Adaptive laboratory evolution and independent component analysis disentangle complex vancomycin adaptation trajectories

Anaelle Fait, Yara Seif, Kasper Mikkelsen, Saugat Poudel, Jerry M. Wells, Bernhard O. Palsson, Hanne Ingmer*

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

Abstract

Human infections with methicillin-resistant Staphylococcus aureus (MRSA) are commonly treated with vancomycin, and strains with decreased susceptibility, designated as vancomycin-intermediate S. aureus (VISA), are associated with treatment failure. Here, we profiled the phenotypic, mutational, and transcriptional landscape of 10 VISA strains adapted by laboratory evolution from one common MRSA ancestor, the USA300 strain JE2. Using functional and independent component analysis, we found that: 1) despite the common genetic background and environmental conditions, the mutational landscape diverged between evolved strains and included mutations previously associated with vancomycin resistance (in vraT, graS, vraFG, walKR, and rpoBCD) as well as novel adaptive mutations (SAUSA300_RS04225, ssaA, pitAR, and sagB); 2) the first wave of mutations affected transcriptional regulators and the second affected genes involved in membrane biosynthesis; 3) expression profiles were predominantly strain-specific except for sceD and lukG, which were the only two genes significantly differentially expressed in all clones; 4) three independent virulence systems (φSa3, SaeR, and T7SS) featured as the most transcriptionally perturbed gene sets across clones; 5) there was a striking variation in oxacillin susceptibility across the evolved lineages (from a 10-fold increase to a 63-fold decrease) that also arose in clinical MRSA isolates exposed to vancomycin and correlated with susceptibility to teichoic acid inhibitors; and 6) constitutive expression of the VraR regulon explained crosssusceptibility, while mutations in walK were associated with cross-resistance. Our results show that adaptation to vancomycin involves a surprising breadth of mutational and transcriptional pathways that affect antibiotic susceptibility and possibly the clinical outcome of infections.

Original languageEnglish
Article numbere2118262119
Pages (from-to)e2118262119
JournalProceedings of the National Academy of Sciences of the United States of America
Volume119
Issue number30
DOIs
Publication statusPublished - 19 Jul 2022

Bibliographical note

Funding Information:
ACKNOWLEDGMENTS. This project has received funding from the European Union’s Horizon 2020 research, number 765147; the National Institutes of Allergies and Infectious Disease, grant number AI124316; and the Olav Thon foundation. We thank Statens Serum Institut for providing us with MRSA clinical isolates.

Funding Information:
This project has received funding from the European Union's Horizon 2020 research, number 765147; the National Institutes of Allergies and Infectious Disease, grant number AI124316; and the Olav Thon foundation. We thank Statens Serum Institut for providing us with MRSA clinical isolates.

Publisher Copyright:
Copyright © 2022 the Author(s).

Other keywords

  • adaptive laboratory evolution
  • Antibiotic resistance
  • transcriptional regulation
  • virulence
  • Anti-Bacterial Agents/chemistry
  • Humans
  • Oxacillin/chemistry
  • Virulence/genetics
  • Staphylococcal Infections/drug therapy
  • Microbial Sensitivity Tests
  • Methicillin-Resistant Staphylococcus aureus/metabolism
  • Vancomycin Resistance/genetics
  • Staphylococcus aureus/drug effects
  • Vancomycin/chemistry
  • Evolution, Molecular

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