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Ji XC, Zhou LF, Li CY, Shi YJ, Wu ML, Zhang Y, Fei XF, Zhao G. Reduction of Human DNA Contamination in Clinical Cerebrospinal Fluid Specimens Improves the Sensitivity of Metagenomic Next-Generation Sequencing. J Mol Neurosci 2020; 70:659-666. [PMID: 32002752 DOI: 10.1007/s12031-019-01472-z] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2019] [Accepted: 12/26/2019] [Indexed: 12/25/2022]
Abstract
Metagenomics next-generation sequencing (mNGS) is increasingly available for the detection of obscure infectious diseases of the central nervous system. However, human DNA contamination from elevated white cells, one of the characteristic cerebrospinal fluid (CSF) features in meningitis patients, greatly reduces the sensitivity of mNGS in the pathogen detection. Currently, effective approaches to selectively reduce host DNA contamination from clinical CSF samples are still lacking. In this study, a total of 20 meningitis patients were enrolled, including 10 definitively diagnosed tuberculous meningitis (TBM) and 10 definite cryptococcal meningitis (CM) cases. To evaluate the effect of reduced human DNA in the sensitivity of mNGS detection, three specimen-processing protocols were performed: (i) To remove human DNA, saponin, a nonionic surfactant, was used to selectively lyse white cells in CSF followed by DNase treatment prior to the extraction of DNA; (ii) to reduce host DNA, CSF was centrifuged to remove human cells, and the supernatant was collected for DNA extraction; and (iii) DNA extraction from the unprocessed specimens was set as the control. We found that saponin processing significantly elevated the NGS unique reads for Cryptococcus (P < 0.01) compared with the control but had no effects for Mycobacterium tuberculosis (P > 0.05). However, detection of centrifuged supernatants improved the NGS unique reads for both TBM and CM compared with controls (P < 0.01). Our results demonstrate that the use of mNGS of centrifuged supernatants from clinical CSF samples in patients with TBM and CM is a simple and effective method to improve the sensitivity of pathogen detection.
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MESH Headings
- Adult
- Aged
- Cerebrospinal Fluid/microbiology
- Cryptococcus/genetics
- Cryptococcus/pathogenicity
- Female
- Genome, Bacterial
- Genome, Human
- High-Throughput Nucleotide Sequencing/methods
- High-Throughput Nucleotide Sequencing/standards
- Humans
- Male
- Meningitis, Cryptococcal/cerebrospinal fluid
- Meningitis, Cryptococcal/diagnosis
- Meningitis, Cryptococcal/microbiology
- Metagenomics/methods
- Metagenomics/standards
- Middle Aged
- Molecular Diagnostic Techniques/methods
- Molecular Diagnostic Techniques/standards
- Mycobacterium tuberculosis/genetics
- Mycobacterium tuberculosis/pathogenicity
- Sensitivity and Specificity
- Sequence Analysis, DNA/methods
- Sequence Analysis, DNA/standards
- Tuberculosis, Meningeal/cerebrospinal fluid
- Tuberculosis, Meningeal/diagnosis
- Tuberculosis, Meningeal/microbiology
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Affiliation(s)
- Xin-Chao Ji
- Department of Neurology, Xijing Hospital, Air Force Military Medical University, Xi'an, China
| | - Lin-Fu Zhou
- Department of Neurology, The 987 Hospital of PLA, Baoji, China
| | - Chao-Yang Li
- Department of Neurology, Xijing Hospital, Air Force Military Medical University, Xi'an, China
| | - Ya-Jun Shi
- Department of Neurology, Xijing Hospital, Air Force Military Medical University, Xi'an, China
| | - Meng-Li Wu
- Department of Neurology, Xijing Hospital, Air Force Military Medical University, Xi'an, China
| | - Yun Zhang
- Department of Neurology, Xijing Hospital, Air Force Military Medical University, Xi'an, China
| | - Xiao-Fei Fei
- Department of Neurology, Xijing Hospital, Air Force Military Medical University, Xi'an, China
| | - Gang Zhao
- Department of Neurology, Xijing Hospital, Air Force Military Medical University, Xi'an, China.
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Sean D, Wang YE, Slater GW. Can gel concentration gradients improve two-dimensional DNA displays? Electrophoresis 2014; 35:736-45. [PMID: 24375111 DOI: 10.1002/elps.201300412] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2013] [Revised: 11/11/2013] [Accepted: 12/09/2013] [Indexed: 11/09/2022]
Abstract
The abrupt reduction in gel electrophoretic mobility that is observed when a dsDNA fragment is partially denatured has recently been predicted to exhibit a dependence upon the gel pore size. Using theoretical modeling, we demonstrate that this dependence can be exploited and used to improve the performance of 2D display of DNA. We report experimental evidence of this dependence and propose a new separation system in which a gel porosity gradient is utilized in a way analogous to temperature or denaturant gradients in traditional 2D display. Such gel porosity gradients can also be used in conjunction with denaturant gradients to improve 2D display results. We test these new ideas by modeling the fragment mobilities and computing the final fragment positions to find optimal 2D separation conditions.
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Affiliation(s)
- David Sean
- Department of Physics, University of Ottawa, Ottawa, Ontario, Canada
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3
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Wang S, He J. Separation of fluorescence-labelled terminal restriction fragment DNA on a two-dimensional gel (T-RFs-2D) - an efficient approach for microbial consortium characterization. Environ Microbiol 2011; 13:2565-75. [PMID: 21824243 DOI: 10.1111/j.1462-2920.2011.02527.x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Fingerprinting techniques provide access to understanding the ecology of uncultured microbial consortia. However, the application of current techniques such as terminal restriction fragment length polymorphism (T-RFLP) and denaturing gradient gel electrophoresis (DGGE) has been hindered due to their limitations in characterizing complex microbial communities. This is due to that different populations possibly share the same terminal restriction fragments (T-RFs) and DNA fragments may co-migrate on DGGE gels. To overcome these limitations, a new approach was developed to separate terminal restriction fragments (T-RFs) of 16S rRNA genes on a two-dimensional gel (T-RFs-2D). T-RFs-2D involves restriction digestion of terminal fluorescence-labelled PCR amplified 16S rRNA gene products and their high-resolution separation via a two-dimensional (2D) gel electrophoresis based on the T-RF fragment size (1(st) D) and its sequence composition on the denaturing gradient gel (2(nd) D). The sequence information of interested T-RFs on 2D gels can be obtained through serial poly(A) tailing reaction, PCR amplification and subsequent DNA sequencing. By employing the T-RFs-2D method, bacteria with MspI digested T-RF size of 436 (±1) bp and 514 (±1) bp were identified to be a Lysobacter sp. and a Dehalococcoides sp. in a polychlorinated biphenyl (PCB) dechlorinating culture. With the high resolution of 2D separation, T-RFs-2D separated 63 DNA fragments in a complex river-sediment microbial community, while traditional DGGE detected only 41 DNA fragments in the same sample. In all, T-RFs-2D has its advantage in obtaining sequence information of interested T-RFs and also in characterization of complex microbial communities.
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Affiliation(s)
- Shanquan Wang
- Department of Civil and Environmental Engineering, National University of Singapore, Singapore 117576
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4
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Lindemann E, Rohde B, Rupp S, Regenbogen J, Sohn K. A multidimensional electrophoretic system of separation for the analysis of gene expression (MESSAGE). Electrophoresis 2010; 31:1330-43. [DOI: 10.1002/elps.200900624] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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5
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Abstract
2-D display is a fast and economical way of visualizing polymorphism and comparing genomes, which is based on the separation of DNA fragments in two steps, first according to their size and then to their sequence composition. In this article, we present an exhaustive study of the numerical issues associated with a model aimed at predicting the final absolute locations of DNA fragments in 2-D display experiments. We show that simple expressions for the mobility of DNA fragments in both dimensions allow one to reproduce experimental final absolute locations better than experimental uncertainties. However, our simulations also point out that the results of 2-D display experiments are not sufficient to determine the best set of parameters for the modeling of fragments separation in the second dimension and that additional detailed measurements of the mobility of a few sequences are necessary to achieve this goal. We hope that this work will help in establishing simulations as a powerful tool to optimize experimental conditions without having to perform a large number of preliminary experiments and to estimate whether 2-D DNA display is suited to identify a mutation or a genetic difference that is expected to exist between the genomes of closely related organisms.
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Affiliation(s)
- Ana-Maria Florescu
- Laboratoire de Spectrométrie Physique, Université Joseph Fourier Grenoble 1, St. Martin d'Hères, France
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Mercier JF, Kingsburry C, Slater GW, Lafay B. Quantitative predictions for DNA two-dimensional display according to size and nucleotide sequence composition. Electrophoresis 2008; 29:1264-72. [DOI: 10.1002/elps.200700407] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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7
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Jones CM, Thies JE. Soil microbial community analysis using two-dimensional polyacrylamide gel electrophoresis of the bacterial ribosomal internal transcribed spacer regions. J Microbiol Methods 2007; 69:256-67. [PMID: 17343936 DOI: 10.1016/j.mimet.2006.12.024] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2006] [Revised: 12/31/2006] [Accepted: 12/31/2006] [Indexed: 10/23/2022]
Abstract
Two-dimensional polyacrylamide gel electrophoresis (2D-PAGE) of digested genomic DNA has been previously used in comparative genomics studies of closely related bacteria species. However, a two-dimensional gel electrophoresis approach for examining microbial community structures in environmental samples has not yet been developed. We determined that it is theoretically possible to separate internal transcribed spacer regions (ITS) of bacterial communities into hundreds of operational taxonomic units (OTUs) using 2D-PAGE. Application of 2D-PAGE for separating Bacterial ITS sequences that have been PCR-amplified from replicate soil samples taken from along a Zn gradient resulted in reproducible gels containing hundreds of spots. Clear differences in spot patterns were observed between soil samples that differed in both sampling location and Zn content. The number of OTUs detected using 2D-PAGE of ITS regions was much greater than that observed using Automated Ribosomal Internal Transcribed Spacer Analysis (ARISA), Terminal Restriction Fragment Length Polymorphism (T-RFLP), or Denaturing Gradient Gel Electrophoresis (DGGE). Principal Component Analysis (PCA) of community spot patterns resulted in similar groupings of samples as those obtained using other molecular methods, however, excised spots were found to contain a far lower diversity of different sequences than excised ITS bands of the same length, as determined by RFLP analysis of excision clone libraries and subsequent sequencing of DNA eluted from excised spots. This increase in resolution makes 2D-PAGE of Bacteria ITS fragments from complex microbial communities a viable method for detecting differences between highly similar communities, as well as in streamlining follow-on sequencing efforts by reducing the level of homoplasy (co-migration of heterogeneous sequences) often seen in band-based community fingerprinting methods.
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Affiliation(s)
- C M Jones
- Department of Crop and Soil Sciences, Cornell University, Ithaca, NY 14853, USA
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Malloff C, Dullaghan E, Li A, Stokes R, Fernandez R, Lam W. Two-dimensional DNA displays for comparisons of bacterial genomes. Biol Proced Online 2003; 5:143-152. [PMID: 14569612 PMCID: PMC162171 DOI: 10.1251/bpo56] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2003] [Revised: 04/04/2003] [Accepted: 04/01/2003] [Indexed: 11/23/2022] Open
Abstract
We have developed two whole genome-scanning techniques to aid in the discovery of polymorphisms as well as horizontally acquired genes in prokaryotic organisms. First, two-dimensional bacterial genomic display (2DBGD) was developed using restriction enzyme fragmentation to separate genomic DNA based on size, and then employing denaturing gradient gel electrophoresis (DGGE) in the second dimension to exploit differences in sequence composition. This technique was used to generate high-resolution displays that enable the direct comparison of > 800 genomic fragments simultaneously and can be adapted for the high-throughput comparison of bacterial genomes. 2DBGDs are capable of detecting acquired and altered DNA, however, only in very closely related strains. If used to compare more distantly related strains (e.g. different species within a genus) numerous small changes (i.e. small deletions and point mutations) unrelated to the interesting phenotype, would encumber the comparison of 2DBGDs. For this reason a second method, bacterial comparative genomic hybridization (BCGH), was developed to directly compare bacterial genomes to identify gain or loss of genomic DNA. BCGH relies on performing 2DBGD on a pooled sample of genomic DNA from 2 strains to be compared and subsequently hybridizing the resulting 2DBGD blot separately with DNA from each individual strain. Unique spots (hybridization signals) represent foreign DNA. The identification of novel DNA is easily achieved by excising the DNA from a dried gel followed by subsequent cloning and sequencing. 2DBGD and BCGH thus represent novel high resolution genome scanning techniques for directly identifying altered and/or acquired DNA.
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Affiliation(s)
- Chad Malloff
- Departments of Pathology and Laboratory Medicine
- British Columbia Cancer Research Center, Vancouver, B.C. Canada
| | - Edie Dullaghan
- Pediatrics
- The Division of Infectious and Immunological Diseases, British Columbia's Children's Hospital
| | - Alice Li
- Departments of Pathology and Laboratory Medicine
- The Division of Infectious and Immunological Diseases, British Columbia's Children's Hospital
| | - Richard Stokes
- Departments of Pathology and Laboratory Medicine
- Pediatrics
- Microbiology and Immunology, University of British Columbia
- The Division of Infectious and Immunological Diseases, British Columbia's Children's Hospital
| | | | - Wan Lam
- Departments of Pathology and Laboratory Medicine
- British Columbia Cancer Research Center, Vancouver, B.C. Canada
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9
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Dullaghan EM, Malloff CA, Li AH, Lam WL, Stokes RW. Two-dimensional bacterial genome display: a method for the genomic analysis of mycobacteria. MICROBIOLOGY (READING, ENGLAND) 2002; 148:3111-3117. [PMID: 12368444 DOI: 10.1099/00221287-148-10-3111] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Annually, Mycobacterium tuberculosis is the cause of approximately three million deaths worldwide. It would appear that currently available therapies for this disease are inadequate. The identification of genes involved in mycobacterial virulence will facilitate the design of new prophylactic and therapeutic interventions. A method for high-resolution comparison of bacterial genomes has been developed to facilitate the identification of genes possibly involved in the virulence of clinically relevant mycobacteria. This 'two-dimensional bacterial genome display' (2DBGD) method utilizes two-dimensional DNA electrophoresis to separate, on the basis of size and G+C content, genomic fragments generated with different restriction endonucleases. The use of this method to identify genomic differences between species, strains and, most importantly, isogenic mutants of mycobacteria is reported. That 2DBGD can be used to identify differences resulting from either insertional mutagenesis using a gentamicin-resistance gene or from a frameshift mutation is demonstrated.
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Affiliation(s)
- Edith M Dullaghan
- The Division of Infectious and Immunological Diseases, British Columbia's Children's Hospital1, and Departments of Paediatrics2 and Pathology & Laboratory Medicine3, University of British Columbia, Vancouver, BC, Canada
| | - Chad A Malloff
- British Columbia Cancer Research Center, 601 West 10th Avenue, Vancouver, BC, V5Z 1L3, Canada4
- The Division of Infectious and Immunological Diseases, British Columbia's Children's Hospital1, and Departments of Paediatrics2 and Pathology & Laboratory Medicine3, University of British Columbia, Vancouver, BC, Canada
| | - Alice H Li
- The Division of Infectious and Immunological Diseases, British Columbia's Children's Hospital1, and Departments of Paediatrics2 and Pathology & Laboratory Medicine3, University of British Columbia, Vancouver, BC, Canada
| | - Wan L Lam
- British Columbia Cancer Research Center, 601 West 10th Avenue, Vancouver, BC, V5Z 1L3, Canada4
- The Division of Infectious and Immunological Diseases, British Columbia's Children's Hospital1, and Departments of Paediatrics2 and Pathology & Laboratory Medicine3, University of British Columbia, Vancouver, BC, Canada
| | - Richard W Stokes
- The Division of Infectious and Immunological Diseases, British Columbia's Children's Hospital1, and Departments of Paediatrics2 and Pathology & Laboratory Medicine3, University of British Columbia, Vancouver, BC, Canada
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