A study of 23 clinical isolates collected in China between 2017 and 2025 has clarified how Nocardia gipuzkoensis should be identified and which antibiotics are most likely to inhibit it. The research, published in Annals of Clinical Microbiology and Antimicrobials, reports that routine 16S rRNA gene sequencing cannot reliably separate N. gipuzkoensis from the closely related species Nocardia abscessus, and that whole-genome sequencing (WGS) was needed to confirm the identity of every isolate in the collection.
N. gipuzkoensis was first described as a novel species in 2020, and infections caused by it have rarely been reported. The authors note that its prevalence may be severely underestimated, because in a previous study the species was misidentified as N. abscessus when 16S rRNA gene sequencing was used. The new study set out to systematically analyze the clinical characteristics, identification, and antimicrobial susceptibility profiles of N. gipuzkoensis to improve understanding of this pathogen.
The team examined 23 strains of N. gipuzkoensis isolated from clinical cases in China between 2017 and 2025. Isolates were identified using both 16S rRNA sequencing and whole-genome sequencing. Clinical data were collected from medical records, and susceptibility to 14 antibiotics was tested with the broth microdilution method.
The sequencing comparison revealed the scale of the identification problem. The 23 N. gipuzkoensis isolates and the reference strain N. abscessus NBRC 100,374 shared 16S rRNA gene sequence similarity ranging from 99.9% to 100%, indicating that routine 16S rRNA sequencing does not distinguish the two species accurately. All 23 isolates were ultimately identified as N. gipuzkoensis with WGS.
Most of the isolates came from the respiratory tract. Of the 23 isolates identified, 20 (87.0%) were recovered from the lower respiratory tract, two (8.7%) from the eye, and one (4.3%) from skin pus. This distribution suggests that, in this collection, N. gipuzkoensis was most often detected in specimens from the lower airways, although the study does not report patient outcomes or establish how the isolates relate to disease severity.
Antimicrobial susceptibility testing showed a clear pattern across the 14 antibiotics tested. The susceptibility rate was highest (100%) for trimethoprim–sulfamethoxazole, linezolid, and amikacin, followed by ceftriaxone, tobramycin, and minocycline, with rates exceeding 90%.
Relatively low inhibitory rates were observed for the fluoroquinolones ciprofloxacin, levofloxacin, and moxifloxacin, followed by clarithromycin. The authors report these susceptibility profiles as laboratory findings from broth microdilution testing of the isolates; the study does not describe treatment outcomes, so the results describe in vitro susceptibility rather than demonstrated clinical efficacy.
The authors conclude that conventional 16S rRNA sequencing contributes to the misidentification of N. gipuzkoensis, and that their study clarified the clinical characteristics, identification, and antimicrobial susceptibility profile of the species. For laboratories, the practical implication is that isolates identified as N. abscessus by 16S rRNA sequencing alone may in fact include N. gipuzkoensis, and that whole-genome sequencing provides the resolution needed to tell the two species apart.
The study is published as an open-access article in Annals of Clinical Microbiology and Antimicrobials, released on 29 August 2026. Because the report covers isolates from a single country over an eight-year period and does not include patient follow-up data, the findings describe the microbiological and susceptibility characteristics of this collection rather than the broader clinical burden of N. gipuzkoensis infection, which the authors suggest may currently be underestimated.
Subject of Research: Identification, clinical characteristics, and antimicrobial susceptibility of Nocardia gipuzkoensis clinical isolates from China
Article Title: Nocardia gipuzkoensis: clinical characterization, identification, and antimicrobial susceptibility
Article References: Zhang, M., Zhang, M., Ren, J., Li, H., Wu, Z., Xin, C., Yang, J., & Shi, D. (2026). Nocardia gipuzkoensis: clinical characterization, identification, and antimicrobial susceptibility. Annals of Clinical Microbiology and Antimicrobials. https://doi.org/10.1186/s12941-026-00882-3
Image Credits: AI Generated
DOI: 10.1186/s12941-026-00882-3
Keywords: Nocardia gipuzkoensis, Nocardia abscessus, whole-genome sequencing, 16S rRNA sequencing, misidentification, antimicrobial susceptibility, broth microdilution, trimethoprim–sulfamethoxazole, linezolid, lower respiratory tract, clinical isolates, China
News Source: Juliet Wilcox. (October 29, 2026). Whole-genome sequencing reveals Nocardia gipuzkoensis misidentified as N. abscessus in Chinese clinical isolates. Scienmag.
