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Graham KA, Gomez J, Primm TP, Houston R. Comparison of nine extraction methods for bacterial identification using the ONT MinION sequencer. Int J Legal Med 2024; 138:351-360. [PMID: 37775594 DOI: 10.1007/s00414-023-03092-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2023] [Accepted: 09/18/2023] [Indexed: 10/01/2023]
Abstract
The Anthrax mailings bioterrorism attack in 2001 revealed the need for universal and rapid microbial forensic analyses on unknown biological evidence. However, the gold standard for bacterial identification includes culturing isolates, which is laborious. Molecular approaches for bacterial identification revolve around 16S ribosomal gene sequencing using Sanger or next generation sequencing (NGS) platforms, but these techniques are laboratory-based and can also be time-consuming. The Oxford Nanopore Technologies (ONT) MinION sequencer can generate long read lengths that span the entire bacterial 16S rRNA gene and accurately identify the species level. This platform can be used in the field, allowing on-site evidence analysis. However, it requires higher quantities of pure DNA compared to other sequencing platforms; thus, the extraction method for bacterial DNA is critical for downstream analysis, which to date are tailored toward a priori knowledge of the species' taxonomic grouping. During an attack, the investigative team may not know what species they are handling; therefore, identifying an extraction method that can handle all bacterial groups and generate clean DNA for the MinION is useful for microbial forensic analysis. The purpose of this study was to identify a "universal" extraction method that can be coupled with ONT MinION sequencing for use in forensic situations for rapid identification. It also evaluated the cloud-based data analysis software provided by ONT, EPI2ME. No "universal" extraction method was identified as optimal for downstream MinION sequencing. However, the DNeasy PowerSoil Kit and Noda et al. Chelex-100 method gave comparable sequencing results and could be used as rapid extraction techniques. This study showed that the ONT 16S Barcoding Kit 1-24 coupled with the 16S FASTQ workflow might not be the best for use in forensic situations where species-level identification needs to be obtained, as most alignments were approximately 89% accurate. In all seven test organisms and nine extraction methods, accurate species identification was only obtained in 63% of the cases.
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Affiliation(s)
- Kari A Graham
- Department of Forensic Science, College of Criminal Justice, Sam Houston State University, 1003 Bowers Blvd., Huntsville, TX, 77340-2525, USA
| | - Javier Gomez
- Department of Biological Sciences, College of Science and Engineering Technology, Sam Houston State University, 2000 Ave I, Huntsville, TX, 77341, USA
| | - Todd P Primm
- Department of Biological Sciences, College of Science and Engineering Technology, Sam Houston State University, 2000 Ave I, Huntsville, TX, 77341, USA
| | - Rachel Houston
- Department of Forensic Science, College of Criminal Justice, Sam Houston State University, 1003 Bowers Blvd., Huntsville, TX, 77340-2525, USA.
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Grimaldo MA, Mendell NL, Bopp NE, Bouyer DH, Mafra C. Mechanisms of Sporicidal Activity Induced by Ionized Hydrogen Peroxide in the Spores of Bacillus atrophaeus. APPLIED BIOSAFETY 2021; 26:130-138. [PMID: 36035543 PMCID: PMC9134323 DOI: 10.1089/apb.20.0060] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Introduction: Ionized hydrogen peroxide (iHP) is a new technology used for the decontamination of surfaces or laboratory areas. It utilizes a low concentration of hydrogen peroxide (H2O2) mixed with air and ionized through a cold plasma arc. This technology generates reactive oxygen species as a means of decontamination. Objectives: The purpose of this study is to review the effects of iHP on the structure of the spores of Bacillus atrophaeus by observing its effects using transmission electron microscopy (TEM) and also by evaluating the existence of DNA damage by fluorescence-based quantitative polymerase chain reaction (qPCR). Methods: Spore samples of B. atrophaeus decontaminated using iHP at different exposure times (Control, 1, 2, 6, and 12 h) were fixed for TEM. In addition, DNA was extracted for evaluation of DNA damages using fluorescence-based qPCR assays. Results: Damages to the spore structures of B. atrophaeus caused by the decontamination process with iHP at different exposure times (Control, 1, 2, 6, and 12 h) can be observed in micrographs. The effects of the decontamination to short DNA segment (132 base pairs [bp]) of the yaaH gene using qPCR present a linear degradation, and for the long DNA segment (680 bp), it presents a biphasic mode. Conclusion: The results of the qPCR analysis show two initial stages of damage to DNA with very noticeable damage at 12 h contact time, which confirms the observations of the TEM micrographs for the B. atrophaeus spores. The study demonstrates damage to the spore core DNA.
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Affiliation(s)
- Miguel A. Grimaldo
- Department of Biochemistry and Molecular Biology, Universidade Federal de Viçosa, Viçosa, Minas Gerais, Brasil
- Department of Pathology, University of Texas Medical Branch, Galveston, Texas, USA
| | - Nicole L. Mendell
- Department of Pathology, University of Texas Medical Branch, Galveston, Texas, USA
| | - Nathen E. Bopp
- Department of Pathology, University of Texas Medical Branch, Galveston, Texas, USA
| | - Donald H. Bouyer
- Department of Pathology, University of Texas Medical Branch, Galveston, Texas, USA
| | - Claudio Mafra
- Department of Biochemistry and Molecular Biology, Universidade Federal de Viçosa, Viçosa, Minas Gerais, Brasil
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Shen J, Wyness AJ, Claire MW, Zerkle AL. Spatial Variability of Microbial Communities and Salt Distributions Across a Latitudinal Aridity Gradient in the Atacama Desert. MICROBIAL ECOLOGY 2021; 82:442-458. [PMID: 33438074 PMCID: PMC8384830 DOI: 10.1007/s00248-020-01672-w] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2020] [Accepted: 12/21/2020] [Indexed: 05/13/2023]
Abstract
Over the past 150 million years, the Chilean Atacama Desert has been transformed into one of the most inhospitable landscapes by geophysical changes, which makes it an ideal Mars analog that has been explored for decades. However, a heavy rainfall that occurred in the Atacama in 2017 provides a unique opportunity to study the response of resident extremophiles to rapid environmental change associated with excessive water and salt shock. Here we combine mineral/salt composition measurements, amendment cell culture experiments, and next-generation sequencing analyses to study the variations in salts and microbial communities along a latitudinal aridity gradient of the Atacama Desert. In addition, we examine the reshuffling of Atacama microbiomes after the rainfall event. Analysis of microbial community composition revealed that soils within the southern arid desert were consistently dominated by Actinobacteria, Chloroflexi, Proteobacteria, Firmicutes, Bacteroidetes, Gemmatimonadetes, Planctomycetes, and Acidobacteria, and Verrucomicrobia. Intriguingly, the hyperarid microbial consortia exhibited a similar pattern to the more southern desert. Salts at the shallow subsurface were dissolved and leached down to a deeper layer, challenging indigenous microorganisms with the increasing osmotic stress. Microbial viability was found to change with aridity and rainfall events. This study sheds light on the structure of xerotolerant, halotolerant, and radioresistant microbiomes from the hyperarid northern desert to the less arid southern transition region, as well as their response to changes in water availability.
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Affiliation(s)
- Jianxun Shen
- School of Earth and Environmental Sciences and Centre for Exoplanet Science, University of St Andrews, St Andrews, KY16 9AL, UK.
| | - Adam J Wyness
- Sediment Ecology Research Group, Scottish Oceans Institute, School of Biology, University of St Andrews, St Andrews, KY16 8LB, UK
- Coastal Research Group, Department of Zoology and Entomology, Rhodes University, Grahamstown, 6139, South Africa
| | - Mark W Claire
- School of Earth and Environmental Sciences and Centre for Exoplanet Science, University of St Andrews, St Andrews, KY16 9AL, UK
| | - Aubrey L Zerkle
- School of Earth and Environmental Sciences and Centre for Exoplanet Science, University of St Andrews, St Andrews, KY16 9AL, UK
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Rodríguez-Alarcón CA, Beristain-Ruiz DM, Olivares-Muñoz A, Quezada-Casasola A, Pérez-Casio F, Álvarez-Martínez JA, Tapia-Alanís J, Lira-Amaya JJ, Rivera-Barreno R, Cera-Hurtado OS, Ibancovichi-Camarillo JA, Soon-Gómez L, Adame-Gallegos JR, Figueroa-Millán JV. Demonstrating the presence of Ehrlichia canis DNA from different tissues of dogs with suspected subclinical ehrlichiosis. Parasit Vectors 2020; 13:518. [PMID: 33059758 PMCID: PMC7561240 DOI: 10.1186/s13071-020-04363-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2020] [Accepted: 09/15/2020] [Indexed: 11/12/2022] Open
Abstract
Background Nowadays, Ehrlichia canis receives increasing attention because of its great morbidity and mortality in animals. Dogs in the subclinical and chronic phases can be asymptomatic, and serological tests show cross-reactivity and fail to differentiate between current and past infections. Moreover, there could be low parasitaemia, and E. canis might be found only in target organs, hence causing results to be negative by polymerase chain reaction (PCR) on blood samples. Methods We evaluated by PCR the prevalence of E. canis in blood, liver, spleen, lymph node and bone marrow samples of 59 recently euthanised dogs that had ticks but were clinically healthy. Results In total, 52.55% of the blood PCRs for E. canis were negative, yet 61.30% yielded positive results from tissue biopsies and were as follows: 63.15% from bone marrow; 52.63% from liver; 47.36% from spleen; and 15.78% from lymph node. In addition, 33% had infection in three tissues (spleen, liver and bone marrow). Conclusions Our results show the prevalence of E. canis from tissues of dogs that were negative by blood PCR. Ehrlichia canis DNA in tissue was 30% lower in dogs that tested negative in PCR of blood samples compared to those that were positive. However, it must be taken into account that some dogs with negative results were positive for E. canis in other tissues.![]()
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Affiliation(s)
- Carlos A Rodríguez-Alarcón
- Veterinary Science Department, Universidad Autónoma de Ciudad Juárez, Anillo Envolvente y Estocolmo s/n, Zona PRONAF, 32310, Juárez, México
| | - Diana M Beristain-Ruiz
- Veterinary Science Department, Universidad Autónoma de Ciudad Juárez, Anillo Envolvente y Estocolmo s/n, Zona PRONAF, 32310, Juárez, México.
| | - Angélica Olivares-Muñoz
- Veterinary and Zootechnic Faculty, Universidad Veracruzana, Miguel Ángel de Quevedo s/n esq. Yáñez, Col. Unidad Veracruzana, 91710, Veracruz, México
| | - Andrés Quezada-Casasola
- Veterinary Science Department, Universidad Autónoma de Ciudad Juárez, Anillo Envolvente y Estocolmo s/n, Zona PRONAF, 32310, Juárez, México
| | - Federico Pérez-Casio
- Veterinary Science Department, Universidad Autónoma de Ciudad Juárez, Anillo Envolvente y Estocolmo s/n, Zona PRONAF, 32310, Juárez, México
| | - Jesús A Álvarez-Martínez
- CENID-Salud Animal e Inocuidad. INIFAP, Km. 11.5 de la Carretera Federal Cuernavaca-Cuautla, 62550, Col. Progreso, Jiutepec, México
| | - Jane Tapia-Alanís
- Veterinary Science Department, Universidad Autónoma de Ciudad Juárez, Anillo Envolvente y Estocolmo s/n, Zona PRONAF, 32310, Juárez, México
| | - José J Lira-Amaya
- CENID-Salud Animal e Inocuidad. INIFAP, Km. 11.5 de la Carretera Federal Cuernavaca-Cuautla, 62550, Col. Progreso, Jiutepec, México
| | - Ramón Rivera-Barreno
- Veterinary Science Department, Universidad Autónoma de Ciudad Juárez, Anillo Envolvente y Estocolmo s/n, Zona PRONAF, 32310, Juárez, México
| | - Orlando S Cera-Hurtado
- Veterinary Science Department, Universidad Autónoma de Ciudad Juárez, Anillo Envolvente y Estocolmo s/n, Zona PRONAF, 32310, Juárez, México
| | - José A Ibancovichi-Camarillo
- Department of Veterinary Anesthesia, Analgesia and Pharmacology, Faculty of Veterinary Medicine, Universidad Autónoma del Estado de México, El Cerrillo Piedras Blancas, 50090, Toluca, México
| | - Luis Soon-Gómez
- Municipal Anti-Rabies Center, Jurisdicción Sanitaria II, Servicios de Salud de Chihuahua, Calle Sevilla 4241, Colonia San Antonio, 32250, Juárez, México
| | - Jaime R Adame-Gallegos
- Faculty of Chemistry, Universidad Autónoma de Chihuahua, Campus 2, Circuito Universitario s/n, 31125, Chihuahua, México
| | - Julio V Figueroa-Millán
- CENID-Salud Animal e Inocuidad. INIFAP, Km. 11.5 de la Carretera Federal Cuernavaca-Cuautla, 62550, Col. Progreso, Jiutepec, México
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Chen YH, Li TJ, Tsai BY, Chen LK, Lai YH, Li MJ, Tsai CY, Tsai PJ, Shieh DB. Vancomycin-Loaded Nanoparticles Enhance Sporicidal and Antibacterial Efficacy for Clostridium difficile Infection. Front Microbiol 2019; 10:1141. [PMID: 31178844 PMCID: PMC6543869 DOI: 10.3389/fmicb.2019.01141] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2019] [Accepted: 05/06/2019] [Indexed: 12/19/2022] Open
Abstract
Current antibiotic treatments fail to eliminate the Clostridium difficile (C. difficile) spores and induce dysbiosis and intestinal inflammation via off-target effect, which causes refractory C. difficile infection raise an unmet need for a spore-specific antimicrobial treatment. We developed a sporicidal and antimicrobial vancomycin-loaded spore-targeting iron oxide nanoparticle (van-IONP) that selectively binds to C. difficile spores. Cryo-electron microscopy showed that vancomycin-loaded nanoparticles can target and completely cover spore surfaces. They not only successfully delayed the germination of the spores but also inhibited ∼50% of vegetative cell outgrowth after 48 h of incubation. The van-IONPs also inhibited the interaction of spores with HT-29 intestinal mucosal cells in vitro. In a murine model of C. difficile infection, the van-IONP significantly protected the mice from infected by C. difficile infection, reducing intestinal inflammation, and facilitated superior mucosal viability compared with equal doses of free vancomycin. This dual-function targeted delivery therapy showed advantages over traditional therapeutics in treating C. difficile infection.
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Affiliation(s)
- Yi-Hsuan Chen
- Department of Medicine, College of Medicine, National Cheng Kung University, Tainan, Taiwan
- Institute of Oral Medicine and Department of Stomatology, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Tsung-Ju Li
- Institute of Basic Medical Sciences, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Bo-Yang Tsai
- Institute of Basic Medical Sciences, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Liang-Kuei Chen
- Department of Medical Laboratory Science and Biotechnology, National Cheng Kung University, Tainan, Taiwan
| | - Yi-Hsin Lai
- Institute of Basic Medical Sciences, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Meng-Jia Li
- Department of Medical Laboratory Science and Biotechnology, National Cheng Kung University, Tainan, Taiwan
| | - Cheng-Yang Tsai
- Institute of Oral Medicine and Department of Stomatology, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Pei-Jane Tsai
- Institute of Basic Medical Sciences, College of Medicine, National Cheng Kung University, Tainan, Taiwan
- Department of Medical Laboratory Science and Biotechnology, National Cheng Kung University, Tainan, Taiwan
- Center of Infectious Disease and Signaling Research, National Cheng Kung University, Tainan, Taiwan
| | - Dar-Bin Shieh
- Institute of Oral Medicine and Department of Stomatology, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan, Taiwan
- Institute of Basic Medical Sciences, College of Medicine, National Cheng Kung University, Tainan, Taiwan
- Advanced Optoelectronic Technology Center, National Cheng Kung University, Tainan, Taiwan
- Center for Micro/Nano Science and Technology, National Cheng Kung University, Tainan, Taiwan
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Nakano M. Multiplex PCR for rapid detection of thermophilicMoorella thermoaceticaandGeobacillus stearothermophilusfrom canned foods and beverages. Int J Food Sci Technol 2017. [DOI: 10.1111/ijfs.13691] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Miyo Nakano
- Division of Food Science; Toyo Institute of Food Technology; 23-2, 4-chome, Minami-hanayashiki Kawanishi-shi Hyogo 666-0026 Japan
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7
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Sedlackova V, Dziedzinska R, Babak V, Kralik P. The detection and quantification of Bacillus thuringiensis
spores from soil and swabs using quantitative PCR as a model system for routine diagnostics of Bacillus anthracis. J Appl Microbiol 2017; 123:116-123. [DOI: 10.1111/jam.13445] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2016] [Revised: 02/14/2017] [Accepted: 03/03/2017] [Indexed: 11/27/2022]
Affiliation(s)
| | | | - V. Babak
- Veterinary Research Institute; Brno Czech Republic
| | - P. Kralik
- Veterinary Research Institute; Brno Czech Republic
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8
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Grass G, Ahrens B, Schleenbecker U, Dobrzykowski L, Wagner M, Krüger C, Wölfel R. Technical Note: Simple, scalable, and sensitive protocol for retrieving Bacillus anthracis (and other live bacteria) from heroin. Forensic Sci Int 2016; 259:32-5. [DOI: 10.1016/j.forsciint.2015.11.017] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2015] [Revised: 11/19/2015] [Accepted: 11/30/2015] [Indexed: 10/22/2022]
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Nakano M. Development of a Quantitative PCR Assay for Thermophilic Spore-Forming Geobacillus stearothermophilus in Canned Food. Biocontrol Sci 2015; 20:221-7. [PMID: 26412704 DOI: 10.4265/bio.20.221] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/01/2022]
Abstract
The thermophilic spore forming bacteria Geobacillus stearothermophilus is recognized as a major cause of spoilage in canned food. A quantitative real-time PCR assay was developed to specifically detect and quantify the species G. stearothermophilus in samples from canned food. The selected primer pairs amplified a 163-bp fragment of the 16S rRNA gene in a specific PCR assay with a detection limit of 12.5 fg of pure culture DNA, corresponding to DNA extracted from approximately 0.7 CFU/mL of G. stearothermophilus. Analysis showed that the bacterial species G. stearothermophilus was not detected in any canned food sample. Our approach presented here will be useful for tracking or quantifying species G. stearotethermophilus in canned food and ingredients.
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Affiliation(s)
- Miyo Nakano
- Division of Food Science, Toyo Institute of Food Technology
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10
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Nakano M. Detection and Quantification of Thermophilic Spore-Forming Moorella thermoacetica in Canned Beverages Using Real-Time PCR. J Food Prot 2015; 78:1392-6. [PMID: 26197294 DOI: 10.4315/0362-028x.jfp-14-547] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
A quantitative real-time PCR assay was developed to specifically detect and quantify Moorella thermoacetica and/or Moorella thermoautotrophica from canned coffee beverages. Six different combinations of newly designed primers were examined, and primer pair v1-1F/v4R was found to specifically amplify M. thermoacetica and M. thermoautotrophica. The minimum detection sensitivity was 15 fg of pure culture DNA from M. thermoacetica. Twenty commercial canned coffee beverages were then screened for the presence of M. thermoacetica, and two were shown to contain >1.3 and >1.0 CFU/ml, respectively. Therefore, the assay developed in this study may be useful for accurately tracking and quantifying M. thermoacetica and M. thermoautotrophica in beverage samples.
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Affiliation(s)
- Miyo Nakano
- Division of Food Science, Toyo Institute of Food Technology, 23-2, 4-chome, Minami-hanayashiki, Kawanishi, Hyogo 666-0026, Japan.
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11
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Recent literature review of soil processing methods for recovery of Bacillus anthracis spores. ANN MICROBIOL 2014. [DOI: 10.1007/s13213-014-0932-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022] Open
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12
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Sella SRBR, Vandenberghe LPS, Soccol CR. Bacillus atrophaeus:main characteristics and biotechnological applications – a review. Crit Rev Biotechnol 2014; 35:533-45. [DOI: 10.3109/07388551.2014.922915] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
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13
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Cross-institute evaluations of inhibitor-resistant PCR reagents for direct testing of aerosol and blood samples containing biological warfare agent DNA. Appl Environ Microbiol 2013; 80:1322-9. [PMID: 24334660 DOI: 10.1128/aem.03478-13] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Rapid pathogen detection is crucial for the timely introduction of therapeutics. Two groups (one in the United Kingdom and one in the United States) independently evaluated inhibitor-resistant PCR reagents for the direct testing of substrates. In the United Kingdom, a multiplexed Bacillus anthracis (target) and Bacillus subtilis (internal-control) PCR was used to evaluate 4 reagents against 5 PCR inhibitors and down-selected the TaqMan Fast Virus 1-Step master mix (Life Technologies Inc.). In the United States, four real-time PCR assays (targeting B. anthracis, Brucella melitensis, Venezuelan equine encephalitis virus [VEEV], and Orthopoxvirus spp.) were used to evaluate 5 reagents (plus the Fast Virus master mix) against buffer, blood, and soil samples and down-selected the KAPA Blood Direct master mix (KAPA Biosystems Inc.) with added Platinum Taq (Life Technologies). The down-selected reagents underwent further testing. In the United Kingdom experiments, both reagents were tested against seven contrived aerosol collector samples containing B. anthracis Ames DNA and B. subtilis spores from a commercial formulation (BioBall). In PCR assays with reaction mixtures containing 40% crude sample, an airfield-collected sample induced inhibition of the B. subtilis PCR with the KAPA reagent and complete failure of both PCRs with the Fast Virus reagent. However, both reagents allowed successful PCR for all other samples-which inhibited PCRs with a non-inhibitor-resistant reagent. In the United States, a cross-assay limit-of-detection (LoD) study in blood was conducted. The KAPA Blood Direct reagent allowed the detection of agent DNA (by four PCRs) at higher concentrations of blood in the reaction mixture (2.5%) than the Fast Virus reagent (0.5%), although LoDs differed between assays and reagent combinations. Across both groups, the KAPA Blood Direct reagent was determined to be the optimal reagent for inhibition relief in PCR.
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Weller SA, Cox V, Essex-Lopresti A, Hartley MG, Parsons TM, Rachwal PA, Stapleton HL, Lukaszewski RA. Evaluation of two multiplex real-time PCR screening capabilities for the detection of Bacillus anthracis, Francisella tularensis and Yersinia pestis in blood samples generated from murine infection models. J Med Microbiol 2012; 61:1546-1555. [DOI: 10.1099/jmm.0.049007-0] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Simon A. Weller
- Defence Science and Technology Laboratory, Porton Down, Salisbury SP4 0JQ, UK
| | - Victoria Cox
- Defence Science and Technology Laboratory, Porton Down, Salisbury SP4 0JQ, UK
| | | | - Margaret G. Hartley
- Defence Science and Technology Laboratory, Porton Down, Salisbury SP4 0JQ, UK
| | - Tanya M. Parsons
- Defence Science and Technology Laboratory, Porton Down, Salisbury SP4 0JQ, UK
| | - Phillip A. Rachwal
- Defence Science and Technology Laboratory, Porton Down, Salisbury SP4 0JQ, UK
| | - Helen L. Stapleton
- Defence Science and Technology Laboratory, Porton Down, Salisbury SP4 0JQ, UK
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Fedick A, Su J, Jalas C, Treff NR. High-throughput real-time PCR-based genotyping without DNA purification. BMC Res Notes 2012; 5:573. [PMID: 23083336 PMCID: PMC3505170 DOI: 10.1186/1756-0500-5-573] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2012] [Accepted: 10/16/2012] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND While improvements in genotyping technology have allowed for increased throughput and reduced time and expense, protocols remain hindered by the slow upstream steps of isolating, purifying, and normalizing DNA. Various methods exist for genotyping samples directly through blood, without having to purify the DNA first. These procedures were designed to be used on smaller throughput systems, however, and have not yet been tested for use on current high-throughput real-time (q)PCR based genotyping platforms. In this paper, a method of quantitative qPCR-based genotyping on blood without DNA purification was developed using a high-throughput qPCR platform. FINDINGS The performances of either DNA purified from blood or the same blood samples without DNA purification were evaluated through qPCR-based genotyping. First, 60 different mutations prevalent in the Ashkenazi Jewish population were genotyped in 12 Ashkenazi Jewish individuals using the QuantStudio™12K Flex Real-Time PCR System. Genotyping directly from blood gave a call rate of 99.21%, and an accuracy of 100%, while the purified DNA gave a call rate of 92.49%, and an accuracy of 99.74%. Although no statistical difference was found for these parameters, an F test comparing the standard deviations of the wild type clusters for the two different methods indicated significantly less variation when genotyping directly from blood instead of after DNA purification. To further establish the ability to perform high-throughput qPCR based genotyping directly from blood, 96 individuals of Ashkenazi Jewish decent were genotyped for the same 60 mutations (5,760 genotypes in 5 hours) and resulted in a call rate of 98.38% and a diagnostic accuracy of 99.77%. CONCLUSION This study shows that accurate qPCR-based high-throughput genotyping can be performed without DNA purification. The direct use of blood may further expedite the entire genotyping process, reduce costs, and avoid tracking errors which can occur during sample DNA purification.
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Affiliation(s)
- Anastasia Fedick
- Department of Molecular Genetics, Microbiology, and Immunology, UMDNJ-Robert Wood Johnson Medical School, Piscataway, NJ, USA.
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Comparison of nucleic acid extraction platforms for detection of select biothreat agents for use in clinical resource limited settings. J Microbiol Methods 2012; 91:179-83. [PMID: 22750394 DOI: 10.1016/j.mimet.2012.06.008] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2012] [Revised: 06/14/2012] [Accepted: 06/14/2012] [Indexed: 10/28/2022]
Abstract
High-quality nucleic acids are critical for optimal PCR-based diagnostics and pathogen detection. Rapid sample processing time is important for the earliest administration of therapeutic and containment measures, especially in the case of biothreat agents. In this context, we compared the Fujifilm QuickGene-Mini80 to Qiagen's QIAamp Mini Purification kits for extraction of DNA and RNA for potential use in austere settings. Qiagen (QIAamp) column-based extraction is the currently recommended purification platform by United States Army Medical Research Institute for Infectious Diseases for both DNA and RNA extraction. However, this sample processing system requires dedicated laboratory equipment including a centrifuge. In this study, we investigated the QuickGene-Mini80, which does not require centrifugation, as a suitable platform for nucleic acid extraction for use in resource-limited locations. Quality of the sample extraction was evaluated using pathogen-specific, real-time PCR assays for nucleic acids extracted from viable and γ-irradiated Bacillus anthracis, Yersinia pestis, vaccinia virus, Venezuelan equine encephalitis virus, or B. anthracis spores in buffer or human whole blood. QuickGene-Mini80 and QIAamp performed similarly for DNA extraction regardless of organism viability. It was noteworthy that γ-irradiation did not have a significant impact on real-time PCR for organism detection. Comparison with QIAamp showed a less than adequate performance of the Fujifilm instrument for RNA extraction. However, QuickGene-Mini80 remains a viable alternative to QIAamp for DNA extraction for use in remote settings due to extraction quality, time efficiency, reduced instrument requirements, and ease of use.
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Rachwal PA, Rose HL, Cox V, Lukaszewski RA, Murch AL, Weller SA. The potential of TaqMan Array Cards for detection of multiple biological agents by real-time PCR. PLoS One 2012; 7:e35971. [PMID: 22540014 PMCID: PMC3334355 DOI: 10.1371/journal.pone.0035971] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2012] [Accepted: 03/24/2012] [Indexed: 12/04/2022] Open
Abstract
The TaqMan Array Card architecture, normally used for gene expression studies, was evaluated for its potential to detect multiple bacterial agents by real-time PCR. Ten PCR assays targeting five biological agents (Bacillus anthracis, Burkholderia mallei, Burkholderia pseudomallei, Francisella tularensis, and Yersinia pestis) were incorporated onto Array Cards. A comparison of PCR performance of each PCR in Array Card and singleplex format was conducted using DNA extracted from pure bacterial cultures. When 100 fg of agent DNA was added to Array Card channels the following levels of agent detection (where at least one agent PCR replicate returned a positive result) were observed: Y. pestis 100%, B. mallei & F. tularensis 93%; B. anthracis 71%; B. pseudomallei 43%. For B. mallei & pseudomallei detection the BPM2 PCR, which detects both species, outperformed PCR assays specific to each organism indicating identification of the respective species would not be reproducible at the 100 fg level. Near 100% levels of detection were observed when 100 fg of DNA was added to each PCR in singleplex format with singleplex PCRs also returning sporadic positives at the 10 fg per PCR level. Before evaluating the use of Array Cards for the testing of environmental and clinical sample types, with potential levels of background DNA and PCR inhibitors, users would therefore have to accept a 10-fold reduction in sensitivity of PCR assays on the Array Card format, in order to benefit for the capacity to test multiple samples for multiple agents. A two PCR per agent strategy would allow the testing of 7 samples for the presence of 11 biological agents or 3 samples for 23 biological agents per card (with negative control channels).
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Affiliation(s)
| | | | | | | | | | - Simon A. Weller
- Defence Science and Technology Laboratory, Porton Down, Salisbury, United Kingdom
- * E-mail:
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Stöckel S, Meisel S, Elschner M, Rösch P, Popp J. Raman spectroscopic detection of anthrax endospores in powder samples. Angew Chem Int Ed Engl 2012; 51:5339-42. [PMID: 22505355 PMCID: PMC3470700 DOI: 10.1002/anie.201201266] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2012] [Indexed: 11/08/2022]
Affiliation(s)
- S Stöckel
- Institut für Physikalische Chemie, Friedrich-Schiller-Universität Jena, Jena, Germany
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Regan JF, Furtado MR, Brevnov MG, Jordan JA. A sample extraction method for faster, more sensitive PCR-based detection of pathogens in blood culture. J Mol Diagn 2012; 14:120-9. [PMID: 22245225 DOI: 10.1016/j.jmoldx.2011.10.001] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2011] [Revised: 10/18/2011] [Accepted: 10/27/2011] [Indexed: 11/25/2022] Open
Abstract
Three mechanistically different sample extraction methodologies, namely, silica spin columns, phenol-chloroform, and an automated magnetic capture of polymer-complexed DNA (via an Automate Express instrument), were compared for their abilities to purify nucleic acids from blood culture fluids for use in TaqMan assays for detection of Staphylococcus aureus. The extracts from silica columns required 100- to 1000-fold dilutions to sufficiently reduce the powerful PCR inhibitory effects of the anticoagulant sodium polyanetholsulfonate, a common additive in blood culture media. In contrast, samples extracted by either phenol-chloroform or the Automate Express instrument required little or no dilution, respectively, allowing for an approximate 100-fold improvement in assay sensitivity. Analysis of 60 blood culture bottles indicated that these latter two methodologies could be used to detect lower numbers of pathogens and that a growing S. aureus culture could be detected 2 hours earlier than when using silica columns. Of the three tested methodologies, the Automate Express instrument had the shortest time to result, requiring only approximately 80 minutes to process 12 samples. These findings highlight the importance of considering the mechanism when selecting a DNA extraction methodology, given that certain PCR inhibitors act in a similar fashion to DNA in certain chemical environments, resulting in copurification, whereas other methodologies use different chemistries that have advantages during the DNA purification of certain types of samples.
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Affiliation(s)
- John F Regan
- Applied Molecular Testing, Life Technologies, Foster City, California, USA
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Rapid filtration separation-based sample preparation method for Bacillus spores in powdery and environmental matrices. Appl Environ Microbiol 2011; 78:1505-12. [PMID: 22210204 DOI: 10.1128/aem.06696-11] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Authorities frequently need to analyze suspicious powders and other samples for biothreat agents in order to assess environmental safety. Numerous nucleic acid detection technologies have been developed to detect and identify biowarfare agents in a timely fashion. The extraction of microbial nucleic acids from a wide variety of powdery and environmental samples to obtain a quality level adequate for these technologies still remains a technical challenge. We aimed to develop a rapid and versatile method of separating bacteria from these samples and then extracting their microbial DNA. Bacillus atrophaeus subsp. globigii was used as a simulant of Bacillus anthracis. We studied the effects of a broad variety of powdery and environmental samples on PCR detection and the steps required to alleviate their interference. With a benchmark DNA extraction procedure, 17 of the 23 samples investigated interfered with bacterial lysis and/or PCR-based detection. Therefore, we developed the dual-filter method for applied recovery of microbial particles from environmental and powdery samples (DARE). The DARE procedure allows the separation of bacteria from contaminating matrices that interfere with PCR detection. This procedure required only 2 min, while the DNA extraction process lasted 7 min, for a total of <10 min. This sample preparation procedure allowed the recovery of cleaned bacterial spores and relieved detection interference caused by a wide variety of samples. Our procedure was easily completed in a laboratory facility and is amenable to field application and automation.
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