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Massa-Buck B, Mendoza S, Keiser J, Mohamed MA. Use of Rapid Molecular Polymerase Chain Reaction in Early Detection of Bacteremia in Neonates Prior to Blood Culture Positivity: A Pilot Study. Am J Perinatol 2024; 41:569-574. [PMID: 35148542 DOI: 10.1055/s-0042-1742743] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/01/2022]
Abstract
OBJECTIVE There has been national strive to decrease the time needed to identify microorganisms in blood culture samples to reduce antibiotic use. This study evaluated rapid molecular polymerase chain reaction (PCR) use in identifying microorganisms in negative culture bottles from neonates with suspected bacterial blood stream infection at 20 to 24 hours of incubation. STUDY DESIGN All blood specimens from neonates with suspected blood stream infection were included. Specimens were incubated using a standard blood culturing instrument that would flag positive if bacterial growth was detected. If the specimen was flagged positive at <20 hours, it was tested by PCR and plated for identification as per standard protocol. In our design, if specimen was not flagged at 20 hours of incubation, the bottle was sterilely accessed and a sample was obtained for PCR testing. The bottle would be returned for incubation for 120 hours or until flagged positive. RESULTS A total of 192 blood specimens were included. Four specimens flagged positive at <20 hours and were all found to be positive by PCR. All other samples did not flag positive by 20 hours of incubation and were tested by PCR between 20 and 24 hours. One sample tested positive via PCR at 21.6 hours then flagged positive on the culturing instrument at 23.5 hours. All other specimens were negative by PCR and remained culture negative at 120 hours. The positive and negative predictive value of PCR verified by blood culture were both equal to 1.0. CONCLUSION Using rapid molecular PCR on blood culture specimens at 20 to 24 hours of incubation provides 100% true negative results possibly allowing providers to discontinue antibiotics at 24 hours. KEY POINTS · Antibiotic overuse leads to adverse neonatal outcomes.. · Molecular PCR may have true negative results.. · Larger study is needed to discontinue antibiotics earlier..
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Affiliation(s)
- Beri Massa-Buck
- Department of Neonatology, Children's National Hospital, Washington, District of Columbia
- Division of Newborn Services, The George Washington University Hospital, Washington, District of Columbia
| | - Salome Mendoza
- Department of Pathology, The George Washington University Hospital, Washington, District of Columbia
| | - John Keiser
- Department of Pathology, The George Washington University Hospital, Washington, District of Columbia
| | - Mohamed A Mohamed
- Department of Neonatology, Cleveland Clinic Children's Hospital, Cleveland, Ohio
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Caunedo-Jiménez M, Fernández-Colomer B, Fernández-Suárez J, Arias-Llorente RP, Lareu-Vidal S, Mantecón-Fernández L, Solís-Sánchez G, Suárez-Rodríguez M. Clinical Utility of the FilmArray® Blood Culture Identification (BCID) Panel for the Diagnosis of Neonatal Sepsis. Microorganisms 2023; 11:microorganisms11030732. [PMID: 36985305 PMCID: PMC10059247 DOI: 10.3390/microorganisms11030732] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Revised: 02/20/2023] [Accepted: 03/10/2023] [Indexed: 03/16/2023] Open
Abstract
This prospective single-center study was designed to assess the clinical utility of the FilmArray® blood culture identification (BCID) panel for improving the diagnostic accuracy in neonatal sepsis. Results obtained using the FilmArray® BCID panel were correlated with results of blood culture in all consecutive neonates with suspicion of early-onset (EOS) and late-onset sepsis (LOS) attended in our service over a two-year period. A total of 102 blood cultures from 92 neonates were included, 69 (67.5%) in cases of EOS and 33 (32.3%) in LOS. The FilmArray® BCID panel was performed in negative culture bottles at a median of 10 h of blood culture incubation (IQR 8–20), without differences by the type of sepsis. The FilmArray® BCID panel showed a 66.7% sensitivity, 100% specificity, 100% positive predictive value, and 95.7% negative predictive value. There were four false-negative cases, three of which were Streptococcus epidermidis in neonates with LOS, and there was one case of Granulicatella adiacens in one neonate with EOS. We conclude that the use of the FilmArray® BCID panel in negative blood cultures from neonates with clinical suspicion of sepsis is useful in decision-making of starting or early withdrawal of empirical antimicrobials because of the high specificity and negative predictive values of this assay.
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Affiliation(s)
- María Caunedo-Jiménez
- Division of Neonatology, Department of Pediatrics, Central University Hospital of Asturias, Av. Roma s/n, E-33011 Oviedo, Spain
| | - Belén Fernández-Colomer
- Division of Neonatology, Department of Pediatrics, Central University Hospital of Asturias, Av. Roma s/n, E-33011 Oviedo, Spain
- Correspondence:
| | - Jonathan Fernández-Suárez
- Department of Microbiology, Central University Hospital of Asturias and Instituto de Investigación Sanitaria del Principado de Asturias, E-33011 Oviedo, Spain
| | - Rosa Patricia Arias-Llorente
- Division of Neonatology, Department of Pediatrics, Central University Hospital of Asturias, Av. Roma s/n, E-33011 Oviedo, Spain
| | - Sonia Lareu-Vidal
- Division of Neonatology, Department of Pediatrics, Central University Hospital of Asturias, Av. Roma s/n, E-33011 Oviedo, Spain
| | - Laura Mantecón-Fernández
- Division of Neonatology, Department of Pediatrics, Central University Hospital of Asturias, Av. Roma s/n, E-33011 Oviedo, Spain
| | - Gonzalo Solís-Sánchez
- Division of Neonatology, Department of Pediatrics, Central University Hospital of Asturias, Av. Roma s/n, E-33011 Oviedo, Spain
| | - Marta Suárez-Rodríguez
- Division of Neonatology, Department of Pediatrics, Central University Hospital of Asturias, Av. Roma s/n, E-33011 Oviedo, Spain
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Pfefferle S, Christner M, Aepfelbacher M, Lütgehetmann M, Rohde H. Implementation of the FilmArray ME panel in laboratory routine using a simple sample selection strategy for diagnosis of meningitis and encephalitis. BMC Infect Dis 2020; 20:170. [PMID: 32087681 PMCID: PMC7036261 DOI: 10.1186/s12879-020-4904-4] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2019] [Accepted: 02/18/2020] [Indexed: 12/13/2022] Open
Abstract
Background Infectious meningitis is a serious disease and patient outcome relies on fast and reliable diagnostics. A syndromic panel testing approach like the FilmArray ME can accelerate diagnosis and therefore decrease the time to pathogen specific therapy. Yet, its clinical utility is controversial, mainly because of a remaining uncertainty in correct interpretation of results, limited data on its performance on clinical specimens and its relatively high costs. The aim of this study was to analyze clinical performance of the assay in a real life setting at a tertiary university hospital using a pragmatic and simple sample selection strategy to reduce the overall cost burden. Methods Over a period of 18 months we received 4623 CSF samples (2338 hospitalizations, 1601 individuals). FilmArray ME analysis was restricted to CSF-samples with a high pretest probability of infectious meningitis, e.g. positive Gram-stain, samples in which leukocytes and/or bacteria were evident or urgent suspicion of infection was communicated by clinicians. N = 171 samples matched to our risk criteria and were subjected to FilmArray ME analysis. Those samples were also analyzed by reference methods: culture only (n = 45), PCR only (n = 20) or both methods (n = 106). Results 56/171 (32.75%) were FilmArray ME positive. Bacterial pathogens were detected in 30/56 (53.57%), viral pathogens were detected in 27/56 (48.21%) and yeast DNA was detected in 1/56 (1.79%) of positive samples. Double detection occurred in 2/56 samples. In 52/56 (92.86%) FilmArray ME positive samples, results could be confirmed by the reference assays (sensitivity = 96.30%, specificity =96.58%). Conclusion The FilmArray ME assay is a fast and reliable diagnostic tool for the management of infectious meningitis and can easily be implemented in routine diagnostic workflows. However, correlation of test results and underlying clinical symptoms requires experienced users and the awareness of potentially false negative or false positive results. Moreover, considering the need for antimicrobial susceptibility testing, the use of molecular tests as a stand-alone diagnostic cannot be recommended.
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Affiliation(s)
- Susanne Pfefferle
- Institut für Medizinische Mikrobiologie, Virologie und Hygiene, Universitätsklinikum Hamburg-Eppendorf, Martinistraße 52, 20246, Hamburg, Germany.
| | - Martin Christner
- Institut für Medizinische Mikrobiologie, Virologie und Hygiene, Universitätsklinikum Hamburg-Eppendorf, Martinistraße 52, 20246, Hamburg, Germany
| | - Martin Aepfelbacher
- Institut für Medizinische Mikrobiologie, Virologie und Hygiene, Universitätsklinikum Hamburg-Eppendorf, Martinistraße 52, 20246, Hamburg, Germany
| | - Marc Lütgehetmann
- Institut für Medizinische Mikrobiologie, Virologie und Hygiene, Universitätsklinikum Hamburg-Eppendorf, Martinistraße 52, 20246, Hamburg, Germany
| | - Holger Rohde
- Institut für Medizinische Mikrobiologie, Virologie und Hygiene, Universitätsklinikum Hamburg-Eppendorf, Martinistraße 52, 20246, Hamburg, Germany
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Comparison of the Fully Automated FilmArray BCID Assay to a 4-Hour Culture Test Coupled to Mass Spectrometry for Day 0 Identification of Microorganisms in Positive Blood Cultures. BIOMED RESEARCH INTERNATIONAL 2018; 2018:7013470. [PMID: 30584536 PMCID: PMC6280299 DOI: 10.1155/2018/7013470] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/09/2018] [Accepted: 11/08/2018] [Indexed: 01/11/2023]
Abstract
Rapid bacterial identification of positive blood culture is important for adapting the antimicrobial therapy in patients with blood stream infection. The aim of this study was to evaluate the performance of the multiplex FilmArray Blood Culture Identification (BCID) assay by comparison to an in-house protocol based on MALDI-TOF MS identification of microcolonies after a 4-hour culture, for identifying on the same day the microorganisms present in positive blood culture bottles. One hundred and fifty-three positive bottles from 123 patients were tested prospectively by the 3 techniques of bacterial identification: 11 bottles yielding negative results by the 3 tests were considered false positive (7.2%). The reference MALDI-TOF MS technique identified 134 monomicrobial (87.6%) and 8 double infections (5.2%), which resulted in a total of 150 microorganisms. Globally, 137 (91.3%) of these 150 pathogens were correctly identified by the fully automated multiplex FilmArray BCID system at the species or genus level on day of growth detection, versus 117 (78.8%) by MALDI-TOF MS identification on nascent microcolonies after a 4-hour culture (P < 0.01). By combining the two approaches, 140 (93.5%) of the positive bottles were identified successfully at day 0. These results confirm the excellent sensitivity of the FilmArray BCID assay, notably in case of multimicrobial infection. Due to the limited number of targets included into the test, it must be coupled to another identification strategy, as that presented in this study relying on MALDI-TOF MS identification of microcolonies obtained after a very short culture period.
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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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Lee AS, de Lencastre H, Garau J, Kluytmans J, Malhotra-Kumar S, Peschel A, Harbarth S. Methicillin-resistant Staphylococcus aureus. Nat Rev Dis Primers 2018; 4:18033. [PMID: 29849094 DOI: 10.1038/nrdp.2018.33] [Citation(s) in RCA: 724] [Impact Index Per Article: 120.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Since the 1960s, methicillin-resistant Staphylococcus aureus (MRSA) has emerged, disseminated globally and become a leading cause of bacterial infections in both health-care and community settings. However, there is marked geographical variation in MRSA burden owing to several factors, including differences in local infection control practices and pathogen-specific characteristics of the circulating clones. Different MRSA clones have resulted from the independent acquisition of staphylococcal cassette chromosome mec (SCCmec), which contains genes encoding proteins that render the bacterium resistant to most β-lactam antibiotics (such as methicillin), by several S. aureus clones. The success of MRSA is a consequence of the extensive arsenal of virulence factors produced by S. aureus combined with β-lactam resistance and, for most clones, resistance to other antibiotic classes. Clinical manifestations of MRSA range from asymptomatic colonization of the nasal mucosa to mild skin and soft tissue infections to fulminant invasive disease with high mortality. Although treatment options for MRSA are limited, several new antimicrobials are under development. An understanding of colonization dynamics, routes of transmission, risk factors for progression to infection and conditions that promote the emergence of resistance will enable optimization of strategies to effectively control MRSA. Vaccine candidates are also under development and could become an effective prevention measure.
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Affiliation(s)
- Andie S Lee
- Departments of Infectious Diseases and Microbiology, Royal Prince Alfred Hospital, Sydney, New South Wales, Australia.,Faculty of Medicine, University of Sydney, Sydney, New South Wales, Australia
| | - Hermínia de Lencastre
- Laboratory of Microbiology and Infectious Diseases, The Rockefeller University, New York, NY, USA.,Laboratory of Molecular Genetics, Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
| | - Javier Garau
- Department of Medicine, Hospital Universitari Mutua de Terrassa, Barcelona, Spain
| | - Jan Kluytmans
- Department of Infection Control, Amphia Hospital, Breda, Netherlands.,Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, Utrecht University, Utrecht, Netherlands
| | - Surbhi Malhotra-Kumar
- Laboratory of Medical Microbiology, Vaccine and Infectious Disease Institute, Universiteit Antwerpen, Wilrijk, Belgium
| | - Andreas Peschel
- Interfaculty Institute of Microbiology and Infection Medicine, Infection Biology Department, University of Tübingen, Tübingen, Germany.,German Center for Infection Research, Partner Site Tübingen, Tübingen, Germany
| | - Stephan Harbarth
- Infection Control Programme, University of Geneva Hospitals and Faculty of Medicine, WHO Collaborating Center, Geneva, Switzerland
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Klingspor L, Lindbäck E, Ullberg M, Özenci V. Seven years of clinical experience with the Yeast Traffic Light PNA FISH: Assay performance and possible implications on antifungal therapy. Mycoses 2017; 61:179-185. [PMID: 29086449 DOI: 10.1111/myc.12722] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2017] [Revised: 10/20/2017] [Accepted: 10/24/2017] [Indexed: 01/02/2023]
Abstract
We evaluated the performance of Yeast Traffic Light PNA FISH (YTL PNA FISH) in identification of Candida spp. from blood cultures. A total of 200 new episodes of candidaemia were analysed prospectively. The YTL PNA FISH results were reported to the clinicians and data on antifungal therapy were documented. In total, there were 164/200 (82%) positive blood culture bottles with monomicrobial growth. Coverage of monomicrobial yeast was 150/164 (91.5%). YTL PNA FISH could identify 23/24 (95.8%) Candida spp. in bottles with concomitant growth of bacteria and one yeast. Growth of two or more different yeast was observed in 12/200 (6%) blood culture bottles and the method could identify all yeast in 8/12 (66.7%). Data on antifungal treatment were available for 181/200 patients (90.5%). In 132/137 (96.4%) samples from patients without antifungal treatment, YTL PNA FISH could identify the Candida spp. or gave a negative result for yeast not included in panel, and based on the result guide appropriate antifungal therapy the same day when the blood culture bottle signalled positive. This study shows that YTL PNA FISH is a rapid, reliable diagnostic method which significantly reduces time delay for choice of appropriate antifungal therapy for critically ill patients.
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Affiliation(s)
- Lena Klingspor
- Division of Clinical Microbiology, Department of Laboratory Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Emma Lindbäck
- Division of Clinical Microbiology, Department of Laboratory Medicine, Karolinska Institutet, Stockholm, Sweden.,Department of Clinical Microbiology, Karolinska University Hospital, Stockholm, Sweden
| | - Måns Ullberg
- Division of Clinical Microbiology, Department of Laboratory Medicine, Karolinska Institutet, Stockholm, Sweden.,Department of Clinical Microbiology, Karolinska University Hospital, Stockholm, Sweden
| | - Volkan Özenci
- Division of Clinical Microbiology, Department of Laboratory Medicine, Karolinska Institutet, Stockholm, Sweden.,Department of Clinical Microbiology, Karolinska University Hospital, Stockholm, Sweden
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Abstract
The recent development of commercial panel-based molecular diagnostics for the rapid detection of pathogens in positive blood culture bottles, respiratory specimens, stool, and cerebrospinal fluid has resulted in a paradigm shift in clinical microbiology and clinical practice. This review focuses on U.S. Food and Drug Administration (FDA)-approved/cleared multiplex molecular panels with more than five targets designed to assist in the diagnosis of bloodstream, respiratory tract, gastrointestinal, or central nervous system infections. While these panel-based assays have the clear advantages of a rapid turnaround time and the detection of a large number of microorganisms and promise to improve health care, they present certain challenges, including cost and the definition of ideal test utilization strategies (i.e., optimal ordering) and test interpretation.
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9
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Messacar K, Hurst AL, Child J, Campbell K, Palmer C, Hamilton S, Dowell E, Robinson CC, Parker SK, Dominguez SR. Clinical Impact and Provider Acceptability of Real-Time Antimicrobial Stewardship Decision Support for Rapid Diagnostics in Children With Positive Blood Culture Results. J Pediatric Infect Dis Soc 2017; 6:267-274. [PMID: 27543412 PMCID: PMC5907879 DOI: 10.1093/jpids/piw047] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/06/2016] [Accepted: 07/12/2016] [Indexed: 12/15/2022]
Abstract
BACKGROUND Rapid diagnostic technologies for infectious diseases have the potential to improve clinical outcomes, but guideline-recommended antimicrobial stewardship (AS) strategies are not currently optimized for rapid intervention. We evaluated the clinical impact and provider acceptability of implementing real-time AS decision support for children with positive blood culture results according to the FilmArray blood culture identification panel (BCID [BioFire Diagnostics]) at Children's Hospital Colorado. METHODS A pre-post quasi-experimental design was used to compare the outcomes of 100 postintervention children with positive blood culture results matched with 200 preintervention control children. Causative organisms in the preintervention group were identified using conventional microbiologic techniques and communicated to providers by a microbiology technologist. Postintervention organisms were identified by the BCID and communicated by an AS provider in real time with interpretation and antimicrobial recommendations. The primary outcome was time to optimal antimicrobial therapy (time from blood culture collection to start of predetermined pathogen-specific regimen or antimicrobial discontinuation for contaminants) compared by a log-rank test and Kaplan-Meier analysis. Provider acceptability of the intervention was assessed via E-mailed surveys. RESULTS The median time to optimal therapy decreased from 60.2 hours before intervention to 26.7 hours after intervention (P = .001). Among children with blood cultures that contained true pathogens, the time to effective antimicrobial therapy decreased from 6.9 to 3.4 hours (P = .03). Unnecessary antibiotic initiation for children with a culture that contained organisms considered to be contaminants decreased from 76% to 26% (P < .001). Providers reported a change in management as a result of BCID results in 73% of the cases and a mean overall satisfaction rating of 4.8 on a 5-point Likert scale. CONCLUSIONS Real-time AS decision support for rapid diagnostics is associated with improved antimicrobial use and high satisfaction ratings by providers.
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Affiliation(s)
- Kevin Messacar
- Department of Pediatrics, Section of Infectious Diseases,Department of Pediatrics, Section of Hospital Medicine, University of Colorado/Children’s Hospital,,Correspondence: K. Messacar, MD, Department of Pediatrics, University of Colorado/Children’s Hospital Colorado, B055, 13123 E 16th Ave, Aurora, CO 80045. E-mail:
| | | | | | - Kristen Campbell
- Department of Biostatistics and Informatics, University of Colorado School of Public Health
| | | | | | - Elaine Dowell
- Department of Pathology and Laboratory Medicine, and
| | | | - Sarah K Parker
- Department of Pediatrics, Section of Infectious Diseases
| | - Samuel R Dominguez
- Department of Pediatrics, Section of Infectious Diseases,Department of Epidemiology, Children’s Hospital Colorado, Aurora
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10
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Decousser JW, Poirel L, Nordmann P. Recent advances in biochemical and molecular diagnostics for the rapid detection of antibiotic-resistant Enterobacteriaceae: a focus on ß-lactam resistance. Expert Rev Mol Diagn 2017; 17:327-350. [DOI: 10.1080/14737159.2017.1289087] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Affiliation(s)
- Jean-Winoc Decousser
- Department of Virology, Bacteriology - Infection Control, Parasitology - Mycology, Assistance Publique - Hôpitaux de Paris, University Hospital Henri Mondor, Créteil, France
- IAME, UMR 1137, INSERM, Paris, France
| | - Laurent Poirel
- Emerging Antibiotic Resistance Unit, Medical and Molecular Microbiology, Department of Medicine, University of Fribourg, Fribourg, Switzerland
- French INSERM European Unit, University of Fribourg (LEA-IAME), Fribourg, Switzerland
- National Reference Center for Emerging Antibiotic Resistance, University of fribourg, fribourg, switzerland
| | - Patrice Nordmann
- Emerging Antibiotic Resistance Unit, Medical and Molecular Microbiology, Department of Medicine, University of Fribourg, Fribourg, Switzerland
- French INSERM European Unit, University of Fribourg (LEA-IAME), Fribourg, Switzerland
- National Reference Center for Emerging Antibiotic Resistance, University of fribourg, fribourg, switzerland
- Institute for Microbiology, University of Lausanne and University hospital Center, Lausanne, Switzerland
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11
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Okeke IN. Laboratory systems as an antibacterial resistance containment tool in Africa. Afr J Lab Med 2016; 5:497. [PMID: 28879140 PMCID: PMC5433813 DOI: 10.4102/ajlm.v5i3.497] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2016] [Accepted: 08/05/2016] [Indexed: 01/02/2023] Open
Abstract
INTRODUCTION As crucial as clinical laboratories are to preventing, identifying and managing resistance problems, laboratory scientists are among the most overlooked stakeholders. This review outlines the contributions that diagnostic laboratory systems should make toward all five of the World Health Organization's 2015 strategic objectives for antimicrobial resistance containment. LABORATORY SYSTEMS IN RESISTANCE CONTAINMENT Antimicrobial susceptibility testing and surveillance are central to antibacterial resistance management and control and need to be implemented more commonly and closer to sick patients. However, the scope of tests that promote judicious antimicrobial use extend beyond susceptibility testing. Laboratory tests for pathogens or their associated biomarkers confirm or rule out specific causes of signs and symptoms associated with infection. Laboratory systems also provide critical support to infection control programmes. All of these functions promote rational antimicrobial use and contain the spread of resistance. Routine laboratory data supports the development of vaccines and other technologies that could ease the pressure placed by antimicrobials. Laboratories are also a rich source of information for health professionals, policymakers and the general public about the urgency of the resistance problem and progress in containing it. CONCLUSION Laboratory systems are integral to antimicrobial resistance containment and contributions from African laboratories to addressing resistance need to be enhanced.
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Affiliation(s)
- Iruka N Okeke
- Department of Pharmaceutical Microbiology, University of Ibadan, Ibadan, Oyo State, Nigeria
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12
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Banerjee R, Özenci V, Patel R. Individualized Approaches Are Needed for Optimized Blood Cultures. Clin Infect Dis 2016; 63:1332-1339. [PMID: 27558570 DOI: 10.1093/cid/ciw573] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2016] [Accepted: 08/14/2016] [Indexed: 01/12/2023] Open
Abstract
Many strategies and technologies are available to improve blood culture (BC)-based diagnostics. The ideal approach to BCs varies between healthcare institutions. Institutions need to examine clinical needs and practices in order to optimize BC-based diagnostics for their site. Before laboratories consider offering rapid matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-ToF MS) or expensive rapid panel-based molecular BC diagnostics, they should optimize preanalytical, analytical, and postanalytical processes and procedures surrounding BC systems. Several factors need to be considered, including local resistance rates, antibiotic prescribing patterns, patient- and provider-types, laboratory staffing, and personnel available to liaise with clinicians to optimize antibiotic use. While there is much excitement surrounding new high-technology diagnostics, cost-neutral benefits can be realized by optimizing existing strategies and using available tools in creative ways. Rapid BC diagnostics should be implemented in a manner that optimizes impact. Strategies to optimize these BC diagnostics in individual laboratories are presented here.
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Affiliation(s)
- Ritu Banerjee
- Department of Pediatric Infections Diseases, Vanderbilt University, Nashville, Tennessee
| | - Volkan Özenci
- Division of Clinical Microbiology, Karolinska Institutet, Karolinska University Hospital, Huddinge, Stockholm, Sweden
| | - Robin Patel
- Division of Clinical Microbiology, Department of Laboratory Medicine and Pathology.,Division of Infectious Diseases, Department of Medicine, Mayo Clinic, Rochester, Minnesota
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Otlu B, Bayindir Y, Ozdemir F, Ince V, Cuglan S, Hopoglu M, Yakupogullari Y, Kizilkaya C, Kuzucu C, Isık B, Yilmaz S. Rapid Detection of Bloodstream Pathogens in Liver Transplantation Patients With FilmArray Multiplex Polymerase Chain Reaction Assays: Comparison With Conventional Methods. Transplant Proc 2016; 47:1926-32. [PMID: 26293075 DOI: 10.1016/j.transproceed.2015.02.025] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2014] [Accepted: 02/10/2015] [Indexed: 02/02/2023]
Abstract
BACKGROUND Bloodstream infection (BSI) is an important concern in transplant patients. Early intervention with appropriate antimicrobial therapy is critical to better clinical outcome; however, there is significant delay when conventional identification methods are used. METHODS We aimed to determine the diagnostic performance of the FilmArray Blood Culture Identification Panel, a recently approved multiplex polymerase chain reaction assay detecting 24 BSI pathogens and 3 resistance genes, in comparison with the performances of conventional identification methods in liver transplant (LT) patients. A total of 52 defined sepsis episodes (signal-positive by blood culture systems) from 45 LT patients were prospectively studied. RESULTS The FilmArray successfully identified 37 of 39 (94.8%) bacterial and 3 of 3 (100%) yeast pathogens in a total of 42 samples with microbial growth, failing to detect only 2 of 39 (5.1%) bacterial pathogens that were not covered by the test panel. The FilmArray could also detect additional pathogens in 3 samples that had been reported as having monomicrobial growth, and it could detect Acinetobacter baumannii in 2 samples suspected of skin flora contamination. The remaining 8 blood cultures showing a positive signal but yielding no growth were also negative by this assay. Results of MecA, KPC, and VanA/B gene detection were in high accordance. The FilmArray produced results with significantly shorter turnaround times (1.33 versus 36.2, 23.6, and 19.5 h; P < .05) than standard identification methods, Vitek II, and Vitek MS, respectively. CONCLUSIONS This study showed that the FilmArray appeared as a reliable alternative diagnostic method with the potential to mitigate problems with protracted diagnosis of the BSI pathogens in LT patients.
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Affiliation(s)
- B Otlu
- Department of Medical Microbiology, Faculty of Medicine, Inonu University, Malatya, Turkey.
| | - Y Bayindir
- Department of Infectious Diseases and Clinical Microbiology, Faculty of Medicine, Inonu University, Malatya, Turkey
| | - F Ozdemir
- Department of Surgery, Liver Transplantation Institute, Faculty of Medicine, Inönü University, Malatya, Turkey
| | - V Ince
- Department of Surgery, Liver Transplantation Institute, Faculty of Medicine, Inönü University, Malatya, Turkey
| | - S Cuglan
- Department of Medical Microbiology, Faculty of Medicine, Inonu University, Malatya, Turkey
| | - M Hopoglu
- Department of Infectious Diseases and Clinical Microbiology, Faculty of Medicine, Inonu University, Malatya, Turkey
| | - Y Yakupogullari
- Department of Medical Microbiology, Faculty of Medicine, Inonu University, Malatya, Turkey
| | - C Kizilkaya
- Department of Medical Microbiology, Faculty of Medicine, Ankara University, Ankara, Turkey
| | - C Kuzucu
- Department of Medical Microbiology, Faculty of Medicine, Inonu University, Malatya, Turkey
| | - B Isık
- Department of Medical Microbiology, Faculty of Medicine, Inonu University, Malatya, Turkey
| | - S Yilmaz
- Department of Surgery, Liver Transplantation Institute, Faculty of Medicine, Inönü University, Malatya, Turkey
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Optimized Use of the MALDI BioTyper System and the FilmArray BCID Panel for Direct Identification of Microbial Pathogens from Positive Blood Cultures. J Clin Microbiol 2015; 54:576-84. [PMID: 26677254 DOI: 10.1128/jcm.02590-15] [Citation(s) in RCA: 57] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2015] [Accepted: 12/13/2015] [Indexed: 01/04/2023] Open
Abstract
Despite the current reliance on blood cultures (BCs), the diagnosis of bloodstream infections (BSIs) can be sped up using new technologies performed directly on positive BC bottles. Two methods (the MALDI BioTyper system and FilmArray blood culture identification [BCID] panel) are potentially applicable. In this study, we performed a large-scale clinical evaluation (1,585 microorganisms from 1,394 BSI episodes) on the combined use of the MALDI BioTyper and FilmArray BCID panel compared to a reference (culture-based) method. As a result, the causative organisms of 97.7% (1,362/1,394) of the BSIs were correctly identified by our MALDI BioTyper and FilmArray BCID-based algorithm. Specifically, 65 (5.3%) out of 1,223 monomicrobial BCs that provided incorrect or invalid identifications with the MALDI BioTyper were accurately detected by the FilmArray BCID panel; additionally, 153 (89.5%) out of 171 polymicrobial BCs achieved complete identification with the FilmArray BCID panel. Conversely, full use of the MALDI BioTyper would have resulted in the identification of only 1 causative organism in 97/171 (56.7%) of the polymicrobial cultures. By applying our diagnostic algorithm, the median time to identification was shortened (19.5 h versus 41.7 h with the reference method; P < 0.001), and the minimized use of the FilmArray BCID panel led to a significant cost savings. Twenty-six out of 31 microorganisms that could not be identified were species/genera not designed to be detected with the FilmArray BCID panel, indicating that subculture was not dispensable for a few of our BSI episodes. In summary, the fast and effective testing of BC bottles is realistically adoptable in the clinical microbiology laboratory workflow, although the usefulness of this testing for the management of BSIs remains to be established.
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15
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Micó M, Navarro F, de Miniac D, González Y, Brell A, López C, Sánchez-Reus F, Mirelis B, Coll P. Efficacy of the FilmArray blood culture identification panel for direct molecular diagnosis of infectious diseases from samples other than blood. J Med Microbiol 2015; 64:1481-1488. [PMID: 26432445 DOI: 10.1099/jmm.0.000180] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Molecular-based techniques reduce the delay in diagnosing infectious diseases and therefore contribute to better patient outcomes. We assessed the FilmArray blood culture identification (BCID) panel (Biofire Diagnostics/bioMérieux) directly on clinical specimens other than blood: cerebrospinal, joint, pleural and ascitic fluids, bronchoscopy samples and abscesses. We compared the results from 88 samples obtained by culture-based techniques. The percentage of agreement between the two methods was 75 % with a Cohen κ value of 0.51. Global sensitivity and specificity using the FilmArray BCID panel were 71 and 97 %, respectively. Sensitivity was poorer in samples with a low bacterial load, such as ascitic and pleural fluids (25 %), whereas the sensitivity for abscess samples was high (89 %). These findings suggest that the FilmArray BCID panel could be useful to perform microbiological diagnosis directly from samples other than positive blood cultures, as it offers acceptable sensitivity and moderate agreement with conventional microbiological methods. Nevertheless, cost-benefit studies should be performed before introducing this method into algorithms for microbiological diagnostics.
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Affiliation(s)
- Miquel Micó
- Servei de Microbiologia. Hospital de la Santa Creu i Sant Pau Barcelona, Spain
| | - Ferran Navarro
- Spanish Network for the Research in Infectious Diseases (REIPI RD12/0015), Instituto de Salud Carlos III, Madrid, Spain.,Servei de Microbiologia. Hospital de la Santa Creu i Sant Pau Barcelona, Spain.,Institut d'Investigació Biomèdica Sant Pau, Barcelona, Spain and Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Daniela de Miniac
- Servei de Microbiologia. Hospital de la Santa Creu i Sant Pau Barcelona, Spain
| | - Yésica González
- Servei de Microbiologia. Hospital de la Santa Creu i Sant Pau Barcelona, Spain
| | - Albert Brell
- Servei de Microbiologia. Hospital de la Santa Creu i Sant Pau Barcelona, Spain
| | - Cristina López
- Servei de Microbiologia. Hospital de la Santa Creu i Sant Pau Barcelona, Spain
| | - Ferran Sánchez-Reus
- Servei de Microbiologia. Hospital de la Santa Creu i Sant Pau Barcelona, Spain.,Institut d'Investigació Biomèdica Sant Pau, Barcelona, Spain and Universitat Autònoma de Barcelona, Barcelona, Spain.,Spanish Network for the Research in Infectious Diseases (REIPI RD12/0015), Instituto de Salud Carlos III, Madrid, Spain
| | - Beatriz Mirelis
- Servei de Microbiologia. Hospital de la Santa Creu i Sant Pau Barcelona, Spain.,Institut d'Investigació Biomèdica Sant Pau, Barcelona, Spain and Universitat Autònoma de Barcelona, Barcelona, Spain.,Spanish Network for the Research in Infectious Diseases (REIPI RD12/0015), Instituto de Salud Carlos III, Madrid, Spain
| | - Pere Coll
- Servei de Microbiologia. Hospital de la Santa Creu i Sant Pau Barcelona, Spain.,Institut d'Investigació Biomèdica Sant Pau, Barcelona, Spain and Universitat Autònoma de Barcelona, Barcelona, Spain.,Spanish Network for the Research in Infectious Diseases (REIPI RD12/0015), Instituto de Salud Carlos III, Madrid, Spain
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Rapid identification of pathogens from pediatric blood cultures by use of the FilmArray blood culture identification panel. J Clin Microbiol 2014; 52:4368-71. [PMID: 25274998 DOI: 10.1128/jcm.02133-14] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The performance of the FilmArray blood culture identification (BCID) panel has been studied in adult patients. We describe here an evaluation of this assay for the rapid identification of pathogens in Bactec Peds Plus/F and Bactec standard anaerobic/F bottles that contained blood samples from pediatric patients at a tertiary care children's hospital.
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