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Zheng H, Chen X, Li W, Lu J, Chen X. Establishment of a Fast Diagnostic Method for Sepsis Pathogens Based on M1 Bead Enrichment. Curr Microbiol 2023; 80:166. [PMID: 37022487 DOI: 10.1007/s00284-023-03280-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2022] [Accepted: 03/21/2023] [Indexed: 04/07/2023]
Abstract
Blood culture-based sepsis diagnostic methods usually cannot obtain positive results in a timely manner. Molecular diagnostic methods, such as real-time PCR without blood culture, would be more time-saving and suitable for pathogenic diagnosis of sepsis, while their sensitivities have always been unsatisfactory for the usually low concentration of pathogens in the blood of sepsis patients. In this study, we established a fast diagnostic method using magnetic beads coated with human recombined mannose-binding lectin that makes it possible to concentrate pathogens from human plasma that have low concentrations of pathogens. With subsequent microculture (MC) and real-time PCR, this method allowed the detection of 1-10 CFUs/ml of Staphylococcus aureus, Group A Streptococcus, Escherichia coli, Pseudomonas aeruginosa, Candida tropicalis, or C. albicans from human plasma within 9.5 h, which was 21-80 h earlier than blood culture. The combination of pathogen enrichment and MC made the detection of sepsis-causing pathogens more time-saving and more sensitive than blood culture or real-time PCR alone.
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Affiliation(s)
- Hao Zheng
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, China
| | - Xiaoli Chen
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, China
| | - Wenge Li
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, China
| | - Jinxing Lu
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, China
| | - Xiaoping Chen
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, China.
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Fiore M, Maraolo AE, Leone S, Gentile I, Cuomo A, Schiavone V, Bimonte S, Pace MC, Cascella M. Spontaneous peritonitis in critically ill cirrhotic patients: a diagnostic algorithm for clinicians and future perspectives. Ther Clin Risk Manag 2017; 13:1409-1414. [PMID: 29081656 PMCID: PMC5652902 DOI: 10.2147/tcrm.s144262] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Spontaneous peritonitis (SP) is the most common infection among decompensated end-stage liver disease patients. SP is the infection of ascitic fluid (neutrophil ascitic count ≥250/mL) without an alternative focus of abdominal infection. According to the causative agent, clinicians can make the diagnosis of spontaneous bacterial peritonitis or spontaneous fungal peritonitis. The mortality rate is very high, ranging from one-fifth of the patients with spontaneous bacterial peritonitis to four-fifths of the patients with spontaneous fungal peritonitis. An immediate and accurate diagnosis can improve the outcome in end-stage liver disease patients. The aim of this work is to provide physicians with a practical diagnostic guidance for SP diagnosis according to current evidence, in order to improve the management of cirrhotic patients with infected ascitic fluid.
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Affiliation(s)
- Marco Fiore
- Department of Anaesthesiological, Surgical and Emergency Sciences, University of Campania "Luigi Vanvitelli", Naples, Italy
| | - Alberto Enrico Maraolo
- Department of Clinical Medicine and Surgery, Section of Infectious Diseases, University of Naples Federico II, Naples, Italy
| | - Sebastiano Leone
- Division of Infectious Diseases, "San Giuseppe Moscati" Hospital, Avellino, Italy
| | - Ivan Gentile
- Department of Clinical Medicine and Surgery, Section of Infectious Diseases, University of Naples Federico II, Naples, Italy
| | - Arturo Cuomo
- Division of Anesthesia, Department of Anesthesia and Pain Medicine, Istituto Nazionale Tumori - IRCCS - Fondazione G. Pascale, Naples, Italy
| | - Vincenzo Schiavone
- Division of Anesthesia and Intensive Care, Hospital "Pineta Grande", Castel Volturno, Italy
| | - Sabrina Bimonte
- Division of Anesthesia, Department of Anesthesia and Pain Medicine, Istituto Nazionale Tumori - IRCCS - Fondazione G. Pascale, Naples, Italy
| | - Maria Caterina Pace
- Department of Anaesthesiological, Surgical and Emergency Sciences, University of Campania "Luigi Vanvitelli", Naples, Italy
| | - Marco Cascella
- Division of Anesthesia, Department of Anesthesia and Pain Medicine, Istituto Nazionale Tumori - IRCCS - Fondazione G. Pascale, Naples, Italy
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Herberg JA, Kaforou M, Wright VJ, Shailes H, Eleftherohorinou H, Hoggart CJ, Cebey-Lopez M, Carter MJ, Janes VA, Gormley S, Shimizu C, Tremoulet AH, Barendregt AM, Salas A, Kanegaye J, Pollard AJ, Faust SN, Patel S, Kuijpers T, Martinon-Torres F, Burns JC, Coin LJM, Levin M. Diagnostic Test Accuracy of a 2-Transcript Host RNA Signature for Discriminating Bacterial vs Viral Infection in Febrile Children. JAMA 2016; 316:835-45. [PMID: 27552617 PMCID: PMC5997174 DOI: 10.1001/jama.2016.11236] [Citation(s) in RCA: 208] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
IMPORTANCE Because clinical features do not reliably distinguish bacterial from viral infection, many children worldwide receive unnecessary antibiotic treatment, while bacterial infection is missed in others. OBJECTIVE To identify a blood RNA expression signature that distinguishes bacterial from viral infection in febrile children. DESIGN, SETTING, AND PARTICIPANTS Febrile children presenting to participating hospitals in the United Kingdom, Spain, the Netherlands, and the United States between 2009-2013 were prospectively recruited, comprising a discovery group and validation group. Each group was classified after microbiological investigation as having definite bacterial infection, definite viral infection, or indeterminate infection. RNA expression signatures distinguishing definite bacterial from viral infection were identified in the discovery group and diagnostic performance assessed in the validation group. Additional validation was undertaken in separate studies of children with meningococcal disease (n = 24) and inflammatory diseases (n = 48) and on published gene expression datasets. EXPOSURES A 2-transcript RNA expression signature distinguishing bacterial infection from viral infection was evaluated against clinical and microbiological diagnosis. MAIN OUTCOMES AND MEASURES Definite bacterial and viral infection was confirmed by culture or molecular detection of the pathogens. Performance of the RNA signature was evaluated in the definite bacterial and viral group and in the indeterminate infection group. RESULTS The discovery group of 240 children (median age, 19 months; 62% male) included 52 with definite bacterial infection, of whom 36 (69%) required intensive care, and 92 with definite viral infection, of whom 32 (35%) required intensive care. Ninety-six children had indeterminate infection. Analysis of RNA expression data identified a 38-transcript signature distinguishing bacterial from viral infection. A smaller (2-transcript) signature (FAM89A and IFI44L) was identified by removing highly correlated transcripts. When this 2-transcript signature was implemented as a disease risk score in the validation group (130 children, with 23 definite bacterial, 28 definite viral, and 79 indeterminate infections; median age, 17 months; 57% male), all 23 patients with microbiologically confirmed definite bacterial infection were classified as bacterial (sensitivity, 100% [95% CI, 100%-100%]) and 27 of 28 patients with definite viral infection were classified as viral (specificity, 96.4% [95% CI, 89.3%-100%]). When applied to additional validation datasets from patients with meningococcal and inflammatory diseases, bacterial infection was identified with a sensitivity of 91.7% (95% CI, 79.2%-100%) and 90.0% (95% CI, 70.0%-100%), respectively, and with specificity of 96.0% (95% CI, 88.0%-100%) and 95.8% (95% CI, 89.6%-100%). Of the children in the indeterminate groups, 46.3% (63/136) were classified as having bacterial infection, although 94.9% (129/136) received antibiotic treatment. CONCLUSIONS AND RELEVANCE This study provides preliminary data regarding test accuracy of a 2-transcript host RNA signature discriminating bacterial from viral infection in febrile children. Further studies are needed in diverse groups of patients to assess accuracy and clinical utility of this test in different clinical settings.
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Affiliation(s)
- Jethro A Herberg
- Section of Paediatrics, Division of Infectious Diseases, Department of Medicine, Imperial College London, London W2 1PG, UK
| | - Myrsini Kaforou
- Section of Paediatrics, Division of Infectious Diseases, Department of Medicine, Imperial College London, London W2 1PG, UK
| | - Victoria J Wright
- Section of Paediatrics, Division of Infectious Diseases, Department of Medicine, Imperial College London, London W2 1PG, UK
| | - Hannah Shailes
- Section of Paediatrics, Division of Infectious Diseases, Department of Medicine, Imperial College London, London W2 1PG, UK
| | - Hariklia Eleftherohorinou
- Section of Paediatrics, Division of Infectious Diseases, Department of Medicine, Imperial College London, London W2 1PG, UK
| | - Clive J Hoggart
- Section of Paediatrics, Division of Infectious Diseases, Department of Medicine, Imperial College London, London W2 1PG, UK
| | - Miriam Cebey-Lopez
- Translational Paediatrics and Infectious Diseases section, Department of Paediatrics, Hospital Clínico Universitario de Santiago, Santiago de Compostela, Galicia, Spain, and Grupo de Investigación en Genética, Vacunas, Infecciones y Pediatría (GENVIP), Healthcare research Institute of Santiago de Compostela and Universidade de Santiago de Compostela, Spain
| | - Michael J Carter
- Section of Paediatrics, Division of Infectious Diseases, Department of Medicine, Imperial College London, London W2 1PG, UK
| | - Victoria A Janes
- Section of Paediatrics, Division of Infectious Diseases, Department of Medicine, Imperial College London, London W2 1PG, UK
| | - Stuart Gormley
- Section of Paediatrics, Division of Infectious Diseases, Department of Medicine, Imperial College London, London W2 1PG, UK
| | - Chisato Shimizu
- Department of Pediatrics, University of California San Diego, La Jolla, California, USA
- Rady Children’s Hospital San Diego, San Diego, California, USA
| | - Adriana H Tremoulet
- Department of Pediatrics, University of California San Diego, La Jolla, California, USA
- Rady Children’s Hospital San Diego, San Diego, California, USA
| | - Anouk M Barendregt
- Emma Children’s Hospital, Department of Paediatric Haematology, Immunology & Infectious Disease, Academic Medical Centre, University of Amsterdam, Amsterdam, The Netherlands
| | - Antonio Salas
- Translational Paediatrics and Infectious Diseases section, Department of Paediatrics, Hospital Clínico Universitario de Santiago, Santiago de Compostela, Galicia, Spain, and Grupo de Investigación en Genética, Vacunas, Infecciones y Pediatría (GENVIP), Healthcare research Institute of Santiago de Compostela and Universidade de Santiago de Compostela, Spain
- Unidade de Xenética, Departamento de Anatomía Patolóxica e Ciencias Forenses, and Instituto de Ciencias Forenses, Grupo de Medicina Xenómica, Spain
| | - John Kanegaye
- Department of Pediatrics, University of California San Diego, La Jolla, California, USA
- Rady Children’s Hospital San Diego, San Diego, California, USA
| | - Andrew J Pollard
- Department of Paediatrics, University of Oxford and the NIHR Oxford Biomedical Research Centre, Oxford, UK
| | - Saul N Faust
- NIHR Wellcome Trust Clinical Research Facility, University of Southampton UK
- University Hospital Southampton NHS Foundation Trust, Southampton, UK
| | - Sanjay Patel
- University Hospital Southampton NHS Foundation Trust, Southampton, UK
| | - Taco Kuijpers
- Emma Children’s Hospital, Department of Paediatric Haematology, Immunology & Infectious Disease, Academic Medical Centre, University of Amsterdam, Amsterdam, The Netherlands
- Sanquin Research and Landsteiner Laboratory, Department of Blood Cell Research, Amsterdam Medical Centre, University of Amsterdam, Amsterdam, The Netherlands
| | - Federico Martinon-Torres
- Translational Paediatrics and Infectious Diseases section, Department of Paediatrics, Hospital Clínico Universitario de Santiago, Santiago de Compostela, Galicia, Spain, and Grupo de Investigación en Genética, Vacunas, Infecciones y Pediatría (GENVIP), Healthcare research Institute of Santiago de Compostela and Universidade de Santiago de Compostela, Spain
| | - Jane C Burns
- Department of Pediatrics, University of California San Diego, La Jolla, California, USA
- Rady Children’s Hospital San Diego, San Diego, California, USA
| | - Lachlan JM Coin
- Institute for Molecular Bioscience, University of Queensland, St Lucia, Queensland, Australia
| | - Michael Levin
- Section of Paediatrics, Division of Infectious Diseases, Department of Medicine, Imperial College London, London W2 1PG, UK
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de Biase D, de Luca C, Gragnano G, Visani M, Bellevicine C, Malapelle U, Tallini G, Troncone G. Fully automated PCR detection of KRAS mutations on pancreatic endoscopic ultrasound fine-needle aspirates. J Clin Pathol 2016; 69:jclinpath-2016-203696. [PMID: 27122185 DOI: 10.1136/jclinpath-2016-203696] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2016] [Accepted: 04/02/2016] [Indexed: 02/05/2023]
Abstract
AIMS In cystic and solid pancreatic lesions, KRAS mutational status refines the diagnosis of uncertain endoscopic ultrasound (EUS) aspirates. This test should have a fast turnaround time and ideally be performed at the centre where the patient is diagnosed. The Idylla KRAS Mutation Test enables standardisation even in units without molecular expertise. METHODS The Idylla test was designed for use with formalin-fixed paraffin-embedded (FFPE) sections. However, we directly pipetted 3 µL (corresponding to 1/10th of a DNA preparation from the aspirate sample) in the cartridge, which was automatically run as if an FFPE sample had been inserted. The performance was compared with Sanger sequencing, Allele Specific Locked Nucleic Acid PCR (ASLNAqPCR), and 454 Next Generation Sequencing (454-NGS) in light of clinicopathological end points. RESULTS Idylla yielded valid results in 49/52 (94.2%) cases, in 2 h. A total of 18/49 cases showed mutation either in KRAS exon 2 (14/18) or in exon 3 (4/18). Idylla KRAS test had 100% specificity and a sensitivity (55.1%) higher than Sanger sequencing (41.3%) and identical to ASLNAqPCR (55.1%). When the low-abundant mutant allele (<5%) cases were excluded from the analysis, the Idylla KRAS Mutation Test clinical sensitivity increased to 61.9% approaching that of 454-NGS (66.6%). CONCLUSIONS This is the first study that applied the novel Idylla KRAS test to the clinical setting of pancreatic cancer. In particular, this system can be easily implemented in the routine assessment of pancreatic EUS-fine-needle aspiration-derived DNA samples to quickly provide information on KRAS mutational status to supplement cytological evaluation.
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Affiliation(s)
- Dario de Biase
- Department of Pharmacy and Biotechnology (FaBiT), Molecular Pathology Unit AUSL di Bologna, Bellaria Hospital, University of Bologna, Bologna, Italy
| | - Caterina de Luca
- Department of Public Health, Anatomic Pathology Unit, University of Napoli Federico II School of Medicine, Napoli, Italy
| | - Gianluca Gragnano
- Department of Public Health, Anatomic Pathology Unit, University of Napoli Federico II School of Medicine, Napoli, Italy
| | - Michela Visani
- Department of Medicine (DIMES), Molecular Pathology Unit AUSL di Bologna, Bellaria Hospital, University of Bologna School of Medicine, Bologna, Italy
| | - Claudio Bellevicine
- Department of Public Health, Anatomic Pathology Unit, University of Napoli Federico II School of Medicine, Napoli, Italy
| | - Umberto Malapelle
- Department of Public Health, Anatomic Pathology Unit, University of Napoli Federico II School of Medicine, Napoli, Italy
| | - Giovanni Tallini
- Department of Medicine (DIMES), Molecular Pathology Unit AUSL di Bologna, Bellaria Hospital, University of Bologna School of Medicine, Bologna, Italy
| | - Giancarlo Troncone
- Department of Public Health, Anatomic Pathology Unit, University of Napoli Federico II School of Medicine, Napoli, Italy
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Aryee A, Edgeworth JD. Carriage, Clinical Microbiology and Transmission of Staphylococcus aureus. Curr Top Microbiol Immunol 2016; 409:1-19. [PMID: 27097812 DOI: 10.1007/82_2016_5] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Staphylococcus aureus is one of the most important bacterial pathogens in clinical practice and a major diagnostic focus for the routine microbiology laboratory. It is carried as a harmless commensal in up to two-thirds of the population at any one time predominantly not only in the anterior nares, but also in multiple other sites such as the groin, axilla, throat, perineum, vagina and rectum. It colonizes skin breach sites, such as ulcers and wounds, and causes superficial and deep skin and soft tissue infections and life-threatening deep seated infections particularly endocarditis and osteomyelitis. S. aureus is constantly evolving through mutation and uptake of mobile genetic elements that confer increasing resistance and virulence. Since the 1960s, hospitals have had to contend with emergence of methicillin-resistant S. aureus (MRSA) strains that spread better in hospitals than methicillin-susceptible S. aureus (MSSA) and are harder to treat. Since the 1980s, distinct community MRSA strains have also emerged that cause severe skin and respiratory infections. Conventional identification of MSSA and MRSA in the microbiology laboratory involves microscopy, culture and biochemical analysis that for most samples is straightforward but slow, taking at least 48 h. This delay has significant consequences for individual patient care and public health, through inadequate or excessive empiric antibiotic use, and failure to implement appropriate infection control measures for MRSA-colonized patients during those first 48 h. This unmet need has driven development of rapid molecular diagnostics that either complement or replace conventional culture techniques in the laboratory, or can be placed in the clinical environment as point-of-care (POC) devices. These new technologies provide results to clinicians anything from within an hour to 24 h, depending on sample and clinical setting, and should transform management of patients with S. aureus and other bacterial diseases; however, uptake is often slow due to the disruptive effect of new technologies, costs of transition and uncertainty of the optimal solution given successive advances. More evidence of the health economic, clinical and antimicrobial resistance benefit will help support introduction of these new technologies. Finally, preventing MRSA transmission has been a priority for healthcare organizations for many years. There have been significant recent reductions in transmission following local and national campaigns to re-enforce basic and heightened infection control interventions such as universal hand hygiene, barrier nursing, decolonization and isolation of MRSA-colonized patients detected through routine culture or screening policies. Developments in whole genome sequencing are providing greater insight into reservoirs and routes of transmission that should help better target interventions to ensure sustainable control of endemic strains and to identify and prevent emergence of new strains.
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Affiliation(s)
- Anna Aryee
- Centre for Clinical Infection and Diagnostics Research, Department of Infectious Diseases, Kings College London and Guy's and St. Thomas' NHS Foundation Trust, 5th Floor North Wing, Westminster Bridge Road, London, SE1 7EH, UK
| | - Jonathan D Edgeworth
- Centre for Clinical Infection and Diagnostics Research, Department of Infectious Diseases, Kings College London and Guy's and St. Thomas' NHS Foundation Trust, 5th Floor North Wing, Westminster Bridge Road, London, SE1 7EH, UK.
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