{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,29]],"date-time":"2026-09-29T06:03:55Z","timestamp":1790661835574,"version":"4.1.0"},"reference-count":72,"publisher":"Frontiers Media SA","license":[{"start":{"date-parts":[[2026,9,29]],"date-time":"2026-09-29T00:00:00Z","timestamp":1790640000000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100023961","name":"Centro de Investigaci\u00f3n Biotecnol\u00f3gica en Red de Enfermedades Infecciosas","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100023961","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["frontiersin.org"],"crossmark-restriction":true},"short-container-title":["Front. Cell. Infect. Microbiol."],"abstract":"<jats:sec>\n                    <jats:title>Introduction<\/jats:title>\n                    <jats:p>\n                      Carbapenemase-producing\n                      <jats:italic>Klebsiella pneumoniae<\/jats:italic>\n                      (CP-KP) represents a major public health threat. The global dissemination of antimicrobial resistance is largely driven by high-risk clones (HRCs), such as ST307\/OXA-48, ST11\/OXA-48 and ST512\/KPC-3, which currently dominate the epidemiology of CP-KP in Spain. This study aimed to describe the emergence, dissemination and genomic evolution of an OXA-48-producing\n                      <jats:italic>K. pneumoniae<\/jats:italic>\n                      ST5994 clone in Cantabria, Spain, and to characterize its genomic, phenotypic and epidemiological features.\n                    <\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Methods<\/jats:title>\n                    <jats:p>A retrospective genomic surveillance study of CP-KP isolates was conducted in Cantabria from 2021 to 2024. Whole-genome sequencing was used to characterize sequence types, resistome, mobilome, virulome, pangenome and phylogenetic relationships. Antimicrobial susceptibility and biofilm production assays were performed. Fourier-transform infrared (FT-IR) spectroscopy combined with machine learning algorithms was used to develop a rapid method for HRCs discrimination.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>\n                      Among 448 non-duplicate CP-KP isolates,\n                      <jats:italic>bla<\/jats:italic>\n                      <jats:sub>OXA-48<\/jats:sub>\n                      was the predominant carbapenemase.\n                      <jats:italic>K. pneumoniae<\/jats:italic>\n                      ST5994 was first detected in the second quarter of 2023 and rapidly became one of the dominant CP-KP clones at both reference hospital and regional levels over a two-year period, displacing previously prevalent HRCs, such as\n                      <jats:italic>K. pneumoniae<\/jats:italic>\n                      ST11 and\n                      <jats:italic>K. pneumoniae<\/jats:italic>\n                      ST307. The newly identified clone harbored two potentially conjugative plasmids carrying\n                      <jats:italic>bla<\/jats:italic>\n                      <jats:sub>OXA-48<\/jats:sub>\n                      carbapenemase and\n                      <jats:italic>bla<\/jats:italic>\n                      <jats:sub>CTX-M-15<\/jats:sub>\n                      extended-spectrum beta-lactamase. At the time of writing, eight ST5994 genomes were publicly available, all from the Americas and none carrying a\n                      <jats:italic>bla<\/jats:italic>\n                      <jats:sub>OXA-48<\/jats:sub>\n                      gene, therefore this study represents both the first description of this ST in Europe and its first association with OXA-48. Genomic and epidemiological analyses were compatible with sustained dissemination within the regional healthcare network, although the specific transmission pathways could not be established with the available data. Comparative analyses supported a close evolutionary relationship between\n                      <jats:italic>K. pneumoniae<\/jats:italic>\n                      ST307 and ST5994.\n                    <\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Conclusions<\/jats:title>\n                    <jats:p>\n                      Our findings highlight the rapid emergence and regional replacement capacity of the novel OXA-48-producing\n                      <jats:italic>K. pneumoniae<\/jats:italic>\n                      ST5994. The integration of genomic and phenotypic data provides insights into its evolutionary trajectory and transmission dynamics. Furthermore, the proposed FT-IR-based approach combined with machine learning offers a promising tool for rapid discrimination of HRCs, supporting surveillance and infection control strategies.\n                    <\/jats:p>\n                  <\/jats:sec>","DOI":"10.3389\/fcimb.2026.1872766","type":"journal-article","created":{"date-parts":[[2026,9,29]],"date-time":"2026-09-29T05:47:35Z","timestamp":1790660855000},"update-policy":"https:\/\/doi.org\/10.3389\/crossmark-policy","source":"Crossref","is-referenced-by-count":0,"title":["Emergence of OXA-48-producing Klebsiella pneumoniae ST5994, a sister lineage of the high-risk ST307 clone"],"prefix":"10.3389","volume":"16","author":[{"given":"Jorge","family":"Rodr\u00edguez-Grande","sequence":"first","affiliation":[{"name":"Servicio de Microbiolog\u00eda, Hospital Universitario Marqu\u00e9s de Valdecilla-Instituto de Investigaci\u00f3n Marqu\u00e9s de Valdecilla (IDIVAL)","place":["Santander, Spain"]},{"name":"Consorcio de Investigaci\u00f3n Biom\u00e9dica en Red (CIBER) de Enfermedades Infecciosas, Instituto de Salud Carlos III","place":["Madrid, Spain"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Domingo","family":"Fern\u00e1ndez-Vecilla","sequence":"additional","affiliation":[{"name":"Servicio de Microbiolog\u00eda, Hospital Universitario Marqu\u00e9s de Valdecilla-Instituto de Investigaci\u00f3n Marqu\u00e9s de Valdecilla (IDIVAL)","place":["Santander, Spain"]},{"name":"Consorcio de Investigaci\u00f3n Biom\u00e9dica en Red (CIBER) de Enfermedades Infecciosas, Instituto de Salud Carlos III","place":["Madrid, Spain"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Rosal\u00eda","family":"Palomino-Cabrera","sequence":"additional","affiliation":[{"name":"Servicio de Microbiolog\u00eda, Hospital Universitario Marqu\u00e9s de Valdecilla-Instituto de Investigaci\u00f3n Marqu\u00e9s de Valdecilla (IDIVAL)","place":["Santander, Spain"]},{"name":"Consorcio de Investigaci\u00f3n Biom\u00e9dica en Red (CIBER) de Enfermedades Infecciosas, Instituto de Salud Carlos III","place":["Madrid, Spain"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Samuel","family":"Garc\u00eda-Garc\u00eda","sequence":"additional","affiliation":[{"name":"Servicio de Microbiolog\u00eda, Hospital Universitario Marqu\u00e9s de Valdecilla-Instituto de Investigaci\u00f3n Marqu\u00e9s de Valdecilla (IDIVAL)","place":["Santander, Spain"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Daniela","family":"Vallejo-Iriarte","sequence":"additional","affiliation":[{"name":"Servicio de Microbiolog\u00eda, Hospital Universitario Marqu\u00e9s de Valdecilla-Instituto de Investigaci\u00f3n Marqu\u00e9s de Valdecilla (IDIVAL)","place":["Santander, Spain"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Nuria","family":"Valc\u00e1rcel-Fraile","sequence":"additional","affiliation":[{"name":"Servicio de Microbiolog\u00eda, Hospital Universitario Marqu\u00e9s de Valdecilla-Instituto de Investigaci\u00f3n Marqu\u00e9s de Valdecilla (IDIVAL)","place":["Santander, Spain"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Mar\u00eda","family":"Siller-Ru\u00edz","sequence":"additional","affiliation":[{"name":"Servicio de Microbiolog\u00eda, Hospital Universitario Marqu\u00e9s de Valdecilla-Instituto de Investigaci\u00f3n Marqu\u00e9s de Valdecilla (IDIVAL)","place":["Santander, Spain"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Mar\u00eda Carmen","family":"Fari\u00f1as","sequence":"additional","affiliation":[{"name":"Consorcio de Investigaci\u00f3n Biom\u00e9dica en Red (CIBER) de Enfermedades Infecciosas, Instituto de Salud Carlos III","place":["Madrid, Spain"]},{"name":"Servicio de Enfermedades Infecciosas, Hospital Universitario Marqu\u00e9s de Valdecilla-Instituto de Investigaci\u00f3n Marqu\u00e9s de Valdecilla (IDIVAL)","place":["Santander, Spain"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Mar\u00eda P\u00eda","family":"Roiz Mesones","sequence":"additional","affiliation":[{"name":"Servicio de Microbiolog\u00eda, Hospital Universitario Marqu\u00e9s de Valdecilla-Instituto de Investigaci\u00f3n Marqu\u00e9s de Valdecilla (IDIVAL)","place":["Santander, Spain"]},{"name":"Consorcio de Investigaci\u00f3n Biom\u00e9dica en Red (CIBER) de Enfermedades Infecciosas, Instituto de Salud Carlos III","place":["Madrid, Spain"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jorge","family":"Calvo-Montes","sequence":"additional","affiliation":[{"name":"Servicio de Microbiolog\u00eda, Hospital Universitario Marqu\u00e9s de Valdecilla-Instituto de Investigaci\u00f3n Marqu\u00e9s de Valdecilla (IDIVAL)","place":["Santander, Spain"]},{"name":"Consorcio de Investigaci\u00f3n Biom\u00e9dica en Red (CIBER) de Enfermedades Infecciosas, Instituto de Salud Carlos III","place":["Madrid, Spain"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Alain","family":"Ocampo-Sosa","sequence":"additional","affiliation":[{"name":"Servicio de Microbiolog\u00eda, Hospital Universitario Marqu\u00e9s de Valdecilla-Instituto de Investigaci\u00f3n Marqu\u00e9s de Valdecilla (IDIVAL)","place":["Santander, Spain"]},{"name":"Consorcio de Investigaci\u00f3n Biom\u00e9dica en Red (CIBER) de Enfermedades Infecciosas, Instituto de Salud Carlos III","place":["Madrid, Spain"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Zaira","family":"Moure","sequence":"additional","affiliation":[{"name":"Servicio de Microbiolog\u00eda, Hospital Universitario Marqu\u00e9s de Valdecilla-Instituto de Investigaci\u00f3n Marqu\u00e9s de Valdecilla (IDIVAL)","place":["Santander, Spain"]},{"name":"Consorcio de Investigaci\u00f3n Biom\u00e9dica en Red (CIBER) de Enfermedades Infecciosas, Instituto de Salud Carlos III","place":["Madrid, Spain"]},{"name":"Departamento de Biolog\u00eda Molecular, Universidad de Cantabria","place":["Santander, Spain"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sergio","family":"Garc\u00eda-Fern\u00e1ndez","sequence":"additional","affiliation":[{"name":"Servicio de Microbiolog\u00eda, Hospital Universitario Marqu\u00e9s de Valdecilla-Instituto de Investigaci\u00f3n Marqu\u00e9s de Valdecilla (IDIVAL)","place":["Santander, Spain"]},{"name":"Consorcio de Investigaci\u00f3n Biom\u00e9dica en Red (CIBER) de Enfermedades Infecciosas, Instituto de Salud Carlos III","place":["Madrid, Spain"]},{"name":"Departamento de Biolog\u00eda Molecular, Universidad de Cantabria","place":["Santander, Spain"]}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1965","published-online":{"date-parts":[[2026,9,29]]},"reference":[{"key":"B1","doi-asserted-by":"publisher","DOI":"10.1093\/GENETICS\/164.4.1279","article-title":"Associations between inverted repeats and the structural evolution of bacterial genomes","volume":"164","author":"Achaz","year":"2003","journal-title":"Genetics"},{"key":"B2","doi-asserted-by":"publisher","DOI":"10.1155\/2015\/414681","article-title":"Diversity and global distribution of IncL\/M plasmids enabling horizontal dissemination of \u03b2-lactam resistance genes among the Enterobacteriaceae","volume":"2015","author":"Adamczuk","year":"2015","journal-title":"BioMed. Res. Int."},{"key":"B3","doi-asserted-by":"publisher","first-page":"D690","DOI":"10.1093\/NAR\/GKAC920","article-title":"CARD 2023: expanded curation, support for machine learning, and resistome prediction at the Comprehensive Antibiotic Resistance Database","volume":"51","author":"Alcock","year":"2023","journal-title":"Nucleic Acids Res."},{"key":"B4","doi-asserted-by":"publisher","DOI":"10.1099\/mgen.0.001132","article-title":"Development of a novel streamlined workflow (AACRE) and database (inCREDBle) for genomic analysis of carbapenem-resistant Enterobacterales","volume":"9","author":"Alioto","year":"2023","journal-title":"Microb. Genom."},{"key":"B5","doi-asserted-by":"publisher","first-page":"328","DOI":"10.1080\/20477724.2022.2121362","article-title":"Global spread and evolutionary convergence of multidrug-resistant and hypervirulent Klebsiella pneumoniae high-risk clones","volume":"117","author":"Arcari","year":"2023","journal-title":"Pathog. Glob. Health"},{"key":"B6","doi-asserted-by":"publisher","first-page":"705","DOI":"10.1111\/j.1574-6976.2011.00293.x","article-title":"Multilevel population genetics in antibiotic resistance","volume":"35","author":"Baquero","year":"2011","journal-title":"FEMS Microbiol. Rev."},{"key":"B7","doi-asserted-by":"publisher","DOI":"10.1128\/aac.01120-24","article-title":"Mutant prevention concentrations, in vitro resistance evolution dynamics, and mechanisms of resistance to imipenem and imipenem\/relebactam in carbapenem-susceptible Klebsiella pneumoniae isolates showing ceftazidime\/avibactam resistance","volume":"68","author":"Blanco-Mart\u00edn","year":"2024","journal-title":"Antimicrob. Agents Chemother."},{"key":"B8","doi-asserted-by":"publisher","first-page":"3491","DOI":"10.1093\/JAC\/DKAA345","article-title":"ResFinder 4.0 for predictions of phenotypes from genotypes","volume":"75","author":"Bortolaia","year":"2020","journal-title":"J. Antimicrob. Chemother."},{"key":"B9","doi-asserted-by":"publisher","first-page":"5092","DOI":"10.1038\/s41467-024-49349-z","article-title":"International and regional spread of carbapenem-resistant Klebsiella pneumoniae in Europe","volume":"15","author":"Budia-Silva","year":"2024","journal-title":"Nat. Commun."},{"key":"B10","doi-asserted-by":"publisher","DOI":"10.1186\/1471-2105-10-421","article-title":"BLAST+: architecture and applications","volume":"10","author":"Camacho","year":"2009","journal-title":"BMC Bioinf."},{"key":"B11","doi-asserted-by":"publisher","first-page":"206","DOI":"10.1016\/j.jgar.2022.01.016","article-title":"Carbapenemase-producing Klebsiella pneumoniae strains in Switzerland: human and non-human settings may share high-risk clones","volume":"28","author":"Campos-Madueno","year":"2022","journal-title":"J. Glob. Antimicrob. Resist."},{"key":"B12","doi-asserted-by":"publisher","first-page":"12","DOI":"10.37201\/req\/s01.03.2021","article-title":"RedLabRA; a Spanish network of microbiology laboratories for the surveillance of antibiotic resistant microorganisms","volume":"34","author":"Ca\u00f1ada-Garc\u00eda","year":"2021","journal-title":"Rev. Espa\u00f1ola Quimioterapia"},{"key":"B13","doi-asserted-by":"publisher","DOI":"10.3389\/fmicb.2022.918362","article-title":"CARB-ES-19 multicenter study of carbapenemase-producing Klebsiella pneumoniae and Escherichia coli from all Spanish provinces reveals interregional spread of high-risk clones such as ST307\/OXA-48 and ST512\/KPC-3","volume":"13","author":"Ca\u00f1ada-Garc\u00eda","year":"2022","journal-title":"Front. Microbiol."},{"key":"B14","doi-asserted-by":"publisher","first-page":"295","DOI":"10.1089\/mdr.2012.0238","article-title":"Rapid expansion of KPC-2-producing Klebsiella pneumoniae isolates in two Texas hospitals due to clonal spread of ST258 and ST307 lineages","volume":"19","author":"Castanheira","year":"2013","journal-title":"Microbial Drug Resistance"},{"key":"B15","doi-asserted-by":"publisher","DOI":"10.1093\/gigascience\/giab008","article-title":"Twelve years of SAMtools and BCFtools","volume":"10","author":"Danecek","year":"2021","journal-title":"GigaScience"},{"key":"B16","doi-asserted-by":"publisher","first-page":"1919","DOI":"10.1038\/s41564-019-0492-8","article-title":"Epidemic of carbapenem-resistant Klebsiella pneumoniae in Europe is driven by nosocomial spread","volume":"4","author":"David","year":"2019","journal-title":"Nat. Microbiol."},{"key":"B17","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btad311","article-title":"NanoPack2: population-scale evaluation of long-read sequencing data","volume":"39","author":"De Coster","year":"2023","journal-title":"Bioinformatics"},{"key":"B18","doi-asserted-by":"publisher","DOI":"10.3390\/antibiotics10050491","article-title":"New sequence type ST3449 in multidrug-resistant Pseudomonas aeruginosa isolates from a cystic fibrosis patient","volume":"10","author":"D\u00edaz-R\u00edos","year":"2021","journal-title":"Antibiotics"},{"key":"B19","doi-asserted-by":"publisher","DOI":"10.1186\/GB-2000-1-6-RESEARCH0011","article-title":"Evidence for symmetric chromosomal inversions around the replication origin in bacteria","volume":"1","author":"Eisen","year":"2000","journal-title":"Genome Biol."},{"key":"B20","doi-asserted-by":"publisher","DOI":"10.1186\/s13104-024-06708-9","article-title":"Investigating the relationship between carbapenemase production and biofilm formation in Klebsiella pneumoniae clinical isolates","volume":"17","author":"El Naggar","year":"2024","journal-title":"BMC Res"},{"key":"B21","doi-asserted-by":"publisher","first-page":"3","DOI":"10.1038\/s41564-020-00834-3","article-title":"Community-led, integrated, reproducible multi-omics with anvi\u2019o","volume":"6","author":"Eren","year":"2020","journal-title":"Nat. Microbiol."},{"key":"B22","article-title":"EUCAST guidelines for detection of resistance mechanisms and specific resistances of clinical and\/or epidemiological importance","author":"EUCAST","year":"2017"},{"key":"B23","doi-asserted-by":"publisher","DOI":"10.3390\/pathogens12030479","article-title":"Emergence of hyper-epidemic clones of Enterobacterales clinical isolates co-producing KPC and metallo-beta-lactamases during the COVID-19 pandemic","volume":"12","author":"Faccone","year":"2023","journal-title":"Pathogens"},{"key":"B24","doi-asserted-by":"publisher","DOI":"10.1099\/mic.0.001369","article-title":"The distribution of fitness effects of plasmid pOXA-48 in clinical enterobacteria","volume":"169","author":"Fern\u00e1ndez-Calvet","year":"2023","journal-title":"Microbiol. (United Kingdom)"},{"key":"B25","doi-asserted-by":"publisher","first-page":"791","DOI":"10.7326\/0003-4819-137-10-200211190-00007","article-title":"Health care\u2013associated bloodstream infections in adults: a reason to change the accepted definition of community-acquired infections","volume":"137","author":"Friedman","year":"2002","journal-title":"Ann. Intern. Med."},{"key":"B26","doi-asserted-by":"publisher","first-page":"6959","DOI":"10.1038\/s41598-019-43464-4","article-title":"Whole-genome sequencing reveals nosocomial Clostridioides difficile transmission and a previously unsuspected epidemic scenario","volume":"9","author":"Garc\u00eda-Fern\u00e1ndez","year":"2019","journal-title":"Sci. Rep."},{"key":"B27","doi-asserted-by":"publisher","first-page":"D243","DOI":"10.1093\/nar\/gkae1038","article-title":"NCBI RefSeq: reference sequence standards through 25 years of curation and annotation","volume":"53","author":"Goldfarb","year":"2025","journal-title":"Nucleic Acids Res."},{"key":"B28","doi-asserted-by":"publisher","first-page":"W484","DOI":"10.1093\/nar\/gkad326","article-title":"Proksee: In-depth characterization and visualization of bacterial genomes","volume":"51","author":"Grant","year":"2023","journal-title":"Nucleic Acids Res."},{"key":"B29","doi-asserted-by":"publisher","DOI":"10.1186\/s13059-018-1618-7","article-title":"An amplicon-based sequencing framework for accurately measuring intrahost virus diversity using PrimalSeq and iVar","volume":"20","author":"Grubaugh","year":"2019","journal-title":"Genome Biol."},{"key":"B30","doi-asserted-by":"publisher","first-page":"307","DOI":"10.1093\/SYSBIO\/SYQ010","article-title":"New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3.0","volume":"59","author":"Guindon","year":"2010","journal-title":"Syst. Biol."},{"key":"B31","doi-asserted-by":"publisher","first-page":"2460","DOI":"10.1093\/jac\/dkw177","article-title":"Glutathione- S -transferase FosA6 of Klebsiella pneumoniae origin conferring fosfomycin resistance in ESBL-producing Escherichia coli","volume":"71","author":"Guo","year":"2016","journal-title":"J. Antimicrob. Chemother."},{"key":"B32","doi-asserted-by":"publisher","first-page":"1072","DOI":"10.1093\/bioinformatics\/btt086","article-title":"QUAST: quality assessment tool for genome assemblies","volume":"29","author":"Gurevich","year":"2013","journal-title":"Bioinformatics"},{"key":"B33","doi-asserted-by":"publisher","DOI":"10.3389\/fmicb.2019.02509","article-title":"Pathogenicity of clinical OXA-48 isolates and impact of the OXA-48 IncL plasmid on virulence and bacterial fitness","volume":"10","author":"Hamprecht","year":"2019","journal-title":"Front. Microbiol."},{"key":"B34","doi-asserted-by":"publisher","first-page":"1343","DOI":"10.1111\/1751-7915.13709","article-title":"Evaluation of the IR Biotyper for Klebsiella pneumoniae typing and its potentials in hospital hygiene management","volume":"14","author":"Hu","year":"2021","journal-title":"Microb. Biotechnol."},{"key":"B35","doi-asserted-by":"publisher","first-page":"1160","DOI":"10.1086\/656747","article-title":"Quantifying interhospital patient sharing as a mechanism for infectious disease spread","volume":"31","author":"Huang","year":"2010","journal-title":"Infect. Control Hosp. Epidemiol."},{"key":"B36","doi-asserted-by":"publisher","first-page":"294","DOI":"10.1186\/s13059-015-0849-0","article-title":"Circlator: automated circularization of genome assemblies using long sequencing reads","volume":"16","author":"Hunt","year":"2015","journal-title":"Genome Biol."},{"key":"B37","doi-asserted-by":"publisher","first-page":"124","DOI":"10.12688\/wellcomeopenres.14826.1","article-title":"Open-access bacterial population genomics: BIGSdb software, the PubMLST.org website and their applications","volume":"3","author":"Jolley","year":"2018","journal-title":"Wellcome Open Res."},{"key":"B38","doi-asserted-by":"publisher","first-page":"587","DOI":"10.1038\/nmeth.4285","article-title":"ModelFinder: fast model selection for accurate phylogenetic estimates","volume":"14","author":"Kalyaanamoorthy","year":"2017","journal-title":"Nat. Methods 2017 14:6"},{"key":"B39","doi-asserted-by":"publisher","DOI":"10.1126\/sciadv.abq4632","article-title":"Structure-informed microbial population genetics elucidate selective pressures that shape protein evolution","volume":"9","author":"Kiefl","year":"2023","journal-title":"Sci. Adv."},{"key":"B40","doi-asserted-by":"publisher","DOI":"10.3390\/pathogens14070648","article-title":"Antibiotic resistance, virulence genes, and molecular diversity of clinical Klebsiella pneumoniae isolates from patients of district hospital in central Poland","volume":"14","author":"Kot","year":"2025","journal-title":"Pathogens"},{"key":"B41","doi-asserted-by":"publisher","first-page":"4188","DOI":"10.1038\/s41467-021-24448-3","article-title":"A genomic surveillance framework and genotyping tool for Klebsiella pneumoniae and its related species complex","volume":"12","author":"Lam","year":"2021","journal-title":"Nat. Commun."},{"key":"B42","doi-asserted-by":"publisher","DOI":"10.1099\/mgen.0.000196","article-title":"Genetic diversity, mobilisation and spread of the yersiniabactin-encoding mobile element ICEKp in Klebsiella pneumoniae populations","volume":"4","author":"Lam","year":"2018","journal-title":"Microb. Genom."},{"key":"B43","doi-asserted-by":"publisher","first-page":"4572","DOI":"10.1093\/bioinformatics\/btab705","article-title":"New strategies to improve minimap2 alignment accuracy","volume":"37","author":"Li","year":"2021","journal-title":"Bioinformatics"},{"key":"B44","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0277575","article-title":"GAMBIT (Genomic Approximation Method for Bacterial Identification and Tracking): a methodology to rapidly leverage whole genome sequencing of bacterial isolates for clinical identification","volume":"18","author":"Lumpe","year":"2023","journal-title":"PloS One"},{"key":"B45","doi-asserted-by":"publisher","first-page":"3052","DOI":"10.1038\/s41467-022-30637-5","article-title":"Whole genome sequencing reveals hidden transmission of carbapenemase-producing Enterobacterales","volume":"13","author":"Marimuthu","year":"2022","journal-title":"Nat. Commun."},{"key":"B46","doi-asserted-by":"publisher","first-page":"565","DOI":"10.1128\/CMR.00116-14","article-title":"The role of epidemic resistance plasmids and international high-risk clones in the spread of multidrug-resistant Enterobacteriaceae","volume":"28","author":"Mathers","year":"2015","journal-title":"Clin. Microbiol. Rev."},{"key":"B47","doi-asserted-by":"publisher","first-page":"64","DOI":"10.1038\/s44259-025-00127-x","article-title":"Epidemiological genomics of Klebsiella pneumoniae isolates from hospitals across Colombia","volume":"3","author":"Medina","year":"2025","journal-title":"NPJ Antimicrobials Resistance"},{"key":"B48","doi-asserted-by":"publisher","first-page":"1530","DOI":"10.1093\/MOLBEV\/MSAA015","article-title":"IQ-TREE 2: new models and efficient methods for phylogenetic inference in the genomic era","volume":"37","author":"Minh","year":"2020","journal-title":"Mol. Biol. Evol."},{"key":"B49","doi-asserted-by":"publisher","first-page":"1863","DOI":"10.1001\/jamainternmed.2017.5506","article-title":"Using spatial and temporal mapping to identify nosocomial disease transmission of Clostridium difficile","volume":"177","author":"Murray","year":"2017","journal-title":"JAMA Intern. Med."},{"key":"B50","doi-asserted-by":"publisher","DOI":"10.3390\/microorganisms10040700","article-title":"IntegronFinder 2.0: identification and analysis of integrons across bacteria, with a focus on antibiotic resistance in Klebsiella","volume":"10","author":"N\u00e9ron","year":"2022","journal-title":"Microorganisms"},{"key":"B51","doi-asserted-by":"publisher","first-page":"732","DOI":"10.1038\/s41597-024-03571-y","article-title":"Exploring and retrieving sequence and metadata for species across the tree of life with NCBI Datasets","volume":"11","author":"O\u2019Leary","year":"2024","journal-title":"Sci. Data"},{"key":"B52","doi-asserted-by":"publisher","first-page":"132","DOI":"10.1186\/S13059-016-0997-X","article-title":"Mash: fast genome and metagenome distance estimation using MinHash","volume":"17","author":"Ondov","year":"2016","journal-title":"Genome Biol."},{"key":"B53","doi-asserted-by":"publisher","DOI":"10.1128\/AAC.01148-20","article-title":"Emerging antimicrobial-resistant high-risk Klebsiella pneumoniae clones ST307 and ST147","volume":"64","author":"Peirano","year":"2020","journal-title":"Antimicrob. Agents Chemother."},{"key":"B54","doi-asserted-by":"publisher","first-page":"559","DOI":"10.1128\/AAC.05289-11","article-title":"Genetic features of the widespread plasmid coding for the carbapenemase OXA-48","volume":"56","author":"Poirel","year":"2012","journal-title":"Antimicrob. Agents Chemother."},{"key":"B55","doi-asserted-by":"publisher","first-page":"119","DOI":"10.1016\/j.diagmicrobio.2010.12.002","article-title":"Multiplex PCR for detection of acquired carbapenemase genes","volume":"70","author":"Poirel","year":"2011","journal-title":"Diagn. Microbiol. Infect. Dis."},{"key":"B56","article-title":"Vigilancia molecular de Klebsiella pneumoniae, Enterobacter cloacae complex y Escherichia coli productores de carbapene\u00acmasas en Espa\u00f1a. Informe anual RedLabRA 2022","volume-title":"Instituto De Salud Carlos III (ISCIII). Centro Nacional De Microbiolog\u00eda (CNM)","author":"Ca\u00f1ada-Garc\u00eda","year":"2023"},{"key":"B57","doi-asserted-by":"publisher","DOI":"10.1099\/mgen.0.000206","article-title":"MOB-suite: software tools for clustering, reconstruction and typing of plasmids from draft assemblies","volume":"4","author":"Robertson","year":"2018","journal-title":"Microb. Genom."},{"key":"B58","doi-asserted-by":"publisher","DOI":"10.1186\/1471-2180-10-179","article-title":"Role of type 1 and type 3 fimbriae in Klebsiella pneumoniae biofilm formation","volume":"10","author":"Schroll","year":"2010","journal-title":"BMC Microbiol."},{"key":"B59","doi-asserted-by":"publisher","DOI":"10.1099\/mgen.0.000685","article-title":"Bakta: rapid and standardized annotation of bacterial genomes via alignment-free sequence identification","volume":"7","author":"Schwengers","year":"2021","journal-title":"Microb. Genom."},{"key":"B60","doi-asserted-by":"publisher","first-page":"492","DOI":"10.1080\/10635150290069913","article-title":"An approximately unbiased test of phylogenetic tree selection","volume":"51","author":"Shimodaira","year":"2002","journal-title":"Syst. Biol."},{"key":"B61","doi-asserted-by":"publisher","DOI":"10.1099\/mgen.0.000166","article-title":"chewBBACA: A complete suite for gene-by-gene schema creation and strain identification","volume":"4","author":"Silva","year":"2018","journal-title":"Microb. Genom."},{"key":"B62","doi-asserted-by":"publisher","first-page":"318","DOI":"10.1016\/S1473-3099(17)30753-3","article-title":"Discovery, research, and development of new antibiotics: the WHO priority list of antibiotic-resistant bacteria and tuberculosis","volume":"18","author":"Tacconelli","year":"2018","journal-title":"Lancet Infect. Dis."},{"key":"B63","doi-asserted-by":"publisher","first-page":"180","DOI":"10.1186\/S13059-020-02090-4","article-title":"Producing polished prokaryotic pangenomes with the Panaroo pipeline","volume":"21","author":"Tonkin-Hill","year":"2020","journal-title":"Genome Biol."},{"key":"B64","doi-asserted-by":"publisher","first-page":"1498","DOI":"10.1093\/jac\/dkab043","article-title":"Activity of imipenem\/relebactam against a Spanish nationwide collection of carbapenemase-producing Enterobacterales","volume":"76","author":"V\u00e1zquez-Ucha","year":"2021","journal-title":"J. Antimicrob. Chemother."},{"key":"B65","doi-asserted-by":"publisher","DOI":"10.3389\/fmicb.2019.02582","article-title":"Fourier-Transform Infrared (FTIR) Spectroscopy for Typing of Clinical Enterobacter cloacae Complex Isolates","volume":"10","author":"Vogt","year":"2019","journal-title":"Front. Microbiol"},{"key":"B66","doi-asserted-by":"publisher","DOI":"10.1128\/mbio.03158-22","article-title":"Insertion sequences determine plasmid adaptation to new bacterial hosts","volume":"14","author":"Wedel","year":"2023","journal-title":"mBio"},{"key":"B67","doi-asserted-by":"publisher","first-page":"266","DOI":"10.1186\/s13059-021-02483-z","article-title":"Trycycler: consensus long-read assemblies for bacterial genomes","volume":"22","author":"Wick","year":"2021","journal-title":"Genome Biol."},{"key":"B68","doi-asserted-by":"publisher","first-page":"W443","DOI":"10.1093\/nar\/gkad382","article-title":"PHASTEST: Faster than PHASTER, better than PHAST","volume":"51","author":"Wishart","year":"2023","journal-title":"Nucleic Acids Res."},{"key":"B69","doi-asserted-by":"publisher","DOI":"10.1186\/s13059-019-1891-0","article-title":"Improved metagenomic analysis with Kraken 2","volume":"20","author":"Wood","year":"2019","journal-title":"Genome Biol."},{"key":"B70","doi-asserted-by":"publisher","first-page":"249","DOI":"10.1007\/s41664-018-0068-2","article-title":"On splitting training and validation set: A comparative study of cross-validation, bootstrap and systematic sampling for estimating the generalization performance of supervised learning","volume":"2","author":"Xu","year":"2018","journal-title":"J. Anal. Test."},{"key":"B71","doi-asserted-by":"publisher","DOI":"10.3389\/fmicb.2025.1543610","article-title":"Comparative genomics reveals key adaptive mechanisms in pathogen host-niche specialization","volume":"16","author":"Zhang","year":"2025","journal-title":"Front. Microbiol."},{"key":"B72","doi-asserted-by":"publisher","first-page":"1395","DOI":"10.1101\/gr.232397.117","article-title":"GrapeTree: visualization of core genomic relationships among 100,000 bacterial pathogens","volume":"28","author":"Zhou","year":"2018","journal-title":"Genome Res."}],"container-title":["Frontiers in Cellular and Infection Microbiology"],"original-title":[],"link":[{"URL":"https:\/\/www.frontiersin.org\/articles\/10.3389\/fcimb.2026.1872766\/full","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,9,29]],"date-time":"2026-09-29T05:47:38Z","timestamp":1790660858000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.frontiersin.org\/articles\/10.3389\/fcimb.2026.1872766\/full"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,9,29]]},"references-count":72,"alternative-id":["10.3389\/fcimb.2026.1872766"],"URL":"https:\/\/doi.org\/10.3389\/fcimb.2026.1872766","relation":{},"ISSN":["2235-2988"],"issn-type":[{"value":"2235-2988","type":"electronic"}],"subject":[],"published":{"date-parts":[[2026,9,29]]},"article-number":"1872766"}}