1
|
Deng QM, Zhang J, Zhang YY, Jia M, Ding DS, Fang YQ, Wang HZ, Gu HC. Diagnosis and treatment of refractory infectious diseases using nanopore sequencing technology: Three case reports. World J Clin Cases 2024; 12:5208-5216. [DOI: 10.12998/wjcc.v12.i22.5208] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/10/2024] [Revised: 05/29/2024] [Accepted: 06/17/2024] [Indexed: 06/30/2024] Open
Abstract
BACKGROUND Infectious diseases are still one of the greatest threats to human health, and the etiology of 20% of cases of clinical fever is unknown; therefore, rapid identification of pathogens is highly important. Traditional culture methods are only able to detect a limited number of pathogens and are time-consuming; serologic detection has window periods, false-positive and false-negative problems; and nucleic acid molecular detection methods can detect several known pathogens only once. Three-generation nanopore sequencing technology provides new options for identifying pathogens.
CASE SUMMARY Case 1: The patient was admitted to the hospital with abdominal pain for three days and cessation of defecation for five days, accompanied by cough and sputum. Nanopore sequencing of the drainage fluid revealed the presence of oral-like bacteria, leading to a clinical diagnosis of bronchopleural fistula. Cefoperazone sodium sulbactam treatment was effective. Case 2: The patient was admitted to the hospital with fever and headache, and CT revealed lung inflammation. Antibiotic treatment for Streptococcus pneumoniae, identified through nanopore sequencing of cerebrospinal fluid, was effective. Case 3: The patient was admitted to our hospital with intermittent fever and an enlarged neck mass that had persisted for more than six months. Despite antibacterial treatment, her symptoms worsened. The nanopore sequencing results indicate that voriconazole treatment is effective for Aspergillus brookii. The patient was diagnosed with mixed cell type classical Hodgkin's lymphoma with infection.
CONCLUSION Three-generation nanopore sequencing technology allows for rapid and accurate detection of pathogens in human infectious diseases.
Collapse
Affiliation(s)
- Qing-Mei Deng
- Science Island Branch, Graduate School of University of Science and Technology of China, Hefei 230031, Anhui Province, China
- Institute of Health and Medical Technology, Hefei Institutes of Physical Science, Chinese Academy of Science, Hefei 230031, Anhui Province, China
- Medical Pathology Center, Hefei Cancer Hospital, Chinese Academy of Sciences, Hefei 230031, Anhui Province, China
| | - Jian Zhang
- Medical Pathology Center, Hefei Cancer Hospital, Chinese Academy of Sciences, Hefei 230031, Anhui Province, China
| | - Yi-Yong Zhang
- Medical Pathology Center, Hefei Cancer Hospital, Chinese Academy of Sciences, Hefei 230031, Anhui Province, China
| | - Min Jia
- Institute of Health and Medical Technology, Hefei Institutes of Physical Science, Chinese Academy of Science, Hefei 230031, Anhui Province, China
- Medical Pathology Center, Hefei Cancer Hospital, Chinese Academy of Sciences, Hefei 230031, Anhui Province, China
| | - Du-Shan Ding
- Medical Pathology Center, Hefei Cancer Hospital, Chinese Academy of Sciences, Hefei 230031, Anhui Province, China
| | - Yu-Qin Fang
- Medical Pathology Center, Hefei Cancer Hospital, Chinese Academy of Sciences, Hefei 230031, Anhui Province, China
| | - Hong-Zhi Wang
- Science Island Branch, Graduate School of University of Science and Technology of China, Hefei 230031, Anhui Province, China
| | - Hong-Cang Gu
- Institute of Health and Medical Technology, Hefei Institutes of Physical Science, Chinese Academy of Science, Hefei 230031, Anhui Province, China
- Medical Pathology Center, Hefei Cancer Hospital, Chinese Academy of Sciences, Hefei 230031, Anhui Province, China
| |
Collapse
|
2
|
Patiño L, Benítez AD, Carrazco-Montalvo A, Regato-Arrata M. Genomics for Arbovirus Surveillance: Considerations for Routine Use in Public Health Laboratories. Viruses 2024; 16:1242. [PMID: 39205216 PMCID: PMC11360194 DOI: 10.3390/v16081242] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2024] [Revised: 07/13/2024] [Accepted: 07/16/2024] [Indexed: 09/04/2024] Open
Abstract
The emergence and re-emergence of arthropod-borne viruses is a public health threat. For routine surveillance in public health laboratories, cost-effective and reproducible methods are essential. In this review, we address the technical considerations of high-throughput sequencing methods (HTS) for arbovirus surveillance in national health laboratories, focusing on pre-sequencing, sequencing, and post-sequencing approaches, underlining the importance of robust wet and dry laboratory workflows for reproducible analysis. We aim to provide insights for researchers and clinicians interested in arbovirus, diagnosis, and surveillance by discussing current advances in sequencing methods and bioinformatics pipelines applied to arboviruses.
Collapse
Affiliation(s)
- Leandro Patiño
- Instituto Nacional de Investigación en Salud Pública “Leopoldo Izquieta Pérez”, Dirección Técnica de Investigación, Desarrollo e Innovación, Guayaquil 090150, Ecuador
- Facultad Ciencias de la Vida, Escuela Superior Politécnica del Litoral, ESPOL, Campus Gustavo Galindo Km. 30.5 Vía Perimetral, Guayaquil 090902, Ecuador
| | - Andrea Denisse Benítez
- Instituto de Microbiología, Universidad San Francisco de Quito USFQ, Quito 170901, Ecuador
| | - Andrés Carrazco-Montalvo
- Instituto Nacional de Investigación en Salud Pública “Leopoldo Izquieta Pérez”, Centro de Referencia Nacional de Genómica, Secuenciación y Bioinformática, Quito 170403, Ecuador;
| | - Mary Regato-Arrata
- Instituto Nacional de Investigación en Salud Pública “Leopoldo Izquieta Pérez”, Centro de Referencia Nacional de Virus Exantemáticos, Gastroentericos y Transmitidos por Vectores, Guayaquil 090150, Ecuador;
| |
Collapse
|
3
|
Si W, Chen J, Zhang Z, Wu G, Zhao J, Sha J. Electroosmotic Sensing of Uncharged Peptides and Differentiating Their Phosphorylated States Using Nanopores. Chemphyschem 2024; 25:e202400281. [PMID: 38686913 DOI: 10.1002/cphc.202400281] [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: 03/18/2024] [Revised: 04/14/2024] [Accepted: 04/29/2024] [Indexed: 05/02/2024]
Abstract
The correct characterization and identification of different kinds of proteins is crucial for the survival and development of living organisms, and proteomics research promotes the analysis and understanding of future genome functions. Nanopore technique has been proved to accurately identify individual nucleotides. However, accurate and rapid protein sequencing is difficult due to the variability of protein structures that contains more than 20 amino acids, and it remains very challenging especially for uncharged peptides as they can not be electrophoretically driven through the nanopore. Graphene nanopores have the advantages of high accuracy, sensitivity and low cost in identifying protein phosphorylation modifications. Here, by using all-atom molecular dynamics simulations, charged graphene nanopores are employed to electroosmotically capture and sense uncharged peptides. By further mimicking AFM manipulation of single molecules, it is also found that the uncharged peptides and their phosphorylated states could also be differentiated by both the ionic current and pulling force signals during their pulling processes through the nanopore with a slow and constant velocity. The results shows ability of using nanopores to detect and discriminate single amino acid and its phosphorylation, which is essential for the future low-cost and high-throughput sequencing of protein residues and their post-translational modifications.
Collapse
Affiliation(s)
- Wei Si
- Jiangsu Key Laboratory for Design and Manufacture of Micro-Nano Biomedical Instruments, School of Mechanical Engineering, Southeast University, Nanjing, 211100, China
| | - Jiayi Chen
- Jiangsu Key Laboratory for Design and Manufacture of Micro-Nano Biomedical Instruments, School of Mechanical Engineering, Southeast University, Nanjing, 211100, China
| | - Zhen Zhang
- Jiangsu Key Laboratory for Design and Manufacture of Micro-Nano Biomedical Instruments, School of Mechanical Engineering, Southeast University, Nanjing, 211100, China
| | - Gensheng Wu
- School of Mechanical and Electronic Engineering, Nanjing Forestry University, Nanjing, 210037, China
| | - Jiajia Zhao
- Department of Pharmacology, Key Laboratory of Neuropsychiatric Diseases, China Pharmaceutical University, Nanjing, 211198, China
| | - Jingjie Sha
- Jiangsu Key Laboratory for Design and Manufacture of Micro-Nano Biomedical Instruments, School of Mechanical Engineering, Southeast University, Nanjing, 211100, China
| |
Collapse
|
4
|
Moreno KMF, de Andrade VA, de Melo Iani FC, Fonseca V, Lima MT, de Castro Barbosa E, Tomé LMR, Guimarães NR, Fritsch HM, Adelino T, Oliveira Fereguetti T, Aspahan MC, Gamarano Barros T, Alcantara LCJ, Giovanetti M. Exploring Microorganisms Associated to Acute Febrile Illness and Severe Neurological Disorders of Unknown Origin: A Nanopore Metagenomics Approach. Genes (Basel) 2024; 15:922. [PMID: 39062701 PMCID: PMC11276239 DOI: 10.3390/genes15070922] [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: 06/18/2024] [Revised: 07/10/2024] [Accepted: 07/12/2024] [Indexed: 07/28/2024] Open
Abstract
Acute febrile illness (AFI) and severe neurological disorders (SNDs) often present diagnostic challenges due to their potential origins from a wide range of infectious agents. Nanopore metagenomics is emerging as a powerful tool for identifying the microorganisms potentially responsible for these undiagnosed clinical cases. In this study, we aim to shed light on the etiological agents underlying AFI and SND cases that conventional diagnostic methods have not been able to fully elucidate. Our approach involved analyzing samples from fourteen hospitalized patients using a comprehensive nanopore metagenomic approach. This process included RNA extraction and enrichment using the SMART-9N protocol, followed by nanopore sequencing. Subsequent steps involved quality control, host DNA/cDNA removal, de novo genome assembly, and taxonomic classification. Our findings in AFI cases revealed a spectrum of disease-associated microbes, including Escherichia coli, Streptococcus sp., Human Immunodeficiency Virus 1 (Subtype B), and Human Pegivirus. Similarly, SND cases revealed the presence of pathogens such as Escherichia coli, Clostridium sp., and Dengue virus type 2 (Genotype-II lineage). This study employed a metagenomic analysis method, demonstrating its efficiency and adaptability in pathogen identification. Our investigation successfully identified pathogens likely associated with AFI and SNDs, underscoring the feasibility of retrieving near-complete genomes from RNA viruses. These findings offer promising prospects for advancing our understanding and control of infectious diseases, by facilitating detailed genomic analysis which is critical for developing targeted interventions and therapeutic strategies.
Collapse
Affiliation(s)
- Keldenn Melo Farias Moreno
- Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte 31270-901, Brazil; (K.M.F.M.); (M.T.L.); (H.M.F.)
| | | | - Felipe Campos de Melo Iani
- Central Public Health Laboratory of the State of Minas Gerais, Ezequiel Dias Foundation, Belo Horizonte 30510-010, Brazil; (F.C.d.M.I.); (T.A.)
| | - Vagner Fonseca
- Department of Exact and Earth Sciences, University of the State of Bahia, Salvador 41150-000, Brazil;
| | - Maurício Teixeira Lima
- Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte 31270-901, Brazil; (K.M.F.M.); (M.T.L.); (H.M.F.)
- René Rachou Institute, Oswaldo Cruz Foundation, Belo Horizonte 30190-002, Brazil; (E.d.C.B.); (L.M.R.T.); (N.R.G.); (L.C.J.A.)
| | - Emerson de Castro Barbosa
- René Rachou Institute, Oswaldo Cruz Foundation, Belo Horizonte 30190-002, Brazil; (E.d.C.B.); (L.M.R.T.); (N.R.G.); (L.C.J.A.)
| | - Luiz Marcelo Ribeiro Tomé
- René Rachou Institute, Oswaldo Cruz Foundation, Belo Horizonte 30190-002, Brazil; (E.d.C.B.); (L.M.R.T.); (N.R.G.); (L.C.J.A.)
| | - Natália Rocha Guimarães
- René Rachou Institute, Oswaldo Cruz Foundation, Belo Horizonte 30190-002, Brazil; (E.d.C.B.); (L.M.R.T.); (N.R.G.); (L.C.J.A.)
| | - Hegger Machado Fritsch
- Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte 31270-901, Brazil; (K.M.F.M.); (M.T.L.); (H.M.F.)
- Morphogenesis and Antigenicity of HIV and Hepatitis Viruses, University of Tours, 37032 Tours, France
| | - Talita Adelino
- Central Public Health Laboratory of the State of Minas Gerais, Ezequiel Dias Foundation, Belo Horizonte 30510-010, Brazil; (F.C.d.M.I.); (T.A.)
| | | | - Maíra Cardoso Aspahan
- Eduardo de Menezes Hospital, Belo Horizonte 30622-020, Brazil; (V.A.d.A.); (T.O.F.); (M.C.A.); (T.G.B.)
| | - Tereza Gamarano Barros
- Eduardo de Menezes Hospital, Belo Horizonte 30622-020, Brazil; (V.A.d.A.); (T.O.F.); (M.C.A.); (T.G.B.)
| | - Luiz Carlos Junior Alcantara
- René Rachou Institute, Oswaldo Cruz Foundation, Belo Horizonte 30190-002, Brazil; (E.d.C.B.); (L.M.R.T.); (N.R.G.); (L.C.J.A.)
| | - Marta Giovanetti
- Department of Sciences and Technologies for Sustainable Development and One Health, Università Campus Bio-Medico di Roma, 00128 Rome, Italy
- Oswaldo Cruz Foundation, Rio de Janeiro 21040-900, Brazil
| |
Collapse
|
5
|
Toxqui-Rodríguez S, Holhorea PG, Naya-Català F, Calduch-Giner JÀ, Sitjà-Bobadilla A, Piazzon C, Pérez-Sánchez J. Differential Reshaping of Skin and Intestinal Microbiota by Stocking Density and Oxygen Availability in Farmed Gilthead Sea Bream ( Sparus aurata): A Behavioral and Network-Based Integrative Approach. Microorganisms 2024; 12:1360. [PMID: 39065128 PMCID: PMC11278760 DOI: 10.3390/microorganisms12071360] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2024] [Revised: 06/21/2024] [Accepted: 06/28/2024] [Indexed: 07/28/2024] Open
Abstract
Fish were kept for six weeks at three different initial stocking densities and water O2 concentrations (low-LD, 8.5 kg/m3 and 95-70% O2 saturation; medium-MD, 17 kg/m3 and 55-75% O2 saturation; high-HD, 25 kg/m3 and 60-45% O2 saturation), with water temperature increasing from 19 °C to 26-27 °C. The improvement in growth performance with the decrease in stocking density was related to changes in skin and intestinal mucosal microbiomes. Changes in microbiome composition were higher in skin, with an increased abundance of Alteromonas and Massilia in HD fish. However, these bacteria genera were mutually exclusive, and Alteromonas abundance was related to a reactive behavior and systemic growth regulation via the liver Gh/Igf system, while Massilia was correlated to a proactive behavior and a growth regulatory transition towards muscle rather than liver. At the intestinal level, microbial abundance showed an opposite trend for two bacteria taxa, rendering in a low abundance of Reyranella and a high abundance of Prauserella in HD fish. This trend was correlated with up-regulated host gene expression, affecting the immune response, epithelial cell turnover, and abiotic stress response. Most of the observed responses are adaptive in nature, and they would serve to infer new welfare indicators for increased stress resilience.
Collapse
Affiliation(s)
- Socorro Toxqui-Rodríguez
- Nutrigenomics and Fish Growth Endocrinology Group, Institute of Aquaculture Torre de la Sal (IATS, CSIC), 12595 Castellón, Spain; (S.T.-R.); (P.G.H.); (F.N.-C.); (J.À.C.-G.)
- Fish Pathology Group, Institute of Aquaculture Torre de la Sal (IATS, CSIC), 12595 Castellón, Spain; (A.S.-B.); (C.P.)
| | - Paul George Holhorea
- Nutrigenomics and Fish Growth Endocrinology Group, Institute of Aquaculture Torre de la Sal (IATS, CSIC), 12595 Castellón, Spain; (S.T.-R.); (P.G.H.); (F.N.-C.); (J.À.C.-G.)
| | - Fernando Naya-Català
- Nutrigenomics and Fish Growth Endocrinology Group, Institute of Aquaculture Torre de la Sal (IATS, CSIC), 12595 Castellón, Spain; (S.T.-R.); (P.G.H.); (F.N.-C.); (J.À.C.-G.)
| | - Josep Àlvar Calduch-Giner
- Nutrigenomics and Fish Growth Endocrinology Group, Institute of Aquaculture Torre de la Sal (IATS, CSIC), 12595 Castellón, Spain; (S.T.-R.); (P.G.H.); (F.N.-C.); (J.À.C.-G.)
| | - Ariadna Sitjà-Bobadilla
- Fish Pathology Group, Institute of Aquaculture Torre de la Sal (IATS, CSIC), 12595 Castellón, Spain; (A.S.-B.); (C.P.)
| | - Carla Piazzon
- Fish Pathology Group, Institute of Aquaculture Torre de la Sal (IATS, CSIC), 12595 Castellón, Spain; (A.S.-B.); (C.P.)
| | - Jaume Pérez-Sánchez
- Nutrigenomics and Fish Growth Endocrinology Group, Institute of Aquaculture Torre de la Sal (IATS, CSIC), 12595 Castellón, Spain; (S.T.-R.); (P.G.H.); (F.N.-C.); (J.À.C.-G.)
| |
Collapse
|
6
|
Ye J, Huang K, Xu Y, Chen N, Tu Y, Huang J, Shao L, Kong W, Zhao D, Xie Y. Clinical application of nanopore-targeted sequencing technology in bronchoalveolar lavage fluid from patients with pulmonary infections. Microbiol Spectr 2024; 12:e0002624. [PMID: 38687074 PMCID: PMC11237526 DOI: 10.1128/spectrum.00026-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2024] [Accepted: 04/13/2024] [Indexed: 05/02/2024] Open
Abstract
The rapid and effective identification of pathogens in patients with pulmonary infections has posed a persistent challenge in medicine, with conventional microbiological tests (CMTs) proving time-consuming and less sensitive, hindering early diagnosis of respiratory infections. While there has been some research on the clinical performance of targeted sequencing technologies, limited focus has been directed toward bronchoalveolar lavage fluid (BALF). This study primarily evaluates the pathogen detection capabilities of nanopore-targeted sequencing (NTS) in BALF, providing a comprehensive analysis. The retrospective study, spanning from January 2022 to November 2023, includes 223 patients exclusively sourced from a single center. We conducted a detailed comparative analysis among NTS, targeted next-generation sequencing (tNGS), and CMTs. Initially, we compared the detection capabilities of NTS and tNGS and found no significant differences in their sensitivity and specificity. Specifically, we observed that the sensitivity of NTS was significantly higher than that of CMTs (74.83% vs 33.11%, P < 0.001). Furthermore, NTS exhibited a higher positivity rate in common pulmonary infections (62.88% vs. 23.48%) and in clinically suspected tuberculosis patients compared to CMTs (87.18% vs. 48.72%). Additionally, NTS showed less susceptibility to antibiotic interference, indicating a more sensitive detection capability, especially in detecting fastidious organisms. It complements GeneXpert in tuberculosis diagnosis and offers excellent advantages in identifying pathogens challenging for CMTs, such as non-tuberculous mycobacteria and viruses. Moreover, NTS significantly shortens the reporting time and is only a quarter of the cost of metagenomic next-generation sequencing. Clearly, NTS can facilitate faster and more cost-effective early diagnosis of respiratory infections.IMPORTANCEThis study holds paramount significance in advancing the field of respiratory infection diagnostics. By assessing the pathogen detection capabilities in bronchoalveolar lavage fluid (BALF) of patients with pulmonary infections, we illuminate the promising potential of nanopore-targeted sequencing (NTS). The findings underscore NTS as a comparable yet distinct alternative to traditional methods like comprehensive conventional microbiological tests (CMTs). Notably, NTS demonstrates a pivotal edge, expanding the spectrum of identified pathogens, particularly excelling in the detection of challenging entities like non-tuberculous mycobacteria and viruses. The study also highlights the complementary role of NTS alongside GeneXpert in the identification of tuberculosis, providing a comprehensive overview of the diagnostic landscape for respiratory infections. This insight carries significant implications for clinicians seeking rapid, cost-effective, and accurate diagnostic tools in the realm of pulmonary infections.
Collapse
Affiliation(s)
- Jiayuan Ye
- Health Science Center, Ningbo University, Ningbo, Zhejiang, China
- Department of Infectious Diseases, Shangyu People’s Hospital Of Shaoxing, Shaoxing, Zhejiang, China
| | - Kai Huang
- Department of General Medicine, The First Affiliated Hospital of Ningbo University, Ningbo, Zhejiang, China
| | - Yaojiang Xu
- Department of Infectious Diseases, Shangyu People’s Hospital Of Shaoxing, Shaoxing, Zhejiang, China
| | - Nan Chen
- Department of Infectious Diseases, Shangyu People’s Hospital Of Shaoxing, Shaoxing, Zhejiang, China
| | - Yifei Tu
- Department of Radiology, Shangyu People’s Hospital Of Shaoxing, Shaoxing, Zhejiang, China
| | - Jing Huang
- Department of Respiratory, Shangyu People’s Hospital Of Shaoxing, Shaoxing, Zhejiang, China
| | - Longfei Shao
- Key Laboratory of Digital Technology in Medical Diagnostics of Zhejiang Province, Dian Diagnostics Group Co., Ltd., Hangzhou, Zhejiang, China
| | - Weiliang Kong
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital of Ningbo University, Ningbo, Zhejiang, China
| | - Dongdong Zhao
- Department of Infectious Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Yilian Xie
- Department of Infectious Diseases, The First Affiliated Hospital of Ningbo University, Ningbo, Zhejiang, China
| |
Collapse
|
7
|
Ota Y, Yasunaga K, Mahazu S, Prah I, Nagai S, Hayashi T, Suzuki M, Yoshida M, Hoshino Y, Akeda Y, Suzuki T, Gu Y, Saito R. Comparative evaluation of analytical pipelines for illumina short- and nanopore long-read 16S rRNA gene amplicon sequencing with mock microbial communities. J Microbiol Methods 2024; 221:106929. [PMID: 38599390 DOI: 10.1016/j.mimet.2024.106929] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2023] [Revised: 04/04/2024] [Accepted: 04/06/2024] [Indexed: 04/12/2024]
Abstract
Utility of a recently developed long-read pipeline, Emu, was assessed using an expectation-maximization algorithm for accurate read classification. We compared it to conventional short- and long-read pipelines, using well-characterized mock bacterial samples. Our findings highlight the necessity of appropriate data-processing for taxonomic descriptions, expanding our understanding of the precise microbiome.
Collapse
Affiliation(s)
- Yusuke Ota
- Department of Molecular Microbiology and Immunology, Tokyo Medical and Dental University, Tokyo, Japan
| | - Kei Yasunaga
- Department of Molecular Microbiology and Immunology, Tokyo Medical and Dental University, Tokyo, Japan
| | - Samiratu Mahazu
- Department of Molecular Microbiology and Immunology, Tokyo Medical and Dental University, Tokyo, Japan; Department of Parasitology and Tropical Medicine, Tokyo Medical and Dental University, Tokyo, Japan
| | - Isaac Prah
- Department of Molecular Microbiology and Immunology, Tokyo Medical and Dental University, Tokyo, Japan
| | - Satoshi Nagai
- Fisheries Technology Institute, Japan Fisheries Research and Education Agency, Kanagawa, Japan
| | - Takaya Hayashi
- Department of Molecular Virology, Tokyo Medical and Dental University, Tokyo, Japan
| | - Masato Suzuki
- Antimicrobial Resistance Research Center, National Institute of Infectious Diseases, Tokyo, Japan
| | - Mitsunori Yoshida
- Department of Mycobacteriology, Leprosy Research Center, National Institute of Infectious Diseases, Tokyo, Japan
| | - Yoshihiko Hoshino
- Department of Mycobacteriology, Leprosy Research Center, National Institute of Infectious Diseases, Tokyo, Japan
| | - Yukihiro Akeda
- Department of Bacteriology I, National Institute of Infectious Diseases, Tokyo, Japan
| | - Toshihiko Suzuki
- Department of Bacterial Pathogenesis, Tokyo Medical and Dental University, Tokyo, Japan
| | - Yoshiaki Gu
- Department of Infectious Diseases, Tokyo Medical and Dental University, Tokyo, Japan
| | - Ryoichi Saito
- Department of Molecular Microbiology and Immunology, Tokyo Medical and Dental University, Tokyo, Japan.
| |
Collapse
|
8
|
Mat-Hussin NH, Siew SW, Maghpor MN, Gan HM, Ahmad HF. Method for detection of pathogenic bacteria from indoor air microbiome samples using high-throughput amplicon sequencing. MethodsX 2024; 12:102636. [PMID: 38439930 PMCID: PMC10909749 DOI: 10.1016/j.mex.2024.102636] [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: 06/29/2023] [Accepted: 02/26/2024] [Indexed: 03/06/2024] Open
Abstract
The exposure of the air microbiome in indoor air posed a detrimental health effect to the building occupants compared to the outdoor air. Indoor air in hospitals has been identified as a reservoir for various pathogenic microbes. The conventional culture-dependent method has been widely used to access the microbial community in the air. However, it has limited capability in enumerating the complex air microbiome communities, as some of the air microbiomes are uncultivable, slow-growers, and require specific media for cultivation. Here, we utilized a culture-independent method via amplicon sequencing to target the V3 region of 16S rRNA from the pool of total genomic DNA extracted from the dust samples taken from hospital interiors. This method will help occupational health practitioners, researchers, and health authorities to efficiently and comprehensively monitor the presence of harmful air microbiome thus take appropriate action in controlling and minimizing the health risks to the hospital occupants. Key features;•Culture-independent methods offer fast, comprehensive, and unbias profiles of pathogenic and non-pathogenic bacteria from the air microbiomes.•Unlike the culture-dependent method, amplicon sequencing allows bacteria identification to the lowest taxonomy levels.
Collapse
Affiliation(s)
- Nor Husna Mat-Hussin
- Faculty of Industrial Sciences and Technology, Universiti Malaysia Pahang, Lebuhraya Persiaran Tun Khalil Yaakob, Gambang, Kuantan, Pahang 26300, Malaysia
| | - Shing Wei Siew
- Faculty of Industrial Sciences and Technology, Universiti Malaysia Pahang, Lebuhraya Persiaran Tun Khalil Yaakob, Gambang, Kuantan, Pahang 26300, Malaysia
| | - Mohd Norhafsam Maghpor
- Laboratory Division, Consultation and Research Department, National Institute of Occupational Safety and Health (NIOSH), Seksyen 15, Bandar Baru Bangi, Selangor 43650, Malaysia
| | - Han Ming Gan
- Patriot Biotech Sdn. Bhd., Bandar Sunway, Subang Jaya, Selangor 47500, Malaysia
| | - Hajar Fauzan Ahmad
- Faculty of Industrial Sciences and Technology, Universiti Malaysia Pahang, Lebuhraya Persiaran Tun Khalil Yaakob, Gambang, Kuantan, Pahang 26300, Malaysia
- Group of Environment, Microbiology and Bioprocessing (GERMS), Universiti Malaysia Pahang, Lebuhraya Persiaran Tun Khalil Yaakob, Gambang, Kuantan, Pahang 26300, Malaysia
| |
Collapse
|
9
|
Niya B, Yaakoubi K, Beraich FZ, Arouch M, Meftah Kadmiri I. Current status and future developments of assessing microbiome composition and dynamics in anaerobic digestion systems using metagenomic approaches. Heliyon 2024; 10:e28221. [PMID: 38560681 PMCID: PMC10979216 DOI: 10.1016/j.heliyon.2024.e28221] [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: 08/17/2023] [Revised: 03/12/2024] [Accepted: 03/13/2024] [Indexed: 04/04/2024] Open
Abstract
The metagenomic approach stands as a powerful technique for examining the composition of microbial communities and their involvement in various anaerobic digestion (AD) systems. Understanding the structure, function, and dynamics of microbial communities becomes pivotal for optimizing the biogas process, enhancing its stability and improving overall performance. Currently, taxonomic profiling of biogas-producing communities relies mainly on high-throughput 16S rRNA sequencing, offering insights into the bacterial and archaeal structures of AD assemblages and their correlations with fed substrates and process parameters. To delve even deeper, shotgun and genome-centric metagenomic approaches are employed to recover individual genomes from the metagenome. This provides a nuanced understanding of collective functionalities, interspecies interactions, and microbial associations with abiotic factors. The application of OMICs in AD systems holds the potential to revolutionize the field, leading to more efficient and sustainable waste management practices particularly through the implementation of precision anaerobic digestion systems. As ongoing research in this area progresses, anticipations are high for further exciting developments in the future. This review serves to explore the current landscape of metagenomic analyses, with focus on advancing our comprehension and critically evaluating biases and recommendations in the analysis of microbial communities in anaerobic digesters. Its objective is to explore how contemporary metagenomic approaches can be effectively applied to enhance our understanding and contribute to the refinement of the AD process. This marks a substantial stride towards achieving a more comprehensive understanding of anaerobic digestion systems.
Collapse
Affiliation(s)
- Btissam Niya
- Plant and Microbial Biotechnology Center, Moroccan Foundation of Advanced Science Innovation and Research MAScIR, Mohammed VI Polytechnic University (UM6P), Lot 660, Hay Moulay Rachid, 43150, Benguerir, Morocco
- Engineering, Industrial Management & Innovation Laboratory IMII, Faculty of Science and Technics (FST), Hassan 1st University of Settat, Morocco
| | - Kaoutar Yaakoubi
- Plant and Microbial Biotechnology Center, Moroccan Foundation of Advanced Science Innovation and Research MAScIR, Mohammed VI Polytechnic University (UM6P), Lot 660, Hay Moulay Rachid, 43150, Benguerir, Morocco
| | - Fatima Zahra Beraich
- Biodome.sarl, Research and Development Design Office of Biogas Technology, Casablanca, Morocco
| | - Moha Arouch
- Engineering, Industrial Management & Innovation Laboratory IMII, Faculty of Science and Technics (FST), Hassan 1st University of Settat, Morocco
| | - Issam Meftah Kadmiri
- Plant and Microbial Biotechnology Center, Moroccan Foundation of Advanced Science Innovation and Research MAScIR, Mohammed VI Polytechnic University (UM6P), Lot 660, Hay Moulay Rachid, 43150, Benguerir, Morocco
| |
Collapse
|
10
|
Fu Y, Gu J, Chen LJ, Xiong M, Zhao J, Xiao X, Zhou J, Li Z, Li Y. A prospective study of nanopore-targeted sequencing in the diagnosis of central nervous system infections. Microbiol Spectr 2024; 12:e0331723. [PMID: 38294222 PMCID: PMC10913467 DOI: 10.1128/spectrum.03317-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2023] [Accepted: 01/04/2024] [Indexed: 02/01/2024] Open
Abstract
Central nervous system (CNS) infections are a leading cause of death in patients. Nanopore-targeted sequencing (NTS) has begun to be used for pathogenic microbial detection. This study aims to evaluate the ability of NTS in the detection of pathogens in cerebrospinal fluid (CSF) through a prospective study. Fifty CSF specimens collected from 50 patients with suspected CNS infections went through three methods including NTS, metagenomic next-generation sequencing (mNGS), and microbial culture in parallel. When there was an inconsistency between NTS results and the results of the mNGS, the 16S rDNA gene was amplified followed by Sanger sequencing to further verify pathogens detected by NTS. Among 50 CSF specimens, 76% were NTS-positive, which is lower than mNGS (94.0%), yet higher than microbial culture (16.0%). The overall validation rate, diagnostic accordance rate (DAR), sensitivity, specificity, positive predictive value (PPV), and negative predictive value (NPV) of NTS were 86.7%, 50.0%, 71.0%, 15.8%, 57.9%, and 25.0%, respectively. In the CSF total nucleated cell (TNC) number ≤10 cells/µL, DAR, specificity, and PPV were 20%, 11.1%, and 11.1%, whereas in that with CSF TNC number >10 cells/µL, DAR, sensitivity, specificity, PPV, and NPV were 57.5%, 70.0%, 20.0%, 72.4%, and 18.2%, respectively. Although NTS has a higher microbial detection rate than microbial culture, it should combine CSF TNC result to evaluate the value of NTS for the diagnosis of CNS infections. IMPORTANCE This study aims to prospectively evaluate the ability of nanopore-targeted sequencing (NTS) in the detection of pathogens in cerebrospinal fluid (CSF). It was the first time combining mNGS and microbial culture to verify the NTS-positive results also using 16S rDNA amplification with Sanger sequencing. Although microbial culture was thought to be the gold standard for pathogens detection and diagnosis of infectious diseases, this study suggested that microbial culture of CSF is not the most appropriate way for diagnosing central nervous system (CNS) infection. NTS should be recommended to be used in CSF for diagnosing CNS infection. When evaluating the value of NTS for diagnosis of CNS infections, the results of CSF TNC should be combined, and NTS-positive result is observed to be more reliable in patients with CSF TNC level >10 cells/μL.
Collapse
Affiliation(s)
- Yu Fu
- Department of Clinical Laboratory, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Jihong Gu
- Department of Clinical Laboratory, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Liang-Jun Chen
- Department of Clinical Laboratory, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Mengyuan Xiong
- Department of Clinical Laboratory, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Jin Zhao
- Department of Clinical Laboratory, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Xiao Xiao
- Department of Clinical Laboratory, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Junying Zhou
- Department of Clinical Laboratory, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Zhiqiang Li
- Department of Neurosurgery, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Yirong Li
- Department of Clinical Laboratory, Zhongnan Hospital of Wuhan University, Wuhan, China
- Wuhan Research Center for Infectious Diseases and Cancer, Chinese Academy of Medical Sciences, Wuhan, China
- Hubei Engineering Center for Infectious Disease Prevention, Control and Treatment, Wuhan, China
| |
Collapse
|
11
|
Graham KA, Gomez J, Primm TP, Houston R. Comparison of nine extraction methods for bacterial identification using the ONT MinION sequencer. Int J Legal Med 2024; 138:351-360. [PMID: 37775594 DOI: 10.1007/s00414-023-03092-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2023] [Accepted: 09/18/2023] [Indexed: 10/01/2023]
Abstract
The Anthrax mailings bioterrorism attack in 2001 revealed the need for universal and rapid microbial forensic analyses on unknown biological evidence. However, the gold standard for bacterial identification includes culturing isolates, which is laborious. Molecular approaches for bacterial identification revolve around 16S ribosomal gene sequencing using Sanger or next generation sequencing (NGS) platforms, but these techniques are laboratory-based and can also be time-consuming. The Oxford Nanopore Technologies (ONT) MinION sequencer can generate long read lengths that span the entire bacterial 16S rRNA gene and accurately identify the species level. This platform can be used in the field, allowing on-site evidence analysis. However, it requires higher quantities of pure DNA compared to other sequencing platforms; thus, the extraction method for bacterial DNA is critical for downstream analysis, which to date are tailored toward a priori knowledge of the species' taxonomic grouping. During an attack, the investigative team may not know what species they are handling; therefore, identifying an extraction method that can handle all bacterial groups and generate clean DNA for the MinION is useful for microbial forensic analysis. The purpose of this study was to identify a "universal" extraction method that can be coupled with ONT MinION sequencing for use in forensic situations for rapid identification. It also evaluated the cloud-based data analysis software provided by ONT, EPI2ME. No "universal" extraction method was identified as optimal for downstream MinION sequencing. However, the DNeasy PowerSoil Kit and Noda et al. Chelex-100 method gave comparable sequencing results and could be used as rapid extraction techniques. This study showed that the ONT 16S Barcoding Kit 1-24 coupled with the 16S FASTQ workflow might not be the best for use in forensic situations where species-level identification needs to be obtained, as most alignments were approximately 89% accurate. In all seven test organisms and nine extraction methods, accurate species identification was only obtained in 63% of the cases.
Collapse
Affiliation(s)
- Kari A Graham
- Department of Forensic Science, College of Criminal Justice, Sam Houston State University, 1003 Bowers Blvd., Huntsville, TX, 77340-2525, USA
| | - Javier Gomez
- Department of Biological Sciences, College of Science and Engineering Technology, Sam Houston State University, 2000 Ave I, Huntsville, TX, 77341, USA
| | - Todd P Primm
- Department of Biological Sciences, College of Science and Engineering Technology, Sam Houston State University, 2000 Ave I, Huntsville, TX, 77341, USA
| | - Rachel Houston
- Department of Forensic Science, College of Criminal Justice, Sam Houston State University, 1003 Bowers Blvd., Huntsville, TX, 77340-2525, USA.
| |
Collapse
|
12
|
Gradisteanu Pircalabioru G, Raileanu M, Dionisie MV, Lixandru-Petre IO, Iliescu C. Fast detection of bacterial gut pathogens on miniaturized devices: an overview. Expert Rev Mol Diagn 2024; 24:201-218. [PMID: 38347807 DOI: 10.1080/14737159.2024.2316756] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2023] [Accepted: 02/06/2024] [Indexed: 03/23/2024]
Abstract
INTRODUCTION Gut microbes pose challenges like colon inflammation, deadly diarrhea, antimicrobial resistance dissemination, and chronic disease onset. Development of early, rapid and specific diagnosis tools is essential for improving infection control. Point-of-care testing (POCT) systems offer rapid, sensitive, low-cost and sample-to-answer methods for microbe detection from various clinical and environmental samples, bringing the advantages of portability, automation, and simple operation. AREAS COVERED Rapid detection of gut microbes can be done using a wide array of techniques including biosensors, immunological assays, electrochemical impedance spectroscopy, mass spectrometry and molecular biology. Inclusion of Internet of Things, machine learning, and smartphone-based point-of-care applications is an important aspect of POCT. In this review, the authors discuss various fast diagnostic platforms for gut pathogens and their main challenges. EXPERT OPINION Developing effective assays for microbe detection can be complex. Assay design must consider factors like target selection, real-time and multiplex detection, sample type, reagent stability and storage, primer/probe design, and optimizing reaction conditions for accuracy and sensitivity. Mitigating these challenges requires interdisciplinary collaboration among scientists, clinicians, engineers, and industry partners. Future efforts are essential to enhance sensitivity, specificity, and versatility of POCT systems for gut microbe detection and quantification, advancing infectious disease diagnostics and management.
Collapse
Affiliation(s)
- Gratiela Gradisteanu Pircalabioru
- eBio-hub Research Centre, National University of Science and Technology "Politehnica" Bucharest, Bucharest, Romania
- Division of Earth, Environmental and Life Sciences, The Research Institute of University of Bucharest (ICUB), Bucharest, Romania
- Academy of Romanian Scientists, Bucharest, Romania
| | - Mina Raileanu
- eBio-hub Research Centre, National University of Science and Technology "Politehnica" Bucharest, Bucharest, Romania
- Department of Life and Environmental Physics, Horia Hulubei National Institute of Physics and Nuclear Engineering, Magurele, Romania
| | - Mihai Viorel Dionisie
- eBio-hub Research Centre, National University of Science and Technology "Politehnica" Bucharest, Bucharest, Romania
| | - Irina-Oana Lixandru-Petre
- eBio-hub Research Centre, National University of Science and Technology "Politehnica" Bucharest, Bucharest, Romania
| | - Ciprian Iliescu
- eBio-hub Research Centre, National University of Science and Technology "Politehnica" Bucharest, Bucharest, Romania
- Academy of Romanian Scientists, Bucharest, Romania
- Microsystems in Biomedical and Environmental Applications, National Research and Development Institute for Microtechnology, Bucharest, Romania
| |
Collapse
|
13
|
Bertolo A, Valido E, Stoyanov J. Optimized bacterial community characterization through full-length 16S rRNA gene sequencing utilizing MinION nanopore technology. BMC Microbiol 2024; 24:58. [PMID: 38365589 PMCID: PMC10870487 DOI: 10.1186/s12866-024-03208-5] [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: 10/31/2023] [Accepted: 01/28/2024] [Indexed: 02/18/2024] Open
Abstract
BACKGROUND Accurate identification of bacterial communities is crucial for research applications, diagnostics, and clinical interventions. Although 16S ribosomal RNA (rRNA) gene sequencing is a widely employed technique for bacterial taxonomic classification, it often results in misclassified or unclassified bacterial taxa. This study sought to refine the full-length 16S rRNA gene sequencing protocol using the MinION sequencer, focusing on the V1-V9 regions. Our methodological enquiry examined several factors, including the number of PCR amplification cycles, choice of primers and Taq polymerase, and specific sequence databases and workflows employed. We used a microbial standard comprising eight bacterial strains (five gram-positive and three gram-negative) in known proportions as a validation control. RESULTS Based on the MinION protocol, we employed the microbial standard as the DNA template for the 16S rRNA gene amplicon sequencing procedure. Our analysis showed that an elevated number of PCR amplification cycles introduced PCR bias, and the selection of Taq polymerase and primer sets significantly affected the subsequent analysis. Bacterial identification at genus level demonstrated Pearson correlation coefficients ranging from 0.73 to 0.79 when assessed using BugSeq, Kraken-Silva and EPI2ME-16S workflows. Notably, the EPI2ME-16S workflow exhibited the highest Pearson correlation with the microbial standard, minimised misclassification, and increased alignment accuracy. At the species taxonomic level, the BugSeq workflow was superior, with a Pearson correlation coefficient of 0.92. CONCLUSIONS These findings emphasise the importance of careful selection of PCR settings and a well-structured analytical framework for 16S rRNA full-length gene sequencing. The results showed a robust correlation between the predicted and observed bacterial abundances at both the genus and species taxonomic levels, making these findings applicable across diverse research contexts and with clinical utility for reliable pathogen identification.
Collapse
Affiliation(s)
- Alessandro Bertolo
- SCI Population Biobanking & Translational Research Group, Swiss Paraplegic Research, Nottwil, Switzerland
- Department of Orthopaedic Surgery, University of Bern, Bern Inselspital, Bern, Switzerland
| | - Ezra Valido
- SCI Population Biobanking & Translational Research Group, Swiss Paraplegic Research, Nottwil, Switzerland
| | - Jivko Stoyanov
- SCI Population Biobanking & Translational Research Group, Swiss Paraplegic Research, Nottwil, Switzerland.
- Institute of Social and Preventive Medicine, University of Bern, Bern, Switzerland.
| |
Collapse
|
14
|
Hosokawa M, Nishikawa Y. Tools for microbial single-cell genomics for obtaining uncultured microbial genomes. Biophys Rev 2024; 16:69-77. [PMID: 38495448 PMCID: PMC10937852 DOI: 10.1007/s12551-023-01124-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Accepted: 08/23/2023] [Indexed: 03/19/2024] Open
Abstract
The advent of next-generation sequencing technologies has facilitated the acquisition of large amounts of DNA sequence data at a relatively low cost, leading to numerous breakthroughs in decoding microbial genomes. Among the various genome sequencing activities, metagenomic analysis, which entails the direct analysis of uncultured microbial DNA, has had a profound impact on microbiome research and has emerged as an indispensable technology in this field. Despite its valuable contributions, metagenomic analysis is a "bulk analysis" technique that analyzes samples containing a wide diversity of microbes, such as bacteria, yielding information that is averaged across the entire microbial population. In order to gain a deeper understanding of the heterogeneous nature of the microbial world, there is a growing need for single-cell analysis, similar to its use in human cell biology. With this paradigm shift in mind, comprehensive single-cell genomics technology has become a much-anticipated innovation that is now poised to revolutionize microbiome research. It has the potential to enable the discovery of differences at the strain level and to facilitate a more comprehensive examination of microbial ecosystems. In this review, we summarize the current state-of-the-art in microbial single-cell genomics, highlighting the potential impact of this technology on our understanding of the microbial world. The successful implementation of this technology is expected to have a profound impact in the field, leading to new discoveries and insights into the diversity and evolution of microbes.
Collapse
Affiliation(s)
- Masahito Hosokawa
- Department of Life Science and Medical Bioscience, Waseda University, 2-2 Wakamatsu-Cho, Shinjuku-Ku, Tokyo, 162-8480 Japan
- Computational Bio Big-Data Open Innovation Laboratory, National Institute of Advanced Industrial Science and Technology, 3-4-1 Okubo, Shinjuku-Ku, Tokyo, 169-8555 Japan
- Research Organization for Nano and Life Innovation, Waseda University, 513 Wasedatsurumaki-Cho, Shinjuku-Ku, Tokyo, 162-0041 Japan
- Institute for Advanced Research of Biosystem Dynamics, Waseda Research Institute for Science and Engineering, 3-4-1 Okubo, Shinjuku-Ku, Tokyo, 169-8555 Japan
- bitBiome, Inc., 513 Wasedatsurumaki-Cho, Shinjuku-Ku, Tokyo, 162-0041 Japan
| | - Yohei Nishikawa
- Computational Bio Big-Data Open Innovation Laboratory, National Institute of Advanced Industrial Science and Technology, 3-4-1 Okubo, Shinjuku-Ku, Tokyo, 169-8555 Japan
- Research Organization for Nano and Life Innovation, Waseda University, 513 Wasedatsurumaki-Cho, Shinjuku-Ku, Tokyo, 162-0041 Japan
| |
Collapse
|
15
|
Lin Q, Yao Y, Li X, Zhang S, Guo H, Ma X, Chen W, Ru C, Wang L, Wang B, Ma Q, Zhu J, Lin X, Chen Q, Lou H, Chen Q, Chen J, Zeng Z, Zhou J, Chen Y, Yu Y, Zhou H. The application of nanopore targeted sequencing for pathogen diagnosis in bronchoalveolar lavage fluid of patients with pneumonia: a prospective multicenter study. Infect Dis (Lond) 2024; 56:128-137. [PMID: 37934028 DOI: 10.1080/23744235.2023.2276785] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/25/2023] [Accepted: 10/12/2023] [Indexed: 11/08/2023] Open
Abstract
OBJECTIVE To evaluate the value of nanopore targeted sequencing in diagnosing pneumonia pathogens. METHODS This large-scale multicentre prospective study performed in 8 hospitals across China from April to October 2022. Hospitalised patients with a diagnosis of pneumonia at admission were included. Complete clinical data were collected, and bronchoalveolar lavage fluid were obtained from each patient. These samples underwent simultaneous testing using conventional microbial testing, metagenomic next-generation sequencing, and nanopore targeted sequencing. RESULTS A total of 218 patients were included. Among the 168 cases of pulmonary infection, 246 strains of pathogens were confirmed. Nanopore targeted sequencing outperformed conventional microbial testing, identifying more pathogens with a sensitivity increase of 47.9% (77.2% vs. 29.3%). Metagenomic next-generation sequencing had a sensitivity of 82.9%. Total of 70.1% patients had consistent results in both metagenomic next-generation sequencing and nanopore targeted sequencing. Nanopore targeted sequencing exhibited significantly higher sensitivity in detecting Pneumocystis jiroveci, cytomegalovirus, Mycobacterium tuberculosis, Nontuberculous mycobacteria, Streptococcus pneumoniae, and Mycoplasma pneumoniae compared to conventional microbial testing. However, metagenomic next-generation sequencing demonstrated higher sensitivity than nanopore targeted sequencing for Aspergillus (88.5% vs. 53.8%). Regarding the detection of co-infections, nanopore targeted sequencing displayed significantly higher sensitivity than conventional microbial testing (76.7% vs. 28.7%) and was on par with metagenomic next-generation sequencing (76.7% vs. 82.9%). CONCLUSION Nanopore targeted sequencing performs equally well as metagenomic next-generation sequencing in bronchoalveolar lavage fluid for pathogen diagnosis in pneumonia, both methods showing higher sensitivity than conventional microbial testing. Nanopore targeted sequencing can be considered a reliable method for diagnosing pathogens in pneumonia.
Collapse
Affiliation(s)
- Qinqing Lin
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
- Department of Critical Care Medicine, Affiliated Hospital of Shaoxing University, Shaoxing, China
| | - Yake Yao
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Xi Li
- Laboratory Medicine Center, Department of Clinical Laboratory, Zhejiang Provincial People's Hospital, Affiliated People's Hospital, Hangzhou Medical College, Hangzhou, Zhejiang, China
| | - Shanshan Zhang
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
- Department of Respiratory and Critical Care Medicine, Beilun People's Hospital, Ningbo, China
| | - Huimin Guo
- Zhejiang Digena Diagnosis Technology CO., Ltd., Hangzhou, Zhejiang, China
- Key Laboratory of Digital Technology in Medical Diagnostics of Zhejiang Province, Dian Diagnostics Group Co., Ltd., Hangzhou, Zhejiang, China
| | - Xiaolong Ma
- Department of Respiratory and Critical Care Medicine, The First Hospital of JiaXing, JiaXing, China
| | - Wenyu Chen
- Key Laboratory of Digital Technology in Medical Diagnostics of Zhejiang Province, Dian Diagnostics Group Co., Ltd., Hangzhou, Zhejiang, China
| | - Chuhui Ru
- Department of Respiratory and Critical Care Medicine, Red Cross Society Hospital of Hangzhou, Hangzhou, China
| | - Limin Wang
- Department of Respiratory and Critical Care Medicine, Affiliated Hangzhou First People's Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Bin Wang
- Department of Respiratory and Critical Care Medicine, Huzhou Central Hospital, Huzhou, China
| | - Qiang Ma
- Department of Respiratory and Critical Care Medicine, The Second People's Hospital of Yuhang District, Hangzhou, China
| | - Junfei Zhu
- Department of Respiratory and Critical Care Medicine, Taizhou Central Hospital, Taizhou, China
| | - Xuemei Lin
- Department of Respiratory and Critical Care Medicine, Jiangshan People's Hospital, Quzhou, China
| | - Qi Chen
- Zhejiang Digena Diagnosis Technology CO., Ltd., Hangzhou, Zhejiang, China
- Key Laboratory of Digital Technology in Medical Diagnostics of Zhejiang Province, Dian Diagnostics Group Co., Ltd., Hangzhou, Zhejiang, China
| | - Hui Lou
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Qi Chen
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Junjun Chen
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Zhu Zeng
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Jianying Zhou
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Yan Chen
- Department of Infectious Disease, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Yunsong Yu
- Department of Infectious Disease, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Hua Zhou
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| |
Collapse
|
16
|
Zhang X, Zhong H, Ran J, Luo J, Chen M, Li H, Wang Y, Cheng S, Yan Y, Huang X. Analysis of winter diet in Guizhou golden monkey ( Rhinopithecus brelichi) using DNA metabarcoding data. Ecol Evol 2024; 14:e10893. [PMID: 38314313 PMCID: PMC10834204 DOI: 10.1002/ece3.10893] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Revised: 01/15/2024] [Accepted: 01/17/2024] [Indexed: 02/06/2024] Open
Abstract
The Guizhou golden monkey (Rhinopithecus brelichi) is a critically endangered wildlife species, and understanding its diet composition may be useful for assessing its feeding strategies. DNA metabarcoding was used to determine the dietary diversity of R. brelichi. DNA was extracted from 31 faecal samples and amplified chloroplast rbcL and mitochondrial COI DNA was sequenced using the Illumina NovaSeq platform. A comparative analysis of the sequences revealed that the five most abundant plant genera were Magnolia, Morinda, Viburnum, Tetradium and Eurya. In winter, R. brelichi mostly consumed shrubs, herbs and shrubs/trees according to the habit of plant genera with higher abundances comparatively. The five most abundant families in animal diet were Psychodidae, Trichinellidae, Staphylinidae, Scarabaeidae and Trichoceridae. This study is the first to show the composition of the winter animal diets of R. brelichi based on DNA metabarcoding. These results provide an important basis for understanding the diet of wild R. brelichi, which inhabits only the Fanjingshan National Nature Reserve, China.
Collapse
Affiliation(s)
- Xu Zhang
- Guizhou Academy of Forestry ScienceGuiyangChina
- Guizhou Fanjingshan Observation and Research Station for Forest EcosystemNational Forestry and Grass‐land AdministrationTongrenChina
- Guizhou Caohai Observation and Research Station for Wet EcosystemNational Forestry and Grassland AdministrationBijieChina
- Key Laboratory of National Forestry and Grassland Administration on Biodiversity Conservation in Karst Mountainous Areas of Southwestern ChinaGuizhou Academy of ForestryGuiyangChina
| | - Huafu Zhong
- Guizhou Fanjingshan Observation and Research Station for Forest EcosystemNational Forestry and Grass‐land AdministrationTongrenChina
- Fanjingshan National Nature Reserve AdministrationTongrenChina
| | - Jingcheng Ran
- Guizhou Academy of Forestry ScienceGuiyangChina
- Guizhou Fanjingshan Observation and Research Station for Forest EcosystemNational Forestry and Grass‐land AdministrationTongrenChina
- Guizhou Caohai Observation and Research Station for Wet EcosystemNational Forestry and Grassland AdministrationBijieChina
- Key Laboratory of National Forestry and Grassland Administration on Biodiversity Conservation in Karst Mountainous Areas of Southwestern ChinaGuizhou Academy of ForestryGuiyangChina
| | - Jiaxin Luo
- College of Life ScienceGuizhou Normal UniversityGuiyangChina
| | - Meifeng Chen
- Guizhou Academy of Forestry ScienceGuiyangChina
- Key Laboratory of National Forestry and Grassland Administration on Biodiversity Conservation in Karst Mountainous Areas of Southwestern ChinaGuizhou Academy of ForestryGuiyangChina
- College of Life ScienceGuizhou Normal UniversityGuiyangChina
| | - Haibo Li
- Guizhou Fanjingshan Observation and Research Station for Forest EcosystemNational Forestry and Grass‐land AdministrationTongrenChina
- Fanjingshan National Nature Reserve AdministrationTongrenChina
| | - Yeying Wang
- College of Life ScienceGuizhou Normal UniversityGuiyangChina
| | - Shaochuan Cheng
- Guizhou Academy of Forestry ScienceGuiyangChina
- Guizhou Fanjingshan Observation and Research Station for Forest EcosystemNational Forestry and Grass‐land AdministrationTongrenChina
- Guizhou Caohai Observation and Research Station for Wet EcosystemNational Forestry and Grassland AdministrationBijieChina
- Key Laboratory of National Forestry and Grassland Administration on Biodiversity Conservation in Karst Mountainous Areas of Southwestern ChinaGuizhou Academy of ForestryGuiyangChina
| | - Yuying Yan
- Guizhou Academy of Forestry ScienceGuiyangChina
- Guizhou Fanjingshan Observation and Research Station for Forest EcosystemNational Forestry and Grass‐land AdministrationTongrenChina
- Guizhou Caohai Observation and Research Station for Wet EcosystemNational Forestry and Grassland AdministrationBijieChina
- Key Laboratory of National Forestry and Grassland Administration on Biodiversity Conservation in Karst Mountainous Areas of Southwestern ChinaGuizhou Academy of ForestryGuiyangChina
| | - Xiaolong Huang
- Guizhou Academy of Forestry ScienceGuiyangChina
- Guizhou Fanjingshan Observation and Research Station for Forest EcosystemNational Forestry and Grass‐land AdministrationTongrenChina
- Guizhou Caohai Observation and Research Station for Wet EcosystemNational Forestry and Grassland AdministrationBijieChina
- Key Laboratory of National Forestry and Grassland Administration on Biodiversity Conservation in Karst Mountainous Areas of Southwestern ChinaGuizhou Academy of ForestryGuiyangChina
| |
Collapse
|
17
|
Huggins LG, Colella V, Young ND, Traub RJ. Metabarcoding using nanopore long-read sequencing for the unbiased characterization of apicomplexan haemoparasites. Mol Ecol Resour 2024; 24:e13878. [PMID: 37837372 DOI: 10.1111/1755-0998.13878] [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: 05/04/2023] [Revised: 08/07/2023] [Accepted: 09/28/2023] [Indexed: 10/16/2023]
Abstract
Apicomplexan haemoparasites generate significant morbidity and mortality in humans and other animals, particularly in many low-to-middle income countries. Malaria caused by Plasmodium remains responsible for some of the highest numbers of annual deaths of any human pathogen, whilst piroplasmids, such as Babesia and Theileria can have immense negative economic effects through livestock loss. Diagnosing haemoparasites via traditional methods like microscopy is challenging due to low-level and transient parasitaemia. PCR-based diagnostics overcome these limitations by being both highly sensitive and specific, but they may be unable to accurately detect coinfections or identify novel species. In contrast, next-generation sequencing (NGS)-based methods can characterize all pathogens from a group of interest concurrently, although, the short-read platforms previously used have been limited in the taxonomic resolution achievable. Here, we used Oxford Nanopore Technologies' (ONT) long-read MinION™ sequencer to conduct apicomplexan haemoparasite metabarcoding via sequencing the near full-length 18S ribosomal RNA gene, demonstrating its ability to detect Babesia, Hepatozoon, Neospora, Plasmodium, Theileria and Toxoplasma species. This method was tested on blood-extracted DNA from 100 dogs and the results benchmarked against qPCR and Illumina-based metabarcoding. For two common haemoparasites, nanopore sequencing performed as well as qPCR (kappa agreement statistics > 0.98), whilst also detecting one pathogen, Hepatozoon felis, missed by the other techniques. The long-reads obtained by nanopore sequencing provide an improved species-level taxonomic resolution whilst the method's broad applicability mean it can be used to explore apicomplexan communities from diverse mammalian hosts, on a portable sequencer that easily permits adaptation to field use.
Collapse
Affiliation(s)
- Lucas G Huggins
- Melbourne Veterinary School, Faculty of Science, University of Melbourne, Parkville, Victoria, Australia
| | - Vito Colella
- Melbourne Veterinary School, Faculty of Science, University of Melbourne, Parkville, Victoria, Australia
| | - Neil D Young
- Melbourne Veterinary School, Faculty of Science, University of Melbourne, Parkville, Victoria, Australia
| | - Rebecca J Traub
- Melbourne Veterinary School, Faculty of Science, University of Melbourne, Parkville, Victoria, Australia
| |
Collapse
|
18
|
Ayeni KI, Berry D, Ezekiel CN, Warth B. Enhancing microbiome research in sub-Saharan Africa. Trends Microbiol 2024; 32:111-115. [PMID: 38212192 DOI: 10.1016/j.tim.2023.11.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Revised: 11/03/2023] [Accepted: 11/13/2023] [Indexed: 01/13/2024]
Abstract
While there are lighthouse examples of microbiome research in sub-Saharan Africa (SSA), a significant proportion of local researchers face several challenges. Here, we highlight prevailing issues limiting microbiome research in SSA and suggest potential technological, societal, and research-based solutions. We emphasize the need for considerable investment in infrastructures, training, and appropriate funding to democratize modern technologies with a view to providing useful data to improve human health.
Collapse
Affiliation(s)
- Kolawole I Ayeni
- University of Vienna, Faculty of Chemistry, Department of Food Chemistry and Toxicology, Währinger Str. 38, A-1090 Vienna, Austria
| | - David Berry
- Centre for Microbiology and Environmental Systems Science, Department of Microbiology and Ecosystem Science, Division of Microbial Ecology, University of Vienna, 1030 Vienna, Austria
| | - Chibundu N Ezekiel
- University of Natural Resources and Life Sciences Vienna (BOKU), Department of Agrobiotechnology (IFA-Tulln), Institute for Bioanalytics and Agro-Metabolomics, Konrad-LorenzStr. 20, 3430, Tulln, Austria; Clifford University, Owerrinta, Ihie Campus, Abia State, Nigeria
| | - Benedikt Warth
- University of Vienna, Faculty of Chemistry, Department of Food Chemistry and Toxicology, Währinger Str. 38, A-1090 Vienna, Austria.
| |
Collapse
|
19
|
Tarquini G, Maestri S, Ermacora P, Martini M. The Oxford Nanopore MinION as a Versatile Technology for the Diagnosis and Characterization of Emerging Plant Viruses. Methods Mol Biol 2024; 2732:235-249. [PMID: 38060129 DOI: 10.1007/978-1-0716-3515-5_16] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/08/2023]
Abstract
The emergence of novel viral epidemics that could affect major crops represents a serious threat to global food security. The early and accurate identification of the causative viral agent is the most important step for a rapid and effective response to disease outbreaks. Over the last years, the Oxford Nanopore Technologies (ONT) MinION sequencer has been proposed as an effective diagnostic tool for the early detection and identification of emerging viruses in plants, providing many advantages compared with different high-throughput sequencing (HTS) technologies. Here, we provide a step-by-step protocol that we optimized to obtain the virome of "Lamon bean" plants (Phaseolus vulgaris L.), an agricultural product with Protected Geographical Indication (PGI) in North-East of Italy, which is frequently subjected to multiple infections caused by different RNA viruses. The conversion of viral RNA in ds-cDNA enabled the use of Genomic DNA Ligation Sequencing Kit and Native Barcoding DNA Kit, which have been originally developed for DNA sequencing. This allowed the simultaneous diagnosis of both DNA- and RNA-based pathogens, providing a more versatile alternative to the use of direct RNA and/or direct cDNA sequencing kits.
Collapse
Affiliation(s)
- Giulia Tarquini
- Department of Agriculture, Food, Environmental and Animal Sciences, University of Udine, Udine, Italy
| | - Simone Maestri
- Center for Genomic Science of IIT@SEMM, Fondazione Istituto Italiano di Tecnologia, Milano, Italy
| | - Paolo Ermacora
- Department of Agriculture, Food, Environmental and Animal Sciences, University of Udine, Udine, Italy
| | - Marta Martini
- Department of Agriculture, Food, Environmental and Animal Sciences, University of Udine, Udine, Italy.
| |
Collapse
|
20
|
Ni J, Pan J, Wang Y, Chen T, Feng X, Li Y, Lin T, Lynch M, Long H, Li W. An integrative protocol for one-step PCR amplicon library construction and accurate demultiplexing of pooled sequencing data. MARINE LIFE SCIENCE & TECHNOLOGY 2023; 5:564-572. [PMID: 38045552 PMCID: PMC10689312 DOI: 10.1007/s42995-023-00182-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Accepted: 06/02/2023] [Indexed: 12/05/2023]
Abstract
High-throughput sequencing of amplicons has been widely used to precisely and efficiently identify species compositions and analyze community structures, greatly promoting biological studies involving large amounts of complex samples, especially those involving environmental and pathogen-monitoring ones. Commercial library preparation kits for amplicon sequencing, which generally require multiple steps, including adapter ligation and indexing, are expensive and time-consuming, especially for applications at a large scale. To overcome these limitations, a "one-step PCR approach" has been previously proposed for constructions of amplicon libraries using long fusion primers. However, efficient amplifications of target genes and accurate demultiplexing of pooled sequencing data remain to be addressed. To tackle these, we present an integrative protocol for one-step PCR amplicon library construction (OSPALC). High-quality reads have been generated by this approach to reliably identify species compositions of mock bacterial communities and environmental samples. With this protocol, the amplicon library is constructed through one regular PCR with long primers, and the total cost per DNA/cDNA sample decreases to just 7% of the typical cost via the multi-step PCR approach. Empirically tested primers and optimized PCR conditions to construct OSPALC libraries for 16S rDNA V4 regions are demonstrated as a case study. Tools to design primers targeting at any genomic regions are also presented. In principle, OSPALC can be readily applied to construct amplicon libraries of any target genes using DNA or RNA samples, and will facilitate research in numerous fields. Supplementary Information The online version contains supplementary material available at 10.1007/s42995-023-00182-1.
Collapse
Affiliation(s)
- Jiahao Ni
- Institute of Evolution and Marine Biodiversity, KLMME, Ocean University of China, Qingdao, 266003 China
- Laboratory for Marine Biology and Biotechnology, Laoshan Laboratory, Qingdao, 266237 China
| | - Jiao Pan
- Institute of Evolution and Marine Biodiversity, KLMME, Ocean University of China, Qingdao, 266003 China
| | - Yaohai Wang
- Institute of Evolution and Marine Biodiversity, KLMME, Ocean University of China, Qingdao, 266003 China
| | - Tianhao Chen
- Institute of Evolution and Marine Biodiversity, KLMME, Ocean University of China, Qingdao, 266003 China
| | - Xinshi Feng
- Institute of Evolution and Marine Biodiversity, KLMME, Ocean University of China, Qingdao, 266003 China
| | - Yichen Li
- Institute of Evolution and Marine Biodiversity, KLMME, Ocean University of China, Qingdao, 266003 China
| | - Tongtong Lin
- Institute of Evolution and Marine Biodiversity, KLMME, Ocean University of China, Qingdao, 266003 China
| | - Michael Lynch
- Biodesign Center for Mechanisms of Evolution, Arizona State University, Tempe, AZ 85281 USA
| | - Hongan Long
- Institute of Evolution and Marine Biodiversity, KLMME, Ocean University of China, Qingdao, 266003 China
- Laboratory for Marine Biology and Biotechnology, Laoshan Laboratory, Qingdao, 266237 China
| | - Weiyi Li
- Department of Biology, Indiana University, Bloomington, IN 47401 USA
- Present Address: SLAC National Accelerator Laboratory, Stanford University, Stanford, 94305 USA
| |
Collapse
|
21
|
Xoconostle-Cázares B, Ramírez-Pool JA, Núñez-Muñoz LA, Calderón-Pérez B, Vargas-Hernández BY, Bujanos-Muñiz R, Ruiz-Medrano R. The Characterization of Melanaphis sacchari Microbiota and Antibiotic Treatment Effect on Insects. INSECTS 2023; 14:807. [PMID: 37887819 PMCID: PMC10607097 DOI: 10.3390/insects14100807] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Revised: 09/23/2023] [Accepted: 10/06/2023] [Indexed: 10/28/2023]
Abstract
Insects are under constant selective pressure, which has resulted in adaptations to novel niches such as crops. This is the case of the pest Melanaphis sacchari, the sugarcane aphid, native to Africa and currently spreading worldwide. The aphid undergoes successful parthenogenesis, causing important damage to a variety of crops and leading to important economic losses for farmers. A natural M. sacchari population grown in sorghum was studied to identify its microbiome through the sequencing of its 16S rDNA metagenome. A high proportion of Proteobacteria, followed by Firmicutes, Bacteroidetes, and Actinobacteria, was observed. We also detected Wolbachia, which correlates with the asexual reproduction of its host. M. sacchari was challenged in a bioassay with the antibiotics oxytetracycline and streptomycin, resulting in a dose-dependent decay of its survival rate. The possibility of controlling this pest by altering its microbiota is proposed.
Collapse
Affiliation(s)
- Beatriz Xoconostle-Cázares
- Departamento de Biotecnología y Bioingeniería, Centro de Investigación y de Estudios Avanzados Av., Instituto Politécnico Nacional 2508, Mexico City 07360, Mexico; (B.X.-C.); (J.A.R.-P.); (L.A.N.-M.); (B.C.-P.)
| | - José Abrahán Ramírez-Pool
- Departamento de Biotecnología y Bioingeniería, Centro de Investigación y de Estudios Avanzados Av., Instituto Politécnico Nacional 2508, Mexico City 07360, Mexico; (B.X.-C.); (J.A.R.-P.); (L.A.N.-M.); (B.C.-P.)
| | - Leandro Alberto Núñez-Muñoz
- Departamento de Biotecnología y Bioingeniería, Centro de Investigación y de Estudios Avanzados Av., Instituto Politécnico Nacional 2508, Mexico City 07360, Mexico; (B.X.-C.); (J.A.R.-P.); (L.A.N.-M.); (B.C.-P.)
| | - Berenice Calderón-Pérez
- Departamento de Biotecnología y Bioingeniería, Centro de Investigación y de Estudios Avanzados Av., Instituto Politécnico Nacional 2508, Mexico City 07360, Mexico; (B.X.-C.); (J.A.R.-P.); (L.A.N.-M.); (B.C.-P.)
| | - Brenda Yazmín Vargas-Hernández
- Departamento de Biotecnología y Bioingeniería, Centro de Investigación y de Estudios Avanzados Av., Instituto Politécnico Nacional 2508, Mexico City 07360, Mexico; (B.X.-C.); (J.A.R.-P.); (L.A.N.-M.); (B.C.-P.)
| | - Rafael Bujanos-Muñiz
- Instituto Nacional de Investigaciones Forestales, Agrícolas y Pecuarias, Carretera Celaya-San Miguel de Allende km 6.5, Celaya Guanajuato 38110, Mexico;
| | - Roberto Ruiz-Medrano
- Departamento de Biotecnología y Bioingeniería, Centro de Investigación y de Estudios Avanzados Av., Instituto Politécnico Nacional 2508, Mexico City 07360, Mexico; (B.X.-C.); (J.A.R.-P.); (L.A.N.-M.); (B.C.-P.)
| |
Collapse
|
22
|
Yu PL, Fulton JC, Hudson OH, Huguet-Tapia JC, Brawner JT. Next-generation fungal identification using target enrichment and Nanopore sequencing. BMC Genomics 2023; 24:581. [PMID: 37784013 PMCID: PMC10544392 DOI: 10.1186/s12864-023-09691-w] [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: 05/15/2023] [Accepted: 09/21/2023] [Indexed: 10/04/2023] Open
Abstract
BACKGROUND Rapid and accurate pathogen identification is required for disease management. Compared to sequencing entire genomes, targeted sequencing may be used to direct sequencing resources to genes of interest for microbe identification and mitigate the low resolution that single-locus molecular identification provides. This work describes a broad-spectrum fungal identification tool developed to focus high-throughput Nanopore sequencing on genes commonly employed for disease diagnostics and phylogenetic inference. RESULTS Orthologs of targeted genes were extracted from 386 reference genomes of fungal species spanning six phyla to identify homologous regions that were used to design the baits used for enrichment. To reduce the cost of producing probes without diminishing the phylogenetic power, DNA sequences were first clustered, and then consensus sequences within each cluster were identified to produce 26,000 probes that targeted 114 genes. To test the efficacy of our probes, we applied the technique to three species representing Ascomycota and Basidiomycota fungi. The efficiency of enrichment, quantified as mean target coverage over the mean genome-wide coverage, ranged from 200 to 300. Furthermore, enrichment of long reads increased the depth of coverage across the targeted genes and into non-coding flanking sequence. The assemblies generated from enriched samples provided well-resolved phylogenetic trees for taxonomic assignment and molecular identification. CONCLUSIONS Our work provides data to support the utility of targeted Nanopore sequencing for fungal identification and provides a platform that may be extended for use with other phytopathogens.
Collapse
Affiliation(s)
- Pei-Ling Yu
- Department of Plant Pathology, University of Florida, Gainesville, FL, 32611, USA
| | - James C Fulton
- Department of Plant Pathology, University of Florida, Gainesville, FL, 32611, USA
- Florida Department of Agriculture and Consumer Services, Division of Plant Industry, Gainesville, FL, 32608, USA
| | - Owen H Hudson
- Department of Plant Pathology, University of Florida, Gainesville, FL, 32611, USA
| | - Jose C Huguet-Tapia
- Department of Plant Pathology, University of Florida, Gainesville, FL, 32611, USA
| | - Jeremy T Brawner
- Department of Plant Pathology, University of Florida, Gainesville, FL, 32611, USA.
| |
Collapse
|
23
|
Rosenzweig AF, Burian J, Brady SF. Present and future outlooks on environmental DNA-based methods for antibiotic discovery. Curr Opin Microbiol 2023; 75:102335. [PMID: 37327680 PMCID: PMC11076179 DOI: 10.1016/j.mib.2023.102335] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Revised: 04/28/2023] [Accepted: 05/17/2023] [Indexed: 06/18/2023]
Abstract
Novel antibiotics are in constant demand to combat a global increase in antibiotic-resistant infections. Bacterial natural products have been a long-standing source of antibiotic compounds, and metagenomic mining of environmental DNA (eDNA) has increasingly provided new antibiotic leads. The metagenomic small-molecule discovery pipeline can be divided into three main steps: surveying eDNA, retrieving a sequence of interest, and accessing the encoded natural product. Improvements in sequencing technology, bioinformatic algorithms, and methods for converting biosynthetic gene clusters into small molecules are steadily increasing our ability to discover metagenomically encoded antibiotics. We predict that, over the next decade, ongoing technological improvements will dramatically increase the rate at which antibiotics are discovered from metagenomes.
Collapse
Affiliation(s)
- Adam F Rosenzweig
- Laboratory of Genetically Encoded Small Molecules, The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA
| | - Ján Burian
- Laboratory of Genetically Encoded Small Molecules, The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA
| | - Sean F Brady
- Laboratory of Genetically Encoded Small Molecules, The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA.
| |
Collapse
|
24
|
Arıkan M, Muth T. Integrated multi-omics analyses of microbial communities: a review of the current state and future directions. Mol Omics 2023; 19:607-623. [PMID: 37417894 DOI: 10.1039/d3mo00089c] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/08/2023]
Abstract
Integrated multi-omics analyses of microbiomes have become increasingly common in recent years as the emerging omics technologies provide an unprecedented opportunity to better understand the structural and functional properties of microbial communities. Consequently, there is a growing need for and interest in the concepts, approaches, considerations, and available tools for investigating diverse environmental and host-associated microbial communities in an integrative manner. In this review, we first provide a general overview of each omics analysis type, including a brief history, typical workflow, primary applications, strengths, and limitations. Then, we inform on both experimental design and bioinformatics analysis considerations in integrated multi-omics analyses, elaborate on the current approaches and commonly used tools, and highlight the current challenges. Finally, we discuss the expected key advances, emerging trends, potential implications on various fields from human health to biotechnology, and future directions.
Collapse
Affiliation(s)
- Muzaffer Arıkan
- Regenerative and Restorative Medicine Research Center (REMER), Research Institute for Health Sciences and Technologies (SABITA), Istanbul Medipol University, Istanbul, Turkey.
- Department of Medical Biology, Faculty of Medicine, Istanbul Medipol University, Istanbul, Turkey
| | - Thilo Muth
- Section eScience (S.3), Federal Institute for Materials Research and Testing (BAM), Berlin, Germany.
| |
Collapse
|
25
|
Arikawa K, Hosokawa M. Uncultured prokaryotic genomes in the spotlight: An examination of publicly available data from metagenomics and single-cell genomics. Comput Struct Biotechnol J 2023; 21:4508-4518. [PMID: 37771751 PMCID: PMC10523443 DOI: 10.1016/j.csbj.2023.09.010] [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: 06/15/2023] [Revised: 09/10/2023] [Accepted: 09/10/2023] [Indexed: 09/30/2023] Open
Abstract
Owing to the ineffectiveness of traditional culture techniques for the vast majority of microbial species, culture-independent analyses utilizing next-generation sequencing and bioinformatics have become essential for gaining insight into microbial ecology and function. This mini-review focuses on two essential methods for obtaining genetic information from uncultured prokaryotes, metagenomics and single-cell genomics. We analyzed the registration status of uncultured prokaryotic genome data from major public databases and assessed the advantages and limitations of both the methods. Metagenomics generates a significant quantity of sequence data and multiple prokaryotic genomes using straightforward experimental procedures. However, in ecosystems with high microbial diversity, such as soil, most genes are presented as brief, disconnected contigs, and lack association of highly conserved genes and mobile genetic elements with individual species genomes. Although technically more challenging, single-cell genomics offers valuable insights into complex ecosystems by providing strain-resolved genomes, addressing issues in metagenomics. Recent technological advancements, such as long-read sequencing, machine learning algorithms, and in silico protein structure prediction, in combination with vast genomic data, have the potential to overcome the current technical challenges and facilitate a deeper understanding of uncultured microbial ecosystems and microbial dark matter genes and proteins. In light of this, it is imperative that continued innovation in both methods and technologies take place to create high-quality reference genome databases that will support future microbial research and industrial applications.
Collapse
Affiliation(s)
- Koji Arikawa
- Department of Life Science and Medical Bioscience, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo 162-8480, Japan
- bitBiome, Inc., 513 Wasedatsurumaki-cho, Shinjuku-ku, Tokyo 162-0041, Japan
| | - Masahito Hosokawa
- Department of Life Science and Medical Bioscience, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo 162-8480, Japan
- bitBiome, Inc., 513 Wasedatsurumaki-cho, Shinjuku-ku, Tokyo 162-0041, Japan
- Research Organization for Nano and Life Innovation, Waseda University, 513 Wasedatsurumaki-cho, Shinjuku-ku, Tokyo 162-0041, Japan
- Institute for Advanced Research of Biosystem Dynamics, Waseda Research Institute for Science and Engineering, 3-4-1 Okubo, Shinjuku-ku, Tokyo 169-8555, Japan
- Computational Bio Big-Data Open Innovation Laboratory, National Institute of Advanced Industrial Science and Technology, 3-4-1 Okubo, Shinjuku-ku, Tokyo 169-8555, Japan
| |
Collapse
|
26
|
Ojala T, Häkkinen AE, Kankuri E, Kankainen M. Current concepts, advances, and challenges in deciphering the human microbiota with metatranscriptomics. Trends Genet 2023; 39:686-702. [PMID: 37365103 DOI: 10.1016/j.tig.2023.05.004] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Revised: 05/24/2023] [Accepted: 05/25/2023] [Indexed: 06/28/2023]
Abstract
Metatranscriptomics refers to the analysis of the collective microbial transcriptome of a sample. Its increased utilization for the characterization of human-associated microbial communities has enabled the discovery of many disease-state related microbial activities. Here, we review the principles of metatranscriptomics-based analysis of human-associated microbial samples. We describe strengths and weaknesses of popular sample preparation, sequencing, and bioinformatics approaches and summarize strategies for their use. We then discuss how human-associated microbial communities have recently been examined and how their characterization may change. We conclude that metatranscriptomics insights into human microbiotas under health and disease have not only expanded our knowledge on human health, but also opened avenues for rational antimicrobial drug use and disease management.
Collapse
Affiliation(s)
- Teija Ojala
- Department of Pharmacology, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | | | - Esko Kankuri
- Department of Pharmacology, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Matti Kankainen
- Hematology Research Unit, University of Helsinki, Helsinki, Finland; Laboratory of Genetics, HUS Diagnostic Center, Hospital District of Helsinki and Uusimaa (HUS), Helsinki, Finland.
| |
Collapse
|
27
|
Desdouits M, Reynaud Y, Philippe C, Guyader FSL. A Comprehensive Review for the Surveillance of Human Pathogenic Microorganisms in Shellfish. Microorganisms 2023; 11:2218. [PMID: 37764063 PMCID: PMC10537662 DOI: 10.3390/microorganisms11092218] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Revised: 08/29/2023] [Accepted: 08/30/2023] [Indexed: 09/29/2023] Open
Abstract
Bivalve molluscan shellfish have been consumed for centuries. Being filter feeders, they may bioaccumulate some microorganisms present in coastal water, either naturally or through the discharge of human or animal sewage. Despite regulations set up to avoid microbiological contamination in shellfish, human outbreaks still occur. After providing an overview showing their implication in disease, this review aims to highlight the diversity of the bacteria or enteric viruses detected in shellfish species, including emerging pathogens. After a critical discussion of the available methods and their limitations, we address the interest of technological developments using genomics to anticipate the emergence of pathogens. In the coming years, further research needs to be performed and methods need to be developed in order to design the future of surveillance and to help risk assessment studies, with the ultimate objective of protecting consumers and enhancing the microbial safety of bivalve molluscan shellfish as a healthy food.
Collapse
Affiliation(s)
| | | | | | - Françoise S. Le Guyader
- Ifremer, Unité Microbiologie Aliment Santé et Environnement, RBE/LSEM, 44311 Nantes, France; (M.D.); (Y.R.); (C.P.)
| |
Collapse
|
28
|
Yao Z, Liu Y, Zhan L, Qiu T, Li G, Chen Z, Fang X, Liu Z, Wu W, Liao Z, Xia W. The utilization of nanopore targeted sequencing proves to be advantageous in the identification of infections present in deceased donors. Front Microbiol 2023; 14:1238666. [PMID: 37664117 PMCID: PMC10469296 DOI: 10.3389/fmicb.2023.1238666] [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: 06/12/2023] [Accepted: 08/03/2023] [Indexed: 09/05/2023] Open
Abstract
Background Nanopore Target Sequencing (NTS) represents a novel iteration of gene sequencing technology; however, its potential utility in the detection of infection in deceased donors has yet to be documented. The present study endeavors to assess the applicability of NTS in this domain. Methods This retrospective study comprised a cohort of 71 patients who were under intensive care at Renmin Hospital of Wuhan University between June 2020 and January 2022. The specimens were subjected to microbiological tests utilizing NTS, culture, and other techniques, and subsequently, the diagnostic accuracy of NTS was compared with conventional methods. Results Blood NTS exhibited a better agreement rate of 52.11% and a greater positive rate of pathogen detection than blood culture (50.70% vs. 5.63%, p < 0.001). In NTS of deceased donors, Klebsiella pneumoniae, Escherichia coli, and Acinetobacter baumannii were the most frequently found bacteria, and Candida was the most frequently found fungus. Blood NTS had a considerably better sensitivity for detecting clinical bloodstream infection than blood culture (62.50%: 7.14%, p < 0.001). These findings were supported by comparisons between blood NTS and conventional microbial detection methods (such as blood culture, glucan testing, galactomannan testing, T cell spot testing for tuberculosis infection, smear, etc.). Conclusion The pathogen detection technology NTS has a high sensitivity and positive rate. It can more accurately and earlier detect infection in deceased donors, which could be very important for raising the donation conversion rate.
Collapse
Affiliation(s)
- Zhiyuan Yao
- Department of Critical Care Medicine, Renmin Hospital of Wuhan University, Wuhan, Hubei, China
| | - Yu Liu
- Department of Cardiology, Renmin Hospital of Wuhan University, Wuhan, Hubei, China
- Cardiovascular Research Institute of Wuhan University, Wuhan, Hubei, China
- Hubei Key Laboratory of Cardiology, Wuhan, Hubei, China
| | - Liying Zhan
- Department of Critical Care Medicine, Renmin Hospital of Wuhan University, Wuhan, Hubei, China
| | - Tao Qiu
- Department of Organ Transplantation, Renmin Hospital of Wuhan University, Wuhan, Hubei, China
| | - Guang Li
- Department of Critical Care Medicine, Renmin Hospital of Wuhan University, Wuhan, Hubei, China
| | - Zhongbao Chen
- Department of Organ Transplantation, Renmin Hospital of Wuhan University, Wuhan, Hubei, China
| | - Xiaoyu Fang
- Department of Critical Care Medicine, Renmin Hospital of Wuhan University, Wuhan, Hubei, China
| | - Zhou Liu
- Department of Critical Care Medicine, Renmin Hospital of Wuhan University, Wuhan, Hubei, China
| | - Wei Wu
- Department of Critical Care Medicine, Renmin Hospital of Wuhan University, Wuhan, Hubei, China
| | - Zhaomin Liao
- Department of Critical Care Medicine, Renmin Hospital of Wuhan University, Wuhan, Hubei, China
| | - Wenfang Xia
- Department of Critical Care Medicine, Renmin Hospital of Wuhan University, Wuhan, Hubei, China
| |
Collapse
|
29
|
Li X, Li Z, Wang M, Fu A, Hao X, Guo X, Gu J, Jin W, Yang A. The diagnostic utility of nanopore targeted sequencing in suspected endophthalmitis. Int Ophthalmol 2023; 43:2653-2668. [PMID: 36941506 PMCID: PMC10371907 DOI: 10.1007/s10792-023-02665-7] [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: 10/26/2022] [Accepted: 02/19/2023] [Indexed: 03/23/2023]
Abstract
PURPOSE This paper aimed to assess the diagnostic utility of a newly developed gene-based technology-nanopore targeted sequencing (NTS) in suspected endophthalmitis patients. METHODS This retrospective study included 43 patients (44 eyes) with suspected endophthalmitis. NTS was applied along with microbiological culture to detect unknown pathogens in intraocular fluid samples. The diagnostic utility of NTS was mainly evaluated from three aspects, including the positivity rate of bacterial/fungal presence, diagnostic turnaround time and the frequency of change in treatment based on etiology test results. Non-parametric, two-sided Wilcoxon rank sum test, the McNemar's test and the kappa statistic were used for statistical comparisons. RESULTS NTS showed significant advantages over traditional culture in positivity rates and diagnostic time (P < 0.001, kappa = 0.082; Z = -5.805, P < 0. 001). As regards antibiotic strategy, 17 patients (39.53%) and 5 patients (11.63%) underwent medication change following NTS and culture results respectively (P < 0.001, kappa = 0.335). With reasonable use of antibiotic and surgical intervention, most patients responded favorably, judged by significantly improved visual acuity (Z = -4.249, P < 0.001). The mean duration of hospitalization was 8.49 ± 2.45 days (range, 1-16 days). CONCLUSION The high efficiency feature of NTS in pathogen detection renders it a valuable supplementary to traditional culture. Additionally, it has facilitated patients' management for the early and precise diagnosis of endophthalmitis.
Collapse
Affiliation(s)
- Xuejie Li
- Eye Center, Renmin Hospital of Wuhan University, Jiefang Road 238#, Wuhan, 430060, Hubei Province, China
| | - Ziyue Li
- Eye Center, Renmin Hospital of Wuhan University, Jiefang Road 238#, Wuhan, 430060, Hubei Province, China
| | - Ming Wang
- Department of Clinical Laboratory, Renmin Hospital of Wuhan University, Wuhan, 430060, Hubei Province, China
| | - Aisi Fu
- Wuhan Dgensee Clinical Laboratory Co, Ltd. Wuhan 430075, Hubei Province, China
| | - Xinlei Hao
- Eye Center, Renmin Hospital of Wuhan University, Jiefang Road 238#, Wuhan, 430060, Hubei Province, China
| | - Xinyang Guo
- Eye Center, Renmin Hospital of Wuhan University, Jiefang Road 238#, Wuhan, 430060, Hubei Province, China
| | - Jiashuang Gu
- Wuhan Dgensee Clinical Laboratory Co, Ltd. Wuhan 430075, Hubei Province, China
| | - Wei Jin
- Eye Center, Renmin Hospital of Wuhan University, Jiefang Road 238#, Wuhan, 430060, Hubei Province, China.
| | - Anhuai Yang
- Eye Center, Renmin Hospital of Wuhan University, Jiefang Road 238#, Wuhan, 430060, Hubei Province, China.
| |
Collapse
|
30
|
Zheng P, Zhou C, Ding Y, Liu B, Lu L, Zhu F, Duan S. Nanopore sequencing technology and its applications. MedComm (Beijing) 2023; 4:e316. [PMID: 37441463 PMCID: PMC10333861 DOI: 10.1002/mco2.316] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Revised: 05/29/2023] [Accepted: 05/31/2023] [Indexed: 07/15/2023] Open
Abstract
Since the development of Sanger sequencing in 1977, sequencing technology has played a pivotal role in molecular biology research by enabling the interpretation of biological genetic codes. Today, nanopore sequencing is one of the leading third-generation sequencing technologies. With its long reads, portability, and low cost, nanopore sequencing is widely used in various scientific fields including epidemic prevention and control, disease diagnosis, and animal and plant breeding. Despite initial concerns about high error rates, continuous innovation in sequencing platforms and algorithm analysis technology has effectively addressed its accuracy. During the coronavirus disease (COVID-19) pandemic, nanopore sequencing played a critical role in detecting the severe acute respiratory syndrome coronavirus-2 virus genome and containing the pandemic. However, a lack of understanding of this technology may limit its popularization and application. Nanopore sequencing is poised to become the mainstream choice for preventing and controlling COVID-19 and future epidemics while creating value in other fields such as oncology and botany. This work introduces the contributions of nanopore sequencing during the COVID-19 pandemic to promote public understanding and its use in emerging outbreaks worldwide. We discuss its application in microbial detection, cancer genomes, and plant genomes and summarize strategies to improve its accuracy.
Collapse
Affiliation(s)
- Peijie Zheng
- Department of Clinical MedicineSchool of MedicineZhejiang University City CollegeHangzhouChina
| | - Chuntao Zhou
- Department of Clinical MedicineSchool of MedicineZhejiang University City CollegeHangzhouChina
| | - Yuemin Ding
- Department of Clinical MedicineSchool of MedicineZhejiang University City CollegeHangzhouChina
- Institute of Translational Medicine, School of MedicineZhejiang University City CollegeHangzhouChina
- Key Laboratory of Novel Targets and Drug Study for Neural Repair of Zhejiang Province, School of MedicineZhejiang University City CollegeHangzhouChina
| | - Bin Liu
- Department of Clinical MedicineSchool of MedicineZhejiang University City CollegeHangzhouChina
| | - Liuyi Lu
- Department of Clinical MedicineSchool of MedicineZhejiang University City CollegeHangzhouChina
| | - Feng Zhu
- Department of Clinical MedicineSchool of MedicineZhejiang University City CollegeHangzhouChina
| | - Shiwei Duan
- Department of Clinical MedicineSchool of MedicineZhejiang University City CollegeHangzhouChina
- Institute of Translational Medicine, School of MedicineZhejiang University City CollegeHangzhouChina
- Key Laboratory of Novel Targets and Drug Study for Neural Repair of Zhejiang Province, School of MedicineZhejiang University City CollegeHangzhouChina
| |
Collapse
|
31
|
Notario E, Visci G, Fosso B, Gissi C, Tanaskovic N, Rescigno M, Marzano M, Pesole G. Amplicon-Based Microbiome Profiling: From Second- to Third-Generation Sequencing for Higher Taxonomic Resolution. Genes (Basel) 2023; 14:1567. [PMID: 37628619 PMCID: PMC10454624 DOI: 10.3390/genes14081567] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Revised: 07/25/2023] [Accepted: 07/27/2023] [Indexed: 08/27/2023] Open
Abstract
The 16S rRNA amplicon-based sequencing approach represents the most common and cost-effective strategy with great potential for microbiome profiling. The use of second-generation sequencing (NGS) technologies has led to protocols based on the amplification of one or a few hypervariable regions, impacting the outcome of the analysis. Nowadays, comparative studies are necessary to assess different amplicon-based approaches, including the full-locus sequencing currently feasible thanks to third-generation sequencing (TGS) technologies. This study compared three different methods to achieve the deepest microbiome taxonomic characterization: (a) the single-region approach, (b) the multiplex approach, covering several regions of the target gene/region, both based on NGS short reads, and (c) the full-length approach, which analyzes the whole length of the target gene thanks to TGS long reads. Analyses carried out on benchmark microbiome samples, with a known taxonomic composition, highlighted a different classification performance, strongly associated with the type of hypervariable regions and the coverage of the target gene. Indeed, the full-length approach showed the greatest discriminating power, up to species level, also on complex real samples. This study supports the transition from NGS to TGS for the study of the microbiome, even if experimental and bioinformatic improvements are still necessary.
Collapse
Affiliation(s)
- Elisabetta Notario
- Department of Biosciences, Biotechnology and Environment, University of Bari Aldo Moro, 70126 Bari, Italy; (E.N.); (B.F.); (C.G.)
| | - Grazia Visci
- Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies, Consiglio Nazionale delle Ricerche, 70126 Bari, Italy;
| | - Bruno Fosso
- Department of Biosciences, Biotechnology and Environment, University of Bari Aldo Moro, 70126 Bari, Italy; (E.N.); (B.F.); (C.G.)
| | - Carmela Gissi
- Department of Biosciences, Biotechnology and Environment, University of Bari Aldo Moro, 70126 Bari, Italy; (E.N.); (B.F.); (C.G.)
- Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies, Consiglio Nazionale delle Ricerche, 70126 Bari, Italy;
- CoNISMa, Consorzio Nazionale Interuniversitario per le Scienze del Mare, 00196 Roma, Italy
| | | | - Maria Rescigno
- IRCCS Humanitas Research Hospital, 20089 Rozzano, Italy;
- Department of Biomedical Sciences, Humanitas University, 20072 Pieve Emanuele, Italy
| | - Marinella Marzano
- Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies, Consiglio Nazionale delle Ricerche, 70126 Bari, Italy;
| | - Graziano Pesole
- Department of Biosciences, Biotechnology and Environment, University of Bari Aldo Moro, 70126 Bari, Italy; (E.N.); (B.F.); (C.G.)
- Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies, Consiglio Nazionale delle Ricerche, 70126 Bari, Italy;
- Consorzio Interuniversitario Biotecnologie, 34148 Trieste, Italy
| |
Collapse
|
32
|
Shih CY, Chen SY, Hsu CR, Chin CH, Chiu WC, Chang MH, Kang LK, Yang CH, Pai TW, Hu CH, Hsu PH, Tzou WS. Distinctive microbial community and genome structure in coastal seawater from a human-made port and nearby offshore island in northern Taiwan facing the Northwestern Pacific Ocean. PLoS One 2023; 18:e0284022. [PMID: 37294811 PMCID: PMC10256201 DOI: 10.1371/journal.pone.0284022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Accepted: 03/21/2023] [Indexed: 06/11/2023] Open
Abstract
Pollution in human-made fishing ports caused by petroleum from boats, dead fish, toxic chemicals, and effluent poses a challenge to the organisms in seawater. To decipher the impact of pollution on the microbiome, we collected surface water from a fishing port and a nearby offshore island in northern Taiwan facing the Northwestern Pacific Ocean. By employing 16S rRNA gene amplicon sequencing and whole-genome shotgun sequencing, we discovered that Rhodobacteraceae, Vibrionaceae, and Oceanospirillaceae emerged as the dominant species in the fishing port, where we found many genes harboring the functions of antibiotic resistance (ansamycin, nitroimidazole, and aminocoumarin), metal tolerance (copper, chromium, iron and multimetal), virulence factors (chemotaxis, flagella, T3SS1), carbohydrate metabolism (biofilm formation and remodeling of bacterial cell walls), nitrogen metabolism (denitrification, N2 fixation, and ammonium assimilation), and ABC transporters (phosphate, lipopolysaccharide, and branched-chain amino acids). The dominant bacteria at the nearby offshore island (Alteromonadaceae, Cryomorphaceae, Flavobacteriaceae, Litoricolaceae, and Rhodobacteraceae) were partly similar to those in the South China Sea and the East China Sea. Furthermore, we inferred that the microbial community network of the cooccurrence of dominant bacteria on the offshore island was connected to dominant bacteria in the fishing port by mutual exclusion. By examining the assembled microbial genomes collected from the coastal seawater of the fishing port, we revealed four genomic islands containing large gene-containing sequences, including phage integrase, DNA invertase, restriction enzyme, DNA gyrase inhibitor, and antitoxin HigA-1. In this study, we provided clues for the possibility of genomic islands as the units of horizontal transfer and as the tools of microbes for facilitating adaptation in a human-made port environment.
Collapse
Affiliation(s)
- Chi-Yu Shih
- Bachelor Degree Program in Marine Biotechnology, National Taiwan Ocean University, Keelung, Taiwan
- Taiwan Ocean Genome Center, National Taiwan Ocean University, Keelung, Taiwan
| | - Shiow-Yi Chen
- Departent of Bioscience and Biotechnology, National Taiwan Ocean University, Keelung, Taiwan
- Center of Excellence for the Oceans, National Taiwan Ocean University, Keelung, Taiwan
| | - Chun-Ru Hsu
- Departent of Bioscience and Biotechnology, National Taiwan Ocean University, Keelung, Taiwan
- Center of Excellence for the Oceans, National Taiwan Ocean University, Keelung, Taiwan
| | - Ching-Hsiang Chin
- Departent of Bioscience and Biotechnology, National Taiwan Ocean University, Keelung, Taiwan
| | - Wei-Chih Chiu
- Departent of Bioscience and Biotechnology, National Taiwan Ocean University, Keelung, Taiwan
| | | | - Lee-Kuo Kang
- Bachelor Degree Program in Marine Biotechnology, National Taiwan Ocean University, Keelung, Taiwan
| | - Cing-Han Yang
- Department of Computer Science and Information Engineering, National Taipei University of Technology, Taipei, Taiwan
- Department of Computer Science and Engineering, National Taiwan Ocean University, Keelung, Taiwan
| | - Tun-Wen Pai
- Department of Computer Science and Information Engineering, National Taipei University of Technology, Taipei, Taiwan
- Department of Computer Science and Engineering, National Taiwan Ocean University, Keelung, Taiwan
| | - Chin-Hwa Hu
- Departent of Bioscience and Biotechnology, National Taiwan Ocean University, Keelung, Taiwan
- Center of Excellence for the Oceans, National Taiwan Ocean University, Keelung, Taiwan
| | - Pang-Hung Hsu
- Departent of Bioscience and Biotechnology, National Taiwan Ocean University, Keelung, Taiwan
- Center of Excellence for the Oceans, National Taiwan Ocean University, Keelung, Taiwan
| | - Wen-Shyong Tzou
- Taiwan Ocean Genome Center, National Taiwan Ocean University, Keelung, Taiwan
- Departent of Bioscience and Biotechnology, National Taiwan Ocean University, Keelung, Taiwan
- Center of Excellence for the Oceans, National Taiwan Ocean University, Keelung, Taiwan
| |
Collapse
|
33
|
Stevens BM, Creed TB, Reardon CL, Manter DK. Comparison of Oxford Nanopore Technologies and Illumina MiSeq sequencing with mock communities and agricultural soil. Sci Rep 2023; 13:9323. [PMID: 37291169 PMCID: PMC10250467 DOI: 10.1038/s41598-023-36101-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2022] [Accepted: 05/30/2023] [Indexed: 06/10/2023] Open
Abstract
Illumina MiSeq is the current standard for characterizing microbial communities in soil. The newer alternative, Oxford Nanopore Technologies MinION sequencer, is quickly gaining popularity because of the low initial cost and longer sequence reads. However, the accuracy of MinION, per base, is much lower than MiSeq (95% versus 99.9%). The effects of this difference in base-calling accuracy on taxonomic and diversity estimates remains unclear. We compared the effects of platform, primers, and bioinformatics on mock community and agricultural soil samples using short MiSeq, and short and full-length MinION 16S rRNA amplicon sequencing. For all three methods, we found that taxonomic assignments of the mock community at both the genus and species level matched expectations with minimal deviation (genus: 80.9-90.5%; species: 70.9-85.2% Bray-Curtis similarity); however, the short MiSeq with error correction (DADA2) resulted in the correct estimate of mock community species richness and much lower alpha diversity for soils. Several filtering strategies were tested to improve these estimates with varying results. The sequencing platform also had a significant influence on the relative abundances of taxa with MiSeq resulting in significantly higher abundances Actinobacteria, Chloroflexi, and Gemmatimonadetes and lower abundances of Acidobacteria, Bacteroides, Firmicutes, Proteobacteria, and Verrucomicrobia compared to the MinION platform. When comparing agricultural soils from two different sites (Fort Collins, CO and Pendleton, OR), methods varied in the taxa identified as significantly different between sites. At all taxonomic levels, the full-length MinION method had the highest similarity to the short MiSeq method with DADA2 correction with 73.2%, 69.3%, 74.1%, 79.3%, 79.4%, and 82.28% of the taxa at the phyla, class, order, family, genus, and species levels, respectively, showing similar patterns in differences between the sites. In summary, although both platforms appear suitable for 16S rRNA microbial community composition, biases for different taxa may make the comparison between studies problematic; and even with a single study (i.e., comparing sites or treatments), the sequencing platform can influence the differentially abundant taxa identified.
Collapse
Affiliation(s)
- Bo Maxwell Stevens
- Water Management and Systems Research Unit, USDA ARS, Fort Collins, CO, 80526, USA
| | - Tim B Creed
- Soil Management and Sugar Beet Research Unit, USDA ARS, Fort Collins, CO, 80526, USA
| | - Catherine L Reardon
- Columbia Plateau Conservation Research Center, USDA ARS, Adams, OR, 97810, USA
| | - Daniel K Manter
- Soil Management and Sugar Beet Research Unit, USDA ARS, Fort Collins, CO, 80526, USA.
| |
Collapse
|
34
|
Andersen MH, Thomsen L, Stokholm-Bjerregaard M, Eriksen S, Hansen SH, Albertsen M, Nielsen PH. Fast DNA-analyses for surveillance of microbial communities in full-scale deammonification tanks: Potential for control and troubleshooting. WATER RESEARCH 2023; 236:119919. [PMID: 37031530 DOI: 10.1016/j.watres.2023.119919] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/07/2022] [Revised: 03/17/2023] [Accepted: 03/26/2023] [Indexed: 06/19/2023]
Abstract
The partial nitritation/anammox process is a popular process for sidestream nitrogen removal, but the process is sensitive to disturbances and requires extensive surveillance and monitoring for optimal performance. We followed two parallel sidestream full-scale deammonification reactors treating digester centrate for a year with high time-resolution of both online sensor data and microbial community as measured by Nanopore DNA sequencing. DNA surveillance revealed system disturbances and allowed for detection of process and equipment upsets, and it facilitated remediating operational actions. Surveillance of anammox bacteria (Ca. Brocadia) revealed unexpected variations, and the composition and dynamics of the flanking community indicated causes for occasional process disturbances with poor nitrogen removal. Monitoring the ammonia oxidizing bacteria (AOB) and nitrite oxidizing bacteria (NOB) could potentially allow reactor operation with increased dissolved oxygen (DO), yielding higher ammonia conversion while keeping NOB in control. The use of fast and frequent DNA sequencing (sampling 3-5 times a week, analysed once per week) was an important supplement, and in many cases superior, to the online sensor data for process surveillance, understanding and control.
Collapse
Affiliation(s)
- Martin Hjorth Andersen
- Center for Microbial Communities, Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark
| | - Lisette Thomsen
- Center for Microbial Communities, Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark
| | | | | | - Susan Hove Hansen
- Center for Microbial Communities, Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark
| | - Mads Albertsen
- Center for Microbial Communities, Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark
| | - Per Halkjær Nielsen
- Center for Microbial Communities, Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark.
| |
Collapse
|
35
|
Qian P, He X, Yang M, Wei L, Zhang L, Xing X. Detection of Severe Murine Typhus by Nanopore Targeted Sequencing, China. Emerg Infect Dis 2023; 29:1275-1277. [PMID: 37209688 DOI: 10.3201/eid2906.221929] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/22/2023] Open
Abstract
We report a case of murine typhus in China caused by Rickettsia typhi and diagnosed by nanopore targeted sequencing of a bronchoalveolar lavage fluid sample. This case highlights that nanopore targeted sequencing can effectively detect clinically unexplained infections and be especially useful for detecting infections in patients without typical signs and symptoms.
Collapse
|
36
|
Wilkinson H, McCarthy HS, Perry J, Smith T, Wright K, Cool P. Genomic Sequencing to Diagnose Prosthetic Joint Infection in the Knee: A Case Report. Cureus 2023; 15:e38788. [PMID: 37303456 PMCID: PMC10250129 DOI: 10.7759/cureus.38788] [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] [Accepted: 05/09/2023] [Indexed: 06/13/2023] Open
Abstract
There is currently no "gold-standard" method to diagnose prosthetic joint infections (PJI), and the current practice of using microbiological cultures has many limitations. The identification of the bacterial species causing the infection is crucial to guide treatment; therefore, a robust method needs to be developed. Here, we attempt to use genomic sequencing with the MinION device from Oxford Nanopore Technologies to identify the species of bacteria causing PJI in a 61-year-old male. Genomic sequencing with the MinION presents an opportunity to produce species identification in real-time and at a smaller cost than current methods. By comparing results with standard hospital microbiological cultures, this study suggests that nanopore sequencing using the MinION could be a faster and more sensitive method to diagnose PJI than microbiological cultures.
Collapse
Affiliation(s)
| | - Helen S McCarthy
- Spinal Studies, The Robert Jones and Agnes Hunt Orthopaedic Hospital, Oswestry, GBR
- School of Pharmacy and Bioengineering, Keele University, Keele, GBR
| | - Jade Perry
- Spinal Studies, The Robert Jones and Agnes Hunt Orthopaedic Hospital, Oswestry, GBR
- School of Pharmacy and Bioengineering, Keele University, Keele, GBR
| | - Tony Smith
- Surgery, The Robert Jones and Agnes Hunt Orthopaedic Hospital, Oswestry, GBR
| | - Karina Wright
- Spinal Studies, The Robert Jones and Agnes Hunt Orthopaedic Hospital, Oswestry, GBR
- School of Pharmacy and Bioengineering, Keele University, Keele, GBR
| | - Paul Cool
- Orthopaedic Oncology, The Robert Jones and Agnes Hunt Orthopaedic Hospital, Oswestry, GBR
- Medical Sciences, Keele University, Keele, GBR
| |
Collapse
|
37
|
Kruasuwan W, Jenjaroenpun P, Arigul T, Chokesajjawatee N, Leekitcharoenphon P, Foongladda S, Wongsurawat T. Nanopore Sequencing Discloses Compositional Quality of Commercial Probiotic Feed Supplements. Sci Rep 2023; 13:4540. [PMID: 36941307 PMCID: PMC10027865 DOI: 10.1038/s41598-023-31626-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2022] [Accepted: 03/15/2023] [Indexed: 03/23/2023] Open
Abstract
The market for the application of probiotics as a livestock health improvement supplement has increased in recent years. However, most of the available products are quality-controlled using low-resolution techniques and un-curated databases, resulting in misidentification and incorrect product labels. In this work, we deployed two workflows and compared results obtained by full-length 16S rRNA genes (16S) and metagenomic (Meta) data to investigate their reliability for the microbial composition of both liquid and solid forms of animal probiotic products using Oxford Nanopore long-read-only (without short-read). Our result revealed that 16S amplicon data permits to detect the bacterial microbiota even with the low abundance in the samples. Moreover, the 16S approach has the potential to provide species-level resolution for prokaryotes but not for assessing yeast communities. Whereas, Meta data has more power to recover of high-quality metagenome-assembled genomes that enables detailed exploration of both bacterial and yeast populations, as well as antimicrobial resistance genes, and functional genes in the population. Our findings clearly demonstrate that implementing these workflows with long-read-only monitoring could be applied to assessing the quality and safety of probiotic products for animals and evaluating the quality of probiotic products on the market. This would benefit the sustained growth of the livestock probiotic industry.
Collapse
Affiliation(s)
- Worarat Kruasuwan
- Division of Medical Bioinformatics, Research Department, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
- Siriraj Long-Read Lab (Si-LoL), Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Piroon Jenjaroenpun
- Division of Medical Bioinformatics, Research Department, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
- Siriraj Long-Read Lab (Si-LoL), Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
- Department of Biomedical Informatics, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - Tantip Arigul
- Division of Medical Bioinformatics, Research Department, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
- Siriraj Long-Read Lab (Si-LoL), Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Nipa Chokesajjawatee
- National Center for Genetic Engineering and Biotechnology (BIOTEC), 113 Thailand Science Park, Phahonyothin Road, Khlong Nueng, Khlong Luang, Pathum Thani, Thailand
| | - Pimlapas Leekitcharoenphon
- Research Group for Genomic Epidemiology, National Food Institute, Technical University of Denmark, 2800, Kgs. Lyngby, Denmark
| | - Suporn Foongladda
- Department of Microbiology, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Thidathip Wongsurawat
- Division of Medical Bioinformatics, Research Department, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand.
- Siriraj Long-Read Lab (Si-LoL), Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand.
- Department of Biomedical Informatics, University of Arkansas for Medical Sciences, Little Rock, AR, USA.
| |
Collapse
|
38
|
Campos-Iglesias D, Freije JMP, López-Otín C. Assessing microbiota composition in the context of aging. Methods Cell Biol 2023; 181:73-85. [PMID: 38302245 DOI: 10.1016/bs.mcb.2022.12.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/10/2023]
Abstract
The gut microbiota is a complex community of different microbial species that influence many aspects of health. Consequently, shifts in the composition of gut microbiome have been proposed to exert negative effects on the host physiology, leading to the pathogenesis of various age-related disorders, including cardiovascular and neurological diseases, type 2 diabetes, obesity, non-alcoholic liver disease, and other pathological conditions. Thus, understanding how the gut microbiota influences the aging-related decline is particularly topical. Advances in next-generation sequencing techniques, together with mechanistic experiments in animal models, have provided substantial improvements in microbiome analysis. However, standardization and best practices are needed to limit experimental variation between different studies. Here, we detail a simple method for microbiota composition analysis in mouse fecal samples using 16S rRNA next-generation sequencing.
Collapse
Affiliation(s)
- Diana Campos-Iglesias
- Departamento de Bioquímica y Biología Molecular, Instituto Universitario de Oncología del Principado de Asturias (IUOPA), Universidad de Oviedo, Oviedo, Spain; Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain; Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Oviedo, Spain
| | - José M P Freije
- Departamento de Bioquímica y Biología Molecular, Instituto Universitario de Oncología del Principado de Asturias (IUOPA), Universidad de Oviedo, Oviedo, Spain; Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain; Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Oviedo, Spain
| | - Carlos López-Otín
- Departamento de Bioquímica y Biología Molecular, Instituto Universitario de Oncología del Principado de Asturias (IUOPA), Universidad de Oviedo, Oviedo, Spain; Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain; Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Oviedo, Spain.
| |
Collapse
|
39
|
Xiao X, Liu S, Deng H, Song Y, Zhang L, Song Z. Advances in the oral microbiota and rapid detection of oral infectious diseases. Front Microbiol 2023; 14:1121737. [PMID: 36814562 PMCID: PMC9939651 DOI: 10.3389/fmicb.2023.1121737] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Accepted: 01/13/2023] [Indexed: 02/09/2023] Open
Abstract
Several studies have shown that the dysregulation of the oral microbiota plays a crucial role in human health conditions, such as dental caries, periodontal disease, oral cancer, other oral infectious diseases, cardiovascular diseases, diabetes, bacteremia, and low birth weight. The use of traditional detection methods in conjunction with rapidly advancing molecular techniques in the diagnosis of harmful oral microorganisms has expanded our understanding of the diversity, location, and function of the microbiota associated with health and disease. This review aimed to highlight the latest knowledge in this field, including microbial colonization; the most modern detection methods; and interactions in disease progression. The next decade may achieve the rapid diagnosis and precise treatment of harmful oral microorganisms.
Collapse
Affiliation(s)
- Xuan Xiao
- Department of Oral Mucosa, Shanghai Stomatological Hospital, Fudan University, Shanghai, China,Shanghai Key Laboratory of Craniomaxillofacial Development and Diseases, Shanghai Stomatological Hospital, Fudan University, Shanghai, China
| | - Shangfeng Liu
- Shanghai Key Laboratory of Craniomaxillofacial Development and Diseases, Shanghai Stomatological Hospital, Fudan University, Shanghai, China
| | - Hua Deng
- Translational Medicine Center, Guangdong Women and Children Hospital, Guangzhou, China
| | - Yuhan Song
- Department of Oral Mucosa, Shanghai Stomatological Hospital, Fudan University, Shanghai, China,Shanghai Key Laboratory of Craniomaxillofacial Development and Diseases, Shanghai Stomatological Hospital, Fudan University, Shanghai, China
| | - Liang Zhang
- Translational Medicine Center, Guangdong Women and Children Hospital, Guangzhou, China,Liang Zhang,
| | - Zhifeng Song
- Department of Oral Mucosa, Shanghai Stomatological Hospital, Fudan University, Shanghai, China,Shanghai Key Laboratory of Craniomaxillofacial Development and Diseases, Shanghai Stomatological Hospital, Fudan University, Shanghai, China,*Correspondence: Zhifeng Song,
| |
Collapse
|
40
|
Arias D, Salazar-Ardiles C, Andrade DC, Rivas M, Panico A, Race M, Cisternas LA, Dorador C. The microbial world in copper sulfide flotation plants (CSFP): Novel insights into bacterial communities and their application as potential pyrite bioreagents. ENVIRONMENTAL RESEARCH 2023; 218:114904. [PMID: 36502904 DOI: 10.1016/j.envres.2022.114904] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Revised: 11/10/2022] [Accepted: 11/21/2022] [Indexed: 06/17/2023]
Abstract
Operations in copper sulfide flotation plants (CSFP) are complex and governed by several variables such as available technologies, reagents, and environmental conditions. However, few investigations are related to studying the microbial communities. These aspects provide a reason to compare the bacterial communities of two CSFP operated with freshwater (FwFlo) and seawater (SwFlo), and study whether indigenous bacteria could be used as pyrite bioreagents. Analyses were determined through next-generation sequencing by Illumina MiSeq System and conducted throughout the entire process: (i) minerals before and after grinding; (ii) final concentrate and concentrate thickener overflow; (iii) final tailings and tailings thickener overflow; and (iv) intake water. Bacterial strains from both plants were tested as potential bioreagents, given their tendency to adhere to pyrite after 5 min. In both CSFP, Proteobacteria (relative abundance from 45.48% to 79.22%), followed by Bacteroidetes (9.37%-44.7%), were the most abundant phyla. Regarding species, Algoriphagus olei (11.35%-43.52%) was present exclusively in FwFlo samples in contact with process water and absent in the mineral before grinding, where Cupriavidus metallidurans (16.05%) and Pseudomonas_uc (11.79%) predominated. In SwFlo samples, Marinobacter flavimaris (3.47%-41.1%), and GU061212-s (10.92%-27.63%), were the most abundant microorganisms. All of them were also detected in intake seawater. The strains with the highest adhesion rate (from 29.84% ± 0.14-100%) were phylogenetically identified as species of the genera Marinobacter, Pseudomonas, Idiomarina, Halomonas, Bacillus, Aerocuccus, and Peribacillus. Our results reveal that bacterial communities are critically dependent on process waters during mining activities, and our data depicted that indigenous bacteria could be used as potential pyrite bioreagents, evidenced by a high adhesion rate. It is thus possible to propose that different indigenous bacterial strains could be considered as new bioreagents to reduce the impact of conventional flotation reagents on health from an environment friendly perspective.
Collapse
Affiliation(s)
- Dayana Arias
- Departamento de Biotecnología, Facultad de Ciencias del Mar y Recursos Biológicos, Universidad de Antofagasta, Av. Angamos 601, Antofagasta, Chile.
| | - Camila Salazar-Ardiles
- Departamento Tecnología Médica, Facultad de Ciencias de Salud, Universidad de Antofagasta, Av. Angamos 601, Antofagasta, Chile; Centro de Investigación en Fisiología y Medicina de Altura, Departamento Biomédico, Facultad de Ciencias de la Salud, Universidad de Antofagasta, Av. Angamos 601, Antofagasta, Chile
| | - David C Andrade
- Centro de Investigación en Fisiología y Medicina de Altura, Departamento Biomédico, Facultad de Ciencias de la Salud, Universidad de Antofagasta, Av. Angamos 601, Antofagasta, Chile
| | - Mariella Rivas
- Departamento de Biotecnología, Facultad de Ciencias del Mar y Recursos Biológicos, Universidad de Antofagasta, Av. Angamos 601, Antofagasta, Chile
| | - Antonio Panico
- Department of Engineering, University of Campania L. Vanvitelli, 81031, Aversa, Italy
| | - Marco Race
- Department of Civil and Mechanical Engineering, University of Cassino and Southern Lazio, Via di Biasio 43, 03043, Cassino, Italy
| | - Luis A Cisternas
- Departamento de Ingeniería Química y Procesos de Minerales, Universidad de Antofagasta, Av. Angamos 601, Antofagasta, Chile
| | - Cristina Dorador
- Departamento de Biotecnología, Facultad de Ciencias del Mar y Recursos Biológicos, Universidad de Antofagasta, Av. Angamos 601, Antofagasta, Chile
| |
Collapse
|
41
|
Zampieri G, Campanaro S, Angione C, Treu L. Metatranscriptomics-guided genome-scale metabolic modeling of microbial communities. CELL REPORTS METHODS 2023; 3:100383. [PMID: 36814842 PMCID: PMC9939383 DOI: 10.1016/j.crmeth.2022.100383] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Revised: 10/07/2022] [Accepted: 12/12/2022] [Indexed: 01/09/2023]
Abstract
Multi-omics data integration via mechanistic models of metabolism is a scalable and flexible framework for exploring biological hypotheses in microbial systems. However, although most microorganisms are unculturable, such multi-omics modeling is limited to isolate microbes or simple synthetic communities. Here, we developed an approach for modeling microbial activity and interactions that leverages the reconstruction of metagenome-assembled genomes and associated genome-centric metatranscriptomes. At its core, we designed a method for condition-specific metabolic modeling of microbial communities through the integration of metatranscriptomic data. Using this approach, we explored the behavior of anaerobic digestion consortia driven by hydrogen availability and human gut microbiota dysbiosis associated with Crohn's disease, identifying condition-dependent amino acid requirements in archaeal species and a reduced short-chain fatty acid exchange network associated with disease, respectively. Our approach can be applied to complex microbial communities, allowing a mechanistic contextualization of multi-omics data on a metagenome scale.
Collapse
Affiliation(s)
- Guido Zampieri
- Department of Biology, University of Padova, Padova 35121, Italy
| | - Stefano Campanaro
- Department of Biology, University of Padova, Padova 35121, Italy
- CRIBI Biotechnology Center, University of Padova, Padova 35121, Italy
| | - Claudio Angione
- School of Computing, Engineering and Digital Technologies, Teesside University, Middlesbrough TS1 3BX, UK
- National Horizons Centre, Teesside University, Darlington DL1 1HG, UK
- Centre for Digital Innovation, Teesside University, Middlesbrough TS1 3BX, UK
| | - Laura Treu
- Department of Biology, University of Padova, Padova 35121, Italy
| |
Collapse
|
42
|
Luo L, Fu A, Shi M, Hu J, Kong D, Liu T, Yuan J, Sun S, Chen C. Species-Level Characterization of the Microbiome in Breast Tissues with Different Malignancy and Hormone-Receptor Statuses Using Nanopore Sequencing. J Pers Med 2023; 13:jpm13020174. [PMID: 36836409 PMCID: PMC9965790 DOI: 10.3390/jpm13020174] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2022] [Revised: 01/13/2023] [Accepted: 01/16/2023] [Indexed: 01/21/2023] Open
Abstract
Unambiguous evidence indicates that microbes are closely linked to various human diseases, including cancer. Most prior work investigating the microbiome of breast tissue describes an association between compositional differences of microbial species in benign and malignant tissues, but few studies have examined the relative abundance of microbial communities within human breast tissue at the species level. In this work, a total of 44 breast tissue samples including benign and malignant tissues with adjacent normal breast tissue pairs were collected, and Oxford Nanopore long-read sequencing was employed to assess breast tissue microbial signatures. Nearly 900 bacterial species were detected from the four dominant phyla: Proteobacteria, Firmicutes, Actinobacteria and Bacteroidetes. The bacteria with the highest abundance in all breast tissues was Ralstonia pickettii, and its relative abundance increased with decreasing malignancy. We further examined the breast-tissue microbiome composition with different hormone-receptor statuses, and the relative abundance of the genus Pseudomonas increased most significantly in breast tissues. Our study provides a rationale for exploring microbiomes associated with breast carcinogenesis and cancer development. Further large-cohort investigation of the breast microbiome is necessary to characterize a microbial risk signature and develop potential microbial-based prevention therapies.
Collapse
Affiliation(s)
- Lan Luo
- Department of Thyroid and Breast Surgery, Renmin Hospital of Wuhan University, Wuhan 430060, China
| | - Aisi Fu
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education and Wuhan University School of Pharmaceutical Sciences, Wuhan 430060, China
| | - Manman Shi
- Department of Thyroid and Breast Surgery, Renmin Hospital of Wuhan University, Wuhan 430060, China
| | - Jiawei Hu
- Department of Thyroid and Breast Surgery, Renmin Hospital of Wuhan University, Wuhan 430060, China
| | - Deguang Kong
- Department of Thyroid and Breast Surgery, Renmin Hospital of Wuhan University, Wuhan 430060, China
| | - Tiangang Liu
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education and Wuhan University School of Pharmaceutical Sciences, Wuhan 430060, China
| | - Jingping Yuan
- Department of Pathology, Renmin Hospital of Wuhan University, Wuhan 430060, China
| | - Shengrong Sun
- Department of Thyroid and Breast Surgery, Renmin Hospital of Wuhan University, Wuhan 430060, China
| | - Chuang Chen
- Department of Thyroid and Breast Surgery, Renmin Hospital of Wuhan University, Wuhan 430060, China
- Correspondence:
| |
Collapse
|
43
|
Neidhöfer C, Sib E, Benhsain AH, Mutschnik-Raab C, Schwabe A, Wollkopf A, Wetzig N, Sieber MA, Thiele R, Döhla M, Engelhart S, Mutters NT, Parčina M. Examining Different Analysis Protocols Targeting Hospital Sanitary Facility Microbiomes. Microorganisms 2023; 11:microorganisms11010185. [PMID: 36677477 PMCID: PMC9867353 DOI: 10.3390/microorganisms11010185] [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: 11/22/2022] [Revised: 01/02/2023] [Accepted: 01/07/2023] [Indexed: 01/15/2023] Open
Abstract
Indoor spaces exhibit microbial compositions that are distinctly dissimilar from one another and from outdoor spaces. Unique in this regard, and a topic that has only recently come into focus, is the microbiome of hospitals. While the benefits of knowing exactly which microorganisms propagate how and where in hospitals are undoubtedly beneficial for preventing hospital-acquired infections, there are, to date, no standardized procedures on how to best study the hospital microbiome. Our study aimed to investigate the microbiome of hospital sanitary facilities, outlining the extent to which hospital microbiome analyses differ according to sample-preparation protocol. For this purpose, fifty samples were collected from two separate hospitals-from three wards and one hospital laboratory-using two different storage media from which DNA was extracted using two different extraction kits and sequenced with two different primer pairs (V1-V2 and V3-V4). There were no observable differences between the sample-preservation media, small differences in detected taxa between the DNA extraction kits (mainly concerning Propionibacteriaceae), and large differences in detected taxa between the two primer pairs V1-V2 and V3-V4. This analysis also showed that microbial occurrences and compositions can vary greatly from toilets to sinks to showers and across wards and hospitals. In surgical wards, patient toilets appeared to be characterized by lower species richness and diversity than staff toilets. Which sampling sites are the best for which assessments should be analyzed in more depth. The fact that the sample processing methods we investigated (apart from the choice of primers) seem to have changed the results only slightly suggests that comparing hospital microbiome studies is a realistic option. The observed differences in species richness and diversity between patient and staff toilets should be further investigated, as these, if confirmed, could be a result of excreted antimicrobials.
Collapse
Affiliation(s)
- Claudio Neidhöfer
- Institute of Medical Microbiology, Immunology and Parasitology, University Hospital Bonn, Venusberg-Campus 1, 53127 Bonn, Germany
- Correspondence:
| | - Esther Sib
- Institute for Hygiene and Public Health, University of Bonn, 53127 Bonn, Germany
| | - Al-Harith Benhsain
- Institute of Medical Microbiology, Immunology and Parasitology, University Hospital Bonn, Venusberg-Campus 1, 53127 Bonn, Germany
| | | | - Anna Schwabe
- Institute for Hygiene and Public Health, University of Bonn, 53127 Bonn, Germany
| | - Alexander Wollkopf
- Institute for Hygiene and Public Health, University of Bonn, 53127 Bonn, Germany
| | - Nina Wetzig
- Institute for Functional Gene Analytics, Bonn-Rhein-Sieg University of Applied Sciences, 53757 Sankt Augustin, Germany
| | - Martin A. Sieber
- Institute for Functional Gene Analytics, Bonn-Rhein-Sieg University of Applied Sciences, 53757 Sankt Augustin, Germany
| | - Ralf Thiele
- Institute for Functional Gene Analytics, Bonn-Rhein-Sieg University of Applied Sciences, 53757 Sankt Augustin, Germany
| | - Manuel Döhla
- Institute for Hygiene and Public Health, University of Bonn, 53127 Bonn, Germany
- Department of Microbiology and Hospital Hygiene, Bundeswehr Central Hospital Koblenz, 56072 Koblenz, Germany
| | - Steffen Engelhart
- Institute for Hygiene and Public Health, University of Bonn, 53127 Bonn, Germany
| | - Nico T. Mutters
- Institute for Hygiene and Public Health, University of Bonn, 53127 Bonn, Germany
| | - Marijo Parčina
- Institute of Medical Microbiology, Immunology and Parasitology, University Hospital Bonn, Venusberg-Campus 1, 53127 Bonn, Germany
| |
Collapse
|
44
|
Ahmadi A, Khezri A, Nørstebø H, Ahmad R. A culture-, amplification-independent, and rapid method for identification of pathogens and antibiotic resistance profile in bovine mastitis milk. Front Microbiol 2023; 13:1104701. [PMID: 36687564 PMCID: PMC9852903 DOI: 10.3389/fmicb.2022.1104701] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Accepted: 12/19/2022] [Indexed: 01/07/2023] Open
Abstract
Introduction Rapid and accurate diagnosis of causative pathogens in mastitis would minimize the imprudent use of antibiotics and, therefore, reduce the spread of antimicrobial resistance. Whole genome sequencing offers a unique opportunity to study the microbial community and antimicrobial resistance (AMR) in mastitis. However, the complexity of milk samples and the presence of a high amount of host DNA in milk from infected udders often make this very challenging. Methods Here, we tested 24 bovine milk samples (18 mastitis and six non-mastitis) using four different commercial kits (Qiagens' DNeasy® PowerFood® Microbial, Norgens' Milk Bacterial DNA Isolation, and Molzyms' MolYsis™ Plus and Complete5) in combination with filtration, low-speed centrifugation, nuclease, and 10% bile extract of male bovine (Ox bile). Isolated DNA was quantified, checked for the presence/absence of host and pathogen using PCR and sequenced using MinION nanopore sequencing. Bioinformatics analysis was performed for taxonomic classification and antimicrobial resistance gene detection. Results The results showed that kits designed explicitly for bacterial DNA isolation from food and dairy matrices could not deplete/minimize host DNA. Following using MolYsis™ Complete 5 + 10% Ox bile + micrococcal nuclease combination, on average, 17% and 66.5% of reads were classified as bovine and Staphylococcus aureus reads, respectively. This combination also effectively enriched other mastitis pathogens, including Escherichia coli and Streptococcus dysgalactiae. Furthermore, using this approach, we identified important AMR genes such as Tet (A), Tet (38), fosB-Saur, and blaZ. We showed that even 40 min of the MinION run was enough for bacterial identification and detecting the first AMR gene. Conclusion We implemented an effective method (sensitivity of 100% and specificity of 92.3%) for host DNA removal and bacterial DNA enrichment (both gram-negative and positive) directly from bovine mastitis milk. To the best of our knowledge, this is the first culture- and amplification-independent study using nanopore-based metagenomic sequencing for real-time detection of the pathogen (within 5 hours) and the AMR profile (within 5-9 hours), in mastitis milk samples. These results provide a promising and potential future on-farm adaptable approach for better clinical management of mastitis.
Collapse
Affiliation(s)
- Asal Ahmadi
- Department of Biotechnology, Inland Norway University of Applied Sciences, Hamar, Norway
| | - Abdolrahman Khezri
- Department of Biotechnology, Inland Norway University of Applied Sciences, Hamar, Norway
| | | | - Rafi Ahmad
- Department of Biotechnology, Inland Norway University of Applied Sciences, Hamar, Norway,Institute of Clinical Medicine, Faculty of Health Sciences, UiT–The Arctic University of Norway, Tromsø, Norway,*Correspondence: Rafi Ahmad,
| |
Collapse
|
45
|
Bağcı C, Albrecht B, Huson DH. MAIRA: Protein-based Analysis of MinION Reads on a Laptop. Methods Mol Biol 2023; 2649:223-234. [PMID: 37258865 DOI: 10.1007/978-1-0716-3072-3_11] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
Third-generation sequencing technologies are being increasingly used in microbiome research and this has given rise to new challenges in computational microbiome analysis. Oxford Nanopore's MinION is a portable sequencer that streams data that can be basecalled on-the-fly. Here we give an introduction to the MAIRA software, which is designed to analyze MinION sequencing reads from a microbiome sample, as they are produced in real-time, on a laptop. The software processes reads in batches and updates the presented analysis after each batch. There are two analysis steps: First, protein alignments are calculated to determine which genera might be present in a sample. When strong evidence for a genus is found, then, in a second step, a more detailed analysis is performed by aligning the reads against the proteins of all species in the detected genus. The program presents a detailed analysis of species, antibiotic resistance genes, and virulence factors.
Collapse
Affiliation(s)
- Caner Bağcı
- Institute for Bioinformatics and Medical Informatics, University of Tübingen, Tübingen, Germany.
- International Max Planck Research School "From Molecules to Organisms", Max Planck Institute for Developmental Biology, Tübingen, Germany.
| | | | - Daniel H Huson
- Institute for Bioinformatics and Medical Informatics, University of Tübingen, Tübingen, Germany.
| |
Collapse
|
46
|
Kryukov K, Imanishi T, Nakagawa S. Nanopore Sequencing Data Analysis of 16S rRNA Genes Using the GenomeSync-GSTK System. Methods Mol Biol 2023; 2632:215-226. [PMID: 36781731 DOI: 10.1007/978-1-0716-2996-3_15] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/27/2023]
Abstract
With the development of nanopore sequencing technology, long reads of DNA sequences can now be determined rapidly from various samples. This protocol introduces the GenomeSync-GSTK system for bacterial species identification in a given sample using nanopore sequencing data of 16S rRNA genes as an example. GenomeSync is a collection of genome sequences designed to provide easy access to genomic data of the species as demanded. GSTK (genome search toolkit) is a set of scripts for managing local homology searches using genomes obtained from the GenomeSync database. Based on this protocol, nanopore sequencing data analyses of metagenomes and amplicons could be efficiently performed. We also noted reanalysis in conjunction with future developments in nanopore sequencing technology and the accumulation of genome sequencing data.
Collapse
Affiliation(s)
- Kirill Kryukov
- Department of Informatics, National Institute of Genetics, Shizuoka, Japan
| | - Tadashi Imanishi
- Department of Molecular Life Science, Tokai University School of Medicine, Kanagawa, Japan
| | - So Nakagawa
- Department of Molecular Life Science, Tokai University School of Medicine, Kanagawa, Japan.
| |
Collapse
|
47
|
Lee AWT, Chan CTM, Wong LLY, Yip CY, Lui WT, Cheng KC, Leung JSL, Lee LK, Wong ITF, Ng TTL, Lao HY, Siu GKH. Identification of microbial community in the urban environment: The concordance between conventional culture and nanopore 16S rRNA sequencing. Front Microbiol 2023; 14:1164632. [PMID: 37125165 PMCID: PMC10133568 DOI: 10.3389/fmicb.2023.1164632] [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: 02/13/2023] [Accepted: 03/14/2023] [Indexed: 05/02/2023] Open
Abstract
Introduction Microbes in the built environment have been implicated as a source of infectious diseases. Bacterial culture is the standard method for assessing the risk of exposure to pathogens in urban environments, but this method only accounts for <1% of the diversity of bacteria. Recently, full-length 16S rRNA gene analysis using nanopore sequencing has been applied for microbial evaluations, resulting in a rise in the development of long-read taxonomic tools for species-level classification. Regarding their comparative performance, there is, however, a lack of information. Methods Here, we aim to analyze the concordance of the microbial community in the urban environment inferred by multiple taxonomic classifiers, including ARGpore2, Emu, Kraken2/Bracken and NanoCLUST, using our 16S-nanopore dataset generated by MegaBLAST, as well as assess their abilities to identify culturable species based on the conventional culture results. Results According to our results, NanoCLUST was preferred for 16S microbial profiling because it had a high concordance of dominant species and a similar microbial profile to MegaBLAST, whereas Kraken2/Bracken, which had similar clustering results as NanoCLUST, was also desirable. Second, for culturable species identification, Emu with the highest accuracy (81.2%) and F1 score (29%) for the detection of culturable species was suggested. Discussion In addition to generating datasets in complex communities for future benchmarking studies, our comprehensive evaluation of the taxonomic classifiers offers recommendations for ongoing microbial community research, particularly for complex communities using nanopore 16S rRNA sequencing.
Collapse
|
48
|
Zhang H, Wang M, Han X, Wang T, Lei Y, Rao Y, Xu P, Wang Y, Gu H. The application of targeted nanopore sequencing for the identification of pathogens and resistance genes in lower respiratory tract infections. Front Microbiol 2022; 13:1065159. [PMID: 36620015 PMCID: PMC9822541 DOI: 10.3389/fmicb.2022.1065159] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Accepted: 11/28/2022] [Indexed: 12/24/2022] Open
Abstract
Objectives Lower respiratory tract infections (LRTIs) are one of the causes of mortality among infectious diseases. Microbial cultures commonly used in clinical practice are time-consuming, have poor sensitivity to unculturable and polymicrobial patterns, and are inadequate to guide timely and accurate antibiotic therapy. We investigated the feasibility of targeted nanopore sequencing (TNPseq) for the identification of pathogen and antimicrobial resistance (AMR) genes across suspected patients with LRTIs. TNPseq is a novel approach, which was improved based on nanopore sequencing for the identification of bacterial and fungal infections of clinical relevance. Methods This prospective study recruited 146 patients suspected of having LRTIs and with a median age of 61 years. The potential pathogens in these patients were detected by both TNPseq and the traditional culture workups. We compared the performance between the two methods among 146 LRTIs-related specimens. AMR genes were also detected by TNPseq to prompt the proper utilization of antibiotics. Results At least one pathogen was detected in 133 (91.1%) samples by TNPseq, but only 37 (25.3%) samples contained positive isolates among 146 cultured specimens. TNPseq possessed higher sensitivity than the conventional culture method (91.1 vs. 25.3%, P < 0.001) in identifying pathogens. It detected more samples with bacterial infections (P < 0.001) and mixed infections (P < 0.001) compared with the clinical culture tests. The most frequent AMR gene identified by TNPseq was bla TEM (n = 29), followed by bla SHV (n = 4), bla KPC (n = 2), bla CTX-M (n = 2), and mecA (n = 2). Furthermore, TNPseq discovered five possible multi-drug resistance specimens. Conclusion TNPseq is efficient to identify pathogens early, thus assisting physicians to conduct timely and precise treatment for patients with suspected LRTIs.
Collapse
Affiliation(s)
- Hongying Zhang
- Department of Pulmonary Medicine, Fuzhou Pulmonary Hospital of Fujian, Fuzhou, China,*Correspondence: Hongying Zhang ✉
| | - Meng Wang
- Institute of Health Education, Hangzhou Center for Disease Control and Prevention, Hangzhou, China
| | - Ximei Han
- Department of Pulmonary Medicine, Fuzhou Pulmonary Hospital of Fujian, Fuzhou, China
| | - Ting Wang
- Department of Pulmonary Medicine, Fuzhou Pulmonary Hospital of Fujian, Fuzhou, China
| | - Yanjuan Lei
- Department of Medicine, Zhejiang ShengTing Biotech Co., Ltd., Hangzhou, China
| | - Yu Rao
- Department of Pulmonary Medicine, Fuzhou Pulmonary Hospital of Fujian, Fuzhou, China
| | - Peisong Xu
- Department of Medicine, Zhejiang ShengTing Biotech Co., Ltd., Hangzhou, China
| | - Yunfei Wang
- Department of Medicine, Zhejiang ShengTing Biotech Co., Ltd., Hangzhou, China
| | - Hongcang Gu
- Institute of Health and Medical Technology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, China,Graduate School, University of Science and Technology of China, Hefei, China,Hongcang Gu ✉
| |
Collapse
|
49
|
Huggins LG, Colella V, Atapattu U, Koehler AV, Traub RJ. Nanopore Sequencing Using the Full-Length 16S rRNA Gene for Detection of Blood-Borne Bacteria in Dogs Reveals a Novel Species of Hemotropic Mycoplasma. Microbiol Spectr 2022; 10:e0308822. [PMID: 36250862 PMCID: PMC9769565 DOI: 10.1128/spectrum.03088-22] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Accepted: 09/26/2022] [Indexed: 01/09/2023] Open
Abstract
Dogs across the globe are afflicted by diverse blood- and vector-borne bacteria (VBB), many of which cause severe disease and can be fatal. Diagnosis of VBB infections can be challenging due to the low concentration of bacteria in the blood, the frequent occurrence of coinfections, and the wide range of known, emerging, and potentially novel VBB species encounterable. Therefore, there is a need for diagnostics that address these challenges by being both sensitive and capable of detecting all VBB simultaneously. We detail the first employment of a nanopore-based sequencing methodology conducted on the Oxford Nanopore Technologies (ONT) MinION device to accurately elucidate the "hemobacteriome" from canine blood through sequencing of the full-length 16S rRNA gene. We detected a diverse range of important canine VBB, including Ehrlichia canis, Anaplasma platys, Mycoplasma haemocanis, Bartonella clarridgeiae, "Candidatus Mycoplasma haematoparvum", a novel species of hemotropic mycoplasma, and Wolbachia endosymbionts of filarial worms, indicative of filariasis. Our nanopore-based protocol was equivalent in sensitivity to both quantitative PCR (qPCR) and Illumina sequencing when benchmarked against these methods, achieving high agreement as defined by the kappa statistics (k > 0.81) for three key VBB. Utilizing the ability of the ONT' MinION device to sequence long read lengths provides an excellent alternative diagnostic method by which the hemobacteriome can be accurately characterized to the species level in a way previously unachievable using short reads. We envision our method to be translatable to multiple contexts, such as the detection of VBB in other vertebrate hosts, including humans, while the small size of the MinION device is highly amenable to field use. IMPORTANCE Blood- and vector-borne bacteria (VBB) can cause severe pathology and even be lethal for dogs in many regions across the globe. Accurate characterization of all the bacterial pathogens infecting a canine host is critical, as coinfections are common and emerging and novel pathogens that may go undetected by traditional diagnostics frequently arise. Deep sequencing using devices from Oxford Nanopore Technologies (ONT) provides a solution, as the long read lengths achievable provide species-level taxonomic identification of pathogens that previous short-read technologies could not accomplish. We developed a protocol using ONT' MinION sequencer to accurately detect and classify a wide spectrum of VBB from canine blood at a sensitivity comparable to that of regularly used diagnostics, such as qPCR. This protocol demonstrates great potential for use in biosurveillance and biosecurity operations for the detection of VBB in a range of vertebrate hosts, while the MinION sequencer's portability allows this method to be used easily in the field.
Collapse
Affiliation(s)
- Lucas G. Huggins
- Faculty of Veterinary and Agricultural Sciences, University of Melbourne, Parkville, Victoria, Australia
| | - Vito Colella
- Faculty of Veterinary and Agricultural Sciences, University of Melbourne, Parkville, Victoria, Australia
| | - Ushani Atapattu
- Faculty of Veterinary and Agricultural Sciences, University of Melbourne, Parkville, Victoria, Australia
| | - Anson V. Koehler
- Faculty of Veterinary and Agricultural Sciences, University of Melbourne, Parkville, Victoria, Australia
| | - Rebecca J. Traub
- Faculty of Veterinary and Agricultural Sciences, University of Melbourne, Parkville, Victoria, Australia
| |
Collapse
|
50
|
González-Plaza JJ, Furlan C, Rijavec T, Lapanje A, Barros R, Tamayo-Ramos JA, Suarez-Diez M. Advances in experimental and computational methodologies for the study of microbial-surface interactions at different omics levels. Front Microbiol 2022; 13:1006946. [PMID: 36519168 PMCID: PMC9744117 DOI: 10.3389/fmicb.2022.1006946] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Accepted: 11/02/2022] [Indexed: 08/31/2023] Open
Abstract
The study of the biological response of microbial cells interacting with natural and synthetic interfaces has acquired a new dimension with the development and constant progress of advanced omics technologies. New methods allow the isolation and analysis of nucleic acids, proteins and metabolites from complex samples, of interest in diverse research areas, such as materials sciences, biomedical sciences, forensic sciences, biotechnology and archeology, among others. The study of the bacterial recognition and response to surface contact or the diagnosis and evolution of ancient pathogens contained in archeological tissues require, in many cases, the availability of specialized methods and tools. The current review describes advances in in vitro and in silico approaches to tackle existing challenges (e.g., low-quality sample, low amount, presence of inhibitors, chelators, etc.) in the isolation of high-quality samples and in the analysis of microbial cells at genomic, transcriptomic, proteomic and metabolomic levels, when present in complex interfaces. From the experimental point of view, tailored manual and automatized methodologies, commercial and in-house developed protocols, are described. The computational level focuses on the discussion of novel tools and approaches designed to solve associated issues, such as sample contamination, low quality reads, low coverage, etc. Finally, approaches to obtain a systems level understanding of these complex interactions by integrating multi omics datasets are presented.
Collapse
Affiliation(s)
- Juan José González-Plaza
- International Research Centre in Critical Raw Materials-ICCRAM, University of Burgos, Burgos, Spain
| | - Cristina Furlan
- Laboratory of Systems and Synthetic Biology, Wageningen University and Research, Wageningen, Netherlands
| | - Tomaž Rijavec
- Department of Environmental Sciences, Jožef Stefan Institute, Ljubljana, Slovenia
| | - Aleš Lapanje
- Department of Environmental Sciences, Jožef Stefan Institute, Ljubljana, Slovenia
| | - Rocío Barros
- International Research Centre in Critical Raw Materials-ICCRAM, University of Burgos, Burgos, Spain
| | | | - Maria Suarez-Diez
- Laboratory of Systems and Synthetic Biology, Wageningen University and Research, Wageningen, Netherlands
| |
Collapse
|