The use of broad-range bacterial PCR in the diagnosis of infectious diseases: a prospective cohort study

Tkadlec, Jan; Peckova, Monika; Šrámková, Lucie; Rohn, Vilém; Jahoda, D; Raszka, D.; Berousek, Jan; Mošna, František; Vymazal, Tomáš; Kvapil, Milan; Dřevı́nek, Pavel

doi:10.1016/j.cmi.2018.10.001

Cited by 30 publications

(21 citation statements)

References 28 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…To improve BSI management, several innovative diagnostic techniques have been developed to optimize direct pathogen detection from whole blood samples (Peker et al, 2018; Poole et al, 2018). Some of them were introduced with limited success (Tkadlec et al, 2020) or with inconclusive validation study results (Tkadlec et al, 2019; Warhurst et al, 2015). In this study, we report real‐world experience with the T2Bacteria Panel (T2Biosystems, USA) which utilizes T2 magnetic resonance (T2MR) to detect six bacterial BSI pathogens ( Enterococcus faecium , Staphylococcus aureus , Klebsiella pneumoniae , Acinetobacter baumannii , Pseudomonas aeruginosa , and Escherichia coli , referred to as ESKAPEc pathogens) directly from whole blood (De Angelis et al, 2018).…”

Section: Introductionmentioning

confidence: 99%

Direct detection of ESKAPEc pathogens from whole blood using the T2Bacteria Panel allows early antimicrobial stewardship intervention in patients with sepsis

et al. 2021

View full text Add to dashboard Cite

In the microbiological diagnosis of bloodstream infections (BSI), blood culture (BC) is considered the gold standard test despite its limitations such as low sensitivity and slow turnaround time. A new FDA‐cleared and CE‐marked platform utilizing magnetic resonance to detect amplified DNA of the six most common and/or problematic BSI pathogens (Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, and Escherichia coli; referred to as ESKAPEc) is available and may shorten the time to diagnosis and potentially improve antimicrobial utilization. Whole blood samples from hospitalized patients with clinical signs of sepsis were analyzed using the T2Bacteria Panel (T2Biosystems) and compared to simultaneously collected BC. Discrepant results were evaluated based on clinical infection criteria, combining supporting culture results and the opinion of treating physicians. A total of 55 samples from 53 patients were evaluated. The sensitivity and specificity of the T2Bacteria panel was 94% (16 out of 17 detections of T2Bacteria‐targeted organisms) and 100%, respectively, with 36.4% (8 of 22) causes of BSI detected only by this method. The T2Bacteria Panel detected pathogens on average 55 hours faster than standard BC. In our study, 9 of 15 patients with positive T2Bacteria Panel results received early‐targeted antibiotic therapy and/or modification of antimicrobial treatment based on T2Bacteria Panel findings. Given the high reliability, faster time to detection, and easy workflow, the technique qualifies as a point‐of‐care testing approach.

show abstract

Section: Introductionmentioning

confidence: 99%

Direct detection of ESKAPEc pathogens from whole blood using the T2Bacteria Panel allows early antimicrobial stewardship intervention in patients with sepsis

et al. 2021

View full text Add to dashboard Cite

show abstract

“…The low level of positive 16S PCR results from CSF was particularly notable, and we question the use of this test in this sample type. Tkadlec et al report consistent data; of the 66 CSF samples tested only 6 additional positive results (9.1%) were returned by 16S PCR where culture was negative 9 . A www.nature.com/scientificreports www.nature.com/scientificreports/ meta-analysis conducted by Srinivasan et al evaluated culture-negative CSF data from 15 studies and found 30% of cases yielded a positive result by 16S PCR, but a wide range between studies (3-100%) possibly reflecting the variation in inclusion criteria 11 .…”

Section: Discussionmentioning

confidence: 68%

Clinical utility and cost-effectiveness of bacterial 16S rRNA and targeted PCR based diagnostic testing in a UK microbiology laboratory network

Aggarwal

Kanitkar

Narouz

et al. 2020

Sci Rep

View full text Add to dashboard Cite

16S ribosomal-ribonucleic acid polymerase chain reaction (PCR) and targeted PCR aid microbiological diagnosis in culture-negative clinical samples. Despite routine clinical use, there remains a paucity of data on their effectiveness across a variety of clinical sample types, and cost-effectiveness. In this 4 year multicentre retrospective observational study, all clinical samples referred for 16S PCR and/or targeted PCR from a laboratory network serving seven London hospitals were identified. Laboratory, clinical, prescribing, and economic variables were analysed. 78/607 samples were 16S PCR positive; pus samples were most frequently positive (29/84; p < 0.0001), and CSF least (8/149; p = 0.003). 210/607 samples had targeted PCR (361 targets requested across 23 organisms) with 43/361 positive; respiratory samples (13/37; p = 0.01) had the highest detection rate. Molecular diagnostics provided a supportive microbiological diagnosis for 21 patients and a new diagnosis for 58. 14/91 patients with prescribing information available and a positive PCR result had antimicrobial de-escalation. For culture-negative samples, mean cost-per-positive 16S PCR result was £568.37 and £292.84 for targeted PCR, equating to £4041.76 and £1506.03 respectively for one prescription change. 16S PCR is more expensive than targeted PCR, with both assisting in microbiological diagnosis but uncommonly enabling antimicrobial change. Rigorous referral pathways for molecular tests may result in significant fiscal savings. Molecular diagnostics have significantly enhanced laboratory ability to detect and identify bacteria in clinical samples 1,2 Whilst bacterial culture is considered the gold standard for microbiological diagnosis, there may be a 24-48 hour delay in providing a result for typical organisms and longer for slow-growing organisms such as Mycobacteria spp 3. Furthermore, false negative culture results may arise from fastidious organisms, non-viable bacteria, or prior use of antimicrobials, potentially affecting patient management. Two methods of Polymerase Chain Reaction (PCR) are recommended as supplementary tests by the United Kingdom Standards of Microbiology Investigations (SMI); targeted PCR and 16S ribosomal ribonucleic acid (rRNA) PCR 4. 16S PCR is a pan-bacterial molecular diagnostic test 5,6 , whilst targeted PCR looks for a finite range of organism targets where specific pathogenic organisms are suspected 7. Identification of causative organisms through targeted PCR or 16S PCR may influence clinical management decisions, serving to support or provide a microbiological diagnosis or impacting antimicrobial prescribing decision-making 8,9. The utility of 16S PCR in identifying causative organisms from specific sterile site samples has been demonstrated in multiple isolated clinical syndromes 10-15. The wider utility of 16S PCR has been evaluated by Rampini et al. 16 , who demonstrated a sensitivity and specificity of 42.9% and 100% for culture-negative bacterial infections respectively. This study did not evaluate the functi...

show abstract

“…These include (i) the fact that they cannot be used to measure antimicrobial susceptibility, (ii) the introduction of bias through the use of general primers for 16 s rRNA sequencing that do not bind equally to all bacteria and (iii) the difficulty in identification beyond the genus due to high similarity among closely related species. Several studies have compared the use of culturing and amplicon sequencing for diagnostics, generally reporting a higher sensitivity for sequencing compared to culturing, especially in the investigation of chronic infections [62][63][64]. If sequencing is to replace culturing as a clinical diagnostic method, it must be standardized, automated and cost-efficient.…”

Section: Examination Methodsmentioning

confidence: 99%

Sampling challenges in diagnosis of chronic bacterial infections

Jakobsen

Bay

et al. 2021

Journal of Medical Microbiology

View full text Add to dashboard Cite

In recent decades there has been an increase in knowledge of the distribution, species diversity and growth patterns of bacteria in human chronic infections. This has challenged standard diagnostic methods, which have undergone a development to both increase the accuracy of testing as well as to decrease the occurrence of contamination. In particular, the introduction of new technologies based on molecular techniques into the clinical diagnostic process has increased detection and identification of infectious pathogens. Sampling is the first step in the diagnostic process, making it crucial for obtaining a successful outcome. However, sampling methods have not developed at the same speed as molecular identification. The heterogeneous distribution and potentially small number of pathogenic bacterial cells in chronic infected tissue makes sampling a complicated task, and samples must be collected judiciously and handled with care. Clinical sampling is a step in the diagnostic process that may benefit from innovative methods based on current knowledge of bacteria present in chronic infections. In the present review, we describe and discuss different aspects that complicate sampling of chronic infections. The purpose is to survey representative scientific work investigating the presence and distribution of bacteria in chronic infections in relation to various clinical sampling methods.

show abstract

The use of broad-range bacterial PCR in the diagnosis of infectious diseases: a prospective cohort study

Cited by 30 publications

References 28 publications

Direct detection of ESKAPEc pathogens from whole blood using the T2Bacteria Panel allows early antimicrobial stewardship intervention in patients with sepsis

Direct detection of ESKAPEc pathogens from whole blood using the T2Bacteria Panel allows early antimicrobial stewardship intervention in patients with sepsis

Clinical utility and cost-effectiveness of bacterial 16S rRNA and targeted PCR based diagnostic testing in a UK microbiology laboratory network

Sampling challenges in diagnosis of chronic bacterial infections

Contact Info

Product

Resources

About