{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,6,10]],"date-time":"2026-06-10T15:09:15Z","timestamp":1781104155179,"version":"3.54.1"},"reference-count":64,"publisher":"Springer Science and Business Media LLC","issue":"1","license":[{"start":{"date-parts":[[2026,6,10]],"date-time":"2026-06-10T00:00:00Z","timestamp":1781049600000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0"},{"start":{"date-parts":[[2026,6,10]],"date-time":"2026-06-10T00:00:00Z","timestamp":1781049600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0"}],"funder":[{"DOI":"10.13039\/100014013","name":"UK Research and Innovation","doi-asserted-by":"publisher","award":["BBSRC BB\/X018156\/1; MRC MR\/X005895\/1; EPSRC EP\/Y018842\/1"],"award-info":[{"award-number":["BBSRC BB\/X018156\/1; MRC MR\/X005895\/1; EPSRC EP\/Y018842\/1"]}],"id":[{"id":"10.13039\/100014013","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100010221","name":"Higher Education Commision, Pakistan","doi-asserted-by":"publisher","award":["HEC\/NRPU\/Project No 99436"],"award-info":[{"award-number":["HEC\/NRPU\/Project No 99436"]}],"id":[{"id":"10.13039\/501100010221","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["Braz J Microbiol"],"published-print":{"date-parts":[[2026,12]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>\n                    <jats:italic>Klebsiella quasipneumoniae<\/jats:italic>\n                    is a Gram-negative, non-motile, capsulated, facultative anaerobic rod within the\n                    <jats:italic>K. pneumoniae<\/jats:italic>\n                    species complex (KpSC) and is increasingly recognized as an opportunistic pathogen associated with bloodstream infections, urinary tract infections (UTIs), and other clinically significant conditions. Because it shares many phenotypic characteristics with\n                    <jats:italic>K. pneumoniae<\/jats:italic>\n                    , accurate diagnosis remains challenging in routine clinical settings, particularly in low-resource laboratories lacking access to molecular identification tools. In this study, we characterized the antimicrobial resistance (AMR) profile of a\n                    <jats:italic>K. quasipneumoniae subsp. quasipneumoniae<\/jats:italic>\n                    isolate obtained from a UTI case in Peshawar, Pakistan. The isolate exhibited a multidrug resistant (MDR) phenotype, with resistance to \u03b2-lactams, carbapenems, fluoroquinolones, and colistin (MIC 4\u00a0\u00b5g\/mL), while remaining susceptible to aminoglycosides (amikacin and gentamicin) and tigecycline (MIC 2\u00a0\u00b5g\/mL). Whole-genome sequencing (WGS) identified chromosomally encoded AMR determinants, including\n                    <jats:italic>bla<\/jats:italic>\n                    OKP-A-8,\n                    <jats:italic>oqxAB<\/jats:italic>\n                    , and fosA6, with no identifiable plasmid replicons detected. Multiple nonsynonymous mutations were observed in\n                    <jats:italic>mgrB<\/jats:italic>\n                    ,\n                    <jats:italic>pmrA\/B<\/jats:italic>\n                    ,\n                    <jats:italic>phoP\/Q<\/jats:italic>\n                    ,\n                    <jats:italic>lpxM<\/jats:italic>\n                    ,\n                    <jats:italic>ompK35\/36<\/jats:italic>\n                    , and\n                    <jats:italic>gyrA\/parC<\/jats:italic>\n                    , which have been previously associated with resistance phenotypes; however, their functional contribution in this isolate was inferred from genomic data and not experimentally validated. Virulence-associated loci such as\n                    <jats:italic>fim<\/jats:italic>\n                    ,\n                    <jats:italic>ecp<\/jats:italic>\n                    ,\n                    <jats:italic>entB<\/jats:italic>\n                    , and\n                    <jats:italic>fepC<\/jats:italic>\n                    were present, consistent with a classical (non-hypervirulent) phenotype. Phylogenomic analysis positioned the isolate (Kq1223) on a distinct branch relative to publicly available genomes, but given that this study is based on a single isolate, no definitive conclusions regarding regional lineage or evolutionary patterns can be established. The allelic profile identified by multilocus sequence typing (MLST) has not been previously reported and may represent an unassigned sequence type pending formal database validation. The presence of chromosomally mediated MDR, including colistin resistance, highlights potential therapeutic challenges and underscores the importance of accurate species identification and expanded genomic surveillance of\n                    <jats:italic>Klebsiella<\/jats:italic>\n                    species in clinical microbiology, particularly in resource limited settings.\n                  <\/jats:p>","DOI":"10.1007\/s42770-026-01982-0","type":"journal-article","created":{"date-parts":[[2026,6,10]],"date-time":"2026-06-10T12:21:30Z","timestamp":1781094090000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["Whole-genome characterization of a colistin-resistant Klebsiella quasipneumoniae subsp. quasipneumoniae isolate from a urinary tract infection in Peshawar, Pakistan"],"prefix":"10.1007","volume":"57","author":[{"given":"Aiman","family":"Waheed","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sumera Afzal","family":"Khan","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sajjad","family":"Ahmad","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Taj Ali","family":"Khan","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Taane G.","family":"Clark","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2026,6,10]]},"reference":[{"key":"1982_CR1","doi-asserted-by":"crossref","unstructured":"Holt KE, Wertheim H, Zadoks RN, Baker S, Whitehouse CA, Dance D et al (2015) Genomic analysis of diversity, population structure, virulence, and antimicrobial resistance in Klebsiella pneumoniae, an urgent threat to public health. Proceedings of the National Academy of Sciences. ;112(27):E3574-E81","DOI":"10.1073\/pnas.1501049112"},{"key":"1982_CR2","doi-asserted-by":"crossref","unstructured":"Asokan S, Jacob T, Jacob J, AlSosowaa AA, Cherian T, Peijnenburg WJ et al (2025) Klebsiella pneumoniae: A growing threat in the era of antimicrobial resistance. Microbe. :100333","DOI":"10.1016\/j.microb.2025.100333"},{"key":"1982_CR3","unstructured":"Castillo LM, Demissie L (2024) Predictors and clinical characteristics of third-generation cephalosporin resistantklebsiella pneumoniae bloodstream infections in pediatric patients admitted to hiwot fana comprehensive specialized hospitalin 2021: a nested case-control study. Haramaya University Harar"},{"issue":"2","key":"1982_CR4","doi-asserted-by":"publisher","first-page":"107","DOI":"10.4161\/viru.22718","volume":"4","author":"AS Shon","year":"2013","unstructured":"Shon AS, Bajwa RP, Russo TA (2013) Hypervirulent (hypermucoviscous) Klebsiella pneumoniae: a new and dangerous breed. Virulence 4(2):107\u2013118","journal-title":"Virulence"},{"issue":"12","key":"1982_CR5","doi-asserted-by":"publisher","first-page":"2548","DOI":"10.3390\/microorganisms12122548","volume":"12","author":"T-A Chen","year":"2024","unstructured":"Chen T-A, Chuang Y-T, Lin C-H (2024) A decade-long review of the virulence, resistance, and epidemiological risks of Klebsiella pneumoniae in ICUs. Microorganisms 12(12):2548","journal-title":"Microorganisms"},{"issue":"1","key":"1982_CR6","doi-asserted-by":"publisher","first-page":"318","DOI":"10.1186\/s12864-025-11509-w","volume":"26","author":"W Jiang","year":"2025","unstructured":"Jiang W, Chen Y, Lai M, Ji Y, Lin S, Shao J et al (2025) Comprehensive genomic epidemiology and antimicrobial resistance profiles of clinical Klebsiella pneumoniae species complex isolates from a tertiary hospital in Wenzhou, China (2019\u20132021). BMC Genomics 26(1):318","journal-title":"BMC Genomics"},{"key":"1982_CR7","doi-asserted-by":"publisher","unstructured":"Long SW, Linson SE, Ojeda Saavedra M, Cantu C, Davis JJ, Brettin T et al (2017) Whole-genome sequencing of human clinical Klebsiella pneumoniae isolates reveals misidentification and misunderstandings of Klebsiella pneumoniae, Klebsiella variicola, and Klebsiella quasipneumoniae. Msphere 2(4). https:\/\/doi.org\/10.1128\/mspheredirect.00290-17","DOI":"10.1128\/mspheredirect.00290-17"},{"key":"1982_CR8","doi-asserted-by":"publisher","first-page":"107040","DOI":"10.1016\/j.micpath.2024.107040","volume":"197","author":"OT Akinola","year":"2024","unstructured":"Akinola OT, Dahunsi SO (2024) Whole genome sequencing reveals antibiotic resistance pattern and virulence factors in Klebsiella quasipneumoniae subsp. Similipneumoniae from Hospital wastewater in South-West, Nigeria. Microb Pathog 197:107040","journal-title":"Microb Pathog"},{"issue":"1","key":"1982_CR9","doi-asserted-by":"publisher","first-page":"112","DOI":"10.3934\/microbiol.2023008","volume":"9","author":"S Kumar","year":"2023","unstructured":"Kumar S, Anwer R, Azzi A (2023) Molecular typing methods & resistance mechanisms of MDR Klebsiella pneumoniae. AIMS Microbiol 9(1):112","journal-title":"AIMS Microbiol"},{"key":"1982_CR10","doi-asserted-by":"publisher","unstructured":"Dinkelacker AG, Vogt S, Oberhettinger P, Mauder N, Rau J, Kostrzewa M et al (2018) Typing and species identification of clinical Klebsiella isolates by Fourier transform infrared spectroscopy and matrix-assisted laser desorption ionization\u2013time of flight mass spectrometry. J Clin Microbiol 56(11). https:\/\/doi.org\/10.1128\/jcm.00843-18","DOI":"10.1128\/jcm.00843-18"},{"issue":"Pt9","key":"1982_CR11","doi-asserted-by":"publisher","first-page":"3146","DOI":"10.1099\/ijs.0.062737-0","volume":"64","author":"S Brisse","year":"2014","unstructured":"Brisse S, Passet V, Grimont PA (2014) Description of Klebsiella quasipneumoniae sp. nov., isolated from human infections, with two subspecies, Klebsiella quasipneumoniae subsp. quasipneumoniae subsp. nov. and Klebsiella quasipneumoniae subsp. similipneumoniae subsp. nov., and demonstration that Klebsiella singaporensis is a junior heterotypic synonym of Klebsiella variicola. Int J Syst Evol MicroBiol 64(Pt9):3146\u20133152","journal-title":"Int J Syst Evol MicroBiol"},{"key":"1982_CR12","doi-asserted-by":"publisher","first-page":"425","DOI":"10.1186\/s12879-022-07384-5","volume":"22","author":"K Imai","year":"2022","unstructured":"Imai K, Ishibashi N, Kodana M, Tarumoto N, Sakai J, Kawamura T et al (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 22:425","journal-title":"BMC Infect Dis"},{"key":"1982_CR13","doi-asserted-by":"publisher","unstructured":"Yuliandari P, Pramono AK, Panjaitan NSD, Pasiana AD, Tyastuti D, Furqoni AH et al (2025) Antimicrobial resistance and virulence factors of klebsiella quasipneumoniae, the Novel Sequence Types (ST) 7979 and 7980 from Indonesia. Microb Pathog 107857. https:\/\/doi.org\/10.1016\/j.micpath.2025.107857","DOI":"10.1016\/j.micpath.2025.107857"},{"key":"1982_CR14","doi-asserted-by":"publisher","first-page":"640408","DOI":"10.3389\/fmicb.2021.640408","volume":"12","author":"P Saxenborn","year":"2021","unstructured":"Saxenborn P, Baxter J, Tilevik A, Fagerlind M, Dyrkell F, Pernestig A-K et al (2021) Genotypic characterization of clinical Klebsiella spp. isolates collected from patients with suspected community-onset sepsis. Swed Front Microbiol 12:640408","journal-title":"Swed Front Microbiol"},{"key":"1982_CR15","doi-asserted-by":"publisher","first-page":"4","DOI":"10.3389\/fcimb.2018.00004","volume":"8","author":"RM Martin","year":"2018","unstructured":"Martin RM, Bachman MA (2018) Colonization, infection, and the accessory genome of Klebsiella pneumoniae. Front Cell Infect Microbiol 8:4","journal-title":"Front Cell Infect Microbiol"},{"issue":"3","key":"1982_CR16","doi-asserted-by":"publisher","first-page":"529","DOI":"10.3201\/eid2203.151466","volume":"22","author":"S Breurec","year":"2016","unstructured":"Breurec S, Melot B, Hoen B, Passet V, Schepers K, Bastian S et al (2016) Liver abscess caused by infection with community-acquired Klebsiella quasipneumoniae subsp. quasipneumoniae. Emerg Infect Dis 22(3):529","journal-title":"Emerg Infect Dis"},{"issue":"9","key":"1982_CR17","doi-asserted-by":"publisher","first-page":"1354","DOI":"10.1038\/s41559-017-0243-2","volume":"1","author":"W Loftie-Eaton","year":"2017","unstructured":"Loftie-Eaton W, Bashford K, Quinn H, Dong K, Millstein J, Hunter S et al (2017) Compensatory mutations improve general permissiveness to antibiotic resistance plasmids. Nat Ecol Evol 1(9):1354\u20131363","journal-title":"Nat Ecol Evol"},{"issue":"4","key":"1982_CR18","doi-asserted-by":"publisher","first-page":"885","DOI":"10.1093\/molbev\/msv339","volume":"33","author":"W Loftie-Eaton","year":"2016","unstructured":"Loftie-Eaton W, Yano H, Burleigh S, Simmons RS, Hughes JM, Rogers LM et al (2016) Evolutionary paths that expand plasmid host-range: implications for spread of antibiotic resistance. Mol Biol Evol 33(4):885\u2013897","journal-title":"Mol Biol Evol"},{"issue":"1","key":"1982_CR19","doi-asserted-by":"publisher","first-page":"2392","DOI":"10.1038\/s41598-019-38943-7","volume":"9","author":"E Heinz","year":"2019","unstructured":"Heinz E, Ejaz H, Bartholdson Scott J, Wang N, Gujaran S, Pickard D et al (2019) Resistance mechanisms and population structure of highly drug resistant Klebsiella in Pakistan during the introduction of the carbapenemase NDM-1. Sci Rep 9(1):2392","journal-title":"Sci Rep"},{"key":"1982_CR20","doi-asserted-by":"publisher","first-page":"1507274","DOI":"10.3389\/fmicb.2024.1507274","volume":"15","author":"E Elashkar","year":"2025","unstructured":"Elashkar E, Alfaraj R, El-Borady OM, Amer MM, Algammal AM, El-Demerdash AS (2025) Novel silver nanoparticle-based biomaterials for combating Klebsiella pneumoniae biofilms. Front Microbiol 15:1507274","journal-title":"Front Microbiol"},{"key":"1982_CR21","doi-asserted-by":"crossref","unstructured":"Algammal A, Hetta HF, Mabrok M, Behzadi P (2023) Emerging multidrug-resistant bacterial pathogens superbugs: A rising public health threat. Frontiers Media SA, p 1135614","DOI":"10.3389\/fmicb.2023.1135614"},{"issue":"1","key":"1982_CR22","doi-asserted-by":"publisher","first-page":"114","DOI":"10.1186\/s12920-025-02181-w","volume":"18","author":"MH Rahman","year":"2025","unstructured":"Rahman MH, Akther S, Ahmed S, Shahadat MN, Munsi MN, Siddique AB (2025) Epidemiological factors associated with the prevalence of mobile genetic elements, and antimicrobial resistance patterns in Klebsiella pneumoniae of farm environments in Bangladesh. BMC Med Genom 18(1):114","journal-title":"BMC Med Genom"},{"key":"1982_CR23","doi-asserted-by":"publisher","first-page":"107317","DOI":"10.1016\/j.micpath.2025.107317","volume":"201","author":"SMJ Mousavi","year":"2025","unstructured":"Mousavi SMJ, Hosseinpour M, Kodori M, Rafiei F, Mahmoudi M, Shahraki H et al (2025) Colistin antibacterial activity, clinical effectiveness, and mechanisms of intrinsic and acquired resistance. Microb Pathog 201:107317","journal-title":"Microb Pathog"},{"issue":"14","key":"1982_CR24","doi-asserted-by":"publisher","first-page":"2950","DOI":"10.3390\/molecules30142950","volume":"30","author":"MA Vlad","year":"2025","unstructured":"Vlad MA, Dan M, Catana AN, Dumitriu S, Tuchilus CG (2025) Trends in Colistin Resistance and Multidrug-Resistant Phenotypes Among Gram-Negative Bacilli: A Retrospective Analysis. Molecules 30(14):2950","journal-title":"Molecules"},{"key":"1982_CR25","doi-asserted-by":"publisher","first-page":"267","DOI":"10.1016\/j.jgar.2024.01.005","volume":"36","author":"Y-t Li","year":"2024","unstructured":"Li Y-t, Xiao Y-h, Liu Y, Hu N, Wu C, Huang X et al (2024) Characterisation of highly virulent and colistin-resistant ST367-KL1 Klebsiella quasipneumoniae subsp. similipneumoniae Strain. J Global Antimicrob Resist 36:267\u2013275","journal-title":"J Global Antimicrob Resist"},{"key":"1982_CR26","doi-asserted-by":"publisher","first-page":"99","DOI":"10.1016\/j.jare.2024.10.013","volume":"74","author":"M Shafiq","year":"2025","unstructured":"Shafiq M, Okoye CO, Nazar M, Khattak WA, Algammal AM (2025) Ecological consequences of antimicrobial residues and bioactive chemicals on antimicrobial resistance in agroecosystems. J Adv Res 74:99\u2013120","journal-title":"J Adv Res"},{"key":"1982_CR27","doi-asserted-by":"publisher","first-page":"1031688","DOI":"10.3389\/fmicb.2022.1031688","volume":"13","author":"M Shafiq","year":"2022","unstructured":"Shafiq M, Zeng M, Permana B, Bilal H, Huang J, Yao F et al (2022) Coexistence of bla NDM\u20135 and tet (X4) in international high-risk Escherichia coli clone ST648 of human origin in China. Front Microbiol 13:1031688","journal-title":"Front Microbiol"},{"issue":"6","key":"1982_CR28","doi-asserted-by":"publisher","first-page":"760","DOI":"10.1089\/mdr.2019.0387","volume":"27","author":"L Hadjadj","year":"2021","unstructured":"Hadjadj L, Syed MA, Abbasi SA, Rolain J-M, Jamil B (2021) Diversity of carbapenem resistance mechanisms in clinical gram-negative bacteria in Pakistan. Microb Drug Resist 27(6):760\u2013767","journal-title":"Microb Drug Resist"},{"key":"1982_CR29","doi-asserted-by":"publisher","unstructured":"Gondal AJ, Saleem S, Jahan S, Choudhry N, Yasmin N (2020) Novel carbapenem-resistant klebsiella pneumoniae ST147 coharboring bla NDM-1, bla OXA-48 and extended-spectrum \u03b2-lactamases from Pakistan. Infect drug Resist 2105\u20132115 https:\/\/doi.org\/10.2147\/IDR.S251532","DOI":"10.2147\/IDR.S251532"},{"issue":"1","key":"1982_CR30","doi-asserted-by":"publisher","first-page":"79","DOI":"10.3390\/pathogens14010079","volume":"14","author":"KTA Azra","year":"2025","unstructured":"Azra KTA, Ul Haq I, Hinthong W, Campino S, Gohar A et al (2025) Antibiotic Susceptibility Patterns and Virulence Profiles of Classical and Hypervirulent Klebsiella pneumoniae Strains Isolated from Clinical Samples in Khyber Pakhtunkhwa, Pakistan. Pathogens 14(1):79","journal-title":"Pathogens"},{"issue":"8","key":"1982_CR31","doi-asserted-by":"publisher","first-page":"2474","DOI":"10.1128\/JCM.00089-07","volume":"45","author":"A Bolmstr\u00f6m","year":"2007","unstructured":"Bolmstr\u00f6m A, Karlsson A, Engelhardt A, Ho P, Petersen PJ, Bradford PA et al (2007) Validation and reproducibility assessment of tigecycline MIC determinations by Etest. J Clin Microbiol 45(8):2474\u20132479","journal-title":"J Clin Microbiol"},{"issue":"3","key":"1982_CR32","doi-asserted-by":"publisher","first-page":"268","DOI":"10.1111\/j.1469-0691.2011.03570.x","volume":"18","author":"A-P Magiorakos","year":"2012","unstructured":"Magiorakos A-P, Srinivasan A, Carey RB, Carmeli Y, Falagas M, Giske C et al (2012) Multidrug-resistant, extensively drug-resistant and pandrug-resistant bacteria: an international expert proposal for interim standard definitions for acquired resistance. Clin Microbiol Infect 18(3):268\u2013281","journal-title":"Clin Microbiol Infect"},{"issue":"3","key":"1982_CR33","doi-asserted-by":"publisher","first-page":"e0265884","DOI":"10.1371\/journal.pone.0265884","volume":"17","author":"S Enany","year":"2022","unstructured":"Enany S, Zakeer S, Diab AA, Bakry U, Sayed AA (2022) Whole genome sequencing of Klebsiella pneumoniae clinical isolates sequence type 627 isolated from Egyptian patients. PLoS ONE 17(3):e0265884","journal-title":"PLoS ONE"},{"key":"1982_CR34","doi-asserted-by":"publisher","first-page":"e16161","DOI":"10.7717\/peerj.16161","volume":"11","author":"L-Y Zhang","year":"2023","unstructured":"Zhang L-Y, Tian B, Huang Y-H, Gu B, Ju P, Luo Y et al (2023) Classification and prediction of Klebsiella pneumoniae strains with different MLST allelic profiles via SERS spectral analysis. PeerJ 11:e16161","journal-title":"PeerJ"},{"issue":"1","key":"1982_CR35","doi-asserted-by":"publisher","first-page":"783","DOI":"10.1186\/s12864-025-11793-6","volume":"26","author":"C Thomas","year":"2025","unstructured":"Thomas C, Brangsch H, Galeone V, H\u00f6lzer M, Marz M, Linde J (2025) Accurately assembling nanopore sequencing data of highly pathogenic bacteria. BMC Genomics 26(1):783","journal-title":"BMC Genomics"},{"issue":"4","key":"1982_CR36","doi-asserted-by":"publisher","first-page":"465","DOI":"10.1007\/s42994-024-00178-0","volume":"5","author":"Y Liu","year":"2024","unstructured":"Liu Y, Ghaffari MH, Ma T, Tu Y (2024) Impact of database choice and confidence score on the performance of taxonomic classification using Kraken2. aBIOTECH 5(4):465\u2013475","journal-title":"aBIOTECH"},{"issue":"1","key":"1982_CR37","doi-asserted-by":"publisher","first-page":"5114","DOI":"10.1038\/s41467-018-07641-9","volume":"9","author":"C Jain","year":"2018","unstructured":"Jain C, Rodriguez-R LM, Phillippy AM, Konstantinidis KT, Aluru S (2018) High throughput ANI analysis of 90K prokaryotic genomes reveals clear species boundaries. Nat Commun 9(1):5114","journal-title":"Nat Commun"},{"issue":"W1","key":"1982_CR38","doi-asserted-by":"publisher","first-page":"W246","DOI":"10.1093\/nar\/gky425","volume":"46","author":"D Couvin","year":"2018","unstructured":"Couvin D, Bernheim A, Toffano-Nioche C, Touchon M, Michalik J, N\u00e9ron B et al (2018) CRISPRCasFinder, an update of CRISRFinder, includes a portable version, enhanced performance and integrates search for Cas proteins. Nucleic Acids Res 46(W1):W246\u2013W51","journal-title":"Nucleic Acids Res"},{"issue":"12","key":"1982_CR39","doi-asserted-by":"publisher","first-page":"3491","DOI":"10.1093\/jac\/dkaa345","volume":"75","author":"V Bortolaia","year":"2020","unstructured":"Bortolaia V, Kaas RS, Ruppe E, Roberts MC, Schwarz S, Cattoir V et al (2020) ResFinder 4.0 for predictions of phenotypes from genotypes. J Antimicrob Chemother 75(12):3491\u20133500","journal-title":"J Antimicrob Chemother"},{"issue":"1","key":"1982_CR40","doi-asserted-by":"publisher","first-page":"12728","DOI":"10.1038\/s41598-021-91456-0","volume":"11","author":"M Feldgarden","year":"2021","unstructured":"Feldgarden M, Brover V, Gonzalez-Escalona N, Frye JG, Haendiges J, Haft DH et al (2021) AMRFinderPlus and the Reference Gene Catalog facilitate examination of the genomic links among antimicrobial resistance, stress response, and virulence. Sci Rep 11(1):12728","journal-title":"Sci Rep"},{"issue":"D1","key":"1982_CR41","doi-asserted-by":"publisher","first-page":"D912","DOI":"10.1093\/nar\/gkab1107","volume":"50","author":"B Liu","year":"2022","unstructured":"Liu B, Zheng D, Zhou S, Chen L, Yang J (2022) VFDB 2022: a general classification scheme for bacterial virulence factors. Nucleic Acids Res 50(D1):D912\u2013D7","journal-title":"Nucleic Acids Res"},{"issue":"7","key":"1982_CR42","doi-asserted-by":"publisher","first-page":"3895","DOI":"10.1128\/AAC.02412-14","volume":"58","author":"A Carattoli","year":"2014","unstructured":"Carattoli A, Zankari E, Garc\u00eda-Fern\u00e1ndez A, Voldby Larsen M, Lund O, Villa L et al (2014) In silico detection and typing of plasmids using PlasmidFinder and plasmid multilocus sequence typing. Antimicrob Agents Chemother 58(7):3895\u20133903","journal-title":"Antimicrob Agents Chemother"},{"issue":"3","key":"1982_CR43","doi-asserted-by":"publisher","first-page":"338","DOI":"10.1007\/s00239-024-10173-0","volume":"92","author":"A Elrashedy","year":"2024","unstructured":"Elrashedy A, Nayel M, Salama A, Zaghawa A, Abdelsalam NR, Hasan ME (2024) Phylogenetic Analysis and Comparative Genomics of Brucella abortus and Brucella melitensis strains in Egypt. J Mol Evol 92(3):338\u2013357","journal-title":"J Mol Evol"},{"issue":"W1","key":"1982_CR44","doi-asserted-by":"publisher","first-page":"W78","DOI":"10.1093\/nar\/gkae268","volume":"52","author":"I Letunic","year":"2024","unstructured":"Letunic I, Bork P (2024) Interactive Tree of Life (iTOL) v6: recent updates to the phylogenetic tree display and annotation tool. Nucleic Acids Res 52(W1):W78\u2013W82","journal-title":"Nucleic Acids Res"},{"issue":"7","key":"1982_CR45","first-page":"585","volume":"40","author":"WW Deng","year":"2018","unstructured":"Deng WW, Long M, Yang SZ, Zou LK (2018) Evolution and the flanking sequences of \u0392-lactamase resistance gene bla OKP. Yi Chuan= Hereditas 40(7):585\u2013592","journal-title":"Yi Chuan= Hereditas"},{"issue":"1","key":"1982_CR46","first-page":"93","volume":"26","author":"F Amereh","year":"2023","unstructured":"Amereh F, Arabestani MR, Shokoohizadeh L (2023) Relationship of OqxAB efflux pump to antibiotic resistance, mainly fluoroquinolones in Klebsiella pneumoniae, isolated from hospitalized patients. Iran J Basic Med Sci 26(1):93","journal-title":"Iran J Basic Med Sci"},{"issue":"9","key":"1982_CR47","doi-asserted-by":"publisher","first-page":"2460","DOI":"10.1093\/jac\/dkw177","volume":"71","author":"Q Guo","year":"2016","unstructured":"Guo Q, Tomich AD, McElheny CL, Cooper VS, Stoesser N, Wang M et al (2016) Glutathione-S-transferase FosA6 of Klebsiella pneumoniae origin conferring fosfomycin resistance in ESBL-producing Escherichia coli. J Antimicrob Chemother 71(9):2460\u20132465","journal-title":"J Antimicrob Chemother"},{"key":"1982_CR48","doi-asserted-by":"publisher","unstructured":"Arena F, Henrici De Angelis L, Pieralli F, Di Pilato V, Giani T, Torricelli F et al (2015) Draft genome sequence of the first hypermucoviscous Klebsiella quasipneumoniae subsp. quasipneumoniae isolate from a bloodstream infection. Genome Announcements 3(5). https:\/\/doi.org\/10.1128\/genomea.00952-15","DOI":"10.1128\/genomea.00952-15"},{"key":"1982_CR49","doi-asserted-by":"publisher","first-page":"302","DOI":"10.1016\/j.jgar.2024.05.022","volume":"38","author":"JTP Silva","year":"2024","unstructured":"Silva JTP, Santos FF, Valiatti TB, Val\u00eancio A, da Silva Ribeiro \u00c1C, Oliveira LFV et al (2024) Unravelling the genomic characteristics of a Klebsiella quasipneumoniae clinical isolate carrying blaNDM-1. J Global Antimicrob Resist 38:302\u2013305","journal-title":"J Global Antimicrob Resist"},{"issue":"6","key":"1982_CR50","doi-asserted-by":"publisher","first-page":"02513","DOI":"10.1128\/aac","volume":"63","author":"AJ Mathers","year":"2019","unstructured":"Mathers AJ, Crook D, Vaughan A, Barry KE, Vegesana K, Stoesser N et al (2019) Klebsiella quasipneumoniae provides a window into carbapenemase gene transfer, plasmid rearrangements, and patient interactions with the hospital environment. Antimicrob Agents Chemother 63(6):02513\u201302518. https:\/\/doi.org\/10.1128\/aac","journal-title":"Antimicrob Agents Chemother"},{"issue":"9","key":"1982_CR51","doi-asserted-by":"publisher","first-page":"426","DOI":"10.1007\/s00284-025-04414-8","volume":"82","author":"A S\u0119kowska","year":"2025","unstructured":"S\u0119kowska A, Konechnyi Y, Carrazco-Montalvo A, S\u0119kowska et al (2025) Curr Microbiol 82(9):426","journal-title":"Curr Microbiol"},{"key":"1982_CR52","first-page":"25","volume-title":"WGS for bacterial identification and susceptibility testing in the clinical lab. Application and Integration of Omics-Powered Diagnostics in Clinical and","author":"S Vourli","year":"2021","unstructured":"Vourli S, Kontos F, Pournaras S (2021) WGS for bacterial identification and susceptibility testing in the clinical lab. Application and Integration of Omics-Powered Diagnostics in Clinical and. Springer, Public Health Microbiology, pp 25\u201344"},{"issue":"12","key":"1982_CR53","doi-asserted-by":"publisher","first-page":"5149","DOI":"10.1128\/AAC.49.12.5149-5152.2005","volume":"49","author":"C Fevre","year":"2005","unstructured":"Fevre C, Passet V, Weill F-X, Grimont PA, Brisse S (2005) Variants of the Klebsiella pneumoniae OKP chromosomal beta-lactamase are divided into two main groups, OKP-A and OKP-B. Antimicrob Agents Chemother 49(12):5149\u20135152","journal-title":"Antimicrob Agents Chemother"},{"issue":"7","key":"1982_CR54","doi-asserted-by":"publisher","first-page":"422","DOI":"10.1016\/j.ijmm.2017.07.006","volume":"307","author":"SP Henson","year":"2017","unstructured":"Henson SP, Boinett CJ, Ellington MJ, Kagia N, Mwarumba S, Nyongesa S et al (2017) Molecular epidemiology of Klebsiella pneumoniae invasive infections over a decade at Kilifi County Hospital in Kenya. Int J Med Microbiol 307(7):422\u2013429","journal-title":"Int J Med Microbiol"},{"issue":"11","key":"1982_CR55","doi-asserted-by":"publisher","first-page":"e0292288","DOI":"10.1371\/journal.pone.0292288","volume":"18","author":"S Aghamohammad","year":"2023","unstructured":"Aghamohammad S, Khazani Asforooshani M, Malek Mohammadi Y, Sholeh M, Badmasti F (2023) Decoding the genetic structure of conjugative plasmids in international clones of Klebsiella pneumoniae: A deep dive into bla KPC, bla NDM, bla OXA-48, and bla GES genes. PLoS ONE 18(11):e0292288","journal-title":"PLoS ONE"},{"issue":"6","key":"1982_CR56","doi-asserted-by":"publisher","first-page":"500","DOI":"10.1016\/j.ijantimicag.2014.07.020","volume":"44","author":"AO Olaitan","year":"2014","unstructured":"Olaitan AO, Diene SM, Kempf M, Berrazeg M, Bakour S, Gupta SK et al (2014) Worldwide emergence of colistin resistance in Klebsiella pneumoniae from healthy humans and patients in Lao PDR, Thailand, Israel, Nigeria and France owing to inactivation of the PhoP\/PhoQ regulator mgrB: an epidemiological and molecular study. Int J Antimicrob Agents 44(6):500\u2013507","journal-title":"Int J Antimicrob Agents"},{"issue":"3","key":"1982_CR57","doi-asserted-by":"publisher","first-page":"252","DOI":"10.1093\/femsre\/fux013","volume":"41","author":"S Navon-Venezia","year":"2017","unstructured":"Navon-Venezia S, Kondratyeva K, Carattoli A (2017) Klebsiella pneumoniae: a major worldwide source and shuttle for antibiotic resistance. FEMS Microbiol Rev 41(3):252\u2013275","journal-title":"FEMS Microbiol Rev"},{"issue":"6","key":"1982_CR58","doi-asserted-by":"publisher","first-page":"898","DOI":"10.1016\/j.ijantimicag.2018.03.020","volume":"52","author":"Z Hamzaoui","year":"2018","unstructured":"Hamzaoui Z, Ocampo-Sosa A, Martinez MF, Landolsi S, Ferjani S, Maamar E et al (2018) Role of association of OmpK35 and OmpK36 alteration and blaESBL and\/or blaAmpC genes in conferring carbapenem resistance among non-carbapenemase-producing Klebsiella pneumoniae. Int J Antimicrob Agents 52(6):898\u2013905","journal-title":"Int J Antimicrob Agents"},{"key":"1982_CR59","doi-asserted-by":"publisher","unstructured":"Su Y, Zou G, Huang X, Bi J, Meng L, Zhao W et al (2025) Molecular characterization and resistance mechanisms of ertapenem-non-susceptible carbapenem-resistant Klebsiella pneumoniae co-harboring ESBLs or AmpC enzymes with porin loss or efflux pump overexpression. J Bacteriol e00148\u2013e00125. https:\/\/doi.org\/10.1128\/jb.00148-25","DOI":"10.1128\/jb.00148-25"},{"key":"1982_CR60","doi-asserted-by":"crossref","unstructured":"Kareem SM, Al-Kadmy IM, Kazaal SS, Mohammed Ali AN, Aziz SN, Makharita RR et al (2021) Detection of gyrA and parC mutations and prevalence of plasmid-mediated quinolone resistance genes in Klebsiella pneumoniae. Infection and drug resistance. :555\u2009\u2013\u200963","DOI":"10.2147\/IDR.S275852"},{"issue":"3","key":"1982_CR61","doi-asserted-by":"publisher","first-page":"318","DOI":"10.3390\/antibiotics15030318","volume":"15","author":"D Karakalpakidis","year":"2026","unstructured":"Karakalpakidis D, Tsitlakidou M-E, Paraskeva M, Mavidi MN, Marinou M, Procter K et al (2026) Molecular Characterization of Colistin-Resistant Clinical Acinetobacter baumannii from Northern Greece: Phenotypic Colistin Susceptibility and lpx\/pmrCAB Mutational Profiles. Antibiotics 15(3):318","journal-title":"Antibiotics"},{"issue":"6","key":"1982_CR62","doi-asserted-by":"publisher","first-page":"344","DOI":"10.1038\/s41579-019-0315-1","volume":"18","author":"KL Wyres","year":"2020","unstructured":"Wyres KL, Lam MM, Holt KE (2020) Population genomics of Klebsiella pneumoniae. Nat Rev Microbiol 18(6):344\u2013359","journal-title":"Nat Rev Microbiol"},{"issue":"1","key":"1982_CR63","doi-asserted-by":"publisher","first-page":"2703","DOI":"10.1038\/s41467-018-05114-7","volume":"9","author":"MM Lam","year":"2018","unstructured":"Lam MM, Wyres KL, Duch\u00eane S, Wick RR, Judd LM, Gan Y-H et al (2018) Population genomics of hypervirulent Klebsiella pneumoniae clonal-group 23 reveals early emergence and rapid global dissemination. Nat Commun 9(1):2703","journal-title":"Nat Commun"},{"issue":"1","key":"1982_CR64","doi-asserted-by":"publisher","first-page":"31644","DOI":"10.1038\/srep31644","volume":"6","author":"T-L Lin","year":"2016","unstructured":"Lin T-L, Pan Y-J, Hsieh P-F, Hsu C-R, Wu M-C, Wang J-T (2016) Imipenem represses CRISPR-Cas interference of DNA acquisition through H-NS stimulation in Klebsiella pneumoniae. Sci Rep 6(1):31644","journal-title":"Sci Rep"}],"container-title":["Brazilian Journal of Microbiology"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1007\/s42770-026-01982-0.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/link.springer.com\/article\/10.1007\/s42770-026-01982-0","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1007\/s42770-026-01982-0.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,6,10]],"date-time":"2026-06-10T14:02:47Z","timestamp":1781100167000},"score":1,"resource":{"primary":{"URL":"https:\/\/link.springer.com\/10.1007\/s42770-026-01982-0"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,6,10]]},"references-count":64,"journal-issue":{"issue":"1","published-print":{"date-parts":[[2026,12]]}},"alternative-id":["1982"],"URL":"https:\/\/doi.org\/10.1007\/s42770-026-01982-0","relation":{},"ISSN":["1517-8382","1678-4405"],"issn-type":[{"value":"1517-8382","type":"print"},{"value":"1678-4405","type":"electronic"}],"subject":[],"published":{"date-parts":[[2026,6,10]]},"assertion":[{"value":"12 December 2025","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"25 May 2026","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"10 June 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 study was conducted in accordance with the Declaration of Helsinki (2013) and approved by the Research Ethics Board of Peshawar University, Peshawar, Pakistan (Approval No. REB-10, dated July 12, 2024). Written informed consent was obtained from the participating patient prior to sample collection and data analysis.","order":2,"name":"Ethics","group":{"name":"EthicsHeading","label":"Ethical approval"}},{"value":"All authors have reviewed and approved the final version of the manuscript and consented to its publication.","order":3,"name":"Ethics","group":{"name":"EthicsHeading","label":"Consent for publication"}},{"value":"The authors declare no conflict of interest.","order":4,"name":"Ethics","group":{"name":"EthicsHeading","label":"Conflict of interest"}}],"article-number":"169"}}