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Mota TF, Brodskyn CI, Morello LG, Marchini FK, Krieger MA, de Cássia Pontello Rampazzo R, Fraga DBM. Multiplex qPCR assay to determine Leishmania infantum load in Lutzomyia longipalpis sandfly samples. MEDICAL AND VETERINARY ENTOMOLOGY 2022; 36:176-184. [PMID: 35089617 DOI: 10.1111/mve.12564] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Revised: 12/27/2021] [Accepted: 01/07/2022] [Indexed: 06/14/2023]
Abstract
The study aimed to develop a multiplex qPCR to detect Leishmania infantum load in different sandfly sample settings using Leishmania kDNA and sandfly vacuolar ATPase (VATP) subunit C as internal control gene. The amplification of Lutzomyia longipalpis VATP gene was evaluated together with Leishmania infantum kDNA in a multiplex reaction. The concentration of VATP gene oligonucleotides was adjusted until no statistically significant difference was observed between all multiplex standard curves and singleplex curves, that is, only kDNA amplification. Limit of detection (LoD) was measured using a probit model and a cut-off defined by receiver operating characteristic analysis. Limit of quantification (LoQ) was assessed by a linear model using the coefficient of variation threshold of 25%. After assuring VATP gene amplification, its primer-probe concentrations were best at 100 nM/10 nM, respectively. The cut-off Cq value for L. infantum kDNA was defined as 35.46 with 100% of sensitivity and specificity. A total of 95% LoD was determined to be of 0.162 parasites while LoQ was 5.858. Our VATP/kDNA multiplex qPCR assay shows that it can be used to evaluate both DNA integrity and determine L. infantum load in L. longipalpis even for low yielded samples, that is, individual midguts.
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Affiliation(s)
- Tiago Feitosa Mota
- Laboratório de Interação Parasito-Hospedeiro e Epidemiologia (LaIPHE), Instituto Gonçalo Moniz (IGM), FIOCRUZ-BA, Rua Waldemar Falcão, Salvador, Brazil
| | - Claudia Ida Brodskyn
- Laboratório de Interação Parasito-Hospedeiro e Epidemiologia (LaIPHE), Instituto Gonçalo Moniz (IGM), FIOCRUZ-BA, Rua Waldemar Falcão, Salvador, Brazil
| | - Luis Gustavo Morello
- Instituto Carlos Chagas (ICC), FIOCRUZ-PR, Rua Prof. Algacyr Munhoz Mader, Curitiba, Brazil
- Instituto de Biologia Molecular do Paraná (IBMP), Rua Professor Algacyr Munhoz Mader, Curitiba, Brazil
| | - Fabricio Klerynton Marchini
- Instituto Carlos Chagas (ICC), FIOCRUZ-PR, Rua Prof. Algacyr Munhoz Mader, Curitiba, Brazil
- Instituto de Biologia Molecular do Paraná (IBMP), Rua Professor Algacyr Munhoz Mader, Curitiba, Brazil
| | - Marco Aurelio Krieger
- Instituto Carlos Chagas (ICC), FIOCRUZ-PR, Rua Prof. Algacyr Munhoz Mader, Curitiba, Brazil
| | | | - Deborah Bittencourt Mothé Fraga
- Laboratório de Interação Parasito-Hospedeiro e Epidemiologia (LaIPHE), Instituto Gonçalo Moniz (IGM), FIOCRUZ-BA, Rua Waldemar Falcão, Salvador, Brazil
- Departamento de Medicina Veterinária Preventiva e Produção Animal, Escola de Medicina Veterinária e Zootecnia, Universidade Federal da Bahia (UFBA), Salvador, Brazil
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PCR enhancers: Types, mechanisms, and applications in long-range PCR. Biochimie 2022; 197:130-143. [DOI: 10.1016/j.biochi.2022.02.009] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Revised: 02/06/2022] [Accepted: 02/24/2022] [Indexed: 12/21/2022]
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Abstract
L. donovani is an intracellular protozoan parasite, that causes visceral leishmaniasis (VL), and consequently, post-kala azar dermal leishmaniasis (PKDL). Diagnosis and treatment of leishmaniasis is crucial for decreasing its transmission. Various diagnostic techniques like microscopy, enzyme-linked immunosorbent assays (ELISA) and PCR-based methods are used to detect leishmaniasis infection. More recently, loop-mediated isothermal amplification (LAMP) assay has emerged as an ideal diagnostic measure for leishmaniasis, primarily due to its accuracy, speed and simplicity. However, point-of-care diagnosis is still not been tested with the LAMP assay. We have developed a portable LAMP device for the monitoring of Leishmania infection. The LAMP assay performed using our device can detect and amplify as little as 100 femtograms of L. donovani DNA. In a preliminary study, we have shown that the device can also amplify L. donovani DNA present in VL and PKDL patient samples with high sensitivity (100%), specificity (98%) and accuracy (99%), and can be used both for diagnostic and prognostic analysis. To our knowledge, this is the first report to describe the development and application of a portable LAMP device which has the potential to evolve as a point-of-care diagnostic and prognostic tool for Leishmania infections in future.
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Queiroz JADS, Rampazzo RDCP, Filho EBDS, Oliveira GS, Oliveira SDC, Souza LFB, Pereira SDS, Rodrigues MMDS, Maia ACS, da Silva CC, Mendonça ALFDM, Lugtenburg CAB, Aguiar FDAA, Rodrigues RDSS, Santos CHN, Guimarães APDS, Máximo FR, Santos ADOD, Krieger MA, Salcedo JMV, Dall'Acqua DSV. Development of a quantitative one-step multiplex RT-qPCR assay for the detection of SARS-CoV-2 in a biological matrix. Int J Infect Dis 2021; 104:373-378. [PMID: 33434663 PMCID: PMC7831874 DOI: 10.1016/j.ijid.2021.01.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2020] [Revised: 11/26/2020] [Accepted: 01/01/2021] [Indexed: 02/07/2023] Open
Abstract
INTRODUCTION Coronavirus disease-2019 (COVID-19) is a disease caused by Severe Acute Respiratory Syndrome Virus 2 (SARS-CoV-2) that emerged in China in late 2019. The rapid viral spread has made the disease a public health emergency of worldwide concern. The gold standard for diagnosing SARS-CoV-2 is reverse transcription followed by qualitative real-time polymerase chain reaction (RT-qPCR); however, the role of viral load quantification has not been thoroughly investigated yet. OBJECTIVE The aim of this study was to develop a high-precision quantitative one-step RT-qPCR reaction using the association of the viral target and the human target in the same reaction. METHODS The assay standardization involved the absolute quantification method, with serial dilutions of a plasmid with the N gene in a biological matrix to build a standard curve. RESULTS AND DISCUSSION The results demonstrated the possibility of quantifying as few as 2.5 copies/reaction and an analysis of 244 patients with known results selected by cross-section that revealed 100% agreement with a qualitative RT-qPCR assay registered by Anvisa. In this population, it was possible to quantify patients with between 2.59 and 3.5 × 107 copies per reaction and negative patients continued to indicate the same result. CONCLUSION This assay can be a useful tool for a proper patient management, because the level and duration of viral replication are important factors to assess the risk of transmission and to guide decisions regarding the isolation and release of patients; an accurate diagnosis is critical information, whereas the current COVID-19 pandemic represents the biggest current global health problem.
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Affiliation(s)
- Jackson Alves da Silva Queiroz
- Fundação Oswaldo Cruz, FIOCRUZ, Unidade Rondônia, Porto Velho, Rondônia, Brazil; Programa de Pós Graduação em Biologia Experimental, Fundação Universidade Federal de Rondônia- PGBIOEXP/UNIR, Porto Velho, Rondônia, Brazil
| | | | - Edivá Basílio da Silva Filho
- Fundação Oswaldo Cruz, FIOCRUZ, Unidade Rondônia, Porto Velho, Rondônia, Brazil; Programa de Pós Graduação em Biologia Experimental, Fundação Universidade Federal de Rondônia- PGBIOEXP/UNIR, Porto Velho, Rondônia, Brazil
| | | | | | - Luan Felipo Botelho Souza
- Laboratório Central de Saúde Pública do Estado de Rondônia - LACEN/RO, Porto Velho, Rondônia, Brazil
| | - Soraya Dos Santos Pereira
- Fundação Oswaldo Cruz, FIOCRUZ, Unidade Rondônia, Porto Velho, Rondônia, Brazil; Programa de Pós Graduação em Biologia Experimental, Fundação Universidade Federal de Rondônia- PGBIOEXP/UNIR, Porto Velho, Rondônia, Brazil
| | | | | | - Cicileia Correia da Silva
- Laboratório Central de Saúde Pública do Estado de Rondônia - LACEN/RO, Porto Velho, Rondônia, Brazil
| | | | | | | | | | | | | | | | | | | | | | - Deusilene Souza Vieira Dall'Acqua
- Fundação Oswaldo Cruz, FIOCRUZ, Unidade Rondônia, Porto Velho, Rondônia, Brazil; Programa de Pós Graduação em Biologia Experimental, Fundação Universidade Federal de Rondônia- PGBIOEXP/UNIR, Porto Velho, Rondônia, Brazil.
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Gonçalves de Albuquerque SDC, da Costa Oliveira CN, Vaitkevicius-Antão V, Silva AC, Luna CF, de Lorena VMB, de Paiva-Cavalcanti M. Study of association of the rs2275913 IL-17A single nucleotide polymorphism and susceptibility to cutaneous leishmaniasis caused by Leishmania braziliensis. Cytokine 2019; 123:154784. [PMID: 31344596 DOI: 10.1016/j.cyto.2019.154784] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2018] [Revised: 05/23/2019] [Accepted: 07/16/2019] [Indexed: 12/14/2022]
Abstract
Cutaneous leishmaniasis (CL) caused by Leishmania braziliensis is the most spread clinical form of leishmaniasis in Brazil. However, only a few part of the people infected develop clinically perceptive disease, suggesting the influence of human genetic components in the CL pathogeny. The rs2275913 SNP is the nucleotide variant of the IL17A gene. The A allele is associated with a vast number of infectious and non-infectious diseases. Here, we investigated the association of the rs2275913 SNP (G/A) from IL-17A and two forms of susceptibility to CL in Brazil by case-control study. Furthermore, we evaluated the functional relevance of this SNP during the immune response of the host and analyzed its impact in the parasite elimination. Weak associations of A allele with susceptibility to L. braziliensis infection or to symptomatic CL were observed, and a tendency of A allele carriers to be more susceptible to infection and cutaneous disease. Functional analysis of the Th17 cell phenotypes revealed lower frequencies of CD4+ IL-17+ cells in samples of infected people with AA/AG genotypes. Furthermore, people carrying the A allele maintain higher parasite loads, reinforcing the genetic susceptibility findings. This study adds knowledge about the influence of a significant genetic variation on IL-17 promoter on CL pathogenesis, and may contribute to enhance the knowledge about the role of IL-17 in the L. braziliensis infections.
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Affiliation(s)
- Suênia da Cunha Gonçalves de Albuquerque
- Department of Microbiology, Aggeu Magalhães Institute, Oswaldo Cruz Foundation, Av. Prof. Moraes Rego S/N, 50670-420 Recife, Pernambuco, Brazil; Central Laboratory of Public Health Dr Milton Bezerra de Sobral, Rua João Fernandes Vieira S/N, 50050-215 Recife, Pernambuco, Brazil
| | - Cíntia Nascimento da Costa Oliveira
- Department of Microbiology, Aggeu Magalhães Institute, Oswaldo Cruz Foundation, Av. Prof. Moraes Rego S/N, 50670-420 Recife, Pernambuco, Brazil
| | - Victor Vaitkevicius-Antão
- Department of Microbiology, Aggeu Magalhães Institute, Oswaldo Cruz Foundation, Av. Prof. Moraes Rego S/N, 50670-420 Recife, Pernambuco, Brazil
| | - Ana Carla Silva
- Department of Microbiology, Aggeu Magalhães Institute, Oswaldo Cruz Foundation, Av. Prof. Moraes Rego S/N, 50670-420 Recife, Pernambuco, Brazil
| | - Carlos Feitosa Luna
- Department of Microbiology, Aggeu Magalhães Institute, Oswaldo Cruz Foundation, Av. Prof. Moraes Rego S/N, 50670-420 Recife, Pernambuco, Brazil
| | - Virgínia Maria Barros de Lorena
- Department of Immunology, Aggeu Magalhães Institute, Oswaldo Cruz Foundation, Av. Prof. Moraes Rego S/N, 50670-420 Recife, Pernambuco, Brazil
| | - Milena de Paiva-Cavalcanti
- Department of Microbiology, Aggeu Magalhães Institute, Oswaldo Cruz Foundation, Av. Prof. Moraes Rego S/N, 50670-420 Recife, Pernambuco, Brazil.
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The diagnosis of canine visceral leishmaniasis in Brazil: Confronting old problems. Exp Parasitol 2019; 199:9-16. [DOI: 10.1016/j.exppara.2019.02.012] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2018] [Revised: 01/01/2019] [Accepted: 02/19/2019] [Indexed: 01/02/2023]
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Dixit KK, Verma S, Singh OP, Singh D, Singh AP, Gupta R, Negi NS, Das P, Sundar S, Singh R, Salotra P. Validation of SYBR green I based closed tube loop mediated isothermal amplification (LAMP) assay and simplified direct-blood-lysis (DBL)-LAMP assay for diagnosis of visceral leishmaniasis (VL). PLoS Negl Trop Dis 2018; 12:e0006922. [PMID: 30439953 PMCID: PMC6264900 DOI: 10.1371/journal.pntd.0006922] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2018] [Revised: 11/29/2018] [Accepted: 10/12/2018] [Indexed: 12/24/2022] Open
Abstract
Background The World Health Organization has targeted elimination of visceral leishmaniasis (VL) in the Indian subcontinent (ISC) by 2020. Despite distinctive decline seen in the number of VL cases in ISC, there is still a quest for development of a diagnostic test which has the utility for detection of active infection and relapse cases and as a test of cure. The present study validated the sensitivity and specificity of SYBR Green I based closed tube LAMP assay reported by us for diagnosis of VL. Methodology The validation study was carried out at two endemic sites in India, located at Rajendra Memorial Research Institute of Medical Sciences (RMRIMS), Patna and Institute of Medical Sciences (IMS), Banaras Hindu University (BHU), Varanasi. Standard operating protocols were provided at the two sites for applying LAMP assay on confirmed VL cases. The diagnostic accuracy of LAMP assay was evaluated by Receiver operator curve (ROC) analysis. Furthermore, a simplified LAMP assay based on direct blood lysis, DBL-LAMP, was developed and verified for its diagnostic accuracy. Principal findings A total of 267 eligible participants were included in the study which comprised of 179 VL cases and 88 controls. Sensitivity and specificity of the LAMP assay were 98.32% (95% C.I– 95.2–99.7%) and 96.59% (95% C.I.-90.4–99.3%), respectively. ROC curve analysis depicted no significant difference between area under curve (AUCROC) for LAMP assay and rK39 RDT, indicative of LAMP as an excellent diagnostic test. DBL-LAMP assay, performed on 67 VL and 100 control samples, yielded a sensitivity of 93.05% (95% C.I- 84.75–97%) and specificity of 100% (95% C.I.- 96.30–100%). Conclusions/Significance The validated closed tube LAMP for diagnosis of VL will provide impetus to the ongoing VL elimination programme in ISC. The assay based on direct blood lysis promotes its scope for application in field settings by further reducing time and cost. Definitive diagnosis of visceral leishmaniasis(VL) by demonstration of amastigotes by microscopy is invasive and risky. Serology based diagnosis using rK39 rapid diagnostic test(RDT) has excellent sensitivity of~97% when combined with clinical symptoms but is inconclusive for detection of active infection and relapses due to persistence of anti-leishmanial antibodies. The developed SYBR Green I based closed tube LAMP assay overcomes these constraints and further, direct blood lysis (DBL)-LAMP, makes it more suitable for field application. The study involved validation of LAMP assay at two endemic sites in India, on a total of 179 VL patients confirmed by rK39 RDT and/ or microscopy and 88 controls. The assay was highly sensitive (98.32%) and specific (96.59%). Further, DBL-LAMP assay yielded a sensitivity and specificity of 93.05% and 100%, respectively. In conclusion, the study has validated the field potential of LAMP assay for diagnosis of VL which will provide momentum to ongoing VL elimination in the Indian subcontinent (ISC).
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Affiliation(s)
- Keerti Kaumudee Dixit
- ICMR-National Institute of Pathology, Safdarjung Hospital Campus, New Delhi, India
- Faculty of Health and Biological Sciences, Symbiosis International (Deemed University), Pune, India
| | - Sandeep Verma
- ICMR-National Institute of Pathology, Safdarjung Hospital Campus, New Delhi, India
| | - Om Prakash Singh
- Department of Medicine, Institute of Medical Sciences, Banaras Hindu University, Varanasi, Uttar Pradesh, India
| | - Dharmendra Singh
- Rajendra Memorial Research Institute of Medical Sciences (RMRIMS), Patna, India
| | - Akhil Pratap Singh
- Department of Medicine, Institute of Medical Sciences, Banaras Hindu University, Varanasi, Uttar Pradesh, India
| | - Ratan Gupta
- Department of Paediatrics, Safdarjung Hospital and Vardhman Mahavir Medical college, New Delhi, India
| | - Narendra Singh Negi
- Department of Medicine, Safdarjung Hospital and Vardhman Mahavir Medical College, New Delhi, India
| | - Pradeep Das
- Rajendra Memorial Research Institute of Medical Sciences (RMRIMS), Patna, India
| | - Shyam Sundar
- Department of Medicine, Institute of Medical Sciences, Banaras Hindu University, Varanasi, Uttar Pradesh, India
| | - Ruchi Singh
- ICMR-National Institute of Pathology, Safdarjung Hospital Campus, New Delhi, India
| | - Poonam Salotra
- ICMR-National Institute of Pathology, Safdarjung Hospital Campus, New Delhi, India
- * E-mail:
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Modarelli JJ, Ferro PJ, Esteve-Gasent MD. Development and application of a canine endogenous internal positive control for use in real-time PCR assays. J Vet Diagn Invest 2018; 30:789-792. [PMID: 30132404 DOI: 10.1177/1040638718795206] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Real-time PCR (rtPCR) tests have become a method of choice in many diagnostic settings, both animal and human. A concern remains, however, regarding rtPCR assay inhibition during nucleic acid extraction and/or rtPCR reaction process that may result in false-negative results. The use of an internal positive control, either endogenous or exogenous, to mitigate this issue has become more commonplace. We identified and standardized an endogenous internal positive control that can be utilized in rtPCR assays targeting canine-specific pathogens in either a singleplex or multiplex format. The target chosen for the endogenous internal positive control (EIPC-K9) was a highly conserved region in canine mitochondrial DNA. Samples from 240 dogs and 11 other species were screened with EIPC-K9; all canine samples were detected, and no cross-amplification with other species tested was observed. Additionally, no inhibition was noted when comparing singleplex to multiplex rtPCR formats.
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Affiliation(s)
- Joseph J Modarelli
- Department of Veterinary Pathobiology, College of Veterinary Medicine and Biomedical Sciences (Modarelli, Esteve-Gasent), Texas A&M University, College Station, TX.,Texas A&M Veterinary Medical Diagnostic Laboratory (Modarelli, Ferro), Texas A&M University, College Station, TX
| | - Pamela J Ferro
- Department of Veterinary Pathobiology, College of Veterinary Medicine and Biomedical Sciences (Modarelli, Esteve-Gasent), Texas A&M University, College Station, TX.,Texas A&M Veterinary Medical Diagnostic Laboratory (Modarelli, Ferro), Texas A&M University, College Station, TX
| | - Maria D Esteve-Gasent
- Department of Veterinary Pathobiology, College of Veterinary Medicine and Biomedical Sciences (Modarelli, Esteve-Gasent), Texas A&M University, College Station, TX.,Texas A&M Veterinary Medical Diagnostic Laboratory (Modarelli, Ferro), Texas A&M University, College Station, TX
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Rampazzo RDCP, Solcà MDS, Santos LCS, Pereira LDN, Guedes JCO, Veras PST, Fraga DBM, Krieger MA, Costa ADT. A ready-to-use duplex qPCR to detect Leishmania infantum DNA in naturally infected dogs. Vet Parasitol 2017; 246:100-107. [PMID: 28969770 DOI: 10.1016/j.vetpar.2017.09.009] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2017] [Revised: 09/07/2017] [Accepted: 09/09/2017] [Indexed: 10/18/2022]
Abstract
Canine visceral leishmaniasis (CVL) is a systemic disease caused by Leishmania infantum. A precise CVL diagnosis would allow for a faster and more specific treatment. Quantitative PCR (qPCR) is a sensitive and specific technique that can diagnose CVL and also monitor parasite load in the animal during the course of the infection or treatment. The aim of this study was to develop a ready-to-use (gelified and freezer-free) duplex qPCR for the identification of infected animals. We combined a new qPCR protocol that detects the canine 18S rRNA gene with an existing protocol for L. infantum kDNA detection, creating a duplex qPCR. This duplex method was then developed into a ready-to-use format. The performance of the duplex and singleplex reactions were compared in the traditional format (liquid and freezer-stored). Furthermore, the duplex qPCR performance was compared between the ready-to-use and traditional formats. The singleplex and new duplex qPCR exhibited the same detection limit in the traditional format (0.1 parasites/reaction). The ready-to-use format showed a detection limit of 1 parasite/reaction without affecting the reaction efficiency. The performance of the new qPCR protocol in the two formats was assessed using canine tissue samples from 82 dogs in an endemic CVL area that were previously characterized by standard serological and parasitological protocols. Splenic aspirates provided a higher rate of positivity (92.9%) followed by skin (50%) and blood (35.7%). The reported detection limits were observed for all tissues studied. Our results show that the amplification of L. infantum kDNA and canine DNA in a single tube, using either the traditional or ready-to-use format, exhibited the same diagnostic performance as amplification of the parasite kDNA alone. The detection of the host gene strengthens the qPCR results by confirming the presence and quality of DNA in the samples and the absence of polymerase inhibitors. The ready-to-use duplex qPCR format has many advantages. By joining two qPCR protocols into one, more results can be obtained in the same amount of time with reduced costs and embedded quality control. Reagents are preloaded and stored on the plate, reducing the operator's hands-on time to set up a reaction, as well as decreasing manipulation steps, which reduces the risk of mistakes or contamination. Thus, the ready-to-use duplex format turns qPCR into a robust, easy-to-use tool, which could help increase the availability of qPCR for CVL diagnosis.
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Affiliation(s)
- Rita de Cássia Pontello Rampazzo
- Instituto Carlos Chagas (ICC), FIOCRUZ-PR, Rua Prof. Algacyr Munhoz Mader, 3775 CIC, 81350-010, Curitiba, Paraná, Brazil; Instituto de Biologia Molecular do Paraná (IBMP), Rua Professor Algacyr Munhoz Mader, 3775 CIC, 81350-010, Curitiba, Paraná, Brazil
| | - Manuela da Silva Solcà
- Laboratório de Patologia e Biointervenção (LPBI), Instituto Gonçalo Moniz (IGM), FIOCRUZ-BA, Rua Waldemar Falcão, 121 Candeal, 40296-710, Salvador, Bahia, Brazil
| | - Liliane Celestino Sales Santos
- Departamento de Medicina Veterinária Preventiva e Produção Animal, Escola de Medicina Veterinária e Zootecnia, Universidade Federal da Bahia (UFBA), Av. Adhemar de Barros, 500 Ondina, 40170-110, Salvador, Bahia, Brazil
| | - Lais de Novaes Pereira
- Departamento de Medicina Veterinária Preventiva e Produção Animal, Escola de Medicina Veterinária e Zootecnia, Universidade Federal da Bahia (UFBA), Av. Adhemar de Barros, 500 Ondina, 40170-110, Salvador, Bahia, Brazil
| | - José Carlos Oliveira Guedes
- Departamento de Medicina Veterinária Preventiva e Produção Animal, Escola de Medicina Veterinária e Zootecnia, Universidade Federal da Bahia (UFBA), Av. Adhemar de Barros, 500 Ondina, 40170-110, Salvador, Bahia, Brazil
| | - Patrícia Sampaio Tavares Veras
- Laboratório de Patologia e Biointervenção (LPBI), Instituto Gonçalo Moniz (IGM), FIOCRUZ-BA, Rua Waldemar Falcão, 121 Candeal, 40296-710, Salvador, Bahia, Brazil; Instituto de Ciência e Tecnologia de Doenças Tropicais, INCT-DT, Salvador, Bahia, Brazil
| | - Deborah Bittencourt Mothé Fraga
- Laboratório de Patologia e Biointervenção (LPBI), Instituto Gonçalo Moniz (IGM), FIOCRUZ-BA, Rua Waldemar Falcão, 121 Candeal, 40296-710, Salvador, Bahia, Brazil; Departamento de Medicina Veterinária Preventiva e Produção Animal, Escola de Medicina Veterinária e Zootecnia, Universidade Federal da Bahia (UFBA), Av. Adhemar de Barros, 500 Ondina, 40170-110, Salvador, Bahia, Brazil; Instituto de Ciência e Tecnologia de Doenças Tropicais, INCT-DT, Salvador, Bahia, Brazil
| | - Marco Aurélio Krieger
- Instituto Carlos Chagas (ICC), FIOCRUZ-PR, Rua Prof. Algacyr Munhoz Mader, 3775 CIC, 81350-010, Curitiba, Paraná, Brazil; Instituto de Biologia Molecular do Paraná (IBMP), Rua Professor Algacyr Munhoz Mader, 3775 CIC, 81350-010, Curitiba, Paraná, Brazil
| | - Alexandre Dias Tavares Costa
- Instituto Carlos Chagas (ICC), FIOCRUZ-PR, Rua Prof. Algacyr Munhoz Mader, 3775 CIC, 81350-010, Curitiba, Paraná, Brazil; Instituto de Biologia Molecular do Paraná (IBMP), Rua Professor Algacyr Munhoz Mader, 3775 CIC, 81350-010, Curitiba, Paraná, Brazil.
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Verma S, Singh R, Sharma V, Bumb RA, Negi NS, Ramesh V, Salotra P. Development of a rapid loop-mediated isothermal amplification assay for diagnosis and assessment of cure of Leishmania infection. BMC Infect Dis 2017; 17:223. [PMID: 28335752 PMCID: PMC5363003 DOI: 10.1186/s12879-017-2318-8] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2016] [Accepted: 03/10/2017] [Indexed: 11/10/2022] Open
Abstract
Background Leishmaniasis is a spectrum of diseases with great relevance to public health. Conventional diagnostic methods are time consuming, needing trained personnel. A robust, rapid and cost effective diagnostic test is warranted for on-time diagnosis and field application. Methods We have developed a loop mediated isothermal amplification (LAMP) assay with primers (n = 6) based on Leishmania donovani kDNA for detection of Leishmania infection, using a closed tube to prevent cross-contamination. The assay was used to detect Leishmania infection in biological samples obtained from patients of visceral leishmaniasis (VL), post kala-azar dermal leishmaniasis (PKDL) and cutaneous leishmaniasis (CL). Results The assay was positive for L. donovani, L. tropica and L. major parasites, with the highest sensitivity towards L. donovani (1 fg DNA). The high sensitivity of the assay for detection of L. donovani was reflected in its ability to detect parasite DNA within 30 min of amplification time with a threshold detection limit of ≥25 copies per reaction. The assay detected parasite in 64 of 66 VL blood samples (sensitivity, 96.9%; 95% CI: 89.6-99.2%), 15 of 15 VL bone marrow aspirate samples (sensitivity, 100%; 95% CI:79.6-100%), 65 of 67 PKDL tissue biopsy samples (sensitivity, 97%; 95% CI:89.7-99.2%). The assay was evaluated in a few cases of CL wherein it was found positive in 8 of 10 tissue biopsies (sensitivity, 80%; 95% CI: 49-94.3%). The assay was negative in all control blood (n = 76) and tissue biopsy (n = 24) samples (specificity, 100%; 95% CI: 96.3-100%). Further, the assay was evaluated for its utility in assessment of cure in treated VL and PKDL patients. The assay detected parasite DNA in 2 of 20VL blood samples and 2 of 21 PKDL tissue samples. Out of 4 cases that were positive for parasite DNA at post treatment stage, 2 patients (1VL and 1 PKDL) returned with relapse. Conclusions The study demonstrated a Leishmania genus specific closed tube LAMP assay for reliable and rapid molecular diagnosis of VL and PKDL with potential for application in assessment of cure.
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Affiliation(s)
- Sandeep Verma
- National Institute of Pathology (ICMR), Safdarjung Hospital Campus, New Delhi, 110029, India
| | - Ruchi Singh
- National Institute of Pathology (ICMR), Safdarjung Hospital Campus, New Delhi, 110029, India
| | - Vanila Sharma
- National Institute of Pathology (ICMR), Safdarjung Hospital Campus, New Delhi, 110029, India
| | - Ram Avtar Bumb
- Department of Skin, STD and Leprosy, S. P. Medical College, Bikaner, India
| | | | - V Ramesh
- Department of Dermatology, Safdarjung Hospital, New Delhi, India
| | - Poonam Salotra
- National Institute of Pathology (ICMR), Safdarjung Hospital Campus, New Delhi, 110029, India.
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de Cássia-Pires R, de Melo MDFAD, Barbosa RDH, Roque ALR. Multiplex PCR as a tool for the diagnosis of Leishmania spp. kDNA and the gapdh housekeeping gene of mammal hosts. PLoS One 2017; 12:e0173922. [PMID: 28301553 PMCID: PMC5354409 DOI: 10.1371/journal.pone.0173922] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2016] [Accepted: 02/28/2017] [Indexed: 12/03/2022] Open
Abstract
Background The PCR assays usually employed for Leishmania diagnosis does not simultaneously detect a constitutive gene that would certify the viability of the DNA sample. We present a multiplex PCR approach for the simultaneous diagnosis of the Leishmania sp. kDNA fragment and a catalytic domain segment of a conserved region of the mammalian gapdh gene. Methodology The proposed multiplex protocol was designed through in silico PCR. The annealing temperature, concentration of primer pairs, number of cycles, distinct polymerase enzymes and premix kit were defined to achieve an optimal reaction. The DNA detection sensitivity was tested with different concentrations of known L. tropica DNA, and the reproducibility of the assay was confirmed using samples from 106 wild mammals that were previously subject to Leishmania sp. kDNA analysis through singleplex reactions. Principal findings The following optimal conditions were established: 95°C for 1 min followed by 30 cycles of 95°C for 30 s, 61°C for 30 s, and 72°C for 30 s and a final extension at 72°C for 1 min. The multiplex PCR system was capable of detecting 0.1 ng of L. tropica diluted in 100 ng of mammalian DNA. Of 51 kDNA samples that were previously found to be positive, 45 (88.2%) were positive for both targets, two were positive only for kDNA and four were negative for both. Of 55 kDNA samples that were previously identified as negative, 38 (69.1%) were positive for gapdh whereas the other 17 were negative for both targets. Conclusions/Significance The proposed multiplex PCR system allows the simultaneous detection of the gapdh gene and Leishmania sp. kDNA in tissue samples derived from distinct wild mammal species. The amplification of the gapdh mammalian gene in the same reaction ensures the quality and viability of the DNA in the sample, eliminating the possibility of false-negative results that would impair an accurate description of the infection rates in a given population.
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Affiliation(s)
- Renata de Cássia-Pires
- Laboratory of Trypanosomatid Biology, Oswaldo Cruz Institute, FIOCRUZ, Rio de Janeiro, Rio de Janeiro, Brazil
| | | | - Raquel da Hora Barbosa
- Center of Medical Sciences, Biomedical Institute, Fluminense Federal University, UFF, Niterói, Rio de Janeiro, Brazil
| | - André Luiz Rodrigues Roque
- Laboratory of Trypanosomatid Biology, Oswaldo Cruz Institute, FIOCRUZ, Rio de Janeiro, Rio de Janeiro, Brazil
- * E-mail:
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Takano E, Shimura N, Akiba T, Kitayama Y, Sunayama H, Abe K, Ikebukuro K, Takeuchi T. Pipette tip biosensors for bacterial double-stranded DNA using bioluminescence induced by zinc finger luciferase. Mikrochim Acta 2017. [DOI: 10.1007/s00604-017-2152-0] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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de Paiva-Cavalcanti M, de Morais RCS, Pessoa-E-Silva R, Trajano-Silva LAM, Gonçalves-de-Albuquerque SDC, Tavares DDHC, Brelaz-de-Castro MCA, Silva RDFE, Pereira VRA. Leishmaniases diagnosis: an update on the use of immunological and molecular tools. Cell Biosci 2015; 5:31. [PMID: 26097678 PMCID: PMC4474361 DOI: 10.1186/s13578-015-0021-2] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2015] [Accepted: 06/05/2015] [Indexed: 11/10/2022] Open
Abstract
Leishmaniases are caused by obligate intracellular protozoan parasites of the genus Leishmania. They cause a spectrum of diseases, most notably visceral (VL), cutaneous (CL), and mucosal (ML) leishmaniasis, which affect millions of people around the world, each year. Despite scientific advances, leishmaniases cases are expanding, constituting an important public health problem. Immunological and molecular diagnostic tools have been increasingly applied for the early detection of these parasitic infections, since the existence of limitations in clinical and parasitological examinations may provide false results, thus interfering in epidemiological research and diseases control. Although there is a great diversity of available immunological assays, important common deficiencies persist, which explains the current exploration of the molecular biology in research fields, especially the Polymerase Chain Reaction (PCR) and its variants, such as real-time quantitative PCR. However, in the last years, significant results have also been reached inside of immunological context (especially by Flow Cytometry), for humans and dogs, demonstrated by research works of the New and Old worlds. In spite of their potential to clarify and minimize the present global situation of the diseases, the implementation of molecular or immunological innovative reference assays for VL and CL at health services is still a challenge due to several reasons, including lack of standardization among laboratories and structural concerns. In this article we bring classical and current information about technological advances for the immunological and molecular leishmaniases diagnosis, their features, and applications.
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Affiliation(s)
- Milena de Paiva-Cavalcanti
- Department of Immunology, Aggeu Magalhães Research Center, Oswaldo Cruz Foundation, Av. Prof. Moraes Rego s / n, 50670-420 Recife, PE Brazil
| | - Rayana Carla Silva de Morais
- Department of Immunology, Aggeu Magalhães Research Center, Oswaldo Cruz Foundation, Av. Prof. Moraes Rego s / n, 50670-420 Recife, PE Brazil
| | - Rômulo Pessoa-E-Silva
- Department of Immunology, Aggeu Magalhães Research Center, Oswaldo Cruz Foundation, Av. Prof. Moraes Rego s / n, 50670-420 Recife, PE Brazil
| | | | | | | | | | - Rafael de Freitas E Silva
- Department of Immunology, Aggeu Magalhães Research Center, Oswaldo Cruz Foundation, Av. Prof. Moraes Rego s / n, 50670-420 Recife, PE Brazil ; Department of Natural and Exact Sciences, University of Pernambuco (UPE), St. Capitão Pedro Rodrigues, 105, 55920-000 São José, Garanhuns, PE Brazil
| | - Valéria Rêgo Alves Pereira
- Department of Immunology, Aggeu Magalhães Research Center, Oswaldo Cruz Foundation, Av. Prof. Moraes Rego s / n, 50670-420 Recife, PE Brazil
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Biswas C, Dey P, Gotyal BS, Satpathy S. A method of multiplex PCR for detection of field released Beauveria bassiana, a fungal entomopathogen applied for pest management in jute (Corchorus olitorius). World J Microbiol Biotechnol 2015; 31:675-9. [PMID: 25680421 DOI: 10.1007/s11274-015-1821-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2014] [Accepted: 02/07/2015] [Indexed: 10/24/2022]
Abstract
The fungal entomopathogen Beauveria bassiana is a promising biocontrol agent for many pests. Some B. bassiana strains have been found effective against jute pests. To monitor the survival of field released B. bassiana a rapid and efficient detection technique is essential. Conventional methods such as plating method or direct culture method which are based on cultivation on selective media followed by microscopy are time consuming and not so sensitive. PCR based methods are rapid, sensitive and reliable. A single primer PCR may fail to amplify some of the strains. However, multiplex PCR increases the possibility of detection as it uses multiple primers. Therefore, in the present investigation a multiplex PCR protocol was developed by multiplexing three primers SCA 14, SCA 15 and SCB 9 to detect field released B. bassiana strains from soil as well as foliage of jute field. Using our multiplex PCR protocol all the five B. bassiana strains could be detected from soil and three strains viz., ITCC 6063, ITCC 4563 and ITCC 4796 could be detected even from the crop foliage after 45 days of spray.
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Affiliation(s)
- Chinmay Biswas
- Central Research Institute for Jute and Allied Fibres (CRIJAF), Barrackpore, Kolkata, 700120, West Bengal, India,
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