Genomic insights into the spread of methicillin-resistant Staphylococcus aureus involved in ear infections

Abstract

Background: Methicillin-resistant Staphylococcus aureus (MRSA) is a major pathogen causing ear infections. However, genomic epidemiology and determinants influencing transmission of ear infections associated MRSA (EIA-MRSA) in community remain unknown.

Methods: In 2020-2021, 105 EIA-MRSA isolates were collected and sequenced from outpatients across different households in Shanghai, China. Antimicrobial susceptibility testing, core genome MLST, and phylodynamic analyses were conducted to characterize EIA-MRSA dissemination.

Results: Quinolone resistance was identified as a risk factor for EIA-MRSA spread (OR 9, [95% CI 3-31]). The ST764 clone and two subclones of ST22-PT hypervirulent clone have developed an extensive quinolone-resistant (eQR) phenotype, conferring additional resistance to advanced quinolones due to the accumulation of four mutations in gyrA (S84L and either S85P, E88K, or E88G) and parC (S80F and either E84K or E84G). These ST764- and ST22-PT-eQR isolates were highly transmissible and showed increased resistance to other commonly used antimicrobials, posing potential high-risk clones. The eQR phenotype may be inherent to the ST764 lineage, which emerged in the late 1980s, coinciding with the widespread fluoroquinolone usage. The ST22-PT-eQR subclones emerged in around 2017 and are accumulating resistance genes.

Conclusion: Vigilance is crucial for eQR high-risk clones, particularly the convergent ST22-PT-eQR subclones that accumulate resistance and virulence traits, posing risks for ear infections.

Clinical trial number: Not applicable.

Keywords: Antimicrobial resistance; Ear infections; Methicillin-resistant staphylococcus aureus; Transmission; Whole genome sequencing.

Fig. 1

Comparison of MICs for different antimicrobials between genetically related (i.e., isolates in cgMLST clusters) and unrelated EIA-MRSA isolates. (A) Distribution of MICs in genetically related (black dots) and unrelated (grey dots) EIA-MRSA isolates across different antimicrobials. (B) Minimum spanning tree based on the core genome of 105 EIA-MRSA isolates. Node colors represent the clonal complex (CC). Thirteen cgMLST clusters, each with at least two isolates and a maximum of eleven allelic differences, are highlighted with a grey background. Dashed outlines around nodes indicate isolates resistant to levofloxacin. Allelic differences between two isolates are indicated on the edges. ST764 and ST22 isolates are enclosed in boxes

Fig. 2

Temporal phylogenetic reconstruction of ST764 MRSA lineage. (A) Bayesian phylogenetic reconstruction of the ST764 MRSA lineage using 1,684 non-recombinant core genome SNPs from 97 isolates (14 from this study). Isolates are represented by dots at the tree tips, colored by isolation country. Strain names of EIA-MRSA isolates are colored in red. Heatmaps show the presence of QRDR mutations and the TSST-1 virulence factor, with colored cells indicating presence and white cells indicating absence. (B) Linear regression plot showing the relationship between date (x-axis) and root-to-tip divergence (y-axis), used to assess the correspondence between the phylogenetic signal (core genome SNPs-based maximum likelihood phylogeny of the ST764 MRSA lineage) and temporal signal (isolation date). (C) Bayesian skyline plot showing changes in the effective population size of the ST764 MRSA population (n = 97) over time. The estimated variations are represented by a blue line, with 95% confidence intervals depicted by a blue shaded area

Fig. 3

Maximum-likelihood phylogeny of the ST22 S. aureus lineage and temporal phylogenetic reconstruction of the ST22-PT hypervirulent MRSA clone. (A) Maximum-likelihood tree of 1,051 ST22 isolates (8 from this study) based on 21,413 non-recombinant core genome SNPs. Rings 1 to 8 (from inside to outside) indicate the presence of QRDR mutations, with colored cells indicating presence and white cells indicating absence. Rings 9 and 10 indicate the presence of PVL and TSST-1 virulence factors, respectively. The tree is midpoint-rooted, and the scale bar represents the number of substitutions. (B) Bayesian phylogenetic reconstruction of the ST22-PT hypervirulent MRSA clone using 818 non-recombinant core SNPs from 29 ST22-PT isolates (7 from this study). Isolates are represented by dots at the tree tips, colored by isolation country. Strain names of EIA-MRSA isolates are colored in red. (C) Linear regression plot showing the relationship between date (x-axis) and root-to-tip divergence (y-axis), used to assess the correspondence between phylogenetic and temporal signals. (D) Comparison of the number of acquired antimicrobial resistance genes in ST22-PT-eQR isolates versus ST22-PT isolates without eQR genotypes