401
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Krähenbühl S, Studer F, Guirou E, Deal A, Mächler P, Hosch S, Mpina M, Mswata S, Daubenberger C, Schindler T. ELIMU-MDx: a web-based, open-source platform for storage, management and analysis of diagnostic qPCR data. Biotechniques 2019; 68:22-27. [PMID: 31588775 DOI: 10.2144/btn-2019-0064] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
The Electronic Laboratory Information and Management Utensil for Molecular Diagnostics (ELIMU-MDx) is a user-friendly platform designed and built to accelerate the turnaround time of diagnostic qPCR assays. ELIMU-MDx is compliant with Minimum Information for Publication of Quantitative Real-Time PCR Experiments (MIQE) guidelines and has extensive data-import capabilities for all major qPCR instruments by using the RDML data standard. This platform was designed as an open-source software tool and can be accessed through the web browser on all major operating systems.
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Affiliation(s)
- Silvan Krähenbühl
- Department of Medical Parasitology & Infection Biology, Swiss Tropical & Public Health Institute, Basel, Switzerland.,University of Basel, Basel, Switzerland
| | - Fabian Studer
- Department of Medical Parasitology & Infection Biology, Swiss Tropical & Public Health Institute, Basel, Switzerland.,University of Basel, Basel, Switzerland
| | - Etienne Guirou
- Department of Medical Parasitology & Infection Biology, Swiss Tropical & Public Health Institute, Basel, Switzerland.,University of Basel, Basel, Switzerland
| | - Anna Deal
- Department of Medical Parasitology & Infection Biology, Swiss Tropical & Public Health Institute, Basel, Switzerland.,University of Basel, Basel, Switzerland.,Equatorial Guinea Malaria Vaccine Initiative, Malabo, Republic of Equatorial Guinea
| | - Philipp Mächler
- Department of Medical Parasitology & Infection Biology, Swiss Tropical & Public Health Institute, Basel, Switzerland.,University of Basel, Basel, Switzerland
| | - Salome Hosch
- Department of Medical Parasitology & Infection Biology, Swiss Tropical & Public Health Institute, Basel, Switzerland.,University of Basel, Basel, Switzerland
| | - Maximilian Mpina
- Department of Medical Parasitology & Infection Biology, Swiss Tropical & Public Health Institute, Basel, Switzerland.,University of Basel, Basel, Switzerland.,Equatorial Guinea Malaria Vaccine Initiative, Malabo, Republic of Equatorial Guinea.,Bagamoyo Research & Training Centre, Ifakara Health Institute, Bagamoyo, United Republic of Tanzania
| | - Sarah Mswata
- Bagamoyo Research & Training Centre, Ifakara Health Institute, Bagamoyo, United Republic of Tanzania
| | - Claudia Daubenberger
- Department of Medical Parasitology & Infection Biology, Swiss Tropical & Public Health Institute, Basel, Switzerland.,University of Basel, Basel, Switzerland
| | - Tobias Schindler
- Department of Medical Parasitology & Infection Biology, Swiss Tropical & Public Health Institute, Basel, Switzerland.,University of Basel, Basel, Switzerland
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402
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Martins L, Fernandes C, Albuquerque P, Tavares F. Assessment of Xanthomonas arboricola pv. juglandis Bacterial Load in Infected Walnut Fruits by Quantitative PCR. PLANT DISEASE 2019; 103:2577-2586. [PMID: 31347945 DOI: 10.1094/pdis-12-18-2253-re] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Xanthomonas arboricola pv. juglandis is the etiologic agent of important walnut (Juglans regia L.) diseases, causing severe fruit drop and high economic losses in walnut production regions. Rapid diagnostics and knowledge of bacterial virulence fitness are key to hinder disease progression and apply timely phytosanitary measures. This work describes an X. arboricola pv. juglandis-specific real-time quantitative PCR (qPCR) using X. arboricola pv. juglandis-specific DNA markers to quantify the bacterial load in infected walnut plant tissues. Method validation was achieved using calibration curves obtained with serial dilutions of X. arboricola pv. juglandis chromosomal DNA and standard curves obtained from walnut samples spiked with X. arboricola pv. juglandis cells. High correlations (R2 > 0.990 and > 0.995) and low limits of detection (35 chromosomes/qPCR reaction and 2.7 CFU/qPCR reaction) were obtained for both markers considering the calibration and standard curves, respectively. Assessment of qPCR repeatability, reproducibility, and specificity allowed us to demonstrate the reliability and consistency of the method. Furthermore, in planta quantification of X. arboricola pv. juglandis bacterial load using infected walnut fruit samples showed a higher detection resolution compared with standard PCR detection. By allowing quantification of virulence fitness of distinct X. arboricola pv. juglandis strains in planta, the proposed qPCR method may contribute to assertive risk assessment of walnut diseases caused by X. arboricola pv. juglandis and ultimately help to improve phytosanitary practices.
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Affiliation(s)
- Leonor Martins
- CIBIO - Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO - Laboratório Associado, Universidade do Porto, Vairão, Portugal
- FCUP - Faculdade de Ciências, Departamento de Biologia, Universidade do Porto, Porto, Portugal
| | - Camila Fernandes
- CIBIO - Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO - Laboratório Associado, Universidade do Porto, Vairão, Portugal
- FCUP - Faculdade de Ciências, Departamento de Biologia, Universidade do Porto, Porto, Portugal
- INIAV - Instituto Nacional de Investigação Agrária e Veterinária, Quinta do Marquês, Oeiras, Portugal
| | - Pedro Albuquerque
- CIBIO - Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO - Laboratório Associado, Universidade do Porto, Vairão, Portugal
- FCUP - Faculdade de Ciências, Departamento de Biologia, Universidade do Porto, Porto, Portugal
| | - Fernando Tavares
- CIBIO - Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO - Laboratório Associado, Universidade do Porto, Vairão, Portugal
- FCUP - Faculdade de Ciências, Departamento de Biologia, Universidade do Porto, Porto, Portugal
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403
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Simple lysis of bacterial cells for DNA-based diagnostics using hydrophilic ionic liquids. Sci Rep 2019; 9:13994. [PMID: 31570727 PMCID: PMC6768989 DOI: 10.1038/s41598-019-50246-5] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2019] [Accepted: 09/09/2019] [Indexed: 12/20/2022] Open
Abstract
The extraction of nucleic acids from microorganisms for subsequent molecular diagnostic applications is still a tedious and time-consuming procedure. We developed a method for the rapid preparation of genomic DNA from bacteria based on hydrophilic ionic liquids (ILs). First, we tested eight ILs in different buffer systems for their inhibitory effects on quantitative PCR. The cell lysis potential of different IL/buffer combinations was assessed by application on Enterococcus faecalis as a model organism for Gram-positive bacteria. The two best ILs, choline hexanoate and 1-ethyl-3-methylimidazolium acetate, were compared with the reference enzymatic method and two commercial DNA extraction kits. All methods were evaluated on four Gram-positive and four Gram-negative bacterial species that are highly relevant for environmental, food, or clinical diagnostics. In comparison to the reference method, extraction yields of the IL-based procedure were within one order of magnitude for most of the strains. The final protocol for DNA extraction using the two ILs is very low-cost, avoids the use of hazardous chemicals and can be performed in five minutes on a simple heating block. This makes the method ideal for high sample throughput and offers the opportunity for DNA extraction from bacteria in resource-limited settings or even in the field.
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404
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Roux G, Ravel C, Varlet-Marie E, Jendrowiak R, Bastien P, Sterkers Y. Inhibition of polymerase chain reaction: Pathogen-specific controls are better than human gene amplification. PLoS One 2019; 14:e0219276. [PMID: 31560697 PMCID: PMC6764677 DOI: 10.1371/journal.pone.0219276] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2019] [Accepted: 08/23/2019] [Indexed: 11/21/2022] Open
Abstract
PCR inhibition is frequent in medical microbiology routine practice and may lead to false-negative results; however there is no consensus on how to detect it. Pathogen-specific and human gene amplifications are widely used to detect PCR inhibition. We aimed at comparing the value of PCR inhibitor detection using these two methods. We analysed Cp shifts (ΔCp) obtained from qPCRs targeting either the albumin gene or the pathogen-specific sequence used in two laboratory-developed microbiological qPCR assays. 3152 samples including various matrixes were included. Pathogen-specific amplification and albumin qPCR identified 62/3152 samples (2.0%), and 409/3152 (13.0%) samples, respectively, as inhibited. Only 16 samples were detected using both methods. In addition, the use of the Youden's index failed to determine adequate Cp thresholds for albumin qPCR, even when we distinguished among the different sample matrixes. qPCR targeting the albumin gene therefore appears not adequate to identify the presence of PCR inhibitors in microbiological PCR assays. Our data may be extrapolated to other heterologous targets and should discourage their use to assess the presence of PCR inhibition in microbiological PCR assays.
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Affiliation(s)
- Guillaume Roux
- Univ. Montpellier, and Laboratoire de Microbiologie, Centre Hospitalier Universitaire (CHU) of Nîmes, Nîmes, France
| | - Christophe Ravel
- Univ. Montpellier, Centre Hospitalier Universitaire (CHU) of Montpellier, Dept. of Parasitology-Mycology, Research Unit MiVEGEC, CNRS, IRD, Montpellier, France
| | - Emmanuelle Varlet-Marie
- Univ. Montpellier, Centre Hospitalier Universitaire (CHU) of Montpellier, Dept. of Parasitology-Mycology, Research Unit MiVEGEC, CNRS, IRD, Montpellier, France
| | - Rachel Jendrowiak
- Univ. Montpellier, Centre Hospitalier Universitaire (CHU) of Montpellier, Dept. of Parasitology-Mycology, Research Unit MiVEGEC, CNRS, IRD, Montpellier, France
| | - Patrick Bastien
- Univ. Montpellier, Centre Hospitalier Universitaire (CHU) of Montpellier, Dept. of Parasitology-Mycology, Research Unit MiVEGEC, CNRS, IRD, Montpellier, France
| | - Yvon Sterkers
- Univ. Montpellier, Centre Hospitalier Universitaire (CHU) of Montpellier, Dept. of Parasitology-Mycology, Research Unit MiVEGEC, CNRS, IRD, Montpellier, France
- * E-mail:
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405
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RNA-based qPCR as a tool to quantify and to characterize dual-species biofilms. Sci Rep 2019; 9:13639. [PMID: 31541147 PMCID: PMC6754382 DOI: 10.1038/s41598-019-50094-3] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2019] [Accepted: 09/06/2019] [Indexed: 12/22/2022] Open
Abstract
While considerable research has focused on studying individual-species, we now face the challenge of determining how interspecies interactions alter bacterial behaviours and pathogenesis. Pseudomonas aeruginosa and Staphylococcus aureus are often found to co-infect cystic-fibrosis patients. Curiously, their interaction is reported as competitive under laboratory conditions. Selecting appropriate methodologies is therefore critical to analyse multi-species communities. Herein, we demonstrated the major biases associated with qPCR quantification of bacterial populations and optimized a RNA-based qPCR able not only to quantify but also to characterize microbial interactions within dual-species biofilms composed by P. aeruginosa and S. aureus, as assessed by gene expression quantification. qPCR quantification was compared with flow-cytometry and culture-based quantification. Discrepancies between culture independent and culture dependent methods could be the result of the presence of viable but not-cultivable bacteria within the biofilm. Fluorescence microscopy confirmed this. A higher sensitivity to detect viable cells further highlights the potentialities of qPCR approach to quantify biofilm communities. By using bacterial RNA and an exogenous mRNA control, it was also possible to characterize bacterial transcriptomic profile, being this a major advantage of this method.
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406
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Inquimbert C, Bourgeois D, Bravo M, Viennot S, Tramini P, Llodra JC, Molinari N, Dussart C, Giraudeau N, Carrouel F. The Oral Bacterial Microbiome of Interdental Surfaces in Adolescents According to Carious Risk. Microorganisms 2019; 7:E319. [PMID: 31491909 PMCID: PMC6780098 DOI: 10.3390/microorganisms7090319] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2019] [Revised: 09/02/2019] [Accepted: 09/04/2019] [Indexed: 12/31/2022] Open
Abstract
Adolescence is closely associated with a high risk of caries. The identification of specific bacteria in an oral microniche, the interdental space of the molars, according to carious risk can facilitate the prediction of future caries and the anticipation of the progression or stabilization of caries in adolescents. A cross-sectional clinical study according to the bacteriological criteria of interdental healthy adolescents and carious risk factors-low and high-using a real-time polymerase chain reaction technique was conducted. The presence of 26 oral pathogens from the interdental microbiota of 50 adolescents aged 15 to 17 years were qualitatively and quantitatively analyzed. Bacteria known to be cariogenic (Bifidobacterium dentium, Lactobacillus spp., Rothia dentocariosa, Streptococcus cristatus, Streptococcus mutans, Streptococcus salivarius, Streptococcus sobrinus, and Streptococcus wiggsiae) did not present differences in abundance according to carious risk. Periodontal bacteria from the red complex are positively correlated with carious risk. However, only 3 bacteria-S. sobrinus, E corrodens and T. forsythia-presented a significant increase in the highest group. Estimating the risk of caries associated with bacterial factors in interdental sites of molars in adolescents contributes to the better definition of carious risk status, periodicity and intensity of diagnostic, prevention and restorative services.
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Affiliation(s)
- Camille Inquimbert
- Laboratory "Systemic Health Care", EA4129, University Lyon 1, University of Lyon, 69008 Lyon, France.
- Department of Public Health, Faculty of Dental Medicine, University of Montpellier, 34090 Montpellier, France.
| | - Denis Bourgeois
- Laboratory "Systemic Health Care", EA4129, University Lyon 1, University of Lyon, 69008 Lyon, France.
| | - Manuel Bravo
- Department of Preventive and Community Dentistry, Faculty of Odontology, University of Granada, 18010 Granada, Spain.
| | - Stéphane Viennot
- Laboratory "Systemic Health Care", EA4129, University Lyon 1, University of Lyon, 69008 Lyon, France.
| | - Paul Tramini
- Department of Public Health, Faculty of Dental Medicine, University of Montpellier, 34090 Montpellier, France.
| | - Juan Carlos Llodra
- Department of Preventive and Community Dentistry, Faculty of Odontology, University of Granada, 18010 Granada, Spain.
| | - Nicolas Molinari
- Service DIM, CHU de Montpellier, UMR 5149 IMAG, University of Montpellier, 34090 Montpellier, France.
| | - Claude Dussart
- Laboratory "Systemic Health Care", EA4129, University Lyon 1, University of Lyon, 69008 Lyon, France.
| | - Nicolas Giraudeau
- Department of Public Health, Faculty of Dental Medicine, University of Montpellier, 34090 Montpellier, France.
| | - Florence Carrouel
- Laboratory "Systemic Health Care", EA4129, University Lyon 1, University of Lyon, 69008 Lyon, France.
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407
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Hage CA, Carmona EM, Epelbaum O, Evans SE, Gabe LM, Haydour Q, Knox KS, Kolls JK, Murad MH, Wengenack NL, Limper AH. Microbiological Laboratory Testing in the Diagnosis of Fungal Infections in Pulmonary and Critical Care Practice. An Official American Thoracic Society Clinical Practice Guideline. Am J Respir Crit Care Med 2019; 200:535-550. [PMID: 31469325 PMCID: PMC6727169 DOI: 10.1164/rccm.201906-1185st] [Citation(s) in RCA: 101] [Impact Index Per Article: 20.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Background: Fungal infections are of increasing incidence and importance in immunocompromised and immunocompetent patients. Timely diagnosis relies on appropriate use of laboratory testing in susceptible patients.Methods: The relevant literature related to diagnosis of invasive pulmonary aspergillosis, invasive candidiasis, and the common endemic mycoses was systematically reviewed. Meta-analysis was performed when appropriate. Recommendations were developed using the Grading of Recommendations Assessment, Development, and Evaluation approach.Results: This guideline includes specific recommendations on the use of galactomannan testing in serum and BAL and for the diagnosis of invasive pulmonary aspergillosis, the role of PCR in the diagnosis of invasive pulmonary aspergillosis, the role of β-d-glucan assays in the diagnosis of invasive candidiasis, and the application of serology and antigen testing in the diagnosis of the endemic mycoses.Conclusions: Rapid, accurate diagnosis of fungal infections relies on appropriate application of laboratory testing, including antigen testing, serological testing, and PCR-based assays.
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408
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Zhang H, Wang Y, Porter E, Lu N, Li Y, Yuan F, Lohman M, Noll L, Zheng W, Stoy C, Lang Y, Huber VC, Ma W, Peddireddi L, Fang Y, Shi J, Anderson G, Liu X, Bai J. Development of a multiplex real-time RT-PCR assay for simultaneous detection and differentiation of influenza A, B, C, and D viruses. Diagn Microbiol Infect Dis 2019; 95:59-66. [PMID: 31130238 PMCID: PMC6697560 DOI: 10.1016/j.diagmicrobio.2019.04.011] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2018] [Revised: 04/08/2019] [Accepted: 04/23/2019] [Indexed: 01/18/2023]
Abstract
Influenza is a common and contagious respiratory disease caused by influenza A, B, C, and D viruses (IAV, IBV, ICV, and IDV). A multiplex real-time RT-PCR assay was developed for simultaneous detection of IAV, IBV, ICV, and IDV. The assay was designed to target unique sequences in the matrix gene of IBV and ICV, the RNA polymerase subunit PB1 of IDV, and combined with USDA and CDC IAV assays, both target the matrix gene. The host 18S rRNA gene was included as an internal control. In silico analyses indicated high strain coverages: 97.9% for IBV, 99.5% for ICV, and 100% for IDV. Transcribed RNA, viral isolates and clinical samples were used for validation. The assay specifically detected target viruses without cross-reactivity, nor detection of other common pathogens. The limit of detection was approximately 30 copies for each viral RNA template, which was equivalent to a threshold cycle value of ~37.
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Affiliation(s)
- Hewei Zhang
- Kansas State Veterinary Diagnostic Laboratory, College of Veterinary Medicine, Kansas State University, Manhattan, KS, USA; College of Food and Drugs, Luoyang Polytechnic, Luo Yang, Henan, China
| | - Yin Wang
- Kansas State Veterinary Diagnostic Laboratory, College of Veterinary Medicine, Kansas State University, Manhattan, KS, USA
| | - Elizabeth Porter
- Kansas State Veterinary Diagnostic Laboratory, College of Veterinary Medicine, Kansas State University, Manhattan, KS, USA
| | - Nanyan Lu
- Kansas State Veterinary Diagnostic Laboratory, College of Veterinary Medicine, Kansas State University, Manhattan, KS, USA
| | - Yanhua Li
- Department of Diagnostic Medicine and Pathobiology, College of Veterinary Medicine, Kansas State University, Manhattan, KS, USA
| | - Fangfeng Yuan
- Kansas State Veterinary Diagnostic Laboratory, College of Veterinary Medicine, Kansas State University, Manhattan, KS, USA
| | - Molly Lohman
- Kansas State Veterinary Diagnostic Laboratory, College of Veterinary Medicine, Kansas State University, Manhattan, KS, USA
| | - Lance Noll
- Kansas State Veterinary Diagnostic Laboratory, College of Veterinary Medicine, Kansas State University, Manhattan, KS, USA
| | - Wanglong Zheng
- Kansas State Veterinary Diagnostic Laboratory, College of Veterinary Medicine, Kansas State University, Manhattan, KS, USA
| | - Colin Stoy
- Kansas State Veterinary Diagnostic Laboratory, College of Veterinary Medicine, Kansas State University, Manhattan, KS, USA
| | - Yuekun Lang
- Department of Diagnostic Medicine and Pathobiology, College of Veterinary Medicine, Kansas State University, Manhattan, KS, USA
| | - Victor C Huber
- Division of Basic Biomedical Sciences, Sanford School of Medicine, The University of South Dakota, Vermillion, SD, USA
| | - Wenjun Ma
- Department of Diagnostic Medicine and Pathobiology, College of Veterinary Medicine, Kansas State University, Manhattan, KS, USA
| | - Lalitha Peddireddi
- Kansas State Veterinary Diagnostic Laboratory, College of Veterinary Medicine, Kansas State University, Manhattan, KS, USA; Department of Diagnostic Medicine and Pathobiology, College of Veterinary Medicine, Kansas State University, Manhattan, KS, USA
| | - Ying Fang
- Department of Diagnostic Medicine and Pathobiology, College of Veterinary Medicine, Kansas State University, Manhattan, KS, USA
| | - Jishu Shi
- Department of Anatomy and Physiology, College of Veterinary Medicine, Kansas State University, Manhattan, KS, USA
| | - Gary Anderson
- Kansas State Veterinary Diagnostic Laboratory, College of Veterinary Medicine, Kansas State University, Manhattan, KS, USA; Department of Diagnostic Medicine and Pathobiology, College of Veterinary Medicine, Kansas State University, Manhattan, KS, USA
| | - Xuming Liu
- Kansas State Veterinary Diagnostic Laboratory, College of Veterinary Medicine, Kansas State University, Manhattan, KS, USA; Department of Diagnostic Medicine and Pathobiology, College of Veterinary Medicine, Kansas State University, Manhattan, KS, USA.
| | - Jianfa Bai
- Kansas State Veterinary Diagnostic Laboratory, College of Veterinary Medicine, Kansas State University, Manhattan, KS, USA; Department of Diagnostic Medicine and Pathobiology, College of Veterinary Medicine, Kansas State University, Manhattan, KS, USA.
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409
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Kang TS. Basic principles for developing real-time PCR methods used in food analysis: A review. Trends Food Sci Technol 2019. [DOI: 10.1016/j.tifs.2019.07.037] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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410
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411
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Jaramillo Ortiz JM, Paoletta MS, Gravisaco MJ, López Arias LS, Montenegro VN, de la Fournière SAM, Valenzano MN, Guillemi EC, Valentini B, Echaide I, Farber MD, Wilkowsky SE. Immunisation of cattle against Babesia bovis combining a multi-epitope modified vaccinia Ankara virus and a recombinant protein induce strong Th1 cell responses but fails to trigger neutralising antibodies required for protection. Ticks Tick Borne Dis 2019; 10:101270. [PMID: 31445874 DOI: 10.1016/j.ttbdis.2019.101270] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2019] [Revised: 08/04/2019] [Accepted: 08/15/2019] [Indexed: 01/01/2023]
Abstract
Protection against the intraerythrocytic protozoan parasite Babesia bovis depends on both strong innate and adaptive immune response, this latter involving the presentation of parasite antigens to CD4+ T-lymphocytes by professional antigen-presenting cells. Secretion of Th1 cytokines by CD4+ T cell is also very important for isotype switching to IgG2, the best opsonising antibody isotype in cattle, to target extracellular parasites and parasite antigens displayed at the erythrocyte surface. In the field of vaccinology, heterologous prime-boost schemes combining protein-adjuvant formulations with a modified vaccinia Ankara vector expressing the same antigen have demonstrated the induction of both humoral and cellular immune responses. It has been previously demonstrated that MVA-infected dendritic cells can present antigens in the context of MHC II and activate CD4+ T cell. These results support the use of the MVA viral vector for a pathogen like Babesia bovis, which only resides within erythrocytes. In this study, 13-15-months-old Holstein-Friesian steers were immunised with a subunit vaccine as a prime and a modified vaccinia Ankara vector as a boost, both expressing a chimeric multi-antigen (rMABbo - rMVA). This antigen includes the immunodominant B and T cell epitopes of three B. bovis proteins: merozoite surface antigen - 2c (MSA - 2c), rhoptry associated protein 1 (RAP - 1) and heat shock protein 20 (HSP20). Responses were compared with the Babesia bovis live attenuated vaccine used in Argentina (R1A). Eleven weeks after the first immunisation, all bovines were challenged by the inoculation of a virulent B. bovis strain. All groups were monitored daily for hyperthermia and reduction of packed cell volume. Both the rMABbo - rMVA and R1A vaccinated animals developed high titters of total IgG antibodies and an antigen-specific Th1 cellular response before and after challenge. However, all rMABbo - rMVA steers showed clinical signs of disease upon challenge. Only the R1A live vaccine group developed an immune response associated with in vitro neutralising antibodies at a level that significantly inhibited the parasite invasion. The lack of protection observed with this recombinant formulation indicates the need to perform further basic and clinical studies in the bovine model in order to achieve the desired effectiveness. This is the first report in which a novel vaccine candidate against Babesia bovis was constructed based on a recombinant and rationally designed viral vector and evaluated in the biological model of the disease.
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Affiliation(s)
- José Manuel Jaramillo Ortiz
- Instituto de Agrobiotecnología y Biología Molecular (IABIMO) INTA - CONICET, De Los Reseros y Dr. Nicolás Repetto s/n, P.O. Box 25 (B1712WAA), Castelar, Buenos Aires, Argentina
| | - Martina Soledad Paoletta
- Instituto de Agrobiotecnología y Biología Molecular (IABIMO) INTA - CONICET, De Los Reseros y Dr. Nicolás Repetto s/n, P.O. Box 25 (B1712WAA), Castelar, Buenos Aires, Argentina
| | - María José Gravisaco
- Instituto de Agrobiotecnología y Biología Molecular (IABIMO) INTA - CONICET, De Los Reseros y Dr. Nicolás Repetto s/n, P.O. Box 25 (B1712WAA), Castelar, Buenos Aires, Argentina
| | - Ludmila Sol López Arias
- Instituto de Agrobiotecnología y Biología Molecular (IABIMO) INTA - CONICET, De Los Reseros y Dr. Nicolás Repetto s/n, P.O. Box 25 (B1712WAA), Castelar, Buenos Aires, Argentina
| | - Valeria Noely Montenegro
- Instituto de Agrobiotecnología y Biología Molecular (IABIMO) INTA - CONICET, De Los Reseros y Dr. Nicolás Repetto s/n, P.O. Box 25 (B1712WAA), Castelar, Buenos Aires, Argentina
| | - Sofía Ana María de la Fournière
- Instituto de Agrobiotecnología y Biología Molecular (IABIMO) INTA - CONICET, De Los Reseros y Dr. Nicolás Repetto s/n, P.O. Box 25 (B1712WAA), Castelar, Buenos Aires, Argentina
| | - Magalí Nicole Valenzano
- Instituto de Agrobiotecnología y Biología Molecular (IABIMO) INTA - CONICET, De Los Reseros y Dr. Nicolás Repetto s/n, P.O. Box 25 (B1712WAA), Castelar, Buenos Aires, Argentina
| | - Eliana Carolina Guillemi
- Instituto de Agrobiotecnología y Biología Molecular (IABIMO) INTA - CONICET, De Los Reseros y Dr. Nicolás Repetto s/n, P.O. Box 25 (B1712WAA), Castelar, Buenos Aires, Argentina
| | - Beatriz Valentini
- Laboratorio de Inmunología y Parasitología Veterinaria, EEA Rafaela, INTA, RN 34, Km 227, CC 22, 2300, Rafaela, Santa Fe, Argentina
| | - Ignacio Echaide
- Laboratorio de Inmunología y Parasitología Veterinaria, EEA Rafaela, INTA, RN 34, Km 227, CC 22, 2300, Rafaela, Santa Fe, Argentina
| | - Marisa Diana Farber
- Instituto de Agrobiotecnología y Biología Molecular (IABIMO) INTA - CONICET, De Los Reseros y Dr. Nicolás Repetto s/n, P.O. Box 25 (B1712WAA), Castelar, Buenos Aires, Argentina
| | - Silvina Elizabeth Wilkowsky
- Instituto de Agrobiotecnología y Biología Molecular (IABIMO) INTA - CONICET, De Los Reseros y Dr. Nicolás Repetto s/n, P.O. Box 25 (B1712WAA), Castelar, Buenos Aires, Argentina.
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412
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Navarro-Gonzalez N, Fourichon C, Blanquefort P, Delafosse A, Joly A, Ngwa-Mbot D, Biet F, Boichard D, Schibler L, Journaux L, Meens E, Guatteo R. Longitudinal study of Mycobacterium avium ssp. paratuberculosis fecal shedding patterns and concurrent serological patterns in naturally infected dairy cattle. J Dairy Sci 2019; 102:9117-9137. [PMID: 31378491 DOI: 10.3168/jds.2018-15897] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2018] [Accepted: 06/12/2019] [Indexed: 11/19/2022]
Abstract
Mycobacterium avium ssp. paratuberculosis (MAP) is the etiological agent of paratuberculosis, a disease that affects ruminants worldwide. Despite global interest in the control of this disease, gaps exist in our knowledge of fecal shedding patterns and concurrent serological patterns. This longitudinal study in dairy cattle herds with high MAP seroprevalence in France aimed at accurately describing fecal shedding patterns over 1 year; relating those shedding patterns to individual animal characteristics (age, breed, parity); and exploring the association between fecal shedding patterns and serological patterns. To describe temporal fecal shedding patterns and continuity of shedding, along with the standard quantitative PCR (qPCR) threshold cycle we used a cutoff value that related to low or nonculturable fecal shedding. We also defined a threshold cycle indicative of shedding in high quantities to describe infection progression patterns. Twenty-one herds completed the study, and 782 cows were tested 4 times each. We obtained 4 sets of paired fecal qPCR and serum ELISA results from 757 cows. Although we targeted highly likely infectious animals, we found a large diversity of shedding patterns, as well as high variability between herds in the proportion of animals showing a given pattern. The fecal qPCR results of almost 20% of the final study sample were positioned at least once in the range that indicated low or nonculturable fecal shedding (between the adjusted and the standard cutoff value). Although these animals would typically be classified as non-shedders, they could be important to infection dynamics on the farm. Animals that shed at least twice consecutively and animals that shed in high quantities rarely reverted to negativity. Repeated fecal qPCR can be used to detect temporal fecal shedding traits, and the decision to cull an animal could practically be based on temporal, semiquantitative results. Overall, we found a mismatch between fecal shedding and ELISA seropositivity (637 animals were ELISA-negative 4 times, but only 13% of those animals were qPCR-negative 4 times). We found that having more than 2 ELISA-positive samples was strongly related to persistent and continuous shedding. We suggest that although serological testing is much less sensitive than qPCR, it can also be used, particularly over the course of multiple testing events, to identify animals that are most likely to contribute to the contamination of the farm environment.
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Affiliation(s)
| | | | | | | | - Alain Joly
- Groupement de Défense Sanitaire Bretagne, 56000 Vannes, France
| | | | - Franck Biet
- ISP, INRA, Université de Tours, 37380, Nouzilly, France
| | - Didier Boichard
- GABI, INRA, AgroParisTech, Université Paris Saclay, 78350 Jouy-en-Josas, France
| | | | | | - Eric Meens
- Groupement de Défense contre les Maladies des Animaux Seine Maritime, 76230 Bois-Guillaume, France
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413
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Yamamoto L, Filho AGA, Queiroz JA, de Carvalho MHB, Rodrigues JC, Kanunfre KA, Francisco RPV, Okay TS. Performance of a Multiplex Nested Polymerase Chain Reaction in Detecting 7 Pathogens Containing DNA in Their Genomes Associated With Congenital Infections. Arch Pathol Lab Med 2019; 144:99-106. [PMID: 31219343 DOI: 10.5858/arpa.2018-0544-oa] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
CONTEXT.— Infections are the leading cause of perinatal and infant mortality in low-income and low-resource countries, which have a higher prevalence of infections. Definitive diagnosis of congenital and perinatal infections is largely dependent upon the results of laboratory tests. OBJECTIVE.— To develop a multiplex nested polymerase chain reaction (PCR) technique for the simultaneous detection of 7 pathogens containing DNA in their genomes in suspected cases of congenital infection. DESIGN.— Eligible participants were pregnant women with positive immunoglobulin M antibodies raised to one of the pathogens in the prenatal serologic screening, associated or not with fetal ultrasound abnormalities or positive fetal serology. Neonates whose mothers did not attend prenatal care were included when they presented with symptomatology and laboratory parameters suggestive of infection. The detection rate of the multiplex nested PCR was compared with maternal, fetal, and neonatal serology, as well as placental immunohistochemistry and noncommercial amplifications. RESULTS.— Of 161 suspected cases, the multiplex nested PCR detected 60 (37.3%), whereas the tests available in hospital laboratories detected 13 of 60 (21.7%) of the cases detected by the multiplex nested PCR, demonstrating a 4.6 times higher detection rate for the multiplex nested PCR (Fisher exact test, P < .001). Positive amplifications were to Toxoplasma gondii (32 cases), cytomegalovirus (14 cases), parvovirus B19 (5 cases), and adenovirus (5 cases). In 4 cases, 2 pathogens were simultaneously detected. All types of biological matrices were suitable for amplification. Sequencing of multiplex nested PCR products confirmed the molecular findings. CONCLUSIONS.— The multiplex nested PCR significantly increased the number of diagnosed congenital infections. Given the scarcity of DNA recovered from amniotic fluid and some neonatal samples, this multiplex nested PCR allows the simultaneous detection of 7 pathogens associated with congenital infections in a reliable, faster, cost-effective, and more sensitive way.
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Affiliation(s)
- Lidia Yamamoto
- From the Laboratory of Seroepidemiology and Immunobiology, Institute of Tropical Medicine (Drs Yamamoto, Rodrigues, Kanunfre, and Okay), the Department of Obstetrics and Gynecology, School of Medicine (Drs Amorim Filho, Queiroz, Carvalho, and Francisco), and LIM 48, Laboratory of Immunology, Department of Infectious and Parasitic Diseases, School of Medicine (Dr Kanunfre), University of São Paulo, São Paulo, Brazil
| | - Antonio G Amorim Filho
- From the Laboratory of Seroepidemiology and Immunobiology, Institute of Tropical Medicine (Drs Yamamoto, Rodrigues, Kanunfre, and Okay), the Department of Obstetrics and Gynecology, School of Medicine (Drs Amorim Filho, Queiroz, Carvalho, and Francisco), and LIM 48, Laboratory of Immunology, Department of Infectious and Parasitic Diseases, School of Medicine (Dr Kanunfre), University of São Paulo, São Paulo, Brazil
| | - Joelma A Queiroz
- From the Laboratory of Seroepidemiology and Immunobiology, Institute of Tropical Medicine (Drs Yamamoto, Rodrigues, Kanunfre, and Okay), the Department of Obstetrics and Gynecology, School of Medicine (Drs Amorim Filho, Queiroz, Carvalho, and Francisco), and LIM 48, Laboratory of Immunology, Department of Infectious and Parasitic Diseases, School of Medicine (Dr Kanunfre), University of São Paulo, São Paulo, Brazil
| | - Mario H B de Carvalho
- From the Laboratory of Seroepidemiology and Immunobiology, Institute of Tropical Medicine (Drs Yamamoto, Rodrigues, Kanunfre, and Okay), the Department of Obstetrics and Gynecology, School of Medicine (Drs Amorim Filho, Queiroz, Carvalho, and Francisco), and LIM 48, Laboratory of Immunology, Department of Infectious and Parasitic Diseases, School of Medicine (Dr Kanunfre), University of São Paulo, São Paulo, Brazil
| | - Jonatas C Rodrigues
- From the Laboratory of Seroepidemiology and Immunobiology, Institute of Tropical Medicine (Drs Yamamoto, Rodrigues, Kanunfre, and Okay), the Department of Obstetrics and Gynecology, School of Medicine (Drs Amorim Filho, Queiroz, Carvalho, and Francisco), and LIM 48, Laboratory of Immunology, Department of Infectious and Parasitic Diseases, School of Medicine (Dr Kanunfre), University of São Paulo, São Paulo, Brazil
| | - Kelly A Kanunfre
- From the Laboratory of Seroepidemiology and Immunobiology, Institute of Tropical Medicine (Drs Yamamoto, Rodrigues, Kanunfre, and Okay), the Department of Obstetrics and Gynecology, School of Medicine (Drs Amorim Filho, Queiroz, Carvalho, and Francisco), and LIM 48, Laboratory of Immunology, Department of Infectious and Parasitic Diseases, School of Medicine (Dr Kanunfre), University of São Paulo, São Paulo, Brazil
| | - Rossana P V Francisco
- From the Laboratory of Seroepidemiology and Immunobiology, Institute of Tropical Medicine (Drs Yamamoto, Rodrigues, Kanunfre, and Okay), the Department of Obstetrics and Gynecology, School of Medicine (Drs Amorim Filho, Queiroz, Carvalho, and Francisco), and LIM 48, Laboratory of Immunology, Department of Infectious and Parasitic Diseases, School of Medicine (Dr Kanunfre), University of São Paulo, São Paulo, Brazil
| | - Thelma Suely Okay
- From the Laboratory of Seroepidemiology and Immunobiology, Institute of Tropical Medicine (Drs Yamamoto, Rodrigues, Kanunfre, and Okay), the Department of Obstetrics and Gynecology, School of Medicine (Drs Amorim Filho, Queiroz, Carvalho, and Francisco), and LIM 48, Laboratory of Immunology, Department of Infectious and Parasitic Diseases, School of Medicine (Dr Kanunfre), University of São Paulo, São Paulo, Brazil
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414
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Buchheister S, Roegener F, Zschemisch NH, Talbot SR, Christensen H, Bleich A. One for two: A novel and highly sensitive virulence factor-based quantitative polymerase chain reaction assay for the simultaneous detection of Rodentibacter pneumotropicus and Rodentibacter heylii in environmental sample material. Lab Anim 2019; 54:239-250. [PMID: 31195883 DOI: 10.1177/0023677219853600] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Hygienic monitoring of laboratory rodents has focused more and more on the analysis of environmental sample material by quantitative polymerase chain reaction (qPCR) assays. This approach requires profound knowledge of specific genetic sequences of the agents to be monitored and the assays need to be permanently adapted to take the latest research into account. [Pasteurella] pneumotropica was recently reclassified into the new genus Rodentibacter, with Rodentibacter (R.) pneumotropicus and R. heylii as the most commonly detected species in laboratory mouse colonies. This study aimed at the development of a specific qPCR assay for the simultaneous detection of both agents. A novel primer probe set, based on detection of the specific virulence factor' 'inclusion body protein A' gene (ibpA), was confirmed by testing the assay on currently described Rodentibacter type species and other Pasteurellaceae. Furthermore, it was validated within four different barrier units and results were compared with the cultural analysis of sentinel mice. The assay was suitable to specifically detect R. pneumotropicus and R. heylii and discriminate them from other murine Rodentibacter spp. In addition, it revealed high sensitivity for the detection of both agents in environmental sampling material including exhaust air dust in individually ventilated cage systems. Altogether, higher pathogen prevalence was detected via qPCR of environmental samples compared with cultural diagnostics of sentinel mice. This study describes a qPCR assay for the simultaneous detection of R. pneumotropicus and R. heylii. This assay was demonstrated to be beneficial during routine health monitoring, especially with regard to environmental sampling strategies.
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Affiliation(s)
| | - Florian Roegener
- Institute of Laboratory Animal Science, Hannover Medical School, Germany
| | | | - Steven R Talbot
- Institute of Laboratory Animal Science, Hannover Medical School, Germany
| | - Henrik Christensen
- Faculty of Health and Medical Sciences, University of Copenhagen, Denmark
| | - André Bleich
- Institute of Laboratory Animal Science, Hannover Medical School, Germany
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415
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Hrytsev О. MULTIPLEX-TOUCHDOWN PCR FOR RAPID SIMULTANEOUS DETECTION OF Rhizoctonia cerealis AND Rhizoctonia solani. BIOTECHNOLOGIA ACTA 2019. [DOI: 10.15407/biotech12.03.075] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
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416
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Angarita‐Díaz MP, Díaz JA, Tupaz HA, López‐López A, Forero D, Mira A, Dávila F, Cerón XA, Ochoa‐Acosta EM, Goméz OL, Gonzalez G. Presence of Streptococcus dentisani in the dental plaque of children from different Colombian cities. Clin Exp Dent Res 2019; 5:184-190. [PMID: 31249697 PMCID: PMC6585583 DOI: 10.1002/cre2.158] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2018] [Revised: 11/29/2018] [Accepted: 12/03/2018] [Indexed: 01/20/2023] Open
Abstract
Streptococcus dentisani has been identified as an oral cavity probiotic due to its beneficial characteristics. One of its beneficial features is the production of bacteriocins, which inhibit the growth of cariogenic bacteria, and another is its buffering capacity through the production of ammonium from arginine. The purpose of this study was to determine the presence of S. dentisani in the dental plaque of Colombian children and whether the presence of this bacterium is related to oral health and other conditions. Dental plaque and information on diet and oral hygiene habits were collected from children between 6 and 12 years of age from four Colombian cities, divided into caries-free children (International Caries Detection and Assessment System [ICDAS] 0, Decayed Missing Filled Teeth index [DMFT] 0), children with ICDAS 1 and 2, and children with ICDAS >3. Plaque DNA was extracted and quantified, and real-time polymerase chain reaction was performed using specific primers. This bacterium was identified in all samples, with a median of 0.46 cells/ng DNA (interquartile range [IQR] 0.13-1.02), without finding significant differences between the groups (P > 0.05). In caries-free children, a median of 0.45 cells/ng DNA (IQR 0.14-1.23) was found. In children with ICDAS 1 and 2, the median was 0.49 cells/ng DNA (IQR 0.11-0.97), and in children with ICDAS >3, the median was 0.35 cells/ng DNA (IQR 0.12-1.07). However, statistically significant differences were found in the origin of children (P < 0.01), the use of fluoride-containing products (P < 0.01), and the frequency of food intake (P < 0.05). In conclusion, the presence of S. dentisani was quantified in children from four Colombian cities, without finding significant differences in oral health status. Nevertheless, three conditions showed a possible relationship with S. dentisani.
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Affiliation(s)
- María P. Angarita‐Díaz
- School of DentistryUniversidad Cooperativa de Colombia, Villavicencio CampusVillavicencioColombia
| | - Jaime A. Díaz
- School of DentistryUniversidad Cooperativa de Colombia, Bogotá CampusBogotáColombia
| | - Herlinto A. Tupaz
- School of DentistryUniversidad Cooperativa de Colombia, Bogotá CampusBogotáColombia
| | - Arantxa López‐López
- Department of Health and GenomicsFoundation for the Promotion of Health and Biomedical Research, FISABIOValenciaSpain
| | - Diana Forero
- School of DentistryUniversidad Cooperativa de Colombia, Villavicencio CampusVillavicencioColombia
| | - Alex Mira
- Department of Health and GenomicsFoundation for the Promotion of Health and Biomedical Research, FISABIOValenciaSpain
| | - Fernando Dávila
- School of DentistryUniversidad Cooperativa de Colombia, Pasto campusPastoColombia
| | - Ximena A. Cerón
- School of DentistryUniversidad Cooperativa de Colombia, Pasto campusPastoColombia
| | | | - Olga L. Goméz
- School of DentistryPontifica Universidad JaverianaBogotáColombia
| | - Gladys Gonzalez
- School of DentistryUniversidad Cooperativa de Colombia, Bogotá CampusBogotáColombia
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417
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Wu F, You Y, Zhang X, Zhang H, Chen W, Yang Y, Werner D, Tao S, Wang X. Effects of Various Carbon Nanotubes on Soil Bacterial Community Composition and Structure. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2019; 53:5707-5716. [PMID: 31046252 DOI: 10.1021/acs.est.8b06909] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Carbon nanotubes (CNTs) have huge industrial potential, and their environmental impacts need to be evaluated. Knowledge of CNT impacts on soil microbial communities is still limited. To address this knowledge gap, we systematically examined dynamic effects of one type of single-walled carbon nanotubes (SWs) and three multiwalled carbon nanotubes (MWs) with different outer diameters on the soil bacterial community in an agricultural soil over 56 days. The results showed that SWs differently affected soil bacterial abundance, diversity, and composition as compared to MWs. The differences could have resulted from the materials' distinct physical structure and surface composition, which in turn affected their bioavailability in soil. For certain treatments, soil bacterial diversity and the relative abundance of certain predominant phyla were correlated with their exposure duration. However, many phyla recovered to their initial relative abundance within 56 days, reflecting resilience of the soil bacterial community in response to CNT-induced disturbance. Further analysis at the genus level showed differential tolerance to MWs, as well as size- and dose-dependent tolerance among bacterial genera. Predictive functional profiling showed that while CNTs initially caused fluctuations in microbial community function, community function largely converged across all treatments by the end of the 56 day exposure.
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Affiliation(s)
- Fan Wu
- Laboratory for Earth Surface Processes, College of Urban and Environmental Sciences , Peking University , Beijing 100871 , China
| | - Yaqi You
- Department of Civil and Environmental Engineering , University of Nevada , Reno , Nevada 89557 , United States
| | - Xinyu Zhang
- Laboratory for Earth Surface Processes, College of Urban and Environmental Sciences , Peking University , Beijing 100871 , China
| | - Haiyun Zhang
- Laboratory for Earth Surface Processes, College of Urban and Environmental Sciences , Peking University , Beijing 100871 , China
| | - Weixiao Chen
- Laboratory for Earth Surface Processes, College of Urban and Environmental Sciences , Peking University , Beijing 100871 , China
| | - Yu Yang
- Department of Civil and Environmental Engineering , University of Nevada , Reno , Nevada 89557 , United States
| | - David Werner
- School of Engineering , Newcastle University , Newcastle upon Tyne NE1 7RU , United Kingdom
| | - Shu Tao
- Laboratory for Earth Surface Processes, College of Urban and Environmental Sciences , Peking University , Beijing 100871 , China
| | - Xilong Wang
- Laboratory for Earth Surface Processes, College of Urban and Environmental Sciences , Peking University , Beijing 100871 , China
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418
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Papaiakovou M, Gasser RB, Littlewood DTJ. Quantitative PCR-Based Diagnosis of Soil-Transmitted Helminth Infections: Faecal or Fickle? Trends Parasitol 2019; 35:491-500. [PMID: 31126720 DOI: 10.1016/j.pt.2019.04.006] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2019] [Revised: 04/16/2019] [Accepted: 04/19/2019] [Indexed: 11/19/2022]
Abstract
Treatment and control programmes tackling soil-transmitted helminth (STH) infections require sensitive, reliable, and accurate diagnostic tools. There is a growing need for measures of infection intensity as programmes approach STH control. Quantitative real-time PCR (qPCR) is well suited to the detection of DNA targets present in stool, even in low-prevalence settings. Detecting low levels of infection becomes increasingly important when the breakpoint of transmission is approached, and is vital when monitoring for recrudescence once control, or possibly 'elimination', is achieved. We address key challenges and questions that remain as barriers to incorporating qPCR as a cornerstone diagnostic tool for STH infections.
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Affiliation(s)
| | - Robin B Gasser
- Department of Veterinary Biosciences, Melbourne Veterinary School, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, Victoria, Australia
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419
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Zhou Y, Wan Z, Yang S, Li Y, Li M, Wang B, Hu Y, Xia X, Jin X, Yu N, Zhang C. A Mismatch-Tolerant Reverse Transcription Loop-Mediated Isothermal Amplification Method and Its Application on Simultaneous Detection of All Four Serotype of Dengue Viruses. Front Microbiol 2019; 10:1056. [PMID: 31139171 PMCID: PMC6518337 DOI: 10.3389/fmicb.2019.01056] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2019] [Accepted: 04/26/2019] [Indexed: 11/25/2022] Open
Abstract
Loop-mediated isothermal amplification (LAMP) has been widely used in the detection of pathogens causing infectious diseases. However, mismatches between primers (especially in the 3′-end) and templates significantly reduced the amplification efficiency of LAMP, and limited its application to genetically diverse viruses. Here, we reported a novel mismatch-tolerant LAMP assay and its application in the detection of dengue viruses (DENV). The novel method features the addition of as little as 0.15 U of high-fidelity DNA polymerase to the standard 25 μl LAMP reaction mixture. This amount was sufficient to remove the mismatched bases at the 3′-end of primers, thereby resulting in excellent tolerance for various mismatches occurring at the 3′-end of the LAMP primers during amplification. This novel LAMP assay has a markedly improved amplification efficiency especially for the mutants forming mismatches with internal primers (FIP/BIP) and loop primers (FLP/BLP). The reaction time of the novel method was about 5.6–22.6 min faster than the conventional LAMP method regardless of the presence or absence of mismatches between primers and templates. Using the novel method, we improved a previously established pan-serotype assay for DENV, and demonstrated greater sensitivity for detection of four DENV serotypes than the previous one. The limit of detection (LOD) of the novel assay was 74, 252, 78, and 35 virus RNA copies per reaction for DENV-1, DENV-2, DENV-3, and DENV-4, respectively. Among 153 clinical samples from patients with suspected DENV infection, the novel assay detected 94.8% samples being DENV positive, higher than that detected by the commercial NS1 antigen assay (92.2%), laboratory-based RT-PCR method (78.4%), and the conventional RT-LAMP assay (86.9%). Furthermore, the novel RT-LAMP assay has been developed into a visual determination method by adding colorimetric dyes. Because of its simplicity, all LAMP-based diagnostic assays may be easily updated to the newly improved version. The novel mismatch-tolerant LAMP method represents a simple, sensitive and promising approach for molecular diagnosis of highly variable viruses, and it is especially suited for application in resource-limited settings.
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Affiliation(s)
- Yi Zhou
- School of Life Sciences, East China Normal University, Shanghai, China.,Pathogen Discovery and Big Data Center, Chinese Academy of Sciences (CAS) Key Laboratory of Molecular Virology and Immunology, Institut Pasteur of Shanghai, Chinese Academy of Sciences, Shanghai, China
| | - Zhenzhou Wan
- Medical Laboratory of Taizhou Fourth People's Hospital, Taizhou, China
| | - Shuting Yang
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, China
| | - Yingxue Li
- Pathogen Discovery and Big Data Center, Chinese Academy of Sciences (CAS) Key Laboratory of Molecular Virology and Immunology, Institut Pasteur of Shanghai, Chinese Academy of Sciences, Shanghai, China
| | - Min Li
- Viral Disease and Vaccine Translational Research Unit, CAS Key Laboratory of Molecular Virology and Immunology, Institut Pasteur of Shanghai, Chinese Academy of Sciences, Shanghai, China
| | - Binghui Wang
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, China
| | - Yihong Hu
- Pathogen Discovery and Big Data Center, Chinese Academy of Sciences (CAS) Key Laboratory of Molecular Virology and Immunology, Institut Pasteur of Shanghai, Chinese Academy of Sciences, Shanghai, China
| | - Xueshan Xia
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, China
| | - Xia Jin
- Viral Disease and Vaccine Translational Research Unit, CAS Key Laboratory of Molecular Virology and Immunology, Institut Pasteur of Shanghai, Chinese Academy of Sciences, Shanghai, China
| | - Na Yu
- School of Life Sciences, East China Normal University, Shanghai, China
| | - Chiyu Zhang
- Pathogen Discovery and Big Data Center, Chinese Academy of Sciences (CAS) Key Laboratory of Molecular Virology and Immunology, Institut Pasteur of Shanghai, Chinese Academy of Sciences, Shanghai, China
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420
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Wisuthiphaet N, Yang X, Young GM, Nitin N. Rapid detection of Escherichia coli in beverages using genetically engineered bacteriophage T7. AMB Express 2019; 9:55. [PMID: 31004244 PMCID: PMC6474890 DOI: 10.1186/s13568-019-0776-7] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2019] [Accepted: 04/09/2019] [Indexed: 11/10/2022] Open
Abstract
Foodborne illness due to bacterial contamination is a significant issue impacting public health that demands new technology which is practical to implement by food industry. Detection of bacteria in food products and production facilities is a crucial strategy supporting food safety assessments. Bacteriophages were investigated as a tool for bacterial detection due to their ability to infect specific strain of host bacteria in order to improve sensitivity, specificity, and rapidity of bacterial detection. The results of this investigation reveal a novel method for rapid detection. The method employs a genetically engineered bacteriophage, phage T7-ALP, which expresses alkaline phosphatase. Upon infection of Escherichia coli, overexpression of alkaline phosphatase provides an opportunity for rapid sensitive detection of a signal indicative of bacterial presence in model beverage samples as low as 100 bacteria per gram. The method employs a fluorescent precipitated substrate, ELF-97, as a substrate for alkaline phosphatase activity coupled with fluorescence imaging and image analysis allowing single-cell imaging results in high detection sensitivity. The method is easily completed within less than 6 h enabling it to be deployed within most large industrial food processing facilities that have routine 8-h operational shifts.
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Affiliation(s)
| | - Xu Yang
- Department of Food Science and Technology, University of California, Davis, CA, USA
| | - Glenn M Young
- Department of Food Science and Technology, University of California, Davis, CA, USA
| | - Nitin Nitin
- Department of Food Science and Technology, University of California, Davis, CA, USA.
- Department of Biological and Agricultural Engineering, University of California, Davis, CA, USA.
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421
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DNA Authentication of St John's Wort ( Hypericum perforatum L.) Commercial Products Targeting the ITS Region. Genes (Basel) 2019; 10:genes10040286. [PMID: 30970623 PMCID: PMC6523358 DOI: 10.3390/genes10040286] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2019] [Revised: 04/03/2019] [Accepted: 04/03/2019] [Indexed: 11/17/2022] Open
Abstract
There is considerable potential for the use of DNA barcoding methods to authenticate raw medicinal plant materials, but their application to testing commercial products has been controversial. A simple PCR test targeting species-specific sequences within the nuclear ribosomal internal transcribed spacer (ITS) region was adapted to screen commercial products for the presence of Hypericum perforatum L. material. DNA differing widely in amount and extent of fragmentation was detected in a number of product types. Two assays were designed to further analyse this DNA using a curated database of selected Hypericum ITS sequences: A qPCR assay based on a species-specific primer pair spanning the ITS1 and ITS2 regions, using synthetic DNA reference standards for DNA quantitation and a Next Generation Sequencing (NGS) assay separately targeting the ITS1 and ITS2 regions. The ability of the assays to detect H. perforatum DNA sequences in processed medicines was investigated. Out of twenty different matrices tested, both assays detected H. perforatum DNA in five samples with more than 103 ITS copies µL−1 DNA extract, whilst the qPCR assay was also able to detect lower levels of DNA in two further samples. The NGS assay confirmed that H. perforatum was the major species in all five positive samples, though trace contaminants were also detected.
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422
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Ou F, McGoverin C, Swift S, Vanholsbeeck F. Near real-time enumeration of live and dead bacteria using a fibre-based spectroscopic device. Sci Rep 2019; 9:4807. [PMID: 30886183 PMCID: PMC6423134 DOI: 10.1038/s41598-019-41221-1] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2018] [Accepted: 02/28/2019] [Indexed: 01/05/2023] Open
Abstract
A rapid, cost-effective and easy method that allows on-site determination of the concentration of live and dead bacterial cells using a fibre-based spectroscopic device (the optrode system) is proposed and demonstrated. Identification of live and dead bacteria was achieved by using the commercially available dyes SYTO 9 and propidium iodide, and fluorescence spectra were measured by the optrode. Three spectral processing methods were evaluated for their effectiveness in predicting the original bacterial concentration in the samples: principal components regression (PCR), partial least squares regression (PLSR) and support vector regression (SVR). Without any sample pre-concentration, PCR achieved the most reliable results. It was able to quantify live bacteria from 108 down to 106.2 bacteria/mL and showed the potential to detect as low as 105.7 bacteria/mL. Meanwhile, enumeration of dead bacteria using PCR was achieved between 108 and 107 bacteria/mL. The general procedures described in this article can be applied or modified for the enumeration of bacteria within populations stained with fluorescent dyes. The optrode is a promising device for the enumeration of live and dead bacterial populations particularly where rapid, on-site measurement and analysis is required.
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Affiliation(s)
- Fang Ou
- Department of Physics, The University of Auckland, Auckland, New Zealand.
- The Dodd-Walls Centre for Photonic and Quantum Technologies, Auckland, New Zealand.
| | - Cushla McGoverin
- Department of Physics, The University of Auckland, Auckland, New Zealand
- The Dodd-Walls Centre for Photonic and Quantum Technologies, Auckland, New Zealand
| | - Simon Swift
- School of Medical Sciences, The University of Auckland, Auckland, New Zealand
| | - Frédérique Vanholsbeeck
- Department of Physics, The University of Auckland, Auckland, New Zealand
- The Dodd-Walls Centre for Photonic and Quantum Technologies, Auckland, New Zealand
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423
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A duplex quantitative real-time PCR assay for the detection and quantification of Xanthomonas phaseoli pv. dieffenbachiae from diseased and latently infected anthurium tissue. J Microbiol Methods 2019; 161:74-83. [PMID: 30858003 DOI: 10.1016/j.mimet.2019.03.003] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2019] [Revised: 03/05/2019] [Accepted: 03/06/2019] [Indexed: 11/22/2022]
Abstract
Anthurium bacterial blight caused by Xanthomonas phaseoli pv. dieffenbachiae (formerly Xanthomonas axonopodis pv. dieffenbachiae) is the major phytosanitary threat in many anthurium growing areas worldwide. Reliable and sensitive diagnostic tools are required for surveillance and certification programs. A duplex real-time quantitative PCR assay was developed for the detection and quantification of X. phaseoli pv. dieffenbachiae from anthurium tissue. This PCR assay targeted a X. phaseoli pv. dieffenbachiae-specific gene encoding an ABC transporter and an internal control encoding for chalcone synthase in Anthurium andreanum. A cycle threshold (Ct), using a receiver-operating characteristic approach (ROC), was implemented to ensure that the declaration of a positive sample was reliable. The duplex real-time assay displayed very high performance with regards to analytical specificity (100% inclusivity, 98.9% exclusivity), analytical sensitivity (LOD95% = 894 bacteria/ml corresponding to 18 bacteria per reaction) and repeatability. We demonstrated the pertinence of this real-time quantitative PCR assay for detecting X. phaseoli pv. dieffenbachiae from diseased leaf tissue (collected from outbreaks on anthurium) and from asymptomatic, latently infected anthurium plants. This assay could be useful for surveillance, as well as for indexing propagative plant material for the presence of X. phaseoli pv. dieffenbachiae.
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424
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Vinayaka AC, Ngo TA, Kant K, Engelsmann P, Dave VP, Shahbazi MA, Wolff A, Bang DD. Rapid detection of Salmonella enterica in food samples by a novel approach with combination of sample concentration and direct PCR. Biosens Bioelectron 2019; 129:224-230. [DOI: 10.1016/j.bios.2018.09.078] [Citation(s) in RCA: 56] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2018] [Revised: 09/11/2018] [Accepted: 09/21/2018] [Indexed: 10/28/2022]
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425
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Appelt S, Aly SS, Tonooka K, Glenn K, Xue Z, Lehenbauer TW, Marco ML. Development and comparison of loop-mediated isothermal amplification and quantitative polymerase chain reaction assays for the detection of Mycoplasma bovis in milk. J Dairy Sci 2019; 102:1985-1996. [DOI: 10.3168/jds.2018-15306] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2018] [Accepted: 11/05/2018] [Indexed: 11/19/2022]
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426
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Martzy R, Kolm C, Krska R, Mach RL, Farnleitner AH, Reischer GH. Challenges and perspectives in the application of isothermal DNA amplification methods for food and water analysis. Anal Bioanal Chem 2019; 411:1695-1702. [PMID: 30617408 PMCID: PMC6453865 DOI: 10.1007/s00216-018-1553-1] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2018] [Revised: 12/09/2018] [Accepted: 12/14/2018] [Indexed: 12/04/2022]
Abstract
Molecular diagnostic tools in the field of food and water quality analysis are becoming increasingly widespread. Usually, based on DNA amplification techniques such as polymerase chain reaction (PCR), these methods are highly sensitive and versatile but require well-equipped laboratories and trained personnel. To reduce analysis time and avoid expensive equipment, isothermal DNA amplification methods for detecting various target organisms have been developed. However, to make molecular diagnostics suitable for low-resource settings and in-field applications, it is crucial to continuously adapt the working steps associated with DNA amplification, namely sample preparation, DNA extraction, and visualization of the results. Many novel approaches have been evaluated in recent years to tackle these challenges, e.g., the use of ionic liquids for the rapid isolation of nucleic acids from organisms relevant for food and water analysis or the integration of entire analytical workflows on microfluidic chips. In any event, the future of applications in the field of isothermal amplification will probably lie in ready-to-use cartridges combined with affordable handheld devices for on-site analysis. This trend article aims to make prospective users more familiar with this technology and its potential for moving molecular diagnostics from the laboratory to the field. Graphical abstract ᅟ.
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Affiliation(s)
- Roland Martzy
- TU Wien, Institute of Chemical, Environmental & Bioscience Engineering, Molecular Diagnostics Group, Department of Agrobiotechnology (IFA-Tulln), 3430, Tulln, Austria
- ICC Interuniversity Cooperation Centre Water & Health, Vienna, Austria
| | - Claudia Kolm
- TU Wien, Institute of Chemical, Environmental & Bioscience Engineering, Molecular Diagnostics Group, Department of Agrobiotechnology (IFA-Tulln), 3430, Tulln, Austria
- ICC Interuniversity Cooperation Centre Water & Health, Vienna, Austria
| | - Rudolf Krska
- University of Natural Resources and Life Sciences, Vienna (BOKU), Department of Agrobiotechnology (IFA-Tulln), Konrad-Lorenz-Str. 20, 3430, Tulln, Austria
- Queen's University Belfast, Institute for Global Food Security, School of Biological Sciences, Belfast, Northern Ireland, BT71NN, UK
| | - Robert L Mach
- TU Wien, Institute of Chemical, Environmental & Bioscience Engineering, Research Area Biochemical Technology, Research Group of Synthetic Biology and Molecular Biotechnology, 1060, Vienna, Austria
| | - Andreas H Farnleitner
- ICC Interuniversity Cooperation Centre Water & Health, Vienna, Austria
- Karl Landsteiner University of Health Sciences, Research Unit Water Quality and Health, 3500, Krems, Austria
- TU Wien, Institute of Chemical, Environmental & Bioscience Engineering, Research Area Biochemical Technology, Research Group of Environmental Microbiology and Molecular Diagnostics, 1060, Vienna, Austria
| | - Georg H Reischer
- TU Wien, Institute of Chemical, Environmental & Bioscience Engineering, Molecular Diagnostics Group, Department of Agrobiotechnology (IFA-Tulln), 3430, Tulln, Austria.
- TU Wien, Institute of Chemical, Environmental & Bioscience Engineering, Research Area Biochemical Technology, Research Group of Environmental Microbiology and Molecular Diagnostics, 1060, Vienna, Austria.
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427
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Real-Time PCR based test for the early diagnosis of Haplosporidium pinnae affecting fan mussel Pinna nobilis. PLoS One 2019; 14:e0212028. [PMID: 30794588 PMCID: PMC6386276 DOI: 10.1371/journal.pone.0212028] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2018] [Accepted: 01/26/2019] [Indexed: 11/19/2022] Open
Abstract
Noble pen shell or fan mussel, Pinna nobilis Linnaeus (1758), protected since 1992, was incorporated into the Spanish Catalogue of Threatened Species (Category: Vulnerable, Royal Decree 139/2011). The status is presently in the process of being catalogued as critically endangered, pending approval by Spanish Government (https://www.mapama.gob.es/es/biodiversidad/participacion-publica/Borrador_OM_situacion_critica.aspx). The International Union for the Conservation of Nature (IUCN) alerted the countries of the Mediterranean basin to the “emergent situation” due to serious mortality events suffered by the fan mussel, putting it in serious risk of extinction. Thus, emergency actions have been implemented by Spanish authorities in which several research institutes from all over the country are involved. The parasite, Haplosporidium pinnae, was recently characterized by histology, TEM, SEM and molecular biology techniques and it was considered responsible for the mass mortality of P. nobilis in the Mediterranean Sea. In this context, the aim of this study has been to develop species-specific quantitative PCR (qPCR) protocol carrying out a fast, specific and effective molecular diagnose of H. pinnae. In this sense, the detection limit for qPCR was equal to 30 copies of SSU rDNA / ng of DNA using plasmid alone and when 100ng DNA of non-infected oyster were added. The qPCR assay revealed that 94% of the 32 analysed mantle tissues of fan mussel were infected by H. pinnae, showing a high sensitivity and specificity for its detection (100% if we don't consider negative and too much degraded samples). This technique will allow us to make quicker follow-ups of the disease, allowing us to get a better understanding of its evolution in order to help in the rescue of P. nobilis populations
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428
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Liu Y, Cao Y, Wang T, Dong Q, Li J, Niu C. Detection of 12 Common Food-Borne Bacterial Pathogens by TaqMan Real-Time PCR Using a Single Set of Reaction Conditions. Front Microbiol 2019; 10:222. [PMID: 30814987 PMCID: PMC6381072 DOI: 10.3389/fmicb.2019.00222] [Citation(s) in RCA: 59] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2018] [Accepted: 01/28/2019] [Indexed: 01/21/2023] Open
Abstract
Food safety has become an important public health issue worldwide. However, conventional methods for detection of food-borne pathogens are complicated, and labor-intensive. Moreover, the sensitivity is often low, and it is difficult to achieve high-throughput detection. This study developed a TaqMan real-time polymerase chain reaction (PCR) assay for the simultaneous detection and quantification of 12 common pathogens in a single reaction, including Escherichia coli O157:H7, Listeria monocytogenes/ivanovii, Salmonella enterica, Vibrio parahaemolyticus, β-streptococcus hemolyticus, Yersinia enterocolitica, Enterococcus faecalis, Shigella spp., Proteus mirabilis, Vibrio fluvialis, Staphylococcus aureus, and Campylobacter jejuni in food and drinking water. Based on published sequence data, specific primers, and fluorescently-labeled hybridization probes were designed targeting based on the virulence genes of the 12 pathogens, and these primers and probes were optimized to achieve consistent reaction conditions. The assay was evaluated using 106 pure bacterial culture strains. There was no cross-reaction among the different pathogens. The analytical sensitivity was 1 copy/μL for E. coli O157:H7, L. monocytogenes/ivanovii, β-streptococcus hemolyticus, Shigella spp., P. mirabilis, and V. fluvialis, 10 copies/μL for S. enterica, V. parahaemolyticus, Y. enterocolitica, E. faecalis, S. aureus, and C. jejuni, respectively. The limit of detection (LOD) was 296, 500, 177, 56, 960, 830, 625, 520, 573, 161, 875, and 495 CFU/mL for E. coli O157:H7, L. monocytogenes/ivanovii, S. enterica, V. parahaemolyticus, β-streptococcus hemolyticus, Y. enterocolitica, E. faecalis, Shigella spp., P. mirabilis, V. fluvialis, S. aureus, and C. jejuni, respectively. The limit of detection for the assay in meat samples was 103 CFU/g for V. parahaemolyticus and 104 CFU/g for other 11 strains. Together, these results indicate that the optimized TaqMan real-time PCR assay will be useful for routine detection of pathogenic bacteria due to its rapid analysis, low cost, high-throughput, high specificity, and sensitivity.
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Affiliation(s)
- Ying Liu
- Department of Environmental Medicine, Tianjin Institute of Environmental and Operational Medicine, Tianjin, China
| | - Yang Cao
- Department of Environmental Medicine, Tianjin Institute of Environmental and Operational Medicine, Tianjin, China
| | - Tao Wang
- Department of Environmental Medicine, Tianjin Institute of Environmental and Operational Medicine, Tianjin, China
| | - Qingyang Dong
- Department of Environmental Medicine, Tianjin Institute of Environmental and Operational Medicine, Tianjin, China
| | - Junwen Li
- Department of Environmental Medicine, Tianjin Institute of Environmental and Operational Medicine, Tianjin, China
| | - Chao Niu
- Department of Environmental Medicine, Tianjin Institute of Environmental and Operational Medicine, Tianjin, China
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429
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Bier NS, Schares G, Johne A, Martin A, Nöckler K, Mayer-Scholl A. Performance of three molecular methods for detection of Toxoplasma gondii in pork. Food Waterborne Parasitol 2019; 14:e00038. [PMID: 32095606 PMCID: PMC7034005 DOI: 10.1016/j.fawpar.2019.e00038] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2018] [Revised: 01/28/2019] [Accepted: 02/04/2019] [Indexed: 11/29/2022] Open
Abstract
Comparison of epidemiological data on the occurrence of Toxoplasma (T.) gondii tissue cysts in meat is hampered by the lack of standardization and a great variety of methods for molecular detection. Therefore, this study aimed to compare and validate three different polymerase chain reaction (PCR) methods for detection of T. gondii DNA in pork. Analytical performance characteristics of two real time PCRs (qPCRs; Tg-qPCR1, Tg-qPCR2) and one conventional endpoint PCR (cPCR), all targeting the 529 repeated element, were assessed using genomic DNA of three clonal T. gondii types prevailing in Europe and North America. qPCR efficiencies for all three clonal types ranged between 93.8 and 94.4% (Tg-qPCR1) and 94.3–95.6% (Tg-qPCR2). Tg-qPCR1 and Tg-qPCR2 showed an overall PCR performance score of 85% and displayed a similar 95% detection limit of 1.067 and 1.561 genome equivalents per PCR reaction (GE/PCR), respectively. However, T. gondii DNA could be detected at concentrations as low as 0.1 GE/PCR. Reliable quantification is possible over 4 log ranges from 105 to 100 GE/PCR with mean repeatability relative standard deviations of ≤11% and reproducibility relative standard deviations of ≤12.7%. Presumably, both qPCRs are similarly suitable for sensitive and specific detection of T. gondii DNA in pork. In contrast, the cPCR using primer pair TOX5/Tox-8 proved to be highly sensitive with a detection limit of 1.41 GE/PCR, but not suitable for detection of T. gondii DNA in pork as unspecific amplification of porcine DNA was observed resulting in bands with similar size to the desired T. gondii-specific PCR product. Comparison of two real time PCRs and one conventional PCR targeting the 529 RE. Both real time PCRs show comparable performance and can be considered equivalent. qPCRs show 95% detection limits of 1.067 and 1.561 genome equivalents per PCR. Reliable quantification is possible over 4 log ranges from 105 to 100 GE/PCR. cPCR using primer pair TOX5/Tox-8 showed non-specific amplification of porcine DNA.
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Affiliation(s)
- Nadja S Bier
- German Federal Institute for Risk Assessment (BfR), Department for Biological Safety, Berlin, Germany
| | - Gereon Schares
- Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Greifswald, Insel Riems, Germany
| | - Annette Johne
- German Federal Institute for Risk Assessment (BfR), Department for Biological Safety, Berlin, Germany
| | - Annett Martin
- German Federal Institute for Risk Assessment (BfR), Department for Exposure, Berlin, Germany
| | - Karsten Nöckler
- German Federal Institute for Risk Assessment (BfR), Department for Biological Safety, Berlin, Germany
| | - Anne Mayer-Scholl
- German Federal Institute for Risk Assessment (BfR), Department for Biological Safety, Berlin, Germany
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430
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Abstract
MicroRNAs (miRNAs) are a class of small, highly conserved, and noncoding RNAs that modulate gene expression by regulating the activity and stability of target mRNAs. MiRNAs play significant roles by controlling fundamental cellular processes and its deregulation is associated with various diseases. Ubiquitous expression and its release into circulation make them interesting biomarkers, which can be measured by different platforms. In this book chapter, we provide a specific protocol that describes the detection of circulating miRNAs in CSF by using RT-qPCR.
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431
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Kozińska A, Seweryn P, Sitkiewicz I. A crash course in sequencing for a microbiologist. J Appl Genet 2019; 60:103-111. [PMID: 30684135 PMCID: PMC6373407 DOI: 10.1007/s13353-019-00482-2] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2018] [Revised: 12/28/2018] [Accepted: 01/06/2019] [Indexed: 12/13/2022]
Abstract
For the last 40 years, "Sanger sequencing" allowed to unveil crucial secrets of life. However, this method of sequencing has been time-consuming, laborious and remains expensive even today. Human Genome Project was a huge impulse to improve sequencing technologies, and unprecedented financial and human effort prompted the development of cheaper high-throughput technologies and strategies called next-generation sequencing (NGS) or whole genome sequencing (WGS). This review will discuss applications of high-throughput methods to study bacteria in a much broader context than simply their genomes. The major goal of next-generation sequencing for a microbiologist is not really resolving another circular genomic sequence. NGS started its infancy from basic structural and functional genomics, to mature into the molecular taxonomy, phylogenetic and advanced comparative genomics. Today, the use of NGS expended capabilities of diagnostic microbiology and epidemiology. The use of RNA sequencing techniques allows studying in detail the complex regulatory processes in the bacterial cells. Finally, NGS is a key technique to study the organization of the bacterial life-from complex communities to single cells. The major challenge in understanding genomic and transcriptomic data lies today in combining it with other sources of global data such as proteome and metabolome, which hopefully will lead to the reconstruction of regulatory networks within bacterial cells that allow communicating with the environment (signalome and interactome) and virtual cell reconstruction.
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Affiliation(s)
- Aleksandra Kozińska
- Department of Drug Biotechnology and Bioinformatics, National Medicines Institute, Chelmska 30/34, 00-725, Warszawa, Poland
| | - Paulina Seweryn
- Department of Microbiology and Antibiotics, National Medicines Institute, Chelmska 30/34, 00-725, Warszawa, Poland
| | - Izabela Sitkiewicz
- Department of Drug Biotechnology and Bioinformatics, National Medicines Institute, Chelmska 30/34, 00-725, Warszawa, Poland.
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432
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Ricke SC, Feye KM, Chaney WE, Shi Z, Pavlidis H, Yang Y. Developments in Rapid Detection Methods for the Detection of Foodborne Campylobacter in the United States. Front Microbiol 2019; 9:3280. [PMID: 30728816 PMCID: PMC6351486 DOI: 10.3389/fmicb.2018.03280] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2018] [Accepted: 12/17/2018] [Indexed: 12/27/2022] Open
Abstract
The accurate and rapid detection of Campylobacter spp. is critical for optimal surveillance throughout poultry processing in the United States. The further development of highly specific and sensitive assays to detect Campylobacter in poultry matrices has tremendous utility and potential for aiding the reduction of foodborne illness. The introduction and development of molecular methods such as polymerase chain reaction (PCR) have enhanced the diagnostic capabilities of the food industry to identify the presence of foodborne pathogens throughout poultry production. Further innovations in various methodologies, such as immune-based typing and detection as well as high throughput analyses, will provide important epidemiological data such as the identification of unique or region-specific Campylobacter. Comparable to traditional microbiology and enrichment techniques, molecular techniques/methods have the potential to have improved sensitivity and specificity, as well as speed of data acquisition. This review will focus on the development and application of rapid molecular methods for identifying and quantifying Campylobacter in U.S. poultry and the emergence of novel methods that are faster and more precise than traditional microbiological techniques.
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Affiliation(s)
- Steven C. Ricke
- Department of Food Science, Center of Food Safety, University of Arkansas, Fayetteville, AR, United States
| | - Kristina M. Feye
- Department of Food Science, Center of Food Safety, University of Arkansas, Fayetteville, AR, United States
| | | | - Zhaohao Shi
- Department of Food Science, Center of Food Safety, University of Arkansas, Fayetteville, AR, United States
| | | | - Yichao Yang
- Department of Poultry Science, University of Arkansas, Fayetteville, AR, United States
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433
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Fan H, Wang J, Komiyama M, Liang X. Effects of secondary structures of DNA templates on the quantification of qPCR. J Biomol Struct Dyn 2019; 37:2867-2874. [PMID: 30101656 DOI: 10.1080/07391102.2018.1498804] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
In the current design of quantitative polymerase chain reaction (qPCR) systems, the sequences of primers are the primary concerns. The secondary structures of DNA templates have not been much considered, although they should be also critically important. In this paper, various hairpins with different stem lengths and loop sizes are placed near primer-binding sites, and their effects on the amplification efficiency of qPCR are systematically investigated. When a hairpin is formed either in the inside of the amplicon or in its outside, the amplification is notably suppressed. The magnitudes of suppression increase with the increase in stem length and the decrease in loop size, and are especially significant for the hairpins formed inside the amplicon. With very long stems (e.g., 20-bp), the effect is still more drastic, and no targeted amplification products are formed. On the basis of melting temperature (Tm) measurements, these suppression effects of hairpins have been mostly ascribed to competitive inhibition of primer binding to the template. It has been concluded that, in order to design precise and reliable qPCR systems, at least 60-bp sequences around primer-binding sites, both inside and outside the amplicons, must be analyzed to confirm that stable secondary structures are not formed in the vicinity of primer-binding sites. Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Huijun Fan
- a College of Food Science and Engineering , Ocean University of China , Qingdao , China
| | - Jing Wang
- a College of Food Science and Engineering , Ocean University of China , Qingdao , China.,b Laboratory for Marine Drugs and Bioproducts , Qingdao National Laboratory for Marine Science and Technology , Qingdao , China
| | - Makoto Komiyama
- a College of Food Science and Engineering , Ocean University of China , Qingdao , China.,c National Institute for Materials Science (NIMS) , Tsukuba , Japan
| | - Xingguo Liang
- a College of Food Science and Engineering , Ocean University of China , Qingdao , China.,b Laboratory for Marine Drugs and Bioproducts , Qingdao National Laboratory for Marine Science and Technology , Qingdao , China
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434
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Guzman-Otazo J, Gonzales-Siles L, Poma V, Bengtsson-Palme J, Thorell K, Flach CF, Iñiguez V, Sjöling Å. Diarrheal bacterial pathogens and multi-resistant enterobacteria in the Choqueyapu River in La Paz, Bolivia. PLoS One 2019; 14:e0210735. [PMID: 30640938 PMCID: PMC6331111 DOI: 10.1371/journal.pone.0210735] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2018] [Accepted: 12/31/2018] [Indexed: 11/18/2022] Open
Abstract
Water borne diarrheal pathogens might accumulate in river water and cause contamination of drinking and irrigation water. The La Paz River basin, including the Choqueyapu River, flows through La Paz city in Bolivia where it is receiving sewage, and residues from inhabitants, hospitals, and industry. Using quantitative real-time PCR (qPCR), we determined the quantity and occurrence of diarrheagenic Escherichia coli (DEC), Salmonella enterica, Klebsiella pneumoniae, Shigella spp. and total enterobacteria in river water, downstream agricultural soil, and irrigated crops, during one year of sampling. The most abundant and frequently detected genes were gapA and eltB, indicating presence of enterobacteria and enterotoxigenic E. coli (ETEC) carrying the heat labile toxin, respectively. Pathogen levels in the samples were significantly positively associated with high water conductivity and low water temperature. In addition, a set of bacterial isolates from water, soil and crops were analyzed by PCR for presence of the genes blaCTX-M, blaKPC, blaNDM, blaVIM and blaOXA-48. Four isolates were found to be positive for blaCTX-M genes and whole genome sequencing identified them as E. coli and one Enterobacter cloacae. The E. coli isolates belonged to the emerging, globally disseminated, multi-resistant E. coli lineages ST648, ST410 and ST162. The results indicate not only a high potential risk of transmission of diarrheal diseases by the consumption of contaminated water and vegetables but also the possibility of antibiotic resistance transfer from the environment to the community.
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Affiliation(s)
- Jessica Guzman-Otazo
- Instituto de Biología Molecular y Biotecnología, Universidad Mayor de San Andrés, La Paz, Bolivia
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
- * E-mail:
| | - Lucia Gonzales-Siles
- Department of Infectious Diseases, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Violeta Poma
- Instituto de Biología Molecular y Biotecnología, Universidad Mayor de San Andrés, La Paz, Bolivia
| | - Johan Bengtsson-Palme
- Department of Infectious Diseases, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
- Centre for Antibiotic Resistance Research (CARe) at the University of Gothenburg, Gothenburg, Sweden
- Wisconsin Institute for Discovery, University of Wisconsin-Madison, Madison, WI, United States of America
| | - Kaisa Thorell
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Carl-Fredrik Flach
- Department of Infectious Diseases, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
- Centre for Antibiotic Resistance Research (CARe) at the University of Gothenburg, Gothenburg, Sweden
| | - Volga Iñiguez
- Instituto de Biología Molecular y Biotecnología, Universidad Mayor de San Andrés, La Paz, Bolivia
| | - Åsa Sjöling
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
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435
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Uwizeyimana JD, Kim MK, Kim D, Byun JH, Yong D. Comparison of Multiplex Real-Time Polymerase Chain Reaction Assays for Detection of Respiratory Viruses in Nasopharyngeal Specimens. ANNALS OF CLINICAL MICROBIOLOGY 2019. [DOI: 10.5145/acm.2019.22.2.35] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022] Open
Affiliation(s)
- Jean Damascene Uwizeyimana
- Department of Laboratory Medicine and Research Institute of Bacterial Resistance, Yonsei University College of Medicine, Seoul, Korea
- Department of Global Health Security, Yonsei University Graduate of Public Health, Seoul, Korea
- Department of Emergency Care, Ruli Hospital, Gakenye, Rwanda
| | - Min Kyung Kim
- Department of Laboratory Medicine and Research Institute of Bacterial Resistance, Yonsei University College of Medicine, Seoul, Korea
| | - Daewon Kim
- Department of Laboratory Medicine and Research Institute of Bacterial Resistance, Yonsei University College of Medicine, Seoul, Korea
| | - Jung-Hyun Byun
- Department of Laboratory Medicine and Research Institute of Bacterial Resistance, Yonsei University College of Medicine, Seoul, Korea
| | - Dongeun Yong
- Department of Laboratory Medicine and Research Institute of Bacterial Resistance, Yonsei University College of Medicine, Seoul, Korea
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436
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Lopes ATS, Albuquerque GR, Maciel BM. Multiplex Real-Time Polymerase Chain Reaction for Simultaneous Quantification of Salmonella spp., Escherichia coli, and Staphylococcus aureus in Different Food Matrices: Advantages and Disadvantages. BIOMED RESEARCH INTERNATIONAL 2018; 2018:6104015. [PMID: 30356394 PMCID: PMC6176325 DOI: 10.1155/2018/6104015] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/03/2018] [Accepted: 09/06/2018] [Indexed: 12/24/2022]
Abstract
Quantitative real-time polymerase chain reactions (qPCRs) of the most prevalent bacteria causing foodborne diseases worldwide, such as Salmonella spp., Escherichia coli, and Staphylococcus aureus, can be an important tool for quantitative microbial risk assessment, which requires numerical data to determine the level of contamination at a specific stage of food production. However, most of qPCR assays described in the literature for these pathogens are qualitative; their objective is pathogen detection and not pathogen quantification. Thus, the aim of our work was to develop a qPCR for the simultaneous quantification of Salmonella spp., E. coli, and S. aureus and to propose its use in the analysis of foods, as a tool for microbiological quality monitoring. For this, a multiplex qPCR was standardized for the simultaneous quantification of specific fragments of target genes (ssf, phoA, and nuc) corresponding to each one of the mentioned bacteria. The limit of detection of the technique was 13, 10, and 12 gene copies for ssf, phoA, and nuc, respectively; standard curves showed R2 > 0.99, with efficiencies ranging from 99 to 110%, and inter- and intraexperiment reproducibility presented a low coefficient of variation in all trials. This methodology was applied in different food matrices (milk, ground beef, and oyster meat), and the results were compared with official microbiological culture methodology and with ready-to-use test. Advantages and disadvantages of each methodology used in this study are pointed out. We suggest that this multiplex qPCR can be used as a rapid screening technique for the analysis of food microbiological quality.
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Affiliation(s)
| | - George Rêgo Albuquerque
- Graduation Program in Animal Science, Santa Cruz State University, Ilhéus (BA), Brazil
- Department of Agricultural and Environmental Sciences, Santa Cruz State University, Ilhéus (BA), Brazil
| | - Bianca Mendes Maciel
- Graduation Program in Animal Science, Santa Cruz State University, Ilhéus (BA), Brazil
- Department of Biological Sciences, Santa Cruz State University, Ilhéus (BA), Brazil
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437
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Lawrence KE, Gibson M, Hickson RE, Gedye K, Hoogenboom A, Fermin L, Draganova I, Pomroy WE. Experimental infection of Friesian bulls with Theileria orientalis (Ikeda) and effects on the haematocrit, live weight, rectal temperature and activity. VETERINARY PARASITOLOGY- REGIONAL STUDIES AND REPORTS 2018; 14:85-93. [PMID: 31014744 DOI: 10.1016/j.vprsr.2018.09.004] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/24/2018] [Revised: 09/11/2018] [Accepted: 09/11/2018] [Indexed: 11/16/2022]
Abstract
Since 2012, New Zealand has suffered from an epidemic of infectious bovine anaemia associated with T. orientalis (Ikeda), an obligate intracellular protozoan parasite of cattle. Despite widespread agreement that T. orientalis (Ikeda) infection has impacted beef and dairy farming in New Zealand there is very little quantitative data to support this conclusion. A randomised controlled experimental study of the effect of T. orientalis (Ikeda) infection on the live weight, haematocrit (HCT), temperature and activity of 2-year-old Friesian bulls was conducted at a Massey University Research farm, Palmerston North. Ten out of seventeen 2-year-old Friesian bulls were injected intravenously with 30 mL whole blood from 2 clinical cases of Theileria-associated bovine anaemia and then followed over a period of 20 weeks. The bulls were blood sampled, had rectal temperature recorded and weighed 3 times weekly for 13 weeks and then once weekly thereafter until the end of the trial. Infection intensity was monitored using qPCR. All 10 inoculated bulls were successfully infected with T. orientalis (Ikeda). The results showed that the live weight response to infection was varied and the bulls could be divided into two groups based on this response. Four infected bulls showed a significant weight reduction of 41.5 kg (p < 0.0001), a financial loss of around NZ$112 per bull, compared with the other 6 bulls in the infected group, which were not different to the 7 uninfected controls. The live weight of the 4 poor growing bulls was significantly lower than the other 6 infected bulls from Day 71 post infection (p < 0.05). All ten infected bulls showed a similar decrease in HCT, with the lowest HCT reached around Day 60 to 80 post-infection, however the four infected bulls that grew poorly did have a significantly elevated HCT for the first 1 to 3 weeks post infection (p < 0.05). The 4 infected bulls which grew poorly also had a significantly higher infection intensity than the other infected bulls from Day 27 to Day 60 post-infection (p < 0.05). There was no pyrexia recorded in the infected group or control groups, instead there was a tendency for the infected group to have a lower rectal temperature from Day 5 to 70 post infection. The infected bulls walked on average 239 steps per day less than the control bulls, although this difference was not significant (p = 0.35). Overall the study clearly showed, by controlling infection date and infectious dose, that a proportion of cattle infected with T. orientalis (Ikeda) have significantly decreased live weight gains.
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Affiliation(s)
- K E Lawrence
- School of Veterinary Science, Massey University, Palmerston North, New Zealand.
| | - M Gibson
- School of Agriculture and Environment, Massey University, Palmerston North, New Zealand
| | - R E Hickson
- School of Agriculture and Environment, Massey University, Palmerston North, New Zealand
| | - K Gedye
- School of Veterinary Science, Massey University, Palmerston North, New Zealand
| | - A Hoogenboom
- School of Veterinary Science, Massey University, Palmerston North, New Zealand
| | - L Fermin
- AgResearch, Hamilton, New Zealand
| | - I Draganova
- School of Agriculture and Environment, Massey University, Palmerston North, New Zealand
| | - W E Pomroy
- School of Veterinary Science, Massey University, Palmerston North, New Zealand
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438
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Comparison of qPCR versus culture for the detection and quantification of Clostridium difficile environmental contamination. PLoS One 2018; 13:e0201569. [PMID: 30161136 PMCID: PMC6116935 DOI: 10.1371/journal.pone.0201569] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2018] [Accepted: 07/17/2018] [Indexed: 12/15/2022] Open
Abstract
Contaminated surfaces serve as an important reservoir for Clostridium difficile transmission. Current strategies to detect environmental contamination of C. difficile rely heavily on culture, and often only indicate presence versus absence of spores. The goal of this study was to compare quantitative PCR (qPCR) to culture for the detection and quantification of C. difficile from inert surfaces. First, we compared the limit of detection (LOD) of a 16S rRNA gene and toxin B gene qPCR assay for detection of C. difficile in solution. Second, we compared the LODs of 16S rRNA gene qPCR versus culture for detection of C. difficile from surfaces. Solution experiments were performed by direct seeding of spores into neutralizing broth, whereas surface experiments involved seeding of spores onto plastic test surfaces, and recovery using sponge swabs. Both experiments were conducted using spores expressing short (NAP1) and long (NAP4) hair lengths. Combining data from both strains, the overall LOD for C. difficile cells in solution was 1.4 cells for 16S rRNA gene and 23.6 cells for toxin B gene qPCR (p<0.001). The overall LOD for C. difficile cells from surfaces was 17.1 cells for 16S rRNA gene qPCR and 54.5 cells for culture (p = 0.05), and was not statistically different between strains for each method (p = 0.52). Overall, the proportion of C. difficile cells recovered from surfaces was good when detected by 16S rRNA gene qPCR and culture (qPCR: 76%, culture: 67%, p = 0.36), but, 16S rRNA gene qPCR was capable of detecting lower levels of surface contamination. Future work attempting to measure the presence of C. difficile on environmental surfaces should consider using qPCR.
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439
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Ayala OD, Wakeman CA, Pence IJ, Gaddy JA, Slaughter JC, Skaar EP, Mahadevan-Jansen A. Drug-Resistant Staphylococcus aureus Strains Reveal Distinct Biochemical Features with Raman Microspectroscopy. ACS Infect Dis 2018; 4:1197-1210. [PMID: 29845863 PMCID: PMC6476553 DOI: 10.1021/acsinfecdis.8b00029] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Staphylococcus aureus ( S. aureus) is a leading cause of hospital-acquired infections, such as bacteremia, pneumonia, and endocarditis. Treatment of these infections can be challenging since strains of S. aureus, such as methicillin-resistant S. aureus (MRSA), have evolved resistance to antimicrobials. Current methods to identify infectious agents in hospital environments often rely on time-consuming, multistep culturing techniques to distinguish problematic strains (i.e., antimicrobial resistant variants) of a particular bacterial species. Therefore, a need exists for a rapid, label-free technique to identify drug-resistant bacterial strains to guide proper antibiotic treatment. Here, our findings demonstrate the ability to characterize and identify microbes at the subspecies level using Raman microspectroscopy, which probes the vibrational modes of molecules to provide a biochemical "fingerprint". This technique can distinguish between different isolates of species such as Streptococcus agalactiae and S. aureus. To determine the ability of this analytical approach to detect drug-resistant bacteria, isogenic variants of S. aureus including the comparison of strains lacking or expressing antibiotic resistance determinants were evaluated. Spectral variations observed may be associated with biochemical components such as amino acids, carotenoids, and lipids. Mutants lacking carotenoid production were distinguished from wild-type S. aureus and other strain variants. Furthermore, spectral biomarkers of S. aureus isogenic bacterial strains were identified. These results demonstrate the feasibility of Raman microspectroscopy for distinguishing between various genetically distinct forms of a single bacterial species in situ. This is important for detecting antibiotic-resistant strains of bacteria and indicates the potential for future identification of other multidrug resistant pathogens with this technique.
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Affiliation(s)
- Oscar D. Ayala
- Biophotonics Center, Vanderbilt University, 410 24th Avenue South, Nashville, Tennessee 37235, United States
- Department of Biomedical Engineering, Vanderbilt University, 5824 Stevenson Center, Nashville, Tennessee 37232, United States
| | - Catherine A. Wakeman
- Department of Biological Sciences, Texas Tech University, 2901 Main Street, Lubbock, Texas 79409, United States
| | - Isaac J. Pence
- Biophotonics Center, Vanderbilt University, 410 24th Avenue South, Nashville, Tennessee 37235, United States
- Department of Biomedical Engineering, Vanderbilt University, 5824 Stevenson Center, Nashville, Tennessee 37232, United States
| | - Jennifer A. Gaddy
- Department of Medicine, Division of Infectious Diseases, Vanderbilt University Medical Center, 1161 21st Avenue South, Medical Center North, Nashville, Tennessee 37232, United States
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, 1161 21st Avenue South, Medical Center North, Nashville, Tennessee 37232, United States
- Tennessee Valley Healthcare Systems, Department of Veterans Affairs, 1310 24th Avenue South, Nashville, Tennessee 37212, United States
| | - James C. Slaughter
- Department of Biostatistics, Vanderbilt University School of Medicine, 2525 West End Avenue, Suite 11000, Nashville, Tennessee 37203, United States
| | - Eric P. Skaar
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, 1161 21st Avenue South, Medical Center North, Nashville, Tennessee 37232, United States
| | - Anita Mahadevan-Jansen
- Biophotonics Center, Vanderbilt University, 410 24th Avenue South, Nashville, Tennessee 37235, United States
- Department of Biomedical Engineering, Vanderbilt University, 5824 Stevenson Center, Nashville, Tennessee 37232, United States
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440
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Changes in salicylic acid content and pathogenesis - related (PR2) gene expression during barley - Pyrenophora teres interaction. ACTA ACUST UNITED AC 2018. [DOI: 10.2478/hppj-2018-0010] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Abstract
Net blotch (NB), caused by the necrotrophic fungal pathogen Pyrenophora teres f. teres, substantially reduces barley grain yield and quality worldwide. The role of salicylic acid (SA) signaling in NB resistance has been poorly documented. In this study, SA levels as well as the expression of the SA-responsive gene PR2 were monitored in infected leaves of two barley genotypes, Banteng (resistant) and WI2291 (susceptible), at different time points of infection. SA signaling was activated in bothgenotypes 24 hours post infection (hpi) as compared with non-inoculated plants. However, with or without pathogen pretreatment, SA signifi cantly increased (P=0.001) in Banteng comparing with WI2291. RT-PCR analysis revealed that PR2 expression increases in the resistant and susceptible genotypes over the inoculation time points, with maximum expression (6.4 and 1.99-fold, respectively) observed 6 dpi. PR2 expression was paralleled by an increase in leaf SA content as shown by the test coincidence (F3, 32 = 4.74, P = 0.001). Based on barley genotype resistance levels, our data strengthen the idea that SA signaling and PR2 play a role in barley NB reduction
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441
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Stakheev AA, Ryazantsev DY, Zvezdina YK, Baranov MS, Zavriev SK. A Novel Fluorescent GFP Chromophore Analog-Based Dye for Quantitative PCR. BIOCHEMISTRY (MOSCOW) 2018; 83:855-860. [DOI: 10.1134/s000629791807009x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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442
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Byrnes SA, Chang TC, Huynh T, Astashkina A, Weigl BH, Nichols KP. Simple Polydisperse Droplet Emulsion Polymerase Chain Reaction with Statistical Volumetric Correction Compared with Microfluidic Droplet Digital Polymerase Chain Reaction. Anal Chem 2018; 90:9374-9380. [DOI: 10.1021/acs.analchem.8b01988] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Affiliation(s)
- Samantha A. Byrnes
- Intellectual Ventures Laboratory, 14360 Southeast Eastgate Way, Bellevue, Washington 98007, United States
| | - Tim C. Chang
- Intellectual Ventures Laboratory, 14360 Southeast Eastgate Way, Bellevue, Washington 98007, United States
| | - Toan Huynh
- Intellectual Ventures Laboratory, 14360 Southeast Eastgate Way, Bellevue, Washington 98007, United States
| | - Anna Astashkina
- Intellectual Ventures Laboratory, 14360 Southeast Eastgate Way, Bellevue, Washington 98007, United States
| | - Bernhard H. Weigl
- Intellectual Ventures Laboratory, 14360 Southeast Eastgate Way, Bellevue, Washington 98007, United States
| | - Kevin P. Nichols
- Intellectual Ventures Laboratory, 14360 Southeast Eastgate Way, Bellevue, Washington 98007, United States
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443
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Galvan DD, Yu Q. Surface-Enhanced Raman Scattering for Rapid Detection and Characterization of Antibiotic-Resistant Bacteria. Adv Healthc Mater 2018; 7:e1701335. [PMID: 29504273 DOI: 10.1002/adhm.201701335] [Citation(s) in RCA: 64] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2017] [Revised: 12/30/2017] [Indexed: 12/19/2022]
Abstract
As the prevalence of antibiotic-resistant bacteria continues to rise, biosensing technologies are needed to enable rapid diagnosis of bacterial infections. Furthermore, understanding the unique biochemistry of resistance mechanisms can facilitate the development of next generation therapeutics. Surface-enhanced Raman scattering (SERS) offers a potential solution to real-time diagnostic technologies, as well as a route to fundamental, mechanistic studies. In the current review, SERS-based approaches to the detection and characterization of antibiotic-resistant bacteria are covered. The commonly used nanomaterials (nanoparticles and nanostructured surfaces) and surface modifications (antibodies, aptamers, reporters, etc.) for SERS bacterial detection and differentiation are discussed first, and followed by a review of SERS-based detection of antibiotic-resistant bacteria from environmental/food processing and clinical sources. Antibiotic susceptibility testing and minimum inhibitory concentration testing with SERS are then summarized. Finally, recent developments of SERS-based chemical imaging/mapping of bacteria are reviewed.
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Affiliation(s)
- Daniel D. Galvan
- Department of Chemical Engineering University of Washington Seattle WA 98195 USA
| | - Qiuming Yu
- Department of Chemical Engineering University of Washington Seattle WA 98195 USA
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444
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Standish I, Leis E, Schmitz N, Credico J, Erickson S, Bailey J, Kerby J, Phillips K, Lewis T. Optimizing, validating, and field testing a multiplex qPCR for the detection of amphibian pathogens. DISEASES OF AQUATIC ORGANISMS 2018; 129:1-13. [PMID: 29916388 DOI: 10.3354/dao03230] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Amphibian populations worldwide are facing numerous threats, including the emergence and spread of infectious diseases. In the past 2 decades, Batrachochytrium dendrobatidis (Bd), a parasitic fungus, and a group of viruses comprising the genus Ranavirus have become widespread and resulted in mass mortality events and extirpations worldwide. In 2013, another novel fungus, B. salamandrivorans (Bsal), was attributed to dramatic declines in populations of fire salamander Salamandra salamandra in the Netherlands. Experimental infections demonstrated that Bsal is highly pathogenic to numerous salamander genera. In an effort to prevent the introduction of Bsal to North America, the US Fish and Wildlife Service (USFWS) listed 201 salamander species as injurious wildlife under the Lacey Act. To determine infection status and accurately assess amphibian health, the development of a sensitive and specific diagnostic assay was needed. We describe the optimization and validation of a multiplex quantitative polymerase chain reaction (qPCR) protocol for the simultaneous detection of Bd, Bsal, and frog virus 3-like ranaviruses. A synthetic genome template (gBlock®) containing the target genes from all 3 pathogens served as the positive control and allowed accurate quantification of pathogen genes. The assay was validated in the field using an established non-lethal swabbing technique to survey local amphibian populations throughout a range of habitats. This multiplex qPCR demonstrates high reproducibility, sensitivity, and was capable of detecting both Bd and ranavirus in numerous locations, species, and life stages. Bsal was not detected at any point during these sampling efforts.
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Affiliation(s)
- Isaac Standish
- US Fish and Wildlife Service, Midwest Fisheries Center, La Crosse Fish Health Center, Onalaska, WI 54650, USA
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445
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Witte AK, Mester P, Fister S, Süß B, Wagner M, Rossmanith P. PCR-Stop analysis as a new tool for qPCR assay validation. Sci Rep 2018; 8:8275. [PMID: 29844518 PMCID: PMC5974342 DOI: 10.1038/s41598-018-26116-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2018] [Accepted: 04/26/2018] [Indexed: 01/01/2023] Open
Abstract
Progressively more qPCR assays have been developed in recent years in numerous fields of application. These assays are routinely validated using calibration curves, but essential validation per se such as Poisson analysis is frequently neglected. However, validation is crucial for determination of resolution and quantitative and qualitative limits. The new test method PCR-Stop analysis presented in this work investigates assay performance during initial qPCR cycles. PCRs with one to five pre-runs are performed while the subsequent main qPCR runs reflect pre-run replication rates. Ideally, DNA doubles according to pre-runs, there is no variation between replicates and qPCR starts immediately at the first cycle with its average efficiency. This study shows two exemplary qPCR assays, both with suitable calibration curves and efficiencies. We demonstrated thereby the benefits of PCR-Stop analysis revealing quantitative and qualitative resolution of both assays, the limits of one of those assays and thus avoiding misinterpretations in qPCR analysis. Furthermore, data displayed that a well performing assay starts indeed with its average efficiency.
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Affiliation(s)
- Anna Kristina Witte
- Christian Doppler Laboratory for Monitoring of Microbial Contaminants, Department of Veterinary Public Health and Food Science, University of Veterinary Medicine, Veterinaerplatz 1, 1210, Vienna, Austria
| | - Patrick Mester
- Christian Doppler Laboratory for Monitoring of Microbial Contaminants, Department of Veterinary Public Health and Food Science, University of Veterinary Medicine, Veterinaerplatz 1, 1210, Vienna, Austria
| | - Susanne Fister
- Christian Doppler Laboratory for Monitoring of Microbial Contaminants, Department of Veterinary Public Health and Food Science, University of Veterinary Medicine, Veterinaerplatz 1, 1210, Vienna, Austria
| | - Beate Süß
- Institute of Milk Hygiene, Milk Technology and Food Science, Department of Veterinary Public Health and Food Science, University of Veterinary Medicine, Veterinaerplatz 1, 1210, Vienna, Austria
| | - Martin Wagner
- Institute of Milk Hygiene, Milk Technology and Food Science, Department of Veterinary Public Health and Food Science, University of Veterinary Medicine, Veterinaerplatz 1, 1210, Vienna, Austria
| | - Peter Rossmanith
- Christian Doppler Laboratory for Monitoring of Microbial Contaminants, Department of Veterinary Public Health and Food Science, University of Veterinary Medicine, Veterinaerplatz 1, 1210, Vienna, Austria. .,Institute of Milk Hygiene, Milk Technology and Food Science, Department of Veterinary Public Health and Food Science, University of Veterinary Medicine, Veterinaerplatz 1, 1210, Vienna, Austria.
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446
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Abstract
Preharvest food safety research and activities have advanced over time with the recognition of the importance and complicated nature of the preharvest phase of food production. In developed nations, implementation of preharvest food safety procedures along with strict monitoring and containment at various postharvest stages such as slaughter, processing, storage, and distribution have remarkably reduced the burden of foodborne pathogens in humans. Early detection and adequate surveillance of pathogens at the preharvest stage is of the utmost importance to ensure a safe meat supply. There is an urgent need to develop rapid, cost-effective, and point-of-care diagnostics which could be used at the preharvest stage and would complement postmortem and other quality checks performed at the postharvest stage. With newer methods and technologies, more efforts need to be directed toward developing rapid, sensitive, and specific methods for detection or screening of foodborne pathogens at the preharvest stage. In this review, we will discuss the molecular methods available for detection and molecular typing of bacterial foodborne pathogens at the farm. Such methods include conventional techniques such as endpoint PCR, real-time PCR, DNA microarray, and more advanced techniques such as matrix-assisted layer desorption ionization-time of flight mass spectrometry and whole-genome sequencing.
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447
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Validation of Biofilm Assays to Assess Antibiofilm Efficacy in Instrumented Root Canals after Syringe Irrigation and Sonic Agitation. J Endod 2018; 44:292-298. [DOI: 10.1016/j.joen.2017.10.005] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2017] [Revised: 10/04/2017] [Accepted: 10/06/2017] [Indexed: 02/06/2023]
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448
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The Effect of Primary, Secondary, and Tertiary Wastewater Treatment Processes on Antibiotic Resistance Gene (ARG) Concentrations in Solid and Dissolved Wastewater Fractions. WATER 2018. [DOI: 10.3390/w10010037] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
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