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 -