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Tavares ER, de Lima TF, Bartolomeu-Gonçalves G, de Castro IM, de Lima DG, Borges PHG, Nakazato G, Kobayashi RKT, Venancio EJ, Tarley CRT, de Almeida ERD, Pelisson M, Vespero EC, Simão ANC, Perugini MRE, Kerbauy G, Fornazieri MA, Tognim MCB, Góes VM, de Souza TDACB, Oliveira DBL, Durigon EL, Faccin-Galhardi LC, Yamauchi LM, Yamada-Ogatta SF. Development of a Melting-Curve-Based Multiplex Real-Time PCR Assay for the Simultaneous Detection of Viruses Causing Respiratory Infection. Microorganisms 2023; 11:2692. [PMID: 38004704 PMCID: PMC10672821 DOI: 10.3390/microorganisms11112692] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2023] [Revised: 10/19/2023] [Accepted: 10/30/2023] [Indexed: 11/26/2023] Open
Abstract
The prompt and accurate identification of the etiological agents of viral respiratory infections is a critical measure in mitigating outbreaks. In this study, we developed and clinically evaluated a novel melting-curve-based multiplex real-time PCR (M-m-qPCR) assay targeting the RNA-dependent RNA polymerase (RdRp) and nucleocapsid phosphoprotein N of SARS-CoV-2, the Matrix protein 2 of the Influenza A virus, the RdRp domain of the L protein from the Human Respiratory Syncytial Virus, and the polyprotein from Rhinovirus B genes. The analytical performance of the M-m-qPCR underwent assessment using in silico analysis and a panel of reference and clinical strains, encompassing viral, bacterial, and fungal pathogens, exhibiting 100% specificity. Moreover, the assay showed a detection limit of 10 copies per reaction for all targeted pathogens using the positive controls. To validate its applicability, the assay was further tested in simulated nasal fluid spiked with the viruses mentioned above, followed by validation on nasopharyngeal swabs collected from 811 individuals. Among them, 13.4% (109/811) tested positive for SARS-CoV-2, and 1.1% (9/811) tested positive for Influenza A. Notably, these results showed 100% concordance with those obtained using a commercial kit. Therefore, the M-m-qPCR exhibits great potential for the routine screening of these respiratory viral pathogens.
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Affiliation(s)
- Eliandro Reis Tavares
- Laboratory of Molecular Biology of Microorganisms, Department of Microbiology, State University of Londrina, Londrina 86057-970, Brazil; (E.R.T.); (D.G.d.L.)
| | - Thiago Ferreira de Lima
- Graduate Program in Microbiology, Department of Microbiology, State University of Londrina, Londrina 86057-970, Brazil; (T.F.d.L.); (I.M.d.C.); (P.H.G.B.); (G.N.); (R.K.T.K.); (L.C.F.-G.)
| | - Guilherme Bartolomeu-Gonçalves
- Graduate Program in Clinical and Laboratory Pathophysiology, Department of Pathology, Clinical and Toxicological Analysis, State University of Londrina, Londrina 86038-350, Brazil; (G.B.-G.); (E.J.V.); (M.P.); (E.C.V.); (A.N.C.S.); (M.R.E.P.)
| | - Isabela Madeira de Castro
- Graduate Program in Microbiology, Department of Microbiology, State University of Londrina, Londrina 86057-970, Brazil; (T.F.d.L.); (I.M.d.C.); (P.H.G.B.); (G.N.); (R.K.T.K.); (L.C.F.-G.)
| | - Daniel Gaiotto de Lima
- Laboratory of Molecular Biology of Microorganisms, Department of Microbiology, State University of Londrina, Londrina 86057-970, Brazil; (E.R.T.); (D.G.d.L.)
| | - Paulo Henrique Guilherme Borges
- Graduate Program in Microbiology, Department of Microbiology, State University of Londrina, Londrina 86057-970, Brazil; (T.F.d.L.); (I.M.d.C.); (P.H.G.B.); (G.N.); (R.K.T.K.); (L.C.F.-G.)
| | - Gerson Nakazato
- Graduate Program in Microbiology, Department of Microbiology, State University of Londrina, Londrina 86057-970, Brazil; (T.F.d.L.); (I.M.d.C.); (P.H.G.B.); (G.N.); (R.K.T.K.); (L.C.F.-G.)
| | - Renata Katsuko Takayama Kobayashi
- Graduate Program in Microbiology, Department of Microbiology, State University of Londrina, Londrina 86057-970, Brazil; (T.F.d.L.); (I.M.d.C.); (P.H.G.B.); (G.N.); (R.K.T.K.); (L.C.F.-G.)
| | - Emerson José Venancio
- Graduate Program in Clinical and Laboratory Pathophysiology, Department of Pathology, Clinical and Toxicological Analysis, State University of Londrina, Londrina 86038-350, Brazil; (G.B.-G.); (E.J.V.); (M.P.); (E.C.V.); (A.N.C.S.); (M.R.E.P.)
| | | | | | - Marsileni Pelisson
- Graduate Program in Clinical and Laboratory Pathophysiology, Department of Pathology, Clinical and Toxicological Analysis, State University of Londrina, Londrina 86038-350, Brazil; (G.B.-G.); (E.J.V.); (M.P.); (E.C.V.); (A.N.C.S.); (M.R.E.P.)
| | - Eliana Carolina Vespero
- Graduate Program in Clinical and Laboratory Pathophysiology, Department of Pathology, Clinical and Toxicological Analysis, State University of Londrina, Londrina 86038-350, Brazil; (G.B.-G.); (E.J.V.); (M.P.); (E.C.V.); (A.N.C.S.); (M.R.E.P.)
| | - Andrea Name Colado Simão
- Graduate Program in Clinical and Laboratory Pathophysiology, Department of Pathology, Clinical and Toxicological Analysis, State University of Londrina, Londrina 86038-350, Brazil; (G.B.-G.); (E.J.V.); (M.P.); (E.C.V.); (A.N.C.S.); (M.R.E.P.)
| | - Márcia Regina Eches Perugini
- Graduate Program in Clinical and Laboratory Pathophysiology, Department of Pathology, Clinical and Toxicological Analysis, State University of Londrina, Londrina 86038-350, Brazil; (G.B.-G.); (E.J.V.); (M.P.); (E.C.V.); (A.N.C.S.); (M.R.E.P.)
| | - Gilselena Kerbauy
- Graduate Program in Nursing, Department of Nursing, State University of Londrina, Londrina 86038-350, Brazil;
| | - Marco Aurélio Fornazieri
- Graduate Program in Health Sciences, Department of Clinical Surgery, State University of Londrina, Londrina 86038-350, Brazil;
| | | | | | | | - Danielle Bruna Leal Oliveira
- Albert Einstein Hospital, São Paulo 05652-900, Brazil;
- Laboratory of Clinical and Molecular Virology, University of São Paulo, São Paulo 05508-000, Brazil;
| | - Edison Luiz Durigon
- Laboratory of Clinical and Molecular Virology, University of São Paulo, São Paulo 05508-000, Brazil;
| | - Lígia Carla Faccin-Galhardi
- Graduate Program in Microbiology, Department of Microbiology, State University of Londrina, Londrina 86057-970, Brazil; (T.F.d.L.); (I.M.d.C.); (P.H.G.B.); (G.N.); (R.K.T.K.); (L.C.F.-G.)
| | - Lucy Megumi Yamauchi
- Laboratory of Molecular Biology of Microorganisms, Department of Microbiology, State University of Londrina, Londrina 86057-970, Brazil; (E.R.T.); (D.G.d.L.)
- Graduate Program in Microbiology, Department of Microbiology, State University of Londrina, Londrina 86057-970, Brazil; (T.F.d.L.); (I.M.d.C.); (P.H.G.B.); (G.N.); (R.K.T.K.); (L.C.F.-G.)
| | - Sueli Fumie Yamada-Ogatta
- Laboratory of Molecular Biology of Microorganisms, Department of Microbiology, State University of Londrina, Londrina 86057-970, Brazil; (E.R.T.); (D.G.d.L.)
- Graduate Program in Microbiology, Department of Microbiology, State University of Londrina, Londrina 86057-970, Brazil; (T.F.d.L.); (I.M.d.C.); (P.H.G.B.); (G.N.); (R.K.T.K.); (L.C.F.-G.)
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Otaguiri ES, Morguette AEB, Morey AT, Tavares ER, Kerbauy G, de Almeida Torres RSL, Chaves Júnior M, Tognim MCB, Góes VM, Krieger MA, Perugini MRE, Yamauchi LM, Yamada-Ogatta SF. Development of a melting-curve based multiplex real-time PCR assay for simultaneous detection of Streptococcus agalactiae and genes encoding resistance to macrolides and lincosamides. BMC Pregnancy Childbirth 2018; 18:126. [PMID: 29724169 PMCID: PMC5934892 DOI: 10.1186/s12884-018-1774-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2017] [Accepted: 04/25/2018] [Indexed: 01/25/2023] Open
Abstract
Background Streptococcus agalactiae or Group B Streptococcus (GBS) remains the leading cause of infections in newborns worldwilde. Prenatal GBS screening of pregnant women for vaginal-rectal colonization is recommended in many countries to manage appropriate intrapartum antimicrobial prophylaxis for those identified as carriers. In this study, a novel melting-curve based multiplex real-time PCR assay for the simultaneous detection of GBS and macrolide and lincosamide resistance markers was developed. The usefulness of the assay was evaluated for rapid and accurate prenatal GBS screening. Methods One hundred two pregnant women who were at 35–37 weeks of gestation were enrolled in this study. The analytical performance of the multiplex real-time PCR was first tested using a panel of reference and clinical bacterial and fungal strains. To test the clinical performance, vaginal-rectal swabs were obtained from pregnant women who were seen at the teaching hospital for regular prenatal care. The results of real-time were compared with those obtained from microbiological analyses. Results The real-time PCR assay showed 100% specificity and a limit of detection of 104 colony forming units equivalent per reaction. The prevalence of GBS colonization among the population studied was 15.7% (16/102) based on a positive culture and the real-time PCR results. Agreement between the two assays was found for 11 (68.75%) GBS colonized women. Using the culture-based results as a reference, the multiplex real-time PCR had a sensitivity of 91.7% (11/12, CI 59.7–99.6%), a specificity of 95.5% (86/90, CI 89.8–98.7%), a positive predictive value of 73.3% (11/15, CI 44.8–91.1%) and a negative predictive value of 98.9% (86/87, CI 92.9–99.9%). Conclusion The multiplex real-time PCR is a rapid, affordable and sensitive assay for direct detection of GBS in vaginal-rectal swabs. Electronic supplementary material The online version of this article (10.1186/s12884-018-1774-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Eliane Saori Otaguiri
- Departamento de Microbiologia, Centro de Ciências Biológicas, Universidade Estadual de Londrina, Londrina, Paraná, Brazil
| | - Ana Elisa Belotto Morguette
- Departamento de Microbiologia, Centro de Ciências Biológicas, Universidade Estadual de Londrina, Londrina, Paraná, Brazil
| | - Alexandre Tadachi Morey
- Departamento de Microbiologia, Centro de Ciências Biológicas, Universidade Estadual de Londrina, Londrina, Paraná, Brazil
| | - Eliandro Reis Tavares
- Departamento de Microbiologia, Centro de Ciências Biológicas, Universidade Estadual de Londrina, Londrina, Paraná, Brazil
| | - Gilselena Kerbauy
- Departamento de Enfermagem, Universidade Estadual de Londrina, Londrina, Paraná, Brazil
| | - Rosângela S L de Almeida Torres
- Laboratory of Bacteriology, Epidemiology Laboratory and Disease Control Division, Laboratório Central do Estado do Paraná - LACEN, Curitiba, PR, Brazil
| | - Mauricio Chaves Júnior
- Departamento de Medicina, Hospital Universitário de Maringá, Universidade Estadual de Maringá, Maringá, Brazil
| | | | | | | | - Marcia Regina Eches Perugini
- Departamento de Patologia, Análises Clínicas e Toxicológicas, Centro de Ciências da Saúde, Universidade Estadual de Londrina, Londrina, Paraná, Brazil
| | - Lucy Megumi Yamauchi
- Departamento de Microbiologia, Centro de Ciências Biológicas, Universidade Estadual de Londrina, Londrina, Paraná, Brazil
| | - Sueli Fumie Yamada-Ogatta
- Departamento de Microbiologia, Centro de Ciências Biológicas, Universidade Estadual de Londrina, Londrina, Paraná, Brazil. .,Departamento de Microbiologia, Universidade Estadual de Londrina, Centro de Ciências Biológicas, Rodovia Celso Garcia Cid, PR 445, km 380. CEP, Londrina, 86057-970, Brazil.
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