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Development and implementation of a customised rapid syndromic diagnostic test for severe pneumonia

Published version
Peer-reviewed

Type

Article

Change log

Authors

Navapurkar, Vilas 
Bartholdson Scott, Josefin  ORCID logo  https://orcid.org/0000-0003-3380-4446
Maes, Mailis 
Hellyer, Thomas P 
Higginson, Ellen 

Abstract

ns4:pns4:boldBackground:</ns4:bold> The diagnosis of pneumonia has been hampered by a reliance on bacterial cultures which take several days to return a result, and are frequently negative. In critically ill patients this leads to the use of empiric, broad-spectrum antimicrobials and compromises good antimicrobial stewardship. The objective of this study wasns4:bold </ns4:bold>tons4:bold </ns4:bold>establish the performance of a syndromic molecular diagnostic approach, using a custom TaqMan array card (TAC) covering 52 respiratory pathogens, and assess its impact on antimicrobial prescribing.</ns4:p>ns4:p </ns4:p>ns4:p ns4:boldMethods:</ns4:bold> The TAC was validated against a retrospective multi-centre cohort of broncho-alveolar lavage samples. The TAC was assessed prospectively in patients undergoing investigation for suspected pneumonia, with a comparator cohort formed of patients investigated when the TAC laboratory team were unavailable.</ns4:p>ns4:p Co-primary outcomes were sensitivity compared to conventional microbiology and, for the prospective study, time to result. Metagenomic sequencing was performed to validate findings in prospective samples. Antibiotic free days (AFD) were compared between the study cohort and comparator group.</ns4:p>ns4:p ns4:boldResults:</ns4:bold> 128 stored samples were tested, with sensitivity of 97% (95% confidence interval (CI) 88-100%). Prospectively, 95 patients were tested by TAC, with 71 forming the comparator group. TAC returned results 51 hours (interquartile range 41-69 hours) faster than culture and with sensitivity of 92% (95% CI 83-98%) compared to conventional microbiology. 94% of organisms identified by sequencing were detected by TAC. There was a significant difference in the distribution of AFDs with more AFDs in the TAC group (p=0.02). TAC group were more likely to experience antimicrobial de-escalation (odds ratio 2.9 (95%1.5-5.5)).</ns4:p>ns4:p ns4:boldConclusions:</ns4:bold> Implementation of a syndromic molecular diagnostic approach to pneumonia led to faster results, with high sensitivity and impact on antibiotic prescribing.</ns4:p>

Description

Keywords

32 Biomedical and Clinical Sciences, 3202 Clinical Sciences, Clinical Research, Pneumonia, Pneumonia & Influenza, Lung, Infectious Diseases, 4.2 Evaluation of markers and technologies, 4 Detection, screening and diagnosis, Infection

Journal Title

Wellcome Open Research

Conference Name

Journal ISSN

2398-502X
2398-502X

Volume Title

6

Publisher

F1000 Research Ltd
Sponsorship
Wellcome Trust (205214/Z/16/Z)
MRC (MR/V006118/1)
Wellcome Trust (094949/Z/10/Z)
Medical Research Council (MR/N029399/1)