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Kajdanek A, Kluska M, Matusiak R, Kazimierczak J, Dastych J. A Rapid and Inexpensive PCR Test for Mastitis Diagnosis Based on NGS Data. Pathogens 2024; 13:423. [PMID: 38787275 DOI: 10.3390/pathogens13050423] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2024] [Revised: 05/02/2024] [Accepted: 05/15/2024] [Indexed: 05/25/2024] Open
Abstract
Mastitis is a common mammary gland disease of dairy cattle caused by a wide range of organisms including bacteria, fungi and algae. Mastitis contributes to economic losses of dairy farms due to reduced yield and poor quality of milk. Since the correct identification of pathogens responsible for the development of mastitis is crucial to the success of treatment, it is necessary to develop a quick and accurate test to distinguish the main pathogens causing this disease. In this paper, we describe the development of a test based on the multiplex polymerase chain reaction (PCR) method allowing for the identification of Streptococcus agalactiae, Streptococcus dysgalactiae, Streptococcus uberis and Staphylococcus aureus. When creating our test, we relied on the results from new generation sequencing (NGS) for accurate determination of species affiliation. The multiplex PCR test was verified on 100 strains including veterinary samples, ATCC and Polish Collection of Microorganisms (PCM) reference strains. The obtained results indicate that this test is accurate and displays high specificity. It may serve as a valuable molecular tool for the detection of major mastitis pathogens.
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Camacho MJ, Albuquerque DC, Inácio ML, Martins VC, Mota M, Freitas PP, de Andrade E. FTA-LAMP based biosensor for a rapid in-field detection of Globodera pallida-the pale potato cyst nematode. Front Bioeng Biotechnol 2024; 12:1337879. [PMID: 38303911 PMCID: PMC10830618 DOI: 10.3389/fbioe.2024.1337879] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Accepted: 01/02/2024] [Indexed: 02/03/2024] Open
Abstract
The combination of a sensitive and specific magnetoresistive sensing device with an easy DNA extraction method and a rapid isothermal amplification is presented here targeting the on-site detection of Globodera pallida, a potato endoparasitic nematode. FTA-cards were used for DNA extraction, LAMP was the method developed for DNA amplification and a nanoparticle functionalized magnetic-biosensor was used for the detection. The combinatorial effect of these three emerging technologies has the capacity to detect G. pallida with a detection limit of one juvenile, even when mixed with other related species. This combined system is far more interesting than what a single technology can provide. Magnetic biosensors can be combined with any DNA extraction protocol and LAMP forming a new solution to target G. pallida. The probe designed in this study consistently distinguished G. pallida (∆Vac binding/Vac sensor above 1%) from other cyst nematodes (∆Vac binding/Vac sensor below 1%). It was confirmed that DNA either extracted with FTA-cards or Lab extraction Kit was of enough quantity and quality to detect G. pallida whenever present (alone or in mixed samples), ensuring probe specificity and sensitivity. This work provides insights for a new strategy to construct advanced devices for pathogens in-field diagnostics. LAMP runs separately but can be easily integrated into a single device.
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Affiliation(s)
- Maria João Camacho
- INIAV—National Institute for Agriculture and Veterinary Research, Oeiras, Portugal
- NemaLab/ MED—Mediterranean Institute for Agriculture, Environment and Development, Institute for Advanced Studies and Research, University of Évora, Évora, Portugal
- INESC Microsistemas e Nanotecnologias, Lisbon, Portugal
| | - Débora C. Albuquerque
- INESC Microsistemas e Nanotecnologias, Lisbon, Portugal
- IST—Instituto Superior Técnico, University of Lisbon, Lisbon, Portugal
| | - Maria L. Inácio
- INIAV—National Institute for Agriculture and Veterinary Research, Oeiras, Portugal
- GREEN-IT Bioresources for Sustainability, ITQB NOVA, Oeiras, Portugal
| | | | - Manuel Mota
- NemaLab/ MED—Mediterranean Institute for Agriculture, Environment and Development, Institute for Advanced Studies and Research, University of Évora, Évora, Portugal
| | - Paulo P. Freitas
- INESC Microsistemas e Nanotecnologias, Lisbon, Portugal
- INL—International Iberian Nanotechnology Laboratory, Braga, Portugal
| | - Eugénia de Andrade
- INIAV—National Institute for Agriculture and Veterinary Research, Oeiras, Portugal
- GREEN-IT Bioresources for Sustainability, ITQB NOVA, Oeiras, Portugal
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Camacho MJ, Albuquerque DC, de Andrade E, Martins VC, Inácio ML, Mota M, Freitas PP. A Lab-on-a-Chip Approach for the Detection of the Quarantine Potato Cyst Nematode Globodera pallida. SENSORS (BASEL, SWITZERLAND) 2023; 23:647. [PMID: 36679443 PMCID: PMC9861625 DOI: 10.3390/s23020647] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/12/2022] [Revised: 12/23/2022] [Accepted: 01/04/2023] [Indexed: 06/17/2023]
Abstract
The potato cyst nematode (PCN), Globodera pallida, has acquired significant importance throughout Europe due to its widespread prevalence and negative effects on potato production. Thus, rapid and reliable diagnosis of PCN is critical during surveillance programs and for the implementation of control measures. The development of innovative technologies to overcome the limitations of current methodologies in achieving early detection is needed. Lab-on-a-chip devices can swiftly and accurately detect the presence of certain nucleotide sequences with high sensitivity and convert the presence of biological components into an understandable electrical signal by combining biosensors with microfluidics-based biochemical analysis. In this study, a specific DNA-probe sequence and PCR primers were designed to be used in a magnetoresistive biosensing platform to amplify the internal transcribed spacer region of the ribosomal DNA of G. pallida. Magnetic nanoparticles were used as the labelling agents of asymmetric PCR product through biotin−streptavidin interaction. Upon target hybridization to sensor immobilized oligo probes, the fringe field created by the magnetic nanoparticles produces a variation in the sensor’s electrical resistance. The detection signal corresponds to the concentration of target molecules present in the sample. The results demonstrate the suitability of the magnetic biosensor to detect PCR target product and the specificity of the probe, which consistently distinguishes G. pallida (DV/V > 1%) from other cyst nematodes (DV/V < 1%), even when DNA mixtures were tested at different concentrations. This shows the magnetic biosensor’s potential as a bioanalytical device for field applications and border phytosanitary inspections.
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Affiliation(s)
- Maria João Camacho
- INIAV, I.P.—National Institute for Agriculture and Veterinary Research, 2780-159 Oeiras, Portugal
- NemaLab, MED–Mediterranean Institute for Agriculture, Environment and Development, Institute for Advanced Studies and Research, University of Évora, 7006-554 Évora, Portugal
| | - Débora C. Albuquerque
- INESC-MN- Microsystems and Nanotechnologies, 1000-029 Lisbon, Portugal
- IST—Instituto Superior Técnico, University of Lisbon, 1049-001 Lisbon, Portugal
| | - Eugénia de Andrade
- INIAV, I.P.—National Institute for Agriculture and Veterinary Research, 2780-159 Oeiras, Portugal
- GREEN-IT Bioresources for Sustainability, ITQB NOVA, 2780-157 Oeiras, Portugal
| | | | - Maria L. Inácio
- INIAV, I.P.—National Institute for Agriculture and Veterinary Research, 2780-159 Oeiras, Portugal
- GREEN-IT Bioresources for Sustainability, ITQB NOVA, 2780-157 Oeiras, Portugal
| | - Manuel Mota
- NemaLab, MED–Mediterranean Institute for Agriculture, Environment and Development, Institute for Advanced Studies and Research, University of Évora, 7006-554 Évora, Portugal
| | - Paulo P. Freitas
- INESC-MN- Microsystems and Nanotechnologies, 1000-029 Lisbon, Portugal
- INL—International Iberian Nanotechnology Laboratory, 4715-330 Braga, Portugal
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Albuquerque DC, Martins VC, Fernandes E, Zé-Zé L, Alves MJ, Cardoso S. Combined detection of molecular and serological signatures of viral infections: The dual assay concept. Biosens Bioelectron 2022; 210:114302. [PMID: 35487137 DOI: 10.1016/j.bios.2022.114302] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Revised: 04/15/2022] [Accepted: 04/20/2022] [Indexed: 11/28/2022]
Abstract
The recent worldwide spread of viral infections has highlighted the need for accurate, fast, and inexpensive disease diagnosis and monitorization methods. Current diagnostics tend to focus either on molecular or serological testing. In this work we propose a dual detection assay approach for viral diseases, where both serological and molecular assays are combined in a single analysis performed on a magnetoresistive system. This type of assay guarantees an accurate assessment of the infection phase, saving time and costs associated with multiple independent tests. Zika and dengue viruses were used as model diseases for the validation of the system. Human IgG anti-zika and anti-dengue antibodies were successfully detected in infected patients' serum, using a novel approach combining competitive and sandwich strategies in a magnetoresistive portable platform. Specificity and sensitivity values of 100% were obtained. Calibration curves with dynamic ranges between 10 ng/mL and 1 μg/mL were established achieving LODs of 1.26 and 1.38 nM for IgG anti-ZIKV and anti-DENV antibodies, respectively. Viral RNA detection down to a few hundreds of pM was also successfully carried out after the design of specific oligo probes and primers for RT-PCR amplification. Dual assays were performed for both viruses, where viral RNA and anti-virus antibodies in serum samples were simultaneously detected. The results obtained for the detection of the molecular and serological targets in the dual assay format show no significant difference between the ones obtained individually, proving the feasibility and accuracy of the dual detection assay. This assay format represents a new paradigm in viral infections diagnostics.
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Affiliation(s)
- Débora C Albuquerque
- IST - Instituto Superior Técnico, University of Lisbon, Lisboa, 1049-001, Portugal; INESC-MN-Instituto de Engenharia de Sistemas E Computadores - Microsistemas e Nanotecnologias, Lisboa, 1000-029, Portugal; INL, International Nanotechnology Laboratory, Braga, 4715-330, Portugal.
| | - Verónica C Martins
- INESC-MN-Instituto de Engenharia de Sistemas E Computadores - Microsistemas e Nanotecnologias, Lisboa, 1000-029, Portugal
| | | | - Líbia Zé-Zé
- INSA- National Institute of Health Doutor Ricardo Jorge, Centre for Vectors and Infectious Diseases Research, Águas de Moura, 2965-575, Portugal; BioISI - Biosystems and Integrative Sciences Institute, Edificio TecLabs, Campus da FCUL, Campo Grande, Lisboa, 1749-016, Portugal
| | - Maria João Alves
- INSA- National Institute of Health Doutor Ricardo Jorge, Centre for Vectors and Infectious Diseases Research, Águas de Moura, 2965-575, Portugal
| | - Susana Cardoso
- IST - Instituto Superior Técnico, University of Lisbon, Lisboa, 1049-001, Portugal; INESC-MN-Instituto de Engenharia de Sistemas E Computadores - Microsistemas e Nanotecnologias, Lisboa, 1000-029, Portugal
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Verma N, Kulkarni R, Pandya A. Microfluidic tools for veterinary and zoonotic disease diagnostics. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2022; 187:281-293. [PMID: 35094778 DOI: 10.1016/bs.pmbts.2021.07.026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
Animal disease diagnostics has linked as the cause and cure of any disease. It also plays a vital role in disease management and prevention. A small outbreak of disease can pose a threat to the entire animal community as we realized in corona pandemic. Thus, to ensure the overall welfare of animals and disease spread monitoring, the development of detection tools for veterinary diagnosis becomes essential. Currently, the animal disease diagnosis is relied on laboratory-based testing. There is a parallel necessity for rapid, reliable and low-cost diagnostic tests to be done by intervention of growing area such as microfluidic platform. Therefore, in this chapter, we have discussed about various microfluidic platform and their application for early diagnosis of veterinary disease. Followed by, we also lightened on future perspective of role of microfluidic in animal disease diagnostics.
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Affiliation(s)
- Nidhi Verma
- Department of Engineering and Physical Sciences, Institute of Advanced Research, Gandhinagar, Gujarat, India
| | - Rutuparna Kulkarni
- Department of Biological Sciences and Biotechnology, Institute of Advanced Research, Gandhinagar, Gujarat, India
| | - Alok Pandya
- Department of Engineering and Physical Sciences, Institute of Advanced Research, Gandhinagar, Gujarat, India.
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Miguéis SDC, Tavares APM, Martins GV, Frasco MF, Sales MGF. Biosensors for European Zoonotic Agents: A Current Portuguese Perspective. SENSORS (BASEL, SWITZERLAND) 2021; 21:4547. [PMID: 34283108 PMCID: PMC8271446 DOI: 10.3390/s21134547] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/06/2021] [Revised: 06/20/2021] [Accepted: 06/25/2021] [Indexed: 01/24/2023]
Abstract
Emerging and recurrent outbreaks caused by zoonotic agents pose a public health risk. They result in morbidity and mortality in humans and significant losses in the livestock and food industries. This highlights the need for rapid surveillance methods. Despite the high reliability of conventional pathogen detection methods, they have high detection limits and are time-consuming and not suitable for on-site analysis. Furthermore, the unpredictable spread of zoonotic infections due to a complex combination of risk factors urges the development of innovative technologies to overcome current limitations in early warning and detection. Biosensing, in particular, is highlighted here, as it offers rapid and cost-effective devices for use at the site of infection while increasing the sensitivity of detection. Portuguese research in biosensors for zoonotic pathogens is the focus of this review. This branch of research produces exciting and innovative devices for the study of the most widespread pathogenic bacteria. The studies presented here relate to the different classes of pathogens whose characteristics and routes of infection are also described. Many advances have been made in recent years, and Portuguese research teams have increased publications in this field. However, biosensing still needs to be extended to other pathogens, including potentially pandemic viruses. In addition, the use of biosensors as part of routine diagnostics in hospitals for humans, in animal infections for veterinary medicine, and food control has not yet been achieved. Therefore, a convergence of Portuguese efforts with global studies on biosensors to control emerging zoonotic diseases is foreseen for the future.
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Affiliation(s)
- Samuel da Costa Miguéis
- BioMark@ISEP, School of Engineering, Polytechnic Institute of Porto, 4249-015 Porto, Portugal; (A.P.M.T.); (G.V.M.); (M.F.F.)
- Centro de Investigação Desenvolvimento e Inovação da Academia Militar, Academia Militar, Instituto Universitário Militar, 1169-203 Lisboa, Portugal
| | - Ana P. M. Tavares
- BioMark@ISEP, School of Engineering, Polytechnic Institute of Porto, 4249-015 Porto, Portugal; (A.P.M.T.); (G.V.M.); (M.F.F.)
- BioMark@UC, Faculty of Sciences and Technology, University of Coimbra, 3030-790 Coimbra, Portugal
- CEB, Centre of Biological Engineering, University of Minho, 4710-057 Braga, Portugal
| | - Gabriela V. Martins
- BioMark@ISEP, School of Engineering, Polytechnic Institute of Porto, 4249-015 Porto, Portugal; (A.P.M.T.); (G.V.M.); (M.F.F.)
- BioMark@UC, Faculty of Sciences and Technology, University of Coimbra, 3030-790 Coimbra, Portugal
- CEB, Centre of Biological Engineering, University of Minho, 4710-057 Braga, Portugal
| | - Manuela F. Frasco
- BioMark@ISEP, School of Engineering, Polytechnic Institute of Porto, 4249-015 Porto, Portugal; (A.P.M.T.); (G.V.M.); (M.F.F.)
- BioMark@UC, Faculty of Sciences and Technology, University of Coimbra, 3030-790 Coimbra, Portugal
- CEB, Centre of Biological Engineering, University of Minho, 4710-057 Braga, Portugal
| | - Maria Goreti Ferreira Sales
- BioMark@ISEP, School of Engineering, Polytechnic Institute of Porto, 4249-015 Porto, Portugal; (A.P.M.T.); (G.V.M.); (M.F.F.)
- BioMark@UC, Faculty of Sciences and Technology, University of Coimbra, 3030-790 Coimbra, Portugal
- CEB, Centre of Biological Engineering, University of Minho, 4710-057 Braga, Portugal
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