Predicting the primary infection source of Escherichia coli bacteremia using virulence-associated genes
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Predicting the primary infection source of Escherichia coli bacteremia using virulence-associated genes. / Ilsby, Christian Schaadt; Hertz, Frederik Boetius; Westh, Henrik; Monk, Jonathan; Worning, Peder; Johansen, Helle Krogh; Hansen, Katrine Hartung; Pinholt, Mette.
In: European Journal of Clinical Microbiology and Infectious Diseases, Vol. 43, No. 4, 2024, p. 641-648.Research output: Contribution to journal › Journal article › Research › peer-review
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TY - JOUR
T1 - Predicting the primary infection source of Escherichia coli bacteremia using virulence-associated genes
AU - Ilsby, Christian Schaadt
AU - Hertz, Frederik Boetius
AU - Westh, Henrik
AU - Monk, Jonathan
AU - Worning, Peder
AU - Johansen, Helle Krogh
AU - Hansen, Katrine Hartung
AU - Pinholt, Mette
N1 - Publisher Copyright: © 2024, The Author(s).
PY - 2024
Y1 - 2024
N2 - Purpose: To investigate the role of E. coli virulence-associated genes (VAGs) in predicting urinary tract infection (UTI) as the source of bacteremia in two distinct hospital populations, one with a large general catchment area and one dominated by referrals. Methods: E. coli bacteremias identified at Department of Clinical Microbiology (DCM), Hvidovre Hospital and DCM, Rigshospitalet in the Capital Region of Denmark from October to December 2018. Using whole genome sequencing (WGS), we identified 358 VAGs from 224 E. coli bacteremia. For predictive analysis, VAGs were paired with clinical source of UTI from local bacteremia databases. Results: VAGs strongly predicting of UTI as primary infection source of bacteremia were primarily found within the pap gene family. papX (PPV 96%, sensitivity 54%) and papGII (PPV 93%, sensitivity 56%) were found highly predictive, but showed low sensitivities. The strength of VAG predictions of UTI as source varied significantly between the two hospital populations. VAGs had weaker predictions in the tertiary referral center (Rigshospitalet), a disparity likely stemming from differences in patient population and department specialization. Conclusion: WGS data was used to predict the primary source of E. coli bacteremia and is an attempt on a new and different type of infection source identification. Genomic data showed potential to be utilized to predict the primary source of infection; however, discrepancy between the best performing profile of VAGs between acute care hospitals and tertiary hospitals makes it difficult to implement in clinical practice.
AB - Purpose: To investigate the role of E. coli virulence-associated genes (VAGs) in predicting urinary tract infection (UTI) as the source of bacteremia in two distinct hospital populations, one with a large general catchment area and one dominated by referrals. Methods: E. coli bacteremias identified at Department of Clinical Microbiology (DCM), Hvidovre Hospital and DCM, Rigshospitalet in the Capital Region of Denmark from October to December 2018. Using whole genome sequencing (WGS), we identified 358 VAGs from 224 E. coli bacteremia. For predictive analysis, VAGs were paired with clinical source of UTI from local bacteremia databases. Results: VAGs strongly predicting of UTI as primary infection source of bacteremia were primarily found within the pap gene family. papX (PPV 96%, sensitivity 54%) and papGII (PPV 93%, sensitivity 56%) were found highly predictive, but showed low sensitivities. The strength of VAG predictions of UTI as source varied significantly between the two hospital populations. VAGs had weaker predictions in the tertiary referral center (Rigshospitalet), a disparity likely stemming from differences in patient population and department specialization. Conclusion: WGS data was used to predict the primary source of E. coli bacteremia and is an attempt on a new and different type of infection source identification. Genomic data showed potential to be utilized to predict the primary source of infection; however, discrepancy between the best performing profile of VAGs between acute care hospitals and tertiary hospitals makes it difficult to implement in clinical practice.
KW - Bacteremia
KW - E. coli
KW - Urosepsis
KW - Virulence-associated genes
KW - WGS
U2 - 10.1007/s10096-024-04754-6
DO - 10.1007/s10096-024-04754-6
M3 - Journal article
C2 - 38273191
AN - SCOPUS:85183042545
VL - 43
SP - 641
EP - 648
JO - European Journal of Clinical Microbiology & Infectious Diseases
JF - European Journal of Clinical Microbiology & Infectious Diseases
SN - 0934-9723
IS - 4
ER -
ID: 381785114