Phenotypic and genotypic correlates of the sodium bicarbonate-responsive phenotype among methicillin-resistant Staphylococcus aureus isolates from skin and soft-tissue infections

Selvi C Ersoy; Sabrina L Madrigal; Liang Chen; Jose Mediavilla; Barry Kreiswirth; Evelyn A Flores; Loren G Miller; Yan Q Xiong; Ewan M Harrison; Beth Blane; Sharon J Peacock; Robin Patel; Henry F Chambers; Arnold S Bayer; Richard A Proctor

doi:10.1016/j.cmi.2024.11.034

Phenotypic and genotypic correlates of the sodium bicarbonate-responsive phenotype among methicillin-resistant Staphylococcus aureus isolates from skin and soft-tissue infections

Clin Microbiol Infect. 2024 Dec 1:S1198-743X(24)00565-2. doi: 10.1016/j.cmi.2024.11.034. Online ahead of print.

Authors

Affiliations

¹ The Lundquist Institute for Biomedical Innovations, Division of Infectious Disease, Harbor-UCLA Medical Center, Torrance, CA, USA; David Geffen School of Medicine, University of California-Los Angeles, Los Angeles, CA, USA. Electronic address: [email protected].
² California State University-Los Angeles, Department of Biological Sciences, Los Angeles, CA, USA.
³ Center for Discovery and Innovation, Hackensack Meridian Health, Nutley, NJ, USA.
⁴ The Lundquist Institute for Biomedical Innovations, Division of Infectious Disease, Harbor-UCLA Medical Center, Torrance, CA, USA.
⁵ The Lundquist Institute for Biomedical Innovations, Division of Infectious Disease, Harbor-UCLA Medical Center, Torrance, CA, USA; David Geffen School of Medicine, University of California-Los Angeles, Los Angeles, CA, USA.
⁶ Wellcome Sanger Institute, Hinxton, United Kingdom; Department of Medicine, University of Cambridge, Cambridge, United Kingdom; Department of Public Health and Primary Care, University of Cambridge, Cambridge, United Kingdom.
⁷ Department of Medicine, University of Cambridge, Cambridge, United Kingdom.
⁸ Wellcome Sanger Institute, Hinxton, United Kingdom; Department of Medicine, University of Cambridge, Cambridge, United Kingdom; London School of Hygiene and Tropical Medicine, London, United Kingdom.
⁹ Department of Microbiology, Mayo Clinic, Rochester, MN, USA.
¹⁰ School of Medicine, University of California-San Francisco, San Francisco, CA, USA.
¹¹ Departments of Medicine and Medical Microbiology/Immunology, University of Wisconsin School of Medicine and Public Health, Madison, WI, USA.

PMID: 39626860
DOI: 10.1016/j.cmi.2024.11.034

Abstract

Objectives: The objective of this study is to assess the frequency of the novel sodium bicarbonate (NaHCO₃)-responsive phenotype, wherein clinical methicillin-resistant Staphylococcus aureus (MRSA) isolates are rendered susceptible to standard-of-care β-lactams in the presence of NaHCO₃, in a collection of 103 clinical U.S. MRSA skin and soft-tissue infection (SSTI) isolates and 22 clinical European SSTI isolates. This study determined the correlation between specific phenotypic and genotypic metrics and the NaHCO₃-responsive phenotype among U.S. SSTI isolates.

Methods: Antimicrobial susceptibility testing was performed to determine susceptibility phenotypes. Targeted and whole-genome sequencing with a genome-wide sequence analysis were conducted to identify specific and novel genotypes of interest that may be associated with the NaHCO₃-responsive phenotype. Gene expression analysis and targeted gene deletion were performed to assess the role of a specific novel genetic locus in the NaHCO₃-responsive phenotype.

Results: The NaHCO₃-responsive phenotype was identified in 78/103 U.S. isolates and 4/22 UK isolates to cefazolin (CFZ), and in 17/103 U.S. isolates and 1/22 UK isolates to oxacillin. In U.S. isolates, a significant association was identified between NaHCO₃-responsiveness to CFZ and: (a) susceptibility to amoxicillin-clavulanate; (b) a specific mecA genotype; (c) clonal complex type 8; and (d) spa type t008. Genome-wide sequence analysis identified single nucleotide polymorphisms (SNPs) in an AraC family regulator (SAUSA300_RS00540) to be exclusively found in NaHCO₃-non-responsive SSTI strains. In vitro HCO₃ exposures of NaHCO₃-responsive strains, but not -non-responsive strains, caused >2-fold upregulated expression of this gene. Deletion of this gene rendered NaHCO₃-responsive strain MRSA 11/11 no longer NaHCO₃-responsive to CFZ; we have termed this gene the staphylococcal AraC bicarbonate-response regulator.

Discussion: NaHCO₃-responsiveness is highly associated with clonal complex type 8/spa type t008, a commonly circulating genetic background in North America. The AraC bicarbonate-response regulator, staphylococcal AraC bicarbonate-response regulator, appears to be associated with the mechanism of NaHCO₃-responsiveness, but more work is needed to verify.

Keywords: Methicillin-resistant Staphylococcus aureus (MRSA); NaHCO(3)-Responsive; Skin and soft-tissue infection (SSTI); Sodium bicarbonate (NaHCO(3)); sabR; β-lactams.