Utility of the biofire filmarray pneumonia panel plus assay for syndromic testing of lower-respiratory tract infections in a low-middle-income setting

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dc.contributor.advisorMoodley, Clinton
dc.contributor.authorVan Der Westhuyzen, Mene
dc.date.accessioned2025-10-02T12:04:05Z
dc.date.available2025-10-02T12:04:05Z
dc.date.issued2025
dc.date.updated2025-10-02T11:06:13Z
dc.description.abstractBackground: Determining lower respiratory tract infection (LRTI) aetiology is complex. Culture-based methods are laborious with poor sensitivity. Molecular assays improve detection of potential pathogens, but incorrect interpretation of results may lead to inappropriate antimicrobial therapy. Methods: The utility of the BioFire® FilmArray® Pneumonia Panel plus (FA-PP) to detect LRTI pathogens, and the potential antimicrobial stewardship impacts in a low resource setting, was assessed. Routine LRT samples were included from adult patients with clinically suspected LRTI or with a concomitant blood culture at Groote Schuur Hospital and referring facilities. Culture and FA-PP results were compared, and pharmacy data analysed to determine appropriateness of antibiotic therapy. Results: There was an 80% correlation between cultured LRTI pathogens and the FA-PP bin ≥107 results. Compared to culture the FA-PP detected substantially more pathogens (86,6% versus 17,9%) and produced a combined 100% positive percent agreement, and 88% negative percent agreement. The FA-PP detected bacterial-viral coinfections in 27% of samples. Correlation of FA-PP results with pharmacy data (n=69) indicated a potential antibiotic change in 75% of cases, but this is difficult to accurately characterise without a ‘gold-standard' for treatment or complete clinical data. Conclusion: The FA-PP increased the number of positive samples with typical bacteria, but the semi-quantitative reporting algorithm does not describe the correlation between the different bin values and colonization versus infection. This complicates result interpretation and may lead to inappropriate antimicrobial treatment. This study highlights the potential positive impact of rapid molecular assays for routine care in lower income settings, but also underscores the interpretive challenges associated with these tests.
dc.identifier.apacitationVan Der Westhuyzen, M. (2025). <i>Utility of the biofire filmarray pneumonia panel plus assay for syndromic testing of lower-respiratory tract infections in a low-middle-income setting</i>. (). University of Cape Town ,Faculty of Health Sciences ,Department of Pathology. Retrieved from http://hdl.handle.net/11427/41980en_ZA
dc.identifier.chicagocitationVan Der Westhuyzen, Mene. <i>"Utility of the biofire filmarray pneumonia panel plus assay for syndromic testing of lower-respiratory tract infections in a low-middle-income setting."</i> ., University of Cape Town ,Faculty of Health Sciences ,Department of Pathology, 2025. http://hdl.handle.net/11427/41980en_ZA
dc.identifier.citationVan Der Westhuyzen, M. 2025. Utility of the biofire filmarray pneumonia panel plus assay for syndromic testing of lower-respiratory tract infections in a low-middle-income setting. . University of Cape Town ,Faculty of Health Sciences ,Department of Pathology. http://hdl.handle.net/11427/41980en_ZA
dc.identifier.ris TY - Thesis / Dissertation AU - Van Der Westhuyzen, Mene AB - Background: Determining lower respiratory tract infection (LRTI) aetiology is complex. Culture-based methods are laborious with poor sensitivity. Molecular assays improve detection of potential pathogens, but incorrect interpretation of results may lead to inappropriate antimicrobial therapy. Methods: The utility of the BioFire® FilmArray® Pneumonia Panel plus (FA-PP) to detect LRTI pathogens, and the potential antimicrobial stewardship impacts in a low resource setting, was assessed. Routine LRT samples were included from adult patients with clinically suspected LRTI or with a concomitant blood culture at Groote Schuur Hospital and referring facilities. Culture and FA-PP results were compared, and pharmacy data analysed to determine appropriateness of antibiotic therapy. Results: There was an 80% correlation between cultured LRTI pathogens and the FA-PP bin ≥107 results. Compared to culture the FA-PP detected substantially more pathogens (86,6% versus 17,9%) and produced a combined 100% positive percent agreement, and 88% negative percent agreement. The FA-PP detected bacterial-viral coinfections in 27% of samples. Correlation of FA-PP results with pharmacy data (n=69) indicated a potential antibiotic change in 75% of cases, but this is difficult to accurately characterise without a ‘gold-standard' for treatment or complete clinical data. Conclusion: The FA-PP increased the number of positive samples with typical bacteria, but the semi-quantitative reporting algorithm does not describe the correlation between the different bin values and colonization versus infection. This complicates result interpretation and may lead to inappropriate antimicrobial treatment. This study highlights the potential positive impact of rapid molecular assays for routine care in lower income settings, but also underscores the interpretive challenges associated with these tests. DA - 2025 DB - OpenUCT DP - University of Cape Town KW - Syndromic testing LK - https://open.uct.ac.za PB - University of Cape Town PY - 2025 T1 - Utility of the biofire filmarray pneumonia panel plus assay for syndromic testing of lower-respiratory tract infections in a low-middle-income setting TI - Utility of the biofire filmarray pneumonia panel plus assay for syndromic testing of lower-respiratory tract infections in a low-middle-income setting UR - http://hdl.handle.net/11427/41980 ER - en_ZA
dc.identifier.urihttp://hdl.handle.net/11427/41980
dc.identifier.vancouvercitationVan Der Westhuyzen M. Utility of the biofire filmarray pneumonia panel plus assay for syndromic testing of lower-respiratory tract infections in a low-middle-income setting. []. University of Cape Town ,Faculty of Health Sciences ,Department of Pathology, 2025 [cited yyyy month dd]. Available from: http://hdl.handle.net/11427/41980en_ZA
dc.language.isoen
dc.language.rfc3066eng
dc.publisher.departmentDepartment of Pathology
dc.publisher.facultyFaculty of Health Sciences
dc.publisher.institutionUniversity of Cape Town
dc.subjectSyndromic testing
dc.titleUtility of the biofire filmarray pneumonia panel plus assay for syndromic testing of lower-respiratory tract infections in a low-middle-income setting
dc.typeThesis / Dissertation
dc.type.qualificationlevelMasters
dc.type.qualificationlevelMMed
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