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Phenotypic and genomic characteristics of oxacillin-susceptible mecA-positive Staphylococcus aureus, rapid selection of high-level resistance to beta-lactams

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Abstract

The aim of this study is to describe the phenotypic and genetic properties of oxacillin-susceptible methicillin-resistant Staphylococcus aureus (OS-MRSA) isolates and their beta-lactam resistant derivatives obtained after selection with oxacillin. A collection of hospital- (HA-) and community-acquired (CA-) MRSA was screened for oxacillin susceptibility. Antibiotic susceptibility testing, population analysis profile (PAP), mecA expression analysis, and whole genome sequencing (WGS) were performed for 60 mecA-positive OS-MRSA isolates. Twelve high-level beta-lactam resistant derivatives selected during PAP were also subjected to WGS. OS-MRSA were more prevalent among CA-MRSA (49/205, 24%) than among HA-MRSA (11/575, 2%). OS-MRSA isolates belonged to twelve sequence types (ST), with a predominance of ST22-t223-SCCmec IVc and ST59-t1950-SCCmec V lineages. OS-MRSA were characterized by mecA promoter mutations at − 33 (C→T) or − 7 (G→T/A) along with PBP2a substitutions (S225R or E246G). The basal and oxacillin-induced levels of mecA expression in OS-MRSA isolates were significantly lower than those in control ST8-HA-MRSA isolates. Most of the OS-MRSA isolates were heteroresistant to oxacillin. High-level beta-lactam resistant OS-MRSA derivatives selected with oxacillin carried mutations in mecA auxiliary factors: relA (metabolism of purines), tyrS, cysS (metabolism of tRNAs), aroK, cysE (metabolism of amino acids and glycolysis). Cefoxitin-based tests demonstrated high specificity for OS-MRSA detection. The highest positive predictive values (PPV > 0.95) were observed for broth microdilution, the VITEK® 2 automatic system, and chromogenic media. Susceptibility testing of CA-MRSA requires special attention due to the high prevalence of difficult-to-detect OS-MRSA among them. Mis-prescription of beta-lactams for the treatment of OS-MRSA may lead to selection of high-level resistance and treatment failures.

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Data availability

Genomic data have been deposited in the NCBI Sequence Read Archive (SRA), under BioProject PRJNA872007.

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Funding

Genomic, phenotypic, and bioinformatic analysis was funded by the Russian Science Foundation (grant no. 18-75-10114-P). Gene expression experiments was supported by the project ID 94030690 of the St. Petersburg State University, St. Petersburg, Russia.

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Authors and Affiliations

  1. Pediatric Research and Clinical Center for Infectious Diseases, Professor Popov Str. 9, Saint Petersburg, 197022, Russia

    Vladimir Gostev, Ksenia Sabinova, Olga Kalinogorskaya, Ofeliia Sulian, Polina Chulkova, Polina Pavlova, Elvira Martens & Sergey Sidorenko

  2. North-Western State Medical University Named After I. I. Mechnikov, Piskarevskij Prospect 47, Saint Petersburg, 195067, Russia

    Vladimir Gostev, Elvira Martens & Sergey Sidorenko

  3. Saint Petersburg State University, Universitetskaya Embankment, Saint Petersburg, 7-9, 199034, Russia

    Julia Sopova, Polina Pavlova & Lavrentii Danilov

  4. Vavilov Institute of General Genetics, Universitetskaya Embankment 7-9, Saint Petersburg, 199034, Russia

    Julia Sopova & Maria Velizhanina

  5. All-Russia Research Institute for Agricultural Microbiology, Podbelsky Chausse 3, Saint Petersburg, Pushkin 8, 196608, Russia

    Maria Velizhanina

  6. Saint Petersburg Pasteur Institute, Mira Str.14, Saint Petersburg, 197101, Russia

    Lyudmila Kraeva & Dmitrii Polev

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  1. Vladimir Gostev
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  2. Ksenia Sabinova
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  4. Olga Kalinogorskaya
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Contributions

Conceptualisation and design: Vladimir Gostev, Sergey Sidorenko and Julia Sopova. Material preparation, data collection and analysis were performed by Olga Kalinogorskaya, Ofeliia Sulian, Polina Chulkova, Lavrentii Danilov, Lyudmila Kraeva, Dmitrii Polev and Elvira Martens. Genome editing: Ksenia Sabinova, Maria Velizhanina and Julia Sopova. Bioinformatics: Polina Pavlova.The first draft of the manuscript was written by Vladimir Gostev and all authors commented on previous versions of the manuscript. All authors read and approved the final manuscript.

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Correspondence to Sergey Sidorenko.

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Supplementary information

ESM 1

Supplementary Table S1. Sequence of primers and probes for the mecA expression assay. (DOCX 13 kb)

ESM 2

Supplementary Table S2. Phenotypes and genotypes of OS-MRSA. (XLSX 43 kb)

ESM 3

Supplementary Table S3. Annotation of the mutations in OS-MRSA derivatives. (XLSX 11 kb)

ESM 4

Supplementary Table S4. MICs and growth rate comparison in OS-MRSA and its derivatives. (XLSX 17 kb)

ESM 5

Supplementary Figure S1. Phylogenetic analysis of mecA-positive oxacillin-susceptible S. aureus. (PNG 723 kb)

ESM 6

Supplementary Figure S2. mecA expression assay data. (PNG 495 kb)

ESM 7

Supplementary Figure S3. Influence of SNPs in the mecA promoter on PAP-AUC data. (PNG 852 kb)

ESM 8

Supplementary Figure S4. mecA expression assay data for parental and derivative isolates. (PNG 700 kb)

ESM 9

Supplementary Figure S5. Correlation analysis of different antibiotic susceptibility tests. (PNG 1655 kb)

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Gostev, V., Sabinova, K., Sopova, J. et al. Phenotypic and genomic characteristics of oxacillin-susceptible mecA-positive Staphylococcus aureus, rapid selection of high-level resistance to beta-lactams. Eur J Clin Microbiol Infect Dis 42, 1125–1133 (2023). https://doi.org/10.1007/s10096-023-04646-1

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