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Ho KL, Ding J, Fan JS, Tsui WNT, Bai J, Fan SK. Digital Microfluidic Multiplex RT-qPCR for SARS-CoV-2 Detection and Variants Discrimination. MICROMACHINES 2023; 14:1627. [PMID: 37630161 PMCID: PMC10456927 DOI: 10.3390/mi14081627] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/04/2023] [Revised: 08/05/2023] [Accepted: 08/11/2023] [Indexed: 08/27/2023]
Abstract
Continuous mutations have occurred in the genome of the SARS-CoV-2 virus since the onset of the COVID-19 pandemic. The increased transmissibility of the mutated viruses has not only imposed medical burdens but also prolonged the duration of the pandemic. A point-of-care (POC) platform that provides multitarget detection will help to track and reduce disease transmissions. Here we detected and discriminated three genotypes of SARS-CoV-2, including the wildtype and two variants of concern (VOCs), the Delta variant and Omicron variant, through reverse transcription quantitative polymerase chain reaction (RT-qPCR) on a digital microfluidics (DMF)-based cartridge. Upon evaluating with the RNA samples of Omicron variant, the DMF RT-qPCR presented a sensitivity of 10 copies/μL and an amplification efficiency of 96.1%, capable for clinical diagnosis. When spiking with SARS-CoV-2 RNA (wildtype, Delta variant, or Omicron variant) and 18S rDNA, the clinical analog samples demonstrated accurate detection and discrimination of different SARS-CoV-2 strains in 49 min.
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Affiliation(s)
- Kuan-Lun Ho
- Department of Mechanical and Nuclear Engineering, Kansas State University, Manhattan, KS 66506, USA; (K.-L.H.); (J.D.)
| | - Jing Ding
- Department of Mechanical and Nuclear Engineering, Kansas State University, Manhattan, KS 66506, USA; (K.-L.H.); (J.D.)
| | - Jia-Shao Fan
- Department of Electrical and Computer Engineering, Kansas State University, Manhattan, KS 66506, USA;
| | - Wai Ning Tiffany Tsui
- Kansas State Veterinary Diagnostic Laboratory, Kansas State University, Manhattan, KS 66506, USA; (W.N.T.T.); (J.B.)
| | - Jianfa Bai
- Kansas State Veterinary Diagnostic Laboratory, Kansas State University, Manhattan, KS 66506, USA; (W.N.T.T.); (J.B.)
- Department of Diagnostic Medicine/Pathobiology, Kansas State University, Manhattan, KS 66506, USA
| | - Shih-Kang Fan
- Department of Mechanical and Nuclear Engineering, Kansas State University, Manhattan, KS 66506, USA; (K.-L.H.); (J.D.)
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Tokamani M, Figgou E, Papamichail L, Sakka E, Toros A, Bouchorikou A, Giannakakis A, Matthaiou EI, Sandaltzopoulos R. A Multiplex PCR Melting-Curve-Analysis-Based Detection Method for the Discrimination of Five Aspergillus Species. J Fungi (Basel) 2023; 9:842. [PMID: 37623613 PMCID: PMC10455196 DOI: 10.3390/jof9080842] [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: 06/17/2023] [Revised: 08/07/2023] [Accepted: 08/07/2023] [Indexed: 08/26/2023] Open
Abstract
Aspergillus mold is a ubiquitously found, airborne pathogen that can cause a variety of diseases from mild to life-threatening in severity. Limitations in diagnostic methods combined with anti-fungal resistance render Aspergillus a global emerging pathogen. In industry, Aspergilli produce toxins, such as aflatoxins, which can cause food spoilage and pose public health risk issues. Here, we report a multiplex qPCR method for the detection and identification of the five most common pathogenic Aspergillus species, Aspergillus fumigatus, Aspergillus flavus, Aspergillus niger, Aspergillus terreus, and Aspergillus nidulans. Our approach exploits species-specific nucleotide polymorphisms within their ITS genomic regions. This novel assay combines multiplex single-color real time qPCR and melting curve analysis and provides a straight-forward, rapid, and cost-effective detection method that can identify five Aspergillus species simultaneously in a single reaction using only six unlabeled primers. Due to their unique fragment lengths, the resulting amplicons are directly linked to certain Aspergillus species like fingerprints, following either electrophoresis or melting curve analysis. Our method is characterized by high analytical sensitivity and specificity, so it may serve as a useful and inexpensive tool for Aspergillus diagnostic applications both in health care and the food industry.
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Affiliation(s)
- Maria Tokamani
- Department of Molecular Biology and Genetics, Faculty of Health Sciences, Democritus University of Thrace, 68100 Alexandroupolis, Greece; (M.T.); (E.F.); (L.P.); (E.S.); (A.T.); (A.B.); (A.G.)
| | - Eleftheria Figgou
- Department of Molecular Biology and Genetics, Faculty of Health Sciences, Democritus University of Thrace, 68100 Alexandroupolis, Greece; (M.T.); (E.F.); (L.P.); (E.S.); (A.T.); (A.B.); (A.G.)
| | - Lito Papamichail
- Department of Molecular Biology and Genetics, Faculty of Health Sciences, Democritus University of Thrace, 68100 Alexandroupolis, Greece; (M.T.); (E.F.); (L.P.); (E.S.); (A.T.); (A.B.); (A.G.)
| | - Eleni Sakka
- Department of Molecular Biology and Genetics, Faculty of Health Sciences, Democritus University of Thrace, 68100 Alexandroupolis, Greece; (M.T.); (E.F.); (L.P.); (E.S.); (A.T.); (A.B.); (A.G.)
| | - Athanasios Toros
- Department of Molecular Biology and Genetics, Faculty of Health Sciences, Democritus University of Thrace, 68100 Alexandroupolis, Greece; (M.T.); (E.F.); (L.P.); (E.S.); (A.T.); (A.B.); (A.G.)
| | - Anastasia Bouchorikou
- Department of Molecular Biology and Genetics, Faculty of Health Sciences, Democritus University of Thrace, 68100 Alexandroupolis, Greece; (M.T.); (E.F.); (L.P.); (E.S.); (A.T.); (A.B.); (A.G.)
| | - Antonis Giannakakis
- Department of Molecular Biology and Genetics, Faculty of Health Sciences, Democritus University of Thrace, 68100 Alexandroupolis, Greece; (M.T.); (E.F.); (L.P.); (E.S.); (A.T.); (A.B.); (A.G.)
| | - Efthymia Iliana Matthaiou
- Department of Medicine, Division of Pulmonary Allergy and Critical Care Medicine, School of Medicine, Stanford University, Stanford, CA 94305, USA;
| | - Raphael Sandaltzopoulos
- Department of Molecular Biology and Genetics, Faculty of Health Sciences, Democritus University of Thrace, 68100 Alexandroupolis, Greece; (M.T.); (E.F.); (L.P.); (E.S.); (A.T.); (A.B.); (A.G.)
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103
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Azzopardi M, Chong YJ, Ng B, Recchioni A, Logeswaran A, Ting DSJ. Diagnosis of Acanthamoeba Keratitis: Past, Present and Future. Diagnostics (Basel) 2023; 13:2655. [PMID: 37627913 PMCID: PMC10453105 DOI: 10.3390/diagnostics13162655] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2023] [Revised: 08/04/2023] [Accepted: 08/09/2023] [Indexed: 08/27/2023] Open
Abstract
Acanthamoeba keratitis (AK) is a painful and sight-threatening parasitic corneal infection. In recent years, the incidence of AK has increased. Timely and accurate diagnosis is crucial during the management of AK, as delayed diagnosis often results in poor clinical outcomes. Currently, AK diagnosis is primarily achieved through a combination of clinical suspicion, microbiological investigations and corneal imaging. Historically, corneal scraping for microbiological culture has been considered to be the gold standard. Despite its technical ease, accessibility and cost-effectiveness, the long diagnostic turnaround time and variably low sensitivity of microbiological culture limit its use as a sole diagnostic test for AK in clinical practice. In this review, we aim to provide a comprehensive overview of the diagnostic modalities that are currently used to diagnose AK, including microscopy with staining, culture, corneal biopsy, in vivo confocal microscopy, polymerase chain reaction and anterior segment optical coherence tomography. We also highlight emerging techniques, such as next-generation sequencing and artificial intelligence-assisted models, which have the potential to transform the diagnostic landscape of AK.
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Affiliation(s)
- Matthew Azzopardi
- Department of Ophthalmology, Royal London Hospital, London E1 1BB, UK;
| | - Yu Jeat Chong
- Birmingham and Midland Eye Centre, Birmingham B18 7QH, UK; (B.N.); (A.R.)
| | - Benjamin Ng
- Birmingham and Midland Eye Centre, Birmingham B18 7QH, UK; (B.N.); (A.R.)
| | - Alberto Recchioni
- Birmingham and Midland Eye Centre, Birmingham B18 7QH, UK; (B.N.); (A.R.)
- Academic Unit of Ophthalmology, Institute of Inflammation and Ageing, University of Birmingham, Birmingham B15 2TT, UK
| | | | - Darren S. J. Ting
- Birmingham and Midland Eye Centre, Birmingham B18 7QH, UK; (B.N.); (A.R.)
- Academic Unit of Ophthalmology, Institute of Inflammation and Ageing, University of Birmingham, Birmingham B15 2TT, UK
- Academic Ophthalmology, School of Medicine, University of Nottingham, Nottingham NG7 2RD, UK
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104
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da Silva Queiroz JA, Roca TP, Souza RB, de Souza LFA, Passos-Silva AM, da Silva ALF, de Castro E Silva E, Borzacov LMP, de Cássia Pontello Rampazzo R, Dos Santos Pereira S, Dantas TO, Mazaro J, Villar LM, Salcedo JMV, da Matta DA, Vieira D. Development of quantitative multiplex RT-qPCR one step assay for detection of hepatitis delta virus. Sci Rep 2023; 13:12073. [PMID: 37495613 PMCID: PMC10372040 DOI: 10.1038/s41598-023-37756-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Accepted: 06/27/2023] [Indexed: 07/28/2023] Open
Abstract
Hepatitis Delta is a disease caused by exposure to hepatitis B (HBV) and hepatitis D (HDV) viruses, usually with a more severe clinical outcome when compared to an HBV monoinfection. To date, the real prevalence of HDV infection is underestimated and detection methods are poorly available, especially in more endemic regions. Therefore, a one-step RT-qPCR method for quantification of HDV-RNA was developed. Biological samples were selected between 2017 and 2023 from patients at the Ambulatório Especializado em Hepatites Virais of the Centro de Pesquisa em Medicina Tropical de Rondônia and Serviço de Assistência Especializada and underwent the test developed by this study and a second quantitative RT-qPCR assay. The slope of the initial quantitative assay was - 3.321 with an efficiency of 100.04% and amplification factor equal to 2. Analysis of the repeatability data revealed a Limit of Quantification of 5 copies/reaction and Limit of Detection (95%) of 2.83 copies per reaction. In the diagnostic sensitivity tests, there was an accuracy of 97.37% when compared to the reference test. This assay proved to be highly efficient and reproducible, making it a valuable tool to monitor hepatitis Delta patients and assess the risk of disease progression, as well as the effectiveness of treatment.
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Affiliation(s)
- Jackson Alves da Silva Queiroz
- Fundação Oswaldo Cruz Rondônia FIOCRUZ/RO, Rua da Beira, 7176, Porto Velho, 76812-245, Brazil
- Programa de Pós-Graduação em Biologia Experimental, Universidade Federal de Rondônia e Fundação Oswaldo Cruz Rondônia - UNIR/FIOCRUZ/RO, 76801-974, Porto Velho, Brazil
| | - Tárcio Peixoto Roca
- Fundação Oswaldo Cruz Rondônia FIOCRUZ/RO, Rua da Beira, 7176, Porto Velho, 76812-245, Brazil
- Programa de Pós-Graduação em Medicina Tropical, Instituto Oswaldo Cruz/IOC, FIOCRUZ, 21041-250, Rio de Janeiro, Brazil
| | - Rutilene Barbosa Souza
- Centro de Infectologia Charles Merieux & Laboratório Rodolphe Merieux (FUNDHACRE), Rio Branco, 69918-340, Brazil
- Universidade Federal da Bahia - UFBA, Salvador, 40110-909, Brazil
| | - Luiz Fellype Alves de Souza
- Programa de Pós-Graduação em Medicina Tropical, Instituto Oswaldo Cruz/IOC, FIOCRUZ, 21041-250, Rio de Janeiro, Brazil
- Centro de Infectologia Charles Merieux & Laboratório Rodolphe Merieux (FUNDHACRE), Rio Branco, 69918-340, Brazil
| | - Ana Maísa Passos-Silva
- Fundação Oswaldo Cruz Rondônia FIOCRUZ/RO, Rua da Beira, 7176, Porto Velho, 76812-245, Brazil
- Programa de Pós-Graduação em Biologia Experimental, Universidade Federal de Rondônia e Fundação Oswaldo Cruz Rondônia - UNIR/FIOCRUZ/RO, 76801-974, Porto Velho, Brazil
| | - André Luiz Ferreira da Silva
- Fundação Oswaldo Cruz Rondônia FIOCRUZ/RO, Rua da Beira, 7176, Porto Velho, 76812-245, Brazil
- Programa de Pós-Graduação em Biologia Experimental, Universidade Federal de Rondônia e Fundação Oswaldo Cruz Rondônia - UNIR/FIOCRUZ/RO, 76801-974, Porto Velho, Brazil
| | - Eugênia de Castro E Silva
- Programa de Pós-Graduação em Medicina Tropical, Instituto Oswaldo Cruz/IOC, FIOCRUZ, 21041-250, Rio de Janeiro, Brazil
- Centro de Pesquisa em Medicina Tropical - CEPEM, Porto Velho, 76812-329, Brazil
| | | | | | - Soraya Dos Santos Pereira
- Fundação Oswaldo Cruz Rondônia FIOCRUZ/RO, Rua da Beira, 7176, Porto Velho, 76812-245, Brazil
- Programa de Pós-Graduação em Biologia Experimental, Universidade Federal de Rondônia e Fundação Oswaldo Cruz Rondônia - UNIR/FIOCRUZ/RO, 76801-974, Porto Velho, Brazil
| | | | - Janaína Mazaro
- Laboratório Central de Saúde Pública do Acre - LACEN/AC, Rio Branco, 69900-614, Brazil
| | - Lívia Melo Villar
- Programa de Pós-Graduação em Medicina Tropical, Instituto Oswaldo Cruz/IOC, FIOCRUZ, 21041-250, Rio de Janeiro, Brazil
| | | | - Daniel Archimedes da Matta
- Centro de Infectologia Charles Merieux & Laboratório Rodolphe Merieux (FUNDHACRE), Rio Branco, 69918-340, Brazil
| | - Deusilene Vieira
- Fundação Oswaldo Cruz Rondônia FIOCRUZ/RO, Rua da Beira, 7176, Porto Velho, 76812-245, Brazil.
- Programa de Pós-Graduação em Biologia Experimental, Universidade Federal de Rondônia e Fundação Oswaldo Cruz Rondônia - UNIR/FIOCRUZ/RO, 76801-974, Porto Velho, Brazil.
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105
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Zambrano-Romero A, Ramirez-Villacis DX, Barriga-Medina N, Sierra-Alvarez R, Trueba G, Ochoa-Herrera V, Leon-Reyes A. Comparative Methods for Quantification of Sulfate-Reducing Bacteria in Environmental and Engineered Sludge Samples. BIOLOGY 2023; 12:985. [PMID: 37508415 PMCID: PMC10375983 DOI: 10.3390/biology12070985] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/02/2023] [Revised: 06/28/2023] [Accepted: 07/06/2023] [Indexed: 07/30/2023]
Abstract
This study aimed to compare microscopic counting, culture, and quantitative or real-time PCR (qPCR) to quantify sulfate-reducing bacteria in environmental and engineered sludge samples. Four sets of primers that amplified the dsrA and apsA gene encoding the two key enzymes of the sulfate-reduction pathway were initially tested. qPCR standard curves were constructed using genomic DNA from an SRB suspension and dilutions of an enriched sulfate-reducing sludge. According to specificity and reproducibility, the DSR1F/RH3-dsr-R primer set ensured a good quantification based on dsrA gene amplification; however, it exhibited inconsistencies at low and high levels of SRB concentrations in environmental and sulfate-reducing sludge samples. Ultimately, we conducted a qPCR method normalized to dsrA gene copies, using a synthetic double-stranded DNA fragment as a calibrator. This method fulfilled all validation criteria and proved to be specific, accurate, and precise. The enumeration of metabolically active SRB populations through culture methods differed from dsrA gene copies but showed a plausible positive correlation. Conversely, microscopic counting had limitations due to distinguishing densely clustered organisms, impacting precision. Hence, this study proves that a qPCR-based method optimized with dsrA gene copies as a calibrator is a sensitive molecular tool for the absolute enumeration of SRB populations in engineered and environmental sludge samples.
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Affiliation(s)
- Aracely Zambrano-Romero
- Instituto de Microbiología, Universidad San Francisco de Quito USFQ, Campus Cumbayá, Diego de Robles y Vía Interoceánica, Quito 17-1200-841, Ecuador
| | - Dario X Ramirez-Villacis
- Instituto de Microbiología, Universidad San Francisco de Quito USFQ, Campus Cumbayá, Diego de Robles y Vía Interoceánica, Quito 17-1200-841, Ecuador
- Colegio de Ciencias e Ingeniería, Universidad San Francisco de Quito USFQ, Campus Cumbayá, Diego de Robles s/n y Vía Interoceánica, Quito 17-1200-841, Ecuador
- Laboratorio de Biotecnología Agrícola y de Alimentos, Ingeniería en Agronomía, Colegio de Ciencias e Ingenierías, Universidad San Francisco de Quito USFQ, Campus Cumbayá, Diego de Robles y Vía Interoceánica, Quito 17-1200-841, Ecuador
| | - Noelia Barriga-Medina
- Colegio de Ciencias e Ingeniería, Universidad San Francisco de Quito USFQ, Campus Cumbayá, Diego de Robles s/n y Vía Interoceánica, Quito 17-1200-841, Ecuador
- Laboratorio de Biotecnología Agrícola y de Alimentos, Ingeniería en Agronomía, Colegio de Ciencias e Ingenierías, Universidad San Francisco de Quito USFQ, Campus Cumbayá, Diego de Robles y Vía Interoceánica, Quito 17-1200-841, Ecuador
| | - Reyes Sierra-Alvarez
- Department of Chemical and Environmental Engineering, The University of Arizona, P.O. Box 210011, Tucson, AZ 85721-0011, USA
| | - Gabriel Trueba
- Instituto de Microbiología, Universidad San Francisco de Quito USFQ, Campus Cumbayá, Diego de Robles y Vía Interoceánica, Quito 17-1200-841, Ecuador
| | - Valeria Ochoa-Herrera
- Colegio de Ciencias e Ingeniería, Universidad San Francisco de Quito USFQ, Campus Cumbayá, Diego de Robles s/n y Vía Interoceánica, Quito 17-1200-841, Ecuador
- Department of Environmental Sciences and Engineering, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599-3280, USA
| | - Antonio Leon-Reyes
- Colegio de Ciencias e Ingeniería, Universidad San Francisco de Quito USFQ, Campus Cumbayá, Diego de Robles s/n y Vía Interoceánica, Quito 17-1200-841, Ecuador
- Laboratorio de Biotecnología Agrícola y de Alimentos, Ingeniería en Agronomía, Colegio de Ciencias e Ingenierías, Universidad San Francisco de Quito USFQ, Campus Cumbayá, Diego de Robles y Vía Interoceánica, Quito 17-1200-841, Ecuador
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599-3280, USA
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106
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Carvalho MJ, S Oliveira AL, Santos Pedrosa S, Pintado M, Pinto-Ribeiro I, Madureira AR. Skin Microbiota and the Cosmetic Industry. MICROBIAL ECOLOGY 2023; 86:86-96. [PMID: 35809121 DOI: 10.1007/s00248-022-02070-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/02/2022] [Accepted: 06/30/2022] [Indexed: 06/15/2023]
Abstract
Skin harbors an important microbial ecosystem - the skin microbiota that is in homeostasis with its host and is beneficial for human health. Cosmetic products have the potential to interfere with this microbial community; therefore their impact should be assessed. The aim of this review is to highlight the importance of skin microbiota in the cosmetic industry. Several studies determined that cosmetic ingredients have the potential to disrupt the skin microbiota equilibrium leading to the development of skin diseases and dysregulation of immune response. These studies led their investigation by using different methodologies and models, concluding that methods must be chosen according to the aim of the study, the skin site to be evaluated, and the target population of the cosmetics. Overall, it is crucial to test the impact of cosmetics in the skin microbiota and to stablish standard procedures, as well as specific criteria that allow to classify a cosmetic product as skin microbiota friendly.
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Affiliation(s)
- Maria João Carvalho
- Escola Superior de Biotecnologia, Universidade Católica Portuguesa, Rua Diogo Botelho 1327, 4169-005, Porto, Portugal
| | - Ana L S Oliveira
- Escola Superior de Biotecnologia, Universidade Católica Portuguesa, Rua Diogo Botelho 1327, 4169-005, Porto, Portugal
| | - Sílvia Santos Pedrosa
- Escola Superior de Biotecnologia, Universidade Católica Portuguesa, Rua Diogo Botelho 1327, 4169-005, Porto, Portugal
| | - Manuela Pintado
- Escola Superior de Biotecnologia, Universidade Católica Portuguesa, Rua Diogo Botelho 1327, 4169-005, Porto, Portugal
| | - Inês Pinto-Ribeiro
- Escola Superior de Biotecnologia, Universidade Católica Portuguesa, Rua Diogo Botelho 1327, 4169-005, Porto, Portugal
- Amyris Bio Products Portugal Unipessoal Lda, Rua Diogo Botelho 1327, 4169-005, Porto, Portugal
| | - Ana Raquel Madureira
- Escola Superior de Biotecnologia, Universidade Católica Portuguesa, Rua Diogo Botelho 1327, 4169-005, Porto, Portugal.
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107
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Olander J, Barkarmo S, Hammarström Johansson P, Wennerberg A, Stenport VF. Inflammatory Gene Profile and Particle Presence in Peri-Implant Mucosa: a Pilot Study on 9 Patients. J Oral Maxillofac Res 2023; 14:e2. [PMID: 37969950 PMCID: PMC10645473 DOI: 10.5037/jomr.2023.14302] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Accepted: 09/27/2023] [Indexed: 11/17/2023]
Abstract
Objectives The purpose of this pilot study is to compare gene expression in mucosa around dental implants with zirconia abutment to titanium and investigate presence of particles in mucosa samples and on implant heads. Material and Methods Ten patients with a single implant supported prosthesis connected to zirconia or titanium abutments were invited at the five-year control. A clinical examination and a survey on experience of function and appearance were conducted. A mucosa biopsy taken in close vicinity to the implant were analysed by real-time polymerase chain reaction (qPCR) and presence of particles in a scanning electron microscope/energy-dispersive X-ray spectroscope (SEM/EDX). Cytological smear samples were collected and analysed through inductively coupled plasma mass spectrometry (ICP-MS) to investigate presence of particles on implant heads. Results In total, 9 patients participated in the study, five with titanium abutments and four with zirconia abutments. All patients were satisfied with function and aesthetics. Titanium and iron particles were detected in mucosa biopsies. The ICP - MS analysis demonstrated presence of zirconia and titanium. Several proinflammatory genes were upregulated in the zirconia abutment group. Conclusions Around zirconia abutments a slight increase in proinflammatory response and amount of wear particles was seen as compared to titanium. Wear particles of titanium were present in all soft tissue samples, however zirconia particles only in the samples from implants heads/mucosa with zirconia abutments.
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Affiliation(s)
- Julia Olander
- Department of Prosthodontics and Dental Materials Science, Institute of Odontology, The Sahlgrenska Academy, University of Gothenburg, GothenburgSweden.
| | - Sargon Barkarmo
- Department of Prosthodontics and Dental Materials Science, Institute of Odontology, The Sahlgrenska Academy, University of Gothenburg, GothenburgSweden.
| | - Petra Hammarström Johansson
- Department of Prosthodontics and Dental Materials Science, Institute of Odontology, The Sahlgrenska Academy, University of Gothenburg, GothenburgSweden.
| | - Ann Wennerberg
- Department of Prosthodontics and Dental Materials Science, Institute of Odontology, The Sahlgrenska Academy, University of Gothenburg, GothenburgSweden.
| | - Victoria Franke Stenport
- Department of Prosthodontics and Dental Materials Science, Institute of Odontology, The Sahlgrenska Academy, University of Gothenburg, GothenburgSweden.
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108
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Chen Z, Halford NG, Liu C. Real-Time Quantitative PCR: Primer Design, Reference Gene Selection, Calculations and Statistics. Metabolites 2023; 13:806. [PMID: 37512513 PMCID: PMC10384377 DOI: 10.3390/metabo13070806] [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: 05/05/2023] [Revised: 06/09/2023] [Accepted: 06/27/2023] [Indexed: 07/30/2023] Open
Abstract
Real-time quantitative PCR is a technique that can measure the content of the target nucleic acid sequence of interest in a given sample. It is mainly divided into absolute and relative quantitative methods. The relative quantification is mainly used in gene expressions for functional genomic and transcriptome studies. However, to use this technology accurately, there are some key points to master. First, specific primers need to be designed to ensure amplification of the gene of interest (GOI). Second, the appropriate reference gene or reference gene combination has to be selected. Finally, scientific gene expression level calculations and statistics are required to obtain accurate results. Therefore, this work proposes a workflow for relative quantitative PCR and introduces the relevant points so that beginners can better understand and use this technology.
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Affiliation(s)
- Zhiwei Chen
- Shanghai Key Laboratory of Agricultural Genetics and Breeding, Biotechnology Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai 201106, China
| | | | - Chenghong Liu
- Shanghai Key Laboratory of Agricultural Genetics and Breeding, Biotechnology Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai 201106, China
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109
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De Tomassi A, Reiter A, Reiger M, Rauer L, Rohayem R, Ck-Care Study Group, Traidl-Hoffmann C, Neumann AU, Hülpüsch C. Combining 16S Sequencing and qPCR Quantification Reveals Staphylococcus aureus Driven Bacterial Overgrowth in the Skin of Severe Atopic Dermatitis Patients. Biomolecules 2023; 13:1030. [PMID: 37509067 PMCID: PMC10377005 DOI: 10.3390/biom13071030] [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: 04/25/2023] [Revised: 06/11/2023] [Accepted: 06/18/2023] [Indexed: 07/30/2023] Open
Abstract
Atopic dermatitis (AD) is an inflammatory skin disease with a microbiome dysbiosis towards a high relative abundance of Staphylococcus aureus. However, information is missing on the actual bacterial load on AD skin, which may affect the cell number driven release of pathogenic factors. Here, we combined the relative abundance results obtained by next-generation sequencing (NGS, 16S V1-V3) with bacterial quantification by targeted qPCR (total bacterial load = 16S, S. aureus = nuc gene). Skin swabs were sampled cross-sectionally (n = 135 AD patients; n = 20 healthy) and longitudinally (n = 6 AD patients; n = 6 healthy). NGS and qPCR yielded highly inter-correlated S. aureus relative abundances and S. aureus cell numbers. Additionally, intra-individual differences between body sides, skin status, and consecutive timepoints were also observed. Interestingly, a significantly higher total bacterial load, in addition to higher S. aureus relative abundance and cell numbers, was observed in AD patients in both lesional and non-lesional skin, as compared to healthy controls. Moreover, in the lesional skin of AD patients, higher S. aureus cell numbers significantly correlated with the higher total bacterial load. Furthermore, significantly more severe AD patients presented with higher S. aureus cell number and total bacterial load compared to patients with mild or moderate AD. Our results indicate that severe AD patients exhibit S. aureus driven increased bacterial skin colonization. Overall, bacterial quantification gives important insights in addition to microbiome composition by sequencing.
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Affiliation(s)
- Amedeo De Tomassi
- Environmental Medicine, Faculty of Medicine, University of Augsburg, 86156 Augsburg, Germany
| | - Anna Reiter
- Environmental Medicine, Faculty of Medicine, University of Augsburg, 86156 Augsburg, Germany
| | - Matthias Reiger
- Environmental Medicine, Faculty of Medicine, University of Augsburg, 86156 Augsburg, Germany
| | - Luise Rauer
- Environmental Medicine, Faculty of Medicine, University of Augsburg, 86156 Augsburg, Germany
- Institute of Environmental Medicine, Helmholtz Zentrum München, 86156 Augsburg, Germany
- Environmental Medicine, Technical University of Munich, 86156 Augsburg, Germany
| | - Robin Rohayem
- Environmental Medicine, Faculty of Medicine, University of Augsburg, 86156 Augsburg, Germany
| | - Ck-Care Study Group
- CK CARE, Christine-Kühne Center for Allergy Research and Education, 7265 Davos, Switzerland
| | - Claudia Traidl-Hoffmann
- Environmental Medicine, Faculty of Medicine, University of Augsburg, 86156 Augsburg, Germany
- Institute of Environmental Medicine, Helmholtz Zentrum München, 86156 Augsburg, Germany
- Environmental Medicine, Technical University of Munich, 86156 Augsburg, Germany
- CK CARE, Christine-Kühne Center for Allergy Research and Education, 7265 Davos, Switzerland
- ZIEL-Institute for Food and Health, Technical University of Munich, 85354 Freising, Germany
| | - Avidan U Neumann
- Environmental Medicine, Faculty of Medicine, University of Augsburg, 86156 Augsburg, Germany
- Institute of Environmental Medicine, Helmholtz Zentrum München, 86156 Augsburg, Germany
- CK CARE, Christine-Kühne Center for Allergy Research and Education, 7265 Davos, Switzerland
| | - Claudia Hülpüsch
- Environmental Medicine, Faculty of Medicine, University of Augsburg, 86156 Augsburg, Germany
- Environmental Medicine, Technical University of Munich, 86156 Augsburg, Germany
- CK CARE, Christine-Kühne Center for Allergy Research and Education, 7265 Davos, Switzerland
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Mohseni N, Chang M, Garcia K, Weakley M, Do T, Mir S. Development of a Syndromic Molecular Diagnostic Assay for Tick-Borne Pathogens Using Barcoded Magnetic Bead Technology. Microbiol Spectr 2023; 11:e0439522. [PMID: 37166314 PMCID: PMC10269837 DOI: 10.1128/spectrum.04395-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Accepted: 04/22/2023] [Indexed: 05/12/2023] Open
Abstract
Infectious disease diagnostics often depend on costly serological testing with poor sensitivity, low specificity, and long turnaround time. Here, we demonstrate proof of the principle for simultaneous detection of two tick-borne pathogens from a single test sample using barcoded magnetic bead technology on the BioCode 2500 system. Specific primer sets complementary to the conserved genes of Anaplasma phagocytophilum and Borrelia burgdorferi were used in PCR amplification of the target, followed by the hybridization of the resulting biotinylated PCR products with specific probes tethered to the barcoded magnetic beads for simultaneous detection, using a fluorophore with high quantum yield. The assay has an extremely high signal to background ratio, with a limit of detection (LOD) of 2.81 50% tissue culture infection dose (TCID50)/mL and 1 CFU/mL for A. phagocytophilum and B. burgdorferi, respectively. The observed LOD for gene blocks was 1.8 copies/reaction for both the pathogens. The assay demonstrated 100% positive and negative agreement on performance evaluation using patient specimens and blood samples spiked with 1 × LOD of pathogen stock. No cross-reactivity was observed with other related tick-borne pathogens and genomic DNA of human, cattle, and canine origin. The assay can be upgraded to a sensitive and cost-effective multiplex diagnostic approach that can simultaneously detect multiple clinically important tick-borne pathogens in a single sample with a short turnaround time. IMPORTANCE The low pathogen load in the tick-borne disease test samples and the lack of highly sensitive multiplex diagnostic approaches have impacted diagnosis during clinical testing and limited surveillance studies to gauge prior insight about the prevalence of tick-borne infections in a geographical area. This article demonstrates proof of the principle for simultaneous detection of two important tick-borne pathogens from a single test sample using digital barcoded magnetic bead technology. Using a fluorophore of high quantum yield, the diagnostic approach showed high sensitivity and specificity. The LOD was 1.8 genome copies per reaction for both A. phagocytophilum and B. burgdorferi. The assay can be upgraded for the detection of all clinically important tick-borne pathogens from a single patient sample with high sensitivity and specificity. The assay can provide a diagnostic answer to the clinician in a short turnaround time to facilitate speedy therapeutic intervention to infected patients and implement public health measures to prevent community spread.
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Affiliation(s)
- Nazleeen Mohseni
- College of Veterinary Medicine, Western University of Health Sciences, Pomona, California, USA
| | - Mariann Chang
- College of Veterinary Medicine, Western University of Health Sciences, Pomona, California, USA
| | - Kathryn Garcia
- College of Veterinary Medicine, Western University of Health Sciences, Pomona, California, USA
| | - Mina Weakley
- College of Veterinary Medicine, Western University of Health Sciences, Pomona, California, USA
| | - Tram Do
- College of Veterinary Medicine, Western University of Health Sciences, Pomona, California, USA
| | - Sheema Mir
- College of Veterinary Medicine, Western University of Health Sciences, Pomona, California, USA
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111
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Kyathanahalli C, Snedden M, Singh L, Regalia C, Keenan-Devlin L, Borders AE, Hirsch E. Maternal plasma and salivary anelloviruses in pregnancy and preterm birth. Front Med (Lausanne) 2023; 10:1191938. [PMID: 37396897 PMCID: PMC10309558 DOI: 10.3389/fmed.2023.1191938] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Accepted: 05/23/2023] [Indexed: 07/04/2023] Open
Abstract
Introduction Human anelloviruses, including torque teno virus (TTV) and torque teno mini virus (TTMV), are ubiquitous in the general population and have no known pathogenicity. We investigated the prevalence and viral load of TTV and TTMV in plasma and saliva over pregnancy, and assessed their association with spontaneous or medically indicated preterm birth. Methods This is a secondary analysis of the Measurement of Maternal Stress (MOMS) study, which recruited 744 individuals with singleton pregnancies from 4 US sites (Chicago, Pittsburgh, San Antonio, and rural Pennsylvania). Baseline outpatient visits took place in the second trimester (between 12'0 and 20'6/7 weeks' gestation), and follow-up visits in the third trimester (between 32'0 and 35'6/7 weeks' gestation). In a case-control study design, participants who delivered preterm (<37 weeks) resulting from spontaneous labor and/or preterm premature rupture of membranes ("sPTB") were compared with participants experiencing medically indicated preterm birth ("iPTB"), or delivery at term ("controls"). Plasma and saliva samples obtained during the second and third trimesters were tested for the presence and quantity of TTV and TTMV using real-time PCR. Demographic data were obtained via self-report, and clinical data via medical record review by trained research personnel. Results TTV was detected in plasma from 81% (second trimester) and 77% (third trimester) of participants, and in saliva from 64 and 60%. Corresponding detection rates for TTMV were 59 and 41% in plasma, and 35 and 24% in saliva. TTV and TTMV concentrations were similar between matched plasma and saliva samples. TTV prevalence and concentrations were not significantly different between groups (sPTB, iPTB, and controls). However, plasma TTMV in the third trimester was associated with sPTB and earlier gestational age at delivery. The iPTB group was not different from either the sPTB or the control group. In saliva, concentrations of TTV and TTMV were similar among the three groups. Both TTV and TTMV were more prevalent with increasing parity and were more common in Black and Hispanic participants compared to non-Hispanic White participants. Conclusion Anellovirus presence (specifically, TTMV) in the third trimester may be associated with preterm birth. Whether this association is causative remains to be determined.
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Affiliation(s)
- Chandrashekara Kyathanahalli
- Department of Obstetrics and Gynecology, NorthShore University HealthSystem, Evanston, IL, United States
- Department of Obstetrics and Gynecology, Pritzker School of Medicine, University of Chicago, Chicago, IL, United States
| | - Madeline Snedden
- Department of Obstetrics and Gynecology, NorthShore University HealthSystem, Evanston, IL, United States
| | - Lavisha Singh
- Department of Statistics, NorthShore University HealthSystem, Evanston, IL, United States
| | - Camilla Regalia
- Department of Obstetrics and Gynecology, NorthShore University HealthSystem, Evanston, IL, United States
| | - Lauren Keenan-Devlin
- Department of Obstetrics and Gynecology, NorthShore University HealthSystem, Evanston, IL, United States
- Department of Obstetrics and Gynecology, Pritzker School of Medicine, University of Chicago, Chicago, IL, United States
| | - Ann E. Borders
- Department of Obstetrics and Gynecology, NorthShore University HealthSystem, Evanston, IL, United States
- Department of Obstetrics and Gynecology, Pritzker School of Medicine, University of Chicago, Chicago, IL, United States
- Center for Healthcare Studies, Institute for Public Health and Medicine, University of Chicago Pritzker School of Medicine, Northwestern University, Evanston, IL, United States
| | - Emmet Hirsch
- Department of Obstetrics and Gynecology, NorthShore University HealthSystem, Evanston, IL, United States
- Department of Obstetrics and Gynecology, Pritzker School of Medicine, University of Chicago, Chicago, IL, United States
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112
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Nikolaou M, Tam VH. Rapid In Vitro Assessment of Antimicrobial Drug Effect Bridging Clinically Relevant Pharmacokinetics: A Comprehensive Methodology. Pharmaceutics 2023; 15:1671. [PMID: 37376120 DOI: 10.3390/pharmaceutics15061671] [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: 04/13/2023] [Revised: 05/24/2023] [Accepted: 06/01/2023] [Indexed: 06/29/2023] Open
Abstract
Rapid in vitro assessment of antimicrobial drug efficacy under clinically relevant pharmacokinetic conditions is an essential element of both drug development and clinical use. Here, we present a comprehensive overview of a recently developed novel integrated methodology for rapid assessment of such efficacy, particularly against the emergence of resistant bacterial strains, as jointly researched by the authors in recent years. This methodology enables rapid in vitro assessment of the antimicrobial efficacy of single or multiple drugs in combination, following clinically relevant pharmacokinetics. The proposed methodology entails (a) the automated collection of longitudinal time-kill data in an optical-density instrument; (b) the processing of collected time-kill data with the aid of a mathematical model to determine optimal dosing regimens under clinically relevant pharmacokinetics for single or multiple drugs; and (c) in vitro validation of promising dosing regimens in a hollow fiber system. Proof-of-concept of this methodology through a number of in vitro studies is discussed. Future directions for the refinement of optimal data collection and processing are discussed.
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Affiliation(s)
- Michael Nikolaou
- Chemical & Biomolecular Engineering Department, University of Houston, Houston, TX 77204, USA
| | - Vincent H Tam
- Chemical & Biomolecular Engineering Department, University of Houston, Houston, TX 77204, USA
- Department of Pharmacy Practice & Translational Research, University of Houston, Houston, TX 77204, USA
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Abdul Rahman NA, Mohd Desa MN, Masri SN, Taib NM, Sulaiman N, Hazman H, John J. The Molecular Approaches and Challenges of Streptococcus pneumoniae Serotyping for Epidemiological Surveillance in the Vaccine Era. Pol J Microbiol 2023; 72:103-115. [PMID: 37314355 DOI: 10.33073/pjm-2023-023] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Accepted: 05/09/2023] [Indexed: 06/15/2023] Open
Abstract
Streptococcus pneumoniae (pneumococcus) belongs to the Gram-positive cocci. This bacterium typically colonizes the nasopharyngeal region of healthy individuals. It has a distinct polysaccharide capsule - a virulence factor allowing the bacteria to elude the immune defense mechanisms. Consequently, it might trigger aggressive conditions like septicemia and meningitis in immunocompromised or older individuals. Moreover, children below five years of age are at risk of morbidity and mortality. Studies have found 101 S. pneumoniae capsular serotypes, of which several correlate with clinical and carriage isolates with distinct disease aggressiveness. Introducing pneumococcal conjugate vaccines (PCV) targets the most common disease-associated serotypes. Nevertheless, vaccine selection pressure leads to replacing the formerly dominant vaccine serotypes (VTs) by non-vaccine types (NVTs). Therefore, serotyping must be conducted for epidemiological surveillance and vaccine assessment. Serotyping can be performed using numerous techniques, either by the conventional antisera-based (Quellung and latex agglutination) or molecular-based approaches (sequetyping, multiplex PCR, real-time PCR, and PCR-RFLP). A cost-effective and practical approach must be used to enhance serotyping accuracy to monitor the prevalence of VTs and NVTs. Therefore, dependable pneumococcal serotyping techniques are essential to precisely monitor virulent lineages, NVT emergence, and genetic associations of isolates. This review discusses the principles, associated benefits, and drawbacks of the respective available conventional and molecular approaches, and potentially the whole genome sequencing (WGS) to be directed for future exploration.
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Affiliation(s)
- Nurul Asyikin Abdul Rahman
- 1Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia, Serdang, Malaysia
- 2School of Biology, Faculty of Applied Sciences, Universiti Teknologi MARA, Kuala Pilah, Malaysia
| | - Mohd Nasir Mohd Desa
- 1Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia, Serdang, Malaysia
| | - Siti Norbaya Masri
- 3Department of Medical Microbiology, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia, Serdang, Malaysia
| | - Niazlin Mohd Taib
- 3Department of Medical Microbiology, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia, Serdang, Malaysia
| | - Nurshahira Sulaiman
- 1Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia, Serdang, Malaysia
| | - Hazmin Hazman
- 1Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia, Serdang, Malaysia
| | - James John
- 4Department of Medical Laboratory Technology, School of Allied Health Science, Sathyabama Institute of Science and Technology, Chennai, India
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Kim LH, Mikolaityte V, Kim S. Establishment of wastewater-based SARS-CoV-2 monitoring system over two years: Case studies in South Korea. JOURNAL OF ENVIRONMENTAL CHEMICAL ENGINEERING 2023; 11:110289. [PMID: 37292384 PMCID: PMC10240911 DOI: 10.1016/j.jece.2023.110289] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Revised: 05/22/2023] [Accepted: 06/03/2023] [Indexed: 06/10/2023]
Abstract
With the global COVID-19 pandemic, wastewater surveillance has received a considerable attention as a method for the early identification of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in wastewater treatment plant (WWTP) and sewer systems. For the first time in Korea, this study utilized the wastewater surveillance technique to monitor the COVID-19 outbreak. Sampling efforts were carried out at the WWTPs in the capital city of Korea, Seoul, and Daegu the place where the first severe outbreak was reported. The RNA of Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has been extracted from the collected wastewater influent and primary sewage sludge samples. The outcomes were contrasted with the COVID-19 cases in the WWTPs served area. Additionally, whole transcriptome sequencing was used to compare the microbial community alterations before and after the COVID-19 outbreak and SARS-CoV-2 variations. The results demonstrated that the changes in SARS-CoV-2 RNA concentrations in the influent and sludge matched the trends of reported COVID-19 cases, especially sludge showed high-resolution data, which is well-matched when fewer COVID-19 cases (0-250) are reported. Interestingly, one month before the clinical report, we found that the SARS-CoV-2 Beta variant (South Africa, B.1.351) in the wastewater. In addition, the Aeromonas bacterial species was dominated (21.2%) among other bacterial species in wastewater after the COVID-19 outbreak, suggesting a potential indirect microbial indicator of the COVID-19 outbreak.
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Affiliation(s)
- Lan Hee Kim
- Research Institute for Advanced Industrial Technology, Korea University, 2511 Sejong-ro, Sejong city 30019, Republic of Korea
| | - Viktorija Mikolaityte
- Research Institute for Advanced Industrial Technology, Korea University, 2511 Sejong-ro, Sejong city 30019, Republic of Korea
| | - Sungpyo Kim
- Research Institute for Advanced Industrial Technology, Korea University, 2511 Sejong-ro, Sejong city 30019, Republic of Korea
- Department of Environmental Systems Engineering, Korea University, 2511 Sejong-ro, Sejong city 30019, Republic of Korea
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115
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de Carvalho NM, Oliveira DL, Costa CM, Pintado ME, Madureira AR. Strategies to Assess the Impact of Sustainable Functional Food Ingredients on Gut Microbiota. Foods 2023; 12:2209. [PMID: 37297454 PMCID: PMC10253045 DOI: 10.3390/foods12112209] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2023] [Revised: 05/27/2023] [Accepted: 05/29/2023] [Indexed: 06/12/2023] Open
Abstract
Nowadays, it is evident that food ingredients have different roles and distinct health benefits to the consumer. Over the past years, the interest in functional foods, especially those targeting gut health, has grown significantly. The use of industrial byproducts as a source of new functional and sustainable ingredients as a response to such demands has raised interest. However, the properties of these ingredients can be affected once incorporated into different food matrices. Therefore, when searching for the least costly and most suitable, beneficial, and sustainable formulations, it is necessary to understand how such ingredients perform when supplemented in different food matrices and how they impact the host's health. As proposed in this manuscript, the ingredients' properties can be first evaluated using in vitro gastrointestinal tract (GIT) simulation models prior to validation through human clinical trials. In vitro models are powerful tools that mimic the physicochemical and physiological conditions of the GIT, enabling prediction of the potentials of functional ingredients per se and when incorporated into a food matrix. Understanding how newly developed ingredients from undervalued agro-industrial sources behave as supplements supports the development of new and more sustainable functional foods while scientifically backing up health-benefits claims.
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Affiliation(s)
- Nelson Mota de Carvalho
- CBQF—Centro de Biotecnologia e Química Fina—Laboratório Associado, Escola Superior de Biotecnologia, Universidade Católica Portuguesa, Rua Diogo Botelho, 1327, 4169-005 Porto, Portugal; (N.M.d.C.); (C.M.C.); (M.E.P.)
| | - Diana Luazi Oliveira
- Research and Innovation Unit—Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Rua Alfredo Allen, 208, 4200-135 Porto, Portugal;
| | - Célia Maria Costa
- CBQF—Centro de Biotecnologia e Química Fina—Laboratório Associado, Escola Superior de Biotecnologia, Universidade Católica Portuguesa, Rua Diogo Botelho, 1327, 4169-005 Porto, Portugal; (N.M.d.C.); (C.M.C.); (M.E.P.)
| | - Manuela Estevez Pintado
- CBQF—Centro de Biotecnologia e Química Fina—Laboratório Associado, Escola Superior de Biotecnologia, Universidade Católica Portuguesa, Rua Diogo Botelho, 1327, 4169-005 Porto, Portugal; (N.M.d.C.); (C.M.C.); (M.E.P.)
| | - Ana Raquel Madureira
- CBQF—Centro de Biotecnologia e Química Fina—Laboratório Associado, Escola Superior de Biotecnologia, Universidade Católica Portuguesa, Rua Diogo Botelho, 1327, 4169-005 Porto, Portugal; (N.M.d.C.); (C.M.C.); (M.E.P.)
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Baumann V, Athanasiou AT, Faridani OR, Schwerdtfeger AR, Wallner B, Steinborn R. Corrigendum: Identification of extremely GC-rich micro RNAs for RT-qPCR data normalization in human plasma. Front Genet 2023; 14:1216150. [PMID: 37323684 PMCID: PMC10264774 DOI: 10.3389/fgene.2023.1216150] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2023] [Accepted: 05/17/2023] [Indexed: 06/17/2023] Open
Abstract
[This corrects the article DOI: 10.3389/fgene.2022.1058668.].
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Affiliation(s)
- Volker Baumann
- Genomics Core Facility, VetCore, University of Veterinary Medicine, Vienna, Austria
| | | | - Omid R. Faridani
- Garvan Institute of Medical Research, Sydney, NSW, Australia
- Lowy Cancer Research Centre, School of Biomedical Sciences, University of New South Wales, Sydney, NSW, Australia
| | | | - Bernard Wallner
- Department of Behavioral and Cognitive Biology, University of Vienna, Vienna, Austria
| | - Ralf Steinborn
- Genomics Core Facility, VetCore, University of Veterinary Medicine, Vienna, Austria
- Department of Microbiology, Immunobiology and Genetics, University of Vienna, Vienna, Austria
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117
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Goldberg TL, Blevins E, Leis EM, Standish IF, Richard JC, Lueder MR, Cer RZ, Bishop-Lilly KA. Plasticity, Paralogy, and Pseudogenization: Rhabdoviruses of Freshwater Mussels Elucidate Mechanisms of Viral Genome Diversification and the Evolution of the Finfish-Infecting Rhabdoviral Genera. J Virol 2023; 97:e0019623. [PMID: 37154732 PMCID: PMC10231222 DOI: 10.1128/jvi.00196-23] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2023] [Accepted: 04/07/2023] [Indexed: 05/10/2023] Open
Abstract
Viruses in the family Rhabdoviridae display remarkable genomic variation and ecological diversity. This plasticity occurs despite the fact that, as negative sense RNA viruses, rhabdoviruses rarely if ever recombine. Here, we describe nonrecombinatorial evolutionary processes leading to genomic diversification in the Rhabdoviridae inferred from two novel rhabdoviruses of freshwater mussels (Mollusca: Bivalvia: Unionida). Killamcar virus 1 (KILLV-1) from a plain pocketbook (Lampsilis cardium) is closely related phylogenetically and transcriptionally to finfish-infecting viruses in the subfamily Alpharhabdovirinae. KILLV-1 offers a novel example of glycoprotein gene duplication, differing from previous examples in that the paralogs overlap. Evolutionary analyses reveal a clear pattern of relaxed selection due to subfunctionalization in rhabdoviral glycoprotein paralogs, which has not previously been described in RNA viruses. Chemarfal virus 1 (CHMFV-1) from a western pearlshell (Margaritifera falcata) is closely related phylogenetically and transcriptionally to viruses in the genus Novirhabdovirus, the sole recognized genus in the subfamily Gammarhabdovirinae, representing the first known gammarhabdovirus of a host other than finfish. The CHMFV-1 G-L noncoding region contains a nontranscribed remnant gene of precisely the same length as the NV gene of most novirhabdoviruses, offering a compelling example of pseudogenization. The unique reproductive strategy of freshwater mussels involves an obligate parasitic stage in which larvae encyst in the tissues of finfish, offering a plausible ecological mechanism for viral host-switching. IMPORTANCE Viruses in the family Rhabdoviridae infect a variety of hosts, including vertebrates, invertebrates, plants and fungi, with important consequences for health and agriculture. This study describes two newly discovered viruses of freshwater mussels from the United States. One virus from a plain pocketbook (Lampsilis cardium) is closely related to fish-infecting viruses in the subfamily Alpharhabdovirinae. The other virus from a western pearlshell (Margaritifera falcata) is closely related to viruses in the subfamily Gammarhabdovirinae, which until now were only known to infect finfish. Genome features of both viruses provide new evidence of how rhabdoviruses evolved their extraordinary variability. Freshwater mussel larvae attach to fish and feed on tissues and blood, which may explain how rhabdoviruses originally jumped between mussels and fish. The significance of this research is that it improves our understanding of rhabdovirus ecology and evolution, shedding new light on these important viruses and the diseases they cause.
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Affiliation(s)
- Tony L. Goldberg
- Department of Pathobiological Sciences, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Emilie Blevins
- Xerces Society for Invertebrate Conservation, Portland, Oregon, USA
| | - Eric M. Leis
- U.S. Fish and Wildlife Service, La Crosse Fish Health Center, Midwest Fisheries Center, Onalaska, Wisconsin, USA
| | - Isaac F. Standish
- U.S. Fish and Wildlife Service, La Crosse Fish Health Center, Midwest Fisheries Center, Onalaska, Wisconsin, USA
| | - Jordan C. Richard
- Department of Pathobiological Sciences, University of Wisconsin-Madison, Madison, Wisconsin, USA
- U.S. Fish and Wildlife Service, Southwestern Virginia Field Office, Abingdon, Virginia, USA
| | - Matthew R. Lueder
- Leidos, Reston, Virginia, USA
- Biological Defense Research Directorate, Naval Medical Research Command–Frederick, Fort Detrick, Maryland, USA
| | - Regina Z. Cer
- Biological Defense Research Directorate, Naval Medical Research Command–Frederick, Fort Detrick, Maryland, USA
| | - Kimberly A. Bishop-Lilly
- Biological Defense Research Directorate, Naval Medical Research Command–Frederick, Fort Detrick, Maryland, USA
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Eriani K, Desriani D, Putri VC, Nursanty R, Mariya S, Umaratusalihah S, Ichsan I, Saidi N. The effect of Cissus quadrangularis Salisb. extract on maturation of rat mesenchymal stem cells. BRAZ J BIOL 2023; 83:e270335. [PMID: 37255198 DOI: 10.1590/1519-6984.270335] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Accepted: 04/17/2023] [Indexed: 06/01/2023] Open
Abstract
Degenerative diseases, such as osteoporosis, could be treated by stem cells. The aim of this study was to identify the gene expression of bone marrow mesenchymal stem cells (BM-MSC) derived from Sprague Dawley rats and to assess the effect of Cissus quadrangularis Salisb. extract on their maturation into bone cells. The BM-MSC were divided into three groups: (a) BM-MSCs + osteoblast cell growth basal medium as the positive control; (b) BM-MSCs + Dulbecco's modified eagle's medium (DMEM) + 0.3 mg/mL methanol extract of C. quadrangularis as methanol group; and (c) BM-MSC + DMEM + 0.3 mg/mL ethyl acetate extract of C. quadrangularis as ethyl acetate group. A relative quantification approach using was used to analyze the expression of the alp (alkaline phosphatase) gene, with the beta-actin gene was used to normalize the expression of the alp gene. The intra-assay variation was calculated to validate the RT-qPCR data. Our study found that the intra-assay variation value was acceptable, with most of the coefficients of variability (CV) value <5. Ethyl acetate solvent outperformed methanol solvent in extracting the active compound C. quadrangularis. In the ethyl acetate extract group, the expression of the alp gene increased three times compared to the positive control. In methanol extract group, the expression of alp gene was lower six times compared to positive control. This study suggests that C. quadrangularis extracts using ethyl acetate could induce the maturation of BM-MSCs. However, further studies are warrant to confirm this effect using different indicators.
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Affiliation(s)
- K Eriani
- Universitas Syiah Kuala, Faculty of Mathematics and Natural Sciences, Department of Biology, Banda Aceh, Indonesia
| | - D Desriani
- Research Center for Genetic Engineering National Research and Innovation Agency, Cibinong, Indonesia
| | - Vianti C Putri
- Universitas Syiah Kuala, Faculty of Mathematics and Natural Sciences, Department of Biology, Banda Aceh, Indonesia
| | - R Nursanty
- Universitas Syiah Kuala, Faculty of Mathematics and Natural Sciences, Department of Biology, Banda Aceh, Indonesia
| | - S Mariya
- IPB University, Primate Research Center, Bogor, Indonesia
| | - S Umaratusalihah
- Universitas Syiah Kuala, Faculty of Mathematics and Natural Sciences, Department of Biology, Banda Aceh, Indonesia
| | - I Ichsan
- Universitas Syiah Kuala, Faculty of Medicine, Banda Aceh, Aceh, Indonesia
| | - N Saidi
- Universitas Syiah Kuala, Department of Chemistry, Banda Aceh, Aceh, Indonesia
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Song Y, Park N, Jo DA, Kim J, Yong D, Song J, Park YM, Lee SJ, Kim YT, Im SG, Choi BG, Kang T, Lee KG. Polyaniline-based 3D network structure promotes entrapment and detection of drug-resistant bacteria. NANO CONVERGENCE 2023; 10:25. [PMID: 37243716 PMCID: PMC10224663 DOI: 10.1186/s40580-023-00370-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Accepted: 05/07/2023] [Indexed: 05/29/2023]
Abstract
Sensitive and accurate capture, enrichment, and identification of drug-resistant bacteria on human skin are important for early-stage diagnosis and treatment of patients. Herein, we constructed a three-dimensional hierarchically structured polyaniline nanoweb (3D HPN) to capture, enrich, and detect drug-resistant bacteria on-site by rubbing infected skins. These unique hierarchical nanostructures enhance bacteria capture efficiency and help severely deform the surface of the bacteria entrapped on them. Therefore, 3D HPN significantly contributes to the effective and reliable recovery of drug-resistant bacteria from the infected skin and the prevention of potential secondary infection. The recovered bacteria were successfully identified by subsequent real-time polymerase chain reaction (PCR) analysis after the lysis process. The molecular analysis results based on a real-time PCR exhibit excellent sensitivity to detecting target bacteria of concentrations ranging from 102 to 107 CFU/mL without any fluorescent signal interruption. To confirm the field applicability of 3D HPN, it was tested with a drug-resistant model consisting of micropig skin similar to human skin and Klebsiella pneumoniae carbapenemase-producing carbapenem-resistant Enterobacteriaceae (KPC-CRE). The results show that the detection sensitivity of this assay is 102 CFU/mL. Therefore, 3D HPN can be extended to on-site pathogen detection systems, along with rapid molecular diagnostics through a simple method, to recover KPC-CRE from the skin.
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Affiliation(s)
- Younseong Song
- Department of Chemical and Biomolecular Engineering, Korea Advanced Institute of Science and Technology, Daejeon, 34141, Republic of Korea
| | - Nahyun Park
- Department of Chemical and Biomolecular Engineering, Korea Advanced Institute of Science and Technology, Daejeon, 34141, Republic of Korea
| | - Da Ae Jo
- Center for Nano Bio Development, National Nanofab Center (NNFC), Daejeon, 34141, Republic of Korea
| | - Jueun Kim
- Center for Nano Bio Development, National Nanofab Center (NNFC), Daejeon, 34141, Republic of Korea
| | - Dongeun Yong
- Department of Laboratory Medicine and Research Institute of Bacterial Resistance, Yonsei University College of Medicine, Seoul, 03722, Republic of Korea
| | - Jayeon Song
- Center for Systems Biology, Massachusetts General Hospital, Boston, MA, 02114, USA
- Department of Radiology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, 02114, USA
- Bionanotechnology Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141, Republic of Korea
| | - Yoo Min Park
- Center for Nano Bio Development, National Nanofab Center (NNFC), Daejeon, 34141, Republic of Korea
| | - Seok Jae Lee
- Center for Nano Bio Development, National Nanofab Center (NNFC), Daejeon, 34141, Republic of Korea
| | - Yong Tae Kim
- Department of Chemical Engineering & Biotechnology, Tech University of Korea, Siheung-Si, 15073, Republic of Korea
| | - Sung Gap Im
- Department of Chemical and Biomolecular Engineering, Korea Advanced Institute of Science and Technology, Daejeon, 34141, Republic of Korea
| | - Bong Gill Choi
- Department of Chemical Engineering, Kangwon National University, Samcheok, 25913, Republic of Korea.
| | - Taejoon Kang
- Bionanotechnology Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141, Republic of Korea.
- School of Pharmacy, Sungkyunkwan University (SKKU), Suwon-Si, 16419, Republic of Korea.
| | - Kyoung G Lee
- Center for Nano Bio Development, National Nanofab Center (NNFC), Daejeon, 34141, Republic of Korea.
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Shim KY, Shin H, Yeo IC, Kim KR, Kwak IS, Jeong CB. Environmental DNA surveillance of biocontamination in a drinking water treatment plant. JOURNAL OF HAZARDOUS MATERIALS 2023; 456:131656. [PMID: 37236104 DOI: 10.1016/j.jhazmat.2023.131656] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Revised: 05/15/2023] [Accepted: 05/16/2023] [Indexed: 05/28/2023]
Abstract
A clean and adequate supply of drinking water is essential to life and good health. However, despite the risk of biologically derived contamination of drinking water, monitoring of invertebrate outbreaks has relied primarily on naked-eye inspections that are prone to errors. In this study, we applied environmental DNA (eDNA) metabarcoding as a biomonitoring tool at seven different stages of drinking water treatment, from prefiltration to release from household faucets. While the composition of invertebrate eDNA communities reflected the communities of the source water in earlier stages of the treatment, several predominant invertebrate taxa (e.g., rotifer) were shown to be introduced during purification, but most were eliminated in later treatment stages. In addition, the limit of detection/quantification of PCR assay and read capacity of high-throughput sequencing was assessed with further microcosm experiments to estimate the applicability eDNA metabarcoding to the biocontamination surveillance in drinking water treatment plants (DWTPs). Here we propose a novel eDNA-based approach for sensitive and efficient surveillance of invertebrate outbreaks in DWTPs.
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Affiliation(s)
- Kyu-Young Shim
- Department of Marine Science, College of Natural Sciences, Incheon National University, Incheon 22012, Republic of Korea
| | - Heesang Shin
- Department of Marine Science, College of Natural Sciences, Incheon National University, Incheon 22012, Republic of Korea
| | - In-Cheol Yeo
- Department of Marine Science, College of Natural Sciences, Incheon National University, Incheon 22012, Republic of Korea
| | - Kyu Ri Kim
- Hoseo Toxicology Research Center, Hoseo University, Asan 31499, Republic of Korea
| | - Ihn-Sil Kwak
- Department of Ocean Integrated Science, Chonnam National University, Yeosu 59626, Republic of Korea
| | - Chang-Bum Jeong
- Department of Marine Science, College of Natural Sciences, Incheon National University, Incheon 22012, Republic of Korea.
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Zhang C, McIntosh KD, Sienkiewicz N, Stelzer EA, Graham JL, Lu J. Using cyanobacteria and other phytoplankton to assess trophic conditions: A qPCR-based, multi-year study in twelve large rivers across the United States. WATER RESEARCH 2023; 235:119679. [PMID: 37011576 PMCID: PMC10123349 DOI: 10.1016/j.watres.2023.119679] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Revised: 01/24/2023] [Accepted: 01/27/2023] [Indexed: 06/19/2023]
Abstract
Phytoplankton is the essential primary producer in fresh surface water ecosystems. However, excessive phytoplankton growth due to eutrophication significantly threatens ecologic, economic, and public health. Therefore, phytoplankton identification and quantification are essential to understanding the productivity and health of freshwater ecosystems as well as the impacts of phytoplankton overgrowth (such as Cyanobacterial blooms) on public health. Microscopy is the gold standard for phytoplankton assessment but is time-consuming, has low throughput, and requires rich experience in phytoplankton morphology. Quantitative polymerase chain reaction (qPCR) is accurate and straightforward with high throughput. In addition, qPCR does not require expertise in phytoplankton morphology. Therefore, qPCR can be a useful alternative for molecular identification and enumeration of phytoplankton. Nonetheless, a comprehensive study is missing which evaluates and compares the feasibility of using qPCR and microscopy to assess phytoplankton in fresh water. This study 1) compared the performance of qPCR and microscopy in identifying and quantifying phytoplankton and 2) evaluated qPCR as a molecular tool to assess phytoplankton and indicate eutrophication. We assessed phytoplankton using both qPCR and microscopy in twelve large freshwater rivers across the United States from early summer to late fall in 2017, 2018, and 2019. qPCR- and microscope-based phytoplankton abundance had a significant positive linear correlation (adjusted R2 = 0.836, p-value < 0.001). Phytoplankton abundance had limited temporal variation within each sampling season and over the three years studied. The sampling sites in the midcontinent rivers had higher phytoplankton abundance than those in the eastern and western rivers. For instance, the concentration (geometric mean) of Bacillariophyta, Cyanobacteria, Chlorophyta, and Dinoflagellates at the sampling sites in the midcontinent rivers was approximately three times that at the sampling sites in the western rivers and approximately 18 times that at the sampling sites in the eastern rivers. Welch's analysis of variance indicates that phytoplankton abundance at the sampling sites in the midcontinent rivers was significantly higher than that at the sampling sites in the eastern rivers (p-value = 0.013) but was comparable to that at the sampling sites in the western rivers (p-value = 0.095). The higher phytoplankton abundance at the sampling sites in the midcontinent rivers was presumably because these rivers were more eutrophic. Indeed, low phytoplankton abundance occurred in oligotrophic or low trophic sites, whereas eutrophic sites had greater phytoplankton abundance. This study demonstrates that qPCR-based phytoplankton abundance can be a useful numerical indicator of the trophic conditions and water quality in freshwater rivers.
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Affiliation(s)
- Chiqian Zhang
- Department of Civil and Environmental Engineering, College of Sciences and Engineering, Southern University and A&M College, Baton Rouge, LA 70813, United States
| | - Kyle D McIntosh
- Oak Ridge Institute for Science and Education at the United States Environmental Protection Agency's Office of Research and Development, Oak Ridge, TN 37830, United States
| | - Nathan Sienkiewicz
- Office of Research and Development, United States Environmental Protection Agency, Cincinnati, OH 45268, United States
| | - Erin A Stelzer
- U.S. Geological Survey, Columbus, OH 43229, United States
| | | | - Jingrang Lu
- Office of Research and Development, United States Environmental Protection Agency, Cincinnati, OH 45268, United States.
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Venbrux M, Crauwels S, Rediers H. Current and emerging trends in techniques for plant pathogen detection. FRONTIERS IN PLANT SCIENCE 2023; 14:1120968. [PMID: 37223788 PMCID: PMC10200959 DOI: 10.3389/fpls.2023.1120968] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/10/2022] [Accepted: 03/21/2023] [Indexed: 05/25/2023]
Abstract
Plant pathogenic microorganisms cause substantial yield losses in several economically important crops, resulting in economic and social adversity. The spread of such plant pathogens and the emergence of new diseases is facilitated by human practices such as monoculture farming and global trade. Therefore, the early detection and identification of pathogens is of utmost importance to reduce the associated agricultural losses. In this review, techniques that are currently available to detect plant pathogens are discussed, including culture-based, PCR-based, sequencing-based, and immunology-based techniques. Their working principles are explained, followed by an overview of the main advantages and disadvantages, and examples of their use in plant pathogen detection. In addition to the more conventional and commonly used techniques, we also point to some recent evolutions in the field of plant pathogen detection. The potential use of point-of-care devices, including biosensors, have gained in popularity. These devices can provide fast analysis, are easy to use, and most importantly can be used for on-site diagnosis, allowing the farmers to take rapid disease management decisions.
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Affiliation(s)
- Marc Venbrux
- Centre of Microbial and Plant Genetics, Laboratory for Process Microbial Ecology and Bioinspirational Management (PME&BIM), Department of Microbial and Molecular Systems (M2S), KU Leuven, Leuven, Belgium
| | - Sam Crauwels
- Centre of Microbial and Plant Genetics, Laboratory for Process Microbial Ecology and Bioinspirational Management (PME&BIM), Department of Microbial and Molecular Systems (M2S), KU Leuven, Leuven, Belgium
- Leuven Plant Institute (LPI), KU Leuven, Leuven, Belgium
| | - Hans Rediers
- Centre of Microbial and Plant Genetics, Laboratory for Process Microbial Ecology and Bioinspirational Management (PME&BIM), Department of Microbial and Molecular Systems (M2S), KU Leuven, Leuven, Belgium
- Leuven Plant Institute (LPI), KU Leuven, Leuven, Belgium
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Garzarelli V, Chiriacò MS, Cereda M, Gigli G, Ferrara F. Ultrasensitive qPCR platform for rapid detection of bacterial contamination of raw biological samples at the point of care. Heliyon 2023; 9:e16229. [PMID: 37234630 PMCID: PMC10205631 DOI: 10.1016/j.heliyon.2023.e16229] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Revised: 05/07/2023] [Accepted: 05/10/2023] [Indexed: 05/28/2023] Open
Abstract
Contamination of cell cultures can result in a significant loss of precious biological material, particularly in long-term processes including amplification of chimeric antigen receptors (CAR)-T cells and differentiation of patient-derived stem cells, for therapeutic purposes. Bacterial contamination can also lead to more complex conditions such as sepsis which can cause morbidity and mortality, despite strict controls and good laboratory/manufacturing practices in the manipulation of complex biological samples such as blood used in autologous and allogeneic stem cells transplantation. The current standard method to identify biological risk is the set-up of microbial cultures, which can be time consuming with the likelihood of wasting large amounts of reagents in the event of contamination. Real-Time Polymerase Chain Reaction (qPCR) is a molecular method able to detect biological agents in a highly sensitive and specific way and in a short time. However, qPCR assays require complex DNA/RNA purification steps and expensive benchtop instruments, which may not always be available. This paper reports an extraction-free and low-volume protocol for qPCR in a standard instrument, which has been demonstrated to be effective on both Gram-positive (Gram+) and Gram-negative (Gram-) bacteria. Detection has been obtained from spiked cell culture samples, reaching a limit of detection (LOD) of 1 colony forming unit (CFU)/ml. To demonstrate the high potential of this optimized procedure, the same samples were also tested on a Point-Of-Care platform, which includes a cartridge with micro-chambers and a compact instrument, capable of performing qPCR with the same efficiency. Staphylococcus aureus (Gram+) was selected as the target for a proof of concept, achieving a LOD of 1 CFU/ml also on the portable device. The availability of these results paves the way for a simplified protocol for DNA extraction and amplification.
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Affiliation(s)
- Valeria Garzarelli
- University of Salento, Dept. of Mathematics & Physics E. de Giorgi, Via Arnesano, 73100, Lecce, Italy
- CNR NANOTEC – Institute of Nanotechnology, via per Monteroni, 73100, Lecce, Italy
| | | | - Marco Cereda
- STMicroelectronics S.r.l., via Olivetti 2, 20864, Agrate Brianza, Italy
| | - Giuseppe Gigli
- University of Salento, Dept. of Mathematics & Physics E. de Giorgi, Via Arnesano, 73100, Lecce, Italy
- CNR NANOTEC – Institute of Nanotechnology, via per Monteroni, 73100, Lecce, Italy
| | - Francesco Ferrara
- CNR NANOTEC – Institute of Nanotechnology, via per Monteroni, 73100, Lecce, Italy
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Jiang K, Wu J, Kim JE, An S, Nam JM, Peng YK, Lee JH. Plasmonic Cross-Linking Colorimetric PCR for Simple and Sensitive Nucleic Acid Detection. NANO LETTERS 2023; 23:3897-3903. [PMID: 37083438 DOI: 10.1021/acs.nanolett.3c00533] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Simple, low-cost, and accurate nucleic acid assay platforms hold great promise for point-of-care (POC) pathogen detection, disease surveillance, and control. Plasmonic photothermal polymerase chain reaction (PPT-PCR) is a powerful and efficient nucleic acid amplification technique, but it lacks a simple and convenient analysis method for POC applications. Herein, we propose a novel plasmonic cross-linking colorimetric PCR (PPT-ccPCR) assay by integrating plasmonic magnetic nanoparticle (PMN)-based PPT-PCR with gold nanoparticle (AuNP)-based cross-linking colorimetry. AuNPs form assembled structures with the PMNs in the presence of amplicons and collect in a magnetic field, resulting in color changes to the supernatant. Target DNA with concentrations as low as 5 copies/μL can be visually detected within 40 min. The achieved limit of detection was 1.8 copies/μL based on the absorption signals. This simple and sensitive strategy needs no expensive instrumentation and demonstrates high potential for POC detection while enabling further applications in clinical diagnostics.
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Affiliation(s)
- Kunlun Jiang
- Department of Chemistry, City University of Hong Kong, Kowloon 999077, Hong Kong, China
| | - Jingrui Wu
- Department of Chemistry, Seoul National University, Seoul 08826, Korea
| | - Ji-Eun Kim
- Department of Chemistry, Seoul National University, Seoul 08826, Korea
| | - Sujin An
- Department of Chemistry, Soonchunhyang University, Asan 31538, Korea
| | - Jwa-Min Nam
- Department of Chemistry, Seoul National University, Seoul 08826, Korea
| | - Yung-Kang Peng
- Department of Chemistry, City University of Hong Kong, Kowloon 999077, Hong Kong, China
| | - Jung-Hoon Lee
- Department of Chemistry, Soonchunhyang University, Asan 31538, Korea
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Leis EM, Dziki S, Standish I, Waller D, Richard J, Weinzinger J, Harris C, Knowles S, Goldberg T. A Bacteriological Comparison of the Hemolymph from Healthy and Moribund Unionid Mussel Populations in the Upper Midwestern U.S.A. Prompts the Development of Diagnostic Assays to Detect Yokenella regensburgei. Microorganisms 2023; 11:microorganisms11041068. [PMID: 37110491 PMCID: PMC10145785 DOI: 10.3390/microorganisms11041068] [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: 03/10/2023] [Revised: 04/07/2023] [Accepted: 04/13/2023] [Indexed: 04/29/2023] Open
Abstract
Recent bacteriological investigations of freshwater mussel mortality events in the southeastern United States have identified a variety of bacteria and differences in bacterial communities between sick and healthy mussels. In particular, Yokenella regensburgei and Aeromonas spp. have been shown to be associated with moribund mussels, although it remains unclear whether these bacteria are causes or consequences of disease. To further understand the role of bacteria in mussel epizootics, we investigated mortality events that occurred in the upper Midwest in the Embarrass River (Wisconsin) and the Huron River (Michigan). For comparison, we also studied mussels from an unaffected population in the St. Croix River (Wisconsin). Diverse bacterial genera were identified from these sites, including Y. regensburgei from moribund mussels in the Embarrass River (Wisconsin). This bacterium has also been consistently isolated during ongoing mortality events in the Clinch River (Virginia). Subsequently, we developed and validated molecular assays for the detection of Yokenella to use in future investigations of mussel mortality events and to identify environmental reservoirs of this bacterium.
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Affiliation(s)
- Eric M Leis
- La Crosse Fish Health Center-Midwest Fisheries Center, U.S. Fish and Wildlife Service, Onalaska, WI 54650, USA
| | - Sara Dziki
- La Crosse Fish Health Center-Midwest Fisheries Center, U.S. Fish and Wildlife Service, Onalaska, WI 54650, USA
| | - Isaac Standish
- La Crosse Fish Health Center-Midwest Fisheries Center, U.S. Fish and Wildlife Service, Onalaska, WI 54650, USA
| | - Diane Waller
- U.S. Geological Survey, Upper Midwest Environmental Sciences Center, La Crosse, WI 54603, USA
| | - Jordan Richard
- Department of Pathobiological Sciences and Freshwater & Marine Sciences Program, University of Wisconsin-Madison, Madison, WI 53711, USA
- Southwestern Virginia Field Office, U.S. Fish and Wildlife Service, Abingdon, VA 24210, USA
| | - Jesse Weinzinger
- Wisconsin Department of Natural Resources, Madison, WI 53703, USA
| | - Cleyo Harris
- Michigan Department of Natural Resources, Waterford, MI 48327, USA
| | - Susan Knowles
- U.S. Geological Survey, National Wildlife Health Center, Madison, WI 53711, USA
| | - Tony Goldberg
- Department of Pathobiological Sciences and Freshwater & Marine Sciences Program, University of Wisconsin-Madison, Madison, WI 53711, USA
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Khan U, Karmakar BC, Basak P, Paul S, Gope A, Sarkar D, Mukhopadhyay AK, Dutta S, Bhattacharya S. Glycyrrhizin, an inhibitor of HMGB1 induces autolysosomal degradation function and inhibits Helicobacter pylori infection. Mol Med 2023; 29:51. [PMID: 37038107 PMCID: PMC10088177 DOI: 10.1186/s10020-023-00641-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Accepted: 03/21/2023] [Indexed: 04/12/2023] Open
Abstract
BACKGROUND Helicobacter pylori is a key agent for causing gastric complications linked with gastric disorders. In response to infection, host cells stimulate autophagy to maintain cellular homeostasis. However, H. pylori have evolved the ability to usurp the host's autophagic machinery. High mobility group box1 (HMGB1), an alarmin molecule is a regulator of autophagy and its expression is augmented during infection and gastric cancer. Therefore, this study aims to explore the role of glycyrrhizin (a known inhibitor of HMGB1) in autophagy during H. pylori infection. MAIN METHODS Human gastric cancer (AGS) cells were infected with the H. pylori SS1 strain and further treatment was done with glycyrrhizin. Western blot was used to examine the expression of autophagy proteins. Autophagy and lysosomal activity were monitored by fluorescence assays. A knockdown of HMGB1 was performed to verify the effect of glycyrrhizin. H. pylori infection in in vivo mice model was established and the effect of glycyrrhizin treatment was studied. RESULTS The autophagy-lysosomal pathway was impaired due to an increase in lysosomal membrane permeabilization during H. pylori infection in AGS cells. Subsequently, glycyrrhizin treatment restored the lysosomal membrane integrity. The recovered lysosomal function enhanced autolysosome formation and concomitantly attenuated the intracellular H. pylori growth by eliminating the pathogenic niche. Additionally, glycyrrhizin treatment inhibited inflammation and improved gastric tissue damage in mice. CONCLUSION This study showed that inhibiting HMGB1 restored lysosomal activity to ameliorate H. pylori infection. It also demonstrated the potential of glycyrrhizin as an antibacterial agent to address the problem of antimicrobial resistance.
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Affiliation(s)
- Uzma Khan
- Division of Biochemistry ICMR-NICED, ICMR-National Institute of Cholera and Enteric Diseases (ICMR-NICED), Kolkata, 700010, India
| | - Bipul Chandra Karmakar
- Division of Bacteriology ICMR-NICED, ICMR-National Institute of Cholera and Enteric Diseases (ICMR-NICED), Kolkata, 700010, India
| | - Priyanka Basak
- Division of Biochemistry ICMR-NICED, ICMR-National Institute of Cholera and Enteric Diseases (ICMR-NICED), Kolkata, 700010, India
| | - Sangita Paul
- Division of Bacteriology ICMR-NICED, ICMR-National Institute of Cholera and Enteric Diseases (ICMR-NICED), Kolkata, 700010, India
| | - Animesh Gope
- Division of Clinical Medicine, ICMR-NICED, ICMR- National Institute of Cholera and Enteric Diseases (ICMR-NICED), Kolkata, India
| | - Deotima Sarkar
- Division of Biochemistry ICMR-NICED, ICMR-National Institute of Cholera and Enteric Diseases (ICMR-NICED), Kolkata, 700010, India
| | - Asish Kumar Mukhopadhyay
- Division of Bacteriology ICMR-NICED, ICMR-National Institute of Cholera and Enteric Diseases (ICMR-NICED), Kolkata, 700010, India
| | - Shanta Dutta
- Division of Bacteriology ICMR-NICED, ICMR-National Institute of Cholera and Enteric Diseases (ICMR-NICED), Kolkata, 700010, India
| | - Sushmita Bhattacharya
- Division of Biochemistry ICMR-NICED, ICMR-National Institute of Cholera and Enteric Diseases (ICMR-NICED), Kolkata, 700010, India.
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Yang S, Xian Q, Liu Y, Zhang Z, Song Q, Gao Y, Wen W. A Silicon-Based PDMS-PEG Copolymer Microfluidic Chip for Real-Time Polymerase Chain Reaction Diagnosis. J Funct Biomater 2023; 14:jfb14040208. [PMID: 37103298 PMCID: PMC10143339 DOI: 10.3390/jfb14040208] [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: 03/15/2023] [Revised: 04/02/2023] [Accepted: 04/07/2023] [Indexed: 04/28/2023] Open
Abstract
Polydimethylsiloxane (PDMS) has been widely used to make lab-on-a-chip devices, such as reactors and sensors, for biological research. Real-time nucleic acid testing is one of the main applications of PDMS microfluidic chips due to their high biocompatibility and transparency. However, the inherent hydrophobicity and excessive gas permeability of PDMS hinder its applications in many fields. This study developed a silicon-based polydimethylsiloxane-polyethylene-glycol (PDMS-PEG) copolymer microfluidic chip, the PDMS-PEG copolymer silicon chip (PPc-Si chip), for biomolecular diagnosis. By adjusting the modifier formula for PDMS, the hydrophilic switch occurred within 15 s after contact with water, resulting in only a 0.8% reduction in transmittance after modification. In addition, we evaluated the transmittance at a wide range of wavelengths from 200 nm to 1000 nm to provide a reference for its optical property study and application in optical-related devices. The improved hydrophilicity was achieved by introducing a large number of hydroxyl groups, which also resulted in excellent bonding strength of PPc-Si chips. The bonding condition was easy to achieve and time-saving. Real-time PCR tests were successfully conducted with higher efficiency and lower non-specific absorption. This chip has a high potential for a wide range of applications in point-of-care tests (POCT) and rapid disease diagnosis.
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Affiliation(s)
- Siyu Yang
- Division of Emerging Interdisciplinary Areas, Interdisciplinary Program Office, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong
- Thrust of Advanced Materials, The Hong Kong University of Science and Technology (Guangzhou), Nansha, Guangzhou 511400, China
- HKUST Shenzhen-Hong Kong Collaborative Innovation Research Institute, Futian, Shenzhen 518000, China
| | - Qingyue Xian
- Division of Emerging Interdisciplinary Areas, Interdisciplinary Program Office, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong
- Thrust of Advanced Materials, The Hong Kong University of Science and Technology (Guangzhou), Nansha, Guangzhou 511400, China
| | - Yiteng Liu
- Division of Emerging Interdisciplinary Areas, Interdisciplinary Program Office, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong
- Thrust of Advanced Materials, The Hong Kong University of Science and Technology (Guangzhou), Nansha, Guangzhou 511400, China
| | - Ziyi Zhang
- Division of Emerging Interdisciplinary Areas, Interdisciplinary Program Office, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong
- Thrust of Advanced Materials, The Hong Kong University of Science and Technology (Guangzhou), Nansha, Guangzhou 511400, China
| | - Qi Song
- Department of Physics, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong
| | - Yibo Gao
- Department of Physics, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong
| | - Weijia Wen
- Thrust of Advanced Materials, The Hong Kong University of Science and Technology (Guangzhou), Nansha, Guangzhou 511400, China
- HKUST Shenzhen-Hong Kong Collaborative Innovation Research Institute, Futian, Shenzhen 518000, China
- Department of Physics, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong
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Adua E. Decoding the mechanism of hypertension through multiomics profiling. J Hum Hypertens 2023; 37:253-264. [PMID: 36329155 PMCID: PMC10063442 DOI: 10.1038/s41371-022-00769-8] [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: 12/29/2021] [Revised: 08/24/2022] [Accepted: 10/17/2022] [Indexed: 11/06/2022]
Abstract
Hypertension, characterised by a constant high blood pressure, is the primary risk factor for multiple cardiovascular events and a major cause of death in adults. Excitingly, innovations in high-throughput technologies have enabled the global exploration of the whole genome (genomics), revealing dysregulated genes that are linked to hypertension. Moreover, post-genomic biomarkers, from the emerging fields of transcriptomics, proteomics, glycomics and lipidomics, have provided new insights into the molecular underpinnings of hypertension. In this paper, we review the pathophysiology of hypertension, and highlight the multi-omics approaches for hypertension prediction and diagnosis.
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Affiliation(s)
- Eric Adua
- School of Clinical Medicine, Medicine & Health, Rural Clinical Campus, University of New South Wales, Wagga Wagga, NSW, Australia.
- School of Medical and Health Sciences, Edith Cowan University, Joondalup, WA, Australia.
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Chen KW, Chen TY, Wang ST, Hou TY, Wang SW, Young KC. Establishment of quantitative and recovery method for detection of dengue virus in wastewater with noncognate spike control. J Virol Methods 2023; 314:114687. [PMID: 36736703 DOI: 10.1016/j.jviromet.2023.114687] [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: 10/24/2022] [Revised: 01/11/2023] [Accepted: 01/17/2023] [Indexed: 02/04/2023]
Abstract
Wastewater-based epidemiology (WBE) represents an efficient approach for public pathogen surveillance as it provides early warning of disease outbreaks; however, it has not yet been applied to dengue virus (DENV), which might cause endemics via mosquito spread. In this study, a working platform was established to provide direct virus recovery and qPCR quantification from wastewater samples that were artificially loaded with target DENV serotypes I to IV and noncognate spike control viral particles. The results showed qPCR efficiencies of 91.2 %, 94.8 %, 92.6 % and 88.7 % for DENV I, II, III, and IV, respectively, and a broad working range over 6 orders of magnitude using the preferred primer sets. Next, the results revealed that the ultrafiltration method was superior to the skimmed milk flocculation method for recovering either DENV or control viral particles from wastewater. Finally, DENV-2 was loaded simultaneously with the noncognate spike control and could be recovered at comparable levels either in PBS or in wastewater, indicating the applicability of noncognate spike control particles to reflect the efficiency of experimental steps. In conclusion, our data suggest that DENV particles in wastewater could be recovered and quantitatively detected in absolute amounts, indicating the feasibility of DENV surveillance using the WBE approach.
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Affiliation(s)
- Kuan-Wei Chen
- Department of Medical Laboratory Science and Biotechnology, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Tzu-Yi Chen
- Department of Medical Laboratory Science and Biotechnology, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Sin-Tian Wang
- Department of Medical Laboratory Science and Biotechnology, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Ting-Yu Hou
- Department of Medical Laboratory Science and Biotechnology, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Shainn-Wei Wang
- Institute of Molecular Medicine, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Kung-Chia Young
- Department of Medical Laboratory Science and Biotechnology, College of Medicine, National Cheng Kung University, Tainan, Taiwan.
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130
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Saleem F, Jiang JL, Atrache R, Paschos A, Edge TA, Schellhorn HE. Cyanobacterial Algal Bloom Monitoring: Molecular Methods and Technologies for Freshwater Ecosystems. Microorganisms 2023; 11:microorganisms11040851. [PMID: 37110273 PMCID: PMC10144707 DOI: 10.3390/microorganisms11040851] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Revised: 03/15/2023] [Accepted: 03/24/2023] [Indexed: 03/29/2023] Open
Abstract
Cyanobacteria (blue-green algae) can accumulate to form harmful algal blooms (HABs) on the surface of freshwater ecosystems under eutrophic conditions. Extensive HAB events can threaten local wildlife, public health, and the utilization of recreational waters. For the detection/quantification of cyanobacteria and cyanotoxins, both the United States Environmental Protection Agency (USEPA) and Health Canada increasingly indicate that molecular methods can be useful. However, each molecular detection method has specific advantages and limitations for monitoring HABs in recreational water ecosystems. Rapidly developing modern technologies, including satellite imaging, biosensors, and machine learning/artificial intelligence, can be integrated with standard/conventional methods to overcome the limitations associated with traditional cyanobacterial detection methodology. We examine advances in cyanobacterial cell lysis methodology and conventional/modern molecular detection methods, including imaging techniques, polymerase chain reaction (PCR)/DNA sequencing, enzyme-linked immunosorbent assays (ELISA), mass spectrometry, remote sensing, and machine learning/AI-based prediction models. This review focuses specifically on methodologies likely to be employed for recreational water ecosystems, especially in the Great Lakes region of North America.
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131
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De Silva S, Ocaña-Rios I, Cagliero C, Gostel MR, Johnson G, Anderson JL. Isolation of DNA from plant tissues using a miniaturized matrix solid-phase dispersion approach featuring ionic liquid and magnetic ionic liquid solvents. Anal Chim Acta 2023; 1245:340858. [PMID: 36737141 DOI: 10.1016/j.aca.2023.340858] [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: 11/19/2022] [Revised: 01/17/2023] [Accepted: 01/18/2023] [Indexed: 01/20/2023]
Abstract
The isolation of high-quality plant genomic DNA is a major prerequisite in many plant biomolecular analyses involving nucleic acid amplification. Conventional plant cell lysis and DNA extraction methods involve lengthy sample preparation procedures that often require large amounts of sample and chemicals, high temperatures and multiple liquid transfer steps which can introduce challenges for high throughput applications. In this study, a simple, rapid, miniaturized ionic liquid (IL)-based extraction method was developed for the isolation of genomic DNA from milligram fragments of Arabidopsis thaliana plant tissue. This method is based on a modification of vortex-assisted matrix solid-phase dispersion (VA-MSPD) in which the trihexyl(tetradecyl)phosphonium bis(trifluoromethylsulfonyl)imide ([P6,6,6,14+][NTf2-]) IL or trihexyl(tetradecyl)phosphonium tris(hexafluoroacetylaceto)nickelate(II) ([P6,6,6,14+][Ni(hfacac)3-]) magnetic IL (MIL) was directly applied to treated plant tissue (∼1.5 mg) and dispersed in an agate mortar to facilitate plant cell lysis and DNA extraction, followed by recovery of the mixture with a qPCR compatible co-solvent. This study represents the first approach to use ILs and MILs in a MSPD procedure to facilitate plant cell lysis and DNA extraction. The DNA-enriched IL- and MIL-cosolvent mixtures were directly integrated into the qPCR buffer without inhibiting the reaction while also circumventing the need for additional purification steps prior to DNA amplification. Under optimum conditions, the IL and MIL yielded 2.87 ± 0.28 and 1.97 ± 0.59 ng of DNA/mg of plant tissue, respectively. Furthermore, the mild extraction conditions used in the method enabled plant DNA in IL- and MIL-cosolvent mixtures to be preserved from degradation at room temperature.
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Affiliation(s)
- Shashini De Silva
- Department of Chemistry, Iowa State University, Ames, IA, 50011, USA
| | - Iran Ocaña-Rios
- Department of Chemistry, Iowa State University, Ames, IA, 50011, USA
| | - Cecilia Cagliero
- Dipartimento di Scienza e Tecnologia del Farmaco, Università di Torino, I-10125, Turin, Italy
| | - Morgan R Gostel
- Botanical Research Institute of Texas, Fort Worth, Texas, 76107-3400, USA
| | | | - Jared L Anderson
- Department of Chemistry, Iowa State University, Ames, IA, 50011, USA.
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132
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Molecular Detection and Identification of Plant-Associated Lactiplantibacillus plantarum. Int J Mol Sci 2023; 24:ijms24054853. [PMID: 36902287 PMCID: PMC10003612 DOI: 10.3390/ijms24054853] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Revised: 02/27/2023] [Accepted: 02/28/2023] [Indexed: 03/06/2023] Open
Abstract
Lactiplantibacillus plantarum is a lactic acid bacterium often isolated from a wide variety of niches. Its ubiquity can be explained by a large, flexible genome that helps it adapt to different habitats. The consequence of this is great strain diversity, which may make their identification difficult. Accordingly, this review provides an overview of molecular techniques, both culture-dependent, and culture-independent, currently used to detect and identify L. plantarum. Some of the techniques described can also be applied to the analysis of other lactic acid bacteria.
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133
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Davis A, Keely SP, Brinkman NE, Bohrer Z, Ai Y, Mou X, Chattopadhyay S, Hershey O, Senko J, Hull N, Lytmer E, Quintero A, Lee J. Evaluation of intra- and inter-lab variability in quantifying SARS-CoV-2 in a state-wide wastewater monitoring network. ENVIRONMENTAL SCIENCE : WATER RESEARCH & TECHNOLOGY 2023; 9:1053-1068. [PMID: 37701755 PMCID: PMC10494892 DOI: 10.1039/d2ew00737a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/14/2023]
Abstract
In December 2019, SARS-CoV-2, the virus that causes coronavirus disease 2019, was first reported and subsequently triggered a global pandemic. Wastewater monitoring, a strategy for quantifying viral gene concentrations from wastewater influents within a community, has served as an early warning and management tool for the spread of SARS-CoV-2 in a community. Ohio built a collaborative statewide wastewater monitoring network that is supported by eight labs (university, government, and commercial laboratories) with unique sample processing workflows. Consequently, we sought to characterize the variability in wastewater monitoring results for network labs. Across seven trials between October 2020 and November 2021, eight participating labs successfully quantified two SARS-CoV-2 RNA targets and human fecal indicator virus targets in wastewater sample aliquots with reproducible results, although recovery efficiencies of spiked surrogates ranged from 3 to 75%. When SARS-CoV-2 gene fragment concentrations were adjusted for recovery efficiency and flow, the proportion of variance between laboratories was minimized, serving as the best model to account for between-lab variance. Another adjustment factor (alone and in different combinations with the above factors) considered to account for sample and measurement variability includes fecal marker normalization. Genetic quantification variability can be attributed to many factors, including the methods, individual samples, and water quality parameters. In addition, statistically significant correlations were observed between SARS-CoV-2 RNA and COVID-19 case numbers, supporting the notion that wastewater surveillance continues to serve as an effective monitoring tool. This study serves as a real-time example of multi-laboratory collaboration for public health preparedness for infectious diseases.
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Affiliation(s)
- Angela Davis
- Division of Environmental Health Sciences, College of Public Health, The Ohio State University, 1841 Neil Avenue, Columbus, OH 43210, USA
| | - Scott P Keely
- United States Environmental Protection Agency, Office of Research and Development, USA
| | - Nichole E Brinkman
- United States Environmental Protection Agency, Office of Research and Development, USA
| | | | - Yuehan Ai
- Department of Food Science & Technology, The Ohio State University, USA
| | - Xiaozhen Mou
- Department of Biological Sciences, Kent State University, USA
| | - Saurabh Chattopadhyay
- Department of Medical Microbiology and Immunology, College of Medicine and Life Sciences, Department of Biology and Department of Geosciences, University of Toledo, USA
| | - Olivia Hershey
- Department of Geosciences and Biology, University of Akron, USA
| | - John Senko
- Department of Geosciences and Biology, University of Akron, USA
| | - Natalie Hull
- Department of Civil, Environmental and Geodetic Engineering and Sustainability Institute, The Ohio State University, USA
| | - Eva Lytmer
- Department of Biological Sciences, Bowling Green State University, USA
| | | | - Jiyoung Lee
- Division of Environmental Health Sciences, College of Public Health, The Ohio State University, 1841 Neil Avenue, Columbus, OH 43210, USA
- Department of Food Science & Technology, The Ohio State University, USA
- Infectious Diseases Institute, The Ohio State University, USA
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134
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Houston G, Blomme A, Harrison O, Bai J, Woodworth J, Jones C, Poulsen-Porter E, Paulk C, Gebhardt J. Evaluating the impact of organic matter and sample processing techniques on RNA detection using environmental samples. JOURNAL OF SWINE HEALTH AND PRODUCTION 2023. [DOI: 10.54846/jshap/1311] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/05/2023]
Abstract
This study evaluated sample processing methods and the presence of organic matter on detection of porcine epidemic diarrhea virus (PEDV) from environmental samples using real-time reverse transcriptase-polymerase chain reaction (qRT-PCR). Steel coupons were inoculated with PEDV and different types of organic material contamination. Surface samples were collected and processed in one of four ways: none, centrifugation, syringe filtration, or combination of centrifugation and syringe filtration, then submitted for PEDV qRT-PCR. There was a surface inoculation type by processing method interaction (P < .001) that impacted the sample cycle threshold value. Centrifugation resulted in the most consistent detection of PEDV RNA.
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135
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Yaung KN, Yeo JG, Kumar P, Wasser M, Chew M, Ravelli A, Law AHN, Arkachaisri T, Martini A, Pisetsky DS, Albani S. Artificial intelligence and high-dimensional technologies in the theragnosis of systemic lupus erythematosus. THE LANCET. RHEUMATOLOGY 2023; 5:e151-e165. [PMID: 38251610 DOI: 10.1016/s2665-9913(23)00010-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2022] [Revised: 12/14/2022] [Accepted: 01/04/2023] [Indexed: 02/22/2023]
Abstract
Systemic lupus erythematosus is a complex, systemic autoimmune disease characterised by immune dysregulation. Pathogenesis is multifactorial, contributing to clinical heterogeneity and posing challenges for diagnosis and treatment. Although strides in treatment options have been made in the past 15 years, with the US Food and Drug Administration approval of belimumab in 2011, there are still many patients who have inadequate responses to therapy. A better understanding of underlying disease mechanisms with a holistic and multiparametric approach is required to improve clinical assessment and treatment. This Review discusses the evolution of genomics, epigenomics, transcriptomics, and proteomics in the study of systemic lupus erythematosus and ways to amalgamate these silos of data with a systems-based approach while also discussing ways to strengthen the overall process. These mechanistic insights will facilitate the discovery of functionally relevant biomarkers to guide rational therapeutic selection to improve patient outcomes.
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Affiliation(s)
- Katherine Nay Yaung
- Translational Immunology Institute, SingHealth Duke-NUS Academic Medical Centre, Singapore; Duke-NUS Medical School, Singapore.
| | - Joo Guan Yeo
- Translational Immunology Institute, SingHealth Duke-NUS Academic Medical Centre, Singapore; Duke-NUS Medical School, Singapore; Rheumatology and Immunology Service, KK Women's and Children's Hospital, Singapore
| | - Pavanish Kumar
- Translational Immunology Institute, SingHealth Duke-NUS Academic Medical Centre, Singapore
| | - Martin Wasser
- Translational Immunology Institute, SingHealth Duke-NUS Academic Medical Centre, Singapore
| | - Marvin Chew
- Translational Immunology Institute, SingHealth Duke-NUS Academic Medical Centre, Singapore
| | - Angelo Ravelli
- Direzione Scientifica, IRCCS Istituto Giannina Gaslini, Genoa, Italy; Dipartimento di Neuroscienze, Riabilitazione, Oftalmologia, Genetica e Scienze Materno-Infantili, Università degli Studi di Genova, Genoa, Italy
| | - Annie Hui Nee Law
- Duke-NUS Medical School, Singapore; Department of Rheumatology and Immunology, Singapore General Hospital, Singapore
| | - Thaschawee Arkachaisri
- Duke-NUS Medical School, Singapore; Rheumatology and Immunology Service, KK Women's and Children's Hospital, Singapore
| | | | - David S Pisetsky
- Department of Medicine and Department of Immunology, Duke University Medical Center, Durham, NC, USA; Medical Research Service, Veterans Administration Medical Center, Durham, NC, USA
| | - Salvatore Albani
- Translational Immunology Institute, SingHealth Duke-NUS Academic Medical Centre, Singapore; Duke-NUS Medical School, Singapore; Rheumatology and Immunology Service, KK Women's and Children's Hospital, Singapore
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136
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Lan WL, Chen CH, Chu YC, Cheng YF, Huang CY. Is There an Association between Concurrent Epstein-Barr Virus Infection and Sudden Hearing Loss?-A Case-Control Study in an East Asian Population. J Clin Med 2023; 12:jcm12051946. [PMID: 36902736 PMCID: PMC10004397 DOI: 10.3390/jcm12051946] [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: 12/10/2022] [Revised: 02/12/2023] [Accepted: 02/27/2023] [Indexed: 03/06/2023] Open
Abstract
Viral infection serves as the crucial etiology for the development of sudden sensorineural hearing loss (SSNHL). We aimed to investigate whether there is an association between concurrent Epstein-Barr virus (EBV) infection and SSNHL in an East Asian population. Patients who were older than 18 years of age and met the criteria of sudden hearing loss without an identifiable etiology were enrolled from July 2021 until June 2022, followed by the serological testing of IgA antibody responses against EBV-specific early antigen (EA) and viral capsid antigen (VCA) with an indirect hemagglutination assay (IHA) and real-time quantitative polymerase chain reaction (qPCR) of EBV DNA in serum before the treatment was initiated. After the treatment for SSNHL, post-treatment audiometry was performed to record the treatment response and degree of recovery. Among the 29 patients included during enrollment, 3 (10.3%) had a positive qPCR result for EBV. In addition, a trend of poor recovery of hearing thresholds was noted for those patients with a higher viral PCR titer. This is the first study to use real-time PCR to detect possible concurrent EBV infection in SSNHL. Our study demonstrated that approximately one-tenth of the enrolled SSNHL patients had evidence of concurrent EBV infection, as reflected by the positive qPCR test results, and a negative trend between hearing gain and the viral DNA PCR level was found within the affected cohort after steroid therapy. These findings indicate a possible role for EBV infection in East Asian patients with SSNHL. Further larger-scale research is needed to better understand the potential role and underlying mechanism of viral infection in the etiology of SSNHL.
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Affiliation(s)
- Wei-Lun Lan
- Department of Otolaryngology-Head and Neck Surgery, Taipei Veterans General Hospital, Taipei 112, Taiwan
| | - Chih-Hao Chen
- Department of Otolaryngology-Head and Neck Surgery, Taipei Veterans General Hospital, Taipei 112, Taiwan
| | - Yuan-Chia Chu
- Information Management Office, Taipei Veterans General Hospital, Taipei 112, Taiwan
- Medical AI Development Center, Taipei Veterans General Hospital, Taipei 112, Taiwan
- Department of Information Management, National Taipei University of Nursing and Health, Taipei 112, Taiwan
| | - Yen-Fu Cheng
- Department of Otolaryngology-Head and Neck Surgery, Taipei Veterans General Hospital, Taipei 112, Taiwan
- School of Medicine, National Yang Ming Chiao Tung University, Taipei 112, Taiwan
- Department of Medical Research, Taipei Veterans General Hospital, Taipei 112, Taiwan
- Institute of Brain Science, National Yang Ming Chiao Tung University, Taipei 112, Taiwan
| | - Chii-Yuan Huang
- Department of Otolaryngology-Head and Neck Surgery, Taipei Veterans General Hospital, Taipei 112, Taiwan
- Information Management Office, Taipei Veterans General Hospital, Taipei 112, Taiwan
- Correspondence:
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137
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Lariviere PJ, Leonard SP, Horak RD, Powell JE, Barrick JE. Honey bee functional genomics using symbiont-mediated RNAi. Nat Protoc 2023; 18:902-928. [PMID: 36460809 DOI: 10.1038/s41596-022-00778-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Accepted: 09/22/2022] [Indexed: 12/03/2022]
Abstract
Honey bees are indispensable pollinators and model organisms for studying social behavior, development and cognition. However, their eusociality makes it difficult to use standard forward genetic approaches to study gene function. Most functional genomics studies in bees currently utilize double-stranded RNA (dsRNA) injection or feeding to induce RNAi-mediated knockdown of a gene of interest. However, dsRNA injection is laborious and harmful, and dsRNA feeding is difficult to scale cheaply. Further, both methods require repeated dsRNA administration to ensure a continued RNAi response. To fill this gap, we engineered the bee gut bacterium Snodgrassella alvi to induce a sustained host RNA interference response that reduces expression of a targeted gene. To employ this functional genomics using engineered symbionts (FUGUES) procedure, a dsRNA expression plasmid is cloned in Escherichia coli using Golden Gate assembly and then transferred to S. alvi. Adult worker bees are then colonized with engineered S. alvi. Finally, gene knockdown is verified through qRT-PCR, and bee phenotypes of interest can be further assessed. Expression of targeted genes is reduced by as much as 50-75% throughout the entire bee body by 5 d after colonization. This protocol can be accomplished in 4 weeks by bee researchers with microbiology and molecular cloning skills. FUGUES currently offers a streamlined and scalable approach for studying the biology of honey bees. Engineering other microbial symbionts to influence their hosts in ways that are similar to those described in this protocol may prove useful for studying additional insect and animal species in the future.
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Affiliation(s)
- Patrick J Lariviere
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA.,Department of Integrative Biology, The University of Texas at Austin, Austin, TX, USA
| | - Sean P Leonard
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA.,Department of Integrative Biology, The University of Texas at Austin, Austin, TX, USA
| | - Richard D Horak
- Department of Integrative Biology, The University of Texas at Austin, Austin, TX, USA
| | - J Elijah Powell
- Department of Integrative Biology, The University of Texas at Austin, Austin, TX, USA
| | - Jeffrey E Barrick
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA.
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138
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Soto-Beltrá N M, Lee BG, Amézquita-López BA, Quiñones B. Overview of methodologies for the culturing, recovery and detection of Campylobacter. INTERNATIONAL JOURNAL OF ENVIRONMENTAL HEALTH RESEARCH 2023; 33:307-323. [PMID: 35168460 DOI: 10.1080/09603123.2022.2029366] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Accepted: 01/11/2022] [Indexed: 06/14/2023]
Abstract
Campylobacter species are responsible for human gastroenteritis with diverse clinical spectra, ranging from acute watery or bloody diarrhea to life-threatening autoimmune disorders. Given the importance of Campylobacter in causing human illness, this article has reviewed the transmission and attribution sources as well as methodologies for the detection and virulence characterization of campylobacteria. The recovery and detection of Campylobacter from clinical, food and environmental samples has been achieved by the combinatorial use of selective enrichment and culturing methods. Biochemical, immunological, and nucleic acid-based methodologies have enabled the detection and differentiation of closely related Campylobacter isolates in foodborne outbreak investigations and have assessed the diversity and phylogenetic relationships of these bacterial pathogens. Analyses of motility, adherence, and invasiveness in host cells have assessed the pathogenic potential of campylobacteria. Further examination of determinants conferring antimicrobial resistance in Campylobacter have supported the growing need to closely monitor antimicrobials use in clinical and agricultural sectors.
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Affiliation(s)
- Marcela Soto-Beltrá N
- Facultad de Ciencias Químico Biológicas, Universidad Autónoma de Sinaloa, Culiacán, México
| | - Bertram G Lee
- Produce Safety and Microbiology Research Unit, United States Department of Agriculture/Agricultural Research Service,Western Regional Research Center, Albany, CA, USA
| | | | - Beatriz Quiñones
- Produce Safety and Microbiology Research Unit, United States Department of Agriculture/Agricultural Research Service,Western Regional Research Center, Albany, CA, USA
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139
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Napoletano S, Battista E, Martone N, Netti PA, Causa F. Direct, precise, enzyme-free detection of miR-103–3p in real samples by microgels with highly specific molecular beacons. Talanta 2023; 259:124468. [PMID: 37011564 DOI: 10.1016/j.talanta.2023.124468] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Revised: 03/13/2023] [Accepted: 03/16/2023] [Indexed: 03/29/2023]
Abstract
Low abundance, small size, and sequence similarities render microRNA (miRNAs) detection challenging, particularly in real samples, where quantifying weakly expressed miRNAs can be arduous due to interference of more abundant molecules. The standard quantitative reverse transcription polymerase chain reaction (qRT-PCR) requires multiple steps, thermal cycles, and costly enzymatic reactions that can negatively affect results. Here we present a direct, precise, enzyme-free assay based on microgels particles conjugating molecular beacons (MB) capable of optically detecting low abundant miRNAs in real samples. We validate the applicability of microgels assay using qRT-PCR as a reference technology. As a relevant case, we chose miR-103-3p, a valuable diagnostic biomarker for breast cancer, both in serum samples and MCF7 cells. As a result, microgels assay quantifies miRNA molecules at room temperature in a single step, 1 h (vs. 4 hrs for qRT-PCR) without complementary DNA synthesis, amplification, or expensive reagents. Microgels assay exhibits femtomolar sensitivity, single nucleotide specificity, and a wide linear range (102-107 fM) (wider than qRT-PCR), with low sample consumption (2 μL) and excellent linearity (R2= 0.98). To test the selectivity of the microgel assay in real samples, MCF7 cells were considered where the pool of 8 other miRNAs were further upregulated with respect to miRNA 103-3p. In such complex environments, microgels assay selectively detects the miRNA target, mainly due to MB advanced stability and specificity as well as high microgel antifouling properties. These results show the reliability of microgels assay to detect miRNAs in real samples.
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140
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Improved DNA Amplification of the Hallmark IS 900 Element in Mycobacterium avium subsp. paratuberculosis: a Reexamination Based on Whole-Genome Sequence Analysis. Appl Environ Microbiol 2023; 89:e0168222. [PMID: 36719222 PMCID: PMC9972922 DOI: 10.1128/aem.01682-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
Amplification of the IS900 multicopy element is a hallmark nucleic acid-based diagnostic test for Mycobacterium avium subsp. paratuberculosis, which causes Johne's disease in ruminants. This assay is frequently used to determine the presence of the bacterium in feces of infected cattle and sheep. Two IS900 primer sets developed in the 1990s were widely used for decades, and their use has continued in current studies. However, these primers were developed prior to the availability of complete genome sequences. Recent sequence analysis of the binding locations for one primer pair (P90/P91) identified errors and binding inefficiencies that can be easily corrected to further increase detection sensitivity. The P90 primer is missing two nucleotides that should be present near the 3' end, and it does not bind all copies of IS900 due to 5' deletions at some IS900 loci. These IS900 primer pairs, along with newly developed primers, were tested by real-time PCR on purified genomic DNA to determine which primer set performed the best and how primer design errors affect amplification efficiencies. The newly designed PCR primer set (JB5) showed increased sensitivity by two to three quantification cycles using purified genomic DNA and was similar in efficiency to 150C/921. These tests were extended using DNA from feces and tissues of infected cows, which showed similar results. Finally, a 167-bp partial duplication of IS900 was found in type I strains. Although P90 and P91 primers successfully amplify M. avium subsp. paratuberculosis DNA, their use should be discontinued in favor of more efficient primer pairs in future studies. IMPORTANCE This study is an example of how applied genomic analysis can aid diagnostic test improvements. Detection of Mycobacterium avium subsp. paratuberculosis infection of livestock prior to the appearance of clinical disease signs is very difficult but essential for identifying animals shedding the bacterium to prevent transmission of Johne's disease. Total M. avium subsp. paratuberculosis quantity in the feces as determined by real-time PCR (qPCR) using the IS900 target indicates bacterial shedding status and potential for transmission of the pathogen. However, legacy primers designed prior to the availability of complete genome sequences that are used in these tests to detect M. avium subsp. paratuberculosis were based on data from only a single copy of IS900 and not considering all copies collectively as a group. This approach resulted in primer design errors which can be easily corrected to improve test sensitivities. We tested original primers that contain these errors and their corrected versions by qPCR and showed improved sensitivity on purified genomic DNA as well as fecal and tissue samples. These findings may help detect the organism from environmental samples on farms where sensitivity is currently lacking.
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141
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Simultaneous Detection of Salmonella spp. and Quantification of Campylobacter spp. in a Real-Time Duplex PCR: Myth or Reality? Pathogens 2023; 12:pathogens12020338. [PMID: 36839610 PMCID: PMC9967202 DOI: 10.3390/pathogens12020338] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2023] [Revised: 02/07/2023] [Accepted: 02/14/2023] [Indexed: 02/18/2023] Open
Abstract
In Europe, there is a process hygiene criterion for Salmonella and Campylobacter on broiler carcasses after chilling. The criterion gives indicative contamination values above which corrective actions are required by food business operators. The reference methods for verifying compliance with the criterion for Salmonella and Campylobacter are international standards EN ISO 6579-1 (2017) and EN ISO 10272-2 (2017), respectively. These methods are time-consuming and expensive for food business operators. Therefore, it would be advantageous to simultaneously detect Salmonella spp. and quantify Campylobacter in the same analysis, using the same sample after the pre-enrichment step for Salmonella recovery. A duplex PCR for Salmonella detection and Campylobacter spp. enumeration was developed. Considering the method as a whole, the LOD and LOQ for Campylobacter enumeration were slightly over the limit of 3 log CFU/g set by the process hygiene criterion. A comparison of the duplex PCR method developed with the ISO method on artificially contaminated bacterial suspensions and on naturally contaminated samples demonstrated a good correlation of the results for Campylobacter enumeration when the duplex PCR was performed on samples taken before or after the pre-enrichment step, but revealed a slight bias with a large standard deviation resulting in widely spaced limits of agreement.
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Higgins O, Chueiri A, O'Connor L, Lahiff S, Burke L, Morris D, Pfeifer NM, Santamarina BG, Berens C, Menge C, Caniça M, Manageiro V, Kisand V, Hassan MM, Gardner B, van Vliet AHM, La Ragione RM, Gonzalez-Zorn B, Smith TJ. Portable Differential Detection of CTX-M ESBL Gene Variants, blaCTX-M-1 and blaCTX-M-15, from Escherichia coli Isolates and Animal Fecal Samples Using Loop-Primer Endonuclease Cleavage Loop-Mediated Isothermal Amplification. Microbiol Spectr 2023; 11:e0331622. [PMID: 36511696 PMCID: PMC9927312 DOI: 10.1128/spectrum.03316-22] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2022] [Accepted: 11/18/2022] [Indexed: 12/15/2022] Open
Abstract
Cefotaximase-Munich (CTX-M) extended-spectrum beta-lactamase (ESBL) enzymes produced by Enterobacteriaceae confer resistance to clinically relevant third-generation cephalosporins. CTX-M group 1 variants, CTX-M-1 and CTX-M-15, are the leading ESBL-producing Enterobacteriaceae associated with animal and human infection, respectively, and are an increasing antimicrobial resistance (AMR) global health concern. The blaCTX-M-1 and blaCTX-M-15 genes encoding these variants have an approximate nucleotide sequence similarity of 98.7%, making effective differential diagnostic monitoring difficult. Loop-primer endonuclease cleavage loop-mediated isothermal amplification (LEC-LAMP) enables rapid real-time multiplex pathogen detection with single-base specificity and portable on-site testing. We have developed an internally controlled multiplex CTX-M-1/15 LEC-LAMP assay for the differential detection of blaCTX-M-1 and blaCTX-M-15. Assay analytical specificity was established using a panel of human, animal, and environmental Escherichia coli isolates positive for blaCTX-M-1 (n = 18), blaCTX-M-15 (n = 35), and other closely related blaCTX-Ms (n = 38) from Ireland, Germany, and Portugal, with analytical sensitivity determined using probit regression analysis. Animal fecal sample testing using the CTX-M-1/15 LEC-LAMP assay in combination with a rapid DNA extraction protocol was carried out on porcine fecal samples previously confirmed to be PCR-positive for E. coli blaCTX-M. Portable instrumentation was used to further analyze each fecal sample and demonstrate the on-site testing capabilities of the LEC-LAMP assay with the rapid DNA extraction protocol. The CTX-M-1/15 LEC-LAMP assay demonstrated complete analytical specificity for the differential detection of both variants with sensitive low-level detection of 8.5 and 9.8 copies per reaction for blaCTX-M-1 and blaCTX-M-15, respectively, and E. coli blaCTX-M-1 was identified in all blaCTX-M positive porcine fecal samples tested. IMPORTANCE CTX-M ESBL-producing E. coli is an increasing AMR public health issue with the transmission between animals and humans via zoonotic pathogens now a major area of interest. Accurate and timely identification of ESBL-expressing E. coli CTX-M variants is essential for disease monitoring, targeted antibiotic treatment and infection control. This study details the first report of portable diagnostics technology for the rapid differential detection of CTX-M AMR markers blaCTX-M-1 and blaCTX-M-15, facilitating improved identification and surveillance of these closely related variants. Further application of this portable internally controlled multiplex CTX-M-1/15 LEC-LAMP assay will provide new information on the transmission and prevalence of these CTX-M ESBL alleles. Furthermore, this transferable diagnostic technology can be applied to other new and emerging relevant AMR markers of interest providing more efficient and specific portable pathogen detection for improved epidemiological surveillance.
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Affiliation(s)
- Owen Higgins
- Molecular Diagnostics Research Group, School of Biological and Chemical Sciences, University of Galway, Galway, Ireland
- Centre for One Health, Ryan Institute, University of Galway, Galway, Ireland
| | - Alexandra Chueiri
- Antimicrobial Resistance and Microbial Ecology Group, School of Medicine, University of Galway, Galway, Ireland
- Centre for One Health, Ryan Institute, University of Galway, Galway, Ireland
| | - Louise O'Connor
- Antimicrobial Resistance and Microbial Ecology Group, School of Medicine, University of Galway, Galway, Ireland
- Centre for One Health, Ryan Institute, University of Galway, Galway, Ireland
| | - Sinéad Lahiff
- Molecular Diagnostics Research Group, School of Biological and Chemical Sciences, University of Galway, Galway, Ireland
- Centre for One Health, Ryan Institute, University of Galway, Galway, Ireland
| | - Liam Burke
- Antimicrobial Resistance and Microbial Ecology Group, School of Medicine, University of Galway, Galway, Ireland
- Centre for One Health, Ryan Institute, University of Galway, Galway, Ireland
| | - Dearbhaile Morris
- Antimicrobial Resistance and Microbial Ecology Group, School of Medicine, University of Galway, Galway, Ireland
- Centre for One Health, Ryan Institute, University of Galway, Galway, Ireland
| | - Nicola Maria Pfeifer
- Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Institute of Molecular Pathogenesis, Jena, Germany
| | - Belén González Santamarina
- Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Institute of Molecular Pathogenesis, Jena, Germany
| | - Christian Berens
- Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Institute of Molecular Pathogenesis, Jena, Germany
| | - Christian Menge
- Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Institute of Molecular Pathogenesis, Jena, Germany
| | - Manuela Caniça
- National Reference Laboratory of Antibiotic Resistances and Healthcare Associated Infections, Department of Infectious Diseases, National Institute of Health Dr. Ricardo Jorge, Lisbon, Portugal
| | - Vera Manageiro
- National Reference Laboratory of Antibiotic Resistances and Healthcare Associated Infections, Department of Infectious Diseases, National Institute of Health Dr. Ricardo Jorge, Lisbon, Portugal
| | - Veljo Kisand
- Institute of Technology, University of Tartu, Tartu, Estonia
| | - Marwa M. Hassan
- Department of Comparative Biomedical Sciences, School of Veterinary Medicine, Faculty of Health and Medical Sciences, University of Surrey, Guildford, Surrey, United Kingdom
| | - Brian Gardner
- Department of Comparative Biomedical Sciences, School of Veterinary Medicine, Faculty of Health and Medical Sciences, University of Surrey, Guildford, Surrey, United Kingdom
| | - Arnoud H. M. van Vliet
- Department of Comparative Biomedical Sciences, School of Veterinary Medicine, Faculty of Health and Medical Sciences, University of Surrey, Guildford, Surrey, United Kingdom
| | - Roberto M. La Ragione
- Department of Comparative Biomedical Sciences, School of Veterinary Medicine, Faculty of Health and Medical Sciences, University of Surrey, Guildford, Surrey, United Kingdom
- Department of Microbial Sciences, School of Biosciences and Medicine, Faculty of Health and Medical Sciences, University of Surrey, Guildford, Surrey, United Kingdom
| | - Bruno Gonzalez-Zorn
- Antimicrobial Resistance Unit, Veterinary School and VISAVET, Complutense University of Madrid, Spain
| | - Terry J. Smith
- Molecular Diagnostics Research Group, School of Biological and Chemical Sciences, University of Galway, Galway, Ireland
- Centre for One Health, Ryan Institute, University of Galway, Galway, Ireland
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143
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Chen H, Zhou X, Wang M, Ren L. Towards Point of Care CRISPR-Based Diagnostics: From Method to Device. J Funct Biomater 2023; 14:jfb14020097. [PMID: 36826896 PMCID: PMC9967495 DOI: 10.3390/jfb14020097] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Revised: 01/27/2023] [Accepted: 02/08/2023] [Indexed: 02/12/2023] Open
Abstract
Rapid, accurate, and portable on-site detection is critical in the face of public health emergencies. Infectious disease control and public health emergency policymaking can both be aided by effective and trustworthy point of care tests (POCT). A very promising POCT method appears to be the clustered regularly interspaced short palindromic repeats and associated protein (CRISPR/Cas)-based molecular diagnosis. For on-site detection, CRISPR/Cas-based detection can be combined with multiple signal sensing methods and integrated into smart devices. In this review, sensing methods for CRISPR/Cas-based diagnostics are introduced and the advanced strategies and recent advances in CRISPR/Cas-based POCT are reviewed. Finally, the future perspectives of CRISPR and POCT are summarized and prospected.
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Affiliation(s)
- Haoxiang Chen
- The Higher Educational Key Laboratory for Biomedical Engineering of Fujian Province, Research Center of Biomedical Engineering of Xiamen, Department of Biomaterials, College of Materials, Xiamen University, Xiamen 361005, China
| | - Xi Zhou
- The Higher Educational Key Laboratory for Biomedical Engineering of Fujian Province, Research Center of Biomedical Engineering of Xiamen, Department of Biomaterials, College of Materials, Xiamen University, Xiamen 361005, China
| | - Miao Wang
- The Higher Educational Key Laboratory for Biomedical Engineering of Fujian Province, Research Center of Biomedical Engineering of Xiamen, Department of Biomaterials, College of Materials, Xiamen University, Xiamen 361005, China
| | - Lei Ren
- The Higher Educational Key Laboratory for Biomedical Engineering of Fujian Province, Research Center of Biomedical Engineering of Xiamen, Department of Biomaterials, College of Materials, Xiamen University, Xiamen 361005, China
- State Key Lab of Physical Chemistry of Solid Surfaces, Xiamen University, Xiamen 361005, China
- Correspondence:
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144
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An Improved Duplex Real-Time Quantitative RT-PCR Assay with a Canine Endogenous Internal Positive Control for More Sensitive and Reliable Detection of Canine Parainfluenza Virus 5. Vet Sci 2023; 10:vetsci10020142. [PMID: 36851445 PMCID: PMC9965950 DOI: 10.3390/vetsci10020142] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2023] [Revised: 02/04/2023] [Accepted: 02/09/2023] [Indexed: 02/12/2023] Open
Abstract
A duplex real-time quantitative reverse transcription-polymerase chain reaction (dqRT-PCR) assay was successfully developed to simultaneously detect canine parainfluenza virus 5 (CPIV5) and a canine endogenous internal positive control (EIPC) in canine clinical samples. Two sets of primers and probes for the CPIV5 L and canine 16S rRNA genes were included in the dqRT-PCR assay to detect CPIV and monitor invalid results throughout the qRT-PCR process. The developed dqRT-PCR assay specifically detected CPIV5 but no other canine pathogens. Furthermore, 16S rRNA was stably amplified by dqRT-PCR assay in all samples containing canine cellular materials. The assay's sensitivity was determined as below ten RNA copies per reaction, with CPIV5 L gene standard RNA and 1 TCID50/mL with the CPIV5 D008 vaccine strain, which was 10-fold higher than that of the previous HN gene-specific qRT-PCR (HN-qRT-PCR) assays and was equivalent to that of the previous N gene-specific qRT-PCR (N-qRT-PCR) assays, respectively. Moreover, the Ct values of the CPIV5-positive samples obtained using the dqRT-PCR assay were lower than those obtained using the previous HN- and N-qRT-PCR assays, indicating that the diagnostic performance of the dqRT-PCR assay was superior to those of previous HN- and N-qRT-PCR assays. The calculated Cohen's kappa coefficient values (95% confidence interval) between dqRT-PCR and the HN- or N-specific qRT-PCR assays were 0.97 (0.90-1.03) or 1.00 (1.00-1.00), respectively. In conclusion, the newly developed dqRT-PCR assay with high sensitivity, specificity, and reliability will be a promising diagnostic tool for the detection of CPIV5 in clinical samples and useful for etiological and epidemiological studies of CPIV5 infection in dogs.
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145
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Nambiar S, Mohan M, Rosin Jose A. Voltammetric Sensors: A Versatile Tool in COVID‐19 Diagnosis and Prognosis. ChemistrySelect 2023. [DOI: 10.1002/slct.202204506] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/11/2023]
Affiliation(s)
- Souparnika Nambiar
- PG and Research Dept. of Chemistry Sacred Heart College (Autonomous) Thevara Kochi Kerala INDIA 682013
| | - Malavika Mohan
- PG and Research Dept. of Chemistry Sacred Heart College (Autonomous) Thevara Kochi Kerala INDIA 682013
| | - Ammu Rosin Jose
- PG and Research Dept. of Chemistry Sacred Heart College (Autonomous) Thevara Kochi Kerala INDIA 682013
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146
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Jonker A, Michel AL. Optimization and Application of Real-Time qPCR Assays in Detection and Identification of Chlamydiales in Products of Domestic Ruminant Abortion. Pathogens 2023; 12:pathogens12020290. [PMID: 36839562 PMCID: PMC9965055 DOI: 10.3390/pathogens12020290] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Revised: 02/07/2023] [Accepted: 02/08/2023] [Indexed: 02/12/2023] Open
Abstract
Domestic ruminant abortions due to infectious agents represent an important cause of economic losses in the agricultural industry. This study aimed to optimise and apply qPCR assays for detection of Chlamydiales in domestic ruminant abortion cases. Primers and probes for detection of the order Chlamydiales, Chlamydia abortus, Chlamydia pecorum, Parachlamydia acanthamoeba and Waddlia chondrophila were taken from the literature to create one singleplex and two duplex assays and the assays were optimised. Placentitis and pneumonia are pathological lesions associated with Chlamydiales infection. In a previous study, twenty-five clinical cases had pathological lesions of placentitis or pneumonia. These cases were investigated further by application of the qPCR assays in this study. Chlamydiales were detected in 16 cases. C. abortus, P. acanthamoeba and W. chondrophila were detected in bovine; and C. pecorum and W. chondrophila in ovine and caprine cases. Chlamydiales were detected in three previously inconclusive cases. Identification was improved from genus to species level (C. pecorum). Four cases remained inconclusive. In conclusion, detection of Chlamydiales and differentiation to species level was improved. This study reports the first detection of P. acanthamoeba and W. chondrophila in abortion cases in South Africa, indicating a potentially significant role in abortions in this country.
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147
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Campos MD, Varanda C, Patanita M, Amaro Ribeiro J, Campos C, Materatski P, Albuquerque A, Félix MDR. A TaqMan ® Assay Allows an Accurate Detection and Quantification of Fusarium spp., the Causal Agents of Tomato Wilt and Rot Diseases. BIOLOGY 2023; 12:biology12020268. [PMID: 36829545 PMCID: PMC9953614 DOI: 10.3390/biology12020268] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Revised: 02/04/2023] [Accepted: 02/06/2023] [Indexed: 02/11/2023]
Abstract
In tomato plants, Fusarium spp. have been increasingly associated with several wilt and rot diseases that are responsible for severe yield losses. Here, we present a real-time PCR TaqMan® MGB (Minor Groove Binder) assay to detect and discriminate Fusarium spp. from other fungal species that affect tomato plants. The methodology used is based on the selective amplification of the internal transcribed spacer (ITS) region of Fusarium spp. This assay revealed to be highly specific and sensitive for Fusarium species, targeting only the 29 Fusarium isolates from the 45 tested isolates associated to tomato diseases. Sensitivity was assessed with serial dilutions of Fusarium genomic DNA, with the limit of detection of 3.05 pg. An absolute DNA quantification method was also established, based on the determination of the absolute number of target copies. Finally, the effectiveness of the assay was successfully validated with the detection and quantification of Fusarium spp. in potentially infected tomato plants from an experimental field and in control plants grown under controlled conditions. The established methodology allows a reliable, sensitive, and reproducible estimation of Fusarium accumulation in infected tomato plants, gaining new insights for disease control and providing an additional tool in the screening of resistant plants.
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Affiliation(s)
- Maria Doroteia Campos
- MED—Mediterranean Institute for Agriculture, Environment and Development & CHANGE—Global Change and Sustainability Institute, Institute for Advanced Studies and Research, Universidade de Évora, Pólo da Mitra, Ap. 94, 7006-554 Évora, Portugal
- Correspondence:
| | - Carla Varanda
- MED—Mediterranean Institute for Agriculture, Environment and Development & CHANGE—Global Change and Sustainability Institute, Institute for Advanced Studies and Research, Universidade de Évora, Pólo da Mitra, Ap. 94, 7006-554 Évora, Portugal
| | - Mariana Patanita
- MED—Mediterranean Institute for Agriculture, Environment and Development & CHANGE—Global Change and Sustainability Institute, Institute for Advanced Studies and Research, Universidade de Évora, Pólo da Mitra, Ap. 94, 7006-554 Évora, Portugal
| | - Joana Amaro Ribeiro
- MED—Mediterranean Institute for Agriculture, Environment and Development & CHANGE—Global Change and Sustainability Institute, Institute for Advanced Studies and Research, Universidade de Évora, Pólo da Mitra, Ap. 94, 7006-554 Évora, Portugal
| | - Catarina Campos
- MED—Mediterranean Institute for Agriculture, Environment and Development & CHANGE—Global Change and Sustainability Institute, Institute for Advanced Studies and Research, Universidade de Évora, Pólo da Mitra, Ap. 94, 7006-554 Évora, Portugal
| | - Patrick Materatski
- MED—Mediterranean Institute for Agriculture, Environment and Development & CHANGE—Global Change and Sustainability Institute, Institute for Advanced Studies and Research, Universidade de Évora, Pólo da Mitra, Ap. 94, 7006-554 Évora, Portugal
| | - André Albuquerque
- MED—Mediterranean Institute for Agriculture, Environment and Development & CHANGE—Global Change and Sustainability Institute, Institute for Advanced Studies and Research, Universidade de Évora, Pólo da Mitra, Ap. 94, 7006-554 Évora, Portugal
| | - Maria do Rosário Félix
- MED—Mediterranean Institute for Agriculture, Environment and Development & CHANGE—Global Change and Sustainability Institute, Departamento de Fitotecnia, Escola de Ciências e Tecnologia, Universidade de Évora, Pólo da Mitra, Ap. 94, 7006-554 Évora, Portugal
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148
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Development of highly accurate digital PCR method and reference material for monkeypox virus detection. Anal Bioanal Chem 2023; 415:1333-1337. [PMID: 36680591 PMCID: PMC9862235 DOI: 10.1007/s00216-023-04518-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Revised: 12/12/2022] [Accepted: 01/04/2023] [Indexed: 01/22/2023]
Abstract
Human monkeypox has attracted attention recently. Monkeypox virus (MPXV) keeps evolving as it spreading around the world rapidly, which may threaten the health of more and more people. Here, we have developed a high order reference method based on digital PCR (dPCR) for MPXV detection, of which the limits of quantification (LoQ) and detection (LoD) are 38 and 6 copies/reaction, respectively. Pseudovirus reference materials (RM) containing the conserved F3L gene has been developed, and the homogeneity assessment showed that the RM was homogeneous. The reference value with its expanded uncertainty determined by the established dPCR is (2.74 ± 0.46) × 103 copies/μL. Six different MPXV test kits were accessed by the RM. Four out of six test kits cannot reach their claimed LoDs. The poor analytical sensitivity might cause false-negative results, which lead to incorrect diagnosis and treatment. The establishment of a high order reference method of dPCR and pseudovirus RM is very useful for improving the accuracy and reliability of MPXV detection.
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149
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Gorrens E, Lecocq A, De Smet J. The Use of Probiotics during Rearing of Hermetia illucens: Potential, Caveats, and Knowledge Gaps. Microorganisms 2023; 11:microorganisms11020245. [PMID: 36838211 PMCID: PMC9960648 DOI: 10.3390/microorganisms11020245] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Revised: 01/10/2023] [Accepted: 01/16/2023] [Indexed: 01/21/2023] Open
Abstract
Given the novelty of the industrial production of the edible insects sector, research has primarily focused on the zootechnical performances of black soldier fly larvae (BSFL) in response to different substrates and rearing conditions as a basis to optimize yield and quality. However recently, research has started to focus more on the associated microbes in the larval digestive system and their substrates and the effect of manipulating the composition of these communities on insect performance as a form of microbiome engineering. Here we present an overview of the existing literature on the use of microorganisms during rearing of the BSFL to optimize the productivity of this insect. These studies have had variable outcomes and potential explanations for this variation are offered to inspire future research that might lead to a better success rate for microbiome engineering in BSFL.
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Affiliation(s)
- Ellen Gorrens
- Research Group for Insect Production and Processing, Department of Microbial and Molecular Systems (M²S), KU Leuven, 2440 Geel, Belgium
| | - Antoine Lecocq
- Department of Plant and Environmental Sciences, University of Copenhagen, 1871 Frederiksberg, Denmark
| | - Jeroen De Smet
- Research Group for Insect Production and Processing, Department of Microbial and Molecular Systems (M²S), KU Leuven, 2440 Geel, Belgium
- Correspondence:
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150
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Shehata HR, Hassane B, Newmaster SG. Real-time polymerase chain reaction methods for strain specific identification and enumeration of strain Lacticaseibacillus paracasei 8700:2. Front Microbiol 2023; 13:1076631. [PMID: 36741903 PMCID: PMC9889646 DOI: 10.3389/fmicb.2022.1076631] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Accepted: 12/21/2022] [Indexed: 01/19/2023] Open
Abstract
Introduction Reliable and accurate methods for probiotic identification and enumeration, at the strain level plays a major role in confirming product efficacy since probiotic health benefits are strain-specific and dose-dependent. In this study, real-time PCR methods were developed for strain specific identification and enumeration of L. paracasei 8700:2, a probiotic strain that plays a role in fighting the common cold. Methods The assay was designed to target a unique region in L. paracasei 8700:2 genome sequence to achieve strain level specificity. The identification assay was evaluated for specificity and sensitivity. The enumeration viability real-time PCR (v-qPCR) method was first optimized for the viability treatment, then the method was evaluated for efficiency, limit of quantification, precision, and its performance was compared to plate count (PC) and viability droplet digital PCR (v-ddPCR) methods. Results The identification method proved to be strain specific and highly sensitive with a limit of detection of 0.5 pg of DNA. The optimal viability dye (PMAxx) concentration was 50 μM. The method was efficient (> 90% with R 2 values > 0.99), with a linear dynamic range between 6*102 and 6*105 copies. The method was highly precise with a relative standard deviation below 5%. The Pearson correlation coefficient (r) was 0.707 for PC and v-qPCR methods, and 0.922 for v-qPCR and v-ddPCR. Bland-Altman method comparison showed that v-qPCR always gave higher values compared to PC method (relative difference ranging from 119% to 184%) and showed no consistent trend (relative difference ranging from -20% to 22%) when comparing v-qPCR and v-ddPCR methods. Discussion The difference between PC and v-PCR methods can potentially be attributed to the proportion of cells that exist in a viable but non culturable (VBNC) state, which can be count by v-PCR but not with PC. The developed v-qPCR method was confirmed to be strain specific, sensitive, efficient, with low variance, able to count VBNC cells, and has shorter time to results compared to plate count methods. Thus, the identification and enumeration methods developed for L. paracasei 8700:2 will be of great importance to achieve high quality and efficacious probiotic products.
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Affiliation(s)
- Hanan R. Shehata
- Natural Health Product Research Alliance, Department of Integrative Biology, College of Biological Science, University of Guelph, Guelph, ON, Canada,Department of Microbiology, Faculty of Pharmacy, Mansoura University, Mansoura, Egypt,Purity-IQ Inc., Guelph, ON, Canada,*Correspondence: Hanan R. Shehata,
| | | | - Steven G. Newmaster
- Natural Health Product Research Alliance, Department of Integrative Biology, College of Biological Science, University of Guelph, Guelph, ON, Canada
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