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Group B streptococci (GBS) strains evading molecular diagnostics showed novel chromosomal deletions encompassing the CAMP-factor (cfb) encoding gene

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Abstract

A highly conserved fragment adjacent to the cfb gene encoding the CAMP factor is the target of PCR-based molecular diagnostic systems for the identification of S. agalactiae (group B streptococci (GBS)). Six PCR-negative, culture-positive GBS strains were whole genome sequenced to assess why they escaped molecular diagnostics. GBS strains did not constitute a clonal cluster and presented variably sized chromosomal deletions (from 7 to 33 kb) which always included the cfb gene, a finding never described before. GBS strains that escape molecular diagnostics are considered rare; however, they can cause false-negative results using molecular diagnostics alone, affecting medical decisions.

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Fig. 1

Data availability

The datasets (raw long reads) generated and analysed during the current study are not publicly available but are available from the corresponding author on reasonable request.

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Acknowledgements

The authors would like to thank Dr. Michele Sonnessa of Bio-Fab Research srl for his help in bioinformatic analyses. We also thank Giovanna Alfarone and Simona Recchia for their valuable technical laboratory support.

This work was partially presented as poster at the 21st Lancefield International Symposium for Streptococci and Streptococcal Diseases, Stockholm 7th - 10th June 2022.

Funding

This work was supported by internal funds. The whole genome sequencing was funded by Accelerate Diagnostics.

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Authors and Affiliations

  1. Antibiotic Resistance and Special Pathogens Unit, Department of Infectious Diseases, Istituto Superiore di Sanità, Viale Regina Elena, 299 –, 00161, Rome, Italy

    Roberta Creti & Monica Imperi

  2. Clinical Microbiology and Virology, Spirito Santo Hospital, Via Fonte Romana 8, 65124, Pescara, Italy

    Andrea Stanziale, Giorgia Giuliani, Paolo Fazii & Vincenzo Savini

Authors
  1. Roberta Creti
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  2. Monica Imperi
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  3. Andrea Stanziale
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  4. Giorgia Giuliani
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  5. Paolo Fazii
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  6. Vincenzo Savini
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Contributions

All authors contributed to the study conception. Roberta Creti and Vincenzo Savini established the experimental design. Vincenzo Savini, Andrea Stanziale, and Giorgia Giuliani isolated and identified the GBS strains. Monica Imperi performed the molecular typing. Roberta Creti performed the genomic analysis. The first draft of the manuscript was written by Roberta Creti, and all authors commented on previous versions of the manuscript. All authors read and approved the final manuscript.

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Correspondence to Roberta Creti.

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Supplementary information

Supplementary file 1

Supplemental Fig. S1. Depiction of reads alignments to the chromosomal deletion encompassing the cfb gene region in the strains ISS9337 (panel a), ISS9782 (Panel b), ISS 9783 (Panel c), ISS 9784 (panel d), ISS9785 (panel E) and ISS9937 (Panel F) with respect to the reference. Depth (coverage), nucleotide matches and nucleotides background mismatches are reported.

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Creti, R., Imperi, M., Stanziale, A. et al. Group B streptococci (GBS) strains evading molecular diagnostics showed novel chromosomal deletions encompassing the CAMP-factor (cfb) encoding gene. Eur J Clin Microbiol Infect Dis 42, 913–916 (2023). https://doi.org/10.1007/s10096-023-04620-x

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  • DOI: https://doi.org/10.1007/s10096-023-04620-x

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