# Comparative phylogenetic, antimicrobial resistance, and clinical characterization of human spondylodiscitis-associated Staphylococcus pseudintermedius

## TL;DR

A rare case of spinal infection caused by Staphylococcus pseudintermedius is analyzed using genome sequencing to track resistance genes and guide treatment.

## Contribution

The study provides a detailed genomic and clinical analysis of a rare S. pseudintermedius infection case, revealing resistance gene profiles and phylogenetic context.

## Key findings

- The isolate belonged to a rare sequence type ST2051 and carried multiple resistance genes but no mecA.
- Genomic comparison revealed three AMR gene clusters, with the isolate in a multidrug-resistant intermediate group.
- Phylogenetic analysis showed high global genomic diversity among S. pseudintermedius isolates.

## Abstract

We report a case of spondylodiscitis caused by methicillin-susceptible Staphylococcus pseudintermedius (MSSP) in a 23-year-old male following lumbar spine stabilization. Despite initial recovery, the patient developed postoperative infection with elevated inflammatory markers and radiological signs of spondylodiscitis. Revision surgery revealed pus extending to the osteosynthesis device. S. pseudintermedius was identified from tissue and blood cultures by MALDI-TOF MS and molecular methods. Whole-genome sequencing (WGS) of three isolates collected at different time points revealed a single clonal strain carrying multiple chromosomal resistance genes [blaZ, cat, ermB, aph-Stph, ant6, aph(3″)-III, sat4A] and a 3.1 kb plasmid of unknown function, but no mecA. Phenotypically, the isolate was susceptible to all tested antibiotics except erythromycin and exhibited inducible clindamycin resistance. Therapy began with clindamycin, later switched to daptomycin, followed by oral levofloxacin and rifampicin, achieving clinical resolution. To contextualize the isolate within the species’ antimicrobial resistance (AMR) landscape, we compared its AMR gene profile with 5,500 publicly available S. pseudintermedius genomes. Thirty-four AMR genes were detected, most frequently aac6-aph2, ant6, aph2, sat, aph-Stph, blaZ, mecA, erm, tetM/tetO, cat, and dfr. Cluster analysis revealed three AMR groups: highly multidrug-resistant (clusters 1–2), intermediate (clusters 3–7), and low-AMR (clusters 8–10). Our isolate fell into cluster 7, enriched for aminoglycoside, β-lactam, macrolide, tetracycline, and phenicol resistance genes. Overall, 42.5% of genomes carried multidrug-resistant gene constellations, whereas 57.5% harbored few AMR genes, with mecA rare in low-AMR clusters. Virulence profiling of our isolate indicated diverse toxins, adhesion factors, biofilm-related autolysins, and immune evasion proteins, supporting pathogenic potential. Phylogenetic analysis using MLST and core-SNPs demonstrated high genomic diversity among S. pseudintermedius worldwide. HGW2412 belonged to the rare sequence type ST2051, previously reported only in Poland. Despite clustering with isolates from multiple continents, precise geographic inference was limited. This case highlights the value of WGS and advanced molecular diagnostics for managing S. pseudintermedius infections and underscores the need for standardized surveillance within a One Health framework.