ORIGINAL RESEARCH article
Front. Cell. Infect. Microbiol.
Sec. Antibiotic Resistance and New Antimicrobial drugs
Volume 15 - 2025 | doi: 10.3389/fcimb.2025.1672889
This article is part of the Research TopicAntibiotic Resistance and Bacterial Infections in Immunocompromised HostsView all articles
Genomic and Phenotypic Characterization of Antimicrobial Resistance in Clinical Nocardia Species Isolates
Provisionally accepted
- 1Wenzhou Medical University, Wenzhou, China
- 2Chinese Center for Disease Control and Prevention, Beijing, China
- 3China-Japan Friendship Hospital, Beijing, China
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Background: Antimicrobial resistance is prevalent across Nocardia species, with varying resistance profiles among different species, which poses significant challenges to effective treatment strategies. Our study aimed to assess the antimicrobial susceptibility profiles of various Nocardia species and investigate the potential correlation between resistance phenotypes and their underlying genotypes. Methods: This study analyzed 148 clinical Nocardia isolates from 13 provinces in China. Minimum inhibitory concentrations (MICs) for 15 antimicrobial agents were determined using the microbroth dilution method. Whole genome sequencing (WGS) was performed for all isolates, followed by bioinformatics analyses integrated with 70 human-sourced Nocardia genomes in the National Center for Biotechnology Information (NCBI), encompassing species verification, phylogenetic analysis, and the identification of antimicrobial resistance genes (ARGs). Results: Average Nucleotide Identity (ANI) analysis reclassified several misidentified isolates and revealed 14 potentially novel Nocardia species, underscoring the taxonomic complexity within this genus. Nocardia species exhibited distinct resistance profiles: Nocardia farcinica demonstrated elevated resistance to cephalosporins and tobramycin; Nocardia otitidiscaviarum showed broad resistance to β-lactams and quinolones; and Nocardia cyriacigeorgica exhibited resistance to quinolones, cefepime, and cefoxitin. Notably, clarithromycin resistance was consistently high across all species. Moreover, 38.51% of Nocardia isolates are resistant to two or more commonly used antibiotics, which revealed widespread multidrug resistance (MDR). Strong genotype – phenotype correlations were observed, including sul1 in sulfamethoxazole/trimethoprim-resistant N. farcinica, blaAST-1 in β-lactam-resistant N. otitidiscaviarum, and tetA/B(58) across tetracycline-intermediate isolates. Additionally, resistance mechanisms beyond ARGs were observed, including species-specific presence of warA and aph(2''), and gyrA mutations largely correlating with ciprofloxacin resistance. Nonetheless, resistance in some strains lacking known resistance determinants indicates the presence of uncharacterized mechanisms. Conclusions: These findings provide critical insights into the drug resistance patterns of Nocardia strains and antimicrobial resistance genes, highlighting the importance of ongoing genomic surveillance and personalized treatments.
Keywords: Nocardia, whole genome sequencing, antimicrobial resistance, Average nucleotide identity, minimum inhibitory concentration
Received: 25 Jul 2025; Accepted: 29 Aug 2025.
Copyright: © 2025 Song, Du, Min, Shen, Xu, Guan, Lu and Li. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) or licensor are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.
* Correspondence:
Wanchun Guan, Wenzhou Medical University, Wenzhou, China
Binghuai Lu, China-Japan Friendship Hospital, Beijing, China
Zhenjun Li, Chinese Center for Disease Control and Prevention, Beijing, China
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