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Ji X, Ni S, Tian G, Zhang L, Wang W. Detection of Microorganisms in Body Fluid Samples. Methods Mol Biol 2023; 2695:73-88. [PMID: 37450112 DOI: 10.1007/978-1-0716-3346-5_5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/18/2023]
Abstract
Next-generation sequencing (NGS) has been widely applied to the identification of microbiome in body fluids. The methodology of 16S rRNA amplicon sequencing is simple, fast, and cost-effective. It overcomes the problem that some microorganisms cannot be isolated or cultured. Low abundant bacteria can also be amplified and sequenced, but the resolution of classification can hardly reach species or sub-species level; moreover, this methodology is mainly used to identify bacterial populations, and other microorganisms like viruses or fungi cannot be sequenced. On the other hand, the microbiome profiling obtained by shotgun metagenomic sequencing is more comprehensive with better resolution, and more accurate classification can be expected due to higher coverage of genomic sequences from microorganisms. By combining the capture-based method with metagenomic sequencing, we can further enrich and detect low abundant microorganisms and identify the viral integration sites in host gDNA at once.
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2
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Yang J, Pu J, Lu S, Bai X, Wu Y, Jin D, Cheng Y, Zhang G, Zhu W, Luo X, Rosselló-Móra R, Xu J. Species-Level Analysis of Human Gut Microbiota With Metataxonomics. Front Microbiol 2020; 11:2029. [PMID: 32983030 PMCID: PMC7479098 DOI: 10.3389/fmicb.2020.02029] [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: 04/02/2020] [Accepted: 07/31/2020] [Indexed: 12/19/2022] Open
Abstract
The current understanding of human gut microbial community is mainly limited to taxonomic features at the genus level. Here, we examined the human gut microbial community at the species level by metataxonomics. To achieve this purpose, a high-throughput approach involving operational phylogenetic unit analysis of the near full-length 16S ribosomal RNA (rRNA) gene sequence was used. A total of 1,235 species-level phylotypes (SLPs) were classified in the feces of 120 Chinese healthy individuals, including 461 previously classified species, 358 potentially new species, and 416 potentially new taxa, which were categorized into low, medium, and high prevalent bacteria groups based on their prevalence. Each individual harbored 186 ± 51 SLPs on average. There was no universal bacterial species shared by all the individuals. However, 90 ± 19 of 116 SLPs were shared in the high prevalent bacteria group. Thirty-two out of thirty-eight species in the high prevalent bacteria group detected in this study were also found in at least one previous study on human gut microbiota based on either culture-dependent or culture-independent approaches. Through compositional analysis, a hierarchical clustering of the prevalence and relative abundance of the 1,235 SLPs revealed two types of gut microbial communities, which were dominated by Prevotella copri and Bacteroides vulgatus, respectively. The type dominated by P. copri was more prevalent in northern China, while the B. vulgatus-dominant type was more prevalent in southern China. Therefore, P- and B-type gut microbial communities in China were proposed. It was found that 166 out of 461 known bacterial species have been previously reported as potential pathogens, and the individuals sampled for this study harbored 20 of these potential pathogenic species on average. The top two most abundant and prevalent potential pathogenic species were Klebsiella pneumoniae and Bacteroides fragilis.
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Affiliation(s)
- Jing Yang
- State Key Laboratory of Infectious Disease Prevention and Control, Chinese Center for Disease Control and Prevention, National Institute for Communicable Disease Control and Prevention, Beijing, China.,Shanghai Public Health Clinical Center, Shanghai Institute for Emerging and Re-emerging Infectious Diseases, Shanghai, China.,Research Units of Discovery of Unknown Bacteria and Function, Chinese Academy of Medical Sciences, Beijing, China
| | - Ji Pu
- State Key Laboratory of Infectious Disease Prevention and Control, Chinese Center for Disease Control and Prevention, National Institute for Communicable Disease Control and Prevention, Beijing, China.,Shanghai Public Health Clinical Center, Shanghai Institute for Emerging and Re-emerging Infectious Diseases, Shanghai, China
| | - Shan Lu
- State Key Laboratory of Infectious Disease Prevention and Control, Chinese Center for Disease Control and Prevention, National Institute for Communicable Disease Control and Prevention, Beijing, China.,Shanghai Public Health Clinical Center, Shanghai Institute for Emerging and Re-emerging Infectious Diseases, Shanghai, China.,Research Units of Discovery of Unknown Bacteria and Function, Chinese Academy of Medical Sciences, Beijing, China
| | - Xiangning Bai
- State Key Laboratory of Infectious Disease Prevention and Control, Chinese Center for Disease Control and Prevention, National Institute for Communicable Disease Control and Prevention, Beijing, China
| | - Yangfeng Wu
- Peking University Clinical Research Institute, Beijing, China
| | - Dong Jin
- State Key Laboratory of Infectious Disease Prevention and Control, Chinese Center for Disease Control and Prevention, National Institute for Communicable Disease Control and Prevention, Beijing, China.,Shanghai Public Health Clinical Center, Shanghai Institute for Emerging and Re-emerging Infectious Diseases, Shanghai, China.,Research Units of Discovery of Unknown Bacteria and Function, Chinese Academy of Medical Sciences, Beijing, China
| | - Yanpeng Cheng
- State Key Laboratory of Infectious Disease Prevention and Control, Chinese Center for Disease Control and Prevention, National Institute for Communicable Disease Control and Prevention, Beijing, China
| | - Gui Zhang
- State Key Laboratory of Infectious Disease Prevention and Control, Chinese Center for Disease Control and Prevention, National Institute for Communicable Disease Control and Prevention, Beijing, China
| | - Wentao Zhu
- State Key Laboratory of Infectious Disease Prevention and Control, Chinese Center for Disease Control and Prevention, National Institute for Communicable Disease Control and Prevention, Beijing, China
| | - Xuelian Luo
- State Key Laboratory of Infectious Disease Prevention and Control, Chinese Center for Disease Control and Prevention, National Institute for Communicable Disease Control and Prevention, Beijing, China
| | - Ramon Rosselló-Móra
- Marine Microbiology Group, Department of Ecology and Marine Resources, Instituto Mediterráneo de Estudios Avanzados (IMEDEA), Esporles, Spain
| | - Jianguo Xu
- State Key Laboratory of Infectious Disease Prevention and Control, Chinese Center for Disease Control and Prevention, National Institute for Communicable Disease Control and Prevention, Beijing, China.,Shanghai Public Health Clinical Center, Shanghai Institute for Emerging and Re-emerging Infectious Diseases, Shanghai, China.,Research Units of Discovery of Unknown Bacteria and Function, Chinese Academy of Medical Sciences, Beijing, China.,Institute of Public Health, Nankai University, Tianjing, China
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3
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Gajdács M, Urbán E. The Pathogenic Role of Actinomyces spp. and Related Organisms in Genitourinary Infections: Discoveries in the New, Modern Diagnostic Era. Antibiotics (Basel) 2020; 9:E524. [PMID: 32824418 PMCID: PMC7459602 DOI: 10.3390/antibiotics9080524] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2020] [Revised: 08/14/2020] [Accepted: 08/15/2020] [Indexed: 12/16/2022] Open
Abstract
Actinomycosis is a chronic, suppurative, granulomatous infectious disease, caused by different species of Actinomyces bacteria. To date, 26 validly published Actinomyces species have been described as part of a normal human microbiota or from human clinical specimens. Due to the rapid spread of new, modern diagnostic procedures, 13 of 26 of these species have been described in this century and the Actinomycetaceae family has undergone several taxonomic revisions, including the introduction of many novel species termed Actinomyces-like organisms (ALOs). There is scarce data available on the role of these novel bacterial species in various infectious processes in human medicine. The aim of this review is to provide a comprehensive overview of Actinomyces and closely related organisms involved in human diseases-with a special focus on newly described species-in particular their role in genitourinary tract infections in females and males.
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Affiliation(s)
- Márió Gajdács
- Department of Pharmacodynamics and Biopharmacy, Faculty of Pharmacy, University of Szeged, 6720 Szeged, Hungary;
- Institute of Medical Microbiology, Faculty of Medicine, Semmelweis University, 1089 Budapest, Hungary
| | - Edit Urbán
- Institute of Translational Medicine, Faculty of Medicine, University of Pécs, 7624 Pécs, Hungary
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Baccari O, Elleuch J, Barkallah M, Boukedi H, Ayed NB, Hammami A, Fendri I, Abdelkafi S. Development of a new TaqMan-based PCR assay for the specific detection and quantification of Simkania negevensis. Mol Cell Probes 2020; 53:101645. [PMID: 32745685 DOI: 10.1016/j.mcp.2020.101645] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2020] [Revised: 07/02/2020] [Accepted: 07/30/2020] [Indexed: 02/07/2023]
Abstract
Simkania negevensis is an emerging Chlamydia-like bacterium related to human respiratory diseases. An early and accurate detection of this pathogen could be useful to monitor the potential infectious risks and to set suitable outbreak control measures. In Tunisia, distribution and abundance of S. negevensis remain until now largely unknown. In the present work, a qPCR assay, targeting the 16S rRNA gene, for fast detection and quantification of S. negevensis was developed and validated. A high specificity for S. negevensis detection displaying no cross-reaction with the closely related Chlamydia spp. or the other tested microorganisms was noticed. qPCR assay performance was considered very satisfying with detection limits of 5 DNA copies per reaction. qPCR assay validation was performed by screening 37 clinical specimens and 35 water samples. S. negevensis wasn't detected in respiratory samples, but it was found in four cases of water samples. We suggest that the qPCR assay developed in this study could be considered sufficiently characterized to initiate the quantification of S. negevensis in environmental samples.
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Affiliation(s)
- Olfa Baccari
- Laboratoire de Génie Enzymatique et Microbiologie, Equipe Biotechnologie des Algues, Ecole Nationale d'Ingénieurs de Sfax, Université de Sfax, Sfax, Tunisia
| | - Jihen Elleuch
- Laboratoire de Génie Enzymatique et Microbiologie, Equipe Biotechnologie des Algues, Ecole Nationale d'Ingénieurs de Sfax, Université de Sfax, Sfax, Tunisia.
| | - Mohamed Barkallah
- Laboratoire de Génie Enzymatique et Microbiologie, Equipe Biotechnologie des Algues, Ecole Nationale d'Ingénieurs de Sfax, Université de Sfax, Sfax, Tunisia
| | - Hanen Boukedi
- Laboratory of Biopesticides, Biotechnology Center of Sfax, University of Sfax, Sfax, Tunisia
| | - Nourelhouda Ben Ayed
- Laboratory of Microbiology, Faculty of Medicine of Sfax, Habib Bourguiba University Hospital, University of Sfax, Tunisia
| | - Adnene Hammami
- Laboratory of Microbiology, Faculty of Medicine of Sfax, Habib Bourguiba University Hospital, University of Sfax, Tunisia
| | - Imen Fendri
- Laboratory of Plant Biotechnology Applied to the Improvement of Cultures, Faculty of Science of Sfax, Tunisia
| | - Slim Abdelkafi
- Laboratoire de Génie Enzymatique et Microbiologie, Equipe Biotechnologie des Algues, Ecole Nationale d'Ingénieurs de Sfax, Université de Sfax, Sfax, Tunisia
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5
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Saltos Rosero N, Seoane Prado R, Aguilera Guirao A, Santos Y. Molecular and serological typing of Streptococcus mutans strains isolated from young Galician population: relationship with the oral health status. Int Microbiol 2020; 23:589-596. [PMID: 32445163 DOI: 10.1007/s10123-020-00132-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2019] [Revised: 04/15/2020] [Accepted: 05/14/2020] [Indexed: 12/12/2022]
Abstract
The aim of this study was to determine the prevalence of Streptococcus mutans and its serotypes in samples from oral cavity of young Galician population and their relationship with the oral health state. The variables generally associated with dental caries, such as salivary flow rate, buffering capacity, eating habits, and lifestyle, were also analysed. No relationship was found between the variables studied and the presence of S. mutans in the oral cavity or the existence of dental caries. Presumptive strains of S. mutans were isolated from saliva samples from 48% of the analysed population. The use of conventional microbiological methods, API 20 Strep system, and species-specific polymerase chain reaction (PCR) allowed to substantiate the identity of the strains as S. mutans. Multiplex PCR protocols, developed in this study for the simultaneous detection of S. mutans and serotypes c, e, and f and for detection of S. mutans and serotype k, also confirmed this result and demonstrated that serotype c was predominant in the studied young Galician population (86%). Serotypes e (8%), k (3%), and f (2%) were also detected. Serotype c was detected in carious and caries-free subjects, while the remaining serotypes were only found in subjects with caries.
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Affiliation(s)
- Nancy Saltos Rosero
- Departamento de Microbiología y Parasitología, Instituto de Análisis Químicos y Biológicos (IAQBUS), Universidade de Santiago de Compostela, Institutos Universitarios Bloque B, C/ Constantino Candeira 5, 15705, Santiago de Compostela, Spain
| | - Rafael Seoane Prado
- Departamento de Microbiología y Parasitología, Facultad de Medicina y Odontología, Universidade de Santiago de Compostela, Santiago de Compostela, Spain
| | - Antonio Aguilera Guirao
- Departamento de Microbiología y Parasitología, Facultad de Medicina y Odontología, Universidade de Santiago de Compostela, Santiago de Compostela, Spain
| | - Ysabel Santos
- Departamento de Microbiología y Parasitología, Instituto de Análisis Químicos y Biológicos (IAQBUS), Universidade de Santiago de Compostela, Institutos Universitarios Bloque B, C/ Constantino Candeira 5, 15705, Santiago de Compostela, Spain.
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6
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da Silva CB, Dos Santos HRM, Marbach PAS, de Souza JT, Cruz-Magalhães V, Argôlo-Filho RC, Loguercio LL. First-tier detection of intragenomic 16S rRNA gene variation in culturable endophytic bacteria from cacao seeds. PeerJ 2019; 7:e7452. [PMID: 31768299 PMCID: PMC6874854 DOI: 10.7717/peerj.7452] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2019] [Accepted: 07/10/2019] [Indexed: 11/20/2022] Open
Abstract
Background Intragenomic variability in 16S rDNA is a limiting factor for taxonomic and diversity characterization of Bacteria, and studies on its occurrence in natural/environmental populations are scarce. In this work, direct DNA amplicon sequencing coupled with frequent-cutter restriction analysis allowed detection of intragenomic 16S rDNA variation in culturable endophytic bacteria from cacao seeds in a fast and attractive manner. Methods Total genomic DNA from 65 bacterial strains was extracted and the 16S rDNA hyper variable V5-V9 regions were amplified for enzyme digestion and direct Sanger-type sequencing. The resulting electropherograms were visually inspected and compared to the corresponding AluI-restriction profiles, as well as to complete genome sequences in databases. Restriction analysis were employed to substitute the need of amplicon cloning and re-sequencing. A specifically improved polyacrylamide-gradient electrophoresis allowed to resolve 5-bp differences in restriction fragment sizes. Chi-square analysis on 2 × 2 contingency table tested for the independence between the 'number of AluI bands' and 'type of eletropherogram'. Results Two types of electropherograms were obtained: unique template, with single peaks per base (clean chromatograms), and heterogeneous template, with various levels of multiple peaks per base (mixed chromatograms). Statistics revealed significant interaction between number of restriction fragments and type of electropherogram for the same amplicons: clean or mixed ones associated to ≤5 or ≥6 bands, respectively. The mixed-template pattern combined with the AluI-restriction profiles indicated a high proportion of 49% of the culturable endophytes from a tropical environment showing evidence of intragenomic 16S rDNA heterogeneity. Conclusion The approach presented here was useful for a rapid, first-tier detection of intragenomic variation in culturable isolates, which can be applied in studies of other natural populations; a preliminary view of intragenomic heterogeneity levels can complement culture-dependent and -independent methods. Consequences of these findings in taxonomic and diversity studies in complex bacterial communities are discussed.
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Affiliation(s)
| | | | - Phellippe Arthur Santos Marbach
- Center for Agricultural, Biological and Environmental Sciences (CCAAB), Federal University of Recôncavo da Bahia (UFRB), Cruz das Almas-BA, Brazil
| | | | - Valter Cruz-Magalhães
- Dept. of Biological Sciences (DCB), State University of Santa Cruz (UESC), Ilhéus-BA, Brazil.,Dept. of Plant Pathology (DFP), Federal University of Lavras (UFLA), Lavras-MG, Brazil
| | | | - Leandro Lopes Loguercio
- Dept. of Biological Sciences (DCB), State University of Santa Cruz (UESC), Ilhéus-BA, Brazil
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Chong YK, Ho CC, Leung SY, Lau SK, Woo PC. Clinical Mass Spectrometry in the Bioinformatics Era: A Hitchhiker's Guide. Comput Struct Biotechnol J 2018; 16:316-334. [PMID: 30237866 PMCID: PMC6138949 DOI: 10.1016/j.csbj.2018.08.003] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2018] [Revised: 08/20/2018] [Accepted: 08/21/2018] [Indexed: 02/06/2023] Open
Abstract
Mass spectrometry (MS) is a sensitive, specific and versatile analytical technique in the clinical laboratory that has recently undergone rapid development. From initial use in metabolic profiling, it has matured into applications including clinical toxicology assays, target hormone and metabolite quantitation, and more recently, rapid microbial identification and antimicrobial resistance detection by matrix assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS). In this mini-review, we first succinctly outline the basics of clinical mass spectrometry. Examples of hard ionization (electron ionization) and soft ionization (electrospray ionization, MALDI) are presented to demonstrate their clinical applications. Next, a conceptual discourse on mass selection and determination is presented: quadrupole mass filter, time-of-flight mass spectrometer and the Orbitrap; and MS/MS (tandem-in-space, tandem-in-time and data acquisition), illustrated with clinical examples. Current applications in (1) bacterial and fungal identification, antimicrobial susceptibility testing and phylogenetic classification, (2) general unknown urine toxicology screening and expanded new-born metabolic screening and (3) clinical metabolic profiling by gas chromatography are outlined. Finally, major limitations of MS-based techniques, including the technical challenges of matrix effect and isobaric interference; and novel challenges in the post-genomic era, such as protein molecular variants, are critically discussed from the perspective of service laboratories. Computer technology and structural biology have played important roles in the maturation of this field. MS-based techniques have the potential to replace current analytical techniques, and existing expertise and instrument will undergo rapid evolution. Significant automation and adaptation to regulatory requirements are underway. Mass spectrometry is unleashing its potentials in clinical laboratories.
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Affiliation(s)
- Yeow-Kuan Chong
- Hospital Authority Toxicology Reference Laboratory, Department of Pathology, Princess Margaret Hospital (PMH), Kowloon, Hong Kong
- Chemical Pathology and Medical Genetics, Department of Pathology, Princess Margaret Hospital (PMH), Kowloon, Hong Kong
| | - Chi-Chun Ho
- Division of Chemical Pathology, Department of Clinical Pathology, Pamela Youde Nethersole Eastern Hospital (PYNEH), Hong Kong
- Division of Clinical Biochemistry, Department of Pathology, Queen Mary Hospital (QMH), Hong Kong
- Centre for Genomic Sciences, The University of Hong Kong, Hong Kong
- Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong
| | - Shui-Yee Leung
- Department of Ocean Science, School of Science, The Hong Kong University of Science and Technology, Kowloon, Hong Kong
| | - Susanna K.P. Lau
- Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong
- State Key Laboratory of Emerging Infectious Diseases, Department of Microbiology, The University of Hong Kong, Hong Kong
- Research Centre of Infection and Immunology, The University of Hong Kong, Hong Kong
- Carol Yu Centre for Infection, The University of Hong Kong, Hong Kong
- Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The University of Hong Kong, Hong Kong
| | - Patrick C.Y. Woo
- Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong
- State Key Laboratory of Emerging Infectious Diseases, Department of Microbiology, The University of Hong Kong, Hong Kong
- Research Centre of Infection and Immunology, The University of Hong Kong, Hong Kong
- Carol Yu Centre for Infection, The University of Hong Kong, Hong Kong
- Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The University of Hong Kong, Hong Kong
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Kotaskova I, Nemec P, Vanerkova M, Malisova B, Tejkalova R, Orban M, Zampachova V, Freiberger T. First report of Sneathia sanguinegens together with Mycoplasma hominis in postpartum prosthetic valve infective endocarditis: a case report. BMC Infect Dis 2017; 17:563. [PMID: 28806998 PMCID: PMC5557263 DOI: 10.1186/s12879-017-2654-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2017] [Accepted: 07/30/2017] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The presence of more than one bacterial agent is relatively rare in infective endocarditis, although more common in prosthetic cases. Molecular diagnosis from a removed heart tissue is considered a quick and effective way to diagnose fastidious or intracellular agents. CASE PRESENTATION Here we describe the case of postpartum polymicrobial prosthetic valve endocarditis in a young woman. Sneathia sanguinegens and Mycoplasma hominis were simultaneously detected from the heart valve sample using broad range 16S rRNA polymerase chain reaction (PCR) followed by sequencing while culture remained negative. Results were confirmed by independent PCR combined with denaturing gradient gel electrophoresis. Before the final agent identification, the highly non-compliant patient left from the hospital against medical advice on empirical intravenous treatment with aminopenicillins, clavulanate and gentamicin switched to oral amoxycillin and clavulanate. Four months after surgery, no signs of inflammation were present despite new regurgitation and valve leaflet flail was detected. However, after another 5 months the patient died from sepsis and recurrent infective endocarditis of unclarified etiology. CONCLUSIONS Mycoplasma hominis is a rare causative agent of infective endocarditis. To the best of our knowledge, presented case is the first report of Sneathia sanguinegens detected in this condition. Molecular techniques were shown to be useful even in polymicrobial infective endocarditis samples.
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Affiliation(s)
- Iva Kotaskova
- Molecular and Genetics Laboratory, Centre for Cardiovascular Surgery and Transplantation, Brno, Czech Republic.,Medical Genomics Research Group, CEITEC, Masaryk University, Brno, Czech Republic
| | - Petr Nemec
- Department of Cardiosurgery, Centre for Cardiovascular Surgery and Transplantation, Brno, Czech Republic
| | - Martina Vanerkova
- Molecular and Genetics Laboratory, Centre for Cardiovascular Surgery and Transplantation, Brno, Czech Republic
| | - Barbora Malisova
- Molecular and Genetics Laboratory, Centre for Cardiovascular Surgery and Transplantation, Brno, Czech Republic
| | - Renata Tejkalova
- Department of Microbiology, Faculty of Medicine, Masaryk University and St. Anne's University Hospital, Brno, Czech Republic
| | - Marek Orban
- Department of Cardiology, Centre for Cardiovascular Surgery and Transplantation, Brno, Czech Republic
| | - Vita Zampachova
- 1st Institute of Pathological Anatomy, Faculty of Medicine, Masaryk University and St. Anne's University Hospital, Brno, Czech Republic
| | - Tomas Freiberger
- Molecular and Genetics Laboratory, Centre for Cardiovascular Surgery and Transplantation, Brno, Czech Republic. .,Medical Genomics Research Group, CEITEC, Masaryk University, Brno, Czech Republic. .,Department of Clinical Immunology and Allergology, Faculty of Medicine, Masaryk University, Brno, Czech Republic.
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Molecular identification of cestodes and nematodes by cox1 gene real-time PCR and sequencing. Diagn Microbiol Infect Dis 2017; 89:185-190. [PMID: 28865743 DOI: 10.1016/j.diagmicrobio.2017.07.012] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2017] [Revised: 07/24/2017] [Accepted: 07/24/2017] [Indexed: 11/22/2022]
Abstract
Unlike bacteria and fungi, identification of helminths by gene sequencing is not well-standardized. No "pan-cestode" or "pan-nematode" PCR primers are available. In this study, we designed 2 pairs of PCR primers for amplifying the cox1 genes of cestodes and nematodes respectively and validated their usefulness for real-time PCR and sequencing identification using clinical samples with cestodes and nematodes collected from a variety of animals and human in 7 countries in Asia, Europe and Africa. The detection limits of the cox1 real-time PCR assays for cestodes and nematodes were 10 copies/reaction of extracted DNA, corresponding to CT values of 33 and 31 respectively. Real-time PCR using the 2 pairs of primers and probes showed positive results for all 20 clinical samples of cestodes and nematodes. Using phenotypic identification results as the reference standard, DNA sequencing successfully identified all the 5 cestodes and 7 nematodes with cox1 gene sequences available in GenBank, with all these names appearing as the best match of the cox1 gene sequences of the corresponding clinical samples. The percentage nucleotide identities between the cox1 gene sequences of the samples and those of the corresponding best match sequences in GenBank were 98-100%. For the remaining 5 cestodes and 3 nematodes, the corresponding cox1 gene sequences were not available in GenBank. cox1 gene sequencing is discriminative enough for accurately identifying most of the cestodes and nematodes in the present study. Further expansion of the cox1 gene sequence database will enable accurate identification of more cestodes and nematodes.
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10
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Use of organism identification by 16S ribosomal RNA polymerase chain reaction to shorten antimicrobial length of therapy. Diagn Microbiol Infect Dis 2017; 88:163-167. [PMID: 28410853 DOI: 10.1016/j.diagmicrobio.2017.03.013] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2016] [Revised: 03/12/2017] [Accepted: 03/24/2017] [Indexed: 11/23/2022]
Abstract
BACKGROUND Organism detection by 16S ribosomal RNA (rRNA) PCR followed by amplicon sequencing identification may help guide antimicrobial treatment in culture-negative patients. The objectives of this study were to assess the effect of a positive versus negative 16S rRNA PCR on antibiotic length of therapy (LOT) and rate of antibiotic discontinuation. METHODS Patients with a sterile site, direct-specimen 16S rRNA PCR negative, and suspected active infection were matched 1:1 with 16S rRNA PCR positive patients based on specimen site and retrospectively evaluated. RESULTS Ninety patients were included (n=45 positive and negative). 16S rRNA PCR negative patients had shorter median LOT (33days [IQR 8-46] versus 43days [IQR 29-51], P=0.02). Antibiotics were discontinued more frequently in 16S rRNA PCR negative patients (38% versus 4%, P<0.01). CONCLUSIONS For culture-negative patients with suspected sterile site infection, a negative, direct-specimen 16S rRNA PCR may help discontinue antibiotics and decrease LOT.
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11
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Meng X, Lu S, Yang J, Jin D, Wang X, Bai X, Wen Y, Wang Y, Niu L, Ye C, Rosselló-Móra R, Xu J. Metataxonomics reveal vultures as a reservoir for Clostridium perfringens. Emerg Microbes Infect 2017; 6:e9. [PMID: 28223683 PMCID: PMC5322324 DOI: 10.1038/emi.2016.137] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2016] [Revised: 11/25/2016] [Accepted: 12/12/2016] [Indexed: 01/21/2023]
Abstract
The Old World vulture may carry and spread pathogens for emerging infections since they feed on the carcasses of dead animals and participate in the sky burials of humans, some of whom have died from communicable diseases. Therefore, we studied the precise fecal microbiome of the Old World vulture with metataxonomics, integrating the high-throughput sequencing of almost full-length small subunit ribosomal RNA (16S rRNA) gene amplicons in tandem with the operational phylogenetic unit (OPU) analysis strategy. Nine vultures of three species were sampled using rectal swabs on the Qinghai-Tibet Plateau, China. Using the Pacific Biosciences sequencing platform, we obtained 54 135 high-quality reads of 16S rRNA amplicons with an average of 1442±6.9 bp in length and 6015±1058 reads per vulture. Those sequences were classified into 314 OPUs, including 102 known species, 50 yet to be described species and 161 unknown new lineages of uncultured representatives. Forty-five species have been reported to be responsible for human outbreaks or infections, and 23 yet to be described species belong to genera that include pathogenic species. Only six species were common to all vultures. Clostridium perfringens was the most abundant and present in all vultures, accounting for 30.8% of the total reads. Therefore, using the new technology, we found that vultures are an important reservoir for C. perfringens as evidenced by the isolation of 107 strains encoding for virulence genes, representing 45 sequence types. Our study suggests that the soil-related C. perfringens and other pathogens could have a reservoir in vultures and other animals.
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Affiliation(s)
- Xiangli Meng
- Department of New Pathogen, State Key Laboratory for Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China.,Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Hangzhou 310003, China
| | - Shan Lu
- Department of New Pathogen, State Key Laboratory for Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China.,Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Hangzhou 310003, China
| | - Jing Yang
- Department of New Pathogen, State Key Laboratory for Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China.,Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Hangzhou 310003, China
| | - Dong Jin
- Department of New Pathogen, State Key Laboratory for Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China.,Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Hangzhou 310003, China
| | - Xiaohong Wang
- Department of New Pathogen, State Key Laboratory for Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China.,Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Hangzhou 310003, China
| | - Xiangning Bai
- Department of New Pathogen, State Key Laboratory for Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China.,Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Hangzhou 310003, China
| | - Yumeng Wen
- Department of New Pathogen, State Key Laboratory for Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China.,Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Hangzhou 310003, China
| | - Yiting Wang
- Department of New Pathogen, State Key Laboratory for Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China.,Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Hangzhou 310003, China
| | - Lina Niu
- Department of New Pathogen, State Key Laboratory for Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China.,Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Hangzhou 310003, China
| | - Changyun Ye
- Department of New Pathogen, State Key Laboratory for Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China.,Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Hangzhou 310003, China
| | - Ramon Rosselló-Móra
- Marine Microbiology Group, Department of Ecology and Marine Resources, Mediterranean Institute for Advanced Studies [Spanish National Research Council (CSIC)-University of the Balearic Islands (UIB)], E-07190 Esporles, Balearic Islands 07190, Spain
| | - Jianguo Xu
- Department of New Pathogen, State Key Laboratory for Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China.,Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Hangzhou 310003, China
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12
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García Carretero R, Luna-Heredia E, Olid-Velilla M, Vazquez-Gomez O. Bacteraemia due to Parvimonas micra, a commensal pathogen, in a patient with an oesophageal tumour. BMJ Case Rep 2016; 2016:bcr-2016-217740. [PMID: 27864301 DOI: 10.1136/bcr-2016-217740] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
A man aged 53 years was admitted to our hospital due to general malaise, fever and chills for the past 24 hours. He had a history of chronic alcoholic liver disease. The blood tests showed leucocytosis with neutrophilia, lactic acidosis and acute-phase reactants. The blood cultures were positive for Parvimonas micra, an anaerobic pathogen which is part of the flora of the oral cavity. There was no evidence of abscess formation in either the examination or the imaging tests, but in the work-up that followed, a gastroscopy showed a stenotic oesophageal mass that turned out to be an invasive squamous cell carcinoma.
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Affiliation(s)
| | - Esther Luna-Heredia
- Department of Internal Medicine, Hospital Universitario de Mostoles, Mostoles, Madrid, Spain
| | - Monica Olid-Velilla
- Department of Internal Medicine, Hospital Universitario de Mostoles, Mostoles, Madrid, Spain
| | - Oscar Vazquez-Gomez
- Department of Internal Medicine, Hospital Universitario de Mostoles, Mostoles, Madrid, Spain
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13
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Chakraborty C, George Priya Doss C, Zhu H, Agoramoorthy G. Rising Strengths Hong Kong SAR in Bioinformatics. Interdiscip Sci 2016; 9:224-236. [PMID: 26961385 PMCID: PMC7091071 DOI: 10.1007/s12539-016-0147-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2015] [Revised: 12/07/2015] [Accepted: 01/08/2016] [Indexed: 12/18/2022]
Abstract
Hong Kong's bioinformatics sector is attaining new heights in combination with its economic boom and the predominance of the working-age group in its population. Factors such as a knowledge-based and free-market economy have contributed towards a prominent position on the world map of bioinformatics. In this review, we have considered the educational measures, landmark research activities and the achievements of bioinformatics companies and the role of the Hong Kong government in the establishment of bioinformatics as strength. However, several hurdles remain. New government policies will assist computational biologists to overcome these hurdles and further raise the profile of the field. There is a high expectation that bioinformatics in Hong Kong will be a promising area for the next generation.
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Affiliation(s)
- Chiranjib Chakraborty
- Department of Bio-informatics, School of Computer and Information Sciences, Galgotias University, Greater Noida, UP, 201306, India
- Department of Computer Sciences, Hong Kong Baptist University, Kowloon Tong, Hong Kong
| | - C George Priya Doss
- Medical Biotechnology Division, School of BioSciences and Technology, VIT University, Vellore, TN, 632014, India
| | - Hailong Zhu
- Department of Computer Sciences, Hong Kong Baptist University, Kowloon Tong, Hong Kong.
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14
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Park G, Jin WY, Jang SJ, Kook JK, Choi JA, Park GC, Lee MJ, Park SN, Li XM, Cho SS, Jang CH, Kang SH, Moon DS. Evaluation of four methods of assigning species and genus to medically important bacteria using 16S rRNA gene sequence analysis. Microbiol Immunol 2016; 59:285-98. [PMID: 25786669 DOI: 10.1111/1348-0421.12254] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2014] [Revised: 03/03/2015] [Accepted: 03/04/2015] [Indexed: 01/08/2023]
Abstract
The four methods for assigning bacterial species are the Clinical and Laboratory Standards Institute (CLSI), modified CLSI (mCLSI), phylogenetic analysis (PA) and closest match (CM) methods, these are used to identify the genus and species using 16S rRNA gene sequence results. In this study, the results of identification by these four methods of 37 aerobic reference strains, 30 anaerobic reference strains, 15 Acinetobacter reference strains and 167 Acinetobacter clinical strains were compared. The rates of accurate identification to the species level using the CLSI, mCLSI, PA and CM methods were as follows: 24.3, 86.5, 86.5 and 89.2%, respectively, for the 37 aerobic reference strains; 73.3%, 96.7%, 90.0% and 93.3%, respectively, for the 30 anaerobic reference strains; 40.0%, 93.3%, 100% and 93.3%, respectively, for the 15 Acinetobacter reference strains; and 53.9%, 90.4%, 95.8% and 90.4%, respectively, for the 167 Acinetobacter clinical strains. The rates of accurate identification to the genus level using the CLSI, mCLSI, PA, and CM methods were as follows: 91.9%, 91.9%, 94.6% and 91.9%, respectively, for the 37 aerobic reference strains; 100%, 100%, 100% and 100%, respectively, for all of the 30 anaerobic reference strains, 15 Acinetobacter reference strains and the 167 Acinetobacter clinical strains. The mCLSI is the most practical and pragmatic method for identification of species based on 16S rRNA sequences for hospital, research or industry laboratories because it performs well and involves a simple procedure.
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Affiliation(s)
- Geon Park
- Department of Laboratory Medicine, College of Medicine, Chosun University, Gwang-Ju, Republic of Korea
| | - Won-Young Jin
- Department of Laboratory Medicine, College of Medicine, Chosun University, Gwang-Ju, Republic of Korea
| | - Sook-Jin Jang
- Department of Laboratory Medicine, College of Medicine, Chosun University, Gwang-Ju, Republic of Korea.,Research Center for Resistant Cells, College of Medicine, Chosun University, Gwang-Ju, Republic of Korea
| | - Joong-Ki Kook
- Korean Collection for Oral Microbiology and Department of Oral Biochemistry, College of Dentistry, Chosun University, Gwang-Ju, Republic of Korea
| | - Ji Ae Choi
- Research Center for Resistant Cells, College of Medicine, Chosun University, Gwang-Ju, Republic of Korea
| | - Gyun Cheol Park
- Department of Laboratory Medicine, College of Medicine, Chosun University, Gwang-Ju, Republic of Korea
| | - Min-Jung Lee
- Research Center for Resistant Cells, College of Medicine, Chosun University, Gwang-Ju, Republic of Korea
| | - Soon-Nang Park
- Korean Collection for Oral Microbiology and Department of Oral Biochemistry, College of Dentistry, Chosun University, Gwang-Ju, Republic of Korea
| | - Xue Min Li
- Department of Internal Medicine, Yantaishan Hospital, Yantai, China
| | - Seong-Sig Cho
- Department of Laboratory Medicine, Chosun University Hospital, Gwang-Ju, Republic of Korea
| | - Chul Ho Jang
- Department of Otolaryngology, Chonnam National University Medical School, Gwangju, 501-757, Republic of Korea
| | - Seong-Ho Kang
- Department of Laboratory Medicine, College of Medicine, Chosun University, Gwang-Ju, Republic of Korea
| | - Dae-Soo Moon
- Department of Laboratory Medicine, College of Medicine, Chosun University, Gwang-Ju, Republic of Korea
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15
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Siu GKH, Chen JHK, Ng TK, Lee RA, Fung KSC, To SWC, Wong BKC, Cheung S, Wong IWF, Tam MMP, Lee SSW, Yam WC. Performance Evaluation of the Verigene Gram-Positive and Gram-Negative Blood Culture Test for Direct Identification of Bacteria and Their Resistance Determinants from Positive Blood Cultures in Hong Kong. PLoS One 2015; 10:e0139728. [PMID: 26431434 PMCID: PMC4592242 DOI: 10.1371/journal.pone.0139728] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2015] [Accepted: 09/15/2015] [Indexed: 12/23/2022] Open
Abstract
BACKGROUND A multicenter study was conducted to evaluate the diagnostic performance and the time to identifcation of the Verigene Blood Culture Test, the BC-GP and BC-GN assays, to identify both Gram-positive and Gram-negative bacteria and their drug resistance determinants directly from positive blood cultures collected in Hong Kong. METHODS AND RESULTS A total of 364 blood cultures were prospectively collected from four public hospitals, in which 114 and 250 cultures yielded Gram-positive and Gram-negative bacteria, and were tested with the BC-GP and BC-GN assay respectively. The overall identification agreement for Gram-positive and Gram-negative bacteria were 89.6% and 90.5% in monomicrobial cultures and 62.5% and 53.6% in polymicrobial cultures, respectively. The sensitivities for most genus/species achieved at least 80% except Enterococcus spp. (60%), K.oxytoca (0%), K.pneumoniae (69.2%), whereas the specificities for all targets ranged from 98.9% to 100%. Of note, 50% (7/14) cultures containing K.pneumoniae that were missed by the BC-GN assay were subsequently identified as K.variicola. Approximately 5.5% (20/364) cultures contained non-target organisms, of which Aeromonas spp. accounted for 25% and are of particular concern. For drug resistance determination, the Verigene test showed 100% sensitivity for identification of MRSA, VRE and carbapenem resistant Acinetobacter, and 84.4% for ESBL-producing Enterobacteriaceae based on the positive detection of mecA, vanA, blaOXA and blaCTXM respectively. CONCLUSION Overall, the Verigene test provided acceptable accuracy for identification of bacteria and resistance markers with a range of turnaround time 40.5 to 99.2 h faster than conventional methods in our region.
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Affiliation(s)
- Gilman K. H. Siu
- Department of Health technology and Informatics, The Hong Kong Polytechnic University, Hong Kong SAR, China
| | - Jonathan H. K. Chen
- Department of Microbiology, Queen Mary Hospital, The University of Hong Kong, Hong Kong SAR, China
| | - T. K. Ng
- Department of Pathology, Princess Margaret Hospital, Hong Kong SAR, China
| | - Rodney A. Lee
- Department of Clinical Pathology, Pamela Youde Nethersole Eastern Hospital, Hong Kong SAR, China
| | - Kitty S. C. Fung
- Department of Pathology, United Christian Hospital, Hong Kong SAR, China
| | - Sabrina W. C. To
- Department of Microbiology, Queen Mary Hospital, The University of Hong Kong, Hong Kong SAR, China
| | - Barry K. C. Wong
- Department of Pathology, United Christian Hospital, Hong Kong SAR, China
| | - Sherman Cheung
- Department of Pathology, Princess Margaret Hospital, Hong Kong SAR, China
| | - Ivan W. F. Wong
- Department of Clinical Pathology, Pamela Youde Nethersole Eastern Hospital, Hong Kong SAR, China
| | - Marble M. P. Tam
- Department of Pathology, United Christian Hospital, Hong Kong SAR, China
| | - Swing S. W. Lee
- Department of Health technology and Informatics, The Hong Kong Polytechnic University, Hong Kong SAR, China
| | - W. C. Yam
- Department of Microbiology, Queen Mary Hospital, The University of Hong Kong, Hong Kong SAR, China
- * E-mail:
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16
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Srinivasan R, Karaoz U, Volegova M, MacKichan J, Kato-Maeda M, Miller S, Nadarajan R, Brodie EL, Lynch SV. Use of 16S rRNA gene for identification of a broad range of clinically relevant bacterial pathogens. PLoS One 2015; 10:e0117617. [PMID: 25658760 PMCID: PMC4319838 DOI: 10.1371/journal.pone.0117617] [Citation(s) in RCA: 211] [Impact Index Per Article: 23.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2014] [Accepted: 12/29/2014] [Indexed: 01/06/2023] Open
Abstract
According to World Health Organization statistics of 2011, infectious diseases remain in the top five causes of mortality worldwide. However, despite sophisticated research tools for microbial detection, rapid and accurate molecular diagnostics for identification of infection in humans have not been extensively adopted. Time-consuming culture-based methods remain to the forefront of clinical microbial detection. The 16S rRNA gene, a molecular marker for identification of bacterial species, is ubiquitous to members of this domain and, thanks to ever-expanding databases of sequence information, a useful tool for bacterial identification. In this study, we assembled an extensive repository of clinical isolates (n = 617), representing 30 medically important pathogenic species and originally identified using traditional culture-based or non-16S molecular methods. This strain repository was used to systematically evaluate the ability of 16S rRNA for species level identification. To enable the most accurate species level classification based on the paucity of sequence data accumulated in public databases, we built a Naïve Bayes classifier representing a diverse set of high-quality sequences from medically important bacterial organisms. We show that for species identification, a model-based approach is superior to an alignment based method. Overall, between 16S gene based and clinical identities, our study shows a genus-level concordance rate of 96% and a species-level concordance rate of 87.5%. We point to multiple cases of probable clinical misidentification with traditional culture based identification across a wide range of gram-negative rods and gram-positive cocci as well as common gram-negative cocci.
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Affiliation(s)
- Ramya Srinivasan
- University of California San Francisco, Department of Medicine, Gastroenterology Division, 513 Parnassus Ave, San Francisco, CA 94143–0538, United States of America
| | - Ulas Karaoz
- Lawrence Berkeley National Laboratory, Earth Sciences Division, 1 Cyclotron Rd., MS70A-3317, Berkeley, CA 94720, United States of America
| | - Marina Volegova
- University of California, Berkeley, CA 94720, United States of America
| | - Joanna MacKichan
- School of Biological Sciences, Victoria University of Wellington, 34 Kenepuru Drive, Porirua, Wellington, New Zealand
| | - Midori Kato-Maeda
- San Francisco General Hospital, Department of Medicine, Bldg 100, San Francisco, CA 94110, United States of America
| | - Steve Miller
- University of California San Francisco, Clinical Microbiology Laboratory, 185 Berry Street, Suite 290, San Francisco, CA 94107, United States of America
| | - Rohan Nadarajan
- University of California San Francisco, Clinical Microbiology Laboratory, 185 Berry Street, Suite 290, San Francisco, CA 94107, United States of America
| | - Eoin L. Brodie
- Lawrence Berkeley National Laboratory, Earth Sciences Division, 1 Cyclotron Rd., MS70A-3317, Berkeley, CA 94720, United States of America
| | - Susan V. Lynch
- University of California San Francisco, Department of Medicine, Gastroenterology Division, 513 Parnassus Ave, San Francisco, CA 94143–0538, United States of America
- * E-mail:
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17
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18
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Luo Y, Siu GKH, Yeung ASF, Chen JHK, Ho PL, Leung KW, Tsang JLY, Cheng VCC, Guo L, Yang J, Ye L, Yam WC. Performance of the VITEK MS matrix-assisted laser desorption ionization-time of flight mass spectrometry system for rapid bacterial identification in two diagnostic centres in China. J Med Microbiol 2015; 64:18-24. [PMID: 25418737 DOI: 10.1099/jmm.0.080317-0] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Yanping Luo
- Department of Microbiology, Chinese People’s Liberation Army General Hospital, Beijing, PR China
| | - Gilman K. H. Siu
- Department of Health Technology and Informatics, The Hong Kong Polytechnic University, Hong Kong Special Administrative Region, PR China
| | - Amy S. F. Yeung
- Department of Microbiology, Queen Mary Hospital, The University of Hong Kong, Hong Kong Special Administrative Region, PR China
| | - Jonathan H. K. Chen
- Department of Microbiology, Queen Mary Hospital, The University of Hong Kong, Hong Kong Special Administrative Region, PR China
| | - Pak Leung Ho
- Carol Yu Centre for Infection, The University of Hong Kong, Hong Kong Special Administrative Region, PR China
- Department of Microbiology, Queen Mary Hospital, The University of Hong Kong, Hong Kong Special Administrative Region, PR China
| | - K. W. Leung
- Department of Microbiology, Queen Mary Hospital, The University of Hong Kong, Hong Kong Special Administrative Region, PR China
| | - Jacqueline L. Y. Tsang
- Department of Microbiology, Queen Mary Hospital, The University of Hong Kong, Hong Kong Special Administrative Region, PR China
| | - Vincent C. C. Cheng
- Carol Yu Centre for Infection, The University of Hong Kong, Hong Kong Special Administrative Region, PR China
- Department of Microbiology, Queen Mary Hospital, The University of Hong Kong, Hong Kong Special Administrative Region, PR China
| | - Ling Guo
- Department of Microbiology, Chinese People’s Liberation Army General Hospital, Beijing, PR China
| | - Jiyong Yang
- Department of Microbiology, Chinese People’s Liberation Army General Hospital, Beijing, PR China
| | - Liyan Ye
- Department of Microbiology, Chinese People’s Liberation Army General Hospital, Beijing, PR China
| | - Wing-Cheong Yam
- Carol Yu Centre for Infection, The University of Hong Kong, Hong Kong Special Administrative Region, PR China
- Department of Microbiology, Queen Mary Hospital, The University of Hong Kong, Hong Kong Special Administrative Region, PR China
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19
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Rhoads DD, Sintchenko V, Rauch CA, Pantanowitz L. Clinical microbiology informatics. Clin Microbiol Rev 2014; 27:1025-47. [PMID: 25278581 PMCID: PMC4187636 DOI: 10.1128/cmr.00049-14] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
The clinical microbiology laboratory has responsibilities ranging from characterizing the causative agent in a patient's infection to helping detect global disease outbreaks. All of these processes are increasingly becoming partnered more intimately with informatics. Effective application of informatics tools can increase the accuracy, timeliness, and completeness of microbiology testing while decreasing the laboratory workload, which can lead to optimized laboratory workflow and decreased costs. Informatics is poised to be increasingly relevant in clinical microbiology, with the advent of total laboratory automation, complex instrument interfaces, electronic health records, clinical decision support tools, and the clinical implementation of microbial genome sequencing. This review discusses the diverse informatics aspects that are relevant to the clinical microbiology laboratory, including the following: the microbiology laboratory information system, decision support tools, expert systems, instrument interfaces, total laboratory automation, telemicrobiology, automated image analysis, nucleic acid sequence databases, electronic reporting of infectious agents to public health agencies, and disease outbreak surveillance. The breadth and utility of informatics tools used in clinical microbiology have made them indispensable to contemporary clinical and laboratory practice. Continued advances in technology and development of these informatics tools will further improve patient and public health care in the future.
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Affiliation(s)
- Daniel D Rhoads
- Department of Pathology, University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania, USA
| | - Vitali Sintchenko
- Marie Bashir Institute for Infectious Diseases and Biosecurity and Sydney Medical School, The University of Sydney, Sydney, New South Wales, Australia Centre for Infectious Diseases and Microbiology-Public Health, Institute of Clinical Pathology and Medical Research, Westmead Hospital, Sydney, New South Wales, Australia
| | - Carol A Rauch
- Department of Pathology, Microbiology and Immunology, Vanderbilt University School of Medicine, Nashville, Tennessee, USA
| | - Liron Pantanowitz
- Department of Pathology, University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania, USA
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20
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GyrB polymorphisms accurately assign invasive viridans group streptococcal species. J Clin Microbiol 2014; 52:2905-12. [PMID: 24899021 DOI: 10.1128/jcm.01068-14] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
Viridans group streptococci (VGS) are a heterogeneous group of medically important bacteria that cannot be accurately assigned to a particular species using conventional phenotypic methods. Although multilocus sequence analysis (MLSA) is considered the gold standard for VGS species-level identification, MLSA is not yet feasible in the clinical setting. Conversely, molecular methods, such as sodA and 16S rRNA gene sequencing, are clinically practical but not sufficiently accurate for VGS species-level identification. Here, we present data regarding the use of an ∼ 400-nucleotide internal fragment of the gene encoding DNA gyrase subunit B (GyrB) for VGS species-level identification. MLSA, internal gyrB, sodA, full-length, and 5' 16S gene sequences were used to characterize 102 unique VGS blood isolates collected from 2011 to 2012. When using the MLSA species assignment as a reference, full-length and 5' partial 16S gene and sodA sequence analyses failed to correctly assign all strains to a species. Precise species determination was particularly problematic for Streptococcus mitis and Streptococcus oralis isolates. However, the internal gyrB fragment allowed for accurate species designations for all 102 strains. We validated these findings using 54 VGS strains for which MLSA, 16S gene, sodA, and gyrB data are available at the NCBI, showing that gyrB is superior to 16S gene and sodA sequence analyses for VGS species identification. We also observed that specific polymorphisms in the 133-amino acid sequence of the internal GyrB fragment can be used to identify invasive VGS species. Thus, the GyrB amino acid sequence may offer a more practical and accurate method for classifying invasive VGS strains to the species level.
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21
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Teng JLL, Ho TCC, Yeung RSY, Wong AYP, Wang H, Chen C, Fung KSC, Lau SKP, Woo PCY. Evaluation of 16SpathDB 2.0, an automated 16S rRNA gene sequence database, using 689 complete bacterial genomes. Diagn Microbiol Infect Dis 2013; 78:105-15. [PMID: 24295571 DOI: 10.1016/j.diagmicrobio.2013.10.019] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2013] [Revised: 10/21/2013] [Accepted: 10/27/2013] [Indexed: 02/04/2023]
Abstract
Interpretation of 16S rRNA sequences is a difficult problem faced by clinical microbiologists and technicians. In this study, we evaluated the updated 16SpathDB 2.0 database, using 689 16S rRNA sequences from 689 complete genomes of medically important bacteria. Among these 689 16S rRNA sequences, none was wrongly identified, with 35.8% reported as a single bacterial species having >98% identity with the query sequence (category 1), 63.9% reported as more than 1 bacterial species having >98% identity with the query sequence (category 2), 0.3% reported to the genus level (category 3), and none reported as no match (category 4). For the 16S rRNA sequences of non-duplicated bacterial species reported as category 1 or 2, the percentage of bacterial species reported as category 1 was significantly higher for anaerobic Gram-positive/Gram-negative bacteria than aerobic/facultative anaerobic Gram-positive/Gram-negative bacteria. 16SpathDB 2.0 is a user-friendly and accurate database for 16S rRNA sequence interpretation in clinical laboratories.
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Affiliation(s)
- Jade L L Teng
- Department of Microbiology, The University of Hong Kong, Hong Kong, China; Research Centre of Infection and Immunology, The University of Hong Kong, Hong Kong, China
| | - Tom C C Ho
- Department of Microbiology, The University of Hong Kong, Hong Kong, China
| | - Ronald S Y Yeung
- Department of Microbiology, The University of Hong Kong, Hong Kong, China; Department of Pathology, United Christian Hospital, Hong Kong, China
| | - Annette Y P Wong
- Department of Microbiology, The University of Hong Kong, Hong Kong, China
| | - Haiyin Wang
- National Institute for Communicable Disease Control and Prevention, Center for Disease Control and Prevention/State Key Laboratory for Infectious Disease Prevention and Control, Beijing, China
| | - Chen Chen
- National Institute for Communicable Disease Control and Prevention, Center for Disease Control and Prevention/State Key Laboratory for Infectious Disease Prevention and Control, Beijing, China
| | - Kitty S C Fung
- Department of Pathology, United Christian Hospital, Hong Kong, China
| | - Susanna K P Lau
- Department of Microbiology, The University of Hong Kong, Hong Kong, China; Research Centre of Infection and Immunology, The University of Hong Kong, Hong Kong, China; State Key Laboratory of Emerging Infectious Diseases, Hong Kong, China; Carol Yu Centre for Infection, The University of Hong Kong, Hong Kong, China.
| | - Patrick C Y Woo
- Department of Microbiology, The University of Hong Kong, Hong Kong, China; Research Centre of Infection and Immunology, The University of Hong Kong, Hong Kong, China; State Key Laboratory of Emerging Infectious Diseases, Hong Kong, China; Carol Yu Centre for Infection, The University of Hong Kong, Hong Kong, China.
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22
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Lau SKP, Tang BSF, Teng JLL, Chan TM, Curreem SOT, Fan RYY, Ng RHY, Chan JFW, Yuen KY, Woo PCY. Matrix-assisted laser desorption ionisation time-of-flight mass spectrometry for identification of clinically significant bacteria that are difficult to identify in clinical laboratories. J Clin Pathol 2013; 67:361-6. [PMID: 24143023 DOI: 10.1136/jclinpath-2013-201818] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
AIMS Although the revolutionary matrix-assisted laser desorption ionisation time-of-flight mass spectrometry (MALDI-TOF MS) has been evaluated for identification of various groups of bacteria, its application in bacteria that are 'difficult-to-identify' by phenotypic tests has been less well studied. We aim to evaluate the usefulness of MALDI-TOF MS for identification of 'difficult-to-identify' bacterial isolates. METHODS We evaluated the performance of the Bruker MALDI-TOF MS system for a collection of 67 diverse clinically important bacterial isolates that were less commonly encountered, possessed ambiguous biochemical profiles or belonged to newly discovered species. The results were compared with 16S rRNA gene sequencing as a reference method for species identification. RESULTS Using 16S rRNA gene sequencing as the reference method, 30 (45%) isolates were identified correctly to species level (score ≥2.0), 20 (30%) were only identified to genus level (score ≥1.7), four (6%) were misidentified (incorrect species with score ≥2.0 or incorrect genus with score ≥1.7) and 13 (19%) showed 'no identification' (score <1.7). Aerobic Gram-positive bacteria showed the highest percentage of correct species identification, followed by aerobic Gram-negative, anaerobic Gram-positive and anaerobic Gram-negative bacteria. Sixteen isolates identified to genus level actually showed the correct species but with scores below the threshold for species identification. Most isolates which showed 'no identification' were due to the absence of the corresponding species in the Bruker database. CONCLUSIONS Expansion of commercial databases to include reference spectra of less commonly encountered and newly discovered species and to increase available spectra for each species is required to improve the accuracy of MALDI-TOF MS for identifying 'difficult-to-identify' bacteria.
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Affiliation(s)
- Susanna K P Lau
- State Key Laboratory of Emerging Infectious Diseases, The University of Hong Kong, , Hong Kong, China
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23
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Actinomyces urogenitalis bacteremia and tubo-ovarian abscess after an in vitro fertilization (IVF) procedure. J Clin Microbiol 2013; 51:4252-4. [PMID: 24025912 DOI: 10.1128/jcm.02142-13] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
We describe the first case of bacteremia due to Actinomyces urogenitalis. Bacteremia was secondary to a tubo-ovarian abscess following transvaginal oocyte retrieval. Identification was established by matrix-assisted desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) and confirmed by 16S rRNA gene sequencing. A. urogenitalis should be considered as a potential causative agent of infection after gynecological procedures.
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Romance of the three domains: how cladistics transformed the classification of cellular organisms. Protein Cell 2013; 4:664-76. [PMID: 23873078 PMCID: PMC4875529 DOI: 10.1007/s13238-013-3050-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2013] [Accepted: 07/01/2013] [Indexed: 11/23/2022] Open
Abstract
Cladistics is a biological philosophy that uses genealogical relationship among species and an inferred sequence of divergence as the basis of classification. This review critically surveys the chronological development of biological classification from Aristotle through our postgenomic era with a central focus on cladistics. In 1957, Julian Huxley coined cladogenesis to denote splitting from subspeciation. In 1960, the English translation of Willi Hennig’s 1950 work, Systematic Phylogenetics, was published, which received strong opposition from pheneticists, such as numerical taxonomists Peter Sneath and Robert Sokal, and evolutionary taxonomist, Ernst Mayr, and sparked acrimonious debates in 1960–1980. In 1977–1990, Carl Woese pioneered in using small subunit rRNA gene sequences to delimitate the three domains of cellular life and established major prokaryotic phyla. Cladistics has since dominated taxonomy. Despite being compatible with modern microbiological observations, i.e. organisms with unusual phenotypes, restricted expression of characteristics and occasionally being uncultivable, increasing recognition of pervasiveness and abundance of horizontal gene transfer has challenged relevance and validity of cladistics. The mosaic nature of eukaryotic and prokaryotic genomes was also gradually discovered. In the mid-2000s, high-throughput and whole-genome sequencing became routine and complex geneologies of organisms have led to the proposal of a reticulated web of life. While genomics only indirectly leads to understanding of functional adaptations to ecological niches, computational modeling of entire organisms is underway and the gap between genomics and phenetics may soon be bridged. Controversies are not expected to settle as taxonomic classifications shall remain subjective to serve the human scientist, not the classified.
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García-Sánchez JE, García-Sánchez E, Martín-Del-Rey Á, García-Merino E. [Anaerobic bacteria 150 years after their discovery by Pasteur]. Enferm Infecc Microbiol Clin 2013; 33:119-28. [PMID: 23648369 DOI: 10.1016/j.eimc.2013.03.012] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2013] [Revised: 03/07/2013] [Accepted: 03/11/2013] [Indexed: 01/05/2023]
Abstract
In 2011 we celebrated the 150th anniversary of the discovery of anaerobic bacteria by Louis Pasteur. The interest of the biomedical community on such bacteria is still maintained, and is particularly focused on Clostridium difficile. In the past few years important advances in taxonomy have been made due to the genetic, technological and computing developments. Thus, a significant number of new species related to human infections have been characterised, and some already known have been reclassified. At pathogenic level some specimens of anaerobic microflora, that had not been isolated from human infections, have been now isolated in some clinical conditions. There was emergence (or re-emergence) of some species and clinical conditions. Certain anaerobic bacteria have been associated with established infectious syndromes. The virulence of certain strains has increased, and some hypotheses on their participation in certain diseases have been given. In terms of diagnosis, the routine use of MALDI-TOF has led to a shortening of time and a cost reduction in the identification, with an improvement directly related to the improvement of data bases. The application of real-time PCR has been another major progress, and the sequencing of 16srRNA gene and others is currently a reality for several laboratories. Anaerobes have increased their resistance to antimicrobial agents, and the emergence of resistance to carbapenems and metronidazole, and multi-resistance is a current reality. In this situation, linezolid could be an effective alternative for Bacteroides. Fidaxomicin is the only anti-anaerobic agent introduced in the recent years, specifically for the diarrhoea caused by C.difficile. Moreover, some mathematical models have also been proposed in relation with this species.
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Affiliation(s)
- José Elías García-Sánchez
- Departamento de Medicina Preventiva, Salud Pública y Microbiología Médica, Facultad de Medicina, Universidad de Salamanca, Salamanca, España.
| | - Enrique García-Sánchez
- Departamento de Medicina Preventiva, Salud Pública y Microbiología Médica, Facultad de Medicina, Universidad de Salamanca, Salamanca, España
| | - Ángel Martín-Del-Rey
- Departamento de Matemática Aplicada, Escuela Politécnica Superior de Ávila, Universidad de Salamanca, Ávila, España
| | - Enrique García-Merino
- Departamento de Salud, Instituto de Educación Secundaria Ramón y Cajal, Valladolid, España
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Direct bacterial identification in positive blood cultures by use of two commercial matrix-assisted laser desorption ionization-time of flight mass spectrometry systems. J Clin Microbiol 2013; 51:1733-9. [PMID: 23515548 DOI: 10.1128/jcm.03259-12] [Citation(s) in RCA: 115] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) for the identification of bacteria and fungi was recently introduced in microbiology laboratories. This technology could greatly improve the clinical management of patients and guidance for chemotherapy. In this study, we used a commercial MALDI Sepsityper extraction method to evaluate the performance of two commercial MALDI-TOF MS systems, the Vitek MS IVD (bioMérieux) and the Microflex LT Biotyper (Bruker Daltonics) for direct bacterial identification in positive blood cultures. In 181 monomicrobial cultures, both systems generated genus to species level identifications for >90% of the specimens (Biotyper, 177/181 [97.8%]; Vitek MS IVD, 167/181 [92.3%]). Overall, the Biotyper system generated significantly more accurate identifications than the Vitek MS IVD system (P = 0.016; 177 versus 167 out of 181 specimens). The Biotyper system identified the minority species among polymicrobial blood cultures. We also compared the performance of an in-house extraction method with that of the Sepsityper on both MALDI-TOF MS systems. The in-house method generated more correct identifications at the genus level than the Sepsityper (96.7% versus 93.5%) on the Biotyper system, whereas the two methods exhibited the same performance level (88.0% versus 88.0%) on the Vitek MS IVD system. Our study confirmed the practical advantages of MALDI-TOF MS, and our in-house extraction method reduced the reagent cost to $1 per specimen, with a shorter turnaround time of 3 h, which is highly cost-effective for a diagnostic microbiology service.
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Wang Y, Hayatsu M, Fujii T. Extraction of bacterial RNA from soil: challenges and solutions. Microbes Environ 2012; 27:111-21. [PMID: 22791042 PMCID: PMC4036013 DOI: 10.1264/jsme2.me11304] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Detection of bacterial gene expression in soil emerged in the early 1990s and provided information on bacterial responses in their original soil environments. As a key procedure in the detection, extraction of bacterial RNA from soil has attracted much interest, and many methods of soil RNA extraction have been reported in the past 20 years. In addition to various RT-PCR-based technologies, new technologies for gene expression analysis, such as microarrays and high-throughput sequencing technologies, have recently been applied to examine bacterial gene expression in soil. These technologies are driving improvements in RNA extraction protocols. In this mini-review, progress in the extraction of bacterial RNA from soil is summarized with emphasis on the major difficulties in the development of methodologies and corresponding strategies to overcome them.
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Affiliation(s)
- Yong Wang
- Environmental Biofunction Division, National Institute for Agro-Environmental Sciences, 3-1-3 Kannondai, Tsukuba, Ibaraki 305-8604, Japan.
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Automated pangenomic analysis in target selection for PCR detection and identification of bacteria by use of ssGeneFinder Webserver and its application to Salmonella enterica serovar Typhi. J Clin Microbiol 2012; 50:1905-11. [PMID: 22442318 DOI: 10.1128/jcm.06843-11] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
With the advent of high-throughput DNA sequencing, more than 4,000 bacterial genomes have been sequenced and are publicly available. We report a user-friendly web platform, ssGeneFinder Webserver (http://147.8.74.24/ssGeneFinder/), which is updated weekly for the automated pangenomic selection of specific targets for direct PCR detection and the identification of clinically important bacteria without the need of gene sequencing. To apply the ssGeneFinder Webserver for identifying specific targets for Salmonella enterica serovar Typhi, we analyzed 11 S. Typhi genomes, generated two specific targets, and validated them using 40 S. Typhi, 110 non-Typhi Salmonella serovars (serovar Paratyphi A, n = 4; Paratyphi B, n = 1; Typhimurium, n = 5; Enteritidis, n = 12; non-Paratyphi group A, n = 6; non-Paratyphi group B, n = 29; non-Paratyphi group C, n = 12; non-Typhi group D, n = 35; group E and others, n = 6), 115 Enterobacteriaceae isolates (Escherichia, n = 78; Shigella, n = 2; Klebsiella, n = 13; Enterobacter, n = 9; others, n = 13), and 66 human stool samples that were culture negative for S. Typhi. Both targets successfully detected all typical and atypical S. Typhi isolates, including an H1-j flagellin gene mutant, an aflagellated mutant which reacted with 2O Salmonella antiserum, and the Vi-negative attenuated vaccine strain Ty21a. No false positive was detected from any of the bacterial isolates and stool samples. DNA sequencing confirmed the identity of all positive amplicons. The PCR assays have detection limits as low as 100 CFU per reaction and were tested using spiked stool samples. Using a pangenomic approach, ssGeneFinder Webserver generated targets specific to S. Typhi. These and other validated targets should be applicable to the identification and direct PCR detection of bacterial pathogens from uncultured, mixed, and environmental samples.
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Molecular characterization of a catalase-negative Staphylococcus aureus subsp. aureus Strain collected from a patient with mitral valve endocarditis and pericarditis revealed a novel nonsense mutation in the katA gene. J Clin Microbiol 2011; 49:3398-402. [PMID: 21715584 DOI: 10.1128/jcm.00849-11] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
We report a case of endocarditis and pericarditis caused by catalase-negative Staphylococcus aureus. Molecular characterization revealed a novel nonsense mutation in the katA gene, leading to a loss of 238 amino acids (47% of the wild-type catalase protein), including the heme-binding site, NADPH-binding region, and Tyr-337, essential for catalysis.
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