{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,21]],"date-time":"2026-10-21T22:49:07Z","timestamp":1792622947843,"version":"4.5.0"},"reference-count":49,"publisher":"Frontiers Media SA","license":[{"start":{"date-parts":[[2025,9,18]],"date-time":"2025-09-18T00:00:00Z","timestamp":1758153600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100012166","name":"National Key Research and Development Program of China","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100012166","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["frontiersin.org"],"crossmark-restriction":true},"short-container-title":["Front. Cell. Infect. Microbiol."],"abstract":"\n Background<\/jats:title>\n \n Antimicrobial resistance is prevalent across\n Nocardia<\/jats:italic>\n 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\n Nocardia<\/jats:italic>\n species and investigate the potential correlation between resistance phenotypes and their underlying genotypes.\n <\/jats:p>\n <\/jats:sec>\n \n Methods<\/jats:title>\n \n This study analyzed 148 clinical\n Nocardia<\/jats:italic>\n 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\n Nocardia<\/jats:italic>\n genomes in the National Center for Biotechnology Information (NCBI), encompassing species verification, phylogenetic analysis, and the identification of antimicrobial resistance genes (ARGs).\n <\/jats:p>\n <\/jats:sec>\n \n Results<\/jats:title>\n \n Average Nucleotide Identity (ANI) analysis reclassified several misidentified isolates and revealed 14 potentially novel\n Nocardia<\/jats:italic>\n species, underscoring the taxonomic complexity within this genus.\n Nocardia<\/jats:italic>\n species exhibited distinct resistance profiles:\n Nocardia farcinica<\/jats:italic>\n demonstrated elevated resistance to cephalosporins and tobramycin;\n Nocardia otitidiscaviarum<\/jats:italic>\n showed broad resistance to\n \u03b2<\/jats:italic>\n -lactams and quinolones; and\n Nocardia cyriacigeorgica<\/jats:italic>\n exhibited resistance to quinolones, cefepime, and cefoxitin. Notably, clarithromycin resistance was consistently high across all species. Moreover, 38.51% of\n Nocardia<\/jats:italic>\n isolates are resistant to two or more commonly used antibiotics, which revealed widespread multidrug resistance (MDR). Strong genotype\u2013phenotype correlations were observed, including\n sul1<\/jats:italic>\n in sulfamethoxazole\/trimethoprim-resistant\n N. farcinica<\/jats:italic>\n ,\n bla<\/jats:italic>\n AST-1<\/jats:sub>\n in\n \u03b2<\/jats:italic>\n -lactam-resistant\n N. otitidiscaviarum<\/jats:italic>\n , and\n tetA\/B(58)<\/jats:italic>\n across tetracycline-intermediate isolates. Additionally, resistance mechanisms beyond ARGs were observed, including species-specific presence of\n warA<\/jats:italic>\n and\n aph(2\u2019\u2019)<\/jats:italic>\n , and\n gyrA<\/jats:italic>\n mutations largely correlating with ciprofloxacin resistance. Nonetheless, resistance in some strains lacking known resistance determinants indicates the presence of uncharacterized mechanisms.\n <\/jats:p>\n <\/jats:sec>\n \n Conclusions<\/jats:title>\n \n These findings provide critical insights into the drug resistance patterns of\n Nocardia<\/jats:italic>\n strains and antimicrobial resistance genes, highlighting the importance of ongoing genomic surveillance and personalized treatments.\n <\/jats:p>\n <\/jats:sec>","DOI":"10.3389\/fcimb.2025.1672889","type":"journal-article","created":{"date-parts":[[2025,9,18]],"date-time":"2025-09-18T05:32:05Z","timestamp":1758173525000},"update-policy":"https:\/\/doi.org\/10.3389\/crossmark-policy","source":"Crossref","is-referenced-by-count":15,"title":["Genomic and phenotypic characterization of antimicrobial resistance in clinical Nocardia species isolates"],"prefix":"10.3389","volume":"15","author":[{"given":"Ziyu","family":"Song","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Bingqian","family":"Du","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Min","family":"Yuan","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jirao","family":"Shen","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Shuai","family":"Xu","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Wanchun","family":"Guan","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Binghuai","family":"Lu","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Zhenjun","family":"Li","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1965","published-online":{"date-parts":[[2025,9,18]]},"reference":[{"key":"B1","doi-asserted-by":"publisher","first-page":"117","DOI":"10.4056\/sigs.531120","article-title":"Digital DNA-DNA hybridization for microbial species delineation by means of genome-to-genome sequence comparison","volume":"2","author":"Auch","year":"2010","journal-title":"Stand Genomic Sci."},{"key":"B2","doi-asserted-by":"publisher","first-page":"1035","DOI":"10.1016\/j.tim.2018.08.004","article-title":"From theory to practice: translating whole-genome sequencing (WGS) into the clinic","volume":"26","author":"Balloux","year":"2018","journal-title":"Trends Microbiol."},{"key":"B3","doi-asserted-by":"publisher","first-page":"455","DOI":"10.1089\/cmb.2012.0021","article-title":"SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing","volume":"19","author":"Bankevich","year":"2012","journal-title":"J. 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