affinity nanogel H5N1-MIPs is prepared by solid phase imprinting technique. When H5N1-MIPs is combined with MagNP-H5N1, different concentrations of H5N1 are added for competitive substitution. The quantitative detection of H5N1 is realized by the change of fluorescence intensity of supernatant. As expected, the constructed sensor shows satisfactory selectivity, and can identify the target virus from highly similar IAV subtypes, such as H1N1, H7N9 and H9N2. The sensor was highly sensitive, with a detection limit of 0.58 fM, and a selectivity factor that is comparable to that of other small MIPs sensors is achieved. In addition, the proposed sensor is cheap, with a cost of only RMB 0.08 yuan. The proposed monoclonal sensor provides a new method for the specific recognition of designated virus subtype, which is expected to be used for large-scale screening and accurate treatment of infected people.
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Affiliation(s)
- Hang Gong
- College of Chemistry and Chemical Engineering, Yunnan Normal University, Kunming, 650500, China; The Key Laboratory for Green Organic Synthesis and Application of Hunan Province, College of Chemistry, Xiangtan University, Xiangtan, 411105, China.
| | - Ganping Cai
- The Key Laboratory for Green Organic Synthesis and Application of Hunan Province, College of Chemistry, Xiangtan University, Xiangtan, 411105, China
| | - Chunyan Chen
- The Key Laboratory for Green Organic Synthesis and Application of Hunan Province, College of Chemistry, Xiangtan University, Xiangtan, 411105, China
| | - Feng Chen
- The Key Laboratory for Green Organic Synthesis and Application of Hunan Province, College of Chemistry, Xiangtan University, Xiangtan, 411105, China
| | - Changqun Cai
- The Key Laboratory for Green Organic Synthesis and Application of Hunan Province, College of Chemistry, Xiangtan University, Xiangtan, 411105, China.
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Zhang D, Yang A, Sheng K, Fang S, Zhou L. Application of the second-generation sequencing technology of metagenomics in the detection of pathogens in respiratory patients. J Microbiol Methods 2024; 225:107021. [PMID: 39147284 DOI: 10.1016/j.mimet.2024.107021] [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: 03/29/2024] [Revised: 08/11/2024] [Accepted: 08/12/2024] [Indexed: 08/17/2024]
Abstract
OBJECTIVE To explore the application value of the second-generation metagenomic next-generation sequencing (mNGS) in the detection of pathogens in patients with pulmonary infection. METHODS We conducted a retrospective analysis of 65 pulmonary infection cases treated at our institution and the Fifth People's Hospital of Shanghai between January 2021 and May 2023. All subjects were subjected to mNGS, targeted next-generation sequencing (tNGS), and conventional microbiological culture. A comparative analysis was performed to evaluate the diversity and quantity of pathogens identified by these methodologies and to appraise their respective diagnostic capabilities in pulmonary infection diagnostics. RESULTS The mNGS successfully identified etiological agents in 60 of the 65 cases, compared to tNGS, which yielded positive results in 42 cases, and conventional laboratory cultures, which detected pathogens in 24 cases. At the bacterial genus level, mNGS discerned 9 genera, 11 species, and 92 isolates of pathogenic bacteria, whereas tNGS identified 8 genera, 8 species, and 71 isolates. Conventional methods were less sensitive, detecting only 6 genera, 7 species, and 33 isolates. In terms of fungal detection, mNGS identified 4 fungal species, tNGS detected 4 isolates of the Candida genus, and conventional methods identified 2 isolates of the same genus. Viral detection at the species level revealed 10 species and 46 isolates by mNGS, whereas tNGS detected only 3 species and 7 isolates. The area under the receiver operating characteristic curve (AUC) with 95% confidence intervals for diagnosing pulmonary infections was 0.818 (0.671 to 0.966) for mNGS, 0.668 (0.475 to 0.860) for tNGS, and 0.721 (0.545 to 0.897) for conventional culture.The mNGS demonstrates superior diagnostic efficacy and pathogen detection breadth in critically ill patients with respiratory infections, offering a significant advantage by reducing the time to diagnosis. The enhanced sensitivity and comprehensive pathogen profiling of mNGS underscore its potential as a leading diagnostic tool in clinical microbiology.
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Affiliation(s)
- Danfeng Zhang
- Department of Geriatrics, Tongren Hospital, Shanghai Jiao Tong University School of Medicine, 1111 XianXia Road, Shanghai 200336, China
| | - Ali Yang
- Department of Geriatric, Shanghai YangZhi Rehabilitation Hospital (Shanghai Sunshine Rehabilitation Center), No.2209 GuangXing Road, Shanghai 201600, China
| | - Kai Sheng
- Department of Geriatrics, Tongren Hospital, Shanghai Jiao Tong University School of Medicine, 1111 XianXia Road, Shanghai 200336, China
| | - Shuyu Fang
- Department of Geriatrics, Tongren Hospital, Shanghai Jiao Tong University School of Medicine, 1111 XianXia Road, Shanghai 200336, China.
| | - Liang Zhou
- Department of Neurosurgery, Shanghai Fifth People's Hospital, Fudan University, No.128 RuiLi Road, Shanghai 200240, China.
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12
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Wang K, Guo W, Zhu J, Guo Y, Gao W. Clinical Characteristics and Risk Factors of Sepsis in Patients with Liver Abscess. Br J Hosp Med (Lond) 2024; 85:1-15. [PMID: 39347671 DOI: 10.12968/hmed.2024.0206] [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] [Indexed: 10/01/2024]
Abstract
Aims/Background Liver abscess (LA) is a serious medical condition that predisposes patients to sepsis. However, predicting sepsis in LA patients has rarely been explored. This study employed univariate and multivariate logistic regression analyses to identify independent risk factors for sepsis, which would provide guidance for clinical diagnosis and treatment. Methods A total of 122 patients with LA treated in Peking University People's Hospital from 1 January 2016 to 31 October 2022 were recruited. Among the cases, 35 patients had sepsis (sepsis group) while the remaining 87 did not have sepsis (non-sepsis group). Clinical data were collected for all enrolled cases. Univariate analysis was performed to identify potential predictors, which were tested in multivariable logistic analysis to pinpoint the independent risk factors for sepsis in LA patients; these findings were utilized to develop a prediction model. Receiver operating characteristic (ROC) curve was used to evaluate the diagnostic efficacy of the prediction model. Informed consent to participate was obtained from the patients or their relatives. Results The incidence of shivering in the sepsis group was significantly higher than that in the non-sepsis group (p < 0.05). Through the univariate analysis, it was found that the reduction in platelet count and prothrombin time activity and the elevation of glycosylated hemoglobin (HbAlc) and procalcitonin (PCT) were more significant in the sepsis group than in the non-sepsis group (p < 0.05). Multivariate logistic regression analysis revealed that PCT and HbAlc were independent risk predictors of sepsis in LA patients within the derivation cohort (p < 0.05). Conclusion Elevated levels of HbAlc and PCT were independent risk factors for sepsis associated with LA. Patients with LA exhibiting elevated PCT levels demonstrated a 21% increased susceptibility to sepsis, and those with elevated HbAlc levels showed a 38% heightened risk for sepsis.
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Affiliation(s)
- Kai Wang
- Department of Emergency, Peking University People's Hospital, Beijing, China
| | - Wei Guo
- Department of Emergency, Peking University People's Hospital, Beijing, China
| | - Jihong Zhu
- Department of Emergency, Peking University People's Hospital, Beijing, China
| | - Yang Guo
- Department of Emergency, Peking University People's Hospital, Beijing, China
| | - Weibo Gao
- Department of Emergency, Peking University People's Hospital, Beijing, China
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13
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Smart K, Pieper JB, Viall AK, Noxon JO, Berger DJ. Comparison of commercial next-generation sequencing assays to conventional culture methods for bacterial identification and antimicrobial susceptibility of samples obtained from clinical cases of canine superficial bacterial folliculitis. Vet Dermatol 2024. [PMID: 39323044 DOI: 10.1111/vde.13299] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2024] [Revised: 04/19/2024] [Accepted: 09/10/2024] [Indexed: 09/27/2024]
Abstract
BACKGROUND Bacterial identification and antimicrobial susceptibility testing is an important step in timely therapeutic decisions for canine superficial bacterial folliculitis (SBF), commonly caused by Staphylococcus pseudintermedius. Next-generation sequencing (NGS) offers the appeal of potentially expedited results with complete detection of bacterial organisms and associated resistance genes compared to culture. Limited studies exist comparing the two methodologies for clinical samples. HYPOTHESIS/OBJECTIVES To compare and contrast genotypic and phenotypic methods for bacterial identification and antimicrobial susceptibility from cases of canine SBF. ANIMALS Twenty-four client-owned dogs with lesions consistent with SBF were enrolled. MATERIALS AND METHODS A sterile culturette swab was used to sample dogs with SBF lesions. The swab was rinsed in 0.9 mL of sterile phosphate-buffered saline and vortexed to create a homogenous solution. Two swabs for NGS laboratories (Labs) and one swab for culture (Culture Lab) were randomly sampled from this solution and submitted for bacterial identification and antimicrobial susceptibility. RESULTS No statistical difference regarding turnaround time for NGS Labs compared to Culture Lab was found. NGS Lab 1 identified more organisms than NGS Lab 2 and Culture Lab, which were both statistically significant. There was no statistical difference in detection frequency for Staphylococcus spp. among all laboratories. There was poor agreement for the presence of meticillin resistance and most antimicrobials among all laboratories. CONCLUSIONS AND CLINICAL RELEVANCE Utilisation of NGS as a replacement for traditional culture when sampling canine SBF lesions is not supported at this time.
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Affiliation(s)
- Kimberly Smart
- Department of Veterinary Clinical Sciences, Iowa State University, Ames, Iowa, USA
| | - Jason B Pieper
- Department of Veterinary Clinical Sciences, Iowa State University, Ames, Iowa, USA
| | - Austin K Viall
- Department of Pathology, Microbiology, and Immunology, University of California Davis, Davis, California, USA
| | - James O Noxon
- Department of Veterinary Clinical Sciences, Iowa State University, Ames, Iowa, USA
| | - Darren J Berger
- Department of Veterinary Clinical Sciences, Iowa State University, Ames, Iowa, USA
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He S, Liu H, Hu X, Zhao J, Liang J, Zhang X, Chen J, Zeng H, Sun G. Exploring the clinical and diagnostic value of metagenomic next-generation sequencing for urinary tract infection: a systematic review and meta-analysis. BMC Infect Dis 2024; 24:1000. [PMID: 39294577 PMCID: PMC11412013 DOI: 10.1186/s12879-024-09914-9] [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: 05/03/2024] [Accepted: 09/10/2024] [Indexed: 09/20/2024] Open
Abstract
BACKGROUND A new pathogen detection tool, metagenomic next-generation sequencing (mNGS), has been widely used for infection diagnosis, but the clinical and diagnostic value of mNGS in urinary tract infection (UTI) remains inconclusive. This systematic review with meta-analysis aimed to investigate the efficacy of mNGS in treating UTIs. METHODS A comprehensive literature search was performed in PubMed, Web of Science, Embase, and the Cochrane Library, and eligible studies were selected based on the predetermined criteria. The quality of the included studies was assessed via the Quality Assessment of Diagnostic Accuracy Studies-2 (QUADAS-2) tool, and the certainty of evidence (CoE) was measured by the Grading of Recommendations, Assessment, Development, and Evaluations (GRADE) score. Then, the positive detection rate (PDR), pooled sensitivity, specificity, positive likelihood ratio (PLR), negative likelihood ratio (NLR), diagnostic odds ratio (DOR), and area under the curve of the summary receiver operating characteristic curve (AUROC) was estimated in Review Manager, Stata, and MetaDisc. Subgroup analysis, meta-regression, and sensitivity analysis were performed to reveal the potential factors that influence internal heterogeneity. RESULTS A total of 17 studies were selected for further analysis. The PDR of mNGS was markedly greater than that of culture (odds ratio (OR) = 2.87, 95% confidence interval [CI]: 1.72-4.81, p < 0.001, I2 = 90%). The GRADE score presented a very low CoE. Then, the pooled sensitivity was 0.89 (95% CI: 0.86-0.91, I2 = 39.65%, p = 0.06), and the pooled specificity was 0.75 (95% CI: 0.51-0.90, I2 = 88.64%, p < 0.001). The AUROC of the studies analyzed was 0.89 (95% CI: 0.86-0.92). The GRADE score indicated a low CoE. CONCLUSION The current evidence shows that mNGS has favorable diagnostic performance for UTIs. More high-quality prospective randomized controlled trials (RCTs) are expected to verify these findings and provide more information about mNGS in UTI treatment and prognosis.
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Affiliation(s)
- Sike He
- Department of Urology, Institute of Urology, West China Hospital, Sichuan University, Chengdu, China
| | - Haolin Liu
- Department of Urology, Institute of Urology, West China Hospital, Sichuan University, Chengdu, China
| | - Xu Hu
- Department of Urology, Institute of Urology, West China Hospital, Sichuan University, Chengdu, China
| | - Jinge Zhao
- Department of Urology, Institute of Urology, West China Hospital, Sichuan University, Chengdu, China
| | - Jiayu Liang
- Department of Urology, Institute of Urology, West China Hospital, Sichuan University, Chengdu, China
| | - Xingming Zhang
- Department of Urology, Institute of Urology, West China Hospital, Sichuan University, Chengdu, China
| | - Junru Chen
- Department of Urology, Institute of Urology, West China Hospital, Sichuan University, Chengdu, China
| | - Hao Zeng
- Department of Urology, Institute of Urology, West China Hospital, Sichuan University, Chengdu, China.
| | - Guangxi Sun
- Department of Urology, Institute of Urology, West China Hospital, Sichuan University, Chengdu, China.
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Lou H, Wang X, Jiang Q, Li X, Yao Y, Chen Q, Chen L, Zhang S, Yu Y, Liu C, Zhou H. Clinical evaluation of a highly multiplexed CRISPR-based diagnostic assay for diagnosing lower respiratory tract infection: a prospective cohort study. Infect Dis (Lond) 2024:1-11. [PMID: 39264585 DOI: 10.1080/23744235.2024.2402921] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/24/2024] [Revised: 08/28/2024] [Accepted: 09/06/2024] [Indexed: 09/13/2024] Open
Abstract
OBJECTIVE Accurate and rapid identification of causative pathogens is essential to guide the clinical management of lower respiratory tract infections (LRTIs). Here we conducted a single-centre prospective study in 284 patients suspected of lower respiratory tract infections to evaluate the utility of a nucleic acid test based on highly multiplexed polymerase chain reaction (PCR) and CRISPR-Cas12a. METHODS We determined the analytical and diagnostic performance of the CRISPR assay using a combination of reference standards, including conventional microbiological tests (CMTs), metagenomic Next-Generation Sequencing (mNGS), and clinical adjudication by a panel of experts on infectious diseases and microbiology. RESULTS The CRISPR assay showed a higher detection rate (63.0%) than conventional microbiological tests (38.4%) and was lower than metagenomic Next-Generation Sequencing (72.9%). In detecting polymicrobial infections, the positivity rate of the CRISPR assay (19.4%) was higher than conventional microbiological tests (3.5%) and lower than metagenomic Next-Generation Sequencing (28.9%). The overall diagnostic sensitivity of the CRISPR assay (67.8%) was higher than conventional microbiological tests (41.8%), and lower than metagenomic Next-Generation Sequencing (93.2%). CONCLUSIONS Considering the low cost, ease of operation, short turnaround time, and broad range of pathogens detected in a single test, the CRISPR assay has the potential to be implemented as a screening tool for the aetiological diagnosis of lower respiratory tract infections patients, especially in cases where atypical bacteria or coinfections are suspected.
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Affiliation(s)
- Hui Lou
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Xiaojia Wang
- Medical Department, Hangzhou Matridx Biotechnology Co., Ltd, Hangzhou, Zhejiang, China
| | - Qiuting Jiang
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Xi Li
- Department of Clinical Laboratory, Laboratory Medicine Center, Zhejiang Provincial People's Hospital, Affiliated People's Hospital, Hangzhou Medical College, Hangzhou, Zhejiang, China
| | - Yake Yao
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Qi Chen
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Linxing Chen
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Shanshan Zhang
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Yunsong Yu
- Department of Infectious Disease, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Chao Liu
- Medical Department, Hangzhou Matridx Biotechnology Co., Ltd, Hangzhou, Zhejiang, China
| | - Hua Zhou
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
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Liu H, Ran Q, Ma J, Zhang J, Tan N, Xi L, Li X, Zhang J, Lu S. Retrospective clinical and microbiologic analysis of metagenomic next-generation sequencing in the microbiological diagnosis of cutaneous infectious granulomas. Ann Clin Microbiol Antimicrob 2024; 23:84. [PMID: 39267031 PMCID: PMC11395180 DOI: 10.1186/s12941-024-00744-w] [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: 12/03/2023] [Accepted: 09/05/2024] [Indexed: 09/14/2024] Open
Abstract
BACKGROUND Cutaneous infectious granulomas (CIG) are localized and chronic skin infection caused by a variety of pathogens such as protozoans, bacteria, worms, viruses and fungi. The diagnosis of CIG is difficult because microbiological examination shows low sensitivity and the histomorphological findings of CIG caused by different pathogens are commonly difficult to be distinguished. OBJECTIVE The objective of this study is to explore the application of mNGS in tissue sample testing for CIG cases, and to compare mNGS with traditional microbiological methods by evaluating sensitivity and specificity. METHODS We conducted a retrospective study at the Department of Dermatology of Sun Yat-sen Memorial Hospital, Sun Yat-sen University from January 1st, 2020, to May 31st, 2024. Specimens from CIG patients with a clinical presentation of cutaneous infection that was supported by histological examination were retrospectively enrolled. Specimens were delivered to be tested for microbiological examinations and mNGS. RESULTS Our data show that mNGS detected Non-tuberculosis mycobacteria, Mycobacterium tuberculosis, fungi and bacteria in CIG. Compared to culture, mNGS showed a higher positive rate (80.77% vs. 57.7%) with high sensitivity rate (100%) and negative predictive value (100%). In addition, mNGS can detect more pathogens in one sample and can be used to detect variable samples including the samples of paraffin-embedded tissue with shorter detective time. Of the 21 patients who showed clinical improvement within a 30-day follow-up, eighteen had their treatments adjusted, including fifteen who continued treatment based on the results of mNGS. CONCLUSIONS mNGS could provide a potentially rapid and effective alternative detection method for diagnosis of cutaneous infectious granulomas and mNGS results may affect the clinical prognosis resulting from enabling the patients to initiate timely treatment.
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Affiliation(s)
- Hsingmei Liu
- Department of Dermatology and Venereology, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, #107 Yanjiang West Rd., Guangzhou, 510120, Guangdong, China
| | - Qiao Ran
- Department of Dermatology and Venereology, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, #107 Yanjiang West Rd., Guangzhou, 510120, Guangdong, China
- The Third People's Hospital of Zhuhai, Hezheng Road, Xiangzhou District, Zhuhai City, 519075, Guangdong, China
| | - Jianchi Ma
- Department of Dermatology and Venereology, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, #107 Yanjiang West Rd., Guangzhou, 510120, Guangdong, China
| | - Jing Zhang
- Department of Dermatology and Venereology, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, #107 Yanjiang West Rd., Guangzhou, 510120, Guangdong, China
| | - Ni Tan
- Department of Dermatology and Venereology, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, #107 Yanjiang West Rd., Guangzhou, 510120, Guangdong, China
- Cellular and Molecular Diagnostics Center, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, 510120, Guangdong, China
| | - Liyan Xi
- Department of Dermatology and Venereology, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, #107 Yanjiang West Rd., Guangzhou, 510120, Guangdong, China
| | - Xiqing Li
- Department of Dermatology and Venereology, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, #107 Yanjiang West Rd., Guangzhou, 510120, Guangdong, China
| | - Junmin Zhang
- Department of Dermatology and Venereology, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, #107 Yanjiang West Rd., Guangzhou, 510120, Guangdong, China
| | - Sha Lu
- Department of Dermatology and Venereology, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, #107 Yanjiang West Rd., Guangzhou, 510120, Guangdong, China.
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17
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Dong H, Qin B, Zhang H, Lei L, Wu S. Current Treatment Methods for Charcot-Marie-Tooth Diseases. Biomolecules 2024; 14:1138. [PMID: 39334903 PMCID: PMC11430469 DOI: 10.3390/biom14091138] [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: 07/21/2024] [Revised: 08/21/2024] [Accepted: 08/29/2024] [Indexed: 09/30/2024] Open
Abstract
Charcot-Marie-Tooth (CMT) disease, the most common inherited neuromuscular disorder, exhibits a wide phenotypic range, genetic heterogeneity, and a variable disease course. The diverse molecular genetic mechanisms of CMT were discovered over the past three decades with the development of molecular biology and gene sequencing technologies. These methods have brought new options for CMT reclassification and led to an exciting era of treatment target discovery for this incurable disease. Currently, there are no approved disease management methods that can fully cure patients with CMT, and rehabilitation, orthotics, and surgery are the only available treatments to ameliorate symptoms. Considerable research attention has been given to disease-modifying therapies, including gene silencing, gene addition, and gene editing, but most treatments that reach clinical trials are drug treatments, while currently, only gene therapies for CMT2S have reached the clinical trial stage. In this review, we highlight the pathogenic mechanisms and therapeutic investigations of different subtypes of CMT, and promising therapeutic approaches are also discussed.
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Affiliation(s)
- Hongxian Dong
- Department of Orthopedic Surgery and Orthopedic Research Institute, West China Hospital, Sichuan University, Chengdu 610041, China; (H.D.); (B.Q.); (H.Z.)
| | - Boquan Qin
- Department of Orthopedic Surgery and Orthopedic Research Institute, West China Hospital, Sichuan University, Chengdu 610041, China; (H.D.); (B.Q.); (H.Z.)
| | - Hui Zhang
- Department of Orthopedic Surgery and Orthopedic Research Institute, West China Hospital, Sichuan University, Chengdu 610041, China; (H.D.); (B.Q.); (H.Z.)
| | - Lei Lei
- State Key Laboratory of Oral Diseases & National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu 610041, China
| | - Shizhou Wu
- Department of Orthopedic Surgery and Orthopedic Research Institute, West China Hospital, Sichuan University, Chengdu 610041, China; (H.D.); (B.Q.); (H.Z.)
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18
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Liu J, Bao C, Zhang J, Han Z, Fang H, Lu H. Artificial intelligence with mass spectrometry-based multimodal molecular profiling methods for advancing therapeutic discovery of infectious diseases. Pharmacol Ther 2024; 263:108712. [PMID: 39241918 DOI: 10.1016/j.pharmthera.2024.108712] [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: 05/31/2024] [Revised: 07/22/2024] [Accepted: 09/03/2024] [Indexed: 09/09/2024]
Abstract
Infectious diseases, driven by a diverse array of pathogens, can swiftly undermine public health systems. Accurate diagnosis and treatment of infectious diseases-centered around the identification of biomarkers and the elucidation of disease mechanisms-are in dire need of more versatile and practical analytical approaches. Mass spectrometry (MS)-based molecular profiling methods can deliver a wealth of information on a range of functional molecules, including nucleic acids, proteins, and metabolites. While MS-driven omics analyses can yield vast datasets, the sheer complexity and multi-dimensionality of MS data can significantly hinder the identification and characterization of functional molecules within specific biological processes and events. Artificial intelligence (AI) emerges as a potent complementary tool that can substantially enhance the processing and interpretation of MS data. AI applications in this context lead to the reduction of spurious signals, the improvement of precision, the creation of standardized analytical frameworks, and the increase of data integration efficiency. This critical review emphasizes the pivotal roles of MS based omics strategies in the discovery of biomarkers and the clarification of infectious diseases. Additionally, the review underscores the transformative ability of AI techniques to enhance the utility of MS-based molecular profiling in the field of infectious diseases by refining the quality and practicality of data produced from omics analyses. In conclusion, we advocate for a forward-looking strategy that integrates AI with MS-based molecular profiling. This integration aims to transform the analytical landscape and the performance of biological molecule characterization, potentially down to the single-cell level. Such advancements are anticipated to propel the development of AI-driven predictive models, thus improving the monitoring of diagnostics and therapeutic discovery for the ongoing challenge related to infectious diseases.
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Affiliation(s)
- Jingjing Liu
- School of Chinese Medicine, Hong Kong Traditional Chinese Medicine Phenome Research Center, State Key Laboratory of Environmental and Biological Analysis, Hong Kong Baptist University, Hong Kong 999077, China
| | - Chaohui Bao
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Jiaxin Zhang
- School of Chinese Medicine, Hong Kong Traditional Chinese Medicine Phenome Research Center, State Key Laboratory of Environmental and Biological Analysis, Hong Kong Baptist University, Hong Kong 999077, China
| | - Zeguang Han
- Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, Shanghai 200240, China.
| | - Hai Fang
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China.
| | - Haitao Lu
- School of Chinese Medicine, Hong Kong Traditional Chinese Medicine Phenome Research Center, State Key Laboratory of Environmental and Biological Analysis, Hong Kong Baptist University, Hong Kong 999077, China; Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China; Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, Shanghai 200240, China.
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Xu RF, Gao WN, Hu TL, Wang XF, Zhao JR, Meng Y. Pathogenic microorganism DNA high-throughput genetic sequencing to diagnose peritoneal dialysis-associated peritonitis due to Mycobacterium tuberculosis infection. BMC Nephrol 2024; 25:290. [PMID: 39227867 PMCID: PMC11373123 DOI: 10.1186/s12882-024-03727-3] [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: 10/27/2023] [Accepted: 08/23/2024] [Indexed: 09/05/2024] Open
Abstract
Peritoneal dialysis-associated peritonitis is a serious complication of peritoneal dialysis, and the prevention and treatment of this condition are important for improving the long-term survival and quality of life of patients. However, peritoneal dialysis-associated peritonitis due to Mycobacterium tuberculosis infection is relatively rare and not easily diagnosed. Here, we present a case of peritoneal dialysis-associated peritonitis caused by Mycobacterium tuberculosis identified by pathogenic microbial DNA high-throughput genetic sequencing. This case demonstrates that pathogenic microbial DNA high-throughput genetic sequencing could be used to improve the detection rate of pathogenic microorganisms in patients with complex conditions, thereby allowing for earlier initiation of treatment.
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Affiliation(s)
- Rui-Feng Xu
- Department of Nephrology, The Affiliated Hospital of Inner Mongolia Medical University, Hohhot, 010050, Inner Mongolia, PR China
| | - Wu-Niri Gao
- Department of Nephrology, The Affiliated Hospital of Inner Mongolia Medical University, Hohhot, 010050, Inner Mongolia, PR China
| | - Ta-la Hu
- Department of Nephrology, The Affiliated Hospital of Inner Mongolia Medical University, Hohhot, 010050, Inner Mongolia, PR China
| | - Xi-Feng Wang
- Department of Nephrology, No. 2 Hospital of Hohhot, Hohhot, PR China
| | - Jian-Rong Zhao
- Department of Nephrology, The Affiliated Hospital of Inner Mongolia Medical University, Hohhot, 010050, Inner Mongolia, PR China
| | - Yan Meng
- Department of Nephrology, The Affiliated Hospital of Inner Mongolia Medical University, Hohhot, 010050, Inner Mongolia, PR China.
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20
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Qin W, Guo T, You T, Tian R, Cui X, Wang P. Metagenomic next generation sequencing of bronchoalveolar lavage fluids for the identification of pathogens in patients with pulmonary infection: A retrospective study. Diagn Microbiol Infect Dis 2024; 110:116402. [PMID: 38878340 DOI: 10.1016/j.diagmicrobio.2024.116402] [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: 04/14/2024] [Revised: 06/10/2024] [Accepted: 06/11/2024] [Indexed: 07/30/2024]
Abstract
Due to the limitations of traditional laboratory methods (TMs), identification of causative pathogens of numerous pulmonary infections (PIs) remains difficult. This study evaluated the value of metagenomic next generation sequencing (mNGS) in the identification of various respiratory pathogens. A total of 207 patients with TMs and mNGS data were collected for this retrospective study. TMs included sputum culture, blood, and bronchoalveolar lavage fluid (BALF) analysis, or polymerase chain reaction analysis of throat swabs. Otherwise, BALF was collected and analyzed using mNGS. For bacterial pathogens, sensitivities of mNGS as compared to TMs were 76.74 % and 58.14 % (P=0.012). For fungal pathogens, the detection rate of mNGS sensitivity was higher as compared to that of TMs (93.68 % vs 22.11 %; P<0.001). The positive predictive value and negative predictive value were also greater for mNGS. Use of mNGS for BALF analysis offers good specificity and thus facilitates to the clinical diagnosis of PIs.
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Affiliation(s)
- Wenwen Qin
- Department of Respiratory Medicine, The Fourth Hospital of Hebei Medical University, Shijiazhuang, 050011, China
| | - Tai Guo
- Department of Respiratory Medicine, The Fourth Hospital of Hebei Medical University, Shijiazhuang, 050011, China
| | - Tiebin You
- Department of Respiratory Medicine, The Fourth Hospital of Hebei Medical University, Shijiazhuang, 050011, China
| | - Ruixin Tian
- Department of Respiratory Medicine, The Fourth Hospital of Hebei Medical University, Shijiazhuang, 050011, China
| | - Xiaoman Cui
- Department of Respiratory Medicine, The Fourth Hospital of Hebei Medical University, Shijiazhuang, 050011, China
| | - Ping Wang
- Department of Respiratory Medicine, The Fourth Hospital of Hebei Medical University, Shijiazhuang, 050011, China.
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Yeh TK, Huang YT, Liu PY, Mao YC, Lai CS, Lai KL, Tseng CH, Liu CW, Huang WH, Huang HP, Lin KP. Pathogenic Detection by Metagenomic Next-generation Sequencing in Skin and Soft Tissue Infection. In Vivo 2024; 38:2364-2373. [PMID: 39187328 PMCID: PMC11363772 DOI: 10.21873/invivo.13703] [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: 05/27/2024] [Revised: 07/02/2024] [Accepted: 07/03/2024] [Indexed: 08/28/2024]
Abstract
BACKGROUND/AIM Skin and soft tissue infections (SSTIs) can be life-threatening, but the conventional bacterial cultures have low sensitivity and are time-consuming. Metagenomic next-generation sequencing (mNGS) is widely used as a diagnostic tool for detecting pathogens from infection sites. However, the use of mNGS for pathogen detection in SSTIs and related research is still relatively limited. PATIENTS AND METHODS From January 2020 to October 2021, 19 SSTI samples from 16 patients were collected in a single center (Taichung Veterans General Hospital, Taichung, Taiwan). The clinical samples were simultaneously subjected to mNGS and conventional bacterial culture methods to detect pathogens. Clinical characteristics were prospectively collected through electronic chart review. The microbiological findings from conventional bacterial culture and mNGS were analyzed and compared. RESULTS The mNGS method detected a higher proportion of multiple pathogens in SSTIs compared to conventional bacterial culture methods. Pseudomonas spp. was among the most commonly identified Gram-negative bacilli using mNGS. Additionally, the mNGS method identified several rare pathogens in patients with SSTIs, including Granulicatella adiacens, Bacillus thuringiensis, and Bacteroides fragilis. Antimicrobial resistance genes were detected in 10 samples (52.6%) using the mNGS method, including genes for extended-spectrum beta-lactamase, Ambler class C β-lactamases, and carbapenemase. CONCLUSION mNGS not only plays an important role in the detection of pathogens in soft tissue infections, but also informs clinical professionals about the presence of additional microbes that may be important for treatment decisions. Further studies comparing conventional pathogen culture with the mNGS method in SSTIs are required.
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Affiliation(s)
- Ting-Kuang Yeh
- Division of Infectious Diseases, Department of Internal Medicine, Taichung Veterans General Hospital, Taichung, Taiwan, R.O.C
- Genomic Center for Infectious Diseases, Taichung Veterans General Hospital, Taichung, Taiwan, R.O.C
| | - Yao-Ting Huang
- Department of Computer Science and Information Engineering, National Chung Cheng University, Chiayi, Taiwan, R.O.C
| | - Po-Yu Liu
- Division of Infectious Diseases, Department of Internal Medicine, Taichung Veterans General Hospital, Taichung, Taiwan, R.O.C
- Genomic Center for Infectious Diseases, Taichung Veterans General Hospital, Taichung, Taiwan, R.O.C
- Ph.D. Program in Translational Medicine, National Chung Hsing University, Taichung, Taiwan, R.O.C
- Rong Hsing Research Center for Translational Medicine, National Chung Hsing University, Taichung, Taiwan, R.O.C
- Department of Post-Baccalaureate Medicine, College of Medicine, National Chung Hsing University, Taichung, Taiwan, R.O.C
| | - Yan-Chiao Mao
- Division of Clinical Toxicology, Department of Emergency Medicine, Taichung Veterans General Hospital, Taichung, Taiwan, R.O.C
| | - Chih-Sheng Lai
- Division of Plastic and Reconstructive Surgery, Department of Surgery, Taichung Veterans General Hospital, Taichung, Taiwan, R.O.C
| | - Kuo-Lung Lai
- Division of Allergy, Immunology and Rheumatology, Department of Medicine, Taichung Veterans General Hospital, Taichung, Taiwan, R.O.C
| | - Chien-Hao Tseng
- Division of Infectious Diseases, Department of Internal Medicine, Taichung Veterans General Hospital, Taichung, Taiwan, R.O.C
| | - Chia-Wei Liu
- Division of Infectious Diseases, Department of Internal Medicine, Taichung Veterans General Hospital, Taichung, Taiwan, R.O.C
| | - Wei-Hsuan Huang
- Division of Infectious Diseases, Department of Internal Medicine, Taichung Veterans General Hospital, Taichung, Taiwan, R.O.C
| | - Hsien-Po Huang
- Division of Infectious Diseases, Department of Internal Medicine, Taichung Veterans General Hospital, Taichung, Taiwan, R.O.C
| | - Kuan-Pei Lin
- Division of Infectious Diseases, Department of Internal Medicine, Taichung Veterans General Hospital, Taichung, Taiwan, R.O.C.;
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Wei L, Luo J, Wu W, Yin J, Sun Z, Xu X, Gong W, Xu J. Clinical diagnostic value of metagenomic next-generation sequencing in patients with acute infection in emergency department. Heliyon 2024; 10:e35802. [PMID: 39220937 PMCID: PMC11365312 DOI: 10.1016/j.heliyon.2024.e35802] [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: 06/13/2024] [Revised: 08/04/2024] [Accepted: 08/05/2024] [Indexed: 09/04/2024] Open
Abstract
Objective To explore the value of metagenomic next-generation sequencing (mNGS) and culture in microbial diagnosis of patients with acute infection. Methods We retrospectively analyzed 206 specimens from 163 patients who were admitted to the emergency department of The First Affiliated Hospital of Sun Yat-sen University between July 2020, and July 2021. We evaluated the diagnostic efficacy of mNGS and in-hospital traditional culture. Results The total positive rate of mNGS was significantly higher than that culture methods (71.4 % vs 40.8 %, p < 0.001), while the sensitivity and accuracy of mNGS were found to be 92.9 % and 88.2 % respectively. However, culture exhibited superior specificity with a value of 92.6 % compared to 75.9 % for mNGS. The detection efficiency of mNGS and culture for fungi was comparable, but mNGS showed superior performance for bacterial detection. In the analysis of sepsis samples, mNGS outperformed traditional culture methods in diagnosing various types of samples, especially for sputum and bronchoalveolar lavage fluid. Among the identified infections, bacterial infections were the most common single infection (37.5 %). Additionally, bacterial-fungal infections represented the most prevalent form of mixed infection (77.3 %). Candida albicans and Staphylococcus aureus were identified as the predominant pathogens in the survival and death groups, respectively. No significant differences in microbial diversity were observed. Conclusion Compared to culture methods, mNGS demonstrates superior positive rates, sensitivity, and accuracy in the rapid detection of acute infections, particularly in critically ill patients such as those with sepsis. This capability establishes a foundation for the swift and precise identification of pathogens, allowing for the analysis of clinical indicators and patient prognosis based on the extensive data generated from mNGS.
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Affiliation(s)
- Lingyu Wei
- Department of Emergency, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, 510080, China
| | - Jieyu Luo
- Department of Emergency, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, 510080, China
| | - Weiwei Wu
- Dinfectome Inc., Nanjing, Jiangsu, 210044, China
| | - Jia Yin
- Dinfectome Inc., Nanjing, Jiangsu, 210044, China
| | - Zaiyuan Sun
- Department of Emergency, The Seventh Affiliated Hospital, Sun Yat-sen University, Guangdong, 518107, China
| | - Xue Xu
- Department of Neurology, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, 510080, China
| | - Wenqian Gong
- Department of Emergency, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, 510080, China
| | - Jia Xu
- Department of Emergency, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, 510080, China
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Batovska J, Brohier ND, Mee PT, Constable FE, Rodoni BC, Lynch SE. The Australian Biosecurity Genomic Database: a new resource for high-throughput sequencing analysis based on the National Notifiable Disease List of Terrestrial Animals. Database (Oxford) 2024; 2024:baae084. [PMID: 39197058 PMCID: PMC11352597 DOI: 10.1093/database/baae084] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2024] [Revised: 06/21/2024] [Accepted: 08/07/2024] [Indexed: 08/30/2024]
Abstract
The Australian Biosecurity Genomic Database (ABGD) is a curated collection of reference viral genome sequences based on the Australian National Notifiable Disease List of Terrestrial Animals. It was created to facilitate the screening of high-throughput sequencing (HTS) data for the potential presence of viruses associated with notifiable disease. The database includes a single verified sequence (the exemplar species sequence, where relevant) for each of the 60 virus species across 21 viral families that are associated with or cause these notifiable diseases, as recognized by the World Organisation for Animal Health. The open-source ABGD on GitHub provides usage guidance documents and is intended to support building a culture in Australian HTS communities that promotes the use of quality-assured, standardized, and verified databases for Australia's national biosecurity interests. Future expansion of the database will include the addition of more strains or subtypes for highly variable viruses, viruses causing diseases of aquatic animals, and genomes of other types of pathogens associated with notifiable diseases, such as bacteria. Database URL: https://github.com/ausbiopathgenDB/AustralianBiosecurityGenomicDatabase.
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Affiliation(s)
- Jana Batovska
- Agriculture Victoria Research, AgriBio Centre for AgriBioscience, 5 Ring Road, Bundoora, Victoria 3083, Australia
| | - Natasha D Brohier
- Agriculture Victoria Research, AgriBio Centre for AgriBioscience, 5 Ring Road, Bundoora, Victoria 3083, Australia
| | - Peter T Mee
- Agriculture Victoria Research, AgriBio Centre for AgriBioscience, 5 Ring Road, Bundoora, Victoria 3083, Australia
- School of Applied Systems Biology (SASB), La Trobe University, Bundoora, Melbourne, Victoria 3086, Australia
| | - Fiona E Constable
- Agriculture Victoria Research, AgriBio Centre for AgriBioscience, 5 Ring Road, Bundoora, Victoria 3083, Australia
- School of Applied Systems Biology (SASB), La Trobe University, Bundoora, Melbourne, Victoria 3086, Australia
| | - Brendan C Rodoni
- Agriculture Victoria Research, AgriBio Centre for AgriBioscience, 5 Ring Road, Bundoora, Victoria 3083, Australia
- School of Applied Systems Biology (SASB), La Trobe University, Bundoora, Melbourne, Victoria 3086, Australia
| | - Stacey E Lynch
- Agriculture Victoria Research, AgriBio Centre for AgriBioscience, 5 Ring Road, Bundoora, Victoria 3083, Australia
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Fu R, Xu J, Fan Z, Qu H, Jiang Y, Xiong W, Huang F, Xuan L, Xu N, Liu H, Wang Z, Sun J, Liu Q, Lin R. Metagenomic Next-Generation Sequencing in the Diagnosis of Pulmonary Infections after Allogeneic Hematopoietic Stem Cell Transplantation. Transplant Cell Ther 2024:S2666-6367(24)00607-9. [PMID: 39197493 DOI: 10.1016/j.jtct.2024.08.014] [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: 05/25/2024] [Revised: 07/27/2024] [Accepted: 08/19/2024] [Indexed: 09/01/2024]
Abstract
Early and accurate identification of pathogens in pulmonary infections after allogeneic hematopoietic stem cell transplantation (allo-HSCT) is critically important. The clinical usefulness of metagenomic next-generation sequencing (mNGS) in the diagnosis of pulmonary infections after allo-HSCT remains under discussion. This multicenter retrospective study was conducted to compare mNGS and conventional microbiological tests (CMTs) in identifying the pathogens of pulmonary infections in allo-HSCT recipients. One hundred forty allo-HSCT recipients with suspected pulmonary infections who underwent bronchoscopy were included. mNGS and CMTs performed on bronchoalveolar lavage fluid specimens showed 71.4% positivity on mNGS compared to 55.0% positivity on CMTs. mNGS identified 182 pathogens, including bacteria (n = 88), fungi (n = 35) and viruses (n = 59), compared to 106 pathogens detected by CMTs (bacteria, n = 31; fungi, n = 24; viruses, n = 51). Pulmonary infection was finally diagnosed in 98 patients, including 22 bacterial, 7 fungal, 18 viral, and 48 mixed infections and 3 infections with an unknown pathogen. Mixed infections were identified in 50.5% of the patients with pulmonary infection. The sensitivity of mNGS and CMTs for diagnosing pulmonary infections was 88.8% and 69.4%, respectively (P = .001), and the specificity were 81.0% and 85.7%, respectively (P = .688). Our findings suggest that mNGS may be a promising technology for diagnosing pulmonary infections in allo-HSCT recipients.
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Affiliation(s)
- Rong Fu
- Department of Hematology, Nanfang Hospital, Southern Medical University, Clinical Medical Research Center of Hematological Diseases of Guangdong Province, Guangzhou, China
| | - Jun Xu
- Department of Hematology, Nanfang Hospital, Southern Medical University, Clinical Medical Research Center of Hematological Diseases of Guangdong Province, Guangzhou, China
| | - Zhiping Fan
- Department of Hematology, Nanfang Hospital, Southern Medical University, Clinical Medical Research Center of Hematological Diseases of Guangdong Province, Guangzhou, China
| | - Hong Qu
- The Affiliated Panyu Central Hospital of Guangzhou Medical University, Infection Medicine Research Institute of Panyu District, Guangzhou, China
| | | | - Wenjie Xiong
- Foresea Life Insurance Guangzhou General Hospital, Guangzhou, China
| | - Fen Huang
- Department of Hematology, Nanfang Hospital, Southern Medical University, Clinical Medical Research Center of Hematological Diseases of Guangdong Province, Guangzhou, China
| | - Li Xuan
- Department of Hematology, Nanfang Hospital, Southern Medical University, Clinical Medical Research Center of Hematological Diseases of Guangdong Province, Guangzhou, China
| | - Na Xu
- Department of Hematology, Nanfang Hospital, Southern Medical University, Clinical Medical Research Center of Hematological Diseases of Guangdong Province, Guangzhou, China
| | - Hui Liu
- Department of Hematology, Nanfang Hospital, Southern Medical University, Clinical Medical Research Center of Hematological Diseases of Guangdong Province, Guangzhou, China
| | - Zhixiang Wang
- Department of Hematology, Nanfang Hospital, Southern Medical University, Clinical Medical Research Center of Hematological Diseases of Guangdong Province, Guangzhou, China
| | - Jing Sun
- Department of Hematology, Nanfang Hospital, Southern Medical University, Clinical Medical Research Center of Hematological Diseases of Guangdong Province, Guangzhou, China
| | - Qifa Liu
- Department of Hematology, Nanfang Hospital, Southern Medical University, Clinical Medical Research Center of Hematological Diseases of Guangdong Province, Guangzhou, China
| | - Ren Lin
- Department of Hematology, Nanfang Hospital, Southern Medical University, Clinical Medical Research Center of Hematological Diseases of Guangdong Province, Guangzhou, China.
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Huang Z, Hu B, Li J, Feng M, Wang Z, Huang F, Xu H, Liu L, Shang W. Metagenomic versus targeted next-generation sequencing for detection of microorganisms in bronchoalveolar lavage fluid among renal transplantation recipients. Front Immunol 2024; 15:1443057. [PMID: 39253087 PMCID: PMC11381253 DOI: 10.3389/fimmu.2024.1443057] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2024] [Accepted: 08/01/2024] [Indexed: 09/11/2024] Open
Abstract
Background Metagenomic next-generation sequencing (mNGS), which provides untargeted and unbiased pathogens detection, has been extensively applied to improve diagnosis of pulmonary infection. This study aimed to compare the clinical performance between mNGS and targeted NGS (tNGS) for microbial detection and identification in bronchoalveolar lavage fluid (BALF) from kidney transplantation recipients (KTRs). Methods BALF samples with microbiological results from mNGS and conventional microbiological test (CMT) were included. For tNGS, samples were extracted, amplified by polymerase chain reaction with pathogen-specific primers, and sequenced on an Illumina Nextseq. Results A total of 99 BALF from 99 KTRs, among which 93 were diagnosed as pulmonary infection, were analyzed. Compared with CMT, both mNGS and tNGS showed higher positive rate and sensitivity (p<0.001) for overall, bacterial and fungal detection. Although the positive rate for mNGS and tNGS was comparable, mNGS significantly outperformed tNGS in sensitivity (100% vs. 93.55%, p<0.05), particularly for bacteria and virus (p<0.001). Moreover, the true positive rate for detected microbes of mNGS was superior over that of tNGS (73.97% vs. 63.15%, p<0.05), and the difference was also significant when specific for bacteria (94.59% vs. 64.81%, p<0.001) and fungi (93.85% vs. 72.58%, p<0.01). Additionally, we found that, unlike most microbes such as SARS-CoV-2, Aspergillus, and EBV, which were predominantly detected from recipients who underwent surgery over 3 years, Torque teno virus (TTV) were principally detected from recipients within 1-year post-transplant, and as post-transplantation time increased, the percentage of TTV positivity declined. Conclusion Although tNGS was inferior to mNGS owing to lower sensitivity and true positive rate in identifying respiratory pathogens among KTRs, both considerably outperformed CMT.
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Affiliation(s)
- Zhaoru Huang
- Kidney Transplantation Department, the First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Bingxue Hu
- Center for Infectious Diseases, Vision Medicals Co., Ltd, Guangzhou, China
| | - Jinfeng Li
- Kidney Transplantation Department, the First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Min Feng
- Surgical Intensive Care Unit, the First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Zhigang Wang
- Kidney Transplantation Department, the First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Fengxiang Huang
- Respiratory Department, the First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Huan Xu
- Center for Infectious Diseases, Vision Medicals Co., Ltd, Guangzhou, China
| | - Lei Liu
- Kidney Transplantation Department, the First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Wenjun Shang
- Kidney Transplantation Department, the First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
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Ali A, Manzoor S, Ali T, Asim M, Muhammad G, Ahmad A, Jamaludin MI, Devaraj S, Munawar N. Innovative aspects and applications of single cell technology for different diseases. Am J Cancer Res 2024; 14:4028-4048. [PMID: 39267684 PMCID: PMC11387862 DOI: 10.62347/vufu1836] [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: 06/21/2024] [Accepted: 08/24/2024] [Indexed: 09/15/2024] Open
Abstract
Recent developments in single-cell technologies have provided valuable insights from cancer genomics to complex microbial communities. Single-cell technologies including the RNA-seq, next-generation sequencing (NGS), epigenomics, genomics, and transcriptomics can be used to uncover the single cell nature and molecular characterization of individual cells. These technologies also reveal the cellular transition states, evolutionary relationships between genes, the complex structure of single-cell populations, cell-to-cell interaction leading to biological discoveries and more reliable than traditional bulk technologies. These technologies are becoming the first choice for the early detection of inflammatory biomarkers affecting the proliferation and progression of tumor cells in the tumor microenvironment and improving the clinical efficacy of patients undergoing immunotherapy. These technologies also hold a central position in the detection of checkpoint inhibitors and thus determining the signaling pathways evoked by tumor invasion. This review addressed the emerging approaches of single cell-based technologies in cancer immunotherapies and different human diseases at cellular and molecular levels and the emerging role of sequencing technologies leading to drug discovery. Advancements in these technologies paved for discovering novel diagnostic markers for better understanding the pathological and biochemical mechanisms also for controlling the rate of different diseases.
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Affiliation(s)
- Ashiq Ali
- Department of Histology and Embryology, Shantou University Medical College Shantou 515041, Guangdong, China
| | - Saba Manzoor
- Department of Zoology, University of Sialkot Sialkot 51310, Pakistan
| | - Tayyab Ali
- Clinico-Molecular Biochemistry Laboratory, Department of Biochemistry, University of Agriculture Faisalabad 38000, Pakistan
| | - Muhammad Asim
- Clinico-Molecular Biochemistry Laboratory, Department of Biochemistry, University of Agriculture Faisalabad 38000, Pakistan
| | - Ghulam Muhammad
- Jinnah Burn and Reconstructive Surgery Centre, Jinnah Hospital, Allama Iqbal Medical College Lahore 54000, Pakistan
| | - Aftab Ahmad
- Biochemistry/Center for Advanced Studies in Agriculture and Food Security (CAS-AFS), University of Agriculture Faisalabad 38040, Pakistan
| | - Mohamad Ikhwan Jamaludin
- BioInspired Device and Tissue Engineering Research Group (BioInspira), Department of Biomedical Engineering and Health Sciences, Faculty of Electrical Engineering, Universiti Teknologi Malaysia Johor Bahru 81310, Johor, Malaysia
| | - Sutha Devaraj
- Graduate School of Medicine, Perdana University Wisma Chase Perdana, Changkat Semantan, Damansara Heights, Kuala Lumpur 50490, Malaysia
| | - Nayla Munawar
- Department of Chemistry, College of Science, United Arab Emirates University Al-Ain 15551, United Arab Emirates
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Xu X, Zheng Y, Zhang X, Zhang C, Gai W, Yang Z. Utility of Metagenomic Next-Generation Sequencing for Diagnosis of Infectious Diseases in Critically Ill Immunocompromised Pediatric Patients. Infect Drug Resist 2024; 17:3579-3591. [PMID: 39165848 PMCID: PMC11334925 DOI: 10.2147/idr.s472129] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2024] [Accepted: 08/09/2024] [Indexed: 08/22/2024] Open
Abstract
Purpose Infections cause high rates of illness and death in children worldwide. However, studies on the clinical value of metagenomic next-generation sequencing (mNGS) for immunocompromised children are still limited. Patients and Methods From June 2021 to December 2023, 119 samples were collected at Pediatric Intensive Care Unit (PICU) of a single-center pediatric hospital and classified into two groups based on their immune states. We compared the diagnostic performance of mNGS and conventional microbiological test (CMT) for pathogen identification, and assessed the clinical impacts of mNGS. Results Among the 119 samples, 48 (40.34%) belonged to the immunocompromised children. mNGS had a higher positivity rate than CMT (76.47% vs 55.46%, P = 0.0006). The positive percent agreement (PPA) of mNGS for immunocompromised children was higher compared to immunocompetent children (95.24% vs 77.78%). The most common pathogens for immunocompromised patients were gram-negative bacteria and herpesvirus. However, immunocompetent children showed a higher detection rate for gram-positive bacteria and respiratory viruses. Furthermore, the proportions of the positive impact of mNGS results were significantly higher in immunocompromised patients compared to immunocompetent patients for both diagnosis (91.67% vs 57.75%) and treatment (95.83% vs 64.79%) (P < 0.0001). Immunocompromised state, length of hospital stays, times stay in ICU, Pediatric Risk of Mortality (PRISM) score, neutrophil percentage (NEUT%) and the ratio of arterial oxygen partial pressure to fractional inspired oxygen (PaO2/FiO2) were considered independent factors for poor prognosis in critically ill pediatric patients. Conclusion In patients from PICU, mNGS had a greater clinical significance in immunocompromised children compared to immunocompetent children. mNGS technology is an important auxiliary method for achieving accurate diagnosis and treatment of critically ill pediatric patients.
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Affiliation(s)
- Xiangzhi Xu
- Department of Pediatric Intensive Care Unit, Children’s Hospital, Zhejiang University School of Medicine, Hangzhou, People’s Republic of China
| | - Yafeng Zheng
- WillingMed Technology (Beijing) Co., Ltd, Beijing, People’s Republic of China
| | - Xiaojing Zhang
- WillingMed Technology (Beijing) Co., Ltd, Beijing, People’s Republic of China
| | - Chenmei Zhang
- Department of Pediatric Intensive Care Unit, Children’s Hospital, Zhejiang University School of Medicine, Hangzhou, People’s Republic of China
| | - Wei Gai
- WillingMed Technology (Beijing) Co., Ltd, Beijing, People’s Republic of China
| | - Zihao Yang
- Department of Pediatric Intensive Care Unit, Children’s Hospital, Zhejiang University School of Medicine, Hangzhou, People’s Republic of China
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Chen J, Qin Z, Jia Z. The application status of sequencing technology in global respiratory infectious disease diagnosis. Infection 2024:10.1007/s15010-024-02360-4. [PMID: 39152290 DOI: 10.1007/s15010-024-02360-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2024] [Accepted: 07/22/2024] [Indexed: 08/19/2024]
Abstract
Next-generation sequencing (NGS) has revolutionized clinical microbiology, particularly in diagnosing respiratory infectious diseases and conducting epidemiological investigations. This narrative review summarizes conventional methods for routine respiratory infection diagnosis, including culture, smear microscopy, immunological assays, image techniques as well as polymerase chain reaction(PCR). In contrast to conventional methods, there is a new detection technology, sequencing technology, and here we mainly focus on the next-generation sequencing NGS, especially metagenomic NGS(mNGS). NGS offers significant advantages over traditional methods. Firstly, mNGS eliminates assumptions about pathogens, leading to faster and more accurate results, thus reducing diagnostic time. Secondly, it allows unbiased identification of known and novel pathogens, offering broad-spectrum coverage. Thirdly, mNGS not only identifies pathogens but also characterizes microbiomes, analyzes human host responses, and detects resistance genes and virulence factors. It can complement targeted sequencing for bacterial and fungal classification. Unlike traditional methods affected by antibiotics, mNGS is less influenced due to the extended survival of pathogen DNA in plasma, broadening its applicability. However, barriers to full integration into clinical practice persist, primarily due to cost constraints and limitations in sensitivity and turnaround time. Despite these challenges, ongoing advancements aim to improve cost-effectiveness and efficiency, making NGS a cornerstone technology for global respiratory infection diagnosis.
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Affiliation(s)
- Jingyuan Chen
- Department of Global Health, School of Public Health, Peking University, Beijing, China
| | - Zhen Qin
- School of Public Health, Peking University, Beijing, China
| | - Zhongwei Jia
- Department of Global Health, School of Public Health, Peking University, Beijing, China.
- Center for Intelligent Public Health, Institute for Artificial Intelligence, Peking University, Beijing, China.
- Center for Drug Abuse Control and Prevention, National Institute of Health Data Science, Peking University, Beijing, China.
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Tuo J, Shen Y, Jia S, Liu S, Zhang Q, Wang D, He X, Liu P, Zhang XX. HPB-Chip: An accurate high-throughput qPCR-based tool for rapidly profiling waterborne human pathogenic bacteria in the environment. WATER RESEARCH 2024; 260:121927. [PMID: 38941866 DOI: 10.1016/j.watres.2024.121927] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/21/2024] [Revised: 06/03/2024] [Accepted: 06/11/2024] [Indexed: 06/30/2024]
Abstract
Waterborne pathogens are threatening public health globally, but profiling multiple human pathogenic bacteria (HPBs) in various polluted environments is still a challenge due to the absence of rapid, high-throughput and accurate quantification tools. This work developed a novel chip, termed the HPB-Chip, based on high-throughput quantitative polymerase chain reactions (HT-qPCR). The HPB-Chip with 33-nL reaction volume could simultaneously complete 10,752 amplification reactions, quantifying 27 HPBs in up to 192 samples with two technical replicates (including those for generating standard curves). Specific positive bands of target genes across different species and single peak melting curves demonstrated high specificity of the HPB-Chip. The mixed plasmid serial dilution test validated its high sensitivity with the limit of quantification (LoD) of averaged 82 copies per reaction for 25 target genes. PCR amplification efficiencies and R2 coefficients of standard curves of the HPB-Chip averaged 101 % and 0.996, respectively. Moreover, a strong positive correlation (Pearson' r: 0.961-0.994, P < 0.001) of HPB concentrations (log10 copies/L) between HPB-Chip and conventional qPCR demonstrated high accuracy of the HPB-Chip. Subsequently, the HPB-Chip has been successfully applied to absolutely quantify 27 HPBs in municipal and hospital wastewater treatment plants (WWTPs) after PMA treatment. A total of 17 HPBs were detected in the 6 full-scale WWTPs, with an additional 19 in the hospital WWTP. Remarkably, Acinetobacter baumannii, Legionella pneumophila, and Arcobacter butzler were present in the final effluent of each municipal WWTP. Overall, the HPB-Chip is an efficient and accurate high-throughput quantification tool to comprehensively and rapidly quantify 27 HPBs in the environment.
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Affiliation(s)
- Jinhua Tuo
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing 210023, China
| | - Yan Shen
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing 210023, China
| | - Shuyu Jia
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing 210023, China; College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Shengnan Liu
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing 210023, China
| | - Qifeng Zhang
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing 210023, China
| | - Depeng Wang
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing 210023, China
| | - Xiwei He
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing 210023, China
| | - Peng Liu
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing 210023, China.
| | - Xu-Xiang Zhang
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing 210023, China.
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朱 家, 孙 家, 马 博, 张 驰, 曹 逊, 郑 善, 陈 志, 张 超, 沈 计, 夏 天. [Study on effectiveness of antibiotics guided by metagenomic next-generation sequencing to control infection after total knee arthroplasty]. ZHONGGUO XIU FU CHONG JIAN WAI KE ZA ZHI = ZHONGGUO XIUFU CHONGJIAN WAIKE ZAZHI = CHINESE JOURNAL OF REPARATIVE AND RECONSTRUCTIVE SURGERY 2024; 38:995-1000. [PMID: 39175323 PMCID: PMC11335594 DOI: 10.7507/1002-1892.202404044] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Received: 04/10/2024] [Revised: 07/07/2024] [Accepted: 07/15/2024] [Indexed: 08/24/2024]
Abstract
Objective To explore the clinical value of metagenomic next-generation sequencing (mNGS) in diagnosis and treatment of periprosthetic joint infection (PJI) after total knee arthroplasty (TKA). Methods Between April 2020 and March 2023, 10 patients with PJI after TKA were admitted. There were 3 males and 7 females with an average age of 69.9 years (range, 44-83 years). Infection occurred after 8-35 months of TKA (mean, 19.5 months). The duration of infection ranged from 16 to 128 days (mean, 37 days). The preoperative erythrocyte sedimentation rate (ESR) was 15-85 mm/1 h (mean, 50.2 mm/1 h). The C reactive protein (CRP) was 4.4-410.0 mg/L (mean, 192.8 mg/L). The white blood cell counting was (3.4-23.8)×10 9/L (mean, 12.3×10 9/L). The absolute value of neutrophils was (1.1-22.5)×10 9/L (mean, 9.2×10 9/L). After admission, the joint fluid was extracted for bacterial culture method and mNGS test, and sensitive antibiotics were chosen according to the results of the test, and the infection was controlled in combination with surgery. Results Seven cases (70%) were detected as positive by bacterial culture method, and 7 types of pathogenic bacteria were detected; the most common pathogenic bacterium was Streptococcus lactis arrestans. Ten cases (100%) were detected as positive by mNGS test, and 11 types of pathogenic bacteria were detected; the most common pathogenic bacterium was Propionibacterium acnes. The difference in the positive rate between the two methods was significant ( P=0.211). Three of the 7 patients who were positive for both the bacterial culture method and the mNGS test had the same results for the type of pathogenic bacteria, with a compliance rate of 42.86% (3/7). The testing time (from sample delivery to results) was (4.95±2.14) days for bacterial culture method and (1.60±0.52) days for mNGS test, and the difference was significant ( t=4.810, P<0.001). The corresponding sensitive antibiotic treatment was chosen according to the results of bacterial culture method and mNGS test. At 3 days after the one-stage operation, the CRP was 6.8-48.2 mg/L (mean, 23.6 mg/L); the ESR was 17-53 mm/1 h (mean, 35.5 mm/1 h); the white blood cell counting was (4.5-8.1)×10 9/L (mean, 6.1×10 9/L); the absolute value of neutrophils was (2.3-5.7)×10 9/L (mean, 4.1×10 9/L). All patients were followed up 12-39 months (mean, 23.5 months). One case had recurrence of infection at 6 months after operation, and the remaining 9 cases showed no signs of infection, with an infection control rate of 90%. Conclusion Compared with bacterial culture method, mNGS test can more rapidly and accurately detect pathogenic bacteria for PJI after TKA, which is important for guiding antibiotics combined with surgical treatment of PJI.
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Affiliation(s)
- 家庆 朱
- 南京中医药大学附属医院骨伤科(南京 210029)Department of Orthopaedics, Affiliated Hospital of Nanjing University of Chinese Medicine, Nanjing Jiangsu, 210029, P. R. China
| | - 家豪 孙
- 南京中医药大学附属医院骨伤科(南京 210029)Department of Orthopaedics, Affiliated Hospital of Nanjing University of Chinese Medicine, Nanjing Jiangsu, 210029, P. R. China
| | - 博闻 马
- 南京中医药大学附属医院骨伤科(南京 210029)Department of Orthopaedics, Affiliated Hospital of Nanjing University of Chinese Medicine, Nanjing Jiangsu, 210029, P. R. China
| | - 驰宇 张
- 南京中医药大学附属医院骨伤科(南京 210029)Department of Orthopaedics, Affiliated Hospital of Nanjing University of Chinese Medicine, Nanjing Jiangsu, 210029, P. R. China
| | - 逊 曹
- 南京中医药大学附属医院骨伤科(南京 210029)Department of Orthopaedics, Affiliated Hospital of Nanjing University of Chinese Medicine, Nanjing Jiangsu, 210029, P. R. China
| | - 善斌 郑
- 南京中医药大学附属医院骨伤科(南京 210029)Department of Orthopaedics, Affiliated Hospital of Nanjing University of Chinese Medicine, Nanjing Jiangsu, 210029, P. R. China
| | - 志远 陈
- 南京中医药大学附属医院骨伤科(南京 210029)Department of Orthopaedics, Affiliated Hospital of Nanjing University of Chinese Medicine, Nanjing Jiangsu, 210029, P. R. China
| | - 超 张
- 南京中医药大学附属医院骨伤科(南京 210029)Department of Orthopaedics, Affiliated Hospital of Nanjing University of Chinese Medicine, Nanjing Jiangsu, 210029, P. R. China
| | - 计荣 沈
- 南京中医药大学附属医院骨伤科(南京 210029)Department of Orthopaedics, Affiliated Hospital of Nanjing University of Chinese Medicine, Nanjing Jiangsu, 210029, P. R. China
| | - 天卫 夏
- 南京中医药大学附属医院骨伤科(南京 210029)Department of Orthopaedics, Affiliated Hospital of Nanjing University of Chinese Medicine, Nanjing Jiangsu, 210029, P. R. China
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Zhang H, Lu M, Guo C, Wang L, Ye K, Zhao Q, Yang J, Yang L, Li T. Clinical impact of metagenomic next-generation sequencing of bronchoalveolar lavage fluids for the diagnosis of pulmonary infections in respiratory intensive care unit. Heliyon 2024; 10:e35287. [PMID: 39170112 PMCID: PMC11336462 DOI: 10.1016/j.heliyon.2024.e35287] [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: 12/04/2023] [Revised: 07/23/2024] [Accepted: 07/25/2024] [Indexed: 08/23/2024] Open
Abstract
Background The real-world clinical impact of mNGS on BALF in the respiratory intensive care unit (RICU) is not yet fully understood. Methods We investigated the clinical impact of mNGS on BALF samples obtained from 92 patients admitted to the RICU over a 2-year period. We utilized both mNGS and culture methods to evaluate the effectiveness of mNGS in diagnosing pulmonary infections. The clinical impact of mNGS were evaluated by the clinician committees. Results Among the 92 diagnosed patients, 78 cases (84.7 %) were determined to have infectious diseases caused by pathogenic microorganisms, and the bacterial infections constituted the most prevalent diagnostic category. For mixed infection, the most common type was the Pneumocystis jironecii and cytomegalovirus co-infection. The mNGS results had a positive impact on the clinical management of 43 cases (46.7 %). Moreover, 19 cases (44.2 %) of positive clinical impacts were solely based on new diagnoses made possible by mNGS results. These new diagnoses were particularly helpful for identifying rare pathogens, which could not be detected by conventional diagnostic methods. Conclusions The BALF mNGS has a positive real-world impact in RICU. Clinician committee play a critical role in ensuring the appropriate use of mNGS.
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Affiliation(s)
- Heng Zhang
- Department of Emergency, The First Medical Center, Chinese PLA General Hospital, Medical School of Chinese PLA, Beijing, 100853, China
| | - Ming Lu
- Laboratory Medicine Department, Tangshan Nanhu Hospital, Hebei, 063000, China
| | - Chaomin Guo
- Laboratory Medicine Department, The First Medical Center, Chinese PLA General Hospital, Beijing, 100853, China
| | - Lifeng Wang
- Laboratory Medicine Department, The First Medical Center, Chinese PLA General Hospital, Beijing, 100853, China
| | - Kun Ye
- Laboratory Medicine Department, The First Medical Center, Chinese PLA General Hospital, Beijing, 100853, China
| | - Qiang Zhao
- Laboratory Medicine Department, The First Medical Center, Chinese PLA General Hospital, Beijing, 100853, China
| | - Jiyong Yang
- Laboratory Medicine Department, The First Medical Center, Chinese PLA General Hospital, Beijing, 100853, China
| | - Liuyang Yang
- Laboratory Medicine Department, The First Medical Center, Chinese PLA General Hospital, Beijing, 100853, China
| | - Tanshi Li
- Department of Emergency, The First Medical Center, Chinese PLA General Hospital, Medical School of Chinese PLA, Beijing, 100853, China
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Liu Z, Qi CJ, Shi Y, Li T, Fang Y, Zhang Q. Active herpesviruses are associated with intensive care unit (ICU) admission in patients pulmonary infection and alter the respiratory microbiome. Front Microbiol 2024; 15:1441476. [PMID: 39184027 PMCID: PMC11342977 DOI: 10.3389/fmicb.2024.1441476] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2024] [Accepted: 07/08/2024] [Indexed: 08/27/2024] Open
Abstract
Background The Herpesviridae family contains several human-related viruses, which are able to establish colonizing and latency in the human body, posing a significant threat to the prognosis of patients. Pulmonary infections represent one of the predominant infectious diseases globally, characterized by diverse and multifaceted clinical manifestations that have consistently attracted clinician's concern. However, the relationship of herpesviruses on the prognosis of pulmonary infections and the respiratory microbiota remains poorly understood. Methods Here, we retrospectively analyzed respiratory samples from 100 patients with pulmonary infection detected by metagenomic next-generation sequencing (mNGS). Results Employing mNGS, five herpesvirus species were detected: Human alphaherpesvirus 1 (HSV-1), Human gammaherpesvirus 4 (EBV), Human betaherpesvirus 5 (CMV), Human betaherpesvirus 7 (HHV-7), and Human betaherpesvirus 6B (HHV-6B). Regression analysis showed that the age and positivity of herpesviruses in patients were independently correlated with ICU admission rates. In addition, positivity of herpesvirus was related with increased ICU days and total hospital stay. The herpesvirus-positive group demonstrated markedly higher incidences of co-infections and fungi-positive, predominantly involving Pneumocystis jirovecii and Aspergillus fumigatus. Analysis of respiratory microbiota revealed a substantially altered community composition within the herpesvirus-positive group, and herpesviruses were significantly positively correlated with the diverse respiratory opportunistic pathogens. Conclusion Overall results substantiate that the active herpesviruses in patients with pulmonary infections were significantly associated with high ICU admission rate. Moreover, the herpesviruses promotes the dysbiosis of the respiratory microbiota and an increased proportion of co-infections. These insights could contribute to unraveling the underlying mechanisms connecting active herpesviruses to the progression of severe illnesses.
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Affiliation(s)
- Zhiguang Liu
- Department of Respiratory and Critical Care Medicine, The Affiliated Changzhou Second People’s Hospital of Nanjing Medical University, Changzhou, China
| | - Chun-jian Qi
- Department of Radiation Oncology, The Affiliated Changzhou Second People’s Hospital of Nanjing Medical University, Changzhou, China
| | - Yujia Shi
- Department of Respiratory and Critical Care Medicine, The Affiliated Changzhou Second People’s Hospital of Nanjing Medical University, Changzhou, China
| | - Tianyu Li
- Genoxor Medical Science and Technology Inc., Shanghai, China
| | - Yuan Fang
- Genoxor Medical Science and Technology Inc., Shanghai, China
| | - Qian Zhang
- Department of Respiratory and Critical Care Medicine, The Affiliated Changzhou Second People’s Hospital of Nanjing Medical University, Changzhou, China
- Changzhou Medical Center, Nanjing Medical University, Changzhou, China
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Li Z, Hu Y, Wang W, Zou F, Yang J, Gao W, Feng S, Chen G, Shi C, Cai Y, Deng G, Chen X. Integrating pathogen- and host-derived blood biomarkers for enhanced tuberculosis diagnosis: a comprehensive review. Front Immunol 2024; 15:1438989. [PMID: 39185416 PMCID: PMC11341448 DOI: 10.3389/fimmu.2024.1438989] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2024] [Accepted: 07/24/2024] [Indexed: 08/27/2024] Open
Abstract
This review explores the evolving landscape of blood biomarkers in the diagnosis of tuberculosis (TB), focusing on biomarkers derived both from the pathogen and the host. These biomarkers provide critical insights that can improve diagnostic accuracy and timeliness, essential for effective TB management. The document highlights recent advancements in molecular techniques that have enhanced the detection and characterization of specific biomarkers. It also discusses the integration of these biomarkers into clinical practice, emphasizing their potential to revolutionize TB diagnostics by enabling more precise detection and monitoring of the disease progression. Challenges such as variability in biomarker expression and the need for standardized validation processes are addressed to ensure reliability across different populations and settings. The review calls for further research to refine these biomarkers and fully harness their potential in the fight against TB, suggesting a multidisciplinary approach to overcome existing barriers and optimize diagnostic strategies. This comprehensive analysis underscores the significance of blood biomarkers as invaluable tools in the global effort to control and eliminate TB.
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Affiliation(s)
- Zhaodong Li
- Guangdong Key Laboratory of Regional Immunity and Diseases, Department of Pathogen Biology, Shenzhen University School of Medicine, Shenzhen, China
- Guangdong Key Laboratory for Biomedical Measurements and Ultrasound Imaging, National-Regional Key Technology Engineering Laboratory for Medical Ultrasound, School of Biomedical Engineering, Shenzhen University Medical School, Shenzhen, China
| | - Yunlong Hu
- Guangdong Key Laboratory of Regional Immunity and Diseases, Department of Pathogen Biology, Shenzhen University School of Medicine, Shenzhen, China
| | - Wenfei Wang
- National Clinical Research Center for Infectious Disease, The Third People's Hospital of Shenzhen, Southern University of Science and Technology, Shenzhen, China
| | - Fa Zou
- Guangdong Key Laboratory of Regional Immunity and Diseases, Department of Pathogen Biology, Shenzhen University School of Medicine, Shenzhen, China
| | - Jing Yang
- Guangdong Key Laboratory of Regional Immunity and Diseases, Department of Pathogen Biology, Shenzhen University School of Medicine, Shenzhen, China
| | - Wei Gao
- Guangdong Key Laboratory of Regional Immunity and Diseases, Department of Pathogen Biology, Shenzhen University School of Medicine, Shenzhen, China
| | - SiWan Feng
- Guangdong Key Laboratory of Regional Immunity and Diseases, Department of Pathogen Biology, Shenzhen University School of Medicine, Shenzhen, China
| | - Guanghuan Chen
- Guangdong Key Laboratory of Regional Immunity and Diseases, Department of Pathogen Biology, Shenzhen University School of Medicine, Shenzhen, China
| | - Chenyan Shi
- Department of Preventive Medicine, School of Public Health, Shenzhen University, Shenzhen, China
| | - Yi Cai
- Guangdong Key Laboratory of Regional Immunity and Diseases, Department of Pathogen Biology, Shenzhen University School of Medicine, Shenzhen, China
| | - Guofang Deng
- Guangdong Key Lab for Diagnosis & Treatment of Emerging Infectious Diseases, Shenzhen Third People's Hospital, Shenzhen, China
| | - Xinchun Chen
- Guangdong Key Laboratory of Regional Immunity and Diseases, Department of Pathogen Biology, Shenzhen University School of Medicine, Shenzhen, China
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Jiang C, He Y, Chen X, Xia F, Shi F, Xu X, Sun T, You K. X-linked severe combined immunodeficiency complicated by disseminated bacillus Calmette-Guérin disease caused by a novel pathogenic mutation in exon 3 of the IL2RG gene: a case report and literature review. Front Immunol 2024; 15:1453046. [PMID: 39176082 PMCID: PMC11338812 DOI: 10.3389/fimmu.2024.1453046] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2024] [Accepted: 07/26/2024] [Indexed: 08/24/2024] Open
Abstract
X-linked severe combined immunodeficiency (X-SCID), caused by mutations in the gamma-chain gene of the interleukin-2 receptor (IL2RG), is a prevalent form of SCID characterized by recurrent and fatal opportunistic infections that occur early in life. The incidence of disseminated bacillus Calmette-Guérin (BCG) disease among children with SCID is much higher than in the general population. Here, we report the case of a 4-month-old male infant who presented with subcutaneous induration, fever, an unhealed BCG vaccination site, and hepatosplenomegaly. Metagenomic next-generation sequencing in blood, and the detection of gastric juice and skin nodule pus all confirmed the infection of Mycobacterium tuberculosis. Lymphocyte subset analysis confirmed the presence of T-B+NK immunodeficiency. Whole-exome and Sanger sequencing revealed a novel microdeletion insertion mutation (c.316_318delinsGTGAT p.Leu106ValfsTer42) in the IL2RG gene, resulting in a rare shift in the amino acid sequence of the coding protein. Consequently, the child was diagnosed with X-SCID caused by a novel mutation in IL2RG, complicated by systemic disseminated BCG disease. Despite receiving systemic anti-infection treatment and four days of hospitalization, the patient died three days after discharge. To the best of our knowledge, this specific IL2RG mutation has not been previously reported. In our systemic review, we outline the efficacy of systemic anti-tuberculosis therapy, hematopoietic stem cell transplantation, and gene therapy in children with SCID and BCG diseases caused by IL2RG gene mutation.
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Affiliation(s)
- Chunxue Jiang
- Department of Pediatrics, Shengjing Hospital of China Medical University, Shenyang, China
| | - Yunhan He
- Department of Pediatrics, Shengjing Hospital of China Medical University, Shenyang, China
| | - Xin Chen
- Department of Pediatrics, Shengjing Hospital of China Medical University, Shenyang, China
| | - Fei Xia
- Computer Center, Shengjing Hospital of China Medical University, Shenyang, China
| | - Feng Shi
- Computer Center, Shengjing Hospital of China Medical University, Shenyang, China
| | - Xuewen Xu
- Department of Urology, Shengjing Hospital of China Medical University, Shenyang, China
| | - Tingting Sun
- Department of Pediatrics, Shengjing Hospital of China Medical University, Shenyang, China
| | - Kai You
- Department of Pediatrics, Shengjing Hospital of China Medical University, Shenyang, China
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Deng QM, Zhang J, Zhang YY, Jia M, Ding DS, Fang YQ, Wang HZ, Gu HC. Diagnosis and treatment of refractory infectious diseases using nanopore sequencing technology: Three case reports. World J Clin Cases 2024; 12:5208-5216. [DOI: 10.12998/wjcc.v12.i22.5208] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/10/2024] [Revised: 05/29/2024] [Accepted: 06/17/2024] [Indexed: 06/30/2024] Open
Abstract
BACKGROUND Infectious diseases are still one of the greatest threats to human health, and the etiology of 20% of cases of clinical fever is unknown; therefore, rapid identification of pathogens is highly important. Traditional culture methods are only able to detect a limited number of pathogens and are time-consuming; serologic detection has window periods, false-positive and false-negative problems; and nucleic acid molecular detection methods can detect several known pathogens only once. Three-generation nanopore sequencing technology provides new options for identifying pathogens.
CASE SUMMARY Case 1: The patient was admitted to the hospital with abdominal pain for three days and cessation of defecation for five days, accompanied by cough and sputum. Nanopore sequencing of the drainage fluid revealed the presence of oral-like bacteria, leading to a clinical diagnosis of bronchopleural fistula. Cefoperazone sodium sulbactam treatment was effective. Case 2: The patient was admitted to the hospital with fever and headache, and CT revealed lung inflammation. Antibiotic treatment for Streptococcus pneumoniae, identified through nanopore sequencing of cerebrospinal fluid, was effective. Case 3: The patient was admitted to our hospital with intermittent fever and an enlarged neck mass that had persisted for more than six months. Despite antibacterial treatment, her symptoms worsened. The nanopore sequencing results indicate that voriconazole treatment is effective for Aspergillus brookii. The patient was diagnosed with mixed cell type classical Hodgkin's lymphoma with infection.
CONCLUSION Three-generation nanopore sequencing technology allows for rapid and accurate detection of pathogens in human infectious diseases.
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Affiliation(s)
- Qing-Mei Deng
- Science Island Branch, Graduate School of University of Science and Technology of China, Hefei 230031, Anhui Province, China
- Institute of Health and Medical Technology, Hefei Institutes of Physical Science, Chinese Academy of Science, Hefei 230031, Anhui Province, China
- Medical Pathology Center, Hefei Cancer Hospital, Chinese Academy of Sciences, Hefei 230031, Anhui Province, China
| | - Jian Zhang
- Medical Pathology Center, Hefei Cancer Hospital, Chinese Academy of Sciences, Hefei 230031, Anhui Province, China
| | - Yi-Yong Zhang
- Medical Pathology Center, Hefei Cancer Hospital, Chinese Academy of Sciences, Hefei 230031, Anhui Province, China
| | - Min Jia
- Institute of Health and Medical Technology, Hefei Institutes of Physical Science, Chinese Academy of Science, Hefei 230031, Anhui Province, China
- Medical Pathology Center, Hefei Cancer Hospital, Chinese Academy of Sciences, Hefei 230031, Anhui Province, China
| | - Du-Shan Ding
- Medical Pathology Center, Hefei Cancer Hospital, Chinese Academy of Sciences, Hefei 230031, Anhui Province, China
| | - Yu-Qin Fang
- Medical Pathology Center, Hefei Cancer Hospital, Chinese Academy of Sciences, Hefei 230031, Anhui Province, China
| | - Hong-Zhi Wang
- Science Island Branch, Graduate School of University of Science and Technology of China, Hefei 230031, Anhui Province, China
| | - Hong-Cang Gu
- Institute of Health and Medical Technology, Hefei Institutes of Physical Science, Chinese Academy of Science, Hefei 230031, Anhui Province, China
- Medical Pathology Center, Hefei Cancer Hospital, Chinese Academy of Sciences, Hefei 230031, Anhui Province, China
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Zalewska M, Błażejewska A, Gawor J, Adamska D, Goryca K, Szeląg M, Kalinowski P, Popowska M. A newly identified IncY plasmid from multi-drug-resistant Escherichia coli isolated from dairy cattle feces in Poland. Microbiol Spectr 2024; 12:e0087724. [PMID: 39012117 PMCID: PMC11302260 DOI: 10.1128/spectrum.00877-24] [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: 04/09/2024] [Accepted: 06/27/2024] [Indexed: 07/17/2024] Open
Abstract
Comprehensive whole-genome sequencing was performed on two multi-drug-resistant Escherichia coli strains isolated from cattle manure from a typical dairy farm in Poland in 2020. The identified strains are resistant to beta-lactams, aminoglycosides, tetracyclines, trimethoprim/sulfamethoxazole, and fluoroquinolones. The complete sequences of the harbored plasmids revealed antibiotic-resistance genes located within many mobile genetic elements (e.g., insertional sequences or transposons) and genes facilitating conjugal transfer or promoting horizontal gene transfer. These plasmids are hitherto undescribed. Similar plasmids have been identified, but not in Poland. The identified plasmids carried resistance genes, including the tetracycline resistance gene tet(A), aph family aminoglycoside resistance genes aph(3″)-lb and aph (6)-ld, beta-lactam resistance genes blaTEM-1 and blaCTX-M-15, sulfonamide resistance gene sul2, fluoroquinolone resistance gene qnrS1, and the trimethoprim resistance gene dfrA14. The characterized resistance plasmids were categorized into the IncY incompatibility group, indicating a high possibility for dissemination among the Enterobacteriaceae. While similar plasmids (99% identity) have been found in environmental and clinical samples, none have been identified in farm animals. These findings are significant within the One Health framework, as they underline the potential for antimicrobial-resistant E. coli from livestock and food sources to be transmitted to humans and vice versa. It highlights the need for careful monitoring and strategies to limit the spread of antibiotic resistance in the One Health approach. IMPORTANCE This study reveals the identification of new strains of antibiotic-resistant Escherichia coli in cattle manure from a dairy farm in Poland, offering critical insights into the spread of drug resistance. Through whole-genome sequencing, researchers discovered novel plasmids within these bacteria, which carry genes resistant to multiple antibiotics. These findings are particularly alarming, as these plasmids can transfer between different bacterial species, potentially escalating the spread of antibiotic resistance. This research underscores the vital connection between the health of humans, animals, and the environment, emphasizing the concept of One Health. It points to the critical need for global vigilance and strategies to curb the proliferation of antibiotic resistance. By showcasing the presence of these strains and their advanced resistance mechanisms, the study calls for enhanced surveillance and preventive actions in both agricultural practices and healthcare settings to address the imminent challenge of antibiotic-resistant bacteria.
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Affiliation(s)
- Magdalena Zalewska
- Department of Bacterial Physiology, Institute of Microbiology, Faculty of Biology, University of Warsaw, Warsaw, Poland
| | - Aleksandra Błażejewska
- Department of Bacterial Physiology, Institute of Microbiology, Faculty of Biology, University of Warsaw, Warsaw, Poland
| | - Jan Gawor
- DNA Sequencing and Synthesis Facility, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
| | - Dorota Adamska
- Genomics Core Facility, Centre of New Technologies, University of Warsaw, Warsaw, Poland
| | - Krzysztof Goryca
- Genomics Core Facility, Centre of New Technologies, University of Warsaw, Warsaw, Poland
| | - Michał Szeląg
- Genomics Core Facility, Centre of New Technologies, University of Warsaw, Warsaw, Poland
| | - Patryk Kalinowski
- Department of Bacterial Physiology, Institute of Microbiology, Faculty of Biology, University of Warsaw, Warsaw, Poland
| | - Magdalena Popowska
- Department of Bacterial Physiology, Institute of Microbiology, Faculty of Biology, University of Warsaw, Warsaw, Poland
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Wu X, Qin N, Peng X, Wang L. Exploring odontogenic brain abscesses: a comprehensive review. Acta Neurol Belg 2024; 124:1155-1165. [PMID: 38722527 DOI: 10.1007/s13760-024-02569-y] [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: 02/04/2024] [Accepted: 04/29/2024] [Indexed: 07/25/2024]
Abstract
INTRODUCTION Whether in neurology or dentistry, odontogenic brain abscess stands as an ailment demanding undivided attention. The onset of this disease is insidious, with a relatively low incidence rate but a markedly high fatality rate. Moreover, its symptoms lack specificity, easily leading to misdiagnosis, oversight, and treatment delays. Hence, clinicians should maintain heightened vigilance when faced with pathogenic bacteria of dental origin in patients. AREAS COVERED This paper encapsulates the latest research findings on the clinical manifestations and essential treatment points of odontogenic brain abscess. It may offer a crucial reference for prompt diagnosis and improved therapeutic approaches. EXPERT OPINIONS Odontogenic brain abscess, an infection of the cerebral parenchyma, usually appears in immunocompromised patients with dental ailments or postdental surgeries. The main pathogenic microorganisms include Streptococcus intermedius, Fusobacterium nucleatum, Streptococcus anginosus, and Millerella. Given the undetectable and nonspecific symptoms in patients, the diagnostic process relies on microbiological methods. Therefore, clinicians should actively investigate and identify the pathogenic microorganisms of odontogenic brain abscess for early detection and selection of appropriate treatment regimens to avoid disease management delays.
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Affiliation(s)
- Xingguo Wu
- Department of Neurology, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Ningxiang Qin
- Department of Neurology, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Xi Peng
- Department of Neurology, The Second Affiliated Hospital of Chongqing Medical University, Chongqing, China.
| | - Liang Wang
- Department of Neurology, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China.
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Zhang F, Wang Z, Men S, Zhang J, Wang L. Two novel compound heterozygous loss-of-function mutations cause fetal IRAK-4 deficiency presenting with Pseudomonas Aeruginosa sepsis. Clin Immunol 2024; 265:110268. [PMID: 38838930 DOI: 10.1016/j.clim.2024.110268] [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: 11/26/2023] [Revised: 03/29/2024] [Accepted: 06/02/2024] [Indexed: 06/07/2024]
Abstract
PURPOSE To report a case of a five-month-old Chinese infant who died of interleukin-1 receptor-associated kinase-4 (IRAK-4) deficiency presenting with rapid and progressive Pseudomonas aeruginosa sepsis. METHODS The genetic etiology of IRAK-4 deficiency was confirmed through trio-whole exome sequencing and Sanger sequencing. Functional consequences were invested using an in vitro minigene splicing assay. RESULTS Trio-whole exome sequencing of genomic DNA identified two novel compound heterozygous mutations, IRAK-4 (NM_016123.3): c.942-1G > A and c.644_651+ 6delTTGCAGCAGTAAGT in the proband, which originated from his symptom-free parents. These mutations were predicted to cause frameshifts and generate three truncated proteins without enzyme activity. CONCLUSIONS Our findings expand the range of IRAK-4 mutations and provide functional support for the pathogenic effects of splice-site mutations. Additionally, this case highlights the importance of considering the underlying genetic defects of immunity when dealing with unusually overwhelming infections in previously healthy children and emphasizes the necessity for timely treatment with wide-spectrum antimicrobials.
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Affiliation(s)
- Fang Zhang
- Department of Prenatal Diagnosis, Lianyungang Maternal and Child Health Hospital, Lianyungang, Jiangsu 222000, People's Republic of China
| | - Zhiwei Wang
- Department of Prenatal Diagnosis, Lianyungang Maternal and Child Health Hospital, Lianyungang, Jiangsu 222000, People's Republic of China
| | - Shuai Men
- Department of Prenatal Diagnosis, Lianyungang Maternal and Child Health Hospital, Lianyungang, Jiangsu 222000, People's Republic of China
| | - Jinglu Zhang
- Department of Prenatal Diagnosis, Lianyungang Maternal and Child Health Hospital, Lianyungang, Jiangsu 222000, People's Republic of China
| | - Leilei Wang
- Department of Prenatal Diagnosis, Lianyungang Maternal and Child Health Hospital, Lianyungang, Jiangsu 222000, People's Republic of China.
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Wang J, Liu L, Li J, Feng X, Yi H, Jiang E, Zheng Y, Zhang F, Zhu X, Mi Y, Han M, Wang J, Feng S. Clinical Characteristics, Prognosis Factors and Metagenomic Next-Generation Sequencing Diagnosis of Mucormycosis in patients With Hematologic Diseases. Mycopathologia 2024; 189:71. [PMID: 39088077 DOI: 10.1007/s11046-024-00875-w] [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: 06/06/2024] [Accepted: 07/02/2024] [Indexed: 08/02/2024]
Abstract
INTRODUCTION New diagnostic methods and antifungal strategies may improve prognosis of mucormycosis. We describe the diagnostic value of metagenomic next⁃generation sequencing (mNGS) and identify the prognostic factors of mucormycosis. METHODS We conducted a retrospective study of hematologic patients suffered from mucormycosis and treated with monotherapy [amphotericin B (AmB) or posaconazole] or combination therapy (AmB and posaconazole). The primary outcome was 84-day all-cause mortality after diagnosis. RESULTS Ninety-five patients were included, with "proven" (n = 27), "probable" (n = 16) mucormycosis confirmed by traditional diagnostic methods, and "possible" (n = 52) mucormycosis with positive mNGS results. The mortality rate at 84 days was 44.2%. Possible + mNGS patients and probable patients had similar diagnosis processes, overall survival rates (44.2% vs 50.0%, p = 0.685) and overall response rates to effective drugs (44.0% vs 37.5%, p = 0.647). Furthermore, the median diagnostic time was shorter in possible + mNGS patients than proven and probable patients (14 vs 26 days, p < 0.001). Combination therapy was associated with better survival compared to monotherapy at six weeks after treatment (78.8% vs 53.1%, p = 0.0075). Multivariate analysis showed that combination therapy was the protective factor (HR = 0.338, 95% CI: 0.162-0.703, p = 0.004), though diabetes (HR = 3.864, 95% CI: 1.897-7.874, p < 0.001) and hypoxemia (HR = 3.536, 95% CI: 1.874-6.673, p < 0.001) were risk factors for mortality. CONCLUSIONS Mucormycosis is a life-threatening infection. Early management of diabetes and hypoxemia may improve the prognosis. Exploring effective diagnostic and treatment methods is important, and combination antifungal therapy seems to hold potential benefits.
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Affiliation(s)
- Jieru Wang
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, China
- Tianjin Institutes of Health Science, Tianjin, China
| | - Li Liu
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, China
- Tianjin Institutes of Health Science, Tianjin, China
| | - Jia Li
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, China
- Tianjin Institutes of Health Science, Tianjin, China
| | - Xiaomeng Feng
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, China
- Tianjin Institutes of Health Science, Tianjin, China
| | - Huiming Yi
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, China
- Tianjin Institutes of Health Science, Tianjin, China
| | - Erlie Jiang
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, China
- Tianjin Institutes of Health Science, Tianjin, China
| | - Yizhou Zheng
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, China
- Tianjin Institutes of Health Science, Tianjin, China
| | - Fengkui Zhang
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, China
- Tianjin Institutes of Health Science, Tianjin, China
| | - Xiaofan Zhu
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, China
- Tianjin Institutes of Health Science, Tianjin, China
| | - Yingchang Mi
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, China
- Tianjin Institutes of Health Science, Tianjin, China
| | - Mingzhe Han
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, China
- Tianjin Institutes of Health Science, Tianjin, China
| | - Jianxiang Wang
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, China
- Tianjin Institutes of Health Science, Tianjin, China
| | - Sizhou Feng
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, China.
- Tianjin Institutes of Health Science, Tianjin, China.
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Cao H, Chen Y, Ge L, Kwong JSW, Lai H, Hu F, Zhang R, Zhao H, Hu L, He R, Zheng W, Zhang J. An umbrella review of the diagnostic value of next-generation sequencing in infectious diseases. Int J Clin Pharm 2024; 46:780-794. [PMID: 38570474 DOI: 10.1007/s11096-024-01704-2] [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: 12/15/2023] [Accepted: 01/18/2024] [Indexed: 04/05/2024]
Abstract
BACKGROUND An increasing number of systematic reviews (SRs) have evaluated the diagnostic values of next-generation sequencing (NGS) in infectious diseases (IDs). AIM This umbrella analysis aimed to assess the potential risk of bias in existing SRs and to summarize the published diagnostic values of NGS in different IDs. METHOD We searched PubMed, Embase, and the Cochrane Library until September 2023 for SRs assessing the diagnostic validity of NGS for IDs. Two investigators independently determined review eligibility, extracted data, and evaluated reporting quality, risk of bias, methodological quality, and evidence certainty in the included SRs. RESULTS Eleven SRs were analyzed. Most SRs exhibited a moderate level of reporting quality, while a serious risk of bias was observed in all SRs. The diagnostic performance of NGS in detecting pneumocystis pneumonia and periprosthetic/prosthetic joint infection was notably robust, showing excellent sensitivity (pneumocystis pneumonia: 0.96, 95% CI 0.90-0.99, very low certainty; periprosthetic/prosthetic joint infection: 0.93, 95% CI 0.83-0.97, very low certainty) and specificity (pneumocystis pneumonia: 0.96, 95% CI 0.92-0.98, very low certainty; periprosthetic/prosthetic joint infection: 0.95, 95% CI 0.92-0.97, very low certainty). NGS exhibited high specificity for central nervous system infection, bacterial meningoencephalitis, and tuberculous meningitis. The sensitivity to these infectious diseases was moderate. NGS demonstrated moderate sensitivity and specificity for multiple infections and pulmonary infections. CONCLUSION This umbrella analysis indicates that NGS is a promising technique for diagnosing pneumocystis pneumonia and periprosthetic/prosthetic joint infection with excellent sensitivity and specificity. More high-quality original research and SRs are needed to verify the current findings.
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Affiliation(s)
- Hong Cao
- School of Pharmaceutical Sciences, Guizhou University, 2708 South of Huaxi Avenue Road, Guiyang, Guizhou Province, China
- Department of Pharmacy, Guizhou Provincial People's Hospital, No.83 Zhongshandong Road, Guiyang, Guizhou Province, China
| | - Yan Chen
- School of Pharmaceutical Sciences, Guizhou University, 2708 South of Huaxi Avenue Road, Guiyang, Guizhou Province, China
- Department of Pharmacy, Guizhou Provincial People's Hospital, No.83 Zhongshandong Road, Guiyang, Guizhou Province, China
| | - Long Ge
- Evidence-Based Social Science Research Center, School of Public Health, Lanzhou University, Lanzhou, China
- Key Laboratory of Evidence Based Medicine and Knowledge Translation of Gansu Province, No. 199, Donggang West Road, Chengguan District, Lanzhou City, Gansu Province, China
| | - Joey Sum-Wing Kwong
- Global Health Nursing, Graduate School of Nursing Science, St. Luke's International University, 10-1 Akashi-Cho, Chuo-Ku, Tokyo, 104-0044, Japan
| | - Honghao Lai
- Evidence-Based Social Science Research Center, School of Public Health, Lanzhou University, Lanzhou, China
- Key Laboratory of Evidence Based Medicine and Knowledge Translation of Gansu Province, No. 199, Donggang West Road, Chengguan District, Lanzhou City, Gansu Province, China
| | - Fangfang Hu
- Department of Laboratory, Guizhou Provincial People's Hospital, No.83 Zhongshandong Road, Guiyang, 550002, Guizhou Province, China
| | - Rui Zhang
- Department of Pharmacy, Guizhou Provincial People's Hospital, No.83 Zhongshandong Road, Guiyang, Guizhou Province, China
| | - Huaye Zhao
- Department of Pharmacy, Guizhou Provincial People's Hospital, No.83 Zhongshandong Road, Guiyang, Guizhou Province, China
| | - Linfang Hu
- Department of Pharmacy, Guizhou Provincial People's Hospital, No.83 Zhongshandong Road, Guiyang, Guizhou Province, China
| | - Rui He
- Experimental Cancer Medicine, Department of Laboratory Medicine, Karolinska Institute, Room 601, Novum PI 6, Hälsovägen 7, Huddinge, 14157, Stockholm, Sweden
| | - Wenyi Zheng
- Experimental Cancer Medicine, Department of Laboratory Medicine, Karolinska Institute, Room 601, Novum PI 6, Hälsovägen 7, Huddinge, 14157, Stockholm, Sweden
| | - Jiaxing Zhang
- Department of Pharmacy, Guizhou Provincial People's Hospital, No.83 Zhongshandong Road, Guiyang, Guizhou Province, China.
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Yuan L, Zhu XY, Lai LM, Chen Q, Liu Y, Zhao R. Clinical application and evaluation of metagenomic next-generation sequencing in pathogen detection for suspected central nervous system infections. Sci Rep 2024; 14:16961. [PMID: 39043813 PMCID: PMC11266612 DOI: 10.1038/s41598-024-68034-1] [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: 03/13/2024] [Accepted: 07/18/2024] [Indexed: 07/25/2024] Open
Abstract
Central nervous system Infections (CNSIs) is a disease characterized by complex pathogens, rapid disease progression, high mortality rate and high disability rate. Here, we evaluated the clinical value of metagenomic next generation sequencing (mNGS) in the diagnosis of central nervous system infections and explored the factors affecting the results of mNGS. We conducted a retrospective study to compare mNGS with conventional methods including culture, smear and etc. 111 suspected CNS infectious patients were enrolled in this study, and clinical data were recorded. Chi-square test were used to evaluate independent binomial variables, taking p < 0.05 as statistically significant threshold. Of the 111 enrolled cases, 57.7% (64/111) were diagnosed with central nervous system infections. From these cases, mNGS identified 39.6% (44/111) true-positive cases, 7.2% (8/111) false-positive case, 35.1% (39/111) true-negative cases, and 18.0% (20/111) false-negative cases. The sensitivity and specificity of mNGS were 68.7% (44/64) and 82.9% (39/47), respectively. Compared with culture, mNGS provided a higher pathogen detection rate in CNSIs patients (68.7% (44/64) vs. 26.5% (17/64), p < 0.0001). Compared to conventional methods, positive percent agreement and negative percent agreement was 84.60% (44/52) and 66.1% (39/59) separately. At a species-specific read number (SSRN) ≥ 2, mNGS performance in the diagnosis of definite viral encephalitis and/or meningitis was optimal (area under the curve [AUC] 0.758, 95% confidence interval [CI] 0.663-0.854). In bacterial CNSIs patients with significant CSF abnormalities (CSF WBC > 300*106/L), the positive rate of CSF mNGS is higher. To sum up, conventional microbiologic testing is insufficient to detect all neuroinvasive pathogens, and mNGS exhibited satisfactory diagnostic performance in CNSIs and with an overall detection rate higher than culture (p < 0.0001).
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Affiliation(s)
- Lei Yuan
- Department of Clinical Laboratory, The First Affiliated Hospital, Jiangxi Medical College, Nanchang University, Nanchang, 330006, People's Republic of China
| | - Xin Yu Zhu
- Department of Clinical Laboratory, The First Affiliated Hospital, Jiangxi Medical College, Nanchang University, Nanchang, 330006, People's Republic of China
| | - Lan Min Lai
- Department of Clinical Laboratory, The First Affiliated Hospital, Jiangxi Medical College, Nanchang University, Nanchang, 330006, People's Republic of China
| | - Qiang Chen
- Department of Clinical Laboratory, The First Affiliated Hospital, Jiangxi Medical College, Nanchang University, Nanchang, 330006, People's Republic of China
| | - Yang Liu
- Department of Clinical Laboratory, The First Affiliated Hospital, Jiangxi Medical College, Nanchang University, Nanchang, 330006, People's Republic of China
| | - Rui Zhao
- Department of Clinical Laboratory, The First Affiliated Hospital, Jiangxi Medical College, Nanchang University, Nanchang, 330006, People's Republic of China.
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Yang Z, Ma J, Han J, Li A, Liu G, Sun Y, Zheng J, Zhang J, Chen G, Xu R, Sun L, Meng C, Gao J, Bai Z, Deng W, Zhang C, Su J, Yao H, Zhang Z. Gut microbiome model predicts response to neoadjuvant immunotherapy plus chemoradiotherapy in rectal cancer. MED 2024:S2666-6340(24)00261-7. [PMID: 39047732 DOI: 10.1016/j.medj.2024.07.002] [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: 07/05/2023] [Revised: 02/18/2024] [Accepted: 07/01/2024] [Indexed: 07/27/2024]
Abstract
BACKGROUND Accurate evaluation of the response to preoperative treatment enables the provision of a more appropriate personalized therapeutic schedule for locally advanced rectal cancer (LARC), which remains an enormous challenge, especially neoadjuvant immunotherapy plus chemoradiotherapy (nICRT). METHODS This prospective, multicenter cohort study enrolled patients with LARC from 6 centers who received nICRT. The dynamic variation in the gut microbiome during nICRT was evaluated. A species-level gut microbiome prediction (SPEED) model was developed and validated to predict the pathological complete response (pCR) to nICRT. FINDINGS A total of 50 patients were enrolled, 75 fecal samples were collected from 33 patients at different time points, and the pCR rate reached 42.4% (14/33). Lactobacillus and Eubacterium were observed to increase after nICRT. Additionally, significant differences in the gut microbiome were observed between responders and non-responders at baseline. Significantly higher abundances of Lachnospiraceaebacterium and Blautiawexlerae were found in responders, while Bacteroides, Prevotella, and Porphyromonas were found in non-responders. The SPEED model showcased a superior predictive performance with areas under the curve of 98.80% (95% confidence interval [CI]: 95.67%-100%) in the training cohort and 77.78% (95% CI: 65.42%-88.29%) in the validation cohort. CONCLUSIONS Programmed death 1 (PD-1) blockade plus concurrent long-course CRT showed a favorable pCR rate and is well tolerated in microsatellite-stable (MSS)/mismatch repair-proficient (pMMR) patients with LARC. The SPEED model can be used to predict the pCR to nICRT based on the baseline gut microbiome with high robustness and accuracy, thereby assisting clinical physicians in providing individualized management for patients with LARC. FUNDING This research was funded by the China National Natural Science Foundation (82202884).
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Affiliation(s)
- Zhengyang Yang
- Department of General Surgery, Beijing Friendship Hospital, Capital Medical University, State Key Lab of Digestive Health, National Clinical Research Center for Digestive Diseases, Beijing, China
| | - Jingxin Ma
- Department of Clinical Laboratory, Beijing Friendship Hospital, Capital Medical University, Beijing, China
| | - Jiagang Han
- Department of General Surgery, Beijing Chaoyang Hospital, Capital Medical University, Beijing, China
| | - Ang Li
- Department of General Surgery, Beijing Xuanwu Hospital, Capital Medical University, Beijing, China
| | - Gang Liu
- Department of General Surgery, Tianjin Medical University General Hospital, Tianjin, China
| | - Yi Sun
- Department of Anorectal, Tianjin People's Hospital, Tianjin, China
| | - Jianyong Zheng
- Department of Gastrointestinal Surgery, The First Affiliated Hospital of Air Force Medical University, Xi'an, China
| | - Jie Zhang
- Department of Radiology, Beijing Friendship Hospital, Capital Medical University, Beijing, China
| | - Guangyong Chen
- Department of Pathology, Beijing Friendship Hospital, Capital Medical University, Beijing, China
| | - Rui Xu
- Department of Pathology, Beijing Friendship Hospital, Capital Medical University, Beijing, China
| | - Liting Sun
- Department of General Surgery, Beijing Friendship Hospital, Capital Medical University, State Key Lab of Digestive Health, National Clinical Research Center for Digestive Diseases, Beijing, China
| | - Cong Meng
- Department of General Surgery, Beijing Friendship Hospital, Capital Medical University, State Key Lab of Digestive Health, National Clinical Research Center for Digestive Diseases, Beijing, China
| | - Jiale Gao
- Department of General Surgery, Beijing Friendship Hospital, Capital Medical University, State Key Lab of Digestive Health, National Clinical Research Center for Digestive Diseases, Beijing, China
| | - Zhigang Bai
- Department of General Surgery, Beijing Friendship Hospital, Capital Medical University, State Key Lab of Digestive Health, National Clinical Research Center for Digestive Diseases, Beijing, China
| | - Wei Deng
- Department of General Surgery, Beijing Friendship Hospital, Capital Medical University, State Key Lab of Digestive Health, National Clinical Research Center for Digestive Diseases, Beijing, China
| | - Chenlin Zhang
- Department of General Surgery, Beijing Friendship Hospital, Capital Medical University, State Key Lab of Digestive Health, National Clinical Research Center for Digestive Diseases, Beijing, China
| | - Jianrong Su
- Department of Clinical Laboratory, Beijing Friendship Hospital, Capital Medical University, Beijing, China.
| | - Hongwei Yao
- Department of General Surgery, Beijing Friendship Hospital, Capital Medical University, State Key Lab of Digestive Health, National Clinical Research Center for Digestive Diseases, Beijing, China.
| | - Zhongtao Zhang
- Department of General Surgery, Beijing Friendship Hospital, Capital Medical University, State Key Lab of Digestive Health, National Clinical Research Center for Digestive Diseases, Beijing, China.
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Li H, Chen X, Li J, Chen L, Liu X, Chen C, Xie D, Chen Y, Yuan J, Tao E. Case Report: Taking action or standing by: managing a preterm neonate at the risk of neonatal varicella by metagenomic next-generation sequencing. Front Pediatr 2024; 12:1345338. [PMID: 39100652 PMCID: PMC11294073 DOI: 10.3389/fped.2024.1345338] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/24/2024] [Accepted: 07/10/2024] [Indexed: 08/06/2024] Open
Abstract
Neonatal varicella is indeed a rare condition, and most infants born to mothers with varicella have a good prognosis. However, in exceptional cases, neonatal varicella can be life-threatening, particularly for preterm infants. Therefore, it is vital to make an early diagnosis or predict the risk of neonatal varicella to ensure prompt treatment and improve prognosis. This report made an effort to early predict neonatal vericalla by using metagenomic next-generation sequencing (mNGS) in a preterm infant who was at risk for vericalla infection. A preterm infant born from a mother with varicella with symptom onset at 8 days before delivery, putting the infant at risk for varicella infection. Importantly, the patient develop pneumonia and pneumothorax, and neonatal vericella was suspected. Fortunately, the use of mNGS for testing the varicella gene in the serum promptly ruled out varicella zoster virus (VZV) infection in the patient, as indicated by a negative mNGS result. Subsequent follow-up, which included a 14-day stay in the hospital followed by an additional 7 days at home, confirmed this finding. Throughout this period, the patient did not exhibit any rash or other symptoms associated with varicella. Therefore, the novel approach of using mNGS allows neonatologists to predict and promptly address potential neonatal infections. This early detection is crucial, as delayed diagnosis or treatment could pose life-threatening risks, as exemplified by the case of neonatal varicella. In such cases, neonatologists can take proactive measures instead of standing by for at-risk neonates. Furthermore, given the severity of neonatal varicella as a life-threatening condition, the early exclusion of subsequent varicella infection by mNGS can offer reassurance to both family members and healthcare professionals.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | - Enfu Tao
- Department of Neonatology and NICU, Wenling Maternal and Child Health Care Hospital, Wenling, Zhejiang, China
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Liu Z, Chen H, Chen D, Wu X, Xu H, Chen P, Wang R, Chen Y. Metagenomic next-generation sequencing for the diagnosis of invasive pulmonary aspergillosis in type 2 diabetes mellitus patients. Sci Rep 2024; 14:16618. [PMID: 39025875 PMCID: PMC11258266 DOI: 10.1038/s41598-024-67174-8] [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: 03/18/2024] [Accepted: 07/09/2024] [Indexed: 07/20/2024] Open
Abstract
Invasive pulmonary aspergillosis (IPA) in patients with diabetes mellitus has high incidence, especially in Type 2 diabetes mellitus (T2DM). The aim of this study was to evaluate the diagnostic efficacy of metagenomic next-generation sequencing (mNGS) for IPA in patients with T2DM. A total of 66 patients with T2DM were included, including 21 IPA and 45 non-IPA patients, from January 2022 to December 2022. The demographic characteristics, comorbidities, laboratory test results, antibiotic treatment response, and 30-day mortality rate of patients were analyzed. The diagnostic accuracy of mNGS and conventional methods was compared, including sensitivity, specificity, positive predictive value and negative predictive value. The sensitivity and specificity of mNGS were 66.7% and 100.0%, respectively, which were significantly higher than those of fluorescence staining (42.1% and 100%), serum 1,3-β-D-glucan detection (38.1% and 90.9%), serum galactomannan detection (14.3% and 94.9%) and BALF galactomannan detection (47.3% and 70.7%). Although the sensitivity of BALF culture (75.0%) was higher than that of mNGS (66.7%), the turnover time of mNGS was significantly shorter than that of traditional culture (1.6 days vs. 5.0 days). The sensitivity of mNGS combined with BALF culture reached 100.0%. In addition, mNGS has a stronger ability to detect co-pathogens with IPA. 47.6% of T2DM patients with IPA were adjusted the initial antimicrobial therapy according to the mNGS results. This is the first study to focus on the diagnostic performance of mNGS in IPA infection in T2DM patients. MNGS can be used as a supplement to conventional methods for the diagnosis of IPA in patients with T2DM.
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Affiliation(s)
- Zhiyun Liu
- Department of Clinical Laboratory, Huizhou Central People's Hospital, Huizhou, 516001, Guangdong, China
| | - Hengxin Chen
- Department of Laboratory Medicine, The First Affiliated Hospital of Sun Yat-Sen University, Guangzhou, 510080, Guangdong, China
| | - Dubo Chen
- Department of Laboratory Medicine, The First Affiliated Hospital of Sun Yat-Sen University, Guangzhou, 510080, Guangdong, China
| | - Xianjin Wu
- Department of Clinical Laboratory, Huizhou Central People's Hospital, Huizhou, 516001, Guangdong, China
| | - Hongxu Xu
- Department of Laboratory Medicine, The First Affiliated Hospital of Sun Yat-Sen University, Guangzhou, 510080, Guangdong, China
| | - Peisong Chen
- Department of Laboratory Medicine, The First Affiliated Hospital of Sun Yat-Sen University, Guangzhou, 510080, Guangdong, China
| | - Ruizhi Wang
- Department of Laboratory Medicine, The First Affiliated Hospital of Sun Yat-Sen University, Guangzhou, 510080, Guangdong, China.
| | - Yili Chen
- Department of Laboratory Medicine, The First Affiliated Hospital of Sun Yat-Sen University, Guangzhou, 510080, Guangdong, China.
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Chen J, Liu Y, Huang S, Pang Z, Wei Q, Liu Y, Qin H, Chen Y. Spinal Infections? mNGS Combined with Microculture and Pathology for Answers. Infect Drug Resist 2024; 17:3025-3034. [PMID: 39050835 PMCID: PMC11268561 DOI: 10.2147/idr.s466738] [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: 04/26/2024] [Accepted: 07/05/2024] [Indexed: 07/27/2024] Open
Abstract
Introduction This study evaluates the efficacy of metagenomic next-generation sequencing (mNGS) in diagnosing spinal infections and developing therapeutic regimens that combine mNGS, microbiological cultures, and pathological investigations. Methods Data were collected from 108 patients with suspected spinal infections between January 2022 and December 2023. Lesion tissues were obtained via C-arm assisted puncture or open surgery for mNGS, conventional microbiological culture, and pathological analysis. Personalized antimicrobial therapies were tailored based on these findings, with follow-up evaluations 7 days postoperatively. The sensitivity and specificity of mNGS were assessed, along with its impact on treatment and prognosis. Results mNGS showed a significantly higher positive detection rate (61.20%) compared to conventional microbiological culture (30.80%) and PCT (28%). mNGS demonstrated greater sensitivity (79.41%) and negative predictive value (63.16%) than cultures (25% and 22.58%, respectively), with no significant difference in specificity and positive predictive value. Seven days post-surgery, a significant reduction in neutrophil percentage (NEUT%) was observed, though decreases in white blood cell count (WBC), erythrocyte sedimentation rate (ESR), and C-reactive protein (CRP) were not statistically significant. At the last follow-up, significant improved in Visual Analogue Scale (VAS) scores, Oswestry Disability Index (ODI), and Japanese Orthopaedic Association (JOA) scores were noted. Conclusion mNGS outperforms traditional microbiological culture in pathogen detection, especially for rare and critical pathogens. Treatment protocols combining mNGS, microbiological cultures, and pathological examinations are effective and provide valuable clinical insights for treating spinal infections.
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Affiliation(s)
- Jiayi Chen
- Department of Spinal Orthopedics, The Second Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, People’s Republic of China
| | - Yonghong Liu
- Department of Preventive Health Care, The Second Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, People’s Republic of China
| | - Shengsheng Huang
- Department of Spinal Orthopedics, The Second Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, People’s Republic of China
| | - Zixiang Pang
- Department of Spinal Orthopedics, The Second Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, People’s Republic of China
| | - Qian Wei
- Department of Spinal Orthopedics, The Second Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, People’s Republic of China
| | - Yuzhen Liu
- Department of Spinal Orthopedics, The Second Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, People’s Republic of China
| | - Hongyuan Qin
- Department of Spinal Orthopedics, The Second Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, People’s Republic of China
| | - Yuanming Chen
- Department of Spinal Orthopedics, The Second Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, People’s Republic of China
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Ugwu OPC, Alum EU, Ugwu JN, Eze VHU, Ugwu CN, Ogenyi FC, Okon MB. Harnessing technology for infectious disease response in conflict zones: Challenges, innovations, and policy implications. Medicine (Baltimore) 2024; 103:e38834. [PMID: 38996110 PMCID: PMC11245197 DOI: 10.1097/md.0000000000038834] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/13/2024] [Accepted: 06/14/2024] [Indexed: 07/14/2024] Open
Abstract
Epidemic outbreaks of infectious diseases in conflict zones are complex threats to public health and humanitarian activities that require creativity approaches of reducing their damage. This narrative review focuses on the technology intersection with infectious disease response in conflict zones, and complexity of healthcare infrastructure, population displacement, and security risks. This narrative review explores how conflict-related destruction is harmful towards healthcare systems and the impediments to disease surveillance and response activities. In this regards, the review also considered the contributions of technological innovations, such as the improvement of epidemiological surveillance, mobile health (mHealth) technologies, genomic sequencing, and surveillance technologies, in strengthening infectious disease management in conflict settings. Ethical issues related to data privacy, security and fairness are also covered. By advisement on policy that focuses on investment in surveillance systems, diagnostic capacity, capacity building, collaboration, and even ethical governance, stakeholders can leverage technology to enhance the response to infectious disease in conflict settings and, thus, protect the global health security. This review is full of information for researchers, policymakers, and practitioners who are dealing with the issues of infectious disease outbreaks in conflicts worn areas.
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Affiliation(s)
| | - Esther Ugo Alum
- Department of Publication and Extension, Kampala International University, Uganda, Kampala, Uganda
| | - Jovita Nnenna Ugwu
- Department of Publication and Extension, Kampala International University, Uganda, Kampala, Uganda
| | - Val Hyginus Udoka Eze
- Department of Publication and Extension, Kampala International University, Uganda, Kampala, Uganda
| | - Chinyere N Ugwu
- Department of Publication and Extension, Kampala International University, Uganda, Kampala, Uganda
| | - Fabian C Ogenyi
- Department of Publication and Extension, Kampala International University, Uganda, Kampala, Uganda
| | - Michael Ben Okon
- Department of Publication and Extension, Kampala International University, Uganda, Kampala, Uganda
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Elgayar FA, Gouda MK, Badran AA, El Halfawy NM. Pathogenomics analysis of high-risk clone ST147 multidrug-resistant Klebsiella pneumoniae isolated from a patient in Egypt. BMC Microbiol 2024; 24:256. [PMID: 38987681 PMCID: PMC11234735 DOI: 10.1186/s12866-024-03389-z] [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: 03/13/2024] [Accepted: 06/19/2024] [Indexed: 07/12/2024] Open
Abstract
BACKGROUND The emergence of multi-drug-resistant Klebsiella pneumoniae (MDR-KP) represents a serious clinical health concern. Antibiotic resistance and virulence interactions play a significant role in the pathogenesis of K. pneumoniae infections. Therefore, tracking the clinical resistome and virulome through monitoring antibiotic resistance genes (ARG) and virulence factors in the bacterial genome using computational analysis tools is critical for predicting the next epidemic. METHODS In the current study, one hundred extended spectrum β-lactamase (ESBL)-producing clinical isolates were collected from Mansoura University Hospital, Egypt, in a six-month period from January to June 2022. One isolate was selected due to the high resistance phenotype, and the genetic features of MDR-KP recovered from hospitalized patient were investigated. Otherwise, the susceptibility to 25 antimicrobials was determined using the DL Antimicrobial Susceptibility Testing (AST) system. Whole genome sequencing (WGS) using Illumina NovaSeq 6000 was employed to provide genomic insights into K. pneumoniae WSF99 clinical isolate. RESULTS The isolate K. pneumoniae WSF99 was phenotypically resistant to the antibiotics under investigation via antibiotic susceptibility testing. WGS analysis revealed that WSF99 total genome length was 5.7 Mb with an estimated 5,718 protein-coding genes and a G + C content of 56.98 mol%. Additionally, the allelic profile of the WSF99 isolate was allocated to the high-risk clone ST147. Furthermore, diverse antibiotic resistance genes were determined in the genome that explain the high-level resistance phenotypes. Several β-lactamase genes, including blaCTX-M-15, blaTEM-1, blaTEM-12, blaSHV-11, blaSHV-67, and blaOXA-9, were detected in the WSF99 isolate. Moreover, a single carbapenemase gene, blaNDM-5, was predicted in the genome, positioned within a mobile cassette. In addition, other resistance genes were predicted in the genome including, aac(6')-Ib, aph(3')-VI, sul1, sul2, fosA, aadA, arr-2, qnrS1, tetA and tetC. Four plasmid replicons CoIRNAI, IncFIB(K), IncFIB(pQil), and IncR were predicted in the genome. The draft genome analysis revealed the occurrence of genetic mobile elements positioned around the ARGs, suggesting the ease of dissemination via horizontal gene transfer. CONCLUSIONS This study reports a comprehensive pathogenomic analysis of MDR-KP isolated from a hospitalized patient. These findings could be relevant for future studies investigating the diversity of antimicrobial resistance and virulence in Egypt.
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Affiliation(s)
- Fatma A Elgayar
- Department of Botany and Microbiology, Faculty of Science, Alexandria University, Moharram Bek 21511, Alexandria, Egypt
| | - Mona K Gouda
- Department of Botany and Microbiology, Faculty of Science, Alexandria University, Moharram Bek 21511, Alexandria, Egypt
| | - Alaa Aboelnour Badran
- Department of Clinical Pathology, Faculty of Medicine, Mansoura University, Mansoura, Egypt
| | - Nancy M El Halfawy
- Department of Botany and Microbiology, Faculty of Science, Alexandria University, Moharram Bek 21511, Alexandria, Egypt.
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Han X, Huang B, Yang L, Wu J, Zhang H. Metagenomic next-generation sequencing in the early diagnosis of leptospirosis infection presenting as acalculous cholecystitis and septic shock in a non-epidemic area after typhoons: A case report. Clin Case Rep 2024; 12:e9095. [PMID: 38911922 PMCID: PMC11192643 DOI: 10.1002/ccr3.9095] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2024] [Revised: 05/28/2024] [Accepted: 06/05/2024] [Indexed: 06/25/2024] Open
Abstract
Key Clinical Message Leptospirosis is an important zoonosis worldwide. Due to nonspecific clinical manifestation and poor recognition in non-epidemic area, there is often a delay in diagnosis and treatment. Early diagnosis from Metagenomic next-generation sequencing test is crucial for timely intervention. Abstract We presented a case of a 19-year-old male patient who developed leptospirosis infection characterized by acalculous cholecystitis and septic shock after typhoon events. Metagenomic next-generation sequencing (mNGS) helped to early diagnose leptospirosis infection. Finally, the patient achieved full recovery following the antibiotic treatment in addition to supportive care and was discharged.
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Affiliation(s)
- Xueying Han
- Department of Critical Care MedicineShenzhen Nanshan HospitalShenzhenChina
- Department of Critical Care MedicineThe 6th Affiliated Hospital of Shenzhen UniversityShenzhenChina
| | - Bihan Huang
- Department of CardiologyShenzhen Nanshan HospitalShenzhenChina
- Department of CardiologyThe 6th Affiliated Hospital of Shenzhen UniversityShenzhenChina
| | - Lilei Yang
- Department of Critical Care MedicineShenzhen Nanshan HospitalShenzhenChina
- Department of Critical Care MedicineThe 6th Affiliated Hospital of Shenzhen UniversityShenzhenChina
| | - Jinglan Wu
- Department of Critical Care MedicineShenzhen Nanshan HospitalShenzhenChina
- Department of Critical Care MedicineThe 6th Affiliated Hospital of Shenzhen UniversityShenzhenChina
| | - Haigang Zhang
- Department of Critical Care MedicineShenzhen Nanshan HospitalShenzhenChina
- Department of Critical Care MedicineThe 6th Affiliated Hospital of Shenzhen UniversityShenzhenChina
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Ghirardelli S, Scaggiante F, Troi C, Valpiana P, Cristofolini G, Aloisi G, Violante B, Russo A, Schaller S, Indelli PF. Multiplex PCR in septic arthritis and periprosthetic joint infections microorganism identification: Results from the application of a new molecular testing diagnostic algorithm. J Exp Orthop 2024; 11:e12097. [PMID: 39035845 PMCID: PMC11260279 DOI: 10.1002/jeo2.12097] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/25/2024] [Revised: 05/16/2024] [Accepted: 06/04/2024] [Indexed: 07/23/2024] Open
Abstract
Purpose Pathogen identification is key in the treatment of septic arthritis (SA) and periprosthetic joint infections (PJI). This study evaluates the outcome of the application of a new, score-based SA and PJI diagnostic algorithm, which includes the execution of molecular testing on synovial fluid. Methods A score-based diagnostic algorithm, which includes serologic and synovial fluid markers determination using multiplex PCR (mPCR) and Next Generation Sequencing (NGS) molecular testing, has been applied to a consecutive series of patients with clinically suspected SA or PJI. Patients with a score ≥6 underwent synovial fluid molecular testing, together with traditional culture, to identify the pathogen and its genetically determined antibiotic resistance. Results One hundred and seventeen joints in 117 patients (62.5% women; average age 73 years) met the criteria for possible SA/PJI. The affected joint was the knee in 87.5% (joint replacement 66.5%; native joint 21%) and the hip in 12.5% (all replaced joints). 43/117 patients (36.7%) were ultimately diagnosed with SA/PJI. Among the various testing technologies applied, mPCR was the main determinant for pathogen identification in 63%, standard culture in 26%, and mNGS in 11%. Staphylococcus aureus and Enterococcus faecalis were the top two microorganisms identified by mPCR, while Staphylococcus epidermidis was the prevalent organism identified by NGS. mPCR detected the presence/absence of the genetically determined antibiotic resistance of all identified microorganisms. The average timeframe for pathogen identification was 3.13 h for mPCR, 4.5 days for culture, and 3.2 days for NGS. Conclusions Molecular diagnostic technologies represent an innovative screening for fast microorganism identification when a joint infection is clinically suspected. Level of Evidence Level IV, case series.
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Affiliation(s)
- Stefano Ghirardelli
- Südtiroler SanitätsbetriebBrixenItaly
- Paracelsus Medical University (PMU), Institute of BiomechanicsParacelsus Medical UniversitySalzburgAustria
| | | | | | - Pieralberto Valpiana
- Südtiroler SanitätsbetriebBrixenItaly
- Paracelsus Medical University (PMU), Institute of BiomechanicsParacelsus Medical UniversitySalzburgAustria
| | | | - Giuseppe Aloisi
- Dipartimento di Medicina Clinica, Sanita' Pubblica, Scienze della Vita e dell'AmbienteUniversita' degli Studi dell'AquilaL'AquilaItaly
| | - Bruno Violante
- Ospedale Isola Tiberina, Gemelli IsolaUOC Chirurgia Protesica e TraumatologicaRomeItaly
| | | | - Sebastian Schaller
- Paracelsus Medical University (PMU), Institute of BiomechanicsParacelsus Medical UniversitySalzburgAustria
| | - Pier F. Indelli
- Südtiroler SanitätsbetriebBrixenItaly
- Paracelsus Medical University (PMU), Institute of BiomechanicsParacelsus Medical UniversitySalzburgAustria
- CESAT, Azienda Sanitaria Toscana CentroFucecchioItaly
- Department of Orthopaedic SurgeryStanford University School of MedicineRedwood CityCaliforniaUSA
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Lv H, Liao S, Shi Z, Guo Y, Zhou J, Chen H, Luo F, Xu J, Zhang Z, Zhang Z. Application of metagenomic next-generation sequencing for rapid molecular identification in spinal infection diagnosis. Front Cell Infect Microbiol 2024; 14:1382635. [PMID: 39011516 PMCID: PMC11247381 DOI: 10.3389/fcimb.2024.1382635] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2024] [Accepted: 06/10/2024] [Indexed: 07/17/2024] Open
Abstract
Objective This study aimed to determine the sensitivity and specificity of metagenomic next-generation sequencing (mNGS) for detecting pathogens in spinal infections and to identify the differences in the diagnostic performance between mNGS and targeted next-generation sequencing (tNGS). Methods A total of 76 consecutive patients with suspected spinal infections who underwent mNGS, culture, and histopathological examinations were retrospectively studied. The final diagnosis of the patient was determined by combining the clinical treatment results, pathological examinations, imaging changes and laboratory indicators. The sensitivity and specificity of mNGS and culture were determined. Results The difference between the two detection rates was statistically significant (p < 0.001), with mNGS exhibiting a significantly higher detection rate (77.6% versus 18.4%). The average diagnosis time of mNGS was significantly shorter than that of bacterial culture (p < 0.001, 1.65 versus 3.07 days). The sensitivity and accuracy of mNGS were significantly higher than that of the culture group (p < 0.001, 82.3% versus 17.5%; 75% versus 27.6%), whereas the specificity of mNGS (42.9%) was lower than that of the culture group (p > 0.05, 42.9% versus 76.9%). The sensitivity, specificity, accuracy, and positive predictive value (PPV) of pus were higher than those of tissue samples for mNGS, whereas for culture, the sensitivity, specificity, accuracy, and PPV of tissue samples were higher than those of pus. tNGS demonstrated higher sensitivity and accuracy in diagnosing tuberculosis (TB) than mNGS (80% versus 50%; 87.5% versus 68.8%). Conclusion mNGS for spinal infection demonstrated better diagnostic value in developing an antibiotic regimen earlier, and it is recommended to prioritize pus samples for testing through mNGS. Moreover, tNGS outperformed other methods for diagnosing spinal TB and identifying antibiotic-resistance genes in drug-resistant TB.
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Affiliation(s)
- Hui Lv
- Department of Spine Surgery, Jiangbei Branch of Southwest Hospital, 958th Hospital of the PLA Army, Chongqing, China
- Department of Orthopaedic, Southwest Hospital, The First Affiliated Hospital of Army Medical University, Chongqing, China
| | - Sheng Liao
- Department of Spine Surgery, Jiangbei Branch of Southwest Hospital, 958th Hospital of the PLA Army, Chongqing, China
| | - Zhenzhen Shi
- Department of Medecine, Dinfectome Inc., Nanjing, Jiangsu, China
| | - Yuan Guo
- Department of Spine Surgery, Jiangbei Branch of Southwest Hospital, 958th Hospital of the PLA Army, Chongqing, China
| | - JianHong Zhou
- Department of Spine Surgery, Jiangbei Branch of Southwest Hospital, 958th Hospital of the PLA Army, Chongqing, China
| | - Hui Chen
- Department of Spine Surgery, Jiangbei Branch of Southwest Hospital, 958th Hospital of the PLA Army, Chongqing, China
| | - Fei Luo
- Department of Spine Surgery, Jiangbei Branch of Southwest Hospital, 958th Hospital of the PLA Army, Chongqing, China
- Department of Orthopaedic, Southwest Hospital, The First Affiliated Hospital of Army Medical University, Chongqing, China
| | - JianZhong Xu
- Department of Spine Surgery, Jiangbei Branch of Southwest Hospital, 958th Hospital of the PLA Army, Chongqing, China
- Department of Orthopaedic, Southwest Hospital, The First Affiliated Hospital of Army Medical University, Chongqing, China
| | - ZhongRong Zhang
- Department of Spine Surgery, Jiangbei Branch of Southwest Hospital, 958th Hospital of the PLA Army, Chongqing, China
- Department of Orthopaedic, Southwest Hospital, The First Affiliated Hospital of Army Medical University, Chongqing, China
| | - ZeHua Zhang
- Department of Spine Surgery, Jiangbei Branch of Southwest Hospital, 958th Hospital of the PLA Army, Chongqing, China
- Department of Orthopaedic, Southwest Hospital, The First Affiliated Hospital of Army Medical University, Chongqing, China
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