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Jagannath A, Li Y, Cong H, Hassan J, Gonzalez G, Wang W, Zhang N, Gilchrist MD. UV-Assisted Hyperbranched Poly(β-amino ester) Modification of a Silica Membrane for Two-Step Microfluidic DNA Extraction from Blood. ACS APPLIED MATERIALS & INTERFACES 2023. [PMID: 37319124 DOI: 10.1021/acsami.3c03523] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
Integrating nucleic acid extraction in amplification-based point-of-care diagnostics will be a significant feature for next-generation point-of-care virus detection devices. However, extracting DNA efficiently on a microfluidic chip poses many technological and commercialization challenges, including manual steps, multiple instruments, pretreatment processes, and the use of organic solvents (ethanol, IPA) that inhibit detection, which is not viable with routine testing such as viral load monitoring of transplant patients for post-operative care. This paper presents a microfluidic system capable of two-step DNA extraction from blood using a UV-assisted hyperbranched poly(β-amino ester) (HPAE)-modified silica membrane for cytomegalovirus (CMV) detection in a rapid and instrument-free manner without the presence of amplification inhibitors. HPAEs of varying branch ratios were synthesized, screened, and coated on a silica membrane and bonded between two layers of poly(methyl methacrylate) (PMMA) substrates. Our system could selectively extract DNA from blood with an efficiency of 94% and a lower limit viral load of 300 IU/mL in 20 min. The extracted DNA was used as the template for real-time loop-mediated isothermal amplification (LAMP)-based detection of CMV and was found to produce a fluorescent signal intensity that was comparable with commercially extracted templates. This system can be integrated easily with a nucleic acid amplification system and used for routine rapid testing of viral load in patient blood samples.
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Affiliation(s)
- Akshaya Jagannath
- School of Mechanical and Materials Engineering, University College Dublin, Belfield, Dublin 4, Ireland
| | - Yinghao Li
- The Charles Institute of Dermatology, School of Medicine, University College Dublin, Belfield, Dublin 4, Ireland
| | - Hengji Cong
- School of Mechanical and Materials Engineering, University College Dublin, Belfield, Dublin 4, Ireland
| | - Jaythoon Hassan
- National Virus Reference Laboratory, University College Dublin, Belfield, Dublin 4, Ireland
| | - Gabriel Gonzalez
- National Virus Reference Laboratory, University College Dublin, Belfield, Dublin 4, Ireland
- International Collaboration Unit, Research Center for Zoonosis Control, Hokkaido University, N20 W10, Kita-ku, Sapporo 001-0020, Japan
| | - Wenxin Wang
- The Charles Institute of Dermatology, School of Medicine, University College Dublin, Belfield, Dublin 4, Ireland
| | - Nan Zhang
- School of Mechanical and Materials Engineering, University College Dublin, Belfield, Dublin 4, Ireland
- MiNAN Technologies Ltd., NovaUCD, Belfield, Dublin 4, Ireland
| | - Michael D Gilchrist
- School of Mechanical and Materials Engineering, University College Dublin, Belfield, Dublin 4, Ireland
- MiNAN Technologies Ltd., NovaUCD, Belfield, Dublin 4, Ireland
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2
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Bocchetti M, Ferraro MG, Melisi F, Grisolia P, Scrima M, Cossu AM, Yau TO. Overview of current detection methods and microRNA potential in Clostridioides difficile infection screening. World J Gastroenterol 2023; 29:3385-3399. [PMID: 37389232 PMCID: PMC10303512 DOI: 10.3748/wjg.v29.i22.3385] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/25/2023] [Revised: 03/23/2023] [Accepted: 05/04/2023] [Indexed: 06/06/2023] Open
Abstract
Clostridioides difficile (formerly called Clostridium difficile, C. difficile) infection (CDI) is listed as an urgent threat on the 2019 antibiotic resistance threats report in the United States by the Centers for Disease Control and Prevention. Early detection and appropriate disease management appear to be essential. Meanwhile, although the majority of cases are hospital-acquired CDI, community-acquired CDI cases are also on the rise, and this vulnerability is not limited to immunocompromised patients. Gastrointestinal treatments and/or gastrointestinal tract surgeries may be required for patients diagnosed with digestive diseases. Such treatments could suppress or interfere with the patient’s immune system and disrupt gut flora homeostasis, creating a suitable microecosystem for C. difficile overgrowth. Currently, stool-based non-invasive screening is the first-line approach to CDI diagnosis, but the accuracy is varied due to different clinical microbiology detection methods; therefore, improving reliability is clearly required. In this review, we briefly summarised the life cycle and toxicity of C. difficile, and we examined existing diagnostic approaches with an emphasis on novel biomarkers such as microRNAs. These biomarkers can be easily detected through non-invasive liquid biopsy and can yield crucial information about ongoing pathological phenomena, particularly in CDI.
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Affiliation(s)
- Marco Bocchetti
- Department of Precision Medicine, University of Campania “Luigi Vanvitelli,” Naples 80138, Italy
- Department of Molecular Oncology, Precision Medicine Laboratory and COVID19 Laboratory, Biogem Scarl, Ariano Irpino 83031, Italy
| | - Maria Grazia Ferraro
- School of Infection and Immunity, College of Medical Veterinary and Life Sciences, University of Glasgow, Glasgow G12 8QQ, United Kingdom
- Department of Pharmacy, School of Medicine and Surgery, University of Naples “Federico II,” Naples 80131, Italy
| | - Federica Melisi
- Department of Precision Medicine, University of Campania “Luigi Vanvitelli,” Naples 80138, Italy
- Department of Molecular Oncology, Precision Medicine Laboratory and COVID19 Laboratory, Biogem Scarl, Ariano Irpino 83031, Italy
| | - Piera Grisolia
- Department of Precision Medicine, University of Campania “Luigi Vanvitelli,” Naples 80138, Italy
- Department of Molecular Oncology, Precision Medicine Laboratory and COVID19 Laboratory, Biogem Scarl, Ariano Irpino 83031, Italy
| | - Marianna Scrima
- Department of Molecular Oncology, Precision Medicine Laboratory and COVID19 Laboratory, Biogem Scarl, Ariano Irpino 83031, Italy
| | - Alessia Maria Cossu
- Department of Precision Medicine, University of Campania “Luigi Vanvitelli,” Naples 80138, Italy
- Department of Molecular Oncology, Precision Medicine Laboratory and COVID19 Laboratory, Biogem Scarl, Ariano Irpino 83031, Italy
| | - Tung On Yau
- School of Science and Technology, Nottingham Trent University, Nottingham NG11 8NS, United Kingdom
- Department of Rural Land Use, Scotland’s Rural College, Aberdeen AB21 9YA, Scotland, United Kingdom
- Department of Health Science, University of the People, Pasadena, CA 9110112, United States
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3
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Gopal A, Yan L, Kashif S, Munshi T, Roy VAL, Voelcker NH, Chen X. Biosensors and Point-of-Care Devices for Bacterial Detection: Rapid Diagnostics Informing Antibiotic Therapy. Adv Healthc Mater 2022; 11:e2101546. [PMID: 34850601 DOI: 10.1002/adhm.202101546] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Revised: 11/20/2021] [Indexed: 02/06/2023]
Abstract
With an exponential rise in antimicrobial resistance and stagnant antibiotic development pipeline, there is, more than ever, a crucial need to optimize current infection therapy approaches. One of the most important stages in this process requires rapid and effective identification of pathogenic bacteria responsible for diseases. Current gold standard techniques of bacterial detection include culture methods, polymerase chain reactions, and immunoassays. However, their use is fraught with downsides with high turnaround time and low accuracy being the most prominent. This imposes great limitations on their eventual application as point-of-care devices. Over time, innovative detection techniques have been proposed and developed to curb these drawbacks. In this review, a systematic summary of a range of biosensing platforms is provided with a strong focus on technologies conferring high detection sensitivity and specificity. A thorough analysis is performed and the benefits and drawbacks of each type of biosensor are highlighted, the factors influencing their potential as point-of-care devices are discussed, and the authors' insights for their translation from proof-of-concept systems into commercial medical devices are provided.
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Affiliation(s)
- Ashna Gopal
- School of Engineering Institute for Bioengineering The University of Edinburgh Edinburgh EH9 3JL UK
| | - Li Yan
- College of Health Science and Environmental Engineering Shenzhen Technology University Shenzhen 518118 China
| | - Saima Kashif
- School of Engineering Institute for Bioengineering The University of Edinburgh Edinburgh EH9 3JL UK
| | - Tasnim Munshi
- School of Chemistry University of Lincoln, Brayford Pool Lincoln Lincolnshire LN6 7TS UK
| | | | - Nicolas H. Voelcker
- Drug Delivery Disposition and Dynamics Monash Institute of Pharmaceutical Sciences Monash University Parkville Victoria VIC 3052 Australia
- Melbourne Centre for Nanofabrication Victorian Node of the Australian National Fabrication Facility Clayton Victoria 3168 Australia
- Commonwealth Scientific and Industrial Research Organisation (CSIRO) Clayton Victoria 3168 Australia
| | - Xianfeng Chen
- School of Engineering Institute for Bioengineering The University of Edinburgh Edinburgh EH9 3JL UK
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4
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Zhang X, Das S, Dunbar S, Tang YW. Molecular and non-molecular approaches to etiologic diagnosis of gastroenteritis. Adv Clin Chem 2020; 99:49-85. [PMID: 32951639 DOI: 10.1016/bs.acc.2020.02.007] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Gastroenteritis is a major cause of mortality and morbidity globally and rapid identification of the causative pathogen is important for appropriate treatment and patient management, implementation of effective infection control measures, reducing hospital length of stay, and reducing overall medical costs. Although stool culture and microscopic examination of diarrheal stool has been the primary method for laboratory diagnosis, culture-independent proteomic and genomic tests are receiving increased attention. Antigen tests for stool pathogens are routinely implemented as rapid and simple analytics whereas molecular tests are now available in various formats from high complexity to waived point-of-care tests. In addition, metagenomic next-generation sequencing stands poised for use as a method for both diagnosis and routine characterization of the gut microbiome in the very near future. Analysis of host biomarkers as indicators of infection status and pathogenesis may also become important for prediction, diagnosis, and monitoring of gastrointestinal infection. Here we review current methods and emerging technologies for the etiologic diagnosis of gastroenteritis in the clinical laboratory. Benefits and limitations of these evolving methods are highlighted.
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Affiliation(s)
- Xin Zhang
- Sichuan Academy of Medical Sciences & Sichuan Provincial People's Hospital, University of Electronic Science and Technology of China, Chengdu, China; Memorial Sloan Kettering Cancer Center, New York, NY, United States
| | | | | | - Yi-Wei Tang
- Memorial Sloan Kettering Cancer Center, New York, NY, United States; Weill Medical College of Cornell University, New York, NY, United States; Cepheid, Danaher Diagnostic Platform, Shanghai, China.
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5
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An Overview of the Molecular Methods in the Diagnosis of Gastrointestinal Infectious Diseases. Int J Microbiol 2020; 2020:8135724. [PMID: 32280346 PMCID: PMC7128059 DOI: 10.1155/2020/8135724] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2019] [Revised: 01/24/2020] [Accepted: 03/02/2020] [Indexed: 12/14/2022] Open
Abstract
Gastrointestinal infectious diseases are very common worldwide and an important cause of morbidity and mortality, particularly in infants in developing countries. Diarrhea and other intestinal infections are caused by a wide range of bacteria, viruses, protozoa, and parasites. Conventional diagnosis of these infections is performed by culture, microscopy, and antigen detection immunoassays. The traditional culture and microscopy procedures are time-consuming, lack sensitivity, and require special laboratory setup and well-trained staff. However, based on the advancement in the molecular diagnostics and with the introduction of commercially available tests, traditional diagnostic techniques have been continuously replaced by these newer rapid antigen detection and molecular-based methods. This review summarizes and discusses the availability, advantages, and disadvantages of molecular methods in the detection and identification of human gastrointestinal pathogens.
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6
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Azrad M, Tkhawkho L, Hamo Z, Peretz A. The diagnostic performance and accuracy of 3 molecular assays for the detection of Clostridium difficile in stool samples, compared with the Xpert® C. difficile assay. J Microbiol Methods 2019; 168:105784. [PMID: 31758952 DOI: 10.1016/j.mimet.2019.105784] [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: 06/24/2019] [Revised: 11/19/2019] [Accepted: 11/19/2019] [Indexed: 11/19/2022]
Abstract
This research compares the performance and diagnostic accuracy of three molecular tests for the detection of Clostridium difficile in stool samples, with the Xpert® C. difficile assay. Fifty-nine positive and twenty-five stool negative samples were analyzed by the BDmax™ Cdiff, the Simplexa C. difficile Direct, and the GenomEra™ C. difficile, and compared with the Xpert® C. difficile routinely used in our laboratory. The highest sensitivity was 94.9% for the BDmax™ Cdiff, followed by GenomEra™ C. difficile with 93.2%, and Simplexa™ C. difficile Direct with 89.8%. The specificities of all assays were 100%. GenomEra™ C. difficile had the highest retesting rate (12%). Simplexa™ C. difficile Direct benefits from both short hands-on time and total-turnaround time and 0% retesting. The differences in performance and accuracy between these three molecular assays are insignificant and all may be used as part of the routine algorithm for detection of C. difficile.
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Affiliation(s)
- Maya Azrad
- Clinical Microbiology Laboratory, The Baruch Padeh Medical Center, Poriya, Tiberias, Israel
| | - Linda Tkhawkho
- Clinical Microbiology Laboratory, The Baruch Padeh Medical Center, Poriya, Tiberias, Israel
| | - Zohar Hamo
- Clinical Microbiology Laboratory, The Baruch Padeh Medical Center, Poriya, Tiberias, Israel
| | - Avi Peretz
- Clinical Microbiology Laboratory, The Baruch Padeh Medical Center, Poriya, Tiberias, Israel; The Azrieli Faculty of Medicine, Bar-Ilan University, Safed, Israel.
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7
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Evaluation of 4 molecular assays as part of a 2-step algorithm for the detection of Clostridium difficile in stool specimens. Diagn Microbiol Infect Dis 2018; 91:1-5. [DOI: 10.1016/j.diagmicrobio.2017.12.018] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2017] [Revised: 12/20/2017] [Accepted: 12/21/2017] [Indexed: 12/19/2022]
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8
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Gomez EJ, Montgomery S, Alby K, Robinson DP, Roundtree SS, Blecker-Shelly D, Sullivan KV. Poor yield of Clostridium difficile testing algorithms using glutamate dehydrogenase antigen and C. difficile toxin enzyme immunoassays in a pediatric population with declining prevalence of clostridium difficile strain BI/NAP1/027. Diagn Microbiol Infect Dis 2018; 91:229-232. [PMID: 29567127 DOI: 10.1016/j.diagmicrobio.2018.02.016] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2017] [Revised: 02/14/2018] [Accepted: 02/21/2018] [Indexed: 01/05/2023]
Abstract
We compared the performance of algorithmic Clostridium difficile infection (CDI) diagnosis with four molecular tests in children. Stool samples in patients 1-18 years old were tested with an algorithm (C. Diff Quik Chek Complete (QCC) reflexed to illumigene C. difficile); AmpliVue C. difficile (ACD); Lyra Direct C. difficile (Lyra); BD MAX C diff (BDM); and Xpert C. difficile (XCD). The gold standard was positivity by two tests. Sensitivity, specificity, positive predictive value, and negative predictive value were 85%, 99%, 93%, 97% for the algorithm; 21%, 99%, 78%, 87% for QCC's toxin component; 94%, 99%, 94%, 99% for ACD; 88%, 99%, 94%, 98% for Lyra; 94%, 100%, 100%, 99% for BDM, and 94%, 99%, 94% and 99% for XCD. 9.6% of samples were ribotype 027. Algorithms may detect CDI with lower sensitivity compared to molecular methods in children. This may be related to low prevalence of NAP-1/ribotype 027.
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Affiliation(s)
- Emily J Gomez
- Department of Pathology and Laboratory Medicine, The Children's Hospital of Philadelphia, 3401 Civic Center Blvd, Philadelphia, PA, USA, 19103; Author's location has changed to Clinical Laboratory, Abington-Jefferson Health, 1200 Old York Rd, Abington, PA, USA, 19001
| | - Sandra Montgomery
- Department of Pathology and Laboratory Medicine, The Children's Hospital of Philadelphia, 3401 Civic Center Blvd, Philadelphia, PA, USA, 19103
| | - Kevin Alby
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, 3400 Spruce St., Philadelphia, PA, USA, 20104
| | - Diana P Robinson
- Department of Pathology and Laboratory Medicine, The Children's Hospital of Philadelphia, 3401 Civic Center Blvd, Philadelphia, PA, USA, 19103
| | - Sylvester S Roundtree
- Department of Pathology and Laboratory Medicine, The Children's Hospital of Philadelphia, 3401 Civic Center Blvd, Philadelphia, PA, USA, 19103
| | - Deborah Blecker-Shelly
- Department of Pathology and Laboratory Medicine, Penn Medicine Princeton Medical Center, 1 Plainsboro Rd, Plainsboro Township, NJ, USA, 08536
| | - Kaede V Sullivan
- Department of Pathology and Laboratory Medicine, Lewis Katz School of Medicine at Temple University, Temple University Health System, 3401 N Broad St., Philadelphia, PA, USA, 19140.
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9
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Lai H, Huang C, Cai J, Ye J, She J, Zheng Y, Wang L, Wei Y, Fang W, Wang X, Tang YW, Luo Y, Jin D. Simultaneous detection and characterization of toxigenic Clostridium difficile directly from clinical stool specimens. Front Med 2017; 12:196-205. [PMID: 29058256 DOI: 10.1007/s11684-017-0560-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2017] [Accepted: 05/17/2017] [Indexed: 02/08/2023]
Abstract
We employed a multiplex polymerase chain reaction (PCR) coupled with capillary electrophoresis (mPCR-CE) targeting six Clostridium difficile genes, including tpi, tcdA, tcdB, cdtA, cdtB, and a deletion in tcdC for simultaneous detection and characterization of toxigenic C. difficile directly from fecal specimens. The mPCR-CE had a limit of detection of 10 colony-forming units per reaction with no cross-reactions with other related bacterial genes. Clinical validation was performed on 354 consecutively collected stool specimens from patients with suspected C. difficile infection and 45 isolates. The results were compared with a reference standard combined with BD MAX Cdiff, real-time cell analysis assay (RTCA), and mPCR-CE. The toxigenic C. difficile species were detected in 36 isolates and 45 stool specimens by the mPCR-CE, which provided a positive rate of 20.3% (81/399). The mPCR-CE had a specificity of 97.2% and a sensitivity of 96.0%, which was higher than RTCA (x2 = 5.67, P = 0.017) but lower than BD MAX Cdiff (P = 0.245). Among the 45 strains, 44 (97.8%) were determined as nonribotype 027 by the mPCR-CE, which was fully agreed with PCR ribotyping. Even though ribotypes 017 (n = 8, 17.8%), 001 (n = 6, 13.3%), and 012 (n = 7, 15.6%) were predominant in this region, ribotype 027 was an important genotype monitored routinely. The mPCR-CE provided an alternative diagnosis tool for the simultaneous detection of toxigenic C. difficile in stool and potentially differentiated between RT027 and non-RT027.
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Affiliation(s)
- Hanjiang Lai
- The First People's Hospital of Xiaoshan District, Hangzhou, 311021, China
| | - Chen Huang
- Department of Microbiology, Zhejiang Provincial Center for Disease Control and Prevention, Hangzhou, 310051, China
| | - Jian Cai
- Department of Disease Control and Prevention, Zhejiang Provincial Center for Disease Control and Prevention, Hangzhou, 310051, China
| | - Julian Ye
- Department of Microbiology, Zhejiang Provincial Center for Disease Control and Prevention, Hangzhou, 310051, China
| | - Jun She
- The First People's Hospital of Xiaoshan District, Hangzhou, 311021, China
| | - Yi Zheng
- Biotherapy Center for Medical Oncology, the First Affiliated Hospital, Zhejiang University, Hangzhou, 310003, China
| | - Liqian Wang
- Department of Laboratory Medicine, Hangzhou First People's Hospital, Hangzhou, 310006, China
| | - Yelin Wei
- The First People's Hospital of Xiaoshan District, Hangzhou, 311021, China
| | - Weijia Fang
- Biotherapy Center for Medical Oncology, the First Affiliated Hospital, Zhejiang University, Hangzhou, 310003, China
| | - Xianjun Wang
- Department of Laboratory Medicine, Hangzhou First People's Hospital, Hangzhou, 310006, China
| | - Yi-Wei Tang
- Department of Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA.,Department of Pathology and Laboratory Medicine, Weill Medical College of Cornell University, New York, NY, 10065, USA
| | - Yun Luo
- Department of Microbiology, Zhejiang Provincial Center for Disease Control and Prevention, Hangzhou, 310051, China.
| | - Dazhi Jin
- Department of Microbiology, Zhejiang Provincial Center for Disease Control and Prevention, Hangzhou, 310051, China.
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10
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Comparative performance study of six commercial molecular assays for rapid detection of toxigenic Clostridium difficile. Clin Microbiol Infect 2017; 23:567-572. [DOI: 10.1016/j.cmi.2017.02.016] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2016] [Revised: 02/13/2017] [Accepted: 02/14/2017] [Indexed: 12/19/2022]
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11
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The risk for Clostridium difficile colitis during hospitalization in asymptomatic carriers. J Hosp Infect 2017; 95:442-443. [DOI: 10.1016/j.jhin.2017.01.013] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2016] [Accepted: 01/23/2017] [Indexed: 11/17/2022]
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Martínez-Meléndez A, Camacho-Ortiz A, Morfin-Otero R, Maldonado-Garza HJ, Villarreal-Treviño L, Garza-González E. Current knowledge on the laboratory diagnosis of Clostridium difficile infection. World J Gastroenterol 2017; 23:1552-1567. [PMID: 28321156 PMCID: PMC5340807 DOI: 10.3748/wjg.v23.i9.1552] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/15/2016] [Revised: 01/21/2017] [Accepted: 02/17/2017] [Indexed: 02/06/2023] Open
Abstract
Clostridium difficile (C. difficile) is a spore-forming, toxin-producing, gram-positive anaerobic bacterium that is the principal etiologic agent of antibiotic-associated diarrhea. Infection with C. difficile (CDI) is characterized by diarrhea in clinical syndromes that vary from self-limited to mild or severe. Since its initial recognition as the causative agent of pseudomembranous colitis, C. difficile has spread around the world. CDI is one of the most common healthcare-associated infections and a significant cause of morbidity and mortality among older adult hospitalized patients. Due to extensive antibiotic usage, the number of CDIs has increased. Diagnosis of CDI is often difficult and has a substantial impact on the management of patients with the disease, mainly with regards to antibiotic management. The diagnosis of CDI is primarily based on the clinical signs and symptoms and is only confirmed by laboratory testing. Despite the high burden of CDI and the increasing interest in the disease, episodes of CDI are often misdiagnosed. The reasons for misdiagnosis are the lack of clinical suspicion or the use of inappropriate tests. The proper diagnosis of CDI reduces transmission, prevents inadequate or unnecessary treatments, and assures best antibiotic treatment. We review the options for the laboratory diagnosis of CDI within the settings of the most accepted guidelines for CDI diagnosis, treatment, and prevention of CDI.
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Abstract
Alteration in the host microbiome at skin and mucosal surfaces plays a role in the function of the immune system, and may predispose immunocompromised patients to infection. Because obligate anaerobes are the predominant type of bacteria present in humans at skin and mucosal surfaces, immunocompromised patients are at increased risk for serious invasive infection due to anaerobes. Laboratory approaches to the diagnosis of anaerobe infections that occur due to pyogenic, polymicrobial, or toxin-producing organisms are described. The clinical interpretation and limitations of anaerobe recovery from specimens, anaerobe-identification procedures, and antibiotic-susceptibility testing are outlined. Bacteriotherapy following analysis of disruption of the host microbiome has been effective for treatment of refractory or recurrent Clostridium difficile infection, and may become feasible for other conditions in the future.
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Affiliation(s)
- Deirdre L Church
- Departments of Pathology & Laboratory Medicine and Medicine, University of Calgary, and Division of Microbiology, Calgary Laboratory Services, Calgary, Alberta, Canada T2N 1N4
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14
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Han S, Shannahan S, Pellish R. Fecal Microbiota Transplant. J Intensive Care Med 2016; 31:577-86. [DOI: 10.1177/0885066615594344] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2014] [Accepted: 05/14/2015] [Indexed: 12/16/2022]
Abstract
Clostridium difficile infection (CDI) has steadily increased in incidence since the 1990s, with an associated increase in recurrence and severity, which has in turn lead to more intensive care unit (ICU) admissions. The development of recurrent CDI, in particular, has been associated with increasing patient morbidity and mortality as well as an immense financial burden on the health care system. Recently, fecal microbiota transplantation (FMT) has received much publicity as an effective means of treatment for recurrent CDI. The goal of this review is to provide evidence-based recommendations for the diagnosis and management of CDI, with a particular focus on FMT and its utilization in the ICU.
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Affiliation(s)
- Samuel Han
- University of Massachusetts Medical School, Worcester, MA, USA
| | - Sarah Shannahan
- University of Massachusetts Medical School, Worcester, MA, USA
| | - Randall Pellish
- University of Massachusetts Medical School, Worcester, MA, USA
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15
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Neuendorf M, Guadarrama-Gonzalez R, Lamik B, MacKenzie CR. A prospective study of two isothermal amplification assays compared with real-time PCR, CCNA and toxigenic culture for the diagnosis of Clostridium difficile infection. BMC Microbiol 2016; 16:19. [PMID: 26868647 PMCID: PMC4751656 DOI: 10.1186/s12866-016-0635-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2015] [Accepted: 02/03/2016] [Indexed: 01/04/2023] Open
Abstract
Background New molecular methods of detecting Clostridium difficile infection (CDI) provide the routine lab with a sensitive random access method to produce results that are available in a shorter time than traditional methods. Methods In this prospective study a total of 989 stool specimens were tested over a period of 16 months in parallel using two isothermal amplification assays, AmpliVue® (Quidel) and Illumigene® (Meridian) and the results compared to those from toxigenic culture. In addition all specimens were tested using a cytotoxic cell neutralisation assay (CCNA) and three different Real-time PCR targeting a C. difficile-specific 16S rDNA sequence or the toxin genes tcdA, tcdB/tcdB027 or cdtB. Results AmpliVue® was positive in 242 (24.5 %) and Illumigene® in 228 (23.1 %) specimens. 167 (16.9 %) specimens were positive in toxigenic culture. Real-time-tcdA and -tcdB PCR was positive in 211 (21.3 %) specimens, Real-time-cdtB PCR was positive in 101 (10.2 %) specimens and C. difficile-PCR (16S rDNA) in 267 (27.0 %) specimens. Conclusions The respective sensitivity, specificity, positive predictive value and negative predictive value compared to toxigenic culture were 91, 89, 62 and 98 % for AmpliVue® and 91, 91, 67 and 98 % for Illumigene®.
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Affiliation(s)
- Martina Neuendorf
- Institute of Medical Microbiology and Hospital Hygiene, University Hospital, Heinrich-Heine University, Düsseldorf, Germany.
| | - Raquel Guadarrama-Gonzalez
- Institute of Medical Microbiology and Hospital Hygiene, University Hospital, Heinrich-Heine University, Düsseldorf, Germany.
| | - Birgit Lamik
- Institute of Medical Microbiology and Hospital Hygiene, University Hospital, Heinrich-Heine University, Düsseldorf, Germany.
| | - Colin R MacKenzie
- Institute of Medical Microbiology and Hospital Hygiene, University Hospital, Heinrich-Heine University, Düsseldorf, Germany.
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16
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Molecular Diagnostics for Clostridium difficile. Mol Microbiol 2016. [DOI: 10.1128/9781555819071.ch16] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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Goret J, Blanchi J, Eckert C, Lacome S, Petit A, Barbut F, Bébéar C, Mégraud F. Comparison of a novel chemiluminescent based algorithm to three algorithmic approaches for the laboratory diagnosis of Clostridium difficile infection. Gut Pathog 2015; 7:33. [PMID: 26705425 PMCID: PMC4690238 DOI: 10.1186/s13099-015-0079-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/09/2015] [Accepted: 12/01/2015] [Indexed: 01/05/2023] Open
Abstract
Background Rapid commercial assays, including nucleic acid amplification tests and immunoassays for Clostridium. difficile toxins, have replaced the use of older assays. They are included in a two-step algorithm diagnosis, including first the detection of the glutamate dehydrogenase (GDH) as a screening method and second the detection of toxins as a confirmatory method. Although assays that detect the presence of free toxins in feces are known to lack sensitivity, they are preferable to confirm infection. We evaluated the accuracy of the chemiluminescence-based method detecting C.difficile GDH and free toxins A/B (DiaSorin algorithm) to an enzyme-immunoassay (EIA) for GDH with a molecular toxins test (Meridian algorithm), EIA-GDH and an EIA-toxins A/B algorithm (Alere algorithm) with and without toxigenic culture for confirmation. Findings A total of 468 diarrhoeal and loose stool samples were included in the study. A positive result was defined by a positive GDH and a positive toxin test. Discordant samples were resolved using an enriched toxigenic culture considered as the reference method. After resolution, the DiaSorin algorithm showed a high sensitivity (86.7 %) compared to that of the Alere algorithm with (60.0 %) and without (50.0 %) confirmation by culture and was as sensitive as the Meridian algorithm (90.0 %), while the specificities were similar: 99.1, 99.5, 99.5 and 98.9 %, respectively. Conclusions The DiaSorin algorithm was as sensitive as an algorithm including nucleic acid amplification test for toxins. Chemiluminescence toxin-enhanced signal assay compensates the lack of sensitivity usually observed for EIA tests for toxins.
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Affiliation(s)
- J Goret
- Laboratoire de Bactériologie, C.H.U. de Bordeaux, Hôspital Pellegrin, 33076 Bordeaux Cedex, France
| | - J Blanchi
- Laboratoire de Bactériologie, C.H.U. de Bordeaux, Hôspital Pellegrin, 33076 Bordeaux Cedex, France
| | - C Eckert
- National Reference Laboratory for Clostridium difficile, Assistance Publique-Hôpitaux de Paris, Hôpital Saint-Antoine, Paris, France
| | - S Lacome
- Laboratoire de Bactériologie, C.H.U. de Bordeaux, Hôspital Pellegrin, 33076 Bordeaux Cedex, France
| | - A Petit
- National Reference Laboratory for Clostridium difficile, Assistance Publique-Hôpitaux de Paris, Hôpital Saint-Antoine, Paris, France
| | - F Barbut
- National Reference Laboratory for Clostridium difficile, Assistance Publique-Hôpitaux de Paris, Hôpital Saint-Antoine, Paris, France
| | - C Bébéar
- Laboratoire de Bactériologie, C.H.U. de Bordeaux, Hôspital Pellegrin, 33076 Bordeaux Cedex, France
| | - Francis Mégraud
- Laboratoire de Bactériologie, C.H.U. de Bordeaux, Hôspital Pellegrin, 33076 Bordeaux Cedex, France
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Evaluation of 3 automated real-time PCR (Xpert C. difficile assay, BD MAX Cdiff, and IMDx C. difficile for Abbott m2000 assay) for detecting Clostridium difficile toxin gene compared to toxigenic culture in stool specimens. Diagn Microbiol Infect Dis 2015; 83:7-10. [PMID: 26081240 DOI: 10.1016/j.diagmicrobio.2015.05.005] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2014] [Revised: 04/18/2015] [Accepted: 05/09/2015] [Indexed: 01/05/2023]
Abstract
We evaluated the performance of the 3 automated systems (Cepheid Xpert, BD MAX, and IMDx C. difficile for Abbott m2000) detecting Clostridium difficile toxin gene compared to toxigenic culture. Of the 254 stool specimens tested, 87 (48 slight, 35 moderate, and 4 heavy growth) were toxigenic culture positive. The overall sensitivities and specificities were 82.8% and 98.8% for Xpert, 81.6% and 95.8% for BD MAX, and 62.1% and 99.4% for IMDx, respectively. The specificity was significantly higher in IMDx than BD MAX (P= 0.03). All stool samples underwent toxin A/B enzyme immunoassay testing, and of the 254 samples, only 29 samples were positive and 2 of them were toxigenic culture negative. Considering the rapidity and high specificity of the real-time PCR assays compared to the toxigenic culture, they can be used as the first test method for C. difficile infection/colonization.
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A large scale clinical evaluation of the AmpliVue and Illumigene molecular tests for the identification of Clostridium difficile-associated diarrhea in adult and pediatric patients. Diagn Microbiol Infect Dis 2015; 82:265-8. [PMID: 26008122 DOI: 10.1016/j.diagmicrobio.2015.03.007] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2014] [Revised: 02/11/2015] [Accepted: 03/07/2015] [Indexed: 02/04/2023]
Abstract
The AmpliVue (Quidel, San Diego, CA, USA) and Illumigene (Meridian Biosciences, Cincinnati, OH, USA) molecular tests were compared for the detection of C. difficile toxin in fresh fecal samples from adult and pediatric patients. A total of 758 samples were collected, in 3 clinical sites: Nationwide Children's (Columbus, OH, USA), Penn State Hershey (Hershey, PA, USA), Primary Children's (Salt Lake City, UT, USA). Each site tested the fecal specimens using both assays. Any discordant results were resolved by performing toxigenic culture. There were 16 discordant samples among the 3 sites. Following discordant resolution, the combined performance for all 3 sites for sensitivity, specificity, PPV, and NPV for AmpliVue was 96.1%, 99.2%, 96.1%, and 99.2%, respectively, while for Illumigene was 96.1%, 99.8%, 99.2%, and 99.2%, respectively. The AmpliVue and Illumigene methods are both relatively rapid and simple to use, sensitive, and specific for detection of C. difficile toxin and demonstrate similar performance.
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Gilbreath JJ, Verma P, Abbott AN, Butler-Wu SM. Comparison of the Verigene Clostridium difficile, Simplexa C. difficile Universal Direct, BD MAX Cdiff, and Xpert C. difficile assays for the detection of toxigenic C. difficile. Diagn Microbiol Infect Dis 2014; 80:13-8. [PMID: 25027069 DOI: 10.1016/j.diagmicrobio.2014.06.001] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2014] [Revised: 05/31/2014] [Accepted: 06/02/2014] [Indexed: 01/05/2023]
Abstract
We compared the Verigene Clostridium difficile test (Nanosphere, Northbrook, IL, USA), the Simplexa C. difficile Universal Direct (Focus Diagnostics, Cypress, CA, USA), the BD MAX Cdiff (Becton Dickinson, Franklin Lakes, NJ, USA), and the Xpert C. difficile (Cepheid, Sunnyvale, CA, USA) assays for the detection of toxigenic C. difficile. One hundred and ninety deidentified, remnant diarrheal specimens were included in this study. After resolution of discordant results by toxigenic culture, the Xpert C. difficile assay displayed the highest sensitivity (100%), with a specificity of 98.8%. The sensitivity and specificity were 95.2% and 99.4% and 87% and 100% for the Verigene CDF and Simplexa Universal Direct assays, respectively. Finally, the BD MAX assay showed a sensitivity of 87% and a specificity of 98.8%. Despite differences in the overall performance of these assays, these results support the routine use of these platforms for the detection of toxigenic C. difficile in the clinical laboratory.
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Affiliation(s)
- Jeremy J Gilbreath
- Department of Laboratory Medicine, University of Washington, Seattle, WA 98195
| | - Punam Verma
- Department of Pathology and Clinical Laboratories, Virginia Mason Medical Center, Seattle, WA 98101
| | - April N Abbott
- Department of Laboratory Medicine, University of Washington, Seattle, WA 98195
| | - Susan M Butler-Wu
- Department of Laboratory Medicine, University of Washington, Seattle, WA 98195.
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Clostridium difficile Infection (CDI) in Solid Organ and Hematopoietic Stem Cell Transplant Recipients. Curr Infect Dis Rep 2014; 16:414. [DOI: 10.1007/s11908-014-0414-0] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
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Molecular test based on isothermal helicase-dependent amplification for detection of the Clostridium difficile toxin A gene. J Clin Microbiol 2014; 52:2386-9. [PMID: 24759714 DOI: 10.1128/jcm.00353-14] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
The AmpliVue Clostridium difficile assay and a glutamate dehydrogenase (GDH)-illumigene algorithm were evaluated using 308 diarrheal stool specimens of patients suspected of having C. difficile infection. Compared to the enriched toxigenic culture method, the sensitivities, specificities, and positive and negative predictive values of the AmpliVue C. difficile assay and the GDH-illumigene-based algorithm were 91.7% (95% confidence interval [CI], 76.4 to 97.8), 100% (95% CI, 98.3 to 100), 100% (95% CI, 87 to 100), and 98.9% (95% CI, 96.6 to 99.7), respectively.
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