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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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Koeffer J, Kolb M, Sorel O, Ulekleiv C, Feenstra JDM, Eigner U. Clinical performance evaluation of TAQPATH Enteric Bacterial Select Panel for the detection of common enteric bacterial pathogens in comparison to routine stool culture and other qPCR-based diagnostic tests. Microbiol Spectr 2024; 12:e0317223. [PMID: 38054723 PMCID: PMC10783074 DOI: 10.1128/spectrum.03172-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Accepted: 11/01/2023] [Indexed: 12/07/2023] Open
Abstract
IMPORTANCE Enteric bacterial infections caused by Salmonella, Shigella, pathogenic Escherichia coli, and Campylobacter represent one of the most common causes of infectious enteritis worldwide. The timely and accurate diagnosis of pathogens causing gastroenteritis is crucial for patient care, public health, and disease surveillance. While stool culture has long been the standard and highly specific method for detecting enteric pathogens, it is labor-intensive and time-consuming with limited sensitivity. To improve patient outcomes, there is a need to implement new cost-effective approaches for the detection of bacterial enteric pathogens with higher sensitivity and faster time to result. This study shows that multiplex real-time polymerase chain reaction-based tests, such as the TAQPATH Enteric Bacterial Select Panel, are accurate and cost-effective diagnostic alternatives for the detection and differentiation of the most common enteric bacterial pathogens, offering quicker time to result and higher sensitivity compared to routine stool culture.
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Affiliation(s)
- Jasmin Koeffer
- Department of Infectious Diseases, MVZ Labor Dr. Limbach & Kollegen GbR, Heidelberg, Germany
| | - Melissa Kolb
- Department of Infectious Diseases, MVZ Labor Dr. Limbach & Kollegen GbR, Heidelberg, Germany
| | - Oceane Sorel
- Thermo Fisher Scientific, South San Francisco, California, USA
| | | | | | - Ulrich Eigner
- Department of Infectious Diseases, MVZ Labor Dr. Limbach & Kollegen GbR, Heidelberg, Germany
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Shasha D, Grupel D, Treigerman O, Prajgrod G, Paran Y, Hacham D, Ben-Ami R, Albukrek D, Zacay G. The clinical significance of Dientamoeba fragilis and Blastocystis in human stool-retrospective cohort study. Clin Microbiol Infect 2024; 30:130-136. [PMID: 37689266 DOI: 10.1016/j.cmi.2023.09.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Revised: 08/30/2023] [Accepted: 09/04/2023] [Indexed: 09/11/2023]
Abstract
OBJECTIVES The aim of this study was to assess the clinical significance of Dientamoeba fragilis (DF) and Blastocystis species (Bs) in human stool. METHODS Observational study of patients ≥18 years, who were tested by stool multiplex PCR for bacteria and parasites between April 2019 and March 2022. Although DF and Bs are part of the PCR kit, these results are not routinely reported to the patient or the ordering physician. The main outcomes were the incidence of symptoms during 14 days before the referral to stool PCR test, and the incidence of several clinical outcomes during 60 days after the PCR test (symptoms, referrals to further evaluation, prescription of symptomatic, or antibiotic treatment). RESULTS A total of 27 918 patients were tested by stool PCR during the 3 study years. A total of 6215 (22.3%) and 5337 (19.2%) were positive for DF and Bs, respectively. The incidence of symptoms before the test was similar in those positive for Bs or DF and those with all-negative PCR (adjusted OR and 95% CI of 0.87 [0.80-0.95] and 0.82 [0.76-0.88] for Bs and DF, respectively), whereas significantly higher (2.47 [2.23-2.73]) in those positive for the other multiplex PCR assay components. During the 60 days after the test, the prevalence of any of the outcomes was similar in those positive for Bs or DF and those with negative PCR (adjusted OR and 95% CI of 0.92 [0.83-1.02] and 0.89 [0.81-0.97] for symptoms, 0.84 [0.75-0.94] and 0.93 [0.85-1.01] for referrals, 0.88 [0.75-1.03] and 0.82 [0.71-0.94] for symptomatic treatment, and 0.88 [0.75-1.02] and 0.86 [0.75-0.98] for antibiotic treatment in the Bs and DF positive individuals, respectively). The PCR cycle threshold was not associated with any of the outcomes. DISCUSSION Positive stool PCR for DF or Bs was not associated with any of the measured clinical outcomes.
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Affiliation(s)
- David Shasha
- Head Office, Medical Division, Meuhedet Health Services, Tel Aviv, Israel; Infectious Disease Unit, Tel-Aviv Sourasky Medical Center, Tel Aviv, Israel; Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel.
| | - Daniel Grupel
- Department of Clinical Microbiology and Infectious Diseases, Hadassah-Hebrew University Medical Center, Jerusalem, Israel
| | - Orit Treigerman
- Head Office, Medical Division, Meuhedet Health Services, Tel Aviv, Israel
| | - George Prajgrod
- Head Office, Medical Division, Meuhedet Health Services, Tel Aviv, Israel
| | - Yael Paran
- Infectious Disease Unit, Tel-Aviv Sourasky Medical Center, Tel Aviv, Israel; Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Dror Hacham
- Head Office, Medical Division, Meuhedet Health Services, Tel Aviv, Israel
| | - Ronen Ben-Ami
- Infectious Disease Unit, Tel-Aviv Sourasky Medical Center, Tel Aviv, Israel; Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Dov Albukrek
- Head Office, Medical Division, Meuhedet Health Services, Tel Aviv, Israel
| | - Galia Zacay
- Head Office, Medical Division, Meuhedet Health Services, Tel Aviv, Israel; Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
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Hu X, Lin C, Li G, Jiang T, Shen J. A microfluidic chip-based multiplex PCR-reverse dot blot hybridization technique for rapid detection of enteropathogenic bacteria. J Microbiol Methods 2023; 211:106785. [PMID: 37459923 DOI: 10.1016/j.mimet.2023.106785] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2023] [Revised: 07/11/2023] [Accepted: 07/11/2023] [Indexed: 07/23/2023]
Abstract
Diarrhea caused by enteropathogenic bacteria is a major public health issue worldwide, especially in developing countries. In this study, a microfluidic chip-based multiplex polymerase chain reaction (PCR)-reverse dot blot hybridization technology for the rapid and simultaneous detection of 11 enteropathogenic bacteria was developed and the entire process was completed within 3-4 h. The specificity of this method was analyzed using 11 types of pure target bacterial colonies and another 7 types of pure bacterial colonies, and its sensitivity was evaluated with the serial 10-fold dilution of 11 types of pure target bacterial colonies. The detection limit of this method was as low as 103-102 CFU/mL, and it exhibited high specificity for enteropathogenic bacteria. A total of 60 clinical diarrheal fecal samples were detected using this method, the results of which were compared with those of the conventional reference method, which resulted in a positive coincident rate of 100% and a negative coincident rate of 93.75%. Based on the findings, it could be concluded that multiplex PCR-reverse dot blot hybridization based on the microfluidic chip is a rapid, economical, sensitive, specific, and high-throughput method for detecting enteropathogenic bacteria.
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Affiliation(s)
- Xinyi Hu
- The First Affiliated Hospital of Anhui Medical University, Hefei, Anhui 230022, China; Anhui Public Health Clinical Center, Hefei, Anhui 230012, China
| | - Chunhui Lin
- The First Affiliated Hospital of Anhui Medical University, Hefei, Anhui 230022, China; Anhui Public Health Clinical Center, Hefei, Anhui 230012, China
| | - Ge Li
- The First Affiliated Hospital of Anhui Medical University, Hefei, Anhui 230022, China; Anhui Public Health Clinical Center, Hefei, Anhui 230012, China
| | - Tong Jiang
- The First Affiliated Hospital of Anhui Medical University, Hefei, Anhui 230022, China; Anhui Public Health Clinical Center, Hefei, Anhui 230012, China
| | - Jilu Shen
- The First Affiliated Hospital of Anhui Medical University, Hefei, Anhui 230022, China; Anhui Public Health Clinical Center, Hefei, Anhui 230012, China.
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Peiró-Mestres A, Fuertes I, Camprubí-Ferrer D, Marcos MÁ, Vilella A, Navarro M, Rodriguez-Elena L, Riera J, Català A, Martínez MJ, Blanco JL. Frequent detection of monkeypox virus DNA in saliva, semen, and other clinical samples from 12 patients, Barcelona, Spain, May to June 2022. Euro Surveill 2022; 27. [PMID: 35837964 DOI: 10.2807/1560-7917.es.2022.27.28.2200503/cite/plaintext] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/24/2023] Open
Abstract
A monkeypox (MPX) outbreak has expanded worldwide since May 2022. We tested 147 clinical samples collected at different time points from 12 patients by real-time PCR. MPX DNA was detected in saliva from all cases, sometimes with high viral loads. Other samples were frequently positive: rectal swab (11/12 cases), nasopharyngeal swab (10/12 cases), semen (7/9 cases), urine (9/12 cases) and faeces (8/12 cases). These results improve knowledge on virus shedding and the possible role of bodily fluids in disease transmission.
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Affiliation(s)
- Aida Peiró-Mestres
- Barcelona Institute for Global Health (ISGlobal), Hospital Clínic-Universitat de Barcelona, Barcelona, Spain
| | - Irene Fuertes
- Dermatology Department, Hospital Clínic-Universitat de Barcelona, Barcelona, Spain
| | - Daniel Camprubí-Ferrer
- Barcelona Institute for Global Health (ISGlobal), Hospital Clínic-Universitat de Barcelona, Barcelona, Spain
| | - María Ángeles Marcos
- Barcelona Institute for Global Health (ISGlobal), Hospital Clínic-Universitat de Barcelona, Barcelona, Spain
- Microbiology Department, Hospital Clínic-Universitat de Barcelona, Barcelona, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III, Madrid, Spain
| | - Anna Vilella
- Barcelona Institute for Global Health (ISGlobal), Hospital Clínic-Universitat de Barcelona, Barcelona, Spain
- Preventive Medicine and Epidemiology Department, Hospital Clínic-Universitat de Barcelona, Barcelona, Spain
| | - Mireia Navarro
- Microbiology Department, Hospital Clínic-Universitat de Barcelona, Barcelona, Spain
| | | | - Josep Riera
- Dermatology Department, Hospital Clínic-Universitat de Barcelona, Barcelona, Spain
| | - Alba Català
- Dermatology Department, Hospital Clínic-Universitat de Barcelona, Barcelona, Spain
| | - Miguel J Martínez
- Barcelona Institute for Global Health (ISGlobal), Hospital Clínic-Universitat de Barcelona, Barcelona, Spain
- Microbiology Department, Hospital Clínic-Universitat de Barcelona, Barcelona, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III, Madrid, Spain
| | - Jose L Blanco
- Centro de Investigación Biomédica en Red de Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III, Madrid, Spain
- Infectious Diseases Department, Hospital Clínic-IDIBAPS, Universitat de Barcelona, Barcelona, Spain
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Peiró-Mestres A, Fuertes I, Camprubí-Ferrer D, Marcos MÁ, Vilella A, Navarro M, Rodriguez-Elena L, Riera J, Català A, Martínez MJ, Blanco JL. Frequent detection of monkeypox virus DNA in saliva, semen, and other clinical samples from 12 patients, Barcelona, Spain, May to June 2022. Euro Surveill 2022; 27:2200503. [PMID: 35837964 PMCID: PMC9284919 DOI: 10.2807/1560-7917.es.2022.27.28.2200503] [Citation(s) in RCA: 171] [Impact Index Per Article: 85.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2022] [Accepted: 07/14/2022] [Indexed: 12/29/2022] Open
Abstract
A monkeypox (MPX) outbreak has expanded worldwide since May 2022. We tested 147 clinical samples collected at different time points from 12 patients by real-time PCR. MPX DNA was detected in saliva from all cases, sometimes with high viral loads. Other samples were frequently positive: rectal swab (11/12 cases), nasopharyngeal swab (10/12 cases), semen (7/9 cases), urine (9/12 cases) and faeces (8/12 cases). These results improve knowledge on virus shedding and the possible role of bodily fluids in disease transmission.
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Affiliation(s)
- Aida Peiró-Mestres
- Barcelona Institute for Global Health (ISGlobal), Hospital Clínic-Universitat de Barcelona, Barcelona, Spain
| | - Irene Fuertes
- Dermatology Department, Hospital Clínic-Universitat de Barcelona, Barcelona, Spain
| | - Daniel Camprubí-Ferrer
- Barcelona Institute for Global Health (ISGlobal), Hospital Clínic-Universitat de Barcelona, Barcelona, Spain
| | - María Ángeles Marcos
- Barcelona Institute for Global Health (ISGlobal), Hospital Clínic-Universitat de Barcelona, Barcelona, Spain
- Microbiology Department, Hospital Clínic-Universitat de Barcelona, Barcelona, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III, Madrid, Spain
| | - Anna Vilella
- Barcelona Institute for Global Health (ISGlobal), Hospital Clínic-Universitat de Barcelona, Barcelona, Spain
- Preventive Medicine and Epidemiology Department, Hospital Clínic-Universitat de Barcelona, Barcelona, Spain
| | - Mireia Navarro
- Microbiology Department, Hospital Clínic-Universitat de Barcelona, Barcelona, Spain
| | | | - Josep Riera
- Dermatology Department, Hospital Clínic-Universitat de Barcelona, Barcelona, Spain
| | - Alba Català
- Dermatology Department, Hospital Clínic-Universitat de Barcelona, Barcelona, Spain
| | - Miguel J Martínez
- Barcelona Institute for Global Health (ISGlobal), Hospital Clínic-Universitat de Barcelona, Barcelona, Spain
- Microbiology Department, Hospital Clínic-Universitat de Barcelona, Barcelona, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III, Madrid, Spain
| | - Jose L Blanco
- Centro de Investigación Biomédica en Red de Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III, Madrid, Spain
- Infectious Diseases Department, Hospital Clínic-IDIBAPS, Universitat de Barcelona, Barcelona, Spain
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