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Nafea AM, Wang Y, Wang D, Salama AM, Aziz MA, Xu S, Tong Y. Application of next-generation sequencing to identify different pathogens. Front Microbiol 2024; 14:1329330. [PMID: 38348304 PMCID: PMC10859930 DOI: 10.3389/fmicb.2023.1329330] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2023] [Accepted: 12/18/2023] [Indexed: 02/15/2024] Open
Abstract
Early and precise detection and identification of various pathogens are essential for epidemiological monitoring, disease management, and reducing the prevalence of clinical infectious diseases. Traditional pathogen detection techniques, which include mass spectrometry, biochemical tests, molecular testing, and culture-based methods, are limited in application and are time-consuming. Next generation sequencing (NGS) has emerged as an essential technology for identifying pathogens. NGS is a cutting-edge sequencing method with high throughput that can create massive volumes of sequences with a broad application prospects in the field of pathogen identification and diagnosis. In this review, we introduce NGS technology in detail, summarizes the application of NGS in that identification of different pathogens, including bacteria, fungi, and viruses, and analyze the challenges and outlook for using NGS to identify clinical pathogens. Thus, this work provides a theoretical basis for NGS studies and provides evidence to support the application of NGS in distinguishing various clinical pathogens.
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Affiliation(s)
- Aljuboori M. Nafea
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, China
- College of Medicine, Department of Microbiology, Ibn Sina University of Medical and Pharmaceutical Science, Baghdad, Iraq
| | - Yuer Wang
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, China
| | - Duanyang Wang
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, China
| | - Ahmed M. Salama
- State Key Laboratory of Chemical Resource Engineering, Beijing University of Chemical Technology, Beijing, China
- Medical Laboratory at Sharkia Health Directorate, Ministry of Health, Sharkia, Egypt
| | - Manal A. Aziz
- College of Medicine, Department of Microbiology, Ibn Sina University of Medical and Pharmaceutical Science, Baghdad, Iraq
| | - Shan Xu
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, China
| | - Yigang Tong
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, China
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Optimization of specific multiplex DNA primers to detect variable CLU genomic lesions in patients with Alzheimer’s disease. BIOCHIP JOURNAL 2015. [DOI: 10.1007/s13206-015-9306-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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Midtvedt T, Zabarovsky E, Norin E, Bark J, Gizatullin R, Kashuba V, Ljungqvist O, Zabarovska V, Möllby R, Ernberg I. Increase of faecal tryptic activity relates to changes in the intestinal microbiome: analysis of Crohn's disease with a multidisciplinary platform. PLoS One 2013; 8:e66074. [PMID: 23840402 PMCID: PMC3688706 DOI: 10.1371/journal.pone.0066074] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2013] [Accepted: 04/30/2013] [Indexed: 12/13/2022] Open
Abstract
Objective To investigate—by molecular, classical and functional methods—the microbiota in biopsies and faeces from patients with active Crohn's disease (CD) and controls. Design The microbiota in biopsies was investigated utilizing a novel molecular method and classical cultivation technology. Faecal samples were investigated by classical technology and four functional methods, reflecting alterations in short chain fatty acids pattern, conversion of cholesterol and bilirubin and inactivation of trypsin. Results By molecular methods we found more than 92% similarity in the microbiota on the biopsies from the two groups. However, 4.6% of microbes found in controls were lacking in CD patients. Furthermore, NotI representation libraries demonstrate two different clusters representing CD patients and controls, respectively. Utilizing conventional technology, Bacteroides (alt. Parabacteroides) was less frequently detected in the biopsies from CD patients than from controls. A similar reduction in the number of Bacteroides was found in faecal samples. Bacteroides is the only group of bacteria known to be able to inactivate pancreatic trypsin. Faecal tryptic activity was high in CD patients, and inversely correlated to the levels of Bacteroides. Conclusions CD patients have compositional and functional alterations in their intestinal microbiota, in line with the global description hypothesis rather than the candidate microorganism theory. The most striking functional difference was high amount of faecal tryptic activity in CD patients, inversely correlated to the levels of Bacteroides in faeces.
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Affiliation(s)
- Tore Midtvedt
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Eugene Zabarovsky
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Elisabeth Norin
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Johan Bark
- Inflammatory Bowel Disease (IBD) Unit, Stockholm Gastro Center, Sophiahemmet Hospital, Stockholm, Sweden
| | - Rinat Gizatullin
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Vladimir Kashuba
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Olle Ljungqvist
- Department of Surgery, Örebro University Hospital, Örebro, Sweden
| | - Veronika Zabarovska
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Roland Möllby
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Ingemar Ernberg
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
- * E-mail:
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Haraldson K, Kashuba VI, Dmitriev AA, Senchenko VN, Kudryavtseva AV, Pavlova TV, Braga EA, Pronina IV, Kondratov AG, Rynditch AV, Lerman MI, Zabarovsky ER. LRRC3B gene is frequently epigenetically inactivated in several epithelial malignancies and inhibits cell growth and replication. Biochimie 2012; 94:1151-7. [PMID: 22321817 DOI: 10.1016/j.biochi.2012.01.019] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2011] [Accepted: 01/26/2012] [Indexed: 12/11/2022]
Abstract
Chromosome 3 specific NotI microarrays containing 180 NotI linking clones associated with 188 genes were hybridized to NotI representation probes prepared using matched tumor/normal samples from major epithelial cancers: breast (47 pairs), lung (40 pairs) cervical (43 pairs), kidney (34 pairs of clear cell renal cell carcinoma), colon (24 pairs), ovarian (25 pairs) and prostate (18 pairs). In all tested primary tumors (compared to normal controls) methylation and/or deletions was found. For the first time we showed that the gene LRRC3B was frequently methylated and/or deleted in breast carcinoma - 32% of samples, cervical - 35%, lung - 40%, renal - 35%, ovarian - 28%, colon - 33% and prostate cancer - 44%. To check these results bisulfite sequencing using cloned PCR products with representative two breast, one cervical, two renal, two ovarian and two colon cancer samples was performed. In all cases methylation was confirmed. Expression analysis using RT-qPCR showed that LRRC3B is strongly down-regulated at the latest stages of RCC and ovarian cancers. In addition we showed that LRRC3B exhibit strong cell growth inhibiting activity (more than 95%) in colony formation experiments in vitro in KRC/Y renal cell carcinoma line. All these data suggest that LRRC3B gene could be involved in the process of carcinogenesis as a tumor suppressor gene.
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Affiliation(s)
- Klas Haraldson
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institute, Stockholm, Sweden
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Kilian A, Wenzl P, Huttner E, Carling J, Xia L, Blois H, Caig V, Heller-Uszynska K, Jaccoud D, Hopper C, Aschenbrenner-Kilian M, Evers M, Peng K, Cayla C, Hok P, Uszynski G. Diversity arrays technology: a generic genome profiling technology on open platforms. Methods Mol Biol 2012; 888:67-89. [PMID: 22665276 DOI: 10.1007/978-1-61779-870-2_5] [Citation(s) in RCA: 401] [Impact Index Per Article: 33.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/25/2023]
Abstract
In the last 20 years, we have observed an exponential growth of the DNA sequence data and simular increase in the volume of DNA polymorphism data generated by numerous molecular marker technologies. Most of the investment, and therefore progress, concentrated on human genome and genomes of selected model species. Diversity Arrays Technology (DArT), developed over a decade ago, was among the first "democratizing" genotyping technologies, as its performance was primarily driven by the level of DNA sequence variation in the species rather than by the level of financial investment. DArT also proved more robust to genome size and ploidy-level differences among approximately 60 organisms for which DArT was developed to date compared to other high-throughput genotyping technologies. The success of DArT in a number of organisms, including a wide range of "orphan crops," can be attributed to the simplicity of underlying concepts: DArT combines genome complexity reduction methods enriching for genic regions with a highly parallel assay readout on a number of "open-access" microarray platforms. The quantitative nature of the assay enabled a number of applications in which allelic frequencies can be estimated from DArT arrays. A typical DArT assay tests for polymorphism tens of thousands of genomic loci with the final number of markers reported (hundreds to thousands) reflecting the level of DNA sequence variation in the tested loci. Detailed DArT methods, protocols, and a range of their application examples as well as DArT's evolution path are presented.
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Affiliation(s)
- Andrzej Kilian
- Diversity Arrays Technology Pty Ltd, Yarralumla, Canberra, ACT, Australia.
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Paliy O, Agans R. Application of phylogenetic microarrays to interrogation of human microbiota. FEMS Microbiol Ecol 2011; 79:2-11. [PMID: 22092522 DOI: 10.1111/j.1574-6941.2011.01222.x] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2011] [Revised: 09/09/2011] [Accepted: 09/28/2011] [Indexed: 12/22/2022] Open
Abstract
Human-associated microbiota is recognized to play vital roles in maintaining host health, and it is implicated in many disease states. While the initial surge in the profiling of these microbial communities was achieved with Sanger and next-generation sequencing, many oligonucleotide microarrays have also been developed recently for this purpose. Containing probes complementary to small ribosomal subunit RNA gene sequences of community members, such phylogenetic arrays provide direct quantitative comparisons of microbiota composition among samples and between sample groups. Some of the developed microarrays including PhyloChip, Microbiota Array, and HITChip can simultaneously measure the presence and abundance of hundreds and thousands of phylotypes in a single sample. This review describes the currently available phylogenetic microarrays that can be used to analyze human microbiota, delineates the approaches for the optimization of microarray use, and provides examples of recent findings based on microarray interrogation of human-associated microbial communities.
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Affiliation(s)
- Oleg Paliy
- Department of Biochemistry and Molecular Biology, Wright State University, Dayton, OH 45435, USA.
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SNPs detection by a single-strand specific nuclease on a PNA zip-code microarray. Biosens Bioelectron 2008; 24:1706-11. [PMID: 18930386 DOI: 10.1016/j.bios.2008.08.049] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2008] [Revised: 08/16/2008] [Accepted: 08/29/2008] [Indexed: 11/23/2022]
Abstract
In this report, a reliable peptide nucleic acid (PNA) microarray-based method for accurately detecting single nucleotide polymorphism (SNP) in human genes is described. The technique relies on the mismatched cleavage activity of a single-strand specific (SSS) nuclease. PCR amplification was performed to prepare gene fragments containing the mutation sites. The amplified fragments were then employed as templates for the SSS nuclease reaction using chimeric probes, modified with biotin at the 5' end and extended with a unique anchoring zip-code complement sequence at the 3' end. The SSS nuclease promotes cleavage of heteroduplex DNAs at base mismatched positions to produce crumbled chimeric probes in the presence of imperfectly matching template strands. In contrast, the probes remain intact when they interact with perfectly matched template strands. Only the non-fragmented probes generate fluorescence signals after treatment with streptavidin-Cy3 on the PNA zip-code array. This methodology was used to successfully genotype selected Korean-specific BRCA mutation sites with wild type and mutant samples. The investigation has led to the development of a reliable SSS nuclease-based system for the diagnosis of human genetic mutations or SNPs.
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Girigoswami A, Jung C, Mun HY, Park HG. PCR-free mutation detection of BRCA1 on a zip-code microarray using ligase chain reaction. ACTA ACUST UNITED AC 2008; 70:897-902. [DOI: 10.1016/j.jprot.2008.01.005] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2007] [Revised: 10/07/2007] [Accepted: 01/09/2008] [Indexed: 01/16/2023]
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Sulimova GE, Rakhmanaliev ER, Klimov EA, Kompaniytsev AA, Udina IG, Zabarovsky ER, Kisselev LL. NotI Sequence-Tagged Sites as Markers of Genes on Human Chromosome 3. Mol Biol 2005. [DOI: 10.1007/s11008-005-0075-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Song JY, Park HG, Jung SO, Park J. Diagnosis of HNF-1alpha mutations on a PNA zip-code microarray by single base extension. Nucleic Acids Res 2005; 33:e19. [PMID: 15687377 PMCID: PMC548378 DOI: 10.1093/nar/gni020] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
In the present study, we exploited the superior features of peptide nucleic acids (PNAs) to develop an efficient PNA zip-code microarray for the detection of hepatocyte nuclear factor-1α (HNF-1α) mutations that cause type 3 maturity onset diabetes of the young (MODY). A multi-epoxy linker compound was synthesized and used to achieve an efficient covalent linking of amine-modified PNA to an aminated glass surface. PCR was performed to amplify the genomic regions containing the mutation sites. The PCR products were then employed as templates in a subsequent multiplex single base extension reaction using chimeric primers with 3′ complementarity to the specific mutation site and 5′ complementarity to the respective PNA zip-code sequence on the microarray. The primers were extended by a single base at each corresponding mutation site in the presence of biotin-labeled ddNTPs, and the products were hybridized to the PNA microarray. Compared to the corresponding DNA, the PNA zip-code sequence showed a much higher duplex specificity for the complementary DNA sequence. The PNA zip-code microarray was finally stained with streptavidin-R-phycoerythrin to generate a fluorescent signal. Using this strategy, we were able to correctly diagnose several mutation sites in exon 2 of HNF-1α with a wild-type and mutant samples including a MODY3 patient. This work represents one of the few successful applications of PNA in DNA chip technology.
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Affiliation(s)
| | - Hyun Gyu Park
- To whom correspondence should be addressed. Tel: +82 42869 3932; Fax: +82 42869 3910;
| | - Sung-Ouk Jung
- Samsung Advanced Institute of TechnologySan 14-1, Nongseo-Ri, Kiheung, Kyunggi-Do, 449-712, Republic of Korea
| | - JaeChan Park
- Samsung Advanced Institute of TechnologySan 14-1, Nongseo-Ri, Kiheung, Kyunggi-Do, 449-712, Republic of Korea
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