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Srivastava S, Sharad N, Kiro VV, Ningombam A, Shrivastava S, Farooque K, Mathur P. Utility of a multiplex pathogen detection system directly from respiratory specimens for treatment and diagnostic stewardship. Microbiol Spectr 2024; 12:e0375923. [PMID: 38712971 PMCID: PMC11237763 DOI: 10.1128/spectrum.03759-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2023] [Accepted: 03/29/2024] [Indexed: 05/08/2024] Open
Abstract
The availability of syndrome-based panels for various ailments has widened the scope of diagnostics in many clinical settings. These panels can detect a multitude of pathogens responsible for a particular condition, which can lead to a timely diagnosis and better treatment outcomes. In contrast to traditional identification methods based on pathogen growth on culture, syndrome-based panels offer a quicker diagnosis, which can be especially beneficial in situations requiring urgent care, such as intensive care units. One such panel is the Biofire Filmarray Pneumonia plus Panel (BFP), which we have compared against microbiological culture and identification. The lower respiratory samples from patients were tested with BFP, culture, and identification with culture considered the gold standard. The phenotypic antibiotic susceptibility results (Vitek 2) were compared with the antimicrobial resistance (AMR) genes detected in BFP. Statistical analysis was carried out using GraphPad 7.0 and MS Excel (Microsoft Inc.). The results showed a positive percent agreement of 100% and a negative percent agreement of 47.8% with an overall agreement of 76.72% compared to culture. BFP was better at identifying fastidious bacteria, and the agreement with culture was higher for high bacterial identification numbers (107 and 106). There was also a correlation between the number of pathogens detected and growth in culture. Carbapenemase genes were detected in around 80% of phenotypically resistant samples and correlated with in-house PCR 60% of the time. Hence, BFP results need to be interpreted with caution especially when multiple pathogens are detected. Similarly, the presence or absence of AMR genes should be used to guide the therapy while being watchful of unusual resistance or susceptibility. The cost constraints and low throughput call for patient selection criteria and prioritization in emergency or resource-limited conditions.IMPORTANCEApplication of syndrome-based panels in clinical microbiology is of huge support in infectious conditions requiring urgent interventions, such as pneumonia. Interpreting the results requires caution; hence, we have compared the results obtained from Biofire Filmarray Pneumonia plus Panel with standard microbiological methods.
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Affiliation(s)
| | - Neha Sharad
- Department of Microbiology, AIIMS, New Delhi, India
| | | | - Aparna Ningombam
- Department of Laboratory Medicine, JPNATC, AIIMS, New Delhi, India
| | | | | | - Purva Mathur
- Department of Laboratory Medicine, JPNATC, AIIMS, New Delhi, India
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Walker AM, Timbrook TT, Hommel B, Prinzi AM. Breaking Boundaries in Pneumonia Diagnostics: Transitioning from Tradition to Molecular Frontiers with Multiplex PCR. Diagnostics (Basel) 2024; 14:752. [PMID: 38611665 PMCID: PMC11012095 DOI: 10.3390/diagnostics14070752] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2024] [Revised: 03/24/2024] [Accepted: 03/27/2024] [Indexed: 04/14/2024] Open
Abstract
The advent of rapid molecular microbiology testing has revolutionized infectious disease diagnostics and is now impacting pneumonia diagnosis and management. Molecular platforms offer highly multiplexed assays for diverse viral and bacterial detection, alongside antimicrobial resistance markers, providing the potential to significantly shape patient care. Despite the superiority in sensitivity and speed, debates continue regarding the clinical role of multiplex molecular testing, notably in comparison to standard methods and distinguishing colonization from infection. Recent guidelines endorse molecular pneumonia panels for enhanced sensitivity and rapidity, but implementation requires addressing methodological differences and ensuring clinical relevance. Diagnostic stewardship should be leveraged to optimize pneumonia testing, emphasizing pre- and post-analytical strategies. Collaboration between clinical microbiologists and bedside providers is essential in developing implementation strategies to maximize the clinical utility of multiplex molecular diagnostics in pneumonia. This narrative review explores these multifaceted issues, examining the current evidence on the clinical performance of multiplex molecular assays in pneumonia, and reflects on lessons learned from previous microbiological advances. Additionally, given the complexity of pneumonia and the sensitivity of molecular diagnostics, diagnostic stewardship is discussed within the context of current literature, including implementation strategies that consider pre-analytical and post-analytical modifications to optimize the clinical utility of advanced technologies like multiplex PCR.
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Affiliation(s)
| | - Tristan T. Timbrook
- bioMerieux, 69280 Marcy L’etoile, France (A.M.P.)
- Department of Pharmacotherapy, College of Pharmacy, University of Utah, Salt Lake City, UT 84112, USA
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Jose Lucar, Rebecca Yee. Diagnostic Stewardship for Multiplex Respiratory Testing: What We Know and What Needs to Be Done. Clin Lab Med 2024; 44:45-61. [PMID: 38280797 DOI: 10.1016/j.cll.2023.10.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2024]
Abstract
Syndromic respiratory panels are now widely available in clinical microbiology laboratories and health care institutions. These panels can rapidly diagnose infections and detect antimicrobial resistance genes allowing for more rapid therapeutic optimization compared to standard microbiology approaches. However, given reimbursement concerns and limitations of multiplex molecular testing and results interpretation, maximum clinical utility and positive clinical outcomes depend on active diagnostic stewardship. Here, the authors review clinical outcomes of both upper and lower respiratory panels and present diagnostic stewardship strategies for optimal use of respiratory panels.
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Affiliation(s)
- Jose Lucar
- Division of Infectious Diseases, George Washington University School of Medicine and Health Sciences, 2150 Pennsylvania Avenue Northeast, Washington, DC 20037, USA
| | - Rebecca Yee
- Department of Pathology, George Washington University School of Medicine and Health Sciences, 900 23rd Street Northwest, Washington, DC 20037, USA.
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Falsey AR, Branche AR, Croft DP, Formica MA, Peasley MR, Walsh EE. Real-life Assessment of BioFire FilmArray Pneumonia Panel in Adults Hospitalized With Respiratory Illness. J Infect Dis 2024; 229:214-222. [PMID: 37369370 PMCID: PMC10786250 DOI: 10.1093/infdis/jiad221] [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: 04/03/2023] [Revised: 06/09/2023] [Accepted: 06/22/2023] [Indexed: 06/29/2023] Open
Abstract
BACKGROUND Inability to identify the microbial etiology of lower respiratory tract infection leads to unnecessary antibiotic use. We evaluated the utility of the BioFire FilmArray Pneumonia Panel (BioFire PN) to inform microbiologic diagnosis. METHODS Hospitalized adults with respiratory illness were recruited; sputa and clinical/laboratory data were collected. Sputa were cultured for bacteria and tested with BioFire PN. Microbial etiology was adjudicated by 4 physicians. Bacterial polymerase chain reaction (PCR) was compared with culture and clinical adjudication. RESULTS Of 298 sputa tested, BioFire PN detected significantly more pathogens (350 bacteria, 16 atypicals, and 164 viruses) than sputum culture plus any standard-of-care testing (91% vs 60%, P < .0001). When compared with culture, the sensitivity of BioFire PN for individual bacteria was 46% to 100%; specificity, 61% to 100%; and negative predictive value, 92% to 100%. Cases were adjudicated as viral (n = 58) and bacterial (n = 100). PCR detected bacteria in 55% of viral cases and 95% of bacterial (P < .0001). High serum procalcitonin and bacterial adjudication were more often associated with sputa with 106 or 107 copies detected. CONCLUSIONS Multiplex PCR testing of sputa for bacteria is useful to rule out bacterial infection with added value to detect viruses and atypical bacteria.
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Affiliation(s)
| | | | - Daniel P Croft
- Department of Pulmonary and Critical Medicine, University of Rochester
| | - Maria A Formica
- Infectious Disease Unit, Rochester General Hospital, Rochester, New York, USA
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Pope CE, Whitlock KB, Hodor P, Limbrick DD, McDonald PJ, Hauptman J, Hoffman LR, Simon TD. A Refined, Controlled 16S rRNA Gene Sequencing Approach Reveals Limited Detection of Cerebrospinal Fluid Microbiota in Children with Bacterial Meningitis. Microbiol Spectr 2023; 11:e0036123. [PMID: 37140368 PMCID: PMC10269467 DOI: 10.1128/spectrum.00361-23] [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: 01/25/2023] [Accepted: 04/12/2023] [Indexed: 05/05/2023] Open
Abstract
Advances in both laboratory and computational components of high-throughput 16S amplicon sequencing (16S HTS) have markedly increased its sensitivity and specificity. Additionally, these refinements have better delineated the limits of sensitivity, and contributions of contamination to these limits, for 16S HTS that are particularly relevant for samples with low bacterial loads, such as human cerebrospinal fluid (CSF). The objectives of this work were to (i) optimize the performance of 16S HTS in CSF samples with low bacterial loads by defining and addressing potential sources of error, and (ii) perform refined 16S HTS on CSF samples from children diagnosed with bacterial meningitis and compare results with those from microbiological cultures. Several bench and computational approaches were taken to address potential sources of error for low bacterial load samples. We compared DNA yields and sequencing results after applying three different DNA extraction approaches to an artificially constructed mock-bacterial community. We also compared two postsequencing computational contaminant removal strategies, decontam R and full contaminant sequence removal. All three extraction techniques followed by decontam R yielded similar results for the mock community. We then applied these methods to 22 CSF samples from children diagnosed with meningitis, which has low bacterial loads relative to other clinical infection samples. The refined 16S HTS pipelines identified the cultured bacterial genus as the dominant organism for only 3 of these samples. We found that all three DNA extraction techniques followed by decontam R generated similar DNA yields for mock communities at the low bacterial loads representative of CSF samples. However, the limits of detection imposed by reagent contaminants and methodologic bias precluded the accurate detection of bacteria in CSF from children with culture-confirmed meningitis using these approaches, despite rigorous controls and sophisticated computational approaches. Although we did not find current DNA-based diagnostics to be useful for pediatric meningitis samples, the utility of these methods for CSF shunt infection remains undefined. Future advances in sample processing methods to minimize or eliminate contamination will be required to improve the sensitivity and specificity of these methods for pediatric meningitis. IMPORTANCE Advances in both laboratory and computational components of high-throughput 16S amplicon sequencing (16S HTS) have markedly increased its sensitivity and specificity. These refinements have better delineated the limits of sensitivity, and contributions of contamination to these limits, for 16S HTS that are particularly relevant for samples with low bacterial loads such as human cerebrospinal fluid (CSF). The objectives of this work were to (i) optimize the performance of 16S HTS in CSF samples by defining and addressing potential sources of error, and (ii) perform refined 16S HTS on CSF samples from children diagnosed with bacterial meningitis and compare results with those from microbiological cultures. We found that the limits of detection imposed by reagent contaminants and methodologic bias precluded the accurate detection of bacteria in CSF from children with culture-confirmed meningitis using these approaches, despite rigorous controls and sophisticated computational approaches.
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Affiliation(s)
- Christopher E. Pope
- Department of Pediatrics, University of Washington, Seattle, Washington, USA
| | | | - Paul Hodor
- Seattle Children's Research Institute, Seattle, Washington, USA
| | - David D. Limbrick
- Department of Neurosurgery, Washington University in St. Louis, St. Louis, Missouri, USA
- St. Louis Children’s Hospital, St. Louis, Missouri, USA
| | - Patrick J. McDonald
- Division of Neurosurgery, University of British Columbia, Vancouver, British Columbia, Canada
- British Columbia Children’s Hospital, Vancouver, British Columbia, Canada
| | - Jason Hauptman
- Seattle Children's Research Institute, Seattle, Washington, USA
- Department of Neurosurgery, University of Washington, Seattle, Washington, USA
- Seattle Children's Hospital, Seattle, Washington, USA
| | - Lucas R. Hoffman
- Department of Pediatrics, University of Washington, Seattle, Washington, USA
- Seattle Children's Research Institute, Seattle, Washington, USA
- Seattle Children's Hospital, Seattle, Washington, USA
| | - Tamara D. Simon
- Department of Pediatrics, University of Southern California, Los Angeles, California, USA
- The Saban Research Institute, Los Angeles, California, USA
- Children’s Hospital Los Angeles, Los Angeles, California, USA
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Yen TY, Chen JF, Lu CY, Wu ET, Wang CC, Lu FL, Huang LM, Chang LY. Application of nested multiplex polymerase chain reaction respiratory and pneumonia panels in children with severe community-acquired pneumonia. J Med Virol 2023; 95:e28334. [PMID: 36418155 PMCID: PMC10108056 DOI: 10.1002/jmv.28334] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2022] [Revised: 09/22/2022] [Accepted: 11/22/2022] [Indexed: 11/25/2022]
Abstract
Community-acquired pneumonia (CAP) is a serious clinical concern. A lack of accurate diagnosis could hinder pathogen-directed therapeutic strategies. To solve this problem, we evaluated clinical application of nested multiplex polymerase chain reaction (PCR) in children with severe CAP. We prospectively enrolled 60 children with severe CAP requiring intensive care between December 2019 and November 2021 at a tertiary medical center. Nested multiplex PCR respiratory panel (RP) and pneumonia panel (PP) were performed on upper and lower respiratory tract specimens. We integrated standard-of-care tests and quantitative PCR for validation. The combination of RP, PP, and standard-of-care tests could detect at least one pathogen in 98% of cases and the mixed viral-bacterial detection rate was 65%. The positive percent agreement (PPA), and negative percent agreement (NPA) for RP were 94% and 99%; the PPA and NPA for PP were 89% and 98%. The distribution of pathogens was similar in the upper and lower respiratory tracts, and the DNA or RNA copies of pathogens in the lower respiratory tract were equal to or higher than those in the upper respiratory tract. PP detected bacterial pathogens in 40 (67%) cases, and clinicians tended to increase bacterial diagnosis and escalate antimicrobial therapy for them. RP and PP had satisfactory performance to help pediatricians make pathogenic diagnoses and establish therapy earlier. The pathogens in the upper respiratory tract had predictive diagnostic values for lower respiratory tract infections in children with severe CAP.
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Affiliation(s)
- Ting-Yu Yen
- Department of Pediatrics, National Taiwan University Hospital, College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Jian-Fu Chen
- Department of Pediatrics, National Taiwan University Hospital, College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Chun-Yi Lu
- Department of Pediatrics, National Taiwan University Hospital, College of Medicine, National Taiwan University, Taipei, Taiwan
| | - En-Ting Wu
- Department of Pediatrics, National Taiwan University Hospital, College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Ching-Chia Wang
- Department of Pediatrics, National Taiwan University Hospital, College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Frank Leigh Lu
- Department of Pediatrics, National Taiwan University Hospital, College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Li-Min Huang
- Department of Pediatrics, National Taiwan University Hospital, College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Luan-Yin Chang
- Department of Pediatrics, National Taiwan University Hospital, College of Medicine, National Taiwan University, Taipei, Taiwan
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Jitmuang A, Puttinad S, Hemvimol S, Pansasiri S, Horthongkham N. A multiplex pneumonia panel for diagnosis of hospital-acquired and ventilator-associated pneumonia in the era of emerging antimicrobial resistance. Front Cell Infect Microbiol 2022; 12:977320. [PMID: 36310855 PMCID: PMC9597303 DOI: 10.3389/fcimb.2022.977320] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2022] [Accepted: 09/27/2022] [Indexed: 11/24/2022] Open
Abstract
Background Antimicrobial resistance (AMR), including multidrug (MDR) and extensively drug-resistant (XDR) bacteria, is an essential consideration in the prevention and management of hospital-acquired pneumonia (HAP) and ventilator-associated pneumonia (VAP). In the AMR era, the clinical utility of the BioFire FilmArray Pneumonia Panel Plus (BFPP) to diagnose HAP/VAP has not been thoroughly evaluated. Methods We enrolled adult hospitalized patients with HAP or VAP at Siriraj Hospital and Saraburi Hospital from July 2019–October 2021. Respiratory samples were collected for standard microbiological assays, antimicrobial susceptibility testing (AST), and the BFPP analysis. Results Of 40 subjects, 21 were men. The median duration of HAP/VAP diagnoses was 10.5 (5, 21.5) days, and 36 endotracheal aspirate and 4 sputum samples were collected. Standard cultures isolated 54 organisms—A. baumannii (37.0%), P. aeruginosa (29.6%), and S. maltophilia (16.7%). 68.6% of Gram Negatives showed an MDR or XDR profile. BFPP detected 77 bacterial targets—A. baumannii 32.5%, P. aeruginosa 26.3%, and K. pneumoniae 17.5%. Of 28 detected AMR gene targets, CTX-M (42.5%), OXA-48-like (25%), and NDM (14.3%) were the most common. Compared with standard testing, the BFPP had an overall sensitivity of 98% (88-100%), specificity of 81% (74-87%), positive predictive value of 60% (47-71%), negative predictive value of 99% (96-100%), and kappa (κ) coefficient of 0.64 (0.53-0.75). The concordance between phenotypic AST and detected AMR genes in Enterobacterales was 0.57. There was no concordance among A. baumannii, P. aeruginosa, and S. aureus Conclusions The BFPP has excellent diagnostic sensitivity to detect HAP/VAP etiology. The absence of S. maltophilia and discordance of AMR gene results limit the test performance.
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Affiliation(s)
- Anupop Jitmuang
- Department of Medicine, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
- *Correspondence: Anupop Jitmuang,
| | - Soravit Puttinad
- Department of Medicine, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | | | - Siri Pansasiri
- Saraburi Hospital Research Center, Saraburi Hospital, Saraburi, Thailand
| | - Navin Horthongkham
- Department of Microbiology, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
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What’s new in antibiotic stewardship for pneumonia in ICU? Anaesth Crit Care Pain Med 2022; 41:101135. [DOI: 10.1016/j.accpm.2022.101135] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Accepted: 05/19/2022] [Indexed: 11/23/2022]
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Empiric Treatment in HAP/VAP: “Don’t You Want to Take a Leap of Faith?”. Antibiotics (Basel) 2022; 11:antibiotics11030359. [PMID: 35326822 PMCID: PMC8944836 DOI: 10.3390/antibiotics11030359] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Revised: 03/04/2022] [Accepted: 03/06/2022] [Indexed: 12/26/2022] Open
Abstract
Ventilator-associated pneumonia is a frequent cause of ICU-acquired infections. These infections are associated with high morbidity and mortality. The increase in antibiotic resistance, particularly among Gram-negative bacilli, makes the choice of empiric antibiotic therapy complex for physicians. Multidrug-resistant organisms (MDROs) related infections are associated with a high risk of initial therapeutic inadequacy. It is, therefore, necessary to quickly identify the bacterial species involved and their susceptibility to antibiotics. New diagnostic tools have recently been commercialized to assist in the management of these infections. Moreover, the recent enrichment of the therapeutic arsenal effective on Gram-negative bacilli raises the question of their place in the therapeutic management of these infections. Most national and international guidelines recommend limiting their use to microbiologically documented infections. However, many clinical situations and, in particular, the knowledge of digestive or respiratory carriage by MDROs should lead to the discussion of the use of these new molecules, especially the new combinations with beta-lactamase inhibitors in empirical therapy. In this review, we present the current epidemiological data, particularly in terms of MDRO, as well as the clinical and microbiological elements that may be taken into account in the discussion of empirical antibiotic therapy for patients managed for ventilator-associated pneumonia.
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Fireizen Y, Babbitt CJ, Adams S, Morphew T, Ferro ET, Randhawa I. The Impact of Pneumonia PCR Panel Testing in the PICU: A Quality Improvement Study. J Pediatr Intensive Care 2022. [DOI: 10.1055/s-0042-1743178] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022] Open
Abstract
AbstractInappropriate antibiotic usage can contribute to the promotion of resistant bacteria. In an effort to reduce antibiotic length of therapy (LOT), we initiated a performance improvement project utilizing pneumonia polymerase chain reaction (PCR) testing in ventilated pediatric intensive care unit (PICU) patients suspected of tracheitis or pneumonia. This is a single-center cohort intervention study that compared pre- and postimplementation patients. The intervention was the use of a pneumonia PCR panel on all PICU patients undergoing an evaluation for acute tracheitis or pneumonia during the postimplementation period. The inclusion criteria were either acute or acute on chronic respiratory failure. After an 8-month period, the charts were reviewed from both cohorts and baseline data, and outcome data were compared by statistical analysis. A total of 41 preimplementation and 30 postimplementation patients were compared, and no baseline differences were found except postimplementation patients being slightly older (133 vs. 56 months, p-value = 0.040). Analysis of the primary outcome measures found that the time to identification of organism (5 vs. 67 hours) and LOT (5 vs. 9 days, p < 0.001) were shorter in postimplementation patients compared with preimplementation patients. Antibiotics were changed based on the results of the pneumonia PCR on 18 of 30 patients (60%). There was no difference in ventilator-free days, PICU length of stay, or mortality. In conclusion, pneumonia PCR panel testing leads to more rapid results and is associated with reduced antibiotic LOT.
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Affiliation(s)
- Yaron Fireizen
- Department of Pediatric Pulmonology, Miller Children's and Women's Hospital of Long Beach, University of California, Irvine School of Medicine, Irvine, California, United States
| | - Christopher J. Babbitt
- Department of Pediatric Critical Care, Miller Children's and Women's Hospital of Long Beach, Long Beach, California, United States
| | - Susan Adams
- Department of Pediatric Pharmacy, Miller Children's and Women's Hospital of Long Beach, Long Beach, California, United States
| | - Tricia Morphew
- Morphew Consulting LLC, Bothell, Washington, United States
- MemorialCare Health System, Fountain Valley, California, United States
| | - Emanuel T. Ferro
- Department of Pathology, Long Beach Memorial Medical Center, Long Beach, California, United States
| | - Inderpal Randhawa
- Department of Pediatric Pulmonology, Miller Children's and Women's Hospital of Long Beach, University of California, Irvine School of Medicine, Irvine, California, United States
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