Predicting β-lactam susceptibility from the genome of Streptococcus pneumoniae and other mitis group streptococci

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  • Helle Brander Eriksen
  • Kurt Fuursted
  • Anders Jensen
  • Christian Salgård Jensen
  • Xiaohui Nielsen
  • Jens Jørgen Christensen
  • Patricia Shewmaker
  • Ana Rita Rebelo
  • Frank Møller Aarestrup
  • Schønning, Kristian
  • Hans Christian Slotved
  • the One Day in Denmark (ODiD) Consortium

Introduction: For Streptococcus pneumoniae, β-lactam susceptibility can be predicted from the amino acid sequence of the penicillin-binding proteins PBP1a, PBP2b, and PBP2x. The combination of PBP-subtypes provides a PBP-profile, which correlates to a phenotypic minimal inhibitory concentration (MIC). The non-S. pneumoniae Mitis-group streptococci (MGS) have similar PBPs and exchange pbp-alleles with S. pneumoniae. We studied whether a simple BLAST analysis could be used to predict phenotypic susceptibility in Danish S. pneumoniae isolates and in internationally collected MGS. Method: Isolates with available WGS and phenotypic susceptibility data were included. For each isolate, the best matching PBP-profile was identified by BLAST analysis. The corresponding MICs for penicillin and ceftriaxone was retrieved. Category agreement (CA), minor-, major-, and very major discrepancy was calculated. Genotypic-phenotypic accuracy was examined with Deming regression. Results: Among 88 S. pneumoniae isolates, 55 isolates had a recognized PBP-profile, and CA was 100% for penicillin and 98.2% for ceftriaxone. In 33 S. pneumoniae isolates with a new PBP-profile, CA was 90.9% (penicillin) and 93.8% (ceftriaxone) using the nearest recognized PBP-profile. Applying the S. pneumoniae database to non-S. pneumoniae MGS revealed that none had a recognized PBP-profile. For Streptococcus pseudopneumoniae, CA was 100% for penicillin and ceftriaxone in 19 susceptible isolates. In 33 Streptococcus mitis isolates, CA was 75.8% (penicillin) and 86.2% (ceftriaxone) and in 25 Streptococcus oralis isolates CA was 8% (penicillin) and 100% (ceftriaxone). Conclusion: Using a simple BLAST analysis, genotypic susceptibility prediction was accurate in Danish S. pneumoniae isolates, particularly in isolates with recognized PBP-profiles. Susceptibility was poorly predicted in other MGS using the current database.

OriginalsprogEngelsk
Artikelnummer1120023
TidsskriftFrontiers in Microbiology
Vol/bind14
Antal sider15
ISSN1664-302X
DOI
StatusUdgivet - 2023

Bibliografisk note

Funding Information:
Members of the One Day in Denmark (ODiD) Consortium are as follows: Valeria Bortolaia; Pimlapas Leekitcharoenphon, Technical University of Denmark, National Food Institute, Kongens Lyngby, Denmark; Dennis Schrøder Hansen; Herlev Hospital, Department of Clinical Microbiology, Herlev, Denmark; Hans Linde Nielsen; Aalborg University Hospital, Department of Clinical Microbiology, Aalborg, Denmark; Svend Ellermann-Eriksen and Niels Nørskov-Lauritsen; Aarhus University Hospital, Department of Clinical Microbiology, Aarhus, Denmark; Michael Kemp; Odense University Hospital, Department of Clinical Microbiology, Odense, Denmark; Bent Løwe Røder; Slagelse Hospital, Department of Clinical Microbiology, Slagelse, Denmark; Niels Frimodt-Møller; Rigshospitalet, Department of Clinical Microbiology, København, Denmark; Turid Snekloth Søndergaard; Hospital of Southern Jutland, Department of Clinical Microbiology, Sønderborg, Denmark; John Eugenio Coia; Sydvestjysk Hospital, Department of Clinical Microbiology, Esbjerg, Denmark; Claus Østergaard; Vejle Hospital, Department of Clinical Microbiology, Vejle, Denmark; Henrik Westh; Hvidovre Hospital, Department of Clinical Microbiology, Hvidovre, Denmark, and Department of Clinical Medicine, University of Copenhagen, Copenhagen, Denmark. Kirsten Burmeister and Karina Kaae are acknowledged for their skilled laboratory work and guidance in this study. We acknowledge the Danish Departments of Clinical Microbiology for submitting invasive pneumococcal isolates for national surveillance throughout the study period.

Funding Information:
H-CS is involved with projects supported by Pfizer.

Publisher Copyright:
Copyright © 2023 Eriksen, Fuursted, Jensen, Jensen, Nielsen, Christensen, Shewmaker, Rebelo, Aarestrup, Schønning, Slotved and the One Day in Denmark (ODiD) Consortium.

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