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

Autor:	Eriksen HB; Department of Clinical Microbiology, Herlev and Gentofte Hospital, Herlev, Denmark., Fuursted K; Department of Bacteria, Parasites, and Fungi, Statens Serum Institut, Copenhagen, Denmark., Jensen A; Department of Clinical Microbiology, Sygehus Lillebælt, Vejle, Denmark., Jensen CS; Department of Clinical Microbiology, Rigshospitalet, Copenhagen, Denmark., Nielsen X; The Regional Department of Clinical Microbiology, Slagelse, Denmark.; Department of Clinical Medicine, University of Copenhagen, Copenhagen, Denmark., Christensen JJ; The Regional Department of Clinical Microbiology, Slagelse, Denmark.; Department of Clinical Medicine, University of Copenhagen, Copenhagen, Denmark., Shewmaker P; Centers for Disease Control and Prevention, Atlanta, GA, United States., Rebelo AR; Research Group for Genomic Epidemiology, National Food Institute, Technical University of Denmark, Kongens Lyngby, Denmark., Aarestrup FM; Research Group for Genomic Epidemiology, National Food Institute, Technical University of Denmark, Kongens Lyngby, Denmark., Schønning K; Department of Clinical Microbiology, Rigshospitalet, Copenhagen, Denmark., Slotved HC; Department of Bacteria, Parasites, and Fungi, Statens Serum Institut, Copenhagen, Denmark.
Jazyk:	angličtina
Zdroj:	Frontiers in microbiology [Front Microbiol] 2023 Mar 02; Vol. 14, pp. 1120023. Date of Electronic Publication: 2023 Mar 02 (Print Publication: 2023).
DOI:	10.3389/fmicb.2023.1120023
Abstrakt:	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. Competing Interests: H-CS is involved with projects supported by Pfizer. The remaining authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest. (Copyright © 2023 Eriksen, Fuursted, Jensen, Jensen, Nielsen, Christensen, Shewmaker, Rebelo, Aarestrup, Schønning, Slotved and the One Day in Denmark (ODiD) Consortium.)
Databáze:	MEDLINE
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