{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,15]],"date-time":"2026-10-15T20:20:38Z","timestamp":1792095638299,"version":"4.4.0"},"reference-count":66,"publisher":"Springer Science and Business Media LLC","issue":"1","license":[{"start":{"date-parts":[[2026,3,6]],"date-time":"2026-03-06T00:00:00Z","timestamp":1772755200000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.springernature.com\/gp\/researchers\/text-and-data-mining"},{"start":{"date-parts":[[2026,3,6]],"date-time":"2026-03-06T00:00:00Z","timestamp":1772755200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/www.springernature.com\/gp\/researchers\/text-and-data-mining"}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["Mol Genet Genomics"],"published-print":{"date-parts":[[2026,12]]},"DOI":"10.1007\/s00438-026-02382-7","type":"journal-article","created":{"date-parts":[[2026,3,6]],"date-time":"2026-03-06T03:19:37Z","timestamp":1772767177000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":3,"title":["Global in silico genomic epidemiology of tetracycline resistance in Staphylococcus aureus: one health dynamics and genotype\u2013phenotype associations"],"prefix":"10.1007","volume":"301","author":[{"given":"Saleh A. S.","family":"AlAbdulhadi","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5516-3160","authenticated-orcid":false,"given":"Lina A.","family":"Hassan","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Dhuha D. M.","family":"Alrawi","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Istabraq H.","family":"Badr","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Amr Ali Mohamed Abdelgawwad","family":"El-Sehrawy","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Rajashree","family":"Panigrahi","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Amit Kumar","family":"Singh","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"D. Roselin","family":"Jenifer","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Vipasha","family":"Sharma","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1748-7225","authenticated-orcid":false,"given":"Mohammad","family":"Sholeh","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2026,3,6]]},"reference":[{"issue":"9","key":"2382_CR1","doi-asserted-by":"publisher","first-page":"1856","DOI":"10.1002\/iub.2325","volume":"72","author":"R Mirzaei","year":"2020","unstructured":"Mirzaei R, Mohammadzadeh R, Mirzaei H, Sholeh M, Karampoor S, Abdi M et al (2020) Role of MicroRNAs in Staphylococcus aureus infection: potential biomarkers and mechanism. IUBMB Life 72(9):1856\u20131869","journal-title":"IUBMB Life"},{"key":"2382_CR2","doi-asserted-by":"crossref","unstructured":"Navidifar T, Zare Banadkouki A, Parvizi E, Mofid M, Golab N, Beig M et al (2025) Global prevalence of macrolide-resistant Staphylococcus spp.: a comprehensive systematic review and meta-analysis. Front Microbiol. ;Volume 16\u20132025","DOI":"10.3389\/fmicb.2025.1524452"},{"issue":"11","key":"2382_CR3","doi-asserted-by":"publisher","first-page":"2628","DOI":"10.1128\/AAC.38.11.2628","volume":"38","author":"GE Kenny","year":"1994","unstructured":"Kenny GE, Cartwright FD (1994) Susceptibilities of Mycoplasma hominis, Mycoplasma pneumoniae, and Ureaplasma urealyticum to new glycylcyclines in comparison with those to older tetracyclines. Antimicrob Agents Chemother 38(11):2628\u20132632","journal-title":"Antimicrob Agents Chemother"},{"key":"2382_CR4","doi-asserted-by":"crossref","unstructured":"Choi BJ, Choi U, Ryu D-B, Lee C-R (2024) PhoPQ-mediated lipopolysaccharide modification regulates intrinsic resistance to Tetracycline and Glycylcycline antibiotics in Escherichia coli.mSystems. 9(10):e0096424","DOI":"10.1128\/msystems.00964-24"},{"issue":"1","key":"2382_CR5","doi-asserted-by":"publisher","first-page":"220","DOI":"10.1128\/AAC.49.1.220-229.2005","volume":"49","author":"G Muralidharan","year":"2005","unstructured":"Muralidharan G, Micalizzi M, Speth J, Raible D, Troy S (2005) Pharmacokinetics of Tigecycline after single and multiple doses in healthy subjects. Antimicrob Agents Chemother 49(1):220\u2013229","journal-title":"Antimicrob Agents Chemother"},{"issue":"5","key":"2382_CR6","doi-asserted-by":"publisher","first-page":"319","DOI":"10.1159\/000221939","volume":"22","author":"SA Lewis","year":"1976","unstructured":"Lewis SA, Altemeier WA (1976) Correlation of in vitro resistance of Staphylococcus aureus to tetracycline, doxycycline, and Minocycline with in vivo use. Chemotherapy 22(5):319\u2013323","journal-title":"Chemotherapy"},{"issue":"3","key":"2382_CR7","doi-asserted-by":"publisher","first-page":"972","DOI":"10.1128\/AAC.47.3.972-978.2003","volume":"47","author":"CR Dean","year":"2003","unstructured":"Dean CR, Visalli MA, Projan SJ, Sum PE, Bradford PA (2003) Efflux-mediated resistance to Tigecycline (GAR-936) in Pseudomonas aeruginosa PAO1. Antimicrob Agents Chemother 47(3):972\u2013978","journal-title":"Antimicrob Agents Chemother"},{"issue":"8","key":"2382_CR8","doi-asserted-by":"publisher","first-page":"1871","DOI":"10.1093\/jac\/dkad174","volume":"78","author":"Y Chen","year":"2023","unstructured":"Chen Y, Sun L, Hong Y, Chen M, Zhang H, Peng Y et al (2023) Exploring the third-generation Tetracycline resistance of multidrug-resistant livestock-associated methicillin-resistant Staphylococcus aureus ST9 across healthcare settings in China. J Antimicrob Chemother 78(8):1871\u20131881","journal-title":"J Antimicrob Chemother"},{"issue":"3","key":"2382_CR9","doi-asserted-by":"publisher","first-page":"534","DOI":"10.1128\/AAC.38.3.534","volume":"38","author":"GM Eliopoulos","year":"1994","unstructured":"Eliopoulos GM, Wennersten CB, Cole G, Moellering RC (1994) In vitro activities of two glycylcyclines against gram-positive bacteria. Antimicrob Agents Chemother 38(3):534\u2013541","journal-title":"Antimicrob Agents Chemother"},{"key":"2382_CR10","doi-asserted-by":"crossref","unstructured":"Zhanel G, Critchley I, Lin LY, Alvandi N (2019) Microbiological profile of Sarecycline, a novel targeted spectrum Tetracycline for the treatment of acne vulgaris. Antimicrob Agents Chemother. ;63(1)e01297-18","DOI":"10.1128\/AAC.01297-18"},{"issue":"4","key":"2382_CR11","first-page":"e4577","volume":"11","author":"M Arget","year":"2019","unstructured":"Arget M, Kosar J, Suen B, Peermohamed S (2019) Successful treatment of legionnaires\u2019 disease with Tigecycline in an immunocompromised man with a legion of antibiotic allergies. Cureus 11(4):e4577","journal-title":"Cureus"},{"issue":"12","key":"2382_CR12","doi-asserted-by":"publisher","first-page":"5955","DOI":"10.1111\/jcmm.13865","volume":"22","author":"R Ma","year":"2018","unstructured":"Ma R, Zhang Y, Wang W, Wu J, Yang Q, Xu W et al (2018) Inhibition of autophagy enhances the antitumour activity of Tigecycline in multiple myeloma. J Cell Mol Med 22(12):5955\u20135963","journal-title":"J Cell Mol Med"},{"issue":"1","key":"2382_CR13","doi-asserted-by":"publisher","first-page":"216","DOI":"10.1128\/AAC.47.1.216-222.2003","volume":"47","author":"A Lefort","year":"2003","unstructured":"Lefort A, Lafaurie M, Massias L, Petegnief Y, Saleh-Mghir A, Muller-Serieys C et al (2003) Activity and diffusion of Tigecycline (GAR-936) in experimental enterococcal endocarditis. Antimicrob Agents Chemother 47(1):216\u2013222","journal-title":"Antimicrob Agents Chemother"},{"issue":"10","key":"2382_CR14","doi-asserted-by":"publisher","first-page":"3164","DOI":"10.1128\/AAC.46.10.3164-3167.2002","volume":"46","author":"RJ Wallace Jr","year":"2002","unstructured":"Wallace RJ Jr., Brown-Elliott BA, Crist CJ, Mann L, Wilson RW (2002) Comparison of the in vitro activity of the Glycylcycline Tigecycline (formerly GAR-936) with those of tetracycline, minocycline, and Doxycycline against isolates of nontuberculous mycobacteria. Antimicrob Agents Chemother 46(10):3164\u20133167","journal-title":"Antimicrob Agents Chemother"},{"issue":"1","key":"2382_CR15","doi-asserted-by":"publisher","first-page":"116088","DOI":"10.1016\/j.diagmicrobio.2023.116088","volume":"108","author":"M Heidary","year":"2024","unstructured":"Heidary M, Sholeh M, koupaei M, Asadi A, Khah SM, Kheirabadi F et al (2024) Prevalence of Tigecycline resistance in methicillin-resistant Staphylococcus aureus: a systematic review and meta-analysis. Diagn Microbiol Infect Dis 108(1):116088","journal-title":"Diagn Microbiol Infect Dis"},{"issue":"11","key":"2382_CR16","doi-asserted-by":"publisher","first-page":"1153","DOI":"10.1177\/1060028019856721","volume":"53","author":"J Hong","year":"2019","unstructured":"Hong J, Ensom MHH, Lau TTY (2019) What is the evidence for Co-trimoxazole, Clindamycin, Doxycycline, and Minocycline in the treatment of Methicillin-Resistant Staphylococcus aureus (MRSA) pneumonia? Ann Pharmacother 53(11):1153\u20131161","journal-title":"Ann Pharmacother"},{"issue":"5","key":"2382_CR17","doi-asserted-by":"publisher","first-page":"1096","DOI":"10.1128\/AAC.38.5.1096","volume":"38","author":"R Wise","year":"1994","unstructured":"Wise R, Andrews JM (1994) In vitro activities of two glycylcyclines. Antimicrob Agents Chemother 38(5):1096\u20131102","journal-title":"Antimicrob Agents Chemother"},{"issue":"1","key":"2382_CR18","doi-asserted-by":"publisher","first-page":"6267","DOI":"10.1038\/s41598-017-06595-0","volume":"7","author":"N Wang","year":"2017","unstructured":"Wang N, Hang X, Zhang M, Liu X, Yang H (2017) Analysis of newly detected Tetracycline resistance genes and their flanking sequences in human intestinal bifidobacteria. Sci Rep 7(1):6267","journal-title":"Sci Rep"},{"key":"2382_CR20","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1186\/1471-2105-11-595","volume":"11","author":"KA Jolley","year":"2010","unstructured":"Jolley KA, Maiden MC (2010) BIGSdb: scalable analysis of bacterial genome variation at the population level. BMC Bioinformatics 11:1\u201311","journal-title":"BMC Bioinformatics"},{"key":"2382_CR22","first-page":"100446","volume":"23","author":"NL Sherry","year":"2022","unstructured":"Sherry NL, Gorrie CL, Kwong JC, Higgs C, Stuart RL, Marshall C et al (2022) Multi-site implementation of whole genome sequencing for hospital infection control: A prospective genomic epidemiological analysis. Lancet Reg Health West Pac 23:100446","journal-title":"Lancet Reg Health West Pac"},{"issue":"8","key":"2382_CR23","doi-asserted-by":"publisher","first-page":"e328","DOI":"10.1016\/S2666-5247(20)30149-X","volume":"1","author":"F Coll","year":"2020","unstructured":"Coll F, Raven KE, Knight GM, Blane B, Harrison EM, Leek D et al (2020) Definition of a genetic relatedness cutoff to exclude recent transmission of meticillin-resistant Staphylococcus aureus: a genomic epidemiology analysis. Lancet Microbe 1(8):e328\u2013e35","journal-title":"Lancet Microbe"},{"issue":"4","key":"2382_CR24","doi-asserted-by":"publisher","first-page":"876","DOI":"10.1128\/AAC.36.4.876","volume":"36","author":"B Oliva","year":"1992","unstructured":"Oliva B, Chopra I (1992) Tet determinants provide poor protection against some tetracyclines: further evidence for division of tetracyclines into two classes. Antimicrob Agents Chemother 36(4):876\u2013878","journal-title":"Antimicrob Agents Chemother"},{"issue":"3","key":"2382_CR25","doi-asserted-by":"publisher","first-page":"237","DOI":"10.1128\/AAC.4.3.237","volume":"4","author":"D Sompolinsky","year":"1973","unstructured":"Sompolinsky D, Krausz J (1973) Action of 12 tetracyclines on susceptible and resistant strains of Staphylococcus aureus. Antimicrob Agents Chemother 4(3):237\u2013247","journal-title":"Antimicrob Agents Chemother"},{"issue":"6","key":"2382_CR26","doi-asserted-by":"publisher","first-page":"763","DOI":"10.1093\/jac\/45.6.763","volume":"45","author":"K Trzcinski","year":"2000","unstructured":"Trzcinski K, Cooper BS, Hryniewicz W, Dowson CG (2000) Expression of resistance to tetracyclines in strains of methicillin-resistant Staphylococcus aureus. J Antimicrob Chemother 45(6):763\u2013770","journal-title":"J Antimicrob Chemother"},{"key":"2382_CR27","doi-asserted-by":"crossref","unstructured":"Truong-Bolduc QC, Wang Y, Hooper DC (2021) Staphylococcus aureus Tet38 efflux pump structural modeling and roles of essential residues in drug efflux and host cell internalization. Infect Immun 89(5):e00811\u2013e00820","DOI":"10.1128\/IAI.00811-20"},{"issue":"11","key":"2382_CR28","doi-asserted-by":"publisher","first-page":"4362","DOI":"10.1128\/IAI.00723-15","volume":"83","author":"QC Truong-Bolduc","year":"2015","unstructured":"Truong-Bolduc QC, Bolduc GR, Medeiros H, Vyas JM, Wang Y, Hooper DC (2015) Role of the Tet38 efflux pump in Staphylococcus aureus internalization and survival in epithelial cells. Infect Immun 83(11):4362\u20134372","journal-title":"Infect Immun"},{"issue":"5","key":"2382_CR29","doi-asserted-by":"publisher","first-page":"1865","DOI":"10.1128\/AAC.49.5.1865-1871.2005","volume":"49","author":"F McAleese","year":"2005","unstructured":"McAleese F, Petersen P, Ruzin A, Dunman PM, Murphy E, Projan SJ et al (2005) A novel MATE family efflux pump contributes to the reduced susceptibility of laboratory-derived Staphylococcus aureus mutants to Tigecycline. Antimicrob Agents Chemother 49(5):1865\u20131871","journal-title":"Antimicrob Agents Chemother"},{"key":"2382_CR30","doi-asserted-by":"publisher","first-page":"1043736","DOI":"10.3389\/fmicb.2022.1043736","volume":"13","author":"W Zeng","year":"2022","unstructured":"Zeng W, Zhang X, Liu Y, Zhang Y, Xu M, Wang S et al (2022) In vitro antimicrobial activity and resistance mechanisms of the new generation Tetracycline agents, eravacycline, omadacycline, and Tigecycline against clinical Staphylococcus aureus isolates. Front Microbiol 13:1043736","journal-title":"Front Microbiol"},{"key":"2382_CR31","doi-asserted-by":"publisher","first-page":"663835","DOI":"10.3389\/fmicb.2021.663835","volume":"12","author":"N Izghirean","year":"2021","unstructured":"Izghirean N, Waidacher C, Kittinger C, Chyba M, Koraimann G, Pertschy B et al (2021) Effects of ribosomal protein S10 flexible loop mutations on Tetracycline and Tigecycline susceptibility of Escherichia coli. Front Microbiol 12:663835","journal-title":"Front Microbiol"},{"issue":"12","key":"2382_CR32","doi-asserted-by":"publisher","first-page":"e0277866","DOI":"10.1371\/journal.pone.0277866","volume":"17","author":"M Aerts","year":"2022","unstructured":"Aerts M, Tzu-Yun Teng K, Jaspers S, Sanchez JA (2022) A multicategory logit model detecting Temporal changes in antimicrobial resistance. PLoS ONE 17(12):e0277866","journal-title":"PLoS ONE"},{"issue":"8","key":"2382_CR33","doi-asserted-by":"publisher","first-page":"e0200719","DOI":"10.1371\/journal.pone.0200719","volume":"13","author":"JG Conner","year":"2018","unstructured":"Conner JG, Smith J, Erol E, Locke S, Phillips E, Carter CN et al (2018) Temporal trends and predictors of antimicrobial resistance among Staphylococcus spp. Isolated from canine specimens submitted to a diagnostic laboratory. PLoS ONE 13(8):e0200719","journal-title":"PLoS ONE"},{"issue":"5","key":"2382_CR34","doi-asserted-by":"publisher","first-page":"505","DOI":"10.2460\/ajvr.77.5.505","volume":"77","author":"KJ Cummings","year":"2016","unstructured":"Cummings KJ, Perkins GA, Khatibzadeh SM, Warnick LD, Aprea VA, Altier C (2016) Antimicrobial resistance trends among Salmonella isolates obtained from horses in the Northeastern united States (2001\u20132013). Am J Vet Res 77(5):505\u2013513","journal-title":"Am J Vet Res"},{"issue":"1","key":"2382_CR35","doi-asserted-by":"publisher","first-page":"1452","DOI":"10.1038\/s41467-025-56425-5","volume":"16","author":"KS Blake","year":"2025","unstructured":"Blake KS, Xue YP, Gillespie VJ, Fishbein SRS, Tolia NH, Wencewicz TA et al (2025) The Tetracycline resistome is shaped by selection for specific resistance mechanisms by each antibiotic generation. Nat Commun 16(1):1452","journal-title":"Nat Commun"},{"issue":"2","key":"2382_CR36","doi-asserted-by":"publisher","first-page":"559","DOI":"10.1038\/s41396-018-0276-9","volume":"13","author":"MJ Bottery","year":"2019","unstructured":"Bottery MJ, Wood AJ, Brockhurst MA (2019) Temporal dynamics of bacteria-plasmid Coevolution under antibiotic selection. ISME J 13(2):559\u2013562","journal-title":"ISME J"},{"issue":"1","key":"2382_CR37","doi-asserted-by":"publisher","first-page":"21","DOI":"10.1186\/s13756-020-0678-0","volume":"9","author":"HH Balkhy","year":"2020","unstructured":"Balkhy HH, El-Saed A, Alshamrani MM, Alsaedi A, Al Nasser W, El Gammal A et al (2020) Ten-year resistance trends in pathogens causing healthcare-associated infections; reflection of infection control interventions at a multi-hospital healthcare system in Saudi Arabia, 2007\u20132016. Antimicrob Resist Infect Control 9(1):21","journal-title":"Antimicrob Resist Infect Control"},{"issue":"13","key":"2382_CR38","doi-asserted-by":"publisher","first-page":"2400512","DOI":"10.2807\/1560-7917.ES.2025.30.13.2400512","volume":"30","author":"J Powell","year":"2025","unstructured":"Powell J, Sharma S, Johnson A, Barrett S, Garvan C, O\u2019Connell NH et al (2025) Evidence for antimicrobial stewardship and reduced antimicrobial resistance in the Mid-West of Ireland, 2012 to 2023: findings from a one health study. Euro Surveill 30(13):2400512","journal-title":"Euro Surveill"},{"issue":"1","key":"2382_CR39","doi-asserted-by":"publisher","first-page":"47","DOI":"10.1186\/s40813-023-00341-x","volume":"9","author":"A Vilaro","year":"2023","unstructured":"Vilaro A, Novell E, Enrique-Tarancon V, Baliellas J, Fraile L (2023) Susceptibility trends of swine respiratory pathogens from 2019 to 2022 to antimicrobials commonly used in Spain. Porcine Health Manag 9(1):47","journal-title":"Porcine Health Manag"},{"key":"2382_CR40","doi-asserted-by":"publisher","first-page":"1911","DOI":"10.3389\/fmicb.2018.01911","volume":"9","author":"L Lu","year":"2018","unstructured":"Lu L, Liu J, Li Z, Liu Z, Guo J, Xiao Y et al (2018) Occurrence and distribution of Tetracycline antibiotics and resistance genes in longshore sediments of the three Gorges Reservoir, China. Front Microbiol 9:1911","journal-title":"Front Microbiol"},{"issue":"9","key":"2382_CR41","doi-asserted-by":"publisher","first-page":"3052","DOI":"10.1128\/AEM.02260-10","volume":"77","author":"MA Argudin","year":"2011","unstructured":"Argudin MA, Tenhagen BA, Fetsch A, Sachsenroder J, Kasbohrer A, Schroeter A et al (2011) Virulence and resistance determinants of German Staphylococcus aureus ST398 isolates from nonhuman sources. Appl Environ Microbiol 77(9):3052\u20133060","journal-title":"Appl Environ Microbiol"},{"issue":"1","key":"2382_CR42","doi-asserted-by":"publisher","first-page":"6","DOI":"10.1186\/s13756-016-0105-8","volume":"5","author":"A Heikinheimo","year":"2016","unstructured":"Heikinheimo A, Johler S, Karvonen L, Julmi J, Fredriksson-Ahomaa M, Stephan R (2016) New dominant spa type t2741 in livestock-associated MRSA (CC398-MRSA-V) in Finnish fattening pigs at slaughter. Antimicrob Resist Infect Control 5(1):6","journal-title":"Antimicrob Resist Infect Control"},{"key":"2382_CR43","doi-asserted-by":"publisher","first-page":"585","DOI":"10.3389\/fmicb.2018.00585","volume":"9","author":"DK Zhu","year":"2018","unstructured":"Zhu DK, Luo HY, Liu MF, Zhao XX, Jia RY, Chen S et al (2018) Various profiles of tet genes addition to tet(X) in Riemerella anatipestifer isolates from ducks in China. Front Microbiol 9:585","journal-title":"Front Microbiol"},{"issue":"1","key":"2382_CR44","doi-asserted-by":"publisher","first-page":"103","DOI":"10.1186\/s40168-017-0324-0","volume":"5","author":"C Wang","year":"2017","unstructured":"Wang C, Dong D, Strong PJ, Zhu W, Ma Z, Qin Y et al (2017) Microbial phylogeny determines transcriptional response of resistome to dynamic composting processes. Microbiome 5(1):103","journal-title":"Microbiome"},{"key":"2382_CR45","doi-asserted-by":"crossref","unstructured":"Mittelstaedt R, Kanjilal S, Helekal D, Robbins GK, Grad YH (2024) Staphylococcus aureus Tetracycline Resistance and Co-resistance in a Doxy-PEP-Eligible Population. medRxiv","DOI":"10.1101\/2024.08.22.24312434"},{"issue":"8","key":"2382_CR46","first-page":"912","volume":"20","author":"SS Khoramrooz","year":"2017","unstructured":"Khoramrooz SS, Dolatabad SA, Dolatabad FM, Marashifard M, Mirzaii M, Dabiri H et al (2017) Detection of Tetracycline resistance genes, aminoglycoside modifying enzymes, and coagulase gene typing of clinical isolates of Staphylococcus aureus in the Southwest of Iran. Iran J Basic Med Sci 20(8):912\u2013919","journal-title":"Iran J Basic Med Sci"},{"issue":"11","key":"2382_CR47","doi-asserted-by":"publisher","first-page":"1127","DOI":"10.7164\/antibiotics.49.1127","volume":"49","author":"UC Warsa","year":"1996","unstructured":"Warsa UC, Nonoyama M, Ida T, Okamoto R, Okubo T, Shimauchi C et al (1996) Detection of tet(K) and tet(M) in Staphylococcus aureus of Asian countries by the polymerase chain reaction. J Antibiot (Tokyo) 49(11):1127\u20131132","journal-title":"J Antibiot (Tokyo)"},{"issue":"1","key":"2382_CR48","doi-asserted-by":"publisher","first-page":"35","DOI":"10.1038\/s44259-024-00052-5","volume":"2","author":"KPT Silva","year":"2024","unstructured":"Silva KPT, Khare A (2024) Antibiotic resistance mediated by gene amplifications. NPJ Antimicrob Resist 2(1):35","journal-title":"NPJ Antimicrob Resist"},{"issue":"1","key":"2382_CR49","doi-asserted-by":"publisher","first-page":"521","DOI":"10.1038\/s42003-021-02052-x","volume":"4","author":"C Pereira","year":"2021","unstructured":"Pereira C, Larsson J, Hjort K, Elf J, Andersson DI (2021) The highly dynamic nature of bacterial heteroresistance impairs its clinical detection. Commun Biol 4(1):521","journal-title":"Commun Biol"},{"issue":"6","key":"2382_CR50","doi-asserted-by":"publisher","first-page":"1441","DOI":"10.1093\/jac\/dkab056","volume":"76","author":"K Yadav","year":"2021","unstructured":"Yadav K, Garoff L, Huseby DL, Hughes D (2021) Phenotypic and genetic barriers to establishment of horizontally transferred genes encoding ribosomal protection proteins. J Antimicrob Chemother 76(6):1441\u20131447","journal-title":"J Antimicrob Chemother"},{"key":"2382_CR51","doi-asserted-by":"publisher","first-page":"592","DOI":"10.3389\/fmicb.2018.00592","volume":"9","author":"S Neuert","year":"2018","unstructured":"Neuert S, Nair S, Day MR, Doumith M, Ashton PM, Mellor KC et al (2018) Prediction of phenotypic antimicrobial resistance profiles from whole genome sequences of Non-typhoidal Salmonella enterica. Front Microbiol 9:592","journal-title":"Front Microbiol"},{"key":"2382_CR52","doi-asserted-by":"publisher","first-page":"311","DOI":"10.3389\/fmicb.2017.00311","volume":"8","author":"JT Bosse","year":"2017","unstructured":"Bosse JT, Li Y, Rogers J, Fernandez Crespo R, Li Y, Chaudhuri RR et al (2017) Whole genome sequencing for surveillance of antimicrobial resistance in Actinobacillus pleuropneumoniae. Front Microbiol 8:311","journal-title":"Front Microbiol"},{"issue":"8","key":"2382_CR53","first-page":"401","volume":"9","author":"N Rusenova","year":"2022","unstructured":"Rusenova N, Vasilev N, Rusenov A, Milanova A, Sirakov I (2022) Comparison between some phenotypic and genotypic methods for assessment of antimicrobial resistance trend of bovine mastitis Staphylococcus aureus isolates from Bulgaria. Vet Sci 9(8):401","journal-title":"Vet Sci"},{"issue":"3","key":"2382_CR54","doi-asserted-by":"publisher","first-page":"e02140","DOI":"10.1128\/AAC.02140-16","volume":"61","author":"GH Tyson","year":"2017","unstructured":"Tyson GH, Zhao S, Li C, Ayers S, Sabo JL, Lam C et al (2017) Establishing genotypic cutoff values to measure antimicrobial resistance in Salmonella. Antimicrob Agents Chemother 61(3):e02140\u2013e02116","journal-title":"Antimicrob Agents Chemother"},{"key":"2382_CR55","doi-asserted-by":"publisher","first-page":"6155","DOI":"10.2147\/IDR.S429687","volume":"16","author":"A Abdeta","year":"2023","unstructured":"Abdeta A, Beyene D, Negeri AA (2023) Antimicrobial resistance patterns of Staphylococcus aureus and Enterococcus species at the Ethiopian public health Institute, ethiopia: A Five-Year retrospective analysis. Infect Drug Resist 16:6155\u20136166","journal-title":"Infect Drug Resist"},{"issue":"1","key":"2382_CR56","doi-asserted-by":"publisher","first-page":"21","DOI":"10.1186\/s12941-016-0135-3","volume":"15","author":"A Kassim","year":"2016","unstructured":"Kassim A, Omuse G, Premji Z, Revathi G (2016) Comparison of clinical laboratory standards Institute and European committee on antimicrobial susceptibility testing guidelines for the interpretation of antibiotic susceptibility at a university teaching hospital in Nairobi, kenya: a cross-sectional study. Ann Clin Microbiol Antimicrob 15(1):21","journal-title":"Ann Clin Microbiol Antimicrob"},{"issue":"11","key":"2382_CR57","doi-asserted-by":"publisher","first-page":"e79130","DOI":"10.1371\/journal.pone.0079130","volume":"8","author":"A Wolfensberger","year":"2013","unstructured":"Wolfensberger A, Sax H, Weber R, Zbinden R, Kuster SP, Hombach M (2013) Change of antibiotic susceptibility testing guidelines from CLSI to EUCAST: influence on cumulative hospital antibiograms. PLoS ONE 8(11):e79130","journal-title":"PLoS ONE"},{"key":"2382_CR58","doi-asserted-by":"publisher","first-page":"715500","DOI":"10.3389\/fmicb.2021.715500","volume":"12","author":"C Park","year":"2021","unstructured":"Park C, Kim SB, Choi SH, Kim S (2021) Comparison of 16S rRNA gene based microbial profiling using five Next-Generation sequencers and various primers. Front Microbiol 12:715500","journal-title":"Front Microbiol"},{"issue":"5","key":"2382_CR59","doi-asserted-by":"publisher","first-page":"1187","DOI":"10.1093\/jac\/dkab017","volume":"76","author":"F Fernandez-Cuenca","year":"2021","unstructured":"Fernandez-Cuenca F, Lopez-Hernandez I, Cercenado E, Conejo C, Tormo N, Gimeno C et al (2021) Reporting antimicrobial susceptibilities and resistance phenotypes in Staphylococcus spp.: a nationwide proficiency study. J Antimicrob Chemother 76(5):1187\u20131196","journal-title":"J Antimicrob Chemother"},{"issue":"7","key":"2382_CR60","first-page":"2038","volume":"11","author":"V Silva","year":"2021","unstructured":"Silva V, Vieira-Pinto M, Saraiva C, Manageiro V, Reis L, Ferreira E et al (2021) Prevalence and characteristics of Multidrug-Resistant Livestock-Associated Methicillin-Resistant Staphylococcus aureus (LA-MRSA) CC398 isolated from quails (Coturnix coturnix Japonica) slaughtered for human consumption. Anim (Basel) 11(7):2038","journal-title":"Anim (Basel)"},{"issue":"5","key":"2382_CR61","doi-asserted-by":"publisher","first-page":"986","DOI":"10.1101\/gr.275894.121","volume":"32","author":"N Shalon","year":"2022","unstructured":"Shalon N, Relman DA, Yaffe E (2022) Precise genotyping of circular mobile elements from metagenomic data uncovers human-associated plasmids with recent common ancestors. Genome Res 32(5):986\u20131003","journal-title":"Genome Res"},{"issue":"12","key":"2382_CR62","doi-asserted-by":"publisher","first-page":"e1004766","DOI":"10.1371\/journal.pgen.1004766","volume":"10","author":"VF Lanza","year":"2014","unstructured":"Lanza VF, de Toro M, Garcillan-Barcia MP, Mora A, Blanco J, Coque TM et al (2014) Plasmid flux in Escherichia coli ST131 sublineages, analyzed by plasmid constellation network (PLACNET), a new method for plasmid reconstruction from whole genome sequences. PLoS Genet 10(12):e1004766","journal-title":"PLoS Genet"},{"issue":"2","key":"2382_CR63","doi-asserted-by":"publisher","first-page":"e0112824","DOI":"10.1128\/msystems.01128-24","volume":"10","author":"I Akintayo","year":"2025","unstructured":"Akintayo I, Siroglavic M, Frolova D, Silva MB, Grundmann H, Iqbal Z et al (2025) Tracking clonal and plasmid transmission in colistin- and carbapenem-resistant Klebsiella pneumoniae. mSystems 10(2):e0112824","journal-title":"mSystems"},{"issue":"3","key":"2382_CR64","doi-asserted-by":"publisher","first-page":"222","DOI":"10.1289\/ehp.1307009","volume":"122","author":"JA Port","year":"2014","unstructured":"Port JA, Cullen AC, Wallace JC, Smith MN, Faustman EM (2014) Metagenomic frameworks for monitoring antibiotic resistance in aquatic environments. Environ Health Perspect 122(3):222\u2013228","journal-title":"Environ Health Perspect"},{"issue":"9","key":"2382_CR65","doi-asserted-by":"publisher","first-page":"152","DOI":"10.1007\/s11274-022-03334-0","volume":"38","author":"C Mutuku","year":"2022","unstructured":"Mutuku C, Gazdag Z, Melegh S (2022) Occurrence of antibiotics and bacterial resistance genes in wastewater: resistance mechanisms and antimicrobial resistance control approaches. World J Microbiol Biotechnol 38(9):152","journal-title":"World J Microbiol Biotechnol"},{"key":"2382_CR66","doi-asserted-by":"crossref","unstructured":"Rojas-Villalta D, Calder\u00f3n-Osorno M, Barrantes-Jim\u00e9nez K, Arias-Andres M, Rojas-Jim\u00e9nez K (2023) Benchmarking AI-based Plasmid Annotation Tools for Antibiotic Resistance Genes Mining From Metagenome of the Virilla River, Costa Rica","DOI":"10.1101\/2023.08.24.554652"},{"issue":"4","key":"2382_CR67","doi-asserted-by":"publisher","first-page":"1541","DOI":"10.1128\/AAC.01688-09","volume":"54","author":"I Cuesta","year":"2010","unstructured":"Cuesta I, Bielza C, Cuenca-Estrella M, Larranaga P, Rodriguez-Tudela JL (2010) Evaluation by data mining techniques of fluconazole breakpoints established by the clinical and laboratory standards Institute (CLSI) and comparison with those of the European committee on antimicrobial susceptibility testing (EUCAST). Antimicrob Agents Chemother 54(4):1541\u20131546","journal-title":"Antimicrob Agents Chemother"},{"issue":"3","key":"2382_CR68","doi-asserted-by":"publisher","first-page":"845","DOI":"10.1128\/JCM.02441-10","volume":"49","author":"MA Pfaller","year":"2011","unstructured":"Pfaller MA, Espinel-Ingroff A, Boyken L, Hollis RJ, Kroeger J, Messer SA et al (2011) Comparison of the broth microdilution (BMD) method of the European committee on antimicrobial susceptibility testing with the 24-hour CLSI BMD method for testing susceptibility of Candida species to fluconazole, posaconazole, and voriconazole by use of epidemiological cutoff values. J Clin Microbiol 49(3):845\u2013850","journal-title":"J Clin Microbiol"}],"container-title":["Molecular Genetics and Genomics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1007\/s00438-026-02382-7.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/link.springer.com\/article\/10.1007\/s00438-026-02382-7","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1007\/s00438-026-02382-7.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,3,6]],"date-time":"2026-03-06T05:01:54Z","timestamp":1772773314000},"score":1,"resource":{"primary":{"URL":"https:\/\/link.springer.com\/10.1007\/s00438-026-02382-7"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,3,6]]},"references-count":66,"journal-issue":{"issue":"1","published-print":{"date-parts":[[2026,12]]}},"alternative-id":["2382"],"URL":"https:\/\/doi.org\/10.1007\/s00438-026-02382-7","relation":{},"ISSN":["1617-4615","1617-4623"],"issn-type":[{"value":"1617-4615","type":"print"},{"value":"1617-4623","type":"electronic"}],"subject":[],"published":{"date-parts":[[2026,3,6]]},"assertion":[{"value":"30 December 2025","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"8 February 2026","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"6 March 2026","order":3,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}},{"order":1,"name":"Ethics","group":{"name":"EthicsHeading","label":"Declarations"}},{"value":"The authors declare that they have no competing interests.","order":2,"name":"Ethics","group":{"name":"EthicsHeading","label":"Conflict of interests"}}],"article-number":"56"}}