1
|
Patel HM, Kaur MR, Haris Ali M, Hadi Z, Parikh A, Khan SH, Kamireddy M, Faiz H, Kamani YG, Agarwal A, Al Hasibuzzaman M. Evaluation of non-invasive diagnostic tools for diarrhea: a systematic review of point-of-care tests and biomarkers. Ann Med Surg (Lond) 2024; 86:2951-2962. [PMID: 38694383 PMCID: PMC11060204 DOI: 10.1097/ms9.0000000000001946] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2023] [Accepted: 03/02/2024] [Indexed: 05/04/2024] Open
Abstract
Background Diarrhea is a prevalent condition affecting millions worldwide. However, current standard diagnostic methods have many drawbacks. This review examines various non-invasive point-of-care (POC) tests and biomarkers aiding rapid diagnosis of diarrhea from different causes. Methods PubMed, PubMed Central, ScienceDirect, Cochrane Library, and Google Scholar were searched from 2013 to present for relevant literature. Two reviewers independently assessed included studies' quality using the Critical Appraisal Skills Programme (CASP) checklist. Results The search yielded 1453 studies, of which 39 were included after screening and applying eligibility criteria. Polymerase chain reaction (PCR) was the POC test in 25 studies, providing consistent sensitivity and specificity. For biomarkers, C-reactive protein (CRP), fecal calprotectin, and procalcitonin offered high sensitivity and specificity for conditions like acute pediatric diarrhea, microscopic colitis, and inflammatory diarrhea, respectively. Conclusion PCR proved the ideal POC test for rapid diarrhea diagnosis, while the procalcitonin biomarker helps differentiate inflammatory from non-inflammatory diarrhea. Other reviewed tools also demonstrated promising diagnostic performance, though improvements in sensitivity, specificity, and usability are still needed.
Collapse
Affiliation(s)
| | | | - Mohammad Haris Ali
- Shaikh Khalifa Bin Zayed Al-Nahyan Medical and Dental College, Lahore, Punjab
| | | | | | | | | | - Haseeb Faiz
- Department of Medicine, Jinnah Hospital, Lahore
| | - Yashkumar G. Kamani
- Cagayan State University College of Medicine, Tuguegarao, Cagayan Valley, Philippines
| | | | - Md. Al Hasibuzzaman
- Institute of Nutrition and Food Science, University of Dhaka, Dhaka
- Med Research Hub, Panchagarh, Bangladesh
- The First Affiliated Hospital of Ningbo University, Ningbo, Zhejiang Province, People’s Republic of China
| |
Collapse
|
2
|
Bhat A, Rao SS, Bhat S, Vidyalakshmi K, Dhanashree B. Molecular diagnosis of bacterial and viral diarrhoea using multiplex-PCR assays: An observational prospective study among paediatric patients from India. Indian J Med Microbiol 2023; 41:64-70. [PMID: 36870754 DOI: 10.1016/j.ijmmb.2023.01.002] [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: 06/19/2022] [Revised: 12/24/2022] [Accepted: 01/02/2023] [Indexed: 01/24/2023]
Abstract
PURPOSE In developing countries, the aetiology of diarrhoea goes undiagnosed as only microscopy, stool culture or enzyme immunoassay are done to find the causative agent. The present study aims to detect common paediatric viral and bacterial diarrhoea pathogens by microscopy, stool culture for bacteria, and multiplex polymerase chain reaction (mPCR) for bacteria and virus detections. MATERIALS AND METHODS Diarrheal stool samples (n = 109) received at the laboratory from paediatric patients aged one month to 18 years were included in the study. They were cultured for common bacterial pathogens and simultaneously subjected to two multiplex PCRs one for the detection of Salmonella spp., Shigella spp., Enteroinvasive E.coli and Enteropathogenic E.coli, another for the detection of adenovirus, astrovirus, rotavirus and norovirus. RESULTS Of the 109 samples cultured for bacterial aetiology, 0.9% (1/109) grew Salmonella enterica ser.Typhi and 2% (2/109) Shigella flexneri. By mPCR, 16% of samples (17/109) were positive for Shigella spp., 0.9% (1/109) for Salmonella spp., and 21% (23/109) for rotavirus. One sample (0.9%) had rotavirus and Shigella spp., which indicates mixed aetiology. CONCLUSIONS Shigella spp. and rotavirus are the prime causative agents of childhood diarrhoea in our region. The rate of detection of bacterial aetiology by culture was poor. Isolation of pathogens by conventional culture helps to know the species, serotypes and antibiotic susceptibility of the pathogens. Virus isolation is cumbersome, time-consuming, and not available for routine diagnostic use. Therefore, real-time mPCR would be a better choice for early detection of pathogens, thereby ensuring timely diagnosis, treatment, and a reduction in mortality.
Collapse
Affiliation(s)
- Archana Bhat
- Department of Microbiology, Kasturba Medical College, Mangalore, Manipal Academy of Higher Education, Manipal, India.
| | - Suchetha S Rao
- Department of Paediatrics, Kasturba Medical College, Mangalore, Manipal Academy of Higher Education, Manipal, India.
| | - Sevitha Bhat
- Department of Microbiology, Kasturba Medical College, Mangalore, Manipal Academy of Higher Education, Manipal, India.
| | - Katara Vidyalakshmi
- Department of Microbiology, Kasturba Medical College, Mangalore, Manipal Academy of Higher Education, Manipal, India.
| | - Biranthabail Dhanashree
- Department of Microbiology, Kasturba Medical College, Mangalore, Manipal Academy of Higher Education, Manipal, India.
| |
Collapse
|
3
|
Tatte VS, Gopalkrishna V. Detection of different enteric viruses in children with diarrheal disease: evidence of the high frequency of mixed infections. Access Microbiol 2019; 1:e000010. [PMID: 32974508 PMCID: PMC7470349 DOI: 10.1099/acmi.0.000010] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2019] [Accepted: 02/08/2019] [Indexed: 01/19/2023] Open
Abstract
Enteric viruses play a major role in causing diarrhea in children. Early identification of the causative pathogen is still a challenge in the clinical laboratory. A multiplex PCR assay is a useful tool to screen a large number of clinical samples especially in an outbreak situation. In this study, a multiplex reverse transcription (RT)-PCR assay was developed to detect nine enteric viruses such as group A rotavirus, norovirus GGII, sapovirus, adenovirus, astrovirus, aichivirus, parechovirus, bocavirus and enterovirus in clinical samples of diarrheal cases. Stool samples (n=185) collected from infants and children with acute gastroenteritis cases in Pune, western India were analysed for nine different enteric viruses by currently developed multiplex RT- PCR. Predominance of group A rotavirus (76%) followed by enterovirus (11.5%), astrovirus (4.5%), adenovirus (2.7%) and norovirus GII (1.6%) was observed. A total of 44.8 % (82/185) samples analysed by this method showed high frequency of mixed infections. These results highlighted high prevalence and diversity of different enteric viruses in children. The multiplex PCR showed good concordance with monoplex RT-PCR for detection of these enteric viruses in clinical samples. This is the first report on the development of a multiplex RT-PCR assay for detection of multiple enteric viruses in diarrheal diseases from India.
Collapse
Affiliation(s)
- Vaishali S Tatte
- Enteric Viruses Group, National Institute of Virology, Pune, India
| | | |
Collapse
|
4
|
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.
Collapse
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.
| |
Collapse
|
5
|
Bergallo M, Galliano I, Montanari P, Brusin MR, Finotti S, Paderi G, Gabiano C. Development of a quantitative real-time PCR assay for sapovirus in children under 5-years-old in Regina Margherita Hospital of Turin, Italy. Can J Microbiol 2017; 63:296-302. [DOI: 10.1139/cjm-2016-0482] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Gastroenteritis is a common disease in children. It is characterized by diarrhea, vomiting, abdominal pain, and fever. Sapovirus (SaV) is a causative agent of acute gastroenteritis, but it causes milder illness than do rotavirus and norovirus. There is high variability in the analytical performance of quantitative PCR-based assays among clinical laboratories. This study developed a reverse transcription real-time PCR method to detect SaV in fecal specimens collected from children under 5-years-old with acute gastroenteritis. Of 137 episodes of acute gastroenteritis, 15 (10.9%) were associated with SaV genomic detection, with a median viral load of 6.6(log10) ± 7.1(log10) genomes/mg fecal specimens. There was a significant difference in detection rate between males and females (9.48% (13/15) vs. 1.46% (2/15), p = 0.0232). Among the 15 SaV-positive cases, 6 were also positive for rotavirus. Viral RNA recovery rate ranged from 46% to 77% in the manual RNAzol protocol and from 31% to 90% in the automated Maxwell protocol. We also studied whether human genomic DNA influences the sensitivity of the assay: its presence caused a decrease in PCR sensitivity. The development of a laboratory-designed real-time PCR TaqMan assay for quantitative detection of SaV and the optimization and standardization of this assay, using stools of children with acute gastroenteritis, are described.
Collapse
Affiliation(s)
- Massimiliano Bergallo
- Department of Public Health and Pediatric Sciences, University of Turin, Medical School, 10136 Turin, Italy
| | - Ilaria Galliano
- Department of Public Health and Pediatric Sciences, University of Turin, Medical School, 10136 Turin, Italy
| | - Paola Montanari
- Department of Public Health and Pediatric Sciences, University of Turin, Medical School, 10136 Turin, Italy
| | - Martina Rosa Brusin
- Struttura Complessa, Pediatric University Regina Margherita Hospital, Piazza Polonia 94, 1016 Turin, Italy
| | - Serena Finotti
- Department of Public Health and Pediatric Sciences, University of Turin, Medical School, 10136 Turin, Italy
| | - Giulia Paderi
- Department of Public Health and Pediatric Sciences, University of Turin, Medical School, 10136 Turin, Italy
| | - Clara Gabiano
- Struttura Complessa, Pediatric University Regina Margherita Hospital, Piazza Polonia 94, 1016 Turin, Italy
| |
Collapse
|
6
|
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.
Collapse
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.
| |
Collapse
|
7
|
A Melting Curve-Based Multiplex RT-qPCR Assay for Simultaneous Detection of Four Human Coronaviruses. Int J Mol Sci 2016; 17:ijms17111880. [PMID: 27886052 PMCID: PMC5133880 DOI: 10.3390/ijms17111880] [Citation(s) in RCA: 57] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2016] [Revised: 10/30/2016] [Accepted: 11/01/2016] [Indexed: 01/17/2023] Open
Abstract
Human coronaviruses HCoV-OC43, HCoV-229E, HCoV-NL63 and HCoV-HKU1 are common respiratory viruses associated with acute respiratory infection. They have a global distribution. Rapid and accurate diagnosis of HCoV infection is important for the management and treatment of hospitalized patients with HCoV infection. Here, we developed a melting curve-based multiplex RT-qPCR assay for simultaneous detection of the four HCoVs. In the assay, SYTO 9 was used to replace SYBR Green I as the fluorescent dye, and GC-modified primers were designed to improve the melting temperature (Tm) of the specific amplicon. The four HCoVs were clearly distinguished by characteristic melting peaks in melting curve analysis. The detection sensitivity of the assay was 3 × 102 copies for HCoV-OC43, and 3 × 101 copies for HCoV-NL63, HCoV-229E and HCoV-HKU1 per 30 μL reaction. Clinical evaluation and sequencing confirmation demonstrated that the assay was specific and reliable. The assay represents a sensitive and reliable method for diagnosis of HCoV infection in clinical samples.
Collapse
|