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Dippenaar A, Ismail N, Heupink TH, Grobbelaar M, Loubser J, Van Rie A, Warren RM. Droplet based whole genome amplification for sequencing minute amounts of purified Mycobacterium tuberculosis DNA. Sci Rep 2024; 14:9931. [PMID: 38689002 PMCID: PMC11061190 DOI: 10.1038/s41598-024-60545-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2023] [Accepted: 04/24/2024] [Indexed: 05/02/2024] Open
Abstract
Implementation of whole genome sequencing (WGS) for patient care is hindered by limited Mycobacterium tuberculosis (Mtb) in clinical specimens and slow Mtb growth. We evaluated droplet multiple displacement amplification (dMDA) for amplification of minute amounts of Mtb DNA to enable WGS as an alternative to other Mtb enrichment methods. Purified genomic Mtb-DNA (0.1, 0.5, 1, and 5 pg) was encapsulated and amplified using the Samplix Xdrop-instrument and sequenced alongside a control sample using standard Illumina protocols followed by MAGMA-analysis. The control and 5 pg input dMDA samples underwent nanopore sequencing followed by Nanoseq and TB-profiler analysis. dMDA generated 105-2400 ng DNA from the 0.1-5 pg input DNA, respectively. Followed by Illumina WGS, dMDA raised mean sequencing depth from 7 × for 0.1 pg input DNA to ≥ 60 × for 5 pg input and the control sample. Bioinformatic analysis revealed a high number of false positive and false negative variants when amplifying ≤ 0.5 pg input DNA. Nanopore sequencing of the 5 pg dMDA sample presented excellent coverage depth, breadth, and accurate strain characterization, albeit elevated false positive and false negative variants compared to Illumina-sequenced dMDA sample with identical Mtb DNA input. dMDA coupled with Illumina WGS for samples with ≥ 5 pg purified Mtb DNA, equating to approximately 1000 copies of the Mtb genome, offers precision for drug resistance, phylogeny, and transmission insights.
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Affiliation(s)
- Anzaan Dippenaar
- Tuberculosis Omics Research Consortium, Department of Family Medicine and Population Health, Global Health Institute, Faculty of Medicine and Health Sciences, University of Antwerp, Antwerp, Belgium.
| | - Nabila Ismail
- South African Medical Research Council Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Tim H Heupink
- Tuberculosis Omics Research Consortium, Department of Family Medicine and Population Health, Global Health Institute, Faculty of Medicine and Health Sciences, University of Antwerp, Antwerp, Belgium
| | - Melanie Grobbelaar
- South African Medical Research Council Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Johannes Loubser
- South African Medical Research Council Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Annelies Van Rie
- Tuberculosis Omics Research Consortium, Department of Family Medicine and Population Health, Global Health Institute, Faculty of Medicine and Health Sciences, University of Antwerp, Antwerp, Belgium
| | - Robin M Warren
- South African Medical Research Council Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
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NISHIMURA H, SHIWA Y, TOMITA S, ENDO A. Microbial composition and metabolic profiles during machine-controlled intra-factory fermentation of cocoa beans harvested in semitropical area of Japan. BIOSCIENCE OF MICROBIOTA, FOOD AND HEALTH 2023; 43:29-42. [PMID: 38188660 PMCID: PMC10767318 DOI: 10.12938/bmfh.2023-036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Accepted: 08/13/2023] [Indexed: 01/09/2024]
Abstract
Cocoa bean fermentation is typically performed in a spontaneous manner on farms in tropical countries or areas and involves several microbial groups. Metabolism by microbes markedly affects the quality of cocoa beans fermented and the chocolate produced thereof. The present study characterized the microbiota and their metabolic profiles in temperature- and humidity-controlled intra-factory cocoa fermentation in a semitropical area of Japan. Although environmental factors were uniform, the microbiota of cocoa beans subjected to intra-factory fermentation was not stable between tests, particularly in terms of the cell count levels and species observed. Fermentation was sometimes delayed, and fermenting microbes were present at very low levels after 24 hr of fermentation. Due to the unstable microbiota, the profiles of water-soluble compounds differed between tests, indicating the unstable qualities of the fermented cocoa beans. These results suggest the necessity of starter cultures not only in on-farm fermentation but also in machine-controlled intra-factory cocoa fermentation.
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Affiliation(s)
- Hiroya NISHIMURA
- Department of Food, Aroma and Cosmetic Chemistry, Faculty of
Bioindustry, Tokyo University of Agriculture, 196 Yasaka, Abashiri-shi, Hokkaido 099-2493,
Japan
| | - Yuh SHIWA
- Department of Molecular Microbiology, Faculty of Life
Sciences, Tokyo University of Agriculture, 1-1-1 Sakuragaoka, Setagaya-ku, Tokyo 156-8502,
Japan
- NODAI Genome Research Centre, Tokyo University of
Agriculture, 1-1-1 Sakuragaoka, Setagaya-ku, Tokyo 156-8502, Japan
| | - Satoru TOMITA
- Institute of Food Research, National Agriculture and Food
Research Organization (NARO), 2-1-12 Kannondai, Tsukuba, Ibaraki 305-8642, Japan
| | - Akihito ENDO
- Department of Food, Aroma and Cosmetic Chemistry, Faculty of
Bioindustry, Tokyo University of Agriculture, 196 Yasaka, Abashiri-shi, Hokkaido 099-2493,
Japan
- Department of Nutritional Science and Food Safety, Faculty of
Applied Bioscience, Tokyo University of Agriculture, 1-1-1 Sakuragaoka, Setagaya-ku, Tokyo
156-8502, Japan
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Characterization and Demonstration of Mock Communities as Control Reagents for Accurate Human Microbiome Community Measurements. Microbiol Spectr 2022; 10:e0191521. [PMID: 35234490 PMCID: PMC8941912 DOI: 10.1128/spectrum.01915-21] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Standardization and quality assurance of microbiome community analysis by high-throughput DNA sequencing require widely accessible and well-characterized reference materials. Here, we report on newly developed DNA and whole-cell mock communities to serve as control reagents for human gut microbiota measurements by shotgun metagenomics and 16S rRNA gene amplicon sequencing. The mock communities were formulated as near-even blends of up to 20 bacterial species prevalent in the human gut, span a wide range of genomic guanine-cytosine (GC) contents, and include multiple strains with Gram-positive type cell walls. Through a collaborative study, we carefully characterized the mock communities by shotgun metagenomics, using previously developed standardized protocols for DNA extraction and sequencing library construction. Further, we validated fitness of the mock communities for revealing technically meaningful differences among protocols for DNA extraction and metagenome/16S rRNA gene amplicon library construction. Finally, we used the mock communities to reveal varying performance of metagenome-based taxonomic profilers and the impact of trimming and filtering of sequencing reads on observed species profiles. The latter showed that aggressive preprocessing of reads may result in substantial GC-dependent bias and should thus be carefully evaluated to minimize unintended effects on species abundances. Taken together, the mock communities are expected to support a myriad of applications that rely on well-characterized control reagents, ranging from evaluation and optimization of methods to assessment of reproducibility in interlaboratory studies and routine quality control. IMPORTANCE Application of high-throughput DNA sequencing has greatly accelerated human microbiome research and its translation into new therapeutic and diagnostic capabilities. Microbiome community analyses results can, however, vary considerably across studies or laboratories, and establishment of measurement standards to improve accuracy and reproducibility has become a priority. The here-developed mock communities, which are available from the NITE Biological Resource Center (NBRC) at the National Institute of Technology and Evaluation (NITE, Japan), provide well-characterized control reagents that allow users to judge the accuracy of their measurement results. Widespread and consistent adoption of the mock communities will improve reproducibility and comparability of microbiome community analyses, thereby supporting and accelerating human microbiome research and development.
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Commensal-Related Changes in the Epidermal Barrier Function Lead to Alterations in the Benzo[ a]Pyrene Metabolite Profile and Its Distribution in 3D Skin. mBio 2021; 12:e0122321. [PMID: 34579573 PMCID: PMC8546866 DOI: 10.1128/mbio.01223-21] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
Polycyclic aromatic hydrocarbons (PAH) such as benzo[a]pyrene (B[a]P) are among the most abundant environmental pollutants, resulting in continuous exposure of human skin and its microbiota. However, effects of the latter on B[a]P toxicity, absorption, metabolism, and distribution in humans remain unclear. Here, we demonstrate that the skin microbiota does metabolize B[a]P on and in human skin in situ, using a recently developed commensal skin model. In this model, microbial metabolism leads to high concentrations of known microbial B[a]P metabolites on the surface as well as in the epidermal layers. In contrast to what was observed for uncolonized skin, B[a]P and its metabolites were subject to altered rates of skin penetration and diffusion, resulting in up to 58% reduction of metabolites recovered from basal culture medium. The results indicate the reason for this altered behavior to be a microbially induced strengthening of the epidermal barrier. Concomitantly, colonized models showed decreased formation and penetration of the ultimate carcinogen B[a]P-7,8-dihydrodiol-9,10-epoxide (BPDE), leading, in consequence, to fewer BPDE-DNA adducts being formed. Befittingly, transcript and expression levels of key proteins for repairing environmentally induced DNA damage such as xeroderma pigmentosum complementation group C (XPC) were also found to be reduced in the commensal models, as was expression of B[a]P-associated cytochrome P450-dependent monooxygenases (CYPs). The results show that the microbiome can have significant effects on the toxicology of external chemical impacts. The respective effects rely on a complex interplay between microbial and host metabolism and microbe-host interactions, all of which cannot be adequately assessed using single-system studies.
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Emran MY, Shenashen MA, El-Safty SA, Selim MM. Design of porous S-doped carbon nanostructured electrode sensor for sensitive and selective detection of guanine from DNA samples. MICROPOROUS AND MESOPOROUS MATERIALS 2021; 320:111097. [DOI: 10.1016/j.micromeso.2021.111097] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/01/2023]
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Tourlousse DM, Narita K, Miura T, Sakamoto M, Ohashi A, Shiina K, Matsuda M, Miura D, Shimamura M, Ohyama Y, Yamazoe A, Uchino Y, Kameyama K, Arioka S, Kataoka J, Hisada T, Fujii K, Takahashi S, Kuroiwa M, Rokushima M, Nishiyama M, Tanaka Y, Fuchikami T, Aoki H, Kira S, Koyanagi R, Naito T, Nishiwaki M, Kumagai H, Konda M, Kasahara K, Ohkuma M, Kawasaki H, Sekiguchi Y, Terauchi J. Validation and standardization of DNA extraction and library construction methods for metagenomics-based human fecal microbiome measurements. MICROBIOME 2021; 9:95. [PMID: 33910647 PMCID: PMC8082873 DOI: 10.1186/s40168-021-01048-3] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Accepted: 03/12/2021] [Indexed: 05/27/2023]
Abstract
BACKGROUND Validation and standardization of methodologies for microbial community measurements by high-throughput sequencing are needed to support human microbiome research and its industrialization. This study set out to establish standards-based solutions to improve the accuracy and reproducibility of metagenomics-based microbiome profiling of human fecal samples. RESULTS In the first phase, we performed a head-to-head comparison of a wide range of protocols for DNA extraction and sequencing library construction using defined mock communities, to identify performant protocols and pinpoint sources of inaccuracy in quantification. In the second phase, we validated performant protocols with respect to their variability of measurement results within a single laboratory (that is, intermediate precision) as well as interlaboratory transferability and reproducibility through an industry-based collaborative study. We further ascertained the performance of our recommended protocols in the context of a community-wide interlaboratory study (that is, the MOSAIC Standards Challenge). Finally, we defined performance metrics to provide best practice guidance for improving measurement consistency across methods and laboratories. CONCLUSIONS The validated protocols and methodological guidance for DNA extraction and library construction provided in this study expand current best practices for metagenomic analyses of human fecal microbiota. Uptake of our protocols and guidelines will improve the accuracy and comparability of metagenomics-based studies of the human microbiome, thereby facilitating development and commercialization of human microbiome-based products. Video Abstract.
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Affiliation(s)
- Dieter M Tourlousse
- Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Ibaraki, 305-8566, Japan
| | - Koji Narita
- Japan Microbiome Consortium (JMBC), Osaka, Osaka, 530-0011, Japan
- Chitose Laboratory Corp., Kawasaki, Kanagawa, 216-0041, Japan
| | - Takamasa Miura
- Biological Resource Center, National Institute of Technology and Evaluation (NITE), Kisarazu, Chiba, 292-0818, Japan
| | - Mitsuo Sakamoto
- Microbe Division/Japan Collection of Microorganisms, RIKEN BioResource Research Center, Tsukuba, Ibaraki, 305-0074, Japan
| | - Akiko Ohashi
- Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Ibaraki, 305-8566, Japan
| | - Keita Shiina
- Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Ibaraki, 305-8566, Japan
| | - Masami Matsuda
- Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Ibaraki, 305-8566, Japan
| | - Daisuke Miura
- Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Ibaraki, 305-8566, Japan
| | - Mamiko Shimamura
- Biological Resource Center, National Institute of Technology and Evaluation (NITE), Kisarazu, Chiba, 292-0818, Japan
| | - Yoshifumi Ohyama
- Biological Resource Center, National Institute of Technology and Evaluation (NITE), Kisarazu, Chiba, 292-0818, Japan
| | - Atsushi Yamazoe
- Biological Resource Center, National Institute of Technology and Evaluation (NITE), Kisarazu, Chiba, 292-0818, Japan
| | - Yoshihito Uchino
- Biological Resource Center, National Institute of Technology and Evaluation (NITE), Kisarazu, Chiba, 292-0818, Japan
| | - Keishi Kameyama
- Japan Microbiome Consortium (JMBC), Osaka, Osaka, 530-0011, Japan
- Institute of Food Sciences and Technologies, Ajinomoto Co., Inc., Kawasaki, Kanagawa, 210-8681, Japan
| | - Shingo Arioka
- Japan Microbiome Consortium (JMBC), Osaka, Osaka, 530-0011, Japan
- Laboratory for Innovative Therapy Research, Shionogi and Co., Ltd., Toyonaka, Osaka, 561-0825, Japan
| | - Jiro Kataoka
- Japan Microbiome Consortium (JMBC), Osaka, Osaka, 530-0011, Japan
- Japan Tobacco Inc., Minato, Tokyo, 105-6927, Japan
| | - Takayoshi Hisada
- Japan Microbiome Consortium (JMBC), Osaka, Osaka, 530-0011, Japan
- TechnoSuruga Laboratory Co., Ltd., Shizuoka, Shizuoka, 424-0065, Japan
| | - Kazuyuki Fujii
- Japan Microbiome Consortium (JMBC), Osaka, Osaka, 530-0011, Japan
- Infectious Diseases Unit, Department of Medical Innovations, New Drug Research Division, Otsuka Pharmaceutical Co., Ltd., Tokushima, Tokushima, 771-0192, Japan
| | - Shunsuke Takahashi
- Japan Microbiome Consortium (JMBC), Osaka, Osaka, 530-0011, Japan
- TechnoSuruga Laboratory Co., Ltd., Shizuoka, Shizuoka, 424-0065, Japan
| | - Miho Kuroiwa
- Japan Microbiome Consortium (JMBC), Osaka, Osaka, 530-0011, Japan
- Laboratory for Innovative Therapy Research, Shionogi and Co., Ltd., Toyonaka, Osaka, 561-0825, Japan
| | - Masatomo Rokushima
- Japan Microbiome Consortium (JMBC), Osaka, Osaka, 530-0011, Japan
- Laboratory for Innovative Therapy Research, Shionogi and Co., Ltd., Toyonaka, Osaka, 561-0825, Japan
| | - Mitsue Nishiyama
- Japan Microbiome Consortium (JMBC), Osaka, Osaka, 530-0011, Japan
- Tsumura Kampo Research Laboratories, Tsumura & Co., Ami, Ibaraki, 300-1192, Japan
| | - Yoshiki Tanaka
- Japan Microbiome Consortium (JMBC), Osaka, Osaka, 530-0011, Japan
- Biofermin Pharmaceutical Co., Ltd., Kobe, Hyogo, 650-0021, Japan
| | - Takuya Fuchikami
- Japan Microbiome Consortium (JMBC), Osaka, Osaka, 530-0011, Japan
- CDM Center Division 4, Takara Bio Inc., Kusatsu, Shiga, 525-0058, Japan
| | - Hitomi Aoki
- Japan Microbiome Consortium (JMBC), Osaka, Osaka, 530-0011, Japan
- CDM Center Division 4, Takara Bio Inc., Kusatsu, Shiga, 525-0058, Japan
| | - Satoshi Kira
- Japan Microbiome Consortium (JMBC), Osaka, Osaka, 530-0011, Japan
- CDM Center Division 4, Takara Bio Inc., Kusatsu, Shiga, 525-0058, Japan
| | - Ryo Koyanagi
- Japan Microbiome Consortium (JMBC), Osaka, Osaka, 530-0011, Japan
- Molecular Genetic Research Department, Advanced Technology Center, LSI Medience Corporation, Chiyoda, Tokyo, 101-8517, Japan
| | - Takeshi Naito
- Japan Microbiome Consortium (JMBC), Osaka, Osaka, 530-0011, Japan
- H.U. Group Research Institute G.K., Hachioji, Tokyo, 192-0031, Japan
| | - Morie Nishiwaki
- Japan Microbiome Consortium (JMBC), Osaka, Osaka, 530-0011, Japan
- H.U. Group Research Institute G.K., Hachioji, Tokyo, 192-0031, Japan
| | - Hirotaka Kumagai
- Japan Microbiome Consortium (JMBC), Osaka, Osaka, 530-0011, Japan
- JSR-Keio University Medical and Chemical Innovation Center, Shinjuku, Tokyo, 160-8582, Japan
| | - Mikiko Konda
- Japan Microbiome Consortium (JMBC), Osaka, Osaka, 530-0011, Japan
- JSR-Keio University Medical and Chemical Innovation Center, Shinjuku, Tokyo, 160-8582, Japan
| | - Ken Kasahara
- Japan Microbiome Consortium (JMBC), Osaka, Osaka, 530-0011, Japan
- Chitose Laboratory Corp., Kawasaki, Kanagawa, 216-0041, Japan
| | - Moriya Ohkuma
- Microbe Division/Japan Collection of Microorganisms, RIKEN BioResource Research Center, Tsukuba, Ibaraki, 305-0074, Japan
| | - Hiroko Kawasaki
- Biological Resource Center, National Institute of Technology and Evaluation (NITE), Kisarazu, Chiba, 292-0818, Japan
| | - Yuji Sekiguchi
- Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Ibaraki, 305-8566, Japan.
| | - Jun Terauchi
- Japan Microbiome Consortium (JMBC), Osaka, Osaka, 530-0011, Japan.
- Ono Pharmaceutical Co., Ltd., Osaka, Osaka, 541-8564, Japan.
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Li N, Cai Q, Miao Q, Song Z, Fang Y, Hu B. High-Throughput Metagenomics for Identification of Pathogens in the Clinical Settings. SMALL METHODS 2021; 5:2000792. [PMID: 33614906 PMCID: PMC7883231 DOI: 10.1002/smtd.202000792] [Citation(s) in RCA: 88] [Impact Index Per Article: 29.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Revised: 10/24/2020] [Indexed: 05/25/2023]
Abstract
The application of sequencing technology is shifting from research to clinical laboratories owing to rapid technological developments and substantially reduced costs. However, although thousands of microorganisms are known to infect humans, identification of the etiological agents for many diseases remains challenging as only a small proportion of pathogens are identifiable by the current diagnostic methods. These challenges are compounded by the emergence of new pathogens. Hence, metagenomic next-generation sequencing (mNGS), an agnostic, unbiased, and comprehensive method for detection, and taxonomic characterization of microorganisms, has become an attractive strategy. Although many studies, and cases reports, have confirmed the success of mNGS in improving the diagnosis, treatment, and tracking of infectious diseases, several hurdles must still be overcome. It is, therefore, imperative that practitioners and clinicians understand both the benefits and limitations of mNGS when applying it to clinical practice. Interestingly, the emerging third-generation sequencing technologies may partially offset the disadvantages of mNGS. In this review, mainly: a) the history of sequencing technology; b) various NGS technologies, common platforms, and workflows for clinical applications; c) the application of NGS in pathogen identification; d) the global expert consensus on NGS-related methods in clinical applications; and e) challenges associated with diagnostic metagenomics are described.
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Affiliation(s)
- Na Li
- Department of Infectious DiseasesZhongshan HospitalFudan UniversityShanghai200032China
| | - Qingqing Cai
- Genoxor Medical Science and Technology Inc.Zhejiang317317China
| | - Qing Miao
- Department of Infectious DiseasesZhongshan HospitalFudan UniversityShanghai200032China
| | - Zeshi Song
- Genoxor Medical Science and Technology Inc.Zhejiang317317China
| | - Yuan Fang
- Genoxor Medical Science and Technology Inc.Zhejiang317317China
| | - Bijie Hu
- Department of Infectious DiseasesZhongshan HospitalFudan UniversityShanghai200032China
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8
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Paniagua Voirol LR, Valsamakis G, Yu M, Johnston PR, Hilker M. How the 'kitome' influences the characterization of bacterial communities in lepidopteran samples with low bacterial biomass. J Appl Microbiol 2020; 130:1780-1793. [PMID: 33128818 DOI: 10.1111/jam.14919] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Revised: 10/02/2020] [Accepted: 10/23/2020] [Indexed: 12/26/2022]
Abstract
AIMS We aimed to elucidate whether the DNA extraction kit and bacteria therein affect the characterization of bacterial communities associated with butterfly samples harbouring different bacterial abundancies. METHODS AND RESULTS We analysed bacteria associated with eggs of Pieris brassicae and with adults of this butterfly, which were either untreated or treated with antibiotics (ABs). Three DNA extraction kits were used. Regardless of the extraction kit used, PCR amplification of the bacterial 16S rRNA gene detected very low bacterial presence in eggs and AB-treated butterflies. In untreated butterflies, bacterial signal intensity varied according to the kit and primers used. Sequencing (MiSeq) of the bacterial communities in untreated and AB-treated butterflies revealed a low alpha diversity in untreated butterflies because of the dominance of few bacteria genera, which were detectable regardless of the kit. However, a significantly greater alpha diversity was found in AB-treated butterflies, evidencing a true bias of the results due to bacterial contaminants in the kit. CONCLUSIONS The so-called 'kitome' can impact the profiling of Lepidoptera-associated bacteria in samples with low bacterial biomass. SIGNIFICANCE AND IMPACT OF THE STUDY Our study highlights the necessity of method testing and analysis of negative controls when investigating Lepidoptera-associated bacterial communities.
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Affiliation(s)
- L R Paniagua Voirol
- Applied Zoology/Animal Ecology, Institute of Biology, Freie Universitaet Berlin, Berlin, Germany
| | - G Valsamakis
- Applied Zoology/Animal Ecology, Institute of Biology, Freie Universitaet Berlin, Berlin, Germany
| | - M Yu
- Applied Zoology/Animal Ecology, Institute of Biology, Freie Universitaet Berlin, Berlin, Germany
| | - P R Johnston
- Evolutionary Biology, Institute of Biology, Freie Universitaet Berlin, Berlin, Germany.,Berlin Center for Genomics in Biodiversity Research (BeGenDiv), Berlin, Germany.,Leibniz-Institute of Freshwater Ecology and Inland Fisheries, Berlin, Germany
| | - M Hilker
- Applied Zoology/Animal Ecology, Institute of Biology, Freie Universitaet Berlin, Berlin, Germany
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Lima WG, de Brito JCM, Cardoso VN, Fernandes SOA. In-depth characterization of antibacterial activity of melittin against Staphylococcus aureus and use in a model of non-surgical MRSA-infected skin wounds. Eur J Pharm Sci 2020; 156:105592. [PMID: 33049305 DOI: 10.1016/j.ejps.2020.105592] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2020] [Revised: 10/07/2020] [Accepted: 10/08/2020] [Indexed: 12/12/2022]
Abstract
Skin infections caused by methicillin-resistant Staphylococcus aureus (MRSA) require the development of new and effective topical antibiotics. In this context, melittin, the main component of apitoxin, has a potent antibacterial effect. However, little is known regarding the anti-inflammatory potential this peptide in infection models, or its ability to induce clinically important resistance. Here, we aimed to conduct an in-depth characterization of the antibacterial potential of melittin in vitro and evaluate the pharmaceutical potential of an ointment containing melittin for the treatment of non-surgical infections induced by MRSA. The minimum inhibitory concentration of melittin varied from 0.12 to 4 μM. The antibacterial effect was mainly bactericidal and fast (approximately 0.5 h after incubation) and was maintained even in stationary cells and mature MRSA biofilms. Melittin interacts synergistically with beta-lactams and aminoglycosides, and its ability to form pores in the membrane reverses the resistance of vancomycin-intermediate Staphylococcus aureus (VISA) to amoxicillin, and vancomycin. Its ability to induce resistance in vitro was absent, and melittin was stable in several conditions often associated with infected wounds. In vivo, aointment containing melittin reduced bacterial load and the content of pro-inflammatory cytokines, such as tumor necrosis factor-α, interleukin-6 (IL-6), and IL-1 beta. Collectively, these data point to melittin as a potential candidate for topical formulations aimed at the treatment of non-surgical infections caused by MRSA.
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Affiliation(s)
- William Gustavo Lima
- Laboratório de Radioisótopos, Departamento de Análises Clinicas e Toxicológicas, Faculdade de Farmácia, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brazil
| | | | - Valbert Nascimento Cardoso
- Laboratório de Radioisótopos, Departamento de Análises Clinicas e Toxicológicas, Faculdade de Farmácia, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brazil
| | - Simone Odília Antunes Fernandes
- Laboratório de Radioisótopos, Departamento de Análises Clinicas e Toxicológicas, Faculdade de Farmácia, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brazil.
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10
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Bacterial mock communities as standards for reproducible cytometric microbiome analysis. Nat Protoc 2020; 15:2788-2812. [PMID: 32770154 DOI: 10.1038/s41596-020-0362-0] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2020] [Accepted: 05/27/2020] [Indexed: 11/09/2022]
Abstract
Flow cytometry has recently established itself as a tool to track short-term dynamics in microbial community assembly and link those dynamics with ecological parameters. However, instrumental configurations of commercial cytometers and variability introduced through differential handling of the cells and instruments frequently cause data set variability at the single-cell level. This is especially pronounced with microorganisms, which are in the lower range of optical resolution. Although alignment beads are valuable to generally minimize instrumental noise and align overall machine settings, an artificial microbial cytometric mock community (mCMC) is mandatory for validating lab workflows and enabling comparison of data between experiments, thus representing a necessary reference standard for the reproducible cytometric characterization of microbial communities, especially in long-term studies. In this study, the mock community consisted of two Gram-positive and two Gram-negative bacterial strains, which can be assembled with respective subsets of cells, including spores, in any selected ratio or concentration. The preparation of the four strains takes a maximum of 5 d, and the stains are storable with either PFA/ethanol fixation at -20 °C or drying at 4 °C for at least 6 months. Starting from this stock, an mCMC can be assembled within 1 h. Fluorescence staining methods are presented and representatively applied with two high-resolution cell sorters and three benchtop flow cytometers. Benchmarked data sets allow the use of bioinformatic evaluation procedures to decode community behavior or convey qualified cell sorting decisions for subsequent high-resolution sequencing or proteomic routines.
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11
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Zemb O, Achard CS, Hamelin J, De Almeida ML, Gabinaud B, Cauquil L, Verschuren LMG, Godon JJ. Absolute quantitation of microbes using 16S rRNA gene metabarcoding: A rapid normalization of relative abundances by quantitative PCR targeting a 16S rRNA gene spike-in standard. Microbiologyopen 2020; 9:e977. [PMID: 31927795 PMCID: PMC7066463 DOI: 10.1002/mbo3.977] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2019] [Revised: 11/15/2019] [Accepted: 11/15/2019] [Indexed: 12/14/2022] Open
Abstract
Metabarcoding of the 16S rRNA gene is commonly used to characterize microbial communities, by estimating the relative abundance of microbes. Here, we present a method to retrieve the concentrations of the 16S rRNA gene per gram of any environmental sample using a synthetic standard in minuscule amounts (100 ppm to 1% of the 16S rRNA sequences) that is added to the sample before DNA extraction and quantified by two quantitative polymerase chain reaction (qPCR) reactions. This allows normalizing by the initial microbial density, taking into account the DNA recovery yield. We quantified the internal standard and the total load of 16S rRNA genes by qPCR. The qPCR for the latter uses the exact same primers as those used for Illumina sequencing of the V3‐V4 hypervariable regions of the 16S rRNA gene to increase accuracy. We are able to calculate the absolute concentration of the species per gram of sample, taking into account the DNA recovery yield. This is crucial for an accurate estimate as the yield varied between 40% and 84%. This method avoids sacrificing a high proportion of the sequencing effort to quantify the internal standard. If sacrificing a part of the sequencing effort to the internal standard is acceptable, we however recommend that the internal standard accounts for 30% of the environmental 16S rRNA genes to avoid the PCR bias associated with rare phylotypes. The method proposed here was tested on a feces sample but can be applied more broadly on any environmental sample. This method offers a real improvement of metabarcoding of microbial communities since it makes the method quantitative with limited efforts.
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Affiliation(s)
- Olivier Zemb
- GenPhySE, Université de Toulouse, INRA, INPT, ENVT, Castanet Tolosan, France
| | | | | | | | - Béatrice Gabinaud
- GenPhySE, Université de Toulouse, INRA, INPT, ENVT, Castanet Tolosan, France
| | - Laurent Cauquil
- GenPhySE, Université de Toulouse, INRA, INPT, ENVT, Castanet Tolosan, France
| | - Lisanne M G Verschuren
- Topigs Norsvin Research Center B.V., Beuningen, The Netherlands.,Wageningen UR, Livestock Research, Wageningen, The Netherlands.,Agrocampus Ouest, Saint-Gilles, France
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12
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Rodríguez A, Guillemyn B, Coucke P, Vaneechoutte M. Nucleic acids enrichment of fungal pathogens to study host-pathogen interactions. Sci Rep 2019; 9:18037. [PMID: 31792282 PMCID: PMC6889467 DOI: 10.1038/s41598-019-54608-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2019] [Accepted: 11/15/2019] [Indexed: 12/11/2022] Open
Abstract
Fungal infections, ranging from superficial to life-threatening infections, represent a major public health problem that affects 25% of the worldwide population. In this context, the study of host-pathogen interactions within the host is crucial to advance antifungal therapy. However, since fungal cells are usually outnumbered by host cells, the fungal transcriptome frequently remains uncovered. We compared three different methods to selectively lyse human cells from in vitro mixes, composed of Candida cells and peripheral blood mononuclear cells. In order to prevent transcriptional modification, the mixes were stored in RNAlater. We evaluated the enrichment of fungal cells through cell counting using microscopy and aimed to further enrich fungal nucleic acids by centrifugation and by reducing contaminant nucleic acids from the host. We verified the enrichment of fungal DNA and RNA through qPCR and RT-qPCR respectively and confirmed that the resulting RNA has high integrity scores, suitable for downstream applications. The enrichment method provided here, i.e., lysis with Buffer RLT followed by centrifugation, may contribute to increase the proportion of nucleic acids from fungi in clinical samples, thus promoting more comprehensive analysis of fungal transcriptional profiles. Although we focused on C. albicans, the enrichment may be applicable to other fungal pathogens.
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Affiliation(s)
- Antonio Rodríguez
- Laboratory Bacteriology Research, Department of Diagnostic Sciences, Faculty of Medicine and Health Sciences, Ghent University, Ghent, 9000, Belgium.
| | - Brecht Guillemyn
- Center for Medical Genetics Ghent, Ghent University Hospital, Department of Biomolecular Medicine, Ghent, 9000, Belgium
| | - Paul Coucke
- Center for Medical Genetics Ghent, Ghent University Hospital, Department of Biomolecular Medicine, Ghent, 9000, Belgium
| | - Mario Vaneechoutte
- Laboratory Bacteriology Research, Department of Diagnostic Sciences, Faculty of Medicine and Health Sciences, Ghent University, Ghent, 9000, Belgium
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13
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Lowenthal MS, Quittman E, Phinney KW. Absolute Quantification of RNA or DNA Using Acid Hydrolysis and Mass Spectrometry. Anal Chem 2019; 91:14569-14576. [PMID: 31638773 DOI: 10.1021/acs.analchem.9b03625] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Accurate, traceable quantification of ribonucleotide or deoxyribonucleotide oligomers is achievable using acid hydrolysis and isotope dilution mass spectrometry (ID-MS). In this work, formic acid hydrolysis is demonstrated to generate stoichiometric release of nucleobases from intact oligonucleotides, which then can be measured by ID-MS, facilitating true and precise absolute quantification of RNA, short linearized DNA, or genomic DNA. Surrogate nucleobases are quantified with a liquid chromatography-tandem mass spectrometry (LC-MS/MS) workflow, using multiple reaction monitoring (MRM). Nucleobases were chromatographically resolved using a novel cation-exchange separation, incorporating a pH gradient. Trueness of this quantitative assay is estimated from agreement among the surrogate nucleobases and by comparison to concentrations provided for commercial materials or Standard Reference Materials (SRMs) from the National Institute of Standards and Technology (NIST). Comparable concentration estimates using NanoDrop spectrophotometry or established from droplet-digital polymerase chain reaction (ddPCR) techniques agree well with the results. Acid hydrolysis-ID-LC-MS/MS provides excellent quantitative selectivity and accuracy while enabling traceability to mass unit. Additionally, this approach can be uniquely useful for quantifying modified nucleobases or mixtures.
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Affiliation(s)
- Mark S Lowenthal
- Biomolecular Measurement Division , National Institute of Standards and Technology , 100 Bureau Drive, Stop 8314 , Gaithersburg , Maryland 20899 , United States
| | - Eva Quittman
- Biomolecular Measurement Division , National Institute of Standards and Technology , 100 Bureau Drive, Stop 8314 , Gaithersburg , Maryland 20899 , United States
| | - Karen W Phinney
- Biomolecular Measurement Division , National Institute of Standards and Technology , 100 Bureau Drive, Stop 8314 , Gaithersburg , Maryland 20899 , United States
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14
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Lin L, Agyemang K, Abdel‐Samie MA, Cui H. Antibacterial mechanism of
Tetrapleura tetraptera
extract against
Escherichia coli
and
Staphylococcus aureus
and its application in pork. J Food Saf 2019. [DOI: 10.1111/jfs.12693] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Lin Lin
- School of Food and Biological EngineeringJiangsu University Zhenjiang China
| | - Kwabena Agyemang
- School of Food and Biological EngineeringJiangsu University Zhenjiang China
| | | | - Haiying Cui
- School of Food and Biological EngineeringJiangsu University Zhenjiang China
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15
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Yin H, Lin Y, Lin C, Tsai W, Wen H. Rapid and sensitive detection ofStaphylococcus aureusin processed foods using a field‐deployed device to perform an insulated isothermal polymerase chain reaction‐based assay. J Food Saf 2019. [DOI: 10.1111/jfs.12690] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Hsin‐Yi Yin
- Department of Food Science and BiotechnologyNational Chung Hsing University Taichung Taiwan, ROC
| | - Yu‐Yi Lin
- Department of Food Science and BiotechnologyNational Chung Hsing University Taichung Taiwan, ROC
| | | | - Wen‐Che Tsai
- Department of Food Science and BiotechnologyNational Chung Hsing University Taichung Taiwan, ROC
| | - Hsiao‐Wei Wen
- Department of Food Science and BiotechnologyNational Chung Hsing University Taichung Taiwan, ROC
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16
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de Bruin OM, Chiefari A, Wroblewski D, Egan C, Kelly-Cirino CD. A novel chemical lysis method for maximum release of DNA from difficult-to-lyse bacteria. Microb Pathog 2018; 126:292-297. [PMID: 30414838 DOI: 10.1016/j.micpath.2018.11.008] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2017] [Revised: 11/02/2018] [Accepted: 11/05/2018] [Indexed: 10/27/2022]
Abstract
Molecular detection of microorganisms requires releasing DNA from cells. However, since certain microbial organisms are refractory to lysis by chemical or enzymatic methods, mechanical lysis by bead-beating is typically employed to disrupt difficult-to-lyse microbes. A newly developed chemical lysis method called sporeLYSE enables release of DNA from difficult-to-lyse microbes without bead-beating. The sporeLYSE method was compared to bead-beating and an alkaline/detergent lysis solution for releasing DNA from microbes grown in vitro, including surrogates of Category A bioterrorism agents. sporeLYSE released 83% to 100% of DNA from Mycobacterium smegmatis, Francisella philomiragia, Yersinia enterocolitica, Bacillus thuringiensis, Pseudomonas aeruginosa, Moraxella catarrhalis and Klebsiella pneumoniae. qPCR results indicated that sporeLYSE extracted an equal or greater amount of DNA than either bead-beating or alkaline/detergent lysis from Gram-positive and Gram-negative bacteria. When sporeLYSE was used to extract DNA from saliva and sputum spiked with M. smegmatis and M. tuberculosis, respectively, the qPCR Ct values were 4-8 cycles lower than those for extractions via alkaline/detergent lysis and heat. Mean Ct values for sporesLYSE extractions from spores of Clostridium difficile and C. botulinum were approximately two cycles lower than those of MagNA Pure DNA extractions. Our results suggest that sporeLYSE is an easy-to-use liquid reagent that can efficiently release large amounts of DNA from a variety of bacteria, including spores.
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Affiliation(s)
- Olle M de Bruin
- DNA Genotek Inc., 3000 - 500 Palladium Drive, Ottawa, ON, K2V 1C2, Canada.
| | - Amy Chiefari
- Wadsworth Center, New York State Department of Health, 120 New Scotland Avenue, Albany, NY, 12208, USA
| | - Danielle Wroblewski
- Wadsworth Center, New York State Department of Health, 120 New Scotland Avenue, Albany, NY, 12208, USA
| | - Christina Egan
- Wadsworth Center, New York State Department of Health, 120 New Scotland Avenue, Albany, NY, 12208, USA
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17
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Quigley CTC, Morrison HG, Mendonça IR, Brawley SH. A common garden experiment with Porphyra umbilicalis (Rhodophyta) evaluates methods to study spatial differences in the macroalgal microbiome. JOURNAL OF PHYCOLOGY 2018; 54:653-664. [PMID: 29981525 DOI: 10.1111/jpy.12763] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2018] [Accepted: 06/27/2018] [Indexed: 06/08/2023]
Abstract
While macroalgal microbiomes are the focus of many recent studies, there is little information about microbial spatial diversity across the thallus. Reliance on field material makes it difficult to discern whether recovered microbiomes belong to the host or its epiphytes, and technical comparisons of macroalgal samples for microbial studies are needed. Here, we use a common garden approach that avoids the problem of epiphytes, particularly at holdfasts, to examine the microbiome of Porphyra umbilicalis (strain Pum1). We used the V6 hypervariable region of the 16S rDNA with Illumina HiSeq sequencing and developed PNA clamps to block recovery of organelle V6 sequences. The common garden approach allowed us to determine differences in the microbiome at the holdfast versus blade margin. We found a notable increase in the relative abundance of Planctomycetes and Alphaproteobacteria at the holdfast, particularly of the possible symbiont Sulfitobacter sp. Nonadjacent 1.5 cm2 samples of blade margin had microbiomes that were not statistically different. The most abundant phylum in the overall microbiome was Proteobacteria, followed by Bacteroidetes. Because phycologists often work in remote sites, we compared three stabilization and preparation techniques and found silica gel desiccation/bead-beating and flash-freezing/lyophilization/bead-beating to be interchangeable. Core taxa (≥0.1% of sequences) across treatments were similar and accounted for ≥95% of all sequences. Finally, statistical conclusions for all comparisons were the same, regardless of which microbial community analysis tool was used: mothur or minimum entropy decomposition.
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Affiliation(s)
- Charlotte T C Quigley
- School of Marine Sciences, University of Maine, 5735 Hitchner Hall, Orono, Maine, 04469-5735, USA
| | - Hilary G Morrison
- Josephine Bay Paul Center for Comparative Molecular Biology and Evolution, Marine Biological Laboratory, Woods Hole, Massachusetts, 02543, USA
| | - Inara R Mendonça
- School of Marine Sciences, University of Maine, 5735 Hitchner Hall, Orono, Maine, 04469-5735, USA
| | - Susan H Brawley
- School of Marine Sciences, University of Maine, 5735 Hitchner Hall, Orono, Maine, 04469-5735, USA
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18
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Durie D, Yeh E, McIntosh N, Fisher L, Bulman DE, Birnboim HC, Chakraborty P, Al-Dirbashi OY. Quantification of DNA in Neonatal Dried Blood Spots by Adenine Tandem Mass Spectrometry. Anal Chem 2017; 90:801-806. [PMID: 29190072 DOI: 10.1021/acs.analchem.7b03265] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Newborn screening programs have expanded to include molecular-based assays as first-tier tests and the success of these assays depends on the quality and yield of DNA extracted from neonatal dried blood spots (DBS). To meet high throughput and rapid turnaround time requirements, newborn screening laboratories adopted rapid DNA extraction methods that produce crude extracts. Quantification of DNA in neonatal DBS is not routinely performed due to technical challenges; however, this may enhance the performance of assays that are sensitive to amounts of input DNA. In this study, we developed a novel high throughput method to quantify total DNA in DBS. It is based on specific acid-catalyzed depurination of DNA followed by mass spectrometric quantification of adenine. The amount of adenine was used to calculate DNA quantity per 3.2 mm DBS. Reference intervals were established using archived, neonatal DBS (n = 501) and a median of 130.6 ng of DNA per DBS was obtained, which is in agreement with literature values. The intra- and interday variations were <15%. The limits of detection and quantification were 12.5 and 37.8 nmol/L adenine, respectively. We demonstrated that DNA from neonatal DBS can be successfully quantified in high throughput settings using instruments currently deployed in NBS laboratories.
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Affiliation(s)
- Danielle Durie
- Newborn Screening Ontario, Ottawa, Ontario K1H 8L1, Canada
| | - Ed Yeh
- Newborn Screening Ontario, Ottawa, Ontario K1H 8L1, Canada
| | | | | | - Dennis E Bulman
- Newborn Screening Ontario, Ottawa, Ontario K1H 8L1, Canada.,Department of Pediatrics, University of Ottawa , Ottawa, Ontario K1H8M5, Canada.,Ottawa Hospital Research Institute , Ottawa, Ontario K1H 8L6, Canada.,Research Institute, Children's Hospital of Eastern Ontario , Ottawa, Ontario K1H 5B2, Canada
| | | | - Pranesh Chakraborty
- Newborn Screening Ontario, Ottawa, Ontario K1H 8L1, Canada.,Department of Pediatrics, University of Ottawa , Ottawa, Ontario K1H8M5, Canada.,Research Institute, Children's Hospital of Eastern Ontario , Ottawa, Ontario K1H 5B2, Canada
| | - Osama Y Al-Dirbashi
- Newborn Screening Ontario, Ottawa, Ontario K1H 8L1, Canada.,Research Institute, Children's Hospital of Eastern Ontario , Ottawa, Ontario K1H 5B2, Canada.,College of Medicine and Health Sciences, United Arab Emirates University , Al Ain, 17172, United Arab Emirates
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