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Thanapirom K, Suksawatamnuay S, Wejnaruemarn S, Thaimai P, Siripon N, Ananchuensook P, Sriphoosanaphan S, Vanichanan J, Treeprasertsuk S, Poovorawan Y, Komolmit P. Bacterial DNA Translocation Is Associated With Overt Hepatic Encephalopathy and Mortality in Patients With Cirrhosis. Clin Transl Gastroenterol 2024; 15:e00697. [PMID: 38488171 PMCID: PMC11124729 DOI: 10.14309/ctg.0000000000000697] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/02/2023] [Accepted: 03/11/2024] [Indexed: 05/26/2024] Open
Abstract
INTRODUCTION Data on the relationship between bacterial translocation, hepatic encephalopathy (HE), and mortality are scarce. This study aimed to assess the association between bacterial DNA (bactDNA) translocation, inflammatory response, ammonia levels, and severity of HE in patients with cirrhosis, as well as the role of bactDNA translocation in predicting mortality. METHODS Cirrhotic patients without bacterial infection were prospectively enrolled between June 2022 and January 2023. Grading of HE was classified by the West Haven Criteria and Psychometric Hepatic Encephalopathy Score ≤ -5. RESULTS Overall, 294 cirrhotic patients were enrolled, with 92 (31.3%) and 58 (19.7%) having covert and overt HE, respectively. BactDNA translocation was detected in 36.1% of patients (n = 106). Patients with overt HE had more bactDNA translocation and higher serum lipopolysaccharide-binding protein (LBP), tumor necrosis factor-α, interleukin-6 (IL-6), and ammonia levels than those without HE. Patients with detectable bactDNA had higher white cell counts and serum LBP and IL-6 levels than those without. By contrast, bactDNA, serum LBP, and soluble CD14 levels were comparable between patients with covert HE and those without HE. The multivariate Cox regression analysis revealed that bactDNA translocation (hazard ratio [HR] = 2.49, 95% confidence interval [CI]: 1.22-5.11), Model for End-Stage Liver Disease score (HR = 1.12, 95% CI: 1.09-1.16), age (HR = 1.05, 95% CI: 1.000-1.002), and baseline IL-6 (HR = 1.001, 95% CI: 1.000-1.002) were independent factors associated with 6-month mortality. DISCUSSION Apart from hyperammonemia, bactDNA translocation is a possible factor associated with overt HE in cirrhotic patients. BactDNA translocation and IL-6 are independent factors associated with 6-month mortality.
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Affiliation(s)
- Kessarin Thanapirom
- Division of Gastroenterology, Department of Medicine, Faculty of Medicine, Chulalongkorn University and King Chulalongkorn Memorial Hospital, Bangkok, Thailand
- Center of Excellence in Hepatic Fibrosis and Cirrhosis, Chulalongkorn University, Bangkok, Thailand
- Excellence Center in Liver Diseases, King Chulalongkorn Memorial Hospital, Thai Red Cross Society, Bangkok, Thailand
| | - Sirinporn Suksawatamnuay
- Division of Gastroenterology, Department of Medicine, Faculty of Medicine, Chulalongkorn University and King Chulalongkorn Memorial Hospital, Bangkok, Thailand
- Center of Excellence in Hepatic Fibrosis and Cirrhosis, Chulalongkorn University, Bangkok, Thailand
- Excellence Center in Liver Diseases, King Chulalongkorn Memorial Hospital, Thai Red Cross Society, Bangkok, Thailand
| | - Salisa Wejnaruemarn
- Division of Gastroenterology, Department of Medicine, Faculty of Medicine, Chulalongkorn University and King Chulalongkorn Memorial Hospital, Bangkok, Thailand
| | - Panarat Thaimai
- Division of Gastroenterology, Department of Medicine, Faculty of Medicine, Chulalongkorn University and King Chulalongkorn Memorial Hospital, Bangkok, Thailand
- Center of Excellence in Hepatic Fibrosis and Cirrhosis, Chulalongkorn University, Bangkok, Thailand
- Excellence Center in Liver Diseases, King Chulalongkorn Memorial Hospital, Thai Red Cross Society, Bangkok, Thailand
| | - Nipaporn Siripon
- Division of Gastroenterology, Department of Medicine, Faculty of Medicine, Chulalongkorn University and King Chulalongkorn Memorial Hospital, Bangkok, Thailand
- Excellence Center in Liver Diseases, King Chulalongkorn Memorial Hospital, Thai Red Cross Society, Bangkok, Thailand
| | - Prooksa Ananchuensook
- Division of Gastroenterology, Department of Medicine, Faculty of Medicine, Chulalongkorn University and King Chulalongkorn Memorial Hospital, Bangkok, Thailand
- Center of Excellence in Hepatic Fibrosis and Cirrhosis, Chulalongkorn University, Bangkok, Thailand
- Excellence Center in Liver Diseases, King Chulalongkorn Memorial Hospital, Thai Red Cross Society, Bangkok, Thailand
| | - Supachaya Sriphoosanaphan
- Division of Gastroenterology, Department of Medicine, Faculty of Medicine, Chulalongkorn University and King Chulalongkorn Memorial Hospital, Bangkok, Thailand
- Excellence Center in Liver Diseases, King Chulalongkorn Memorial Hospital, Thai Red Cross Society, Bangkok, Thailand
| | - Jakapat Vanichanan
- Division of Infectious Disease, Department of Medicine, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Sombat Treeprasertsuk
- Division of Gastroenterology, Department of Medicine, Faculty of Medicine, Chulalongkorn University and King Chulalongkorn Memorial Hospital, Bangkok, Thailand
| | - Yong Poovorawan
- Centers of Excellence in Clinical Virology, Chulalongkorn University, Bangkok, Thailand
| | - Piyawat Komolmit
- Division of Gastroenterology, Department of Medicine, Faculty of Medicine, Chulalongkorn University and King Chulalongkorn Memorial Hospital, Bangkok, Thailand
- Center of Excellence in Hepatic Fibrosis and Cirrhosis, Chulalongkorn University, Bangkok, Thailand
- Excellence Center in Liver Diseases, King Chulalongkorn Memorial Hospital, Thai Red Cross Society, Bangkok, Thailand
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Bacterial agents (3rd section). Transfusion 2024; 64 Suppl 1:S208-S242. [PMID: 38394040 DOI: 10.1111/trf.17693] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2023] [Accepted: 12/13/2023] [Indexed: 02/25/2024]
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Moagi I, Mabasa L, Maputle SM, Ndwandwe D, Raliphaswa NS, Netshikweta LM, Malwela T, Samie A. The impact of DNA methylation as a factor of Adverse Pregnancy and Birth Outcomes (APBOs): a systematic review protocol. Syst Rev 2024; 13:4. [PMID: 38167510 PMCID: PMC10759365 DOI: 10.1186/s13643-023-02416-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Accepted: 12/05/2023] [Indexed: 01/05/2024] Open
Abstract
BACKGROUND Deoxyribonucleic acid (DNA) methylation is one of the epigenetic modifications that has gained a lot of interest as a factor influencing fetal programming and as a biomarker for adverse pregnancy and birth outcomes (APBOs). Epidemiological studies have demonstrated that DNA methylation can result in adverse pregnancy and birth outcomes (APBOs) including miscarriage, intrauterine growth restriction (IUGR), low birth weight (LBW), sepsis, and preterm birth (PTB), which may later result in diseases in adulthood. However, the mechanism by which DNA methylation influences these APBOs remains unclear. The systematic review will assess the association between global and gene-specific DNA methylation with adverse pregnancy outcomes. METHOD The Preferred Reporting Items for Systematic Review and Meta-Analysis (PRISMA) 2020 checklist will be followed when conducting this systematic review. To develop the search strategy the PI(E)COS (population, intervention/exposure, comparator/control, outcome, and study designs) framework will be followed. Thus far, the research team has retrieved 4721 from Cochrane Library, PubMed, Web of Sciences, and MEDLINE. Out of these, 584 studies have been screened for eligibility, and approximately 124 studies meet the inclusion criteria. Pending the search results identified from the grey literature. For identification of unpublished studies in journals indexed in electronic databases, Google Scholar will be used. I.M and A.S will separately extract data from the articles and screen them, if there are any disagreements between I.M and A.S, then the L.M will resolve them. The methodological quality and bias risk of the included studies will be evaluated using the Critical Appraisal Skill Programme CASP) checklist. [Formula: see text] and [Formula: see text] alpha = 0.10 statistic will be used for assessing statistical heterogeneity between studies. The Grading of Recommendations, Assessment, Development, and Evaluation (GRADE) approach will be used to assess and grade the overall quality of extracted data. ETHICS AND DISSEMINATION Ethical approval is not required. The systematic review will assess available literature on possible associations between DNA methylation with adverse pregnancy and birth outcomes (APBOs) including LBW, IUGR, miscarriage, sepsis, and PTB. The findings could help guide future research assessing DNA methylation and other APBOs. SYSTEMATIC REVIEW REGISTRATION PROSPERO CRCRD42022370647.
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Affiliation(s)
- Innocent Moagi
- Faculty of Sciences, Engineering and Agriculture, Department of Biochemistry and Microbiology, University of Venda, Private Bag X5050, Thohoyandou, 0950, South Africa.
| | - Lawrence Mabasa
- Biomedical Research and Innovation Platform (BRIP), South Africa Medical Research Council, Tygerberg, P.O Box 19070, Cape Town, 7505, South Africa
| | - Sonto Maria Maputle
- Faculty of Health Sciences, Department of Advanced Nursing Sciences, University of Venda, Private Bag X5050, Thohoyandou, 0950, South Africa
| | - Duduzile Ndwandwe
- Cochrane South Africa, South Africa Medical Research Council, Parow Valley, Cape Town, 7501, South Africa
| | - Ndidzulafhi Selina Raliphaswa
- Faculty of Health Sciences, Department of Advanced Nursing Sciences, University of Venda, Private Bag X5050, Thohoyandou, 0950, South Africa
| | - Lizzy Mutshinyalo Netshikweta
- Faculty of Health Sciences, Department of Advanced Nursing Sciences, University of Venda, Private Bag X5050, Thohoyandou, 0950, South Africa
| | - Thivhulawi Malwela
- Faculty of Health Sciences, Department of Advanced Nursing Sciences, University of Venda, Private Bag X5050, Thohoyandou, 0950, South Africa
| | - Amidou Samie
- Faculty of Sciences, Engineering and Agriculture, Department of Biochemistry and Microbiology, University of Venda, Private Bag X5050, Thohoyandou, 0950, South Africa.
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Kashyap R, Boro PR, Yasmin R, Nath J, Sonowal D, Doley R, Mondal B. Multiple protein-patterned surface plasmon resonance biochip for the detection of human immunoglobulin-G. JOURNAL OF BIOPHOTONICS 2023; 16:e202200263. [PMID: 36683194 DOI: 10.1002/jbio.202200263] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Revised: 11/18/2022] [Accepted: 01/02/2023] [Indexed: 05/17/2023]
Abstract
A portable surface plasmon resonance (SPR) measurement prototype integrated with a multiple protein-patterned SPR biochip is introduced for label-free and selective detection of human immunoglobulin-G (H-IgG). The polyclonal anti-H-IgG antibodies derived from goat, rabbit, and mouse were immobilized through polydimethylsiloxane (PDMS) microchannels to fabricate the patterned SPR biochip. The PDMS surface was functionalized using 3-aminopropyltrimethoxysilane and bonded to carbodiimide-activated gold substrates to construct irreversibly bonded hydrophilic microfluidic chip at room temperature. For SPR measurement, a custom-made system is developed with a high angular scanning accuracy of 0.005° and a wide scanning range of 30°-80° that avoids the conventional requirement of expensive goniometric stages and detector arrays. The SPR biochip immobilized with 750 μg/mL goat anti-H-IgG demonstrated detection of H-IgG with a detection limits of 15 μg/mL, and linear response through a wide concentration range (15-225 μg/mL) of high coefficient of determination (R2 = 0.99661). The selectivity of the sensor was investigated by exposing them to two different non-specific targets (bovine serum albumin and polyvalent antivenom). The results indicate negligible sensor response towards nonspecific targets (0.25° for 30 μg/mL bovine serum albumin (BSA) and 0.25° for 30 μg/mL polyvalent antivenom) in comparison to H-IgG (1.5° for 30 μg/mL).
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Affiliation(s)
- Ritayan Kashyap
- Department of Electronics and Communication Engineering, Tezpur University, Tezpur, Assam, India
| | - Pearleshwari Rani Boro
- Department of Electronics and Communication Engineering, Tezpur University, Tezpur, Assam, India
| | - Rafika Yasmin
- Department of Molecular Biology and Biotechnology, Tezpur University, Tezpur, Assam, India
| | - Jugabrat Nath
- Department of Electronics and Communication Engineering, Tezpur University, Tezpur, Assam, India
| | - Durlav Sonowal
- Department of Electronics and Communication Engineering, Tezpur University, Tezpur, Assam, India
| | - Robin Doley
- Department of Molecular Biology and Biotechnology, Tezpur University, Tezpur, Assam, India
| | - Biplob Mondal
- Department of Electronics and Communication Engineering, Tezpur University, Tezpur, Assam, India
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Adampourezare M, Hasanzadeh M, Hoseinpourefeizi MA, Seidi F. Iron/iron oxide-based magneto-electrochemical sensors/biosensors for ensuring food safety: recent progress and challenges in environmental protection. RSC Adv 2023; 13:12760-12780. [PMID: 37153517 PMCID: PMC10157298 DOI: 10.1039/d2ra07415j] [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: 11/22/2022] [Accepted: 03/09/2023] [Indexed: 05/09/2023] Open
Abstract
Foodborne diseases have arisen due to the globalization of industry and the increase in urban population, which has led to increased demand for food and has ultimately endangered the quality of food. Foodborne diseases have caused some of the most common public health problems and led to significant social and economic issues worldwide. Food quality and safety are affected by microbial contaminants, growth-promoting feed additives (β-agonists and antibiotics), food allergens, and toxins in different stages from harvesting to storage and marketing of products. Electrochemical biosensors, due to their reduced size and portability, low cost, and low consumption of reagents and samples, can quickly provide valuable quantitative and qualitative information about food contamination. In this regard, using nanomaterials can increase the sensitivity of the assessment. Magnetic nanoparticle (MNP)-based biosensors, especially, are receiving significant attention due to their low-cost production, physicochemical stability, biocompatibility, and eco-friendly catalytic characteristics, along with magnetic, biological, chemical and electronic sensing features. Here, we provide a review on the application of iron-based magnetic nanoparticles in the electrochemical sensing of food contamination. The types of nanomaterials used in order to improve the methods and increase the sensitivity of the methods have been discussed. Then, we stated the advantages and limitations of each method and tried to state the research gaps for each platform/method. Finally, the role of microfluidic and smartphone-based methods in the rapid detection of food contamination is stated. Then, various techniques like label-free and labelled regimes for the sensitive monitoring of food contamination were surveyed. Next, the critical role of antibody, aptamer, peptide, enzyme, DNA, cells and so on for the construction of specific bioreceptors for individual and simultaneous recognition by electrochemical methods for food contamination were discussed. Finally, integration of novel technologies such as microfluidic and smartphones for the identification of food contaminations were investigated. It is important to point out that, in the last part of each sub-section, attained results of different reports for each strategy were compared and advantages/limitations were mentioned.
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Affiliation(s)
- Mina Adampourezare
- Department of Biology, Faculty of Natural Science, University of Tabriz Tabriz Iran
| | - Mohammad Hasanzadeh
- Pharmaceutical Analysis Research Center, Tabriz University of Medical Sciences Tabriz Iran
- Nutrition Research Center, Tabriz University of Medical Sciences Tabriz Iran
| | | | - Farzad Seidi
- Jiangsu Co-Innovation Center for Efficient Processing and Utilization of Forest Resources and International Innovation Center for Forest Chemicals and Materials, Nanjing Forestry University Nanjing 210037 China
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Li Y, Wang C, Chen M. Metabolomics-based study of potential biomarkers of sepsis. Sci Rep 2023; 13:585. [PMID: 36631483 PMCID: PMC9834301 DOI: 10.1038/s41598-022-24878-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2022] [Accepted: 11/22/2022] [Indexed: 01/13/2023] Open
Abstract
The purpose of our study was to explore potential characteristic biomarkers in patients with sepsis. Peripheral blood specimens from sepsis patients and normal human volunteers were processed by liquid chromatography-mass spectrometry-based analysis. Outlier data were excluded by principal component analysis and orthogonal partial least squares-discriminant analysis using the metabolomics R software package metaX and MetaboAnalyst 5.0 ( https://www.metaboanalyst.ca/home.xhtml ) online analysis software, and differential metabolite counts were identified by using volcano and heatmaps. The obtained differential metabolites were combined with KEGG (Kyoto Gene and Kyoto Encyclopedia) analysis to screen out potential core differential metabolites, and ROC curves were drawn to analyze the changes in serum metabolites in sepsis patients and to explore the potential value of the metabolites in the diagnosis of sepsis patients. By metabolomic analysis, nine differential metabolites were screened for their significance in guiding the diagnosis and differential diagnosis of sepsis namely: 3-phenyl lactic acid, N-phenylacetylglutamine, phenylethylamine, traumatin, xanthine, methyl jasmonate, indole, l-tryptophan and 1107116. In this study, nine metabolites were finally screened based on metabolomic analysis and used as potential characteristic biomarkers for the diagnosis of sepsis.
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Affiliation(s)
- Yang Li
- grid.488387.8Department of Emergency Medicine, The Affiliated Hospital of Southwest Medical University, Luzhou, 646000 Sichuan China
| | - Chenglin Wang
- grid.488387.8Department of Emergency Medicine, The Affiliated Hospital of Southwest Medical University, Luzhou, 646000 Sichuan China
| | - Muhu Chen
- Department of Emergency Medicine, The Affiliated Hospital of Southwest Medical University, Luzhou, 646000, Sichuan, China.
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Chen L, Zhao Y, Wei J, Huang W, Ma Y, Yang X, Liu Y, Wang J, Xia H, Lou Z. Metagenomic Next-Generation Sequencing for the Diagnosis of Neonatal Infectious Diseases. Microbiol Spectr 2022; 10:e0119522. [PMID: 36409152 PMCID: PMC9769891 DOI: 10.1128/spectrum.01195-22] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Accepted: 10/28/2022] [Indexed: 11/23/2022] Open
Abstract
Infectious diseases pose a fatal risk to neonates. Timely and accurate pathogen detection is crucial for proper clinical diagnosis and therapeutic strategies. Limited sample volumes from neonatal patients seriously hindered the accurate detection of pathogens. Here, we unravel that metagenomic next-generation sequencing (mNGS) of cell-free DNA (cfDNA) and RNA can achieve unbiased detection of trace pathogens from different kinds of body fluid samples and blood samples. We enrolled 168 neonatal patients with suspected infections from whom blood samples (n = 153), cerebrospinal fluid samples (n = 127), and respiratory tract samples (RTSs) (including bronchoalveolar lavage fluids, sputa, and respiratory secretions) (n = 51) were collected and analyzed using mNGS. High rates of positivity (70.2%; 118/168) of mNGS were observed, and the coincidence rate against the final clinical diagnosis in positive mNGS cases reached 68.6% (81/118). The most common causative pathogens were Klebsiella pneumoniae (n = 12), Escherichia coli (n = 12), and Streptococcus pneumoniae (n = 8). mNGS using cfDNA and RNA can identify microbes that cannot be detected by conventional methods in different body fluid and blood samples, and more than 50% of these microbes were identified as causative pathogens. Further local polynomial regression fitting analysis revealed that the best timing for mNGS detection ranged from 1 to 3 days after the start of continuous antimicrobial therapy. Diagnosed and guided by mNGS results, the therapeutic regimens for 86 out of 117 neonatal patients were changed, most of whom (80/86) completely recovered and were discharged, while 44 out of 86 patients completely or partially stopped unnecessary medication. Our findings highlight the importance of mNGS in detecting causative DNA and RNA pathogens in infected neonatal patients. IMPORTANCE To the best of our knowledge, this is the first report on evaluating the performance of mNGS using cfDNA and RNA from body fluid and blood samples for diagnosing neonatal infections. mNGS of RNA and cfDNA can achieve the unbiased detection and identification of trace pathogens from different kinds of neonatal body fluid and blood samples with a high total coincidence rate (226/331; 68.3%) against final clinical diagnoses by sample. The best timing for mNGS detection in neonatal infections ranged from 1 to 3 days, rather than 0 days, after the start of continuous antimicrobial therapy. Our findings highlight the importance of mNGS in detecting causative DNA and RNA pathogens, and the extensive application of mNGS for the diagnosis of neonatal infections can be expected.
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Affiliation(s)
- Lu Chen
- Xi’an Children’s Hospital, Xi’an, China
| | | | | | | | - Ying Ma
- Xi’an Children’s Hospital, Xi’an, China
| | - Xuefeng Yang
- Neonatal Intensive Care Department, Xi’an Children’s Hospital, Xi’an, China
| | - Yang Liu
- Xi’an Children’s Hospital, Xi’an, China
| | - Jing Wang
- Department of Scientific Affairs, Hugobiotech Co., Ltd., Beijing, China
| | - Han Xia
- Department of Scientific Affairs, Hugobiotech Co., Ltd., Beijing, China
| | - Zheng Lou
- Department of Scientific Affairs, Hugobiotech Co., Ltd., Beijing, China
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Khnouf R, Al Shami F, Albiss BA, Salem N, Ababneh H, Mahasneh A. Enhancement of Salmonella Enteritidis Detection Using Nanoparticle-Assisted Real-Time Polymerase Chain Reaction. J Biomed Nanotechnol 2022. [DOI: 10.1166/jbn.2022.3401] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Improved; fast; and specific detection of pathogens has always been of great importance; more so with the increase of human population and human interaction. In this work we investigate the application of metal oxide nanoparticles (ZnO; Fe2O3; and TiO2)
in the detection of the pathogen Salmonella enteritidis using real-time quantitative PCR (qPCR). The nanoparticles were synthesized and characterized; and then they were added at different concentrations to qPCR for Salmonella enteritidis detection. qPCR provides numerical data such
as threshold cycle (Ct); efficiency; and DNA yield which make comparing the different tested conditions easier and more accurate. It has been observed that adding all three types of NPs at an optimum concentration 4×10−11 M for ZnO NPs, and 4×10−9
for Fe2O3 and TiO2 nanoparticles has led to increasing the efficiency of the reaction to 100% and to lowering the threshold cycle value by up to 6.6 for ZnO nanoparticles; hence increasing the DNA yield of the reaction; and lowering the detection time of the
pathogen by up to 50%.
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Affiliation(s)
- Ruba Khnouf
- Department of Biomedical Engineering, Jordan University of Science and Technology, Irbid, 22110, Jordan
| | - Farah Al Shami
- Department of Applied Biological Sciences, Jordan University of Science and Technology, Irbid, 22110, Jordan
| | - Borhan A. Albiss
- Department of Applied Physics, Jordan University of Science and Technology, Irbid, 22110, Jordan
| | - Nida’ Salem
- Department of Plant Protection, The University of Jordan, Amman, 11942, Jordan
| | - Haneen Ababneh
- Department of Applied Biological Sciences, Jordan University of Science and Technology, Irbid, 22110, Jordan
| | - Amjad Mahasneh
- Department of Applied Biological Sciences, Jordan University of Science and Technology, Irbid, 22110, Jordan
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Doualeh M, Payne M, Litton E, Raby E, Currie A. Molecular Methodologies for Improved Polymicrobial Sepsis Diagnosis. Int J Mol Sci 2022; 23:ijms23094484. [PMID: 35562877 PMCID: PMC9104822 DOI: 10.3390/ijms23094484] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Revised: 04/14/2022] [Accepted: 04/14/2022] [Indexed: 12/19/2022] Open
Abstract
Polymicrobial sepsis is associated with worse patient outcomes than monomicrobial sepsis. Routinely used culture-dependent microbiological diagnostic techniques have low sensitivity, often leading to missed identification of all causative organisms. To overcome these limitations, culture-independent methods incorporating advanced molecular technologies have recently been explored. However, contamination, assay inhibition and interference from host DNA are issues that must be addressed before these methods can be relied on for routine clinical use. While the host component of the complex sepsis host–pathogen interplay is well described, less is known about the pathogen’s role, including pathogen–pathogen interactions in polymicrobial sepsis. This review highlights the clinical significance of polymicrobial sepsis and addresses how promising alternative molecular microbiology methods can be improved to detect polymicrobial infections. It also discusses how the application of shotgun metagenomics can be used to uncover pathogen/pathogen interactions in polymicrobial sepsis cases and their potential role in the clinical course of this condition.
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Affiliation(s)
- Mariam Doualeh
- Centre for Molecular Medicine & Innovative Therapeutics, Murdoch University, Murdoch, WA 6150, Australia;
- Wesfarmers Centre of Vaccines and Infectious Diseases, Telethon Kids Institute, Perth, WA 6009, Australia
- Women and Infants Research Foundation, Perth, WA 6008, Australia;
| | - Matthew Payne
- Women and Infants Research Foundation, Perth, WA 6008, Australia;
- Division of Obstetrics and Gynaecology, University of Western Australia, Perth, WA 6008, Australia
| | - Edward Litton
- Intensive Care Unit, Fiona Stanley Hospital, Murdoch, WA 6150, Australia;
- Intensive Care Unit, St. John of God Hospital, Subiaco, WA 6009, Australia
| | - Edward Raby
- State Burns Unit, Fiona Stanley Hospital, Murdoch, WA 6150, Australia;
- Microbiology Department, Path West Laboratory Medicine, Murdoch, WA 6150, Australia
| | - Andrew Currie
- Centre for Molecular Medicine & Innovative Therapeutics, Murdoch University, Murdoch, WA 6150, Australia;
- Wesfarmers Centre of Vaccines and Infectious Diseases, Telethon Kids Institute, Perth, WA 6009, Australia
- Women and Infants Research Foundation, Perth, WA 6008, Australia;
- Correspondence: ; Tel.: +61-(08)-9360-7426
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Vilén A, Nilson B, Petersson AC, Cigut M, Nielsen C, Ström H. Detection of bacterial DNA in synovial fluid in dogs with arthritis: a comparison between bacterial culture and 16S rRNA polymerase chain reaction. Acta Vet Scand 2021; 63:34. [PMID: 34461947 PMCID: PMC8404341 DOI: 10.1186/s13028-021-00599-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2020] [Accepted: 08/22/2021] [Indexed: 12/03/2022] Open
Abstract
Background Septic arthritis (SA) is a serious condition in dogs that requires a prompt diagnosis and treatment to minimize long-term joint pathology. Although bacterial detection in synovial fluid (SF) through culture or cytology is often performed to confirm diagnosis, the sensitivity of these tests is low. The need for a reliable diagnostic tool to confirm the presence of bacteria in SF in humans has led to the increased use of 16S rRNA (i.e., ribosomal RNA) gene sequencing by polymerase chain reaction (16S rRNA PCR). The aim of this prospective clinical study was to compare the sensitivity and specificity of 16S rRNA PCR with bacterial culture on blood agar plates after pre-incubation of SF in paediatric blood bacterial culture bottles to identify bacteria in dogs with clinical signs of SA and to investigate the usefulness of these methods as diagnostic tools. Results Ten dogs with clinical signs of SA, nine with osteoarthritis (OA, control group) and nine with clinical signs of immune-mediated polyarthritis (IMPA, second control group) were examined. Bacterial culture was positive in seven of 10 dogs with clinical SA, of which only two were positive by 16S rRNA PCR. The sensitivity of 16S rRNA PCR and bacterial culture analysis for dogs with clinical SA were 20% and 70%, respectively. All SF samples collected from control group (n = 9) and second control group (n = 14) animals were negative on culture, and 16S rRNA PCR rendered a specificity of 100%. Conclusions Our study showed a lower sensitivity of 16S rRNA PCR than bacterial culture for dogs with clinical SA. Our findings suggest that there is currently no advantage in using 16S rRNA PCR as a diagnostic tool for dogs with clinical SA. Furthermore, our study indicates that pre-incubation in paediatric blood bacterial culture bottles before bacterial cultivation on blood agar plates might enhance bacterial culture sensitivity compared to other culture methods.
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Vajpeyee M, Yadav LB, Tiwari S, Tank P. To understand the reproductive tract microbiome associated with infertility through metagenomics analysis. MIDDLE EAST FERTILITY SOCIETY JOURNAL 2021. [DOI: 10.1186/s43043-021-00078-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
Abstract
Background
Knowledge of the microbiome is in its infancy in health and human illness, especially concerning human reproduction. We will be better able to treat dysbiosis of the reproductive tract clinically if it is better explained and understood. It has been shown that altered vaginal microbiota affects parturition, and its function is uncertain in assisted reproductive technologies. However, the effects of recognized microbes such as Mycoplasma tuberculosis, Chlamydia trachomatis, and Neisseria gonorrhoeae are well established, resulting in subclinical changes which are considered to be risk factors for infertility and poor reproductive outcomes.
Main body
Recent studies indicate that the vaginal tract comprises several different organisms of the microbiome. Some microbiota can play an important role not only in the reproductive tract but also in overall health. The microbiome of the female reproductive tract has been identified mainly based on studies that examine vaginal samples across many reproductive technologies, using a metagenomics approach.
Conclusion
Alteration of reproductive tract microbiota or presence of certain microbiota irrespective of the level of pathogenicity may interfere with fertilization, implantation, and subsequent embryo development. This may lead to failed fertility treatments and reduced live birth rate (LBR).
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Kalimuthu P, Gonzalez-Martinez JF, Jakubauskas D, Cárdenas M, Ruzgas T, Sotres J. Battery-free radio frequency wireless sensor for bacteria based on their degradation of gelatin-fatty acid composite films. Electrochim Acta 2021. [DOI: 10.1016/j.electacta.2021.138275] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
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13
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Le J, Greenberg RG, Benjamin DK, Yoo Y, Zimmerman KO, Cohen-Wolkowiez M, Wade KC. Prolonged Post-Discontinuation Antibiotic Exposure in Very Low Birth Weight Neonates at Risk for Early-Onset Sepsis. J Pediatric Infect Dis Soc 2021; 10:615-621. [PMID: 33491088 PMCID: PMC8163059 DOI: 10.1093/jpids/piaa172] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/12/2020] [Accepted: 12/28/2020] [Indexed: 11/13/2022]
Abstract
BACKGROUND Premature, very low birth weight (VLBW) neonates are at risk for early-onset sepsis and receive ampicillin and gentamicin post-birth. Antimicrobial stewardship supports short-course antibiotics, but how long antibiotic concentrations remain therapeutic post-last dose is unknown. METHODS Using Monte Carlo simulations (NONMEM 7.3), we analyzed antibiotic exposures in a retrospective cohort of 34 689 neonates (<1500 g, 22-27 weeks of gestation). Therapeutic exposure for ampicillin and gentamicin was evaluated relative to the minimum inhibitory concentration (MIC) for common pathogens (MIC 0.25-8 mcg/mL for group B streptococcus [GBS] and Escherichia coli). Post-discontinuation antibiotic exposure (PDAE) was defined as the time from the last dose to time when concentration decreased below MIC. RESULTS Neonates had a median (range) gestational age of 26 (22-27) weeks and BW, 790 g (400-1497) . All ampicillin dosing regimens (50-100 mg/kg every 8-12 hours for 2-6 doses) achieved therapeutic exposures > MIC range. After the last dose, the PDAE mean (95% confidence interval [CI]) ranged from 34 to 50 hours (17-79) for E. coli (MIC 8) and 82 to 104 hours (95% CI: 39-122) for GBS (MIC 0.25); longer PDAE occurred with higher dose, shorter interval, and longer course. Short-course ampicillin (2 doses, 50 mg/kg every 12 hours) provided PDAE 34 hours for E. coli and 82 hours for GBS. Single-dose 5 mg/kg gentamicin provided PDAE > MIC 2 for 26 hours. CONCLUSIONS In VLBW neonates, ampicillin exposure remains therapeutic long after the last dose. Short-course ampicillin provided therapeutic exposures throughout the typical blood culture incubation period.
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Affiliation(s)
- Jennifer Le
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California–San Diego, La Jolla, California, USA
| | - Rachel G Greenberg
- Department of Pediatrics, Duke University Medical Center, Durham, North Carolina, USA
- Duke Clinical Research Institute, Durham, North Carolina, USA
| | - Daniel K Benjamin
- Department of Pediatrics, Duke University Medical Center, Durham, North Carolina, USA
- Duke Clinical Research Institute, Durham, North Carolina, USA
| | - YoungJun Yoo
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California–San Diego, La Jolla, California, USA
| | - Kanecia O Zimmerman
- Department of Pediatrics, Duke University Medical Center, Durham, North Carolina, USA
- Duke Clinical Research Institute, Durham, North Carolina, USA
| | - Michael Cohen-Wolkowiez
- Department of Pediatrics, Duke University Medical Center, Durham, North Carolina, USA
- Duke Clinical Research Institute, Durham, North Carolina, USA
| | - Kelly C Wade
- Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
- Department of Pediatrics, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
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14
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The Accuracy of 16S rRNA Polymerase Chain Reaction for the Diagnosis of Neonatal Sepsis: A Meta-Analysis. BIOMED RESEARCH INTERNATIONAL 2021; 2021:5550387. [PMID: 34095300 PMCID: PMC8140837 DOI: 10.1155/2021/5550387] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Accepted: 04/29/2021] [Indexed: 11/18/2022]
Abstract
Objective To determine the accuracy of 16S rRNA polymerase chain reaction (PCR) for the diagnosis of neonatal sepsis through a systematic review and meta-analysis. Methods Studies involving 16S rRNA PCR tests for the diagnosis of neonatal sepsis were searched in the PubMed, Medline, Embase, and Cochrane Library databases. The methodological quality of the identified studies was evaluated using the Quality Assessment of Diagnostic Accuracy Studies-2 (QUADAS-2), and the sensitivity, the specificity, the positive likelihood ratio (PLR), the negative likelihood ratio (NLR), the diagnostic odds ratio (DOR), and the area under the curve (AUC) of operator characteristic (SROC) curves were determined. Heterogeneity between studies was analyzed by metaregression. Stata 14.0 and Meta-disc 1.4 software were used for the analyses. Results This meta-analysis included 19 related studies. The analysis found a sensitivity of 0.98 (95% CI: 0.85-1), specificity of 0.94 (95% CI: 0.87-0.97), PLR of 16.0 (95% CI: 7.6-33.9), NLR of 0.02 (95% CI: 0.00-0.18), DOR of 674 (95% CI: 89-5100), and AUC of 0.99 (95% CI: 0.97-0.99). Metaregression analysis identified Asian countries, arterial blood in blood samples, and sample size > 200 as the main sources of heterogeneity. This meta-analysis did not uncover publication bias. Sensitivity analysis showed that the study was robust. Fagan's nomogram results showed clinical usability. Conclusions The results from this meta-analysis indicate that 16S rRNA PCR testing is effective for the rapid diagnosis of neonatal sepsis.
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15
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Pérez-Torralba C, Ruiz-Olivares M, Sanbonmatsu-Gámez S, Expósito-Ruíz M, Navarro-Marí JM, Gutiérrez-Fernández J. [Increased infections by herpes simplex virus type 1 and polymicrobials of the genital tract, in the general population of a Spanish middle city]. REVISTA ESPANOLA DE QUIMIOTERAPIA 2021; 34:320-329. [PMID: 33886170 PMCID: PMC8329564 DOI: 10.37201/req/004.2021] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Introducción Las infecciones por genitopatógenos son un motivo de consulta frecuente en Atención Primaria y en las especialidades de Enfermedades Infecciosas, Urología, Ginecología y Dermatología. Las causas más comunes son los microorganismos oportunistas y los responsables de las infecciones de transmisión sexual asociadas a prácticas sin protección. El objetivo de este trabajo es determinar los microorganismos que causan estas infecciones en los pacientes atendidos en el Hospital Universitario Virgen de las Nieves de Granada y la sensibilidad a los antibióticos de Neisseria gonorrhoeae. Material y métodos Se realizó un estudio transversal y retrospectivo, en el que se incluyeron los resultados emitidos, entre enero de 2018 y diciembre de 2019, en el Laboratorio de Microbiología a partir de todos los episodios estudiados mediante procedimiento normalizados de trabajo. Resultados: Los microorganismos más frecuentemente detectados fueron Gardnerella vaginalis (23,81%) seguido de Candida spp. (20,9%), sobre todo en mujeres, N. gonorrhoeae (11,36%) y Ureaplasma urealyticum (11,99%), sobre todo en hombres. En multitud de ocasiones se presentaron de forma combinada. En cuanto a los virus del herpes simple, en hombres la infección por ambas especies tuvo una presencia similar (50%), mientras que en mujeres el tipo 1 fue más prevalente (76,52%). Los antibióticos más activos frente a N. gonorrhoeae fueron cefotaxima (98%) y cefixima (100%), siendo poco activo tetraciclina (39,02%). Conclusiones Los patógenos más frecuentes correspondieron a aquellos que han causado habitualmente infecciones en las mujeres, aunque N. gonorrhoeae fue el más frecuente en varones y las infecciones mixtas no son un hallazgo casual. Las infecciones por VHS-1 fueron más frecuentes que por VHS-2, lo cual confirma la tendencia de un cambio en la epidemiología del herpes genital.
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Affiliation(s)
| | | | | | | | | | - J Gutiérrez-Fernández
- José Gutiérrez-Fernández. Laboratorio de Microbiología. Hospital Universitario Virgen de las Nieves. Avenida de las Fuerzas Armadas, 2. E-18012 Granada, Spain.
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16
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Siles-Guerrero V, Cardona-Benavides I, Liébana-Martos C, Vázquez-Alonso F, Expósito-Ruiz M, Navarro-Marí JM, Gutiérrez-Fernández J. Recent clinical relevance of mono-genital colonization/infection by Ureaplasma parvum. Eur J Clin Microbiol Infect Dis 2020; 39:1899-1905. [PMID: 32436116 DOI: 10.1007/s10096-020-03928-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2020] [Accepted: 05/12/2020] [Indexed: 12/14/2022]
Abstract
Ureaplasma parvum is the most prevalent genital mycoplasma in women of childbearing age. There is debate around the relevance of its presence in male or female genitals for disease development and as a cofactor. The objective of this study was to determine the prevalence of colonization/infection by U. parvum and its possible relationship with reproductive tract infections. We retrospectively analyzed the presence of U. parvum in patients referred by specialist clinicians for suspicion of genitourinary tract infection. U. parvum was detected in 23.8% of samples, significantly more frequently in females (39.9%) than in males (6%). Among the males, U. parvum was found alone in 68.4% of episodes, with Ct < 30. Among the females, U. parvum was detected in 88.6% of cases, with Ct < 30, including 22 cases with premature rupture of membranes and 6 cases with threat of preterm labor. Co-infection was significantly more frequent in females (62.6%) than in males (31.6%). Given the high prevalence of U. parvum as sole isolate in males and females with genitourinary symptoms, it should be considered in the diagnosis and treatment of genital infections, although its pathogenic role in some diseases has not been fully elucidated.
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Affiliation(s)
- Víctor Siles-Guerrero
- Department of Microbiology, School of Medicine, University of Granada-Instituto de Investigación Biosanitaria de Granada.ibs, Granada, Spain
| | - Inmaculada Cardona-Benavides
- Department of Obstetrics and Gynecology, University Hospital Virgen de las Nieves- Instituto de Investigación Biosanitaria de Granada, ibs Granada, Granada, Spain
| | - Carmen Liébana-Martos
- Department of Microbiology, University Hospital Ciudad de Jaén -Instituto de Investigación Biosanitaria de Granada, ibs Granada, Jaén, Spain
| | - Fernando Vázquez-Alonso
- Department of Urology, University Hospital Virgen de las Nieves-Instituto de Investigación Biosanitaria de Granada, ibs Granada, Granada, Spain
| | - Manuela Expósito-Ruiz
- Research and Biostatistics Methodology Unit, University Hospital Virgen de las Nieves- Instituto de Investigación Biosanitaria de Granada, ibs Granada, Granada, Spain
| | - José María Navarro-Marí
- Department of Microbiology, University Hospital Virgen de las Nieves-Instituto de Investigación Biosanitaria de Granada, ibs Granada, Granada, Spain
| | - José Gutiérrez-Fernández
- Department of Microbiology, School of Medicine, University of Granada-Instituto de Investigación Biosanitaria de Granada.ibs, Granada, Spain.
- Department of Microbiology, University Hospital Virgen de las Nieves-Instituto de Investigación Biosanitaria de Granada, ibs Granada, Granada, Spain.
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17
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The Pathogenesis of Sepsis and Potential Therapeutic Targets. Int J Mol Sci 2019; 20:ijms20215376. [PMID: 31671729 PMCID: PMC6862039 DOI: 10.3390/ijms20215376] [Citation(s) in RCA: 357] [Impact Index Per Article: 71.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2019] [Revised: 10/05/2019] [Accepted: 10/25/2019] [Indexed: 02/06/2023] Open
Abstract
Sepsis is defined as “a life-threatening organ dysfunction caused by a host’s dysfunctional response to infection”. Although the treatment of sepsis has developed rapidly in the past few years, sepsis incidence and mortality in clinical treatment is still climbing. Moreover, because of the diverse manifestations of sepsis, clinicians continue to face severe challenges in the diagnosis, treatment, and management of patients with sepsis. Here, we review the recent development in our understanding regarding the cellular pathogenesis and the target of clinical diagnosis of sepsis, with the goal of enhancing the current understanding of sepsis. The present state of research on targeted therapeutic drugs is also elaborated upon to provide information for the treatment of sepsis.
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18
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Correlates of Gut Function in Children Hospitalized for Severe Acute Malnutrition, a Cross-sectional Study in Uganda. J Pediatr Gastroenterol Nutr 2019; 69:292-298. [PMID: 31169661 DOI: 10.1097/mpg.0000000000002381] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/10/2022]
Abstract
OBJECTIVE Children with severe acute malnutrition (SAM) may have impaired intestinal function, which can result in malabsorption, diarrhoea, and poor growth. This study evaluated the gut function of children with SAM using fecal and blood biomarkers and assessed their correlates. METHODS A cross-sectional study, nested in a randomized trial (www.isrctn.com, ISRCTN 16454889), was conducted at Mulago hospital, Uganda among subgroups of 400 children with complicated SAM and 30 community controls. Gut function was evaluated by 5 biomarkers: plasma citrulline, fecal myeloperoxidase and fecal neopterin, bacterially derived 16S rRNA gene and internal transcribed Spacer region (ITS) specific for Candida spp. in blood. RESULTS Compared with controls, children with SAM had lower median plasma citrulline (5.14 vs 27.4 μmol/L, P < 0.001), higher median fecal myeloperoxidase (18083 vs 7482 ng/mL, P = 0.001), and fecal neopterin (541 vs 210 nmol/L, P < 0.001). A higher blood concentration of 16S rRNA gene copy numbers was observed among children with SAM (95 vs 28 copies/μl, P = 0.05), whereas there was no difference in the blood concentration of Candida-specific ITS fragment.Among those with SAM, plasma citrulline was lower in children with edema, diarrhoea, dermatosis, and plasma C-reactive protein (CRP) >10 mg/L. Fecal neopterin was positively correlated with symptoms of fever and cough whereas it was negatively correlated with mid-upper arm circumference (MUAC), weight-for-height z score (WHZ), edema, and dermatosis. CONCLUSIONS Children with complicated SAM seem to have impaired gut function characterized by reduced enterocyte mass, intestinal inflammation, and increased bacterial translocation.
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19
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Reece E, McClean S, Greally P, Renwick J. The prevalence of Aspergillus fumigatus in early cystic fibrosis disease is underestimated by culture-based diagnostic methods. J Microbiol Methods 2019; 164:105683. [PMID: 31386863 DOI: 10.1016/j.mimet.2019.105683] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2019] [Revised: 07/31/2019] [Accepted: 08/02/2019] [Indexed: 11/28/2022]
Abstract
Aspergillus fumigatus is the most common fungus infecting/colonising people with cystic fibrosis (CF) and can negatively impact clinical status. Diagnostic laboratories rely on culture to detect A. fumigatus which is known to be less sensitive than molecular approaches. Therefore, A. fumigatus colonisation in the CF population may be underestimated. Sputum (n = 60) from 25 children with CF were collected and A. fumigatus was detected using routine culture (CM1), enhanced culture (CM2) and ITS1 qPCR. The prevalence of A. fumigatus in this young CF population was 68% by qPCR and only 16% by CM1. CM1, CM2 and qPCR detected A. fumigatus in 8%, 22% and 53% of samples, respectively. qPCR had a 94.2% and 77.4% increased odds of detecting A. fumigatus over CM1 and CM2, respectively. Molecular methods proved superior for detecting A. fumigatus in CF sputum. A. fumigatus is likely more prevalent in early CF disease than is currently reported.
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Affiliation(s)
- Emma Reece
- Department of Clinical Microbiology, Trinity College Dublin, Trinity Centre for Health Science, Tallaght University Hospital, Dublin 24, Ireland
| | - Siobhán McClean
- School of Biomolecular and Biomedical Sciences, University College Dublin, Ireland
| | - Peter Greally
- Department of Respiratory Medicine, The National Children's Hospital, Tallaght University Hospital, Dublin 24, Ireland
| | - Julie Renwick
- Department of Clinical Microbiology, Trinity College Dublin, Trinity Centre for Health Science, Tallaght University Hospital, Dublin 24, Ireland.
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20
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Tuzun F, Ozkan H, Cetinkaya M, Yucesoy E, Kurum O, Cebeci B, Cakmak E, Ozkutuk A, Keskinoglu P, Baysal B, Kumral A, Duman N. Is European Medicines Agency (EMA) sepsis criteria accurate for neonatal sepsis diagnosis or do we need new criteria? PLoS One 2019; 14:e0218002. [PMID: 31170237 PMCID: PMC6553766 DOI: 10.1371/journal.pone.0218002] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2019] [Accepted: 05/22/2019] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND Currently, there is a lack of clear definition for neonatal sepsis. The Pediatric Committee of the European Medicines Agency (EMA) developed consensus criteria to ensure a standardization for neonatal sepsis definition. However, there is no evidence supporting the accuracy of the EMA sepsis criteria in neonatal sepsis diagnosis. The main objective of this study was to evaluate the diagnostic accuracy of EMA sepsis criteria for proven neonatal sepsis. METHODS A multicenter prospective cohort study was conducted from October 2015 to November 2018. Infants with a gestational age over 34th weeks, diagnosed with clinical sepsis and received antibiotics according to the EMA criteria or experienced neonatologists' opinion were included. Blood culture or multiplex real time-PCR or 16S-rRNA positive infants were accepted as "proven sepsis". The predictive performance of EMA criteria for proven sepsis was evaluated by sensitivity, specificity, accuracy, and area under the curve measures of receiver operator characteristic curves. Data-mining methods were used for further analysis. RESULTS Among the 245 included infants, the EMA criteria were positive in 97 infants (39.6%), while proven sepsis was diagnosed in 113 infants (46.1%). The sensitivity, specificity, and accuracy of the EMA criteria for proven sepsis were 44.2% (95%CI: 34.9-53.9), 64.4% (95%CI: 55.6-72.5), 55.1% (95%CI: 46.6-59.4) respectively. None of the clinical and laboratory parameters had sufficient performance individually in terms of sensitivity, specificity and accuracy measures. The diagnostic performance was similar when different clinical findings were added to the EMA sepsis criteria or assessment of the score was interpreted in different ways. CONCLUSIONS Results highlighted that clinician opinion and standard laboratory tests are limited in the neonatal sepsis diagnosis. The EMA criteria also did not efficiently meet the diagnostic accuracy measures for neonatal sepsis. A predictive sepsis definition and rapid bedside point-of care tests are urgently needed.
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Affiliation(s)
- Funda Tuzun
- Department of Pediatrics, Division of Neonatology, Dokuz Eylul University Faculty of Medicine, Izmir, Turkey
| | - Hasan Ozkan
- Department of Pediatrics, Division of Neonatology, Dokuz Eylul University Faculty of Medicine, Izmir, Turkey
- * E-mail:
| | - Merih Cetinkaya
- Department of Pediatrics, Division of Neonatology, Kanuni Sultan Süleyman Training and Research Hospital, Istanbul, Turkey
| | - Ebru Yucesoy
- Department of Pediatrics, Division of Neonatology, Urfa Maternity and Children Hospital, Urfa, Turkey
| | - Ozge Kurum
- Department of Pediatrics, Division of Neonatology, Kanuni Sultan Süleyman Training and Research Hospital, Istanbul, Turkey
| | - Burcu Cebeci
- Department of Pediatrics, Division of Neonatology, Kanuni Sultan Süleyman Training and Research Hospital, Istanbul, Turkey
| | - Ertan Cakmak
- Department of Clinical Microbiology, Dokuz Eylul University Faculty of Medicine, Izmir, Turkey
| | - Aydan Ozkutuk
- Department of Clinical Microbiology, Dokuz Eylul University Faculty of Medicine, Izmir, Turkey
| | - Pembe Keskinoglu
- Department of Biostatistics and Bioinformatics, Dokuz Eylul University Faculty of Medicine, Izmir, Turkey
| | - Bora Baysal
- Department of Pediatrics, Division of Neonatology, Dokuz Eylul University Faculty of Medicine, Izmir, Turkey
| | - Abdullah Kumral
- Department of Pediatrics, Division of Neonatology, Dokuz Eylul University Faculty of Medicine, Izmir, Turkey
| | - Nuray Duman
- Department of Pediatrics, Division of Neonatology, Dokuz Eylul University Faculty of Medicine, Izmir, Turkey
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21
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Wilson D, Materón EM, Ibáñez-Redín G, Faria RC, Correa DS, Oliveira ON. Electrical detection of pathogenic bacteria in food samples using information visualization methods with a sensor based on magnetic nanoparticles functionalized with antimicrobial peptides. Talanta 2018; 194:611-618. [PMID: 30609580 DOI: 10.1016/j.talanta.2018.10.089] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2018] [Revised: 10/23/2018] [Accepted: 10/26/2018] [Indexed: 01/27/2023]
Abstract
Outbreaks of foodborne diseases demand simple, rapid techniques for detecting pathogenic bacteria beyond the standard methods that are not applicable to routine analysis in the food industry and in the points of food consumption. In this work, we developed a sensitive, rapid and low-cost assay for detecting Escherichia coli (E. coli), Staphylococcus aureus (S. aureus) and Salmonella typhimurium (S. typhi) in potable water and apple juice. The assay is based on electrical impedance spectroscopy measurements with screen-printed interdigitated electrodes coupled with magnetite nanoparticles functionalized with the antimicrobial peptide melittin (MLT). The data were analyzed with the information visualization methods Sammon's Mapping and Interactive Document Map to distinguish samples at two levels of contamination from food suitable for consumption. With this approach it has been possible to detect E. coli concentration down to 1 CFU mL-1 in potable water and 3.5 CFU mL-1 in apple juice without sample preparation, within only 25 min. This approach may serve as a low-cost, quick screening procedure to detect bacteria-related food poisoning, especially if the impedance data of several sensing units are combined.
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Affiliation(s)
- Deivy Wilson
- São Carlos Institute of Physics, University of São Paulo, Av. Trabalhador São-carlense, 400, 13566-590 São Carlos, SP, Brazil; Nanotechnology National Laboratory for Agriculture (LNNA), Embrapa Instrumentação, 13560-970 São Carlos, SP, Brazil.
| | - Elsa M Materón
- São Carlos Institute of Physics, University of São Paulo, Av. Trabalhador São-carlense, 400, 13566-590 São Carlos, SP, Brazil; Department of Chemistry, Federal University of São Carlos, Rod Washington Luiz, km 235, 13565-970 São Carlos, SP, Brazil
| | - Gisela Ibáñez-Redín
- São Carlos Institute of Physics, University of São Paulo, Av. Trabalhador São-carlense, 400, 13566-590 São Carlos, SP, Brazil
| | - Ronaldo C Faria
- Department of Chemistry, Federal University of São Carlos, Rod Washington Luiz, km 235, 13565-970 São Carlos, SP, Brazil
| | - Daniel S Correa
- Nanotechnology National Laboratory for Agriculture (LNNA), Embrapa Instrumentação, 13560-970 São Carlos, SP, Brazil
| | - Osvaldo N Oliveira
- São Carlos Institute of Physics, University of São Paulo, Av. Trabalhador São-carlense, 400, 13566-590 São Carlos, SP, Brazil.
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Stranieri I, Kanunfre KA, Rodrigues JC, Yamamoto L, Nadaf MIV, Palmeira P, Okay TS. Assessment and comparison of bacterial load levels determined by quantitative amplifications in blood culture-positive and negative neonatal sepsis. Rev Inst Med Trop Sao Paulo 2018; 60:e61. [PMID: 30379228 PMCID: PMC6201740 DOI: 10.1590/s1678-9946201860061] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2018] [Accepted: 10/02/2018] [Indexed: 12/17/2022] Open
Abstract
Bacterial sepsis remains a major cause of mortality and blood cultures are the
gold standard of laboratory diagnosis even though they lack sensitivity in
neonates. Culturenegative sepsis, also known as clinical sepsis, has long been
considered a diagnosis in neonatal intensive care units because, as well as
culture-positive infants, culture-negative neonates have worse prognosis in
comparison with non-infected ones. Quantitative amplifications are used to
detect bacterial infections in neonates but results are considered only in a
qualitative way (positive or negative). The aim of the present study was to
determine and compare bacterial load levels in blood culture-positive and
culture-negative neonatal sepsis. Seventy neonates with clinical and laboratory
evidence of infection admitted at three neonatal intensive care units were
classified as blood culture-positive or culture-negative. Blood samples obtained
at the same time of blood cultures had bacterial load levels assessed through a
16S rDNA qPCR. Blood cultures were positive in 29 cases (41.4%) and qPCR in 64
(91.4%). In the 29 culture-positive cases, 100% were also positive by qPCR,
while in the 41 culture-negative cases, 35 (85.4%) were positive by qPCR.
Bacterial load levels were in general < 50 CFU/mL, but were significantly
higher in culture-positive cases (Mann-Whitney, p = 0.013), although clinical
and laboratory findings were similar, excepting for deaths. In conclusion, the
present study has shown that blood culture-negative neonates have lower bacteria
load levels in their bloodstream when compared to blood culture-positive
infants.
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Affiliation(s)
- Inês Stranieri
- Universidade Federal de Mato Grosso, Hospital Universitário Julio Muller, Laboratório de Análises Clínicas, Divisão de Microbiologia, Cuiabá, Mato Grosso, Brazil
| | - Kelly Aparecida Kanunfre
- Universidade de São Paulo, Instituto de Medicina Tropical de São Paulo, Laboratório de Soroepidemiologia e Imunobiologia, São Paulo, São Paulo, Brazil.,Universidade de São Paulo, Faculdade de Medicina, Departamento de Moléstias Infecciosas e Parasitárias, LIM 48, São Paulo, São Paulo, Brazil
| | - Jonatas Cristian Rodrigues
- Universidade de São Paulo, Instituto de Medicina Tropical de São Paulo, Laboratório de Soroepidemiologia e Imunobiologia, São Paulo, São Paulo, Brazil.,Universidade de São Paulo, Faculdade de Medicina, Departamento de Moléstias Infecciosas e Parasitárias, LIM 48, São Paulo, São Paulo, Brazil
| | - Lidia Yamamoto
- Universidade de São Paulo, Instituto de Medicina Tropical de São Paulo, Laboratório de Soroepidemiologia e Imunobiologia, São Paulo, São Paulo, Brazil
| | - Maria Isabel Valdomir Nadaf
- Universidade Federal do Mato Grosso, Faculdade de Medicina, Departamento de Pediatria, Cuiabá, Mato Grosso, Brazil
| | - Patricia Palmeira
- Universidade de São Paulo, Faculdade de Medicina, Departamento de Pediatria, São Paulo, São Paulo, Brazil.,Universidade de São Paulo, Faculdade de Medicina, Hospital das Clínicas, Instituto da Criança, Laboratório de Pediatria Clínica, LIM 36, São Paulo, São Paulo, Brazil
| | - Thelma Suely Okay
- Universidade de São Paulo, Instituto de Medicina Tropical de São Paulo, Laboratório de Soroepidemiologia e Imunobiologia, São Paulo, São Paulo, Brazil
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23
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Rutanga JP, Van Puyvelde S, Heroes AS, Muvunyi CM, Jacobs J, Deborggraeve S. 16S metagenomics for diagnosis of bloodstream infections: opportunities and pitfalls. Expert Rev Mol Diagn 2018; 18:749-759. [PMID: 29985081 DOI: 10.1080/14737159.2018.1498786] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
INTRODUCTION Bacterial bloodstream infections (BSI) form a large public health threat worldwide. Current routine diagnosis is based on blood culture (BC) but this technique suffers from limited sensitivity. Molecular diagnostic tools have been developed for identification of bacteria in the blood of BSI patients. 16S metagenomics is an open-ended technique that can detect simultaneously all bacteria in a given sample based on PCR amplification of the 16S ribosomal RNA gene (rDNA) followed by sequencing of the PCR amplicons and taxonomic labeling of the sequence reads at genus or species level. Areas covered: Here we review the studies that have used 16S metagenomics for the identification of bacteria in human blood samples. We also discuss the potential added value of 16S metagenomics in the diagnosis of BSI, challenges as well as future directions for implementation in clinical settings. Expert commentary: 16S metagenomics has the potential to complement conventional BC; however, the technique currently suffers from several technical limitations jeopardizing implementation in routine clinical microbiology laboratories. Further studies are required to assess the cost-efficiency and clinical impact of 16S metagenomics in comparison to BC which remains the gold standard diagnostic method for BSI.
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Affiliation(s)
- Jean Pierre Rutanga
- a College of Science and Technology , University of Rwanda , Kigali , Rwanda.,b Department of Biomedical Sciences , Institute of Tropical Medicine , Antwerp , Belgium.,d Department of Microbiology and Immunology , KU Leuven , Leuven , Belgium
| | - Sandra Van Puyvelde
- b Department of Biomedical Sciences , Institute of Tropical Medicine , Antwerp , Belgium.,c Wellcome Trust Sanger Institute , Hinxton , United Kingdom
| | - Anne-Sophie Heroes
- d Department of Microbiology and Immunology , KU Leuven , Leuven , Belgium.,e Department of Clinical Sciences , Institute of Tropical Medicine , Antwerp , Belgium
| | - Claude Mambo Muvunyi
- f College of Medicine and Health Sciences , University of Rwanda , Kigali , Rwanda
| | - Jan Jacobs
- d Department of Microbiology and Immunology , KU Leuven , Leuven , Belgium.,e Department of Clinical Sciences , Institute of Tropical Medicine , Antwerp , Belgium
| | - Stijn Deborggraeve
- b Department of Biomedical Sciences , Institute of Tropical Medicine , Antwerp , Belgium
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van den Brand M, van den Dungen FAM, Bos MP, van Weissenbruch MM, van Furth AM, de Lange A, Rubenjan A, Peters RPH, Savelkoul PHM. Evaluation of a real-time PCR assay for detection and quantification of bacterial DNA directly in blood of preterm neonates with suspected late-onset sepsis. CRITICAL CARE : THE OFFICIAL JOURNAL OF THE CRITICAL CARE FORUM 2018; 22:105. [PMID: 29679983 PMCID: PMC5911371 DOI: 10.1186/s13054-018-2010-4] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/15/2017] [Accepted: 03/05/2018] [Indexed: 11/29/2022]
Abstract
Background Rapid and accurate diagnosis of neonatal sepsis is highly warranted because of high associated morbidity and mortality. The aim of this study was to evaluate the performance of a novel multiplex PCR assay for diagnosis of late-onset sepsis and to investigate the value of bacterial DNA load (BDL) determination as a measure of infection severity. Methods This cross-sectional study was conducted in a neonatal intensive care unit. Preterm and/or very low birth weight infants suspected for late-onset sepsis were included. Upon suspicion of sepsis, a whole blood sample was drawn for multiplex PCR to detect the eight most common bacteria causing neonatal sepsis, as well as for blood culture. BDL was determined in episodes with a positive multiplex PCR. Results In total, 91 episodes of suspected sepsis were investigated, and PCR was positive in 53 (58%) and blood culture in 60 (66%) episodes, yielding no significant difference in detection rate (p = 0.17). Multiplex PCR showed a sensitivity of 77%, specificity of 81%, positive predictive value of 87%, and negative predictive value of 68% compared with blood culture. Episodes with discordant results of PCR and blood culture included mainly detection of coagulase-negative staphylococci (CoNS). C-reactive protein (CRP) level and immature to total neutrophil (I/T) ratio were lower in these episodes, indicating less severe disease or even contamination. Median BDL was high (4.1 log10 cfu Eq/ml) with a wide range, and was it higher in episodes with a positive blood culture than in those with a negative blood culture (4.5 versus 2.5 log10 cfu Eq/ml; p < 0.0001). For CoNS infection episodes BDL and CRP were positively associated (p = 0.004), and for Staphylococcus aureus infection episodes there was a positive association between BDL and I/T ratio (p = 0.049). Conclusions Multiplex PCR provides a powerful assay to enhance rapid identification of the causative pathogen in late-onset sepsis. BDL measurement may be a useful indicator of severity of infection. Electronic supplementary material The online version of this article (10.1186/s13054-018-2010-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Marre van den Brand
- Department of Medical Microbiology and Infection Control, VU University Medical Center, De Boelelaan 1117, 1081HV, Amsterdam, The Netherlands.
| | - Frank A M van den Dungen
- Department of Pediatrics, VU University Medical Center, De Boelelaan 1117, 1081HV, Amsterdam, The Netherlands
| | - Martine P Bos
- Microbiome Ltd., De Boelelaan 1108, 1081HZ, Amsterdam, The Netherlands
| | - Mirjam M van Weissenbruch
- Department of Pediatrics, VU University Medical Center, De Boelelaan 1117, 1081HV, Amsterdam, The Netherlands
| | - A Marceline van Furth
- Department of Pediatrics, VU University Medical Center, De Boelelaan 1117, 1081HV, Amsterdam, The Netherlands
| | - Annemieke de Lange
- Department of Pediatrics, VU University Medical Center, De Boelelaan 1117, 1081HV, Amsterdam, The Netherlands
| | - Anna Rubenjan
- Department of Medical Microbiology and Infection Control, VU University Medical Center, De Boelelaan 1117, 1081HV, Amsterdam, The Netherlands
| | - Remco P H Peters
- Department of Medical Microbiology, University of Pretoria, Lynnwood Road and Roper Street, Hatfield, South Africa.,Department of Medical Microbiology, Maastricht University Medical Centre+, P. Debyelaan 25, 6229HX, Maastricht, The Netherlands
| | - Paul H M Savelkoul
- Department of Medical Microbiology and Infection Control, VU University Medical Center, De Boelelaan 1117, 1081HV, Amsterdam, The Netherlands.,Department of Medical Microbiology, Maastricht University Medical Centre+, P. Debyelaan 25, 6229HX, Maastricht, The Netherlands
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Microfluidic-Based Bacteria Isolation from Whole Blood for Diagnostics of Blood Stream Infection. Methods Mol Biol 2018; 1547:175-186. [PMID: 28044296 DOI: 10.1007/978-1-4939-6734-6_14] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/14/2023]
Abstract
Bacterial blood stream infection (BSI) potentially leads to life-threatening clinical conditions and medical emergencies such as severe sepsis, septic shock, and multi organ failure syndrome. Blood culturing is currently the gold standard for the identification of microorganisms and, although it has been automated over the decade, the process still requires 24-72 h to complete. This long turnaround time, especially for the identification of antimicrobial resistance, is driving the development of rapid molecular diagnostic methods. Rapid detection of microbial pathogens in blood related to bloodstream infections will allow the clinician to decide on or adjust the antimicrobial therapy potentially reducing the morbidity, mortality, and economic burden associated with BSI. For molecular-based methods, there is a lot to gain from an improved and straightforward method for isolation of bacteria from whole blood for downstream processing.We describe a microfluidic-based sample-preparation approach that rapidly and selectively lyses all blood cells while it extracts intact bacteria for downstream analysis. Whole blood is exposed to a mild detergent, which lyses most blood cells, and then to osmotic shock using deionized water, which eliminates the remaining white blood cells. The recovered bacteria are 100 % viable, which opens up possibilities for performing drug susceptibility tests and for nucleic-acid-based molecular identification.
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Florio W, Morici P, Ghelardi E, Barnini S, Lupetti A. Recent advances in the microbiological diagnosis of bloodstream infections. Crit Rev Microbiol 2017; 44:351-370. [PMID: 29185372 DOI: 10.1080/1040841x.2017.1407745] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Rapid identification (ID) and antimicrobial susceptibility testing (AST) of the causative agent(s) of bloodstream infections (BSIs) are essential for the prompt administration of an effective antimicrobial therapy, which can result in clinical and financial benefits. Immediately after blood sampling, empirical antimicrobial therapy, chosen on clinical and epidemiological data, is administered. When ID and AST results are available, the clinician decides whether to continue or streamline the antimicrobial therapy, based on the results of the in vitro antimicrobial susceptibility profile of the pathogen. The aim of the present study is to review and discuss the experimental data, advantages, and drawbacks of recently developed technological advances of culture-based and molecular methods for the diagnosis of BSI (including mass spectrometry, magnetic resonance, PCR-based methods, direct inoculation methods, and peptide nucleic acid fluorescence in situ hybridization), the understanding of which could provide new perspectives to improve and fasten the diagnosis and treatment of septic patients. Although blood culture remains the gold standard to diagnose BSIs, newly developed methods can significantly shorten the turnaround time of reliable microbial ID and AST, thus substantially improving the diagnostic yield.
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Affiliation(s)
- Walter Florio
- a Dipartimento di Ricerca Traslazionale e delle Nuove Tecnologie in Medicina e Chirurgia , Università di Pisa , Pisa , Italy
| | - Paola Morici
- a Dipartimento di Ricerca Traslazionale e delle Nuove Tecnologie in Medicina e Chirurgia , Università di Pisa , Pisa , Italy
| | - Emilia Ghelardi
- a Dipartimento di Ricerca Traslazionale e delle Nuove Tecnologie in Medicina e Chirurgia , Università di Pisa , Pisa , Italy
| | - Simona Barnini
- b U.O. Microbiologia Universitaria Azienda Ospedaliero-Universitaria Pisana , Pisa , Italy
| | - Antonella Lupetti
- a Dipartimento di Ricerca Traslazionale e delle Nuove Tecnologie in Medicina e Chirurgia , Università di Pisa , Pisa , Italy
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Varadhan KK, Constantin-Teodosiu D, Constantin D, Greenhaff PL, Lobo DN. Inflammation-mediated muscle metabolic dysregulation local and remote to the site of major abdominal surgery. Clin Nutr 2017; 37:2178-2185. [PMID: 29129636 PMCID: PMC6295976 DOI: 10.1016/j.clnu.2017.10.020] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2017] [Revised: 10/24/2017] [Accepted: 10/26/2017] [Indexed: 11/06/2022]
Abstract
Background & aims Postoperative hyperglycaemia is common in patients having major surgery and is associated with adverse outcomes. This study aimed to determine whether bacteraemia contributed to postoperative systemic inflammation, and whether increases in the expression of muscle mRNAs and proteins reflecting increased muscle inflammation, atrophy and impaired carbohydrate oxidation were evident at the time of surgery, and both local and distant to the site of trauma, and could be associated with impaired glucoregulation. Methods Fifteen adult patients without diabetes undergoing major abdominal surgery participated in this observational study set in a university teaching hospital. Arterialised-venous blood samples and muscle biopsies were obtained before and after major elective abdominal surgery, from sites local (rectus abdominis – RA) and remote to the site of surgery (vastus lateralis – VL). The main outcome measures included blood glucose concentrations, gut permeability and changes in expression of muscle mRNAs and proteins linked to inflammation and glucose regulation. Results Immediately postoperatively, RA demonstrated markedly increased mRNA expression levels of cathepsin-L (7.5-fold, P < 0.05), FOXO1 (10.5-fold, P < 0.05), MAFbx (11.5-fold, P < 0.01), PDK4 (7.8-fold, P < 0.05), TNF-α (16.5-fold, P < 0.05) and IL-6 (1058-fold, P < 0.001). A similar, albeit blunted, response was observed in VL. Surgery also increased expression of proteins linked to inflammation (IL-6; 6-fold, P < 0.01), protein degradation (MAFbx; 4.5-fold, P < 0.5), and blunted carbohydrate oxidation (PDK4; 4-fold, P < 0.05) in RA but not VL. Increased systemic inflammation (TNF-α, P < 0.05; IL-6, P < 0.001), and impaired postoperative glucose tolerance (P < 0.001), but not bacteraemia (although gut permeability was increased significantly, P < 0.05) or increased plasma cortisol, were noted 48 h postoperatively. Conclusions A systemic postoperative proinflammatory response was accompanied by muscle inflammation and metabolic dysregulation both local and remote to the site of surgery, and was not accompanied by bacteraemia. Clinical trial registration Registered at http://clinicaltrials.gov (NCT01134809).
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Affiliation(s)
- Krishna K Varadhan
- Gastrointestinal Surgery, Nottingham Digestive Diseases Centre, National Institute of Health Research (NIHR) Nottingham Biomedical Research Centre, Nottingham University Hospitals and University of Nottingham, Queen's Medical Centre, Nottingham NG7 2UH, UK
| | - Dumitru Constantin-Teodosiu
- MRC/ARUK Centre for Musculoskeletal Ageing Research, National Institute of Health Research (NIHR) Nottingham Biomedical Research Centre, School of Life Sciences, University of Nottingham, Queen's Medical Centre, Nottingham NG7 2UH, UK
| | - Despina Constantin
- MRC/ARUK Centre for Musculoskeletal Ageing Research, National Institute of Health Research (NIHR) Nottingham Biomedical Research Centre, School of Life Sciences, University of Nottingham, Queen's Medical Centre, Nottingham NG7 2UH, UK
| | - Paul L Greenhaff
- MRC/ARUK Centre for Musculoskeletal Ageing Research, National Institute of Health Research (NIHR) Nottingham Biomedical Research Centre, School of Life Sciences, University of Nottingham, Queen's Medical Centre, Nottingham NG7 2UH, UK
| | - Dileep N Lobo
- Gastrointestinal Surgery, Nottingham Digestive Diseases Centre, National Institute of Health Research (NIHR) Nottingham Biomedical Research Centre, Nottingham University Hospitals and University of Nottingham, Queen's Medical Centre, Nottingham NG7 2UH, UK.
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Vergis N, Atkinson SR, Knapp S, Maurice J, Allison M, Austin A, Forrest EH, Masson S, McCune A, Patch D, Richardson P, Gleeson D, Ryder SD, Wright M, Thursz MR. In Patients With Severe Alcoholic Hepatitis, Prednisolone Increases Susceptibility to Infection and Infection-Related Mortality, and Is Associated With High Circulating Levels of Bacterial DNA. Gastroenterology 2017; 152:1068-1077.e4. [PMID: 28043903 PMCID: PMC6381387 DOI: 10.1053/j.gastro.2016.12.019] [Citation(s) in RCA: 121] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/23/2016] [Revised: 11/16/2016] [Accepted: 12/03/2016] [Indexed: 12/16/2022]
Abstract
BACKGROUND & AIMS Infections are common in patients with severe alcoholic hepatitis (SAH), but little information is available on how to predict their development or their effects on patients. Prednisolone is advocated for treatment of SAH, but can increase susceptibility to infection. We compared the effects of infection on clinical outcomes of patients treated with and without prednisolone, and identified risk factors for development of infection in SAH. METHODS We analyzed data from 1092 patients enrolled in a double-blind placebo-controlled trial to evaluate the efficacy of treatment with prednisolone (40 mg daily) or pentoxifylline (400 mg 3 times each day) in patients with SAH. The 2 × 2 factorial design led to 547 patients receiving prednisolone; 546 were treated with pentoxifylline. The trial was conducted in the United Kingdom from January 2011 through February 2014. Data on development of infection were collected at evaluations performed at screening, baseline, weekly during admission, on discharge, and after 90 days. Patients were diagnosed with infection based on published clinical and microbiologic criteria. Risk factors for development of infection and effects on 90-day mortality were evaluated separately in patients treated with prednisolone (n = 547) and patients not treated with prednisolone (n = 545) using logistic regression. Pretreatment blood levels of bacterial DNA (bDNA) were measured in 731 patients. RESULTS Of the 1092 patients in the study, 135 had an infection at baseline, 251 developed infections during treatment, and 89 patients developed an infection after treatment. There was no association between pentoxifylline therapy and the risk of serious infection (P = .084), infection during treatment (P = .20), or infection after treatment (P = .27). Infections classified as serious were more frequent in patients treated with prednisolone (odds ratio [OR], 1.27; 95% confidence interval [CI], 1.27-2.92; P = .002). There was no association between prednisolone therapy and infection during treatment (OR, 1.04; 95% CI, 0.78-1.37; P = .80). However, a higher proportion (10%) of patients receiving prednisolone developed an infection after treatment than of patients not given prednisolone (6%) (OR, 1.70; 95% CI, 1.07-2.69; P = .024). Development of infection was associated with increased 90-day mortality in patients with SAH treated with prednisolone, independent of model for end-stage liver disease or Lille score (OR, 2.46; 95% CI, 1.41-4.30; P = .002). High circulating bDNA predicted infection that developed within 7 days of prednisolone therapy, independent of Model for End-Stage Liver Disease and white blood cell count (OR, 4.68; 95% CI, 1.80-12.17; P = .001). In patients who did not receive prednisolone, infection was not independently associated with 90-day mortality (OR, 0.94; 95% CI, 0.54-1.62; P = .82) or levels of bDNA (OR, 0.83; 95% CI, 0.39-1.75; P = .62). CONCLUSIONS Patients with SAH given prednisolone are at greater risk for developing serious infections and infections after treatment than patients not given prednisolone, which may offset its therapeutic benefit. Level of circulating bDNA before treatment could identify patients at high risk of infection if given prednisolone; these data could be used to select therapies for patients with SAH. EudraCT no: 2009-013897-42; Current Controlled Trials no: ISRCTN88782125.
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Affiliation(s)
| | - Stephen R. Atkinson
- Imperial College, London, United Kingdom,Reprint requests Address requests for reprints to: Stephen Atkinson, PhD, St Mary’s Hospital, Imperial College, London, W2 1NY, UK. fax: +4420 7724 9369.
| | | | | | | | | | | | - Steven Masson
- Freeman Hospital, The Newcastle Upon Tyne Hospitals, National Health Service Foundation Trust, Newcastle Upon Tyne, United Kingdom
| | - Anne McCune
- Bristol Royal Infirmary, Bristol, United Kingdom
| | | | - Paul Richardson
- Royal Liverpool University National Health Service Trust, Liverpool, United Kingdom
| | - Dermot Gleeson
- Sheffield Teaching Hospitals Foundation Trust, Sheffield, United Kingdom
| | - Stephen D. Ryder
- NIHR Biomedical Research Unit in Gastrointestinal and Liver Diseases at Nottingham University Hospitals National Health Service Trust and The University of Nottingham, Nottingham, United Kingdom
| | - Mark Wright
- Southampton University Hospital, Southampton, United Kingdom
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Abstract
BACKGROUND Microbial cultures for diagnosis of neonatal sepsis have low sensitivity and reporting delay. Advances in molecular microbiology have fostered new molecular assays that are rapid and may improve neonatal outcomes. OBJECTIVES To assess the diagnostic accuracy of various molecular methods for the diagnosis of culture-positive bacterial and fungal sepsis in neonates and to explore heterogeneity among studies by analyzing subgroups classified by gestational age and type of sepsis onset and compare molecular tests with one another. SEARCH METHODS We performed the systematic review as recommended by the Cochrane Diagnostic Test Accuracy Working Group. On 19 January 2016, we searched electronic bibliographic databases (the Cochrane Library, PubMed (from 1966), Embase (from 1982), and CINAHL (from 1982)), conference proceedings of the Pediatric Academic Societies annual conference (from 1990), clinical trial registries (ClinicalTrials.gov, International Standard Randomised Controlled Trial Number (ISRCTN) registry, and World Health Organization (WHO) International Clinical Trials Platform (ICTRP) Search portal), and Science Citation Index. We contacted experts in the field for studies. SELECTION CRITERIA We included studies that were prospective or retrospective, cohort or cross-sectional design, which evaluated molecular assays (index test) in neonates with suspected sepsis (participants) in comparison with microbial cultures (reference standard). DATA COLLECTION AND ANALYSIS Two review authors independently assessed the methodologic quality of the studies and extracted data. We performed meta-analyses using the bivariate and hierarchical summary receiver operating characteristic (HSROC) models and entered data into Review Manager 5. MAIN RESULTS Thirty-five studies were eligible for inclusion and the summary estimate of sensitivity was 0.90 (95% confidence interval (CI) 0.82 to 0.95) and of specificity was 0.93 (95% CI 0.89 to 0.96) (moderate quality evidence). We explored heterogeneity by subgroup analyses of type of test, gestational age, type of sepsis onset, and prevalence of sepsis and we did not find sufficient explanations for the heterogeneity (moderate to very low quality evidence). Sensitivity analyses by including studies that analyzed blood samples and by good methodology revealed similar results (moderate quality evidence). AUTHORS' CONCLUSIONS Molecular assays have the advantage of producing rapid results and may perform well as 'add-on' tests.
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Affiliation(s)
- Mohan Pammi
- Baylor College of MedicineSection of Neonatology, Department of Pediatrics6621, Fannin, MC.WT 6‐104HoustonTexasUSA77030
| | - Angela Flores
- Pediatrix Medical Group ‐ NW Houston Practice9250 Pinecroft St.The WoodlandsTexasUSA77380
| | - James Versalovic
- Texas Children’s Hospital and Baylor College of MedicinePathologyHoustonTexasUSA
| | - Mariska MG Leeflang
- Academic Medical Center, University of AmsterdamDepartment of Clinical Epidemiology, Biostatistics and BioinformaticsP.O. Box 22700AmsterdamNetherlands1100 DE
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Vitrenko Y, Kostenko I, Kulebyakina K, Duda A, Klunnyk M, Sorochynska K. Fetal Tissues Tested for Microbial Sterility by Culture- and PCR-Based Methods Can be Safely Used in Clinics. Cell Transplant 2016; 26:339-350. [PMID: 27501947 DOI: 10.3727/096368916x692735] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Cell preparations to be used in clinical practice must be free of infectious agents. Safety concerns are especially elevated upon the use of human fetal tissues, which are otherwise highly advantageous in cell therapy. We demonstrate that treating fetal samples with antibiotic, extensive washing, and homogenization prior to cryoconservation efficiently removes microbes in general. Screening a large collection by an automatic culture system showed that 89.2% fetal tissue samples were sterile, while contamination was detected in 10.8% samples. Liver and chorion were contaminated more than the brain, kidney, lung, and soft tissues. Broad-range PCR from the bacterial 16s rRNA gene was adopted as a confirmatory assay; however, the concordance between the culture-based and PCR assays was weak. Taxonomic identification was done for contaminated samples by bacteriological methods and sequencing 16s rRNA PCR products. The two approaches revealed different spectra of taxonomic groups sharing only Lactobacillus, the most frequently found genus. In addition, other representatives of vaginal microbiota were detected by culture-based identification, while PCR product sequencing has also revealed a subset of nosocomial microorganisms. Importantly, species known to cause sepsis were identified by both techniques, arguing for their indispensability and mutual complementarity. We suggest that most contaminations are taken up during collection of fetal material rather than originating from an in utero infection. In conclusion, a rigorous microbiological control by culture and PCR is a prerequisite for safe clinical use of fetal tissue suspensions.
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Targeted next-generation sequencing for the detection of ciprofloxacin resistance markers using molecular inversion probes. Sci Rep 2016; 6:25904. [PMID: 27174456 PMCID: PMC4865750 DOI: 10.1038/srep25904] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2015] [Accepted: 04/25/2016] [Indexed: 02/07/2023] Open
Abstract
Antibiotic resistance (AR) is an epidemic of increasing magnitude requiring rapid identification and profiling for appropriate and timely therapeutic measures and containment strategies. In this context, ciprofloxacin is part of the first-line of countermeasures against numerous high consequence bacteria. Significant resistance can occur via single nucleotide polymorphisms (SNP) and deletions within ciprofloxacin targeted genes. Ideally, use of ciprofloxacin would be prefaced with AR determination to avoid overuse or misuse of the antibiotic. Here, we describe the development and evaluation of a panel of 44 single-stranded molecular inversion probes (MIPs) coupled to next-generation sequencing (NGS) for the detection of genetic variants known to confer ciprofloxacin resistance in Bacillus anthracis, Yersinia pestis, and Francisella tularensis. Sequencing results demonstrate MIPs capture and amplify targeted regions of interest at significant levels of coverage. Depending on the genetic variant, limits of detection (LOD) for high-throughput pooled sequencing ranged from approximately 300–1800 input genome copies. LODs increased 10-fold in the presence of contaminating human genome DNA. In addition, we show that MIPs can be used as an enrichment step with high resolution melt (HRM) real-time PCR which is a sensitive assay with a rapid time-to-answer. Overall, this technology is a multiplexable upfront enrichment applicable with multiple downstream molecular assays for the detection of targeted genetic regions.
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Park KS, Huang CH, Lee K, Yoo YE, Castro CM, Weissleder R, Lee H. Rapid identification of health care-associated infections with an integrated fluorescence anisotropy system. SCIENCE ADVANCES 2016; 2:e1600300. [PMID: 28861468 PMCID: PMC5565941 DOI: 10.1126/sciadv.1600300] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/12/2016] [Accepted: 04/06/2016] [Indexed: 05/21/2023]
Abstract
Health care-associated infections (HAIs) and drug-resistant pathogens have become a major health care issue with millions of reported cases every year. Advanced diagnostics would allow clinicians to more quickly determine the most effective treatment, reduce the nonspecific use of broad-spectrum antimicrobials, and facilitate enrollment in new antibiotic treatments. We present a new integrated system, polarization anisotropy diagnostics (PAD), for rapid detection of HAI pathogens. The PAD uses changes of fluorescence anisotropy when detection probes recognize target bacterial nucleic acids. The technology is inherently robust against environmental noise and economically scalable for parallel measurements. The assay is fast (2 hours) and performed on-site in a single-tube format. When applied to clinical samples obtained from interventional procedures, the PAD determined the overall bacterial burden, differentiated HAI bacterial species, and identified drug resistance and virulence status. The PAD system holds promise as a powerful tool for near-patient, rapid HAI testing.
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Affiliation(s)
- Ki Soo Park
- Center for Systems Biology, Massachusetts General
Hospital and Harvard Medical School, Boston, MA 02114, USA
- Department of Radiology, Harvard Medical School, Boston,
MA 02114, USA
| | - Chen-Han Huang
- Center for Systems Biology, Massachusetts General
Hospital and Harvard Medical School, Boston, MA 02114, USA
- Department of Radiology, Harvard Medical School, Boston,
MA 02114, USA
| | - Kyungheon Lee
- Center for Systems Biology, Massachusetts General
Hospital and Harvard Medical School, Boston, MA 02114, USA
- Department of Radiology, Harvard Medical School, Boston,
MA 02114, USA
| | - Yeong-Eun Yoo
- Department of Nanomanufacturing Technology, Korea
Institute of Machinery and Materials, Daejeon 305-343, Korea
| | - Cesar M. Castro
- Center for Systems Biology, Massachusetts General
Hospital and Harvard Medical School, Boston, MA 02114, USA
- Department of Medicine, Harvard Medical School, Boston,
MA 02114, USA
| | - Ralph Weissleder
- Center for Systems Biology, Massachusetts General
Hospital and Harvard Medical School, Boston, MA 02114, USA
- Department of Radiology, Harvard Medical School, Boston,
MA 02114, USA
- Department of Systems Biology, Harvard Medical School,
Boston, MA 02115, USA
- Corresponding author.
(R.W.);
(H.L.)
| | - Hakho Lee
- Center for Systems Biology, Massachusetts General
Hospital and Harvard Medical School, Boston, MA 02114, USA
- Department of Radiology, Harvard Medical School, Boston,
MA 02114, USA
- Corresponding author.
(R.W.);
(H.L.)
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Gupta MD, Kaur H, Ray P, Gautam V, Puri GD. Ribosomal RNA-based panbacterial polymerase chain reaction for rapid diagnosis of septicaemia in Intensive Care Unit patients. Indian J Med Microbiol 2016; 34:219-21. [PMID: 27080778 DOI: 10.4103/0255-0857.180351] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Abstract
Early diagnosis and treatment of sepsis by appropriate antibiotics is of utmost importance. Therefore, we evaluated 16S rRNA panbacterial polymerase chain reaction (PCR) for rapid diagnosis of sepsis in 49 adult patients in Intensive Care Units (ICUs) and compared it with an automated blood culture. 8 ml of 10 ml blood collected was inoculated into BACTEC® aerobic bottle and the remaining 2 ml was used for DNA extraction and PCR. 109 of 115 (93%) episodes of suspected sepsis showed concordant results between automated culture and PCR. Six episodes were positive by PCR only. Panbacterial PCR reduces turnaround time with rapid differentiation between systemic inflammatory response syndrome and sepsis.
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Affiliation(s)
| | | | | | - Vikas Gautam
- Department of Medical Microbiology, Postgraduate Institute of Medical Education and Research, Chandigarh, India
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Scharf VF, Lewis DD, Wellehan JF, Wamsley HL, Richardson R. Comparison of synovial fluid culture and 16S rRNA PCR in dogs with suspected septic arthritis. Aust Vet J 2016; 93:204-7. [PMID: 26010926 DOI: 10.1111/avj.12329] [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] [Received: 05/14/2014] [Revised: 09/15/2014] [Accepted: 09/28/2014] [Indexed: 11/29/2022]
Abstract
OBJECTIVE To prospectively compare the sensitivity and specificity of 16S rRNA PCR with culture for identifying the causative organism in synovial fluid obtained from dogs with suspected septic arthritis. METHODS Synovial fluid cytology, PCR analysis and aerobic, anaerobic and Mycoplasma culture of samples from the affected joints of 18 dogs presenting with suspected septic arthritis were performed. Synovial fluid samples from the corresponding contralateral joints of 7 dogs were also analysed as negative controls. RESULTS There was no significant difference between the sensitivity of bacterial detection via culture (63.2%) versus PCR (73.7%) of synovial fluid (P=0.728) or between culture and combined PCR and culture (89.5%) of synovial fluid (P=0.124). The specificity of PCR (42.9%) was significantly lower than culture specificity (100%) (P=0.07). CONCLUSION Although 16S PCR may hold potential as an ancillary diagnostic test for identifying the causative organism in dogs with septic arthritis, our study failed to demonstrate improved accuracy compared with traditional synovial fluid culture.
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Affiliation(s)
- V F Scharf
- Department of Small Animal Clinical Sciences, College of Veterinary Medicine, University of Florida, Gainesville, Florida, USA
| | - D D Lewis
- Department of Small Animal Clinical Sciences, College of Veterinary Medicine, University of Florida, Gainesville, Florida, USA
| | - J F Wellehan
- Department of Small Animal Clinical Sciences, College of Veterinary Medicine, University of Florida, Gainesville, Florida, USA
| | - H L Wamsley
- Department of Physiologic Sciences, College of Veterinary Medicine, University of Florida, Gainesville, Florida, USA
| | - R Richardson
- Department of Small Animal Clinical Sciences, College of Veterinary Medicine, University of Florida, Gainesville, Florida, USA
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Buehler SS, Madison B, Snyder SR, Derzon JH, Cornish NE, Saubolle MA, Weissfeld AS, Weinstein MP, Liebow EB, Wolk DM. Effectiveness of Practices To Increase Timeliness of Providing Targeted Therapy for Inpatients with Bloodstream Infections: a Laboratory Medicine Best Practices Systematic Review and Meta-analysis. Clin Microbiol Rev 2016; 29:59-103. [PMID: 26598385 PMCID: PMC4771213 DOI: 10.1128/cmr.00053-14] [Citation(s) in RCA: 177] [Impact Index Per Article: 22.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
BACKGROUND Bloodstream infection (BSI) is a major cause of morbidity and mortality throughout the world. Rapid identification of bloodstream pathogens is a laboratory practice that supports strategies for rapid transition to direct targeted therapy by providing for timely and effective patient care. In fact, the more rapidly that appropriate antimicrobials are prescribed, the lower the mortality for patients with sepsis. Rapid identification methods may have multiple positive impacts on patient outcomes, including reductions in mortality, morbidity, hospital lengths of stay, and antibiotic use. In addition, the strategy can reduce the cost of care for patients with BSIs. OBJECTIVES The purpose of this review is to evaluate the evidence for the effectiveness of three rapid diagnostic practices in decreasing the time to targeted therapy for hospitalized patients with BSIs. The review was performed by applying the Centers for Disease Control and Prevention's (CDC's) Laboratory Medicine Best Practices Initiative (LMBP) systematic review methods for quality improvement (QI) practices and translating the results into evidence-based guidance (R. H. Christenson et al., Clin Chem 57:816-825, 2011, http://dx.doi.org/10.1373/clinchem.2010.157131). SEARCH STRATEGY A comprehensive literature search was conducted to identify studies with measurable outcomes. A search of three electronic bibliographic databases (PubMed, Embase, and CINAHL), databases containing "gray" literature (unpublished academic, government, or industry evidence not governed by commercial publishing) (CIHI, NIHR, SIGN, and other databases), and the Cochrane database for English-language articles published between 1990 and 2011 was conducted in July 2011. DATES OF SEARCH The dates of our search were from 1990 to July 2011. SELECTION CRITERIA Animal studies and non-English publications were excluded. The search contained the following medical subject headings: bacteremia; bloodstream infection; time factors; health care costs; length of stay; morbidity; mortality; antimicrobial therapy; rapid molecular techniques, polymerase chain reaction (PCR); in situ hybridization, fluorescence; treatment outcome; drug therapy; patient care team; pharmacy service, hospital; hospital information systems; Gram stain; pharmacy service; and spectrometry, mass, matrix-assisted laser desorption-ionization. Phenotypic as well as the following key words were searched: targeted therapy; rapid identification; rapid; Gram positive; Gram negative; reduce(ed); cost(s); pneumoslide; PBP2; tube coagulase; matrix-assisted laser desorption/ionization time of flight; MALDI TOF; blood culture; EMR; electronic reporting; call to provider; collaboration; pharmacy; laboratory; bacteria; yeast; ICU; and others. In addition to the electronic search being performed, a request for unpublished quality improvement data was made to the clinical laboratory community. MAIN RESULTS Rapid molecular testing with direct communication significantly improves timeliness compared to standard testing. Rapid phenotypic techniques with direct communication likely improve the timeliness of targeted therapy. Studies show a significant and homogeneous reduction in mortality associated with rapid molecular testing combined with direct communication. AUTHORS' CONCLUSIONS No recommendation is made for or against the use of the three assessed practices of this review due to insufficient evidence. The overall strength of evidence is suggestive; the data suggest that each of these three practices has the potential to improve the time required to initiate targeted therapy and possibly improve other patient outcomes, such as mortality. The meta-analysis results suggest that the implementation of any of the three practices may be more effective at increasing timeliness to targeted therapy than routine microbiology techniques for identification of the microorganisms causing BSIs. Based on the included studies, results for all three practices appear applicable across multiple microorganisms, including methicillin-resistant Staphylococcus aureus (MRSA), methicillin-sensitive S. aureus (MSSA), Candida species, and Enterococcus species.
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Affiliation(s)
| | - Bereneice Madison
- Battelle Center for Analytics and Public Health, Atlanta, Georgia, USA
| | - Susan R Snyder
- Battelle Center for Analytics and Public Health, Atlanta, Georgia, USA
| | - James H Derzon
- Battelle Center for Analytics and Public Health, Atlanta, Georgia, USA
| | - Nancy E Cornish
- Centers for Disease Control and Prevention, Center for Surveillance, Epidemiology and Laboratory Services (CSELS), Atlanta, Georgia, USA
| | - Michael A Saubolle
- Banner Good Samaritan Medical Center, Banner Health, Phoenix, Arizona, USA, and University of Arizona College of Medicine, Phoenix, and University of Arizona College of Medicine, Tucson, Arizona, USA
| | | | - Melvin P Weinstein
- Rutgers Robert Wood Johnson Medical School, New Brunswick, New Jersey, USA
| | - Edward B Liebow
- Battelle Center for Analytics and Public Health, Atlanta, Georgia, USA
| | - Donna M Wolk
- Geisinger Health System, Danville, Pennsylvania, USA
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Poon DCH, Ho YS, You R, Tse HL, Chiu K, Chang RCC. PKR deficiency alters E. coli-induced sickness behaviors but does not exacerbate neuroimmune responses or bacterial load. J Neuroinflammation 2015; 12:212. [PMID: 26585788 PMCID: PMC4653925 DOI: 10.1186/s12974-015-0433-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2015] [Accepted: 11/14/2015] [Indexed: 11/15/2022] Open
Abstract
Background Systemic inflammation induces neuroimmune activation, ultimately leading to sickness (e.g., fever, anorexia, motor impairments, exploratory deficits, and social withdrawal). In this study, we evaluated the role of protein kinase R (PKR), a serine-threonine kinase that can control systemic inflammation, on neuroimmune responses and sickness. Methods Wild-type (WT) PKR+/+ mice and PKR−/− mice were subcutaneously injected with live Escherichia coli (E. coli) or vehicle. Food consumption, rotarod test performance, burrowing, open field activity, object investigation, and social interaction were monitored. Plasma TNF-α and corticosterone were measured by ELISA. The percentage of neutrophils in blood was deduced from blood smears. Inflammatory gene expression (IL-1β, TNF-α, IL-6, cyclooxygenase (COX)-2, iNOS) in the liver and the brain (hypothalamus and hippocampus) were quantified by real-time PCR. Blood and lavage fluid (injection site) were collected for microbiological plate count and for real-time PCR of bacterial 16S ribosomal DNA (rDNA). Corticotrophin-releasing hormone (CRH) expression in the hypothalamus was also determined by real-time PCR. Results Deficiency of PKR diminished peripheral inflammatory responses following E. coli challenge. However, while the core components of sickness (anorexia and motor impairments) were similar between both strains of mice, the behavioral components of sickness (reduced burrowing, exploratory activity deficits, and social withdrawal) were only observable in PKR−/− mice but not in WT mice. Such alteration of behavioral components was unlikely to be caused by exaggerated neuroimmune activation, by an impaired host defense to the infection, or due to a dysregulated corticosterone response, because both strains of mice displayed similar neuroimmune responses, bacterial titers, and plasma corticosterone profiles throughout the course of infection. Nevertheless, the induction of hypothalamic corticotrophin-releasing hormone (CRH) by E. coli was delayed in PKR−/− mice relative to WT mice, suggesting that PKR deficiency may postpone the CRH response during systemic inflammation. Conclusions Taken together, our findings show that (1) loss of PKR could alter E. coli-induced sickness behaviors and (2) this was unlikely to be due to exacerbated neuroimmune activation, (3) elevated bacterial load, or (4) dysregulation in the corticosterone response. Further studies can address the role of PKR in the CRH response together with its consequence on sickness.
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Affiliation(s)
- David Chun-Hei Poon
- Laboratory of Neurodegenerative Diseases, School of Biomedical Sciences, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China.
| | - Yuen-Shan Ho
- School of Nursing, Faculty of Health and Social Sciences, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong SAR, China.
| | - Ran You
- Laboratory of Neurodegenerative Diseases, School of Biomedical Sciences, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China.
| | - Hei-Long Tse
- Laboratory of Neurodegenerative Diseases, School of Biomedical Sciences, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China.
| | - Kin Chiu
- Department of Ophthalmology, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China.
| | - Raymond Chuen-Chung Chang
- Laboratory of Neurodegenerative Diseases, School of Biomedical Sciences, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China. .,Research Centre of Heart, Brain, Hormone and Healthy Aging, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China. .,State Key Laboratory of Brain and Cognitive Sciences, The University of Hong Kong, Hong Kong SAR, China. .,Rm. L1-49, Laboratory Block, Faculty of Medicine Building, 21 Sassoon Road, Pokfulam, Hong Kong SAR, China.
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Direct Screening of Blood by PCR and Pyrosequencing for a 16S rRNA Gene Target from Emergency Department and Intensive Care Unit Patients Being Evaluated for Bloodstream Infection. J Clin Microbiol 2015; 54:99-105. [PMID: 26511737 DOI: 10.1128/jcm.02394-15] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2015] [Accepted: 10/22/2015] [Indexed: 11/20/2022] Open
Abstract
Here we compared the results of PCR/pyrosequencing to those of culture for detecting bacteria directly from blood. DNA was extracted from 1,130 blood samples from 913 patients suspected of bacteremia (enrollment criteria were physician-ordered blood culture and complete blood count [CBC]), and 102 controls (healthy blood donors). Real-time PCR assays for beta-globin and Universal 16S rRNA gene targets were performed on all 1,232 extracts. Specimens identified by Universal 16S rRNA gene PCR/pyrosequencing as containing staphylococci, streptococci, or enteric Gram-negative rods had target-specific PCR/pyrosequencing performed. Amplifiable beta-globin (melting temperature [Tm], 87.2°C ± 0.2°C) occurred in 99.1% (1,120/1,130) of patient extracts and 100% (102/102) of controls. Concordance between PCR/pyrosequencing and culture was 96.9% (1,085/1,120) for Universal 16S rRNA gene targets, with positivity rates of 9.4% (105/1,120) and 11.3% (126/1,120), respectively. Bacteria cultured included staphylococci (59/126, 46.8%), Gram-negative rods (34/126, 27%), streptococci (32/126, 25.4%), and a Gram-positive rod (1/126, 0.8%). All controls screened negative by PCR/pyrosequencing. Clinical performance characteristics (95% confidence interval [CI]) for Universal 16S rRNA gene PCR/pyrosequencing included sensitivity of 77.8% (69.5 to 84.7), specificity of 99.3% (98.6 to 99.7), positive predictive value (PPV) of 93.3% (86.8 to 97.3), and negative predictive value (NPV) of 97.2% (96.0 to 98.2). Bacteria were accurately identified in 77.8% (98/126) of culture-confirmed sepsis samples with Universal 16S PCR/pyrosequencing and in 76.4% (96/126) with follow-up target-specific PCR/pyrosequencing. The initial PCR/pyrosequencing took ∼5.5 h to complete or ∼7.5 h when including target-specific PCR/pyrosequencing compared to 27.9 ± 13.6 h for Gram stain or 81.6 ± 24.0 h for phenotypic identification. In summary, this molecular approach detected the causative bacteria in over three-quarters of all culture-confirmed cases of bacteremia directly from blood in significantly less time than standard culture but cannot be used to rule out infection.
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Real-time polymerase chain reaction and culture in the diagnosis of invasive group B streptococcal disease in infants: a retrospective study. Eur J Clin Microbiol Infect Dis 2015; 34:2413-20. [PMID: 26433745 DOI: 10.1007/s10096-015-2496-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2015] [Accepted: 09/21/2015] [Indexed: 12/12/2022]
Abstract
Group B streptococcus (GBS) is a leading cause of invasive disease in infants. Accurate and rapid diagnosis is crucial to reduce morbidity and mortality. Real-time polymerase chain reaction (PCR) targeting the dltR gene was utilised for the direct detection of GBS DNA in blood and cerebrospinal fluid (CSF) from infants at an Irish maternity hospital. A retrospective review of laboratory and patient records during the period 2011-2013 was performed in order to evaluate PCR and culture for the diagnosis of invasive GBS disease. A total of 3570 blood and 189 CSF samples from 3510 infants had corresponding culture and PCR results. Culture and PCR exhibited concordance in 3526 GBS-negative samples and 13 (25%) GBS-positive samples (n = 53). Six (11%) and 34 (64%) GBS-positive samples were positive only in culture or PCR, respectively. Culture and PCR identified more GBS-positive infants (n = 47) than PCR (n = 43) or culture (n = 16) alone. Using culture as the reference standard, the sensitivity, specificity, and positive and negative predictive values for PCR on blood samples were 71.4%, 99.2%, 25% and 99.9%, and for CSF samples, they were 60%, 97.8%, 42.9% and 98.9%, respectively. The sensitivity and positive predictive values were improved (blood: 84.6% and 55%; CSF: 77.8% and 100%, respectively) when maternal risk factors and other laboratory test results were considered. The findings in this study recommend the use of direct GBS real-time PCR for the diagnosis of GBS infection in infants with a clinical suspicion of invasive disease and as a complement to culture, but should be interpreted in the light of other laboratory and clinical findings.
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Su G, Fu Z, Hu L, Wang Y, Zhao Z, Yang W. 16S Ribosomal Ribonucleic Acid Gene Polymerase Chain Reaction in the Diagnosis of Bloodstream Infections: A Systematic Review and Meta-Analysis. PLoS One 2015; 10:e0127195. [PMID: 25996771 PMCID: PMC4440735 DOI: 10.1371/journal.pone.0127195] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2015] [Accepted: 04/12/2015] [Indexed: 01/08/2023] Open
Abstract
Objective We aim to evaluate the accuracy of the 16S ribosomal ribonucleic acid (rRNA) gene polymerase chain reaction (PCR) test in the diagnosis of bloodstream infections through a systematic review and meta-analysis. Methods A computerized literature search was conducted to identify studies that assessed the diagnostic value of 16S rRNA gene PCR test for bloodstream infections. Study quality was assessed using the revised Quality Assessment of Diagnostic Accuracy Studies (QUADAS-2) tool. We calculated the sensitivity, specificity, positive likelihood ratio (PLR), negative likelihood ratio (NLR), diagnostic odds ratio (DOR) and their 95% confidence intervals (95% CI) for each study. Summary receiver operating characteristic (SROC) curve was used to summarize overall test performance. Statistical analysis was performed in Meta-DiSc 1.4 and Stata/SE 12.0 software. Results Twenty-eight studies were included in our meta-analysis. Using random-effect model analysis, the pooled sensitivity, specificity, PLR, NLR, and DOR were 0.87 (95% CI, 0.85–0.89), 0.94 (95% CI, 0.93–0.95), 12.65 (95% CI, 8.04–19.90), 0.14 (95% CI, 0.08–0.24), and 116.76 (95% CI, 52.02–262.05), respectively. The SROC curve indicated that the area under the curve (AUC) was 0.9690 and the maximum joint sensitivity and specificity (Q*) was 0.9183. In addition, heterogeneity was statistically significant but was not caused by the threshold effect. Conclusion Existing data suggest that 16S rRNA gene PCR test is a practical tool for the rapid screening of sepsis. Further prospective studies are needed to assess the diagnostic value of PCR amplification and DNA microarray hybridization of 16S rRNA gene in the future.
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Affiliation(s)
- Guoming Su
- Guangdong Provincial Key Laboratory of Medical Molecular Diagnostics, Guangdong Medical College, Dongguan, China
| | - Zhuqing Fu
- Department of Microbiology and Immunology, Guangdong Medical College, Zhanjiang, China
| | - Liren Hu
- Department of Epidemiology and Health Statistics, School of Public Health, Guangdong Medical College, Zhanjiang, China
| | - Yueying Wang
- Guangdong Provincial Key Laboratory of Medical Molecular Diagnostics, Guangdong Medical College, Dongguan, China
| | - Zuguo Zhao
- Department of Microbiology and Immunology, Guangdong Medical College, Zhanjiang, China
| | - Weiqing Yang
- Guangdong Provincial Key Laboratory of Medical Molecular Diagnostics, Guangdong Medical College, Dongguan, China
- * E-mail:
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Tokel O, Yildiz UH, Inci F, Durmus NG, Ekiz OO, Turker B, Cetin C, Rao S, Sridhar K, Natarajan N, Shafiee H, Dana A, Demirci U. Portable microfluidic integrated plasmonic platform for pathogen detection. Sci Rep 2015; 5:9152. [PMID: 25801042 PMCID: PMC4371189 DOI: 10.1038/srep09152] [Citation(s) in RCA: 106] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2013] [Accepted: 01/26/2015] [Indexed: 01/22/2023] Open
Abstract
Timely detection of infectious agents is critical in early diagnosis and treatment of infectious diseases. Conventional pathogen detection methods, such as enzyme linked immunosorbent assay (ELISA), culturing or polymerase chain reaction (PCR) require long assay times, and complex and expensive instruments, which are not adaptable to point-of-care (POC) needs at resource-constrained as well as primary care settings. Therefore, there is an unmet need to develop simple, rapid, and accurate methods for detection of pathogens at the POC. Here, we present a portable, multiplex, inexpensive microfluidic-integrated surface plasmon resonance (SPR) platform that detects and quantifies bacteria, i.e., Escherichia coli (E. coli) and Staphylococcus aureus (S. aureus) rapidly. The platform presented reliable capture and detection of E. coli at concentrations ranging from ~10(5) to 3.2 × 10(7) CFUs/mL in phosphate buffered saline (PBS) and peritoneal dialysis (PD) fluid. The multiplexing and specificity capability of the platform was also tested with S. aureus samples. The presented platform technology could potentially be applicable to capture and detect other pathogens at the POC and primary care settings.
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Affiliation(s)
- Onur Tokel
- Demirci Bio-Acoustic-MEMS in Medicine (BAMM) Laboratory, Center for Biomedical Engineering, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Umit Hakan Yildiz
- Demirci Bio-Acoustic-MEMS in Medicine (BAMM) Laboratory, Stanford University School of Medicine, Canary Center at Stanford for Cancer Early Detection, Palo Alto, CA, USA
| | - Fatih Inci
- Demirci Bio-Acoustic-MEMS in Medicine (BAMM) Laboratory, Stanford University School of Medicine, Canary Center at Stanford for Cancer Early Detection, Palo Alto, CA, USA
| | - Naside Gozde Durmus
- Department of Biochemistry, Stanford School of Medicine, Stanford, CA, USA
- Stanford Genome Technology Center, Stanford University, Palo Alto, CA, USA
| | - Okan Oner Ekiz
- UNAM Institute of Materials Science and Nanotechnology, Bilkent University, 06800 Ankara, Turkey
| | - Burak Turker
- UNAM Institute of Materials Science and Nanotechnology, Bilkent University, 06800 Ankara, Turkey
| | - Can Cetin
- Demirci Bio-Acoustic-MEMS in Medicine (BAMM) Laboratory, Center for Biomedical Engineering, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Shruthi Rao
- Demirci Bio-Acoustic-MEMS in Medicine (BAMM) Laboratory, Center for Biomedical Engineering, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Kaushik Sridhar
- Demirci Bio-Acoustic-MEMS in Medicine (BAMM) Laboratory, Center for Biomedical Engineering, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Nalini Natarajan
- Demirci Bio-Acoustic-MEMS in Medicine (BAMM) Laboratory, Center for Biomedical Engineering, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Hadi Shafiee
- Demirci Bio-Acoustic-MEMS in Medicine (BAMM) Laboratory, Center for Biomedical Engineering, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Aykutlu Dana
- UNAM Institute of Materials Science and Nanotechnology, Bilkent University, 06800 Ankara, Turkey
| | - Utkan Demirci
- Demirci Bio-Acoustic-MEMS in Medicine (BAMM) Laboratory, Center for Biomedical Engineering, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
- Demirci Bio-Acoustic-MEMS in Medicine (BAMM) Laboratory, Stanford University School of Medicine, Canary Center at Stanford for Cancer Early Detection, Palo Alto, CA, USA
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Evaluation of real-time PCR and pyrosequencing for screening incubating blood culture bottles from adults with suspected bloodstream infection. Diagn Microbiol Infect Dis 2014; 81:158-62. [PMID: 25534615 DOI: 10.1016/j.diagmicrobio.2014.11.014] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2014] [Revised: 11/05/2014] [Accepted: 11/24/2014] [Indexed: 11/24/2022]
Abstract
Several molecular platforms can identify bacteria associated with bloodstream infections but require positive culture bottles as starting material. Here, we describe results of screening 1140 blood cultures at 8h postinoculation, from 918 eligible adults being evaluated for bloodstream infection. DNA was extracted and analyzed by 16S and/or 23S rRNA real-time PCR/pyrosequencing. Compared to culture, PCR/pyrosequencing displayed 90.9% sensitivity, 99.6% specificity, 95.7% positive predictive value, and 99.1% negative predictive value. Overall concordance rate was 98.9% (1127/1140). In 4 cases with molecular-positive/culture-negative results, medical chart reviews provided evidence of identical bacteria from subsequent blood or concomitant urine/sputum cultures. Nine culture-positive/molecular-negative cases were associated with either polymicrobial growth, grew only in the anaerobic bottle of the clinical pair, and/or were detected by PCR/pyrosequencing after 8h. In summary, this approach accurately detected and identified bacteria in ~91% of culture-confirmed cases significantly sooner than the phenotypic identification was available, having the potential to improve antibiotic stewardship.
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Park SD, Lee G, Wang HY, Park M, Kim S, Kim H, Kim J, Kim YK, Kim HY, Lee H, Uh Y, Kim JB. Evaluation of PCR-reverse blot hybridization assay, REBA Sepsis-ID test, for simultaneous identification of bacterial pathogens and mecA and van genes from blood culture bottles. Ann Lab Med 2014; 34:446-55. [PMID: 25368820 PMCID: PMC4215418 DOI: 10.3343/alm.2014.34.6.446] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2014] [Revised: 04/13/2014] [Accepted: 08/27/2014] [Indexed: 11/19/2022] Open
Abstract
Background The aim of this study was to evaluate a newly developed PCR-based reverse blot hybridization assay (PCR-REBA), REBA Sepsis-ID (M&D, Wonju, Korea), to rapidly detect the presence of bacteremia and antimicrobial resistance gene in blood culture samples. Methods One thousand four hundred consecutive blood culture samples from patients with a delta neutrophil index greater than 2.7% were selected from March to July in 2013. Three hundred positive and 1,100 negative for bacterial growth in blood culture bottles samples were tested by conventional and real-time PCR-REBA, respectively. Results The overall agreement between the conventional identification test and the REBA Sepsis-ID test was 95.3% (286/300). Agreement for gram-positive bacteria, gram-negative bacteria, fungi, and polymicrobials was 94.5% (190/201), 97.3% (71/73), 100% (14/14), and 91.7% (11/12), respectively. The detection rate of the mecA gene from methicillin-resistant Staphylococcus isolates was 97.8% (90/92). The vanA gene was detected in one blood culture sample from which vancomycin-resistant Enterococcus was isolated. When the cycle threshold for real-time PCR was defined as 30.0, 2.4% (26/1,100) of negative blood culture samples tested positive by real-time PCR. Conclusions The REBA Sepsis-ID test is capable of simultaneously and quickly detecting both causative agents and antimicrobial resistance genes, such as mecA and van, in blood culture positive samples.
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Affiliation(s)
- Soon Deok Park
- Department of Laboratory Medicine, Yonsei University Wonju College of Medicine, Wonju, Korea
| | - Gyusang Lee
- Department of Biomedical Laboratory Science, College of Health Sciences, Yonsei University, Wonju, Korea
| | - Hye-Young Wang
- M&D, Inc., Wonju Eco Environmental Technology Center, Wonju, Korea
| | - Min Park
- Department of Biomedical Laboratory Science, College of Health Sciences, Yonsei University, Wonju, Korea
| | - Sunghyun Kim
- Department of Biomedical Laboratory Science, College of Health Sciences, Yonsei University, Wonju, Korea
| | - Hyunjung Kim
- Department of Biomedical Laboratory Science, College of Health Sciences, Yonsei University, Wonju, Korea
| | - Jungho Kim
- Department of Biomedical Laboratory Science, College of Health Sciences, Yonsei University, Wonju, Korea
| | - Young Keun Kim
- Department of Internal Medicine, Yonsei University Wonju College of Medicine, Wonju, Korea
| | - Hyo Youl Kim
- Department of Internal Medicine, Yonsei University Wonju College of Medicine, Wonju, Korea
| | - Hyeyoung Lee
- Department of Biomedical Laboratory Science, College of Health Sciences, Yonsei University, Wonju, Korea
| | - Young Uh
- Department of Laboratory Medicine, Yonsei University Wonju College of Medicine, Wonju, Korea
| | - Jong Bae Kim
- Department of Biomedical Laboratory Science, College of Health Sciences, Yonsei University, Wonju, Korea
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Weng SL, Chiu CM, Lin FM, Huang WC, Liang C, Yang T, Yang TL, Liu CY, Wu WY, Chang YA, Chang TH, Huang HD. Bacterial communities in semen from men of infertile couples: metagenomic sequencing reveals relationships of seminal microbiota to semen quality. PLoS One 2014; 9:e110152. [PMID: 25340531 PMCID: PMC4207690 DOI: 10.1371/journal.pone.0110152] [Citation(s) in RCA: 156] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2014] [Accepted: 08/21/2014] [Indexed: 12/12/2022] Open
Abstract
Some previous studies have identified bacteria in semen as being a potential factor in male infertility. However, only few types of bacteria were taken into consideration while using PCR-based or culturing methods. Here we present an analysis approach using next-generation sequencing technology and bioinformatics analysis to investigate the associations between bacterial communities and semen quality. Ninety-six semen samples collected were examined for bacterial communities, measuring seven clinical criteria for semen quality (semen volume, sperm concentration, motility, Kruger's strict morphology, antisperm antibody (IgA), Atypical, and leukocytes). Computer-assisted semen analysis (CASA) was also performed. Results showed that the most abundant genera among all samples were Lactobacillus (19.9%), Pseudomonas (9.85%), Prevotella (8.51%) and Gardnerella (4.21%). The proportion of Lactobacillus and Gardnerella was significantly higher in the normal samples, while that of Prevotella was significantly higher in the low quality samples. Unsupervised clustering analysis demonstrated that the seminal bacterial communities were clustered into three main groups: Lactobacillus, Pseudomonas, and Prevotella predominant group. Remarkably, most normal samples (80.6%) were clustered in Lactobacillus predominant group. The analysis results showed seminal bacteria community types were highly associated with semen health. Lactobacillus might not only be a potential probiotic for semen quality maintenance, but also might be helpful in countering the negative influence of Prevotella and Pseudomonas. In this study, we investigated whole seminal bacterial communities and provided the most comprehensive analysis of the association between bacterial community and semen quality. The study significantly contributes to the current understanding of the etiology of male fertility.
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Affiliation(s)
- Shun-Long Weng
- Institute of Bioinformatics and Systems Biology, National Chiao Tung University, Hsinchu, Taiwan
- Department of Biological Science and Technology, National Chiao Tung University, Hsinchu, Taiwan
- Department of Obstetrics and Gynecology, Hsinchu Mackay Memorial Hospital, Hsinchu, Taiwan
- Mackay Junior College of Medicine, Nursing and Management, Taipei, Taiwan
- Department of Medicine, Mackay Medical College, New Taipei City, Taiwan
| | - Chih-Min Chiu
- Institute of Bioinformatics and Systems Biology, National Chiao Tung University, Hsinchu, Taiwan
| | - Feng-Mao Lin
- Institute of Bioinformatics and Systems Biology, National Chiao Tung University, Hsinchu, Taiwan
| | - Wei-Chih Huang
- Institute of Bioinformatics and Systems Biology, National Chiao Tung University, Hsinchu, Taiwan
| | - Chao Liang
- Institute of Bioinformatics and Systems Biology, National Chiao Tung University, Hsinchu, Taiwan
| | - Ting Yang
- Institute of Bioinformatics and Systems Biology, National Chiao Tung University, Hsinchu, Taiwan
| | - Tzu-Ling Yang
- Institute of Bioinformatics and Systems Biology, National Chiao Tung University, Hsinchu, Taiwan
| | - Chia-Yu Liu
- Institute of Bioinformatics and Systems Biology, National Chiao Tung University, Hsinchu, Taiwan
| | - Wei-Yun Wu
- Institute of Bioinformatics and Systems Biology, National Chiao Tung University, Hsinchu, Taiwan
| | - Yi-An Chang
- Institute of Bioinformatics and Systems Biology, National Chiao Tung University, Hsinchu, Taiwan
- Health GeneTech Corporation, Taoyuan, Taiwan
| | - Tzu-Hao Chang
- Graduate Institute of Biomedical Informatics, Taipei Medical University, Taipei, Taiwan
| | - Hsien-Da Huang
- Institute of Bioinformatics and Systems Biology, National Chiao Tung University, Hsinchu, Taiwan
- Department of Biological Science and Technology, National Chiao Tung University, Hsinchu, Taiwan
- Department of Biomedical Science and Environmental Biology, Kaohsiung Medical University, Kaohsiung, Taiwan
- Center for Bioinformatics Research, National Chiao Tung University, HsinChu, Taiwan
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45
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Bhandari V. Effective Biomarkers for Diagnosis of Neonatal Sepsis. J Pediatric Infect Dis Soc 2014; 3:234-45. [PMID: 26625387 DOI: 10.1093/jpids/piu063] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/21/2014] [Accepted: 05/22/2014] [Indexed: 01/05/2023]
Abstract
Infection in neonates continues to be a global problem with significant morbidity and mortality. The diagnosis of neonatal sepsis is complicated by nonspecific clinical symptomatology, a high-false negative rate, and a delay in obtaining blood culture results. An ideal biomarker needs to have a high degree of accuracy in recognizing the presence or absence of definite infection at an early stage, to guide the initiation and duration of antibiotic therapy. The diagnostic utility of the following biomarkers seems to be most practical in the early (interleukin [IL]-6, IL-8, tumor necrosis factor-alpha, neutrophil CD64), mid (procalcitonin) and late (C-reactive protein) phases of neonatal sepsis. Future research studies to assess reliability of these biomarkers should be (1) adequately powered for sample size and (2) use the gold-standard definition of blood-culture proven pathogen-specific sepsis. Significant advances in diagnostic accuracy of novel biomarkers to allow early, accurate, and cost-effective identification of pathogens responsible for neonatal sepsis is anticipated in the next 5 years.
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Affiliation(s)
- Vineet Bhandari
- Division of Perinatal Medicine, Department of Pediatrics, Yale University School of Medicine, New Haven, Connecticut
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46
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van den Brand M, Peters RPH, Catsburg A, Rubenjan A, Broeke FJ, van den Dungen FAM, van Weissenbruch MM, van Furth AM, Kõressaar T, Remm M, Savelkoul PHM, Bos MP. Development of a multiplex real-time PCR assay for the rapid diagnosis of neonatal late onset sepsis. J Microbiol Methods 2014; 106:8-15. [PMID: 25102109 DOI: 10.1016/j.mimet.2014.07.034] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2014] [Revised: 07/25/2014] [Accepted: 07/25/2014] [Indexed: 01/20/2023]
Abstract
The diagnosis of late onset sepsis (LOS), a severe condition with high prevalence in preterm infants, is hampered by the suboptimal sensitivity and long turnaround time of blood culture. Detection of the infecting pathogen directly in blood by PCR would provide a much more timely result. Unfortunately, PCR-based assays reported so far are labor intensive and often lack direct species identification. Therefore we developed a real-time multiplex PCR assay tailored to LOS diagnosis which is easy-to-use, is applicable on small blood volumes and provides species-specific results within 4h. Species-specific PCR assays were selected from literature or developed using bioinformatic tools for the detection of the most prevalent etiologic pathogens: Enterococcus faecalis, Staphylococcus aureus, Staphylococcus spp., Streptococcus agalactiae, Escherichia coli, Pseudomonas aeruginosa, Klebsiella spp. and Serratia marcescens. The PCR assays showed 100% specificity, full coverage of the target pathogens and a limit of detection (LOD) of ≤10CFUeq./reaction. These LOD values were maintained in the multiplex format or when bacterial DNA was isolated from blood. Clinical evaluation showed high concordance between the multiplex PCR and blood culture. In conclusion, we developed a multiplex PCR that allows the direct detection of the most important bacterial pathogens causing LOS in preterm infants.
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Affiliation(s)
- Marre van den Brand
- Department of Medical Microbiology and Infection Control, VU University Medical Center, De Boelelaan 1118, 1081HZ Amsterdam, The Netherlands.
| | - Remco P H Peters
- Department of Medical Microbiology, Maastricht University Medical Centre, P. Debyelaan 25, 6229HX Maastricht, The Netherlands.
| | - Arnold Catsburg
- Microbiome, Troubadoursborgh 59, 3992BE Houten, The Netherlands.
| | - Anna Rubenjan
- Department of Medical Microbiology and Infection Control, VU University Medical Center, De Boelelaan 1118, 1081HZ Amsterdam, The Netherlands.
| | - Ferdi J Broeke
- Department of Medical Microbiology and Infection Control, VU University Medical Center, De Boelelaan 1118, 1081HZ Amsterdam, The Netherlands.
| | - Frank A M van den Dungen
- Department of Pediatrics, VU University Medical Center, De Boelelaan 1118, 1081HZ Amsterdam, The Netherlands.
| | - Mirjam M van Weissenbruch
- Department of Pediatrics, VU University Medical Center, De Boelelaan 1118, 1081HZ Amsterdam, The Netherlands.
| | - A Marceline van Furth
- Department of Pediatrics, VU University Medical Center, De Boelelaan 1118, 1081HZ Amsterdam, The Netherlands.
| | - Triinu Kõressaar
- Department of Bioinformatics, University of Tartu, Ülikooli 18, 50090 Tartu, Estonia.
| | - Maido Remm
- Department of Bioinformatics, University of Tartu, Ülikooli 18, 50090 Tartu, Estonia.
| | - Paul H M Savelkoul
- Department of Medical Microbiology and Infection Control, VU University Medical Center, De Boelelaan 1118, 1081HZ Amsterdam, The Netherlands; Department of Medical Microbiology, Maastricht University Medical Centre, P. Debyelaan 25, 6229HX Maastricht, The Netherlands; Microbiome, Troubadoursborgh 59, 3992BE Houten, The Netherlands.
| | - Martine P Bos
- Microbiome, Troubadoursborgh 59, 3992BE Houten, The Netherlands.
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Song Y, Giske CG, Gille-Johnson P, Emanuelsson O, Lundeberg J, Gyarmati P. Nuclease-assisted suppression of human DNA background in sepsis. PLoS One 2014; 9:e103610. [PMID: 25076135 PMCID: PMC4116218 DOI: 10.1371/journal.pone.0103610] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2014] [Accepted: 06/29/2014] [Indexed: 11/18/2022] Open
Abstract
Sepsis is a severe medical condition characterized by a systemic inflammatory response of the body caused by pathogenic microorganisms in the bloodstream. Blood or plasma is typically used for diagnosis, both containing large amount of human DNA, greatly exceeding the DNA of microbial origin. In order to enrich bacterial DNA, we applied the C0t effect to reduce human DNA background: a model system was set up with human and Escherichia coli (E. coli) DNA to mimic the conditions of bloodstream infections; and this system was adapted to plasma and blood samples from septic patients. As a consequence of the C0t effect, abundant DNA hybridizes faster than rare DNA. Following denaturation and re-hybridization, the amount of abundant DNA can be decreased with the application of double strand specific nucleases, leaving the non-hybridized rare DNA intact. Our experiments show that human DNA concentration can be reduced approximately 100,000-fold without affecting the E. coli DNA concentration in a model system with similarly sized amplicons. With clinical samples, the human DNA background was decreased 100-fold, as bacterial genomes are approximately 1,000-fold smaller compared to the human genome. According to our results, background suppression can be a valuable tool to enrich rare DNA in clinical samples where a high amount of background DNA can be found.
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Affiliation(s)
- Yajing Song
- Royal Institute of Technology, Science for Life Laboratory, Stockholm, Sweden
| | - Christian G. Giske
- Karolinska Institutet, Department of Microbiology, Tumor and Cell Biology, Stockholm, Sweden
- Karolinska University Hospital, Department of Clinical Microbiology, Stockholm, Sweden
| | - Patrik Gille-Johnson
- Division of Infectious Diseases, Department of Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Olof Emanuelsson
- Royal Institute of Technology, Science for Life Laboratory, Stockholm, Sweden
| | - Joakim Lundeberg
- Royal Institute of Technology, Science for Life Laboratory, Stockholm, Sweden
| | - Peter Gyarmati
- Royal Institute of Technology, Science for Life Laboratory, Stockholm, Sweden
- Karolinska Institutet, Department of Microbiology, Tumor and Cell Biology, Stockholm, Sweden
- Karolinska University Hospital, Department of Clinical Microbiology, Stockholm, Sweden
- * E-mail:
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48
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Emonet S, Schrenzel J, Martinez de Tejada B. Molecular-based screening for perinatal group B streptococcal infection: implications for prevention and therapy. Mol Diagn Ther 2014; 17:355-61. [PMID: 23832874 DOI: 10.1007/s40291-013-0047-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Group B streptococci (GBS) are a leading cause of infectious neonatal morbidity and mortality. Timely and accurate identification of colonized pregnant women is imperative to implement intrapartum antibioprophylaxis (IAP) to reduce the risk of early neonatal sepsis. Current guidelines recommend screening for GBS carriage with vaginal-rectal cultures. However, cultures require 24-72 h, thus precluding their use for intrapartum screening and these are only performed at 35-37 weeks gestation. New rapid molecular-based tests can detect GBS within hours. They have the potential to be used intrapartum and to allow for selective IAP in women carrying GBS. An advantage is that they can sometimes be performed by non-laboratory staff in the labor suite, thus avoiding delays in sample transfers to the microbiology laboratory. Another possible use of molecular-based assays is for the diagnosis of neonatal sepsis, where tests with a short turnaround time and high sensitivity and specificity are crucial. In this situation, the detection of microorganisms once antibiotic therapy has already been started is important, as treatment is started immediately once sepsis is suspected without waiting for microbiological confirmation. In this article, we discuss the state-of-the-art molecular-based tests available for GBS screening during pregnancy, as well as their implications for IAP for the diagnosis and prevention of neonatal sepsis.
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Affiliation(s)
- Stéphane Emonet
- Department of Genetics and Laboratory Medicine, University Hospitals of Geneva and Faculty of Medicine, Geneva, Switzerland
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49
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Abstract
Early-onset sepsis remains a common and serious problem for neonates, especially preterm infants. Group B streptococcus (GBS) is the most common etiologic agent, while Escherichia coli is the most common cause of mortality. Current efforts toward maternal intrapartum antimicrobial prophylaxis have significantly reduced the rates of GBS disease but have been associated with increased rates of Gram-negative infections, especially among very-low-birth-weight infants. The diagnosis of neonatal sepsis is based on a combination of clinical presentation; the use of nonspecific markers, including C-reactive protein and procalcitonin (where available); blood cultures; and the use of molecular methods, including PCR. Cytokines, including interleukin 6 (IL-6), interleukin 8 (IL-8), gamma interferon (IFN-γ), and tumor necrosis factor alpha (TNF-α), and cell surface antigens, including soluble intercellular adhesion molecule (sICAM) and CD64, are also being increasingly examined for use as nonspecific screening measures for neonatal sepsis. Viruses, in particular enteroviruses, parechoviruses, and herpes simplex virus (HSV), should be considered in the differential diagnosis. Empirical treatment should be based on local patterns of antimicrobial resistance but typically consists of the use of ampicillin and gentamicin, or ampicillin and cefotaxime if meningitis is suspected, until the etiologic agent has been identified. Current research is focused primarily on development of vaccines against GBS.
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50
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Sun Z, Peng Y, Zhang M, Wang K, Bai J, Li X, Ning B, Gao Z. Simultaneous and highly sensitive detection of six different foodborne pathogens by high-throughput suspension array technology. Food Control 2014. [DOI: 10.1016/j.foodcont.2013.11.028] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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