Multicenter comparative genomic study of Klebsiella oxytoca complex reveals a highly antibiotic-resistant subspecies of Klebsiella michiganensis

Högenauer, 2006, Klebsiella oxytoca as a causative organism of antibiotic-associated hemorrhagic colitis, N Engl J Med, 355, 2418, 10.1056/NEJMoa054765 Yang, 2022, Klebsiella oxytoca complex: update on taxonomy, antimicrobial resistance, and virulence, Clin Microbiol Rev, 35, 10.1128/CMR.00006-21 Ghasemian, 2019, Expression of adhesin genes and biofilm formation among Klebsiella oxytoca clinical isolates from patients with antibiotic-associated haemorrhagic colitis, J Med Microbiol, 68, 978, 10.1099/jmm.0.000965 Bouchillon, 2013, Antimicrobial susceptibility of inpatient urinary tract isolates of gram-negative bacilli in the United States: results from the study for monitoring antimicrobial resistance trends (SMART) program: 2009-2011, Clin Therapeut, 35, 872, 10.1016/j.clinthera.2013.03.022 Hoban, 2014, In vitro susceptibility and distribution of beta-lactamases in Enterobacteriaceae causing intra-abdominal infections in North America 2010-2011, Diagn Microbiol Infect Dis, 79, 367, 10.1016/j.diagmicrobio.2014.03.026 Rønning, 2019, Investigation of an outbreak caused by antibiotic-susceptible Klebsiella oxytoca in a neonatal intensive care unit in Norway, Acta Paediatr, 108, 76, 10.1111/apa.14584 Herruzo, 2017, VIM-Klebsiella oxytoca outbreak in a Neonatal Intensive Care Unit. This time it wasn't the drain, J Prev Med Hyg, 58 Ayan, 2003, Analysis of three outbreaks due to Klebsiella species in a neonatal intensive care unit, Infect Control Hosp Epidemiol, 24, 495, 10.1086/502245 Jeong, 2001, Neonatal intensive care unit outbreak caused by a strain of Klebsiella oxytoca resistant to aztreonam due to overproduction of chromosomal beta-lactamase, J Hosp Infect, 48, 281, 10.1053/jhin.2001.1018 Berthelot, 2001, Nosocomial colonization of premature babies with Klebsiella oxytoca: probable role of enteral feeding procedure in transmission and control of the outbreak with the use of gloves, Infect Control Hosp Epidemiol, 22, 148, 10.1086/501881 Reiss, 2000, Disinfectant contaminated with Klebsiella oxytoca as a source of sepsis in babies, Lancet, 356, 310, 10.1016/S0140-6736(00)02509-5 Smith, 1984, Gentamicin-resistant Klebsiella oxytoca on a special care baby unit, Lancet, 2, 586, 10.1016/S0140-6736(84)90812-2 Cuénod, 2021, Whole-genome sequence-informed MALDI-TOF MS diagnostics reveal importance of Klebsiella oxytoca group in invasive infections: a retrospective clinical study, Genome Med, 13, 150, 10.1186/s13073-021-00960-5 Richter, 2009, Shifting the genomic gold standard for the prokaryotic species definition, Proc Natl Acad Sci U S A, 106, 19126, 10.1073/pnas.0906412106 2018, Methods for dilution antimicrobial susceptibility tests for bacteria that grow aerobically 2022 Bankevich, 2012, SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing, J Comput Biol, 19, 455, 10.1089/cmb.2012.0021 Seemann, 2014, Prokka: rapid prokaryotic genome annotation, Bioinformatics, 30, 2068, 10.1093/bioinformatics/btu153 Page, 2015, Roary: rapid large-scale prokaryote pan genome analysis, Bioinformatics, 31, 3691, 10.1093/bioinformatics/btv421 Price, 2010, FastTree 2--approximately maximum-likelihood trees for large alignments, PLoS One, 5, 10.1371/journal.pone.0009490 Kumar, 2018, Molecular evolutionary genetics analysis across computing platforms, Mol Biol Evol, 35, 1547, 10.1093/molbev/msy096 Lam, 2021, A genomic surveillance framework and genotyping tool for Klebsiella pneumoniae and its related species complex, Nat Commun, 12, 4188, 10.1038/s41467-021-24448-3 Liu, 2022, Vfdb 2022: a general classification scheme for bacterial virulence factors, Nucleic Acids Res, 50 Alcock, 2020, Card 2020: antibiotic resistome surveillance with the comprehensive antibiotic resistance database, Nucleic Acids Res, 48 Carattoli, 2014, In silico detection and typing of plasmids using PlasmidFinder and plasmid multilocus sequence typing, Antimicrob Agents Chemother, 58, 3895, 10.1128/AAC.02412-14 Johansson, 2021, Detection of mobile genetic elements associated with antibiotic resistance in Salmonella enterica using a newly developed web tool: MobileElementFinder, J Antimicrob Chemother, 76, 101, 10.1093/jac/dkaa390 Liu, 2022, Correlation of Moraxella catarrhalis macrolide susceptibility with the ability to adhere and invade human respiratory epithelial cells, Emerg Microb Infect, 11, 2055, 10.1080/22221751.2022.2108341 Heesemann, 1993, Virulence of Yersinia enterocolitica is closely associated with siderophore production, expression of an iron-repressible outer membrane polypeptide of 65,000 Da and pesticin sensitivity, Mol Microbiol, 8, 397, 10.1111/j.1365-2958.1993.tb01583.x Garcia, 2011, Redundancy and specificity of Escherichia coli iron acquisition systems during urinary tract infection, Infect Immun, 79, 1225, 10.1128/IAI.01222-10 Yeom, 2020, Small proteins regulate Salmonella survival inside macrophages by controlling degradation of a magnesium transporter, Proc Natl Acad Sci U S A, 117, 20235, 10.1073/pnas.2006116117