{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,10,10]],"date-time":"2025-10-10T01:32:28Z","timestamp":1760059948281,"version":"build-2065373602"},"reference-count":35,"publisher":"MDPI AG","issue":"8","license":[{"start":{"date-parts":[[2025,7,22]],"date-time":"2025-07-22T00:00:00Z","timestamp":1753142400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100000614","name":"FEMS","doi-asserted-by":"publisher","award":["2668"],"award-info":[{"award-number":["2668"]}],"id":[{"id":"10.13039\/501100000614","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Antibiotics"],"abstract":"<jats:p>Background:\u00a0Klebsiella variicola is a Gram-negative, capsulated, nonmotile, facultative anaerobic rod. It is one of the species belonging to the K. pneumoniae complex. The objective of this study was to gain insights into the antimicrobial resistance and virulence of K. variicola strains isolated from clinical samples from oncologic patients. Methods: Strain identification was performed using a mass spectrometry method. Whole genome sequencing was conducted for all analyzed strains. Antimicrobial susceptibility was determined using an automated method. The presence of antimicrobial resistance mechanisms and genes encoding extended-spectrum beta-lactamases (ESBL) was assessed using the double-disc synergy test and genotypic methods. Results: All isolates were identified as K. variicola using mass spectrometry and whole genome sequencing (WGS). All isolates were ESBL-positive, and two of them harbored the blaCTX-M-15 gene. In our study, the blaLEN-17 gene was detected in all strains. Genome sequence analysis of the K. variicola isolates revealed the presence of virulence factor genes, including entAB, fepC, ompA, ykgK, and yagWXYZ. Two different plasmids, IncFIB(K) and IncFII, were identified in all of the analyzed K. variicola strains. The detected virulence factors suggest the ability of the bacteria to survive in the environment and infect host cells. All isolates demonstrated in vitro susceptibility to carbapenems. Conclusions: Further studies are needed to confirm whether multidrug-resistant K. variicola strains represent an important pathogen in infections among oncologic patients.<\/jats:p>","DOI":"10.3390\/antibiotics14080735","type":"journal-article","created":{"date-parts":[[2025,7,22]],"date-time":"2025-07-22T15:00:42Z","timestamp":1753196442000},"page":"735","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["Whole Genome Sequencing of Klebsiella variicola Strains Isolated from Patients with Cancer"],"prefix":"10.3390","volume":"14","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-6380-3968","authenticated-orcid":false,"given":"Alicja","family":"S\u0119kowska","sequence":"first","affiliation":[{"name":"Department of Microbiology, Ludwik Rydygier Collegium Medicum in Bydgoszcz, Nicolaus Copernicus University in Toru\u0144, 85-094 Bydgoszcz, Poland"},{"name":"Department of Clinical Microbiology, Dr. A. Jurasz University Hospital No. 1 in Bydgoszcz, 85-094 Bydgoszcz, Poland"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3581-7761","authenticated-orcid":false,"given":"Andr\u00e9s","family":"Carrazco-Montalvo","sequence":"additional","affiliation":[{"name":"Centro de Referencia Nacional de Gen\u00f3mica, Secuenciaci\u00f3n y Bioinform\u00e1tica, Instituto Nacional de Investigaci\u00f3n en Salud P\u00fablica \u201cLeopoldo Izquieta P\u00e9rez\u201d, Quito 170403, Ecuador"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4789-1675","authenticated-orcid":false,"given":"Yulian","family":"Konechnyi","sequence":"additional","affiliation":[{"name":"Department of Microbiology, Danylo Halytsky Lviv National Medical University, 79010 Lviv, Ukraine"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"1968","published-online":{"date-parts":[[2025,7,22]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","unstructured":"Long, S.W., Linson, S.E., Ojeda Saavedra, M., Cantu, C., Davis, J.J., Brettin, T., and Olsen, R.J. (2017). Whole-Genome Sequencing of Human Clinical Klebsiella pneumoniae Isolates Reveals Misidentification and Misunderstandings of Klebsiella pneumoniae, Klebsiella variicola, and Klebsiella quasipneumoniae. mSphere, 2.","DOI":"10.1128\/mSphereDirect.00290-17"},{"key":"ref_2","doi-asserted-by":"crossref","unstructured":"Garza-Ramos, U., Silva-S\u00e1nchez, J., Mart\u00ednez-Romero, E., Tinoco, P., Pina-Gonzales, M., Barrios, H., Mart\u00ednez-Barnetche, J., G\u00f3mez-Barreto, R.E., and Tellez-Sosa, J. (2015). Development of a Multiplex-PCR Probe System for the Proper Identification of Klebsiella variicola. BMC Microbiol., 15.","DOI":"10.1186\/s12866-015-0396-6"},{"key":"ref_3","doi-asserted-by":"crossref","first-page":"973","DOI":"10.1080\/22221751.2019.1634981","article-title":"Klebsiella variicola: An Emerging Pathogen in Humans","volume":"8","year":"2019","journal-title":"Emerg. Microbes Infect."},{"key":"ref_4","doi-asserted-by":"crossref","unstructured":"Potter, R.F., Lainhart, W., Twentyman, J., Wallace, M.A., Wang, B., Burnham, C.A., Rosen, D.A., and Dantas, G. (2018). Population Structure, Antibiotic Resistance, and Uropathogenicity of Klebsiella variicola. mBio, 9.","DOI":"10.1128\/mBio.02481-18"},{"key":"ref_5","doi-asserted-by":"crossref","unstructured":"Maatallah, M., Vading, M., Kabir, M.H., Bakhrouf, A., Kalin, M., Naucl\u00e9r, P., Brisse, S., and Giske, C.G. (2014). Klebsiella variicola Is a Frequent Cause of Bloodstream Infection in the Stockholm Area, and Associated with Higher Mortality Compared to K. pneumoniae. PLoS ONE, 9.","DOI":"10.1371\/journal.pone.0113539"},{"key":"ref_6","doi-asserted-by":"crossref","first-page":"2793","DOI":"10.1128\/JCM.00841-15","article-title":"An Investigation into Laboratory Misidentification of a Bloodstream Klebsiella variicola Infection","volume":"53","author":"Berry","year":"2015","journal-title":"J. Clin. Microbiol."},{"key":"ref_7","doi-asserted-by":"crossref","first-page":"3001","DOI":"10.1093\/jac\/dky301","article-title":"Occurrence of Colistin-Resistant Hypervirulent Klebsiella variicola","volume":"73","author":"Lu","year":"2018","journal-title":"J. Antimicrob. Chemother."},{"key":"ref_8","doi-asserted-by":"crossref","unstructured":"Imai, K., Ishibashi, N., Kodana, M., Tarumoto, N., Sakai, J., Kawamura, T., Takeuchi, S., Taji, Y., Ebihara, Y., and Ikebuchi, K. (2022). Correction to: Clinical Characteristics in Blood Stream Infections Caused by Klebsiella pneumoniae, Klebsiella variicola, and Klebsiella quasipneumoniae: A Comparative Study, Japan, 2014\u20132017. BMC Infect. Dis., 22.","DOI":"10.1186\/s12879-022-07384-5"},{"key":"ref_9","doi-asserted-by":"crossref","first-page":"e238896","DOI":"10.1136\/bcr-2020-238896","article-title":"Severe Sepsis Caused by a Gas-Forming Clostridium Perfringens and Klebsiella variicola Liver Abscess Following Total Pancreatectomy","volume":"13","author":"Dahl","year":"2020","journal-title":"BMJ Case Rep."},{"key":"ref_10","doi-asserted-by":"crossref","first-page":"4503","DOI":"10.2147\/IDR.S330977","article-title":"Co-Occurrence of Klebsiella variicola and Klebsiella pneumoniae Both Carrying Bla KPC from a Respiratory Intensive Care Unit Patient","volume":"14","author":"Huang","year":"2021","journal-title":"Infect. Drug Resist."},{"key":"ref_11","doi-asserted-by":"crossref","first-page":"665","DOI":"10.1093\/jac\/dkab463","article-title":"A Nationwide Genomic Study of Clinical Klebsiella pneumoniae in Norway 2001-15: Introduction and Spread of ESBLs Facilitated by Clonal Groups CG15 and CG307","volume":"77","author":"Fostervold","year":"2022","journal-title":"J. Antimicrob. Chemother."},{"key":"ref_12","doi-asserted-by":"crossref","unstructured":"Watanabe, N., Watari, T., Otsuka, Y., Yamagata, K., and Fujioka, M. (2022). Clinical Characteristics and Antimicrobial Susceptibility of Klebsiella pneumoniae, Klebsiella variicola and Klebsiella quasipneumoniae Isolated from Human Urine in Japan. J. Med. Microbiol., 71.","DOI":"10.1099\/jmm.0.001546"},{"key":"ref_13","doi-asserted-by":"crossref","unstructured":"Harada, S., Aoki, K., Yamamoto, S., Ishii, Y., Sekiya, N., Kurai, H., Furukawa, K., Doi, A., Tochitani, K., and Kubo, K. (2019). Clinical and Molecular Characteristics of Klebsiella pneumoniae Isolates Causing Bloodstream Infections in Japan: Occurrence of Hypervirulent Infections in Health Care. J. Clin. Microbiol., 57.","DOI":"10.1128\/JCM.01206-19"},{"key":"ref_14","doi-asserted-by":"crossref","first-page":"2462","DOI":"10.1093\/jac\/dkad255","article-title":"Carbapenem Resistance in Enterobacterales Bloodstream Infections among Children with Cancer or Post-Haematopoietic Stem Cell Transplant: A Retrospective Cohort Study","volume":"78","author":"Cantor","year":"2023","journal-title":"J. Antimicrob. Chemother."},{"key":"ref_15","doi-asserted-by":"crossref","unstructured":"Madney, Y., Aboubakr, S., Khedr, R., Hafez, H., Ahmed, N., Elsheshtawy, K., Elanany, M., Salahelden, A., Shalaby, L., and Galal Behairy, O. (2023). Carbapenem-Resistant Enterobacteriaceae (CRE) among Children with Cancer: Predictors of Mortality and Treatment Outcome. Antibiotics, 12.","DOI":"10.3390\/antibiotics12020405"},{"key":"ref_16","doi-asserted-by":"crossref","first-page":"1225","DOI":"10.1093\/cid\/ciy778","article-title":"Outbreak of Hypervirulent Multidrug-Resistant Klebsiella variicola Causing High Mortality in Neonates in Bangladesh","volume":"68","author":"Farzana","year":"2019","journal-title":"Clin. Infect. Dis."},{"key":"ref_17","doi-asserted-by":"crossref","first-page":"11","DOI":"10.1016\/j.jgar.2023.08.009","article-title":"Prevalence, Clonal Diversity, and Antimicrobial Resistance of Hypervirulent Klebsiella pneumoniae and Klebsiella variicola Clinical Isolates in Northern Japan","volume":"35","author":"Matsuda","year":"2023","journal-title":"J. Glob. Antimicrob. Resist."},{"key":"ref_18","doi-asserted-by":"crossref","first-page":"396","DOI":"10.1099\/jmm.0.001143","article-title":"Klebsiella variicola Causing Nosocomial Transmission among Neonates\u2014An Emerging Pathogen?","volume":"69","author":"Piepenbrock","year":"2020","journal-title":"J. Med. Microbiol."},{"key":"ref_19","doi-asserted-by":"crossref","unstructured":"de Campos, T.A., de Almeida, F.M., de Almeida, A.P.C., Nakamura-Silva, R., Oliveira-Silva, M., de Sousa, I.F.A., Cerdeira, L., Lincopan, N., Pappas, G.J., and Pitondo-Silva, A. (2021). Multidrug-Resistant (MDR) Klebsiella variicola Strains Isolated in a Brazilian Hospital Belong to New Clones. Front. Microbiol., 12.","DOI":"10.3389\/fmicb.2021.604031"},{"key":"ref_20","doi-asserted-by":"crossref","unstructured":"Barrios-Camacho, H., Aguilar-Vera, A., Beltran-Rojel, M., Aguilar-Vera, E., Duran-Bedolla, J., Rodriguez-Medina, N., Lozano-Aguirre, L., Perez-Carrascal, O.M., Rojas, J., and Garza-Ramos, U. (2019). Molecular Epidemiology of Klebsiella variicola Obtained from Different Sources. Sci. Rep., 9.","DOI":"10.1038\/s41598-019-46998-9"},{"key":"ref_21","doi-asserted-by":"crossref","first-page":"27","DOI":"10.1078\/0723-2020-00261","article-title":"Klebsiella variicola, a Novel Species with Clinical and Plant-Associated Isolates","volume":"27","author":"Rosenblueth","year":"2004","journal-title":"Syst. Appl. Microbiol."},{"key":"ref_22","doi-asserted-by":"crossref","first-page":"801","DOI":"10.1099\/jmm.0.051334-0","article-title":"Fatal Sepsis Caused by an Unusual Klebsiella Species That Was Misidentified by an Automated Identification System","volume":"62","author":"Seki","year":"2013","journal-title":"J. Med. Microbiol."},{"key":"ref_23","doi-asserted-by":"crossref","unstructured":"Fontana, L., Bonura, E., Lyski, Z., and Messer, W. (2019). Closing the Brief Case: Klebsiella variicola-Identifying the Misidentified. J. Clin. Microbiol., 57.","DOI":"10.1128\/JCM.00825-18"},{"key":"ref_24","doi-asserted-by":"crossref","unstructured":"Garza-Ramos, U., Silva-Sanchez, J., Barrios, H., Rodriguez-Medina, N., Mart\u00ednez-Barnetche, J., and Andrade, V. (2015). Draft Genome Sequence of the First Hypermucoviscous Klebsiella variicola Clinical Isolate. Genome Announc., 3.","DOI":"10.1128\/genomeA.01352-14"},{"key":"ref_25","doi-asserted-by":"crossref","first-page":"35","DOI":"10.1080\/21505594.2020.1859274","article-title":"Hypervirulent and Hypermucoviscous Extended-Spectrum \u03b2-Lactamase-Producing Klebsiella pneumoniae and Klebsiella variicola in Chile","volume":"12","author":"Caro","year":"2021","journal-title":"Virulence"},{"key":"ref_26","doi-asserted-by":"crossref","unstructured":"Muraya, A., Kyany\u2019a, C., Kiyaga, S., Smith, H.J., Kibet, C., Martin, M.J., Kimani, J., and Musila, L. (2022). Antimicrobial Resistance and Virulence Characteristics of Klebsiella pneumoniae Isolates in Kenya by Whole-Genome Sequencing. Pathogens, 11.","DOI":"10.1101\/2022.02.01.478614"},{"key":"ref_27","doi-asserted-by":"crossref","unstructured":"Wareth, G., Linde, J., Hammer, P., Pletz, M.W., Neubauer, H., and Sprague, L.D. (2022). WGS-Based Phenotyping and Molecular Characterization of the Resistome, Virulome and Plasmid Replicons in Klebsiella pneumoniae Isolates from Powdered Milk Produced in Germany. Microorganisms, 10.","DOI":"10.3390\/microorganisms10030564"},{"key":"ref_28","doi-asserted-by":"crossref","first-page":"e211","DOI":"10.1016\/S2666-5247(23)00342-7","article-title":"fosA7: A Silent Fosfomycin Resistance Gene in Salmonella?","volume":"5","author":"Wang","year":"2024","journal-title":"Lancet Microbe"},{"key":"ref_29","doi-asserted-by":"crossref","unstructured":"Saxenborn, P., Baxter, J., Tilevik, A., Fagerlind, M., Dyrkell, F., Pernestig, A.-K., Enroth, H., and Tilevik, D. (2021). Genotypic Characterization of Clinical Klebsiella Spp. Isolates Collected from Patients with Suspected Community-Onset Sepsis, Sweden. Front. Microbiol., 12.","DOI":"10.3389\/fmicb.2021.640408"},{"key":"ref_30","doi-asserted-by":"crossref","unstructured":"Cao, X., Xu, X., Zhang, Z., Shen, H., Chen, J., and Zhang, K. (2014). Molecular Characterization of Clinical Multidrug-Resistant Klebsiella pneumoniae Isolates. Ann. Clin. Microbiol. Antimicrob., 13.","DOI":"10.1186\/1476-0711-13-16"},{"key":"ref_31","doi-asserted-by":"crossref","unstructured":"Long, S.W., Linson, S.E., Ojeda Saavedra, M., Cantu, C., Davis, J.J., Brettin, T., and Olsen, R.J. (2017). Whole-Genome Sequencing of a Human Clinical Isolate of the Novel Species Klebsiella quasivariicola Sp. Nov. Genome Announc., 5.","DOI":"10.1128\/genomeA.01057-17"},{"key":"ref_32","doi-asserted-by":"crossref","unstructured":"Folgori, L., Di Carlo, D., Comandatore, F., Piazza, A., Witney, A.A., Bresesti, I., Hsia, Y., Laing, K., Monahan, I., and Bielicki, J. (2021). Antibiotic Susceptibility, Virulome, and Clinical Outcomes in European Infants with Bloodstream Infections Caused by Enterobacterales. Antibiotics, 10.","DOI":"10.3390\/antibiotics10060706"},{"key":"ref_33","unstructured":"(2023, December 07). Eucast. Available online: https:\/\/www.eucast.org\/."},{"key":"ref_34","doi-asserted-by":"crossref","unstructured":"Garza-Ramos, U., Rodriguez-Medina, N., Lozano-Aguirre, L., Silva-Sanchez, J., Sanchez-Arias, M., Rodriguez-Olguin, J., and Mart\u00ednez-Romero, E. (2021). Klebsiella variicola Reference Strain F2R9 (ATCC BAA-830) Genome Sequence. Microbiol. Resour. Announc., 10.","DOI":"10.1128\/MRA.00329-21"},{"key":"ref_35","doi-asserted-by":"crossref","first-page":"3691","DOI":"10.1093\/bioinformatics\/btv421","article-title":"Roary: Rapid Large-Scale Prokaryote Pan Genome Analysis","volume":"31","author":"Page","year":"2015","journal-title":"Bioinformatics"}],"container-title":["Antibiotics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.mdpi.com\/2079-6382\/14\/8\/735\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,10,9]],"date-time":"2025-10-09T18:14:10Z","timestamp":1760033650000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.mdpi.com\/2079-6382\/14\/8\/735"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2025,7,22]]},"references-count":35,"journal-issue":{"issue":"8","published-online":{"date-parts":[[2025,8]]}},"alternative-id":["antibiotics14080735"],"URL":"https:\/\/doi.org\/10.3390\/antibiotics14080735","relation":{},"ISSN":["2079-6382"],"issn-type":[{"type":"electronic","value":"2079-6382"}],"subject":[],"published":{"date-parts":[[2025,7,22]]}}}