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Ambrosius-Eichner J, Hogardt M, Berger A, Dultz G, Idris R, Kempf VAJ, Wichelhaus TA. Comparative evaluation of the detection rate, workflow and associated costs of a multiplex PCR panel versus conventional methods in diagnosis of infectious gastroenteritis. J Med Microbiol 2024; 73. [PMID: 38362908 DOI: 10.1099/jmm.0.001795] [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: 02/17/2024] Open
Abstract
Introduction. Infectious gastroenteritis is a common reason for consulting a physician. Although most cases of gastrointestinal illness are self-limiting, the identification of the etiologic pathogen by stool specimen analysis is important in cases of more severe illness and for epidemiological reasons.Due to the broad range of causative pathogens, the conventional examination of a stool specimen is labour-intensive and usually requires different diagnostic methods. Multiplex PCR tests [e.g. BioFire Gastrointestinal (GI) Panel] allow the rapid detecting of up to 22 pathogens in one test.Hypothesis. Using a multiplex PCR panel to test stool specimens for infectious gastroenteritis pathogens can improve the detection rate, reduce the time-to-result and hands-on time and lower the costs of a microbiology laboratory.Aim. This study was aimed at evaluating the detection rate, the workflow and associated costs of stool specimen management using the BioFire GI Panel versus conventional methods.Methodology. Stool specimens were evaluated prospectively during the routine operation. Pathogen detection rate, hands-on time, time-to-result and material and personnel costs were determined for the BioFire GI Panel and conventional methods-the latter based on physician request and excluding viral testing.Results. Analysing 333 specimens collected between 2019 and 2020, the detection rate of enteropathogens was significantly higher with a positivity rate of 39.9 % using the multiplex PCR panel compared with 15.0 % using the conventional methods. The BioFire GI Panel presented results in a median time of 2.2 h compared with 77.5 h for culture and 22.1 h for antigen testing, noting that no tests were performed at weekends except for toxinogenic Clostridioides difficile. Based on list prices, the BioFire GI Panel was nine times more expensive compared with conventional methods, whereas hands-on-time was significantly lower using the BioFire GI Panel.Conclusion. Multiplex PCR panels are valuable tools for laboratory identification of infectious agents causing diarrhoea. The higher costs of such a multiplex PCR panel might be outweighed by the higher detection rate, ease of handling, rapid results and most likely improved patient management. However, these panels do not provide information on antimicrobial susceptibility testing. Therefore, if this is necessary for targeted therapy or if outbreak monitoring and control is required, specimens must still be cultured.
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Affiliation(s)
- J Ambrosius-Eichner
- Institute of Medical Microbiology and Infection Control, Goethe University Frankfurt, University Hospital, Frankfurt, Germany
- University Center for Infectious Diseases, Goethe University Frankfurt, University Hospital, Frankfurt, Germany
| | - M Hogardt
- Institute of Medical Microbiology and Infection Control, Goethe University Frankfurt, University Hospital, Frankfurt, Germany
- University Center for Infectious Diseases, Goethe University Frankfurt, University Hospital, Frankfurt, Germany
| | - A Berger
- University Center for Infectious Diseases, Goethe University Frankfurt, University Hospital, Frankfurt, Germany
- Institute of Medical Virology, Goethe University Frankfurt, University Hospital, Frankfurt, Germany
| | - G Dultz
- University Center for Infectious Diseases, Goethe University Frankfurt, University Hospital, Frankfurt, Germany
- Department of Medicine I, Goethe University Frankfurt, University Hospital, Frankfurt, Germany
| | - R Idris
- University Center for Infectious Diseases, Goethe University Frankfurt, University Hospital, Frankfurt, Germany
- Department of Medicine II-Infectious Diseases, Goethe University Frankfurt, University Hospital, Frankfurt, Germany
| | - V A J Kempf
- Institute of Medical Microbiology and Infection Control, Goethe University Frankfurt, University Hospital, Frankfurt, Germany
- University Center for Infectious Diseases, Goethe University Frankfurt, University Hospital, Frankfurt, Germany
| | - T A Wichelhaus
- Institute of Medical Microbiology and Infection Control, Goethe University Frankfurt, University Hospital, Frankfurt, Germany
- University Center for Infectious Diseases, Goethe University Frankfurt, University Hospital, Frankfurt, Germany
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Lewinski MA, Alby K, Babady NE, Butler-Wu SM, Bard JD, Greninger AL, Hanson K, Naccache SN, Newton D, Temple-Smolkin RL, Nolte F. Exploring the Utility of Multiplex Infectious Disease Panel Testing for Diagnosis of Infection in Different Body Sites: A Joint Report of the Association for Molecular Pathology, American Society for Microbiology, Infectious Diseases Society of America, and Pan American Society for Clinical Virology. J Mol Diagn 2023; 25:857-875. [PMID: 37757952 DOI: 10.1016/j.jmoldx.2023.08.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Revised: 06/08/2023] [Accepted: 08/30/2023] [Indexed: 09/29/2023] Open
Abstract
The use of clinical molecular diagnostic methods for detecting microbial pathogens continues to expand and, in some cases, supplant conventional identification methods in various scenarios. Analytical and clinical benefits of multiplex molecular panels for the detection of respiratory pathogens have been demonstrated in various studies. The use of these panels in managing different patient populations has been incorporated into clinical guidance documents. The Association for Molecular Pathology's Infectious Diseases Multiplex Working Group conducted a review of the current benefits and challenges to using multiplex PCR for the detection of pathogens from gastrointestinal tract, central nervous system, lower respiratory tract, and joint specimens. The Working Group also discusses future directions and novel approaches to detection of pathogens in alternate specimen types, and outlines challenges associated with implementation of these multiplex PCR panels.
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Affiliation(s)
- Michael A Lewinski
- Infectious Diseases Multiplex Working Group of the Clinical Practice Committee, Association for Molecular Pathology, Rockville, Maryland; Roche Molecular Systems, San Clemente, California.
| | - Kevin Alby
- Infectious Diseases Multiplex Working Group of the Clinical Practice Committee, Association for Molecular Pathology, Rockville, Maryland; Department of Pathology and Laboratory Medicine, University of North Carolina School of Medicine, Chapel Hill, North Carolina
| | - N Esther Babady
- Infectious Diseases Multiplex Working Group of the Clinical Practice Committee, Association for Molecular Pathology, Rockville, Maryland; Clinical Microbiology Service, Departments of Laboratory Medicine and Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Susan M Butler-Wu
- Infectious Diseases Multiplex Working Group of the Clinical Practice Committee, Association for Molecular Pathology, Rockville, Maryland; Department of Clinical Pathology, Keck School of Medicine, University of Southern California, Los Angeles, California
| | - Jennifer Dien Bard
- Infectious Diseases Multiplex Working Group of the Clinical Practice Committee, Association for Molecular Pathology, Rockville, Maryland; Department of Pathology and Laboratory Medicine, Children's Hospital Los Angeles and Keck School of Medicine, University of Southern California, Los Angeles, California
| | - Alexander L Greninger
- Infectious Diseases Multiplex Working Group of the Clinical Practice Committee, Association for Molecular Pathology, Rockville, Maryland; Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington
| | - Kimberly Hanson
- Infectious Diseases Multiplex Working Group of the Clinical Practice Committee, Association for Molecular Pathology, Rockville, Maryland; University of Utah School of Medicine and ARUP Laboratories, Salt Lake City, Utah
| | - Samia N Naccache
- Infectious Diseases Multiplex Working Group of the Clinical Practice Committee, Association for Molecular Pathology, Rockville, Maryland; Department of Microbiology, LabCorp Seattle, Seattle, Washington
| | - Duane Newton
- Infectious Diseases Multiplex Working Group of the Clinical Practice Committee, Association for Molecular Pathology, Rockville, Maryland; Bio-Rad Laboratories, Irvine, California
| | | | - Frederick Nolte
- Infectious Diseases Multiplex Working Group of the Clinical Practice Committee, Association for Molecular Pathology, Rockville, Maryland; Department of Pathology and Laboratory Medicine, Medical University of South Carolina, Charleston, South Carolina
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Powell EA, Hata DJ, Starolis MW. Viral pathogen detection using multiplex gastrointestinal molecular panels: The pros and cons of viral target inclusion. J Clin Virol 2023; 169:105612. [PMID: 37866093 DOI: 10.1016/j.jcv.2023.105612] [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: 05/08/2023] [Revised: 07/31/2023] [Accepted: 10/14/2023] [Indexed: 10/24/2023]
Abstract
Diagnosis of gastrointestinal infections has been revolutionized by the development of in vitro diagnostic (IVD) multiplex molecular panels for the detection of viral nucleic acids. In addition to a high degree of accuracy, these panels are commercially available and relatively simple to perform in the clinical laboratory. However, use of these panels must be carefully considered owing to the laboratory costs of the test, limited reimbursement, and potential for overuse. In this review from the Pan American Society for Clinical Virology, we focus on the viral components of GI multiplex panels (GIPs), presenting a brief overview of pathogens included on most panels and a discussion of advantages and challenges of the inclusion of viral targets on GIPs that should be considered before implementation in the clinical laboratory.
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Affiliation(s)
- Eleanor A Powell
- Department of Pathology and Laboratory Medicine, University of Cincinnati College of Medicine, 234 Goodman St., Cincinnati, OH 45219, United States.
| | - D Jane Hata
- Department of Laboratory Medicine and Pathology, Mayo Clinic Florida, 4500 San Pablo Rd., Jacksonville, FL 32266, United States
| | - Meghan W Starolis
- Quest Diagnostics, 14225 Newbrook Dr., Chantilly, VA 20155, United States
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Hata DJ, Powell EA, Starolis MW. Utility and Recommendations for the Use of Multiplex Molecular Gastrointestinal Pathogen Panels. J Appl Lab Med 2023; 8:1148-1159. [PMID: 37102500 DOI: 10.1093/jalm/jfad009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Accepted: 01/27/2023] [Indexed: 04/28/2023]
Abstract
BACKGROUND Many molecular gastrointestinal pathogen panels (GIPs) are Food and Drug Administration (FDA) cleared but it is still unclear how to best utilize these new diagnostic tools. GIPs are highly sensitive and specific, simultaneously detect multiple pathogens in one reaction, and can shorten the overall time of diagnosis for infectious gastroenteritis but are also expensive with relatively poor insurance reimbursement. CONTENT In this review, we take a comprehensive approach to discuss issues with utilization of GIPs from a physician perspective, and implementation from a laboratory perspective. The information presented is to assist physicians in deciding on appropriate use of GIPs in diagnostic algorithms for their patients, and to provide information to laboratories that may be considering the addition of these powerful diagnostic assays to their test menu. Some of the important topics discussed are inpatient vs outpatient use, the appropriate panel size and organisms to include, interpretation of results, laboratory validation, and reimbursement. SUMMARY The information in this review provides clear guidance to both clinicians and laboratories in deciding the best use of GIPs for a specific patient population. While this technology provides many benefits over traditional methods, it can also complicate result interpretation and comes with a high cost, which necessitates the need for use recommendations.
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Affiliation(s)
- D Jane Hata
- Department of Laboratory Medicine and Pathology, Mayo Clinic Florida, Jacksonville, FL, United States
| | - Eleanor A Powell
- Department of Pathology and Laboratory Medicine, University of Cincinnati College of Medicine, Cincinnati, OH, United States
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Berkhout A, Cheng DR, McNab S, Lee LY, Daley AJ, Clifford V. Clinical and Health System Impact of Biofire Filmarray Meningitis/Encephalitis Routine Testing of CSF in a Pediatric Hospital: An Observational Study. Pediatr Infect Dis J 2023; 42:281-285. [PMID: 36728816 DOI: 10.1097/inf.0000000000003812] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
BACKGROUND Rapid cartridge-based molecular test panels targeting multiple pathogens are increasingly available, improve pathogen detection and reduce turn-around-time but are more expensive than standard testing. Confirmation that these test panels contribute to improved patient or health service outcomes is required. METHODS In March 2021, our pediatric hospital laboratory implemented the BioFire Filmarray™ meningitis/encephalitis (M/E) panel as an additional routine test for all cerebrospinal fluid (CSF) samples collected from infants <90 days or from any patient in the emergency department. A retrospective chart review was done to ascertain changes in clinical outcomes, antimicrobial prescribing practices, and hospital length of stay, comparing two discrete 6-month periods: preimplementation (March-August 2019) and postimplementation (March-August 2021). RESULTS Both pre- and postimplementation groups were similar at baseline, except the preimplementation group had a higher proportion of infants with enterovirus and parechovirus meningitis. There was no significant difference between the groups in terms of median length of stay (2.94 vs 3.47 days, p = 0.41), duration of antibiotic treatment (2.0 vs 2.3 days, p = 0.25), need for central venous access (12.9% vs 17%, p = 0.38) or hospital-in-the-home admission (9.4% vs 9%, p = 0.92). A similar proportion of infants received aciclovir (33% vs 31%), however, a reduction in duration was observed (1.36 vs 0.90 days, p = 0.03) in the postimplementation period. CONCLUSIONS Introduction of the Biofire Filmarray™ M/E panel for routine testing of CSF samples reduced the duration of antiviral prescribing but had only a minor impact on antibiotic prescribing practices or health service outcomes in our pediatric hospital. The introduction of new laboratory testing needs to be supported by a comprehensive stewardship program to see optimal outcomes from new testing platforms.
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Affiliation(s)
- Angela Berkhout
- Laboratory Services, Royal Children's Hospital, Parkville, Victoria, Australia
- Murdoch Children's Research Institute, Parkville, Victoria, Australia
- General Medicine, Royal Children's Hospital, Parkville, Victoria, Australia
- The University of Queensland, Faculty of Medicine, Brisbane. Queensland, Australia
- Department of Paediatrics, University of Melbourne, Victoria, Australia
- Infection Management & Prevention Service, The Queensland Children's Hospital, Brisbane, Queensland, Australia
| | - Daryl R Cheng
- General Medicine, Royal Children's Hospital, Parkville, Victoria, Australia
- The University of Queensland, Faculty of Medicine, Brisbane. Queensland, Australia
- Department of Paediatrics, University of Melbourne, Victoria, Australia
| | - Sarah McNab
- General Medicine, Royal Children's Hospital, Parkville, Victoria, Australia
- The University of Queensland, Faculty of Medicine, Brisbane. Queensland, Australia
- Department of Paediatrics, University of Melbourne, Victoria, Australia
| | - Lai-Yang Lee
- Laboratory Services, Royal Children's Hospital, Parkville, Victoria, Australia
| | - Andrew J Daley
- Laboratory Services, Royal Children's Hospital, Parkville, Victoria, Australia
- General Medicine, Royal Children's Hospital, Parkville, Victoria, Australia
- The University of Queensland, Faculty of Medicine, Brisbane. Queensland, Australia
| | - Vanessa Clifford
- Laboratory Services, Royal Children's Hospital, Parkville, Victoria, Australia
- Murdoch Children's Research Institute, Parkville, Victoria, Australia
- General Medicine, Royal Children's Hospital, Parkville, Victoria, Australia
- The University of Queensland, Faculty of Medicine, Brisbane. Queensland, Australia
- Department of Paediatrics, University of Melbourne, Victoria, Australia
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6
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Carmon D, Rohana H, Azrad M, Peretz A. The Impact of a Positive Biofire® FilmArray® Gastrointestinal Panel Result on Clinical Management and Outcomes. Diagnostics (Basel) 2023; 13:diagnostics13061094. [PMID: 36980402 PMCID: PMC10046972 DOI: 10.3390/diagnostics13061094] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Revised: 03/02/2023] [Accepted: 03/10/2023] [Indexed: 03/17/2023] Open
Abstract
The gold standard diagnostic method for gastrointestinal infections is stool culture, which has limited sensitivity and long turnaround time. Infection diagnosis recently shifted to syndrome-based panel assays. This study employed the FilmArray® Gastrointestinal Panel, which detects 22 pathogens simultaneously, to investigate gastrointestinal infection and pathogen distribution in 91 stool samples of patients hospitalized at the Tzafon Medical Center, Israel, during 2020, and to compare the clinical and demographic data of negative vs. positive samples. Among the 61 positive samples (67%), the most common pathogen was Campylobacter (34.4%). Positive test results were associated with a slightly younger patient age (p = 0.012), significantly higher post-diagnosis use of antibiotics (63.9% vs. 36.7%; p = 0.014), and shorter length of stay and time to discharge (p = 0.035, p = 0.003, respectively) than negative test results. To conclude, the FilmArray® Gastrointestinal Panel enabled the early identification of causative infectious agents and enhanced clinical management and outcomes.
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Affiliation(s)
- David Carmon
- Azrieli Faculty of Medicine, Bar-Ilan University, Safed 1311502, Israel
| | - Hanan Rohana
- Azrieli Faculty of Medicine, Bar-Ilan University, Safed 1311502, Israel
- The Clinical Microbiology Laboratory, Tzafon Medical Center, Poriya, Tiberias 1528001, Israel
| | - Maya Azrad
- Azrieli Faculty of Medicine, Bar-Ilan University, Safed 1311502, Israel
- The Clinical Microbiology Laboratory, Tzafon Medical Center, Poriya, Tiberias 1528001, Israel
| | - Avi Peretz
- Azrieli Faculty of Medicine, Bar-Ilan University, Safed 1311502, Israel
- The Clinical Microbiology Laboratory, Tzafon Medical Center, Poriya, Tiberias 1528001, Israel
- Correspondence: ; Tel.: +972-4-665-2322
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Relationship between Diagnostic Method and Pathogen Detection, Healthcare Resource Use, and Cost in U.S. Adult Outpatients Treated for Acute Infectious Gastroenteritis. J Clin Microbiol 2023; 61:e0162822. [PMID: 36645308 PMCID: PMC9945572 DOI: 10.1128/jcm.01628-22] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
A retrospective observational study was performed to assess the relationship between diagnostic method (traditional work-up [TW], multiplex PCR panel with < 12 target pathogens [PCR < 12], or multiplex PCR panel with ≥ 12 target pathogens [PCR12]), and diagnostic yield, health care resource use (HRU), and cost in adult outpatients visiting U.S. hospitals for acute infectious gastroenteritis (AGE). Using data from PINC AI Healthcare Database during January 1, 2016-June 30, 2021, we analyzed adult patients with an AGE diagnosis and stool testing performed during an outpatient visit. Detection rates for different pathogens were analyzed for those with microbiology data available. Among 36,787 patients, TW was most often performed (57.0%). PCR12 testing was more frequent in patients from large, urban, and teaching hospitals, compared to TW (all P < 0.01). PCR12 was associated with a higher mean index visit cost (by $97) but lower mean 30-day AGE-related follow-up cost (by $117) than TW. Patients with PCR12 had a lower 30-day AGE-related hospitalization risk than TW (1.7% versus 2.7% P < 0.01). Among the 8,451 patients with microbiology data, PCR12 was associated with fewer stool tests per patient (mean 1.61 versus 1.26), faster turnaround time (mean 6.3 versus 25.7 h) and lower likelihood of receiving in-hospital antibiotics (39.4% versus 47.1%, all P < 0.01) than TW. A higher percentage of patients with PCR12 had a target pathogen detected (73.1%) compared to PCR < 12 (63.6%) or TW (45.4%, P < 0.01). Thus, we found that large multiplex PCR panels were associated with lower 30-day AGE-related follow-up cost and risk of AGE-related hospitalization, and increased diagnostic yield compared to TW.
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8
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Capraro GA. Replacement of Culture with Molecular Testing for Diagnosis Infectious Diseases. Clin Lab Med 2022; 42:547-555. [PMID: 36368781 DOI: 10.1016/j.cll.2022.09.010] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Gerald A Capraro
- Clinical Microbiology Laboratory, Carolinas Pathology Group, Atrium Health, 5040 Airport Center Parkway, Building H, Suite A, Charlotte, NC 28208, USA.
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9
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DiDiodato G, Allen A, Bradbury N, Brown J, Cruise K, Jedrzejko C, MacDonald V, Pigeon J, Sturgeon A, Yellenik D. The Efficacy of the BioFire FilmArray Gastrointestinal Panel to Reduce Hospital Costs Associated With Contact Isolation: A Pragmatic Randomized Controlled Trial. Cureus 2022; 14:e27931. [PMID: 36120274 PMCID: PMC9464456 DOI: 10.7759/cureus.27931] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/12/2022] [Indexed: 11/05/2022] Open
Abstract
Background: Molecular syndromic panels can rapidly detect common pathogens responsible for acute gastroenteritis in hospitalized patients. Their impact on both patient and healthcare system outcomes is uncertain compared to conventional stool testing. This randomized trial evaluates the impact of molecular testing on in-hospital resource utilization compared to conventional stool testing. Methods: Hospitalized patients with acute diarrheal illness were randomized 1:1 to either conventional or molecular stool testing with the BioFire FilmArray gastrointestinal panel (FGP). The primary outcome was the duration of contact isolation, and secondary outcomes included other in-hospital resource utilization such as diagnostic imaging and antimicrobial use. Results: A total of 156 patients were randomized. Randomization resulted in a balanced allocation of patients across all three age strata (<18, 18-69, ≥70 years old). The proportion of positive stools was 20.5% vs 29.5% in the control and FGP groups, respectively (p=0.196). The median duration of contact isolation was 51 hours (interquartile range [iqr] 66) and 69 hours (iqr 81) in the conventional and FGP groups, respectively (p=0.0513). There were no significant differences in other in-hospital resource utilization between groups. Conclusions: There were no differences in in-hospital resource utilization observed between the FGP and conventional stool testing groups.
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10
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Acute Viral Gastrointestinal (GI) Infections in the Tropics—A Role for Cartridge-Based Multiplex PCR Panels? Trop Med Infect Dis 2022; 7:tropicalmed7050080. [PMID: 35622707 PMCID: PMC9143240 DOI: 10.3390/tropicalmed7050080] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Revised: 05/16/2022] [Accepted: 05/17/2022] [Indexed: 02/04/2023] Open
Abstract
Acute gastroenteritis (AGE) contributes to increased morbidity and mortality worldwide. In particular, children in resource-poor settings suffer from frequent episodes of diarrhea. A variety of pathogens, including bacteria, viruses, fungi, and protozoa, can cause AGE. Common viruses associated with AGE are norovirus, rotavirus, astrovirus, adenovirus, and sapovirus. Due to their similar clinical presentation, AGE pathogens cannot be distinguished on clinical grounds rendering the etiological diagnosis challenging. However, reliable diagnosis is essential for individual and public health reasons, e.g., to limit transmission, for appropriate antibiotic use, prognostic appreciation, and vaccination programs. Therefore, high-quality data derived by accurate diagnostics are important to improve global health. In Western industrialized countries, diagnosis relies on microbiological testing, including culture methods, microscopy, immunochromatography, and single-target molecular methods. Recently, multiplex PCR or syndromic panels have been introduced, which simultaneously analyze for multiple pathogens in a very short time. A further technological advancement is cartridge-based syndromic panels, which allow for near patient/point-of-care testing independently from a laboratory. In resource-poor tropical regions, however, laboratory diagnosis is rarely established, and there are little routine laboratory data on the epidemiology of viral AGE pathogens. Limiting factors for the implementation of syndromic panels are high costs, sophisticated equipment, and the need for trained personnel. In addition, pilot studies have shown a large number of viral (co-)detections among healthy controls, thus further challenging their clinical utilization. Hence, there are little evidence-based data on the impact of multiplex syndromic panels from resource-limited regions. Here, we aim to provide a brief overview of what is known about the use of syndromic panels for virus-associated AGE in tropical regions and to address future challenges.
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11
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Meltzer AC, Newton S, Lange J, Hall NC, Vargas NM, Huang Y, Moran S, Ma Y. A randomized control trial of a multiplex gastrointestinal PCR panel versus usual testing to assess antibiotics use for patients with infectious diarrhea in the emergency department. J Am Coll Emerg Physicians Open 2022; 3:e12616. [PMID: 35072157 PMCID: PMC8760946 DOI: 10.1002/emp2.12616] [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: 08/12/2021] [Revised: 11/08/2021] [Accepted: 11/12/2021] [Indexed: 11/23/2022] Open
Abstract
OBJECTIVE This study analyzed physician treating behavior through the use of a multiplex gastrointestinal polymerase chain reaction (GI PCR) test compared with usual testing in emergency department (ED) patients with suspected acute infectious diarrhea to assess differences in antibiotic management. METHODS A prospective, single-center, randomized control trial was designed to investigate antibiotic use in ED patients with moderate to severe suspected infectious diarrhea, comparing those who received GI PCR to those who received usual testing. ED patients with signs of dehydration, inflammation, or persistent symptoms were randomized to either the experimental arm (GI PCR) or the control arm (usual testing or no testing). RESULTS A total of 74 patients met study criteria and were randomized to either the experimental GI PCR arm (n = 38) or to the control arm (n = 36). Participants in the GI PCR arm received antibiotics in 87% of bacterial or protozoal diarrheal infections (13/15) whereas those in the control arm received antibiotics in 46% of bacterial or protozoal infections (6/13) (P value 0.042) with 2-proportion difference 0.41 (95% confidence interval 0.07 and 0.68). CONCLUSIONS ED use of multiplex GI PCR led to an increase in antibiotic use for bacterial and protozoal causes of infectious diarrhea compared to usual testing. This increase in antibiotics appears to be appropriate given patients' moderate to severe symptoms and a definitive identification of a likely bacterial or protozoal cause of symptoms. Results should be interpreted with caution because of the small sample size.
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Affiliation(s)
- Andrew C. Meltzer
- Department of Emergency MedicineGeorge Washington University (GWU) School of Medicine & Health SciencesWashingtonDistrict of ColumbiaUSA
| | - Sophia Newton
- Department of Emergency MedicineGeorge Washington University (GWU) School of Medicine & Health SciencesWashingtonDistrict of ColumbiaUSA
| | - Joel Lange
- Department of Emergency MedicineGeorge Washington University (GWU) School of Medicine & Health SciencesWashingtonDistrict of ColumbiaUSA
| | - Nicole C. Hall
- Department of Emergency MedicineGeorge Washington University (GWU) School of Medicine & Health SciencesWashingtonDistrict of ColumbiaUSA
| | - Nataly Montano Vargas
- Department of Emergency MedicineGeorge Washington University (GWU) School of Medicine & Health SciencesWashingtonDistrict of ColumbiaUSA
| | - Yihe Huang
- Department of Biostatistics and BioinformaticsGeorge Washington University (GWU) Milken Institute School of Public HealthWashingtonDistrict of ColumbiaUSA
| | - Seamus Moran
- Department of Emergency MedicineGeorge Washington University (GWU) School of Medicine & Health SciencesWashingtonDistrict of ColumbiaUSA
| | - Yan Ma
- Department of Biostatistics and BioinformaticsGeorge Washington University (GWU) Milken Institute School of Public HealthWashingtonDistrict of ColumbiaUSA
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12
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Teh R, Tee WD, Tan E, Fan K, Koh CJ, Tambyah PA, Oon J, Tee N, Soh AYS, Siah KTH. Review of the role of gastrointestinal multiplex polymerase chain reaction in the management of diarrheal illness. J Gastroenterol Hepatol 2021; 36:3286-3297. [PMID: 34129249 DOI: 10.1111/jgh.15581] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Revised: 05/19/2021] [Accepted: 06/13/2021] [Indexed: 01/25/2023]
Abstract
Acute and chronic diarrheal illness secondary to gastrointestinal infection is a significant cause of morbidity and mortality around the world. A cornerstone of management includes prompt diagnosis and appropriate treatment of culprit pathogens. Timely diagnosis can improve patient care, assist in infection control, and prevent disease outbreaks. Historical methods of diagnosis include traditional culture methods and stool analysis. These are limited by long turnaround time and inability to simultaneously assess multiple pathogens. The advent of multiplexed nucleic acid amplification tests first began with the Food and Drug Administration-approved respiratory virus multiplex polymerase chain reaction (PCR) panel in 2009, followed by gastrointestinal infections in 2013, and neurological infections in 2014. We conducted a review of current literature pertaining to the clinical utility of a gastrointestinal multiplex PCR in management of acute and chronic diarrhea in patients. To date, seven platforms approved by the US Food and Drug Administration are used in detection of various bacterial, viral, and parasitic causative organisms for diagnosis of gastrointestinal infections. The sensitivity and specificity of each assay vary depending on the tested organism. Interpretation of a positive result has to be tailored to the clinical context. Further studies are required to establish the utility of gastrointestinal multiplex PCR from a cost-based perspective, whether specific enteropathogens such as Clostridioides difficile are better assessed with toxin gene detection and whether new parameters such as cycle threshold values can improve clinical application of test results.
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Affiliation(s)
- Readon Teh
- Division of Gastroenterology and Hepatology, National University Hospital, Singapore
| | - Wei De Tee
- Division of Gastroenterology and Hepatology, Ng Teng Fong General Hospital, Singapore.,Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Eunice Tan
- Division of Gastroenterology and Hepatology, National University Hospital, Singapore.,Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Kristie Fan
- Division of Gastroenterology and Hepatology, National University Hospital, Singapore.,Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Calvin Jianyi Koh
- Division of Gastroenterology and Hepatology, National University Hospital, Singapore.,Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Paul Ananth Tambyah
- Division of Infectious Diseases, National University Hospital, Singapore.,Infectious Diseases Translational Research Programme, Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Jolene Oon
- Division of Infectious Diseases, National University Hospital, Singapore
| | - Nancy Tee
- Department of Laboratory Medicine, National University Hospital, Singapore
| | - Alex Yu Sen Soh
- Division of Gastroenterology and Hepatology, National University Hospital, Singapore.,Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Kewin Tien Ho Siah
- Division of Gastroenterology and Hepatology, National University Hospital, Singapore.,Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
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13
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Kwon JH, O'Neil CA, Hink T, Reske KA, Bosserman RE, Dubberke ER, Burnham CAD. Alternative Causes of Infectious Diarrhea in Patients with Negative Tests for Clostridoides Difficile. J Appl Lab Med 2021; 7:437-443. [PMID: 34609483 DOI: 10.1093/jalm/jfab110] [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: 04/30/2021] [Accepted: 08/09/2021] [Indexed: 11/12/2022]
Abstract
BACKGROUND Hospitalized patients with diarrhea who have a negative Clostridoides difficile (C. difficile) test are not routinely evaluated for alternative causes of infectious diarrhea. This study assessed for potential infectious causes of diarrhea in hospitalized patients with an order for repeat C. difficile toxin enzyme immunoassay (tEIA) testing after an initial tEIA test was negative. METHODS For patients age ≥18 years who had a second C. difficile tEIA test ordered within 96 h after a negative tEIA test, remnant fecal specimens from the first (negative) tEIA test were evaluated using the BioFire FilmArray Gastrointestinal Panel PCR, C. difficile toxigenic culture, and culture on a blood agar plate (BAP) to identify other potential causes of infectious diarrhea. Growth of organisms on the BAP was also used to assess potential disruptions in the gastrointestinal microbiota. RESULTS Among 84 remnant specimens, toxigenic C. difficile was identified in 9 (11%) by culture or PCR, while potential alternative causes of infectious diarrhea, including norovirus, rotavirus, enteropathogenic Escherichia coli, and Salmonella, were identified in 11 specimens (13%) by PCR. For the majority of patients, no infectious cause of diarrhea was identified, but 84% exhibited disrupted gastrointestinal microbiota, which may contribute to diarrhea. CONCLUSIONS When a hospitalized patient has a negative C. difficile tEIA test but continues to have diarrhea, alternative infectious and noninfectious causes of diarrhea should be considered. If the patient has clinical signs and symptoms suggestive of infection or risk factors for gastrointestinal infection, laboratory testing for other etiologic agents may be appropriate.
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Affiliation(s)
- Jennie H Kwon
- Department of Medicine, Division of Infectious Diseases, Washington University School of Medicine, St. Louis, MO, USA
| | - Caroline A O'Neil
- Department of Medicine, Division of Infectious Diseases, Washington University School of Medicine, St. Louis, MO, USA
| | - Tiffany Hink
- Department of Medicine, Division of Infectious Diseases, Washington University School of Medicine, St. Louis, MO, USA
| | - Kimberly A Reske
- Department of Medicine, Division of Infectious Diseases, Washington University School of Medicine, St. Louis, MO, USA
| | - Rachel E Bosserman
- Department of Medicine, Division of Infectious Diseases, Washington University School of Medicine, St. Louis, MO, USA
| | - Erik R Dubberke
- Department of Medicine, Division of Infectious Diseases, Washington University School of Medicine, St. Louis, MO, USA
| | - Carey-Ann D Burnham
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, USA
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14
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Engberg J, Vejrum LK, Madsen TV, Nielsen XC. Verification of analytical bacterial spectrum of QIAstat-Dx® GI V2 and Novodiag® Bacterial GE+ V2-0 diagnostic panels. J Antimicrob Chemother 2021; 76:iii50-iii57. [PMID: 34555154 PMCID: PMC8460093 DOI: 10.1093/jac/dkab242] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
Background Implementing multiplex PCR or syndromic panel-based testing platforms to detect microbial species that cause acute diarrhoea may guide patient management more effectively and efficiently. Objectives To assess and compare the performance of two syndromic panel-based testing systems, QIAstat-Dx® Gastrointestinal Panel V2 (QGI) and the Novodiag® Bacterial GE+ V2-0 (NGE). Methods The QGI and NGE panels include 16 and 14 bacterial gastrointestinal pathogens, respectively. The performance of the panels was tested retrospectively using 141 positive clinical stool specimens, External Quality Assessment (EQA) panels and spiked faecal specimens. Results For Campylobacter jejuni and coli (n = 20), Salmonella (n = 24), Shigella (n = 13), Yersinia enterocolitica (non-1A biotypes) (n = 8), Clostridioides difficile (n = 24) and Vibrio parahaemolyticus (n = 2), QGI correctly verified 19/20, 20/24, 13/13, 8/8, 23/24 and 2/2, whereas NGE correctly verified 20/20, 17/24, 13/13, 8/8, 14/24 and 1/2. Among diarrhoeagenic Escherichia coli (n = 29), QGI reported one Shiga toxin-producing E. coli (STEC) stx1a O26:H11 as STEC serotype O157:H7 and NGE failed on one enteropathogenic E. coli, one enteroaggregative E. coli and one STEC (stx2e). Y. enterocolitica biotype 1A (non-pathogenic) (n = 6) were all positive in QGI, but negative in NGE. Conclusions Both QGI and NGE testing panels can improve laboratory workflow and patient management by providing user-friendly platforms that can rapidly detect a number of targets with one specimen. QGI was significantly more sensitive in identifying C. difficile. Both methods had suboptimal detection of Salmonella and this needs to be examined further. The short hands-on time and turnaround time are of value for on-demand testing and use in a high-throughput setting.
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Affiliation(s)
- Jørgen Engberg
- Department of Clinical Microbiology, Zealand University Hospital, Koege, Ingemannsvej 46, DK-4200 Slagelse, Denmark
| | - Laus Krems Vejrum
- Department of Clinical Microbiology, Zealand University Hospital, Koege, Ingemannsvej 46, DK-4200 Slagelse, Denmark
| | - Tina Vasehus Madsen
- Department of Clinical Microbiology, Zealand University Hospital, Koege, Ingemannsvej 46, DK-4200 Slagelse, Denmark
| | - Xiaohui Chen Nielsen
- Department of Clinical Microbiology, Zealand University Hospital, Koege, Ingemannsvej 46, DK-4200 Slagelse, Denmark
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15
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Maldonado-Garza HJ, Garza-González E, Bocanegra-Ibarias P, Flores-Treviño S. Diagnostic syndromic multiplex approaches for gastrointestinal infections. Expert Rev Gastroenterol Hepatol 2021; 15:743-757. [PMID: 33682566 DOI: 10.1080/17474124.2021.1899807] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
Introduction: Gastrointestinal diseases due to infectious pathogens currently represent an important global health concern, especially in children and developing countries. Early and accurate detection of gastrointestinal pathogens is important to initiate the appropriate type of therapy. Multiplex molecular gastrointestinal panels rapidly detect several gastrointestinal pathogens at once with high sensitivity.Areas covered: We assess the scope and limitations of several multiplex gastrointestinal panels approved by the Food and Drug Administration or marked by Conformité Européenne-in vitro diagnostic. We compare 10 syndromic gastrointestinal panels, 14 bacteria-specific multiplex panels, seven parasite-specific multiplex panels, and eight virus-specific multiplex panels.Expert opinion: Thanks to the advances made in the diagnostic approaches for gastrointestinal infections, there are various panels to choose. The choice of a specific syndromic gastrointestinal multiplex panel should be made to improve patient care. Diagnostic syndromic multiplex approaches for gastrointestinal infections should be customized; each hospital should develop its diagnostic algorithm for gastrointestinal infections tailored to its setting, study population, and geographical site. Current multiplex gastrointestinal panels could be improved by including the detection of antimicrobial resistance, toxigenic Clostridioides difficile, and severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2, the virus responsible for the COVID-19 pandemic).
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Affiliation(s)
- Héctor Jesús Maldonado-Garza
- Departamento de Medicina Interna, Universidad Autónoma De Nuevo León, Hospital Universitario Dr. José Eleuterio González Y Facultad De Medicina, Servicio De Gastroenterología, Monterrey, Nuevo León, Mexico
| | - Elvira Garza-González
- Departamento de Medicina Interna, Universidad Autónoma De Nuevo León, Hospital Universitario Dr. José Eleuterio González Y Facultad De Medicina, Servicio De Gastroenterología, Monterrey, Nuevo León, Mexico
| | - Paola Bocanegra-Ibarias
- Departamento de Medicina Interna, Universidad Autónoma De Nuevo León, Hospital Universitario Dr. José Eleuterio González Y Facultad De Medicina, Servicio De Gastroenterología, Monterrey, Nuevo León, Mexico
| | - Samantha Flores-Treviño
- Departamento de Medicina Interna, Universidad Autónoma De Nuevo León, Hospital Universitario Dr. José Eleuterio González Y Facultad De Medicina, Servicio De Gastroenterología, Monterrey, Nuevo León, Mexico
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16
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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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17
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Stone JM, Savage A, Hudspeth M, Twombley K, Kasi N, Quiros JA, Arbizu RA, Curry S. Multi-organism gastrointestinal polymerase chain reaction positivity among pediatric transplant vs non-transplant populations: A single-center experience. Pediatr Transplant 2020; 24:e13771. [PMID: 32639105 PMCID: PMC8103891 DOI: 10.1111/petr.13771] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/11/2020] [Revised: 05/01/2020] [Accepted: 05/26/2020] [Indexed: 12/19/2022]
Abstract
BACKGROUND Diarrhea is a common problem in the pediatric post-solid organ transplant and post-hematopoietic stem cell transplant populations. Infectious etiology incidences are poorly defined, and the possibility of multi-organism positivity is often uninvestigated. The aim of this study is to utilize stool multiplex GIP assays to compare the PTP and NTP regarding the incidence and profiles of single-organism and multi-organism infectious diarrhea. METHODS A single-center retrospective review was conducted, investigating stool multiplex GIP panel results over a more than 3-year period, for pediatric patients. Assays test for 23 viral, bacterial, and protozoal organisms. RESULTS Positive assays in the PTP and NTP were 70/101 (69.3%) and 962/1716 (56.1%), respectively (P = .009). Thirty-two percent (32/101) of assays within the PTP were multi-organism positive, significantly more than 14.8% (254/1716) in the NTP (P < .00001). There was no significant difference in the incidence of single-organism positives, 37.6% (38/101) in PTP and 41.3% (708/1716) in the NTP. The PTP demonstrated a statistically significantly higher incidence of the following organisms within multi-agent positive GIPs (P < .05 for each): Clostridioides difficile, Cryptosporidium, EPEC, norovirus, and sapovirus. CONCLUSIONS The pediatric PTP demonstrates higher incidence of positive GIPs, higher rate of multi-organism positivity, and unique infectious organism incidence profiles. These data can provide a framework for understanding organism-specific pathogenicity factors, assessing the clinical impact of enteric co-infection, and understanding the utility of this testing modality in this unique population.
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Affiliation(s)
- John M. Stone
- Department of Pediatric Gastroenterology Hepatology and Nutrition, Medical University of South Carolina, Charleston, South Carolina, USA
| | - Andrew Savage
- Department of Pediatric Cardiology, Medical University of South Carolina, Charleston, South Carolina, USA
| | - Michelle Hudspeth
- Department of Pediatric Hematology and Oncology, Medical University of South Carolina, Charleston, South Carolina, USA
| | - Katherine Twombley
- Department of Pediatric Nephrology, Medical University of South Carolina, Charleston, South Carolina, USA
| | - Nagraj Kasi
- Department of Pediatric Gastroenterology Hepatology and Nutrition, Medical University of South Carolina, Charleston, South Carolina, USA
| | - Jose Antonio Quiros
- Department of Pediatric Gastroenterology Hepatology and Nutrition, Mount Sinai Kravis Children’s Hospital, New York, New York, USA
| | - Ricardo A. Arbizu
- Department of Pediatric Gastroenterology Hepatology and Nutrition, Medical University of South Carolina, Charleston, South Carolina, USA
| | - Scott Curry
- Department of Infectious Disease, Medical University of South Carolina, Charleston, South Carolina, USA
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18
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Torres-Miranda D, Akselrod H, Karsner R, Secco A, Silva-Cantillo D, Siegel MO, Roberts AD, Simon GL. Use of BioFire FilmArray gastrointestinal PCR panel associated with reductions in antibiotic use, time to optimal antibiotics, and length of stay. BMC Gastroenterol 2020; 20:246. [PMID: 32727381 PMCID: PMC7392718 DOI: 10.1186/s12876-020-01394-w] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/09/2020] [Accepted: 07/22/2020] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND Rapid and accurate diagnostic tools are needed for appropriate management of infectious diarrhea. METHODS We evaluated the impact of the introduction of rapid multiplex PCR testing using the FilmArray gastrointestinal (GI) panel (BioFire Diagnostics, LLC, Salt Lake City, UT) at our institution, and compared the results to those of standard stool cultures. RESULTS The most common pathogens detected by the FilmArray GI panel were Clostridium difficile (55.0%), Campylobacter species (20.9%), Salmonella species (12.4%), and Shigella/EIEC species (12.4%). Rates of reproducibility in stool culture for these pathogens ranged from 56.3 to 77.8%. Co-detection of two or more organisms was common (24.2%), most commonly involving EPEC, EAEC, ETEC, and STEC. The time from arrival in the Emergency Department to discharge or admission to the hospital was unchanged after the introduction of FilmArray GI panel, but length of hospital stay was shorter (3 vs. 7.5 days, p = 0.0002) for the FilmArray group. The time to empiric antibiotics did not differ significantly, but optimal antibiotics were started earlier after introduction of the FilmArray GI panel (hospital day 1 vs. 2, p < 0.0001). More patients were discharged without antibiotics after introduction of the FilmArray GI panel (14.0% vs. 4.5%; p < 0.001). CONCLUSION Our results demonstrate that the FilmArray GI panel is an important tool for improving both patient care and antibiotic stewardship, despite the tendency for positive results with multiple pathogens.
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Affiliation(s)
- Daisy Torres-Miranda
- Division of Infectious Diseases, George Washington University School of Medicine and Health Sciences, 2150 Pennsylvania Avenue NW, Washington, DC, 20037, USA
| | - Hana Akselrod
- Division of Infectious Diseases, George Washington University School of Medicine and Health Sciences, 2150 Pennsylvania Avenue NW, Washington, DC, 20037, USA.
| | - Ryan Karsner
- Division of Infectious Diseases, George Washington University School of Medicine and Health Sciences, 2150 Pennsylvania Avenue NW, Washington, DC, 20037, USA
| | - Alessandra Secco
- Division of Infectious Diseases, George Washington University School of Medicine and Health Sciences, 2150 Pennsylvania Avenue NW, Washington, DC, 20037, USA
| | - Diana Silva-Cantillo
- Division of Infectious Diseases, George Washington University School of Medicine and Health Sciences, 2150 Pennsylvania Avenue NW, Washington, DC, 20037, USA
| | - Marc O Siegel
- Division of Infectious Diseases, George Washington University School of Medicine and Health Sciences, 2150 Pennsylvania Avenue NW, Washington, DC, 20037, USA
| | - Afsoon D Roberts
- Division of Infectious Diseases, George Washington University School of Medicine and Health Sciences, 2150 Pennsylvania Avenue NW, Washington, DC, 20037, USA
| | - Gary L Simon
- Division of Infectious Diseases, George Washington University School of Medicine and Health Sciences, 2150 Pennsylvania Avenue NW, Washington, DC, 20037, USA
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19
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20
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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: 25] [Impact Index Per Article: 6.3] [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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21
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Machiels JD, Cremers AJH, van Bergen-Verkuyten MCGT, Paardekoper-Strijbosch SJM, Frijns KCJ, Wertheim HFL, Rahamat-Langendoen J, Melchers WJG. Impact of the BioFire FilmArray gastrointestinal panel on patient care and infection control. PLoS One 2020; 15:e0228596. [PMID: 32027698 PMCID: PMC7004333 DOI: 10.1371/journal.pone.0228596] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2019] [Accepted: 01/18/2020] [Indexed: 12/20/2022] Open
Abstract
Objectives Conventional routine PCR testing for gastrointestinal infections is generally based on pathogen related panels specifically requested by clinicians and can be erroneous and time consuming. The BioFire FilmArray gastrointestinal (GI) panel combines 22 pathogens into a single cartridge-based test on a random-access system, thereby reducing the turnaround time to less than 2 hours. We described the clinical impact of implementing the BioFire FilmArray on patients with gastroenteritis in our hospital. Methods Patients attending a Dutch tertiary care center (Radboud University Medical Center), from whom stool samples were obtained, were eligible for inclusion. The clinicians selected one or a combination of different routinely performed PCR panels (bacterial panel, viral panel, clostridium testing, and three parasitic panels) based on clinical history and symptoms. All samples were in parallel tested with the FilmArray. We retrospectively collected patient data regarding infection control and patient management to assess the potential impact of implementing the FilmArray. Results In total 182 patients were included. Routine PCR detected one or more pathogens in 52 (28.6%) patients compared to 72 (39.6%) using the FilmArray. Turnaround time (including transport) decreased from median 53 hours for the routine PCR to 16 hours for the FilmArray. Twenty-six patients could have been removed from isolation 29 hours sooner, 3.6 antibiotic days could have been saved and in five patients additional imaging testing (including colonoscopies) could have been prevented. Conclusion The theoretical implementation of the BioFire FilmArray GI panel in patients with clinical suspicion of gastroenteritis resulted in a significant better patient management.
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Affiliation(s)
- Julian D. Machiels
- Department of Medical Microbiology & Radboudumc Center for Infectious Diseases, Radboud university medical center, Nijmegen, The Netherlands
- * E-mail:
| | - Amelieke J. H. Cremers
- Department of Medical Microbiology & Radboudumc Center for Infectious Diseases, Radboud university medical center, Nijmegen, The Netherlands
| | | | - Sandra J. M. Paardekoper-Strijbosch
- Department of Medical Microbiology & Radboudumc Center for Infectious Diseases, Radboud university medical center, Nijmegen, The Netherlands
| | - Kelly C. J. Frijns
- Department of Medical Microbiology & Radboudumc Center for Infectious Diseases, Radboud university medical center, Nijmegen, The Netherlands
| | - Heiman F. L. Wertheim
- Department of Medical Microbiology & Radboudumc Center for Infectious Diseases, Radboud university medical center, Nijmegen, The Netherlands
| | - Janette Rahamat-Langendoen
- Department of Medical Microbiology & Radboudumc Center for Infectious Diseases, Radboud university medical center, Nijmegen, The Netherlands
| | - Willem J. G. Melchers
- Department of Medical Microbiology & Radboudumc Center for Infectious Diseases, Radboud university medical center, Nijmegen, The Netherlands
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22
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Abstract
The clinical microbiology laboratory relies on traditional diagnostic methods such as culturing, Gram stains, and biochemical testing. Receipt of a high-quality specimen with an appropriate test order is integral to accurate testing. Recent technological advancements have led to decreased time to results and improved diagnostic accuracy. Examples of advancements discussed in this chapter include automation of bacterial culture processing and incubation, as well as introduction of mass spectrometry for the proteomic identification of microorganisms. In addition, molecular testing is increasingly common in the clinical laboratory. Commercially available multiplex molecular assays simultaneously test for a broad array of syndromic-related pathogens, providing rapid and sensitive diagnostic results. Molecular advancements have also transformed point-of-care (POC) microbiology testing, and molecular POC assays may largely supplant traditional rapid antigen testing in the future. Integration of new technologies with traditional testing methods has led to improved quality and value in the clinical microbiology laboratory. After reviewing this chapter, the reader will be able to:List key considerations for specimen collection for microbiology testing. Discuss the advantages and limitations of automation in the clinical microbiology laboratory. Describe the evolution of microorganism identification methods. Discuss the benefits and limitations of molecular microbiology point-of-care testing. Summarize currently available multiplex molecular microbiology testing options.
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23
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Young BA, Hanson KE, Gomez CA. Molecular Diagnostic Advances in Transplant Infectious Diseases. Curr Infect Dis Rep 2019; 21:52. [PMID: 31773290 DOI: 10.1007/s11908-019-0704-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
PURPOSE OF REVIEW The infectious complications of transplantation can have devastating consequences for patients. Early and accurate diagnosis is essential to good outcomes. This review describes recent advances in pathogen-directed diagnostic testing and discusses the role of new methods for transplant infectious diseases. RECENT FINDINGS Several molecular assays have been introduced into clinical practice in recent years. When the results of rapid testing are linked to patient-specific interventions, improved outcomes can be realized. Syndromic testing along with metagenomic next-generation sequencing (mNGS) represents novel approaches to infection diagnosis. However, the optimal use of these tests for transplant patients along with an overall assessment of cost-effectiveness demands further study. Molecular diagnostics are revolutionizing transplant care. Clinicians need to be aware of the current diagnostic landscape and have a working knowledge of the nuances related to test performance, result interpretation, and cost.
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Affiliation(s)
- Brittany A Young
- Department of Pathology, University of Utah, Salt Lake City, UT, USA.,Associated Regional and University Pathologists Laboratories (ARUP), Salt Lake City, UT, USA
| | - Kimberly E Hanson
- Department of Pathology, University of Utah, Salt Lake City, UT, USA.,Associated Regional and University Pathologists Laboratories (ARUP), Salt Lake City, UT, USA.,Department of Medicine, Division of Infectious Diseases, University of Utah, Salt Lake City, UT, USA
| | - Carlos A Gomez
- Department of Medicine, Division of Infectious Diseases, University of Utah, Salt Lake City, UT, USA. .,University of Utah School of Medicine, 30 North 1900 East, Room 4B319, Salt Lake City, UT, 84132, USA.
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24
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Leli C, Di Matteo L, Gotta F, Vay D, Cavallo V, Mazzeo R, Busso S, Carrabba L, Rocchetti A. Evaluation of a multiplex gastrointestinal PCR panel for the aetiological diagnosis of infectious diarrhoea. Infect Dis (Lond) 2019; 52:114-120. [DOI: 10.1080/23744235.2019.1688861] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Affiliation(s)
- Christian Leli
- Microbiology Laboratory, SS. Antonio e Biagio e C. Arrigo Hospital, Alessandria, Italy
| | - Luigi Di Matteo
- Microbiology Laboratory, SS. Antonio e Biagio e C. Arrigo Hospital, Alessandria, Italy
| | - Franca Gotta
- Microbiology Laboratory, SS. Antonio e Biagio e C. Arrigo Hospital, Alessandria, Italy
| | - Daria Vay
- Pathology Unit, SS. Antonio e Biagio e C. Arrigo Hospital, Alessandria, Italy
| | - Valeria Cavallo
- Microbiology Laboratory, SS. Antonio e Biagio e C. Arrigo Hospital, Alessandria, Italy
| | - Roberta Mazzeo
- Microbiology Laboratory, SS. Antonio e Biagio e C. Arrigo Hospital, Alessandria, Italy
| | - Simone Busso
- Microbiology Laboratory, SS. Antonio e Biagio e C. Arrigo Hospital, Alessandria, Italy
| | - Laura Carrabba
- Microbiology Laboratory, SS. Antonio e Biagio e C. Arrigo Hospital, Alessandria, Italy
| | - Andrea Rocchetti
- Microbiology Laboratory, SS. Antonio e Biagio e C. Arrigo Hospital, Alessandria, Italy
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25
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Barrado L, Aguinaga A, Herrera-León S, Ezpeleta Baquedano C. Traveller's diarrhoea by Vibrio cholerae in patients returning from the Dominican Republic. Enferm Infecc Microbiol Clin 2019; 37:548-550. [DOI: 10.1016/j.eimc.2018.08.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2018] [Revised: 08/01/2018] [Accepted: 08/15/2018] [Indexed: 10/28/2022]
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26
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Wang EW, Bhatti M, Cantu S, Okhuysen PC. Diagnosis of Yersinia enterocolitica Infection in Cancer Patients With Diarrhea in the Era of Molecular Diagnostics for Gastrointestinal Infections. Open Forum Infect Dis 2019; 6:ofz116. [PMID: 31049362 PMCID: PMC6488527 DOI: 10.1093/ofid/ofz116] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2019] [Accepted: 03/01/2019] [Indexed: 12/03/2022] Open
Abstract
Background Yersinia enterocolitica is an uncommon cause of diarrhea, mesenteric adenitis and bacteremia in the United States. There is limited information regarding the clinical course in immunocompromised patients. We describe the clinical presentations and outcomes in patients with cancer with Y. enterocolitica diagnosed at a US cancer center before and after introduction of gastrointestinal multiplex panel (GIMP) nucleic acid amplification tests (NAATs). Methods We reviewed medical records of all patients with Y. enterocolitica isolated from cultures or identified by means of NAATs from 2000 to 2018. We then extracted demographic information, clinical characteristics, treatment, and overall mortality rate at 30 days after the diagnosis of yersiniosis. Results We identified 17 cases: 6 cases by culture before April 2016 and 11 cases by NAATs after that; 4 of the latter were confirmed by means of culture (36%). This represented an 8-fold increase for overall detection and a 3-fold increase in culture-proved infections when adjusted per 1000 admissions. The most common presenting symptom was diarrhea (11 of 14 [79%]), followed by abdominal pain (9 of 14 [64%]) and nausea and vomiting (6 of 14 [43%]). In 1 patient, the infection resolved spontaneously; the other patients received antibiotic treatment, the majority with a fluoroquinolone. The 30-day mortality rate was 7.1%, and the cause of death was a complication of advanced cancer. Conclusion Since implementing use of the GIMP, we observed an increase in Y. enterocolitica cases, possibly related to increasing number of patients with cancer at our institution who are receiving intensive immunosuppression, increased testing due to ease and availability, and increased sensitivity of NAATs. GIMP NAATs are redefining the epidemiology of Y. enterocolitica infection in patients with cancer.
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Affiliation(s)
- Elizabeth Wenqian Wang
- Department of Medicine, Section of Infectious Diseases, Baylor College of Medicine.,Department of Infectious Diseases, Infection Control and Employee Health, The University of Texas MD Anderson Cancer Center, Houston
| | - Micah Bhatti
- Department of Infectious Diseases, Infection Control and Employee Health, The University of Texas MD Anderson Cancer Center, Houston
| | - Sherry Cantu
- Department of Infectious Diseases, Infection Control and Employee Health, The University of Texas MD Anderson Cancer Center, Houston
| | - Pablo C Okhuysen
- Department of Medicine, Section of Infectious Diseases, Baylor College of Medicine.,Department of Infectious Diseases, Infection Control and Employee Health, The University of Texas MD Anderson Cancer Center, Houston
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Henderson WA, Xiang L, Fourie NH, Abey SK, Ferguson EG, Diallo AF, Kenea ND, Kim CH. Simple lateral flow assays for microbial detection in stool. ANALYTICAL METHODS : ADVANCING METHODS AND APPLICATIONS 2018; 10:5358-5363. [PMID: 31241058 PMCID: PMC6253687 DOI: 10.1039/c8ay01475b] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/03/2018] [Accepted: 08/30/2018] [Indexed: 06/09/2023]
Abstract
Diarrheal diseases claim the lives of 1300 children daily, mostly in the developing world. We have developed a simple lateral flow assay capable of detecting E. coli and EPEC DNA and RNA rapidly (<15 minutes) at the point-of-need, directly from stool without nucleic acid extraction or molecular amplification. The limit of detection of the method is 1 nM using synthetic DNA target substrates spiked into stool. However, due to the endogenous amplification of the 23S rRNA targets, we were able to detect the endogenous EPEC in pea-sized (5 mg) stool without labor-intensive and time-consuming nucleic acid purification or target amplification using enzymes. The significance of this method is that it is rapid (<15 minutes) and simple (without nucleic acid purification or molecular amplification) and does not require instrumentation, or access to a laboratory, cold chain or electric power. Thus, it is well-suited for point-of-need use in remote and/or resource-limited settings in the developing world where the mortality due to diarrheal diseases is especially high. The rapid testing of stool pathogens in real time at the point-of-need will decrease the loss of patients to follow-up, and enable patients to be treated earlier with the appropriate therapeutics in both the developed and developing world settings.
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Affiliation(s)
- Wendy A Henderson
- Division of Intramural Research , National Institute of Nursing Research , National Institutes of Health , Department of Health and Human Services , Bethesda , MD 20892 , USA .
| | - Lichen Xiang
- Division of Intramural Research , National Institute of Nursing Research , National Institutes of Health , Department of Health and Human Services , Bethesda , MD 20892 , USA .
- GoDx , 510 Charmany Drive, Suite 257 , Madison , WI 53719 , USA .
| | - Nicolaas H Fourie
- Division of Intramural Research , National Institute of Nursing Research , National Institutes of Health , Department of Health and Human Services , Bethesda , MD 20892 , USA .
| | - Sarah K Abey
- Division of Intramural Research , National Institute of Nursing Research , National Institutes of Health , Department of Health and Human Services , Bethesda , MD 20892 , USA .
| | - Eric G Ferguson
- Division of Intramural Research , National Institute of Nursing Research , National Institutes of Health , Department of Health and Human Services , Bethesda , MD 20892 , USA .
| | - Ana F Diallo
- Division of Intramural Research , National Institute of Nursing Research , National Institutes of Health , Department of Health and Human Services , Bethesda , MD 20892 , USA .
| | - Natnael D Kenea
- Division of Intramural Research , National Institute of Nursing Research , National Institutes of Health , Department of Health and Human Services , Bethesda , MD 20892 , USA .
| | - Chang Hee Kim
- GoDx , 510 Charmany Drive, Suite 257 , Madison , WI 53719 , USA .
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Madigan VM, Sinickas VG, Giltrap D, Kyriakou P, Ryan K, Chan HT, Clifford V. Health service impact of testing for respiratory pathogens using cartridge-based multiplex array versus molecular batch testing. Pathology 2018; 50:758-763. [PMID: 30389216 PMCID: PMC7111697 DOI: 10.1016/j.pathol.2018.08.012] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2018] [Revised: 08/18/2018] [Accepted: 08/23/2018] [Indexed: 12/26/2022]
Abstract
There is increasing demand for access to rapid microbiological testing, with a view to improving clinical outcomes. The possibility of rapid testing has been facilitated by development of cartridge-based random access molecular technologies that are now widely available. Whether the expense of cartridge-based assays is justified in terms of clinical or laboratory cost savings is controversial. This prospective study evaluated the impact of the Biofire FilmArray Respiratory Panel (‘FilmArray’), a cartridge-based random access molecular test, compared with standard batched molecular testing using an ‘in-house’ respiratory polymerase chain reaction (PCR) on laboratory and health service outcomes for adult patients at a tertiary-level adult hospital in Melbourne, Australia. Laboratory result turnaround time was significantly reduced with the FilmArray (median 4.4 h) compared to a standard validated in-house respiratory PCR assay (median 21.6 h, p < 0.0001) and there was a significant increase in diagnostic yield with the Filmarray (71/124, 57.3%) compared to in-house PCR (79/200; 39.5%; p = 0.002). Despite improved result turnaround time and increased diagnostic yield from testing, there was no corresponding reduction in hospital length of stay or use of isolation beds. Although cartridge-based molecular testing reduced turnaround time to result for respiratory pathogen testing, it did not impact on health service outcomes such as hospital length of stay. Further work is warranted to determine whether cartridge-based tests at the point of care can improve clinical and health service impacts.
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Affiliation(s)
- Victoria M Madigan
- Microbiology Department, Royal Melbourne Hospital, Melbourne, Vic, Australia.
| | - Vincent G Sinickas
- Microbiology Department, Royal Melbourne Hospital, Melbourne, Vic, Australia
| | - Dawn Giltrap
- Microbiology Department, Royal Melbourne Hospital, Melbourne, Vic, Australia
| | - Peter Kyriakou
- Microbiology Department, Royal Melbourne Hospital, Melbourne, Vic, Australia
| | - Katherine Ryan
- Microbiology Department, Royal Melbourne Hospital, Melbourne, Vic, Australia
| | - Hiu-Tat Chan
- Microbiology Department, Royal Melbourne Hospital, Melbourne, Vic, Australia
| | - Vanessa Clifford
- Microbiology Department, Royal Melbourne Hospital, Melbourne, Vic, Australia; The University of Melbourne, Melbourne, Vic, Australia; Murdoch Children's Research Institute, Parkville, Vic, Australia
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29
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Tam CC, Offeddu V, Anderson KB, Weg AL, Macareo LR, Ellison DW, Rangsin R, Fernandez S, Gibbons RV, Yoon IK, Simasathien S. Association between semi-quantitative microbial load and respiratory symptoms among Thai military recruits: a prospective cohort study. BMC Infect Dis 2018; 18:462. [PMID: 30217168 PMCID: PMC6137728 DOI: 10.1186/s12879-018-3358-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2018] [Accepted: 08/23/2018] [Indexed: 02/04/2023] Open
Abstract
BACKGROUND Multiplex real-time polymerase chain reaction assays have improved diagnostic sensitivity for a wide range of pathogens. However, co-detection of multiple agents and bacterial colonization make it difficult to distinguish between asymptomatic infection or illness aetiology. We assessed whether semi-quantitative microbial load data can differentiate between symptomatic and asymptomatic states for common respiratory pathogens. METHODS We obtained throat and nasal swab samples from military trainees at two Thai Army barracks. Specimens were collected at the start and end of 10-week training periods (non-acute samples), and from individuals who developed upper respiratory tract infection during training (acute samples). We analysed the samples using a commercial multiplex respiratory panel comprising 33 bacterial, viral and fungal targets. We used random effects tobit models to compare cycle threshold (Ct) value distributions from non-acute and acute samples. RESULTS We analysed 341 non-acute and 145 acute swab samples from 274 participants. Haemophilus influenzae type B was the most commonly detected microbe (77.4% of non-acute and 64.8% of acute samples). In acute samples, nine specific microbe pairs were detected more frequently than expected by chance. Regression models indicated significantly lower microbial load in non-acute relative to acute samples for H. influenzae non-type B, Streptococcus pneumoniae and rhinovirus, although it was not possible to identify a Ct-value threshold indicating causal etiology for any of these organisms. CONCLUSIONS Semi-quantitative measures of microbial concentration did not reliably differentiate between illness and asymptomatic colonization, suggesting that clinical symptoms may not always be directly related to microbial load for common respiratory infections.
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Affiliation(s)
- Clarence C Tam
- Saw Swee Hock School of Public Health, National University of Singapore and National University Health System, Singapore, 117549, Singapore. .,London School of Hygiene & Tropical Medicine, WC1E7HT, London, UK.
| | - Vittoria Offeddu
- Saw Swee Hock School of Public Health, National University of Singapore and National University Health System, Singapore, 117549, Singapore
| | - Kathryn B Anderson
- University of Minnesota, Minneapolis, 55455, USA.,Armed Forces Research Institute of Medical Sciences, Bangkok, 10400, Thailand
| | - Alden L Weg
- Armed Forces Research Institute of Medical Sciences, Bangkok, 10400, Thailand
| | - Louis R Macareo
- Armed Forces Research Institute of Medical Sciences, Bangkok, 10400, Thailand
| | - Damon W Ellison
- Armed Forces Research Institute of Medical Sciences, Bangkok, 10400, Thailand
| | - Ram Rangsin
- Phramongkutklao College of Medicine, Bangkok, 10400, Thailand
| | - Stefan Fernandez
- Armed Forces Research Institute of Medical Sciences, Bangkok, 10400, Thailand
| | | | - In-Kyu Yoon
- International Vaccine Institute, Seoul, 08826, South Korea
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Rationale of using multiplex polymerase chain reaction (PCR) panels for etiological diagnosis of infective diarrhea in the tropics. Indian J Gastroenterol 2018; 37:381-384. [PMID: 30406887 DOI: 10.1007/s12664-018-0908-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
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31
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Clinical Impact of a Multiplex Gastrointestinal Polymerase Chain Reaction Panel in Patients With Acute Gastroenteritis. Clin Infect Dis 2018; 67:1688-1696. [DOI: 10.1093/cid/ciy357] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2018] [Accepted: 04/20/2018] [Indexed: 02/06/2023] Open
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32
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Freeman K, Mistry H, Tsertsvadze A, Royle P, McCarthy N, Taylor-Phillips S, Manuel R, Mason J. Multiplex tests to identify gastrointestinal bacteria, viruses and parasites in people with suspected infectious gastroenteritis: a systematic review and economic analysis. Health Technol Assess 2018; 21:1-188. [PMID: 28619124 DOI: 10.3310/hta21230] [Citation(s) in RCA: 58] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
BACKGROUND Gastroenteritis is a common, transient disorder usually caused by infection and characterised by the acute onset of diarrhoea. Multiplex gastrointestinal pathogen panel (GPP) tests simultaneously identify common bacterial, viral and parasitic pathogens using molecular testing. By providing test results more rapidly than conventional testing methods, GPP tests might positively influence the treatment and management of patients presenting in hospital or in the community. OBJECTIVE To systematically review the evidence for GPP tests [xTAG® (Luminex, Toronto, ON, Canada), FilmArray (BioFire Diagnostics, Salt Lake City, UT, USA) and Faecal Pathogens B (AusDiagnostics, Beaconsfield, NSW, Australia)] and to develop a de novo economic model to compare the cost-effectiveness of GPP tests with conventional testing in England and Wales. DATA SOURCES Multiple electronic databases including MEDLINE, EMBASE, Web of Science and the Cochrane Database were searched from inception to January 2016 (with supplementary searches of other online resources). REVIEW METHODS Eligible studies included patients with acute diarrhoea; comparing GPP tests with standard microbiology techniques; and patient, management, test accuracy or cost-effectiveness outcomes. Quality assessment of eligible studies used tailored Quality Assessment of Diagnostic Accuracy Studies-2, Consolidated Health Economic Evaluation Reporting Standards and Philips checklists. The meta-analysis included positive and negative agreement estimated for each pathogen. A de novo decision tree model compared patients managed with GPP testing or comparable coverage with patients managed using conventional tests, within the Public Health England pathway. Economic models included hospital and community management of patients with suspected gastroenteritis. The model estimated costs (in 2014/15 prices) and quality-adjusted life-year losses from a NHS and Personal Social Services perspective. RESULTS Twenty-three studies informed the review of clinical evidence (17 xTAG, four FilmArray, two xTAG and FilmArray, 0 Faecal Pathogens B). No study provided an adequate reference standard with which to compare the test accuracy of GPP with conventional tests. A meta-analysis (of 10 studies) found considerable heterogeneity; however, GPP testing produces a greater number of pathogen-positive findings than conventional testing. It is unclear whether or not these additional 'positives' are clinically important. The review identified no robust evidence to inform consequent clinical management of patients. There is considerable uncertainty about the cost-effectiveness of GPP panels used to test for suspected infectious gastroenteritis in hospital and community settings. Uncertainties in the model include length of stay, assumptions about false-positive findings and the costs of tests. Although there is potential for cost-effectiveness in both settings, key modelling assumptions need to be verified and model findings remain tentative. LIMITATIONS No test-treat trials were retrieved. The economic model reflects one pattern of care, which will vary across the NHS. CONCLUSIONS The systematic review and cost-effectiveness model identify uncertainties about the adoption of GPP tests within the NHS. GPP testing will generally correctly identify pathogens identified by conventional testing; however, these tests also generate considerable additional positive results of uncertain clinical importance. FUTURE WORK An independent reference standard may not exist to evaluate alternative approaches to testing. A test-treat trial might ascertain whether or not additional GPP 'positives' are clinically important or result in overdiagnoses, whether or not earlier diagnosis leads to earlier discharge in patients and what the health consequences of earlier intervention are. Future work might also consider the public health impact of different testing treatments, as test results form the basis for public health surveillance. STUDY REGISTRATION This study is registered as PROSPERO CRD2016033320. FUNDING The National Institute for Health Research Health Technology Assessment programme.
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Affiliation(s)
- Karoline Freeman
- Division of Health Sciences, Warwick Medical School, University of Warwick, Coventry, UK
| | - Hema Mistry
- Division of Health Sciences, Warwick Medical School, University of Warwick, Coventry, UK
| | - Alexander Tsertsvadze
- Division of Health Sciences, Warwick Medical School, University of Warwick, Coventry, UK
| | - Pam Royle
- Division of Health Sciences, Warwick Medical School, University of Warwick, Coventry, UK
| | - Noel McCarthy
- Division of Health Sciences, Warwick Medical School, University of Warwick, Coventry, UK
| | - Sian Taylor-Phillips
- Division of Health Sciences, Warwick Medical School, University of Warwick, Coventry, UK
| | | | - James Mason
- Division of Health Sciences, Warwick Medical School, University of Warwick, Coventry, UK
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The role of multiplex molecular panels for the diagnosis of gastrointestinal infections in immunocompromised patients. Curr Opin Infect Dis 2018; 29:359-65. [PMID: 27191200 DOI: 10.1097/qco.0000000000000276] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
PURPOSE OF REVIEW An increasing number of laboratories have implemented multiplex molecular panels for the diagnosis of gastrointestinal infections. This review focuses on recent data addressing the performance of US Food and Drug Administration-cleared multiplex gastrointestinal panels and discusses the advantages and limitations of these tests in the immunocompromised population. RECENT FINDINGS Testing for gastrointestinal pathogens using multiplex molecular panels increases sensitivity and detection of coinfections compared with routine testing methods. Furthermore, multiplex panels reduce turnaround time and may allow for more informed decisions regarding treatment and infection control measures. However, the routine use of multiplex gastrointestinal panels has led to an increase in the detection of certain organisms, such as enteroaggregative Escherichia coli and sapovirus, which many clinical laboratories did not specifically test for in the past. This has created a degree of confusion on how to best interpret the results of multiplex panels, especially in the immunocompromised host. SUMMARY Multiplex molecular panels provide a rapid and sensitive tool for the diagnosis of infectious diarrhea, and may allow for more timely decisions regarding the management of immunosuppressed patients. However, there are limitations associated with multiplex panels, including the interpretation of results and the cost associated with testing. Clinical microbiologists should work closely with clinicians to develop evidence-based algorithms to guide test utilization in this area.
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34
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Tang YW, Stratton CW. Multiplex PCR for Detection and Identification of Microbial Pathogens. ADVANCED TECHNIQUES IN DIAGNOSTIC MICROBIOLOGY 2018. [PMCID: PMC7121544 DOI: 10.1007/978-3-319-95111-9_19] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Multiplexed nucleic acid-based tests for infectious disease have become a standard part of clinical laboratory practice. These tests provide a comprehensive syndrome-based approach to determine the etiological agent of disease. The technology underlying these different systems is reviewed here with a special focus on the BioFire FilmArray® platform. The literature on the clinical utility and cost-effectiveness of these platforms for respiratory, blood culture, and gastrointestinal infections is discussed. Although there are reports showing a clear benefit to the patient or to the healthcare system from adopting a syndromic molecular approach, it is also apparent that clinical laboratories and healthcare providers are still learning how to take full advantage of the new systems. Finally, some improvements to this technology that should appear in the next few years are discussed. These include automated pathogen-specific surveillance based on aggregating the data from these systems, a move toward point-of-care syndromic testing, and further decreases in time to result of the tests.
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Affiliation(s)
- Yi-Wei Tang
- Departments of Laboratory Medicine and Internal Medicine, Memorial Sloan Kettering Cancer Center, New York, NY USA
| | - Charles W. Stratton
- Department of Pathology, Microbiology and Immunology and Medicine, Vanderbilt University Medical Center, Nashville, TN USA
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35
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A Gastrointestinal PCR Panel Improves Clinical Management and Lowers Health Care Costs. J Clin Microbiol 2017; 56:JCM.01457-17. [PMID: 29093106 DOI: 10.1128/jcm.01457-17] [Citation(s) in RCA: 76] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2017] [Accepted: 10/26/2017] [Indexed: 11/20/2022] Open
Abstract
Conventional methods for the identification of gastrointestinal pathogens are time-consuming and expensive and have limited sensitivity. The aim of this study was to determine the clinical impact of a comprehensive molecular test, the BioFire FilmArray gastrointestinal (GI) panel, which tests for many of the most common agents of infectious diarrhea in approximately 1 h. Patients with stool cultures submitted were tested on the GI panel (n = 241) and were compared with control patients (n = 594) from the year prior. The most common organisms detected by the GI panel were enteropathogenic Escherichia coli (EPEC, n = 21), norovirus (n = 21), rotavirus (n = 15), sapovirus (n = 9), and Salmonella (n = 8). Patients tested on the GI panel had an average of 0.58 other infectious stool tests compared with 3.02 in the control group (P = 0.0001). The numbers of days on antibiotic(s) per patient were 1.73 in the cases and 2.12 in the controls (P = 0.06). Patients with the GI panel had 0.18 abdomen and/or pelvic imaging studies per patient compared with 0.39 (P = 0.0002) in the controls. The average length of time from stool culture collection to discharge was 3.4 days in the GI panel group versus 3.9 days in the controls (P = 0.04). The overall health care cost could have decreased by $293.61 per patient tested. The GI panel improved patient care by rapidly identifying a broad range of pathogens which may not have otherwise been detected, reducing the need for other diagnostic tests, reducing unnecessary use of antibiotics, and leading to a reduction in hospital length of stay.
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Abstract
The recent development of commercial panel-based molecular diagnostics for the rapid detection of pathogens in positive blood culture bottles, respiratory specimens, stool, and cerebrospinal fluid has resulted in a paradigm shift in clinical microbiology and clinical practice. This review focuses on U.S. Food and Drug Administration (FDA)-approved/cleared multiplex molecular panels with more than five targets designed to assist in the diagnosis of bloodstream, respiratory tract, gastrointestinal, or central nervous system infections. While these panel-based assays have the clear advantages of a rapid turnaround time and the detection of a large number of microorganisms and promise to improve health care, they present certain challenges, including cost and the definition of ideal test utilization strategies (i.e., optimal ordering) and test interpretation.
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37
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Abbott AN, Fang FC. Clinical Impact of Multiplex Syndromic Panels in the Diagnosis of Bloodstream, Gastrointestinal, Respiratory, and Central Nervous System Infections. ACTA ACUST UNITED AC 2017. [DOI: 10.1016/j.clinmicnews.2017.08.004] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
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38
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Chhabra P, Gregoricus N, Weinberg GA, Halasa N, Chappell J, Hassan F, Selvarangan R, Mijatovic-Rustempasic S, Ward ML, Bowen M, Payne DC, Vinjé J. Comparison of three multiplex gastrointestinal platforms for the detection of gastroenteritis viruses. J Clin Virol 2017; 95:66-71. [PMID: 28889082 DOI: 10.1016/j.jcv.2017.08.012] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2017] [Revised: 08/22/2017] [Accepted: 08/25/2017] [Indexed: 02/04/2023]
Abstract
BACKGROUND Viruses are major etiological agents of childhood gastroenteritis. In recent years, several molecular platforms for the detection of viral enteric pathogens have become available. OBJECTIVE/STUDY DESIGN We evaluated the performance of three multiplex platforms including Biofire's Gastrointestinal Panel (FilmArray), Luminex xTAG® Gastrointestinal Pathogen Panel (GPP), and the TaqMan Array Card (TAC) for the detection of five gastroenteritis viruses using a coded panel of 300 archived stool samples. RESULTS The FilmArray detected a virus in 199 (96.1%) and the TAC in 172 (83.1%) of the 207 samples (187 samples positive for a single virus and 20 samples positive for more than one virus) whereas the GPP detected a virus in 100 (78.7%) of the 127 (97 positive for one virus and three positive for more than one virus) samples. Overall the clinical accuracy was highest for the FilmArray (98%) followed by TAC (97.2%) and GPP (96.9%). The sensitivity of the FilmArray, GPP and TAC platforms was highest for rotavirus (100%, 95.8%, and 89.6%, respectively) and lowest for adenovirus type 40/41 (97.4%, 57.9% and 68.4%). The specificity of the three platforms ranged from 95.6% (rotavirus) to 99.6% (norovirus/sapovirus) for the FilmArray, 99.6% (norovirus) to 100% (rotavirus/adenovirus) for GPP, and 98.9% (astrovirus) to 100% (rotavirus/sapovirus) for TAC. CONCLUSION The FilmArray demonstrated the best analytical performance followed by TAC. In recent years, the availability of multi-enteric molecular testing platforms has increased significantly and our data highlight the strengths and weaknesses of these platforms.
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Affiliation(s)
- Preeti Chhabra
- Synergy America, Inc., Atlanta, GA, United States; Division of Viral Diseases, National Center for Immunizations and Respiratory Disease, Centers for Disease Control and Prevention, Atlanta, GA, United States
| | - Nicole Gregoricus
- Division of Viral Diseases, National Center for Immunizations and Respiratory Disease, Centers for Disease Control and Prevention, Atlanta, GA, United States
| | - Geoffrey A Weinberg
- University of Rochester School of Medicine and Dentistry, Golisano Children's Hospital, Rochester, NY, United States
| | - Natasha Halasa
- Department of Pediatrics, Vanderbilt Vaccine Research Program, Vanderbilt University Medical Center, Nashville, TN, United States
| | - James Chappell
- Department of Pediatrics, Vanderbilt Vaccine Research Program, Vanderbilt University Medical Center, Nashville, TN, United States
| | - Ferdaus Hassan
- Department of Pathology and Laboratory Medicine, Children's Mercy Hospitals, Kansas City, MO, United States
| | - Rangaraj Selvarangan
- Department of Pathology and Laboratory Medicine, Children's Mercy Hospitals, Kansas City, MO, United States
| | - Slavica Mijatovic-Rustempasic
- Division of Viral Diseases, National Center for Immunizations and Respiratory Disease, Centers for Disease Control and Prevention, Atlanta, GA, United States
| | - M Leanne Ward
- Division of Viral Diseases, National Center for Immunizations and Respiratory Disease, Centers for Disease Control and Prevention, Atlanta, GA, United States
| | - Michael Bowen
- Division of Viral Diseases, National Center for Immunizations and Respiratory Disease, Centers for Disease Control and Prevention, Atlanta, GA, United States
| | - Daniel C Payne
- Division of Viral Diseases, National Center for Immunizations and Respiratory Disease, Centers for Disease Control and Prevention, Atlanta, GA, United States
| | - Jan Vinjé
- Division of Viral Diseases, National Center for Immunizations and Respiratory Disease, Centers for Disease Control and Prevention, Atlanta, GA, United States.
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Chao AW, Bhatti M, DuPont HL, Nataro JP, Carlin LG, Okhuysen PC. Clinical features and molecular epidemiology of diarrheagenic Escherichia coli pathotypes identified by fecal gastrointestinal multiplex nucleic acid amplification in patients with cancer and diarrhea. Diagn Microbiol Infect Dis 2017; 89:235-240. [PMID: 28931467 DOI: 10.1016/j.diagmicrobio.2017.08.004] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2017] [Accepted: 08/06/2017] [Indexed: 01/29/2023]
Abstract
Diarrheagenic Escherichia coli (DEC) pathotypes with differing epidemiology and clinical features, are known causes of disease with worldwide occurrence. At a major cancer center in the U.S., we studied patients with cancer and diarrhea for whom a GI Biofire FilmArray multiplex GI panel (BFM) was performed. An enteropathogen was identified in 382 of 2017 (19%) samples distributed across 311 patients. Of these, 60/311(19%) were positive for DEC. Patients receiving hematopoietic stem cell transplants (HSCT) 29/60 (48%) or with a hematologic malignancy 17/60 (28%) accounted for the majority of DEC cases. Enteropathogenic E. coli (EPEC, n=35 [58%]), enteroaggregative E. coli (EAEC, n=10 [17%]) and Shiga toxin producing E. coli (STEC, n=3 [5%]) were the most common DEC identified and peaked in the summer months. Stool cultures confirmed infections in 6/10 (60%) EAEC (five typical AggR+), and EPEC was recovered in 8/35 (22%) samples (all atypical eaeA+, bfp-). DEC was identified in 22 cases (37%) that developed diarrhea >48hours after admission suggesting health care acquisition. Chronic infections were found in 2 EPEC and 1 EAEC cases that were tested at 1month or beyond with shedding that ranged from 58 to >125days. Two patients that underwent hematopoietic stem cell transplantation carried EAEC strains resistant to multiple antibiotics including fluoroquinolones and expressed extended spectrum beta lactamases. While in some instances BFM results were not verified in culture and could represent false positives, DEC pathotypes, especially EPEC and EAEC, caused chronic infections with antimicrobial-resistant strains in a subset of immunosuppressed cancer patients.
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Affiliation(s)
- Andrew W Chao
- Department of Infectious Diseases, Infection Control and Employee Health, The University of Texas M.D. Anderson Cancer Center, Houston, TX; Section of Infectious Diseases, Baylor College of Medicine, Houston, TX
| | - Micah Bhatti
- Department of Laboratory Medicine, The University of Texas M.D. Anderson Cancer Center, Houston, TX
| | - Herbert L DuPont
- Section of Infectious Diseases, Baylor College of Medicine, Houston, TX; Department of Epidemiology, Human Genetics and Environmental Health, The University of Texas School of Public Health, Houston, TX
| | - James P Nataro
- Department of Pediatrics, The University of Virginia School of medicine, Charlottesville, VA
| | - Lily G Carlin
- Department of Infectious Diseases, Infection Control and Employee Health, The University of Texas M.D. Anderson Cancer Center, Houston, TX
| | - Pablo C Okhuysen
- Department of Infectious Diseases, Infection Control and Employee Health, The University of Texas M.D. Anderson Cancer Center, Houston, TX; Section of Infectious Diseases, Baylor College of Medicine, Houston, TX; Department of Epidemiology, Human Genetics and Environmental Health, The University of Texas School of Public Health, Houston, TX.
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40
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Vila J. New molecular diagnostic tools in traveller's diarrhea. J Travel Med 2017; 24:S23-S28. [PMID: 28520995 DOI: 10.1093/jtm/taw071] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/21/2016] [Accepted: 09/16/2016] [Indexed: 12/31/2022]
Abstract
Traveller's diarrhea can be caused by bacteria, protozoa, helminths and viruses. Globally, the most common causes of traveller's diarrhea are two pathotypes of Escherichia coli (enterotoxigenic and enteroaggregative) and Shigella, although there are significant variations according to the geographic area visited. While traveller's diarrhea is usually a mild, self-limiting disease, half of the travellers with traveller's diarrhea have some limitation in their activities during the journey and up to 10% present persistent diarrhea or other complications, making microbiological diagnosis necessary. The aim of this article is to describe the application of new molecular diagnostic tools mainly based on multiplex PCR, including their advantages and disadvantages as well as the current gaps that requiring further study.
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Affiliation(s)
- Jordi Vila
- Department of Clinical Microbiology, Biomedical Diagnostic Centre (CDB), Hospital Clinic, School of Medicine, University of Barcelona, Villarroel, 170, 08036 Barcelona, Spain.,ISGlobal, Barcelona Centre for International Health Research (CRESIB), Barcelona, Spain
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Pérot P, Lecuit M, Eloit M. Astrovirus Diagnostics. Viruses 2017; 9:v9010010. [PMID: 28085120 PMCID: PMC5294979 DOI: 10.3390/v9010010] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2016] [Revised: 12/23/2016] [Accepted: 12/30/2016] [Indexed: 01/25/2023] Open
Abstract
Various methods exist to detect an astrovirus infection. Current methods include electron microscopy (EM), cell culture, immunoassays, polymerase chain reaction (PCR) and various other molecular approaches that can be applied in the context of diagnostic or in surveillance studies. With the advent of metagenomics, novel human astrovirus (HAstV) strains have been found in immunocompromised individuals in association with central nervous system (CNS) infections. This work reviews the past and current methods for astrovirus detection and their uses in both research laboratories and for medical diagnostic purposes.
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Affiliation(s)
- Philippe Pérot
- Institut Pasteur, Biology of Infection Unit, Inserm U1117, Laboratory of Pathogen Discovery, 75015 Paris, France.
- Institut Pasteur, Centre d'innovation et de Recherche Technologique (Citech), 75015 Paris, France.
| | - Marc Lecuit
- Institut Pasteur, Biology of Infection Unit, Inserm U1117, Laboratory of Pathogen Discovery, 75015 Paris, France.
- Paris Descartes University, Sorbonne Paris Cité, 75005, Paris, France.
- Necker-Enfants Malades University Hospital, Division of Infectious Diseases and Tropical Medicine, 75015 Paris, France.
| | - Marc Eloit
- Institut Pasteur, Biology of Infection Unit, Inserm U1117, Laboratory of Pathogen Discovery, 75015 Paris, France.
- Ecole Nationale Vétérinaire d'Alfort, 94700 Maisons-Alfort, France.
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42
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Vila J, Gómez MD, Salavert M, Bosch J. [Methods of rapid diagnosis in clinical microbiology: Clinical needs]. Enferm Infecc Microbiol Clin 2016; 35:41-46. [PMID: 27993417 DOI: 10.1016/j.eimc.2016.11.004] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2016] [Accepted: 11/16/2016] [Indexed: 11/30/2022]
Abstract
The diagnostic methods of infectious diseases should be fast, accurate, simple and affordable. The speed of diagnosis can play a crucial role in healing the patient, allowing the administration of appropriate antibiotic treatment. One aspect that increasingly determines the need for rapid diagnostic techniques is the increased rates of serious infections caused by multidrug resistant bacteria, which cause a high probability of error in the empirical treatment. Some of the conventional methods such as Gram staining or antigen detection can generate results in less than 1 hour but lack sensitivity. Today we are witnessing a major change in clinical microbiology laboratories with the technological advances such as molecular diagnostics, digital microbiology and mass spectrometry. There are several studies showing that these changes in the microbiological diagnosis reduce the generation time of the test results, which has an obvious clinical impact. However, if we look into the future, other new technologies which will cover the needs required for a rapid microbiological diagnosis are on the horizon. This review provides an in depth analysis of the clinical impact that the implementation of rapid diagnostic techniques will have on unmet clinical needs.
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Affiliation(s)
- Jordi Vila
- ISGlobal, Barcelona Ctr. Int. Health Res. (CRESIB), Hospital Clínic - Universitat de Barcelona, Barcelona, España; Servicio de Microbiología, Centro de Diagnóstico Biomédico, Hospital Clínic, Barcelona, España.
| | - María Dolores Gómez
- Servicio de Microbiología, Hospital Universitario y Politécnico La Fe, Valencia, España
| | - Miguel Salavert
- Unidad de Enfermedades Infecciosas, Hospital Universitario y Politécnico La Fe, Valencia, España
| | - Jordi Bosch
- ISGlobal, Barcelona Ctr. Int. Health Res. (CRESIB), Hospital Clínic - Universitat de Barcelona, Barcelona, España; Servicio de Microbiología, Centro de Diagnóstico Biomédico, Hospital Clínic, Barcelona, España
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43
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Murphy CN, Fowler RC, Iwen PC, Fey PD. Evaluation of the BioFire FilmArray® GastrointestinalPanel in a Midwestern Academic Hospital. Eur J Clin Microbiol Infect Dis 2016; 36:747-754. [PMID: 27957599 DOI: 10.1007/s10096-016-2858-7] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2016] [Accepted: 11/28/2016] [Indexed: 01/05/2023]
Abstract
The BioFire FilmArray® Gastrointestinal Panel (GIP) was implemented to replace traditional stool culture and enzyme immunoassay (EIA) testing for stool pathogens. The purpose of this study was to evaluate the detection rate, incidence of coinfection, and culture recovery rate of gastrointestinal (GI) pathogens detected by the GIP over a 1-year period. A total of 2257 stools collected from January to December 2015 were tested using the GIP. Clostridium difficile colonization was also evaluated by an antigen/toxin EIA and confirmatory polymerase chain reaction (PCR). The GIP detected one pathogen in 911 (40.4%) specimens. Coinfections were detected in 176 (7.8%) of these specimens. The most frequently detected pathogens were C. difficile (15.2%), norovirus (8.9%), enteropathogenic Escherichia coli (7.1%), enteroaggregative E. coli (3.4%), Campylobacter spp. (2.3%), and sapovirus (2.0%). Each of the remaining GIP targets had a detection rate of ≤1.6%. The recovery of bacteria for public health investigations varied, with rates as high as 77% for Salmonella to as low as 30% for Yersinia enterocolitica. Of stools positive for C. difficile on the GIP that were tested by EIA, only 42.7% (88/206) were found to be producing detectable toxin. Overall, the implementation of the GIP resulted in high detection rates of GI pathogens, including the frequent detection of coinfections. This is a promising test to streamline the testing of agents causing infectious gastroenteritis from multiple tests down to a single order with limited hands-on time. Ongoing studies will need to assess the impact that the GIP has on downstream patient care and public health practices.
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Affiliation(s)
- C N Murphy
- Department of Pathology and Microbiology, University of Nebraska Medical Center, 985900 Nebraska Medical Center, Omaha, NE, 68198-5900, USA.
| | - R C Fowler
- Department of Pathology and Microbiology, University of Nebraska Medical Center, 985900 Nebraska Medical Center, Omaha, NE, 68198-5900, USA
| | - P C Iwen
- Department of Pathology and Microbiology, University of Nebraska Medical Center, 985900 Nebraska Medical Center, Omaha, NE, 68198-5900, USA
- Nebraska Public Health Laboratory, University of Nebraska Medical Center, Omaha, NE, 68198-5900, USA
| | - P D Fey
- Department of Pathology and Microbiology, University of Nebraska Medical Center, 985900 Nebraska Medical Center, Omaha, NE, 68198-5900, USA
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Multiplex Molecular Panels for Diagnosis of Gastrointestinal Infection: Performance, Result Interpretation, and Cost-Effectiveness. J Clin Microbiol 2016; 53:3723-8. [PMID: 26311866 DOI: 10.1128/jcm.02103-15] [Citation(s) in RCA: 125] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Gastrointestinal disease is a major cause of morbidity and mortality worldwide, especially among young children and immunocompromised patients. Diarrhea may result from infection with a variety of microbial pathogens, including bacteria, viruses, or parasites. Historically, the diagnosis of infectious diarrhea has been made using microscopy, antigen tests, culture, and real-time PCR. A combination of these traditional tests is often required due to the inability to distinguish between infectious etiologies based on the clinical presentation alone. Recently, several multiplex molecular assays have been developed for the detection of gastrointestinal pathogens directly from clinical stool samples. These panels allow for the detection and identification of up to 20 pathogens in as little as 1 h. This review will focus on the multiplex molecular panels that have received clearance from the FDA for the diagnosis of diarrheal disease and will highlight issues related to test performance, result interpretation, and cost-effectiveness of these new molecular diagnostic tools.
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Point-Counterpoint: A Nucleic Acid Amplification Test for Streptococcus pyogenes Should Replace Antigen Detection and Culture for Detection of Bacterial Pharyngitis. J Clin Microbiol 2016; 54:2413-9. [PMID: 27440817 DOI: 10.1128/jcm.01472-16] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
Nucleic acid amplification tests (NAATs) have frequently been the standard diagnostic approach when specific infectious agents are sought in a clinic specimen. They can be applied for specific agents such as S. pyogenes, or commercial multiplex NAATs for detection of a variety of pathogens in gastrointestinal, bloodstream, and respiratory infections may be used. NAATs are both rapid and sensitive. For many years, S. pyogenes testing algorithms used a rapid and specific group A streptococcal antigen test to screen throat specimens, followed, in some clinical settings, by a throat culture for S. pyogenes to increase the sensitivity of its detection. Now S. pyogenes NAATs are being used with increasing frequency. Given their accuracy, rapidity, and ease of use, should they replace antigen detection and culture for the detection of bacterial pharyngitis? Bobbi Pritt and Robin Patel of the Mayo Clinic, where S. pyogenes NAATs have been used for well over a decade with great success, will explain the advantages of this approach, while Richard (Tom) Thomson and Tom Kirn of the NorthShore University HealthSystem will discuss their concerns about this approach to diagnosing bacterial pharyngitis.
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Salmona M, Jolivet S, Duprilot M, Akpabie AC, Fourati S, Decousser JW. Laboratory-based strategy using a new marketed polymerase chain reaction assay to manage diarrheic episodes among patients from rehabilitation and long-term care facilities. Am J Infect Control 2016; 44:716-8. [PMID: 26921013 DOI: 10.1016/j.ajic.2015.12.027] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2015] [Revised: 12/09/2015] [Accepted: 12/14/2015] [Indexed: 12/25/2022]
Abstract
Management of Norovirus and Clostridium difficile gastroenteritis is challenging for rehabilitation and long-term care facilities. We evaluated the contribution of a 2-step laboratory-based strategy, including a new ready-to-use Norovirus polymerase chain reaction assay to promote isolation precautions. C difficile and Norovirus were successively identified from 17% and 23% of 52 episodes of diarrhea, respectively, during the winter season, leading to 100% adequate isolation measures. In patient populations with numerous risk factors for diarrhea, a combined laboratory-based approach could improve infection control.
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Affiliation(s)
- Maud Salmona
- Department of Microbiology, Assistance Publique-Hôpitaux de Paris, University Hospital Henri Mondor, Créteil, France
| | - Sarah Jolivet
- Department of Infection Control, Assistance Publique-Hôpitaux de Paris, University Hospital Henri Mondor, Créteil, France; University Paris East Créteil, Créteil, France
| | - Marion Duprilot
- Department of Microbiology, Assistance Publique-Hôpitaux de Paris, University Hospital Henri Mondor, Créteil, France
| | - Anani Clément Akpabie
- Department of Infection Control, Assistance Publique-Hôpitaux de Paris, Emile-Roux Hospital, Limeil-Brevannes, France
| | - Slim Fourati
- Department of Microbiology, Assistance Publique-Hôpitaux de Paris, University Hospital Henri Mondor, Créteil, France; University Paris East Créteil, Créteil, France
| | - Jean-Winoc Decousser
- Department of Microbiology, Assistance Publique-Hôpitaux de Paris, University Hospital Henri Mondor, Créteil, France; University Paris East Créteil, Créteil, France.
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Zboromyrska Y, Vila J. Advanced PCR-based molecular diagnosis of gastrointestinal infections: challenges and opportunities. Expert Rev Mol Diagn 2016; 16:631-40. [PMID: 26986537 DOI: 10.1586/14737159.2016.1167599] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Acute infections of the gastrointestinal tract are among the most common infectious diseases. The etiological agents of gastroenteritis may be bacteria, viruses or protozoa. Identification of the etiological agents of acute diarrhea is important for the treatment and management of diarrheal diseases. Conventional stool culture for bacteria shows a low sensitivity and requires more than 24 hours. In addition, other approaches to detect viruses and protozoa mainly involve antigen detection, but this is not available for all enteropathogens, and microscopic observation requires training and is of low sensitivity. In this review, the authors describe currently available molecular methods to detect different enteropathogens and analyze the main advantages and disadvantages of these methods for laboratory diagnosis of gastroenteritis.
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Affiliation(s)
- Yuliya Zboromyrska
- a Department of Clinical Microbiology, Biomedical Diagnostic Centre (CDB), Hospital Clínic, School of Medicine , University of Barcelona , Barcelona , Spain.,b ISGlobal, Barcelona Centre for International Health Research (CRESIB), Hospital Clínic, University of Barcelona , Barcelona , Spain
| | - Jordi Vila
- a Department of Clinical Microbiology, Biomedical Diagnostic Centre (CDB), Hospital Clínic, School of Medicine , University of Barcelona , Barcelona , Spain.,b ISGlobal, Barcelona Centre for International Health Research (CRESIB), Hospital Clínic, University of Barcelona , Barcelona , Spain
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Beal SG, Assarzadegan N, Rand KH. Sample-to-result molecular infectious disease assays: clinical implications, limitations and potential. Expert Rev Mol Diagn 2016; 16:323-41. [PMID: 26689497 PMCID: PMC7103687 DOI: 10.1586/14737159.2016.1134325] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2015] [Accepted: 12/17/2015] [Indexed: 01/01/2023]
Abstract
Molecular infectious disease diagnostic tests have undergone major advances in the past decade and will continue to rapidly evolve. Assays have become extraordinarily simple to perform, eliminating the need for pre-analytic sample preparation and post-amplification analysis. This allows these tests to be performed in settings without sophisticated expertise in molecular biology, including locations with limited resources. Additionally, the sensitivity and specificity of these assays is superb and many offer extremely fast turn-around times. These tests have major impacts on patient care, but also have some limitations.
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Affiliation(s)
- Stacy G. Beal
- Department of Pathology, Immunology and Laboratory Medicine,
University of Florida College of Medicine, Gainesville, FL,
USA
| | - Naziheh Assarzadegan
- Department of Pathology, Immunology and Laboratory Medicine,
University of Florida College of Medicine, Gainesville, FL,
USA
| | - Kenneth H. Rand
- Department of Pathology, Immunology and Laboratory Medicine,
University of Florida College of Medicine, Gainesville, FL,
USA
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Human Trichuriasis: Whipworm Genetics, Phylogeny, Transmission and Future Research Directions. CURRENT TROPICAL MEDICINE REPORTS 2015. [DOI: 10.1007/s40475-015-0062-y] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
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