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Li N, Cai QM, Hu NY, Jiang SL, Chen FQ, Hu QQ, Yang F, He CZ. Pyrosequencing analysis of bacterial community changes in dental unit waterlines after chlorogenic acid treatment. Front Cell Infect Microbiol 2024; 14:1303099. [PMID: 38299116 PMCID: PMC10828043 DOI: 10.3389/fcimb.2024.1303099] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2023] [Accepted: 01/02/2024] [Indexed: 02/02/2024] Open
Abstract
Introduction The contamination of dental unit waterlines (DUWLs) poses a significant risk of cross-infection in dentistry. Although chemical disinfectants have been effective in reducing number of bacteria, they do have limitations. Methods This study aimed to investigate the potential of chlorogenic acid, a natural substance with broadspectrum antibacterial properties, for treating DUWLs. Over a period of three months, we analyzed the microbial communities in 149 DUWLs samples collected from 5 dental units using high-throughput pyrophosphate sequencing. Results The results revealed that chlorogenic acid treatment had a significant impact on the microbial community profile in the DUWLs, with the most significant changes occurring within the first 15 days and stabilization observed in the last 30 days. The predominant genera detected in the samples were Bacteroides, Lactobacillus, Streptococcus, Methylobacterium, and Phreatobacter. Additionally, the relative abundance of certain beneficial bacteria, such as Alloprevotella, Roseburia, and Blautia, increased, while the presence of opportunistic pathogens like Mycobacteria significantly decreased. The functional prediction analysis using the KEGG database indicated a decrease in the pathogenicity of the bacterial community in the DUWLs following chlorogenic acid treatment. Discussion This study introduces a novel approach for the prevention and treatment of infections associated with dental care.
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Affiliation(s)
- Na Li
- Department of Stomatology, The First Affiliated Hospital, Jiangxi Medical College, Nanchang University, Nanchang, China
- Nursing School, Nanchang University, Nanchang, China
| | - Qin-Ming Cai
- The First Affiliated Hospital of Nanchang University, School of Public Health, Nanchang University, Nanchang, China
- The Second School of Clinical Medicine, Southern Medical University, Guangzhou, China
| | - Ni-Ya Hu
- The First Affiliated Hospital of Nanchang University, School of Public Health, Nanchang University, Nanchang, China
| | - Shu-ling Jiang
- Department of Stomatology, The First Affiliated Hospital, Jiangxi Medical College, Nanchang University, Nanchang, China
- Nursing School, Nanchang University, Nanchang, China
| | - Fu-Qing Chen
- Department of Stomatology, The First Affiliated Hospital, Jiangxi Medical College, Nanchang University, Nanchang, China
| | - Qiao-Qiao Hu
- Department of Stomatology, The First Affiliated Hospital, Jiangxi Medical College, Nanchang University, Nanchang, China
| | - Fen Yang
- Department of Stomatology, The First Affiliated Hospital, Jiangxi Medical College, Nanchang University, Nanchang, China
| | - Chao-Zhu He
- Nursing School, Nanchang University, Nanchang, China
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Deng X, Zhao X, Liang Y, Zhang L, Jiang J, Zhao G, Zhou Y. Modification of the genome topology network and its application to the comparison of group B Streptococcus genomes. BMC Genomics 2019; 20:886. [PMID: 31752672 PMCID: PMC6868693 DOI: 10.1186/s12864-019-6234-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2019] [Accepted: 10/28/2019] [Indexed: 11/30/2022] Open
Abstract
Background The genome topology network (GTN) is a new approach for studying the phylogenetics of bacterial genomes by analysing their gene order. The previous GTN tool gives a phylogenetic tree and calculate the different degrees (DD) of various adjacent gene families with complete genome data, but it is limited to the gene family level. Result In this study, we collected 51 published complete and draft group B Streptococcus (GBS) genomes from the NCBI database as the case study data. The phylogenetic tree obtained from the GTN method assigned the genomes into six main clades. Compared with single nucleotide polymorphism (SNP)-based method, the GTN method exhibited a higher resolution in two clades. The gene families located at unique node connections in these clades were associated with the clusters of orthologous groups (COG) functional categories of “[G] Carbohydrate transport and metabolism,”, “[L] Replication, recombination, and repair” and “[J] translation, ribosomal structure and biogenesis”. Thus, these genes were the major factors affecting the differentiation of these six clades in the phylogenetic tree obtained from the GTN. Conclusion The modified GTN analyzes draft genomic data and exhibits greater functionality than the previous version. The gene family clustering algorithm embedded in the GTN tool is optimized by introducing the Markov cluster algorithm (MCL) tool to assign genes to functional gene families. A bootstrap test is performed to verify the credibility of the clades when allowing users to adjust the relationships of the clades accordingly. The GTN tool gives additional evolutionary information that is a useful complement to the SNP-based method. Information on the differences in the connections between a gene and its adjacent genes in species or clades is easily obtained. The modified GTN tool can be downloaded from https://github.com/0232/Genome_topology_network
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Affiliation(s)
- Xiao Deng
- Institutes of Biology and Medical Sciences, Medical College of Soochow University, Suzhou, 215123, China
| | - Xuechao Zhao
- Institutes of Biology and Medical Sciences, Medical College of Soochow University, Suzhou, 215123, China
| | - Yuan Liang
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, 200433, China
| | - Liang Zhang
- Shanghai-MOST Key Laboratory of Health and Disease Genomics, Chinese National Human Genome Center at Shanghai, Shanghai, 201203, China
| | - Jianping Jiang
- SJTU-Yale Joint Center for Biostatistics, Shanghai Jiaotong University, Shanghai, 200240, China
| | - Guoping Zhao
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, 200433, China.,Shanghai-MOST Key Laboratory of Health and Disease Genomics, Chinese National Human Genome Center at Shanghai, Shanghai, 201203, China
| | - Yan Zhou
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, 200433, China. .,Shanghai-MOST Key Laboratory of Health and Disease Genomics, Chinese National Human Genome Center at Shanghai, Shanghai, 201203, China.
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Ryoo S, Lee J, Oh JY, Kim BK, Kim Y, Kim JH, Shin C, Lee SH. Comparing Two Mycobacterium tuberculosis Genomes from Chinese Immigrants with Native Genomes Using Mauve Alignments. Tuberc Respir Dis (Seoul) 2018; 81:216-221. [PMID: 29926541 PMCID: PMC6030666 DOI: 10.4046/trd.2017.0091] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2017] [Revised: 10/01/2017] [Accepted: 11/01/2017] [Indexed: 01/24/2023] Open
Abstract
BACKGROUND The number of immigrants with tuberculosis (TB) increases each year in South Korea. Determining the transmission dynamics based on whole genome sequencing (WGS) to cluster the strains has been challenging. METHODS WGS, annotation refinement, and orthology assignment for the GenBank accession number acquisition were performed on two clinical isolates from Chinese immigrants. In addition, the genomes of the two isolates were compared with the genomes of Mycobacterium tuberculosis isolates, from two native Korean and five native Chinese individuals using a phylogenetic topology tree based on the Multiple Alignment of Conserved Genomic Sequence with Rearrangements (Mauve) package. RESULTS The newly assigned accession numbers for two clinical isolates were CP020381.2 (a Korean-Chinese from Yanbian Province) and CP022014.1 (a Chinese from Shandong Province), respectively. Mauve alignment classified all nine TB isolates into a discriminative collinear set with matched regions. The phylogenetic analysis revealed a rooted phylogenetic tree grouping the nine strains into two lineages: strains from Chinese individuals and strains from Korean individuals. CONCLUSION Phylogenetic trees based on the Mauve alignments were supposed to be useful in revealing the dynamics of TB transmission from immigrants in South Korea, which can provide valuable information for scaling up the TB screening policy for immigrants.
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Affiliation(s)
- Sungweon Ryoo
- Clinical Research Centre, Masan National Tuberculosis Hospital, Changwon, Korea
| | | | - Jee Youn Oh
- Division of Pulmonary, Sleep, and Critical Care Medicine, Department of Internal Medicine, Korea University Guro Hospital, Korea University College of Medicine, Seoul, Korea
| | - Byeong Ki Kim
- Division of Pulmonary, Sleep, and Critical Care Medicine, Department of Internal Medicine, Korea University Ansan Hospital, Korea University College of Medicine, Ansan, Korea
| | - Young Kim
- Division of Pulmonary, Sleep, and Critical Care Medicine, Department of Internal Medicine, Korea University Ansan Hospital, Korea University College of Medicine, Ansan, Korea
| | - Je Hyeong Kim
- Division of Pulmonary, Sleep, and Critical Care Medicine, Department of Internal Medicine, Korea University Ansan Hospital, Korea University College of Medicine, Ansan, Korea
| | - Chol Shin
- Division of Pulmonary, Sleep, and Critical Care Medicine, Department of Internal Medicine, Korea University Ansan Hospital, Korea University College of Medicine, Ansan, Korea
| | - Seung Heon Lee
- Division of Pulmonary, Sleep, and Critical Care Medicine, Department of Internal Medicine, Korea University Ansan Hospital, Korea University College of Medicine, Ansan, Korea.
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Eckert SE, Chan JZM, Houniet D, The Pathseek Consortium, Breuer J, Speight G. Enrichment by hybridisation of long DNA fragments for Nanopore sequencing. Microb Genom 2016; 2:e000087. [PMID: 28785419 PMCID: PMC5537632 DOI: 10.1099/mgen.0.000087] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2016] [Accepted: 08/26/2016] [Indexed: 12/11/2022] Open
Abstract
Enrichment of DNA by hybridisation is an important tool which enables users to gather target-focused next-generation sequence data in an economical fashion. Current in-solution methods capture short fragments of around 200–300 nt, potentially missing key structural information such as recombination or translocations often found in viral or bacterial pathogens. The increasing use of long-read third-generation sequencers requires methods and protocols to be adapted for their specific requirements. Here, we present a variation of the traditional bait–capture approach which can selectively enrich large fragments of DNA or cDNA from specific bacterial and viral pathogens, for sequencing on long-read sequencers. We enriched cDNA from cultured influenza virus A, human cytomegalovirus (HCMV) and genomic DNA from two strains of Mycobacterium tuberculosis (M. tb) from a background of cell line or spiked human DNA. We sequenced the enriched samples on the Oxford Nanopore MinION™ and the Illumina MiSeq platform and present an evaluation of the method, together with analysis of the sequence data. We found that unenriched influenza A and HCMV samples had no reads matching the target organism due to the high background of DNA from the cell line used to culture the pathogen. In contrast, enriched samples sequenced on the MinION™ platform had 57 % and 99 % best-quality on-target reads respectively.
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Affiliation(s)
- Sabine E Eckert
- 1Oxford Gene Technology, Begbroke Science Park, Begbroke Hill, Woodstock Road, Begbroke, Oxfordshire OX5 1PF, UK
| | - Jackie Z-M Chan
- 1Oxford Gene Technology, Begbroke Science Park, Begbroke Hill, Woodstock Road, Begbroke, Oxfordshire OX5 1PF, UK
| | - Darren Houniet
- 1Oxford Gene Technology, Begbroke Science Park, Begbroke Hill, Woodstock Road, Begbroke, Oxfordshire OX5 1PF, UK
| | | | - Judy Breuer
- 3UCL Division of Infection & Immunity, Cruciform Building, Gower Street, University College London, London WC1E 6BT, UK
| | - Graham Speight
- 1Oxford Gene Technology, Begbroke Science Park, Begbroke Hill, Woodstock Road, Begbroke, Oxfordshire OX5 1PF, UK
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