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Manthey CF, Epple HJ, Keller KM, Lübbert C, Posovszky C, Ramharter M, Reuken P, Suerbaum S, Vehreschild M, Weinke T, Addo MM, Stallmach A, Lohse AW. S2k-Leitlinie Gastrointestinale Infektionen der Deutschen Gesellschaft für Gastroenterologie, Verdauungs- und Stoffwechselkrankheiten (DGVS). ZEITSCHRIFT FUR GASTROENTEROLOGIE 2024; 62:1090-1149. [PMID: 38976986 DOI: 10.1055/a-2240-1428] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/10/2024]
Affiliation(s)
- Carolin F Manthey
- I. Medizinische Klinik und Poliklinik - Schwerpunkt Gastroenterologie; Sektionen Infektions- und Tropenmedizin, Universitätsklinikum Hamburg-Eppendorf, Hamburg, Deutschland
- Gemeinschaftspraxis Innere Medizin Witten, Witten, Deutschland
| | - Hans-Jörg Epple
- Antibiotic Stewardship, Vorstand Krankenversorgung, Universitätsmedizin Berlin, Berlin, Deutschland
| | - Klaus-Michael Keller
- Klinik für Kinder- und Jugendmedizin, Helios Dr. Horst Schmidt Kliniken, Klinik für Kinder- und Jugendmedizin, Wiesbaden, Deutschland
| | - Christoph Lübbert
- Bereich Infektiologie und Tropenmedizin, Medizinische Klinik I (Hämatologie, Zelltherapie, Infektiologie und Hämostaseologie), Universitätsklinikum Leipzig, Leipzig, Deutschland
| | | | - Michael Ramharter
- I. Medizinische Klinik und Poliklinik - Schwerpunkt Gastroenterologie; Sektionen Infektions- und Tropenmedizin, Universitätsklinikum Hamburg-Eppendorf, Hamburg, Deutschland
| | - Philipp Reuken
- Klinik für Innere Medizin IV (Gastroenterologie, Hepatologie, Infektiologie, Zentrale Endoskopie), Universitätsklinikum Jena, Jena, Deutschland
| | - Sebastian Suerbaum
- Universität München, Max von Pettenkofer-Institut für Hygiene und Medizinische Mikrobiologie, München, Deutschland
| | - Maria Vehreschild
- Medizinische Klinik II, Universitätsklinikum Frankfurt, Frankfurt, Deutschland
| | - Thomas Weinke
- Klinik für Gastroenterologie und Infektiologie, Klinikum Ernst von Bergmann, Potsdam, Deutschland
| | - Marylyn M Addo
- I. Medizinische Klinik und Poliklinik - Schwerpunkt Gastroenterologie; Sektionen Infektions- und Tropenmedizin, Universitätsklinikum Hamburg-Eppendorf, Hamburg, Deutschland
- Institut für Infektionsforschung und Impfstoffentwicklung Sektion Infektiologie, I. Med. Klinik, Zentrum für Innere Medizin, Universitätsklinikum Hamburg-Eppendorf, Hamburg, Deutschland
| | - Andreas Stallmach
- Klinik für Innere Medizin IV (Gastroenterologie, Hepatologie, Infektiologie, Zentrale Endoskopie), Universitätsklinikum Jena, Jena, Deutschland
| | - Ansgar W Lohse
- I. Medizinische Klinik und Poliklinik - Schwerpunkt Gastroenterologie; Sektionen Infektions- und Tropenmedizin, Universitätsklinikum Hamburg-Eppendorf, Hamburg, Deutschland
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Dashti A, Alonso H, Escolar-Miñana C, Köster PC, Bailo B, Carmena D, González-Barrio D. Evaluation of the Use of Singleplex and Duplex CerTest VIASURE Real-Time PCR Assays to Detect Common Intestinal Protist Parasites. Diagnostics (Basel) 2024; 14:319. [PMID: 38337835 PMCID: PMC10855428 DOI: 10.3390/diagnostics14030319] [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: 12/18/2023] [Revised: 01/24/2024] [Accepted: 01/30/2024] [Indexed: 02/12/2024] Open
Abstract
Cryptosporidium spp., Giardia duodenalis and Entamoeba histolytica are species of protozoa- causing diarrhoea that are common worldwide, while Entamoeba dispar, Dientamoeba fragilis and Blastocystis sp. appear to be commensal parasites whose role in pathogenicity remains controversial. We conducted the clinical evaluation of five singleplex and one duplex CerTest VIASURE Real-Time PCR Assays against a large panel of positive DNA samples (n = 358), and specifically to Cryptosporidium spp. (n = 96), G. duodenalis (n = 115), E. histolytica (n = 25) E. dispar (n = 11), Blastocystis sp. (n = 42), D. fragilis (n = 37), and related parasitic phylum species such as Apicomplexa, Euglenozoa, Microsporidia and Nematoda. DNA samples were obtained from clinical stool specimens or cultured isolates in a national reference centre. Estimated diagnostic sensitivity and specificity values were 0.94-1 for Cryptosporidium spp., 0.96-0.99 for G. duodenalis, 0.96-1 for E. histolytica, 1-1 for E. dispar, and 1-0.99 for D. fragilis in the evaluated singleplex assays. In the duplex assay for the simultaneous detection of Blastocystis sp. and D. fragilis these values were 1-0.98 and 1-0.99, respectively. Measures of diagnostic precision for repeatability and reproducibility were found to be under acceptable ranges. The assays identified six Cryptosporidium species (C. hominis, C. parvum, C. canis, C. felis, C. scrofarum, and C. ryanae), four G. duodenalis assemblages (A, B, C, and F), and six Blastocystis subtypes (ST1-ST5, and ST8). The evaluated singleplex and duplex VIASURE Real-Time PCR assays provide sensitive, practical, and cost-effective choices to the molecular diagnosis of the main diarrhoea-causing intestinal protists in clinical microbiology and research laboratories.
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Affiliation(s)
- Alejandro Dashti
- Parasitology Reference and Research Laboratory, National Centre for Microbiology, Health Institute Carlos III, 28220 Majadahonda, Spain; (A.D.); (P.C.K.); (B.B.); (D.G.-B.)
| | - Henar Alonso
- Department of Microbiology, Paediatrics, Radiology, and Public Health, Faculty of Medicine, University of Zaragoza, 50009 Saragossa, Spain
| | - Cristina Escolar-Miñana
- Department of Animal Production and Food Science, Faculty of Veterinary, University of Zaragoza, 50013 Saragossa, Spain
| | - Pamela C. Köster
- Parasitology Reference and Research Laboratory, National Centre for Microbiology, Health Institute Carlos III, 28220 Majadahonda, Spain; (A.D.); (P.C.K.); (B.B.); (D.G.-B.)
- Faculty of Health Sciences, Alfonso X El Sabio University (UAX), 28691 Villanueva de la Cañada, Spain
- Faculty of Medicine, Alfonso X El Sabio University (UAX), 28691 Villanueva de la Cañada, Spain
| | - Begoña Bailo
- Parasitology Reference and Research Laboratory, National Centre for Microbiology, Health Institute Carlos III, 28220 Majadahonda, Spain; (A.D.); (P.C.K.); (B.B.); (D.G.-B.)
| | - David Carmena
- Parasitology Reference and Research Laboratory, National Centre for Microbiology, Health Institute Carlos III, 28220 Majadahonda, Spain; (A.D.); (P.C.K.); (B.B.); (D.G.-B.)
- CIBER Infectious Diseases (CIBERINFEC), Health Institute Carlos III, 28008 Madrid, Spain
| | - David González-Barrio
- Parasitology Reference and Research Laboratory, National Centre for Microbiology, Health Institute Carlos III, 28220 Majadahonda, Spain; (A.D.); (P.C.K.); (B.B.); (D.G.-B.)
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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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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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Sánchez I, Dashti A, Köster PC, Bailo B, González N, Allende J, Stensvold CR, Carmena D, González-Barrio D. Development, Optimisation and Validation of a Novel Multiplex Real-Time PCR Method for the Simultaneous Detection of Cryptosporidium spp., Giardia duodenalis and Dientamoeba fragilis. Pathogens 2022; 11:1277. [PMID: 36365028 PMCID: PMC9693193 DOI: 10.3390/pathogens11111277] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Revised: 10/28/2022] [Accepted: 10/30/2022] [Indexed: 07/03/2024] Open
Abstract
The enteric protozoan parasites Cryptosporidium spp., Giardia duodenalis and Dientamoeba fragilis are-to various extents-contributors to the burden of gastrointestinal illness in high-income countries. Detection of these pathogens by microscopy examination is challenging because of the limited sensitivity and need for specific staining procedures. We developed and optimised a new multiplex real-time PCR assay for the simultaneous detection of Cryptosporidium spp., G. duodenalis and D. fragilis in clinical (stool) samples. The diagnostic performance of the assay was evaluated against a large panel of well-characterised DNA samples positive for Cryptosporidium spp. (n = 126), G. duodenalis (n = 132) and D. fragilis (n = 49). The specificity of the test was assessed against a DNA panel from other intestinal or phylogenetically related parasites (n = 105) and faecal DNA from individuals without clinical manifestations (n = 12). The assay exhibited a diagnostic sensitivity of 0.90-0.97 and a diagnostic specificity of 1. The limit of detection was estimated for Cryptosporidium (1 oocyst) and G. duodenalis (5 × 10-4 cysts). The method allowed the detection of four Cryptosporidium species (C. hominis, C. parvum, C. meleagridis and C. cuniculus) and five G. duodenalis assemblages (A-E) without cross-reacting with other parasites belonging to the phyla Amoebozoa, Apicomplexa, Euglenozoa, Microsporidia, Nematoda and Platyhelminthes. This newly developed multiplex real-time PCR assay represents a novel alternative for the rapid and accurate detection of Cryptosporidium, G. duodenalis and D. fragilis in clinical settings.
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Affiliation(s)
| | - Alejandro Dashti
- Parasitology Reference and Research Laboratory, Spanish National Centre for Microbiology, Health Institute Carlos III, Majadahonda, 28220 Madrid, Spain
| | - Pamela C. Köster
- Parasitology Reference and Research Laboratory, Spanish National Centre for Microbiology, Health Institute Carlos III, Majadahonda, 28220 Madrid, Spain
| | - Begoña Bailo
- Parasitology Reference and Research Laboratory, Spanish National Centre for Microbiology, Health Institute Carlos III, Majadahonda, 28220 Madrid, Spain
| | | | | | - Christen Rune Stensvold
- Department of Bacteria, Parasites and Fungi, Infectious Disease Preparedness, Statens Serum Institute, 2300 Copenhagen, Denmark
| | - David Carmena
- Parasitology Reference and Research Laboratory, Spanish National Centre for Microbiology, Health Institute Carlos III, Majadahonda, 28220 Madrid, Spain
- Center for Biomedical Research Network (CIBER) in Infectious Diseases, Health Institute Carlos III, Majadahonda, 28220 Madrid, Spain
| | - David González-Barrio
- Parasitology Reference and Research Laboratory, Spanish National Centre for Microbiology, Health Institute Carlos III, Majadahonda, 28220 Madrid, Spain
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Montasser K, Osman HA, Abozaid H, Khalil HS, Hatem Amer W, Sabry AMM. Multiplex PCR: Aid to more-timely and directed therapeutic intervention for patients with infectious gastroenteritis. Medicine (Baltimore) 2022; 101:e31022. [PMID: 36254068 PMCID: PMC9575839 DOI: 10.1097/md.0000000000031022] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
BACKGROUND Multiplex PCR is a sensitive and rapid method compared with conventional methods. Therefore, we use multiplex PCR for the rapid detection of the four major intestinal pathogens causing gastroenteritis (Shigella spp., Campylobacter spp., Aeromonas spp. and Enterohemorrhagic Escherichia coli [EHEC]) in stool specimens. MATERIALS AND METHODS A prospective randomized study using 200 stool samples obtained from patients presented with acute gastroenteritis during the study period (between February 2019 and December 2021). Bacteria in stool samples were identified using conventional culture methods and multiplex PCR for stool samples. RESULTS The identified organisms using conventional cultures; were Shigella (27%), Aeromonas species (10%) and EHEC (O157) (8%). Using multiplex PCR. Shigella spp. was the most commonly identified pathogen (detected in 40.5% of positive samples), followed by Aeromonas spp. (30%), EHEC (20%) and Campylobacter species was only detected in (1%) of positive samples. The diagnostic evaluation of multiplex PCR in relation to conventional method in diagnosis of Shigella, EHEC and Aeromonas showed, sensitivity of 100% (for each), specificity of 88.5%, 92.4%, 77.8% respectively. However, the diagnostic evaluation of multiplex PCR in relation to conventional method in diagnosis of Campylobacter showed specificity of 99% and NPV of 100%. CONCLUSIONS Multiplex PCR is an accurate and rapid method for detection of common intestinal pathogens causing severe gastroenteritis. a rapid method that could be used in outbreaks for diagnosis of the common enteric pathogens causing fatal gastroenteritis.
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Affiliation(s)
- Karim Montasser
- Clinical Pathology Department, Faculty of Medicine, Helwan University, Helwan, Egypt
| | - Heba Ahmed Osman
- Tropical Medicine and Gastroenterology Department, Faculty of Medicine, South Valley University, Qena, Egypt
- *Correspondence: Heba Ahmed Osman, Tropical Medicine and Gastroenterology Department, Faculty of Medicine, South Valley University, Qena, Egypt (e-mail: )
| | - Hanan Abozaid
- Clinical Pathology Department, Faculty of Medicine, Helwan University, Helwan, Egypt
| | - Haidy S. Khalil
- Medical Microbiology and Immunology Department, Faculty of Medicine, Helwan University, Helwan, Egypt
| | - Wesam Hatem Amer
- Microbiology and Immunology Department, Faculty of Medicine, Tanta University, Tanta, Egypt
| | - Abeer M. M. Sabry
- Internal Medicine and Gastroenterology Department, Faculty of Medicine, Helwan University, Helwan, Egypt
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Kara Y, Kızıl MC, Kılıç Ö, Us T, Dinleyici EÇ. Investigation of the use of multiplex PCR in childhood diarrhea with clinical and epidemiological features. J Trop Pediatr 2022; 68:6770065. [PMID: 36272732 DOI: 10.1093/tropej/fmac090] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
INTRODUCTION Acute gastroenteritis is one of the most common causes of hospital admission in children. Treatment regimens differ depending on the pathogen. In our study, we aimed to evaluate the epidemiological and clinical features of pediatric patients whose gastrointestinal agents were detected by multiplex PCR. MATERIALS AND METHODS The study included 131 pediatric patients who were followed up at Eskişehir Osmangazi University, Pediatric Department between January 2018 and December 2021.Gastrointestinal pathogens were detected in stool samples by multiplex PCR. The epidemiological and clinical features were reviewed retrospectively. RESULTS A total of 203 gastrointestinal pathogens were detected from the stool samples of 131 cases. Of these cases, 56% were male and 44% were female. The mean age was 66 (2-204) months. The most common symptoms were diarrhea, fever, vomiting and abdominal pain. The pathogen detection rate was 69% by multiplex PCR. A single pathogen was detected in 85 (65%) cases and multiple pathogens were detected in 46 (35%) cases. The most common pathogens were enteropathogenic Escherichia coli (EPEC, 23%), Clostridium difficile (21%), norovirus (17%), rotavirus (15%), salmonella (12%) and enterotoxigenic E. coli (ETEC, 11%). Stool culture was positive in 16 (12%) cases and microscopic examination positive in 17 (13%) cases. Probiotic treatment was given to 119 (92%) cases and antimicrobial treatment (metroinidazole, ceftriaxone, azithromycin and oral vancomycin) to 34 (26%) cases. Of the cases, 56 (42%) had chronic disease, 40 (30%) had a history of previous antibiotic use and 17 (13%) had a history of hospitalization in the intensive care unit. CONCLUSION The sensitivity of the multiplex PCR in the detection of acute gastroenteritis agents is higher than stool microscopy, stool culture and stool antigen tests. However, due to the inability to distinguish between colonization, carrier state and pathogenicity, it should be evaluated together with other diagnostic tests and clinical findings in order to determine whether the determined agent is pathogenic or not and in the regulation of antimicrobial therapy.
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Affiliation(s)
- Yalçın Kara
- Division of Pediatric Infectious Diseases, Department of Pediatrics, Eskişehir Osmangazi University Medical Faculty, Eskişehir, Turkey
| | - Mahmut Can Kızıl
- Division of Pediatric Infectious Diseases, Department of Pediatrics, Eskişehir Osmangazi University Medical Faculty, Eskişehir, Turkey
| | - Ömer Kılıç
- Division of Pediatric Infectious Diseases, Department of Pediatrics, Eskişehir Osmangazi University Medical Faculty, Eskişehir, Turkey
| | - Tercan Us
- Department of Microbiology, Eskişehir Osmangazi University Medical Faculty, Eskişehir, Turkey
| | - Ener Çağrı Dinleyici
- Division of Pediatric Intensive Care Unit, Department of Pediatrics, Eskişehir Osmangazi University Medical Faculty, Eskişehir, Turkey
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Rousou X, Furuya-Kanamori L, Kostoulas P, Doi SAR. Diagnostic accuracy of multiplex nucleic acid amplification tests for Campylobacter infection: a systematic review and meta-analysis. Pathog Glob Health 2022; 117:259-272. [PMID: 35815907 PMCID: PMC10081061 DOI: 10.1080/20477724.2022.2097830] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022] Open
Abstract
Campylobacter infection is one of the most frequently reported foodborne diseases with approximately 230,000 and 1.5 million cases each year in Europe and the USA, respectively. Culture methods are the reference for the diagnosis of Campylobacter infections; however, these methods are complex and time-consuming. Multiplex nucleic acid amplification test is favored due to its rapidity, automatization in the procedure followed and the quick simultaneous testing of numerous foodborne pathogens. The aim of this meta-analysis was to evaluate the accuracy of these tests for the diagnosis of Campylobacter infection. Scopus, Science Direct, PubMed, Web of Science, and Mendeley were searched for peer-reviewed articles. The split component synthesis method with the use of the inverse variance heterogeneity model was chosen for the quantitative meta-analysis. Sensitivity analysis was performed by age category and index test. The literature search found 34 studies involving 28,105 patients with suspected gastroenteritis. The sensitivity and specificity were 95.3% (92.3; 97.1) and 97.1% (95.1; 98.3), respectively, and AUC (area under the curve) was 0.963 (0.947; 0.974). Pediatric patients had a lower sensitivity (87.4, 48.2; 98.1) and higher specificity (99.2, 91.6; 99.9) estimate compared to all ages category (sensitivity 95.3, 91.3; 97.5, specificity 96.7, 93.7; 98.3). Among the various index tests, Seeplex/Allplex and Amplidiag/Novodiag had the lowest estimate for sensitivity (88.9, 73.8; 95.8) and specificity (95.2, 86; 98.4), respectively. BDMax had the highest (sensitivity 98.1, 96.1; 99 and specificity 98.5, 97; 99.3). Multiplex nucleic acid tests showed excellent accuracy and could play an influential role in diagnosing Campylobacter infections.
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Affiliation(s)
- Xanthoula Rousou
- Laboratory of Epidemiology and Artificial Intelligence, Faculty of Public and One Health, School of Health Sciences, University of Thessaly, Karditsa, Greece
| | - Luis Furuya-Kanamori
- UQ Centre for Clinical Research, Faculty of Medicine, the University of Queensland, Herston, Queensland, Australia
| | - Polychronis Kostoulas
- Laboratory of Epidemiology and Artificial Intelligence, Faculty of Public and One Health, School of Health Sciences, University of Thessaly, Karditsa, Greece
| | - Suhail A R Doi
- Department of Population Medicine, College of Medicine, Qatar University, Doha, Qatar
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Dashti A, Alonso H, Escolar-Miñana C, Köster PC, Bailo B, Carmena D, González-Barrio D. Evaluation of a Novel Commercial Real-Time PCR Assay for the Simultaneous Detection of Cryptosporidium spp., Giardia duodenalis, and Entamoeba histolytica. Microbiol Spectr 2022; 10:e0053122. [PMID: 35502919 PMCID: PMC9241732 DOI: 10.1128/spectrum.00531-22] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Accepted: 04/11/2022] [Indexed: 11/20/2022] Open
Abstract
Cryptosporidium spp., Giardia duodenalis, and Entamoeba histolytica are the most common diarrhea-causing protozoan species globally. Misdiagnosis is a concern for asymptomatic and chronic infections. Multiplexing, i.e., the detection of more than one parasite in a single test by real-time PCR, allows high diagnostic performance with favorable cost-effectiveness. We conducted a clinical evaluation of the VIASURE Cryptosporidium, Giardia, & E. histolytica real-time PCR assay (CerTest Biotec, San Mateo de Gállego, Spain) against a large panel (n = 358) of well-characterized DNA samples positive for Cryptosporidium spp. (n = 96), G. duodenalis (n = 115), E. histolytica (n = 25), and other parasitic species of the phyla Amoebozoa (n = 11), Apicomplexa (n = 14), Euglenozoa (n = 8), Heterokonta (n = 42), Metamonada (n = 37), Microsporidia (n = 4), and Nematoda (n = 6). DNA samples were obtained from clinical stool specimens or cultured isolates in a national reference center. Estimated sensitivity and specificity were 0.96 and 0.99 for Cryptosporidium spp., 0.94 and 1 for G. duodenalis, and 0.96 and 1 for E. histolytica, respectively. Positive and negative predictive values were calculated as 1 and 0.98 for Cryptosporidium spp., 0.99 and 0.98 for G. duodenalis, and 1 and 0.99 for E. histolytica, respectively. The assay identified six Cryptosporidium species (Cryptosporidium hominis, Cryptosporidium parvum, Cryptosporidium canis, Cryptosporidium felis, Cryptosporidium scrofarum, and Cryptosporidium ryanae) and four G. duodenalis assemblages (A, B, C, and F). The VIASURE assay provides rapid and accurate simultaneous detection and identification of the most commonly occurring species and genetic variants of diarrhea-causing parasitic protozoa in humans. IMPORTANCE Thorough independent assessment of the diagnostic performance of novel diagnostic assays is essential to ascertain their true usefulness and applicability in routine clinical practice. This is particularly true for commercially available kits based on multiplex real-time PCR aimed to detect and differentiate multiple pathogens in a single biological sample. In this study, we conducted a clinical evaluation of the VIASURE Cryptosporidium, Giardia, & E. histolytica real-time PCR assay (CerTest Biotec) for the detection and identification of the diarrhea-causing enteric protozoan parasites Cryptosporidium spp., G. duodenalis, and E. histolytica. A large panel of well-characterized DNA samples from clinical stool specimens or cultured isolates from a reference center was used for this purpose. The VIASURE assay demonstrated good performance for the routine testing of these pathogens in clinical microbiological laboratories.
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Affiliation(s)
- Alejandro Dashti
- Parasitology Reference and Research Laboratory, National Centre for Microbiology, Carlos III Health Institute, Madrid, Spain
| | - Henar Alonso
- Department of Microbiology, Paediatrics, Radiology, and Public Health, Faculty of Medicine, University of Zaragoza, Saragossa, Spain
| | - Cristina Escolar-Miñana
- Department of Animal Production and Food Science, Faculty of Veterinary, University of Zaragoza, Saragossa, Spain
| | - Pamela C. Köster
- Parasitology Reference and Research Laboratory, National Centre for Microbiology, Carlos III Health Institute, Madrid, Spain
| | - Begoña Bailo
- Parasitology Reference and Research Laboratory, National Centre for Microbiology, Carlos III Health Institute, Madrid, Spain
| | - David Carmena
- Parasitology Reference and Research Laboratory, National Centre for Microbiology, Carlos III Health Institute, Madrid, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Infecciosas, Instituto de Salud Carlos III, Madrid, Spain
| | - David González-Barrio
- Parasitology Reference and Research Laboratory, National Centre for Microbiology, Carlos III Health Institute, Madrid, Spain
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Holliday LR, Perry MD. Network-wide analysis of the Serosep EntericBio Gastro Panel 2 for the detection of enteric pathogens in Public Health Wales microbiology laboratories. J Med Microbiol 2022; 71. [PMID: 35639604 DOI: 10.1099/jmm.0.001555] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Introduction. A retrospective data analysis of 34 months (spanning 2016-2020) of 961573 diagnostic results obtained before and after nucleic acid amplification testing (NAAT) implementation, across the Public Health Wales microbiology network.Hypothesis / Gap Statement. This is the first network-wide analysis of the implementation of enteric NAAT in diagnostic microbiology.Aim. To assess the outcome of replacing microscopy and bacterial culture with NAAT as the primary test in the diagnosis of: Campylobacter spp., Salmonella sp., Shigella spp., Shiga toxin-producing Escherichia coli (STEC), Cryptosporidium spp. and Giardia duodenalis infections.Methodology. Following NAAT introduction, bacterial culture was performed as a secondary test, to provide further information from NAAT positive samples for epidemiological purposes. Primary detection rates and overall bacterial culture rates were calculated for each target pathogen using both testing regimes (Stage I) including a comparison of in-patient and out-patient diagnoses (Stage II).Results. Stage I analysis showed that the primary detection rate significantly increased for Campylobacter spp. (P<0.0001), Salmonella sp. (P=0.0151), Shigella spp. (P<0.0001), STEC (P<0.0001), Cryptosporidium spp. (P<0.0001) and Giardia duodenalis (P<0.0001) when using NAAT compared to microscopy or bacterial culture. A significant decrease was seen in the overall rate of Campylobacter spp. isolation by bacterial culture (P<0.0001), whilst other targets remained unaffected. Stage II analysis showed that NAAT positive out-patient samples were more likely to be supplemented by a positive bacterial culture than NAAT positive in-patient samples for Campylobacter spp. (P<0.0001), Salmonella sp. (P=0.0004) and STEC (P=0.0039). However, Shigella spp. was more frequently isolated from NAAT positive in-patient samples (P=0.0005). A notable increase was seen for G. duodenalis detection from in-patient samples (P=0.0002). Reference laboratory data showed the NAAT assay can detect at least 53 serotypes of STEC but may not be able to detect some of the rarer species of Cryptosporidium seen in human infections.Conclusion. The implementation of NAAT has significantly increased the primary detection rate of all target enteric pathogens in Wales and information gleaned previously from direct culture is largely unaffected.
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Affiliation(s)
- Lucy R Holliday
- Public Health Wales Microbiology, Singleton Hospital, Swansea, UK
| | - Michael D Perry
- Public Health Wales Microbiology, University Hospital of Wales, Heath Park, Cardiff, UK
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Karakusevic A, Devaney P, Enstone A, Kanibir N, Hartwig S, Carias CDS. The burden of rotavirus-associated acute gastroenteritis in the elderly: assessment of the epidemiology in the context of universal childhood vaccination programs. Expert Rev Vaccines 2022; 21:929-940. [PMID: 35535677 DOI: 10.1080/14760584.2022.2066524] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Abstract
INTRODUCTION Rotaviruses (RVs) cause acute gastroenteritis (AGE) in infants and young children worldwide and also in older adults (≥60 years), however the burden among this age group is not well understood. Herd immunity through pediatric RV vaccination may reduce the burden of RVGE across all ages, however the impact of pediatric vaccination on burden in older adults is poorly understood. AREAS COVERED This systematic review was undertaken to identify studies related to the following objectives: understand the burden of RV in older adults, RV seroprevalence, and the impact of pediatric vaccination on this burden and highlight evidence gaps to guide future research. Of studies identified, 59 studies from two databases were included in this analysis following a review by two reviewers. EXPERT OPINION RV is an understudied disease in older adults. We found that 0-62% of patients with AGE tested positive for RV, with results varying by setting, country, and patient age. Results also suggest that pediatric vaccination benefits older adults through herd protection. Several studies showed a reduction in RV incidence after vaccination. However, there was variety in results and lack of consistency in outcomes reported. Further studies targeting older adults are needed to better characterize RV burden.
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Affiliation(s)
| | | | | | - Nabi Kanibir
- Global Medical and Scientific Affairs, Msd International GmbH, Luzern, Switzerland
| | - Susanne Hartwig
- Biostatistical and Research Decision Sciences Epidemiology, MSD Vaccins, France
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12
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Collard JM, Andrianonimiadana L, Habib A, Rakotondrainipiana M, Andriantsalama P, Randriamparany R, Rabenandrasana MAN, Weill FX, Sauvonnet N, Randremanana RV, Guillemot V, Vonaesch P, Sansonetti PJ. High prevalence of small intestine bacteria overgrowth and asymptomatic carriage of enteric pathogens in stunted children in Antananarivo, Madagascar. PLoS Negl Trop Dis 2022; 16:e0009849. [PMID: 35533199 PMCID: PMC9119516 DOI: 10.1371/journal.pntd.0009849] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2021] [Revised: 05/19/2022] [Accepted: 04/01/2022] [Indexed: 11/26/2022] Open
Abstract
Environmental Enteric Dysfunction (EED) refers to an incompletely defined syndrome of inflammation, reduced absorptive capacity, and reduced barrier function in the small intestine. It is widespread among children and adults in low- and middle-income countries and is also associated with poor sanitation and certain gut infections possibly resulting in an abnormal gut microbiota, small intestinal bacterial overgrowth (SIBO) and stunting. We investigated bacterial pathogen exposure in stunted and non-stunted children in Antananarivo, Madagascar by collecting fecal samples from 464 children (96 severely stunted, 104 moderately stunted and 264 non-stunted) and the prevalence of SIBO in 109 duodenal aspirates from stunted children (61 from severely stunted and 48 from moderately stunted children). SIBO assessed by both aerobic and anaerobic plating techniques was very high: 85.3% when selecting a threshold of ≥105 CFU/ml of bacteria in the upper intestinal aspirates. Moreover, 58.7% of the children showed more than 106 bacteria/ml in these aspirates. The most prevalent cultivated genera recovered were Streptococcus, Neisseria, Staphylococcus, Rothia, Haemophilus, Pantoea and Branhamella. Feces screening by qPCR showed a high prevalence of bacterial enteropathogens, especially those categorized as being enteroinvasive or causing mucosal disruption, such as Shigella spp., enterotoxigenic Escherichia coli, enteropathogenic E. coli and enteroaggregative E. coli. These pathogens were detected at a similar rate in stunted children and controls, all showing no sign of severe diarrhea the day of inclusion but both living in a highly contaminated environment (slum-dwelling). Interestingly Shigella spp. was the most prevalent enteropathogen found in this study (83.3%) without overrepresentation in stunted children. About 2 million children under the age of 5 suffer from stunted growth in Madagascar. Although deficient diet is the major cause of undernutrition, impaired absorption or assimilation caused by Environmental Enteric dysfunction (EED) has been proposed to play an important role in stunting. EED is widespread among children and adults in low- and middle-income countries (LMIC) and is also associated with undernutrition, poor sanitation, certain gut infections resulting in an abnormal gut microbiota and small intestinal bacterial overgrowth (SIBO) although the role of SIBO in EED remains unclear. The current study highlights the presence at high concentrations of bacterial taxa usually found in the oro-pharyngeal sphere in a high number of duodenal fluids of stunted children. This uncommon presence suggests a decompartmentalization of the gastrointestinal tract and a possible pro-inflammatory effect due to the ectopic presence of some of these bacteria in the duodenum. The study also points to a high prevalence of enteropathogens (especially Shigella spp.) in the feces of both stunted and control children, hence preventing from proposing a direct association with stunting. This suggests that, beside combatting poverty and improving diet, environmental sanitation, quality of water sources, hygiene promotion and health education are key points to mitigate stunting and restore nutritional benefits.
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Affiliation(s)
- Jean-Marc Collard
- Unité de Bactériologie Expérimentale, Institut Pasteur de Madagascar, Antananarivo, Madagascar
- * E-mail:
| | - Lova Andrianonimiadana
- Unité de Bactériologie Expérimentale, Institut Pasteur de Madagascar, Antananarivo, Madagascar
| | - Azimdine Habib
- Unité de Bactériologie Expérimentale, Institut Pasteur de Madagascar, Antananarivo, Madagascar
| | | | - Prisca Andriantsalama
- Unité d’Epidémiologie et de Recherche Clinique, Institut Pasteur de Madagascar, Antananarivo, Madagascar
| | - Ravaka Randriamparany
- Unité d’Epidémiologie et de Recherche Clinique, Institut Pasteur de Madagascar, Antananarivo, Madagascar
| | - M. A. N. Rabenandrasana
- Unité de Bactériologie Expérimentale, Institut Pasteur de Madagascar, Antananarivo, Madagascar
| | - François-Xavier Weill
- Centre National de Référence des Escherichia coli, Shigella et Salmonella, Unité des Bactéries Pathogènes Entériques, Institut Pasteur, Paris, France
| | - Nathalie Sauvonnet
- Unité de Pathogénie Microbienne Moléculaire, Institut Pasteur, Paris, France
| | | | - Vincent Guillemot
- Hub of Bioinformatics and Biostatistics, Institut Pasteur, Paris, France
| | - Pascale Vonaesch
- Unité de Pathogénie Microbienne Moléculaire, Institut Pasteur, Paris, France
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Argy N, Nourrisson C, Aboubacar A, Poirier P, Valot S, Laude A, Desoubeaux G, Pomares C, Machouart M, Le Govic Y, Dalle F, Botterel F, Bourgeois N, Cateau E, Leterrier M, Le Pape P, Morio F, Houze S. Selecting a multiplex PCR panel for accurate molecular diagnosis of intestinal protists: a comparative study of Allplex ® (Seegene ®), G-DiaParaTrio (Diagenode ®), and RIDA ®GENE (R-Biopharm ®) assays and microscopic examination. Parasite 2022; 29:5. [PMID: 35138245 PMCID: PMC8826582 DOI: 10.1051/parasite/2022003] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Accepted: 01/14/2022] [Indexed: 12/17/2022] Open
Abstract
Commercial multiplex PCR assay panels were developed to overcome the limitations of microscopic examination for parasitological diagnosis on stool samples. However, given the increased supply of this diagnostic approach, these assays must be evaluated to position them in a diagnostic algorithm. Analytical performances of the multiplex PCR assay G-DiaParaTrio, Allplex® GI parasite and RIDA®GENE parasitic stool panel for detecting Blastocystis sp., Entamoeba histolytica, Giardia duodenalis, Cryptosporidium spp., Dientamoeba fragilis, and Cyclospora cayetanensis, were assessed through a retrospective comparative study on 184 stool samples initially sent for parasitological investigation. The composite reference method for parasitological diagnosis was microscopic observation and Entamoeba histolytica-specific adhesion detection when necessary. Multiplex PCR assays were performed on extracted DNA from each stool, following the manufacturer's recommendations. Discrepant results with the composite reference method were investigated with species-specific PCR to approach a final parasitological diagnosis. Overall sensitivity/specificity for the multiplex PCR assays was 93.2%/100% for G-DiaParaTrio, 96.5%/98.3% for Allplex® GI parasite and 89.6%/98.3% for RIDA®GENE, whereas the composite reference method presented an overall sensitivity/specificity of 59.6%/99.8%. These results confirmed the added diagnostic value of the multiplex PCR approach for gastrointestinal protists. Nevertheless, the PCR procedure and the analytical performance for each protist of interest, variable depending on the multiplex PCR assay, must be considered when implementing a PCR-based diagnostic approach.
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Affiliation(s)
- Nicolas Argy
- Parasitology-Mycology Laboratory, Bichat-Claude Bernard hospital, APHP, 75018 Paris, France - IRD MERIT UMR 261, Pharmacy Faculty, Paris University, 75006 Paris, France
| | - Céline Nourrisson
- Parasitology-Mycology Laboratory, CHU de Clermont-Ferrand, 3IHP, INSERM, 63000 Clermont-Ferrand, France
| | - Ahmed Aboubacar
- Parasitology-Mycology Laboratory, CHU de Strasbourg, 67000 Strasbourg, France
| | - Philippe Poirier
- Parasitology-Mycology Laboratory, CHU de Clermont-Ferrand, 3IHP, INSERM, 63000 Clermont-Ferrand, France
| | - Stéphane Valot
- Parasitology-Mycology Laboratory, CHU de Dijon, 21000 Dijon, France
| | - Adrien Laude
- Parasitology-Mycology Laboratory, Institut de Biologie, CHU de Nantes, 44093 Nantes, France
| | - Guillaume Desoubeaux
- Parasitology-Mycology-Tropical Diseases Department, CHU de Tours, 37000 Tours, France
| | | | - Marie Machouart
- Parasitology-Mycology Laboratory, CHU de Nancy, 54511 Vandoeuvre-les-Nancy, France
| | - Yohann Le Govic
- Parasitology-Mycology Laboratory, CHU d'Angers, 49100 Angers, France
| | - Frédéric Dalle
- Parasitology-Mycology Laboratory, CHU de Dijon, 21000 Dijon, France
| | - Françoise Botterel
- Parasitology-Mycology Laboratory, CHU Henri Mondor, APHP, 94000 Créteil, France
| | - Nathalie Bourgeois
- Parasitology-Mycology Laboratory, CHU de Montpellier, 34295 Montpellier, France
| | - Estelle Cateau
- Parasitology-Mycology Laboratory, CHU de Poitiers, 86021 Poitiers, France
| | - Marion Leterrier
- Microbiology Laboratory, CHD de la Roche-Sur-Yon, 85000 la Roche-Sur-Yon, France
| | - Patrice Le Pape
- Parasitology-Mycology Laboratory, Institut de Biologie, CHU de Nantes, 44093 Nantes, France
| | - Florent Morio
- Parasitology-Mycology Laboratory, Institut de Biologie, CHU de Nantes, 44093 Nantes, France
| | - Sandrine Houze
- Parasitology-Mycology Laboratory, Bichat-Claude Bernard hospital, APHP, 75018 Paris, France - IRD MERIT UMR 261, Pharmacy Faculty, Paris University, 75006 Paris, France
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Abstract
Traveler's diarrhea is the most common travel disease in both children and adults. Adult guidelines for traveler's diarrhea have been established, but significant gaps persist in guidance for the evaluation and management of pediatric traveler's diarrhea. Adult guidelines are not necessarily applicable in children, and it is essential for clinicians to account for the differences in pediatric pathophysiology, clinical presentations, and treatment recommendations when evaluating and managing pediatric traveler's diarrhea.
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Affiliation(s)
- Frank Zhu
- Department of Pediatrics, Division of Pediatric Infectious Diseases, Medical College of Wisconsin Suite 450C, 999 North 92nd Street, Wauwatosa, WI 53226, USA.
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15
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Commercial Simplex and Multiplex PCR Assays for the Detection of Intestinal Parasites Giardia intestinalis, Entamoeba spp., and Cryptosporidium spp.: Comparative Evaluation of Seven Commercial PCR Kits with Routine In-House Simplex PCR Assays. Microorganisms 2021; 9:microorganisms9112325. [PMID: 34835453 PMCID: PMC8623296 DOI: 10.3390/microorganisms9112325] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Revised: 11/06/2021] [Accepted: 11/08/2021] [Indexed: 02/04/2023] Open
Abstract
Nowadays, many commercial kits allowing the detection of digestive parasites by DNA amplification methods have been developed, including simplex PCR assays (SimpPCRa) allowing the identification of a single parasite, and multiplex PCR assays (MultPCRa) allowing the identification of several parasites at once. Thus, aimed at improving the diagnosis of intestinal protozoal infections, it is essential to evaluate the performances of these new tools. A total of 174 DNA samples collected between 2007 and 2017 were retrospectively included in this study. Performances of four commercial SimpPCRa (i.e., CerTest-VIASURETM) and three MultPCRa (i.e., CerTest-VIASURETM, FAST-TRACK-Diagnostics-FTD-Stool-ParasiteTM and DIAGENODE-Gastroenteritis/Parasite-panel-ITM) were evaluated for the detection of Cryptosporidium spp., Entamoeba spp., and Giardia intestinalis in stool samples compared to our routinely used in-house SimpPCRa. Globally, the SimpPCRa showed better sensitivity/specificity for the detection of G. intestinalis, E. histolytica, E. dispar, and Cryptosporidium spp. (i.e., 96.9/93.6%; 100/100%; 95.5/100%; and 100/99.3%, respectively), compared to the three commercial MultPCRa tested. All in all, we showed that MultPCRa offer an interesting alternative for the detection of protozoans in stool samples depending on the clinical context.
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16
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Berenger BM, Chui L, Ferrato C, Lloyd T, Li V, Pillai DR. Performance of four commercial real-time PCR assays for the detection of bacterial enteric pathogens in clinical samples. Int J Infect Dis 2021; 114:195-201. [PMID: 34700003 DOI: 10.1016/j.ijid.2021.10.035] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Revised: 10/19/2021] [Accepted: 10/20/2021] [Indexed: 10/20/2022] Open
Abstract
OBJECTIVES Many laboratories use culture-independent diagnostic tests for bacterial gastroenteritis (ie. real-time polymerase chain reaction [RT-PCR]) instead of culture because of better sensitivity, automation, and faster turnaround times. To address some gaps in initial evaluations and lack of intraassay comparisons for many commercial RT-PCRs we compared the ability of four commercially available RT-PCR tests (Ridagene, Fast Track Diagnostics, BD Max, and Prodesse Progastro) to detect five major bacterial enteric pathogens: Campylobacter, Salmonella, Shiga-toxin producing E. coli (STEC), Shigella and Yersinia. METHODS Clinical stool specimens and contrived samples comprising commonly circulating species, serotypes, biovars and/or toxin subtypes were used for the comparison. RESULTS Concordance rates for RT-PCR and culture using culture positive and negative clinical stools were greater than 90% for Campylobacter (97.5-100%), Salmonella (97.5-100%), Shigella (100%) and STEC (90-100%). However, the agreement between RT-PCR and culture for Y. enteroccolitica ranged from 70-90%. For the contrived sample set, stx2f was detected by only 1 of 4 assays. Of note, no assay could detect Yersinia non-enterocolitica and C. upsaliensis. CONCLUSIONS Depending on the prevalence of certain stx sub-types, Yersinia and Campylobacter species in a laboratory's jurisdiction, culture methods remain critical for the detection of these pathogens without further improvement in PCR assays.
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Affiliation(s)
- Byron M Berenger
- South Sector Microbiology, Alberta Precision Laboratories, 3535 Research Road, Calgary, AB, Canada T2L 1Y1; Alberta Public Health Laboratory, Alberta Precision Laboratories, 3300 Hospital Drive NW, Calgary, AB, T2N 4W4; Department of Pathology and Laboratory Medicine, University of Calgary, 3535 Research Road, Calgary, AB, Canada T2L 1Y1.
| | - Linda Chui
- Alberta Public Health Laboratory, Alberta Precision Laboratories, 3300 Hospital Drive NW, Calgary, AB, T2N 4W4; Department of Laboratory Medicine and Pathology, University of Alberta, 116 St. and 85 Ave Edmonton, AB, Canada T6G 2R3.
| | - Christina Ferrato
- Alberta Public Health Laboratory, Alberta Precision Laboratories, 3300 Hospital Drive NW, Calgary, AB, T2N 4W4.
| | - Tracie Lloyd
- South Sector Microbiology, Alberta Precision Laboratories, 3535 Research Road, Calgary, AB, Canada T2L 1Y1.
| | - Vincent Li
- Alberta Public Health Laboratory, Alberta Precision Laboratories, 3300 Hospital Drive NW, Calgary, AB, T2N 4W4.
| | - Dylan R Pillai
- South Sector Microbiology, Alberta Precision Laboratories, 3535 Research Road, Calgary, AB, Canada T2L 1Y1; Department of Pathology and Laboratory Medicine, University of Calgary, 3535 Research Road, Calgary, AB, Canada T2L 1Y1; Department of Medicine, University of Calgary, 3330 Hospital Drive NW, Calgary, AB, Canada T2N 4N1.
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Guan H, Xue P, Zhou H, Sha D, Wang D, Gao H, Li J, Diao B, Zhao H, Kan B, Zhang J. A multiplex PCR assay for the detection of five human pathogenic Vibrio species and Plesiomonas. Mol Cell Probes 2020; 55:101689. [PMID: 33338586 DOI: 10.1016/j.mcp.2020.101689] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Revised: 12/04/2020] [Accepted: 12/10/2020] [Indexed: 01/07/2023]
Abstract
A multiplex PCR (mPCR) assay was established to detect five pathogenic Vibrio species and Plesiomonas shigelloides. Twelve genes were included: ompW, ctxA, rfbN, and wbfR from V. cholerae; tl, tdh, and trh from V. parahaemolyticus; toxR and vmhA from V. mimicus; toxR from V. fluvialis; vvhA from V. vulnificus; and the 23S rRNA gene from P. shigelloides. The specificity of the mPCR assay was 100% for the detection of 136 strains and the limits of detection (LoD) were 12.5-50 pg/reaction. The assay exhibited higher sensitivity than cultivation methods in the detection of APW cultures of 113 diarrhea samples. In the analysis of 369 suspected Vibrio populations from estuarine water samples, the specificity of the mPCR for V. cholerae and V. parahaemolyticus was 100% for both, while the sensitivities were 100% and 96.1%, respectively. The assay can be applied to screen enrichment cultures and suspected colonies from environmental and clinical samples.
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Affiliation(s)
- Hongxia Guan
- Wuxi Center for Disease Control and Prevention, Jiangsu, 214023, China
| | - Panpan Xue
- State Key Laboratory for Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, China
| | - Haijian Zhou
- State Key Laboratory for Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, China
| | - Dan Sha
- Wuxi Center for Disease Control and Prevention, Jiangsu, 214023, China
| | - Duochun Wang
- State Key Laboratory for Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, China
| | - He Gao
- State Key Laboratory for Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, China
| | - Jie Li
- State Key Laboratory for Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, China
| | - Baowei Diao
- State Key Laboratory for Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, China
| | - Hongqun Zhao
- State Key Laboratory for Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, China
| | - Biao Kan
- State Key Laboratory for Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, China; Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Hangzhou, 310003, China
| | - Jingyun Zhang
- State Key Laboratory for Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, China.
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Use of the Multiplex Diagnostic PCR Panel in Diarrheal Disease: Expert Guidance on the Interpretation of Results With a Focus on Travelers' Diarrhea. Am J Gastroenterol 2020; 115:1553-1555. [PMID: 32558686 DOI: 10.14309/ajg.0000000000000735] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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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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20
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Mitra S, Nayak MK, Majumdar A, Sinha A, Chatterjee S, Deb A, Chawla-Sarkar M, Dutta S. Development and evaluation of a multiplex conventional reverse-transcription polymerase chain reaction assay for detection of common viral pathogens causing acute gastroenteritis. Diagn Microbiol Infect Dis 2020; 97:115061. [PMID: 32585545 DOI: 10.1016/j.diagmicrobio.2020.115061] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2020] [Revised: 03/27/2020] [Accepted: 04/12/2020] [Indexed: 12/11/2022]
Abstract
Timely identification of etiological agents of enteric infections is necessary to reduce the burden of infantile diarrheal mortality. Nucleic acid amplification-based detection methods offer a quick, reliable way for diagnosis of microbes in clinical specimens. This study was undertaken to evaluate an easy-to-use, cost-effective multiplex conventional reverse-transcription polymerase chain reaction (RT-PCR) assay developed at the Indian Council of Medical Research-National Institute of Cholera and Enteric Diseases virology laboratory to identify 4 common enteric viruses (rotavirus, norovirus, adenovirus, astrovirus) in stool samples from patients who were being evaluated for acute diarrhea. On comparison with a commercially available real-time PCR method, significant agreement in sensitivity and specificity was observed. Though the turnaround time for RT-PCR was 6-8 h compared to 5-6 h for real-time PCR, the real-time PCR has high test cost (approximately 28 USD/2000 INR) for Fast-Track Diagnostics kit-based quantitative RT-PCR versus 6 USD or 400 INR for conventional multiplex RT-PCR/sample. Thus, the conventional RT-PCR method is expected to be adaptable at local hospitals and health cares in resource-poor settings.
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Affiliation(s)
- Suvrotoa Mitra
- Division of Virology, ICMR-National Institute of Cholera and Enteric Diseases, Kolkata, WB, India
| | | | - Agniva Majumdar
- Regional Virus Research and Diagnostic Lab (VRDL), ICMR-National Institute of Cholera and Enteric Diseases, Kolkata, WB, India
| | - Avisek Sinha
- Division of Virology, ICMR-National Institute of Cholera and Enteric Diseases, Kolkata, WB, India
| | - Soumyadipta Chatterjee
- Division of Virology, ICMR-National Institute of Cholera and Enteric Diseases, Kolkata, WB, India
| | - Alok Deb
- Division of Epidemiology, ICMR-National Institute of Cholera and Enteric Diseases, Kolkata, WB, India
| | - Mamta Chawla-Sarkar
- Division of Virology, ICMR-National Institute of Cholera and Enteric Diseases, Kolkata, WB, India.
| | - Shanta Dutta
- Regional Virus Research and Diagnostic Lab (VRDL), ICMR-National Institute of Cholera and Enteric Diseases, Kolkata, WB, India
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21
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Ashkenazi S, Schwartz E. Traveler's diarrhea in children: New insights and existing gaps. Travel Med Infect Dis 2019; 34:101503. [PMID: 31654742 DOI: 10.1016/j.tmaid.2019.101503] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2019] [Revised: 10/15/2019] [Accepted: 10/21/2019] [Indexed: 01/17/2023]
Abstract
The number of children accompanying their parents in international travel is increasing steadily, and with the rising global migration, children more frequently accompany their parents or caregivers for visiting friends or relatives (VFR). As compared to travel for tourism, VFR children are at higher risk of acquiring local diseases, as they more often stay in rural areas in resource-poor locations, have longer periods of visit, are less likely to attend pre-travel consultations, and less frequently adhere to recommended precautions. Travelers's diarrhea (TD) is the most common travel-associated illnesses in children. This review updates the existing knowledge on TD in children, regarding its distinctive epidemiology, risk factors, preventive measures, clinical manifestations, complications, causative microorganisms and management. Despite the limited focused research on pediatric TD, which challenges the formulation of children-oriented evidence-based guidelines, practical recommendations are suggested.
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Affiliation(s)
- Shai Ashkenazi
- Adelson School of Medicine, Ariel University, Ariel, Israel; Schneider Children's Medical Center of Israel, Petach Tikva, Israel.
| | - Eli Schwartz
- Center for Geographic Medicine and Tropical Diseases, Sheba Medical Center, Tel Hashomer, Israel; Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
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Philip CO, Koech M, Kipkemoi N, Kirera R, Ndonye J, Ombogo A, Kirui M, Kipkirui E, Danboise B, Hulseberg C, Bateman S, Flynn A, Swierczewski B, Magiri E, Odundo E. Evaluation of the performance of a multiplex reverse transcription polymerase chain reaction kit as a potential diagnostic and surveillance kit for rotavirus in Kenya. TROPICAL DISEASES TRAVEL MEDICINE AND VACCINES 2019; 5:12. [PMID: 31346474 PMCID: PMC6631878 DOI: 10.1186/s40794-019-0087-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 01/25/2019] [Accepted: 06/21/2019] [Indexed: 12/12/2022]
Abstract
Background Diarrhea is a serious concern worldwide, especially in developing countries. Rotavirus is implicated in approximately 400,000 infant deaths annually. It is highly contagious elevating the risk of outbreaks especially in enclosed settings such as daycare centers, hospitals, and boarding schools. Reliable testing methods are critical for early detection of infections, better clinical management, pathogen surveillance and evaluation of interventions such as vaccines. Enzyme immunoassays have proved to be reliable and practical in most settings; however, newer multiplex reverse transcription polymerase assays have been introduced in the Kenya market but have not been evaluated locally. Methods Stool samples collected from an ongoing Surveillance of Enteric Pathogens Causing diarrheal illness in Kenya (EPS) study were used to compare an established enzyme immunoassay, Premier™ Rotaclone® (Meridian Bioscience, Cincinnati, Ohio, U.S.A.), that can only detect group A rotavirus against a novel multiplex reverse transcription polymerase chain reaction kit, Seeplex® Diarrhea-V ACE Detection (Seegene, Seoul, Republic of Korea), that can detect rotavirus, astrovirus, adenovirus, and norovirus genogroups I and II. Detection frequency, sensitivity, specificity, turnaround time, and cost were compared to determine the suitability of each assay for clinical work in austere settings versus public health work in well-funded institutes in Kenya. Results The Premier™ Rotaclone® kit had a detection frequency of 11.2%, sensitivity of 77.8%, specificity of 100%, turnaround time of 93 min and an average cost per sample of 13.33 United States dollars (USD). The Seeplex® Diarrhea-V ACE Detection kit had a detection frequency of 16.0%, sensitivity of 100%, specificity of 98.1%, turnaround time of 359 min and an average cost per samples 32.74 United States dollars respectively. The detection frequency sensitivity and specificity of the Seeplex® Diarrhea-V ACE Detection kit mentioned above are for rotavirus only. Conclusions The higher sensitivity and multiplex nature of the Seeplex® Diarrhea-V ACE Detection kit make it suitable for surveillance of enteric viruses circulating in Kenya. However, its higher cost, longer turnaround time and complexity favor well-resourced clinical labs and research applications. The Premier™ Rotaclone®, on the other hand, had a higher specificity, shorter turnaround time, and lower cost making it more attractive for clinical work in low complexity labs in austere regions of the country. It is important to continuously evaluate assay platforms' performance, operational cost, turnaround time, and usability in different settings so as to ensure quality results that are useful to the patients and public health practitioners.
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Affiliation(s)
| | - Margaret Koech
- United States Army Medical Research Directorate-Africa, Nairobi, Kenya
| | - Nancy Kipkemoi
- United States Army Medical Research Directorate-Africa, Nairobi, Kenya
| | - Ronald Kirera
- United States Army Medical Research Directorate-Africa, Nairobi, Kenya
| | - Janet Ndonye
- United States Army Medical Research Directorate-Africa, Nairobi, Kenya
| | - Abigael Ombogo
- United States Army Medical Research Directorate-Africa, Nairobi, Kenya
| | - Mary Kirui
- United States Army Medical Research Directorate-Africa, Nairobi, Kenya
| | - Erick Kipkirui
- United States Army Medical Research Directorate-Africa, Nairobi, Kenya
| | | | - Christine Hulseberg
- 3Center for Genome Sciences, US Army Medical Research Institute of Infectious Diseases, Frederick, Maryland USA
| | | | - Alexander Flynn
- United States Army Medical Research Directorate-Africa, Nairobi, Kenya
| | | | - Esther Magiri
- 6Jomo Kenyatta University of Agriculture and Technology, Juja, Kenya
| | - Elizabeth Odundo
- United States Army Medical Research Directorate-Africa, Nairobi, Kenya
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Performance evaluation of gastrointestinal viral ELIte panel multiplex RT-PCR assay for the diagnosis of rotavirus, adenovirus and astrovirus infection. J Virol Methods 2019; 268:48-52. [DOI: 10.1016/j.jviromet.2019.03.010] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2018] [Revised: 01/22/2019] [Accepted: 03/19/2019] [Indexed: 01/25/2023]
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24
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Kim YJ, Park KH, Park DA, Park J, Bang BW, Lee SS, Lee EJ, Lee HJ, Hong SK, Kim YR. Guideline for the Antibiotic Use in Acute Gastroenteritis. Infect Chemother 2019; 51:217-243. [PMID: 31271003 PMCID: PMC6609748 DOI: 10.3947/ic.2019.51.2.217] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2019] [Indexed: 12/23/2022] Open
Abstract
Acute gastroenteritis is common infectious disease in community in adults. This work represents an update of 'Clinical guideline for the diagnosis and treatment of gastrointestinal infections' that was developed domestically in 2010. The recommendation of this guideline was developed regarding the following; epidemiological factors, test for diagnosis, the indications of empirical antibiotics, and modification of antibiotics after confirming pathogen. Ultimately, it is expected to decrease antibiotic misuse and prevent antibiotic resistance.
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Affiliation(s)
- Youn Jeong Kim
- Division of Infectious Diseases, Department of Internal Medicine, Incheon St. Mary's Hospital, College of Medicine, The Catholic University of Korea, Seoul, Korea
| | - Ki Ho Park
- Division of Infectious Diseases, Department of Internal Medicine, Kyung Hee University Hospital, Kyung Hee University School of Medicine, Seoul, Korea
| | - Dong Ah Park
- Division of Healthcare Technology Assessment Research, National Evidence-Based Healthcare Collaborating Agency, Seoul, Korea
| | - Joonhong Park
- Department of Laboratory Medicine, Daejeon St. Mary's hospital, College of Medicine, The Catholic University of Korea, Daejeon, Korea
| | - Byoung Wook Bang
- Division of Gastroenterology, Department of Internal Medicine, Inha University College of Medicine, Incheon, Korea
| | - Seung Soon Lee
- Division of Infectious Diseases, Department of Internal Medicine, Hallym University Chuncheon Sacred Heart Hospital, Hallym University College of Medicine, Chuncheon, Korea
| | - Eun Jung Lee
- Division of Infectious Diseases, Department of Internal Medicine, Soonchunhyang University Seoul Hospital, Soonchunhyang University College of Medicine, Seoul, Korea
| | - Hyo Jin Lee
- Division of Infectious Diseases, Department of Internal Medicine, Uijeongbu St. Mary's Hospital, College of Medicine, The Catholic University of Korea, Uijeongbu, Korea
| | - Sung Kwan Hong
- Division of Infectious Diseases, Department of Internal Medicine, CHA Bundang Medical Center, CHA University, Seongnam, Korea
| | - Yang Ree Kim
- Division of Infectious Diseases, Department of Internal Medicine, Uijeongbu St. Mary's Hospital, College of Medicine, The Catholic University of Korea, Uijeongbu, Korea.
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25
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Comparative performance evaluation of four commercial multiplex real-time PCR assays for the detection of the diarrhoea-causing protozoa Cryptosporidium hominis/parvum, Giardia duodenalis and Entamoeba histolytica. PLoS One 2019; 14:e0215068. [PMID: 30958837 PMCID: PMC6453453 DOI: 10.1371/journal.pone.0215068] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2018] [Accepted: 03/26/2019] [Indexed: 01/31/2023] Open
Abstract
Background Multiplex molecular panels are relentlessly replacing conventional methods for the detection of enteric pathogens from stool samples in clinical and research laboratories. Here we evaluated four commercial multiplex real-time PCR assays for the detection of Cryptosporidium hominis/parvum, Giardia duodenalis and Entamoeba histolytica. Methods The diagnostic performance of the Gastroenteritis/Parasite Panel I (Diagenode), the RIDAGENE Parasitic Stool Panel (R-Biopharm), the Allplex Gastrointestinal Parasite Panel 4 (Seegene) and the FTD Stool Parasites (Fast Track) real-time PCR methods was assessed against a reference panel of 126 well-characterized DNA samples including Cryptosporidium hominis (n = 29), Cryptosporidium parvum (n = 3), Giardia duodenalis (n = 47), Entamoeba histolytica (n = 3), other parasite species (n = 20), and apparently healthy subjects (n = 24). Principal findings Obtained diagnostic sensitivities ranged from 53–88% for Cryptosporidium hominis/parvum, and from 68–100% for G. duodenalis. The R-Biopharm method achieved the best performance for the detection of Cryptosporidium hominis/parvum both in terms of diagnostic sensitivity (87.5%) and detection limit (a 100-fold increase compared to other tests). The Fast Track method was particularly suited for the detection of G. duodenalis, achieving a 100% sensitivity and a detection limit at least 10-fold superior. Detection of E. histolytica was similarly achieved by all compared methods except Diagenode. Conclusions Diagnostic performance varied largely depending on the method used and the targeted pathogen species. Factors including test sensitivity/specificity, cost, patient population surveyed, laboratory workflow, and diagnostic algorithm should be carefully considered when choosing the most appropriate multiplex PCR platform.
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26
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Pouletty M, De Pontual L, Lopez M, Morin L, Poilane I, Pham LL, Carbonnelle E, Titomanlio L, Faye A, Bonacorsi S. Multiplex PCR reveals a high prevalence of multiple pathogens in traveller's diarrhoea in children. Arch Dis Child 2019; 104:141-146. [PMID: 29982173 DOI: 10.1136/archdischild-2017-314327] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/24/2017] [Revised: 06/04/2018] [Accepted: 06/05/2018] [Indexed: 11/03/2022]
Abstract
OBJECTIVE Traveller's diarrhoea (TD) is one of the most frequent illnesses affecting children returning from tropical countries. The purpose of this study was to assess the distribution of pathogens associated with TD in children using a multiplex PCR assay on stool samples. DESIGN All the children admitted for TD in two university hospitals from 1 August to 15October during 2014 and 2015 were included in a prospective study. Stool samples were tested by a multiplex PCR FilmArray GI panel detecting 22 pathogens. Performances for the detection of major enteropathogenic bacteria (Salmonella, Shigella and Campylobacter spp) by multiplex PCR and conventional culture methods were compared. The prevalence of extended spectrum beta-lactamase (ESBL)-producing Enterobacteriaceae was also determined. RESULTS Fifty-nine children were included. In 58 cases (98%), at least one pathogen was identified, including 9 different enteropathogenic bacteria, 5 viruses and 2 parasites. Multiplex PCR enhanced the enteropathogenic bacteria detection by 25%. The most frequent pathogens were enteroaggregative Escherichia coli (n=32), enteropathogenic E. coli (n=26), enterotoxigenic E. coli (n=19), Salmonella enterica, enteroinvasive E. coli/Shigella (n=16 each), Cryptosporidium, sapovirus (n=11 each), Campylobacter jejuni, norovirus (n=10 each), rotavirus (n=9), Giardia (n=8) and Shiga-toxin-producing E. coli (n=4). Fifty-two coinfections were observed, notably including bacteria and viruses (n=21), multiple bacteria (n=14), or bacteria and parasites (n=10). ESBL were detected in 28 cases. Multiplex PCR could optimise the number of treated patients by 27% compared with stool cultures. CONCLUSION Multiplex PCR on stools revealed a high prevalence of diverse enteric pathogens and coinfections in children with TD. Major enteropathogenic bacteria were more frequently detected by multiplex PCR compared with conventional culture. Finally, this technique allows the start of appropriate and early antibiotic treatment and seems to optimise the number of correctly treated patients.
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Affiliation(s)
- Marie Pouletty
- General Pediatric Department, Robert Debré Hospital, Paris, France
| | - Loïc De Pontual
- General Pediatric and Emergency Department, Hopital Jean Verdier, Bondy, France.,Microbiology Laboratory, Robert Debré Hospital, Paris, France.,Pediatric Emergency Department, Robert Debré Hospital, Paris, France.,Microbiology Laboratory, Jean Verdier Hospital, Paris, France.,University Paris 13, Sorbonne Paris Cité, Paris, France
| | - Moreen Lopez
- Microbiology Laboratory, Robert Debré Hospital, Paris, France
| | - Laurence Morin
- Pediatric Emergency Department, Robert Debré Hospital, Paris, France
| | | | - Luu Ly Pham
- General Pediatric and Emergency Department, Hopital Jean Verdier, Bondy, France
| | - Etienne Carbonnelle
- Microbiology Laboratory, Jean Verdier Hospital, Paris, France.,University Paris 13, Sorbonne Paris Cité, Paris, France.,University Paris Denis Diderot, Sorbonne Paris Cité, Paris, France.,INSERM 1123, Paris, France.,INSERM 1137, Paris, France
| | - Luigi Titomanlio
- Pediatric Emergency Department, Robert Debré Hospital, Paris, France
| | - Albert Faye
- General Pediatric Department, Robert Debré Hospital, Paris, France.,General Pediatric and Emergency Department, Hopital Jean Verdier, Bondy, France.,Microbiology Laboratory, Robert Debré Hospital, Paris, France.,Pediatric Emergency Department, Robert Debré Hospital, Paris, France.,Microbiology Laboratory, Jean Verdier Hospital, Paris, France.,University Paris 13, Sorbonne Paris Cité, Paris, France.,University Paris Denis Diderot, Sorbonne Paris Cité, Paris, France.,INSERM 1123, Paris, France
| | - Stéphane Bonacorsi
- Microbiology Laboratory, Robert Debré Hospital, Paris, France.,Pediatric Emergency Department, Robert Debré Hospital, Paris, France.,Microbiology Laboratory, Jean Verdier Hospital, Paris, France.,University Paris 13, Sorbonne Paris Cité, Paris, France.,University Paris Denis Diderot, Sorbonne Paris Cité, Paris, France
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27
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Kaushik S, Tiwari U, Prashar S, Das B, Sinha RK. Label-free detection of Escherichia coli bacteria by cascaded chirped long period gratings immunosensor. THE REVIEW OF SCIENTIFIC INSTRUMENTS 2019; 90:025003. [PMID: 30831695 DOI: 10.1063/1.5036693] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/18/2018] [Accepted: 01/16/2019] [Indexed: 05/28/2023]
Abstract
An optical fiber based immunosensing platform formed by two identical chirped long period gratings (CLPGs) for sensitive and label-free detection of Escherichia coli (E. coli) is presented. The proposed immunosensor having two CLPGs with an inter-grating space (IGS) works like a Mach-Zehnder interferometer. The important feature of this sensor is that by changing the refractive index (RI) induced phase at the IGS region, a corresponding shift in resonance wavelength can be realized without affecting the actual grating region. Additionally, the confining bandwidth of the interference fringes promotes greater resolution in the resonance wavelength analysis of the transmission spectrum. The main aim of this study was the specific and rapid detection of the E. coli bacteria in phosphate buffer saline (detection range: 10 cfu/ml to 60 cfu/ml) by using the bio-functionalized IGS region as a sensing probe of the dual CLPG structure. The observed detection limit was 7 cfu/ml. For specificity analysis, Salmonella typhimurium and Staphylococcus aureus were tested and no significant shift in resonance wavelength was observed. In addition, the proposed immunosensor has the ability to selectively detect E. coli in real samples including lake water. The high specificity, good sensitivity to ambient RI, and robustness of the developed sensing platform will open a new avenue in optical immunosensing technology, and cascaded long CLPG sensors can contribute significantly to the detection of pathogenic bacteria in water and food samples.
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Affiliation(s)
- Siddharth Kaushik
- Advanced Materials and Sensors (V 4), Central Scientific Instruments Organization, Chandigarh 160030, India
| | - Umesh Tiwari
- Advanced Materials and Sensors (V 4), Central Scientific Instruments Organization, Chandigarh 160030, India
| | | | - Bhargab Das
- Advanced Materials and Sensors (V 4), Central Scientific Instruments Organization, Chandigarh 160030, India
| | - Ravindra K Sinha
- Advanced Materials and Sensors (V 4), Central Scientific Instruments Organization, Chandigarh 160030, India
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Kiemde F, Bonko MDA, Tahita MC, Lompo P, Tinto H, Mens PF, Schallig HDFH, van Hensbroek MB. Can clinical signs or symptoms combined with basic hematology data be used to predict the presence of bacterial infections in febrile children under - 5 years? BMC Pediatr 2018; 18:370. [PMID: 30482171 PMCID: PMC6260750 DOI: 10.1186/s12887-018-1340-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/25/2018] [Accepted: 11/12/2018] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Infectious diseases in children living in resource-limited settings are often presumptively managed on the basis of clinical signs and symptoms. Malaria is an exception. However, the interpretation of clinical signs and symptoms in relation to bacterial infections is often challenging, which may lead to an over prescription of antibiotics when a malaria infection is excluded. The present study aims to determine the association between clinical signs and symptoms and basic hematology data, with laboratory confirmed bacterial infections. METHODS A health survey was done by study nurses to collect clinical signs/symptoms in febrile (axillary temperature ≥ 37.5 °C) children under - 5 years of age. In addition, blood, stool and urine specimen were systematically collected from each child to perform bacterial culture and full blood cell counts. To determine the association between a bacterial infection with clinical signs/symptoms, and if possible supported by basic hematology data (hemoglobin and leucocyte rates), a univariate analysis was done. This was followed by a multivariate analysis only on those variables with a p-value p < 0.1 in the univariate analysis. Only a p-value of < 0.05 was considered as significant for multivariate analysis. RESULTS In total, 1099 febrile children were included. Bacteria were isolated from clinical specimens (blood-, stool- and urine- culture) of 127 (11.6%) febrile children. Multivariate logistical regression analysis revealed that a general bacterial infection (irrespective of the site of infection) was significantly associated with the following clinical signs/symptoms: diarrhea (p = 0.003), edema (p = 0.010) and convulsion (p = 0.021). Bacterial bloodstream infection was significantly associated with fever> 39.5 °C (p = 0.002), diarrhea (p = 0.019) and edema (p = 0.017). There was no association found between bacterial infections and basic haematological findings. If diarrhea and edema were absent, a good negative predictive value (100%) of a bacterial bloodstream infection was found, but the positive predictive value was low (33.3%) and the confidence interval was very large (2.5-100; 7.5-70.1). CONCLUSION Our study demonstrates that clinical signs and symptoms, combined with basic hematology data only, cannot predict bacterial infections in febrile children under - 5 years of age. The development of practical and easy deployable diagnostic tools to diagnose bacterial infections remains a priority.
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Affiliation(s)
- Francois Kiemde
- Institut de Recherche en Science de la Sante-Unité de Recherche Clinique de Nanoro, Nanoro, Burkina Faso. .,Amsterdam University Medical Centers, Academic Medical Centre, Department of Medical Microbiology, Parasitology Unit, University of Amsterdam, Amsterdam, The Netherlands. .,Global Child Health Group, Amsterdam University Medical Centers, Academic Medical Centre, University of Amsterdam, Amsterdam, The Netherlands.
| | - Massa Dit Achille Bonko
- Institut de Recherche en Science de la Sante-Unité de Recherche Clinique de Nanoro, Nanoro, Burkina Faso.,Amsterdam University Medical Centers, Academic Medical Centre, Department of Medical Microbiology, Parasitology Unit, University of Amsterdam, Amsterdam, The Netherlands
| | - Marc Christian Tahita
- Institut de Recherche en Science de la Sante-Unité de Recherche Clinique de Nanoro, Nanoro, Burkina Faso
| | - Palpouguini Lompo
- Institut de Recherche en Science de la Sante-Unité de Recherche Clinique de Nanoro, Nanoro, Burkina Faso
| | - Halidou Tinto
- Institut de Recherche en Science de la Sante-Unité de Recherche Clinique de Nanoro, Nanoro, Burkina Faso
| | - Petra F Mens
- Amsterdam University Medical Centers, Academic Medical Centre, Department of Medical Microbiology, Parasitology Unit, University of Amsterdam, Amsterdam, The Netherlands
| | - Henk D F H Schallig
- Amsterdam University Medical Centers, Academic Medical Centre, Department of Medical Microbiology, Parasitology Unit, University of Amsterdam, Amsterdam, The Netherlands
| | - Michael Boele van Hensbroek
- Global Child Health Group, Amsterdam University Medical Centers, Academic Medical Centre, University of Amsterdam, Amsterdam, The Netherlands
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29
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Valenzuela C, Legarraga P, Peña A, Arenas A, Berkowitz L, Ramírez G, Wozniak A, García P, Álvarez-Lobos M. Etiologic and clinical characterization of community acquired gastroenteritis in adult patients in a Chilean emergency room by the FilmArray GI panel. PLoS One 2018; 13:e0207850. [PMID: 30475924 PMCID: PMC6258233 DOI: 10.1371/journal.pone.0207850] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2018] [Accepted: 11/07/2018] [Indexed: 02/04/2023] Open
Abstract
Infectious diarrhea can be caused by a large number of microorganisms including bacteria virus and parasites. The clinical syndromic approach has been traditionally used to guide therapy. The aim of this study was to characterize the etiology of acute diarrhea by the FilmArray GI panel and to correlate it with its clinical presentation in an adult population presenting to the emergency room in a developing country. Material and Methods: Adult patients attending the ER due to acute diarrhea were selected. All patients included had a FilmArray GI panel performed and the clinical characteristics were recorded. Results: One hundred and ninety-nine patients were included. One hundred and eighteen (59.3%) were females. The mean age was 43 years old. Thirty three percent of the patients presented dysentery, 36.7% fever, 54.8% referred nauseas and 35.7% vomiting. Sixty three percent of the patients presented some degree of dehydration. In total, 221 microorganisms were detected of which 71.5% corresponded to bacteria (158/221), 19.9% to virus (44/221) and 8.6% to parasites (19/221). In 133 (67.0%) of 199 patients at least one microorganism was identified. Infections with more than one microorganism were detected in 27.1% of the patients. Polimicrobial infections were associated with a higher frequency of nausea (50.0% vs 32.0%, p 0.046), abdominal pain (87.0% vs 44.0%, p<0.0001) and travel history (20.0% vs 5.0%, p 0.0102). Bacterial infections occurred without a seasonal distribution with the exception of Salmonella sp whereas viral infections predominated during the autumn–winter months. Diarreicogenic E. coli were present in the context of a co-infection in more than 80.0% of the cases. Discussion: The use of multiplex panels has given us invaluable information regarding the epidemiology of acute diarrhea in adult. It highlighted the importance of polimicrobial infections and the frequency of diarreicogenic E. coli infections. Nevertheless, the lack of severity compared to monomicrobial infections and the usual association with other microorganisms in the latter make their clinical importance debatable.
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Affiliation(s)
- Carlos Valenzuela
- Department of Gastroenterology, Escuela de Medicina, Pontificia Universidad Católica de Chile, Santiago, Chile
- Facultad de Medicina, Universidad Católica de la Santísima Concepción, Concepción, Chile
| | - Paulette Legarraga
- Department of Clinical Laboratories, Escuela de Medicina, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Arturo Peña
- Emergency Room, Escuela de Medicina, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Alex Arenas
- Department of Gastroenterology, Escuela de Medicina, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Loni Berkowitz
- Department of Gastroenterology, Escuela de Medicina, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Gigliola Ramírez
- Department of Gastroenterology, Escuela de Medicina, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Aniela Wozniak
- Department of Clinical Laboratories, Escuela de Medicina, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Patricia García
- Department of Clinical Laboratories, Escuela de Medicina, Pontificia Universidad Católica de Chile, Santiago, Chile
- * E-mail: (MAL); (PG)
| | - Manuel Álvarez-Lobos
- Department of Gastroenterology, Escuela de Medicina, Pontificia Universidad Católica de Chile, Santiago, Chile
- * E-mail: (MAL); (PG)
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Hirvonen JJ. Comparison of three multiplex real-time PCR assays for detection of enteric viruses in patients with diarrhea. Eur J Clin Microbiol Infect Dis 2018; 38:241-244. [DOI: 10.1007/s10096-018-3418-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2018] [Accepted: 10/30/2018] [Indexed: 02/06/2023]
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Hyun J, Ko DH, Lee SK, Kim HS, Kim JS, Song W, Kim HS. Evaluation of a New Multiplex Real-Time PCR Assay for Detecting Gastroenteritis-Causing Viruses in Stool Samples. Ann Lab Med 2018; 38:220-225. [PMID: 29401556 PMCID: PMC5820066 DOI: 10.3343/alm.2018.38.3.220] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2017] [Revised: 08/09/2017] [Accepted: 01/09/2018] [Indexed: 01/13/2023] Open
Abstract
Background Diarrhea has been the second leading cause of death among children under the age of five, and the rapid and accurate pathogen diagnosis in patients with diarrhea is crucial for reducing morbidity and mortality. A newly developed one-step multiplex real-time PCR assay, the Allplex GI-Virus Assay, was evaluated for its ability to detect six diarrhea-causing viruses (rotavirus, norovirus genogroup I (GI) and genogroup II (GII), enteric adenovirus, astrovirus, and sapovirus) in stool samples. Methods The performance of the Allplex assay was compared with those of another multiplex PCR assay (Seeplex Diarrhea-V Ace Detection) and genotyping by sequencing, using 446 stool samples from patients with acute gastroenteritis. Results The overall agreement rates between the results of the Allplex and Seeplex assays were 98.7% for rotavirus, 99.1% for norovirus GI, 93.3% for norovirus GII, 98.0% for adenovirus, and 99.6% for astrovirus. The overall agreement rates between the Allplex assay and genotyping were 99.1% for rotavirus, 99.1% for norovirus GI, 98.7% for norovirus GII, 89.7% for adenovirus, 98.2% for astrovirus, and 99.8% for sapovirus. In addition, eight rotavirus genotypes, three norovirus GI genotypes, four norovirus GII genotypes, eight adenovirus genotypes, two astrovirus genotypes, and two sapovirus genotypes were detected. Conclusions The Allplex assay showed high agreement with Seeplex and genotyping results, and was able to additionally detect sapoviruses. The Allplex assay could be useful in identifying viral gastrointestinal infections in patients with acute gastroenteritis symptoms.
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Affiliation(s)
- Jungwon Hyun
- Department of Laboratory Medicine, Hallym University College of Medicine, Hwaseong, Korea
| | - Dae Hyun Ko
- Department of Laboratory Medicine, Hallym University College of Medicine, Hwaseong, Korea
| | - Su Kyung Lee
- Department of Laboratory Medicine, Hallym University College of Medicine, Hwaseong, Korea
| | - Han Sung Kim
- Department of Laboratory Medicine, Hallym University College of Medicine, Hwaseong, Korea
| | - Jae Seok Kim
- Department of Laboratory Medicine, Hallym University College of Medicine, Hwaseong, Korea
| | - Wonkeun Song
- Department of Laboratory Medicine, Hallym University College of Medicine, Hwaseong, Korea
| | - Hyun Soo Kim
- Department of Laboratory Medicine, Hallym University College of Medicine, Hwaseong, Korea.
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Kinnula S, Hemminki K, Kotilainen H, Ruotsalainen E, Tarkka E, Salmenlinna S, Hallanvuo S, Leinonen E, Jukka O, Rimhanen-Finne R. Outbreak of multiple strains of non-O157 Shiga toxin-producing and enteropathogenic Escherichia coli associated with rocket salad, Finland, autumn 2016. Euro Surveill 2018; 23:1700666. [PMID: 30180926 PMCID: PMC6124187 DOI: 10.2807/1560-7917.es.2018.23.35.1700666] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2017] [Accepted: 05/15/2018] [Indexed: 12/11/2022] Open
Abstract
In August 2016, an outbreak of Shiga toxin-producing Escherichia coli (STEC) and enteropathogenic E. coli (EPEC) with 237 cases occurred in the Helsinki metropolitan area, Finland. Gastroenteritis cases were reported at 11 events served by one catering company. Microbiological and epidemiological investigations suggested rocket salad as the cause of the outbreak. STEC ONT H11 and EPEC O111:H8 strains isolated from food samples containing rocket were identical to the patient isolates. In this outbreak, the reported symptoms were milder than considered before for STEC infection, and the guidelines for STEC control measures need to be updated based on the severity of the illness. Based on our experience in this outbreak, national surveillance criteria for STEC have been updated to meet the practice in reporting laboratories covering both PCR-positive and culture-confirmed findings. We suggest that EPEC could be added to the national surveillance since diagnostics for EPEC are routinely done in clinical laboratories.
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Affiliation(s)
- Sohvi Kinnula
- National Institute for Health and Welfare, Health Security Department, Helsinki, Finland
| | - Kaisa Hemminki
- Environmental Health, Social and Health Services Espoo, Espoo, Finland
| | - Hannele Kotilainen
- City of Helsinki, Communicable Diseases, Epidemiology Unit, Social Services and Health Care Sector, Helsinki, Finland
| | - Eeva Ruotsalainen
- Division of Infectious Diseases, Inflammation Center, Helsinki University Central Hospital, Helsinki, Finland
| | - Eveliina Tarkka
- Department of Clinical Microbiology, University of Helsinki and Helsinki University Hospital, HUSLAB, Helsinki, Finland
| | - Saara Salmenlinna
- National Institute for Health and Welfare, Health Security Department, Helsinki, Finland
| | - Saija Hallanvuo
- Finnish Food Safety Authority Evira, Research and Laboratory Services Department, Microbiology Research Unit, Helsinki, Finland
| | - Elina Leinonen
- Finnish Food Safety Authority Evira, Food Safety Department, Microbiological Food Safety Unit, Helsinki, Finland
| | - Ollgren Jukka
- National Institute for Health and Welfare, Health Security Department, Helsinki, Finland
| | - Ruska Rimhanen-Finne
- National Institute for Health and Welfare, Health Security Department, Helsinki, Finland
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Abstract
BACKGROUND Globally, diarrhea kills almost 1500 children daily. In diagnostics, molecular methods are replacing traditional assays. We aimed to investigate enteropathogens in children with and without diarrhea in Luanda, the capital of Angola. METHODS One hundred and ninety-four stool samples from 98 children with acute diarrhea and 96 children without diarrhea were investigated for 17 enteropathogens with multiplex real-time polymerase chain reaction. RESULTS The median age of children was 10.5 months. Enteropathogens, bacteria, viruses and parasites were detected in 91%, 78%, 50% and 25%, respectively. A positive finding was significantly (P = 0.003) more common in diarrhea when testing for all pathogens combined, for bacteria alone and for viruses alone. More than one pathogen was found more frequently in diarrhea than in non-diarrhea stool samples, in 87% and in 59% (P < 0.0001), respectively. The median number (interquartile range) of pathogens detected was 3 (2) versus 1.5 (2; P < 0.0001), respectively. When age was taken into account, diarrhea was found to be associated with enterotoxigenic and enteroaggregative Escherichia coli, Shigella, Campylobacter, rotavirus, sapovirus and Cryptosporidium. CONCLUSIONS Multiplex polymerase chain reaction detected enteropathogens in almost all stool samples of children in Luanda, albeit this occurred more often in diarrhea. Children with diarrhea showed more mixed infections than children without diarrhea.
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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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Göktaş Ş, Gökmen AA, Şamlıoğlu P. Detection of Acute Gastroenteritis Agents By Molecular Methods. JOURNAL OF CLINICAL AND EXPERIMENTAL INVESTIGATIONS 2018. [DOI: 10.5799/jcei.413060] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
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37
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Gosert R, Heininger U, Hirsch HH. Enterovirus detection in patients with acute gastroenteritis in Switzerland. J Med Virol 2018; 90:685-691. [PMID: 29236304 DOI: 10.1002/jmv.25005] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2017] [Accepted: 11/30/2017] [Indexed: 01/21/2023]
Abstract
Acute gastroenteritis (GE) has a major impact on morbidity and mortality worldwide, yet comprehensive data regarding infectious agents including enteroviruses are scarce. We hypothesized that enteroviruses constitute a significant cause of acute GE. We analyzed 677 stool samples from 504 patients, which had been submitted for suspected infectious GE. 0.2 mL of stool suspension was extracted using the Abbott m2000sp robot and analysed by multiplex nucleic acid testing (NAT) using the Luminex xTAG gastrointestinal pathogen panel (GPP) as well as by specific NATs detecting enteroviruses and polioviruses. Median age of the patients was 6.6 years (IQR 1.1-50.6; pediatric <18 years). 292 of 677 (43%) samples were positive for at least one pathogen. Enterovirus was detected in 5.3% (36/677) as sole pathogen (67%), and more frequently in children (P = 0.0054). Only rotavirus (18.6%) and norovirus (12.1%) were more frequent. Clostridium difficile and Campylobacter jejuni were detected in 5.5% and 2.2% of stools, respectively. Adenovirus, E. coli O157, Salmonella, Shiga toxin-producing E. coli (STEC), Shigella, Giardia lamblia, Cryptosporidium, and Entamoeba histolytica were rare (<1% of samples). Vibrio cholerae, Yersinia enterocolitica, enterotoxigenic E. coli (ETEC) and poliovirus were not detected. Thus, non-polio enteroviruses are the third most frequent pathogen in acute GE suggesting that enteroviruses may play an important role in GE even in developed, industrial health care settings.
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Affiliation(s)
- Rainer Gosert
- Division of Infection Diagnostics, Department Biomedicine - Haus Petersplatz, University of Basel, Basel, Switzerland
| | - Ulrich Heininger
- University of Basel Children's Hospital, Pediatric Infectious Diseases and Vaccinology, Basel, Switzerland
| | - Hans H Hirsch
- Division of Infection Diagnostics, Department Biomedicine - Haus Petersplatz, University of Basel, Basel, Switzerland.,Infectious Diseases and Hospital Epidemiology, University Hospital Basel, Basel, Switzerland
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38
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Multiplex PCR testing for travelers’ diarrhea—friend or foe? Int J Infect Dis 2018; 66:96-98. [DOI: 10.1016/j.ijid.2017.11.022] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2017] [Revised: 11/12/2017] [Accepted: 11/13/2017] [Indexed: 11/22/2022] Open
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Connor BA, Rogova M, Whyte O. Use of a multiplex DNA extraction PCR in the identification of pathogens in travelers' diarrhea. J Travel Med 2018; 25:4780170. [PMID: 29394385 DOI: 10.1093/jtm/tax087] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/19/2017] [Accepted: 11/29/2017] [Indexed: 11/12/2022]
Abstract
BACKGROUND Diarrhea is one of the most common ailments afflicting travelers with attack rates of 30-40% for medium to high-risk destinations. As travelers' diarrhea (TD) is syndromic and caused by a wide range of pathogens, including bacteria, parasites and viruses, multiplex deoxyribonucleic acid (DNA) extraction polymerase chain reaction (PCR) technology can be useful for determining the etiology of TD pathogens. OBJECTIVE The goal of this retrospective study was to produce clinically relevant and useful data on gastrointestinal illness related to travel identified by culture-independent methods of diagnosis-use of the multiplex DNA extraction PCR platform (BioFire FilmArray GI Panel) and to describe the use of this technology in detection of enteric pathogens. METHOD We reviewed our data in returned travelers from May 2014 to March 2017, looking at demographics, country of travel, number of pathogens found and pathogens by specific region. RESULTS Stool analysis by DNA extraction PCR was obtained in 388 post-travel patients. Three hundred and twenty-seven of these had diarrhea or other enteric symptoms. Sixty-one travelers presented with enteric symptoms and were diagnosed with post infectious irritable bowel syndrome (PI-IBS) after stool analyses were negative. Of those with diarrhea or gastrointestinal (GI) symptoms and excluding those diagnosed with PI-IBS, 207 patients tested positive for at least 1 enteric pathogen (63.4%). Eighty of those patients were found to have multiple pathogens. Viral pathogens were identified in 38 patients, 18% of the total number of cases. CONCLUSION The BioFire FilmArray GI Panel was associated with better detection of pathogens than historical controls while also allowing prompt and accurate diagnosis and potential treatment. A higher proportion of viral pathogens compared with historical assumptions was identified as well as mixed infections with multiple pathogens, a phenomenon largely unknown to clinicians before this technology became available.
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Affiliation(s)
- Bradley A Connor
- The New York Center for Travel and Tropical Medicine, New York, NY, USA.,Department of Medicine, Weill Cornell Medical College, New York, NY, USA
| | - Marina Rogova
- The New York Center for Travel and Tropical Medicine, New York, NY, USA
| | - Olga Whyte
- The New York Center for Travel and Tropical Medicine, New York, NY, USA
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Highly sensitive and specific detection of Giardia duodenalis, Entamoeba histolytica, and Cryptosporidium spp. in human stool samples by the BD MAX™ Enteric Parasite Panel. Parasitol Res 2017; 117:447-451. [PMID: 29260297 DOI: 10.1007/s00436-017-5720-7] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2017] [Accepted: 12/11/2017] [Indexed: 02/04/2023]
Abstract
Detection of intestinal protozoan parasites by light microscopy is cumbersome, needs experienced personnel, and may lack sensitivity and/or specificity as compared with molecular-based stool assays. Here, we evaluated the BD MAX™ Enteric Parasite Panel, i.e., a multiplex real-time PCR assay for simultaneous detection of Giardia duodenalis, Entamoeba histolytica, and cryptosporidia (Cryptosporidium parvum and C. hominis), by examining 200 positive human stool samples (138 × G. duodenalis, 27 × E. histolytica, 35 × Cryptosporidium spp.) and 119 controls including 18 samples with E. dispar. The majority of the samples, i.e., 153/200 (76.5%) positive samples and 66/119 (55.5%) controls, were confirmed by multiplex in-house PCR detecting the same parasites as the BD MAX™ Enteric Parasite Panel. The BD MAX™ assay did not yield false-positive results. Sensitivity and specificity were 97.8% (95% CI, 93.3-99.4%) and 100% (95% CI, 97.4-100%) for G. duodenalis, 100% (95% CI, 84.5-100%) and 100% (95% CI, 98.4-100%) for E. histolytica, and 100% (95% CI, 87.7-100%) and 100% (95% CI, 98.3-100%) for cryptosporidia, and similar data were obtained when only the 219 PCR-confirmed samples were analyzed. Thus, the BD MAX™ Enteric Parasite Panel provides a highly sensitive and specific tool for the laboratory diagnosis of three predominant protozoan parasites causing enteritis.
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Moudjahed H, Pinçon C, Alidjinou K, Dewilde A, Goffard A. Comparison of three molecular assays for detection of enteric viruses in stool samples. J Virol Methods 2017; 250:55-58. [DOI: 10.1016/j.jviromet.2017.09.026] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2017] [Revised: 09/15/2017] [Accepted: 09/27/2017] [Indexed: 10/18/2022]
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Schierenberg A, Broekhuizen BDL, Nipshagen MD, Kommer MBJ, Bruijning-Verhagen PCJ, van Delft S, van de Pol AC, Bonten MJM, de Wit NJ. Guideline adherence for diagnostic faeces testing in primary care patients with gastroenteritis. Fam Pract 2017; 34:692-696. [PMID: 28531259 DOI: 10.1093/fampra/cmx042] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
BACKGROUND Gastroenteritis (GE) is a common reason for primary care consultation. Dutch clinical practice guidelines (CPG) recommend diagnostic faeces testing (DFT) only in primary care patients with severe illness, comprised immunity or increased transmission risk. For its superior accuracy, shorter turnaround time and ease of use, polymerase chain reaction (PCR)-based DFT has largely replaced conventional techniques. It is unknown whether this changed CPG adherence. OBJECTIVE To quantify the effect of PCR introduction on adherence to CPG indications for DFT in primary care patients with GE. METHODS We performed a cohort study using routine care data of 225 GPs. Episodes of GE where DFT was performed were extracted from electronic patient records. Presenting symptoms were identified and adherence to CPG indications for DFT assessed in two randomly drawn samples of each 500 patients, one from the period before PCR introduction (2010-11) and one after (2013). The association between PCR introduction and adherence was estimated using multivariable regression analysis. RESULTS In 88% of all episodes relevant presenting symptoms were reported, most often 'frequent watery stool' (58%) and 'illness duration >10 days' (40%). DFT was performed in 15% of episodes before PCR introduction and in 18% after. Overall, in 17% the DFT request was considered adherent to the CPG, 16% before PCR introduction and 18% after (adjusted OR 1.2, 95% CI 0.9-1.7). CONCLUSION Overall adherence to CPG indications when requesting DFT in primary care patient with GE was 17%. Implementation of PCR-based DFT was not associated with a change in CPG adherence.
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Affiliation(s)
- Alwin Schierenberg
- University Medical Center Utrecht, Julius Center for Health Sciences and Primary Care, PO Box 85500, 3508 GA Utrecht, The Netherlands
| | - Berna D L Broekhuizen
- University Medical Center Utrecht, Julius Center for Health Sciences and Primary Care, PO Box 85500, 3508 GA Utrecht, The Netherlands
| | - Martine D Nipshagen
- University Medical Center Utrecht, Department of Medical Microbiology, PO Box 85500, 3508 GA Utrecht, The Netherlands
| | - Maarten B J Kommer
- University Medical Center Utrecht, Julius Center for Health Sciences and Primary Care, PO Box 85500, 3508 GA Utrecht, The Netherlands
| | - Patricia C J Bruijning-Verhagen
- University Medical Center Utrecht, Julius Center for Health Sciences and Primary Care, PO Box 85500, 3508 GA Utrecht, The Netherlands
| | - Sanne van Delft
- Saltro Diagnostic Center, Mississippidreef 83, 3565 CE Utrecht, The Netherlands
| | - Alma C van de Pol
- University Medical Center Utrecht, Julius Center for Health Sciences and Primary Care, PO Box 85500, 3508 GA Utrecht, The Netherlands
| | - Marc J M Bonten
- University Medical Center Utrecht, Julius Center for Health Sciences and Primary Care, PO Box 85500, 3508 GA Utrecht, The Netherlands.,University Medical Center Utrecht, Department of Medical Microbiology, PO Box 85500, 3508 GA Utrecht, The Netherlands
| | - Niek J de Wit
- University Medical Center Utrecht, Julius Center for Health Sciences and Primary Care, PO Box 85500, 3508 GA Utrecht, The Netherlands
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Hahn A, Luetgehetmann M, Landt O, Schwarz NG, Frickmann H. Comparison of one commercial and two in-house TaqMan multiplex real-time PCR assays for detection of enteropathogenic, enterotoxigenic and enteroaggregative Escherichia coli. Trop Med Int Health 2017; 22:1371-1376. [PMID: 28906580 DOI: 10.1111/tmi.12976] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
OBJECTIVE Enteropathogenic, enterotoxigenic and enteroaggregative Escherichia coli (EPEC, ETEC, EAEC) are among the most frequent causes of diarrhoea during travel or on military deployments. Cost-efficient and reliable real-time multiplex PCR (mPCR) assays are desirable for surveillance or point prevalence studies in remote and resource-limited tropical settings. We compared one commercial PCR kit and two in-house assays without using a gold standard to estimate sensitivity and specificity of each assay. METHODS Residual materials from nucleic acid extractions of stool samples from two groups with presumably different prevalences and increased likelihood of being infected or colonised by diarrhoeagenic E. coli were included in the assessment. One group comprised samples from returnees from tropical deployments, the second group was of migrants and study participants from high-endemicity settings. Each sample was assessed with all of the PCR assays. Cycle threshold (Ct) values were descriptively compared. RESULTS The calculated sensitivities for the commercial test vs. the in-house tests were for EPEC 0.84 vs. 0.89 and 0.96, for ETEC 0.83 vs. 0.76 and 0.61, and for EAEC 0.69 vs. 0.54 and 0.69. False positive results were rare - specificity was 0.94 and 0.97 for two EPEC tests and 1.0 for all other tests. Most positive samples had late Ct values corresponding to low quantities of pathogens. Discordant test results were associated with late Ct values. CONCLUSIONS As commercial and in-house assays showed comparable results, in-house tests can be assumed to be safe while affording considerable savings, making them a valuable alternative for surveillance testing in resource-limited tropical areas.
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Affiliation(s)
- Andreas Hahn
- Institute for Microbiology, Charité-University Medicine Berlin, Berlin, Germany
| | - Marc Luetgehetmann
- Institute for Medical Microbiology, Virology and Hygiene, University Hospital Hamburg-Eppendorf, Hamburg, Germany
| | | | - Norbert Georg Schwarz
- Infectious Disease Epidemiology, Bernhard Nocht Institute for Tropical Medicine Hamburg, Hamburg, Germany
| | - Hagen Frickmann
- Department of Tropical Medicine at the Bernhard Nocht Institute, Bundeswehr Hospital Hamburg, Hamburg, Germany.,Institute for Medical Microbiology, Virology and Hygiene, University Medicine Rostock, Rostock, Germany
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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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45
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Riddle CAPTMS, Martin GJ, Murray COLCK, Burgess CAPTTH, Connor CP, Mancuso COLJD, Schnaubelt MER, Ballard LCTP, Fraser J, Tribble DR. Management of Acute Diarrheal Illness During Deployment: A Deployment Health Guideline and Expert Panel Report. Mil Med 2017; 182:34-52. [PMID: 28885922 PMCID: PMC5657341 DOI: 10.7205/milmed-d-17-00077] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
BACKGROUND Acute diarrheal illness during deployment causes significant morbidity and loss of duty days. Effective and timely treatment is needed to reduce individual, unit, and health system performance impacts. METHODS This critical appraisal of the literature, as part of the development of expert consensus guidelines, asked several key questions related to self-care and healthcare-seeking behavior, antibiotics for self-treatment of travelers' diarrhea, what antibiotics/regimens should be considered for treatment of acute watery diarrhea and febrile diarrhea and/or dysentery, and when and what laboratory diagnostics should be used to support management of deployment-related travelers' diarrhea. Studies of acute diarrhea management in military and other travelers were assessed for relevance and quality. On the basis of this critical appraisal, guideline recommendations were developed and graded by the Expert Panel using good standards in clinical guideline development methodology. RESULTS New definitions for defining the severity of diarrhea during deployment were established. A total of 13 graded recommendations on the topics of prophylaxis, therapy and diagnosis, and follow-up were developed. In addition, four non-graded consensus-based statements were adopted. CONCLUSIONS Successful management of acute diarrheal illness during deployment requires action at the provider, population, and commander levels. Strong evidence supports that single-dose antimicrobial therapy is effective in most cases of moderate to severe acute diarrheal illness during deployment. Further studies are needed to address gaps in available knowledge regarding optimal therapies for treatment, prevention, and laboratory testing of acute diarrheal illness.
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Affiliation(s)
- CAPT Mark S. Riddle
- Enteric Disease Department, Naval Medical Research Center, 503 Robert Grant Avenue, Silver Spring, MD 20910, USA
| | - Gregory J. Martin
- Chief, Tropical Medicine-Infectious Diseases, Bureau of Medical Services, US Department of State, 2401 E St NW L209, Washington DC 20037, USA
| | - COL Clinton K. Murray
- Deputy Medical Corps Chief, Medical Corps Specific Branch Proponent Officer, Infectious Disease Consultant to the Army Surgeon General, Brooke Army Medical Center, 3551 Roger Brooke Dr, JBSA Fort Sam Houston, TX 78234, USA
| | - CAPT Timothy H. Burgess
- Infectious Disease Clinical Research Program, Preventive Medicine & Biostatistics Department, Uniformed Services University of the Health Sciences, 4301 Jones Bridge Road, Bethesda, MD 20814, USA
| | - Col Patrick Connor
- Military Enteric Disease Group, Academic Department of Military Medicine, Birmingham Research Park, Vincent Drive, Birmingham B15 2SQ, United Kingdom
| | - COL James D. Mancuso
- Department of Preventive Medicine & Biostatistics, The F. Edward Hébert School of Medicine, Uniformed Services University of the Health Sciences, 4301 Jones Bridge Road, Bethesda, MD 20814, USA
| | - Maj Elizabeth R. Schnaubelt
- Infectious Disease Service, Landstuhl Regional Medical Center, Landstuhl, Germany, CMR 402, APO, AE, 19180, USA [Current Affiliation: Division of Global HIV and TB, Centers for Disease Control and Prevention, 1600 Clifton Rd, Atlanta, GA 30333, USA]
| | - Lt Col Timothy P. Ballard
- Operational Medicine, Defense Institute for Medical Operations, 1320 Truemper St, Bldg 9122, JBSA-Lackland, TX 78236, USA
| | - Jamie Fraser
- Infectious Disease Clinical Research Program, Preventive Medicine & Biostatistics Department, Uniformed Services University of the Health Sciences, 4301 Jones Bridge Road, Bethesda, MD 20814, USA
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., 6720A Rockledge Dr #100, Bethesda, MD 20817, USA
| | - David R. Tribble
- Infectious Disease Clinical Research Program, Preventive Medicine & Biostatistics Department, Uniformed Services University of the Health Sciences, 4301 Jones Bridge Road, Bethesda, MD 20814, USA
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Sow D, Parola P, Sylla K, Ndiaye M, Delaunay P, Halfon P, Camiade S, Dieng T, Tine RCK, Faye B, Ndiaye JL, Dieng Y, Gaye O, Raoult D, Bittar F. Performance of Real-Time Polymerase Chain Reaction Assays for the Detection of 20 Gastrointestinal Parasites in Clinical Samples from Senegal. Am J Trop Med Hyg 2017; 97:173-182. [PMID: 28719290 DOI: 10.4269/ajtmh.16-0781] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Gastrointestinal parasite infections represent one of the biggest public health problems in the world. Therefore, appropriate innovative tools are needed for assessing interventions to control these infections. This study aims to compare the performance of real-time polymerase chain reaction (PCR) assays to microscopic examination for detection of intestinal parasites. A direct microscopic examination and stool concentration was performed on 98 stool samples from patients attending Senegalese hospitals. Negative microscopic control samples were also collected in Nice and Marseille (France). Species-specific primers/probes were used to detect 20 common gastrointestinal protozoans and helminths. Positive frequency and the sensitivity of each real-time PCR assay were compared with conventional microscopic examination. Real-time PCR was positive in 72 of 98 samples (73.5%), whereas microscopic examination was positive in 37 (37.7%) samples (P < 0.001). The real-time PCR assays were more sensitive than microscopy, with 57.4% (31/54) versus 18.5% (10/54), respectively, in the detection of parasites in asymptomatic patients (P < 0.05). In terms of polyparasitism, there were more coinfections detected by real-time PCR assays compared with microscopic methods (25.5% versus 3.06%). In comparison to parasite prevalence on individual samples, the results showed a perfect agreement (100%) between the two techniques for seven species, whereas discrepancies were observed for the others (agreement percentage varying from 64.2% to 98.9%). Real-time PCR appeared to be superior to microscopic examination for the detection of parasites in stool samples. This assay will be useful in diagnostic laboratories and in the field for evaluating the efficacy of mass drug administration programs.
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Affiliation(s)
- Doudou Sow
- Aix Marseille Université, URMITE, UM63, CNRS 7278, IRD 198, INSERM 1095, IHU - Méditerranée Infection, Marseille, France.,Service de Parasitologie-Mycologie, Faculté de Médecine, Université Cheikh Anta Diop (UCAD), Dakar, Senegal
| | - Philippe Parola
- Aix Marseille Université, URMITE, UM63, CNRS 7278, IRD 198, INSERM 1095, IHU - Méditerranée Infection, Marseille, France
| | - Khadime Sylla
- Service de Parasitologie-Mycologie, Faculté de Médecine, Université Cheikh Anta Diop (UCAD), Dakar, Senegal
| | - Magatte Ndiaye
- Service de Parasitologie-Mycologie, Faculté de Médecine, Université Cheikh Anta Diop (UCAD), Dakar, Senegal
| | - Pascal Delaunay
- Parasitologie-Mycologie, Hôpital de l'Archet, Centre Hospitalier Universitaire de Nice, France - MIVEGEC, UMR IRD224 -CNRS 5290-Université de Montpellier, Montpellier Cedex 5, France
| | | | - Sabine Camiade
- Laboratoire Alphabio Hôpital Européen, Marseille, France
| | - Thérèse Dieng
- Service de Parasitologie-Mycologie, Faculté de Médecine, Université Cheikh Anta Diop (UCAD), Dakar, Senegal
| | - Roger C K Tine
- Service de Parasitologie-Mycologie, Faculté de Médecine, Université Cheikh Anta Diop (UCAD), Dakar, Senegal
| | - Babacar Faye
- Service de Parasitologie-Mycologie, Faculté de Médecine, Université Cheikh Anta Diop (UCAD), Dakar, Senegal
| | - Jean Louis Ndiaye
- Service de Parasitologie-Mycologie, Faculté de Médecine, Université Cheikh Anta Diop (UCAD), Dakar, Senegal
| | - Yémou Dieng
- Service de Parasitologie-Mycologie, Faculté de Médecine, Université Cheikh Anta Diop (UCAD), Dakar, Senegal
| | - Oumar Gaye
- Service de Parasitologie-Mycologie, Faculté de Médecine, Université Cheikh Anta Diop (UCAD), Dakar, Senegal
| | - Didier Raoult
- Aix Marseille Université, URMITE, UM63, CNRS 7278, IRD 198, INSERM 1095, IHU - Méditerranée Infection, Marseille, France
| | - Fadi Bittar
- Aix Marseille Université, URMITE, UM63, CNRS 7278, IRD 198, INSERM 1095, IHU - Méditerranée Infection, Marseille, France
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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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Exploiting Bacterial Whole-Genome Sequencing Data for Evaluation of Diagnostic Assays: Campylobacter Species Identification as a Case Study. J Clin Microbiol 2016; 54:2882-2890. [PMID: 27733632 PMCID: PMC5121375 DOI: 10.1128/jcm.01522-16] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2016] [Accepted: 10/03/2016] [Indexed: 01/18/2023] Open
Abstract
The application of whole-genome sequencing (WGS) to problems in clinical microbiology has had a major impact on the field. Clinical laboratories are now using WGS for pathogen identification, antimicrobial susceptibility testing, and epidemiological typing. WGS data also represent a valuable resource for the development and evaluation of molecular diagnostic assays, which continue to play an important role in clinical microbiology. To demonstrate this application of WGS, this study used publicly available genomic data to evaluate a duplex real-time PCR (RT-PCR) assay that targets mapA and ceuE for the detection of Campylobacter jejuni and Campylobacter coli, leading global causes of bacterial gastroenteritis. In silico analyses of mapA and ceuE primer and probe sequences from 1,713 genetically diverse C. jejuni and C. coli genomes, supported by RT-PCR testing, indicated that the assay was robust, with 1,707 (99.7%) isolates correctly identified. The high specificity of the mapA-ceuE assay was the result of interspecies diversity and intraspecies conservation of the target genes in C. jejuni and C. coli Rare instances of a lack of specificity among C. coli isolates were due to introgression in mapA or sequence diversity in ceuE The results of this study illustrate how WGS can be exploited to evaluate molecular diagnostic assays by using publicly available data, online databases, and open-source software.
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Evaluation of the NanoCHIP® Gastrointestinal Panel (GIP) Test for Simultaneous Detection of Parasitic and Bacterial Enteric Pathogens in Fecal Specimens. PLoS One 2016; 11:e0159440. [PMID: 27447173 PMCID: PMC4957780 DOI: 10.1371/journal.pone.0159440] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2016] [Accepted: 07/04/2016] [Indexed: 12/22/2022] Open
Abstract
Infectious gastroenteritis is a global health problem associated with high morbidity and mortality rates. Rapid and accurate diagnosis is crucial to allow appropriate and timely treatment. Current laboratory stool testing has a long turnaround time (TAT) and demands highly qualified personnel and multiple techniques. The need for high throughput and the number of possible enteric pathogens compels the implementation of a molecular approach which uses multiplex technology, without compromising performance requirements. In this work we evaluated the feasibility of the NanoCHIP® Gastrointestinal Panel (GIP) (Savyon Diagnostics, Ashdod, IL), a molecular microarray-based screening test, to be used in the routine workflow of our laboratory, a big outpatient microbiology laboratory. The NanoCHIP® GIP test provides simultaneous detection of nine major enteric bacteria and parasites: Campylobacter spp., Salmonella spp., Shigella spp., Giardia sp., Cryptosporidium spp., Entamoeba histolytica, Entamoeba dispar, Dientamoeba fragilis, and Blastocystis spp. The required high-throughput was obtained by the NanoCHIP® detection system together with the MagNA Pure 96 DNA purification system (Roche Diagnostics Ltd., Switzerland). This combined system has demonstrated a higher sensitivity and detection yield compared to the conventional methods in both, retrospective and prospective samples. The identification of multiple parasites and bacteria in a single test also enabled increased efficiency of detecting mixed infections, as well as reduced hands-on time and work load. In conclusion, the combination of these two automated systems is a proper response to the laboratory needs in terms of improving laboratory workflow, turn-around-time, minimizing human errors and can be efficiently integrated in the routine work of the laboratory.
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Molecular testing for clinical diagnosis and epidemiological investigations of intestinal parasitic infections. Clin Microbiol Rev 2016; 27:371-418. [PMID: 24696439 DOI: 10.1128/cmr.00122-13] [Citation(s) in RCA: 146] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Over the past few decades, nucleic acid-based methods have been developed for the diagnosis of intestinal parasitic infections. Advantages of nucleic acid-based methods are numerous; typically, these include increased sensitivity and specificity and simpler standardization of diagnostic procedures. DNA samples can also be stored and used for genetic characterization and molecular typing, providing a valuable tool for surveys and surveillance studies. A variety of technologies have been applied, and some specific and general pitfalls and limitations have been identified. This review provides an overview of the multitude of methods that have been reported for the detection of intestinal parasites and offers some guidance in applying these methods in the clinical laboratory and in epidemiological studies.
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