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Li Y, Zhao L, Wang J, Qi P, Yang Z, Zou X, Peng F, Li S. A new application of multiplex PCR combined with membrane biochip assay for rapid detection of 9 common pathogens in sepsis. PeerJ 2023; 11:e15325. [PMID: 37197582 PMCID: PMC10184654 DOI: 10.7717/peerj.15325] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Accepted: 04/10/2023] [Indexed: 05/19/2023] Open
Abstract
Rapid and accurate identification of specific sepsis pathogens is critical for patient treatment and disease control. This study aimed to establish a new application for the rapid identification of common pathogens in patients with suspected sepsis and evaluate its role in clinical application. A multiplex PCR assay was designed to simultaneously amplify specific conserved regions of nine common pathogenic microorganisms in sepsis, including Acinetobacter baumannii, Escherichia coli, Klebsiella pneumonia, Pseudomonas aeruginosa, Enterococcus faecalis, Staphylococcus aureus, Staphylococcus epidermidis, Streptococcus pneumonia, and Candida albicans. The PCR products were analyzed by a membrane biochip. The analytical sensitivity of the assay was determined at a range of 5-100 copies/reaction for each standard strain, and the detection range was 20-200 cfu/reaction in a series dilution of simulated clinical samples at different concentrations. Out of the 179 clinical samples, the positive rate for pathogens detected by the membrane biochip assay and blood culture method was 20.11% (36/179) and 18.44% (33/179), respectively. However, by comparing the positive rate of the nine common pathogens we detected, the membrane biochip assay tended to be more sensitive than the blood culture method (20.11% vs 15.64%). The clinical sensitivity, specificity, positive predictive value (PPV), and negative predictive value (NPV) of the membrane biochip assay were 92.9%, 93.2%, 72.2% and 98.6%, respectively. Generally, this multiplex PCR combined membrane biochip assay can be used to detect major sepsis pathogens, and is useful for early initiation of effective antimicrobial treatment, and is feasible for sepsis pathogens identification in routine clinical practice.
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Affiliation(s)
- Yun Li
- School of Basic Medical Sciences, Weifang Medical University, Weifang, China
| | - LuJie Zhao
- School of Basic Medical Sciences, Weifang Medical University, Weifang, China
| | - Jingye Wang
- Department of Pathology, Weifang Maternal and Child Health Care Hospital, Weifang, China
| | - Peipei Qi
- The Third Department of Neurology Weifang People’s Hospital, Weifang, China
| | - Zhongfa Yang
- School of Basic Medical Sciences, Weifang Medical University, Weifang, China
| | - Xiangyu Zou
- School of Basic Medical Sciences, Weifang Medical University, Weifang, China
| | - Fujun Peng
- School of Basic Medical Sciences, Weifang Medical University, Weifang, China
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2
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Pan Y, Fan Q. Clostridium Symbiosum Sepsis Diagnosed Using Next-Generation Sequencing in a 2 Year Old Child: A Case Report. Fetal Pediatr Pathol 2022; 42:518-521. [PMID: 36541613 DOI: 10.1080/15513815.2022.2158696] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Background: Sepsis is a severe illness that can affect preterm, term, and young infants, and is often associated with negative cultures.Case report: A 2-year-old boy, with a previous partial colectomy after birth, presented with abdominal complaints and clinical sepsis. We empirically treated with meropenem and linezolid. Blood cultures were sterile, and fecal cultures demonstrated no pathogenes. Metagenomic next-generation sequencing identified Clostridium symbiosum from blood sample. The result supported the continued use of the antibiotic regimen. After 1 week, CRP and PCT returned to normal and subsequent de-escalation therapy (cefotaxime sodium sulbactam and metronidazole) was used for anaerobic bacteria. Conclusions: mNGS identified an anaerobic agent responsible for sepsis. From the published sensitivities, the organism was sensitive to the original empiric antibiotic therapy.
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Affiliation(s)
- Yan Pan
- Department of Pediatrics, the First Affiliated Hospital of Yangtze University, Jingzhou, China
| | - Qihong Fan
- Department of Pediatrics, the First Affiliated Hospital of Yangtze University, Jingzhou, China
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3
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Costa SP, Nogueira CL, Cunha AP, Lisac A, Carvalho CM. Potential of bacteriophage proteins as recognition molecules for pathogen detection. Crit Rev Biotechnol 2022:1-18. [PMID: 35848817 DOI: 10.1080/07388551.2022.2071671] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
Bacterial pathogens are leading causes of infections with high mortality worldwide having a great impact on healthcare systems and the food industry. Gold standard methods for bacterial detection mainly rely on culture-based technologies and biochemical tests which are laborious and time-consuming. Regardless of several developments in existing methods, the goal of achieving high sensitivity and specificity, as well as a low detection limit, remains unaccomplished. In past years, various biorecognition elements, such as antibodies, enzymes, aptamers, or nucleic acids, have been widely used, being crucial for the pathogens detection in different complex matrices. However, these molecules are usually associated with high detection limits, demand laborious and costly production, and usually present cross-reactivity. (Bacterio)phage-encoded proteins, especially the receptor binding proteins (RBPs) and cell-wall binding domains (CBDs) of endolysins, are responsible for the phage binding to the bacterial surface receptors in different stages of the phage lytic cycle. Due to their remarkable properties, such as high specificity, sensitivity, stability, and ability to be easily engineered, they are appointed as excellent candidates to replace conventional recognition molecules, thereby contributing to the improvement of the detection methods. Moreover, they offer several possibilities of application in a variety of detection systems, such as magnetic, optical, and electrochemical. Herein we provide a review of phage-derived bacterial binding proteins, namely the RBPs and CBDs, with the prospect to be employed as recognition elements for bacteria. Moreover, we summarize and discuss the various existing methods based on these proteins for the detection of nosocomial and foodborne pathogens.
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Affiliation(s)
- Susana P Costa
- Centre of Biological Engineering, University of Minho, Braga, Portugal.,International Iberian Nanotechnology Laboratory, Braga, Portugal.,Instituto de Engenharia de Sistemas e Computadores-Microsistemas e Nanotecnologias (INESC MN), IN-Institute of Nanoscience and Nanotechnolnology, Lisbon, Portugal
| | - Catarina L Nogueira
- International Iberian Nanotechnology Laboratory, Braga, Portugal.,Instituto de Engenharia de Sistemas e Computadores-Microsistemas e Nanotecnologias (INESC MN), IN-Institute of Nanoscience and Nanotechnolnology, Lisbon, Portugal
| | - Alexandra P Cunha
- Centre of Biological Engineering, University of Minho, Braga, Portugal.,International Iberian Nanotechnology Laboratory, Braga, Portugal
| | - Ana Lisac
- Faculty of Chemistry and Chemical Technology, University of Ljubljana, Ljubljana, Slovenia
| | - Carla M Carvalho
- International Iberian Nanotechnology Laboratory, Braga, Portugal
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4
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Costa SP, Carvalho CM. Burden of bacterial bloodstream infections and recent advances for diagnosis. Pathog Dis 2022; 80:6631550. [PMID: 35790126 DOI: 10.1093/femspd/ftac027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Revised: 06/07/2022] [Accepted: 07/01/2022] [Indexed: 11/13/2022] Open
Abstract
Bloodstream infections (BSIs) and subsequent organ dysfunction (sepsis and septic shock) are conditions that rank among the top reasons for human mortality and have a great impact on healthcare systems. Their treatment mainly relies on the administration of broad-spectrum antimicrobials since the standard blood culture-based diagnostic methods remain time-consuming for the pathogen's identification. Consequently, the routine use of these antibiotics may lead to downstream antimicrobial resistance and failure in treatment outcomes. Recently, significant advances have been made in improving several methodologies for the identification of pathogens directly in whole blood especially regarding specificity and time to detection. Nevertheless, for the widespread implementation of these novel methods in healthcare facilities, further improvements are still needed concerning the sensitivity and cost-effectiveness to allow a faster and more appropriate antimicrobial therapy. This review is focused on the problem of BSIs and sepsis addressing several aspects like their origin, challenges, and causative agents. Also, it highlights current and emerging diagnostics technologies, discussing their strengths and weaknesses.
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Affiliation(s)
- Susana P Costa
- Centre of Biological Engineering, University of Minho, Campus de Gualtar, 4710-057, Braga, Portugal.,LABBELS - Associate Laboratory, Braga/Guimarães, Portugal.,International Iberian Nanotechnology Laboratory, Av. Mestre José Veiga s/n, 4715-330, Braga, Portugal.,Instituto de Engenharia de Sistemas e Computadores - Microsistemas e Nanotecnologias (INESC MN) and IN - Institute of Nanoscience and Nanotechnology, Rua Alves Redol, 9 1000-029 Lisbon, Portugal
| | - Carla M Carvalho
- International Iberian Nanotechnology Laboratory, Av. Mestre José Veiga s/n, 4715-330, Braga, Portugal
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5
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Costa SP, Cunha AP, Freitas PP, Carvalho CM. A Phage Receptor-Binding Protein as a Promising Tool for the Detection of Escherichia coli in Human Specimens. Front Microbiol 2022; 13:871855. [PMID: 35722298 PMCID: PMC9202026 DOI: 10.3389/fmicb.2022.871855] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Accepted: 04/26/2022] [Indexed: 02/03/2023] Open
Abstract
Escherichia coli is a problematic pathogen that causes life-threatening diseases, being a frequent causative agent of several nosocomial infections such as urinary tract and bloodstream infections. Proper and rapid bacterial identification is critical for allowing prompt and targeted antimicrobial therapy. (Bacterio)phage receptor-binding proteins (RBPs) display high specificity for bacterial surface epitopes and, therefore, are particularly attractive as biorecognition elements, potentially conferring high sensitivity and specificity in bacterial detection. In this study, we elucidated, for the first time, the potential of a recombinant RBP (Gp17) to recognize E. coli at different viability states, such as viable but not culturable cells, which are not detected by conventional techniques. Moreover, by using a diagnostic method in which we combined magnetic and spectrofluorimetric approaches, we demonstrated the ability of Gp17 to specifically detect E. coli in various human specimens (e.g., whole blood, feces, urine, and saliva) in about 1.5 h, without requiring complex sample processing.
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Affiliation(s)
- Susana P Costa
- Centre of Biological Engineering, University of Minho, Braga, Portugal.,LABBELS -Associate Laboratory, Braga/Guimarães, Portugal.,International Iberian Nanotechnology Laboratory, Braga, Portugal.,Instituto de Engenharia de Sistemas e Computadores - Microsistemas e Nanotecnologias and IN - Institute of Nanoscience and Nanotechnology, Lisbon, Portugal
| | - Alexandra P Cunha
- Centre of Biological Engineering, University of Minho, Braga, Portugal.,LABBELS -Associate Laboratory, Braga/Guimarães, Portugal.,International Iberian Nanotechnology Laboratory, Braga, Portugal
| | - Paulo P Freitas
- International Iberian Nanotechnology Laboratory, Braga, Portugal.,Instituto de Engenharia de Sistemas e Computadores - Microsistemas e Nanotecnologias and IN - Institute of Nanoscience and Nanotechnology, Lisbon, Portugal
| | - Carla M Carvalho
- International Iberian Nanotechnology Laboratory, Braga, Portugal
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6
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Shin J, Shin S, Jung SH, Park C, Cho SY, Lee DG, Chung YJ. Duplex dPCR System for Rapid Identification of Gram-Negative Pathogens in the Blood of Patients with Bloodstream Infection: A Culture-Independent Approach. J Microbiol Biotechnol 2021; 31:1481-1489. [PMID: 34528911 PMCID: PMC9705831 DOI: 10.4014/jmb.2103.03044] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Revised: 08/17/2021] [Accepted: 09/09/2021] [Indexed: 12/15/2022]
Abstract
Early and accurate detection of pathogens is important to improve clinical outcomes of bloodstream infections (BSI), especially in the case of drug-resistant pathogens. In this study, we aimed to develop a culture-independent digital PCR (dPCR) system for multiplex detection of major sepsiscausing gram-negative pathogens and antimicrobial resistance genes using plasma DNA from BSI patients. Our duplex dPCR system successfully detected nine targets (five bacteria-specific targets and four antimicrobial resistance genes) through five reactions within 3 hours. The minimum detection limit was 50 ag of bacterial DNA, suggesting that 1 CFU/ml of bacteria in the blood can be detected. To validate the clinical applicability, cell-free DNA samples from febrile patients were tested with our system and confirmed high consistency with conventional blood culture. This system can support early identification of some drug-resistant gram-negative pathogens, which can help improving treatment outcomes of BSI.
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Affiliation(s)
- Juyoun Shin
- Department of Microbiology, The Catholic University of Korea, College of Medicine, Seoul 06591, Republic of Korea
| | - Sun Shin
- Precision Medicine Research Center, Integrated Research Center for Genome Polymorphism, The Catholic University of Korea, College of Medicine, Seoul 06591, Republic of Korea
| | - Seung-Hyun Jung
- Department of Biochemistry, The Catholic University of Korea, College of Medicine, Seoul 06591, Republic of Korea
| | - Chulmin Park
- Vaccine Bio Research Institute, The Catholic University of Korea, College of Medicine, Seoul St. Mary’s Hospital, Seoul 06591, Republic of Korea
| | - Sung-Yeon Cho
- Vaccine Bio Research Institute, The Catholic University of Korea, College of Medicine, Seoul St. Mary’s Hospital, Seoul 06591, Republic of Korea,Department of Internal Medicine, The Catholic University of Korea, College of Medicine, Seoul St. Mary’s Hospital, Seoul 06591, Republic of Korea
| | - Dong-Gun Lee
- Vaccine Bio Research Institute, The Catholic University of Korea, College of Medicine, Seoul St. Mary’s Hospital, Seoul 06591, Republic of Korea,Department of Internal Medicine, The Catholic University of Korea, College of Medicine, Seoul St. Mary’s Hospital, Seoul 06591, Republic of Korea
| | - Yeun-Jun Chung
- Department of Microbiology, The Catholic University of Korea, College of Medicine, Seoul 06591, Republic of Korea,Precision Medicine Research Center, Integrated Research Center for Genome Polymorphism, The Catholic University of Korea, College of Medicine, Seoul 06591, Republic of Korea,Corresponding author Phone: +82-2-2258-7343 Fax: +82-2-537-0572 E-mail:
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7
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Tourelle KM, Boutin S, Weigand MA, Schmitt FCF. Sepsis and the Human Microbiome. Just Another Kind of Organ Failure? A Review. J Clin Med 2021; 10:jcm10214831. [PMID: 34768350 PMCID: PMC8585089 DOI: 10.3390/jcm10214831] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2021] [Revised: 10/17/2021] [Accepted: 10/18/2021] [Indexed: 01/05/2023] Open
Abstract
Next-generation sequencing (NGS) has been further optimised during the last years and has given us new insights into the human microbiome. The 16S rDNA sequencing, especially, is a cheap, fast, and reliable method that can reveal significantly more microorganisms compared to culture-based diagnostics. It might be a useful method for patients suffering from severe sepsis and at risk of organ failure because early detection and differentiation between healthy and harmful microorganisms are essential for effective therapy. In particular, the gut and lung microbiome in critically ill patients have been probed by NGS. For this review, an iterative approach was used. Current data suggest that an altered microbiome with a decreased alpha-diversity compared to healthy individuals could negatively influence the individual patient’s outcome. In the future, NGS may not only contribute to the diagnosis of complications. Patients at risk could also be identified before surgery or even during their stay in an intensive care unit. Unfortunately, there is still a lack of knowledge to make precise statements about what constitutes a healthy microbiome, which patients exactly have an increased perioperative risk, and what could be a possible therapy to strengthen the microbiome. This work is an iterative review that presents the current state of knowledge in this field.
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Affiliation(s)
- Kevin M. Tourelle
- Department of Anesthesiology, Heidelberg University Hospital, 420, Im Neuenheimer Feld, 69120 Heidelberg, Germany; (K.M.T.); (M.A.W.)
| | - Sebastien Boutin
- Department of Infectious Disease, Medical Microbiology and Hygiene, University Hospital, 324, Im Neuenheimer Feld, 69120 Heidelberg, Germany;
| | - Markus A. Weigand
- Department of Anesthesiology, Heidelberg University Hospital, 420, Im Neuenheimer Feld, 69120 Heidelberg, Germany; (K.M.T.); (M.A.W.)
| | - Felix C. F. Schmitt
- Department of Anesthesiology, Heidelberg University Hospital, 420, Im Neuenheimer Feld, 69120 Heidelberg, Germany; (K.M.T.); (M.A.W.)
- Correspondence:
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Kondori N, Kurtovic A, Piñeiro-Iglesias B, Salvà-Serra F, Jaén-Luchoro D, Andersson B, Alves G, Ogurtsov A, Thorsell A, Fuchs J, Tunovic T, Kamenska N, Karlsson A, Yu YK, Moore ERB, Karlsson R. Mass Spectrometry Proteotyping-Based Detection and Identification of Staphylococcus aureus, Escherichia coli, and Candida albicans in Blood. Front Cell Infect Microbiol 2021; 11:634215. [PMID: 34381737 PMCID: PMC8350517 DOI: 10.3389/fcimb.2021.634215] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2020] [Accepted: 07/09/2021] [Indexed: 12/12/2022] Open
Abstract
Bloodstream infections (BSIs), the presence of microorganisms in blood, are potentially serious conditions that can quickly develop into sepsis and life-threatening situations. When assessing proper treatment, rapid diagnosis is the key; besides clinical judgement performed by attending physicians, supporting microbiological tests typically are performed, often requiring microbial isolation and culturing steps, which increases the time required for confirming positive cases of BSI. The additional waiting time forces physicians to prescribe broad-spectrum antibiotics and empirically based treatments, before determining the precise cause of the disease. Thus, alternative and more rapid cultivation-independent methods are needed to improve clinical diagnostics, supporting prompt and accurate treatment and reducing the development of antibiotic resistance. In this study, a culture-independent workflow for pathogen detection and identification in blood samples was developed, using peptide biomarkers and applying bottom-up proteomics analyses, i.e., so-called "proteotyping". To demonstrate the feasibility of detection of blood infectious pathogens, using proteotyping, Escherichia coli and Staphylococcus aureus were included in the study, as the most prominent bacterial causes of bacteremia and sepsis, as well as Candida albicans, one of the most prominent causes of fungemia. Model systems including spiked negative blood samples, as well as positive blood cultures, without further culturing steps, were investigated. Furthermore, an experiment designed to determine the incubation time needed for correct identification of the infectious pathogens in blood cultures was performed. The results for the spiked negative blood samples showed that proteotyping was 100- to 1,000-fold more sensitive, in comparison with the MALDI-TOF MS-based approach. Furthermore, in the analyses of ten positive blood cultures each of E. coli and S. aureus, both the MALDI-TOF MS-based and proteotyping approaches were successful in the identification of E. coli, although only proteotyping could identify S. aureus correctly in all samples. Compared with the MALDI-TOF MS-based approaches, shotgun proteotyping demonstrated higher sensitivity and accuracy, and required significantly shorter incubation time before detection and identification of the correct pathogen could be accomplished.
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Affiliation(s)
- Nahid Kondori
- Department of Infectious Diseases, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
- Department of Clinical Microbiology, Sahlgrenska University Hospital, Gothenburg, Sweden
| | - Amra Kurtovic
- Department of Clinical Microbiology, Sahlgrenska University Hospital, Gothenburg, Sweden
| | | | - Francisco Salvà-Serra
- Department of Infectious Diseases, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
- Department of Clinical Microbiology, Sahlgrenska University Hospital, Gothenburg, Sweden
- Culture Collection University of Gothenburg (CCUG), Sahlgrenska Academy of the University of Gothenburg, Gothenburg, Sweden
- Microbiology, Department of Biology, University of the Balearic Islands, Palma de Mallorca, Spain
| | - Daniel Jaén-Luchoro
- Department of Infectious Diseases, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
- Culture Collection University of Gothenburg (CCUG), Sahlgrenska Academy of the University of Gothenburg, Gothenburg, Sweden
| | - Björn Andersson
- Bioinformatics Core Facility at Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Gelio Alves
- National Center for Biotechnology Information (NCBI), Bethesda, MD, United States
| | - Aleksey Ogurtsov
- National Center for Biotechnology Information (NCBI), Bethesda, MD, United States
| | - Annika Thorsell
- Proteomics Core Facility at Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Johannes Fuchs
- Proteomics Core Facility at Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Timur Tunovic
- Department of Clinical Microbiology, Sahlgrenska University Hospital, Gothenburg, Sweden
| | - Nina Kamenska
- Norra-Älvsborgs-Länssjukhus (NÄL), Trollhättan, Sweden
| | | | - Yi-Kuo Yu
- National Center for Biotechnology Information (NCBI), Bethesda, MD, United States
| | - Edward R. B. Moore
- Department of Infectious Diseases, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
- Department of Clinical Microbiology, Sahlgrenska University Hospital, Gothenburg, Sweden
- Culture Collection University of Gothenburg (CCUG), Sahlgrenska Academy of the University of Gothenburg, Gothenburg, Sweden
| | - Roger Karlsson
- Department of Infectious Diseases, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
- Department of Clinical Microbiology, Sahlgrenska University Hospital, Gothenburg, Sweden
- Nanoxis Consulting AB, Gothenburg, Sweden
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Schmoch T, Westhoff JH, Decker SO, Skarabis A, Hoffmann GF, Dohna-Schwake C, Felderhoff-Müser U, Skolik C, Feisst M, Klose C, Bruckner T, Luntz S, Weigand MA, Sohn K, Brenner T. Next-generation sequencing diagnostics of bacteremia in pediatric sepsis. Medicine (Baltimore) 2021; 100:e26403. [PMID: 34160425 PMCID: PMC8238315 DOI: 10.1097/md.0000000000026403] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Accepted: 06/03/2021] [Indexed: 01/04/2023] Open
Abstract
INTRODUCTION Sepsis and septic shock are the most severe forms of infection affecting predominantly elderly people, preterm and term neonates, and young infants. Even in high-income countries sepsis causes about 8% of admissions to pediatric intensive care units (PICUs). Early diagnosis, rapid anti-infective treatment, and prompt hemodynamic stabilization are crucial for patient survival. In this context, it is essential to identify the causative pathogen as soon as possible to optimize antimicrobial treatment. To date, culture-based diagnostic procedures (e.g., blood cultures) represent the standard of care. However, they have 2 major problems: on the one hand, in the case of very small sample volumes (and thus usually in children), they are not sufficiently sensitive. On the other hand, with a time-to-result of 2 to 5 days, blood cultures need a relatively long time for the anti-infective therapy to be calculated. To overcome these problems, culture-independent molecular diagnostic procedures such as unbiased sequence analysis of circulating cell-free DNA (cfDNA) from plasma samples of septic patients by next-generation sequencing (NGS) have been tested successfully in adult septic patients. However, these results still need to be transferred to the pediatric setting. METHODS The Next GeneSiPS-Trial is a prospective, observational, non-interventional, multicenter study used to assess the diagnostic performance of an NGS-based approach for the identification of causative pathogens in (preterm and term) neonates (d1-d28, n = 50), infants (d29 to <1 yr, n = 50), and toddlers (1 yr to <5 yr, n = 50) with suspected or proven severe sepsis or septic shock (according to the pediatric sepsis definition) by the use of the quantitative sepsis indicating quantifier (SIQ) score in comparison to standard of care (culture-based) microbiological diagnostics. Potential changes in anti-infective treatment regimens based on these NGS results will be estimated retrospectively by a panel of 3 independent clinical specialists. DISCUSSION Neonates, infants, and young children are significantly affected by sepsis. Fast and more sensitive diagnostic approaches are urgently needed. This prospective, observational, non-interventional, multicenter study seeks to evaluate an NGS-based approach in critically ill children suffering from sepsis. TRIAL REGISTRATION DRKS-ID: DRKS00015705 (registered October 24, 2018). https://www.drks.de/drks_web/navigate.do?navigationId=trial.HTML&TRIAL_ID=DRKS00015705.
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Affiliation(s)
- Thomas Schmoch
- Department of Anesthesiology and Intensive Care Medicine, University Hospital Essen, University Duisburg-Essen, Essen
- Department of Anesthesiology, Heidelberg University Hospital
| | - Jens H. Westhoff
- Department of Pediatrics I, University Children's Hospital Heidelberg, Heidelberg
| | | | - Annabell Skarabis
- Department of Anesthesiology and Intensive Care Medicine, University Hospital Essen, University Duisburg-Essen, Essen
| | - Georg F. Hoffmann
- Department of Pediatrics I, University Children's Hospital Heidelberg, Heidelberg
| | - Christian Dohna-Schwake
- Department of Pediatrics I, Neonatology, Pediatric Intensive Care, Pediatric Neurology, University Hospital Essen, University Duisburg-Essen, Essen
| | - Ursula Felderhoff-Müser
- Department of Pediatrics I, Neonatology, Pediatric Intensive Care, Pediatric Neurology, University Hospital Essen, University Duisburg-Essen, Essen
| | | | - Manuel Feisst
- Institute of Medical Biometry, University of Heidelberg
| | | | | | - Steffen Luntz
- Coordination Centre for Clinical Trials (KKS), Ruprecht-Karls-University, Heidelberg
| | | | - Kai Sohn
- Fraunhofer Institute for Interfacial Engineering and Biotechnology, Stuttgart, Germany
| | - Thorsten Brenner
- Department of Anesthesiology and Intensive Care Medicine, University Hospital Essen, University Duisburg-Essen, Essen
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10
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Saikh KU, Ranji CM, Ulrich RG, Corea E, De Silva AD, Natesan M. An increase in p62/NBR1 levels in melioidosis patients of Sri Lanka exhibit a characteristic of potential host biomarker. J Med Microbiol 2020; 69:1240-1248. [PMID: 32815800 PMCID: PMC7660894 DOI: 10.1099/jmm.0.001242] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2020] [Accepted: 07/23/2020] [Indexed: 12/18/2022] Open
Abstract
Introduction. Melioidosis, caused by Burkholderia pseudomallei, in endemic areas, poses a challenge for treating the diseased populations without accurate diagnosis, and the disease-specific biomarkers linked with the infection have yet to be reported. Due to the invasive nature of the causative agent, Burkholderia pseudomallei, host innate effector mechanisms, including autophagy are known to be activated, resulting in differential expression of cellular proteins and immune markers. Identification of a disease-specific biomarker associated with B. pseudomallei infection will be helpful to facilitate rapid confirmation of melioidosis, which would enable early treatment and therapeutic success.Aim. We aimed to assess the levels of a host autophagy component, p62/NBR1, which function as a cargo-receptor in the process of autophagy activation leading to the degradation of ubiquitin-coated intracellular bacteria in which p62/NBR1 itself is degraded in the clearance of the pathogen. We further probed the extent of intracellular p62/NBR1 degradation and assessed its potential as a melioidosis biomarker.Methodology. We analysed peripheral blood mononuclear cell (PBMC) lysates using an ELISA-based assay for detecting cytosolic autophagy-related proteins p62/NBR1. We measured p62/NBR1 levels in diseased (confirmed B. pseudomallei infection) and non -diseased populations and utilized receiver operating characteristic (ROC) curve and max Youden index analysis for evaluating potential disease biomarker characteristics.Results. Our results revealed a three to fivefold increase in p62/NBR1 levels confirmed melioidosis cases compared to uninfected healthy donors. Comparable to p62/NBR1, levels of cytosolic LC3-I levels also increased, whereas the levels of degraded membrane bound form LC3-II was low, suggesting autophagy deficiency. Proinflammatory serum cytokine response, particularly IL-6, was consistently higher alongside B. pseudomallei infection in comparison to healthy controls.Conclusions. ROC curve and max Youden index analysis suggest that increased p62/NBR1 levels in diseased populations display characteristics of a potential disease biomarker in melioidosis and illustrates that an elevated p62/NBR1 level, in conjunction with B. pseudomallei infection associated with autophagy deficiency.
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Affiliation(s)
- Kamal U. Saikh
- Department of Immunology, United States Army Medical Research Institute of Infectious Diseases, Frederick, MD, USA
| | - Cyra M. Ranji
- Department of Immunology, United States Army Medical Research Institute of Infectious Diseases, Frederick, MD, USA
| | - Robert G. Ulrich
- Department of Immunology, United States Army Medical Research Institute of Infectious Diseases, Frederick, MD, USA
| | - Enoka Corea
- Department of Microbiology, University of Colombo, Colombo, Sri Lanka
| | - Aruna Dharshan De Silva
- Division of Vaccine Discovery, La Jolla Institute of Allergy and Immunology, La Jolla, CA, USA
- Department of Paraclinical Sciences, Faculty of Medicine, Kotelawala Defence University, Ratmalana, Sri Lanka
| | - Mohan Natesan
- Department of Immunology, United States Army Medical Research Institute of Infectious Diseases, Frederick, MD, USA
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11
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Santos SB, Cunha AP, Macedo M, Nogueira CL, Brandão A, Costa SP, Melo LDR, Azeredo J, Carvalho CM. Bacteriophage‐receptor binding proteins for multiplex detection of
Staphylococcus
and
Enterococcus
in blood. Biotechnol Bioeng 2020; 117:3286-3298. [DOI: 10.1002/bit.27489] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Revised: 06/23/2020] [Accepted: 07/10/2020] [Indexed: 02/06/2023]
Affiliation(s)
- Sílvio B. Santos
- Centre of Biological Engineering University of Minho Braga Portugal
| | | | - Mariana Macedo
- Centre of Biological Engineering University of Minho Braga Portugal
| | - Catarina L. Nogueira
- International Iberian Nanotechnology Laboratory Braga Portugal
- Instituto de Engenharia de Sistemas e Computadores – Microsistemas e Nanotecnologias (INESC MN) and IN – Institute of Nanoscience and Nanotechnolnology Lisbon Portugal
| | - Ana Brandão
- Centre of Biological Engineering University of Minho Braga Portugal
| | - Susana P. Costa
- Centre of Biological Engineering University of Minho Braga Portugal
- International Iberian Nanotechnology Laboratory Braga Portugal
- Instituto de Engenharia de Sistemas e Computadores – Microsistemas e Nanotecnologias (INESC MN) and IN – Institute of Nanoscience and Nanotechnolnology Lisbon Portugal
| | - Luís D. R. Melo
- Centre of Biological Engineering University of Minho Braga Portugal
| | - Joana Azeredo
- Centre of Biological Engineering University of Minho Braga Portugal
| | - Carla M. Carvalho
- Centre of Biological Engineering University of Minho Braga Portugal
- International Iberian Nanotechnology Laboratory Braga Portugal
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12
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Abstract
The mortality of patients with sepsis and septic shock is still unacceptably high. An effective calculated antibiotic treatment within 1 h of recognition of sepsis is an important target of sepsis treatment. Delays lead to an increase in mortality; therefore, structured treatment concepts form a rational foundation, taking relevant diagnostic and treatment steps into consideration. In addition to the assumed infection and individual risks of each patient, local resistance patterns and specific problem pathogens must be taken into account during the selection of anti-infective treatment. Many pathophysiologic alterations influence the pharmacokinetics (PK) of antibiotics during sepsis. The principle of standard dosing should be abandoned and replaced by an individual treatment approach with stronger weighting of the pharmacokinetics/pharmacodynamics (PK/PD) index of the substance groups. Although this is not yet the clinical standard, prolonged (or continuous) infusion of β‑lactam antibiotics and therapeutic drug monitoring (TDM) can help to achieve defined PK targets. Prolonged infusion is sufficient without TDM, but for continuous infusion, TDM is generally necessary. A further argument for individual PK/PD-oriented antibiotic approaches is the increasing number of infections due to multidrug-resistant (MDR) pathogens in the intensive care unit. For effective treatment, antibiotic stewardship teams (ABS teams) are becoming more established. Interdisciplinary cooperation of the ABS team with infectious disease (ID) specialists, microbiologists, and clinical pharmacists leads not only to rational administration of antibiotics, but also has a positive influence on treatment outcome. The gold standards for pathogen identification are still culture-based detection and microbiologic resistance testing for the various antibiotic groups. Despite the rapid investigation time, novel polymerase chain reaction(PCR)-based procedures for pathogen identification and resistance determination are currently only an adjunct to routine sepsis diagnostics, due to the limited number of studies, high costs, and limited availability. In complicated septic courses with multiple anti-infective therapies or recurrent sepsis, PCR-based procedures can be used in addition to treatment monitoring and diagnostics. Novel antibiotics represent potent alternatives in the treatment of MDR infections. Due to the often defined spectrum of pathogens and the practically (still) absent resistance, they are suitable for targeted treatment of severe MDR infections (therapy escalation). (Contribution available free of charge by "Free Access" [ https://link.springer.com/article/10.1007/s00101-017-0396-z ].).
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13
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Costa SP, Dias NM, Melo LDR, Azeredo J, Santos SB, Carvalho CM. A novel flow cytometry assay based on bacteriophage-derived proteins for Staphylococcus detection in blood. Sci Rep 2020; 10:6260. [PMID: 32277078 PMCID: PMC7148305 DOI: 10.1038/s41598-020-62533-7] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2019] [Accepted: 12/06/2019] [Indexed: 02/08/2023] Open
Abstract
Bloodstream infections (BSIs) are considered a major cause of death worldwide. Staphylococcus spp. are one of the most BSIs prevalent bacteria, classified as high priority due to the increasing multidrug resistant strains. Thus, a fast, specific and sensitive method for detection of these pathogens is of extreme importance. In this study, we have designed a novel assay for detection of Staphylococcus in blood culture samples, which combines the advantages of a phage endolysin cell wall binding domain (CBD) as a specific probe with the accuracy and high-throughput of flow cytometry techniques. In order to select the biorecognition molecule, three different truncations of the C-terminus of Staphylococcus phage endolysin E-LM12, namely the amidase (AMI), SH3 and amidase+SH3 (AMI_SH3) were cloned fused with a green fluorescent protein. From these, a higher binding efficiency to Staphylococcus cells was observed for AMI_SH3, indicating that the amidase domain possibly contributes to a more efficient binding of the SH3 domain. The novel phage endolysin-based flow cytometry assay provided highly reliable and specific detection of 1-5 CFU of Staphylococcus in 10 mL of spiked blood, after 16 hours of enrichment culture. Overall, the method developed herein presents advantages over the standard BSIs diagnostic methods, potentially contributing to an early and effective treatment of BSIs.
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Affiliation(s)
- Susana P Costa
- Centre of Biological Engineering, University of Minho, Campus de Gualtar, 4710-057, Braga, Portugal
- International Iberian Nanotechnology Laboratory (INL), Av. Mestre José Veiga s/n, 4715-330, Braga, Portugal
| | - Nicolina M Dias
- Centre of Biological Engineering, University of Minho, Campus de Gualtar, 4710-057, Braga, Portugal
| | - Luís D R Melo
- Centre of Biological Engineering, University of Minho, Campus de Gualtar, 4710-057, Braga, Portugal
| | - Joana Azeredo
- Centre of Biological Engineering, University of Minho, Campus de Gualtar, 4710-057, Braga, Portugal
| | - Sílvio B Santos
- Centre of Biological Engineering, University of Minho, Campus de Gualtar, 4710-057, Braga, Portugal
| | - Carla M Carvalho
- Centre of Biological Engineering, University of Minho, Campus de Gualtar, 4710-057, Braga, Portugal.
- International Iberian Nanotechnology Laboratory (INL), Av. Mestre José Veiga s/n, 4715-330, Braga, Portugal.
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14
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Rodrigues C, Siciliano RF, Filho HC, Charbel CE, de Carvalho Sarahyba da Silva L, Baiardo Redaelli M, de Paula Rosa Passetti AP, Franco MRG, Rossi F, Zeigler R, De Backer D, Franco RA, de Almeida JP, Rizk SI, Fukushima JT, Landoni G, Uip DE, Hajjar LA, Strabelli TMV. The effect of a rapid molecular blood test on the use of antibiotics for nosocomial sepsis: a randomized clinical trial. J Intensive Care 2019; 7:37. [PMID: 31367384 PMCID: PMC6647273 DOI: 10.1186/s40560-019-0391-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2019] [Accepted: 07/08/2019] [Indexed: 11/24/2022] Open
Abstract
BACKGROUND Appropriate use of antimicrobials is essential to improve outcomes in sepsis. The aim of this study was to determine whether the use of a rapid molecular blood test-SeptiFast (SF) reduces the antibiotic consumption through early de-escalation in patients with nosocomial sepsis compared with conventional blood cultures (BCs). METHODS This was a prospective, randomized, superiority, controlled trial conducted at Sao Paulo Heart Institute in the period October 2012-May 2016. Adult patients admitted to the hospital for at least 48 h with a diagnosis of nosocomial sepsis underwent microorganism identification by both SF test and BCs. Patients randomized into the intervention group received antibiotic therapy adjustment according to the results of SF. Patients randomized into the control group received standard antibiotic adjustment according to the results of BCs. The primary endpoint was antimicrobial consumption during the first 14 days after randomization. RESULTS A total of 200 patients were included (100 in each group). The intention to treat analysis found no significant differences in median antibiotic consumption. In the subgroup of patients with positive SF and blood cultures (19 and 25 respectively), we found a statistically significant reduction in the median antimicrobial consumption which was 1429 (1071-2000) days of therapy (DOT)/1000 patients-day in the intervention group and 1889 (1357-2563) DOT/1000 patients-day in the control group (p = 0.017), in the median time of antimicrobial de-escalation (8 versus 54 h-p < 0.001), in the duration of antimicrobial therapy (p = 0.039) and in anti-gram-positive antimicrobial costs (p = 0.002). Microorganism identification was possible in 24.5% of patients (45/184) by SF and 21.2% (39/184) by BC (p = 0.45). CONCLUSION This randomized clinical trial showed that the use of a rapid molecular-based pathogen identification test does not reduce the median antibiotic consumption in nosocomial sepsis. However, in patients with positive microbiological tests, the use of SeptiFast reduced antimicrobial consumption through early de-escalation compared to conventional blood cultures. These results were driven by a reduction in the consumption of antimicrobials used for Gram-positive bacteria. TRIAL REGISTRATION The trial was registered at ClinicalTrials.gov (NCT01450358) on 12th October 2011.
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Affiliation(s)
- Cristhieni Rodrigues
- Infectious Diseases Control, Heart Institute, University of Sao Paulo, São Paulo, Brazil
| | | | | | | | | | - Martina Baiardo Redaelli
- Department of Anesthesia and Intensive Care, IRCCS San Raffaele Scientific Institute, Milan, Italy
- Vita-Salute San Raffaele University of Milan, Milan, Italy
| | | | | | - Flávia Rossi
- Microbiology Division, University of Sao Paulo, São Paulo, Brazil
| | - Rogerio Zeigler
- Infectious Diseases Control, Heart Institute, University of Sao Paulo, São Paulo, Brazil
| | - Daniel De Backer
- Department of Intensive Care at the Erasme University, Universite Libre de Bruxelles, Bruxelles, Belgium
| | - Rafael Alves Franco
- Intensive Care Unit, Instituto do Cancer, University of Sao Paulo, São Paulo, Brazil
| | | | - Stéphanie Itala Rizk
- Intensive Care Unit, Instituto do Cancer, University of Sao Paulo, São Paulo, Brazil
| | - Julia Tizue Fukushima
- Intensive Care Unit, Instituto do Cancer, University of Sao Paulo, São Paulo, Brazil
| | - Giovanni Landoni
- Department of Anesthesia and Intensive Care, IRCCS San Raffaele Scientific Institute, Milan, Italy
- Vita-Salute San Raffaele University of Milan, Milan, Italy
| | - David Everson Uip
- Infectious Diseases Control, Heart Institute, University of Sao Paulo, São Paulo, Brazil
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15
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Yoon EJ, Choi MH, Park YS, Lee HS, Kim D, Lee H, Shin KS, Shin JH, Uh Y, Kim YA, Shin JH, Jeong SH. Impact of host-pathogen-treatment tripartite components on early mortality of patients with Escherichia coli bloodstream infection: Prospective observational study. EBioMedicine 2018; 35:76-86. [PMID: 30139627 PMCID: PMC6161478 DOI: 10.1016/j.ebiom.2018.08.029] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2018] [Revised: 08/12/2018] [Accepted: 08/13/2018] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND Risk factors affecting early morality of patients with Escherichia coli bloodstream infection (BSI) were investigated including the host-pathogen-treatment tripartite components. METHODS Six general hospitals in South Korea participated in this multicentre prospective observational study from May 2016 to April 2017 and a total of 1492 laboratory-confirmed E. coli BSI cases were studied. Cox regression was used to estimate risks of the primary endpoint, i.e., all-cause mortality within 30 days from the initial blood culture. Six multivariate analysis models were constructed in accordance to the clinical importance and intra- and inter-component multicollinearity. FINDINGS Among the 1492 E. coli BSI cases, 9.5% (n = 141) patients expired within 30 days. Six models of multivariate analysis indicated risk factors of critical illness, primary infection of peritoneum, and chronic liver disease including cirrhosis for host variables; of phylogenetic group B2, ST131-sublineage H30Rx, multidrug resistance, group 1 CTX-M extended-spectrum beta-lactamase production, and having either of fyuA, afa, and sfa/foc virulence genes for causative E. coli pathogen variables; and of delayed definitive therapy for antimicrobial treatment variables. In addition, as a protective factor, primary urinary tract infection was identified. INTERPRETATION Despite decades' effort searching for the risk factors for E. coli BSI, systemic understanding covering the entire tripartite component is still lacking. This study detailed the organic impact of host-pathogen-treatment tripartite components for early mortality in patients with E. coli BSI.
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Affiliation(s)
- Eun-Jeong Yoon
- Department of Laboratory Medicine, Research Institute of Bacterial Resistance, Yonsei University College of Medicine, Seoul, South Korea
| | - Min Hyuk Choi
- Department of Laboratory Medicine, Research Institute of Bacterial Resistance, Yonsei University College of Medicine, Seoul, South Korea
| | - Yoon Soo Park
- Department of Internal Medicine, National Health Insurance Service Ilsan Hospital, Goyang, South Korea
| | - Hye Sun Lee
- Biostatistics Collaboration Unit, College of Medicine, Yonsei University, Seoul, South Korea
| | - Dokyun Kim
- Department of Laboratory Medicine, Research Institute of Bacterial Resistance, Yonsei University College of Medicine, Seoul, South Korea
| | - Hyukmin Lee
- Department of Laboratory Medicine, Research Institute of Bacterial Resistance, Yonsei University College of Medicine, Seoul, South Korea
| | - Kyeong Seob Shin
- Department of Laboratory Medicine, College of Medicine, Chungbuk National University, Cheongju, South Korea
| | - Jong Hee Shin
- Department of Laboratory Medicine, Chonnam National University Medical School, Gwangju, South Korea
| | - Young Uh
- Department of Laboratory Medicine, College of Medicine, Yonsei University Wonju, Wonju, South Korea
| | - Young Ah Kim
- Department of Internal Medicine, National Health Insurance Service Ilsan Hospital, Goyang, South Korea
| | - Jeong Hwan Shin
- Department of Laboratory Medicine, Paik Institute for Clinical Research, College of Medicine, Inje University, Busan, South Korea
| | - Seok Hoon Jeong
- Department of Laboratory Medicine, Research Institute of Bacterial Resistance, Yonsei University College of Medicine, Seoul, South Korea.
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16
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Richter DC, Heininger A, Brenner T, Hochreiter M, Bernhard M, Briegel J, Dubler S, Grabein B, Hecker A, Krüger WA, Mayer K, Pletz MW, Störzinger D, Pinder N, Hoppe-Tichy T, Weiterer S, Zimmermann S, Brinkmann A, Weigand MA, Lichtenstern C. [Bacterial sepsis : Diagnostics and calculated antibiotic therapy]. Anaesthesist 2018; 66:737-761. [PMID: 28980026 DOI: 10.1007/s00101-017-0363-8] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
The mortality of patients with sepsis and septic shock is still unacceptably high. An effective antibiotic treatment within 1 h of recognition of sepsis is an important target of sepsis treatment. Delays lead to an increase in mortality; therefore, structured treatment concepts form a rational foundation, taking relevant diagnostic and treatment steps into consideration. In addition to the assumed focus and individual risks of each patient, local resistance patterns and specific problem pathogens must be taken into account for selection of anti-infection treatment. Many pathophysiological alterations influence the pharmacokinetics of antibiotics during sepsis. The principle of standard dosing should be abandoned and replaced by an individual treatment approach with stronger weighting of the pharmacokinetics/pharmacodynamics (PK/PD) index of the substance groups. Although this is not yet the clinical standard, prolonged (or continuous) infusion of beta-lactam antibiotics and therapeutic drug monitoring (TDM) can help to achieve defined PK targets. Prolonged infusion is sufficient without TDM but for continuous infusion TDM is basically necessary. A further argument for individual PK/PD-oriented antibiotic approaches is the increasing number of infections due to multidrug resistant pathogens (MDR) in the intensive care unit. For effective treatment antibiotic stewardship teams (ABS team) are becoming more established. Interdisciplinary cooperation of the ABS team with infectiologists, microbiologists and clinical pharmacists leads not only to a rational administration of antibiotics but also has a positive influence on the outcome. The gold standards for pathogen detection are still culture-based detection and microbiological resistance testing for the various antibiotic groups. Despite the rapid investigation time, novel polymerase chain reaction (PCR)-based procedures for pathogen identification and resistance determination, are currently only an adjunct to routine sepsis diagnostics due to the limited number of studies, high costs and limited availability. In complicated septic courses with multiple anti-infective treatment or recurrent sepsis, PCR-based procedures can be used in addition to therapy monitoring and diagnostics. Novel antibiotics represent potent alternatives in the treatment of MDR infections. Due to the often defined spectrum of pathogens and the practically absent resistance, they are suitable for targeted treatment of severe MDR infections (therapy escalation).
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Affiliation(s)
- D C Richter
- Klinik für Anästhesiologie, Universitätsklinikum Heidelberg, Im Neuenheimer Feld 110, 69120, Heidelberg, Deutschland.
| | - A Heininger
- Zentrum für Infektiologie, Sektion für Krankenhaus- und Umwelthygiene, Universitätsklinikum Heidelberg, Heidelberg, Deutschland
| | - T Brenner
- Klinik für Anästhesiologie, Universitätsklinikum Heidelberg, Im Neuenheimer Feld 110, 69120, Heidelberg, Deutschland
| | - M Hochreiter
- Klinik für Anästhesiologie, Universitätsklinikum Heidelberg, Im Neuenheimer Feld 110, 69120, Heidelberg, Deutschland
| | - M Bernhard
- Zentrale Notaufnahme, Universitätsklinikum Leipzig, Leipzig, Deutschland
| | - J Briegel
- Klinik für Anästhesiologie, Klinikum der Universität München, München, Deutschland
| | - S Dubler
- Klinik für Anästhesiologie, Universitätsklinikum Heidelberg, Im Neuenheimer Feld 110, 69120, Heidelberg, Deutschland
| | - B Grabein
- Stabsstelle "Klinische Mikrobiologie und Krankenhaushygiene", Klinikum der Universität München, München, Deutschland
| | - A Hecker
- Klinik für Allgemein‑, Viszeral‑, Thorax‑, Transplantations- und Kinderchirurgie, Universitätsklinikum Gießen und Marburg, Standort Gießen, Gießen, Deutschland
| | - W A Krüger
- Klinik für Anästhesiologie und operative Intensivmedizin, Gesundheitsverbund Landkreis Konstanz, Klinikum Konstanz, Konstanz, Deutschland
| | - K Mayer
- Apotheke des Universitätsklinikums Heidelberg, Heidelberg, Deutschland
| | - M W Pletz
- Zentrum für Infektionsmedizin und Krankenhaushygiene, Universitätsklinikum Jena, Jena, Deutschland
| | - D Störzinger
- Apotheke des Universitätsklinikums Heidelberg, Heidelberg, Deutschland
| | - N Pinder
- Apotheke des Universitätsklinikums Heidelberg, Heidelberg, Deutschland
| | - T Hoppe-Tichy
- Zentrum für Infektiologie, Sektion für Krankenhaus- und Umwelthygiene, Universitätsklinikum Heidelberg, Heidelberg, Deutschland
| | - S Weiterer
- Klinik für Anästhesiologie, Universitätsklinikum Heidelberg, Im Neuenheimer Feld 110, 69120, Heidelberg, Deutschland
| | - S Zimmermann
- Zentrum für Infektiologie, Sektion für Krankenhaus- und Umwelthygiene, Universitätsklinikum Heidelberg, Heidelberg, Deutschland
| | - A Brinkmann
- Klinik für Anästhesie, operative Intensivmedizin und spezielle Schmerztherapie, Klinikum Heidenheim, Heidenheim, Deutschland
| | - M A Weigand
- Klinik für Anästhesiologie, Universitätsklinikum Heidelberg, Im Neuenheimer Feld 110, 69120, Heidelberg, Deutschland
| | - Christoph Lichtenstern
- Klinik für Anästhesiologie, Universitätsklinikum Heidelberg, Im Neuenheimer Feld 110, 69120, Heidelberg, Deutschland
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17
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Zhao S, Cao S, Luo L, Zhang Z, Yuan G, Zhang Y, Yang Y, Guo W, Wang L, Chen F, Wu Q, Li L. A preliminary investigation of metal element profiles in the serum of patients with bloodstream infections using inductively-coupled plasma mass spectrometry (ICP-MS). Clin Chim Acta 2018; 485:323-332. [PMID: 30017616 DOI: 10.1016/j.cca.2018.07.013] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2018] [Revised: 05/30/2018] [Accepted: 07/09/2018] [Indexed: 01/30/2023]
Abstract
BACKGROUND We determined metal element profiles (MEPs) by inductively-coupled plasma mass spectrometry (ICP-MS) in the serum of patients with blood stream infection (BSI) and find out very important (VIP) metal elements in specific infections. METHODS Sixty-eight metal elements were identified in both serum and the bacteria isolated from 14 BSI patients with Staphylococcus infection, 39 with Enterobacteriaceae infection, 5 with Enterococcus infection and 58 healthy subjects without infection by ICP-MS methods. Statistical analysis, Principal Component Analysis (PCA) and Partial Least Squares Discriminant Analysis (PLS-DA) were performed to process data among different groups, select differential metal elements and operate correlation analysis. RESULTS The MEPs in the serum of BSI patients with 4 types of bacteria (Staphylococcus aureus, Escherichia coli, Enterococcus faecium, and Klebsiella pneumonia), and the corresponding MEPs of the bacteria were established. VIP metal elements were screened out in different BSI patients. Correlation analysis showed that there were some correlations between serum concentrations of metal elements and bacterial infection. CONCLUSION We found differential metal elements in the serum of BSI patients compared with controls, thus providing a basis for the diagnosis, prevention and treatment of BSI from the perspective of metallomics.
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Affiliation(s)
- Suying Zhao
- Department of laboratory medicine, The Affiliated hospital of Nanjing university of Traditional ChineseMedicine, Nanjing 210009, China
| | - Shuyuan Cao
- Department of Hygienic Analysis and Detection and Ministry of Education Key Lab for Modern Toxicology, School of Public Health, Nanjing Medical University, Nanjing 211166, China
| | - Lan Luo
- Nanjing entry-exit inspection and quarantine bureau, Nanjing 211106,China
| | - Zhan Zhang
- Department of Hygienic Analysis and Detection and Ministry of Education Key Lab for Modern Toxicology, School of Public Health, Nanjing Medical University, Nanjing 211166, China
| | - Gehui Yuan
- Department of Hygienic Analysis and Detection and Ministry of Education Key Lab for Modern Toxicology, School of Public Health, Nanjing Medical University, Nanjing 211166, China
| | - Yanan Zhang
- Department of Hygienic Analysis and Detection and Ministry of Education Key Lab for Modern Toxicology, School of Public Health, Nanjing Medical University, Nanjing 211166, China
| | - Yanting Yang
- Department of Hygienic Analysis and Detection and Ministry of Education Key Lab for Modern Toxicology, School of Public Health, Nanjing Medical University, Nanjing 211166, China
| | - Weihui Guo
- Department of Hygienic Analysis and Detection and Ministry of Education Key Lab for Modern Toxicology, School of Public Health, Nanjing Medical University, Nanjing 211166, China
| | - Li Wang
- Department of Hygienic Analysis and Detection and Ministry of Education Key Lab for Modern Toxicology, School of Public Health, Nanjing Medical University, Nanjing 211166, China
| | - Feng Chen
- Department of Epidemiology and Biostatistics and Ministry of Education Key Lab for Modern Toxicology, School of Public Health, Nanjing Medical University, Nanjing 211166, China
| | - Qian Wu
- Department of Hygienic Analysis and Detection and Ministry of Education Key Lab for Modern Toxicology, School of Public Health, Nanjing Medical University, Nanjing 211166, China.
| | - Lei Li
- Department of Hygienic Analysis and Detection and Ministry of Education Key Lab for Modern Toxicology, School of Public Health, Nanjing Medical University, Nanjing 211166, China.
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18
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Abstract
Burkholderia pseudomallei is a Gram-negative environmental bacterium and the aetiological agent of melioidosis, a life-threatening infection that is estimated to account for ∼89,000 deaths per year worldwide. Diabetes mellitus is a major risk factor for melioidosis, and the global diabetes pandemic could increase the number of fatalities caused by melioidosis. Melioidosis is endemic across tropical areas, especially in southeast Asia and northern Australia. Disease manifestations can range from acute septicaemia to chronic infection, as the facultative intracellular lifestyle and virulence factors of B. pseudomallei promote survival and persistence of the pathogen within a broad range of cells, and the bacteria can manipulate the host's immune responses and signalling pathways to escape surveillance. The majority of patients present with sepsis, but specific clinical presentations and their severity vary depending on the route of bacterial entry (skin penetration, inhalation or ingestion), host immune function and bacterial strain and load. Diagnosis is based on clinical and epidemiological features as well as bacterial culture. Treatment requires long-term intravenous and oral antibiotic courses. Delays in treatment due to difficulties in clinical recognition and laboratory diagnosis often lead to poor outcomes and mortality can exceed 40% in some regions. Research into B. pseudomallei is increasing, owing to the biothreat potential of this pathogen and increasing awareness of the disease and its burden; however, better diagnostic tests are needed to improve early confirmation of diagnosis, which would enable better therapeutic efficacy and survival.
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Affiliation(s)
- W Joost Wiersinga
- Department of Medicine, Division of Infectious Diseases, Academic Medical Center, Meibergdreef 9, Rm. G2-132, 1105 AZ Amsterdam, The Netherlands
- Centre for Experimental and Molecular Medicine, Academic Medical Center, Amsterdam, The Netherlands
| | - Harjeet S Virk
- Centre for Experimental and Molecular Medicine, Academic Medical Center, Amsterdam, The Netherlands
| | - Alfredo G Torres
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, Texas, USA
| | - Bart J Currie
- Menzies School of Health Research, Charles Darwin University and Royal Darwin Hospital, Darwin, Australia
| | - Sharon J Peacock
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, UK
- Department of Medicine, University of Cambridge, Cambridge, UK
| | - David A B Dance
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, UK
- Lao-Oxford-Mahosot Hospital Wellcome Trust Research Unit, Vientiane, Lao People's Democratic Republic
- Centre for Tropical Medicine and Global Health, University of Oxford, Oxford, UK
| | - Direk Limmathurotsakul
- Centre for Tropical Medicine and Global Health, University of Oxford, Oxford, UK
- Department of Tropical Hygiene and Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok 10400, Thailand
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19
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Chung B, Park C, Cho SY, Shin J, Shin S, Yim SH, Lee DG, Chung YJ. Multiplex identification of sepsis-causing Gram-negative pathogens from the plasma of infected blood. Electrophoresis 2017; 39:645-652. [PMID: 29193166 DOI: 10.1002/elps.201700405] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2017] [Accepted: 11/16/2017] [Indexed: 11/09/2022]
Abstract
Early and accurate detection of bacterial pathogens in the blood is the most crucial step for sepsis management. Gram-negative bacteria are the most common organisms causing severe sepsis and responsible for high morbidity and mortality. We aimed to develop a method for rapid multiplex identification of clinically important Gram-negative pathogens and also validated whether our system can identify Gram-negative pathogens with the cell-free plasm DNA from infected blood. We designed five MLPA probe sets targeting the genes specific to major Gram-negative pathogens (uidA and lacY for E. coli, ompA for A. baumannii, phoE for K. pneumoniae, and ecfX for P. aeruginosa) and one set targeting the CTX-M group 1 to identify the ESBL producing Gram-negative pathogens. All six target-specific peaks were clearly separated without any non-specific peaks in a multiplex reaction condition. The minimum detection limit was 100 fg of pathogen DNA. When we tested 28 Gram-negative clinical isolates, all of them were successfully identified without any non-specific peaks. To evaluate the clinical applicability, we tested seven blood samples from febrile patients. Three blood culture positive cases showed E. coli specific peaks, while no peak was detected in the other four culture negative samples. This technology can be useful for detection of major sepsis-causing, drug-resistant Gram-negative pathogens and also the major ESBL producing Gram-negatives from the blood of sepsis patients in a clinical setting. This system can help early initiation of effective antimicrobial treatment against Gram-negative pathogens for sepsis patients, which is very crucial for better treatment outcomes.
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Affiliation(s)
- Boram Chung
- Department of Microbiology, The Catholic University of Korea, College of Medicine, Seoul, Republic of Korea.,Precision Medicine Research Center, Integrated Research Center for Genome Polymorphism, The Catholic University of Korea, College of Medicine, Seoul, Republic of Korea
| | - Chulmin Park
- Vaccine Bio Research Institute, The Catholic University of Korea, College of Medicine, Seoul St. Mary's Hospital, Seoul, Republic of Korea
| | - Sung-Yeon Cho
- Vaccine Bio Research Institute, The Catholic University of Korea, College of Medicine, Seoul St. Mary's Hospital, Seoul, Republic of Korea.,Department of Internal Medicine, The Catholic University of Korea, College of Medicine, Seoul St. Mary's Hospital, Seoul, Republic of Korea
| | - Juyoun Shin
- Department of Microbiology, The Catholic University of Korea, College of Medicine, Seoul, Republic of Korea
| | - Sun Shin
- Department of Microbiology, The Catholic University of Korea, College of Medicine, Seoul, Republic of Korea.,Precision Medicine Research Center, Integrated Research Center for Genome Polymorphism, The Catholic University of Korea, College of Medicine, Seoul, Republic of Korea
| | - Seon-Hee Yim
- Precision Medicine Research Center, Integrated Research Center for Genome Polymorphism, The Catholic University of Korea, College of Medicine, Seoul, Republic of Korea
| | - Dong-Gun Lee
- Vaccine Bio Research Institute, The Catholic University of Korea, College of Medicine, Seoul St. Mary's Hospital, Seoul, Republic of Korea.,Department of Internal Medicine, The Catholic University of Korea, College of Medicine, Seoul St. Mary's Hospital, Seoul, Republic of Korea
| | - Yeun-Jung Chung
- Department of Microbiology, The Catholic University of Korea, College of Medicine, Seoul, Republic of Korea.,Precision Medicine Research Center, Integrated Research Center for Genome Polymorphism, The Catholic University of Korea, College of Medicine, Seoul, Republic of Korea
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20
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Mihajlovic D, Brkic S, Uvelin A, Draskovic B, Vrsajkov V. Use of presepsin and procalcitonin for prediction of SeptiFast results in critically ill patients. J Crit Care 2017; 40:197-201. [PMID: 28432884 DOI: 10.1016/j.jcrc.2017.04.008] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2016] [Revised: 03/20/2017] [Accepted: 04/06/2017] [Indexed: 12/29/2022]
Abstract
PURPOSE There is a need for identification of marker that could lead physicians to take the right step towards laboratory techniques for documentation of infection. The aim of this study was to investigate whether presepsin and procalcitonin (PCT) levels in patients with suspected sepsis could predict blood culture (BC) and SeptiFast (SF) results. MATERIAL AND METHODS 100 patients were included in our study. PCT, C-reactive protein (CRP), and presepsin levels were determined. Differences between groups of patients were assessed by Mann-Whitney U test. Categorical variables were compared using chi-square test. Receiver operating characteristic (ROC) curves were plotted to determine predictive values of biomarkers for prediction of positive SF results. RESULTS PCT (70.9±106.36 vs. 16.35±26.79) and presepsin (4899.73±5207.81 vs. 1751.59±2830.62) were significantly higher in patients with positive SF in contrast to patients with negative SF. There was no significant difference between patients who had positive and negative BC for PCT and presepsin values. PCT and presepsin showed a similar performance in predicting positive SF results with AUC of 0.75 for PCT and 0.73 for presepsin. CONCLUSION Presepsin can serve as good predictor of bacteremia detected by SF and it should be included with PCT in protocols for sepsis diagnosing.
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Affiliation(s)
- Dunja Mihajlovic
- Medical faculty, University of Novi Sad, Clinical center of Vojvodina, Emergency center, Department of anesthesia and reanimation, Novi Sad, Serbia.
| | - Snezana Brkic
- Medical faculty, University of Novi Sad, Clinical center of Vojvodina, Clinic for infectious diseases, Novi Sad, Serbia
| | - Arsen Uvelin
- Medical faculty, University of Novi Sad, Clinical center of Vojvodina, Emergency center, Department of anesthesia and reanimation, Novi Sad, Serbia
| | - Biljana Draskovic
- Medical faculty, University of Novi Sad, Institute of Child and Adolescent Health Care of Vojvodina, Clinic of Pediatric Surgery, Novi Sad, Serbia
| | - Vladimir Vrsajkov
- Medical faculty, University of Novi Sad, Clinical center of Vojvodina, Emergency center, Department of anesthesia and reanimation, Novi Sad, Serbia
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21
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Maurer FP, Christner M, Hentschke M, Rohde H. Advances in Rapid Identification and Susceptibility Testing of Bacteria in the Clinical Microbiology Laboratory: Implications for Patient Care and Antimicrobial Stewardship Programs. Infect Dis Rep 2017; 9:6839. [PMID: 28458798 PMCID: PMC5391540 DOI: 10.4081/idr.2017.6839] [Citation(s) in RCA: 87] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/16/2016] [Revised: 12/30/2016] [Accepted: 01/12/2017] [Indexed: 12/11/2022] Open
Abstract
Early availability of information on bacterial pathogens and their antimicrobial susceptibility is of key importance for the management of infectious diseases patients. Currently, using traditional approaches, it usually takes at least 48 hours for identification and susceptibility testing of bacterial pathogens. Therefore, the slowness of diagnostic procedures drives prolongation of empiric, potentially inappropriate, antibacterial therapies. Over the last couple of years, the improvement of available techniques (e.g. for susceptibility testing, DNA amplification assays), and introduction of novel technologies (e.g. MALDI-TOF) has fundamentally changed approaches towards pathogen identification and characterization. Importantly, these techniques offer increased diagnostic resolution while at the same time shorten the time-to-result, and are thus of obvious importance for antimicrobial stewardship. In this review, we will discuss recent advances in medical microbiology with special emphasis on the impact of novel techniques on antimicrobial stewardship programs.
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Affiliation(s)
- Florian P Maurer
- Institute of Medical Microbiology, Virology and Hygiene.,Antibiotic Stewardship Team, University Medical Centre Hamburg-Eppendorf, Hamburg
| | | | | | - Holger Rohde
- Institute of Medical Microbiology, Virology and Hygiene
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22
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Riedel S, Carroll KC. Early Identification and Treatment of Pathogens in Sepsis: Molecular Diagnostics and Antibiotic Choice. Clin Chest Med 2017; 37:191-207. [PMID: 27229637 DOI: 10.1016/j.ccm.2016.01.018] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
Sepsis and septic shock are serious conditions associated with high morbidity and mortality. Rapid molecular methods for detection of microorganisms and antimicrobial resistance genes from positive blood cultures or whole blood have evolved over the past 10 years. Such diagnostic methods coupled with therapeutic interventional programs are desirable to improve the overall clinical outcome and mortality. This article discusses the usefulness of current molecular test methods for the diagnosis of sepsis and their potential to enhance the success of antimicrobial stewardship programs. Clinicians and laboratories alike must appreciate key factors influencing the appropriate use and potential impact of these methods.
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Affiliation(s)
- Stefan Riedel
- Department of Pathology, Harvard Medical School, Beth Israel Deaconess Medical Center, 330 Brookline Avenue, Boston, MA 02215, USA.
| | - Karen C Carroll
- Division of Medical Microbiology, Department of Pathology, The Johns Hopkins Hospital, The Johns Hopkins University School of Medicine, 600 North Wolfe Street, Meyer B1-193, Baltimore, MD 21287, USA
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23
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Gosiewski T, Ludwig-Galezowska AH, Huminska K, Sroka-Oleksiak A, Radkowski P, Salamon D, Wojciechowicz J, Kus-Slowinska M, Bulanda M, Wolkow PP. Comprehensive detection and identification of bacterial DNA in the blood of patients with sepsis and healthy volunteers using next-generation sequencing method - the observation of DNAemia. Eur J Clin Microbiol Infect Dis 2016; 36:329-336. [PMID: 27771780 PMCID: PMC5253159 DOI: 10.1007/s10096-016-2805-7] [Citation(s) in RCA: 108] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2016] [Accepted: 09/26/2016] [Indexed: 12/17/2022]
Abstract
Blood is considered to be a sterile microenvironment, in which bacteria appear only periodically. Previously used methods allowed only for the detection of either viable bacteria with low sensitivity or selected species of bacteria. The Next-Generation Sequencing method (NGS) enables the identification of all bacteria in the sample with their taxonomic classification. We used NGS for the analysis of blood samples from healthy volunteers (n = 23) and patients with sepsis (n = 62) to check whether any bacterial DNA exists in the blood of healthy people and to identify bacterial taxonomic profile in the blood of septic patients. The presence of bacterial DNA was found both in septic and healthy subjects; however, bacterial diversity was significantly different (P = 0.002) between the studied groups. Among healthy volunteers, a significant predominance of anaerobic bacteria (76.2 %), of which most were bacteria of the order Bifidobacteriales (73.0 %), was observed. In sepsis, the majority of detected taxa belonged to aerobic or microaerophilic microorganisms (75.1 %). The most striking difference was seen in the case of Actinobacteria phyla, the abundance of which was decreased in sepsis (P < 0.001) and Proteobacteria phyla which was decreased in the healthy volunteers (P < 0.001). Our research shows that bacterial DNA can be detected in the blood of healthy people and that its taxonomic composition is different from the one seen in septic patients. Detection of bacterial DNA in the blood of healthy people may suggest that bacteria continuously translocate into the blood, but not always cause sepsis; this observation can be called DNAemia.
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Affiliation(s)
- T Gosiewski
- Department of Microbiology, Jagiellonian University Medical College, Krakow, Poland
| | - A H Ludwig-Galezowska
- Center for Medical Genomics OMICRON, Jagiellonian University Medical College, 7C Kopernika Str., 31-034, Krakow, Poland
| | - K Huminska
- Genomic Laboratory, DNA Research Center, Poznan, Poland.,Laboratory of High Throughput Technologies, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, Poznan, Poland
| | - A Sroka-Oleksiak
- Department of Microbiology, Jagiellonian University Medical College, Krakow, Poland
| | - P Radkowski
- Center for Medical Genomics OMICRON, Jagiellonian University Medical College, 7C Kopernika Str., 31-034, Krakow, Poland
| | - D Salamon
- Department of Microbiology, Jagiellonian University Medical College, Krakow, Poland
| | | | | | - M Bulanda
- Department of Microbiology, Jagiellonian University Medical College, Krakow, Poland
| | - P P Wolkow
- Center for Medical Genomics OMICRON, Jagiellonian University Medical College, 7C Kopernika Str., 31-034, Krakow, Poland.
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24
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Tziolos N, Giamarellos-Bourboulis EJ. Contemporary approaches to the rapid molecular diagnosis of sepsis. Expert Rev Mol Diagn 2016; 16:1201-1207. [PMID: 27728986 DOI: 10.1080/14737159.2016.1246958] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
INTRODUCTION Although the administration of appropriate antimicrobials within the very first hour remains the mainstay of sepsis management, the correct selection of antimicrobials is hampered by the delay of conventional microbiology providing results after at least 48 hours. Methods of rapid detection of pathogens are an approach to overcome these difficulties. Areas covered: This review analyzes the advantages and the disadvantages of these approaches with major emphasis on technologies based on multiplex PCR for the rapid detection of pathogens using whole blood. The most broadly studied platform is SeptFast. Sensitivity ranges between 42% and 73% and specificity between 50% and 97%. The main disadvantages are high cost, the risk of contamination and the lack of information for the presence of resistance genes. A brief review of the use of PCR techniques for the diagnosis of endocarditis and of the recognition of the bacterial proteome for the rapid identification of grown colonies (MALDI-TOF) is also provided. Expert commentary: More randomized clinical trials are necessary to validate the use of molecular techniques for decision-making for patients' outcomes, taking into consideration the cost-benefit for the patient.
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Affiliation(s)
- Nikolaos Tziolos
- a 4th Department of Internal Medicine , National and Kapodistrian University of Athens, Medical School , Athens , Greece
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25
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Chung B, Park C, Cho SY, Shin S, Yim SH, Jung GY, Lee DG, Chung YJ. Multiplex identification of drug-resistant Gram-positive pathogens using stuffer-free MLPA system. Electrophoresis 2016; 37:3079-3083. [PMID: 27573990 DOI: 10.1002/elps.201600372] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2016] [Revised: 08/09/2016] [Accepted: 08/22/2016] [Indexed: 11/09/2022]
Abstract
Early detection of pathogens from blood and identification of their drug resistance are essential for sepsis management. However, conventional culture-based methods require relatively longer time to identify drug-resistant pathogens, which delays therapeutic decisions. For precise multiplex detection of drug-resistant Gram-positive pathogens, we developed a method by using stuffer-free multiplex ligation-dependent probe amplification (MLPA) coupled with high-resolution CE single-strand conformation polymorphisms (CE-SSCP) system. We designed three probe sets for genes specific to Gram-positive species (Staphylococcus aureus: nuc, Enterococcus faecium: sodA, and Streptococcus pneumoniae: lytA) and two sets for genes associated with drug resistance (mecA and vanA) to discriminate major Gram-positive pathogens with the resistance. A total of 94 different strains (34 reference strains and 60 clinical isolates) were used to validate this method and strain-specific peaks were successfully observed for all the strains. To improve sensitivity of the method, a target-specific preamplification step was introduced and, consequently, the sensitivity increased from 10 pg to 100 fg. We also reduced a total assay time to 8 h by optimizing hybridization time without compromising test sensitivity. Taken together, our multiplex detection system can improve detection of drug-resistant Gram-positive pathogens from sepsis patients' blood.
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Affiliation(s)
- Boram Chung
- Department of Microbiology, College of Medicine, The Catholic University of Korea Korea, Seoul, Korea.,Integrated Research Center for Genome Polymorphism, College of Medicine, The Catholic University of Korea Korea, Seoul, Korea
| | - Chulmin Park
- Vaccine Bio Research Institute, College of Medicine, The Catholic University of Korea Korea, Seoul, Korea
| | - Sung-Yeon Cho
- Vaccine Bio Research Institute, College of Medicine, The Catholic University of Korea Korea, Seoul, Korea.,Division of Infectious Diseases, Department of Internal Medicine, College of Medicine, The Catholic University of Korea, Seoul, Korea
| | - Sun Shin
- Department of Microbiology, College of Medicine, The Catholic University of Korea Korea, Seoul, Korea.,Integrated Research Center for Genome Polymorphism, College of Medicine, The Catholic University of Korea Korea, Seoul, Korea
| | - Seon-Hee Yim
- Integrated Research Center for Genome Polymorphism, College of Medicine, The Catholic University of Korea Korea, Seoul, Korea
| | - Gyoo Yeol Jung
- School of Interdisciplinary Bioscience and Bioengineering, Pohang University of Science and Technology, Pohang, Gyeongbuk, Korea
| | - Dong-Gun Lee
- Vaccine Bio Research Institute, College of Medicine, The Catholic University of Korea Korea, Seoul, Korea.,Division of Infectious Diseases, Department of Internal Medicine, College of Medicine, The Catholic University of Korea, Seoul, Korea
| | - Yeun-Jun Chung
- Department of Microbiology, College of Medicine, The Catholic University of Korea Korea, Seoul, Korea.,Integrated Research Center for Genome Polymorphism, College of Medicine, The Catholic University of Korea Korea, Seoul, Korea
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26
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Efe İris N, Yıldırmak T, Gedik H, Şimşek F, Aydın D, Demirel N, Yokuş O. Could Neutrophil CD64 Expression Be Used as a Diagnostic Parameter of Bacteremia in Patients with Febrile Neutropenia? Turk J Haematol 2016; 34:167-173. [PMID: 27348760 PMCID: PMC5440869 DOI: 10.4274/tjh.2016.0123] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
OBJECTIVE The aim of this study is to investigate if neutrophil CD64 expression in febrile neutropenia patients could be used as an early indicator of bacteremia. MATERIALS AND METHODS All consecutive patients older than 18 years of age who had developed febrile neutropenia episodes due to hematological malignancies were included in the study. Those patients who had significant growth in their blood cultures constituted the case group, while those who had febrile neutropenia without any growth in their cultures and who did not have any documented infections formed the control group. Blood culture bottles were incubated in the Bact ALERT 3D system (bioMerieux, France), identification and susceptibility testing were performed using an automated broth microdilution method (VITEK 2, bioMerieux), and CD64 expression analysis was performed by the flow cytometry method. C-reactive protein (CRP) was measured by turbidimetric methods (Biosystems, Spain) and erythrocyte sedimentation rate (ESR) was measured by the Wintrobe method. RESULTS In total, we prospectively evaluated 31 febrile episodes. The case group consisted of 17 patients while the control group included 14 patients. CD64 was found on neutrophils of the case group patients with a mean count of 8006 molecules/cell and of control group with a mean count of 2786 molecules/cell. CD64 levels of the case group were significantly higher than those of the control group (p=0.005). In the differentiation of the case group from the control group, a 2500 cut-off value for CD64 had significant [AUC=0.792 (0.619-0.965)] predictive value (p=0.001). In the prediction of patients with a 2500 cut-off value for CD64, sensitivity was 94.1%, positive predictive value was 76.2%, specificity was 64.3%, and negative predictive value was 90.0%. CRP levels and ESR values did not differ significantly between the groups (p=0.005). CONCLUSION Neutrophil CD64 expression could be a good predictor as an immune parameter with high sensitivity and a negative predictive value for bacteremia in febrile neutropenic patients.
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Affiliation(s)
- Nur Efe İris
- İstanbul Bilim University Faculty of Medicine, Department of Infectious Diseases and Clinical Microbiology, İstanbul, Turkey Phone: +90 212 361 88 00 E-mail :
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27
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Rödel J, Karrasch M, Edel B, Stoll S, Bohnert J, Löffler B, Saupe A, Pfister W. Antibiotic treatment algorithm development based on a microarray nucleic acid assay for rapid bacterial identification and resistance determination from positive blood cultures. Diagn Microbiol Infect Dis 2015; 84:252-7. [PMID: 26712265 DOI: 10.1016/j.diagmicrobio.2015.10.021] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2015] [Revised: 10/19/2015] [Accepted: 10/24/2015] [Indexed: 01/04/2023]
Abstract
Rapid diagnosis of bloodstream infections remains a challenge for the early targeting of an antibiotic therapy in sepsis patients. In recent studies, the reliability of the Nanosphere Verigene Gram-positive and Gram-negative blood culture (BC-GP and BC-GN) assays for the rapid identification of bacteria and resistance genes directly from positive BCs has been demonstrated. In this work, we have developed a model to define treatment recommendations by combining Verigene test results with knowledge on local antibiotic resistance patterns of bacterial pathogens. The data of 275 positive BCs were analyzed. Two hundred sixty-three isolates (95.6%) were included in the Verigene assay panels, and 257 isolates (93.5%) were correctly identified. The agreement of the detection of resistance genes with subsequent phenotypic susceptibility testing was 100%. The hospital antibiogram was used to develop a treatment algorithm on the basis of Verigene results that may contribute to a faster patient management.
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Affiliation(s)
- Jürgen Rödel
- Institute of Medical Microbiology, University Hospital of Jena, Erlanger Allee 101, D-07747 Jena, Germany.
| | - Matthias Karrasch
- Institute of Medical Microbiology, University Hospital of Jena, Erlanger Allee 101, D-07747 Jena, Germany
| | - Birgit Edel
- Institute of Medical Microbiology, University Hospital of Jena, Erlanger Allee 101, D-07747 Jena, Germany
| | - Sylvia Stoll
- Institute of Medical Microbiology, University Hospital of Jena, Erlanger Allee 101, D-07747 Jena, Germany
| | - Jürgen Bohnert
- Institute of Medical Microbiology, University Hospital of Jena, Erlanger Allee 101, D-07747 Jena, Germany
| | - Bettina Löffler
- Institute of Medical Microbiology, University Hospital of Jena, Erlanger Allee 101, D-07747 Jena, Germany
| | - Angela Saupe
- Institute of Medical Microbiology, University Hospital of Jena, Erlanger Allee 101, D-07747 Jena, Germany
| | - Wolfgang Pfister
- Institute of Medical Microbiology, University Hospital of Jena, Erlanger Allee 101, D-07747 Jena, Germany
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28
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Abstract
The prevention and treatment of sepsis in the immunocompromised host present a challenging array of diagnostic and management issues. The neutropenic patient has a primary defect in innate immune responses and is susceptible to conventional and opportunistic pathogens. The solid organ transplant patient has a primary defect in adaptive immunity and is susceptible to a myriad of pathogens that require an effective cellular immune response. Risk for infections in organ transplant recipients is further complicated by mechanical, vascular, and rejection of the transplanted organ itself. The immune suppressed state can modify the cardinal signs of inflammation, making accurate and rapid diagnosis of infection and sepsis difficult. Empiric antimicrobial agents can be lifesaving in these patients, but managing therapy in an era of progressive antibiotic resistance has become a real issue. This review discusses the challenges faced when treating severe infections in these high-risk patients.
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Affiliation(s)
- Andre C Kalil
- The Transplant Infectious Disease Program, University of Nebraska Medical Center, Omaha, NE, USA
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Abstract
OBJECTIVE To develop predictive models for early triage of burn patients based on hypersusceptibility to repeated infections. BACKGROUND Infection remains a major cause of mortality and morbidity after severe trauma, demanding new strategies to combat infections. Models for infection prediction are lacking. METHODS Secondary analysis of 459 burn patients (≥16 years old) with 20% or more total body surface area burns recruited from 6 US burn centers. We compared blood transcriptomes with a 180-hour cutoff on the injury-to-transcriptome interval of 47 patients (≤1 infection episode) to those of 66 hypersusceptible patients [multiple (≥2) infection episodes (MIE)]. We used LASSO regression to select biomarkers and multivariate logistic regression to built models, accuracy of which were assessed by area under receiver operating characteristic curve (AUROC) and cross-validation. RESULTS Three predictive models were developed using covariates of (1) clinical characteristics; (2) expression profiles of 14 genomic probes; (3) combining (1) and (2). The genomic and clinical models were highly predictive of MIE status [AUROCGenomic = 0.946 (95% CI: 0.906-0.986); AUROCClinical = 0.864 (CI: 0.794-0.933); AUROCGenomic/AUROCClinical P = 0.044]. Combined model has an increased AUROCCombined of 0.967 (CI: 0.940-0.993) compared with the individual models (AUROCCombined/AUROCClinical P = 0.0069). Hypersusceptible patients show early alterations in immune-related signaling pathways, epigenetic modulation, and chromatin remodeling. CONCLUSIONS Early triage of burn patients more susceptible to infections can be made using clinical characteristics and/or genomic signatures. Genomic signature suggests new insights into the pathophysiology of hypersusceptibility to infection may lead to novel potential therapeutic or prophylactic targets.
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30
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Diagnostic and prognostic value of sCD14-ST--presepsin for patients admitted to hospital intensive care unit (ICU). Wien Klin Wochenschr 2015; 127:521-7. [PMID: 25854904 DOI: 10.1007/s00508-015-0719-5] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2014] [Accepted: 01/19/2015] [Indexed: 01/02/2023]
Abstract
BACKGROUND Sepsis is a serious problem in intensive care units all over the world. Biomarkers could be useful to identify patients at risk. We focused especially on the performance of presepsin (sCD14-ST), compared to C-reactive protein (CRP), procalcitonin (PCT) and CD64, to determine its diagnostic and prognostic indications. METHODS The study was conducted on 47 hospitalized patients after procedures, who were divided into three groups; systemic inflammatory response (SIRS), sepsis and septic shock. Expression of CD64 on neutrophils presented as CD64 index, sCD14-ST, CRP and PCT were measured in whole blood or plasma samples. All patients had standard samples like urine, respiratory tract samples etc. taken for culturing. Blood cultures were drawn to confirm bloodstream infection. RESULTS Forty (85 %) patients had SIRS with bacterial infection and seven (15 %) patients had SIRS with no infection. All infections were confirmed with blood cultures. Biomarkers were evaluated in all patients. In patients with confirmed infection the values were high. The patients with bacterial infection showed statistical significance with CD64 index (p = 0.003), CRP (p = 0.049) and sCD14-ST (p = 0.026), but not with PCT (p = 1.000). The severity of diagnosed SIRS was significant only with PCT (p < 0.001). CONCLUSION CD64 index, CRP and sCD14-ST served as good parameters to determine possible infection in patients that needed intensive care after major procedures. Values of PCT were the only ones to predict SIRS severity and could distinguish between sepsis and severe sepsis or septic shock.
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31
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Bwanga F, Disqué C, Lorenz MG, Allerheiligen V, Worodria W, Luyombya A, Najjingo I, Weizenegger M. Higher blood volumes improve the sensitivity of direct PCR diagnosis of blood stream tuberculosis among HIV-positive patients: an observation study. BMC Infect Dis 2015; 15:48. [PMID: 25656799 PMCID: PMC4326319 DOI: 10.1186/s12879-015-0785-3] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2014] [Accepted: 01/27/2015] [Indexed: 12/14/2022] Open
Abstract
Background Blood stream tuberculosis (TB), caused by Mycobacterium tuberculosis (MTB) is common among HIV-positive patients, turning rapidly fatal unless detected and treated promptly. Blood culture is currently the standard test for the detection of MTB in whole blood but results take weeks; patients deteriorate markedly and often die before a diagnosis of blood stream TB is made. Rapid molecular tests on whole blood, with potential for same day diagnosis of blood stream TB usually show low sensitivity due to the problem of insufficient MTB DNA template when extraction is performed directly on low blood volumes. This study assessed the influence of blood volume on the sensitivity of a HyBeacon PCR assay-the FluoroType® MTB (Hain Lifescience, Nehren, Germany) on direct detection of MTB in whole blood. Methods Prospective recruitment of HIV-positive patients with clinical suspicion of blood stream TB but not on anti-TB or HIV drug treatment was done. Venous blood samples were collected and DNA extracted using the MolYsis (Molzym, Bremen, Germany) methods; for study A, from duplicate 1 ml (42 patients) and for study B (31 patients) from 9 ml EDTA blood samples. The FluoroType® MTB PCR assay targeting an IS6110 sequence was performed and results compared with blood culture. Results The diagnostic sensitivity and specificity of the FluoroType® MTB PCR in study A was 33% and 97%, respectively. Corresponding values in study B were 71% and 96%, respectively. In both studies, one case each of blood culture-negative blood stream TB was detected with the FluoroType® MTB PCR assay. The median time to positivity of blood culture was 20.1 (range 12–32) for study A and 19.9 days (range 15–30) for study B. Conclusion Larger blood volumes (9 ml) improved and gave acceptable sensitivity of direct PCR diagnosis of blood stream TB.
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Affiliation(s)
- Freddie Bwanga
- Makerere University College of Health Sciences, Kampala, Uganda. .,MBN Clinical Laboratories, Kampala, Uganda.
| | | | | | | | - William Worodria
- Makerere University College of Health Sciences, Kampala, Uganda.
| | | | | | - Michael Weizenegger
- Medizinisches Versorgungszentrum Labor Dr. Limbach und Kollegen, Heidelberg, Germany.
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32
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Unterer S, Lechner E, Mueller RS, Wolf G, Straubinger RK, Schulz BS, Hartmann K. Prospective study of bacteraemia in acute haemorrhagic diarrhoea syndrome in dogs. Vet Rec 2015; 176:309. [PMID: 25568184 DOI: 10.1136/vr.102521] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
In dogs with idiopathic acute haemorrhagic diarrhoea syndrome (AHDS), a serious loss of intestinal mucosal barrier integrity occurs. However, the incidence of bacterial translocation in dogs with idiopathic AHDS is not known. Thus, the objectives of this prospective study were to identify the incidence of bacteraemia, to evaluate the frequency of septic events and the influence of bacteraemia on various clinical and laboratory parameters, duration of hospitalisation and survival of dogs with idiopathic AHDS. The study included 87 dogs with idiopathic AHDS. Twenty-one healthy dogs served as control group. To evaluate clinical significance of bacterial translocation, blood culture results were compared between patients and controls. Clinical and laboratory parameters were compared between patients with positive and negative blood cultures. There was no significant difference in either incidence of bacteraemia between patients with idiopathic AHDS (11 per cent) and controls (14 per cent) or in severity of clinical signs, laboratory parameters, duration of hospitalisation or mortality between blood culture-positive and culture-negative dogs with idiopathic AHDS. The results of this study suggest that the incidence of bacteraemia in dogs with idiopathic AHDS is low and not different from that of healthy control dogs. Bacteraemia does not influence the clinical course or survival and thus antibiotic treatment is not indicated to prevent sepsis.
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Affiliation(s)
- S Unterer
- Clinic of Small Animal Medicine, LMU University of Munich, Veterinaerstrasse 13, Munich 80539, Germany
| | - E Lechner
- Clinic of Small Animal Medicine, LMU University of Munich, Veterinaerstrasse 13, Munich 80539, Germany
| | - R S Mueller
- Clinic of Small Animal Medicine, LMU University of Munich, Veterinaerstrasse 13, Munich 80539, Germany
| | - G Wolf
- Department of Veterinary Sciences, Institute for Infectious Diseases and Zoonoses, LMU Munich, Germany
| | - R K Straubinger
- Department of Veterinary Sciences, Institute for Infectious Diseases and Zoonoses, LMU Munich, Germany
| | - B S Schulz
- Clinic of Small Animal Medicine, LMU University of Munich, Veterinaerstrasse 13, Munich 80539, Germany
| | - K Hartmann
- Clinic of Small Animal Medicine, LMU University of Munich, Veterinaerstrasse 13, Munich 80539, Germany
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Comparison of nested, multiplex, qPCR; FISH; SeptiFast and blood culture methods in detection and identification of bacteria and fungi in blood of patients with sepsis. BMC Microbiol 2014; 14:313. [PMID: 25551203 PMCID: PMC4302608 DOI: 10.1186/s12866-014-0313-4] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2014] [Accepted: 11/26/2014] [Indexed: 01/08/2023] Open
Abstract
Background Microbiological diagnosis of sepsis relies primarily on blood culture data. This study compares four diagnostic methods, i.e. those developed by us: nested, multiplex, qPCR (qPCR) and FISH with commercial methods: SeptiFast (Roche) (SF) and BacT/ALERT® 3D blood culture system (bioMérieux). Blood samples were derived from adult patients with clinical symptoms of sepsis, according to SIRS criteria, hospitalized in the Intensive Care Unit. Results Using qPCR, FISH, SF, and culture, microbial presence was found in 71.8%, 29.6%, 25.3%, and 36.6% of samples, respectively. It was demonstrated that qPCR was significantly more likely to detect microorganisms than the remaining methods; qPCR confirmed the results obtained with the SF kit in all cases wherein bacteria were detected with simultaneous confirmation of Gram-typing. All data collected through the FISH method were corroborated by qPCR. Conclusions The qPCR and FISH methods described in this study may constitute alternatives to blood culture and to the few existing commercial molecular assays since they enable the detection of the majority of microbial species, and the qPCR method allows their identification in a higher number of samples than the SF test. FISH made it possible to show the presence of microbes in a blood sample even before its culture.
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Diagnostic accuracy of SeptiFast multi-pathogen real-time PCR in the setting of suspected healthcare-associated bloodstream infection. Intensive Care Med 2014; 41:86-93. [PMID: 25406409 DOI: 10.1007/s00134-014-3551-x] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2014] [Accepted: 11/06/2014] [Indexed: 01/08/2023]
Abstract
PURPOSE SeptiFast is a real-time PCR assay which targets ribosomal DNA sequences of bacteria and fungi, enabling detection and identification of the commonest pathogens in blood within a few hours, including those acquired in healthcare settings. We report here the first detailed assessment of SeptiFast that focuses on healthcare-associated bloodstream infections which develop during routine critical care. METHODS This was a prospective multicentre study designed to compare the clinical diagnostic accuracy of SeptiFast versus microbiological culture and independent clinical adjudication. This Phase III diagnostic study was performed in an adequately sized cohort of adult patients who developed new signs of suspected bloodstream infection while receiving routine critical care. RESULTS Of 1,006 new episodes of suspected bloodstream infection in 853 patients, 922 (92 %) of these episodes in 795 patients met the inclusion criteria of the study. Patients had been exposed to a median of 8 days (interquartile range 4-16) of hospital care and had received high levels of organ support and recent antibiotic exposure. The SeptiFast test, when compared with bloodstream infection at the species/genus level, had a greater specificity [0.86, 95 % confidence interval (CI) 0.83-0.88] than sensitivity (0.50, 95 % CI 0.39-0.61). There was a low prevalence of blood culture-proven pathogens (9.2 %, 95 % CI 7.4-11.2 %), and the post-test probabilities of both a positive (26.3 %, 95 % CI 19.8-33.7 %) and a negative SeptiFast test (5.6 %, 95 % CI 4.1-7.4 %) indicated potential limitations of this technology in diagnosing bloodstream infection. CONCLUSION When compared with blood culture, SeptiFast is likely to have limited utility for the diagnosis of healthcare-associated bloodstream infection in critical care patients despite its potential to deliver results more rapidly.
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Expression of CD64 on neutrophils can be used to predict the severity of bloodstream infection before broad range 16S rRNA PCR. Folia Microbiol (Praha) 2014; 60:111-8. [PMID: 25253263 DOI: 10.1007/s12223-014-0346-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2013] [Accepted: 09/05/2014] [Indexed: 10/24/2022]
Abstract
The aging population and increased incidence of severe bacterial infection can lead to sepsis. Interest to early identification of endangered patients and identification of pathogen do not always confirm the infection. To use biomarkers can help in early identification of infection and opportunity to start therapy timeously. All biomarkers were defined in 33 out of 96 patients. Thirty-two (97 %) patients had bacterial infection and 1 (3 %) patient had systemic inflammatory response syndrome (SIRS) without infection. PCR confirmed the infection in 27 cases and blood cultures in 8. Area under curve (AUC) for CD64 was 1.00, meanwhile other biomarkers showed 2-fold smaller AUC for positive infection. CD64 index was associated with bacterial infection (p<0.001) and could be used to confirm assessment of SIRS severity (p=0.037). As regards to our results, limited to only 33 patients, CD64 index served as a good parameter to predict bacterial infection and determine severity. The use of broad range 16S ribosomal RNA (rRNA) PCR proved to be an excellent tool to confirm bloodstream infection. The CD64 index had the highest AUC, which exceeded all the others, and could be used to predict the outcome of broad range 16S rRNA PCR from whole blood. However, C-reactive protein (CRP), procalcitonin (PCT) and sCD14 are much easier and faster to measure, but the values could be elevated in other clinical assessments.
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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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Fernández-Romero N, Quiles I, Jiménez C, Oliva MOL, Rivas B, Mingorance J, Romero-Gómez MP. Use of multiplex PCR in diagnosis of bloodstream infections in kidney patients. Diagn Microbiol Infect Dis 2014; 80:93-6. [PMID: 25107361 DOI: 10.1016/j.diagmicrobio.2014.07.001] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2014] [Revised: 06/05/2014] [Accepted: 07/02/2014] [Indexed: 10/25/2022]
Abstract
The LightCycler® SeptiFast Test (Roche Diagnostics GmbH, Mannheim, Germany) was prospectively compared with the standard blood culture technique in a series of 86 kidney patients. The sensitivity of the PCR compared with the culture was 71%, and the specificity was 88%. All the species identified by culture in these patients were in the SeptiFast panel. The median time to results was 1 day for the PCR, 3 days for positive cultures, and 5 days for negative cultures.
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Affiliation(s)
- Natalia Fernández-Romero
- Servicio de Microbiología, Hospital Universitario La Paz, IdiPAZ, Paseo de la Castellana, 261, 28046, Madrid, Spain
| | - Inmaculada Quiles
- Servicio de Microbiología, Hospital Universitario La Paz, IdiPAZ, Paseo de la Castellana, 261, 28046, Madrid, Spain
| | - Carlos Jiménez
- Servicio de Nefrología, Hospital Universitario La Paz, IdiPAZ, Paseo de la Castellana, 261, 28046, Madrid, Spain
| | - María Ovidea Lopez Oliva
- Servicio de Nefrología, Hospital Universitario La Paz, IdiPAZ, Paseo de la Castellana, 261, 28046, Madrid, Spain
| | - Begoña Rivas
- Servicio de Nefrología, Hospital Universitario La Paz, IdiPAZ, Paseo de la Castellana, 261, 28046, Madrid, Spain
| | - Jesús Mingorance
- Servicio de Microbiología, Hospital Universitario La Paz, IdiPAZ, Paseo de la Castellana, 261, 28046, Madrid, Spain
| | - María Pilar Romero-Gómez
- Servicio de Microbiología, Hospital Universitario La Paz, IdiPAZ, Paseo de la Castellana, 261, 28046, Madrid, Spain.
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Diagnostic utility of broad range bacterial 16S rRNA gene PCR with degradation of human and free bacterial DNA in bloodstream infection is more sensitive than an in-house developed PCR without degradation of human and free bacterial DNA. Mediators Inflamm 2014; 2014:108592. [PMID: 25120284 PMCID: PMC4120914 DOI: 10.1155/2014/108592] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2014] [Revised: 05/26/2014] [Accepted: 06/22/2014] [Indexed: 12/18/2022] Open
Abstract
We compared a commercial broad range 16S rRNA gene PCR assay (SepsiTest) to an in-house developed assay (IHP). We assessed whether CD64 index, a biomarker of bacterial infection, can be used to exclude patients with a low probability of systemic bacterial infection. From January to March 2010, 23 patients with suspected sepsis were enrolled. CD64 index, procalcitonin, and C-reactive protein were measured on admission. Broad range 16S rRNA gene PCR was performed from whole blood (SepsiTest) or blood plasma (IHP) and compared to blood culture results. Blood samples spiked with Staphylococcus aureus were used to assess sensitivity of the molecular assays in vitro. CD64 index was lower in patients where possible sepsis was excluded than in patients with microbiologically confirmed sepsis (P = 0.004). SepsiTest identified more relevant pathogens than blood cultures (P = 0.008); in three patients (13%) results from blood culture and SepsiTest were congruent, whereas in four cases (17.4%) relevant pathogens were detected by SepsiTest only. In vitro spiking experiments suggested equal sensitivity of SepsiTest and IHP. A diagnostic algorithm using CD64 index as a decision maker to perform SepsiTest shows improved detection of pathogens in patients with suspected blood stream infection and may enable earlier targeted antibiotic therapy.
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