Comparison of Two Real-Time PCR Assays Targeting Ribosomal Sequences for the Identification of Cystoisospora belli in Human Stool Samples
Abstract
:1. Introduction
2. Results
2.1. Sensitivity and Specificity of the Real-Time PCR Assays as well as Accuracy-Adjusted Prevalence Calculated Applying Latent Class Analysis and Agreement Kappa between the Assays
2.2. Comparison of the Recorded Cycle Threshold (Ct) Values
3. Discussion
4. Materials and Methods
4.1. Study Population
4.2. Nucleic Acid Extraction
4.3. Applied Real-Time PCR Assays
4.4. Exclusion Criteria
4.5. Statistics
4.6. Ethics
5. Conclusions
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
Appendix A
Positive Control Sequence Insert |
---|
5′-GGCGCTGTGGGGATATTCCCTGCAGCATGTCTGTTTCAGTGTCTCTGAAGTTTCAAGTTCTGCTCACGCGCTTCTGGGGGTGTCTCTGGAATACGCGTGTGGCAGTGTGACTGGATGTCTTGGGTGTTGAGAAACAAGCTACTTGTGCTTCTAGAAAGCCGAACGTCATCCGAAATAGTCACAGCGGCGTTTACGCGATCAAACAGTGTTGAGTTGTGTCCCGAACATCTTTG-3′ |
References
- Dubey, J.P.; Almeria, S. Cystoisospora belli infections in humans: The past 100 years. Parasitology 2019, 146, 1490–1527. [Google Scholar] [CrossRef]
- Lindsay, D.S. Cystoisospora species insights from development in vitro. Front. Vet. Sci. 2019, 5, 335. [Google Scholar] [CrossRef] [PubMed] [Green Version]
- Gassama, A.; Sow, P.S.; Fall, F.; Camara, P.; Guèye-N’diaye, A.; Seng, R.; Samb, B.; M’Boup, S.; Aïdara-Kane, A. Ordinary and opportunistic enteropathogens associated with diarrhea in Senegalese adults in relation to human immunodeficiency virus serostatus. Int. J. Infect. Dis. 2001, 5, 192–198. [Google Scholar] [CrossRef] [Green Version]
- Wumba, R.; Longo-Mbenza, B.; Menotti, J.; Mandina, M.; Kintoki, F.; Situakibanza, N.H.; Kakicha, M.K.; Zanga, J.; Mbanzulu-Makola, K.; Nseka, T.; et al. Epidemiology, clinical, immune, and molecular profiles of microsporidiosis and cryptosporidiosis among HIV/AIDS patients. Int. J. Gen. Med. 2012, 5, 603–611. [Google Scholar]
- Wumba, R.; Longo-Mbenza, B.; Mandina, M.; Odio, W.T.; Biligui, S.; Sala, J.; Breton, J.; Thellier, M. Intestinal parasites infections in hospitalized AIDS patients in Kinshasa, Democratic Republic of Congo. Parasite 2010, 17, 321–328. [Google Scholar] [CrossRef] [Green Version]
- Rivero-Rodríguez, Z.; Hernández, A.; Bracho, Á.; Salazar, S.; Villalobos, R. Prevalence of intestinal microsporidia and other intestinal parasites in hiv positive patients from Maracaibo, Venezuela. Biomedica 2013, 33, 538–545. [Google Scholar] [PubMed] [Green Version]
- Saksirisampant, W.; Prownebon, J.; Saksirisampant, P.; Mungthin, M.; Siripatanapipong, S.; Leelayoova, S. Intestinal parasitic infections: Prevalences in HIV/AIDS patients in a Thai AIDS-care centre. Ann. Trop. Med. Parasitol. 2009, 103, 573–581. [Google Scholar] [CrossRef] [PubMed]
- Moreno-Camacho, A.; López-Vélez, R.; Muñoz Sanz, A.; Labarga-Echevarría, P. Intestinal parasitic infections and leishmaniasis in patients with HIV infection. Enferm. Infecc. Y Microbiol. Clin. 1998, 16 (Suppl. S1), 52–60. [Google Scholar]
- Raccurt, C.P.; Fouché, B.; Agnamey, P.; Menotti, J.; Chouaki, T.; Totet, A.; Pape, J.W. Presence of Enterocytozoon bieneusi associated with intestinal coccidia in patients with chronic diarrhea visiting an HIV center in Haiti. Am. J. Trop. Med. Hyg. 2008, 79, 579–580. [Google Scholar] [CrossRef] [PubMed] [Green Version]
- Konate, A.; Minta, D.; Diarra, M.; Dolo, A.; Dembele, M.; Diarra, B.; Maiga, M.Y.; Traore, H.A.; Doumbo, O. Intestinal parasitosis during AIDS diarrhoea. Bull. Soc. Pathol. Exot. 2005, 98, 33–35. [Google Scholar] [PubMed]
- Gassama, A.; Thiaw, B.; Dia, N.M.; Fall, F.; Camara, P.; Hovette, P.; Perret, J.L.; Gueye-Ndiaye, A.; Mboup, S.; Sow, P.S.; et al. Infective etiology of diarrhea in adults with HIV infection in Dakar: A case-control study on 594 patients. Dakar Med. 2001, 46, 46–50. [Google Scholar] [PubMed]
- Höfler, W. Current questions in parasitology and infection prevention. Das Offentliche Gesundh. 1990, 52, 432–437. [Google Scholar]
- Koltas, I.S.; Elgun, G.; Demirkazık, M. The importance of real-time polymerase chain reaction method in diagnosis of intestinal parasites in cases with diarrhea. Trop. Biomed. 2017, 34, 895–902. [Google Scholar] [PubMed]
- Dokmaikaw, A.; Suntaravitun, P. Prevalence of Parasitic contamination of cockroaches collected from fresh markets in Chachoengsao province, Thailand. Kobe J. Med. Sci. 2020, 65, E118–E123. [Google Scholar] [PubMed]
- Teichroeb, J.A.; Kutz, S.J.; Parkar, U.; Thompson, R.C.; Sicotte, P. Ecology of the gastrointestinal parasites of Colobus vellerosus at Boabeng-Fiema, Ghana: Possible anthropozoonotic transmission. Am. J. Phys. Anthropol. 2009, 140, 498–507. [Google Scholar] [CrossRef] [PubMed]
- Noor, M.; Katzman, P.J.; Huber, A.R.; Findeis-Hosey, J.J.; Whitney-Miller, C.; Gonzalez, R.S.; Zhou, Z.; N’kodia, H.D.; Skonick, K.; Abell, R.L.; et al. Unexpectedly high prevalence of Cystoisospora belli infection in acalculous gallbladders of immunocompetent patients. Am. J. Clin. Pathol. 2019, 151, 100–107. [Google Scholar] [CrossRef] [PubMed] [Green Version]
- Akateh, C.; Arnold, C.A.; Benissan-Messan, D.; Michaels, A.; Black, S.M. Cystoisospora belli gallbladder infection in a liver transplant donor. Case Rep. Infect. Dis. 2018, 2018, 3170238. [Google Scholar] [CrossRef] [PubMed]
- Swanson, E.A.; March, J.K.; Clayton, F.; Couturier, M.R.; Arcega, R.; Smith, R.; Evason, K.J. Epithelial inclusions in gallbladder specimens mimic parasite infection: Histologic and molecular examination of reported Cystoisospora belli infection in gallbladders of immunocompetent patients. Am. J. Surg. Pathol. 2018, 42, 1346–1352. [Google Scholar] [CrossRef]
- Gopinath, A.; Mubeen, A.; Baskovich, B.; Ginn, A.; Shukri, A.; Menes, M.; Kenneth, K.; Makary, R.; Herrera, G.A.; Masood, S.; et al. Ultrastructural characteristics of gallbladder epithelial inclusions mimicking Cystoisospora. Am. J. Clin. Pathol. 2020, 153, 88–93. [Google Scholar] [CrossRef] [Green Version]
- Velásquez, J.N.; di Risio, C.A.; Etchart, C.B.; Chertcoff, A.V.; Nigro, M.G.; Pantano, M.L.; Ledesma, B.A.; Vittar, N.; Carnevale, S. First report of Cystoisospora belli parasitemia in a patient with acquired immunodeficiency syndrome. Acta Parasitol. 2016, 61, 172–177. [Google Scholar] [CrossRef] [PubMed]
- Cama, V.A.; Mathison, B.A. Infections by intestinal coccidia and Giardia duodenalis. Clin. Lab. Med. 2015, 35, 423–444. [Google Scholar] [CrossRef] [PubMed] [Green Version]
- Curry, A.; Smith, H.V. Emerging pathogens: Isospora, Cyclospora and microsporidia. Parasitology 1998, 117, S143–S159. [Google Scholar] [CrossRef] [PubMed]
- Legua, P.; Seas, C. Cystoisospora and Cyclospora. Curr. Opin. Infect. Dis. 2013, 26, 479–483. [Google Scholar] [CrossRef]
- Woon, S.A.; Yang, R.; Ryan, U.; Boan, P.; Prentice, D. Chronic Cystoisospora belli infection in an immunocompetent Myanmar refugee—Microscopy is not sensitive enough. BMC Infect. Dis. 2016, 16, 221. [Google Scholar] [CrossRef] [PubMed] [Green Version]
- Resende, D.V.; Pedrosa, A.L.; Correia, D.; Cabrine-Santos, M.; Lages-Silva, E.; Meira, W.S.; Oliveira-Silva, M.B. Polymorphisms in the 18S rDNA gene of Cystoisospora belli and clinical features of cystoisosporosis in HIV-infected patients. Parasitol. Res. 2011, 108, 679–685. [Google Scholar] [CrossRef] [PubMed]
- Samarasinghe, B.; Johnson, J.; Ryan, U. Phylogenetic analysis of Cystoisospora species at the rRNA ITS1 locus and development of a PCR-RFLP assay. Exp. Parasitol. 2008, 118, 592–595. [Google Scholar] [CrossRef]
- Agholi, M.; Shahabadi, S.N.; Motazedian, M.H.; Hatam, G.R. Prevalence of enteric protozoan oocysts with special reference to Sarcocystis cruzi among fecal samples of diarrheic immunodeficient patients in Iran. Korean J. Parasitol. 2016, 54, 339–344. [Google Scholar] [CrossRef] [PubMed] [Green Version]
- Taniuchi, M.; Verweij, J.J.; Sethabutr, O.; Bodhidatta, L.; Garcia, L.; Maro, A.; Kumburu, H.; Gratz, J.; Kibiki, G.; Houpt, E.R. Multiplex polymerase chain reaction method to detect Cyclospora, Cystoisospora, and microsporidia in stool samples. Diagn. Microbiol. Infect. Dis. 2011, 71, 386–390. [Google Scholar] [CrossRef] [PubMed] [Green Version]
- Verweij, J.J.; Stensvold, C.R. Molecular testing for clinical diagnosis and epidemiological investigations of intestinal parasitic infections. Clin. Microbiol. Rev. 2014, 27, 371–418. [Google Scholar] [CrossRef] [PubMed] [Green Version]
- Murphy, S.C.; Hoogestraat, D.R.; Sengupta, D.J.; Prentice, J.; Chakrapani, A.; Cookson, B.T. Molecular diagnosis of cystoisosporiasis using extended-range PCR screening. J. Mol. Diagn. 2011, 13, 359–362. [Google Scholar] [CrossRef] [PubMed]
- Müller, A.; Bialek, R.; Fätkenheuer, G.; Salzberger, B.; Diehl, V.; Franzen, C. Detection of Isospora belli by polymerase chain reaction using primers based on small-subunit ribosomal RNA sequences. Eur. J. Clin. Microbiol. Infect. Dis. 2000, 19, 631–634. [Google Scholar] [CrossRef] [PubMed]
- Lalonde, L.F.; Reyes, J.; Gajadhar, A.A. Application of a qPCR assay with melting curve analysis for detection and differentiation of protozoan oocysts in human fecal samples from Dominican Republic. Am. J. Trop. Med. Hyg. 2013, 89, 892–898. [Google Scholar] [CrossRef] [PubMed] [Green Version]
- Ten Hove, R.J.; van Lieshout, L.; Brienen, E.A.; Perez, M.A.; Verweij, J.J. Real-time polymerase chain reaction for detection of Isospora belli in stool samples. Diagn. Microbiol. Infect. Dis. 2008, 61, 280–283. [Google Scholar] [CrossRef] [PubMed]
- Stark, D.; Roberts, T.; Ellis, J.T.; Marriott, D.; Harkness, J. Evaluation of the EasyScreen™ enteric parasite detection kit for the detection of Blastocystis spp., Cryptosporidium spp., Dientamoeba fragilis, Entamoeba complex, and Giardia intestinalis from clinical stool samples. Diagn. Microbiol. Infect. Dis. 2014, 78, 149–152. [Google Scholar] [CrossRef] [PubMed]
- Huibers, M.H.W.; Moons, P.; Maseko, N.; Gushu, M.B.; Iwajomo, O.H.; Heyderman, R.S.; Boele van Hensbroek, M.; Brienen, E.A.; van Lieshout, L.; Calis, J.C.J. Multiplex real-time PCR detection of intestinal protozoa in HIV-infected children in Malawi: Enterocytozoon bieneusi is common and associated with gastrointestinal complaints and may delay BMI (nutritional status) recovery. Pediatr. Infect. Dis. J. 2018, 37, 910–915. [Google Scholar] [CrossRef] [Green Version]
- Menu, E.; Mary, C.; Toga, I.; Raoult, D.; Ranque, S.; Bittar, F. Evaluation of two DNA extraction methods for the PCR-based detection of eukaryotic enteric pathogens in fecal samples. BMC Res. Notes 2018, 11, 206. [Google Scholar] [CrossRef] [Green Version]
- Hahn, A.; Podbielski, A.; Meyer, T.; Zautner, A.E.; Loderstädt, U.; Schwarz, N.G.; Krüger, A.; Cadar, D.; Frickmann, H. On detection thresholds-a review on diagnostic approaches in the infectious disease laboratory and the interpretation of their results. Acta Trop. 2020, 205, 105377. [Google Scholar] [CrossRef] [PubMed]
- Qu, Y.; Tan, M.; Kutner, M.H. Random effects models in latent class analysis for evaluating accuracy of diagnostic tests. Biometrics 1996, 52, 797–810. [Google Scholar] [CrossRef] [PubMed]
- Landis, J.R.; Koch, G.G. The measurement of observer agreement for categorical data. Biometrics 1977, 33, 159–174. [Google Scholar] [CrossRef] [PubMed] [Green Version]
- Eberhardt, K.A.; Sarfo, F.S.; Dompreh, A.; Kuffour, E.O.; Geldmacher, C.; Soltau, M.; Schachscheider, M.; Drexler, J.F.; Eis-Hübinger, A.M.; Häussinger, D.; et al. Helicobacter pylori coinfection is associated with decreased markers of immune activation in ART-naive HIV-positive and in HIV-negative individuals in Ghana. Clin. Infect. Dis. 2015, 61, 1615–1623. [Google Scholar] [CrossRef] [PubMed] [Green Version]
- Sarfo, F.S.; Eberhardt, K.A.; Dompreh, A.; Kuffour, E.O.; Soltau, M.; Schachscheider, M.; Drexler, J.F.; Eis-Hübinger, A.M.; Häussinger, D.; Oteng-Seifah, E.E.; et al. Helicobacter pylori infection is associated with higher CD4 T cell counts and lower HIV-1 viral loads in ART-naïve HIV-positive patients in Ghana. PLoS ONE 2015, 10, e0143388. [Google Scholar] [CrossRef] [Green Version]
- Tanida, K.; Hahn, A.; Eberhardt, K.A.; Tannich, E.; Landt, O.; Kann, S.; Feldt, T.; Sarfo, F.S.; Di Cristanziano, V.; Frickmann, H.; et al. Comparative assessment of in-house real-time PCRs targeting enteric disease-associated microsporidia in human stool samples. Pathogens 2021, 10, 656. [Google Scholar] [CrossRef]
- Schawaller, M.; Wiemer, D.; Hagen, R.M.; Frickmann, H. Infectious diseases in German military personnel after predominantly tropical deployments: A retrospective assessment over 13 years. BMJ Mil Health 2020. [Google Scholar] [CrossRef]
- Utzinger, J.; Botero-Kleiven, S.; Castelli, F.; Chiodini, P.L.; Edwards, H.; Köhler, N.; Gulletta, M.; Lebbad, M.; Manser, M.; Matthys, B.; et al. Microscopic diagnosis of sodium acetate-acetic acid-formalin-fixed stool samples for helminths and intestinal protozoa: A comparison among European reference laboratories. Clin. Microbiol. Infect. 2010, 16, 267–273. [Google Scholar] [CrossRef] [Green Version]
- Frickmann, H.; Hoffmann, T.; Köller, T.; Hahn, A.; Podbielski, A.; Landt, O.; Loderstädt, U.; Tannich, E. Comparison of five commercial real-time PCRs for in-vitro diagnosis of Entamoeba histolytica, Giardia duodenalis, Cryptosporidium spp., Cyclospora cayetanensis, and Dientamoeba fragilis in human stool samples. Travel. Med. Infect. Dis. 2021, 41, 102042. [Google Scholar] [CrossRef] [PubMed]
- Frickmann, H.; Hinz, R.; Hagen, R.M. Comparison of an automated nucleic acid extraction system with the column-based procedure. Eur. J. Microbiol. Immunol. 2015, 5, 94–102. [Google Scholar] [CrossRef] [PubMed] [Green Version]
- Loderstädt, U.; Hagen, R.M.; Hahn, A.; Frickmann, H. New developments in PCR-based diagnostics for bacterial pathogens causing gastrointestinal infections-a narrative mini-review on challenges in the tropics. Trop. Med. Infect. Dis. 2021, 6, 96. [Google Scholar] [CrossRef] [PubMed]
- Bossuyt, P.M.; Reitsma, J.B.; Bruns, D.E.; Gatsonis, C.A.; Glasziou, P.P.; Irwig, L.; Lijmer, J.G.; Moher, D.; Rennie, D.; De Vet, H.C.W.; et al. STARD 2015: An updated list of essential items for reporting diagnostic accuracy studies. BMJ 2015, 351, h5527. [Google Scholar] [CrossRef] [PubMed] [Green Version]
- Niesters, H.G. Quantitation of viral load using real-time amplification techniques. Methods 2001, 25, 419–429. [Google Scholar] [CrossRef]
PCR | n | Positives (%) | Sensitivity (0.95 CI) | Specificity (0.95 CI) | Kappa (0.95 CI) |
---|---|---|---|---|---|
5.8S rRNA gene/ITS-2 sequence PCR | 967 | 29 (3.00) | 0.928 (0, 1) | 1 (n.e.) | 0.933 (0.868, 0.998) |
ITS-2 sequence PCR | 967 | 33 (3.41) | 1 (0, 1) | 0.998 (0,1) | |
Prevalence (0.95 CI) | 0.032 (0.010, 0.092) |
PCR | n | Mean (SD) | Median (Min, Max) |
---|---|---|---|
5.8S rRNA gene/ITS-2 sequence PCR | 29 | 31.57 (4.14) | 31.45 (23.98, 38.24) |
ITS-2 sequence PCR | 33 | 30.66 (4.27) | 31.33 (23.62, 36.89) |
Forward Primer Name | Forward Primer Sequence | Reverse Primer Name | Reverse Primer Sequence | Probe Name | Probe Sequence |
---|---|---|---|---|---|
Real-time PCR targeting a combined 5.8S rRNA gene/ITS-2 sequence fragment of C. belli | |||||
Cys Ib-213-F | 5′-GGATATTCCCTGCAGCATGT-3′ | Cys Ib-213-R | 5′-CGGGACACAACTCAACACTG-3′ | Cys Ib-213-P | 5′-GTCACAGCGGCGTTTACGC-3′ |
Real-time PCR targeting the ITS-2 sequence of C. belli | |||||
Cys Ib-40-F | 5′-ATATTCCCTGCAGCATGTCTGTTT-3′ | Cys Ib-129-R | 5′-CCACACGCGTATTCCAGAGA-3′ | Cys Ib-81-P | 5′-CAAGTTCTGCTCACGCGCTTCTGG-3′ |
Publisher’s Note: MDPI stays neutral with regard to jurisdictional claims in published maps and institutional affiliations. |
© 2021 by the authors. Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https://creativecommons.org/licenses/by/4.0/).
Share and Cite
Blohm, M.; Hahn, A.; Hagen, R.M.; Eberhardt, K.A.; Rohde, H.; Leboulle, G.; Feldt, T.; Sarfo, F.S.; Di Cristanziano, V.; Frickmann, H.; et al. Comparison of Two Real-Time PCR Assays Targeting Ribosomal Sequences for the Identification of Cystoisospora belli in Human Stool Samples. Pathogens 2021, 10, 1053. https://doi.org/10.3390/pathogens10081053
Blohm M, Hahn A, Hagen RM, Eberhardt KA, Rohde H, Leboulle G, Feldt T, Sarfo FS, Di Cristanziano V, Frickmann H, et al. Comparison of Two Real-Time PCR Assays Targeting Ribosomal Sequences for the Identification of Cystoisospora belli in Human Stool Samples. Pathogens. 2021; 10(8):1053. https://doi.org/10.3390/pathogens10081053
Chicago/Turabian StyleBlohm, Martin, Andreas Hahn, Ralf Matthias Hagen, Kirsten Alexandra Eberhardt, Holger Rohde, Gérard Leboulle, Torsten Feldt, Fred Stephen Sarfo, Veronica Di Cristanziano, Hagen Frickmann, and et al. 2021. "Comparison of Two Real-Time PCR Assays Targeting Ribosomal Sequences for the Identification of Cystoisospora belli in Human Stool Samples" Pathogens 10, no. 8: 1053. https://doi.org/10.3390/pathogens10081053
APA StyleBlohm, M., Hahn, A., Hagen, R. M., Eberhardt, K. A., Rohde, H., Leboulle, G., Feldt, T., Sarfo, F. S., Di Cristanziano, V., Frickmann, H., & Loderstädt, U. (2021). Comparison of Two Real-Time PCR Assays Targeting Ribosomal Sequences for the Identification of Cystoisospora belli in Human Stool Samples. Pathogens, 10(8), 1053. https://doi.org/10.3390/pathogens10081053