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Li L, Baker J, Saavedra A, Suster C, Moscova M, Iredell J, Shetty A. Comparison of clinical characteristics and outcomes of patients with sepsis identified by the Sepsis-3 criteria by blood and urine culture results: A multicentre retrospective cohort study. Health Sci Rep 2024; 7:e2162. [PMID: 38899001 PMCID: PMC11186038 DOI: 10.1002/hsr2.2162] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2023] [Revised: 09/22/2023] [Accepted: 05/15/2024] [Indexed: 06/21/2024] Open
Abstract
Background and Aims Blood and urine are the most common culture testing for sepsis patients. This study aimed to compare clinical characteristics and outcomes of sepsis patients by blood and urine culture positivity and to identify factors associated with positive cultures. Methods This retrospective study included patients aged ≥16 years with sepsis identified by the Sepsis-3 criteria presenting to the emergency department at four hospitals between 2017 and 2019 in Australia. Patient clinical outcomes were in-hospital mortality, intensive care unit (ICU) admission, hospital length of stay, and representation following discharge. Four culture groups were defined based on the positivity of blood cultures (BC) and urine cultures (UC) ordered within 24 h of triage. Results Of 4109 patient encounters with sepsis, 2730 (66%) were nonbacteremic, urine culture-negative (BC-UC-); 767 (19%) nonbacteremic, urine culture-positive (BC-UC+); 359 (9%) bacteremic, urine culture-negative (BC+UC-); and 253 (6%) bacteremic, urine culture-positive (BC+UC+). Compared with BC-UC- patients, BC+UC- patients had the highest risk of ICU admission (adjusted odds ratio [AOR] 95% CI: 1.60 [1.18-2.18]) while BC-UC+ patients had lowest risk (adjusted odds ratio [AOR]: 0.56 [0.41-0.76]). BC+UC- patients had the highest risk of 3-day representation (AOR: 1.51 [1.02-2.25]) and second longest hospital stay (adjusted relative risk 1.17 [1.03-1.34]). Antibiotic administration before sample collection for culture was associated with lower odds of positive blood or urine culture results (AOR: 0.38, p < 0.0001). Conclusions Enhanced clinical care should be beneficial for nongenitourinary sepsis patients (BC+UC-) who had the highest comparative risk of adverse clinical outcomes. Every effort needs to be made to collect relevant culture samples before antibiotic administration, to follow up on culture results, and tailor treatment accordingly.
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Affiliation(s)
- Ling Li
- Australian Institute of Health InnovationMacquarie UniversitySydneyNew South WalesAustralia
| | - Jannah Baker
- Australian Institute of Health InnovationMacquarie UniversitySydneyNew South WalesAustralia
| | - Aldo Saavedra
- The University of SydneySydneyNew South WalesAustralia
| | - Carl Suster
- The University of SydneySydneyNew South WalesAustralia
| | | | | | - Amith Shetty
- Australian Institute of Health InnovationMacquarie UniversitySydneyNew South WalesAustralia
- NSW Ministry of HealthSydneyNew South WalesAustralia
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2
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Horn J, Höhn P, Strotmann J, Majchrzak-Stiller B, Buchholz M, Uhl W, Herzog T. Next-generation microbiological testing in intraabdominal infections with PCR technology. Langenbecks Arch Surg 2024; 409:108. [PMID: 38570375 PMCID: PMC10990981 DOI: 10.1007/s00423-024-03298-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Accepted: 03/22/2024] [Indexed: 04/05/2024]
Abstract
PURPOSE Intraabdominal infections (IAI) are increasing worldwide and are a major contributor to morbidity and mortality. Among IAI, the number of multi-drug resistant organisms (MDRO) is increasing globally. We tested the Unyvero A50® for intraabdominal infections, compared the detected microorganisms and antibiotic resistance, and compared the results with those of routine microbiology. METHODS We prospectively compared samples obtained from surgical patients using PCR-based Unyvero IAI cartridges against routine microbiology for the detection of microorganisms. Additionally, we identified clinical parameters that correlated with the microbiological findings. Data were analyzed using the t-test and Mann-Whitney U test. RESULTS Sixty-two samples were analyzed. The PCR system identified more microorganisms, mostly Bacteroides species, Escherichia coli, and Enterococcus spp. For bacterial resistance, the PCR system results were fully concordant with those of routine microbiology, resulting in a sensitivity, specificity, and positive and negative predictive value (PPV, NPV) of 100%. The sensitivity, specificity, PPV, and NPV for the detection of microorganisms were 74%, 58%, 60%, and 72%, respectively. CRP levels were significantly higher in patients with detectable microorganisms. We identified more microorganisms and bacterial resistance in hospital-acquired intra-abdominal infections by using the PCR system. DISCUSSION IAI warrants early identification of the microorganisms involved and their resistance to allow for adequate antibiotic therapy. PCR systems enable physicians to rapidly adjust their antibiotic treatment. Conventional microbiological culture and testing remain essential for determining the minimal growth inhibition concentrations for antibiotic therapy.
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Affiliation(s)
- Julian Horn
- Department of General and Visceral Surgery, St. Josef-Hospital Bochum, Ruhr University Bochum, Gudrunstraße 56, 44791, Bochum, Germany.
| | - Philipp Höhn
- Department of General and Visceral Surgery, Division of Molecular and Clinical Research, St. Josef-Hospital Bochum, Ruhr University Bochum, Gudrunstraße 56, 44791, Bochum, Germany
| | - Johanna Strotmann
- Department of General and Visceral Surgery, Division of Molecular and Clinical Research, St. Josef-Hospital Bochum, Ruhr University Bochum, Gudrunstraße 56, 44791, Bochum, Germany
| | - Britta Majchrzak-Stiller
- Department of General and Visceral Surgery, Division of Molecular and Clinical Research, St. Josef-Hospital Bochum, Ruhr University Bochum, Gudrunstraße 56, 44791, Bochum, Germany
| | - Marie Buchholz
- Department of General and Visceral Surgery, Division of Molecular and Clinical Research, St. Josef-Hospital Bochum, Ruhr University Bochum, Gudrunstraße 56, 44791, Bochum, Germany
| | - Waldemar Uhl
- Department of General and Visceral Surgery, St. Josef-Hospital Bochum, Ruhr University Bochum, Gudrunstraße 56, 44791, Bochum, Germany
| | - Torsten Herzog
- Department of General Surgery and Visceral Surgery, Klinikum Vest, Ruhr University Bochum, Recklinghausen, Germany
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O'Grady NP, Alexander E, Alhazzani W, Alshamsi F, Cuellar-Rodriguez J, Jefferson BK, Kalil AC, Pastores SM, Patel R, van Duin D, Weber DJ, Deresinski S. Society of Critical Care Medicine and the Infectious Diseases Society of America Guidelines for Evaluating New Fever in Adult Patients in the ICU. Crit Care Med 2023; 51:1570-1586. [PMID: 37902340 DOI: 10.1097/ccm.0000000000006022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2023]
Abstract
RATIONALE Fever is frequently an early indicator of infection and often requires rigorous diagnostic evaluation. OBJECTIVES This is an update of the 2008 Infectious Diseases Society of America and Society (IDSA) and Society of Critical Care Medicine (SCCM) guideline for the evaluation of new-onset fever in adult ICU patients without severe immunocompromise, now using the Grading of Recommendations Assessment, Development, and Evaluation (GRADE) methodology. PANEL DESIGN The SCCM and IDSA convened a taskforce to update the 2008 version of the guideline for the evaluation of new fever in critically ill adult patients, which included expert clinicians as well as methodologists from the Guidelines in Intensive Care, Development and Evaluation Group. The guidelines committee consisted of 12 experts in critical care, infectious diseases, clinical microbiology, organ transplantation, public health, clinical research, and health policy and administration. All task force members followed all conflict-of-interest procedures as documented in the American College of Critical Care Medicine/SCCM Standard Operating Procedures Manual and the IDSA. There was no industry input or funding to produce this guideline. METHODS We conducted a systematic review for each population, intervention, comparison, and outcomes question to identify the best available evidence, statistically summarized the evidence, and then assessed the quality of evidence using the GRADE approach. We used the evidence-to-decision framework to formulate recommendations as strong or weak or as best-practice statements. RESULTS The panel issued 12 recommendations and 9 best practice statements. The panel recommended using central temperature monitoring methods, including thermistors for pulmonary artery catheters, bladder catheters, or esophageal balloon thermistors when these devices are in place or accurate temperature measurements are critical for diagnosis and management. For patients without these devices in place, oral or rectal temperatures over other temperature measurement methods that are less reliable such as axillary or tympanic membrane temperatures, noninvasive temporal artery thermometers, or chemical dot thermometers were recommended. Imaging studies including ultrasonography were recommended in addition to microbiological evaluation using rapid diagnostic testing strategies. Biomarkers were recommended to assist in guiding the discontinuation of antimicrobial therapy. All recommendations issued were weak based on the quality of data. CONCLUSIONS The guidelines panel was able to formulate several recommendations for the evaluation of new fever in a critically ill adult patient, acknowledging that most recommendations were based on weak evidence. This highlights the need for the rapid advancement of research in all aspects of this issue-including better noninvasive methods to measure core body temperature, the use of diagnostic imaging, advances in microbiology including molecular testing, and the use of biomarkers.
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Affiliation(s)
- Naomi P O'Grady
- Internal Medicine Services, National Institutes of Health Clinical Center, Bethesda, MD
| | - Earnest Alexander
- Clinical Pharmacy Services, Department of Pharmacy, Tampa General Hospital, Tampa, FL
| | - Waleed Alhazzani
- Department of Medicine, McMaster University, Hamilton, ON, Canada
| | - Fayez Alshamsi
- Department of Internal Medicine, College of Medicine and Health Sciences, United Arab Emirates University, Al Ain, United Arab Emirates
| | - Jennifer Cuellar-Rodriguez
- Laboratory of Clinical Immunology and Microbiology, National Institutes of Allergy and Infectious Diseases, Bethesda, MD
| | - Brian K Jefferson
- Division of Hepatobiliary and Pancreatic Surgery, Department of Internal Medicine-Critical Care Services, Atrium Health Cabarrus, Concord, NC
| | - Andre C Kalil
- Infectious Diseases Division, University of Nebraska Medical Center, Omaha, NE
| | - Stephen M Pastores
- Department of Anesthesiology and Critical Care Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Robin Patel
- Division of Clinical Microbiology, Department of Laboratory Medicine and Pathology, Rochester, MN
- Division of Infectious Diseases, Department of Medicine, Mayo Clinic, Rochester, MN
| | - David van Duin
- Division of Infectious Diseases, University of North Carolina, Chapel Hill, NC
| | - David J Weber
- Division of Infectious Diseases, University of North Carolina, Chapel Hill, NC
| | - Stanley Deresinski
- Division of Infectious Diseases and Geographic Medicine, Stanford University School of Medicine, Stanford, CA
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Lee SJ, Park SY, Lee KH, Lee MW, Yu CY, Maeng J, Kim HD, Kim SW. Development of a Simple Direct and Hot-Start PCR Using Escherichia coli-Expressing Taq DNA Polymerase. Int J Mol Sci 2023; 24:11405. [PMID: 37511160 PMCID: PMC10379934 DOI: 10.3390/ijms241411405] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2023] [Revised: 07/06/2023] [Accepted: 07/11/2023] [Indexed: 07/30/2023] Open
Abstract
Taq DNA polymerases have played an important role in molecular biology for several years and are frequently used for polymerase chain reaction (PCR); hence, there is an increasing interest in developing a convenient method for preparing Taq DNA polymerase for routine use in laboratories. We developed a method using Escherichia coli (E. coli) that expresses thermostable Taq DNA polymerase directly in the PCR without purification. The Taq gene was transformed into E. coli and expressed. After overnight incubation and washing, E. coli-expressing Taq DNA polymerase (EcoliTaq) was used as the DNA polymerase without purification. EcoliTaq showed activity comparable to that of commercial DNA polymerase and remained stable for 3 months. With a high-pH buffer containing 2% Tween 20 and 0.4 M trehalose, EcoliTaq facilitated direct PCR amplification from anticoagulated whole blood samples. EcoliTaq exhibited good performance in allele-specific PCR using both purified DNA and whole blood samples. Furthermore, it proved to be useful as a DNA polymerase in hot-start PCR by effectively minimizing non-specific amplification. We developed a simple and cost-effective direct and hot-start PCR method in which EcoliTaq was used directly as a PCR enzyme, thus eliminating the laborious and time-consuming steps of polymerase purification.
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Affiliation(s)
- Sun Ju Lee
- Department of Health and Safety Convergence Science, Graduate School, Korea University, 145 Anam-ro, Seoul 02841, Republic of Korea
- L-HOPE Program for Community-Based Total Learning Health Systems, Korea University, 145 Anam-ro, Seoul 02841, Republic of Korea
| | - Sang-Yong Park
- Department of Health and Safety Convergence Science, Graduate School, Korea University, 145 Anam-ro, Seoul 02841, Republic of Korea
| | - Kwang-Ho Lee
- Department of Health and Safety Convergence Science, Graduate School, Korea University, 145 Anam-ro, Seoul 02841, Republic of Korea
- Department of Laboratory Medicine, ASAN Medical Center, 88 Olympic-ro 43-gil, Songpa-gu, Seoul 05505, Republic of Korea
| | - Min-Woo Lee
- Department of Health and Safety Convergence Science, Graduate School, Korea University, 145 Anam-ro, Seoul 02841, Republic of Korea
| | - Chae-Yeon Yu
- Department of Health and Safety Convergence Science, Graduate School, Korea University, 145 Anam-ro, Seoul 02841, Republic of Korea
- L-HOPE Program for Community-Based Total Learning Health Systems, Korea University, 145 Anam-ro, Seoul 02841, Republic of Korea
- Graduate School of Particulate Matter Specialization, Korea University, 145 Anam-ro, Seoul 02841, Republic of Korea
| | - Jaeyoung Maeng
- Department of Health and Safety Convergence Science, Graduate School, Korea University, 145 Anam-ro, Seoul 02841, Republic of Korea
- L-HOPE Program for Community-Based Total Learning Health Systems, Korea University, 145 Anam-ro, Seoul 02841, Republic of Korea
- Graduate School of Particulate Matter Specialization, Korea University, 145 Anam-ro, Seoul 02841, Republic of Korea
| | - Hyeong-Dong Kim
- Department of Health and Safety Convergence Science, Graduate School, Korea University, 145 Anam-ro, Seoul 02841, Republic of Korea
| | - Suhng Wook Kim
- Department of Health and Safety Convergence Science, Graduate School, Korea University, 145 Anam-ro, Seoul 02841, Republic of Korea
- L-HOPE Program for Community-Based Total Learning Health Systems, Korea University, 145 Anam-ro, Seoul 02841, Republic of Korea
- Graduate School of Particulate Matter Specialization, Korea University, 145 Anam-ro, Seoul 02841, Republic of Korea
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Zapata-Farfan J, Kafshgari MH, Patskovsky S, Meunier M. Dynamic multispectral detection of bacteria with nanoplasmonic markers. NANOSCALE 2023; 15:3309-3317. [PMID: 36625354 DOI: 10.1039/d2nr03047k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
Culture-based diagnosis of bacterial diseases is a time-consuming technique that can lead not only to antibiotic resistance or bacterial mutation but also to fast-spreading diseases. Such mutations contribute to the fast deterioration of the patient's health and in some cases the death depending on the complexity of the infection. There is great interest in developing widely available molecular-level diagnostics that provide accurate and rapid diagnosis at the individual level and that do not require sophisticated analysis or expensive equipment. Here, we present a promising analytical approach to detect the presence of pathogenic bacteria based on their dynamic properties enhanced with nanoplasmonic biomarkers. These markers have shown greater photostability and biocompatibility compared to fluorescent markers and quantum dots, and serve as both a selective marker and an amplifying agent in optical biomedical detection. We show that a simple dark-field side- illumination technique can provide sufficiently high-contrast dynamic images of individual plasmonic nanoparticles attached to Escherichia coli (E. coli) for multiplex biodetection. Combined with numerical dynamic filtering, our proposed system shows great potential for the deployment of portable commercial devices for rapid diagnostic tests available to physicians in emergency departments, clinics and public hospitals as point-of-care devices.
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Affiliation(s)
- Jennyfer Zapata-Farfan
- Department of Engineering Physics, Polytechnique Montréal, Montréal, Québec, H3C 3A7, Canada.
| | | | - Sergiy Patskovsky
- Department of Engineering Physics, Polytechnique Montréal, Montréal, Québec, H3C 3A7, Canada.
| | - Michel Meunier
- Department of Engineering Physics, Polytechnique Montréal, Montréal, Québec, H3C 3A7, Canada.
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Badran S, Chen M, Coia JE. Multiplex Droplet Digital Polymerase Chain Reaction Assay for Rapid Molecular Detection of Pathogens in Patients With Sepsis: Protocol for an Assay Development Study. JMIR Res Protoc 2021; 10:e33746. [PMID: 34898460 PMCID: PMC8713102 DOI: 10.2196/33746] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Accepted: 10/24/2021] [Indexed: 12/19/2022] Open
Abstract
BACKGROUND Blood cultures are the cornerstone of diagnosis for detecting the presence of bacteria or fungi in the blood, with an average detection time of 48 hours and failure to detect a pathogen occurring in approximately 50% of patients with sepsis. Rapid diagnosis would facilitate earlier treatment and/or an earlier switch to narrow-spectrum antibiotics. OBJECTIVE The aim of this study is to develop and implement a multiplex droplet digital polymerase chain reaction (ddPCR) assay as a routine diagnostic tool in the detection and identification of pathogens from whole blood and/or blood culture after 3 hours of incubation. METHODS The study consists of three phases: (1) design of primer-probe pairs for accurate and reliable quantification of the most common sepsis-causing microorganisms using a multiplex reaction, (2) determination of the analytical sensitivity and specificity of the multiplex ddPCR assay, and (3) a clinical study in patients with sepsis using the assay. The QX200 Droplet Digital PCR System will be used for the detection of the following species-specific genes in blood from patients with sepsis: coa (staphylocoagulase) in Staphylococcus aureus, cpsA (capsular polysaccharide) in Streptococcus pneumoniae, uidA (beta-D-glucuronidase) in Escherichia coli, oprL (peptidoglycan-associated lipoprotein) in Pseudomonas aeruginosa, and the highly conserved regions of the 16S rRNA gene for Gram-positive and Gram-negative bacteria. All data will be analyzed using QuantaSoft Analysis Pro Software. RESULTS In phase 1, to determine the optimal annealing temperature for the designed primer-probe pairs, results from a gradient temperature experiment will be collected and the limit of detection (LOD) of the assay will be determined. In phase 2, results for the analytical sensitivity and specificity of the assay will be obtained after an optimization of the extraction and purification method in spiked blood. In phase 3, clinical sensitivity and specificity as compared to the standard blood culture technique will be determined using 301 clinical samples. CONCLUSIONS Successful design of primer-probe pairs in the first phase and subsequent optimization and determination of the LOD will allow progression to phase 3 to compare the novel method with existing blood culture methods. INTERNATIONAL REGISTERED REPORT IDENTIFIER (IRRID) PRR1-10.2196/33746.
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Affiliation(s)
- Samir Badran
- Research Unit in Clinical Microbiology, Department of Clinical Diagnostics, Hospital South West Jutland, University Hospital of Southern Denmark, Esbjerg, Denmark
- Department of Regional Health Research, Faculty of Health Sciences, University of Southern Denmark, Odense, Denmark
| | - Ming Chen
- Department of Regional Health Research, Faculty of Health Sciences, University of Southern Denmark, Odense, Denmark
- Department of Clinical Microbiology, Hospital of Southern Jutland, University Hospital of Southern Denmark, Aabenraa, Denmark
| | - John E Coia
- Research Unit in Clinical Microbiology, Department of Clinical Diagnostics, Hospital South West Jutland, University Hospital of Southern Denmark, Esbjerg, Denmark
- Department of Regional Health Research, Faculty of Health Sciences, University of Southern Denmark, Odense, Denmark
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7
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Culture independent detection systems for bloodstream infection. Clin Microbiol Infect 2021; 28:195-201. [PMID: 34687856 DOI: 10.1016/j.cmi.2021.09.039] [Citation(s) in RCA: 49] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Revised: 08/30/2021] [Accepted: 09/28/2021] [Indexed: 12/14/2022]
Abstract
BACKGROUND Sepsis and bloodstream infection are associated with significant morbidity and mortality, and early effective antimicrobial therapy has been demonstrated to improve patient outcomes. Traditional culture-based methods, however, have several limitations which hamper a prompt diagnosis in bloodstream infection, including long turnaround times and limited sensitivity. In the last years, advances have been made in the development of several technologies which allow the identification of pathogens and their resistance markers directly from whole blood, possibly representing promising alternatives to conventional culture methods. OBJECTIVES To review the currently commercially available emerging assays for the diagnosis of bloodstream infections directly from whole blood, including their performance and the available data about their impact on patients' outcome. SOURCES Peer-reviewed publications relevant to the topic have been searched through PubMed; manufacturers' websites have also been consulted as a data source. CONTENT We have reviewed available data about the following technologies: multiplex real-time PCR working directly from whole blood (Magicplex Sepsis Real-Time test, Seegene), PCR combined with T2 Magnetic Resonance (T2Candida and T2Bacteria panel, T2Biosystem), and metagenomics-based assays (including SepsiTest, Molzym; iDTECT Dx Blood, PathoQuest; Karius NGS plasma Test, Karius). Performance characteristics, advantages and pitfalls of each method are described, and available data about their impact on patients' clinical outcomes are discussed. IMPLICATIONS The potential of rapid diagnostic tests applied on whole blood in improving the management of patients with bloodstream infection and sepsis is high, both in terms of reducing turnaround times and improving the sensitivity of pathogen and antimicrobial resistance detection. However, overall, there is still a scarcity of data about the real-life performance of such tests, and well-designed studies are awaited for assessing the impact of these emerging technologies on patients' outcomes.
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8
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Singhal C, Bruno JG, Kaushal A, Sharma TK. Recent Advances and a Roadmap to Aptamer-Based Sensors for Bloodstream Infections. ACS APPLIED BIO MATERIALS 2021; 4:3962-3984. [PMID: 35006817 DOI: 10.1021/acsabm.0c01358] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The present review is intended to describe bloodstream infections (BSIs), the major pathogens responsible for BSIs, conventional tests and their limitations, commercially available methods used, and the aptamer and nanomaterials-based approaches developed so far for the detection of BSIs. The advantages associated with aptamers and the aptamer-based sensors, the comparison between the aptamers and the antibodies, and the various types of aptasensors developed so far for the detection of bloodstream infections have been described in detail in the present review. Also, the future outlook and roadmap toward aptamer-based sensors and the challenges associated with the aptamer development have also been concluded in this review.
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Affiliation(s)
- Chaitali Singhal
- Aptamer Technology and Diagnostic Laboratory, Multidisciplinary Clinical and Translational Research Group, Translational Health Science and Technology Institute (THSTI), Faridabad, Haryana 121001, India
| | - John G Bruno
- Nanohmics, Inc., Austin, Texas 78741, United States
| | - Ankur Kaushal
- Centre of Nanotechnology, Amity University, Manesar, Gurugram, Haryana 122413, India
| | - Tarun K Sharma
- Aptamer Technology and Diagnostic Laboratory, Multidisciplinary Clinical and Translational Research Group, Translational Health Science and Technology Institute (THSTI), Faridabad, Haryana 121001, India
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9
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Li Y, Guo J, Yang H, Li H, Shen Y, Zhang D. Comparison of culture-negative and culture-positive sepsis or septic shock: a systematic review and meta-analysis. CRITICAL CARE : THE OFFICIAL JOURNAL OF THE CRITICAL CARE FORUM 2021; 25:167. [PMID: 33964934 PMCID: PMC8106121 DOI: 10.1186/s13054-021-03592-8] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/07/2021] [Accepted: 04/30/2021] [Indexed: 11/15/2022]
Abstract
Background Mortality and other clinical outcomes between culture-negative and culture-positive septic patients have been documented inconsistently and are very controversial. A systematic review and meta-analysis was performed to compare the clinical outcomes of culture-negative and culture-positive sepsis or septic shock. Methods We searched the PubMed, Cochrane and Embase databases for studies from inception to the 1st of January 2021. We included studies involving patients with sepsis or septic shock. All authors reported our primary outcome of all-cause mortality and clearly compared culture-negative versus culture-positive patients with clinically relevant secondary outcomes (ICU length of stay, hospital length of stay, mechanical ventilation requirements, mechanical ventilation duration and renal replacement requirements). Results were expressed as odds ratio (OR) and mean difference (MD) with accompanying 95% confidence interval (CI). Results Seven studies including 22,655 patients were included. The primary outcome of this meta-analysis showed that there was no statistically significant difference in the all-cause mortality between two groups (OR = 0.95; 95% CI, 0.88 to 1.01; P = 0.12; Chi-2 = 30.71; I2 = 80%). Secondary outcomes demonstrated that there was no statistically significant difference in the ICU length of stay (MD = − 0.19;95% CI, − 0.42 to 0.04; P = 0.10;Chi-2 = 5.73; I2 = 48%), mechanical ventilation requirements (OR = 1.02; 95% CI, 0.94 to 1.11; P = 0.61; Chi2 = 6.32; I2 = 53%) and renal replacement requirements (OR = 0.82; 95% CI, 0.67 to 1.01; P = 0.06; Chi-2 = 1.21; I2 = 0%) between two groups. The hospital length of stay of culture-positive group was longer than that of the culture-negative group (MD = − 3.48;95% CI, − 4.34 to − 2.63; P < 0.00001;Chi-2 = 1.03; I2 = 0%). The mechanical ventilation duration of culture-positive group was longer than that of the culture-negative group (MD = − 0.64;95% CI, − 0.88 to − 0.4; P < 0.00001;Chi-2 = 4.86; I2 = 38%). Conclusions Culture positivity or negativity was not associated with mortality of sepsis or septic shock patients. Furthermore, culture-positive septic patients had similar ICU length of stay, mechanical ventilation requirements and renal replacement requirements as those culture-negative patients. The hospital length of stay and mechanical ventilation duration of culture-positive septic patients were both longer than that of the culture-negative patients. Further large-scale studies are still required to confirm these results.
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Affiliation(s)
- Yuting Li
- Department of Intensive Care Unit, The First Hospital of Jilin University, Changchun, 130021, Jilin, China
| | - Jianxing Guo
- Department of Intensive Care Unit, The First Hospital of Jilin University, Changchun, 130021, Jilin, China
| | - Hongmei Yang
- Department of Intensive Care Unit, The First Hospital of Jilin University, Changchun, 130021, Jilin, China
| | - Hongxiang Li
- Department of Intensive Care Unit, The First Hospital of Jilin University, Changchun, 130021, Jilin, China
| | - Yangyang Shen
- Department of Intensive Care Unit, The First Hospital of Jilin University, Changchun, 130021, Jilin, China
| | - Dong Zhang
- Department of Intensive Care Unit, The First Hospital of Jilin University, Changchun, 130021, Jilin, China.
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10
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Rello J, Alonso-Tarrés C. Emerging Technologies for Microbiologic Diagnosis of Sepsis: The rapid determination of resistance to antimicrobial agents should be the key. Clin Infect Dis 2021; 73:1173-1175. [PMID: 33895796 DOI: 10.1093/cid/ciab355] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Indexed: 11/13/2022] Open
Affiliation(s)
- Jordi Rello
- Clinical Research in Pneumonia & Sepsis (CRIPS). Vall d'Hebron Institute of Research (VHIR), Barcelona, Spain.,Clinical Research. CHU Maribeau. Nîmes, France
| | - Carles Alonso-Tarrés
- Microbiology Department, Laboratory. Fundació Puigvert. Barcelona, Spain.,Universitat Autònoma de Barcelona, Spain
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11
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Emerging Microbiology Diagnostics for Transplant Infections: On the Cusp of a Paradigm Shift. Transplantation 2020; 104:1358-1384. [PMID: 31972701 DOI: 10.1097/tp.0000000000003123] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
In light of the heightened risk for infection associated with solid organ and hematopoietic stem cell transplantation, rapid and accurate microbiology diagnostics are essential to the practice of transplant clinicians, including infectious diseases specialists. In the last decade, diagnostic microbiology has seen a shift toward culture-independent techniques including single-target and multiplexed molecular testing, mass-spectrometry, and magnetic resonance-based methods which have together greatly expanded the array of pathogens identified, increased processing speed and throughput, allowed for detection of resistance determinants, and ultimately improved the outcomes of infected transplant recipients. More recently, a newer generation of diagnostics with immense potential has emerged, including multiplexed molecular panels directly applicable to blood and blood culture specimens, next-generation metagenomics, and gas chromatography mass spectrometry. Though these methods have some recognized drawbacks, many have already demonstrated improved sensitivity and a positive impact on clinical outcomes in transplant and immunocompromised patients.
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12
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D'Onofrio V, Salimans L, Bedenić B, Cartuyvels R, Barišić I, Gyssens IC. The Clinical Impact of Rapid Molecular Microbiological Diagnostics for Pathogen and Resistance Gene Identification in Patients With Sepsis: A Systematic Review. Open Forum Infect Dis 2020; 7:ofaa352. [PMID: 33033730 PMCID: PMC7528559 DOI: 10.1093/ofid/ofaa352] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2020] [Accepted: 08/10/2020] [Indexed: 12/12/2022] Open
Abstract
Fast microbiological diagnostics (MDx) are needed to ensure early targeted antimicrobial treatment in sepsis. This systematic review focuses on the impact on antimicrobial management and patient outcomes of MDx for pathogen and resistance gene identification compared with blood cultures. PubMed was searched for clinical studies using either whole blood directly or after short-term incubation. Twenty-five articles were retrieved describing the outcomes of 8 different MDx. Three interventional studies showed a significant increase in appropriateness of antimicrobial therapy and a nonsignificant change in time to appropriate therapy. Impact on mortality was conflicting. Length of stay was significantly lower in 2 studies. A significant decrease in antimicrobial cost was demonstrated in 6 studies. The limitations of this systematic review include the low number and observed heterogeneity of clinical studies. In conclusion, potential benefits of MDx regarding antimicrobial management and some patient outcomes were reported. More rigorous intervention studies are needed focusing on the direct benefits for patients.
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Affiliation(s)
- Valentino D'Onofrio
- Faculty of Medicine and Life Sciences, Hasselt University, Hasselt, Belgium.,Department of Infectious Diseases and Immunity, Jessa Hospital, Hasselt, Belgium.,Department of Internal Medicine and Radboud Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Lene Salimans
- Faculty of Medicine and Life Sciences, Hasselt University, Hasselt, Belgium
| | - Branka Bedenić
- Department of Microbiology, School of Medicine, University of Zagreb, Zagreb, Croatia
| | | | - Ivan Barišić
- Molecular diagnostics, Austrian Institute of Technology, Vienna, Austria
| | - Inge C Gyssens
- Faculty of Medicine and Life Sciences, Hasselt University, Hasselt, Belgium.,Department of Internal Medicine and Radboud Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, the Netherlands
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13
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Black LP, Puskarich MA, Henson M, Miller T, Reddy ST, Fernandez R, Guirgis FW. Quantitative and Qualitative Assessments of Cholesterol Association With Bacterial Infection Type in Sepsis and Septic Shock. J Intensive Care Med 2020; 36:808-817. [PMID: 32578468 DOI: 10.1177/0885066620931473] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
BACKGROUND Reduced cholesterol levels are associated with increased organ failure and mortality in sepsis. Cholesterol levels may vary by infection type (gram negative vs positive), possibly reflecting differences in cholesterol-mediated bacterial clearance. METHODS This was a secondary analysis of a combined data set of 2 prospective cohort studies of adult patients meeting Sepsis-3 criteria. Infection types were classified as gram negative, gram positive, or culture negative. We investigated quantitative (levels) and qualitative (dysfunctional high-density lipoprotein [HDL]) cholesterol differences. We used multivariable logistic regression to control for disease severity. RESULTS Among 171 patients with sepsis, infections were gram negative in 67, gram positive in 46, and culture negative in 47. Both gram-negative and gram-positive infections occurred in 11 patients. Total cholesterol (TC), low-density lipoprotein cholesterol (LDL-C), and HDL cholesterol (HDL-C) levels were lower for culture-positive sepsis at enrollment (TC, P < .001; LDL-C, P < .001; HDL-C, P = .011) and persisted after controlling for disease severity. Similarly, cholesterol levels were lower among culture-positive patients at 48 hours (TC, P = .012; LDL-C, P = .029; HDL-C, P = .002). Triglyceride (TG) levels were lower at enrollment (P =.033) but not at 48 hours (P = .212). There were no differences in dysfunctional HDL. Among bacteremic patients, cholesterol levels were lower at enrollment (TC, P = .010; LDL-C, P = .010; HDL-C, P ≤ .001; TG, P = .005) and at 48 hours (LDL-C, P = .027; HDL-C, P < .001; TG, P = .020), except for 48 hour TC (P = .051). In the bacteremia subgroup, enrollment TC and LDL-C were lower for gram-negative versus gram-positive infections (TC, P = .039; LDL-C, P = .023). CONCLUSION Cholesterol levels are significantly lower among patients with culture-positive sepsis and bacteremia.
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Affiliation(s)
- Lauren Page Black
- Department of Emergency Medicine, 137869University of Florida College of Medicine - Jacksonville, Jacksonville, FL, USA
| | - Michael A Puskarich
- Department of Emergency Medicine, Hennepin County Medical Center, Minneapolis, MN, USA.,Department of Emergency Medicine, 5635University of Minnesota, Minneapolis, MN, USA
| | - Morgan Henson
- Department of Emergency Medicine, 137869University of Florida College of Medicine - Jacksonville, Jacksonville, FL, USA
| | - Taylor Miller
- Department of Emergency Medicine, 137869University of Florida College of Medicine - Jacksonville, Jacksonville, FL, USA
| | - Srinivasa T Reddy
- Department of Medicine, Molecular & Medical Pharmacology, University of California, Los Angeles, CA, USA
| | - Rosemarie Fernandez
- Department of Emergency Medicine, University of Florida College of Medicine, Gainesville, FL, USA.,Center for Experiential Learning and Simulation, University of Florida College of Medicine, Gainesville, FL, USA
| | - Faheem W Guirgis
- Department of Emergency Medicine, 137869University of Florida College of Medicine - Jacksonville, Jacksonville, FL, USA
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14
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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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15
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Schwarzenbacher J, Kuhn SO, Vollmer M, Scheer C, Fuchs C, Rehberg S, Balau V, Hahnenkamp K, Bohnert JA, Gründling M. On-site blood culture incubation shortens the time to knowledge of positivity and microbiological results in septic patients. PLoS One 2019; 14:e0225999. [PMID: 31826003 PMCID: PMC6905563 DOI: 10.1371/journal.pone.0225999] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2019] [Accepted: 11/19/2019] [Indexed: 12/29/2022] Open
Abstract
Introduction To determine whether on-site incubation of blood cultures at the intensive care unit (ICU) improves not only the time to incubation but also time to positivity, time to knowledge of positivity and time to results (identification and antibiotic susceptibility testing). Methods This observational single-centre study in ICU patients with severe sepsis and septic shock investigated the impact of blood culture incubation immediately on-site at the ICU (ICU group) by comparison with traditional processing in a remote laboratory (LAB group) on different time intervals of blood culture diagnostics from obtaining blood to clinician notification of final result. The effect of on-site incubation was evaluated in Kaplan-Meier estimates for the time to positivity, time to knowledge of positivity and time to microbiological results and a linear mixed model was built. Results A total of 3,549 blood culture sets from 657 ICU patients were analysed: 2,381 in the LAB group and 1,168 in the ICU group. Overall, 660 (18.6%) blood culture sets were positive and 2,889 (81.4%) sets remained negative. On-site incubation was associated with reduced time to knowledge of positivity (46.9 h [CI 43.4–50.8 h] vs. 28.0 h [CI 23.6–32.2 h], p < 0.001) and reduced time to result (61.4 h [CI 58.4–64.8 h] vs. 42.1 h [CI 39.1–47.5 h], p < 0.001). In blood cultures processed instantaneously at the ICU compared to incubation in the remote laboratory within 4 h, the time to microbiological result was significantly reduced by 8.5 h (p < 0.001). Pre-existing anti-infective therapy had no significant impact on diagnostic time intervals. Conclusions Instantaneous incubation of blood cultures in the ICU compared to incubation in a remote laboratory significantly improves time to knowledge to positivity and time to result. These effects are even more pronounced during off-hours of the microbiological laboratory. The results underline the importance of 24/7 diagnostics to provide round-the-clock processing of blood culture samples in patients with sepsis and septic shock and an immediate to communication of the results to the clinicians.
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Affiliation(s)
| | - Sven-Olaf Kuhn
- Department of Anesthesiology, University Hospital of Greifswald, Greifswald, Germany
- * E-mail:
| | - Marcus Vollmer
- Institute of Bioinformatics, University Medicine Greifswald, Greifswald, Germany
| | - Christian Scheer
- Department of Anesthesiology, University Hospital of Greifswald, Greifswald, Germany
| | - Christian Fuchs
- Department of Anesthesiology, University Hospital of Greifswald, Greifswald, Germany
| | - Sebastian Rehberg
- Department of Anesthesiology, Intensive Care, Emergency Medicine, Transfusion Medicine and Pain Therapy, Protestant Hospital of the Bethel Foundation, Bielefeld, Germany
| | - Veronika Balau
- IMD Labor Greifswald, MVZ Labor Greifswald GmbH, Greifswald, Germany
| | - Klaus Hahnenkamp
- Department of Anesthesiology, University Hospital of Greifswald, Greifswald, Germany
| | - Jürgen A. Bohnert
- Friedrich Loeffler Institute of Microbiology, University Hospital Greifswald, Greifswald, Germany
| | - Matthias Gründling
- Department of Anesthesiology, University Hospital of Greifswald, Greifswald, Germany
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16
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16S rDNA droplet digital PCR for monitoring bacterial DNAemia in bloodstream infections. PLoS One 2019; 14:e0224656. [PMID: 31721817 PMCID: PMC6853374 DOI: 10.1371/journal.pone.0224656] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2019] [Accepted: 10/18/2019] [Indexed: 12/20/2022] Open
Abstract
Repeated quantitative measurement of bacterial DNA on whole blood has been shown to be a promising method for monitoring bloodstream infection (BSI) with selected bacterial species. To enable broad use of this method, we developed a quantitative droplet digital PCR (ddPCR) method for 16S rDNA. It was validated with species-specific ddPCRs for Staphylococcus aureus (nuc), Streptococcus pneumoniae (lytA), and Escherichia coli (uidA) on spiked whole blood samples and on repeated whole blood samples (days 0, 1–2, 3–4, 6–8, and 13–15) from 83 patients with BSI with these pathogens. In these patients, 16S rDNA and species-specific DNA were detected in 60% and 61%, respectively, at least at one time-point. The highest positivity rates were seen in S. aureus BSI, where 92% of the patients were 16S rDNA-positive and 85% nuc-positive. Quantitative 16S rDNA and species-specific DNA showed strong correlations in spiked samples (r = 0.98; p < 0.0001) and clinical samples (r = 0.84; p < 0.0001). Positivity for 16S rDNA was rapidly cleared in patients with S. pneumoniae and E. coli BSI, but more slowly and sometimes persisted, in those with S. aureus BSI. The initial 16S rDNA load was higher in BSI patients with sepsis (Sepsis-3 definition) than without sepsis (median 2.38 vs. 0 lg10 copies/mL; p = 0.031) and in non-survivors than in survivors (median 2.83 vs. 0 lg10 copies/mL; p = 0.006). 16S rDNA ddPCR appears to be a promising method for bacterial DNA monitoring during BSI. The clinical value of such monitoring should be further studied.
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17
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Rapid microbiological tests for bloodstream infections due to multidrug resistant Gram-negative bacteria: therapeutic implications. Clin Microbiol Infect 2019; 26:713-722. [PMID: 31610299 DOI: 10.1016/j.cmi.2019.09.023] [Citation(s) in RCA: 49] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2019] [Revised: 09/20/2019] [Accepted: 09/27/2019] [Indexed: 12/13/2022]
Abstract
BACKGROUND Treating severe infections due to multidrug-resistant Gram-negative bacteria (MDR-GNB) is one of the most important challenges for clinicians worldwide, partly because resistance may remain unrecognized until identification of the causative agent and/or antimicrobial susceptibility testing (AST). Recently, some novel rapid test for identification and/or AST of MDR-GNB from positive blood cultures or the blood of patients with bloodstream infections (BSIs) have become available. OBJECTIVES The objective of this narrative review is to discuss the advantages and limitations of different rapid tests for identification and/or AST of MDR-GNB from positive blood cultures or the blood of patients with BSI, as well as the available evidence on their possible role to improve therapeutic decisions and antimicrobial stewardship. SOURCES Inductive PubMed search for publications relevant to the topic. CONTENT The present review is structured in the following way: (a) rapid tests on positive blood cultures; (b) rapid tests directly on whole blood; (c) therapeutic implications. IMPLICATIONS Novel molecular and phenotypic rapid tests for identification and AST show the potential for favourably influencing patients' outcomes and results of antimicrobial stewardship interventions by reducing both the time to effective treatment and the misuse of antibiotics, although the interpretation about their impact on actual therapeutic decisions and patients' outcomes is still complex. Factors such as feasibility and personnel availability, as well as the detailed knowledge of the local microbiological epidemiology, need to be considered very carefully when implementing novel rapid tests in laboratory workflows and algorithms. Providing high-level, comparable evidence on the clinical impact of rapid identification and AST is becoming of paramount importance for MDR-GNB infections, since in the near future rapid identification of specific resistance mechanisms could be crucial for guiding rapid, effective, and targeted therapy against specific resistance mechanisms.
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18
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Trung NT, Thau NS, Bang MH, Song LH. PCR-based Sepsis@Quick test is superior in comparison with blood culture for identification of sepsis-causative pathogens. Sci Rep 2019; 9:13663. [PMID: 31541157 PMCID: PMC6754458 DOI: 10.1038/s41598-019-50150-y] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2018] [Accepted: 09/05/2019] [Indexed: 12/17/2022] Open
Abstract
Sepsis is an acute, often fatal syndrome that requires early diagnosis and proper treatment. Blood culture (BC) is the gold standard for the identification of pathogens, however it has marked limitations, including that it is time-consuming (delaying treatment) and can only detect microbes that readily grow under culture conditions. Alternatively, non-culture-based methodologies like polymerase chain reaction (PCR) are faster but also have limitations; e.g., the reaction is often inhibited by the abundance of human DNA and thus can only detect limited known target pathogens. In our previous publication, we have demonstrated a proof-of-concept of a simple pre-analytical tool to remove human DNA from patients’ blood specimens, hence allowing downstream PCRs to detect rare bacterial genetic materials. In the current study, we reported a better performance of a novel prototype diagnosis kit named Sepsis@Quick that combines human DNA removal step with real-time PCRs compared to blood-culture for identifying sepsis causative bacteria. Our data showed that Sepsis@Quick is superior to blood culture in which the novel diagnostic kit could identify more pathogens and even polymicrobial infection, faster and less influenced by the empirical administration of broad spectrum antibiotic therapy (single administration or combination of cephalosporin III and fluoroquinolon). Additionally, for the first time, we demonstrated that positive results achieved by Sepsis@Quick are significantly associated with a reduction of sepsis-related mortality.
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Affiliation(s)
- Ngo Tat Trung
- Vietnamese-German Center for Medical Research (VG-CARE), 108 Military Central Hospital, Hà Nội, Vietnam. .,Centre for Genetic Consultation and Cancer Screening, 108 Military Central Hospital, Hà Nội, Vietnam. .,Department of Molecular Biology, 108 Military Central Hospital, Hà Nội, Vietnam.
| | - Nguyen Sy Thau
- Vietnamese-German Center for Medical Research (VG-CARE), 108 Military Central Hospital, Hà Nội, Vietnam.,Faculty of Tropical and Infectious Diseases, 108 Military Central Hospital, Hà Nội, Vietnam
| | - Mai Hong Bang
- Vietnamese-German Center for Medical Research (VG-CARE), 108 Military Central Hospital, Hà Nội, Vietnam
| | - Le Huu Song
- Vietnamese-German Center for Medical Research (VG-CARE), 108 Military Central Hospital, Hà Nội, Vietnam. .,Faculty of Tropical and Infectious Diseases, 108 Military Central Hospital, Hà Nội, Vietnam.
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19
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Zboromyrska Y, Cillóniz C, Cobos-Trigueros N, Almela M, Hurtado JC, Vergara A, Mata C, Soriano A, Mensa J, Marco F, Vila J. Evaluation of the Magicplex™ Sepsis Real-Time Test for the Rapid Diagnosis of Bloodstream Infections in Adults. Front Cell Infect Microbiol 2019; 9:56. [PMID: 30931259 PMCID: PMC6423426 DOI: 10.3389/fcimb.2019.00056] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2018] [Accepted: 02/20/2019] [Indexed: 12/12/2022] Open
Abstract
Sepsis is a serious health condition worldwide, affecting more than 30 million people globally each year. Blood culture (BC) is generally used to diagnose sepsis because of the low quantity of microbes occurring in the blood during such infections. However, ~50% of bloodstream infections (BSI) give negative BC, this figure being higher for sepsis, which delays the start of appropriate antimicrobial therapy. This prospective study evaluated a multiplex real-time polymerase chain reaction, the MagicplexTM Sepsis test (MP), for the detection of pathogens from whole blood, comparing it to routine BC. We analyzed 809 blood samples from 636 adult patients, with 132/809 (16.3%) of the samples positive for one or more relevant microorganism according to BC and/or MP. The sensitivity and specificity of MP were 29 and 95%, respectively, while the level of agreement between BC and MP was 87%. The rate of contaminated samples was higher for BC (10%) than MP (4.8%) (P < 0.001). Patients with only MP-positive samples were more likely to be on antimicrobial treatment (47%) than those with only BC-positive samples (18%) (P = 0.002). In summary, the MP test could be useful in some clinical setting, such as among patients on antibiotic therapy. Nevertheless, a low sensitivity demonstrated impairs its use as a part of a routine diagnostic algorithm.
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Affiliation(s)
- Yuliya Zboromyrska
- The Consortium of the Intercomarcal Laboratory of the Alt Penedès, Department of Microbiology, Vilafranca del Penedès, Spain
| | - Catia Cillóniz
- Department of Pneumology, Hospital Clinic of Barcelona, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Networked Biomedical Research Center for Respiratory Diseases (CIBERES), University of Barcelona, Barcelona, Spain
| | - Nazaret Cobos-Trigueros
- Department of Infectious Diseases, Hospital Clinic, University of Barcelona, Barcelona, Spain
| | - Manel Almela
- The Consortium of the Intercomarcal Laboratory of the Alt Penedès, Department of Microbiology, Vilafranca del Penedès, Spain
| | - Juan Carlos Hurtado
- Department of Microbiology, ISGlobal, Barcelona Centre for International Health Research, Hospital Clinic, University of Barcelona, Barcelona, Spain
| | - Andrea Vergara
- Department of Microbiology, ISGlobal, Barcelona Centre for International Health Research, Hospital Clinic, University of Barcelona, Barcelona, Spain
| | - Caterina Mata
- Sample Preparation Team, Centre Nacional d'Anàlisi Genòmica, Parc Científic de Barcelona – Torre I, Barcelona, Spain
| | - Alex Soriano
- Department of Infectious Diseases, Hospital Clinic, University of Barcelona, Barcelona, Spain
| | - Josep Mensa
- Department of Infectious Diseases, Hospital Clinic, University of Barcelona, Barcelona, Spain
| | - Francesc Marco
- Department of Microbiology, ISGlobal, Barcelona Centre for International Health Research, Hospital Clinic, University of Barcelona, Barcelona, Spain
| | - Jordi Vila
- Department of Microbiology, ISGlobal, Barcelona Centre for International Health Research, Hospital Clinic, University of Barcelona, Barcelona, Spain
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20
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Substantial diagnostic impact of blood culture independent molecular methods in bloodstream infections: Superior performance of PCR/ESI-MS. Sci Rep 2018; 8:16024. [PMID: 30375435 PMCID: PMC6207717 DOI: 10.1038/s41598-018-34298-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2018] [Accepted: 09/28/2018] [Indexed: 02/06/2023] Open
Abstract
This study analyzed the performance of different molecular technologies along with blood culture (BC) in the diagnosis of bloodstream infections (BSI) in patients from internal medicine wards - including intensive care units (ICUs) - and the emergency room. Patients with systemic inflammatory response syndrome were prospectively included. BCs and EDTA whole blood were obtained simultaneously. The latter was analyzed by PCR combined with electrospray ionization mass spectrometry (PCR/ESI-MS; IRIDICA BAC BSI assay, Abbott) and by SeptiFast (Roche). Cases were classified as BSI according to adapted European Centre for Disease Prevention and Control criteria. Out of 462 analyzed episodes, 193 with valid test results fulfilled the inclusion criteria and were further evaluated. Sixty-nine (35.8%) were classified as BSI. PCR/ESI-MS showed a significantly better overall performance than BC (p = 0.004) or SeptiFast (p = 0.034). Only in patients from the ICU the performance of SeptiFast was comparable to that of PCR/ESI-MS. Mainly due to the negative effect of antimicrobial pre-treatment on BC results, the cumulative performance of each of the molecular tests with BC was significantly higher than that of BC alone (p < 0.001). SeptiFast and in particular the broad-range pathogen detection system PCR/ESI-MS proved to be an essential addition to BC-based diagnostics in BSI.
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21
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Ashikawa S, Tarumoto N, Imai K, Sakai J, Kodana M, Kawamura T, Ikebuchi K, Murakami T, Mitsutake K, Maesaki S, Maeda T. Rapid identification of pathogens from positive blood culture bottles with the MinION nanopore sequencer. J Med Microbiol 2018; 67:1589-1595. [PMID: 30311873 DOI: 10.1099/jmm.0.000855] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
PURPOSE Bloodstream infections are major causes of morbidity and mortality that lead to prolonged hospital stays and higher medical costs. In this study, we aimed to evaluate the MinION nanopore sequencer for the identification of the most dominant pathogens in positive blood culture bottles. METHODOLOGY 16S and ITS1-5.8S-ITS2 rRNA genes were amplified by PCR reactions with barcoded primers using nine clinical isolates obtained from positive blood bottles and 11 type strains, including five types of Candida species. Barcoded amplicons were mixed, and multiplex sequencing with the MinION sequencer was performed. In addition, barcoded PCR amplicons were sequenced by Sanger sequencing to validate the performance of the MinION. RESULTS The bacterial and Candida spp. identified by MinION sequencing, based on the highest homology of reference sequences from the NCBI gene databases, agreed with the matrix-assisted laser desorption ionization time of flight mass spectrometry results, excepting the closely related species Streptococcusand Escherichia coli. The 'pass' reads obtained within about 10 min of sequencing were sufficient to identify the pathogens. The average values of sequence identities with 1D2 chemistry and the R9.5 flow cell were around 99 %; thus, frequent sequence errors did not affect species identification based on amplicon sequencing. CONCLUSION We have established a rapid, portable and economical technique for the identification of pathogens in positive blood culture bottles through a novel MinION nanopore sequencer amplicon sequencing scheme, which replaces traditional Sanger sequencing.
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Affiliation(s)
- Sae Ashikawa
- 1School of Medical Technology, Faculty of Health and Medical Care, Saitama Medical University, Saitama, Japan
| | - Norihito Tarumoto
- 2Department of Infectious Disease and Infection Control, Saitama Medical University, Saitama, Japan.,3Center for Clinical Infectious Diseases and Research, Saitama Medical University, Saitama, Japan
| | - Kazuo Imai
- 2Department of Infectious Disease and Infection Control, Saitama Medical University, Saitama, Japan.,3Center for Clinical Infectious Diseases and Research, Saitama Medical University, Saitama, Japan
| | - Jun Sakai
- 2Department of Infectious Disease and Infection Control, Saitama Medical University, Saitama, Japan.,3Center for Clinical Infectious Diseases and Research, Saitama Medical University, Saitama, Japan
| | - Masahiro Kodana
- 4Clinical Laboratory Medicine, Saitama Medical University Hospital, Saitama, Japan
| | - Toru Kawamura
- 4Clinical Laboratory Medicine, Saitama Medical University Hospital, Saitama, Japan
| | - Kenji Ikebuchi
- 4Clinical Laboratory Medicine, Saitama Medical University Hospital, Saitama, Japan
| | - Takashi Murakami
- 3Center for Clinical Infectious Diseases and Research, Saitama Medical University, Saitama, Japan.,5Department of Microbiology, Saitama Medical University, Saitama, Japan
| | - Kotaro Mitsutake
- 3Center for Clinical Infectious Diseases and Research, Saitama Medical University, Saitama, Japan.,6Department of Infectious Diseases and Infection Control, International Medical Center, Saitama Medical University, Saitama, Japan
| | - Shigefumi Maesaki
- 2Department of Infectious Disease and Infection Control, Saitama Medical University, Saitama, Japan.,3Center for Clinical Infectious Diseases and Research, Saitama Medical University, Saitama, Japan
| | - Takuya Maeda
- 3Center for Clinical Infectious Diseases and Research, Saitama Medical University, Saitama, Japan.,5Department of Microbiology, Saitama Medical University, Saitama, Japan
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22
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Machine learning for fast identification of bacteraemia in SIRS patients treated on standard care wards: a cohort study. Sci Rep 2018; 8:12233. [PMID: 30111827 PMCID: PMC6093921 DOI: 10.1038/s41598-018-30236-9] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2018] [Accepted: 07/16/2018] [Indexed: 01/09/2023] Open
Abstract
Bacteraemia is a life-threating condition requiring immediate diagnostic and therapeutic actions. Blood culture (BC) analyses often result in a low true positive result rate, indicating its improper usage. A predictive model might assist clinicians in deciding for whom to conduct or to avoid BC analysis in patients having a relevant bacteraemia risk. Predictive models were established by using linear and non-linear machine learning methods. To obtain proper data, a unique data set was collected prior to model estimation in a prospective cohort study, screening 3,370 standard care patients with suspected bacteraemia. Data from 466 patients fulfilling two or more systemic inflammatory response syndrome criteria (bacteraemia rate: 28.8%) were finally used. A 29 parameter panel of clinical data, cytokine expression levels and standard laboratory markers was used for model training. Model tuning was performed in a ten-fold cross validation and tuned models were validated in a test set (80:20 random split). The random forest strategy presented the best result in the test set validation (ROC-AUC: 0.729, 95%CI: 0.679–0.779). However, procalcitonin (PCT), as the best individual variable, yielded a similar ROC-AUC (0.729, 95%CI: 0.679–0.779). Thus, machine learning methods failed to improve the moderate diagnostic accuracy of PCT.
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23
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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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Karrasch M, Geraci J, Sachse S, Rödel J, Löffler B, Bauer M, Thomas-Rüddel D, Hagel S, Aschenbach R, Bloos F. Early adjustment of antimicrobial therapy after PCR/electrospray ionization mass spectrometry-based pathogen detection in critically ill patients with suspected sepsis. ACTA ACUST UNITED AC 2018; 56:e207-e209. [DOI: 10.1515/cclm-2017-1110] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2017] [Accepted: 01/22/2018] [Indexed: 11/15/2022]
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25
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Rello J, van Engelen TSR, Alp E, Calandra T, Cattoir V, Kern WV, Netea MG, Nseir S, Opal SM, van de Veerdonk FL, Wilcox MH, Wiersinga WJ. Towards precision medicine in sepsis: a position paper from the European Society of Clinical Microbiology and Infectious Diseases. Clin Microbiol Infect 2018; 24:1264-1272. [PMID: 29581049 DOI: 10.1016/j.cmi.2018.03.011] [Citation(s) in RCA: 84] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2017] [Revised: 03/06/2018] [Accepted: 03/10/2018] [Indexed: 12/30/2022]
Abstract
BACKGROUND Our current understanding of the pathophysiology and management of sepsis is associated with a lack of progress in clinical trials, which partly reflects insufficient appreciation of the heterogeneity of this syndrome. Consequently, more patient-specific approaches to treatment should be explored. AIMS To summarize the current evidence on precision medicine in sepsis, with an emphasis on translation from theory to clinical practice. A secondary objective is to develop a framework enclosing recommendations on management and priorities for further research. SOURCES A global search strategy was performed in the MEDLINE database through the PubMed search engine (last search December 2017). No restrictions of study design, time, or language were imposed. CONTENT The focus of this Position Paper is on the interplay between therapies, pathogens, and the host. Regarding the pathogen, microbiologic diagnostic approaches (such as blood cultures (BCs) and rapid diagnostic tests (RDTs)) are discussed, as well as targeted antibiotic treatment. Other topics include the disruption of host immune system and the use of biomarkers in sepsis management, patient stratification, and future clinical trial design. Lastly, personalized antibiotic treatment and stewardship are addressed (Fig. 1). IMPLICATIONS A road map provides recommendations and future perspectives. RDTs and identifying drug-response phenotypes are clear challenges. The next step will be the implementation of precision medicine to sepsis management, based on theranostic methodology. This highly individualized approach will be essential for the design of novel clinical trials and improvement of care pathways.
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Affiliation(s)
- J Rello
- CIBERES, Vall d'Hebron Barcelona Campus Hospital, European Study Group of Infections in Critically Ill Patients (ESGCIP), Barcelona, Spain.
| | - T S R van Engelen
- Centre for Experimental Molecular Medicine, Academic Medical Centre, University of Amsterdam, Amsterdam, The Netherlands
| | - E Alp
- Department of Infectious Diseases, Infection Control Committee, Faculty of Medicine, Erciyes University, Kayseri, Turkey
| | - T Calandra
- Infectious Diseases Service, Department of Medicine, Centre Hospitalier Universitaire Vaudois and University of Lausanne, Lausanne, Switzerland
| | - V Cattoir
- University Hospital of Rennes, Department of Clinical Microbiology, Rennes, France and National Reference Center for Antimicrobial Resistance (lab Enterococci), Rennes, France
| | - W V Kern
- Division of Infectious Diseases, Department of Medicine, University Hospital and Medical Centre, Albert-Ludwigs-University Faculty of Medicine, Freiburg, Germany; Executive Committee of ESCMID Study Group for Bloodstream Infections and Sepsis (ESGBIS), The Netherlands
| | - M G Netea
- Department of Internal Medicine and Radboud Centre for Infectious Diseases (RCI), Radboud University Nijmegen Medical Centre, Nijmegen, The Netherlands; Human Genomics Laboratory, Craiova University of Medicine and Pharmacy, Craiova, Romania
| | - S Nseir
- Faculté de Médecine, University of Lille and Centre de Réanimation, CHU Lille, Lille, France
| | - S M Opal
- Brown University, Infectious Diseases, Providence, RI, USA
| | - F L van de Veerdonk
- Department of Internal Medicine and Radboud Centre for Infectious Diseases (RCI), Radboud University Nijmegen Medical Centre, Nijmegen, The Netherlands
| | - M H Wilcox
- Department of Microbiology, Leeds Teaching Hospitals NHS Trust, University of Leeds, Leeds, UK
| | - W J Wiersinga
- Centre for Experimental Molecular Medicine, Academic Medical Centre, University of Amsterdam, Amsterdam, The Netherlands; Department of Medicine, Division of Infectious Diseases, Academic Medical Centre, University of Amsterdam, Amsterdam, The Netherlands; Executive Committee of ESCMID Study Group for Bloodstream Infections and Sepsis (ESGBIS), The Netherlands.
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26
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Maubon D, Dard C, Garnaud C, Cornet M. Profile of GenMark's ePlex® blood culture identification fungal pathogen panel. Expert Rev Mol Diagn 2017; 18:119-132. [PMID: 29284316 DOI: 10.1080/14737159.2018.1420476] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
INTRODUCTION Fungemia presents high morbi-mortality and thus rapid microbiological diagnosis may contribute to appropriate patient management. In the last decade, kits based on molecular technologies have become available and health care institutes are increasingly facing critical investment choices. Although all these tools aim to achieve rapid fungal detection and species identification, they display different inherent characteristics. Areas covered: Considering technologies allowing detection and identification of fungal species in a sepsis context, the market proposes either tests on positive blood culture or tests on patient's whole blood. In this review, the authors describe and compare the ePlex® Blood Culture Identification Fungal Pathogen (BCID-FP) test, a fully automated one-step single-use cartridge assay that has been designed to detect identify frequent or rare but emerging, fungal species, from positive blood culture. A comparison with the competing kits is provided. Expert commentaries: The ePlex BCID-FP test provides a diversified and rather relevant panel. Its easy-to-use cartridges allow flexible use around the clock. Nevertheless, prospective clinical studies assessing the time-to-result benefit on antifungal stewardship and on hospital length of stay are not available yet. New tools aim to benefit clinicians and patients, but they should be accompanied by supervision of result interpretation and adaptation of antifungal stewardship.
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Affiliation(s)
- Danièle Maubon
- a Univsité Grenoble Alpes, CNRS, Grenoble INP*, TIMC-IMAG , Grenoble , France.,b Parasitology-Mycology Laboratory, Infectious Agents Department , CHU Grenoble-Alpes , Grenoble , France
| | - Céline Dard
- b Parasitology-Mycology Laboratory, Infectious Agents Department , CHU Grenoble-Alpes , Grenoble , France
| | - Cécile Garnaud
- a Univsité Grenoble Alpes, CNRS, Grenoble INP*, TIMC-IMAG , Grenoble , France.,b Parasitology-Mycology Laboratory, Infectious Agents Department , CHU Grenoble-Alpes , Grenoble , France
| | - Muriel Cornet
- a Univsité Grenoble Alpes, CNRS, Grenoble INP*, TIMC-IMAG , Grenoble , France.,b Parasitology-Mycology Laboratory, Infectious Agents Department , CHU Grenoble-Alpes , Grenoble , France
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27
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Tat Trung N, Van Tong H, Lien TT, Van Son T, Thanh Huyen TT, Quyen DT, Hoan PQ, Meyer CG, Song LH. Clinical utility of an optimised multiplex real-time PCR assay for the identification of pathogens causing sepsis in Vietnamese patients. Int J Infect Dis 2017; 67:122-128. [PMID: 29253706 DOI: 10.1016/j.ijid.2017.12.015] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2017] [Revised: 12/07/2017] [Accepted: 12/09/2017] [Indexed: 11/30/2022] Open
Abstract
INTRODUCTION For the identification of bacterial pathogens, blood culture is still the gold standard diagnostic method. However, several disadvantages apply to blood cultures, such as time and rather large volumes of blood sample required. We have previously established an optimised multiplex real-time PCR method in order to diagnose bloodstream infections. MATERIAL AND METHODS In the present study, we evaluated the diagnostic performance of this optimised multiplex RT-PCR in blood samples collected from 110 septicaemia patients enrolled at the 108 Military Central Hospital, Hanoi, Vietnam. RESULTS Positive results were obtained by blood culture, the Light Cylcler-based SeptiFast® assay and our multiplex RT-PCR in 35 (32%), 31 (28%), and 31 (28%) samples, respectively. Combined use of the three methods confirmed 50 (45.5%) positive cases of bloodstream infection, a rate significantly higher compared to the exclusive use of one of the three methods (P=0.052, 0.012 and 0.012, respectively). The sensitivity, specificity and area under the curve (AUC) of our assay were higher compared to that of the SeptiFast® assay (77.4%, 86.1% and 0.8 vs. 67.7%, 82.3% and 0.73, respectively). Combined use of blood culture and multiplex RT-PCR assay showed a superior diagnostic performance, as the sensitivity, specificity, and AUC reached 83.3%, 100%, and 0.95, respectively. The concordance between blood culture and the multiplex RT-PCR assay was highest for Klebsiella pneumonia (100%), followed by Streptococcus spp. (77.8%), Escherichia coli (66.7%), Staphylococcus spp. (50%) and Salmonella spp. (50%). In addition, the use of the newly established multiplex RT-PCR assay increased the spectrum of identifiable agents (Acintobacter baumannii, 1/32; Proteus mirabilis, 1/32). CONCLUSION The combination of culture and the multiplex RT-PCR assay provided an excellent diagnostic accomplishment and significantly supported the identification of causative pathogens in clinical samples obtained from septic patients.
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Affiliation(s)
- Ngo Tat Trung
- Department of Molecular Biology, 108 Military Central Hospital, No 1, Tran Hung Dao Street, Hai Ba Trung Dist, Hanoi, Vietnam; Vietnamese - German Centre for Medical Research (VG-CARE), Hanoi, Vietnam.
| | - Hoang Van Tong
- Vietnamese - German Centre for Medical Research (VG-CARE), Hanoi, Vietnam; Biomedical and Pharmaceutical Applied Research Center, Vietnam Military Medical University, Hanoi, Vietnam.
| | - Tran Thi Lien
- Faculty of Infectious diseases, Hai Phong Medical University, 72A Nguyen Binh Khiem, Ngo Quyen District, Hai Phong, Vietnam.
| | - Trinh Van Son
- Vietnamese - German Centre for Medical Research (VG-CARE), Hanoi, Vietnam; Institute of Clinical Infectious Diseases, 108 Military Central Hospital, No 1, Tran Hung Dao Street, Hai Ba Trung Dist, Hanoi, Vietnam.
| | - Tran Thi Thanh Huyen
- Department of Molecular Biology, 108 Military Central Hospital, No 1, Tran Hung Dao Street, Hai Ba Trung Dist, Hanoi, Vietnam.
| | - Dao Thanh Quyen
- Department of Molecular Biology, 108 Military Central Hospital, No 1, Tran Hung Dao Street, Hai Ba Trung Dist, Hanoi, Vietnam.
| | - Phan Quoc Hoan
- Department of Molecular Biology, 108 Military Central Hospital, No 1, Tran Hung Dao Street, Hai Ba Trung Dist, Hanoi, Vietnam.
| | - Christian G Meyer
- Vietnamese - German Centre for Medical Research (VG-CARE), Hanoi, Vietnam; Institute of Tropical Medicine, Eberhard Karls University Tübingen, Wilhelmstr. 27, 72074, Tübingen, Germany; Faculty of Medicine, Duy Tan University, Da Nang, Vietnam.
| | - Le Huu Song
- Vietnamese - German Centre for Medical Research (VG-CARE), Hanoi, Vietnam; Institute of Clinical Infectious Diseases, 108 Military Central Hospital, No 1, Tran Hung Dao Street, Hai Ba Trung Dist, Hanoi, Vietnam.
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Florio W, Morici P, Ghelardi E, Barnini S, Lupetti A. Recent advances in the microbiological diagnosis of bloodstream infections. Crit Rev Microbiol 2017; 44:351-370. [PMID: 29185372 DOI: 10.1080/1040841x.2017.1407745] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Rapid identification (ID) and antimicrobial susceptibility testing (AST) of the causative agent(s) of bloodstream infections (BSIs) are essential for the prompt administration of an effective antimicrobial therapy, which can result in clinical and financial benefits. Immediately after blood sampling, empirical antimicrobial therapy, chosen on clinical and epidemiological data, is administered. When ID and AST results are available, the clinician decides whether to continue or streamline the antimicrobial therapy, based on the results of the in vitro antimicrobial susceptibility profile of the pathogen. The aim of the present study is to review and discuss the experimental data, advantages, and drawbacks of recently developed technological advances of culture-based and molecular methods for the diagnosis of BSI (including mass spectrometry, magnetic resonance, PCR-based methods, direct inoculation methods, and peptide nucleic acid fluorescence in situ hybridization), the understanding of which could provide new perspectives to improve and fasten the diagnosis and treatment of septic patients. Although blood culture remains the gold standard to diagnose BSIs, newly developed methods can significantly shorten the turnaround time of reliable microbial ID and AST, thus substantially improving the diagnostic yield.
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Affiliation(s)
- Walter Florio
- a Dipartimento di Ricerca Traslazionale e delle Nuove Tecnologie in Medicina e Chirurgia , Università di Pisa , Pisa , Italy
| | - Paola Morici
- a Dipartimento di Ricerca Traslazionale e delle Nuove Tecnologie in Medicina e Chirurgia , Università di Pisa , Pisa , Italy
| | - Emilia Ghelardi
- a Dipartimento di Ricerca Traslazionale e delle Nuove Tecnologie in Medicina e Chirurgia , Università di Pisa , Pisa , Italy
| | - Simona Barnini
- b U.O. Microbiologia Universitaria Azienda Ospedaliero-Universitaria Pisana , Pisa , Italy
| | - Antonella Lupetti
- a Dipartimento di Ricerca Traslazionale e delle Nuove Tecnologie in Medicina e Chirurgia , Università di Pisa , Pisa , Italy
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29
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Markota A, Sinkovič A. Mortality, intensive care treatment, and cost evaluation: Role of a polymerase chain reaction assay in patients with sepsis. J Int Med Res 2017; 46:79-88. [PMID: 28730906 PMCID: PMC6011302 DOI: 10.1177/0300060517719768] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
Objective We examined whether patients with a positive SeptiFast (SF) assay (LightCycler SeptiFast; Roche Diagnostics, Basel, Switzerland) developed higher long-term mortality, a more difficult course of treatment, and a higher antimicrobial treatment cost than patients with a negative SF assay. Methods We performed a post-hoc analysis of data collected in a 1-year prospective interventional study of adults with severe sepsis and septic shock. In addition to the standard treatment, an additional 5 ml of blood was obtained for an SF assay, and the antimicrobial treatment was changed according to the SF results. Results We included 57 patients, and the SF assay was positive (SF+) in 10 (17.5%) and negative (SF−) in 47 (82.5%) patients. A trend toward a higher 6-month, 1-year, and 2-year mortality rate was observed in the SF+ group. In the SF+ group, we observed a significantly greater need for second-line vasopressor therapy, a higher initial procalcitonin concentration, and higher maximum C-reactive protein and lactate concentrations. We found no significant differences in cost of antimicrobial treatment between the SF+ and SF− groups. Conclusions We observed a trend toward higher long-term mortality and a more difficult course of treatment but no difference in the cost of antimicrobial treatment.
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Affiliation(s)
- Andrej Markota
- Medical Intensive Care Unit, University Medical Centre Maribor, Ljubljanska 5, Maribor, Slovenia
| | - Andreja Sinkovič
- Medical Intensive Care Unit, University Medical Centre Maribor, Ljubljanska 5, Maribor, Slovenia
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30
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Marco F. Molecular methods for septicemia diagnosis. Enferm Infecc Microbiol Clin 2017; 35:586-592. [PMID: 28427796 DOI: 10.1016/j.eimc.2017.03.002] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2017] [Accepted: 03/06/2017] [Indexed: 12/12/2022]
Abstract
Septicemia remains a major cause of hospital mortality. Blood culture remains the best approach to identify the etiological microorganisms when a bloodstream infection is suspected but it takes long time because it relies on bacterial or fungal growth. The introduction in clinical microbiology laboratories of the matrix-assisted laser desorption ionization time-of-flight mass spectrometry technology, DNA hybridization, microarrays or rapid PCR-based test significantly reduce the time to results. Tests for direct detection in whole blood samples are highly desirable because of their potential to identify bloodstream pathogens without waiting for blood cultures to become positive. Nonetheless, limitations of current molecular diagnostic methods are substantial. This article reviews these new molecular approaches (LightCycler SeptiFast, Magicplex sepsis real time, Septitest, VYOO, PCR/ESI-MS analysis, T2Candida).
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Affiliation(s)
- Francesc Marco
- Servicio de Microbiología, Centro de Diagnóstico Biomédico, Hospital Clínic, Barcelona, España; ISGlobal, Barcelona Institute for Global Health, Hospital Clínic-Universitat de Barcelona, Barcelona, España.
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31
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Cambau E, Durand-Zaleski I, Bretagne S, Brun-Buisson C, Cordonnier C, Duval X, Herwegh S, Pottecher J, Courcol R, Bastuji-Garin S. Performance and economic evaluation of the molecular detection of pathogens for patients with severe infections: the EVAMICA open-label, cluster-randomised, interventional crossover trial. Intensive Care Med 2017; 43:1613-1625. [PMID: 28374097 PMCID: PMC5633620 DOI: 10.1007/s00134-017-4766-4] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2017] [Accepted: 03/08/2017] [Indexed: 12/19/2022]
Abstract
Purpose Microbiological diagnosis (MD) of infections remains insufficient. The resulting empirical antimicrobial therapy leads to multidrug resistance and inappropriate treatments. We therefore evaluated the cost-effectiveness of direct molecular detection of pathogens in blood for patients with severe sepsis (SES), febrile neutropenia (FN) and suspected infective endocarditis (SIE). Methods Patients were enrolled in a multicentre, open-label, cluster-randomised crossover trial conducted during two consecutive periods, randomly assigned as control period (CP; standard diagnostic workup) or intervention period (IP; additional testing with LightCycler®SeptiFast). Multilevel models used to account for clustering were stratified by clinical setting (SES, FN, SIE). Results A total of 1416 patients (907 SES, 440 FN, 69 SIE) were evaluated for the primary endpoint (rate of blood MD). For SES patients, the MD rate was higher during IP than during CP [42.6% (198/465) vs. 28.1% (125/442), odds ratio (OR) 1.89, 95% confidence interval (CI) 1.43–2.50; P < 0.001], with an absolute increase of 14.5% (95% CI 8.4–20.7). A trend towards an association was observed for SIE [35.4% (17/48) vs. 9.5% (2/21); OR 6.22 (0.98–39.6)], but not for FN [32.1% (70/218) vs. 30.2% (67/222), P = 0.66]. Overall, turn-around time was shorter during IP than during CP (22.9 vs. 49.5 h, P < 0.001) and hospital costs were similar (median, mean ± SD: IP €14,826, €18,118 ± 17,775; CP €17,828, €18,653 ± 15,966). Bootstrap analysis of the incremental cost-effectiveness ratio showed weak dominance of intervention in SES patients. Conclusion Addition of molecular detection to standard care improves MD and thus efficiency of healthcare resource usage in patients with SES. ClinicalTrials.gov registration number: NCT00709358. Electronic supplementary material The online version of this article (doi:10.1007/s00134-017-4766-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Emmanuelle Cambau
- APHP-Lariboisière, Bacteriology Laboratory, 75010, Paris, France. .,Univ Paris Diderot, Sorbonne Paris Cité, INSERM, UMR1137 IAME, 75018, Paris, France.
| | - Isabelle Durand-Zaleski
- APHP-URC ECO, Créteil, France.,Université Paris Est, UFR de Médecine, 94010, Créteil, France
| | - Stéphane Bretagne
- APHP-Henri Mondor, Parasitology and Mycology Laboratory, 94010, Créteil, France.,APHP-Saint Louis, Parasitology and Mycology Laboratory, 75010, Paris, France.,Sorbonne Paris Cité, University Paris Diderot, Paris, France.,Molecular Mycology Unit, Institut Pasteur, National Reference Center of Invasive Mycoses and Antifungals, Paris, France
| | | | - Catherine Cordonnier
- APHP- Henri Mondor, Haematology Department and University Paris-Est Créteil, 94010, Créteil, France
| | - Xavier Duval
- APHP-Bichat, Centre d'investigation Clinique CIC 1425, INSERM UMR 1137 IAME, University Paris Diderot, 75018, Paris, France
| | | | - Julien Pottecher
- Hôpitaux Universitaires de Strasbourg, Hôpital de Hautepierre, Service d'Anesthésie-Réanimation chirurgicale, Université de Strasbourg, FMTS, EA 3072, 67098, Strasbourg, France
| | - René Courcol
- CHU Lille, Microbiology Institute, 59000, Lille, France
| | - Sylvie Bastuji-Garin
- APHP-Henri Mondor, Public Health Department, 94010, Créteil, France.,University Paris Est (UPE), IMRB, CEpiA (Clinical Epidemiology and Ageing Unit, EA7376), 94010, Créteil, France.,APHP, Henri Mondor Hospital, Clinical Research Unit (URC Mondor), 94010, Créteil, France
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Ginn AN, Hazelton B, Shoma S, Cullen M, Solano T, Iredell JR. Quantitative multiplexed-tandem PCR for direct detection of bacteraemia in critically ill patients. Pathology 2017; 49:304-308. [PMID: 28238416 DOI: 10.1016/j.pathol.2016.10.014] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2016] [Revised: 10/12/2016] [Accepted: 10/18/2016] [Indexed: 10/20/2022]
Abstract
Culture remains the gold standard for diagnosis of blood stream infections (BSI), but its clinical utility is limited by slow turnaround times. Here we describe a method for rapid quantitative detection of bacterial DNA directly extracted from whole blood using a multiplexed tandem real-time PCR (MT-PCR) assay targeting Staphylococcus, Streptococcus, Pseudomonas, Enterococcus and Enterobacteriaceae 16S rDNA genes. Results were available less than 3.5 hours after blood collection with all five bacterial targets having limits of detection between 101 and 103 CFU/mL. A small-scale clinical evaluation of the assay using blood samples collected from 15 patients admitted to the Intensive Care Unit at our institution demonstrated 93.3% (14/15) concordance between MT-PCR and blood culture when detection of persistent bacterial DNAemia by MT- PCR was considered a true result. Further evaluation with clinical samples is needed; however, this method has potential as an effective rule-in diagnostic tool for bacteraemic sepsis and septic shock.
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Affiliation(s)
- Andrew N Ginn
- Centre for Infectious Diseases and Microbiology, The Westmead Institute for Medical Research, The University of Sydney and Westmead Hospital, Westmead, NSW, Australia; Centre for Infectious Diseases and Microbiology Laboratory Services, Institute of Clinical Pathology and Medical Research, Westmead Hospital, Westmead, NSW, Australia
| | - Briony Hazelton
- Centre for Infectious Diseases and Microbiology Laboratory Services, Institute of Clinical Pathology and Medical Research, Westmead Hospital, Westmead, NSW, Australia
| | - Shereen Shoma
- Centre for Infectious Diseases and Microbiology, The Westmead Institute for Medical Research, The University of Sydney and Westmead Hospital, Westmead, NSW, Australia
| | - Martin Cullen
- Intensive Care Unit, Westmead Hospital, Westmead, NSW, Australia
| | - Thomas Solano
- Intensive Care Unit, Westmead Hospital, Westmead, NSW, Australia
| | - Jonathan R Iredell
- Centre for Infectious Diseases and Microbiology, The Westmead Institute for Medical Research, The University of Sydney and Westmead Hospital, Westmead, NSW, Australia; Centre for Infectious Diseases and Microbiology Laboratory Services, Institute of Clinical Pathology and Medical Research, Westmead Hospital, Westmead, NSW, Australia.
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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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34
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Ziegler I, Fagerström A, Strålin K, Mölling P. Evaluation of a Commercial Multiplex PCR Assay for Detection of Pathogen DNA in Blood from Patients with Suspected Sepsis. PLoS One 2016; 11:e0167883. [PMID: 27997618 PMCID: PMC5172567 DOI: 10.1371/journal.pone.0167883] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2015] [Accepted: 11/22/2016] [Indexed: 11/24/2022] Open
Abstract
The Magicplex Sepsis Real-time Test (MST) is a commercial multiplex PCR that can detect more than 90 different pathogens in blood, with an analysis time of six hours. The aim of the present study was to evaluate this method for the detection of bloodstream infection (BSI). An EDTA whole blood sample for MST was collected together with blood cultures (BC) from patients with suspected sepsis at the Emergency Department of a university hospital. Among 696 study patients, 322 (46%) patients were positive with at least one method; 128 (18%) were BC positive and 268 (38%) were MST positive. Considering BC to be the gold standard, MST had an overall sensitivity of 47%, specificity of 66%, positive predictive value (PPV) of 23%, and a negative predictive value of 87%. Among the MST positive samples with a negative BC, coagulase-negative staphylococci (CoNS) and species that rarely cause community-acquired BSI were frequently noted. However, the quantification cycle (Cq) values of the MST+/BC- results were often high. We thus hypothesized that the performance of the MST test could be improved if the Cq cut-off level was adjusted downwards. With a lower Cq cut-off value, i.e. 6.0 for Staphylococcus species and 9.0 for all other species, the number of MST positive cases decreased to 83 (12%) and the overall sensitivity decreased to 38%. However, the PPV increased to 59% and the specificity increased to 96%, as many MST positive results for CoNS and bacteria that rarely cause community-acquired BSI turned MST negative. In conclusion, our study shows that with a lower Cq cut-off value, the MST will detect less contaminants and findings with unclear relevance, but to the cost of a lower sensitivity. Consequently, we consider that a positive MST results with a Cq value above the adjusted cut-off should be interpreted with caution, as the result might be clinically irrelevant. In a correspondent way, quantitative results could probably be useful in the interpretation of positive results from other molecular assays for the detection of BSI.
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Affiliation(s)
- Ingrid Ziegler
- Department of Infectious Diseases, Örebro University Hospital, Örebro, Sweden
- School of Health and Medical Sciences, Örebro University, Örebro, Sweden
- * E-mail:
| | - Anna Fagerström
- School of Health and Medical Sciences, Örebro University, Örebro, Sweden
- Department of Laboratory Medicine, Örebro University Hospital, Örebro, Sweden
| | - Kristoffer Strålin
- School of Health and Medical Sciences, Örebro University, Örebro, Sweden
- Department of Infectious Diseases, Karolinska University Hospital, Stockholm, Sweden
- Department of Medicine Huddinge, Karolinska Institutet, Stockholm, Sweden
| | - Paula Mölling
- School of Health and Medical Sciences, Örebro University, Örebro, Sweden
- Department of Laboratory Medicine, Örebro University Hospital, Örebro, Sweden
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35
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Contou D, Roux D, Jochmans S, Coudroy R, Guérot E, Grimaldi D, Ricome S, Maury E, Plantefève G, Mayaux J, Mekontso Dessap A, Brun-Buisson C, de Prost N. Septic shock with no diagnosis at 24 hours: a pragmatic multicenter prospective cohort study. CRITICAL CARE : THE OFFICIAL JOURNAL OF THE CRITICAL CARE FORUM 2016; 20:360. [PMID: 27816060 PMCID: PMC5097846 DOI: 10.1186/s13054-016-1537-5] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/13/2016] [Accepted: 10/19/2016] [Indexed: 12/20/2022]
Abstract
Background The lack of a patent source of infection after 24 hours of management of shock considered septic is a common and disturbing scenario. We aimed to determine the prevalence and the causes of shock with no diagnosis 24 hours after its onset, and to compare the outcomes of patients with early-confirmed septic shock to those of others. Methods We conducted a pragmatic, prospective, multicenter observational cohort study in ten intensive care units (ICU) in France. We included all consecutive patients admitted to the ICU with suspected septic shock defined by clinical suspicion of infection leading to antibiotic prescription plus acute circulatory failure requiring vasopressor support. Results A total of 508 patients were admitted with suspected septic shock. Among them, 374 (74 %) had early-confirmed septic shock, while the 134 others (26 %) had no source of infection identified nor microbiological documentation retrieved 24 hours after shock onset. Among these, 37/134 (28 %) had late-confirmed septic shock diagnosed after 24 hours, 59/134 (44 %) had a condition mimicking septic (septic shock mimicker, mainly related to adverse drug reactions, acute mesenteric ischemia and malignancies) and 38/134 (28 %) had shock of unknown origin by the end of the ICU stay. There were no differences between patients with early-confirmed septic shock and the remainder in ICU mortality and the median duration of ICU stay, of tracheal intubation and of vasopressor support. The multivariable Cox model showed that the risk of day-60 mortality did not differ between patients with or without early-confirmed septic shock. A sensitivity analysis was performed in the subgroup (n = 369/508) of patients meeting the Sepsis-3 definition criteria and displayed consistent results. Conclusions One quarter of the patients admitted in the ICU with suspected septic shock had no infection identified 24 hours after its onset and almost half of them were eventually diagnosed with a septic shock mimicker. Outcome did not differ between patients with early-confirmed septic shock and other patients. Electronic supplementary material The online version of this article (doi:10.1186/s13054-016-1537-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Damien Contou
- Service de réanimation Médicale, Groupe de Recherche CARMAS, Centre Hospitalier Universitaire Henri Mondor, Assistance Publique-Hôpitaux de Paris, 51, avenue du Maréchal de Lattre de Tassigny, Créteil, 94010, France. .,INSERM U955, Institut Mondor de Recherche Biomedicale, Equipe 8, Faculté de Médecine de Créteil, Université Paris Est-Créteil, Créteil, France.
| | - Damien Roux
- Service de réanimation médico-chirurgicale, Centre Hospitalier Universitaire Louis Mourier, Assistance Publique-Hôpitaux de Paris, 178 rue des Renouillers, Colombes, 92700, France
| | - Sébastien Jochmans
- Service de réanimation, Centre Hospitalier Marc Jacquet, 2 rue Fréteau de Peny, Melun, 77011, France
| | - Rémi Coudroy
- Service de réanimation médicale, Centre Hospitalier Universitaire de Poitiers, 2 rue de la Milétrie, Poitiers, 86021, France
| | - Emmanuel Guérot
- Service de réanimation médicale, Centre Hospitalier Universitaire Georges Pompidou, Assistance Publique-Hôpitaux de Paris, 20 rue Leblanc, Paris, 75015, France
| | - David Grimaldi
- Service de réanimation médico-chirurgicale, Centre Hospitalier André Mignot, 177 rue de Versailles, Le Chesnay, 78150, France
| | - Sylvie Ricome
- Service de réanimation, Centre Hospitalier Robert Ballanger, Boulevard Robert Ballanger, Aulnay-sous-Bois, 93600, France
| | - Eric Maury
- Service de réanimation médicale, Centre Hospitalier Universitaire Saint-Antoine, Assistance Publique-Hôpitaux de Paris, 184 rue du Faubourg Saint-Antoine, Paris, 75012, France
| | - Gaëtan Plantefève
- Service de réanimation polyvalente, Centre Hospitalier Victor Dupouy, 69 rue du Lieutenant-Colonel Prudhon, Argenteuil, 95107, France
| | - Julien Mayaux
- Service de réanimation médicale, Centre Hospitalier Universitaire Pitié Salpétrière, Assistance Publique-Hôpitaux de Paris, 47-83 Boulevard de l'Hôpital, Paris, 75013, France
| | - Armand Mekontso Dessap
- Service de réanimation Médicale, Groupe de Recherche CARMAS, Centre Hospitalier Universitaire Henri Mondor, Assistance Publique-Hôpitaux de Paris, 51, avenue du Maréchal de Lattre de Tassigny, Créteil, 94010, France.,INSERM U955, Institut Mondor de Recherche Biomedicale, Equipe 8, Faculté de Médecine de Créteil, Université Paris Est-Créteil, Créteil, France
| | - Christian Brun-Buisson
- Service de réanimation Médicale, Groupe de Recherche CARMAS, Centre Hospitalier Universitaire Henri Mondor, Assistance Publique-Hôpitaux de Paris, 51, avenue du Maréchal de Lattre de Tassigny, Créteil, 94010, France.,INSERM U955, Institut Mondor de Recherche Biomedicale, Equipe 8, Faculté de Médecine de Créteil, Université Paris Est-Créteil, Créteil, France
| | - Nicolas de Prost
- Service de réanimation Médicale, Groupe de Recherche CARMAS, Centre Hospitalier Universitaire Henri Mondor, Assistance Publique-Hôpitaux de Paris, 51, avenue du Maréchal de Lattre de Tassigny, Créteil, 94010, France.,INSERM U955, Institut Mondor de Recherche Biomedicale, Equipe 8, Faculté de Médecine de Créteil, Université Paris Est-Créteil, Créteil, France
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36
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Ohlsson P, Evander M, Petersson K, Mellhammar L, Lehmusvuori A, Karhunen U, Soikkeli M, Seppä T, Tuunainen E, Spangar A, von Lode P, Rantakokko-Jalava K, Otto G, Scheding S, Soukka T, Wittfooth S, Laurell T. Integrated Acoustic Separation, Enrichment, and Microchip Polymerase Chain Reaction Detection of Bacteria from Blood for Rapid Sepsis Diagnostics. Anal Chem 2016; 88:9403-9411. [DOI: 10.1021/acs.analchem.6b00323] [Citation(s) in RCA: 86] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Pelle Ohlsson
- Department
of Biomedical Engineering, Lund University, Box 118, SE-221 00 Lund, Sweden
| | - Mikael Evander
- Department
of Biomedical Engineering, Lund University, Box 118, SE-221 00 Lund, Sweden
| | - Klara Petersson
- Department
of Biomedical Engineering, Lund University, Box 118, SE-221 00 Lund, Sweden
| | - Lisa Mellhammar
- Stem Cell Center, Lund University, BMC B10, Klinikgatan 24, SE-222 42 Lund, Sweden
| | - Ari Lehmusvuori
- Department
of Biochemistry/Biotechnology, University of Turku, Tykistökatu
6 A, FI-20520 Turku, Finland
| | - Ulla Karhunen
- Department
of Biochemistry/Biotechnology, University of Turku, Tykistökatu
6 A, FI-20520 Turku, Finland
| | - Minna Soikkeli
- Department
of Biochemistry/Biotechnology, University of Turku, Tykistökatu
6 A, FI-20520 Turku, Finland
| | - Titta Seppä
- Department
of Biochemistry/Biotechnology, University of Turku, Tykistökatu
6 A, FI-20520 Turku, Finland
| | - Emilia Tuunainen
- Department
of Biochemistry/Biotechnology, University of Turku, Tykistökatu
6 A, FI-20520 Turku, Finland
| | - Anni Spangar
- Department
of Biochemistry/Biotechnology, University of Turku, Tykistökatu
6 A, FI-20520 Turku, Finland
| | - Piia von Lode
- Abacus Diagnostica Oy, Tykistökatu 4 D, FI-20520 Turku, Finland
| | | | | | - Stefan Scheding
- Stem Cell Center, Lund University, BMC B10, Klinikgatan 24, SE-222 42 Lund, Sweden
| | - Tero Soukka
- Department
of Biochemistry/Biotechnology, University of Turku, Tykistökatu
6 A, FI-20520 Turku, Finland
| | - Saara Wittfooth
- Department
of Biochemistry/Biotechnology, University of Turku, Tykistökatu
6 A, FI-20520 Turku, Finland
| | - Thomas Laurell
- Department
of Biomedical Engineering, Lund University, Box 118, SE-221 00 Lund, Sweden
- Department
of Biomedical Engineering, Dongguk University, Seoul, Korea
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37
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Trung NT, Hien TTT, Huyen TTT, Quyen DT, Van Son T, Hoan PQ, Phuong NTK, Lien TT, Binh MT, Van Tong H, Meyer CG, Velavan TP, Song LH. Enrichment of bacterial DNA for the diagnosis of blood stream infections. BMC Infect Dis 2016; 16:235. [PMID: 27246723 PMCID: PMC4888298 DOI: 10.1186/s12879-016-1568-1] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2015] [Accepted: 05/16/2016] [Indexed: 12/31/2022] Open
Abstract
Background Blood cultures are commonly employed to identify bacterial pathogens causing sepsis. PCR assays to diagnose septicemia require extraction of bacterial DNA from blood samples and thus, delay the initiation of appropriate antimicrobial treatment. The presence of abundant human DNA may hamper the sensitivity of PCR in the detection of bacteria. Methods We used serial dilutions of E. Coli spiked pseudo-blood-sepsis samples to develop a simple method that combines the use of a polar detergent solvent and adjustment of the basic pH to remove human DNA. A 16S rRNA gene-based screening algorithm was established to differentiate Gram-positive and Gram-negative groups of bacteria and the family of Enterobacteriaceae. A stringent validation with appropriate controls was implemented. The method of human DNA removal was then applied on 194 sepsis blood samples and 44 cerebrospinal fluid (CSF) samples by real-time PCR. Results This uncomplicated and straightforward approach allows to remove up to 98 % of human DNA from peripheral blood of septic patients. The inhibitory effect of human DNA is efficiently prevented and the detection limit of real-time PCR is increased to 10 E. Coli CFUs/ml. This sensitivity is 10 times higher compared to conventional real-time PCR assays. The classical blood culture detected 58/194 (30 %) of sepsis and 9/44 (21 %) of CSF samples. Out of the 194 blood samples tested, the conventional real-time PCR targeting 13 common sepsis causing pathogens correctly detected the bacterial DNA in 16/194 (8 %) only and 14/44 (32 %) in cerebrospinal fluid samples. Our newly established approach was able to provide correct diagnoses in 78 (40 %) of the 194 blood samples and in 14 (32 %) of the CSF samples. The combination of both blood cultures and our technique raised the rate of sepsis diagnoses to 112/194 (58 %). Of the total group tested positive, 46 (24 %) cases showed overlap with the classical methodology. Conclusion We report a simple optimized in-house protocol for removal of human DNA from blood sepsis samples as a pre-analytical tool to prepare DNA for subsequent PCR assays. With the detection increase of our in-house DNA removal approach, subsequent PCR assays can reach detection limits of 10 E. coli CFUs/ml and significantly improve the diagnostic rate in blood sepsis cases. Electronic supplementary material The online version of this article (doi:10.1186/s12879-016-1568-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Ngo Tat Trung
- Department of Molecular Biology, 108 Military Central Hospital, Hanoi, Vietnam.,Vietnamese - German Centre for Medical Research (VG-CARE), Hanoi, Vietnam
| | - Tran Thi Thu Hien
- Department of Molecular Biology, 108 Military Central Hospital, Hanoi, Vietnam
| | | | - Dao Thanh Quyen
- Department of Molecular Biology, 108 Military Central Hospital, Hanoi, Vietnam
| | - Trinh Van Son
- Institute of Clinical Infectious Diseases, 108 Military Central Hospital, Hanoi, Vietnam.,Vietnamese - German Centre for Medical Research (VG-CARE), Hanoi, Vietnam
| | - Phan Quoc Hoan
- Department of Molecular Biology, 108 Military Central Hospital, Hanoi, Vietnam
| | | | - Tran Thi Lien
- Faculty of Infectious Diseases, Hai Phong Medical University, Hai Phong, Vietnam
| | - Mai Thanh Binh
- Department of Gastroenterology, 108 Military Central Hospital, Hanoi, Vietnam.,Vietnamese - German Centre for Medical Research (VG-CARE), Hanoi, Vietnam
| | - Hoang Van Tong
- Institute of Tropical Medicine, University of Tübingen, Tübingen, Germany.,Vietnamese - German Centre for Medical Research (VG-CARE), Hanoi, Vietnam
| | - Christian G Meyer
- Institute of Tropical Medicine, University of Tübingen, Tübingen, Germany.,Vietnamese - German Centre for Medical Research (VG-CARE), Hanoi, Vietnam
| | - Thirumalaisamy P Velavan
- Institute of Tropical Medicine, University of Tübingen, Tübingen, Germany. .,Vietnamese - German Centre for Medical Research (VG-CARE), Hanoi, Vietnam.
| | - Le Huu Song
- Department of Molecular Biology, 108 Military Central Hospital, Hanoi, Vietnam. .,Institute of Clinical Infectious Diseases, 108 Military Central Hospital, Hanoi, Vietnam. .,Vietnamese - German Centre for Medical Research (VG-CARE), Hanoi, Vietnam.
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38
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Barlam TF, Cosgrove SE, Abbo LM, MacDougall C, Schuetz AN, Septimus EJ, Srinivasan A, Dellit TH, Falck-Ytter YT, Fishman NO, Hamilton CW, Jenkins TC, Lipsett PA, Malani PN, May LS, Moran GJ, Neuhauser MM, Newland JG, Ohl CA, Samore MH, Seo SK, Trivedi KK. Implementing an Antibiotic Stewardship Program: Guidelines by the Infectious Diseases Society of America and the Society for Healthcare Epidemiology of America. Clin Infect Dis 2016; 62:e51-77. [PMID: 27080992 PMCID: PMC5006285 DOI: 10.1093/cid/ciw118] [Citation(s) in RCA: 1842] [Impact Index Per Article: 230.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2016] [Accepted: 02/23/2016] [Indexed: 12/11/2022] Open
Abstract
Evidence-based guidelines for implementation and measurement of antibiotic stewardship interventions in inpatient populations including long-term care were prepared by a multidisciplinary expert panel of the Infectious Diseases Society of America and the Society for Healthcare Epidemiology of America. The panel included clinicians and investigators representing internal medicine, emergency medicine, microbiology, critical care, surgery, epidemiology, pharmacy, and adult and pediatric infectious diseases specialties. These recommendations address the best approaches for antibiotic stewardship programs to influence the optimal use of antibiotics.
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Affiliation(s)
- Tamar F Barlam
- Section of Infectious Diseases, Boston University School of Medicine, Boston, Massachusetts
| | - Sara E Cosgrove
- Division of Infectious Diseases, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Lilian M Abbo
- Division of Infectious Diseases, University of Miami Miller School of Medicine, Miami, Florida
| | - Conan MacDougall
- Department of Clinical Pharmacy, School of Pharmacy, University of California, San Francisco
| | - Audrey N Schuetz
- Department of Medicine, Weill Cornell Medical Center/New York-Presbyterian Hospital, New York, New York
| | - Edward J Septimus
- Department of Internal Medicine, Texas A&M Health Science Center College of Medicine, Houston
| | - Arjun Srinivasan
- Division of Healthcare Quality Promotion, Centers for Disease Control and Prevention, Atlanta, Georgia
| | - Timothy H Dellit
- Division of Allergy and Infectious Diseases, University of Washington School of Medicine, Seattle
| | - Yngve T Falck-Ytter
- Department of Medicine, Case Western Reserve University and Veterans Affairs Medical Center, Cleveland, Ohio
| | - Neil O Fishman
- Department of Medicine, University of Pennsylvania Health System, Philadelphia
| | | | | | - Pamela A Lipsett
- Department of Anesthesiology and Critical Care Medicine, Johns Hopkins University Schools of Medicine and Nursing, Baltimore, Maryland
| | - Preeti N Malani
- Division of Infectious Diseases, University of Michigan Health System, Ann Arbor
| | - Larissa S May
- Department of Emergency Medicine, University of California, Davis
| | - Gregory J Moran
- Department of Emergency Medicine, David Geffen School of Medicine, University of California, Los Angeles Medical Center, Sylmar
| | | | - Jason G Newland
- Department of Pediatrics, Washington University School of Medicine in St. Louis, Missouri
| | - Christopher A Ohl
- Section on Infectious Diseases, Wake Forest University School of Medicine, Winston-Salem, North Carolina
| | - Matthew H Samore
- Department of Veterans Affairs and University of Utah, Salt Lake City
| | - Susan K Seo
- Infectious Diseases, Memorial Sloan Kettering Cancer Center, New York, New York
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39
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Ratzinger F, Tsirkinidou I, Haslacher H, Perkmann T, Schmetterer KG, Mitteregger D, Makristathis A, Burgmann H. Evaluation of the Septifast MGrade Test on Standard Care Wards--A Cohort Study. PLoS One 2016; 11:e0151108. [PMID: 26986826 PMCID: PMC4795709 DOI: 10.1371/journal.pone.0151108] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2015] [Accepted: 02/22/2016] [Indexed: 12/22/2022] Open
Abstract
Background The immediate need for appropriate antimicrobial therapy in septic patients requires the detection of the causative pathogen in a timely and reliable manner. In this study, the real-time PCR Septifast MGrade test was evaluated in adult patients meeting the systemic inflammatory response syndrome (SIRS) criteria that were treated at standard care wards. Methods Patients with clinical suspected infection, drawn blood cultures (BC), the Septifast MGrade test (SF) and sepsis biomarkers were prospectively screened for fulfillment of SIRS criteria and evaluated using the criteria of the European Centre of Disease Control (ECDC) for infection point prevalence studies. Results In total, 220 patients with SIRS were prospectively enrolled, including 56 patients with detection of bacteria in the blood (incidence: 25.5%). BC analysis resulted in 75.0% sensitivity (95% confidence interval, CI: 61.6%– 85.6%) with 97.6% specificity (CI: 93.9%– 99.3%) for detecting bacteria in the blood. In comparison to BC, SF presented with 80.4% sensitivity (CI: 67.6%– 89.8%) and with 97.6% specificity (CI: 93.9%– 99.3%). BC and SF analysis yielded comparable ROC-AUCs (0.86, 0.89), which did not differ significantly (p = 0.558). A trend of a shorter time-to-positivity of BC analysis was not seen in bacteremic patients with a positive SF test than those with a negative test result. Sepsis biomarkers, including PCT, IL-6 or CRP, did not help to explain discordant test results for BC and SF. Conclusion Since negative results do not exclude bacteremia, the Septifast MGrade test is not suited to replacing BC, but it is a valuable tool with which to complement BC for faster detection of pathogens.
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Affiliation(s)
- Franz Ratzinger
- Department of Laboratory Medicine, Division of Medical and Chemical Laboratory Diagnostics, Medical University of Vienna, Vienna, Austria
| | - Irene Tsirkinidou
- Department of Medicine I, Division of Infectious Diseases and Tropical Medicine, Medical University of Vienna, Vienna, Austria
| | - Helmuth Haslacher
- Department of Laboratory Medicine, Division of Medical and Chemical Laboratory Diagnostics, Medical University of Vienna, Vienna, Austria
| | - Thomas Perkmann
- Department of Laboratory Medicine, Division of Medical and Chemical Laboratory Diagnostics, Medical University of Vienna, Vienna, Austria
| | - Klaus G. Schmetterer
- Department of Laboratory Medicine, Division of Medical and Chemical Laboratory Diagnostics, Medical University of Vienna, Vienna, Austria
| | - Dieter Mitteregger
- Department of Laboratory Medicine, Division of Clinical Microbiology, Medical University of Vienna, Vienna, Austria
| | - Athanasios Makristathis
- Department of Laboratory Medicine, Division of Clinical Microbiology, Medical University of Vienna, Vienna, Austria
| | - Heinz Burgmann
- Department of Medicine I, Division of Infectious Diseases and Tropical Medicine, Medical University of Vienna, Vienna, Austria
- * E-mail:
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40
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Rapid Diagnosis of Infection in the Critically Ill, a Multicenter Study of Molecular Detection in Bloodstream Infections, Pneumonia, and Sterile Site Infections. Crit Care Med 2016; 43:2283-91. [PMID: 26327198 PMCID: PMC4603364 DOI: 10.1097/ccm.0000000000001249] [Citation(s) in RCA: 133] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Supplemental Digital Content is available in the text. Early identification of causative microorganism(s) in patients with severe infection is crucial to optimize antimicrobial use and patient survival. However, current culture-based pathogen identification is slow and unreliable such that broad-spectrum antibiotics are often used to insure coverage of all potential organisms, carrying risks of overtreatment, toxicity, and selection of multidrug-resistant bacteria. We compared the results obtained using a novel, culture-independent polymerase chain reaction/electrospray ionization-mass spectrometry technology with those obtained by standard microbiological testing and evaluated the potential clinical implications of this technique.
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41
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Warhurst G, Dunn G, Chadwick P, Blackwood B, McAuley D, Perkins GD, McMullan R, Gates S, Bentley A, Young D, Carlson GL, Dark P. Rapid detection of health-care-associated bloodstream infection in critical care using multipathogen real-time polymerase chain reaction technology: a diagnostic accuracy study and systematic review. Health Technol Assess 2016; 19:1-142. [PMID: 25961752 DOI: 10.3310/hta19350] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
BACKGROUND There is growing interest in the potential utility of real-time polymerase chain reaction (PCR) in diagnosing bloodstream infection by detecting pathogen deoxyribonucleic acid (DNA) in blood samples within a few hours. SeptiFast (Roche Diagnostics GmBH, Mannheim, Germany) is a multipathogen probe-based system targeting ribosomal DNA sequences of bacteria and fungi. It detects and identifies the commonest pathogens causing bloodstream infection. As background to this study, we report a systematic review of Phase III diagnostic accuracy studies of SeptiFast, which reveals uncertainty about its likely clinical utility based on widespread evidence of deficiencies in study design and reporting with a high risk of bias. OBJECTIVE Determine the accuracy of SeptiFast real-time PCR for the detection of health-care-associated bloodstream infection, against standard microbiological culture. DESIGN Prospective multicentre Phase III clinical diagnostic accuracy study using the standards for the reporting of diagnostic accuracy studies criteria. SETTING Critical care departments within NHS hospitals in the north-west of England. PARTICIPANTS Adult patients requiring blood culture (BC) when developing new signs of systemic inflammation. MAIN OUTCOME MEASURES SeptiFast real-time PCR results at species/genus level compared with microbiological culture in association with independent adjudication of infection. Metrics of diagnostic accuracy were derived including sensitivity, specificity, likelihood ratios and predictive values, with their 95% confidence intervals (CIs). Latent class analysis was used to explore the diagnostic performance of culture as a reference standard. RESULTS Of 1006 new patient episodes of systemic inflammation in 853 patients, 922 (92%) met the inclusion criteria and provided sufficient information for analysis. Index test assay failure occurred on 69 (7%) occasions. Adult patients had been exposed to a median of 8 days (interquartile range 4-16 days) of hospital care, had high levels of organ support activities and recent antibiotic exposure. SeptiFast real-time PCR, when compared with culture-proven bloodstream infection at species/genus level, had better specificity (85.8%, 95% CI 83.3% to 88.1%) than sensitivity (50%, 95% CI 39.1% to 60.8%). When compared with pooled diagnostic metrics derived from our systematic review, our clinical study revealed lower test accuracy of SeptiFast real-time PCR, mainly as a result of low diagnostic sensitivity. There was a low prevalence of BC-proven pathogens in these patients (9.2%, 95% CI 7.4% to 11.2%) such that the post-test probabilities of both a positive (26.3%, 95% CI 19.8% to 33.7%) and a negative SeptiFast test (5.6%, 95% CI 4.1% to 7.4%) indicate the potential limitations of this technology in the diagnosis of bloodstream infection. However, latent class analysis indicates that BC has a low sensitivity, questioning its relevance as a reference test in this setting. Using this analysis approach, the sensitivity of the SeptiFast test was low but also appeared significantly better than BC. Blood samples identified as positive by either culture or SeptiFast real-time PCR were associated with a high probability (> 95%) of infection, indicating higher diagnostic rule-in utility than was apparent using conventional analyses of diagnostic accuracy. CONCLUSION SeptiFast real-time PCR on blood samples may have rapid rule-in utility for the diagnosis of health-care-associated bloodstream infection but the lack of sensitivity is a significant limiting factor. Innovations aimed at improved diagnostic sensitivity of real-time PCR in this setting are urgently required. Future work recommendations include technology developments to improve the efficiency of pathogen DNA extraction and the capacity to detect a much broader range of pathogens and drug resistance genes and the application of new statistical approaches able to more reliably assess test performance in situation where the reference standard (e.g. blood culture in the setting of high antimicrobial use) is prone to error. STUDY REGISTRATION The systematic review is registered as PROSPERO CRD42011001289. FUNDING The National Institute for Health Research Health Technology Assessment programme. Professor Daniel McAuley and Professor Gavin D Perkins contributed to the systematic review through their funded roles as codirectors of the Intensive Care Foundation (UK).
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Affiliation(s)
- Geoffrey Warhurst
- Infection, Injury and Inflammation Research Group, Salford Royal NHS Foundation Trust, Manchester Academic Health Sciences Centre (MAHSC), University of Manchester, Salford, UK
| | - Graham Dunn
- Centre for Biostatistics, Institute of Population Health, Faculty of Medical and Human Sciences, Manchester Academic Health Sciences Centre (MAHSC), University of Manchester, Salford, UK
| | - Paul Chadwick
- Microbiology Department, Salford Royal NHS Foundation Trust, Manchester Academic Health Sciences Centre (MAHSC), University of Manchester, Salford, UK
| | - Bronagh Blackwood
- Centre for Infection and Immunity, Queen's University Belfast, Belfast, UK
| | - Daniel McAuley
- Centre for Infection and Immunity, Queen's University Belfast, Belfast, UK
| | - Gavin D Perkins
- Clinical Trials Unit, Medical School, Warwick University, Coventry, UK
| | - Ronan McMullan
- Medical Microbiology, Royal Victoria Hospital, Belfast, UK
| | - Simon Gates
- Clinical Trials Unit, Medical School, Warwick University, Coventry, UK
| | - Andrew Bentley
- Institue of Inflammation and Repair, Faculty of Medical and Human Sciences, Manchester Academic Health Sciences Centre (MAHSC), University of Manchester, Salford, UK
| | - Duncan Young
- Nuffield Department of Clinical Neurosciences, John Radcliffe Hospital, Oxford, UK
| | - Gordon L Carlson
- Infection, Injury and Inflammation Research Group, Salford Royal NHS Foundation Trust, Manchester Academic Health Sciences Centre (MAHSC), University of Manchester, Salford, UK
| | - Paul Dark
- Infection, Injury and Inflammation Research Group, Salford Royal NHS Foundation Trust, Manchester Academic Health Sciences Centre (MAHSC), University of Manchester, Salford, UK
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Molecular and Mass Spectrometry Detection and Identification of Causative Agents of Bloodstream Infections. Mol Microbiol 2016. [DOI: 10.1128/9781555819071.ch26] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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Dubourg G, Raoult D. Emerging methodologies for pathogen identification in positive blood culture testing. Expert Rev Mol Diagn 2015; 16:97-111. [PMID: 26559655 DOI: 10.1586/14737159.2016.1112274] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Bloodstream infections (BSIs) represent a major cause of death in developed countries and are associated with long-term loss of functions. Blood culture remains the gold standard for BSI diagnosis, as it is easy to perform and displays a good analytical sensitivity. However, its major drawback remains the long turnaround time, which can result in inappropriate therapy, fall of survival rate, emergence of antibiotic resistance and increase of medical costs. Over the last 10 years, molecular tools have been the alternative to blood cultures, allowing early identification of pathogens involved in sepsis, as well detection of critical antibiotic resistance genes. Besides, the advent of MALDI-TOF revolutionized practice in routine microbiology significantly reduced the time to result. Reviewed here are recent improvements in early BSI diagnosis and these authors' view for the future is presented, including innovative high-throughput technologies.
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Affiliation(s)
- Grégory Dubourg
- a Pôle des Maladies Infectieuses et Tropicales Clinique et Biologique, Fédération de Bactériologie-Hygiène-Virologie, University, Hospital Centre Timone, Institut Hospitalo-Universitaire (IHU) Méditerranée Infection, Assistance Publique - Hôpitaux de Marseille , Marseille , France.,b Université Aix-Marseille, Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes (URMITE) UM 63 CNRS 7278 IRD 198 INSERM U1095, Facultés de Médecine et de Pharmacie , Marseille , France
| | - Didier Raoult
- a Pôle des Maladies Infectieuses et Tropicales Clinique et Biologique, Fédération de Bactériologie-Hygiène-Virologie, University, Hospital Centre Timone, Institut Hospitalo-Universitaire (IHU) Méditerranée Infection, Assistance Publique - Hôpitaux de Marseille , Marseille , France.,b Université Aix-Marseille, Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes (URMITE) UM 63 CNRS 7278 IRD 198 INSERM U1095, Facultés de Médecine et de Pharmacie , Marseille , France
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Neither Single nor a Combination of Routine Laboratory Parameters can Discriminate between Gram-positive and Gram-negative Bacteremia. Sci Rep 2015; 5:16008. [PMID: 26522966 PMCID: PMC4629184 DOI: 10.1038/srep16008] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2015] [Accepted: 10/05/2015] [Indexed: 12/18/2022] Open
Abstract
Adequate early empiric antibiotic therapy is pivotal for the outcome of patients with bloodstream infections. In clinical practice the use of surrogate laboratory parameters is frequently proposed to predict underlying bacterial pathogens; however there is no clear evidence for this assumption. In this study, we investigated the discriminatory capacity of predictive models consisting of routinely available laboratory parameters to predict the presence of Gram-positive or Gram-negative bacteremia. Major machine learning algorithms were screened for their capacity to maximize the area under the receiver operating characteristic curve (ROC-AUC) for discriminating between Gram-positive and Gram-negative cases. Data from 23,765 patients with clinically suspected bacteremia were screened and 1,180 bacteremic patients were included in the study. A relative predominance of Gram-negative bacteremia (54.0%), which was more pronounced in females (59.1%), was observed. The final model achieved 0.675 ROC-AUC resulting in 44.57% sensitivity and 79.75% specificity. Various parameters presented a significant difference between both genders. In gender-specific models, the discriminatory potency was slightly improved. The results of this study do not support the use of surrogate laboratory parameters for predicting classes of causative pathogens. In this patient cohort, gender-specific differences in various laboratory parameters were observed, indicating differences in the host response between genders.
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Sircar M, Ranjan P, Gupta R, Jha OK, Gupta A, Kaur R, Chavhan N, Singh M, Singh SK. Impact of bronchoalveolar lavage multiplex polymerase chain reaction on microbiological yield and therapeutic decisions in severe pneumonia in intensive care unit. J Crit Care 2015; 31:227-32. [PMID: 26611381 DOI: 10.1016/j.jcrc.2015.10.012] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2015] [Revised: 09/23/2015] [Accepted: 10/11/2015] [Indexed: 12/12/2022]
Abstract
PURPOSE The purpose of the study is to evaluate the impact of adding bronchoalveolar lavage multiplex polymerase chain reaction (M-PCR) to conventional cultures (CC) on microbiological yield and therapeutic decisions in adult intensive care unit patients with pneumonia and severe sepsis or septic shock. MATERIAL AND METHODS In this retrospective case-control study, bronchoalveolar lavage cultures were taken for control (58 patients, 58 admissions) and study arms (57 patients, 58 admissions). Bronchoalveolar lavage M-PCR was sent simultaneously for the latter. RESULTS A total of 267 microorganisms were identified (M-PCR alone, 211; CC alone, 15; both, 41) in the study arm vs 64 in controls. Concordance between M-PCR and culture was complete in 32 (55.17%), partial in 4 (6.9%), and discordant in 22 (37.93%) including 17 with positive M-PCR but negative CC. Time to antibiotic therapy modification was significantly less (P < .001) in M-PCR group compared to controls (32.40 ± 14.41 vs 41.74 ± 45.61 hours). There was no significant difference in index episode resolution (48.3% vs 50%; P = 1), intensive care unit mortality (57.4% vs 51.2%; P = .67), and hospital mortality (59.6% vs 61.5%; P = 1) in study and control arms, respectively, despite more septic shock patients in the study arm (89.7% vs 75.9%; P = .05). CONCLUSION Bronchoalveolar lavage M-PCR with culture leads to higher microbiological yield and earlier modification of antibiotics compared to conventional culture.
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Affiliation(s)
- Mrinal Sircar
- Department of Pulmonology and Critical Care Medicine, Fortis Hospital, Noida, Uttar Pradesh, India.
| | - Prashant Ranjan
- Department of Pulmonology and Critical Care Medicine, Fortis Hospital, Noida, Uttar Pradesh, India.
| | - Rajesh Gupta
- Department of Pulmonology and Critical Care Medicine, Fortis Hospital, Noida, Uttar Pradesh, India.
| | - Onkar Kumar Jha
- Department of Pulmonology and Critical Care Medicine, Fortis Hospital, Noida, Uttar Pradesh, India
| | - Amit Gupta
- Department of Pulmonology and Critical Care Medicine, Fortis Hospital, Noida, Uttar Pradesh, India.
| | | | - Neela Chavhan
- Department of Pulmonology and Critical Care Medicine, Fortis Hospital, Noida, Uttar Pradesh, India.
| | - Mukta Singh
- Department of Pulmonology and Critical Care Medicine, Fortis Hospital, Noida, Uttar Pradesh, India.
| | - Sujeet Kumar Singh
- Department of Pulmonology and Critical Care Medicine, Fortis Hospital, Noida, Uttar Pradesh, India.
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Kell D, Potgieter M, Pretorius E. Individuality, phenotypic differentiation, dormancy and 'persistence' in culturable bacterial systems: commonalities shared by environmental, laboratory, and clinical microbiology. F1000Res 2015; 4:179. [PMID: 26629334 PMCID: PMC4642849 DOI: 10.12688/f1000research.6709.2] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 09/04/2015] [Indexed: 01/28/2023] Open
Abstract
For bacteria, replication mainly involves growth by binary fission. However, in a very great many natural environments there are examples of phenotypically dormant, non-growing cells that do not replicate immediately and that are phenotypically 'nonculturable' on media that normally admit their growth. They thereby evade detection by conventional culture-based methods. Such dormant cells may also be observed in laboratory cultures and in clinical microbiology. They are usually more tolerant to stresses such as antibiotics, and in clinical microbiology they are typically referred to as 'persisters'. Bacterial cultures necessarily share a great deal of relatedness, and inclusive fitness theory implies that there are conceptual evolutionary advantages in trading a variation in growth rate against its mean, equivalent to hedging one's bets. There is much evidence that bacteria exploit this strategy widely. We here bring together data that show the commonality of these phenomena across environmental, laboratory and clinical microbiology. Considerable evidence, using methods similar to those common in environmental microbiology, now suggests that many supposedly non-communicable, chronic and inflammatory diseases are exacerbated (if not indeed largely caused) by the presence of dormant or persistent bacteria (the ability of whose components to cause inflammation is well known). This dormancy (and resuscitation therefrom) often reflects the extent of the availability of free iron. Together, these phenomena can provide a ready explanation for the continuing inflammation common to such chronic diseases and its correlation with iron dysregulation. This implies that measures designed to assess and to inhibit or remove such organisms (or their access to iron) might be of much therapeutic benefit.
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Affiliation(s)
- Douglas Kell
- School of Chemistry and The Manchester Institute of Biotechnology, The University of Manchester, Manchester, Lancashire, M1 7DN, UK
| | - Marnie Potgieter
- Department of Physiology, Faculty of Health Sciences, University of Pretoria, Arcadia, 0007, South Africa
| | - Etheresia Pretorius
- Department of Physiology, Faculty of Health Sciences, University of Pretoria, Arcadia, 0007, South Africa
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47
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Kell D, Potgieter M, Pretorius E. Individuality, phenotypic differentiation, dormancy and 'persistence' in culturable bacterial systems: commonalities shared by environmental, laboratory, and clinical microbiology. F1000Res 2015; 4:179. [PMID: 26629334 DOI: 10.12688/f1000research.6709.1] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 06/29/2015] [Indexed: 01/28/2023] Open
Abstract
For bacteria, replication mainly involves growth by binary fission. However, in a very great many natural environments there are examples of phenotypically dormant, non-growing cells that do not replicate immediately and that are phenotypically 'nonculturable' on media that normally admit their growth. They thereby evade detection by conventional culture-based methods. Such dormant cells may also be observed in laboratory cultures and in clinical microbiology. They are usually more tolerant to stresses such as antibiotics, and in clinical microbiology they are typically referred to as 'persisters'. Bacterial cultures necessarily share a great deal of relatedness, and inclusive fitness theory implies that there are conceptual evolutionary advantages in trading a variation in growth rate against its mean, equivalent to hedging one's bets. There is much evidence that bacteria exploit this strategy widely. We here bring together data that show the commonality of these phenomena across environmental, laboratory and clinical microbiology. Considerable evidence, using methods similar to those common in environmental microbiology, now suggests that many supposedly non-communicable, chronic and inflammatory diseases are exacerbated (if not indeed largely caused) by the presence of dormant or persistent bacteria (the ability of whose components to cause inflammation is well known). This dormancy (and resuscitation therefrom) often reflects the extent of the availability of free iron. Together, these phenomena can provide a ready explanation for the continuing inflammation common to such chronic diseases and its correlation with iron dysregulation. This implies that measures designed to assess and to inhibit or remove such organisms (or their access to iron) might be of much therapeutic benefit.
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Affiliation(s)
- Douglas Kell
- School of Chemistry and The Manchester Institute of Biotechnology, The University of Manchester, Manchester, Lancashire, M1 7DN, UK
| | - Marnie Potgieter
- Department of Physiology, Faculty of Health Sciences, University of Pretoria, Arcadia, 0007, South Africa
| | - Etheresia Pretorius
- Department of Physiology, Faculty of Health Sciences, University of Pretoria, Arcadia, 0007, South Africa
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Bloos F. Clinical diagnosis of sepsis and the combined use of biomarkers and culture- and non-culture-based assays. Methods Mol Biol 2015; 1237:247-60. [PMID: 25319792 DOI: 10.1007/978-1-4939-1776-1_19] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Sepsis is among the most common causes of death in hospitalized patients, and early recognition followed by immediate initiation of therapy is an important concept to improve survival in these patients. According to the definition of sepsis, diagnosis of sepsis requires the recognition of the systemic inflammatory response syndrome (SIRS) caused by infection as well as recognition of possible infection-related organ dysfunctions for diagnosis of severe sepsis or septic shock. Both SIRS and organ dysfunctions may occur frequently in hospitalized patients for various reasons. However, the fast recognition of acute infection as a cause of SIRS and newly developed organ dysfunction may be a demanding task since culture-based results of microbiological samples will be available only days after onset of symptoms. Biomarkers and PCR-based pathogen detection may help the physician in differentiating SIRS from sepsis. Procalcitonin (PCT) is the best investigated biomarker for this purpose. Furthermore, the current data support the usage of PCT for guidance of antimicrobial therapy. C-reactive protein (CRP) may be used to monitor the course of infection but has only limited discriminative capabilities. Interleukin-6 is widely used for its fast response to the infectious stimulus, but conclusive data for the application of this biomarker are missing. None of the available biomarkers can by itself reliably differentiate SIRS from sepsis but can aid and shorten the decision process. PCR-based pathogen detection can theoretically shorten the recognition of the underlying pathogen to about 8 h. However, this technique is expensive and requires additional staff in the laboratory; controlled prospective studies are missing. Although current studies suggest that PCR-based pathogen detection may be useful to shorten time to adequate antimicrobial therapy and diagnose invasive Candida infections, no general recommendations about the application of PCR for the diagnosis of sepsis can be given.
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Affiliation(s)
- Frank Bloos
- Department of Anesthesiology and Intensive Care Medicine, University Hospital of Jena, Erlanger Allee 101, 07747, Jena, Germany,
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Clinical evaluation of commercial nucleic acid amplification tests in patients with suspected sepsis. BMC Infect Dis 2015; 15:199. [PMID: 25928122 PMCID: PMC4419503 DOI: 10.1186/s12879-015-0938-4] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2015] [Accepted: 04/22/2015] [Indexed: 12/15/2022] Open
Abstract
Background Sepsis is a serious medical condition requiring timely administered, appropriate antibiotic therapy. Blood culture is regarded as the gold standard for aetiological diagnosis of sepsis, but it suffers from low sensitivity and long turnaround time. Thus, nucleic acid amplification tests (NAATs) have emerged to shorten the time to identification of causative microbes. The aim of the present study was to evaluate the clinical utility in everyday practice in the emergency department of two commercial NAATs in patients suspected with sepsis. Methods During a six-week period, blood samples were collected consecutively from all adult patients admitted to the general emergency department for suspicion of a community-onset sepsis and treated with intravenous antibiotics. Along with conventional blood cultures, multiplex PCR (Magicplex™) was performed on whole blood specimens whereas portions from blood culture bottles were used for analysis by microarray-based assay (Prove-it™). The aetiological significance of identified organisms was determined by two infectious disease physicians based on clinical presentation and expected pathogenicity. Results Among 382 episodes of suspected sepsis, clinically relevant microbes were detected by blood culture in 42 episodes (11%), by multiplex PCR in 37 episodes (9.7%), and by microarray in 32 episodes (8.4%). Although moderate agreement with blood culture (kappa 0.50), the multiplex PCR added diagnostic value by timely detection of 15 clinically relevant findings in blood culture-negative specimens. Results of the microarray corresponded very well to those of blood culture (kappa 0.90), but were available just marginally prior to blood culture results. Conclusions The use of NAATs on whole blood specimens in adjunct to current culture-based methods provides a clinical add-on value by allowing for detection of organisms missed by blood culture. However, the aetiological significance of findings detected by NAATs should be interpreted with caution as the high analytical sensitivity may add findings that do not necessarily corroborate with the clinical diagnosis. Electronic supplementary material The online version of this article (doi:10.1186/s12879-015-0938-4) contains supplementary material, which is available to authorized users.
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Mwaigwisya S, Assiri RAM, O'Grady J. Emerging commercial molecular tests for the diagnosis of bloodstream infection. Expert Rev Mol Diagn 2015; 15:681-92. [PMID: 25866124 DOI: 10.1586/14737159.2015.1029459] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Bloodstream infection (BSI) by microorganisms can lead to sepsis. This condition has a high mortality rate, which rises significantly with delays in initiation of appropriate antimicrobial treatment. Current culture methods for diagnosing BSI have long turnaround times and poor clinical sensitivity. While clinicians wait for culture diagnosis, patients are treated empirically, which can result in inappropriate treatment, undesirable side effects and contribute to drug resistance development. Molecular diagnostics assays that target pathogen DNA can identify pathogens and resistance markers within hours. Early diagnosis improves antibiotic stewardship and is associated with favorable clinical outcomes. Nonetheless, limitations of current molecular diagnostic methods are substantial. This article reviews recent commercially available molecular methods that use pathogen DNA to diagnose BSI, either by testing positive blood cultures or directly testing patient blood. We critically assess these tests and their application in clinical microbiology. A view of future directions in BSI diagnosis is also provided.
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