1
|
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.
Collapse
|
2
|
Affiliation(s)
- Marilynn Ransom Fairfax
- Department of Pathology, Wayne State University School of Medicine, 540 East Canfield Street, Detroit, MI 48201, USA; Clinical Microbiology Laboratories, DMC University Laboratories, 4201 St. Antoine Street, Detroit, MI 48201, USA.
| | - Martin H Bluth
- Department of Pathology, Wayne State University School of Medicine, 540 East Canfield Street, Detroit, MI 48201, USA; Pathology Laboratories, Michigan Surgical Hospital, 21230 Dequindre Road, Warren, MI 48091, USA
| | - Hossein Salimnia
- Department of Pathology, Wayne State University School of Medicine, 540 East Canfield Street, Detroit, MI 48201, USA; Clinical Microbiology Laboratories, DMC University Laboratories, 4201 St. Antoine Street, Detroit, MI 48201, USA
| |
Collapse
|
3
|
Reitz A, Poppert S, Rieker M, Frickmann H. Evaluation of FISH for Blood Cultures under Diagnostic Real-Life Conditions. Eur J Microbiol Immunol (Bp) 2018; 8:135-141. [PMID: 30719330 PMCID: PMC6348703 DOI: 10.1556/1886.2018.00024] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2018] [Accepted: 09/18/2018] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND The study assessed a spectrum of previously published in-house fluorescence in-situ hybridization (FISH) probes in a combined approach regarding their diagnostic performance with incubated blood culture materials. METHODS Within a two-year interval, positive blood culture materials were assessed with Gram and FISH staining. Previously described and new FISH probes were combined to panels for Gram-positive cocci in grape-like clusters and in chains, as well as for Gram-negative rod-shaped bacteria. Covered pathogens comprised Staphylococcus spp., such as S. aureus, Micrococcus spp., Enterococcus spp., including E. faecium, E. faecalis, and E. gallinarum, Streptococcus spp., like S. pyogenes, S. agalactiae, and S. pneumoniae, Enterobacteriaceae, such as Escherichia coli, Klebsiella pneumoniae and Salmonella spp., Pseudomonas aeruginosa, Stenotrophomonas maltophilia, and Bacteroides spp. RESULTS A total of 955 blood culture materials were assessed with FISH. In 21 (2.2%) instances, FISH reaction led to non-interpretable results. With few exemptions, the tested FISH probes showed acceptable test characteristics even in the routine setting, with a sensitivity ranging from 28.6% (Bacteroides spp.) to 100% (6 probes) and a specificity of >95% in all instances. CONCLUSION If sophisticated rapid diagnostic methods like mass spectrometry from blood culture materials are not available, FISH provides an option for rapid differentiation for laboratories in resource-limited settings.
Collapse
Affiliation(s)
- Annalena Reitz
- University Hospital of the Goethe University, Frankfurt/Main, Germany
| | - Sven Poppert
- Swiss Tropical and Public Health Institute, Basel, Switzerland.,Faculty of Medicine, University Basel, Basel, Switzerland
| | | | - Hagen Frickmann
- Department of Microbiology and Hospital Hygiene, Bundeswehr Hospital Hamburg, Hamburg, Germany.,Institute for Medical Microbiology, Virology and Hygiene, University Hospital Rostock, Rostock, Germany
| |
Collapse
|
4
|
She RC, Bender JM. Advances in Rapid Molecular Blood Culture Diagnostics: Healthcare Impact, Laboratory Implications, and Multiplex Technologies. J Appl Lab Med 2018; 3:617-630. [PMID: 31639730 DOI: 10.1373/jalm.2018.027409] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2018] [Accepted: 09/28/2018] [Indexed: 01/11/2023]
Abstract
BACKGROUND For far too long, the diagnosis of bloodstream infections has relied on time-consuming blood cultures coupled with traditional organism identification and susceptibility testing. Technologies to define the culprit in bloodstream infections have gained sophistication in recent years, notably by application of molecular methods. CONTENT In this review, we summarize the tests available to clinical laboratories for molecular rapid identification and resistance marker detection in blood culture bottles that have flagged positive. We explore the cost-benefit ratio of such assays, covering aspects that include performance characteristics, effect on patient care, and relevance to antibiotic stewardship initiatives. SUMMARY Rapid blood culture diagnostics represent an advance in the care of patients with bloodstream infections, particularly those infected with resistant organisms. These diagnostics are relatively easy to implement and appear to have a positive cost-benefit balance, particularly when fully incorporated into a hospital's antimicrobial stewardship program.
Collapse
Affiliation(s)
- Rosemary C She
- Department of Pathology, Keck School of Medicine of the University of Southern California, Los Angeles, CA;
| | - Jeffrey M Bender
- Division of Infectious Diseases of the Department of Pediatrics, Keck School of Medicine of the University of Southern California, Los Angeles, CA
| |
Collapse
|
5
|
Otašević S, Momčilović S, Stojanović NM, Skvarč M, Rajković K, Arsić-Arsenijević V. Non-culture based assays for the detection of fungal pathogens. J Mycol Med 2018; 28:236-248. [PMID: 29605542 PMCID: PMC7110445 DOI: 10.1016/j.mycmed.2018.03.001] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2018] [Revised: 03/05/2018] [Accepted: 03/05/2018] [Indexed: 01/05/2023]
Abstract
Traditional, culture based methods for the diagnosis of fungal infections are still considered as gold standard, but they are time consuming and low sensitive. Therefore, in order to overcome the limitations, many researchers have focused on the development of new immunological and molecular based rapid assays that could enable early diagnosis of infection and accurate identification of fungal pathogens causing superficial and invasive infection. In this brief review, we highlighted the advantages and disadvantages of conventional diagnostic methods and possibility of non-culture based assays in diagnosis of superficial fungal infections and presented the overview on currently available immunochromatographic assays as well as availability of biomarkers detection by immunodiagnostic procedures in prompt and accurate diagnosis of invasive fungal infections. In addition, we presented diagnostic efficiency of currently available molecular panels and researches in this area.
Collapse
Affiliation(s)
- S Otašević
- Center of Microbiology and Parasitology, Public Health Institute Niš, Serbia, boulevard Zorana Djindjica 50, 18000 Niš, Serbia; Department of Microbiology and Immunology, Faculty of Medicine, University of Niš, Serbia, boulevard Zorana Djindjica 81, 18000 Niš, Serbia.
| | - S Momčilović
- Department of Microbiology and Immunology, Faculty of Medicine, University of Niš, Serbia, boulevard Zorana Djindjica 81, 18000 Niš, Serbia
| | - N M Stojanović
- Faculty of Medicine, University of Niš, Serbia, boulevard Zorana Djindjica 81, 18000 Niš, Serbia
| | - M Skvarč
- University of Ljubljana, Faculty of Medicine, Institute of Microbiology and Immunology, Zaloska 4, Ljubljana, Slovenia
| | - K Rajković
- High Chemical and Technological School for Professional Studies, Kosančićeva 36, 37000 Kruševac, Serbia
| | - V Arsić-Arsenijević
- Department for Microbiology and Immunology, Faculty of Medicine, University of Belgrade, Serbia, Dr Subotića 1, 11000 Belgrade, Serbia
| |
Collapse
|
6
|
Frickmann H, Zautner AE, Moter A, Kikhney J, Hagen RM, Stender H, Poppert S. Fluorescence in situ hybridization (FISH) in the microbiological diagnostic routine laboratory: a review. Crit Rev Microbiol 2017; 43:263-293. [PMID: 28129707 DOI: 10.3109/1040841x.2016.1169990] [Citation(s) in RCA: 126] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Early identification of microbial pathogens is essential for rational and conservative antibiotic use especially in the case of known regional resistance patterns. Here, we describe fluorescence in situ hybridization (FISH) as one of the rapid methods for easy identification of microbial pathogens, and its advantages and disadvantages for the diagnosis of pathogens in human infections in the laboratory diagnostic routine. Binding of short fluorescence-labeled DNA or nucleic acid-mimicking PNA probes to ribosomes of infectious agents with consecutive analysis by fluorescence microscopy allows identification of bacterial and eukaryotic pathogens at genus or species level. FISH analysis leads to immediate differentiation of infectious agents without delay due to the need for microbial culture. As a microscopic technique, FISH has the unique potential to provide information about spatial resolution, morphology and identification of key pathogens in mixed species samples. On-going automation and commercialization of the FISH procedure has led to significant shortening of the time-to-result and increased test reliability. FISH is a useful tool for the rapid initial identification of microbial pathogens, even from primary materials. Among the rapidly developing alternative techniques, FISH serves as a bridging technology between microscopy, microbial culture, biochemical identification and molecular diagnostic procedures.
Collapse
Affiliation(s)
- Hagen Frickmann
- a German Armed Forces Hospital of Hamburg, Department of Tropical Medicine at the Bernhard Nocht Institute , Hamburg , Germany
| | - Andreas Erich Zautner
- b Department of Medical Microbiology, University Medical Center Göttingen , Göttingen , Germany
| | - Annette Moter
- c University Medical Center Berlin, Biofilmcenter at the German Heart Institute Berlin , Berlin , Germany
| | - Judith Kikhney
- c University Medical Center Berlin, Biofilmcenter at the German Heart Institute Berlin , Berlin , Germany
| | - Ralf Matthias Hagen
- a German Armed Forces Hospital of Hamburg, Department of Tropical Medicine at the Bernhard Nocht Institute , Hamburg , Germany
| | | | - Sven Poppert
- e Institute for Medical Microbiology, Justus-Liebig-University Giessen , Giessen , Germany
| |
Collapse
|
7
|
Rapid detection of Gram-negative bacteria and their drug resistance genes from positive blood cultures using an automated microarray assay. Diagn Microbiol Infect Dis 2014; 81:153-7. [PMID: 25591999 DOI: 10.1016/j.diagmicrobio.2014.10.009] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2014] [Revised: 09/25/2014] [Accepted: 10/22/2014] [Indexed: 12/25/2022]
Abstract
We evaluated the performance of the Verigene Gram-negative blood culture (BC-GN) assay (CE-IVD version) for identification of Gram-negative (GN) bacteria and detection of resistance genes. A total of 163 GN organisms (72 characterized strains and 91 clinical isolates from 86 patients) were tested; among the clinical isolates, 86 (94.5%) isolates were included in the BC-GN panel. For identification, the agreement was 98.6% (146/148, 95% confidence interval [CI], 92.1-100) and 70% (7/10, 95% CI, 53.5-100) for monomicrobial and polymicrobial cultures, respectively. Of the 48 resistance genes harbored by 43 characterized strains, all were correctly detected. Of the 19 clinical isolates harboring resistance genes, 1 CTX-M-producing Escherichia coli isolated in polymicrobial culture was not detected. Overall, BC-GN assay provides acceptable accuracy for rapid identification of Gram-negative bacteria and detection of resistance genes, compared with routine laboratory methods despite that it has limitations in the number of genus/species and resistance gene included in the panel and it shows lower sensitivity in polymicrobial cultures.
Collapse
|
8
|
Tojo M, Fujita T, Ainoda Y, Nagamatsu M, Hayakawa K, Mezaki K, Sakurai A, Masui Y, Yazaki H, Takahashi H, Miyoshi-Akiyama T, Totsuka K, Kirikae T, Ohmagari N. Evaluation of an automated rapid diagnostic assay for detection of Gram-negative bacteria and their drug-resistance genes in positive blood cultures. PLoS One 2014; 9:e94064. [PMID: 24705449 PMCID: PMC3976387 DOI: 10.1371/journal.pone.0094064] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2013] [Accepted: 03/11/2014] [Indexed: 02/04/2023] Open
Abstract
We evaluated the performance of the Verigene Gram-Negative Blood Culture Nucleic Acid Test (BC-GN; Nanosphere, Northbrook, IL, USA), an automated multiplex assay for rapid identification of positive blood cultures caused by 9 Gram-negative bacteria (GNB) and for detection of 9 genes associated with β-lactam resistance. The BC-GN assay can be performed directly from positive blood cultures with 5 minutes of hands-on and 2 hours of run time per sample. A total of 397 GNB positive blood cultures were analyzed using the BC-GN assay. Of the 397 samples, 295 were simulated samples prepared by inoculating GNB into blood culture bottles, and the remaining were clinical samples from 102 patients with positive blood cultures. Aliquots of the positive blood cultures were tested by the BC-GN assay. The results of bacterial identification between the BC-GN assay and standard laboratory methods were as follows: Acinetobacter spp. (39 isolates for the BC-GN assay/39 for the standard methods), Citrobacter spp. (7/7), Escherichia coli (87/87), Klebsiella oxytoca (13/13), and Proteus spp. (11/11); Enterobacter spp. (29/30); Klebsiella pneumoniae (62/72); Pseudomonas aeruginosa (124/125); and Serratia marcescens (18/21); respectively. From the 102 clinical samples, 104 bacterial species were identified with the BC-GN assay, whereas 110 were identified with the standard methods. The BC-GN assay also detected all β-lactam resistance genes tested (233 genes), including 54 blaCTX-M, 119 blaIMP, 8 blaKPC, 16 blaNDM, 24 blaOXA-23, 1 blaOXA-24/40, 1 blaOXA-48, 4 blaOXA-58, and 6 blaVIM. The data shows that the BC-GN assay provides rapid detection of GNB and β-lactam resistance genes in positive blood cultures and has the potential to contributing to optimal patient management by earlier detection of major antimicrobial resistance genes.
Collapse
Affiliation(s)
- Masayoshi Tojo
- Disease Control and Prevention Center, Research Institute, National Center for Global Health and Medicine, Tokyo, Japan
- Department of Infectious Diseases, Research Institute, National Center for Global Health and Medicine, Tokyo, Japan
| | - Takahiro Fujita
- Department of Infectious Diseases, Tokyo Women's Medical University, Tokyo, Japan
| | - Yusuke Ainoda
- Department of Infectious Diseases, Tokyo Women's Medical University, Tokyo, Japan
| | - Maki Nagamatsu
- Disease Control and Prevention Center, Research Institute, National Center for Global Health and Medicine, Tokyo, Japan
- Department of Infectious Diseases, Research Institute, National Center for Global Health and Medicine, Tokyo, Japan
| | - Kayoko Hayakawa
- Disease Control and Prevention Center, Research Institute, National Center for Global Health and Medicine, Tokyo, Japan
| | - Kazuhisa Mezaki
- Department of Clinical Laboratory, National Center for Global Health and Medicine, Tokyo, Japan
| | - Aki Sakurai
- Department of Pulmonary Medicine, Kohnodai Hospital, National Center for Global Health and Medicine, Chiba, Japan
| | - Yoshinori Masui
- Department of Internal Medicine, Kohnodai Hospital, National Center for Global Health and Medicine, Chiba, Japan
| | - Hirohisa Yazaki
- AIDS Clinical Center, National Center for Global Health and Medicine, Tokyo, Japan
| | - Hiroshi Takahashi
- East-West Diagnostics/Theranostics, LLC, San Francisco, California, United States of America
| | - Tohru Miyoshi-Akiyama
- Department of Infectious Diseases, Research Institute, National Center for Global Health and Medicine, Tokyo, Japan
| | - Kyoichi Totsuka
- Department of Infectious Diseases, Tokyo Women's Medical University, Tokyo, Japan
| | - Teruo Kirikae
- Department of Infectious Diseases, Research Institute, National Center for Global Health and Medicine, Tokyo, Japan
- * E-mail:
| | - Norio Ohmagari
- Disease Control and Prevention Center, Research Institute, National Center for Global Health and Medicine, Tokyo, Japan
| |
Collapse
|
9
|
Calderaro A, Martinelli M, Motta F, Larini S, Arcangeletti MC, Medici MC, Chezzi C, De Conto F. Comparison of peptide nucleic acid fluorescence in situ hybridization assays with culture-based matrix-assisted laser desorption/ionization-time of flight mass spectrometry for the identification of bacteria and yeasts from blood cultures and cerebrospinal fluid cultures. Clin Microbiol Infect 2014; 20:O468-75. [PMID: 24304149 DOI: 10.1111/1469-0691.12490] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2013] [Revised: 11/29/2013] [Accepted: 11/29/2013] [Indexed: 11/29/2022]
Abstract
Peptide nucleic acid fluorescence in situ hybridization (PNA FISH) is a molecular diagnostic tool for the rapid detection of pathogens directly from liquid media. The aim of this study was to prospectively evaluate PNA FISH assays in comparison with culture-based matrix-assisted laser desorption/ionization-time of flight mass spectrometry (MALDI-TOF MS) identification, as a reference method, for both blood and cerebrospinal fluid (CSF) cultures, during a 1-year investigation. On the basis of the Gram stain microscopy results, four different PNA FISH commercially available assays were used ('Staphylococcus aureus/CNS', 'Enterococcus faecalis/OE', 'GNR Traffic Light' and 'Yeasts Traffic Light' PNA FISH assays, AdvanDx). The four PNA FISH assays were applied to 956 positive blood cultures (921 for bacteria and 35 for yeasts) and 11 CSF cultures. Among the 921 blood samples positive for bacteria, PNA FISH gave concordant results with MALDI-TOF MS in 908/921 (98.64%) samples, showing an agreement of 99.4% in the case of monomicrobial infections. As regards yeasts, the PNA FISH assay showed a 100% agreement with the result obtained by MALDI-TOF MS. When PNA FISH assays were tested on the 11 CSF cultures, the results agreed with the reference method in all cases (100%). PNA FISH assays provided species identification at least one work-day before the MALDI-TOF MS culture-based identification. PNA FISH assays showed an excellent efficacy in the prompt identification of main pathogens, yielding a significant reduction in reporting time and leading to more appropriate patient management and therapy in cases of sepsis and severe infections.
Collapse
Affiliation(s)
- A Calderaro
- Unit of Microbiology and Virology, Department of Clinical and Experimental Medicine, Faculty of Medicine and Surgery, University of Parma, Parma, Italy
| | | | | | | | | | | | | | | |
Collapse
|
10
|
Epidemiology and new developments in the diagnosis of prosthetic joint infection. Int J Artif Organs 2013; 35:923-34. [PMID: 23138706 DOI: 10.5301/ijao.5000168] [Citation(s) in RCA: 154] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/15/2012] [Indexed: 12/12/2022]
Abstract
Although prosthetic joint infection (PJI) is a rare event after arthroplasty, it represents a significant complication that is associated with high morbidity, need for complex treatment, and substantial healthcare costs. An accurate and rapid diagnosis of PJI is crucial for treatment success. Current diagnostic methods in PJI are insufficient with 10-30% false-negative cultures. Consequently, there is a need for research and development into new methods aimed at improving diagnostic accuracy and speed of detection. In this article, we review available conventional diagnostic methods for the diagnosis of PJI (laboratory markers, histopathology, synovial fluid and periprosthetic tissue cultures), new diagnostic methods (sonication of implants, specific and multiplex PCR, mass spectrometry) and innovative techniques under development (new laboratory markers, microcalorimetry, electrical method, reverse transcription [RT]-PCR, fluorescence in situ hybridization [FISH], biofilm microscopy, microarray identification, and serological tests). The results of highly sensitive diagnostic techniques with unknown specificity should be interpreted with caution. The organism identified by a new method may represent a real pathogen that was unrecognized by conventional diagnostic methods or contamination during specimen sampling, transportation, or processing. For accurate interpretation, additional studies are needed, which would evaluate the long-term outcome (usually >2 years) with or without antimicrobial treatment. It is expected that new rapid, accurate, and fully automatic diagnostic tests will be developed soon.
Collapse
|
11
|
Harris DM, Hata DJ. Rapid identification of bacteria and Candida using PNA-FISH from blood and peritoneal fluid cultures: a retrospective clinical study. Ann Clin Microbiol Antimicrob 2013; 12:2. [PMID: 23295014 PMCID: PMC3553016 DOI: 10.1186/1476-0711-12-2] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2012] [Accepted: 01/05/2013] [Indexed: 11/16/2022] Open
Abstract
Background Peptide nucleic acid fluorescent in situ hybridization (PNA-FISH) is a rapid and established method for identification of Candida sp., Gram positive, and Gram negative bacteria from positive blood cultures. This study reports clinical experience in the evaluation of 103 positive blood cultures and 17 positive peritoneal fluid cultures from 120 patients using PNA-FISH. Our study provides evidence as to potential pharmaceutical cost savings based on rapid pathogen identification, in addition to the novel application of PNA-FISH to peritoneal fluid specimens. Methods Identification accuracy and elapsed time to identification of Gram positives, Gram negatives, and Candida sp., isolated from blood and peritoneal fluid cultures were assessed using PNA-FISH (AdvanDx), as compared to standard culture methods. Patient charts were reviewed to extrapolate potential pharmaceutical cost savings due to adjustment of antimicrobial or antifungal therapy, based on identification by PNA-FISH. Results In blood cultures, time to identification by standard culture methods for bacteria and Candida sp., averaged 83.6 hours (95% CI 56.7 to 110.5). Identification by PNA-FISH averaged 11.2 hours (95% CI 4.8 to 17.6). Overall PNA-FISH identification accuracy was 98.8% (83/84, 95% CI 93.5% to 99.9%) as compared to culture. In peritoneal fluid, identification of bacteria by culture averaged 87.4 hours (95% CI −92.4 to 267.1). Identification by PNA-FISH averaged 16.4 hours (95% CI −57.3 to 90.0). Overall PNA-FISH identification accuracy was 100% (13/13, 95% CI 75.3% to 100%). For Candida sp., pharmaceutical cost savings based on PNA-FISH identification could be $377.74/day. For coagulase-negative staphylococcus (CoNS), discontinuation of vancomycin could result in savings of $20.00/day. Conclusions In this retrospective study, excellent accuracy of PNA-FISH in blood and peritoneal fluids with reduced time to identification was observed, as compared to conventional culture-based techniques. Species-level identification based on PNA-FISH could contribute to notable cost savings due to adjustments in empiric antimicrobial or antifungal therapy as appropriate to the pathogen identified.
Collapse
Affiliation(s)
- Dana M Harris
- Department of Laboratory Medicine and Pathology, Mayo Clinic College of Medicine, 4500 San Pablo Rd, Jacksonville, Florida 32224, USA
| | | |
Collapse
|
12
|
Blaschke AJ, Heyrend C, Byington CL, Fisher MA, Barker E, Garrone NF, Thatcher SA, Pavia AT, Barney T, Alger GD, Daly JA, Ririe KM, Ota I, Poritz MA. Rapid identification of pathogens from positive blood cultures by multiplex polymerase chain reaction using the FilmArray system. Diagn Microbiol Infect Dis 2012; 74:349-55. [PMID: 22999332 DOI: 10.1016/j.diagmicrobio.2012.08.013] [Citation(s) in RCA: 149] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2012] [Revised: 07/21/2012] [Accepted: 08/20/2012] [Indexed: 01/09/2023]
Abstract
Sepsis is a leading cause of death. Rapid and accurate identification of pathogens and antimicrobial resistance directly from blood culture could improve patient outcomes. The FilmArray® (FA; Idaho Technology, Salt Lake City, UT, USA) Blood Culture (BC) panel can identify >25 pathogens and 4 antibiotic resistance genes from positive blood cultures in 1 h. We compared a development version of the panel to conventional culture and susceptibility testing on 102 archived blood cultures from adults and children with bacteremia. Of 109 pathogens identified by culture, 95% were identified by FA. Among 111 prospectively collected blood cultures, the FA identified 84 (91%) of 92 pathogens covered by the panel. Among 25 Staphylococcus aureus and 21 Enterococcus species detected, FA identified all culture-proven methicillin-resistant S. aureus and vancomycin-resistant enterococci. The FA BC panel is an accurate method for the rapid identification of pathogens and resistance genes from blood culture.
Collapse
Affiliation(s)
- Anne J Blaschke
- Department of Pediatrics, University of Utah, Salt Lake City, UT, USA.
| | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
13
|
Goff DA, Jankowski C, Tenover FC. Using Rapid Diagnostic Tests to Optimize Antimicrobial Selection in Antimicrobial Stewardship Programs. Pharmacotherapy 2012; 32:677-87. [DOI: 10.1002/j.1875-9114.2012.01137.x] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Affiliation(s)
- Debra A. Goff
- Department of Pharmacy; The Ohio State University Medical Center; Columbus; Ohio
| | | | | |
Collapse
|
14
|
Novel, improved sample preparation for rapid, direct identification from positive blood cultures using matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) mass spectrometry. J Mol Diagn 2011; 13:701-6. [PMID: 21889611 DOI: 10.1016/j.jmoldx.2011.07.004] [Citation(s) in RCA: 120] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2011] [Revised: 07/03/2011] [Accepted: 07/12/2011] [Indexed: 11/24/2022] Open
Abstract
Matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS) is widely used for rapid and reliable identification of bacteria and yeast grown on agar plates. Moreover, MALDI-TOF MS also holds promise for bacterial identification from blood culture (BC) broths in hospital laboratories. The most important technical step for the identification of bacteria from positive BCs by MALDI-TOF MS is sample preparation to remove blood cells and host proteins. We present a method for novel, rapid sample preparation using differential lysis of blood cells. We demonstrate the efficacy and ease of use of this sample preparation and subsequent MALDI-TOF MS identification, applying it to a total of 500 aerobic and anaerobic BCs reported to be positive by a Bactec 9240 system. In 86.5% of all BCs, the microorganism species were correctly identified. Moreover, in 18/27 mixed cultures at least one isolate was correctly identified. A novel method that adjusts the score value for MALDI-TOF MS results is proposed, further improving the proportion of correctly identified samples. The results of the present study show that the MALDI-TOF MS-based method allows rapid (<20 minutes) bacterial identification directly from positive BCs and with high accuracy.
Collapse
|
15
|
Identification of Escherichia coli, Klebsiella pneumoniae, and Pseudomonas aeruginosa in blood cultures: a multicenter performance evaluation of a three-color peptide nucleic acid fluorescence in situ hybridization assay. J Clin Microbiol 2011; 49:2259-61. [PMID: 21490185 DOI: 10.1128/jcm.02250-10] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
A multicenter evaluation was undertaken to evaluate the performance of a new three-color peptide nucleic acid fluorescence in situ hybridization assay that identifies isolates directly from blood cultures positive for Gram-negative bacilli (GNB). The assay correctly identified 100% (186/186) of the Escherichia coli isolates, 99.1% (109/110) of the Klebsiella pneumoniae isolates, and 95.8% (46/48) of the Pseudomonas aeruginosa isolates in this study. Negative assay results were correctly obtained for 162 of 165 other GNB (specificity, 98.2%).
Collapse
|
16
|
Tenover FC. Potential impact of rapid diagnostic tests on improving antimicrobial use. Ann N Y Acad Sci 2010; 1213:70-80. [DOI: 10.1111/j.1749-6632.2010.05827.x] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
|