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Gao P, Wu C, Zhang J, Wang S, Huang Y, Dong Y, Liu T, Ye C, Xu X, Xin W. Evaluation and Optimization of Microdrop Digital PCR for Detection of Serotype A and B Clostridium botulinum. Front Microbiol 2022; 13:860992. [PMID: 35615503 PMCID: PMC9125207 DOI: 10.3389/fmicb.2022.860992] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Accepted: 02/11/2022] [Indexed: 12/02/2022] Open
Abstract
Clostridium botulinum is the causative pathogen of botulism. Laboratory detection of C. botulinum is essential for clinical therapy treatment of botulism due to the difficulty in diagnosis, especially in infant botulism. The extreme toxicity of botulinum neurotoxin (BoNT) requires a sensitive detection method. Due to the detection limit of real-time quantitative PCR (q-PCR), a more sensitive detection method, micro-drop digital PCR (ddPCR) was applied in C. botulinum main serotypes A and B. The following performance criteria were evaluated by ddPCR: analytical sensitivity; repeatability; and diagnostic specificity. The limit of detection (LOD) was 0.84 and 0.88 copies/μl for BoNT A and B genes, respectively, by ddPCR with high specificity, compared to 5.04×102 and 6.91×102 copies/μl by q-PCR. It was increased 10 times compared with q-PCR in spiked stool samples. This improvement in sensitivity was especially important in clinical samples as more positive samples were detected by digital PCR compared with q-PCR. Meanwhile, enrichment time for low bacteria content samples was shortened by four hours both in serotypes A and B C. botulinum by ddPCR compared with q-PCR, which are important for laboratory diagnosis and epidemiology work.
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Affiliation(s)
- Pengya Gao
- State Key Laboratory for Infectious Disease Prevention and Control and National Institute for Communicable Diseases Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
- College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang, China
| | - Changde Wu
- College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang, China
| | - Jin Zhang
- Criminal Investigation School, People's Public Security University of China, Beijing, China
| | - Shuping Wang
- College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang, China
| | - Ying Huang
- State Key Laboratory for Infectious Disease Prevention and Control and National Institute for Communicable Diseases Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Yinping Dong
- NHC Key Laboratory of Food Safety Risk Assessment, China National Center for Food Safety Risk Assessment, Beijing, China
| | - Tingting Liu
- State Key Laboratory of Pathogen and Biosecurity, Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences, Beijing, China
| | - Changyun Ye
- State Key Laboratory for Infectious Disease Prevention and Control and National Institute for Communicable Diseases Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Xuefang Xu
- State Key Laboratory for Infectious Disease Prevention and Control and National Institute for Communicable Diseases Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
- *Correspondence: Xuefang Xu
| | - Wenwen Xin
- State Key Laboratory of Pathogen and Biosecurity, Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences, Beijing, China
- Wenwen Xin
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Hoj TR, McNeely B, Webber K, Welling E, Pitt WG, Ford LC, Robison RA. A pentaplex real-time PCR assay for rapid identification of major beta-lactamase genes KPC, NDM, CTX, CMY, and OXA-48 directly from bacteria in blood. J Med Microbiol 2021; 70:001465. [PMID: 34878374 PMCID: PMC8744273 DOI: 10.1099/jmm.0.001465] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2021] [Accepted: 10/17/2021] [Indexed: 11/18/2022] Open
Abstract
Introduction. Antibiotic resistance, particularly in cases of sepsis, has emerged as a growing global public health concern and economic burden. Current methods of blood culture and antimicrobial susceptibility testing of agents involved in sepsis can take as long as 3-5 days. It is vital to rapidly identify which antimicrobials can be used to effectively treat sepsis cases on an individual basis. Here, we present a pentaplex, real-time PCR-based assay that can quickly identify the most common beta-lactamase genes (Klebsiella pneumoniae carbapenemase (KPC); New Delhi metallo-beta-lactamase (NDM); cefotaximase-Munich (CTX-M); cephamycin AmpC beta-lactamases (CMY); and Oxacillinase-48 (OXA-48)) from pathogens derived directly from the blood of patients presenting with bacterial septicemia.Aim. To develop an assay which can rapidly identify the most common beta-lactamase genes in Carbapenem-resistant Enterobacteriaceae bacteria (CREs) from the United States.Hypothesis/Gap Statement. Septicemia caused by carbapenem-resistant bacteria has a death rate of 40-60 %. Rapid diagnosis of antibiotic susceptibility directly from bacteria in blood by identification of beta-lactamase genes will greatly improve survival rates. In this work, we develop an assay capable of concurrently identifying the five most common beta-lactamase and carbapenemase genes.Methodology. Primers and probes were created which can identify all subtypes of Klebsiella pneumoniae carbapenemase (KPC); New Delhi metallo-beta-lactamase (NDM); cefotaximase-Munich (CTX); cephamycin AmpC beta-lactamase (CMY); and oxacillinase-48 (OXA-48). The assay was validated using 13 isolates containing various PCR targets from the Centre for Disease Control Antimicrobial Resistance Isolate Bank Enterobacterales Carbapenemase Diversity Panel. Blood obtained from volunteers was spiked with CREs and bacteria were separated, lysed, and subjected to analysis via the pentaplex assay.Results. This pentaplex assay successfully identified beta-lactamase genes derived from bacteria separated from blood at concentrations of 4-8 c.f.u. ml-1.Conclusion. This assay will improve patient outcomes by supplying physicians with critical drug resistance information within 2 h of septicemia onset, allowing them to prescribe effective antimicrobials corresponding to the resistance gene(s) present in the pathogen. In addition, information supplied by this assay will lessen the inappropriate use of broad-spectrum antimicrobials and prevent the evolution of further antibiotic resistance.
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Affiliation(s)
- Taalin R. Hoj
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, UT 84602, USA
| | - Bradley McNeely
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, UT 84602, USA
| | - Kylie Webber
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, UT 84602, USA
| | - Evelyn Welling
- Chemical Engineering Department, Brigham Young University, Provo, UT, USA
| | - William G. Pitt
- Chemical Engineering Department, Brigham Young University, Provo, UT, USA
| | - Larry C. Ford
- Infectious Diseases, Intermountain Healthcare, Provo, UT USA
| | - Richard A. Robison
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, UT 84602, USA
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Rajkovic A, Jovanovic J, Monteiro S, Decleer M, Andjelkovic M, Foubert A, Beloglazova N, Tsilla V, Sas B, Madder A, De Saeger S, Uyttendaele M. Detection of toxins involved in foodborne diseases caused by Gram‐positive bacteria. Compr Rev Food Sci Food Saf 2020; 19:1605-1657. [DOI: 10.1111/1541-4337.12571] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2019] [Revised: 04/10/2020] [Accepted: 04/14/2020] [Indexed: 12/11/2022]
Affiliation(s)
- Andreja Rajkovic
- Laboratory of Food Microbiology and Food Preservation, Department of Food Technology, Safety and Health, Faculty of Bioscience EngineeringGhent University Ghent Belgium
| | - Jelena Jovanovic
- Laboratory of Food Microbiology and Food Preservation, Department of Food Technology, Safety and Health, Faculty of Bioscience EngineeringGhent University Ghent Belgium
| | - Silvia Monteiro
- Laboratorio Analises, Instituto Superior TecnicoUniversidade de Lisboa Lisbon Portugal
| | - Marlies Decleer
- Laboratory of Food Microbiology and Food Preservation, Department of Food Technology, Safety and Health, Faculty of Bioscience EngineeringGhent University Ghent Belgium
- Laboratory of Food Analysis, Department of Bioanalysis, Faculty of Pharmaceutical SciencesGhent University Ghent Belgium
| | - Mirjana Andjelkovic
- Operational Directorate Food, Medicines and Consumer SafetyService for Chemical Residues and Contaminants Brussels Belgium
| | - Astrid Foubert
- Laboratory of Food Analysis, Department of Bioanalysis, Faculty of Pharmaceutical SciencesGhent University Ghent Belgium
| | - Natalia Beloglazova
- Laboratory of Food Analysis, Department of Bioanalysis, Faculty of Pharmaceutical SciencesGhent University Ghent Belgium
- Nanotechnology Education and Research CenterSouth Ural State University Chelyabinsk Russia
| | - Varvara Tsilla
- Laboratory of Food Microbiology and Food Preservation, Department of Food Technology, Safety and Health, Faculty of Bioscience EngineeringGhent University Ghent Belgium
| | - Benedikt Sas
- Laboratory of Food Microbiology and Food Preservation, Department of Food Technology, Safety and Health, Faculty of Bioscience EngineeringGhent University Ghent Belgium
| | - Annemieke Madder
- Laboratorium for Organic and Biomimetic Chemistry, Department of Organic and Macromolecular ChemistryGhent University Ghent Belgium
| | - Sarah De Saeger
- Laboratory of Food Analysis, Department of Bioanalysis, Faculty of Pharmaceutical SciencesGhent University Ghent Belgium
| | - Mieke Uyttendaele
- Laboratory of Food Microbiology and Food Preservation, Department of Food Technology, Safety and Health, Faculty of Bioscience EngineeringGhent University Ghent Belgium
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Keisam S, Tuikhar N, Ahmed G, Jeyaram K. Toxigenic and pathogenic potential of enteric bacterial pathogens prevalent in the traditional fermented foods marketed in the Northeast region of India. Int J Food Microbiol 2019; 296:21-30. [PMID: 30826539 DOI: 10.1016/j.ijfoodmicro.2019.02.012] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2018] [Revised: 09/27/2018] [Accepted: 02/18/2019] [Indexed: 01/02/2023]
Abstract
The microbial risk involved with natural food fermentation is largely unknown. Here, we report the prevalence of enteric bacterial pathogens in the traditional fermented foods marketed in Northeast region of India. A total of 682 samples of 39 food types (broadly categorized into fermented soybean, bamboo shoot, fish, milk and pork products) collected over four different seasons from seven states of India were analyzed in this study. Cultivation-independent analysis by MiSeq amplicon sequencing of V4-V5 region of the 16S rRNA gene showed the bacterial community structure in the foods. Among the WHO prioritized foodborne bacterial pathogens, we detected the prevalence of phylotypes related to Clostridium botulinum, Bacillus cereus, Staphylococcus aureus, Clostridium perfringens, Listeria monocytogenes, and Escherichia coli in these ethnic foods. We also observed the occurrence of other well known human enteric pathogens like Proteus mirabilis, Clostridium difficile, and Yersinia enterocolitica. Further pathogen-specific qPCR assays confirmed a higher population (>107 cells/g) of B. cereus, P. mirabilis, and a C. botulinum related phylotype in the fermented soybean, fish, and pork products. We noticed a general trend of higher pathogen occurrence during the colder months without any seasonal variation of total bacterial load in the fermented foods. Further qPCR analysis on toxigenic and pathogenic potential, and toxins production by immunoassays showed that all the soybean samples and the isolated B. cereus cultures were positive for diarrheal toxins (Nhe and Hb1), and nearly half of the samples were positive for emetic toxin (cereulide). Similarly, the food samples and associated swarming P. mirabilis cultures were positive with the pathogenic factors like hemolysin (hpm), urease (ure) and multidrug resistance. However, we could not confirm the presence of botulinum neurotoxin (toxins A, B, E, and F) in the C. botulinum positive food samples. This is the first baseline data of the enteric bacterial pathogens prevalent in the traditional fermented foods of India, which will support the sustained effort of WHO to estimate the global foodborne disease burden. The unusual presence of P. mirabilis in the fermented foods marketed in the Indian region with high incidence of urolithiasis cases is a concern. Our study emphasizes the need of the hour to have a coordinated action to control and prevent the spread of enteric bacterial pathogens through fermented foods marketed in India. Moreover, replacing the indigenous process with a defined starter culture based controlled fermentation will enhance the safety of Indian fermented foods.
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Affiliation(s)
- Santosh Keisam
- Microbial Resources Division, Institute of Bioresources and Sustainable Development, Takyelpat, Imphal 795001, India; Department of Biotechnology, Gauhati University, Guwahati 781014, India
| | - Ngangyola Tuikhar
- Microbial Resources Division, Institute of Bioresources and Sustainable Development, Takyelpat, Imphal 795001, India; Department of Biotechnology, Gauhati University, Guwahati 781014, India
| | - Giasuddin Ahmed
- Department of Biotechnology, Gauhati University, Guwahati 781014, India
| | - Kumaraswamy Jeyaram
- Microbial Resources Division, Institute of Bioresources and Sustainable Development, Takyelpat, Imphal 795001, India.
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Chellapandi P, Prisilla A. PCR-based molecular diagnosis of botulism (types C and D) outbreaks in aquatic birds. ANN MICROBIOL 2018. [DOI: 10.1007/s13213-018-1390-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
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Lowe CW, Satterfield BA, Nelson DB, Thiriot JD, Heder MJ, March JK, Drake DS, Lew CS, Bunnell AJ, Moore ES, O'Neill KL, Robison RA. A Quadruplex Real-Time PCR Assay for the Rapid Detection and Differentiation of the Most Relevant Members of the B. pseudomallei Complex: B. mallei, B. pseudomallei, and B. thailandensis. PLoS One 2016; 11:e0164006. [PMID: 27736903 PMCID: PMC5063335 DOI: 10.1371/journal.pone.0164006] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2015] [Accepted: 09/19/2016] [Indexed: 11/24/2022] Open
Abstract
The Burkholderia pseudomallei complex classically consisted of B. mallei, B. pseudomallei, and B. thailandensis, but has now expanded to include B. oklahomensis, B. humptydooensis, and three unassigned Burkholderia clades. Methods for detecting and differentiating the B. pseudomallei complex has been the topic of recent research due to phenotypic and genotypic similarities of these species. B. mallei and B. pseudomallei are recognized as CDC Tier 1 select agents, and are the causative agents of glanders and melioidosis, respectively. Although B. thailandensis and B. oklahomensis are generally avirulent, both display similar phenotypic characteristics to that of B. pseudomallei. B. humptydooensis and the Burkholderia clades are genetically similar to the B. pseudomallei complex, and are not associated with disease. Optimal identification of these species remains problematic, and PCR-based methods can resolve issues with B. pseudomallei complex detection and differentiation. Currently, no PCR assay is available that detects the major species of the B. pseudomallei complex. A real-time PCR assay in a multiplex single-tube format was developed to simultaneously detect and differentiate B. mallei, B. pseudomallei, and B. thailandensis, and a common sequence found in B. pseudomallei, B. mallei, B. thailandensis, and B. oklahomensis. A total of 309 Burkholderia isolates and 5 other bacterial species were evaluated. The assay was 100% sensitive and specific, demonstrated sensitivity beyond culture and GC methods for the isolates tested, and is completed in about an hour with a detection limit between 2.6pg and 48.9pg of gDNA. Bioinformatic analyses also showed the assay is likely 100% specific and sensitive for all 84 fully sequenced B. pseudomallei, B. mallei, B. thailandensis, and B. oklahomensis strains currently available in GenBank. For these reasons, this assay could be a rapid and sensitive tool in the detection and differentiation for those species of the B. pseudomallei complex with recognized clinical and practical significance.
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Affiliation(s)
- Chinn-Woan Lowe
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, UT, 84602, United States of America
| | - Benjamin A. Satterfield
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, UT, 84602, United States of America
| | - Daniel B. Nelson
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, UT, 84602, United States of America
| | - Joseph D. Thiriot
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, UT, 84602, United States of America
| | - Michael J. Heder
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, UT, 84602, United States of America
| | - Jordon K. March
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, UT, 84602, United States of America
| | - David S. Drake
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, UT, 84602, United States of America
| | - Cynthia S. Lew
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, UT, 84602, United States of America
| | - Annette J. Bunnell
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, UT, 84602, United States of America
| | - Emily S. Moore
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, UT, 84602, United States of America
| | - Kim L. O'Neill
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, UT, 84602, United States of America
| | - Richard A. Robison
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, UT, 84602, United States of America
- * E-mail:
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Smith TJ, Hill KK, Raphael BH. Historical and current perspectives on Clostridium botulinum diversity. Res Microbiol 2015; 166:290-302. [PMID: 25312020 PMCID: PMC11302483 DOI: 10.1016/j.resmic.2014.09.007] [Citation(s) in RCA: 91] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2014] [Revised: 09/24/2014] [Accepted: 09/24/2014] [Indexed: 11/19/2022]
Abstract
For nearly one hundred years, researchers have attempted to categorize botulinum neurotoxin-producing clostridia and the toxins that they produce according to biochemical characterizations, serological comparisons, and genetic analyses. Throughout this period the bacteria and their toxins have defied such attempts at categorization. Below is a description of both historic and current Clostridium botulinum strain and neurotoxin information that illustrates how each new finding has significantly added to the knowledge of the botulinum neurotoxin-containing clostridia and their diversity.
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Affiliation(s)
- Theresa J Smith
- Molecular and Translational Sciences, United States Army Medical Research Institute of Infectious Diseases, Fort Detrick, MD 21702, USA.
| | - Karen K Hill
- Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
| | - Brian H Raphael
- Enteric Diseases Laboratory Branch, Centers for Disease Control and Prevention, Atlanta, GA 30329, USA
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Woudstra C, Tevell Åberg A, Skarin H, Anniballi F, De Medici D, Bano L, Koene M, Löfström C, Hansen T, Hedeland M, Fach P. Animal botulism outcomes in the AniBioThreat project. Biosecur Bioterror 2014; 11 Suppl 1:S177-82. [PMID: 23971804 DOI: 10.1089/bsp.2012.0074] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Botulism disease in both humans and animals is a worldwide concern. Botulinum neurotoxins produced by Clostridium botulinum and other Clostridium species are the most potent biological substances known and are responsible for flaccid paralysis leading to a high mortality rate. Clostridium botulinum and botulinum neurotoxins are considered potential weapons for bioterrorism and have been included in the Australia Group List of Biological Agents. In 2010 the European Commission (DG Justice, Freedom and Security) funded a 3-year project named AniBioThreat to improve the EU's capacity to counter animal bioterrorism threats. A detection portfolio with screening methods for botulism agents and incidents was needed to improve tracking and tracing of accidental and deliberate contamination of the feed and food chain with botulinum neurotoxins and other Clostridia. The complexity of this threat required acquiring new genetic information to better understand the diversity of these Clostridia and develop detection methods targeting both highly specific genetic markers of these Clostridia and the neurotoxins they are able to produce. Several European institutes participating in the AniBioThreat project collaborated on this program to achieve these objectives. Their scientific developments are discussed here.
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DERMAN Y, KORKEALA H, SALO E, LÖNNQVIST T, SAXEN H, LINDSTRÖM M. Infant botulism with prolonged faecal excretion of botulinum neurotoxin and Clostridium botulinum for 7 months. Epidemiol Infect 2014; 142:335-9. [PMID: 23688392 PMCID: PMC9151104 DOI: 10.1017/s0950268813001258] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2013] [Revised: 04/25/2013] [Accepted: 05/01/2013] [Indexed: 11/07/2022] Open
Abstract
In Finland in April 2010, a 3-month old baby was diagnosed with type A infant botulism. He excreted botulinum neurotoxin and/or Clostridium botulinum in his faeces until November 2010. Five months of excretion was after clinical recovery and discharge from hospital. C. botulinum isolates recovered from the household dust in the patient's home were genetically identical to those found in the infant's stool samples. Long-term faecal excretion of C. botulinum may pose a possible health risk for the parents and others in close contact with the infant.
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Affiliation(s)
- Y. DERMAN
- Department of Food Hygiene and Environmental Health, University of Helsinki, Finland
| | - H. KORKEALA
- Department of Food Hygiene and Environmental Health, University of Helsinki, Finland
| | - E. SALO
- Children's Hospital, University of Helsinki and Helsinki University Central Hospital, Finland
| | - T. LÖNNQVIST
- Children's Hospital, University of Helsinki and Helsinki University Central Hospital, Finland
| | - H. SAXEN
- Children's Hospital, University of Helsinki and Helsinki University Central Hospital, Finland
| | - M. LINDSTRÖM
- Department of Food Hygiene and Environmental Health, University of Helsinki, Finland
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Chiu CM, Lin FM, Chang TH, Huang WC, Liang C, Yang T, Wu WY, Yang TL, Weng SL, Huang HD. Clinical detection of human probiotics and human pathogenic bacteria by using a novel high-throughput platform based on next generation sequencing. J Clin Bioinforma 2014; 4:1. [PMID: 24418497 PMCID: PMC3901789 DOI: 10.1186/2043-9113-4-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2013] [Accepted: 12/13/2013] [Indexed: 02/08/2023] Open
Abstract
BACKGROUND The human body plays host to a vast array of bacteria, found in oral cavities, skin, gastrointestinal tract and the vagina. Some bacteria are harmful while others are beneficial to the host. Despite the availability of many methods to identify bacteria, most of them are only applicable to specific and cultivable bacteria and are also tedious. Based on high throughput sequencing technology, this work derives 16S rRNA sequences of bacteria and analyzes probiotics and pathogens species. RESULTS We constructed a database that recorded the species of probiotics and pathogens from literature, along with a modified Smith-Waterman algorithm for assigning the taxonomy of the sequenced 16S rRNA sequences. We also constructed a bacteria disease risk model for seven diseases based on 98 samples. Applicability of the proposed platform is demonstrated by collecting the microbiome in human gut of 13 samples. CONCLUSIONS The proposed platform provides a relatively easy means of identifying a certain amount of bacteria and their species (including uncultivable pathogens) for clinical microbiology applications. That is, detecting how probiotics and pathogens inhabit humans and how affect their health can significantly contribute to develop a diagnosis and treatment method.
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Affiliation(s)
- Chih-Min Chiu
- Institute of Bioinformatics and Systems Biology, National Chiao Tung University, Hsin-Chu 300, Taiwan
| | - Feng-Mao Lin
- Institute of Bioinformatics and Systems Biology, National Chiao Tung University, Hsin-Chu 300, Taiwan
| | - Tzu-Hao Chang
- Graduate Institute of Biomedical Informatics, Taipei Medical University, Taipei, Taiwan
| | - Wei-Chih Huang
- Institute of Bioinformatics and Systems Biology, National Chiao Tung University, Hsin-Chu 300, Taiwan
| | - Chao Liang
- Institute of Bioinformatics and Systems Biology, National Chiao Tung University, Hsin-Chu 300, Taiwan
| | - Ting Yang
- Institute of Bioinformatics and Systems Biology, National Chiao Tung University, Hsin-Chu 300, Taiwan
| | - Wei-Yun Wu
- Institute of Bioinformatics and Systems Biology, National Chiao Tung University, Hsin-Chu 300, Taiwan
| | - Tzu-Ling Yang
- Institute of Bioinformatics and Systems Biology, National Chiao Tung University, Hsin-Chu 300, Taiwan
| | - Shun-Long Weng
- Institute of Bioinformatics and Systems Biology, National Chiao Tung University, Hsin-Chu 300, Taiwan.,Department of Obstetrics and Gynecology, Hsinchu Mackay Memorial Hospital, Hsinchu, Taiwan.,Mackay Medicine, Nursing and Management College, Taipei, Taiwan.,Department of Medicine, Mackay Medical College, New Taipei City, Taiwan
| | - Hsien-Da Huang
- Institute of Bioinformatics and Systems Biology, National Chiao Tung University, Hsin-Chu 300, Taiwan.,Department of Biological Science and Technology, National Chiao Tung University, Hsin-Chu 300, Taiwan
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11
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Wang L, Zhang C, Gong F, Li H, Xie X, Xia C, Chen J, Song Y, Shen A, Song J. Influence of Pseudomonas aeruginosa pvdQ gene on altering antibiotic susceptibility under swarming conditions. Curr Microbiol 2012; 66:152-61. [PMID: 23090643 DOI: 10.1007/s00284-012-0217-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2011] [Accepted: 06/24/2011] [Indexed: 11/24/2022]
Abstract
In Pseudomonas aeruginosa PAO1, the pvdQ gene has been shown to have at least two functions. It encodes the acylase enzyme and hydrolyzes 3-oxo-C12-HSL, the key signaling molecule of quorum sensing system. In addition, pvdQ is involved in swarming motility. It is required and up-regulated during swarming motility, which is triggered by high cell densities. As high density bacterial populations also display elevated antibiotics resistance, studies have demonstrated swarm-cell differentiation in P. aeruginosa promotes increased resistance to various antibiotics. PvdQ acts as a signal during swarm-cell differentiation, and thus may play a role in P. aeruginosa antibiotic resistance. The aim of this study was to examine whether pvdQ was involved in modifying antibiotic susceptibility during swarming conditions and to investigate the mechanism by which this occurred. We constructed the PAO1pMEpvdQ strain, which overproduces PvdQ. PAO1pMEpvdQ promotes swarming motility, while PAO1ΔpvdQ abolishes swarming motility. In addition, both PAO1 and PAO1pMEpvdQ acquired resistance to ceftazidime, ciprofloxacin, meropenem, polymyxin B, and gentamicin, though PAO1pMEpvdQ exhibited a twofold to eightfold increase in antibiotic resistance compared to PAO1. These results indicate that pvdQ plays an important role in elevating antibiotic resistance via swarm-cell differentiation and possibly other mechanisms as well. We analyzed outer membrane permeability. Our data also suggest that pvdQ decreases P. aeruginosa outer membrane permeability, thereby elevating antibiotic resistance under swarming conditions. Our results suggest new approaches for reducing P. aeruginosa resistance.
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Affiliation(s)
- Lili Wang
- Department of Infectious Diseases, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, Hubei Province, China.
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Singh AK, Stanker LH, Sharma SK. Botulinum neurotoxin: where are we with detection technologies? Crit Rev Microbiol 2012; 39:43-56. [PMID: 22676403 DOI: 10.3109/1040841x.2012.691457] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Because of its high toxicity, botulinum neurotoxin (BoNT) poses a significant risk to humans and it represents a possible biological warfare agent. Nevertheless, BoNT serotypes A and B are considered an effective treatment for a variety of neurological disorders. The growing applicability of BoNT as a drug, and its potential use as a biological threat agent, highlight the urgent need to develop sensitive detection assays and therapeutic counter measures. In the last decade, significant progress has been made in BoNT detection technologies but none have fully replaced the mouse lethality assay, the current "gold standard". Recently, new advances in robotics and the availability of new reagents have allowed development of methods for rapid toxin analysis. These technologies while promising need further refinement.
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Affiliation(s)
- Ajay K Singh
- Food and Drug Administration, Center for Food Safety and Applied Nutrition, College Park, MD 20740, USA
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Neurotoxin gene profiling of clostridium botulinum types C and D native to different countries within Europe. Appl Environ Microbiol 2012; 78:3120-7. [PMID: 22344654 DOI: 10.1128/aem.07568-11] [Citation(s) in RCA: 73] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Clostridium botulinum types C and D, as well as their mosaic variants C-D and D-C, are associated with avian and mammalian botulism. This study reports on the development of low-density macroarrays based on the GeneDisc cycler platform (Pall-GeneDisc Technologies) applied to the simultaneous detection of the C. botulinum subtypes C, C-D, D, and D-C. The limit of detection of the PCR assays was 38 fg of total DNA, corresponding to 15 genome copies. Artificially contaminated samples of cecum showed a limit of detection below 50 spores/g. The tests were performed with a large variety of bacterial strains, including C. botulinum types C (n = 12), C-D (n = 29), D (n = 5), and D-C (n = 10), other botulinum neurotoxin (BoNT)-producing Clostridium strains (n = 20), non-BoNT-producing clostridia (n = 20), and other bacterial species (n = 23), and showed a high specificity. These PCR assays were compared to previously published real-time PCRs for the detection of C. botulinum in 292 samples collected from cases of botulism events in four European regions. The majority of the samples originated from wild birds (n = 108), poultry (n = 60), and bovines (n = 56). Among the 292 samples, 144 were positive for either the bont/C-D or the bont/D-C gene by using the GeneDisc arrays. The reliability of the results tallied to 97.94%. Interestingly, only BoNT mosaics, types C-D and D-C, were found in naturally contaminated samples whatever their animal origin and their geographical location. Further investigations should now be performed in order to check that mosaic types dominate in Europe and that acquisition of mosaic types helps in survival or adaptation to particular niche.
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Antibodies against a synthetic peptide designed to mimic a surface area of the H chain of botulinum neurotoxin A. Immunol Lett 2012; 142:20-7. [DOI: 10.1016/j.imlet.2011.11.002] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2011] [Revised: 11/07/2011] [Accepted: 11/14/2011] [Indexed: 11/23/2022]
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Dorner MB, Schulz KM, Kull S, Dorner BG. Complexity of Botulinum Neurotoxins: Challenges for Detection Technology. Curr Top Microbiol Immunol 2012. [DOI: 10.1007/978-3-662-45790-0_11] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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Parks BA, Shearer JD, Baudys J, Kalb SR, Sanford DC, Pirkle JL, Barr JR. Quantification of botulinum neurotoxin serotypes A and B from serum using mass spectrometry. Anal Chem 2011; 83:9047-53. [PMID: 22017298 DOI: 10.1021/ac201910q] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Botulinum neurotoxins (BoNT) are the deadliest agents known. Previously, we reported an endopeptidase activity based method (Endopep-MS) that detects and differentiates BoNT serotypes A-G. This method uses serotype specific monoclonal antibodies and the specific enzymatic activity of BoNT against peptide substrates which mimic the toxin's natural target. Cleavage products from the reaction are detected by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry. We have now developed a multiple reaction monitoring method to quantify the biological activity of BoNT serotypes A (BoNT/A) and B (BoNT/B) present in 0.5 mL of serum using electrospray mass spectrometry. The limit of quantification for each serotype is 1 mouse intraperitoneal lethal dose (MIPLD(50)) corresponding to 31 pg of BoNT/A and 15 pg of BoNT/B in this study. This method was applied to serum from rhesus macaques with inhalational botulism following exposure to BoNT/B, showing a maximum activity of 6.0 MIPLD(50)/mL in surviving animals and 653.6 MIPLD(50)/mL in animals that died in the study. The method detects BoNT/B in serum 2-5 h after exposure and up to 14 days. This is the first report of a quantitative method with sufficient sensitivity, selectivity, and low sample size requirements to measure circulating BoNT activity at multiple times during the course of botulism.
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Affiliation(s)
- Bryan A Parks
- Centers for Disease Control and Prevention, 4770 Buford Highway, Atlanta, Georgia, USA
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Influence of Pseudomonas aeruginosa pvdQ gene on altering antibiotic susceptibility under swarming conditions. Curr Microbiol 2011; 63:377-86. [PMID: 21833667 DOI: 10.1007/s00284-011-9979-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2011] [Accepted: 06/24/2011] [Indexed: 10/17/2022]
Abstract
In Pseudomonas aeruginosa PAO1, the pvdQ gene has been shown to have at least two functions. It encodes the acylase enzyme and hydrolyzes 3-oxo-C12-HSL, the key signaling molecule of quorum sensing system. In addition, pvdQ is involved in swarming motility. It is required for up-regulated during swarming motility, which is triggered by high cell densities. As high-density bacterial populations also display elevated antibiotic resistance, studies have demonstrated that swarm-cell differentiation in P. aeruginosa promotes increased resistance to various antibiotics. PvdQ acts as a signal during swarm-cell differentiation, and thus may play a role in P. aeruginosa antibiotic resistance. The aim of this study is to examine whether pvdQ was involved in modifying antibiotic susceptibility during swarming conditions, and to investigate the mechanism by which this occurred. We constructed the PAO1pMEpvdQ strain, which overproduced PvdQ. PAO1pMEpvdQ promotes swarming motility, while PAO1ΔpvdQ abolishes swarming motility. In addition, both PAO1 and PAO1pMEpvdQ acquired resistance to ceftazidime, ciprofloxacin, meropenem, polymyxin B, and gentamicin, though PAO1pMEpvdQ exhibited a two to eightfold increase in antibiotic resistance compared to PAO1. These results indicate that pvdQ plays an important role in elevating antibiotic resistance via swarm-cell differentiation and possibly other mechanisms as well. We analyzed outer membrane permeability. Our data also suggest that pvdQ decreases P. aeruginosa outer membrane permeability, thereby elevating antibiotic resistance under swarming conditions. Our results suggest new approaches for reducing P. aeruginosa resistance.
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Fach P, Fenicia L, Knutsson R, Wielinga PR, Anniballi F, Delibato E, Auricchio B, Woudstra C, Agren J, Segerman B, de Medici D, van Rotterdam BJ. An innovative molecular detection tool for tracking and tracing Clostridium botulinum types A, B, E, F and other botulinum neurotoxin producing Clostridia based on the GeneDisc cycler. Int J Food Microbiol 2010; 145 Suppl 1:S145-51. [PMID: 20471128 DOI: 10.1016/j.ijfoodmicro.2010.04.006] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2010] [Revised: 04/01/2010] [Accepted: 04/02/2010] [Indexed: 10/19/2022]
Abstract
Rapid and specific detection of botulinum neurotoxin (BoNT) producing Clostridia is a priority for public health authorities, in case of both natural and intentional botulism outbreaks. This study reports on the evaluation of a detection system based on the GeneDisc Cycler designed for simultaneously testing the bont/A, bont/B, bont/E and bont/F genes encoding for the botulinum neurotoxins types A, B, E and F. BoNT-producing Clostridia (n = 102) and non-BoNT-producing bacteria (n = 52) isolated from clinical, food and environmental samples were tested using this macro-array and results were compared to the reference lethality test on mice. The bont genes were correctly detected in all C. botulinum type A, B, E and F strains available, as well as in toxigenic C. baratii type F and toxigenic C. butyricum type E. No cross reactivity was observed with non human-toxigenic bacteria, C. botulinum types C, D and G. The identification of the bont genotype using the macro-array was correlated to toxino-typing of the BoNTs as determined by the mouse bioassay. An "evaluation trial" of the GeneDisc array performed blind in four European laboratories with 77 BoNT-producing Clostridia as well as 10 food and clinical samples showed that the developed macro-array is specific and reliable for identifying BoNT/A-, BoNT/B-, BoNT/E- and BoNT/F-producing clostridial strains and for screening naturally contaminated food and fecal samples. The test is robust, has a low detection limit (c.a. 5 to 50 genome copies in the PCR reaction microwell) and is promising for monitoring BoNT-producing Clostridia in different kinds of samples including food and clinical samples.
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Affiliation(s)
- P Fach
- French Food Safety Agency, Laboratory for Study and Research on Food Quality and Processes, 23 Av du Général De Gaulle, Fr-94706 Maisons-Alfort, France.
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