Phylogenetic and Genomic Feature Analysis of Cutaneous Nocardia Isolates

Cutaneous nocardiosis differs from pulmonary and disseminated nocardiosis in that it can occur in immunocompetent individuals and is usually localized with a favorable prognosis. However, the phylogenetic relationships, genomic characteristics, and virulence and antimicrobial resistance profiles of human cutaneous Nocardia isolates remain poorly understood.

This study aimed to characterize the phylogenetic relationships and genomic features of human cutaneous Nocardia isolates and to investigate their virulence-associated and antimicrobial resistance determinants, as well as their phenotypic antimicrobial susceptibility profiles.

A total of 31 human cutaneous Nocardia genomes were included for comparative genomic analysis, comprising nine clinical isolates sequenced in this study and 22 publicly available genomes retrieved from the NCBI database. Phylogenetic reconstruction, average nucleotide identity (ANI) analysis, and pan-genome analysis were performed to investigate the genomic relationships and diversity of the isolates. Putative virulence-associated and antimicrobial resistance genes were identified through genome-based annotation. In vitro antimicrobial susceptibility testing was performed for 13 isolates against 15 antimicrobial agents.

Phylogenetic analysis demonstrated clear species-level clustering and identified a potentially novel cutaneous pathogen, Nocardia sp. NK_136. Pan-genome analysis revealed an open pan-genome with substantial genomic plasticity. Virulence profiling identified a broadly conserved core framework mainly associated with stress response, immune evasion, iron acquisition, secretion systems, and host interaction, together with variable virulence-associated modules distributed in a species- or strain-specific manner. A total of 40 antimicrobial resistance genes were identified, showing marked species-dependent distribution. Phenotypic antimicrobial susceptibility testing demonstrated that all tested isolates were susceptible to trimethoprim-sulfamethoxazole (TMP-SMX) and linezolid, whereas variable resistance was observed to cefepime, cefoxitin, ciprofloxacin, tobramycin, and clarithromycin.

Human cutaneous Nocardia isolates possess a conserved core virulence-associated genomic framework accompanied by variable virulence modules, while their antimicrobial resistance determinants and phenotypic resistance profiles show substantial species-dependent variation. These findings provide genomic insights into the diversity, potential pathogenicity, and antimicrobial resistance of cutaneous Nocardia isolates and provide a basis for further investigation of the pathogenesis and clinical management of cutaneous nocardiosis.