{"doi":"10.1128/jcm.01511-25","title":"Genomic population structure, antimicrobial susceptibility, and clinical features of\n                    <i>Mycobacterium xenopi</i>\n                    isolates, Frankfurt, Germany, 1995–2020","abstract":"<i>Mycobacterium xenopi</i> causes non-tuberculous mycobacterial pulmonary disease (NTM-PD) that is difficult to treat. However, data on the genomic population structure, antimicrobial susceptibility, and the clinical significance of this pathogen remain scarce. We analyzed 76 clinical <i>M. xenopi</i> isolates from 70 patients collected between 1995 and 2020 in Frankfurt am Main, Germany. All isolates underwent phenotypic drug susceptibility testing and whole-genome sequencing. Cluster analysis, including isolates from this study and all hitherto available high-quality <i>M. xenopi</i> genome data sets in the Sequence Read Archive (<i>n</i> = 11), was performed by core genome multilocus sequence typing. In our cohort, only 26.5% of patients met criteria for clinically relevant NTM-PD. Phylogenetic analysis identified three large hospital-associated clusters (≤10 allelic difference), each involving between 7 and 20 patients and persisting for over 18 years, suggesting prolonged transmission chains or a common environmental source. We also defined three major clades (≤50 allelic difference), two of which contained isolates from the United Kingdom. Clofazimine and guideline-recommended antimycobacterial agents showed good <i>in vitro</i> efficacy, except rifampicin, with 23.6% resistance. This study represents a major expansion of <i>M. xenopi</i> genomic resources and provides insights into the genomic population structure, phenotypic susceptibility, and clinical characteristics of <i>M. xenopi</i>. Guideline-recommended antimycobacterials show good <i>in vitro</i> activity, while clofazimine may be a valuable addition to <i>M. xenopi</i> therapy. The identified clusters underscore the need for further investigation into transmission dynamics and globally successful clones.IMPORTANCE<i>Mycobacterium xenopi</i> is an increasingly recognized opportunistic lung pathogen that is difficult to treat. Infections often occur in patients with pre-existing health conditions and can present substantial diagnostic and therapeutic challenges. A deeper understanding of its genetic diversity and resistance mechanisms is essential for optimal patient management and for clarifying potential transmission routes. By analyzing 76 whole-genome sequences together with detailed clinical information and phenotypic drug-susceptibility data, this study substantially expands the available genomic repertoire for <i>M. xenopi</i>. While clinical relevance was limited in our cohort, most guideline-recommended antimicrobial agents showed good efficacy <i>in vitro</i>. The detection of closely related strains might point toward a common environmental source of infection. These findings highlight the need for continued surveillance and provide a comprehensive foundation that supports more accurate monitoring, improved understanding of disease behavior, and future investigations into <i>M. xenopi</i> pathogenicity.","journal":"Journal of Clinical Microbiology","year":2026,"id":12067,"datarank":0.0,"base_score":0.0,"endowment":0.0,"self_citation_contribution":0.0,"citation_network_contribution":0.0,"self_endowment_contribution":0.0,"citer_contribution":0.0,"corpus_percentile":0.0,"corpus_rank":765,"citation_count":0,"citer_count":0,"citers_with_citation_signal":0,"citers_with_endowment":0,"datacite_reuse_total":0,"is_dataset":true,"is_dataset_confidence":0.6441,"is_oa":true,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":"2026-02-09","fair_score":49.7917,"fair_percentile":77.9023746701847,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":96117,"name":"Lisa Marschall","orcid":null,"position":1,"is_corresponding":false},{"id":96118,"name":"Teodora Biciusca","orcid":"0000-0002-7423-2926","position":2,"is_corresponding":false},{"id":96119,"name":"Ann-Sophie Zielbauer","orcid":"0000-0003-3507-9217","position":3,"is_corresponding":false},{"id":96120,"name":"Max Kevane-Campbell","orcid":null,"position":4,"is_corresponding":false},{"id":96121,"name":"Martin Kuhns","orcid":null,"position":5,"is_corresponding":false},{"id":96122,"name":"Sönke Andres","orcid":null,"position":6,"is_corresponding":false},{"id":96123,"name":"Stefan Niemann","orcid":"0000-0002-6604-0684","position":7,"is_corresponding":false},{"id":96124,"name":"Thomas A. Wichelhaus","orcid":"0000-0002-4029-2955","position":8,"is_corresponding":false},{"id":96125,"name":"Nils Wetzstein","orcid":"0000-0002-5589-4668","position":9,"is_corresponding":false},{"id":96116,"name":"Margo Diricks","orcid":"0000-0002-5428-1456","position":0,"is_corresponding":true}],"reference_count":50,"raw_metadata":{"citation_network_status":"fetched"},"created_at":"2026-03-01T18:20:47.508186Z","pmid":"41660834","pmcid":"PMC12977513","fwci":null,"citation_percentile":null,"influential_citations":0,"oa_status":"diamond","license":"cc-by","views":0,"total_file_size_bytes":0,"version_count":0,"fair_f":65.0,"fair_a":55.0,"fair_i":37.5,"fair_r":41.6667,"fair_zscore":0.4143,"fair_rationale":{"fair_score":49.79,"has_llm":true,"dimensions":{"F":{"name":"Findable","score":65.0,"criteria":[{"key":"f_has_doi","label":"Has a persistent DOI","kind":"deterministic","weight":1.0,"fraction":1.0,"signal":"DOI present","rationale":null},{"key":"f_repository_presence","label":"Indexed in repositories / literature DBs","kind":"deterministic","weight":1.0,"fraction":1.0,"signal":"datacite=0, pmcid=True, pmid=True","rationale":null},{"key":"f_persistent_ids","label":"Resolvable scholarly identifiers (OpenAlex)","kind":"deterministic","weight":0.5,"fraction":0.0,"signal":"no OpenAlex id","rationale":null},{"key":"f_metadata_richness","label":"Rich, machine-readable metadata","kind":"llm","weight":1.0,"fraction":0.5,"signal":null,"rationale":"The paper provides accession numbers and supplemental tables, but lacks structured machine-readable metadata or use of ontologies."}]},"A":{"name":"Accessible","score":55.0,"criteria":[{"key":"a_open_access","label":"Open Access / files deposited","kind":"deterministic","weight":1.5,"fraction":1.0,"signal":"Open Access","rationale":null},{"key":"a_retrievable","label":"Free full text retrievable","kind":"deterministic","weight":1.0,"fraction":0.0,"signal":"0 OA location(s)","rationale":null},{"key":"a_access_protocol","label":"Clear data/code access protocol","kind":"llm","weight":1.0,"fraction":0.5,"signal":null,"rationale":"Sequence data access via ENA is stated, but no protocol for code or other data is provided, and no explicit access instructions beyond the link."}]},"I":{"name":"Interoperable","score":37.5,"criteria":[{"key":"i_linked_data","label":"Linked datasets / DataCite relations","kind":"deterministic","weight":1.0,"fraction":0.0,"signal":"linked_datasets=0, datacite=0","rationale":null},{"key":"i_standard_ids","label":"References data via standard accessions","kind":"deterministic","weight":1.0,"fraction":0.0,"signal":"accessions=0, trials=0","rationale":null},{"key":"i_standards","label":"Standard formats, vocabularies & identifiers","kind":"llm","weight":1.0,"fraction":0.75,"signal":null,"rationale":"Standard formats (FASTQ, ENA identifiers) and vocabularies (CLSI breakpoints) are used, but no explicit mention of ontologies or formal interoperability standards."}]},"R":{"name":"Reusable","score":41.67,"criteria":[{"key":"r_license","label":"Clear, open reuse license","kind":"deterministic","weight":1.5,"fraction":0.0,"signal":"no license","rationale":null},{"key":"r_downloads","label":"Demonstrated reuse (downloads)","kind":"deterministic","weight":0.5,"fraction":0.0,"signal":"downloads=0","rationale":null},{"key":"r_version","label":"Versioned / maintained","kind":"deterministic","weight":0.5,"fraction":0.0,"signal":"no version chain","rationale":null},{"key":"r_dataset","label":"Classified as a data resource","kind":"deterministic","weight":0.5,"fraction":1.0,"signal":"is_dataset","rationale":null},{"key":"r_reusability","label":"Data-availability statement, license & reproducibility","kind":"llm","weight":2.0,"fraction":0.667,"signal":null,"rationale":"Data availability statement with ENA accession and CC BY 4.0 license are provided, but code is not shared and reproducibility details are incomplete."}]}},"suggestions":["Provide machine-readable metadata (e.g., ISA-Tab or JSON-LD) for all datasets.","Include a code availability statement with a link to a public repository (e.g., GitHub).","Use standardized ontologies for clinical and phenotypic terms to enhance interoperability.","Add a data dictionary for supplemental tables to clarify column meanings and units.","Ensure all supplemental files are in non-proprietary, open formats (e.g., CSV instead of XLSX)."],"model":"deepseek/deepseek-v4-flash","agent_version":"fair_agent_v2","fulltext_source":"epmc_xml"},"fair_model":"deepseek/deepseek-v4-flash","fair_agent_version":"fair_agent_v2","fair_fulltext_source":"epmc_xml","fair_has_llm":true,"fair_computed_at":"2026-06-18T06:57:54.990409Z","clinical_trials":[],"software_tools":[],"db_accessions":[],"linked_datasets":[],"topics":[]}