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

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Standard

Predicting β-lactam susceptibility from the genome of Streptococcus pneumoniae and other mitis group streptococci. / Eriksen, Helle Brander; Fuursted, Kurt; Jensen, Anders; Jensen, Christian Salgård; Nielsen, Xiaohui; Christensen, Jens Jørgen; Shewmaker, Patricia; Rebelo, Ana Rita; Aarestrup, Frank Møller; Schønning, Kristian; Slotved, Hans Christian; the One Day in Denmark (ODiD) Consortium.

I: Frontiers in Microbiology, Bind 14, 1120023, 2023.

Publikation: Bidrag til tidsskrift › Tidsskriftartikel › Forskning › fagfællebedømt

Harvard

Eriksen, HB, Fuursted, K, Jensen, A, Jensen, CS, Nielsen, X, Christensen, JJ, Shewmaker, P, Rebelo, AR, Aarestrup, FM, Schønning, K, Slotved, HC & the One Day in Denmark (ODiD) Consortium 2023, 'Predicting β-lactam susceptibility from the genome of Streptococcus pneumoniae and other mitis group streptococci', Frontiers in Microbiology, bind 14, 1120023. https://doi.org/10.3389/fmicb.2023.1120023

APA

Eriksen, H. B., Fuursted, K., Jensen, A., Jensen, C. S., Nielsen, X., Christensen, J. J., Shewmaker, P., Rebelo, A. R., Aarestrup, F. M., Schønning, K., Slotved, H. C., & the One Day in Denmark (ODiD) Consortium (2023). Predicting β-lactam susceptibility from the genome of Streptococcus pneumoniae and other mitis group streptococci. Frontiers in Microbiology, 14, [1120023]. https://doi.org/10.3389/fmicb.2023.1120023

Vancouver

Eriksen HB, Fuursted K, Jensen A, Jensen CS, Nielsen X, Christensen JJ o.a. Predicting β-lactam susceptibility from the genome of Streptococcus pneumoniae and other mitis group streptococci. Frontiers in Microbiology. 2023;14. 1120023. https://doi.org/10.3389/fmicb.2023.1120023

Author

Eriksen, Helle Brander ; Fuursted, Kurt ; Jensen, Anders ; Jensen, Christian Salgård ; Nielsen, Xiaohui ; Christensen, Jens Jørgen ; Shewmaker, Patricia ; Rebelo, Ana Rita ; Aarestrup, Frank Møller ; Schønning, Kristian ; Slotved, Hans Christian ; the One Day in Denmark (ODiD) Consortium. / Predicting β-lactam susceptibility from the genome of Streptococcus pneumoniae and other mitis group streptococci. I: Frontiers in Microbiology. 2023 ; Bind 14.

Bibtex

@article{467157025f88470988cc39ed7a998855,

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

abstract = "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.",

keywords = "genotypic susceptibility, penicillin, penicillin-binding proteins, pneumococcus, Streptococcus",

author = "Eriksen, {Helle Brander} and Kurt Fuursted and Anders Jensen and Jensen, {Christian Salg{\aa}rd} and Xiaohui Nielsen and Christensen, {Jens J{\o}rgen} and Patricia Shewmaker and Rebelo, {Ana Rita} and Aarestrup, {Frank M{\o}ller} and Kristian Sch{\o}nning and Slotved, {Hans Christian} and {the One Day in Denmark (ODiD) Consortium}",

note = "Publisher Copyright: Copyright {\textcopyright} 2023 Eriksen, Fuursted, Jensen, Jensen, Nielsen, Christensen, Shewmaker, Rebelo, Aarestrup, Sch{\o}nning, Slotved and the One Day in Denmark (ODiD) Consortium.",

year = "2023",

doi = "10.3389/fmicb.2023.1120023",

language = "English",

volume = "14",

journal = "Frontiers in Microbiology",

issn = "1664-302X",

publisher = "Frontiers Media S.A.",

}

RIS

TY - JOUR

T1 - Predicting β-lactam susceptibility from the genome of Streptococcus pneumoniae and other mitis group streptococci

AU - Eriksen, Helle Brander

AU - Fuursted, Kurt

AU - Jensen, Anders

AU - Jensen, Christian Salgård

AU - Nielsen, Xiaohui

AU - Christensen, Jens Jørgen

AU - Shewmaker, Patricia

AU - Rebelo, Ana Rita

AU - Aarestrup, Frank Møller

AU - Schønning, Kristian

AU - Slotved, Hans Christian

AU - the One Day in Denmark (ODiD) Consortium

PY - 2023

Y1 - 2023

N2 - 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.

AB - 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.

KW - genotypic susceptibility

KW - penicillin

KW - penicillin-binding proteins

KW - pneumococcus

KW - Streptococcus

UR - http://www.scopus.com/inward/record.url?scp=85150505229&partnerID=8YFLogxK

U2 - 10.3389/fmicb.2023.1120023

DO - 10.3389/fmicb.2023.1120023

M3 - Journal article

C2 - 36937294

AN - SCOPUS:85150505229

VL - 14

JO - Frontiers in Microbiology

JF - Frontiers in Microbiology

SN - 1664-302X

M1 - 1120023

ER -

ID: 364546980