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Mohtar J, Mallah H, Mardirossian JM, El-Bikai R, Jisr TE, Soussi S, Naoufal R, Alam G, Chaar ME. Enhancing enteric pathogen detection: implementation and impact of multiplex PCR for improved diagnosis and surveillance. BMC Infect Dis 2024; 24:171. [PMID: 38326773 PMCID: PMC10848388 DOI: 10.1186/s12879-024-09047-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Accepted: 01/23/2024] [Indexed: 02/09/2024] Open
Abstract
BACKGROUND Syndromic surveillance of acute gastroenteritis plays a significant role in the diagnosis and management of gastrointestinal infections that are responsible for a substantial number of deaths globally, especially in developing countries. In Lebanon, there is a lack of national surveillance for acute gastroenteritis, and limited data exists regarding the prevalence of pathogens causing diarrhea. The one-year study aims to investigate the epidemiology of common gastrointestinal pathogens and compare our findings with causative agents of diarrhea reported by our study collaborative centers. METHODS A multicenter, cross-sectional study was conducted over a one-year period. A total of 271 samples were obtained from outpatients and inpatients presenting with symptoms of acute gastroenteritis at various healthcare facilities. The samples were then analyzed using Allplex gastrointestinal assay that identifies a panel of enteric pathogens. RESULTS Overall, enteropathogens were detected in 71% of the enrolled cases, 46% of those were identified in patients as single and 54% as mixed infections. Bacteria were observed in 48%, parasites in 12% and viruses in 11%. Bacterial infections were the most prevalent in all age groups. Enteroaggregative E. coli (26.5%), Enterotoxigenic E. coli (23.2%) and Enteropathogenic E. coli (20.3%) were the most frequently identified followed by Blastocystis hominis (15.5%) and Rotavirus (7.7%). Highest hospitalization rate occurred with rotavirus (63%), Enterotoxigenic E. coli (50%), Blastocystis hominis (45%) and Enteropathogenic E. coli (43%). Enteric pathogens were prevalent during summer, fall and winter seasons. CONCLUSIONS The adoption of multiplex real-time PCR assays in the diagnosis of gastrointestinal infections has identified gaps and improved the rates of detection for multiple pathogens. Our findings highlight the importance of conducting comprehensive surveillance to monitor enteric infections. The implementation of a syndromic testing panel can therefore provide healthcare professionals with timely and accurate information for more effective treatment and public health interventions.
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Affiliation(s)
- Jad Mohtar
- Faculty of Health Sciences, University of Balamand, Beirut, Lebanon
| | - Hiba Mallah
- Faculty of Health Sciences, University of Balamand, Beirut, Lebanon
| | - Jean Marc Mardirossian
- Faculty of Health Sciences, University of Balamand, Beirut, Lebanon
- Mayo Clinic Discovery and Translational Polycystic Kidney Disease Center, Florida, USA
| | - Rana El-Bikai
- Faculty of Health Sciences, University of Balamand, Beirut, Lebanon
| | - Tamima El Jisr
- Clinical Laboratory Department, Makassed General Hospital, Beirut, Lebanon
| | - Shatha Soussi
- Clinical Laboratory Department, Makassed General Hospital, Beirut, Lebanon
| | - Rania Naoufal
- Clinical Laboratory Department, Saint Georges Hospital University Medical Center, Beirut, Lebanon
| | - Gabriella Alam
- Clinical Laboratory Department, Saint Georges Hospital University Medical Center, Beirut, Lebanon
| | - Mira El Chaar
- Faculty of Health Sciences, University of Balamand, Beirut, Lebanon.
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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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Çetin S, Telli E, Şahin AM, Uğur M, Aydın E, Şenel İ, Yetkin MA. Gastrointestinal PCR panel results and antibiotic use in acute gastroenteritis cases: How appropriate are we in our usage? Indian J Med Microbiol 2024; 47:100536. [PMID: 38316393 DOI: 10.1016/j.ijmmb.2024.100536] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Revised: 01/22/2024] [Accepted: 02/03/2024] [Indexed: 02/07/2024]
Abstract
BACKGROUND We aimed to determine the pathogens detected by the Gastrointestinal (GI) PCR panel in patients with acute gastroenteritis (AGE), the evaluation of antibiotic use in these patients, and the investigation of the role of laboratory parameters in differentiating viral and bacterial etiologies. METHODS The demographic characteristics, GI PCR panel results, laboratory investigations, antibiotic usage, and appropriateness of antibiotic treatment were investigated in AGE patients. RESULTS A total of 175 adult patients with AGE and GI PCR panel results were included in the study. The most common pathogens were EPEC (24.6%) and C. difficile (18.3%). Among the 102 patients receiving antibiotic treatment, 34.3% were evaluated as inappropriate antibiotic use. WBC, CRP, procalcitonin, CRP/albumin ratio, and procalcitonin/albumin ratio were found to be significantly higher in cases with bacterial origin. CONCLUSIONS The utilization of GI PCR panels in AGE patients has revolutionized the field of diagnostics by providing rapid and accurate identification of pathogens. In units without the possibility of GI PCR testing, CRP, procalcitonin, CRP/albumin ratio and procalcitonin/albumin ratio may be useful in the decision of antibiotic treatment.
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Affiliation(s)
- Sinan Çetin
- Department of Infectious Diseases and Clinical Microbiology, Giresun University, Giresun, Turkey.
| | - Enes Telli
- Department of Infectious Diseases and Clinical Microbiology, Giresun University, Giresun, Turkey.
| | - Ahmet Melih Şahin
- Department of Infectious Diseases and Clinical Microbiology, Giresun University, Giresun, Turkey.
| | - Mediha Uğur
- Department of Medical Microbiology, Giresun University, Giresun, Turkey.
| | - Emsal Aydın
- Department of Infectious Diseases and Clinical Microbiology, Giresun University, Giresun, Turkey.
| | - İlknur Şenel
- Department of Infectious Diseases and Clinical Microbiology, Giresun University, Giresun, Turkey.
| | - Meltem Arzu Yetkin
- Department of Infectious Diseases and Clinical Microbiology, Giresun University, Giresun, Turkey.
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Giffen SR, Sadler JM, Miller MB. QIAstat-Dx gastrointestinal panel and Luminex xTAG gastrointestinal pathogen panel comparative evaluation. J Clin Microbiol 2023; 61:e0085923. [PMID: 37921475 PMCID: PMC10662366 DOI: 10.1128/jcm.00859-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Accepted: 09/28/2023] [Indexed: 11/04/2023] Open
Abstract
The diagnosis of acute gastroenteritis is an ongoing clinical challenge in terms of identification of the etiologic agent, time to results, and appropriate treatment. Rapid detection of gastrointestinal pathogens is needed to improve patient care. This study evaluates the performance of the QIAstat-Dx gastrointestinal panel (Q-GP; Investigational Use Only) compared to the Luminex xTAG gastrointestinal pathogen panel (L-GPP; US-IVD). Using 245 stool specimens, we evaluated 10 different targets including rotavirus, norovirus, Salmonella, Shigella, Campylobacter, Giardia, Cryptosporidium, Escherichia coli O157, enterotoxigenic E. coli (ETEC), and Shiga toxin-producing E. coli (STEC). For the viral targets, the percent positive agreement (PPA) for rotavirus was 100% (n = 19) and that for norovirus was 91% (20/22). For the parasitic targets, the PPA was 100% for Giardia and Cryptosporidium (n = 18 and n = 23, respectively). The PPA was 96% for Salmonella (22/23) and Campylobacter (22/23), and the PPA for Shigella was 100% (n = 23). For the E. coli targets, a PPA of 94% was achieved for STEC (32/34) and 96% for ETEC (24/25). We did not assess PPA for the E. coli O157 target as the Q-GP O157 call is stx dependent. The negative percent agreement across all targets was 99.1%. Our study suggests that QIAstat-Dx GP provides comparable results to Luminex GPP based on the analysis of targets found on both panels.
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Affiliation(s)
- Samantha R. Giffen
- McLendon Clinical Microbiology Laboratories, University of North Carolina Medical Center, Chapel Hill, North Carolina, USA
| | - Jacob M. Sadler
- McLendon Clinical Microbiology Laboratories, University of North Carolina Medical Center, Chapel Hill, North Carolina, USA
| | - Melissa B. Miller
- McLendon Clinical Microbiology Laboratories, University of North Carolina Medical Center, Chapel Hill, North Carolina, USA
- Department of Pathology and Laboratory Medicine, University of North Carolina Chapel Hill School of Medicine, Chapel Hill, North Carolina, USA
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Hu L, Fu Y, Zhang S, Pan Z, Xia J, Zhu P, Guo J. An Assay Combining Droplet Digital PCR With Propidium Monoazide Treatment for the Accurate Detection of Live Cells of Vibrio vulnificus in Plasma Samples. Front Microbiol 2022; 13:927285. [PMID: 35910629 PMCID: PMC9335127 DOI: 10.3389/fmicb.2022.927285] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2022] [Accepted: 06/24/2022] [Indexed: 11/17/2022] Open
Abstract
Vibrio vulnificus (V. vulnificus) is one of the most common pathogenic Vibrio species to humans; therefore, the establishment of timely and credible detection methods has become an urgent requirement for V. vulnificus illness surveillance. In this study, an assay combining droplet digital PCR (ddPCR) with propidium monoazide (PMA) treatment was developed for detecting V. vulnificus. The primers/probes targeting the V. vulnificus hemolysin A (vvhA) gene, amplification procedures, and PMA processing conditions involved in the assay were optimized. Then, we analyzed the specificity, sensitivity, and ability to detect live cell DNA while testing the performance of PMA-ddPCR in clinical samples. The optimal concentrations of primers and probes were 1.0 and 0.3 μM, respectively. The annealing temperature achieving the highest accuracy in ddPCR assay was 60°C. With an initial V. vulnificus cell concentration of 108 CFU/mL (colony-forming units per milliliter), the optimal strategy to distinguish live cells from dead cells was to treat samples with 100 μM PMA for 15 min in the dark and expose them to LED light with an output wavelength of 465 nm for 10 min. The specificity of the PMA-ddPCR assay was tested on 27 strains, including seven V. vulnificus strains and 20 other bacterial strains. Only the seven V. vulnificus strains were observed with positive signals in specificity analysis. Comparative experiments on the detection ability of PMA-ddPCR and PMA-qPCR in pure cultures and plasma samples were performed. The limit of detection (LOD) and the limit of quantitation (LOQ) in pure culture solutions of V. vulnificus were 29.33 and 53.64 CFU/mL in PMA-ddPCR, respectively. For artificially clinical sample tests in PMA-ddPCR, V. vulnificus could be detected at concentrations as low as 65.20 CFU/mL. The sensitivity of the PMA-ddPCR assay was 15- to 40-fold more sensitive than the PMA-qPCR in this study. The PMA-ddPCR assay we developed provides a new insight to accurately detect live cells of V. vulnificus in clinical samples, which is of great significance to enhance public health safety and security capability and improve the emergency response level for V. vulnificus infection.
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Affiliation(s)
- Ling Hu
- Hangzhou Medical College, Hangzhou, China
- Ningbo Stomatology Hospital, Ningbo, China
| | - Yidong Fu
- Hwa Mei Hospital, University of Chinese Academy of Sciences, Ningbo, China
- Ningbo Institute of Life and Health Industry, University of Chinese Academy of Sciences, Ningbo, China
- Key Laboratory of Diagnosis and Treatment of Digestive System Tumors of Zhejiang Province, Ningbo, China
| | - Shun Zhang
- Hwa Mei Hospital, University of Chinese Academy of Sciences, Ningbo, China
- Ningbo Institute of Life and Health Industry, University of Chinese Academy of Sciences, Ningbo, China
- Key Laboratory of Diagnosis and Treatment of Digestive System Tumors of Zhejiang Province, Ningbo, China
| | - Zhilei Pan
- Hwa Mei Hospital, University of Chinese Academy of Sciences, Ningbo, China
| | - Jiang Xia
- Pilot Gene Technologies (Hangzhou) Co., Ltd., Hangzhou, China
| | - Peng Zhu
- Hwa Mei Hospital, University of Chinese Academy of Sciences, Ningbo, China
- Ningbo Institute of Life and Health Industry, University of Chinese Academy of Sciences, Ningbo, China
- Key Laboratory of Diagnosis and Treatment of Digestive System Tumors of Zhejiang Province, Ningbo, China
- *Correspondence: Peng Zhu,
| | - Jing Guo
- Hangzhou Medical College, Hangzhou, China
- Ningbo Stomatology Hospital, Ningbo, China
- Jing Guo,
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6
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Chiu SC, Hu SC, Liao LM, Chen YH, Liao HW, Cheng JC, Lin JH. Evaluation of a New Norovirus Genogroups GI and GII In Vitro Molecular Diagnostic Assay Using Clinical Specimens Collected from Acute Diarrheal Outbreaks. Foodborne Pathog Dis 2022; 19:311-315. [PMID: 35404143 DOI: 10.1089/fpd.2021.0097] [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: 11/12/2022] Open
Abstract
Norovirus is a leading cause of acute gastroenteritis (AGE) in Taiwan. To improve diagnosis as part of laboratory surveillance, AGE surveillance was conducted using a new fluorescent probe hydrolysis-based insulated isothermal polymerase chain reaction (PCR) method, the POCKIT system, and the results were compared with those obtained from conventional methods. A total of 119 clinical stool samples from reported AGE outbreaks were collected for this study. From 83 real-time reverse transcription PCR (rRT-PCR) norovirus-positive cases, the POCKIT system identified 78 with a sensitivity of 90.3% in GI genogroup and 96.7% in GII genogroup. The specificity for both GI and GII genogroups was 100%. Overall, the POCKIT system is faster and easier to use than the conventional rRT-PCR method, and because of its high sensitivity and specificity, this system is a promising alternative for the detection of norovirus in patients with AGE, and would benefit public health laboratories for near real-time surveillance of AGE epidemic outbreaks.
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Affiliation(s)
- Shu-Chun Chiu
- Center for Diagnostics and Vaccine Development, Centers for Disease Control, Taiwan, Taipei, Taiwan
| | - Szu-Chieh Hu
- Center for Diagnostics and Vaccine Development, Centers for Disease Control, Taiwan, Taipei, Taiwan
| | - Ling-Min Liao
- Center for Diagnostics and Vaccine Development, Centers for Disease Control, Taiwan, Taipei, Taiwan
| | - Yu-Hua Chen
- Center for Diagnostics and Vaccine Development, Centers for Disease Control, Taiwan, Taipei, Taiwan
| | - Hui-Wen Liao
- Center for Diagnostics and Vaccine Development, Centers for Disease Control, Taiwan, Taipei, Taiwan
| | - Ju-Chien Cheng
- Department of Medical Laboratory Science and Biotechnology, China Medical University, Taichung, Taiwan
| | - Jih-Hui Lin
- Center for Diagnostics and Vaccine Development, Centers for Disease Control, Taiwan, Taipei, Taiwan
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7
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Teh R, Tee WD, Tan E, Fan K, Koh CJ, Tambyah PA, Oon J, Tee N, Soh AYS, Siah KTH. Review of the role of gastrointestinal multiplex polymerase chain reaction in the management of diarrheal illness. J Gastroenterol Hepatol 2021; 36:3286-3297. [PMID: 34129249 DOI: 10.1111/jgh.15581] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Revised: 05/19/2021] [Accepted: 06/13/2021] [Indexed: 01/25/2023]
Abstract
Acute and chronic diarrheal illness secondary to gastrointestinal infection is a significant cause of morbidity and mortality around the world. A cornerstone of management includes prompt diagnosis and appropriate treatment of culprit pathogens. Timely diagnosis can improve patient care, assist in infection control, and prevent disease outbreaks. Historical methods of diagnosis include traditional culture methods and stool analysis. These are limited by long turnaround time and inability to simultaneously assess multiple pathogens. The advent of multiplexed nucleic acid amplification tests first began with the Food and Drug Administration-approved respiratory virus multiplex polymerase chain reaction (PCR) panel in 2009, followed by gastrointestinal infections in 2013, and neurological infections in 2014. We conducted a review of current literature pertaining to the clinical utility of a gastrointestinal multiplex PCR in management of acute and chronic diarrhea in patients. To date, seven platforms approved by the US Food and Drug Administration are used in detection of various bacterial, viral, and parasitic causative organisms for diagnosis of gastrointestinal infections. The sensitivity and specificity of each assay vary depending on the tested organism. Interpretation of a positive result has to be tailored to the clinical context. Further studies are required to establish the utility of gastrointestinal multiplex PCR from a cost-based perspective, whether specific enteropathogens such as Clostridioides difficile are better assessed with toxin gene detection and whether new parameters such as cycle threshold values can improve clinical application of test results.
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Affiliation(s)
- Readon Teh
- Division of Gastroenterology and Hepatology, National University Hospital, Singapore
| | - Wei De Tee
- Division of Gastroenterology and Hepatology, Ng Teng Fong General Hospital, Singapore.,Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Eunice Tan
- Division of Gastroenterology and Hepatology, National University Hospital, Singapore.,Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Kristie Fan
- Division of Gastroenterology and Hepatology, National University Hospital, Singapore.,Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Calvin Jianyi Koh
- Division of Gastroenterology and Hepatology, National University Hospital, Singapore.,Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Paul Ananth Tambyah
- Division of Infectious Diseases, National University Hospital, Singapore.,Infectious Diseases Translational Research Programme, Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Jolene Oon
- Division of Infectious Diseases, National University Hospital, Singapore
| | - Nancy Tee
- Department of Laboratory Medicine, National University Hospital, Singapore
| | - Alex Yu Sen Soh
- Division of Gastroenterology and Hepatology, National University Hospital, Singapore.,Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Kewin Tien Ho Siah
- Division of Gastroenterology and Hepatology, National University Hospital, Singapore.,Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
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Engberg J, Vejrum LK, Madsen TV, Nielsen XC. Verification of analytical bacterial spectrum of QIAstat-Dx® GI V2 and Novodiag® Bacterial GE+ V2-0 diagnostic panels. J Antimicrob Chemother 2021; 76:iii50-iii57. [PMID: 34555154 PMCID: PMC8460093 DOI: 10.1093/jac/dkab242] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
Background Implementing multiplex PCR or syndromic panel-based testing platforms to detect microbial species that cause acute diarrhoea may guide patient management more effectively and efficiently. Objectives To assess and compare the performance of two syndromic panel-based testing systems, QIAstat-Dx® Gastrointestinal Panel V2 (QGI) and the Novodiag® Bacterial GE+ V2-0 (NGE). Methods The QGI and NGE panels include 16 and 14 bacterial gastrointestinal pathogens, respectively. The performance of the panels was tested retrospectively using 141 positive clinical stool specimens, External Quality Assessment (EQA) panels and spiked faecal specimens. Results For Campylobacter jejuni and coli (n = 20), Salmonella (n = 24), Shigella (n = 13), Yersinia enterocolitica (non-1A biotypes) (n = 8), Clostridioides difficile (n = 24) and Vibrio parahaemolyticus (n = 2), QGI correctly verified 19/20, 20/24, 13/13, 8/8, 23/24 and 2/2, whereas NGE correctly verified 20/20, 17/24, 13/13, 8/8, 14/24 and 1/2. Among diarrhoeagenic Escherichia coli (n = 29), QGI reported one Shiga toxin-producing E. coli (STEC) stx1a O26:H11 as STEC serotype O157:H7 and NGE failed on one enteropathogenic E. coli, one enteroaggregative E. coli and one STEC (stx2e). Y. enterocolitica biotype 1A (non-pathogenic) (n = 6) were all positive in QGI, but negative in NGE. Conclusions Both QGI and NGE testing panels can improve laboratory workflow and patient management by providing user-friendly platforms that can rapidly detect a number of targets with one specimen. QGI was significantly more sensitive in identifying C. difficile. Both methods had suboptimal detection of Salmonella and this needs to be examined further. The short hands-on time and turnaround time are of value for on-demand testing and use in a high-throughput setting.
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Affiliation(s)
- Jørgen Engberg
- Department of Clinical Microbiology, Zealand University Hospital, Koege, Ingemannsvej 46, DK-4200 Slagelse, Denmark
| | - Laus Krems Vejrum
- Department of Clinical Microbiology, Zealand University Hospital, Koege, Ingemannsvej 46, DK-4200 Slagelse, Denmark
| | - Tina Vasehus Madsen
- Department of Clinical Microbiology, Zealand University Hospital, Koege, Ingemannsvej 46, DK-4200 Slagelse, Denmark
| | - Xiaohui Chen Nielsen
- Department of Clinical Microbiology, Zealand University Hospital, Koege, Ingemannsvej 46, DK-4200 Slagelse, Denmark
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9
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O'Leary JK, Sleator RD, Lucey B. Cryptosporidium spp. diagnosis and research in the 21 st century. Food Waterborne Parasitol 2021; 24:e00131. [PMID: 34471706 PMCID: PMC8390533 DOI: 10.1016/j.fawpar.2021.e00131] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Revised: 08/06/2021] [Accepted: 08/17/2021] [Indexed: 01/01/2023] Open
Abstract
The protozoan parasite Cryptosporidium has emerged as a leading cause of diarrhoeal illness worldwide, posing a significant threat to young children and immunocompromised patients. While endemic in the vast majority of developing countries, Cryptosporidium also has the potential to cause waterborne epidemics and large scale outbreaks in both developing and developed nations. Anthroponontic and zoonotic transmission routes are well defined, with the ingestion of faecally contaminated food and water supplies a common source of infection. Microscopy, the current diagnostic mainstay, is considered by many to be suboptimal. This has prompted a shift towards alternative diagnostic techniques in the advent of the molecular era. Molecular methods, particularly PCR, are gaining traction in a diagnostic capacity over microscopy in the diagnosis of cryptosporidiosis, given the laborious and often tedious nature of the latter. Until now, developments in the field of Cryptosporidium detection and research have been somewhat hampered by the intractable nature of this parasite. However, recent advances in the field have taken the tentative first steps towards bringing Cryptosporidium research into the 21st century. Herein, we provide a review of these advances.
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Affiliation(s)
- Jennifer K. O'Leary
- Department of Biological Sciences, Munster Technological University, Bishopstown Campus, Cork, Ireland
| | - Roy D. Sleator
- Department of Biological Sciences, Munster Technological University, Bishopstown Campus, Cork, Ireland
| | - Brigid Lucey
- Department of Biological Sciences, Munster Technological University, Bishopstown Campus, Cork, Ireland
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Ahmad-Nejad P, Ashavaid T, Vacaflores Salinas A, Huggett J, Harris K, Linder MW, Baluchova K, Steimer W, Payne DA. Current and future challenges in quality assurance in molecular diagnostics. Clin Chim Acta 2021; 519:239-246. [PMID: 33971158 DOI: 10.1016/j.cca.2021.05.004] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Revised: 05/04/2021] [Accepted: 05/05/2021] [Indexed: 02/08/2023]
Abstract
The development and performance of molecular genetic assays has required increasingly complex quality assurance in recent years and continues to pose new challenges. Quality management officers, as well as academic and technical personnel are confronted with new molecular genetic parameters, methods, changing regulatory environments, questions regarding appropriate validation, and quality control for these innovative assays that are increasingly applying quantification and/or multiplex formats. Yet, quality assurance and quality control guidelines are still not widely available or in some circumstances have become outdated. For these reasons, the need for solutions to provide test confidence continues to grow. In order to integrate new test procedures into existing quality assurance measures, the ISO 15189 guideline can serve as an orientation. The ISO 15189 guideline describes requirements for medical laboratories and thus includes those performing molecular diagnostics. This article gives an overview of the possibilities and challenges in quality assurance of molecular parameters and shows possible solutions.
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Affiliation(s)
- Parviz Ahmad-Nejad
- Institute for Medicine Laboratory Diagnostics, Centre for Clinical and Translational Research (CCTR), HELIOS University Hospital, Wuppertal, Witten/Herdecke University, Germany.
| | - Tester Ashavaid
- Department of Laboratory Medicine, P.D. Hinduja National Hospital and Medical Research Center, Mumbai, India
| | | | - Jim Huggett
- National Measurement Laboratory (NML) at LGC, Queens Rd, Teddington, TW11 0LY, United Kingdom; School of Biosciences & Medicine, Faculty of Health & Medical Science, University of Surrey, Guildford GU2 7XH, United Kingdom
| | - Kathryn Harris
- Microbiology Department, Great Ormond Street Hospital NHS Foundation Trust, London, UK
| | - Mark W Linder
- Department of Pathology and Laboratory Medicine, University of Louisville School of Medicine, Louisville, KY, USA
| | - Katarina Baluchova
- OncoLab Diagnostics GmbH Technologie- und Forschungszentrum, Viktor-Kaplan-Straße 2, 2700 Wiener Neustadt, Austria
| | - Werner Steimer
- Institute for Clinical Chemistry and Pathobiochemistry, Munich University of Technology, Klinikum rechts der Isar, D-81675 Munich, Germany
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11
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Castany-Feixas M, Simo S, Garcia-Garcia S, Fernandez de Sevilla M, Launes C, Kalkgruber M, Gene A, Muñoz-Almagro C, Brotons P. Rapid molecular syndromic testing for aetiological diagnosis of gastrointestinal infections and targeted antimicrobial prescription: experience from a reference paediatric hospital in Spain. Eur J Clin Microbiol Infect Dis 2021; 40:2153-2160. [PMID: 33963926 PMCID: PMC8449766 DOI: 10.1007/s10096-021-04266-7] [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: 12/11/2020] [Accepted: 04/28/2021] [Indexed: 11/30/2022]
Abstract
Aetiological diagnosis of gastrointestinal infections is challenging since a wide range of bacteria, parasites and viruses can be causal agents and derived clinical manifestations appear quite similar. Our aim was to evaluate contribution of the novel QIAstat-DxGastrointestinal Panel (GIP) to aetiological diagnosis of gastrointestinal infections and rational antimicrobial prescription in a reference paediatric hospital. Evaluation included comparison of diagnostic yield and agreement of results of QIAstat-Dx GIP and conventional microbiological methods. Parallel testing was performed on stool samples collected prospectively from children admitted to Sant Joan de Deu Barcelona Hospital (Spain) during the period February-March 2019. Influence of the panel test use on antimicrobial prescription was assessed using a pre-post study design. Eighty-six (68.8%) out of 125 specimens were positive by QIAstat-Dx GIP versus 44 (35.2%) positive by a composite of conventional methods (p<0.001). Global agreement of panel test results with rotavirus-adenovirus antigen detection (92.8%) and a two-step antigen/toxin and PCR-based algorithm for toxigenic Clostridioides difficile detection (87.5%) was greater than that with bacterial culture (76.0%) and parasite microscopic identification (64.3%). Panel test results orientated antimicrobial prescription changes in 18 (14.4%) patients, including antimicrobial start in 11 cases initially untreated, targeted antimicrobial prescription in 5 and discontinuation in 2 cases empirically treated. Results showed that QIAstat-Dx GIP significantly expanded aetiological diagnosis of gastrointestinal infections compared to conventional microbiological methods while orientating a more judicious use of antimicrobial drugs in hospitalised children.
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Affiliation(s)
| | - Silvia Simo
- Institut de Recerca Sant Joan de Deu, Barcelona, Spain.,CIBER de Epidemiología y Salud Pública CIBERESP, Madrid, Spain
| | - Selene Garcia-Garcia
- Institut de Recerca Sant Joan de Deu, Barcelona, Spain.,Universitat Internacional de Catalunya, Barcelona, Spain
| | - Mariona Fernandez de Sevilla
- Institut de Recerca Sant Joan de Deu, Barcelona, Spain.,CIBER de Epidemiología y Salud Pública CIBERESP, Madrid, Spain.,University Hospital Sant Joan de Deu, P° Sant Joan de Déu, n° 2 08950 Esplugues, Barcelona, Spain.,Universitat de Barcelona, Barcelona, Spain
| | - Cristian Launes
- Institut de Recerca Sant Joan de Deu, Barcelona, Spain.,CIBER de Epidemiología y Salud Pública CIBERESP, Madrid, Spain.,University Hospital Sant Joan de Deu, P° Sant Joan de Déu, n° 2 08950 Esplugues, Barcelona, Spain.,Universitat de Barcelona, Barcelona, Spain
| | | | - Amadeu Gene
- University Hospital Sant Joan de Deu, P° Sant Joan de Déu, n° 2 08950 Esplugues, Barcelona, Spain
| | - Carmen Muñoz-Almagro
- Institut de Recerca Sant Joan de Deu, Barcelona, Spain. .,CIBER de Epidemiología y Salud Pública CIBERESP, Madrid, Spain. .,Universitat Internacional de Catalunya, Barcelona, Spain. .,University Hospital Sant Joan de Deu, P° Sant Joan de Déu, n° 2 08950 Esplugues, Barcelona, Spain.
| | - Pedro Brotons
- Institut de Recerca Sant Joan de Deu, Barcelona, Spain.,CIBER de Epidemiología y Salud Pública CIBERESP, Madrid, Spain.,Universitat Internacional de Catalunya, Barcelona, Spain
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12
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Chirambo AC, Nyirenda TS, Jambo N, Msefula C, Kamng'ona A, Molina S, Mandala WL, Heyderman RS, Iturizza-Gomara M, Henrion MYR, Gordon MA. Performance of molecular methods for the detection of Salmonella in human stool specimens. Wellcome Open Res 2021; 5:237. [PMID: 34017923 PMCID: PMC8108707 DOI: 10.12688/wellcomeopenres.16305.2] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/21/2021] [Indexed: 11/28/2022] Open
Abstract
Background: The relationship between asymptomatic
Salmonella exposure within the gastrointestinal tract and
Salmonella bacteraemia is poorly understood, in part due to the low sensitivity of stool culture and the lack of validated molecular diagnostic tests for the detection of
Salmonella in the stool. The study aimed to determine a reliable molecular diagnostic test for
Salmonella in stool specimens. Methods: We optimised an in-house monoplex real-time polymerase chain reaction (PCR) for the detection of
Salmonellattr and
InvA genes in stool by including a selenite broth pre-culture step for
Salmonella before DNA extraction and validated their specificity against other local common pathogens. Then we assessed their performance against a well-validated multiplex PCR targeting the same
ttr and
InvA genes and against stool culture using clinical stool specimens collected from a cohort of 50 asymptomatic healthy Malawian children that were sampled at 1-month intervals over 12 months. We employed a latent Markov model to estimate the specificities and sensitivities of PCR methods. Results:
Ttr and
InvA primers were both able to detect all the different
Salmonella serovars tested and had superior limits of detection when DNA was extracted after selenite pre-culture. T
tr sensitivity and specificity for monoplex-PCR were (99.53%, 95.46%) and for multiplex-PCR (90.30%, 99.30%) respectively.
InvA specificity and specificity for using monoplex-PCR was (95.06%, 90.31%) and multiplex-PCRs (89.41%, 98.00%) respectively. Sensitivity and specificity for standard stool culture were 62.88% and 99.99%, respectively. Culture showed the highest PPV (99.73%), and monoplex-
ttr had the highest NPV (99.67%). Conclusion: Test methods demonstrated high concordance, although stool culture and monoplexed
ttr primers had superior specificity and sensitivity, respectively. The use of selenite pre-enrichment step increased
Salmonella detection rate. Taken together, molecular detection methods used here could be used to reveal the true extent of both asymptomatic and symptomatic
Salmonella exposure events.
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Affiliation(s)
- Angeziwa Chunga Chirambo
- Malawi-Liverpool-Wellcome (MLW) Programme, Blantyre, +265, Malawi.,Pathology Department, College of Medicine, Malawi, Blantyre, Malawi.,Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, L69 3BX, UK
| | - Tonney S Nyirenda
- Malawi-Liverpool-Wellcome (MLW) Programme, Blantyre, +265, Malawi.,Pathology Department, College of Medicine, Malawi, Blantyre, Malawi
| | - Ndaru Jambo
- Malawi-Liverpool-Wellcome (MLW) Programme, Blantyre, +265, Malawi.,Pathology Department, College of Medicine, Malawi, Blantyre, Malawi.,Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, L69 3BX, UK
| | - Chisomo Msefula
- Malawi-Liverpool-Wellcome (MLW) Programme, Blantyre, +265, Malawi.,Pathology Department, College of Medicine, Malawi, Blantyre, Malawi
| | - Arox Kamng'ona
- Malawi-Liverpool-Wellcome (MLW) Programme, Blantyre, +265, Malawi.,Biomedical Sciences Department, College of Medicine, Malawi, Blantyre, Malawi
| | - Sandra Molina
- London School of Hygiene and Tropical Medicine, London, WC1E 7HT, UK
| | - Wilson L Mandala
- Malawi University of Science and Technology, Thyolo, +265, Malawi
| | - Robert S Heyderman
- Research Department of Infection, Division of Infection and Immunity, University College London, London, WC1E 6EJ, UK
| | - Miren Iturizza-Gomara
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, L69 3BX, UK
| | - Marc Y R Henrion
- Malawi-Liverpool-Wellcome (MLW) Programme, Blantyre, +265, Malawi.,Department of Clinical Sciences, Liverpool School of Tropical Medicine, Liverpool, L3 5QA, UK
| | - Melita A Gordon
- Malawi-Liverpool-Wellcome (MLW) Programme, Blantyre, +265, Malawi.,Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, L69 3BX, UK
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13
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Chirambo AC, Nyirenda TS, Jambo N, Msefula C, Kamng'ona A, Molina S, Mandala WL, Heyderman RS, Iturizza-Gomara M, Henrion MY, Gordon MA. Performance of molecular methods for the detection of Salmonella in human stool specimens. Wellcome Open Res 2020; 5:237. [DOI: 10.12688/wellcomeopenres.16305.1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/01/2020] [Indexed: 11/20/2022] Open
Abstract
Background: The relationship between asymptomatic Salmonella exposure within the gastrointestinal tract and Salmonella bacteraemia is poorly understood, in part due to the low sensitivity of stool culture, and the lack of validated molecular diagnostic tests for the detection of Salmonella in stool. The study aimed to determine a reliable molecular diagnostic test for Salmonella in stool specimens. Methods: We optimized an in-house monoplex real time polymerase chain reaction (PCR) for the detection of Salmonella TTR and InvA genes in stool by including a selenite broth pre-culture step for Salmonella before DNA extraction, and validated their specificity against other local common pathogens. Then we assessed their performance against a well-validated multiplex PCR targeting the same TTR and InvA genes, and against stool culture using clinical stool specimens collected from a cohort of 50 asymptomatic healthy Malawian children that were sampled at 1-month intervals over a period of 12 months. We employed a latent Markov model to estimate the specificities and sensitivities of PCR methods. Results: TTR and InvA primers were both able to detect all the different Salmonella serovars tested, and had superior limits of detection if DNA was extracted after selenite pre-culture. TTR sensitivity and specificity for monoplex-PCR were (99.53%, 95.46%) and for multiplex-PCR (90.30%, 99.30%) respectively. InvA specificity and specificity for using monoplex-PCR was (95.06%, 90.31%) and multiplex-PCRs (89.41%, 98.00%) respectively. Sensitivity and specificity for standard stool culture were 62.88% and 99.99% respectively. Culture showed the highest PPV (99.73%) and mono-TTR had the highest NPV (99.67%). Conclusion: Test methods demonstrated high concordance although stool culture and monoplexed TTR primers had superior specificity and sensitivity respectively. The use of selenite pre-enrichment step increased Salmonella detection rate. Taken together, molecular detection methods used here could be used to reveal the true extent of both asymptomatic and symptomatic Salmonella exposure events.
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14
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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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15
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Performance Evaluation of the Novodiag Bacterial GE+ Multiplex PCR Assay. J Clin Microbiol 2020; 58:JCM.01033-20. [PMID: 32719031 DOI: 10.1128/jcm.01033-20] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2020] [Accepted: 07/15/2020] [Indexed: 11/20/2022] Open
Abstract
The bacteriological diagnosis of intestinal bacterial infections has historically been based on culture on agar plates. However, culture may lack sensitivity, and some enteropathogens, such as pathovars of Escherichia coli, may escape routine diagnosis. Our goal was to evaluate the analytical performance of the Novodiag Bacterial GE+ kit for the detection of enteropathogenic bacteria in acute community diarrhea. We included 251 stools in this study (198 retrospective and 53 prospective). The analytical performance was calculated using a composite reference standard (CRS) in the absence of a perfect gold standard (lack of sensitivity of culture). The CRS was defined as positive if culture was positive or, in case of a negative culture, if the BD Max extended enteric bacterial panel and/or other real-time PCR (RT-PCR) tests were positive. Of the 251 samples, 200 were positive, and 51 were negative. Overall sensitivities of the Novodiag Bacterial GE+ kit for Campylobacter sp., Salmonella sp., Shigella sp./enteroinvasive E. coli (EIEC), Yersinia enterocolitica, enterohemorrhagic E. coli (EHEC), and enterotoxigenic E. coli (ETEC) ranged from 98.98 to 100%, specificities ranged from 98.08 to 100%, positive predictive values (PPVs) ranged from 88.24 to 100%, and negative predictive values (NVPs) ranged from 99.36 to 100%. The analytical performance of the Novodiag Bacterial GE+ kit is excellent. It can be used as a routine tool in the rapid diagnosis of bacterial gastroenteritis. Despite the eNAT tube dilution of the primary sample, the detection of Salmonella sp. and EHEC was perfect. The kit has the advantage of only detecting pathogenic Y. enterocolitica Its performance for Campylobacter is very satisfactory.
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16
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De Grazia S, Bonura F, Bonura C, Mangiaracina L, Filizzolo C, Martella V, Giammanco GM. Assessing the burden of viral co-infections in acute gastroenteritis in children: An eleven-year-long investigation. J Clin Virol 2020; 129:104513. [PMID: 32575023 DOI: 10.1016/j.jcv.2020.104513] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Revised: 06/05/2020] [Accepted: 06/14/2020] [Indexed: 12/18/2022]
Abstract
BACKGROUND Acute gastroenteritis is an important cause of childhood morbidity and mortality worldwide. A number of pathogens are responsible for human acute gastroenteritis. The recent introduction of syndromic assays for the diagnosis of enteric infections, including a wide panel of enteric pathogens, has unveiled the frequency of mixed infections. This study was carried out to assess the burden of viral co-infections and the genetic diversity of the viruses detected in children hospitalized with acute gastroenteritis in Italy. METHODS A total of 4161 stool samples collected from diarrheic children over 11 years, from January 2008 to December 2018, were investigated for the presence of four enteric viruses, i.e. group A rotavirus, norovirus, astrovirus and adenovirus. The samples were initially screened by either molecular or immunochromatographic assays and subsequently confirmed by Real-time PCR and sequence analyses. RESULTS At least one viral agent was detected in 48.6 %of specimens. Rotavirus was the most prevalent virus (24.7 %) followed by norovirus (19.6 %), adenovirus (5.3 %) and astrovirus (3%). Co-infections were detected in 8.3 % of virus-positive patients, with common viral combination being rotavirus with norovirus (70.6 % of co-infections) or with astrovirus (9.6 %). A variety of viral genotypes was detected in co-infections and in single infections. Using Real-time PCR cycle thresholds as a proxy measure of fecal viral load, rotavirus was generally detected at higher levels in co-infected patients. CONCLUSIONS Combining and deciphering measurable indicators of viral load and epidemiological information could be useful for an accurate interpretation of viral co-infections.
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Affiliation(s)
- Simona De Grazia
- Dipartimento di Promozione della Salute, Materno-Infantile, di Medicina Interna e Specialistica di Eccellenza "G. D'Alessandro", Università di Palermo, Palermo, Italy.
| | - Floriana Bonura
- Dipartimento di Promozione della Salute, Materno-Infantile, di Medicina Interna e Specialistica di Eccellenza "G. D'Alessandro", Università di Palermo, Palermo, Italy
| | - Celestino Bonura
- Dipartimento di Promozione della Salute, Materno-Infantile, di Medicina Interna e Specialistica di Eccellenza "G. D'Alessandro", Università di Palermo, Palermo, Italy
| | - Leonardo Mangiaracina
- Dipartimento di Promozione della Salute, Materno-Infantile, di Medicina Interna e Specialistica di Eccellenza "G. D'Alessandro", Università di Palermo, Palermo, Italy
| | - Chiara Filizzolo
- Dipartimento di Promozione della Salute, Materno-Infantile, di Medicina Interna e Specialistica di Eccellenza "G. D'Alessandro", Università di Palermo, Palermo, Italy
| | - Vito Martella
- Dipartimento di Medicina Veterinaria, Università Aldo Moro di Bari, Valenzano, Italy
| | - Giovanni M Giammanco
- Dipartimento di Promozione della Salute, Materno-Infantile, di Medicina Interna e Specialistica di Eccellenza "G. D'Alessandro", Università di Palermo, Palermo, Italy
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17
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Clinical evaluation of a non-purified direct molecular assay for the detection of Clostridioides difficile toxin genes in stool specimens. PLoS One 2020; 15:e0234119. [PMID: 32492051 PMCID: PMC7269250 DOI: 10.1371/journal.pone.0234119] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2020] [Accepted: 05/19/2020] [Indexed: 12/22/2022] Open
Abstract
Recently, a new rapid assay for the detection of tcdB gene of Clostridioides difficile was developed using the GENECUBE. The assay can directly detect the tcdB gene from stool samples without a purification in approximately 35 minutes with a few minutes of preparation process. We performed a prospective comparative study of the performance of the assay at eight institutions in Japan. Fresh residual stool samples (Bristol stool scale ≥5) were used and comparisons were performed with the BD MAX Cdiff assay and toxigenic cultures. For the evaluation of 383 stool samples compared with the BD MAX Cdiff assay, the sensitivity, and specificity of the two assays was 99.0% (379/383), 98.1% (52/53), 99.1% (327/330), respectively. In the comparison with toxigenic culture, the total, sensitivity, and specificity were 96.6% (370/383), 85.0% (51/60), and 98.8% (319/323), respectively. The current investigation indicated the GENECUBE Clostridioides difficile assay has equivalent performance with the BD MAX Cdiff assay for the detection of tcdB gene of C. difficile.
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18
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Shima N, Nakamura J, Saito K, Kamata Y, Nagatani K, Nagashima T, Iwamoto M, Akine D, Saito T, Sato K, Minota S. Salmonella enterica Subspecies arizonae Detected from Bilateral Pleural Fluid in a Patient with Systemic Lupus Erythematosus and Malignant Lymphoma. Intern Med 2020; 59:1223-1226. [PMID: 32051382 PMCID: PMC7270754 DOI: 10.2169/internalmedicine.3982-19] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
A 72-year-old woman was admitted to our hospital with bilateral pleural effusions. She had a 31-year history of systemic lupus erythematosus and had been treated with prednisolone and azathioprine. Pleural fluid culture revealed Salmonella enterica subsp. arizonae infection. This pathogen rarely infects humans but is commonly found in the gut flora of reptiles, especially snakes. Our patient had not come in contact with reptiles. Despite antibiotic therapies and negative pleural cultures, the pleural effusion persisted. Colon cancer was detected concomitantly, and she finally died. The autopsy revealed that the pleuritis was due to underlying diffuse large B cell lymphoma.
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Affiliation(s)
- Natsuki Shima
- Division of Rheumatology and Clinical Immunology, Department of Medicine, Jichi Medical University, Japan
| | - Jun Nakamura
- Division of Rheumatology and Clinical Immunology, Department of Medicine, Jichi Medical University, Japan
| | - Keisuke Saito
- Division of Rheumatology and Clinical Immunology, Department of Medicine, Jichi Medical University, Japan
| | - Yasuyuki Kamata
- Division of Rheumatology and Clinical Immunology, Department of Medicine, Jichi Medical University, Japan
| | - Katsuya Nagatani
- Division of Rheumatology and Clinical Immunology, Department of Medicine, Jichi Medical University, Japan
| | - Takao Nagashima
- Division of Rheumatology and Clinical Immunology, Department of Medicine, Jichi Medical University, Japan
| | - Masahiro Iwamoto
- Division of Rheumatology and Clinical Immunology, Department of Medicine, Jichi Medical University, Japan
| | - Dai Akine
- Health Service Center, Jichi Medical University, Japan
- Division of Clinical Infectious Diseases, Department of Infection and Immunity, Jichi Medical University, Japan
| | - Tatsuya Saito
- Division of Pulmonary Medicine, Department of Medicine, Jichi Medical University, Japan
| | - Kojiro Sato
- Division of Rheumatology and Clinical Immunology, Department of Medicine, Jichi Medical University, Japan
| | - Seiji Minota
- Division of Rheumatology and Clinical Immunology, Department of Medicine, Jichi Medical University, Japan
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19
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An Overview of the Molecular Methods in the Diagnosis of Gastrointestinal Infectious Diseases. Int J Microbiol 2020; 2020:8135724. [PMID: 32280346 PMCID: PMC7128059 DOI: 10.1155/2020/8135724] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2019] [Revised: 01/24/2020] [Accepted: 03/02/2020] [Indexed: 12/14/2022] Open
Abstract
Gastrointestinal infectious diseases are very common worldwide and an important cause of morbidity and mortality, particularly in infants in developing countries. Diarrhea and other intestinal infections are caused by a wide range of bacteria, viruses, protozoa, and parasites. Conventional diagnosis of these infections is performed by culture, microscopy, and antigen detection immunoassays. The traditional culture and microscopy procedures are time-consuming, lack sensitivity, and require special laboratory setup and well-trained staff. However, based on the advancement in the molecular diagnostics and with the introduction of commercially available tests, traditional diagnostic techniques have been continuously replaced by these newer rapid antigen detection and molecular-based methods. This review summarizes and discusses the availability, advantages, and disadvantages of molecular methods in the detection and identification of human gastrointestinal pathogens.
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20
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Performance of the QIAstat-Dx Gastrointestinal Panel for Diagnosing Infectious Gastroenteritis. J Clin Microbiol 2020; 58:JCM.01737-19. [PMID: 31915286 PMCID: PMC7041566 DOI: 10.1128/jcm.01737-19] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2019] [Accepted: 12/19/2019] [Indexed: 12/20/2022] Open
Abstract
Detection and identification of enteropathogens that cause infectious gastroenteritis are essential steps for appropriate patient treatment and effective isolation precautions. Several syndrome-based tests have recently become available, with the gastrointestinal panel (GIP) assay on the QIAstat-Dx as the most recent addition to the syndromic testing landscape. Detection and identification of enteropathogens that cause infectious gastroenteritis are essential steps for appropriate patient treatment and effective isolation precautions. Several syndrome-based tests have recently become available, with the gastrointestinal panel (GIP) assay on the QIAstat-Dx as the most recent addition to the syndromic testing landscape. The QIAstat-Dx GIP assay offers simultaneous testing for 24 bacterial, viral, and parasitic enteropathogens using a single test that reports the results in 70 min. In this study, we compared the performance of the GIP assay to laboratory-developed real-time PCR assays (LDTs), using 172 prospectively and retrospectively collected fecal samples from patients suspected to have infectious gastroenteritis. The GIP assay detected 97/107 enteropathogens (91%) that were detected by LDTs, and the overall agreement of results increased to 95% when excluding discrepant results with cycle threshold (CT) values of >35. Further, the GIP assay detected 42 additional enteropathogens that were not detected, or tested, by LDTs. These included 35 diarrheagenic Escherichia coli targets for which the clinical relevance is unclear for most. The main advantage of the QIAstat-Dx system compared to other syndromic testing systems is the ability to generate CT values that could help with the interpretation of results. However, compared to LDTs, the GIP assay is limited by flexibility and high-throughput testing. In conclusion, the GIP assay offers an easy, sample-to-answer workflow with a rapid detection of the most common enteropathogens and therefore has the potential to direct appropriate therapy and infection control precautions.
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21
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Li J, Cui Z, Qi M, Zhang L. Advances in Cyclosporiasis Diagnosis and Therapeutic Intervention. Front Cell Infect Microbiol 2020; 10:43. [PMID: 32117814 PMCID: PMC7026454 DOI: 10.3389/fcimb.2020.00043] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2019] [Accepted: 01/22/2020] [Indexed: 12/22/2022] Open
Abstract
Cyclosporiasis is caused by the coccidian parasite Cyclospora cayetanensis and is associated with large and complex food-borne outbreaks worldwide. Associated symptoms include severe watery diarrhea, particularly in infants, and immune dysfunction. With the globalization of human food supply, the occurrence of cyclosporiasis has been increasing in both food growing and importing countries. As well as being a burden on the health of individual humans, cyclosporiasis is a global public health concern. Currently, no vaccine is available but early detection and treatment could result in a favorable clinical outcome. Clinical diagnosis is based on cardinal clinical symptoms and conventional laboratory methods, which usually involve microscopic examination of wet smears, staining tests, fluorescence microscopy, serological testing, or DNA testing for oocysts in the stool. Detection in the vehicle of infection, which can be fresh produce, water, or soil is helpful for case-linkage and source-tracking during cyclosporiasis outbreaks. Treatment with trimethoprim-sulfamethoxazole (TMP-SMX) can evidently cure C. cayetanensis infection. However, TMP-SMX is not suitable for patients having sulfonamide intolerance. In such case ciprofloxacin, although less effective than TMP-SMX, is a good option. Another drug of choice is nitazoxanide that can be used in the cases of sulfonamide intolerance and ciprofloxacin resistance. More epidemiological research investigating cyclosporiasis in humans should be conducted worldwide, to achieve a better understanding of its characteristics in this regard. It is also necessary to establish in vitro and/or in vivo protocols for cultivating C. cayetanensis, to facilitate the development of rapid, convenient, precise, and economical detection methods for diagnosis, as well as more effective tracing methods. This review focuses on the advances in clinical features, diagnosis, and therapeutic intervention of cyclosporiasis.
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Affiliation(s)
- Junqiang Li
- Academy of Chinese Medical Sciences, Henan University of Chinese Medicine, Zhengzhou, China.,College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou, China
| | - Zhaohui Cui
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou, China
| | - Meng Qi
- College of Animal Science, Tarim University, Alar, China
| | - Longxian Zhang
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou, China
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