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Liang T, Liu Y, Guo N, Li Y, Niu L, Liu J, Ma Q, Zhang J, Shan M. Jinhong decoction ameliorates injury in septic mice without disrupting the equilibrium of gut microbiota. J Pharm Biomed Anal 2024; 251:116404. [PMID: 39154578 DOI: 10.1016/j.jpba.2024.116404] [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: 11/30/2023] [Revised: 06/25/2024] [Accepted: 08/05/2024] [Indexed: 08/20/2024]
Abstract
Sepsis is a life-threatening condition and usually be treated with antibiotics, which however often has severe side effects. This work proposed a novel Chinese traditional medicine JINHONG (JH) decoction for therapy of sepsis. We first identified the chemical constituents of JH decoction by using high-performance liquid chromatography and mass spectrometry (HPLC-MS). Then, we constructed a model mouse for sepsis by using cecal ligation and puncture (CLP). Metagenomic sequencing method was used to compare the diversity and abundance of the gut microbiota between normal, disease model, JH decoction-treatment and antibiotic-treatment mice. Many indices including the number of platelets, CD62p and CD63 content, AQP2 and AQP8 level, as well as the expression level of protein C confirmed that the sepsis resulted in serious pathological damage, while all of these indices could be reversed by JH decoction and antibiotics. The diversity and abundance of intestinal flora decreased in CLP mice, and the decrements aggravated after antibiotic treatment while can be recovered by JH decoction treatment. The abundance of anti-inflammatory Ruminococcaceae increased after JH decoction treatment, indicating that JH decoction could ameliorate pathology associated with sepsis in CLP model via modulating the intestinal flora. This study demonstrates that JH decoction could treat sepsis clinically without obvious adverse effects on gut microbiota.
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Affiliation(s)
- Tengxiao Liang
- Department of Emergency, Dongzhimen Hospital, Beijing University of Chinese Medicine, Beijing 100007, China
| | - Yang Liu
- Center for Integrated Chinese and Western Medicine, Beijing Youan Hospital, Capital Medical University, Beijing 100069, China
| | - Nan Guo
- Intensive Care Unit, Dongzhimen Hospital, Beijing University of Chinese Medicine, Beijing 100007, China
| | - Yanpeng Li
- Department of Emergency, Dongzhimen Hospital, Beijing University of Chinese Medicine, Beijing 100007, China
| | - Liqiang Niu
- Department of Emergency, Dongzhimen Hospital, Beijing University of Chinese Medicine, Beijing 100007, China
| | - Jin Liu
- Intensive Care Unit, Dongzhimen Hospital, Beijing University of Chinese Medicine, Beijing 100007, China
| | - Qian Ma
- Department of Emergency, Dongzhimen Hospital, Beijing University of Chinese Medicine, Beijing 100007, China
| | - Jiaqi Zhang
- Department of Emergency, Dongzhimen Hospital, Beijing University of Chinese Medicine, Beijing 100007, China
| | - Minmin Shan
- Department of Emergency, Dongzhimen Hospital, Beijing University of Chinese Medicine, Beijing 100007, China.
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2
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Williamson CHD, Vazquez AJ, Nunnally AE, Kyger K, Fofanov VY, Furstenau TN, Hornstra HM, Terriquez J, Keim P, Sahl JW. ColiSeq: a multiplex amplicon assay that provides strain level resolution of Escherichia coli directly from clinical specimens. Microbiol Spectr 2024; 12:e0413923. [PMID: 38651881 PMCID: PMC11237721 DOI: 10.1128/spectrum.04139-23] [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: 12/06/2023] [Accepted: 04/01/2024] [Indexed: 04/25/2024] Open
Abstract
Escherichia coli is a diverse pathogen, causing a range of disease in humans, from self-limiting diarrhea to urinary tract infections (UTIs). Uropathogenic E. coli (UPEC) is the most frequently observed uropathogen in UTIs, a common disease in high-income countries, incurring billions of dollars yearly in treatment costs. Although E. coli is easily grown and identified in the clinical laboratory, genotyping the pathogen is more complicated, yet critical for reducing the incidence of disease. These goals can be achieved through whole-genome sequencing of E. coli isolates, but this approach is relatively slow and typically requires culturing the pathogen in the laboratory. To genotype E. coli rapidly and inexpensively directly from clinical samples, including but not limited to urine, we developed and validated a multiplex amplicon sequencing assay, called ColiSeq. The assay consists of targets designed for E. coli species confirmation, high resolution genotyping, and mixture deconvolution. To demonstrate its utility, we screened the ColiSeq assay against 230 clinical urine samples collected from a hospital system in Flagstaff, Arizona, USA. A limit of detection analysis demonstrated the ability of ColiSeq to identify E. coli at a concentration of ~2 genomic equivalent (GEs)/mL and to generate high-resolution genotyping at a concentration of 1 × 105 GEs/mL. The results of this study suggest that ColiSeq could be a valuable method to understand the source of UPEC strains and guide infection mitigation efforts. As sequence-based diagnostics become accepted in the clinical laboratory, workflows such as ColiSeq will provide actionable information to improve patient outcomes.IMPORTANCEUrinary tract infections (UTIs), caused primarily by Escherichia coli, create an enormous health care burden in the United States and other high-income countries. The early detection of E. coli from clinical samples, including urine, is important to target therapy and prevent further patient complications. Additionally, understanding the source of E. coli exposure will help with future mitigation efforts. In this study, we developed, tested, and validated an amplicon sequencing assay focused on direct detection of E. coli from urine. The resulting sequence data were demonstrated to provide strain level resolution of the pathogen, not only confirming the presence of E. coli, which can focus treatment efforts, but also providing data needed for source attribution and contact tracing. This assay will generate inexpensive, rapid, and reproducible data that can be deployed by public health agencies to track, diagnose, and potentially mitigate future UTIs caused by E. coli.
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Affiliation(s)
| | - Adam J. Vazquez
- Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, USA
| | - Amalee E. Nunnally
- Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, USA
| | - Kristen Kyger
- Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, USA
| | - Viacheslav Y. Fofanov
- Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, USA
- School of Informatics, Computing, and Cyber Systems, Northern Arizona University, Flagstaff, Arizona, USA
| | - Tara N. Furstenau
- Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, USA
- School of Informatics, Computing, and Cyber Systems, Northern Arizona University, Flagstaff, Arizona, USA
| | - Heidie M. Hornstra
- Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, USA
| | | | - Paul Keim
- Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, USA
| | - Jason W. Sahl
- Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, USA
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3
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Levine ZC, Sene A, Mkandawire W, Deme AB, Ndiaye T, Sy M, Gaye A, Diedhiou Y, Mbaye AM, Ndiaye IM, Gomis J, Ndiop M, Sene D, Faye Paye M, MacInnis BL, Schaffner SF, Park DJ, Badiane AS, Colubri A, Ndiaye M, Sy N, Sabeti PC, Ndiaye D, Siddle KJ. Investigating the etiologies of non-malarial febrile illness in Senegal using metagenomic sequencing. Nat Commun 2024; 15:747. [PMID: 38272885 PMCID: PMC10810818 DOI: 10.1038/s41467-024-44800-7] [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: 08/22/2023] [Accepted: 01/04/2024] [Indexed: 01/27/2024] Open
Abstract
The worldwide decline in malaria incidence is revealing the extensive burden of non-malarial febrile illness (NMFI), which remains poorly understood and difficult to diagnose. To characterize NMFI in Senegal, we collected venous blood and clinical metadata in a cross-sectional study of febrile patients and healthy controls in a low malaria burden area. Using 16S and untargeted sequencing, we detected viral, bacterial, or eukaryotic pathogens in 23% (38/163) of NMFI cases. Bacteria were the most common, with relapsing fever Borrelia and spotted fever Rickettsia found in 15.5% and 3.8% of cases, respectively. Four viral pathogens were found in a total of 7 febrile cases (3.5%). Sequencing also detected undiagnosed Plasmodium, including one putative P. ovale infection. We developed a logistic regression model that can distinguish Borrelia from NMFIs with similar presentation based on symptoms and vital signs (F1 score: 0.823). These results highlight the challenge and importance of improved diagnostics, especially for Borrelia, to support diagnosis and surveillance.
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Affiliation(s)
- Zoë C Levine
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Harvard Graduate Program in Biological and Biomedical Science, Boston, MA, USA
- Harvard/MIT MD-PhD Program, Boston, MA, USA
| | - Aita Sene
- Department of Parasitology, Cheikh Anta Diop University Dakar, Dakar, Senegal
- Centre International de Recherche et de Formation en Génomique Appliquée et de la Surveillance Sanitaire, Dakar, Senegal
| | - Winnie Mkandawire
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
- University of Massachusetts Medical School, Worcester, MA, USA
| | - Awa B Deme
- Centre International de Recherche et de Formation en Génomique Appliquée et de la Surveillance Sanitaire, Dakar, Senegal
| | - Tolla Ndiaye
- Department of Parasitology, Cheikh Anta Diop University Dakar, Dakar, Senegal
- Centre International de Recherche et de Formation en Génomique Appliquée et de la Surveillance Sanitaire, Dakar, Senegal
| | - Mouhamad Sy
- Department of Parasitology, Cheikh Anta Diop University Dakar, Dakar, Senegal
- Centre International de Recherche et de Formation en Génomique Appliquée et de la Surveillance Sanitaire, Dakar, Senegal
| | - Amy Gaye
- Department of Parasitology, Cheikh Anta Diop University Dakar, Dakar, Senegal
- Centre International de Recherche et de Formation en Génomique Appliquée et de la Surveillance Sanitaire, Dakar, Senegal
| | - Younouss Diedhiou
- Department of Parasitology, Cheikh Anta Diop University Dakar, Dakar, Senegal
- Centre International de Recherche et de Formation en Génomique Appliquée et de la Surveillance Sanitaire, Dakar, Senegal
| | - Amadou M Mbaye
- Department of Parasitology, Cheikh Anta Diop University Dakar, Dakar, Senegal
- Centre International de Recherche et de Formation en Génomique Appliquée et de la Surveillance Sanitaire, Dakar, Senegal
| | - Ibrahima M Ndiaye
- Department of Parasitology, Cheikh Anta Diop University Dakar, Dakar, Senegal
- Centre International de Recherche et de Formation en Génomique Appliquée et de la Surveillance Sanitaire, Dakar, Senegal
| | - Jules Gomis
- Department of Parasitology, Cheikh Anta Diop University Dakar, Dakar, Senegal
- Centre International de Recherche et de Formation en Génomique Appliquée et de la Surveillance Sanitaire, Dakar, Senegal
| | - Médoune Ndiop
- Programme National de lutte contre le Paludisme, Ministère de la Santé, Dakar Fann, Senegal
| | - Doudou Sene
- Programme National de lutte contre le Paludisme, Ministère de la Santé, Dakar Fann, Senegal
| | | | - Bronwyn L MacInnis
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Harvard University, Boston, MA, USA
| | - Stephen F Schaffner
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Harvard University, Boston, MA, USA
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, USA
| | - Daniel J Park
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Aida S Badiane
- Department of Parasitology, Cheikh Anta Diop University Dakar, Dakar, Senegal
- Centre International de Recherche et de Formation en Génomique Appliquée et de la Surveillance Sanitaire, Dakar, Senegal
| | - Andres Colubri
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
- University of Massachusetts Medical School, Worcester, MA, USA
| | - Mouhamadou Ndiaye
- Department of Parasitology, Cheikh Anta Diop University Dakar, Dakar, Senegal
- Centre International de Recherche et de Formation en Génomique Appliquée et de la Surveillance Sanitaire, Dakar, Senegal
| | - Ngayo Sy
- Service de Lutte Anti Parasitaire, Thies, Senegal
| | - Pardis C Sabeti
- Broad Institute of Harvard and MIT, Cambridge, MA, USA.
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Harvard University, Boston, MA, USA.
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, USA.
- Howard Hughes Medical Institute, Chevy Chase, MD, USA.
| | - Daouda Ndiaye
- Department of Parasitology, Cheikh Anta Diop University Dakar, Dakar, Senegal.
- Centre International de Recherche et de Formation en Génomique Appliquée et de la Surveillance Sanitaire, Dakar, Senegal.
| | - Katherine J Siddle
- Broad Institute of Harvard and MIT, Cambridge, MA, USA.
- Department of Molecular Microbiology and Immunology, Brown University, Providence, RI, USA.
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4
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Burban A, Słupik D, Reda A, Szczerba E, Grabowski M, Kołodzińska A. Novel Diagnostic Methods for Infective Endocarditis. Int J Mol Sci 2024; 25:1245. [PMID: 38279244 PMCID: PMC10816594 DOI: 10.3390/ijms25021245] [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: 12/15/2023] [Revised: 01/14/2024] [Accepted: 01/15/2024] [Indexed: 01/28/2024] Open
Abstract
Infective endocarditis (IE) remains a dangerous disease and continues to have a high mortality rate. Unfortunately, despite continuous improvements in diagnostic methods, in many cases, blood cultures remain negative, and the pathogen causing endocarditis is unknown. This makes targeted therapy and the selection of appropriate antibiotics impossible. Therefore, we present what methods can be used to identify the pathogen in infective endocarditis. These are mainly molecular methods, including PCR and MGS, as well as imaging methods using radiotracers, which offer more possibilities for diagnosing IE. However, they are still not widely used in the diagnosis of IE. The article summarizes in which cases we should choose them and what we are most hopeful about in further research into the diagnosis of IE. In addition, registered clinical trials that are currently underway for the diagnosis of IE are also presented.
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Affiliation(s)
- Anna Burban
- 1st Chair and Department of Cardiology, Medical University of Warsaw, 02-097 Warsaw, Poland
- Doctoral School, Medical University of Warsaw, 02-091 Warsaw, Poland
| | - Dorota Słupik
- 1st Chair and Department of Cardiology, Medical University of Warsaw, 02-097 Warsaw, Poland
| | - Aleksandra Reda
- 1st Chair and Department of Cardiology, Medical University of Warsaw, 02-097 Warsaw, Poland
| | - Ewa Szczerba
- 1st Chair and Department of Cardiology, Medical University of Warsaw, 02-097 Warsaw, Poland
| | - Marcin Grabowski
- 1st Chair and Department of Cardiology, Medical University of Warsaw, 02-097 Warsaw, Poland
| | - Agnieszka Kołodzińska
- 1st Chair and Department of Cardiology, Medical University of Warsaw, 02-097 Warsaw, Poland
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5
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Levine ZC, Sene A, Mkandawire W, Deme AB, Ndiaye T, Sy M, Gaye A, Diedhiou Y, Mbaye AM, Ndiaye I, Gomis J, Ndiop M, Sene D, Paye MF, MacInnis B, Schaffner SF, Park DJ, Badiane AS, Colubri A, Ndiaye M, Sy N, Sabeti PC, Ndiaye D, Siddle KJ. Improving diagnosis of non-malarial fevers in Senegal: Borrelia and the contribution of tick-borne bacteria. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.08.24.23294564. [PMID: 37662407 PMCID: PMC10473814 DOI: 10.1101/2023.08.24.23294564] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/05/2023]
Abstract
The worldwide decline in malaria incidence is revealing the extensive burden of non-malarial febrile illness (NMFI), which remains poorly understood and difficult to diagnose. To characterize NMFI in Senegal, we collected venous blood and clinical metadata from febrile patients and healthy controls in a low malaria burden area. Using 16S and unbiased sequencing, we detected viral, bacterial, or eukaryotic pathogens in 29% of NMFI cases. Bacteria were the most common, with relapsing fever Borrelia and spotted fever Rickettsia found in 15% and 3.7% of cases, respectively. Four viral pathogens were found in a total of 7 febrile cases (3.5%). Sequencing also detected undiagnosed Plasmodium, including one putative P. ovale infection. We developed a logistic regression model to distinguish Borrelia from NMFIs with similar presentation based on symptoms and vital signs. These results highlight the challenge and importance of improved diagnostics, especially for Borrelia, to support diagnosis and surveillance.
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Affiliation(s)
- Zoë C Levine
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Harvard Graduate Program in Biological and Biomedical Science, Boston, MA, USA
- Harvard/MIT MD-PhD Program, Boston, MA, 02115, USA
| | - Aita Sene
- Centre International de recherche, de formation en Génomique Appliquée et de Surveillance Sanitaire (CIGASS), Dakar, Senegal
| | - Winnie Mkandawire
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
- University of Massachusetts Medical School, Worcester, MA, USA
| | - Awa B Deme
- Centre International de recherche, de formation en Génomique Appliquée et de Surveillance Sanitaire (CIGASS), Dakar, Senegal
| | - Tolla Ndiaye
- Centre International de recherche, de formation en Génomique Appliquée et de Surveillance Sanitaire (CIGASS), Dakar, Senegal
| | - Mouhamad Sy
- Centre International de recherche, de formation en Génomique Appliquée et de Surveillance Sanitaire (CIGASS), Dakar, Senegal
| | - Amy Gaye
- Centre International de recherche, de formation en Génomique Appliquée et de Surveillance Sanitaire (CIGASS), Dakar, Senegal
| | - Younouss Diedhiou
- Centre International de recherche, de formation en Génomique Appliquée et de Surveillance Sanitaire (CIGASS), Dakar, Senegal
| | - Amadou M Mbaye
- Centre International de recherche, de formation en Génomique Appliquée et de Surveillance Sanitaire (CIGASS), Dakar, Senegal
| | - Ibrahima Ndiaye
- Centre International de recherche, de formation en Génomique Appliquée et de Surveillance Sanitaire (CIGASS), Dakar, Senegal
| | - Jules Gomis
- Centre International de recherche, de formation en Génomique Appliquée et de Surveillance Sanitaire (CIGASS), Dakar, Senegal
| | - Médoune Ndiop
- Programme National de Lutte contre le Paludisme (PNLP), Ministère de la Santé, Dakar Fann, Senegal
| | - Doudou Sene
- Programme National de Lutte contre le Paludisme (PNLP), Ministère de la Santé, Dakar Fann, Senegal
| | | | - Bronwyn MacInnis
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Harvard University, Boston, MA, USA
| | - Stephen F Schaffner
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Harvard University, Boston, MA, USA
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, USA
| | - Daniel J Park
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Aida S Badiane
- Centre International de recherche, de formation en Génomique Appliquée et de Surveillance Sanitaire (CIGASS), Dakar, Senegal
| | - Andres Colubri
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
- University of Massachusetts Medical School, Worcester, MA, USA
| | - Mouhamadou Ndiaye
- Centre International de recherche, de formation en Génomique Appliquée et de Surveillance Sanitaire (CIGASS), Dakar, Senegal
| | - Ngayo Sy
- Service de Lutte Anti Parasitaire, Thies, Senegal
| | - Pardis C Sabeti
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Harvard University, Boston, MA, USA
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - Daouda Ndiaye
- Centre International de recherche, de formation en Génomique Appliquée et de Surveillance Sanitaire (CIGASS), Dakar, Senegal
| | - Katherine J Siddle
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Department of Molecular Microbiology and Immunology, Brown University, Providence, RI, USA
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6
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Paulose AK, Hou YJ, Huang YS, Chakkalaparambil Dileep N, Chiu CL, Pal A, Kalaimani VM, Lin ZH, Chang CR, Chen CP, Lin YC, Cheng CY, Cheng SH, Cheng CM, Wang YL. Rapid Escherichia coli Cloned DNA Detection in Serum Using an Electrical Double Layer-Gated Field-Effect Transistor-Based DNA Sensor. Anal Chem 2023; 95:6871-6878. [PMID: 37080900 DOI: 10.1021/acs.analchem.2c05719] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/22/2023]
Abstract
In this study, a rapid diagnosis platform was developed for the detection of Escherichia coli O157:H7. An electrical double layer (EDL)-gated field-effect transistor-based biosensor (BioFET) as a point-of-care testing device is demonstrated with its high sensitivity, portability, high selectivity, quick response, and ease of use. The specially designed ssDNA probe was immobilized on the extended gate electrode to bind the target complementary DNA segment of E. coli, resulting in a sharp drain current change within minutes. The limit of detection for target DNA is validated to a concentration of 1 fM in buffer solution and serum. Meanwhile, the results of a Kelvin probe force microscope were shown to have reduced surface potential of the DNA immobilized sensors before and after the cDNA detection, which is consistent with the decreased drain current of the BioFET. A 1.2 kb E. coli duplex DNA synthesized in plasmid was sonicated and detected in serum samples with the sensor array. Gel electrophoresis was used to confirm the efficiency of sonication by elucidating the length of DNA. Those results show that the EDL-gated BioFET system is a promising platform for rapid identification of pathogens for future clinical needs.
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Affiliation(s)
- Akhil K Paulose
- Institute of Nanoengineering and Microsystems, National Tsing Hua University, Hsinchu 30013, Taiwan, ROC
| | - Yueh-Ju Hou
- Department of Life Sciences, National University of Kaohsiung, Kaohsiung 811726, Taiwan, ROC
| | - Yu-Shan Huang
- Institute of Nanoengineering and Microsystems, National Tsing Hua University, Hsinchu 30013, Taiwan, ROC
| | | | - Chia-Lin Chiu
- Department of Power Mechanical Engineering, National Tsing Hua University, Hsinchu 30013, Taiwan, ROC
| | - Arnab Pal
- International Intercollegiate PhD Program, National Tsing Hua University, Hsinchu 30013, Taiwan, ROC
| | - Vishal Mani Kalaimani
- Institute of Nanoengineering and Microsystems, National Tsing Hua University, Hsinchu 30013, Taiwan, ROC
| | - Zong-Hong Lin
- Department of Biomedical Engineering, National Taiwan University, Taipei 10617, Taiwan, ROC
| | - Chuang-Rung Chang
- Institute of Biotechnology, National Tsing Hua University, Hsinchu 30013, Taiwan, ROC
| | - Cheng-Pin Chen
- Department of Infectious Diseases, Taoyuan General Hospital, Ministry of Health and Welfare, Taoyuan 32748, Taiwan
| | - Yi-Chun Lin
- Department of Infectious Diseases, Taoyuan General Hospital, Ministry of Health and Welfare, Taoyuan 32748, Taiwan
| | - Chien-Yu Cheng
- Department of Infectious Diseases, Taoyuan General Hospital, Ministry of Health and Welfare, Taoyuan 32748, Taiwan
| | - Shu-Hsing Cheng
- Department of Infectious Diseases, Taoyuan General Hospital, Ministry of Health and Welfare, Taoyuan 32748, Taiwan
| | - Chao-Min Cheng
- Institute of Biomedical Engineering, National Tsing Hua University, Hsinchu 30013, Taiwan, ROC
| | - Yu-Lin Wang
- Institute of Nanoengineering and Microsystems, National Tsing Hua University, Hsinchu 30013, Taiwan, ROC
- Department of Power Mechanical Engineering, National Tsing Hua University, Hsinchu 30013, Taiwan, ROC
- College of Semiconductor Research, National Tsing Hua University, Hsinchu 30013, Taiwan, ROC
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7
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Tao S, Zhou D, Chen H, Li N, Zheng L, Fang Y, Xu Y, Jiang Q, Liang W. Analysis of genetic structure and function of clustered regularly interspaced short palindromic repeats loci in 110 Enterococcus strains. Front Microbiol 2023; 14:1177841. [PMID: 37168121 PMCID: PMC10165109 DOI: 10.3389/fmicb.2023.1177841] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Accepted: 04/05/2023] [Indexed: 05/13/2023] Open
Abstract
Clustered regularly interspaced short palindromic repeats (CRISPR) and their CRISPR-associated proteins (Cas) are an adaptive immune system involved in specific defenses against the invasion of foreign mobile genetic elements, such as plasmids and phages. This study aims to analyze the gene structure and to explore the function of the CRISPR system in the Enterococcus genome, especially with regard to drug resistance. The whole genome information of 110 enterococci was downloaded from the NCBI database to analyze the distribution and the structure of the CRISPR-Cas system including the Cas gene, repeat sequences, and spacer sequence of the CRISPR-Cas system by bioinformatics methods, and to find drug resistance-related genes and analyze the relationship between them and the CRISPR-Cas system. Multilocus sequence typing (MLST) of enterococci was performed against the reference MLST database. Information on the drug resistance of Enterococcus was retrieved from the CARD database, and its relationship to the presence or absence of CRISPR was statistically analyzed. Among the 110 Enterococcus strains, 39 strains (35.45%) contained a complete CRISPR-Cas system, 87 CRISPR arrays were identified, and 62 strains contained Cas gene clusters. The CRISPR system in the Enterococcus genome was mainly type II-A (59.68%), followed by type II-C (33.87%). The phylogenetic analysis of the cas1 gene sequence was basically consistent with the typing of the CRISPR-Cas system. Of the 74 strains included in the study for MLST typing, only 19 (25.68%) were related to CRISPR-Cas typing, while the majority of the strains (74.32%) of MLST typing were associated with the untyped CRISPR system. Additionally, the CRISPR-Cas system may only be related to the carrying rate of some drug-resistant genes and the drug-resistant phenotype. In conclusion, the distribution of the enterococcus CRISPR-Cas system varies greatly among different species and the presence of CRISPR loci reduces the horizontal transfer of some drug resistance genes.
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Affiliation(s)
- Shuan Tao
- School of Medicine, Jiangsu University, Zhenjiang, China
- Department of Clinical Laboratory, Ningbo First Hospital, Ningbo, China
| | - Dongdong Zhou
- Department of General Medicine, Ningbo First Hospital, Ningbo, China
| | - Huimin Chen
- School of Medicine, Jiangsu University, Zhenjiang, China
| | - Na Li
- Bengbu Medical College, Bengbu, China
| | - Lin Zheng
- Department of Clinical Laboratory, Ningbo First Hospital, Ningbo, China
| | - Yewei Fang
- Department of Clinical Laboratory, Ningbo First Hospital, Ningbo, China
| | - Yao Xu
- School of Medicine, Ningbo University, Ningbo, China
| | - Qi Jiang
- Department of Gastroenterology, Ningbo First Hospital, Ningbo, China
- *Correspondence: Qi Jiang,
| | - Wei Liang
- Department of Clinical Laboratory, Ningbo First Hospital, Ningbo, China
- Wei Liang,
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8
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Toward predictive engineering of gene circuits. Trends Biotechnol 2022; 41:760-768. [PMID: 36435671 DOI: 10.1016/j.tibtech.2022.11.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Revised: 10/26/2022] [Accepted: 11/02/2022] [Indexed: 11/25/2022]
Abstract
Many synthetic biology applications rely on programming living cells using gene circuits - the assembly and wiring of genetic elements to control cellular behaviors. Extensive progress has been made in constructing gene circuits with diverse functions and applications. For many circuit functions, however, it remains challenging to ensure that the circuits operate in a predictable manner. Although the notion of predictability may appear intuitive, close inspection suggests that it is not always clear what constitutes predictability. We dissect this concept and how it can be confounded by the complexity of a circuit, the complexity of the context, and the interplay between the two. We discuss circuit engineering strategies, in both computation and experiment, that have been used to improve the predictability of gene circuits.
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9
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Yu Y, Huang Q, Liu A. Analysis of pathogens, drug resistance, sensitive antibiotic treatment and risk factors of early-onset sepsis in very low birth weight infants. Am J Transl Res 2021; 13:12939-12948. [PMID: 34956509 PMCID: PMC8661145] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Accepted: 08/22/2021] [Indexed: 06/14/2023]
Abstract
The clinical manifestations, types of infectious pathogens, and drug-resistant strains of sepsis in infants with very low birth weight (VLBWIs) vary greatly in different regions and hospitals. In order to improve the level of diagnosis and treatment, this study analyzed the distribution and drug resistance of the pathogenic bacteria of sepsis in VLBWIs in our hospital. A total of 69 cases of VLBWIs in Qilu Hospital (Qingdao), Cheeloo College of Medicine, Shandong University from January 01, 2014 to December 31, 2020 were included. Among them, 34 VLBWIs with early-onset sepsis (EOS) were assigned to the EOS group, and 14 VLBWIs with late-onset sepsis (LOS) were included in the LOS group. The distribution of pathogens and the drug resistance of antibiotics were analyzed. The results showed that fluorescent nanoparticles detected pathogenic bacteria in 48 cases, and the blood cultures were all positive. A total of 49 pathogenic bacteria were isolated, including 27 gram-negative bacteria (55.1%), 21 gram-positive bacteria (42.86%), and 1 fungus (2.04%, Candida albicans). Gram-negative bacteria comprised of E.coli and Klebsiella pneumoniae, which were highly sensitive to compound preparations containing β-lactamase inhibitors, and carbapenem antibacterial drugs, were the first choice. Gram-positive bacteria were mainly Staphylococcus epidermidis and Streptococcus agalactiae. Staphylococcus epidermidis was highly resistant to penicillins and can be treated with vancomycin. Streptococcus agalactiae was highly resistant to penicillins and can be treated with penicillin and vancomycin. Amniotic fluid pollution, intrauterine distress, premature rupture of membranes, and maternal fever were risk factors for EOS in VLBWIs, with odds ratios (ORs) of 9.369, 6.217, 5.638, and 4.267, respectively. In summary, timely and reasonable treatment should be given based on the types and drug resistance characteristics of pathogens of neonatal sepsis and the risk factors of EOS.
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Affiliation(s)
- Yingying Yu
- Department of Pharmacy, Qilu Hospital (Qingdao), Cheeloo College of Medicine, Shandong UniversityQingdao 266035, Shandong Province, China
| | - Qikun Huang
- Department of Pediatrics, Qilu Hospital (Qingdao), Cheeloo College of Medicine, Shandong UniversityQingdao 266035, Shandong Province, China
| | - Anchang Liu
- Department of Pharmacy, Qilu Hospital (Qingdao), Cheeloo College of Medicine, Shandong UniversityQingdao 266035, Shandong Province, China
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10
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Liu WD, Yen TY, Liu PY, Wu UI, Bhan P, Li YC, Chi CH, Sheng WH. Clinical Application of Metagenomic Next-Generation Sequencing in Patients with Hematologic Malignancies Suffering from Sepsis. Microorganisms 2021; 9:microorganisms9112309. [PMID: 34835435 PMCID: PMC8624204 DOI: 10.3390/microorganisms9112309] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2021] [Revised: 11/02/2021] [Accepted: 11/05/2021] [Indexed: 11/21/2022] Open
Abstract
Background: Sepsis remains a common but fatal complication among patients with immune suppression. We aimed to investigate the performance of metagenomic next-generation sequencing (mNGS) compared with standard microbiological diagnostics in patients with hematologic malignancies. Methods: We performed a prospective study from June 2019 to December 2019. Adult patients with hematologic malignancies and a clinical diagnosis of sepsis were enrolled. Conventional diagnostic methods included blood cultures, serum galactomannan for Aspergillus, cryptococcal antigen and cytomegalovirus (CMV) viral loads. Blood samples for mNGS were collected within 24 h after hypotension developed. Results: Of 24 patients enrolled, mNGS and conventional diagnostic methods (blood cultures, serology testing and virus RT-PCR) reached comparable positive results in 9 cases. Of ten patients, mNGS was able to identify additional pathogens compared with conventional methods; most of the pathogens were virus. Conclusion: Our results show that mNGS may serve as adjunctive diagnostic tool for the identification of pathogens of hematologic patients with clinically sepsis.
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Affiliation(s)
- Wang-Da Liu
- Department of Internal Medicine, National Taiwan University Hospital and National Taiwan University College of Medicine, Taipei 100, Taiwan; (W.-D.L.); (P.-Y.L.); (U.-I.W.)
- Department of Medicine, National Taiwan University Cancer Center, Taipei 106, Taiwan
| | - Ting-Yu Yen
- Department of Pediatrics, National Taiwan University Children’s Hospital, Taipei 100, Taiwan;
| | - Po-Yo Liu
- Department of Internal Medicine, National Taiwan University Hospital and National Taiwan University College of Medicine, Taipei 100, Taiwan; (W.-D.L.); (P.-Y.L.); (U.-I.W.)
- Department of Pathobiology and Population Sciences, Royal Veterinary College, University of London, London AL9 7TA, UK
| | - Un-In Wu
- Department of Internal Medicine, National Taiwan University Hospital and National Taiwan University College of Medicine, Taipei 100, Taiwan; (W.-D.L.); (P.-Y.L.); (U.-I.W.)
- Department of Medicine, National Taiwan University Cancer Center, Taipei 106, Taiwan
| | - Prerana Bhan
- LIHPAO Life Science Cooperation, New Taipei City 251, Taiwan; (P.B.); (Y.-C.L.); (C.-H.C.)
| | - Yu-Chi Li
- LIHPAO Life Science Cooperation, New Taipei City 251, Taiwan; (P.B.); (Y.-C.L.); (C.-H.C.)
| | - Chih-Hung Chi
- LIHPAO Life Science Cooperation, New Taipei City 251, Taiwan; (P.B.); (Y.-C.L.); (C.-H.C.)
| | - Wang-Huei Sheng
- Department of Internal Medicine, National Taiwan University Hospital and National Taiwan University College of Medicine, Taipei 100, Taiwan; (W.-D.L.); (P.-Y.L.); (U.-I.W.)
- Department of Medical Education, National Taiwan University Hospital, Taipei 100, Taiwan
- School of Medicine, National Taiwan University College of Medicine, Taipei 100, Taiwan
- Correspondence:
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11
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Wilson-Nieuwenhuis J, El-Mohtadi M, Edwards K, Whitehead K, Dempsey-Hibbert N. Factors Involved in the onset of infection following bacterially contaminated platelet transfusions. Platelets 2021; 32:909-918. [PMID: 32762589 DOI: 10.1080/09537104.2020.1803253] [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: 10/23/2022]
Abstract
Transfusion of platelet concentrates (PCs) is associated with several adverse patient reactions, the most common of which are febrile non-hemolytic transfusion reactions (FNHTRs) and transfusion-associated bacterial-infection/transfusion-associated sepsis (T-ABI/TA-S). Diagnosis of T-ABI/T-AS requires a positive blood culture (BC) result from the transfusion recipient and also a positive identification of bacterial contamination within a test aliquot of the transfused PC. In a significant number of cases, clinical symptoms post-transfusion are reported by the clinician, yet the BCs from the patient and/or PC are negative. The topic of 'missed bacterial detection' has therefore been the focus of several primary research studies and review articles, suggesting that biofilm formation in the blood bag and the presence of viable but non-culturable (VBNC) pathogens are the major causes of this missed detection. However, platelets are emerging as key players in early host responses to infection and as such, the aforementioned biofilm formation could elicit 'platelet priming', which could lead to significant immunological reactions in the host, in the absence of planktonic bacteria in the host bloodstream. This review reflects on what is known about missed detection and relates this to the emerging understanding of the effect of bacterial contamination on the platelets themselves and the significant role played by platelets in exacerbation of an immune response to infection within the transfusion setting.
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Affiliation(s)
| | - Mohamed El-Mohtadi
- Centre for Bioscience, Manchester Metropolitan University, Manchester, UK
| | - Kurtis Edwards
- Centre for Bioscience, Manchester Metropolitan University, Manchester, UK
| | - Kathryn Whitehead
- Centre for Bioscience, Manchester Metropolitan University, Manchester, UK
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12
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Yan G, Liu J, Chen W, Chen Y, Cheng Y, Tao J, Cai X, Zhou Y, Wang Y, Wang M, Lu G. Metagenomic Next-Generation Sequencing of Bloodstream Microbial Cell-Free Nucleic Acid in Children With Suspected Sepsis in Pediatric Intensive Care Unit. Front Cell Infect Microbiol 2021; 11:665226. [PMID: 34504805 PMCID: PMC8421769 DOI: 10.3389/fcimb.2021.665226] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2021] [Accepted: 08/05/2021] [Indexed: 11/21/2022] Open
Abstract
Bloodstream infection is a life-threatening complication in critically ill patients. Multi-drug resistant bacteria or fungi may increase the risk of invasive infections in hospitalized children and are difficult to treat in intensive care units. The purpose of this study was to use metagenomic next-generation sequencing (mNGS) to understand the bloodstream microbiomes of children with suspected sepsis in a pediatric intensive care unit (PICU). mNGS were performed on microbial cell-free nucleic acid from 34 children admitted to PICU, and potentially pathogenic microbes were identified. The associations of serological inflammation indicators, lymphocyte subpopulations, and other clinical phenotypes were also examined. mNGS of blood samples from children in PICU revealed potential eukaryotic microbial pathogens. The abundance of Pneumocystis jirovecii was positively correlated with a decrease in total white blood cell count and immunodeficiency. Hospital-acquired pneumonia patients showed a significant increase in blood bacterial species richness compared with community-acquired pneumonia children. The abundance of bloodstream bacteria was positively correlated with serum procalcitonin level. Microbial genome sequences from potential pathogens were detected in the bloodstream of children with suspected sepsis in PICU, suggesting the presence of bloodstream infections in these children.
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Affiliation(s)
- Gangfeng Yan
- Paediatric Intensive Care Unit, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai, China
| | - Jing Liu
- Paediatric Intensive Care Unit, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai, China
| | - Weiming Chen
- Paediatric Intensive Care Unit, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai, China
| | - Yang Chen
- Paediatric Intensive Care Unit, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai, China
| | - Ye Cheng
- Paediatric Intensive Care Unit, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai, China
| | - Jinhao Tao
- Paediatric Intensive Care Unit, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai, China
| | - Xiaodi Cai
- Paediatric Intensive Care Unit, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai, China
| | - Yang Zhou
- BGI PathoGenesis Pharmaceutical Technology Co., Ltd, BGI-Shenzhen, Shenzhen, China
| | - Yixue Wang
- Paediatric Intensive Care Unit, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai, China
| | - Mingbang Wang
- Shanghai Key Laboratory of Birth Defects, National Health Commission (NHC) Key Laboratory of Neonatal Diseases, Division of Neonatology, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai, China
| | - Guoping Lu
- Paediatric Intensive Care Unit, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai, China
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13
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Kondori N, Kurtovic A, Piñeiro-Iglesias B, Salvà-Serra F, Jaén-Luchoro D, Andersson B, Alves G, Ogurtsov A, Thorsell A, Fuchs J, Tunovic T, Kamenska N, Karlsson A, Yu YK, Moore ERB, Karlsson R. Mass Spectrometry Proteotyping-Based Detection and Identification of Staphylococcus aureus, Escherichia coli, and Candida albicans in Blood. Front Cell Infect Microbiol 2021; 11:634215. [PMID: 34381737 PMCID: PMC8350517 DOI: 10.3389/fcimb.2021.634215] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2020] [Accepted: 07/09/2021] [Indexed: 12/12/2022] Open
Abstract
Bloodstream infections (BSIs), the presence of microorganisms in blood, are potentially serious conditions that can quickly develop into sepsis and life-threatening situations. When assessing proper treatment, rapid diagnosis is the key; besides clinical judgement performed by attending physicians, supporting microbiological tests typically are performed, often requiring microbial isolation and culturing steps, which increases the time required for confirming positive cases of BSI. The additional waiting time forces physicians to prescribe broad-spectrum antibiotics and empirically based treatments, before determining the precise cause of the disease. Thus, alternative and more rapid cultivation-independent methods are needed to improve clinical diagnostics, supporting prompt and accurate treatment and reducing the development of antibiotic resistance. In this study, a culture-independent workflow for pathogen detection and identification in blood samples was developed, using peptide biomarkers and applying bottom-up proteomics analyses, i.e., so-called "proteotyping". To demonstrate the feasibility of detection of blood infectious pathogens, using proteotyping, Escherichia coli and Staphylococcus aureus were included in the study, as the most prominent bacterial causes of bacteremia and sepsis, as well as Candida albicans, one of the most prominent causes of fungemia. Model systems including spiked negative blood samples, as well as positive blood cultures, without further culturing steps, were investigated. Furthermore, an experiment designed to determine the incubation time needed for correct identification of the infectious pathogens in blood cultures was performed. The results for the spiked negative blood samples showed that proteotyping was 100- to 1,000-fold more sensitive, in comparison with the MALDI-TOF MS-based approach. Furthermore, in the analyses of ten positive blood cultures each of E. coli and S. aureus, both the MALDI-TOF MS-based and proteotyping approaches were successful in the identification of E. coli, although only proteotyping could identify S. aureus correctly in all samples. Compared with the MALDI-TOF MS-based approaches, shotgun proteotyping demonstrated higher sensitivity and accuracy, and required significantly shorter incubation time before detection and identification of the correct pathogen could be accomplished.
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Affiliation(s)
- Nahid Kondori
- Department of Infectious Diseases, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
- Department of Clinical Microbiology, Sahlgrenska University Hospital, Gothenburg, Sweden
| | - Amra Kurtovic
- Department of Clinical Microbiology, Sahlgrenska University Hospital, Gothenburg, Sweden
| | | | - Francisco Salvà-Serra
- Department of Infectious Diseases, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
- Department of Clinical Microbiology, Sahlgrenska University Hospital, Gothenburg, Sweden
- Culture Collection University of Gothenburg (CCUG), Sahlgrenska Academy of the University of Gothenburg, Gothenburg, Sweden
- Microbiology, Department of Biology, University of the Balearic Islands, Palma de Mallorca, Spain
| | - Daniel Jaén-Luchoro
- Department of Infectious Diseases, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
- Culture Collection University of Gothenburg (CCUG), Sahlgrenska Academy of the University of Gothenburg, Gothenburg, Sweden
| | - Björn Andersson
- Bioinformatics Core Facility at Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Gelio Alves
- National Center for Biotechnology Information (NCBI), Bethesda, MD, United States
| | - Aleksey Ogurtsov
- National Center for Biotechnology Information (NCBI), Bethesda, MD, United States
| | - Annika Thorsell
- Proteomics Core Facility at Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Johannes Fuchs
- Proteomics Core Facility at Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Timur Tunovic
- Department of Clinical Microbiology, Sahlgrenska University Hospital, Gothenburg, Sweden
| | - Nina Kamenska
- Norra-Älvsborgs-Länssjukhus (NÄL), Trollhättan, Sweden
| | | | - Yi-Kuo Yu
- National Center for Biotechnology Information (NCBI), Bethesda, MD, United States
| | - Edward R. B. Moore
- Department of Infectious Diseases, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
- Department of Clinical Microbiology, Sahlgrenska University Hospital, Gothenburg, Sweden
- Culture Collection University of Gothenburg (CCUG), Sahlgrenska Academy of the University of Gothenburg, Gothenburg, Sweden
| | - Roger Karlsson
- Department of Infectious Diseases, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
- Department of Clinical Microbiology, Sahlgrenska University Hospital, Gothenburg, Sweden
- Nanoxis Consulting AB, Gothenburg, Sweden
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14
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Young RB, Marcelino VR, Chonwerawong M, Gulliver EL, Forster SC. Key Technologies for Progressing Discovery of Microbiome-Based Medicines. Front Microbiol 2021; 12:685935. [PMID: 34239510 PMCID: PMC8258393 DOI: 10.3389/fmicb.2021.685935] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Accepted: 05/25/2021] [Indexed: 12/22/2022] Open
Abstract
A growing number of experimental and computational approaches are illuminating the “microbial dark matter” and uncovering the integral role of commensal microbes in human health. Through this work, it is now clear that the human microbiome presents great potential as a therapeutic target for a plethora of diseases, including inflammatory bowel disease, diabetes and obesity. The development of more efficacious and targeted treatments relies on identification of causal links between the microbiome and disease; with future progress dependent on effective links between state-of-the-art sequencing approaches, computational analyses and experimental assays. We argue determining causation is essential, which can be attained by generating hypotheses using multi-omic functional analyses and validating these hypotheses in complex, biologically relevant experimental models. In this review we discuss existing analysis and validation methods, and propose best-practice approaches required to enable the next phase of microbiome research.
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Affiliation(s)
- Remy B Young
- Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research, Clayton, VIC, Australia.,Infection and Immunity Program, Monash Biomedicine Discovery Institute and Department of Microbiology, Monash University, Clayton, VIC, Australia
| | - Vanessa R Marcelino
- Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research, Clayton, VIC, Australia.,Department of Molecular and Translational Sciences, Monash University, Clayton, VIC, Australia
| | - Michelle Chonwerawong
- Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research, Clayton, VIC, Australia.,Department of Molecular and Translational Sciences, Monash University, Clayton, VIC, Australia
| | - Emily L Gulliver
- Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research, Clayton, VIC, Australia.,Infection and Immunity Program, Monash Biomedicine Discovery Institute and Department of Microbiology, Monash University, Clayton, VIC, Australia.,Department of Molecular and Translational Sciences, Monash University, Clayton, VIC, Australia
| | - Samuel C Forster
- Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research, Clayton, VIC, Australia.,Infection and Immunity Program, Monash Biomedicine Discovery Institute and Department of Microbiology, Monash University, Clayton, VIC, Australia.,Department of Molecular and Translational Sciences, Monash University, Clayton, VIC, Australia
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15
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Rivera-Urbalejo AP, Vázquez D, Fernández Vázquez JL, Rosete Enríquez M, Cesa-Luna C, Morales-García YE, Muñoz Rojas J, Quintero Hernández V. APORTES Y DIFICULTADES DE LA METAGENÓMICA DE SUELOS Y SU IMPACTO EN LA AGRICULTURA. ACTA BIOLÓGICA COLOMBIANA 2021. [DOI: 10.15446/abc.v26n3.85760] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
Los microorganismos son de gran interés porque colonizan todo tipo de ambiente, sin embargo, uno de los problemas al que nos enfrentamos para conocer su diversidad biológica es que no todos los microorganismos son cultivables. El desarrollo de nuevas tecnologías como la generación de vectores de clonación aunado al desarrollo de técnicas de secuenciación de alto rendimiento ha favorecido el surgimiento de una nueva herramienta llamada metagenómica, la cual nos permite estudiar genomas de comunidades enteras de microorganismos. Debido a que ningún ambiente es idéntico a otro, es importante mencionar que dependiendo del tipo de muestra a analizar será el tipo de reto al cual nos enfrentaremos al trabajar con metagenómica, en el caso específico del suelo existen diversas variantes como la contaminación del suelo con metales pesados o diversos compuestos químicos que podrían limitar los estudios. Sin embargo, pese a las limitaciones que el mismo ambiente presenta, la metagenómica ha permitido tanto el descubrimiento de nuevos genes como la caracterización de las comunidades microbianas que influyen positivamente en el desarrollo de plantas, lo cual en un futuro podría generar un gran impacto en la agricultura. En este artículo se realizó una revisión de diversas investigaciones que han empleado metagenómica, reportadas en las bases de datos de PudMed y Google Schoolar, con el objetivo de examinar los beneficios y limitaciones de las diversas metodologías empleadas en el tratamiento del ADN metagenómico de suelo y el impacto de la metagenómica en la agricultura.
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16
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Targeted metagenomics using next generation sequencing in laboratory diagnosis of culture negative endophthalmitis. Heliyon 2021; 7:e06780. [PMID: 33997374 PMCID: PMC8099753 DOI: 10.1016/j.heliyon.2021.e06780] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Revised: 03/22/2021] [Accepted: 04/08/2021] [Indexed: 11/29/2022] Open
Abstract
To study the feasibility of 16S rRNA metagenomics using next generation sequencing (NGS) along with broad range PCR assay for 762 bp region of 16S rRNA gene with Sanger's sequencing, in microbial diagnosis of culture negative endophthalmitis. Vitreous fluid from 16 culture negative and one culture positive endophthalmitis patients, admitted to a tertiary care hospital were processed for targeted metagenomics. NGS of 7 variable regions of 16S rRNA gene was done using Ion Torrent Personal Genome Machine (PGM). Sequence data were analyzed using Ion Reporter software using QIIME and BLSATN tools and Greengenes and NCBI–Genbank databases. Bacterial genome sequences were detected in 15 culture negative and culture positive vitreous specimens. The sequence reads varied between 25,245–540,916 with read length between 142bp–228bp and coverage depth was 41.0X and 81.2X. Operational taxonomic unit (OTUs) of multiple bacterial genera and species were detected in 13 culture negative vitreous specimens and OTUs of a single bacterial species were detected in 2 culture negative and 1 culture positive specimens; one negative specimen had no bacterial DNA. Maximum numbers of OTUs detected by NGS for a bacterial species from any vitreous specimen was the one which was detected and identified by Sanger's sequencing in broad range PCR. All the bacteria were belonging to clinically relevant species. Broad range PCR with sequencing failed to identify bacteria from 5 of the 16 (31.25%) culture negative vitreous specimens. Metagenomics could detect and identify bacterial pathogens in 15 of the 16 culture negative vitreous specimen's up to species level. With rapidly decreasing cost, metagenomics has a potential to be used widely in endophthalmitis diagnosis, in which culture negativity is usually high.
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17
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Shiraishi Y, Kryukov K, Tomomatsu K, Sakamaki F, Inoue S, Nakagawa S, Imanishi T, Asano K. Diagnosis of pleural empyema/parapneumonic effusion by next-generation sequencing. Infect Dis (Lond) 2021; 53:450-459. [PMID: 33689538 DOI: 10.1080/23744235.2021.1892178] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
Abstract
BACKGROUND Although a microbiological diagnosis of pleural infection is clinically important, it is often complicated by prior antibiotic treatment and/or difficulties with culturing some bacterial species. Therefore, we aimed to identify probable causative bacteria in pleural empyema/parapneumonic effusions by combining 16S ribosomal RNA (rRNA) gene amplification and next-generation sequencing (NGS). METHODS Pleural fluids were collected from 19 patients with infectious effusions and nine patients with non-infectious malignant effusions. We analysed DNA extracted from the pleural fluid supernatant by NGS using the Genome Search Toolkit and GenomeSync database, either directly or after PCR amplification of the 16S rRNA gene. Infectious and non-infectious effusions were distinguished by semi-quantitative PCR of the 16S rRNA gene. RESULTS Only 8 (42%) effusions were culture-positive, however, NGS of the 16S rRNA gene amplicon identified 14 anaerobes and 7 aerobes/facultative anaerobes in all patients, including Streptococcus sp. (n = 6), Fusobacterium sp. (n = 5), Porphyromonas sp. (n = 5), and Prevotella sp. (n = 4), accounting for >10% of the total genomes. The culture and NGS results were discordant for 3 out of 8 patients, all of whom had previously been treated with antibiotics. Total (2ΔCT value in semi-quantitative PCR of the 16S rRNA gene) and specific (total bacterial load multiplied by the proportion of primary bacteria in NGS) bacterial loads could efficiently distinguish empyema/parapneumonic effusion from non-infectious effusion. CONCLUSION Combining NGS with semi-quantitative PCR can facilitate the diagnosis of pleural empyema/parapneumonic effusion and its causal bacteria.
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Affiliation(s)
- Yoshiki Shiraishi
- Division of Pulmonary Medicine, Department of Medicine, Tokai University School of Medicine, Isehara, Japan
| | - Kirill Kryukov
- Department of Molecular Life Science, Tokai University School of Medicine, Isehara, Japan.,Department of Genomics and Evolutionary Biology, National Institute of Genetics, Mishima, Japan
| | - Katsuyoshi Tomomatsu
- Division of Pulmonary Medicine, Department of Medicine, Tokai University School of Medicine, Isehara, Japan
| | - Fumio Sakamaki
- Division of Respiratory Disease, Department of Medicine, Tokai University Hachioji Hospital, Tokyo, Japan
| | - Shigeaki Inoue
- Department of Emergency and Critical Care Medicine, Tokai University School of Medicine, Isehara, Japan
| | - So Nakagawa
- Department of Molecular Life Science, Tokai University School of Medicine, Isehara, Japan
| | - Tadashi Imanishi
- Department of Molecular Life Science, Tokai University School of Medicine, Isehara, Japan
| | - Koichiro Asano
- Division of Pulmonary Medicine, Department of Medicine, Tokai University School of Medicine, Isehara, Japan
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18
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Corduneanu A, Mihalca AD, Sándor AD, Hornok S, Malmberg M, Viso NP, Bongcam-Rudloff E. The heart microbiome of insectivorous bats from Central and South Eastern Europe. Comp Immunol Microbiol Infect Dis 2021; 75:101605. [PMID: 33421678 DOI: 10.1016/j.cimid.2020.101605] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2020] [Revised: 09/22/2020] [Accepted: 12/03/2020] [Indexed: 02/03/2023]
Abstract
Host associated microbiome not only may affect the individual health-status or provide insights into the species- or group specific bacterial communities but may act as early warning signs in the assessment of zoonotic reservoirs, offering clues to predict, prevent and control possible episodes of emerging zoonoses. Bats may be carriers and reservoirs of multiple pathogens such as viruses, bacteria and parasites, showing in the same time robust immunity against many of them. The microbiota plays a fundamental role on the induction, training and function of the host immune system and the immune system has largely evolved in order to maintain the symbiotic relationship of the host with these diverse microbes. Thus, expanding our knowledge on bat-associated microbiome it can be usefully in understanding bats' outstanding immune capacities. The aim of this study was to investigate the presence of different bacterial communities in heart tissue of insectivorous bats, Nyctalus noctula, Pipistrellus pipistrellus and Rhinoplophus hipposideros, from Central and Eastern Europe using high-throughput sequencing of variable regions of the 16S rRNA. In addition, species-specific PCRs were used to validate the presence of the vector-borne pathogens Bartonella spp. and Rickettsia spp. In this study we identified a wide variety of bacterial groups, with the most abundant phyla being Proteobacteria and Firmicutes. The results showed that at individual level, the year or location had no effect on the diversity and composition of the microbiome, however host species determined both structure and abundance of the bacterial community. We report the presence of vector-borne bacteria Bartonella spp. in samples of N. noctula and indications of Rickettsia spp. in R. hipposideros. Our results provide a first insight into the bacterial community found in heart tissue of bats from Central and South Eastern Europe.
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Affiliation(s)
- Alexandra Corduneanu
- Department of Parasitology and Parasitic Diseases, University of Agricultural Sciences and Veterinary Medicine of Cluj-Napoca, Romania
| | - Andrei Daniel Mihalca
- Department of Parasitology and Parasitic Diseases, University of Agricultural Sciences and Veterinary Medicine of Cluj-Napoca, Romania
| | - Attila D Sándor
- Department of Parasitology and Parasitic Diseases, University of Agricultural Sciences and Veterinary Medicine of Cluj-Napoca, Romania; Department of Parasitology and Zoology, University of Veterinary Medicine, Budapest, Hungary.
| | - Sándor Hornok
- Department of Parasitology and Zoology, University of Veterinary Medicine, Budapest, Hungary
| | - Maja Malmberg
- Section of Virology, Department of Biomedical Sciences and Veterinary Public Health, Swedish University of Agricultural Sciences, Box 7028, 750 07, Uppsala, Sweden; SLU Global Bioinformatics Centre, Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Box 7023, 750 07, Uppsala, Sweden
| | - Natalia Pin Viso
- Consejo Nacional de Investigaciones Científicas y Técnicas, Godoy Cruz 2290, 1425, Ciudad Autónoma de Buenos Aires, Argentina; Instituto de Agrobiotecnología y Biología Molecular, IABiMo, INTA-CONICET, Calle Las Cabañas y Los Reseros s/n, Casilla de Correo 25, Castelar, 1712, Buenos Aires, Argentina
| | - Erik Bongcam-Rudloff
- SLU Global Bioinformatics Centre, Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Box 7023, 750 07, Uppsala, Sweden
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19
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Targeted Metagenomics Offers Insights into Potential Tick-Borne Pathogens. J Clin Microbiol 2020; 58:JCM.01893-20. [PMID: 32878948 DOI: 10.1128/jcm.01893-20] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Tick-borne disease pathogen identification remains a diagnostic challenge due to the multiple tests necessary for diagnosis. Targeted metagenomic sequencing is an evolving method to detect multiple different pathogens with a single test. In this issue of the Journal of Clinical Microbiology, L. Kingry, S. Sheldon, S. Oatman, B. Pritt, et al. (J Clin Microbiol 58:e00147-20, 2020, https://doi.org/10.1128/JCM.00147-20) explore 16S rRNA gene-targeted metagenomics to identify bacterial pathogens in 881 of more than 13,000 specimens submitted for tick-borne pathogen testing, giving new insights into suspected tick-borne pathogens.
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20
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Advantages and Limitations of 16S rRNA Next-Generation Sequencing for Pathogen Identification in the Diagnostic Microbiology Laboratory: Perspectives from a Middle-Income Country. Diagnostics (Basel) 2020; 10:diagnostics10100816. [PMID: 33066371 PMCID: PMC7602188 DOI: 10.3390/diagnostics10100816] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2020] [Revised: 09/18/2020] [Accepted: 10/11/2020] [Indexed: 12/19/2022] Open
Abstract
Bacterial culture and biochemical testing (CBtest) have been the cornerstone of pathogen identification in the diagnostic microbiology laboratory. With the advent of Sanger sequencing and later, next-generation sequencing, 16S rRNA next-generation sequencing (16SNGS) has been proposed to be a plausible platform for this purpose. Nevertheless, usage of the 16SNGS platform has both advantages and limitations. In addition, transition from the traditional methods of CBtest to 16SNGS requires procurement of costly equipment, timely and sustainable maintenance of these platforms, specific facility infrastructure and technical expertise. All these factors pose a challenge for middle-income countries, more so for countries in the lower middle-income range. In this review, we describe the basis for CBtest and 16SNGS, and discuss the limitations, challenges, advantages and future potential of using 16SNGS for bacterial pathogen identification in diagnostic microbiology laboratories of middle-income countries.
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21
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Arunachalam PS, Wimmers F, Mok CKP, Perera RAPM, Scott M, Hagan T, Sigal N, Feng Y, Bristow L, Tak-Yin Tsang O, Wagh D, Coller J, Pellegrini KL, Kazmin D, Alaaeddine G, Leung WS, Chan JMC, Chik TSH, Choi CYC, Huerta C, Paine McCullough M, Lv H, Anderson E, Edupuganti S, Upadhyay AA, Bosinger SE, Maecker HT, Khatri P, Rouphael N, Peiris M, Pulendran B. Systems biological assessment of immunity to mild versus severe COVID-19 infection in humans. Science 2020; 369:1210-1220. [PMID: 32788292 DOI: 10.1126/science.abc6261] [Citation(s) in RCA: 796] [Impact Index Per Article: 199.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2020] [Revised: 07/10/2020] [Accepted: 08/04/2020] [Indexed: 02/06/2023]
Abstract
Coronavirus disease 2019 (COVID-19) represents a global crisis, yet major knowledge gaps remain about human immunity to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). We analyzed immune responses in 76 COVID-19 patients and 69 healthy individuals from Hong Kong and Atlanta, Georgia, United States. In the peripheral blood mononuclear cells (PBMCs) of COVID-19 patients, we observed reduced expression of human leukocyte antigen class DR (HLA-DR) and proinflammatory cytokines by myeloid cells as well as impaired mammalian target of rapamycin (mTOR) signaling and interferon-α (IFN-α) production by plasmacytoid dendritic cells. By contrast, we detected enhanced plasma levels of inflammatory mediators-including EN-RAGE, TNFSF14, and oncostatin M-which correlated with disease severity and increased bacterial products in plasma. Single-cell transcriptomics revealed a lack of type I IFNs, reduced HLA-DR in the myeloid cells of patients with severe COVID-19, and transient expression of IFN-stimulated genes. This was consistent with bulk PBMC transcriptomics and transient, low IFN-α levels in plasma during infection. These results reveal mechanisms and potential therapeutic targets for COVID-19.
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Affiliation(s)
- Prabhu S Arunachalam
- Institute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Florian Wimmers
- Institute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Chris Ka Pun Mok
- HKU-Pasteur Research Pole, School of Public Health, HKU Li Ka Shing Faculty of Medicine, The University of Hong Kong (HKU), Hong Kong
| | - Ranawaka A P M Perera
- Centre of Influenza Research, School of Public Health, HKU Li Ka Shing Faculty of Medicine, HKU, Hong Kong
| | - Madeleine Scott
- Institute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, CA 94305, USA.,Center for Biomedical Informatics, Department of Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Thomas Hagan
- Institute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Natalia Sigal
- Institute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Yupeng Feng
- Institute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Laurel Bristow
- Hope Clinic of the Emory Vaccine Center, Department of Medicine, Division of Infectious Diseases, Emory University School of Medicine, Decatur, GA 30030, USA
| | - Owen Tak-Yin Tsang
- Infectious Diseases Centre, Princess Margaret Hospital, Hospital Authority of Hong Kong, Hong Kong
| | - Dhananjay Wagh
- Stanford Functional Genomics Facility, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - John Coller
- Stanford Functional Genomics Facility, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Kathryn L Pellegrini
- Emory Vaccine Center, Yerkes National Primate Research Center, Atlanta, GA 30329, USA
| | - Dmitri Kazmin
- Institute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Ghina Alaaeddine
- Hope Clinic of the Emory Vaccine Center, Department of Medicine, Division of Infectious Diseases, Emory University School of Medicine, Decatur, GA 30030, USA
| | - Wai Shing Leung
- Infectious Diseases Centre, Princess Margaret Hospital, Hospital Authority of Hong Kong, Hong Kong
| | - Jacky Man Chun Chan
- Infectious Diseases Centre, Princess Margaret Hospital, Hospital Authority of Hong Kong, Hong Kong
| | - Thomas Shiu Hong Chik
- Infectious Diseases Centre, Princess Margaret Hospital, Hospital Authority of Hong Kong, Hong Kong
| | - Chris Yau Chung Choi
- Infectious Diseases Centre, Princess Margaret Hospital, Hospital Authority of Hong Kong, Hong Kong
| | - Christopher Huerta
- Hope Clinic of the Emory Vaccine Center, Department of Medicine, Division of Infectious Diseases, Emory University School of Medicine, Decatur, GA 30030, USA
| | - Michele Paine McCullough
- Hope Clinic of the Emory Vaccine Center, Department of Medicine, Division of Infectious Diseases, Emory University School of Medicine, Decatur, GA 30030, USA
| | - Huibin Lv
- HKU-Pasteur Research Pole, School of Public Health, HKU Li Ka Shing Faculty of Medicine, The University of Hong Kong (HKU), Hong Kong
| | - Evan Anderson
- Department of Pediatrics, Division of Infectious Disease, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Srilatha Edupuganti
- Hope Clinic of the Emory Vaccine Center, Department of Medicine, Division of Infectious Diseases, Emory University School of Medicine, Decatur, GA 30030, USA
| | - Amit A Upadhyay
- Emory Vaccine Center, Yerkes National Primate Research Center, Atlanta, GA 30329, USA
| | - Steve E Bosinger
- Emory Vaccine Center, Yerkes National Primate Research Center, Atlanta, GA 30329, USA.,Department of Pathology and Laboratory Medicine, Emory University, Atlanta, GA 30329, USA
| | - Holden Terry Maecker
- Institute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Purvesh Khatri
- Institute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, CA 94305, USA.,Center for Biomedical Informatics, Department of Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Nadine Rouphael
- Hope Clinic of the Emory Vaccine Center, Department of Medicine, Division of Infectious Diseases, Emory University School of Medicine, Decatur, GA 30030, USA
| | - Malik Peiris
- HKU-Pasteur Research Pole, School of Public Health, HKU Li Ka Shing Faculty of Medicine, The University of Hong Kong (HKU), Hong Kong.,Centre of Influenza Research, School of Public Health, HKU Li Ka Shing Faculty of Medicine, HKU, Hong Kong
| | - Bali Pulendran
- Institute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, CA 94305, USA. .,Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305, USA.,Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA
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22
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Źródłowski T, Sobońska J, Salamon D, McFarlane IM, Ziętkiewicz M, Gosiewski T. Classical Microbiological Diagnostics of Bacteremia: Are the Negative Results Really Negative? What is the Laboratory Result Telling Us About the "Gold Standard"? Microorganisms 2020; 8:microorganisms8030346. [PMID: 32121353 PMCID: PMC7143506 DOI: 10.3390/microorganisms8030346] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2020] [Revised: 02/25/2020] [Accepted: 02/27/2020] [Indexed: 12/29/2022] Open
Abstract
Standard blood cultures require at least 24–120 h to be reported as preliminary positive. The objective of this study was to compare the reliability of Gram staining and fluorescent in-situ hybridization (FISH) for detecting bacteria in otherwise negative blood culture bottles. Ninety-six sets were taken from patients with a diagnosis of sepsis. Six incomplete blood culture sets and eight blood cultures sets demonstrating positive growth were excluded. We performed Gram stain and FISH on 82 sets taken from post-operative septic patients: 82 negative aerobic blood cultures, 82 anaerobic blood cultures, and 82 blood samples, as well as 57 blood samples taken from healthy volunteers. From the eighty-two blood sets analyzed from the septic patients, Gram stain visualized bacteria in 62.2% of blood samples, 35.4% of the negative aerobic bottles, and in 31.7% of the negative anaerobic bottles. Utilizing FISH, we detected bacteria in 75.6%, 56.1%, and 64.6% respectively. Among the blood samples from healthy volunteers, FISH detected bacteria in 64.9%, while Gram stain detected bacteria in only 38.6%. The time needed to obtain the study results using Gram stain was 1 h, for FISH 4 h, and for the culture method, considering the duration of growth, 5 days. Gram stain and FISH allow quick detection of bacteria in the blood taken directly from a patient. Finding phagocytosed bacteria, which were also detected among healthy individuals, confirms the hypothesis that blood microbiome exists.
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Affiliation(s)
- Tomasz Źródłowski
- Thoracic Anesthesia and Respiratory Intensive Care Unit, John Paul II Hospital, 31- 202 Kraków, Poland;
- Department of Internal Medicine, St. John’s Episcopal Hospital, Far Rockaway, NY 11691, USA
| | - Joanna Sobońska
- Department of Molecular Medical Microbiology, Chair of Microbiology, Faculty of Medicine, Jagiellonian University Medical College, 31-121 Krakow, Poland
| | - Dominika Salamon
- Department of Molecular Medical Microbiology, Chair of Microbiology, Faculty of Medicine, Jagiellonian University Medical College, 31-121 Krakow, Poland
| | - Isabel M. McFarlane
- Department of Medicine, SUNY Downstate Medical Center, Brooklyn, NY 11203, USA
| | - Mirosław Ziętkiewicz
- Thoracic Anesthesia and Respiratory Intensive Care Unit, John Paul II Hospital, 31- 202 Kraków, Poland;
- Department of Anesthesiology and Intensive Care, Faculty of Medicine, Jagiellonian University Medical College, 31-501 Krakow, Poland
- Correspondence: (M.Z.); (T.G.)
| | - Tomasz Gosiewski
- Department of Molecular Medical Microbiology, Chair of Microbiology, Faculty of Medicine, Jagiellonian University Medical College, 31-121 Krakow, Poland
- Correspondence: (M.Z.); (T.G.)
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23
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Ishihara T, Watanabe N, Inoue S, Aoki H, Tsuji T, Yamamoto B, Yanagi H, Oki M, Kryukov K, Nakagawa S, Inokuchi S, Ozawa H, Imanishi T. Usefulness of next-generation DNA sequencing for the diagnosis of urinary tract infection. Drug Discov Ther 2020; 14:42-49. [PMID: 32101813 DOI: 10.5582/ddt.2020.01000] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Acute urinary tract infection (UTI) is a highly common clinical condition. Although bacterial culture is the gold standard diagnostic test, false negative results may be possible, leading to the pathogen being unidentified. In recent years, bacterial DNA sequencing analysis has garnered much attention, but clinical studies are rare in Japan. In this study, we assessed the usefulness of next-generation DNA sequencing (NGS) analysis for acute UTI patients. We thus performed an observational, retrospective case series study. Urine and blood samples were collected from ten acute UTI patients, of whom four had also been diagnosed with urosepsis. Seven variable regions of bacterial 16S rRNA genes were amplified by PCR and then sequenced by IonPGM. The identified bacterial species were compared with those identified using the culture tests and the clinical parameters were analyzed. As a result, the NGS method effectively identified predominant culture-positive bacteria in urine samples. The urine NGS also detected several culture-negative species, which have been reported to be potentially pathogenic. Out of four urosepsis cases, three were pathogen-positive in blood NGS results, while two were pathogen-negative in blood culture. In one sepsis case, although blood culture was negative for Escherichia coli, this species was detected by blood NGS. For non-sepsis cases, however, blood NGS, as well as blood culture, was less effective in detecting bacterial signals. In conclusion, NGS is potentially useful for identifying pathogenic bacteria in urine from acute UTI patients but is less applicable in patients who do not meet clinical criteria for sepsis.
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Affiliation(s)
- Toru Ishihara
- Department of General Internal Medicine, Tokai University School of Medicine, Isehara, Kanagawa, Japan
| | - Nobuo Watanabe
- Department of Emergency and Critical Care Medicine, Tokai University School of Medicine, Isehara, Kanagawa, Japan
| | - Shigeaki Inoue
- Department of Emergency and Critical Care Medicine, Tokai University School of Medicine, Isehara, Kanagawa, Japan
| | - Hiromichi Aoki
- Department of Emergency and Critical Care Medicine, Tokai University School of Medicine, Isehara, Kanagawa, Japan
| | - Tomoatsu Tsuji
- Department of Emergency and Critical Care Medicine, Tokai University School of Medicine, Isehara, Kanagawa, Japan
| | - Bunsei Yamamoto
- Department of Emergency and Critical Care Medicine, Tokai University School of Medicine, Isehara, Kanagawa, Japan
| | - Hidetaka Yanagi
- Department of General Internal Medicine, Tokai University School of Medicine, Isehara, Kanagawa, Japan
| | - Masayuki Oki
- Department of General Internal Medicine, Tokai University School of Medicine, Isehara, Kanagawa, Japan
| | - Kirill Kryukov
- Department of Molecular Life Science, Tokai University School of Medicine, Isehara, Kanagawa, Japan
| | - So Nakagawa
- Department of Molecular Life Science, Tokai University School of Medicine, Isehara, Kanagawa, Japan
| | - Sadaki Inokuchi
- Department of Emergency and Critical Care Medicine, Tokai University School of Medicine, Isehara, Kanagawa, Japan
| | - Hideki Ozawa
- Department of General Internal Medicine, Tokai University School of Medicine, Isehara, Kanagawa, Japan
| | - Tadashi Imanishi
- Department of Molecular Life Science, Tokai University School of Medicine, Isehara, Kanagawa, Japan
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24
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Nakagawa S, Inoue S, Kryukov K, Yamagishi J, Ohno A, Hayashida K, Nakazwe R, Kalumbi M, Mwenya D, Asami N, Sugimoto C, Mutengo MM, Imanishi T. Rapid sequencing-based diagnosis of infectious bacterial species from meningitis patients in Zambia. Clin Transl Immunology 2019; 8:e01087. [PMID: 31709051 PMCID: PMC6831930 DOI: 10.1002/cti2.1087] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2019] [Revised: 10/05/2019] [Accepted: 10/10/2019] [Indexed: 12/13/2022] Open
Abstract
OBJECTIVES We have developed a portable system for the rapid determination of bacterial composition for the diagnosis of infectious diseases. Our system comprises of a nanopore technology-based sequencer, MinION, and two laptop computers. To examine the accuracy and time efficiency of our system, we provided a proof-of-concept for the detection of the causative bacteria of 11 meningitis patients in Zambia. METHODS We extracted DNA from cerebrospinal fluid samples of each patient and amplified the 16S rRNA gene regions. The sequencing library was prepared, and the sequenced reads were simultaneously processed for bacterial composition determination using the minimap2 software and the representative prokaryote genomes. RESULTS The sequencing results of four of the six culture-positive samples were consistent with those of conventional culture-based methods. The dominant bacterial species in each of these samples were identified from the sequencing data within only 3 min. Although the major bacterial species were also detected from the other two culture-positive samples and five culture-negative samples, their presence could not be confirmed. Moreover, as a whole, although the number of sequencing reads obtained within a short sequencing run was small, there was no change in the major bacterial species over time with prolonged sequencing. In addition, the processing time strongly correlated with the number of sequencing reads used for the analysis. CONCLUSION Our results suggest that time-effective analysis could be achieved by determining the number of sequencing reads required for the rapid diagnosis of infectious bacterial species depending on the complexity of bacterial species in a sample.
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Affiliation(s)
- So Nakagawa
- Department of Molecular Life ScienceTokai University School of MedicineIseharaJapan
- Micro/Nano Technology CenterTokai UniversityHiratsukaJapan
| | - Shigeaki Inoue
- Department of Emergency and Critical Care MedicineTokai University School of MedicineIseharaJapan
- Department of Disaster and Emergency MedicineKobe University Graduate School of MedicineKobeJapan
| | - Kirill Kryukov
- Department of Molecular Life ScienceTokai University School of MedicineIseharaJapan
| | - Junya Yamagishi
- Research Center for Zoonosis ControlHokkaido UniversitySapporoJapan
- Global Station for Zoonosis ControlGI‐CoREHokkaido UniversitySapporoJapan
| | - Ayumu Ohno
- Department of Molecular Life ScienceTokai University School of MedicineIseharaJapan
| | - Kyoko Hayashida
- Research Center for Zoonosis ControlHokkaido UniversitySapporoJapan
| | - Ruth Nakazwe
- Department of Pathology and MicrobiologyUniversity Teaching HospitalLusakaZambia
| | - Mox Kalumbi
- Department of Pathology and MicrobiologyUniversity Teaching HospitalLusakaZambia
- Institute of Basic and Biomedical SciencesLevy Mwanawasa Medical UniversityLusakaZambia
| | - Darlington Mwenya
- Department of Pathology and MicrobiologyUniversity Teaching HospitalLusakaZambia
| | - Nana Asami
- Department of Molecular Life ScienceTokai University School of MedicineIseharaJapan
| | - Chihiro Sugimoto
- Research Center for Zoonosis ControlHokkaido UniversitySapporoJapan
- Global Station for Zoonosis ControlGI‐CoREHokkaido UniversitySapporoJapan
| | - Mable M Mutengo
- Department of Pathology and MicrobiologyUniversity Teaching HospitalLusakaZambia
- Institute of Basic and Biomedical SciencesLevy Mwanawasa Medical UniversityLusakaZambia
| | - Tadashi Imanishi
- Department of Molecular Life ScienceTokai University School of MedicineIseharaJapan
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25
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Watts GS, Thornton JE, Youens-Clark K, Ponsero AJ, Slepian MJ, Menashi E, Hu C, Deng W, Armstrong DG, Reed S, Cranmer LD, Hurwitz BL. Identification and quantitation of clinically relevant microbes in patient samples: Comparison of three k-mer based classifiers for speed, accuracy, and sensitivity. PLoS Comput Biol 2019; 15:e1006863. [PMID: 31756192 PMCID: PMC6897419 DOI: 10.1371/journal.pcbi.1006863] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2019] [Revised: 12/06/2019] [Accepted: 10/10/2019] [Indexed: 12/15/2022] Open
Abstract
Infections are a serious health concern worldwide, particularly in vulnerable populations such as the immunocompromised, elderly, and young. Advances in metagenomic sequencing availability, speed, and decreased cost offer the opportunity to supplement or even replace culture-based identification of pathogens with DNA sequence-based diagnostics. Adopting metagenomic analysis for clinical use requires that all aspects of the workflow are optimized and tested, including data analysis and computational time and resources. We tested the accuracy, sensitivity, and resource requirements of three top metagenomic taxonomic classifiers that use fast k-mer based algorithms: Centrifuge, CLARK, and KrakenUniq. Binary mixtures of bacteria showed all three reliably identified organisms down to 1% relative abundance, while only the relative abundance estimates of Centrifuge and CLARK were accurate. All three classifiers identified the organisms present in their default databases from a mock bacterial community of 20 organisms, but only Centrifuge had no false positives. In addition, Centrifuge required far less computational resources and time for analysis. Centrifuge analysis of metagenomes obtained from samples of VAP, infected DFUs, and FN showed Centrifuge identified pathogenic bacteria and one virus that were corroborated by culture or a clinical PCR assay. Importantly, in both diabetic foot ulcer patients, metagenomic sequencing identified pathogens 4-6 weeks before culture. Finally, we show that Centrifuge results were minimally affected by elimination of time-consuming read quality control and host screening steps.
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Affiliation(s)
- George S. Watts
- University of Arizona Cancer Center and Department of Pharmacology, University of Arizona, Tucson, Arizona, United States of America
| | - James E. Thornton
- Department of Biosystems Engineering, University of Arizona, Tucson, Arizona, United States of America
| | - Ken Youens-Clark
- Department of Biosystems Engineering, University of Arizona, Tucson, Arizona, United States of America
| | - Alise J. Ponsero
- Department of Biosystems Engineering, University of Arizona, Tucson, Arizona, United States of America
| | - Marvin J. Slepian
- Department of Medicine, University of Arizona, Tucson, Arizona, United States of America
- Department of Biomedical Engineering, University of Arizona, Tucson, Arizona, United States of America
- Arizona Center for Accelerated Biomedical Innovation, University of Arizona, Tucson, Arizona, United States of America
| | - Emmanuel Menashi
- Honor Health Hospital, Scottsdale, Arizona, United States of America
| | - Charles Hu
- Dignity Health Chandler Regional Medical Center, Chandler, Arizona, United States of America
| | - Wuquan Deng
- Department of Endocrinology, Multidisciplinary Diabetic Foot Medical Center, Affiliated Central Hospital of Chongqing University, Chongqing, China
| | - David G. Armstrong
- Southwestern Academic Limb Salvage Alliance (SALSA), Department of Surgery, Keck School of Medicine of University of Southern California, Los Angeles, California, United States of America
| | - Spenser Reed
- University of Arizona Department of Family and Community Medicine, Tucson, Arizona, United States of America
| | - Lee D. Cranmer
- Department of Medicine, University of Washington and Fred Hutchinson Cancer Research Center, and Seattle Cancer Care Alliance, Seattle, Washington, United States of America
| | - Bonnie L. Hurwitz
- Department of Biosystems Engineering, University of Arizona, Tucson, Arizona, United States of America
- BIO5 Institute, University of Arizona, Tucson, Arizona, United States of America
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26
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Zhu ZZ, Zhu J, Zhu K, Wang H, Xu Q, Bai C. Next generation sequencing-guided anti-infective therapy of large liver abscess due to Edwardsiella tarda: a case report. J LAB MED 2019. [DOI: 10.1515/labmed-2019-0070] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
AbstractBackgroundLiver abscess is a potentially fatal disease, however identification of its causative pathogen remains challenging, which is crucial for guiding appropriate antibiotic therapy. To the best of our knowledge, the use of plasma next-generation sequencing (NGS) based pathogen analysis in patients with liver abscess has never been reported.Case presentationWe report a case with large liver abscess due toEdwardsiella tardathat was diagnosed by the plasma-based NGS assay within 24 h. After a 2-week single agent anti-infection therapy, the patient completely recovered. A second NGS assay following anti-infection therapy failed to detect the pathogenic DNA. Follow-up magnetic resonance imaging (MRI) of the abdomen on 1 month and 3 months showed a gradually decrease in size of the liver abscess, and the 6-month MRI showed that the abscess disappeared completely.ConclusionsOur data indicated that the plasma NGS test can sensitively and minimal-invasively detect pathogens within a clinically actionable timeframe, and antibiotic alone is an alternative to first-line treatment for large liver abscess with the aid of NGS for accurate detection of the pathogenic bacterial genome.
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27
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Abstract
Objective: Sepsis is a deadly infection that causes injury to tissues and organs. Infection and anti-infective treatment are the eternal themes of sepsis. The successful control of infection is a key factor of resuscitation for sepsis and septic shock. This review examines evidence for the treatment of sepsis. This evidence is combined with clinical experiments to reveal the rules and a standard flowchart of anti-infection therapy for sepsis. Data Sources: We retrieved information from the PubMed database up to October 2018 using various search terms and their combinations, including sepsis, septic shock, infection, antibiotics, and anti-infection. Study Selection: We included data from peer-reviewed journals printed in English on the relationships between infections and antibiotics. Results: By combining the literature review and clinical experience, we propose a 6Rs rule for sepsis and septic shock management: right patients, right time, right target, right antibiotics, right dose, and right source control. This rule encompasses rational decisions regarding the timing of treatment, the identification of the correct pathogen, the selection of appropriate antibiotics, the formulation of a scientifically based antibiotic dosage regimen, and the adequate control of infectious foci. Conclusions: This review highlights how to recognize and treat sepsis and septic shock and provides rules and a standard flowchart for anti-infection therapy for sepsis and septic shock for use in the clinical setting.
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