Phenotypic Plasticity of Staphylococcus aureus in Liquid Medium Containing Vancomycin

Abstract

Phenotypic plasticity enables individuals to develop different phenotypes in a changing environment and promotes adaptive evolution. Genome-wide association study (GWAS) facilitates the study of the genetic basis of bacterial phenotypes, and provides a new opportunity for bacterial phenotypic plasticity research. To investigate the relationship between growth plasticity and genotype in bacteria, 41 Staphylococcus aureus strains, including 29 vancomycin-intermediate S. aureus (VISA) strains, were inoculated in the absence or presence of vancomycin for 48 h. Growth curves and maximum growth rates revealed that strains with the same minimum inhibitory concentration (MIC) showed different levels of plasticity in response to vancomycin. A bivariate GWAS was performed to map single-nucleotide polymorphisms (SNPs) associated with growth plasticity. In total, 227 SNPs were identified from 14 time points, while 15 high-frequency SNPs were mapped to different annotated genes. The P-values and growth variations between the two cultures suggest that non-coding region (SNP 738836), ebh (SNP 1394043), drug transporter (SNP 264897), and pepV (SNP 1775112) play important roles in the growth plasticity of S. aureus. Our study provides an alternative strategy for dissecting the adaptive growth of S. aureus in vancomycin and highlights the feasibility of bivariate GWAS in bacterial phenotypic plasticity research.

Keywords: Staphylococcus aureus; bivariate GWAS; phenotypic plasticity; vancomycin; whole-genome sequencing.

FIGURE 1

Growth curves of S. aureus. The growth curves of all strains at 0 μg/ml vancomycin culture (A) and 2 μg/ml vancomycin culture (B). (C–F) The growth curves of S1’, S3’, S5’, and S22’ at 0 and 2 μg/ml.

FIGURE 2

Maximum growth rates of 41 S. aureus. The maximum growth rates of strains in 0 and 2 μg/ml vancomycin treatments were sorted and compared.

FIGURE 3

The emergence time of the maximum growth rate. The maximum growth rate emergence time of six strains in the growth process. Circle: S1’; triangle: S26’; rhombus: S29’; square: S32’; hexagon: S34’; pentagon: S39’.

FIGURE 4

Manhattan plots of the four significant SNPs The x-axis showed SNP positions (Mb) and the y-axis was the –logP-value resulting from the association test. Each dot in the plot represented an SNP, and a reference line was used on the y-axis to reflect genome-wide significance. (A) Time point 3 (4 h). (B) Time point 4 (6 h).

FIGURE 5

Differences of the growth of two genotypes The x-axis represented two genotypes and the y-axis showed the growth variation between the two cultures.

FIGURE 6

Schematic overview of the partial reaction of lysine formation The enzyme encoded by the SAOUHSC_01868 (in red) regulates the production of lysine.