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Anifowose OR, Oladosu GA, Omotosho OO. Occurrence and characterization of Proteus mirabilis from infected farmed African catfish in Ogun State, Nigeria. Mol Biol Rep 2024; 51:446. [PMID: 38532199 DOI: 10.1007/s11033-023-08973-6] [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: 08/23/2023] [Accepted: 10/23/2023] [Indexed: 03/28/2024]
Abstract
BACKGROUND Bacterial pathogens are the causative agents of some of the most serious disease problems in cultured fish causing mortalities and severe economic losses. This study was conducted to determine the occurrence and characterization of Proteus mirabilis from infected farmed African catfish in Ogun State, Nigeria. METHODOLOGY The bacteria were isolated from diseased farmed African catfish (Clarias gariepinus, n=128) with clinical signs of skin haemorrhages, ulceration, and ascites purposively sampled from farms within three senatorial districts namely Ogun East (OE; n=76), Ogun Central (OC; n=30) and Ogun West (OW; n=22) in Ogun State. The isolates were identified based on morphological characteristics, biochemical tests, and 16S rRNA gene characterisation. The 16S rRNA gene sequences were analysed using BLAST, submitted to the NCBI database, and an accession number was generated. RESULTS The occurrence of Proteus mirabilis in infected Clarias gariepinus was 13.16%, 25%, and 31.25% in OE, OC, and OW, respectively. A significantly higher incidence was recorded in OW compared to other areas. All the Proteus mirabilis isolates were motile, gram-negative, short rod, non-lactose fermenter bacteria that showed positive catalase reactions, negative oxidase, and positive for methyl-red. The Proteus mirabilis isolates (OP 594726.1) were closely related to isolates from Pakistan, Italy, and India CONCLUSIONS: We conclude that Proteus mirabilis colonises farmed Clarias gariepinus in Ogun State, Nigeria and the identified strain showed an evolutionary relationship with known pathogenic NCBI reference strains from other countries.
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Affiliation(s)
| | - Gbolahanmi Akinola Oladosu
- Department of Veterinary Medicine, Faculty of Veterinary Medicine, University of Ibadan, Ibadan, Nigeria
| | - Oladipo Olufemi Omotosho
- Department of Veterinary Medicine, Faculty of Veterinary Medicine, University of Ibadan, Ibadan, Nigeria
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2
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Lal J, Kaul G, Akhir A, Saxena D, Dubkara H, Shekhar S, Chopra S, Reddy DN. β-Turn editing in Gramicidin S: Activity impact on replacing proline α-carbon with stereodynamic nitrogen. Bioorg Chem 2023; 138:106641. [PMID: 37300963 DOI: 10.1016/j.bioorg.2023.106641] [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: 12/23/2022] [Revised: 05/15/2023] [Accepted: 05/26/2023] [Indexed: 06/12/2023]
Abstract
Gramicidin S, natural antimicrobial peptide is used commercially in medicinal lozenges for sore throat and Gram-negative and Gram-positive bacterial infections. However, its clinical potential is limited to topical applications because of its high red blood cells (RBC) cytotoxicity. Given the importance of developing potential antibiotics and inspired by the cyclic structure and druggable features of Gramicidin S, we edited proline α-carbon with stereodynamic nitrogen to examine the direct impact on biological activity and cytotoxicity with respect to prolyl counterpart. Natural Gramicidin S (12), proline-edited peptides 13-16 and wild-type d-Phe-d-Pro β-turn mimetics (17 and 18) were synthesized using solid phase peptide synthesis and investigated their activity against clinically relevant bacterial pathogens. Interestingly, mono-proline edited analogous peptide 13 showed moderate improvement in antimicrobial activity against E. coli ATCC 25922 and K.pneumoniae BAA 1705 as compared to Gramicidin S. Furthermore, proline edited peptide 13 exhibited equipotent antimicrobial effect against MDR S. aureus and Enterococcus spp. Analysis of cytotoxicity against VERO cells and RBC, reveals that proline edited peptides showed two-fivefold lesser cytotoxicity than the counterpart Gramicidin S. Our study suggests that introducing single azPro/Pro mutation in Gramicidin S marginally improved the activity and lessens the cytotoxicity as compared with the parent peptide.
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Affiliation(s)
- Jhajan Lal
- Division of Medicinal and Process Chemistry, CSIR-CDRI, Lucknow 226031, India; Academy of Scientific & Innovative Research (AcSIR), Ghaziabad, UP 201002, India
| | - Grace Kaul
- Division of Molecular Microbiology and Immunology, CSIR-Central Drug Research Institute, Lucknow 226031, India; Academy of Scientific & Innovative Research (AcSIR), Ghaziabad, UP 201002, India
| | - Abdul Akhir
- Division of Molecular Microbiology and Immunology, CSIR-Central Drug Research Institute, Lucknow 226031, India
| | - Deepanshi Saxena
- Division of Molecular Microbiology and Immunology, CSIR-Central Drug Research Institute, Lucknow 226031, India
| | - Harshita Dubkara
- Division of Medicinal and Process Chemistry, CSIR-CDRI, Lucknow 226031, India; Academy of Scientific & Innovative Research (AcSIR), Ghaziabad, UP 201002, India
| | - Shashank Shekhar
- Division of Medicinal and Process Chemistry, CSIR-CDRI, Lucknow 226031, India; Academy of Scientific & Innovative Research (AcSIR), Ghaziabad, UP 201002, India
| | - Sidharth Chopra
- Division of Molecular Microbiology and Immunology, CSIR-Central Drug Research Institute, Lucknow 226031, India; Academy of Scientific & Innovative Research (AcSIR), Ghaziabad, UP 201002, India.
| | - Damodara N Reddy
- Division of Medicinal and Process Chemistry, CSIR-CDRI, Lucknow 226031, India; Academy of Scientific & Innovative Research (AcSIR), Ghaziabad, UP 201002, India.
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Ma H, Wang X, Yan H, Liu Q, Yang D, Bian T. Dual intracranial infection with Nocardia farcinica and Cryptococcus neoformans diagnosed by next-generation sequencing in a patient with nephrotic syndrome: A case report. Medicine (Baltimore) 2022; 101:e30325. [PMID: 36107518 PMCID: PMC9439795 DOI: 10.1097/md.0000000000030325] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
RATIONALE Intracranial infections are associated with high morbidity and mortality in immunocompromised patients, due to delayed diagnosis and treatment. Establishing a rapid, accurate diagnosis and a precise therapeutic regimen is crucial for management of the patients. Our report described a rare intracranial infection of patient with nephrotic syndrome. PATIENT CONCERNS A 66-year-old woman with a history of nephrotic syndrome presented symptoms in central nervous system for 1 month, followed by headache and fever over several days. DIAGNOSIS Neurological examination, brain imaging, and cerebrospinal fluid (CSF) tests exhibited resemblance to intracranial infection. Subsequently, CSF cultures confirmed the presence of Cryptococcus. Fortunately, next-generation sequencing revealed the concomitant infection with Nocardia farcinica in addition to Cryptococcus neoformans. INTERVENTIONS The treatment with intravenous fluconazole combined with amphotericin could not immediately ameliorate her symptoms. The patient's condition improved significantly with minimal deficits after timely administration of antibiotics against N farcinica. OUTCOMES One month later, cranial MRI indicated that basal ganglia lesions ameliorated. The patient has recovered well. LESSONS SUBSECTIONS To our best knowledge, this is the first case report of intracranial infection caused by both N farcinica and C neoformans in a patient with nephrotic syndrome. Remarkably, extensive application of next-generation sequencing can facilitate investigation on the potential role of various pathogenic organisms in infectious diseases.
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Affiliation(s)
- Hongmei Ma
- Department of Neurology, Beijing Fengtai You’anmen Hospital, BeijingChina
- *Correspondence: Hongmei Ma, Department of Neurology, Beijing Fengtai You’anmen Hospital, No. 199 You’anmen Wai Avenue, Fengtai District, Beijing 100069, China (e-mail: )
| | - Xiangbo Wang
- Department of Neurology, Xuanwu Hospital of Capital Medical University, Beijing, China
| | - Heli Yan
- Department of Neurology, Xuanwu Hospital of Capital Medical University, Beijing, China
| | - Qing Liu
- Department of Neurology, Beijing Fengtai You’anmen Hospital, BeijingChina
| | - Dan Yang
- Department of Neurology, Beijing Fengtai You’anmen Hospital, BeijingChina
| | - Tingting Bian
- Department of Neurology, Beijing Fengtai You’anmen Hospital, BeijingChina
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Alves G, Yu YK. Robust Accurate Identification and Biomass Estimates of Microorganisms via Tandem Mass Spectrometry. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2020; 31:85-102. [PMID: 32881514 PMCID: PMC10501333 DOI: 10.1021/jasms.9b00035] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Rapid and accurate identification of microorganisms and estimation of their biomasses are of extreme importance to public health. Mass spectrometry has become an important technique for these purposes. Previously we published a workflow named Microorganism Classification and Identification (MiCId v.12.26.2017) that was shown to perform no worse than other workflows. This manuscript presents MiCId v.12.13.2018 that, in comparison with the earlier version v.12.26.2017, allows for biomass estimates, provides more accurate microorganism identifications (better controls the number of false positives), and is robust against database size increase. This significant advance is made possible by several new ingredients introduced: first, we apply a modified expectation-maximization method to compute for each taxon considered a prior probability, which can be used for biomass estimate; second, we introduce a new concept called ownership, through which the participation ratio is computed and use it as the number of taxa to be kept within a cluster of closely related taxa; third, based on confidently identified peptides, we calculate for each taxon its degree of independence from the rest of taxa considered to determine whether or not to split this taxon off the cluster. Using 270 data files, each containing a large number of MS/MS spectra, we show that, in comparison with v.12.26.2017, version v.12.13.2018 yields superior retrieval results. We also show that MiCId v.12.13.2018 can estimate species biomass reasonably well. The new MiCId v.12.13.2018, designed to run in Linux environment, is freely available for download at https://www.ncbi.nlm.nih.gov/CBBresearch/Yu/downloads.html.
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Affiliation(s)
- Gelio Alves
- National Center for Biotehnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland 20894, United States
| | - Yi-Kuo Yu
- National Center for Biotehnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland 20894, United States
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5
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Rana A, Thakur S, Kumar G, Akhter Y. Recent Trends in System-Scale Integrative Approaches for Discovering Protective Antigens Against Mycobacterial Pathogens. Front Genet 2018; 9:572. [PMID: 30538722 PMCID: PMC6277634 DOI: 10.3389/fgene.2018.00572] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2018] [Accepted: 11/06/2018] [Indexed: 11/21/2022] Open
Abstract
Mycobacterial infections are one of the deadliest infectious diseases still posing a major health burden worldwide. The battle against these pathogens needs to focus on novel approaches and key interventions. In recent times, availability of genome scale data has revolutionized the fields of computational biology and immunoproteomics. Here, we summarize the cutting-edge ‘omics’ technologies and innovative system scale strategies exploited to mine the available data. These may be targeted using high-throughput technologies to expedite the identification of novel antigenic candidates for the rational next generation vaccines and serodiagnostic development against mycobacterial pathogens for which traditional methods have been failing.
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Affiliation(s)
- Aarti Rana
- School of Life Sciences, Central University of Himachal Pradesh, Shahpur, India
| | - Shweta Thakur
- School of Life Sciences, Central University of Himachal Pradesh, Shahpur, India
| | - Girish Kumar
- School of Life Sciences, Central University of Himachal Pradesh, Shahpur, India
| | - Yusuf Akhter
- Department of Biotechnology, Babasaheb Bhimrao Ambedkar University, Lucknow, India
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Guschin VA, Manuilov VA, Makarov VV, Tkachuk AP. The proper structure of a biosafety system as a way of reducing the vulnerability of a society, economy or state in the face of a biogenic threat. BULLETIN OF RUSSIAN STATE MEDICAL UNIVERSITY 2018. [DOI: 10.24075/brsmu.2018.054] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
To understand how vulnerable are a society, an economy and a state in the face of a biohazard, one should attempt to identify any potential holes in the national biosafety system, such as the lack of important components or technologies for biological monitoring and the inadequacy of existing analytical methods used to prevent or counteract biogenic threats. In Russia, biological monitoring is quite advanced. However, the agencies that ensure proper functioning of its components lack collaboration and do not form a well-coordinated network. Each of such agencies alone cannot provide comprehensive information on the subject. In the Russian Federation, there are at least 4 state-funded programs that collect epidemiological data and are quite efficient in performing the narrow task of monitoring infections. But because there is no central database where epidemiological data can be channeled and subsequently shared, these agencies do not complete each other. This leaves the Russian society, economy and state vulnerable to biogenic threats. We need an adequately organized, modern, fully functional and effective system for monitoring biohazards that will serve as a basis for the national biosafety system and also a tool for the identification and elimination of its weaknesses.
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Affiliation(s)
- V. A. Guschin
- Laboratory of Population Variability Mechanisms in Pathogenic Microorganisms, Gamaleya Research Institute of Epidemiology and Microbiology, Moscow; Department of Virology, Faculty of Biology, Lomonosov Moscow State University, Moscow
| | - V. A. Manuilov
- Laboratory of Translational Medicine, Gamaleya Research Institute of Epidemiology and Microbiology, Moscow
| | - V. V. Makarov
- Center for Strategic Planning of the Ministry of Health of the Russian Federation, Moscow
| | - A. P. Tkachuk
- Laboratory of Translational Medicine, Gamaleya Research Institute of Epidemiology and Microbiology, Moscow
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7
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Fournier PE, Drancourt M, Raoult D. New Laboratory Tools for Emerging Bacterial Challenges. Clin Infect Dis 2018; 65:S39-S49. [PMID: 28859351 DOI: 10.1093/cid/cix405] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Since its creation, the Méditerranée-Infection foundation has aimed at optimizing the management of infectious diseases and surveying the local and global epidemiology. This pivotal role was permitted by the development of rational sampling, point-of-care tests, and extended automation as well as new technologies, including mass spectrometry for colony identification, real-time genomics for isolate characterization, and the development of versatile and permissive culture systems. By identifying and characterizing emerging microbial pathogens, these developments provided significant breakthroughs in infectious diseases.
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Affiliation(s)
- Pierre-Edouard Fournier
- URMITE, UM63, CNRS7278, IRD198, Inserm 1095, Institut Hospitalo-Universitaire Méditerranée-Infection, Aix-Marseille Université, Faculté de Médecine, Marseille, France
| | - Michel Drancourt
- URMITE, UM63, CNRS7278, IRD198, Inserm 1095, Institut Hospitalo-Universitaire Méditerranée-Infection, Aix-Marseille Université, Faculté de Médecine, Marseille, France
| | - Didier Raoult
- URMITE, UM63, CNRS7278, IRD198, Inserm 1095, Institut Hospitalo-Universitaire Méditerranée-Infection, Aix-Marseille Université, Faculté de Médecine, Marseille, France
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8
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Boers SA, Hiltemann SD, Stubbs AP, Jansen R, Hays JP. Development and evaluation of a culture-free microbiota profiling platform (MYcrobiota) for clinical diagnostics. Eur J Clin Microbiol Infect Dis 2018; 37:1081-1089. [PMID: 29549470 PMCID: PMC5948305 DOI: 10.1007/s10096-018-3220-z] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2018] [Accepted: 02/20/2018] [Indexed: 12/19/2022]
Abstract
Microbiota profiling has the potential to greatly impact on routine clinical diagnostics by detecting DNA derived from live, fastidious, and dead bacterial cells present within clinical samples. Such results could potentially be used to benefit patients by influencing antibiotic prescribing practices or to generate new classical-based diagnostic methods, e.g., culture or PCR. However, technical flaws in 16S rRNA gene next-generation sequencing (NGS) protocols, together with the requirement for access to bioinformatics, currently hinder the introduction of microbiota analysis into clinical diagnostics. Here, we report on the development and evaluation of an “end-to-end” microbiota profiling platform (MYcrobiota), which combines our previously validated micelle PCR/NGS (micPCR/NGS) methodology with an easy-to-use, dedicated bioinformatics pipeline. The newly designed bioinformatics pipeline processes micPCR/NGS data automatically and summarizes the results in interactive, but simple web reports. In order to explore the utility of MYcrobiota in clinical diagnostics, 47 clinical samples (40 “damaged skin” samples and 7 synovial fluids) were investigated using routine bacterial culture as comparator. MYcrobiota confirmed the presence of bacterial DNA in 37/37 culture-positive samples and detected bacterial taxa in 2/10 culture-negative samples. Moreover, 36/38 potentially relevant aerobic bacterial taxa and 3/3 mixtures of anaerobic bacteria were identified using culture and MYcrobiota, with the sensitivity and specificity being 95%. Interestingly, the majority of the 448 bacterial taxa identified using MYcrobiota were not identified using culture, which could potentially have an impact on clinical decision-making. Taken together, the development of MYcrobiota is a promising step towards the introduction of microbiota analysis into clinical diagnostic laboratories.
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Affiliation(s)
- Stefan A Boers
- Department of Medical Microbiology and Infectious Diseases, Erasmus University Medical Centre Rotterdam (Erasmus MC), Wytemaweg 80, 3015 CN, Rotterdam, the Netherlands
| | - Saskia D Hiltemann
- Department of Bioinformatics, Erasmus University Medical Centre Rotterdam (Erasmus MC), Rotterdam, the Netherlands
| | - Andrew P Stubbs
- Department of Bioinformatics, Erasmus University Medical Centre Rotterdam (Erasmus MC), Rotterdam, the Netherlands
| | - Ruud Jansen
- Department of Molecular Biology, Regional Laboratory of Public Health Kennemerland, Haarlem, the Netherlands
| | - John P Hays
- Department of Medical Microbiology and Infectious Diseases, Erasmus University Medical Centre Rotterdam (Erasmus MC), Wytemaweg 80, 3015 CN, Rotterdam, the Netherlands.
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9
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Abayasekara LM, Perera J, Chandrasekharan V, Gnanam VS, Udunuwara NA, Liyanage DS, Bulathsinhala NE, Adikary S, Aluthmuhandiram JVS, Thanaseelan CS, Tharmakulasingam DP, Karunakaran T, Ilango J. Detection of bacterial pathogens from clinical specimens using conventional microbial culture and 16S metagenomics: a comparative study. BMC Infect Dis 2017; 17:631. [PMID: 28927397 PMCID: PMC5606128 DOI: 10.1186/s12879-017-2727-8] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2017] [Accepted: 09/12/2017] [Indexed: 12/27/2022] Open
Abstract
Background Infectious disease is the leading cause of death worldwide, and diagnosis of polymicrobial and fungal infections is increasingly challenging in the clinical setting. Conventionally, molecular detection is still the best method of species identification in clinical samples. However, the limitations of Sanger sequencing make diagnosis of polymicrobial infections one of the biggest hurdles in treatment. The development of massively parallel sequencing or next generation sequencing (NGS) has revolutionized the field of metagenomics, with wide application of the technology in identification of microbial communities in environmental sources, human gut and others. However, to date there has been no commercial application of this technology in infectious disease diagnostic settings. Methods Credence Genomics Rapid Infection Detection™ test, is a molecular based diagnostic test that uses next generation sequencing of bacterial 16S rRNA gene and fungal ITS1 gene region to provide accurate identification of species within a clinical sample. Here we present a study comparing 16S and ITS1 metagenomic identification against conventional culture for clinical samples. Using culture results as gold standard, a comparison was conducted using patient specimens from a clinical microbiology lab. Results Metagenomics based results show a 91.8% concordance rate for culture positive specimens and 52.8% concordance rate with culture negative samples. 10.3% of specimens were also positive for fungal species which was not investigated by culture. Specificity and sensitivity for metagenomics analysis is 91.8 and 52.7% respectively. Conclusion 16S based metagenomic identification of bacterial species within a clinical specimen is on par with conventional culture based techniques and when coupled with clinical information can lead to an accurate diagnostic tool for infectious disease diagnosis. Electronic supplementary material The online version of this article (10.1186/s12879-017-2727-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
| | - Jennifer Perera
- Dean and Chair Professor of Microbiology, Faculty of Medicine, University of Colombo, P.O. box 271, Colombo, Sri Lanka.,Credence Genomics Pvt. Ltd, 12 - 3/2, Sunethradevi Road, Kohuwala, Nugegoda, Sri Lanka
| | - Vishvanath Chandrasekharan
- Department of Chemistry, Faculty of Science, University of Colombo, Colombo, Sri Lanka.,Credence Genomics Pvt. Ltd, 12 - 3/2, Sunethradevi Road, Kohuwala, Nugegoda, Sri Lanka
| | - Vaz S Gnanam
- Credence Genomics Pvt. Ltd, 12 - 3/2, Sunethradevi Road, Kohuwala, Nugegoda, Sri Lanka
| | - Nisala A Udunuwara
- Credence Genomics Pvt. Ltd, 12 - 3/2, Sunethradevi Road, Kohuwala, Nugegoda, Sri Lanka
| | - Dileepa S Liyanage
- Credence Genomics Pvt. Ltd, 12 - 3/2, Sunethradevi Road, Kohuwala, Nugegoda, Sri Lanka
| | | | - Subhashanie Adikary
- Credence Genomics Pvt. Ltd, 12 - 3/2, Sunethradevi Road, Kohuwala, Nugegoda, Sri Lanka
| | | | | | | | - Tharaga Karunakaran
- Credence Genomics Pvt. Ltd, 12 - 3/2, Sunethradevi Road, Kohuwala, Nugegoda, Sri Lanka
| | - Janahan Ilango
- Credence Genomics Pvt. Ltd, 12 - 3/2, Sunethradevi Road, Kohuwala, Nugegoda, Sri Lanka
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10
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Turvey ME, Weiland F, Keller EJ, Hoffmann P. The changing face of microbial quality control practices in the brewing industry: Introducing mass spectrometry proteomic fingerprinting for microbial identification. JOURNAL OF THE INSTITUTE OF BREWING 2017. [DOI: 10.1002/jib.428] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- M. E. Turvey
- Adelaide Proteomics Centre; The University of Adelaide; Australia
- Institute of Photonics and Advanced Sensing; Australia
- Singapore-MIT Alliance for Research and Technology Centre; Singapore
| | - F. Weiland
- Adelaide Proteomics Centre; The University of Adelaide; Australia
- Institute of Photonics and Advanced Sensing; Australia
| | - E. J. Keller
- Adelaide Proteomics Centre; The University of Adelaide; Australia
- Institute of Photonics and Advanced Sensing; Australia
| | - P. Hoffmann
- Adelaide Proteomics Centre; The University of Adelaide; Australia
- Institute of Photonics and Advanced Sensing; Australia
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11
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Bacterial Genomes. Infect Dis (Lond) 2017. [DOI: 10.1016/b978-0-7020-6285-8.00007-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
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12
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Dubourg G, Fournier PE. Advances in Diagnostic Microbiology. Infect Dis (Lond) 2017. [DOI: 10.1016/b978-0-7020-6285-8.00161-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
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13
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Cimmino T, Le Page S, Raoult D, Rolain JM. Contemporary challenges and opportunities in the diagnosis and outbreak detection of multidrug-resistant infectious disease. Expert Rev Mol Diagn 2016; 16:1163-1175. [PMID: 27690721 DOI: 10.1080/14737159.2016.1244005] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
INTRODUCTION The dissemination of multi-drug resistant bacteria (MDRB) has become a major public health concern worldwide because of the increase in infections caused by MDRB, the difficulty in treating them, and expenditures in patient care. Areas covered: We have reviewed challenges and contemporary opportunities for rapidly confronting infections caused by MDRB in the 21st century, including surveillance, detection, identification of resistance mechanisms, and action steps. Expert commentary: In this context, the first critical point for clinical microbiologists is to be able to rapidly detect an abnormal event, an outbreak and/or the spread of a MDRB with surveillance tools so that healthcare policies and therapies adapted to a new stochastic event that will certainly occur again in the future can be implemented.
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Affiliation(s)
- Teresa Cimmino
- a URMITE UM 63 CNRS 7278 IRD 198 INSERM U1905, IHU Méditerranée Infection, Faculté de Médecine et de Pharmacie , Aix-Marseille University , Marseille , France
| | - Stéphanie Le Page
- a URMITE UM 63 CNRS 7278 IRD 198 INSERM U1905, IHU Méditerranée Infection, Faculté de Médecine et de Pharmacie , Aix-Marseille University , Marseille , France
| | - Didier Raoult
- a URMITE UM 63 CNRS 7278 IRD 198 INSERM U1905, IHU Méditerranée Infection, Faculté de Médecine et de Pharmacie , Aix-Marseille University , Marseille , France
| | - Jean-Marc Rolain
- a URMITE UM 63 CNRS 7278 IRD 198 INSERM U1905, IHU Méditerranée Infection, Faculté de Médecine et de Pharmacie , Aix-Marseille University , Marseille , France
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14
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Bakour S, Sankar SA, Rathored J, Biagini P, Raoult D, Fournier PE. Identification of virulence factors and antibiotic resistance markers using bacterial genomics. Future Microbiol 2016; 11:455-66. [PMID: 26974504 DOI: 10.2217/fmb.15.149] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
In recent years, the number of multidrug-resistant bacteria has increased rapidly and several epidemics were signaled in different regions of the world. Faced with this situation that presents a major global public health concern, the development and the use of new and rapid technologies is more than urgent. The use of the next-generation sequencing platforms by microbiologists and infectious disease specialists has allowed great progress in the medical field. Here, we review the usefulness of whole-genome sequencing for the detection of virulence and antibiotic resistance associated genes.
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Affiliation(s)
- Sofiane Bakour
- Unité de recherche sur les maladies infectieuses et tropicales émergentes (URMITE), UM 63, CNRS 7278, IRD 198, INSERM 1095, IHU Méditerranée Infection, Faculté de Médecine et de Pharmacie, Aix-Marseille-Université, Marseille, France
| | - Senthil Alias Sankar
- Unité de recherche sur les maladies infectieuses et tropicales émergentes (URMITE), UM 63, CNRS 7278, IRD 198, INSERM 1095, IHU Méditerranée Infection, Faculté de Médecine et de Pharmacie, Aix-Marseille-Université, Marseille, France
| | - Jaishriram Rathored
- Unité de recherche sur les maladies infectieuses et tropicales émergentes (URMITE), UM 63, CNRS 7278, IRD 198, INSERM 1095, IHU Méditerranée Infection, Faculté de Médecine et de Pharmacie, Aix-Marseille-Université, Marseille, France
| | - Philippe Biagini
- UMR CNRS 7268 Equipe "Emergence et coévolution virale," Etablissement Français du Sang Alpes-Méditerranée et Aix-Marseille Université, 27 Boulevard Jean Moulin, 13005 Marseille
| | - Didier Raoult
- Unité de recherche sur les maladies infectieuses et tropicales émergentes (URMITE), UM 63, CNRS 7278, IRD 198, INSERM 1095, IHU Méditerranée Infection, Faculté de Médecine et de Pharmacie, Aix-Marseille-Université, Marseille, France
| | - Pierre-Edouard Fournier
- Unité de recherche sur les maladies infectieuses et tropicales émergentes (URMITE), UM 63, CNRS 7278, IRD 198, INSERM 1095, IHU Méditerranée Infection, Faculté de Médecine et de Pharmacie, Aix-Marseille-Université, Marseille, France
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15
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D’Amato F, Eldin C, Raoult D. The contribution of genomics to the study of Q fever. Future Microbiol 2016; 11:253-72. [DOI: 10.2217/fmb.15.137] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
Coxiella burnetii is the etiological agent of Q fever, a worldwide zoonosis that can result in large outbreaks. The birth of genomics and sequencing of C. burnetii strains has revolutionized many fields of study of this infection. Accurate genotyping methods and comparative genomic analysis have enabled description of the diversity of strains around the world and their link with pathogenicity. Genomics has also permitted the development of qPCR tools and axenic culture medium, facilitating the diagnosis of Q fever. Moreover, several pathophysiological mechanisms can now be predicted and therapeutic strategies can be determined thanks to in silico genome analysis. An extensive pan-genomic analysis will allow for a comprehensive view of the clonal diversity of C. burnetii and its link with virulence.
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Affiliation(s)
- Felicetta D’Amato
- Aix-Marseille Université, Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, UM63, CNRS 7278, IRD 198, INSERM 1095, Marseille, France
| | - Carole Eldin
- Aix-Marseille Université, Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, UM63, CNRS 7278, IRD 198, INSERM 1095, Marseille, France
| | - Didier Raoult
- Aix-Marseille Université, Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, UM63, CNRS 7278, IRD 198, INSERM 1095, Marseille, France
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16
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Yang XJ, Wang YB, Zhou ZW, Wang GW, Wang XH, Liu QF, Zhou SF, Wang ZH. High-throughput sequencing of 16S rDNA amplicons characterizes bacterial composition in bronchoalveolar lavage fluid in patients with ventilator-associated pneumonia. DRUG DESIGN DEVELOPMENT AND THERAPY 2015; 9:4883-96. [PMID: 26345636 PMCID: PMC4554422 DOI: 10.2147/dddt.s87634] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Ventilator-associated pneumonia (VAP) is a life-threatening disease that is associated with high rates of morbidity and likely mortality, placing a heavy burden on an individual and society. Currently available diagnostic and therapeutic approaches for VAP treatment are limited, and the prognosis of VAP is poor. The present study aimed to reveal and discriminate the identification of the full spectrum of the pathogens in patients with VAP using high-throughput sequencing approach and analyze the species richness and complexity via alpha and beta diversity analysis. The bronchoalveolar lavage fluid samples were collected from 27 patients with VAP in intensive care unit. The polymerase chain reaction products of the hypervariable regions of 16S rDNA gene in these 27 samples of VAP were sequenced using the 454 GS FLX system. A total of 103,856 pyrosequencing reads and 638 operational taxonomic units were obtained from these 27 samples. There were four dominant phyla, including Proteobacteria, Firmicutes, Actinobacteria, and Bacteroidetes. There were 90 different genera, of which 12 genera occurred in over ten different samples. The top five dominant genera were Streptococcus, Acinetobacter, Limnohabitans, Neisseria, and Corynebacterium, and the most widely distributed genera were Streptococcus, Limnohabitans, and Acinetobacter in these 27 samples. Of note, the mixed profile of causative pathogens was observed. Taken together, the results show that the high-throughput sequencing approach facilitates the characterization of the pathogens in bronchoalveolar lavage fluid samples and the determination of the profile for bacteria in the bronchoalveolar lavage fluid samples of the patients with VAP. This study can provide useful information of pathogens in VAP and assist clinicians to make rational and effective therapeutic decisions.
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Affiliation(s)
- Xiao-Jun Yang
- Department of Intensive Care Unit, General Hospital of Ningxia Medical University, Yinchuan, Ningxia, People's Republic of China
| | - Yan-Bo Wang
- Neurology Center, General Hospital of Ningxia Medical University, Yinchuan, Ningxia, People's Republic of China ; Key Laboratory of Brain Diseases of Ningxia, Yinchuan, Ningxia, People's Republic of China
| | - Zhi-Wei Zhou
- Department of Pharmaceutical Sciences, College of Pharmacy, University of South Florida, Tampa, FL, USA
| | - Guo-Wei Wang
- Neurology Center, General Hospital of Ningxia Medical University, Yinchuan, Ningxia, People's Republic of China
| | - Xiao-Hong Wang
- Department of Intensive Care Unit, General Hospital of Ningxia Medical University, Yinchuan, Ningxia, People's Republic of China
| | - Qing-Fu Liu
- Department of Intensive Care Unit, General Hospital of Ningxia Medical University, Yinchuan, Ningxia, People's Republic of China
| | - Shu-Feng Zhou
- Department of Pharmaceutical Sciences, College of Pharmacy, University of South Florida, Tampa, FL, USA
| | - Zhen-Hai Wang
- Neurology Center, General Hospital of Ningxia Medical University, Yinchuan, Ningxia, People's Republic of China ; Key Laboratory of Brain Diseases of Ningxia, Yinchuan, Ningxia, People's Republic of China
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17
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Liu A, Wang C, Liang Z, Zhou ZW, Wang L, Ma Q, Wang G, Zhou SF, Wang Z. High-throughput sequencing of 16S rDNA amplicons characterizes bacterial composition in cerebrospinal fluid samples from patients with purulent meningitis. Drug Des Devel Ther 2015; 9:4417-29. [PMID: 26300628 PMCID: PMC4535540 DOI: 10.2147/dddt.s82728] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Purulent meningitis (PM) is a severe infectious disease that is associated with high rates of morbidity and mortality. It has been recognized that bacterial infection is a major contributing factor to the pathogenesis of PM. However, there is a lack of information on the bacterial composition in PM, due to the low positive rate of cerebrospinal fluid bacterial culture. Herein, we aimed to discriminate and identify the main pathogens and bacterial composition in cerebrospinal fluid sample from PM patients using high-throughput sequencing approach. The cerebrospinal fluid samples were collected from 26 PM patients, and were determined as culture-negative samples. The polymerase chain reaction products of the hypervariable regions of 16S rDNA gene in these 26 samples of PM were sequenced using the 454 GS FLX system. The results showed that there were 71,440 pyrosequencing reads, of which, the predominant phyla were Proteobacteria and Firmicutes; and the predominant genera were Streptococcus, Acinetobacter, Pseudomonas, and Neisseria. The bacterial species in the cerebrospinal fluid were complex, with 61.5% of the samples presenting with mixed pathogens. A significant number of bacteria belonging to a known pathogenic potential was observed. The number of operational taxonomic units for individual samples ranged from six to 75 and there was a comparable difference in the species diversity that was calculated through alpha and beta diversity analysis. Collectively, the data show that high-throughput sequencing approach facilitates the characterization of the pathogens in cerebrospinal fluid and determine the abundance and the composition of bacteria in the cerebrospinal fluid samples of the PM patients, which may provide a better understanding of pathogens in PM and assist clinicians to make rational and effective therapeutic decisions.
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Affiliation(s)
- Aicui Liu
- Neurology Center, General Hospital of Ningxia Medical University, Yinchuan, Ningxia, People's Republic of China ; Key Laboratory of Brain Diseases of Ningxia, Yinchuan, Ningxia, People's Republic of China
| | - Chao Wang
- Neurology Center, General Hospital of Ningxia Medical University, Yinchuan, Ningxia, People's Republic of China ; Key Laboratory of Brain Diseases of Ningxia, Yinchuan, Ningxia, People's Republic of China
| | - Zhijuan Liang
- Department of Neurology, The First People's Hospital of Lanzhou, Lanzhou, Gansu, People's Republic of China
| | - Zhi-Wei Zhou
- Department of Pharmaceutical Sciences, College of Pharmacy, University of South Florida, Tampa, FL, USA
| | - Lin Wang
- Neurology Center, General Hospital of Ningxia Medical University, Yinchuan, Ningxia, People's Republic of China ; Key Laboratory of Brain Diseases of Ningxia, Yinchuan, Ningxia, People's Republic of China
| | - Qiaoli Ma
- Neurology Center, General Hospital of Ningxia Medical University, Yinchuan, Ningxia, People's Republic of China ; Key Laboratory of Brain Diseases of Ningxia, Yinchuan, Ningxia, People's Republic of China
| | - Guowei Wang
- Neurology Center, General Hospital of Ningxia Medical University, Yinchuan, Ningxia, People's Republic of China ; Key Laboratory of Brain Diseases of Ningxia, Yinchuan, Ningxia, People's Republic of China
| | - Shu-Feng Zhou
- Department of Pharmaceutical Sciences, College of Pharmacy, University of South Florida, Tampa, FL, USA
| | - Zhenhai Wang
- Neurology Center, General Hospital of Ningxia Medical University, Yinchuan, Ningxia, People's Republic of China ; Key Laboratory of Brain Diseases of Ningxia, Yinchuan, Ningxia, People's Republic of China
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18
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Sashidhara KV, Rao KB, Kushwaha P, Modukuri RK, Singh P, Soni I, Shukla PK, Chopra S, Pasupuleti M. Novel Chalcone-Thiazole Hybrids as Potent Inhibitors of Drug Resistant Staphylococcus aureus. ACS Med Chem Lett 2015; 6:809-13. [PMID: 26191371 PMCID: PMC4499817 DOI: 10.1021/acsmedchemlett.5b00169] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2015] [Accepted: 05/29/2015] [Indexed: 11/29/2022] Open
Abstract
A series of novel hybrids possessing chalcone and thiazole moieties were synthesized and evaluated for their antibacterial activities. In general this class of hybrids exhibited potency against Staphylococcus aureus, and in particular, compound 27 exhibited potent inhibitory activity with respect to other synthesized hybrids. Furthermore, the hemolytic and toxicity data demonstrated that the compound 27 was nonhemolytic and nontoxic to mammalian cells. The in vivo studies utilizing a S. aureus septicemia model demonstrated that compound 27 was as potent as vancomycin. The results of antibacterial activities underscore the potential of this scaffold that can be utilized for developing a new class of novel antibiotics.
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Affiliation(s)
- Koneni V. Sashidhara
- Medicinal & Process Chemistry Division and Division of Microbiology, CSIR−Central Drug Research Institute (CSIR-CDRI), Sector 10, Jankipuram extension,
Sitapur Road, Lucknow-226031, Uttar Pradesh, India
| | - K. Bhaskara Rao
- Medicinal & Process Chemistry Division and Division of Microbiology, CSIR−Central Drug Research Institute (CSIR-CDRI), Sector 10, Jankipuram extension,
Sitapur Road, Lucknow-226031, Uttar Pradesh, India
| | - Pragati Kushwaha
- Medicinal & Process Chemistry Division and Division of Microbiology, CSIR−Central Drug Research Institute (CSIR-CDRI), Sector 10, Jankipuram extension,
Sitapur Road, Lucknow-226031, Uttar Pradesh, India
| | - Ram K. Modukuri
- Medicinal & Process Chemistry Division and Division of Microbiology, CSIR−Central Drug Research Institute (CSIR-CDRI), Sector 10, Jankipuram extension,
Sitapur Road, Lucknow-226031, Uttar Pradesh, India
| | - Pratiksha Singh
- Medicinal & Process Chemistry Division and Division of Microbiology, CSIR−Central Drug Research Institute (CSIR-CDRI), Sector 10, Jankipuram extension,
Sitapur Road, Lucknow-226031, Uttar Pradesh, India
| | - Isha Soni
- Medicinal & Process Chemistry Division and Division of Microbiology, CSIR−Central Drug Research Institute (CSIR-CDRI), Sector 10, Jankipuram extension,
Sitapur Road, Lucknow-226031, Uttar Pradesh, India
| | - P. K. Shukla
- Medicinal & Process Chemistry Division and Division of Microbiology, CSIR−Central Drug Research Institute (CSIR-CDRI), Sector 10, Jankipuram extension,
Sitapur Road, Lucknow-226031, Uttar Pradesh, India
| | - Sidharth Chopra
- Medicinal & Process Chemistry Division and Division of Microbiology, CSIR−Central Drug Research Institute (CSIR-CDRI), Sector 10, Jankipuram extension,
Sitapur Road, Lucknow-226031, Uttar Pradesh, India
| | - Mukesh Pasupuleti
- Medicinal & Process Chemistry Division and Division of Microbiology, CSIR−Central Drug Research Institute (CSIR-CDRI), Sector 10, Jankipuram extension,
Sitapur Road, Lucknow-226031, Uttar Pradesh, India
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19
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The rebirth of culture in microbiology through the example of culturomics to study human gut microbiota. Clin Microbiol Rev 2015; 28:237-64. [PMID: 25567229 DOI: 10.1128/cmr.00014-14] [Citation(s) in RCA: 522] [Impact Index Per Article: 58.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Bacterial culture was the first method used to describe the human microbiota, but this method is considered outdated by many researchers. Metagenomics studies have since been applied to clinical microbiology; however, a "dark matter" of prokaryotes, which corresponds to a hole in our knowledge and includes minority bacterial populations, is not elucidated by these studies. By replicating the natural environment, environmental microbiologists were the first to reduce the "great plate count anomaly," which corresponds to the difference between microscopic and culture counts. The revolution in bacterial identification also allowed rapid progress. 16S rRNA bacterial identification allowed the accurate identification of new species. Mass spectrometry allowed the high-throughput identification of rare species and the detection of new species. By using these methods and by increasing the number of culture conditions, culturomics allowed the extension of the known human gut repertoire to levels equivalent to those of pyrosequencing. Finally, taxonogenomics strategies became an emerging method for describing new species, associating the genome sequence of the bacteria systematically. We provide a comprehensive review on these topics, demonstrating that both empirical and hypothesis-driven approaches will enable a rapid increase in the identification of the human prokaryote repertoire.
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20
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Fournier PE, Drancourt M. New Microbes New Infections promotes modern prokaryotic taxonomy: a new section "TaxonoGenomics: new genomes of microorganisms in humans". New Microbes New Infect 2015. [PMID: 26199732 PMCID: PMC4506979 DOI: 10.1016/j.nmni.2015.06.001] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Affiliation(s)
- Pierre-Edouard Fournier
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes URMITE, Institut Hospitalo-Universitaire Méditerranée-Infection, Aix-Marseille Université, UMR63, CNRS 7278, IRD 198, INSERM U1095, Faculté de Médecine, 27 Bd Jean Moulin, 13005, Marseille, France
| | - Michel Drancourt
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes URMITE, Institut Hospitalo-Universitaire Méditerranée-Infection, Aix-Marseille Université, UMR63, CNRS 7278, IRD 198, INSERM U1095, Faculté de Médecine, 27 Bd Jean Moulin, 13005, Marseille, France
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21
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Burke W, Korngiebel DM. Closing the gap between knowledge and clinical application: challenges for genomic translation. PLoS Genet 2015; 11:e1004978. [PMID: 25719903 PMCID: PMC4342348 DOI: 10.1371/journal.pgen.1004978] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Despite early predictions and rapid progress in research, the introduction of personal genomics into clinical practice has been slow. Several factors contribute to this translational gap between knowledge and clinical application. The evidence available to support genetic test use is often limited, and implementation of new testing programs can be challenging. In addition, the heterogeneity of genomic risk information points to the need for strategies to select and deliver the information most appropriate for particular clinical needs. Accomplishing these tasks also requires recognition that some expectations for personal genomics are unrealistic, notably expectations concerning the clinical utility of genomic risk assessment for common complex diseases. Efforts are needed to improve the body of evidence addressing clinical outcomes for genomics, apply implementation science to personal genomics, and develop realistic goals for genomic risk assessment. In addition, translational research should emphasize the broader benefits of genomic knowledge, including applications of genomic research that provide clinical benefit outside the context of personal genomic risk.
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Affiliation(s)
- Wylie Burke
- Department of Bioethics and Humanities, University of Washington, Seattle, Washington, United States of America
- * E-mail:
| | - Diane M. Korngiebel
- Department of Bioinformatics and Medical Education, University of Washington, Seattle, Washington, United States of America
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22
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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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23
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Coinfection of Fusobacterium nucleatum and Actinomyces israelii in mastoiditis diagnosed by next-generation DNA sequencing. J Clin Microbiol 2014; 52:1789-92. [PMID: 24574281 DOI: 10.1128/jcm.03133-13] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Some bacterial infections involve potentially complex mixtures of species that can now be distinguished using next-generation DNA sequencing. We present a case of mastoiditis where Gram stain, culture, and molecular diagnosis were nondiagnostic or discrepant. Next-generation sequencing implicated coinfection of Fusobacterium nucleatum and Actinomyces israelii, resolving these diagnostic discrepancies.
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24
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Sin MLY, Mach KE, Wong PK, Liao JC. Advances and challenges in biosensor-based diagnosis of infectious diseases. Expert Rev Mol Diagn 2014; 14:225-44. [PMID: 24524681 DOI: 10.1586/14737159.2014.888313] [Citation(s) in RCA: 199] [Impact Index Per Article: 19.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Rapid diagnosis of infectious diseases and timely initiation of appropriate treatment are critical determinants that promote optimal clinical outcomes and general public health. Conventional in vitro diagnostics for infectious diseases are time-consuming and require centralized laboratories, experienced personnel and bulky equipment. Recent advances in biosensor technologies have potential to deliver point-of-care diagnostics that match or surpass conventional standards in regards to time, accuracy and cost. Broadly classified as either label-free or labeled, modern biosensors exploit micro- and nanofabrication technologies and diverse sensing strategies including optical, electrical and mechanical transducers. Despite clinical need, translation of biosensors from research laboratories to clinical applications has remained limited to a few notable examples, such as the glucose sensor. Challenges to be overcome include sample preparation, matrix effects and system integration. We review the advances of biosensors for infectious disease diagnostics and discuss the critical challenges that need to be overcome in order to implement integrated diagnostic biosensors in real world settings.
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Affiliation(s)
- Mandy L Y Sin
- Department of Urology, Stanford University School of Medicine , Stanford, CA 94305-5118 , USA
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25
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Padmanabhan R, Mishra AK, Raoult D, Fournier PE. Genomics and metagenomics in medical microbiology. J Microbiol Methods 2013; 95:415-24. [PMID: 24200711 DOI: 10.1016/j.mimet.2013.10.006] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2013] [Revised: 10/08/2013] [Accepted: 10/10/2013] [Indexed: 02/06/2023]
Abstract
Over the last two decades, sequencing tools have evolved from laborious time-consuming methodologies to real-time detection and deciphering of genomic DNA. Genome sequencing, especially using next generation sequencing (NGS) has revolutionized the landscape of microbiology and infectious disease. This deluge of sequencing data has not only enabled advances in fundamental biology but also helped improve diagnosis, typing of pathogen, virulence and antibiotic resistance detection, and development of new vaccines and culture media. In addition, NGS also enabled efficient analysis of complex human micro-floras, both commensal, and pathological, through metagenomic methods, thus helping the comprehension and management of human diseases such as obesity. This review summarizes technological advances in genomics and metagenomics relevant to the field of medical microbiology.
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Affiliation(s)
- Roshan Padmanabhan
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, Aix-Marseille Université, UM63, CNRS 7278, IRD 198, INSERM 1095, Faculté de Médecine, 27 Bd. Jean Moulin, 13005 Marseille, France
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26
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Huang HC, Yao LL, Song ZM, Li XP, Hua QQ, Li Q, Pan CW, Xia CM. Development-specific differences in the proteomics of Angiostrongylus cantonensis. PLoS One 2013; 8:e76982. [PMID: 24204717 PMCID: PMC3808366 DOI: 10.1371/journal.pone.0076982] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2013] [Accepted: 08/27/2013] [Indexed: 11/18/2022] Open
Abstract
Angiostrongyliasis is an emerging communicable disease. Several different hosts are required to complete the life cycle of Angiostrongylus cantonensis. However, we lack a complete understanding of variability of proteins across different developmental stages and their contribution to parasite survival and progression. In this study, we extracted soluble proteins from various stages of the A. cantonensis life cycle [female adults, male adults, the fifth-stage female larvae (FL5), the fifth-stage male larvae (ML5) and third-stage larvae (L3)], separated those proteins using two-dimensional difference gel electrophoresis (2D-DIGE) at pH 4-7, and analyzed the gel images using DeCyder 7.0 software. This proteomic analysis produced a total of 183 different dominant protein spots. Thirty-seven protein spots were found to have high confidence scores (>95%) by matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS). Comparative proteomic analyses revealed that 29 spots represented cytoskeleton-associated proteins and functional proteins. Eight spots were unnamed proteins. Twelve protein spots that were matched to the EST of different-stage larvae of A. cantonensis were identified. Two genes and the internal control 18s were chosen for quantitative real-time PCR (qPCR) and the qPCR results were consistent with those of the DIGE studies. These findings will provide a new basis for understanding the characteristics of growth and development of A. cantonensis and the host-parasite relationship. They may also assist searches for candidate proteins suitable for use in diagnostic assays and as drug targets for the control of eosinophilic meningitis caused by A. cantonensis.
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Affiliation(s)
- Hui-Cong Huang
- Department of Parasitology, Medical College of Soochow University, Suzhou, Jiangsu, P. R. China
- Department of Parasitology, School of Basic Medical Sciences, Wenzhou Medical University, Wenzhou, Zhejiang, P. R. China
| | - Li-Li Yao
- Department of Parasitology, School of Basic Medical Sciences, Wenzhou Medical University, Wenzhou, Zhejiang, P. R. China
| | - Zeng-Mei Song
- Department of Parasitology, School of Basic Medical Sciences, Wenzhou Medical University, Wenzhou, Zhejiang, P. R. China
| | - Xing-Pan Li
- Department of Parasitology, School of Basic Medical Sciences, Wenzhou Medical University, Wenzhou, Zhejiang, P. R. China
| | - Qian-Qian Hua
- Department of Parasitology, School of Basic Medical Sciences, Wenzhou Medical University, Wenzhou, Zhejiang, P. R. China
| | - Qiang Li
- Department of Laboratory Diagnosis, The Third Affiliated Hospital of Wenzhou Medical University, Ruian, Zhejiang, P. R. China
| | - Chang-Wang Pan
- Department of Parasitology, School of Basic Medical Sciences, Wenzhou Medical University, Wenzhou, Zhejiang, P. R. China
| | - Chao-Ming Xia
- Department of Parasitology, Medical College of Soochow University, Suzhou, Jiangsu, P. R. China
- * E-mail:
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27
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Molecular diagnosis of Actinomadura madurae infection by 16S rRNA deep sequencing. J Clin Microbiol 2013; 51:4262-5. [PMID: 24108607 DOI: 10.1128/jcm.02227-13] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
Next-generation DNA sequencing can be used to catalog individual organisms within complex, polymicrobial specimens. Here, we utilized deep sequencing of 16S rRNA to implicate Actinomadura madurae as the cause of mycetoma in a diabetic patient when culture and conventional molecular methods were overwhelmed by overgrowth of other organisms.
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28
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Maiden MCJ, Jansen van Rensburg MJ, Bray JE, Earle SG, Ford SA, Jolley KA, McCarthy ND. MLST revisited: the gene-by-gene approach to bacterial genomics. Nat Rev Microbiol 2013; 11:728-36. [PMID: 23979428 PMCID: PMC3980634 DOI: 10.1038/nrmicro3093] [Citation(s) in RCA: 471] [Impact Index Per Article: 42.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Multilocus sequence typing (MLST) was proposed in 1998 as a portable sequence-based method for identifying clonal relationships among bacteria. Today, in the whole-genome era of microbiology, the need for systematic, standardized descriptions of bacterial genotypic variation remains a priority. Here, to meet this need, we draw on the successes of MLST and 16S rRNA gene sequencing to propose a hierarchical gene-by-gene approach that reflects functional and evolutionary relationships and catalogues bacteria 'from domain to strain'. Our gene-based typing approach using online platforms such as the Bacterial Isolate Genome Sequence Database (BIGSdb) allows the scalable organization and analysis of whole-genome sequence data.
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Affiliation(s)
- Martin C J Maiden
- Department of Zoology, University of Oxford, South Parks Road, Oxford OX1 3PS, UK
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Sentausa E, Fournier PE. Advantages and limitations of genomics in prokaryotic taxonomy. Clin Microbiol Infect 2013; 19:790-5. [DOI: 10.1111/1469-0691.12181] [Citation(s) in RCA: 76] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Fournier PE, Drancourt M, Colson P, Rolain JM, Scola BL, Raoult D. Modern clinical microbiology: new challenges and solutions. Nat Rev Microbiol 2013; 11:574-85. [PMID: 24020074 PMCID: PMC7097238 DOI: 10.1038/nrmicro3068] [Citation(s) in RCA: 208] [Impact Index Per Article: 18.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
In the twenty-first century, the clinical microbiology laboratory plays a central part in optimizing the management of infectious diseases and surveying local and global epidemiology. This pivotal role is made possible by the adoption of rational sampling, point-of-care tests, extended automation and new technologies, including mass spectrometry for colony identification, real-time genomics for isolate characterization, and versatile and permissive culture systems. When balanced with cost, these developments can improve the workflow and output of clinical microbiology laboratories and, by identifying and characterizing microbial pathogens, provide significant input to scientific discovery.
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Affiliation(s)
- Pierre-Edouard Fournier
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, UM63, CNRS7278, IRD198, INSERMU1095, Institut Hospitalo-Universitaire Méditerranée-Infection, Aix-Marseille Université, Faculté de Médecine, 27 Boulevard Jean Moulin, Marseille, 13385 France
| | - Michel Drancourt
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, UM63, CNRS7278, IRD198, INSERMU1095, Institut Hospitalo-Universitaire Méditerranée-Infection, Aix-Marseille Université, Faculté de Médecine, 27 Boulevard Jean Moulin, Marseille, 13385 France
| | - Philippe Colson
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, UM63, CNRS7278, IRD198, INSERMU1095, Institut Hospitalo-Universitaire Méditerranée-Infection, Aix-Marseille Université, Faculté de Médecine, 27 Boulevard Jean Moulin, Marseille, 13385 France
| | - Jean-Marc Rolain
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, UM63, CNRS7278, IRD198, INSERMU1095, Institut Hospitalo-Universitaire Méditerranée-Infection, Aix-Marseille Université, Faculté de Médecine, 27 Boulevard Jean Moulin, Marseille, 13385 France
| | - Bernard La Scola
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, UM63, CNRS7278, IRD198, INSERMU1095, Institut Hospitalo-Universitaire Méditerranée-Infection, Aix-Marseille Université, Faculté de Médecine, 27 Boulevard Jean Moulin, Marseille, 13385 France
| | - Didier Raoult
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, UM63, CNRS7278, IRD198, INSERMU1095, Institut Hospitalo-Universitaire Méditerranée-Infection, Aix-Marseille Université, Faculté de Médecine, 27 Boulevard Jean Moulin, Marseille, 13385 France
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31
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Cell extract-containing medium for culture of intracellular fastidious bacteria. J Clin Microbiol 2013; 51:2599-607. [PMID: 23740722 DOI: 10.1128/jcm.00719-13] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The culture of fastidious microorganisms is a critical step in infectious disease studies. As a proof-of-concept experiment, we evaluated an empirical medium containing eukaryotic cell extracts for its ability to support the growth of Coxiella burnetii. Here, we demonstrate the exponential growth of several bacterial strains, including the C. burnetii Nine Mile phase I and phase II strains, and C. burnetii isolates from humans and animals. Low-oxygen-tension conditions and the presence of small hydrophilic molecules and short peptides were critical for facilitating growth. Moreover, bacterial antigenicity was conserved, revealing the potential for this culture medium to be used in diagnostic tests and in the elaboration of vaccines against C. burnetii. We were also able to grow the majority of previously tested intracellular and fastidious bacterial species, including Tropheryma whipplei, Mycobacterium bovis, Leptospira spp., Borrelia spp., and most putative bioterrorism agents. However, we were unable to culture Rickettsia africae and Legionella spp. in this medium. The versatility of this medium should encourage its use as a replacement for the cell-based culture systems currently used for growing several facultative and putative intracellular bacterial species.
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Salipante SJ, Sengupta DJ, Rosenthal C, Costa G, Spangler J, Sims EH, Jacobs MA, Miller SI, Hoogestraat DR, Cookson BT, McCoy C, Matsen FA, Shendure J, Lee CC, Harkins TT, Hoffman NG. Rapid 16S rRNA next-generation sequencing of polymicrobial clinical samples for diagnosis of complex bacterial infections. PLoS One 2013; 8:e65226. [PMID: 23734239 PMCID: PMC3666980 DOI: 10.1371/journal.pone.0065226] [Citation(s) in RCA: 149] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2013] [Accepted: 04/23/2013] [Indexed: 12/25/2022] Open
Abstract
Classifying individual bacterial species comprising complex, polymicrobial patient specimens remains a challenge for culture-based and molecular microbiology techniques in common clinical use. We therefore adapted practices from metagenomics research to rapidly catalog the bacterial composition of clinical specimens directly from patients, without need for prior culture. We have combined a semiconductor deep sequencing protocol that produces reads spanning 16S ribosomal RNA gene variable regions 1 and 2 (∼360 bp) with a de-noising pipeline that significantly improves the fraction of error-free sequences. The resulting sequences can be used to perform accurate genus- or species-level taxonomic assignment. We explore the microbial composition of challenging, heterogeneous clinical specimens by deep sequencing, culture-based strain typing, and Sanger sequencing of bulk PCR product. We report that deep sequencing can catalog bacterial species in mixed specimens from which usable data cannot be obtained by conventional clinical methods. Deep sequencing a collection of sputum samples from cystic fibrosis (CF) patients reveals well-described CF pathogens in specimens where they were not detected by standard clinical culture methods, especially for low-prevalence or fastidious bacteria. We also found that sputa submitted for CF diagnostic workup can be divided into a limited number of groups based on the phylogenetic composition of the airway microbiota, suggesting that metagenomic profiling may prove useful as a clinical diagnostic strategy in the future. The described method is sufficiently rapid (theoretically compatible with same-day turnaround times) and inexpensive for routine clinical use.
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Affiliation(s)
- Stephen J. Salipante
- Department of Laboratory Medicine, University of Washington, Seattle, Washington, United States of America
- Department of Genome Sciences, University of Washington, Seattle, Washington, United States of America
- * E-mail: (SS); (NH)
| | - Dhruba J. Sengupta
- Department of Laboratory Medicine, University of Washington, Seattle, Washington, United States of America
| | - Christopher Rosenthal
- Department of Laboratory Medicine, University of Washington, Seattle, Washington, United States of America
| | - Gina Costa
- Life Technologies, Beverly, Massachusetts, United States of America
| | - Jessica Spangler
- Life Technologies, Beverly, Massachusetts, United States of America
| | - Elizabeth H. Sims
- Department of Microbiology, University of Washington, Seattle, Washington, United States of America
| | - Michael A. Jacobs
- Department of Microbiology, University of Washington, Seattle, Washington, United States of America
| | - Samuel I. Miller
- Department of Microbiology, University of Washington, Seattle, Washington, United States of America
| | - Daniel R. Hoogestraat
- Department of Laboratory Medicine, University of Washington, Seattle, Washington, United States of America
| | - Brad T. Cookson
- Department of Laboratory Medicine, University of Washington, Seattle, Washington, United States of America
- Department of Microbiology, University of Washington, Seattle, Washington, United States of America
| | - Connor McCoy
- Public Health Science Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - Frederick A. Matsen
- Public Health Science Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - Jay Shendure
- Department of Genome Sciences, University of Washington, Seattle, Washington, United States of America
| | - Clarence C. Lee
- Life Technologies, Beverly, Massachusetts, United States of America
| | | | - Noah G. Hoffman
- Department of Laboratory Medicine, University of Washington, Seattle, Washington, United States of America
- * E-mail: (SS); (NH)
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Whole-genome sequencing of bacterial sexually transmitted infections: implications for clinicians. Curr Opin Infect Dis 2013; 26:90-8. [PMID: 23221768 DOI: 10.1097/qco.0b013e32835c2159] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
PURPOSE OF REVIEW Increasingly, genomics is being used to answer detailed clinical questions. Although genome analysis of bacterial sexually transmitted infections (STIs) lags far behind that of many other bacterial pathogens, genomics can reveal previously inaccessible aspects of pathogen biology. RECENT FINDINGS Comparative genomic studies on the most common bacterial STI, chlamydia, have revolutionized our understanding of this intracellular bacterium, demonstrating that it undergoes extensive recombination and that the traditional typing schemes can be misleading. Genome projects can also help us to understand the recently observed phenomenon of 'diagnostic escape' seen in both Chlamydia trachomatis and Neisseria gonorrhoeae. SUMMARY The routine use of genomics in clinical settings is becoming a reality. For STIs, a primary requirement is an understanding of the diversity of circulating strains and how they change over time. This can help to inform future studies and allow us to address real clinical issues such as outbreak identification, global spread of successful clones and antimicrobial resistance monitoring.
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A review on recent developments in mass spectrometry instrumentation and quantitative tools advancing bacterial proteomics. Appl Microbiol Biotechnol 2013; 97:4749-62. [DOI: 10.1007/s00253-013-4897-7] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2012] [Revised: 03/29/2013] [Accepted: 04/03/2013] [Indexed: 10/26/2022]
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Gemi: PCR primers prediction from multiple alignments. Comp Funct Genomics 2012; 2012:783138. [PMID: 23316117 PMCID: PMC3535827 DOI: 10.1155/2012/783138] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2012] [Accepted: 10/19/2012] [Indexed: 12/31/2022] Open
Abstract
Designing primers and probes for polymerase chain reaction (PCR) is a preliminary and critical step that requires the identification of highly conserved regions in a given set of sequences. This task can be challenging if the targeted sequences display a high level of diversity, as frequently encountered in microbiologic studies. We developed Gemi, an automated, fast, and easy-to-use bioinformatics tool with a user-friendly interface to design primers and probes based on multiple aligned sequences. This tool can be used for the purpose of real-time and conventional PCR and can deal efficiently with large sets of sequences of a large size.
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Zhao J, Xie F, Zhong W, Wu W, Qu S, Gao S, Liu L, Zhao J, Wang M, Zhou J, Jie H, Chen W. Restriction endonuclease-mediated real-time digestion-PCR for somatic mutation detection. Int J Cancer 2012. [PMID: 23180674 DOI: 10.1002/ijc.27968] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
PCR is a powerful platform for clinical and diagnostic applications, but challenges remain in detecting somatic mutations, as mutant cells are often mixed with more numerous wild-type cells at the tissue-sample sites. Here, we describe a novel method that couples PCR with restriction endonuclease digestion (designated real-time digestion-PCR, or RTD-PCR) in a one-step reaction tube for detecting somatic mutations from a minority of cells. The PCR mixture contains a thermostable restriction enzyme that digests wild-type alleles during the PCR program, allowing selective amplification of the mutant alleles. To validate this method, we used real-time digestion-PCR for the specific detection of the EGFR (epidermal growth factor receptor) treatment resistance-inducing mutation, T790M, combining with three different platforms: Sanger sequencing, TaqMan probe PCR and Sequenom MassArray. From 78 clinical samples, seven T790M mutations were consistently detected on all three platforms, indicating that RTD-PCR may be a useful clinical tool for analyzing the T790M point mutation.
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Affiliation(s)
- Jinyin Zhao
- Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
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Tibayrenc M, Ayala FJ. Reproductive clonality of pathogens: a perspective on pathogenic viruses, bacteria, fungi, and parasitic protozoa. Proc Natl Acad Sci U S A 2012; 109:E3305-13. [PMID: 22949662 PMCID: PMC3511763 DOI: 10.1073/pnas.1212452109] [Citation(s) in RCA: 146] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
We propose that clonal evolution in micropathogens be defined as restrained recombination on an evolutionary scale, with genetic exchange scarce enough to not break the prevalent pattern of clonal population structure, a definition already widely used for all kinds of pathogens, although not clearly formulated by many scientists and rejected by others. The two main manifestations of clonal evolution are strong linkage disequilibrium (LD) and widespread genetic clustering ("near-clading"). We hypothesize that this pattern is not mainly due to natural selection, but originates chiefly from in-built genetic properties of pathogens, which could be ancestral and could function as alternative allelic systems to recombination genes ("clonality/sexuality machinery") to escape recombinational load. The clonal framework of species of pathogens should be ascertained before any analysis of biomedical phenotypes (phylogenetic character mapping). In our opinion, this model provides a conceptual framework for the population genetics of any micropathogen.
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Affiliation(s)
- Michel Tibayrenc
- Maladies Infectieuses et Vecteurs Ecologie, Génétique, Evolution et Contrôle, Institut de Rercherche pour le Développement 224, Centre National de la Recherche Scientifique 5290, Universités Montpellier 1 and 2, 34394 Montpellier Cedex 5, France; and
- Department of Ecology and Evolutionary Biology, University of California, Irvine, CA 92697
| | - Francisco J. Ayala
- Department of Ecology and Evolutionary Biology, University of California, Irvine, CA 92697
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Moal V, Zandotti C, Colson P. Emerging viral diseases in kidney transplant recipients. Rev Med Virol 2012; 23:50-69. [PMID: 23132728 PMCID: PMC7169126 DOI: 10.1002/rmv.1732] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2012] [Revised: 09/13/2012] [Accepted: 09/20/2012] [Indexed: 12/22/2022]
Abstract
Viruses are the most important cause of infections and a major source of mortality in Kidney Transplant Recipients (KTRs). These patients may acquire viral infections through exogenous routes including community exposure, donor organs, and blood products or by endogenous reactivation of latent viruses. Beside major opportunistic infections due to CMV and EBV and viral hepatitis B and C, several viral diseases have recently emerged in KTRs. New medical practices or technologies, implementation of new diagnostic tools, and improved medical information have contributed to the emergence of these viral diseases in this special population. The purpose of this review is to summarize the current knowledge on emerging viral diseases and newly discovered viruses in KTRs over the last two decades. We identified viruses in the field of KT that had shown the greatest increase in numbers of citations in the NCBI PubMed database. BKV was the most cited in the literature and linked to an emerging disease that represents a great clinical concern in KTRs. HHV-8, PVB19, WNV, JCV, H1N1 influenza virus A, HEV, and GB virus were the main other emerging viruses. Excluding HHV8, newly discovered viruses have been infrequently linked to clinical diseases in KTRs. Nonetheless, pathogenicity can emerge long after the discovery of the causative agent, as has been the case for BKV. Overall, antiviral treatments are very limited, and reducing immunosuppressive therapy remains the cornerstone of management.
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Affiliation(s)
- Valérie Moal
- Centre de Néphrologie et Transplantation Rénale, APHM, CHU Conception, Marseille, France.
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Van Oudenhove L, De Vriendt K, Van Beeumen J, Mercuri PS, Devreese B. Differential proteomic analysis of the response of Stenotrophomonas maltophilia to imipenem. Appl Microbiol Biotechnol 2012; 95:717-33. [DOI: 10.1007/s00253-012-4167-0] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2012] [Revised: 05/09/2012] [Accepted: 05/10/2012] [Indexed: 11/28/2022]
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Pottiez G, Jagadish T, Yu F, Letendre S, Ellis R, Duarte NA, Grant I, Gendelman HE, Fox HS, Ciborowski P. Plasma proteomic profiling in HIV-1 infected methamphetamine abusers. PLoS One 2012; 7:e31031. [PMID: 22359561 PMCID: PMC3281056 DOI: 10.1371/journal.pone.0031031] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2011] [Accepted: 12/29/2011] [Indexed: 12/21/2022] Open
Abstract
We wanted to determine whether methamphetamine use affects a subset of plasma proteins in HIV-infected persons. Plasma samples from two visits were identified for subjects from four groups: HIV+, ongoing, persistent METH use; HIV+, short-term METH abstinent; HIV+, long term METH abstinence; HIV negative, no history of METH use. Among 390 proteins identified, 28 showed significant changes in expression in the HIV+/persistent METH+ group over the two visits, which were not attributable to HIV itself. These proteins were involved in complement, coagulation pathways and oxidative stress. Continuous METH use is an unstable condition, altering levels of a number of plasma proteins.
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Affiliation(s)
- Gwenael Pottiez
- Department of Pharmacology and Experimental Neuroscience, Omaha, Nebraska, United States of America
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Sibley CD, Peirano G, Church DL. Molecular methods for pathogen and microbial community detection and characterization: current and potential application in diagnostic microbiology. INFECTION GENETICS AND EVOLUTION 2012; 12:505-21. [PMID: 22342514 PMCID: PMC7106020 DOI: 10.1016/j.meegid.2012.01.011] [Citation(s) in RCA: 105] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/10/2011] [Revised: 01/10/2012] [Accepted: 01/12/2012] [Indexed: 12/25/2022]
Abstract
Clinical microbiology laboratories worldwide have historically relied on phenotypic methods (i.e., culture and biochemical tests) for detection, identification and characterization of virulence traits (e.g., antibiotic resistance genes, toxins) of human pathogens. However, limitations to implementation of molecular methods for human infectious diseases testing are being rapidly overcome allowing for the clinical evaluation and implementation of diverse technologies with expanding diagnostic capabilities. The advantages and limitation of molecular techniques including real-time polymerase chain reaction, partial or whole genome sequencing, molecular typing, microarrays, broad-range PCR and multiplexing will be discussed. Finally, terminal restriction fragment length polymorphism (T-RFLP) and deep sequencing are introduced as technologies at the clinical interface with the potential to dramatically enhance our ability to diagnose infectious diseases and better define the epidemiology and microbial ecology of a wide range of complex infections.
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Affiliation(s)
- Christopher D. Sibley
- Department of Microbiology, Immunology & Infectious Diseases, Faculty of Medicine, University of Calgary, Calgary, Alta, Canada
| | - Gisele Peirano
- Division of Microbiology, Calgary Laboratory Services, Calgary, Alta, Canada
| | - Deirdre L. Church
- Department of Pathology & Laboratory Medicine, Faculty of Medicine, University of Calgary, Calgary, Alta, Canada
- Department of Medicine, Faculty of Medicine, University of Calgary, Calgary, Alta, Canada
- Division of Microbiology, Calgary Laboratory Services, Calgary, Alta, Canada
- Corresponding author. Address: c/o Calgary Laboratory Services, 9-3535 Research Rd. N.W., Calgary, Alta, Canada T2L 2K8. Tel.: +1 403 770 3281; fax: +1 403 770 3347.
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