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This study aimed to investigate the genomic characteristics, antimicrobial resistance (AMR) profiles, and temporal dynamics of\n                      <jats:italic>C. difficile<\/jats:italic>\n                      strains isolated from hospitalized patients in a German tertiary hospital over nearly two decades (1997\u20132015).\n                    <\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Methods<\/jats:title>\n                    <jats:p>\n                      Whole-genome sequencing was performed on 46 toxigenic\n                      <jats:italic>C. difficile<\/jats:italic>\n                      isolates to determine sequence types (STs) and phylogenetic relationships and these were compared to national surveillance data on\n                      <jats:italic>C. dificile<\/jats:italic>\n                      . AMR profiling was conducted to identify key resistance determinants at genetic level while epsilometer minimum inhibitory concentration (MIC) analyses were used to correlate genetic resistance markers with phenotypic resistance. Longitudinal antibiotic usage data were analysed to assess potential associations with resistance profiles and strains evolution.\n                    <\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>\n                      Five predominant STs were identified: ST1 (30%), ST54 (24%), ST3 (22%), ST11 (11%), and ST37 (4%). Phylogenetic analysis showed that ST1 (ribotype 027) emerged as the dominant and persistent lineage, replacing ST11 and ST54 over time. AMR profiling detected several resistance genetic markers such as\n                      <jats:italic>CDD-1\/CDD-2<\/jats:italic>\n                      (carbapenem resistance),\n                      <jats:italic>ErmB<\/jats:italic>\n                      (macrolide-lincosamide-streptogramin B resistance\/MLS resistance), and mutations in\n                      <jats:italic>gyrA<\/jats:italic>\n                      (fluoroquinolone resistance) and\n                      <jats:italic>rpoB<\/jats:italic>\n                      (rifampicin resistance). MIC analyses confirmed high resistance rates to moxifloxacin (87%) and rifampicin (59%), while susceptibility to fidaxomicin, metronidazole, and vancomycin remained. The\n                      <jats:italic>tetM<\/jats:italic>\n                      gene, associated with doxycycline resistance, declined as ST11 and ST54 frequencies decreased. Longitudinal analysis revealed a reduction in moxifloxacin resistance following its decreased use, whereas increased doxycycline use paradoxically correlated with reduced resistance.\n                    <\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Conclusion<\/jats:title>\n                    <jats:p>\n                      This study highlights the dynamic strain evolution of\n                      <jats:italic>C. difficile<\/jats:italic>\n                      , reflecting national trends in strain evolution. The findings emphasize the strong correlation between epsilometer MIC values and molecular resistance markers. This observation reinforces the integration of genetic surveillance with antibiotic stewardship in the clinical routine to effectively mitigate CDI recurrence. Further research is needed to better understand the complex interactions between antibiotic exposure and strain evolution in hospital environments.\n                    <\/jats:p>\n                  <\/jats:sec>","DOI":"10.1007\/s15010-025-02576-y","type":"journal-article","created":{"date-parts":[[2025,6,8]],"date-time":"2025-06-08T04:53:29Z","timestamp":1749358409000},"page":"2209-2218","update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":1,"title":["Clostridioides difficile evolution in a tertiary German hospital through a retrospective genomic characterization"],"prefix":"10.1007","volume":"53","author":[{"given":"Fabian","family":"Lorenzo-Diaz","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Tilman E.","family":"Klassert","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Cristina","family":"Zubiria-Barrera","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Amelya","family":"Keles-Slevogt","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Mario","family":"Gonzalez-Carracedo","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Mariano","family":"Hernandez","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Hortense","family":"Slevogt","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Thomas","family":"Gr\u00fcnewald","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2025,6,8]]},"reference":[{"key":"2576_CR1","doi-asserted-by":"publisher","first-page":"1211","DOI":"10.1007\/s10096-019-03539-6","volume":"38","author":"J Czepiel","year":"2019","unstructured":"Czepiel J, Dr\u00f3\u017cd\u017c M, Pituch H, Kuijper EJ, Perucki W, Mielimonka A, et al. 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All analysis performed was solely conducted on bacterial strains and hospital-wide consumption data. No data from humans were accessed.","order":2,"name":"Ethics","group":{"name":"EthicsHeading","label":"Ethics approval and consent to participate"}},{"value":"TEK was awarded the 2024 Hygiene-Price of the Rudolf-Sch\u00fclke-Stiftung and received an honorarium from Sch\u00fclke & Mayr GmbH for a presentation at the 17th Hospital Hygiene Conference. All other authors declare no conflict of interest.","order":3,"name":"Ethics","group":{"name":"EthicsHeading","label":"Competing interests"}}]}}