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Garg P, Bhasin SL, Malhotra P, Rana SS, Singh S, Sethi J, Sehgal R, Khurana S, Datta P. Multiplex PCR for gastrointestinal parasites in stool: Benchmarking against direct microscopy and simplex PCR. Diagn Microbiol Infect Dis 2024; 110:116475. [PMID: 39096665 DOI: 10.1016/j.diagmicrobio.2024.116475] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2024] [Revised: 06/29/2024] [Accepted: 07/29/2024] [Indexed: 08/05/2024]
Abstract
PURPOSE To develop and validate a multiplex conventional PCR assay to simultaneously detect Cryptosporidium spp., Entamoeba histolytica, and Giardia lamblia in diarrheal samples as a rapid, cost-effective, and sensitive diagnostic tool for prevalent co-infections for improved diagnostic accuracy and efficiency in resource-limited settings. METHODS Stool samples collected from patients with gastrointestinal symptoms after taking written consent, processed via wet mount, iodine mount, and PCR assays. Cohen's kappa statistical analysis was done to test agreement. RESULT Among 240 patients, 28.75% showed intestinal protozoa via Microscopy; Single-plex and multiplex PCR demonstrated 100% concordance, detecting 27.9%; confirmed by sequencing. Highest parasite positivity was observed in transplant and immunocompromised patients, with moderate to almost perfect agreement between microscopy and molecular methods. CONCLUSION Multiplex-conventional PCR offers superior sensitivity and specificity over microscopy and 100% concordance with single-plex PCR, enabling rapid, cost-effective diagnosis of multiple parasites from single stool sample. Its adoption could revolutionize parasitic infection management in routine diagnostics.
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Affiliation(s)
- Puja Garg
- Department of Medical Parasitology PGIMER, Chandigarh, 160012, India
| | - Sadhna Lal Bhasin
- Department of Paediatrics Gastroenterology PGIMER, Chandigarh, 160012, India
| | - Pankaj Malhotra
- Department of Clinical Haematology and Oncology PGIMER, Chandigarh, 160012, India
| | | | - Shreya Singh
- Department of Microbiology Dr. BR Ambedkar State Institute of Medical Sciences, Mohali, Punjab, 160062, India
| | - Jasmine Sethi
- Department of Medical Parasitology PGIMER, Chandigarh, 160012, India
| | - Rakesh Sehgal
- Department of Microbiology Aarupudai Veedu Medical College & Hospital, VMRF-DU, Puducherry, 607403, India
| | - Sumeeta Khurana
- Department of Medical Parasitology PGIMER, Chandigarh, 160012, India
| | - Priya Datta
- Department of Medical Parasitology PGIMER, Chandigarh, 160012, India.
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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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Aghazadeh M, Jones M, Perera S, Nair J, Tan L, Clark B, Curtis A, Jones J, Ellem J, Olma T, Stark D, Melki J, Coulston N, Baker R, Millar D. The Application of 3base™ Technology to Diagnose Eight of the Most Clinically Important Gastrointestinal Protozoan Infections. Int J Mol Sci 2023; 24:13387. [PMID: 37686192 PMCID: PMC10487386 DOI: 10.3390/ijms241713387] [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: 07/04/2023] [Revised: 08/15/2023] [Accepted: 08/25/2023] [Indexed: 09/10/2023] Open
Abstract
Globally, over 3.5 billion people are infected with intestinal parasites each year, resulting in over 200,000 deaths. Three of the most common protozoan pathogens that affect the gastrointestinal tract of humans are Cryptosporidium spp., Giardia intestinalis, and Entamoeba histolytica. Other protozoan agents that have been implicated in gastroenteritis in humans include Cyclospora cayetanensis, Dientamoeba fragilis, Blastocystis hominis, and the microsporidia Enterocytozoon bieneusi and Encephalitozoon intestinalis. Genetic Signatures previously developed a 3base™ multiplexed Real-Time PCR (mRT-PCR) enteric protozoan kit (EP001) for the detection of Giardia intestinalis/lamblia/duodenalis, Cryptosporidium spp., E. histolytica, D. fragilis, and B. hominis. We now describe improvements to this kit to produce a more comprehensive assay, including C. cayetanensis, E. bieneusi, and E. intestinalis, termed EP005. The clinical performance of EP005 was assessed using a set of 380 clinical samples against a commercially available PCR test and other in-house nucleic acid amplification tests where commercial tests were not available. All methods provided at least 90% agreement. EP005 had no cross-reactivity against 82 organisms commonly found in the gut. The EP005 method streamlines the detection of gastrointestinal parasites and addresses the many challenges of traditional microscopic detection, resulting in cost savings and significant improvements in patient care.
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Affiliation(s)
- Mahdis Aghazadeh
- Genetic Signatures, 7 Eliza Street, Newtown, NSW 2042, Australia; (M.A.); (M.J.); (S.P.); (J.N.); (B.C.); (A.C.); (J.J.); (J.M.); (N.C.); (R.B.)
| | - Meghan Jones
- Genetic Signatures, 7 Eliza Street, Newtown, NSW 2042, Australia; (M.A.); (M.J.); (S.P.); (J.N.); (B.C.); (A.C.); (J.J.); (J.M.); (N.C.); (R.B.)
| | - Suneth Perera
- Genetic Signatures, 7 Eliza Street, Newtown, NSW 2042, Australia; (M.A.); (M.J.); (S.P.); (J.N.); (B.C.); (A.C.); (J.J.); (J.M.); (N.C.); (R.B.)
| | - Jiny Nair
- Genetic Signatures, 7 Eliza Street, Newtown, NSW 2042, Australia; (M.A.); (M.J.); (S.P.); (J.N.); (B.C.); (A.C.); (J.J.); (J.M.); (N.C.); (R.B.)
| | - Litty Tan
- Genetic Signatures, 7 Eliza Street, Newtown, NSW 2042, Australia; (M.A.); (M.J.); (S.P.); (J.N.); (B.C.); (A.C.); (J.J.); (J.M.); (N.C.); (R.B.)
| | - Brett Clark
- Genetic Signatures, 7 Eliza Street, Newtown, NSW 2042, Australia; (M.A.); (M.J.); (S.P.); (J.N.); (B.C.); (A.C.); (J.J.); (J.M.); (N.C.); (R.B.)
| | - Angela Curtis
- Genetic Signatures, 7 Eliza Street, Newtown, NSW 2042, Australia; (M.A.); (M.J.); (S.P.); (J.N.); (B.C.); (A.C.); (J.J.); (J.M.); (N.C.); (R.B.)
| | - Jackson Jones
- Genetic Signatures, 7 Eliza Street, Newtown, NSW 2042, Australia; (M.A.); (M.J.); (S.P.); (J.N.); (B.C.); (A.C.); (J.J.); (J.M.); (N.C.); (R.B.)
| | - Justin Ellem
- Microbiology Department, Westmead Hospital, Westmead, NSW 2145, Australia; (J.E.); (T.O.)
| | - Tom Olma
- Microbiology Department, Westmead Hospital, Westmead, NSW 2145, Australia; (J.E.); (T.O.)
| | - Damien Stark
- St. Vincent’s Pathology, Level 6, Xavier Building, 390 Victoria Street, Darlinghurst, NSW 2010, Australia;
| | - John Melki
- Genetic Signatures, 7 Eliza Street, Newtown, NSW 2042, Australia; (M.A.); (M.J.); (S.P.); (J.N.); (B.C.); (A.C.); (J.J.); (J.M.); (N.C.); (R.B.)
| | - Neralie Coulston
- Genetic Signatures, 7 Eliza Street, Newtown, NSW 2042, Australia; (M.A.); (M.J.); (S.P.); (J.N.); (B.C.); (A.C.); (J.J.); (J.M.); (N.C.); (R.B.)
| | - Rohan Baker
- Genetic Signatures, 7 Eliza Street, Newtown, NSW 2042, Australia; (M.A.); (M.J.); (S.P.); (J.N.); (B.C.); (A.C.); (J.J.); (J.M.); (N.C.); (R.B.)
| | - Douglas Millar
- Genetic Signatures, 7 Eliza Street, Newtown, NSW 2042, Australia; (M.A.); (M.J.); (S.P.); (J.N.); (B.C.); (A.C.); (J.J.); (J.M.); (N.C.); (R.B.)
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Influence of Selected Factors on the Survival Assessment and Detection of Giardia intestinalis DNA in Axenic Culture. Pathogens 2023; 12:pathogens12020316. [PMID: 36839588 PMCID: PMC9968169 DOI: 10.3390/pathogens12020316] [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: 01/11/2023] [Revised: 02/09/2023] [Accepted: 02/13/2023] [Indexed: 02/17/2023] Open
Abstract
Giardia intestinalis is one of the most common food-borne protozoa. The sensitivity of pathogens to physical and chemical factors is the basis for developing measures to reduce the incidence of the population. Several methods are available to detect the presence of G. intestinalis. The study determines the influence of 22 selected factors on the survival assessment and detection of G. intestinalis DNA in trophozoites axenically cultured. The influence of a given factor on the test result was observed in the case of 17 factors (77.3%) in the microscopic method, while only in the case of 3 (13.6%) substances in the real-time PCR method. Prevention of G. intestinalis infections, e.g., by ensuring food and water safety, is a crucial issue affecting public health. The experiment was conducted on trophozoites as the first approach. It is necessary to continue research and observe the epidemiological situation. In future studies, the impact of the studied factors on the survival assessment and detection of Giardia intestinalis DNA in axenically cultured cysts should be determined.
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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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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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