{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,16]],"date-time":"2026-10-16T16:21:05Z","timestamp":1792167665609,"version":"4.4.0"},"reference-count":147,"publisher":"Frontiers Media SA","license":[{"start":{"date-parts":[[2024,2,14]],"date-time":"2024-02-14T00:00:00Z","timestamp":1707868800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":["frontiersin.org"],"crossmark-restriction":true},"short-container-title":["Front. Microbiol."],"abstract":"<jats:p><jats:italic>Klebsiella aerogenes<\/jats:italic> is an important opportunistic pathogen with the potential to develop resistance against last-line antibiotics, such as carbapenems, limiting the treatment options. Here, we investigated the antibiotic resistance profiles of 10 <jats:italic>K. aerogenes<\/jats:italic> strains isolated from patient samples in the intensive-care unit of a Brazilian tertiary hospital using conventional PCR and a comprehensive genomic characterization of a specific <jats:italic>K. aerogenes<\/jats:italic> strain (CRK317) carrying both the <jats:italic>bla<\/jats:italic><jats:sub>KPC-2<\/jats:sub> and <jats:italic>bla<\/jats:italic><jats:sub>NDM-1<\/jats:sub> genes simultaneously. All isolates were completely resistant to \u03b2-lactam antibiotics, including ertapenem, imipenem, and meropenem with differencing levels of resistance to aminoglycosides, quinolones, and tigecycline also observed. Half of the strains studied were classified as multidrug-resistant. The carbapenemase-producing isolates carried many genes of interest including: \u03b2-lactams (<jats:italic>bla<\/jats:italic><jats:sub>NDM-1<\/jats:sub>, <jats:italic>bla<\/jats:italic><jats:sub>KPC-2<\/jats:sub>, <jats:italic>bla<\/jats:italic><jats:sub>TEM-1<\/jats:sub>, <jats:italic>bla<\/jats:italic><jats:sub>CTX-M-1<\/jats:sub> group, <jats:italic>bla<\/jats:italic><jats:sub>OXA-1<\/jats:sub> group and <jats:italic>bla<\/jats:italic><jats:sub>SHVvariants<\/jats:sub> in 20-80% of the strains), aminoglycoside resistance genes [<jats:italic>aac(6\u2019)-Ib<\/jats:italic> and <jats:italic>aph<\/jats:italic>(<jats:italic>3\u2019)-VI<\/jats:italic>, 70 and 80%], a fluoroquinolone resistance gene (<jats:italic>qnrS<\/jats:italic>, 80%), a sulfonamide resistance gene (<jats:italic>sul-2<\/jats:italic>, 80%) and a multidrug efflux system transporter (<jats:italic>mdtK<\/jats:italic>, 70%) while all strains carried the efflux pumps <jats:italic>Acr<\/jats:italic> (subunit A) and <jats:italic>tolC<\/jats:italic>. Moreover, we performed a comprehensive genomic characterization of a specific <jats:italic>K. aerogenes<\/jats:italic> strain (CRK317) carrying both the <jats:italic>bla<\/jats:italic><jats:sub>KPC-2<\/jats:sub> and <jats:italic>bla<\/jats:italic><jats:sub>NDM-1<\/jats:sub> genes simultaneously. The draft genome assembly of the CRK317 had a total length of 5,462,831\u2009bp and a GC content of 54.8%. The chromosome was found to contain many essential genes. <jats:italic>In silico<\/jats:italic> analysis identified many genes associated with resistance phenotypes, including \u03b2-lactamases (<jats:italic>bla<\/jats:italic><jats:sub>OXA-9<\/jats:sub>, <jats:italic>bla<\/jats:italic><jats:sub>TEM-1<\/jats:sub>, <jats:italic>bla<\/jats:italic><jats:sub>NDM-1<\/jats:sub>, <jats:italic>bla<\/jats:italic><jats:sub>CTX-M-15<\/jats:sub>, <jats:italic>bla<\/jats:italic><jats:sub>AmpC-1<\/jats:sub>, <jats:italic>bla<\/jats:italic><jats:sub>AmpC-2<\/jats:sub>), the bleomycin resistance gene (<jats:italic>ble<\/jats:italic><jats:sub>MBL<\/jats:sub>), an erythromycin resistance methylase (<jats:italic>ermC<\/jats:italic>), aminoglycoside-modifying enzymes [<jats:italic>aac(6\u2019)<\/jats:italic>-<jats:italic>Ib<\/jats:italic>, <jats:italic>aadA\/ant(3\u201d)<\/jats:italic>-<jats:italic>Ia<\/jats:italic>, <jats:italic>aph(3\u2019)-VI<\/jats:italic>], a sulfonamide resistance enzyme (<jats:italic>sul-2<\/jats:italic>), a chloramphenicol acetyltransferase (<jats:italic>catA-<\/jats:italic>like), a plasmid-mediated quinolone resistance protein (<jats:italic>qnrS1<\/jats:italic>), a glutathione transferase (<jats:italic>fosA<\/jats:italic>), PEtN transferases (<jats:italic>eptA<\/jats:italic>, <jats:italic>eptB<\/jats:italic>) and a glycosyltransferase (<jats:italic>arnT<\/jats:italic>). We also detected 22 genomic islands, eight families of insertion sequences, two putative integrative and conjugative elements with a type IV secretion system, and eight prophage regions. This suggests the significant involvement of these genetic structures in the dissemination of antibiotic resistance. The results of our study show that the emergence of carbapenemase-producing <jats:italic>K. aerogenes<\/jats:italic>, co-harboring <jats:italic>bla<\/jats:italic><jats:sub>KPC-2<\/jats:sub> and <jats:italic>bla<\/jats:italic><jats:sub>NDM-1<\/jats:sub>, is a worrying phenomenon which highlights the importance of developing strategies to detect, prevent, and control the spread of these microorganisms.<\/jats:p>","DOI":"10.3389\/fmicb.2024.1352851","type":"journal-article","created":{"date-parts":[[2024,2,15]],"date-time":"2024-02-15T14:25:56Z","timestamp":1708007156000},"update-policy":"https:\/\/doi.org\/10.3389\/crossmark-policy","source":"Crossref","is-referenced-by-count":13,"title":["First report of coexistence of blaKPC-2 and blaNDM-1 in carbapenem-resistant clinical isolates of Klebsiella aerogenes in Brazil"],"prefix":"10.3389","volume":"15","author":[{"given":"Saulo Henrique","family":"Rodrigues","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Gustavo Dantas","family":"Nunes","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Gabriela Guerrera","family":"Soares","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Roumayne Lopes","family":"Ferreira","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Marcelo Silva Folhas","family":"Damas","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Pedro Mendes","family":"Laprega","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Rebecca Elizabeth","family":"Shilling","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Leslie Camelo","family":"Campos","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Andrea Soares","family":"da Costa","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Iran","family":"Malavazi","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Anderson Ferreira","family":"da Cunha","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Maria-Cristina da Silva","family":"Pranchevicius","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1965","published-online":{"date-parts":[[2024,2,14]]},"reference":[{"key":"ref1","doi-asserted-by":"publisher","first-page":"W537","DOI":"10.1093\/nar\/gky379","article-title":"The galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2018 update","volume":"46","author":"Afgan","year":"2018","journal-title":"Nucleic Acids Res."},{"key":"ref2","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkz935","article-title":"CARD 2020: antibiotic resistome surveillance with the comprehensive antibiotic resistance database","author":"Alcock","year":"2019","journal-title":"Nucleic Acids Res."},{"key":"ref3","doi-asserted-by":"publisher","first-page":"4443","DOI":"10.1128\/AAC.00099-14","article-title":"Carbapenem-resistant Klebsiella pneumoniae strains exhibit diversity in aminoglycoside-modifying enzymes, which exert differing effects on Plazomicin and other agents","volume":"58","author":"Almaghrabi","year":"2014","journal-title":"Antimicrob. Agents Chemother."},{"key":"ref4","doi-asserted-by":"publisher","first-page":"2228","DOI":"10.1093\/jac\/dkv105","article-title":"A novel alanine to serine substitution mutation in sox S induces overexpression of efflux pumps and contributes to multidrug resistance in clinical Escherichia coli isolates","volume":"70","author":"Aly","year":"2015","journal-title":"J. Antimicrob. Chemother."},{"key":"ref5","doi-asserted-by":"publisher","first-page":"1487","DOI":"10.3390\/ijerph120201487","article-title":"Multidrug efflux pumps from Enterobacteriaceae, Vibrio cholerae and Staphylococcus aureus bacterial food pathogens","volume":"12","author":"Andersen","year":"2015","journal-title":"Int. J. Environ. Res. Public Health"},{"key":"ref6","doi-asserted-by":"publisher","first-page":"3380","DOI":"10.1093\/bioinformatics\/btw493","article-title":"Plasmid SPAdes: assembling plasmids from whole genome sequencing data","volume":"32","author":"Antipov","year":"2016","journal-title":"Bioinformatics"},{"key":"ref7","doi-asserted-by":"publisher","first-page":"W16","DOI":"10.1093\/nar\/gkw387","article-title":"PHASTER: a better, faster version of the PHAST phage search tool","volume":"44","author":"Arndt","year":"2016","journal-title":"Nucleic Acids Res."},{"key":"ref8","doi-asserted-by":"publisher","first-page":"224","DOI":"10.1016\/j.bjm.2018.04.009","article-title":"Detection of virulence and \u03b2-lactamase encoding genes in Enterobacter aerogenes and Enterobacter cloacae clinical isolates from Brazil","volume":"49","author":"Azevedo","year":"2018","journal-title":"Braz. J. Microbiol."},{"key":"ref9","doi-asserted-by":"publisher","first-page":"75","DOI":"10.1186\/1471-2164-9-75","article-title":"The RAST server: rapid annotations using subsystems technology","volume":"9","author":"Aziz","year":"2008","journal-title":"BMC Genomics"},{"key":"ref10","doi-asserted-by":"publisher","first-page":"455","DOI":"10.1089\/cmb.2012.0021","article-title":"SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing","volume":"19","author":"Bankevich","year":"2012","journal-title":"J. Comput. Biol."},{"key":"ref11","doi-asserted-by":"publisher","first-page":"e1009998","DOI":"10.1371\/journal.pgen.1009998","article-title":"Biology and engineering of integrative and conjugative elements: construction and analyses of hybrid ICEs reveal element functions that affect species-specific efficiencies","volume":"18","author":"Bean","year":"2022","journal-title":"PLoS Genet."},{"key":"ref12","doi-asserted-by":"publisher","first-page":"141","DOI":"10.1038\/417141a","article-title":"Complete genome sequence of the model actinomycete Streptomyces coelicolor A3(2)","volume":"417","author":"Bentley","year":"2002","journal-title":"Nature"},{"key":"ref13","doi-asserted-by":"publisher","first-page":"503","DOI":"10.3390\/antibiotics9080503","article-title":"Development of an NGS-based workflow for improved monitoring of circulating plasmids in support of risk assessment of antimicrobial resistance gene dissemination","volume":"9","author":"Berbers","year":"2020","journal-title":"Antibiotics"},{"key":"ref14","doi-asserted-by":"publisher","first-page":"W30","DOI":"10.1093\/nar\/gkx343","article-title":"Island viewer 4: expanded prediction of genomic islands for larger-scale datasets","volume":"45","author":"Bertelli","year":"2017","journal-title":"Nucleic Acids Res."},{"key":"ref15","doi-asserted-by":"publisher","first-page":"1077","DOI":"10.1093\/molbev\/msu088","article-title":"Automated reconstruction of whole-genome phylogenies from short-sequence reads","volume":"31","author":"Bertels","year":"2014","journal-title":"Mol. Biol. Evol."},{"key":"ref16","doi-asserted-by":"publisher","DOI":"10.1128\/AAC.00764-18","article-title":"In silico typing and comparative genomic analysis of Inc FII K plasmids and insights into the evolution of replicons, plasmid backbones, and resistance determinant profiles","volume":"62","author":"Bi","year":"2018","journal-title":"Antimicrob. Agents Chemother."},{"key":"ref17","doi-asserted-by":"publisher","first-page":"43","DOI":"10.1016\/j.jgar.2020.05.001","article-title":"Multidrug-resistant Klebsiella aerogenes clinical isolates from Brazil carrying Inc Q1 plasmids containing the Bla KPC-2 gene associated with non-Tn4401 elements (NTEKPC-IId)","volume":"22","author":"Bispo Beltr\u00e3o","year":"2020","journal-title":"J. Glob. Antimicrob. Resist."},{"key":"ref18","doi-asserted-by":"publisher","first-page":"578","DOI":"10.1093\/bioinformatics\/btq683","article-title":"Scaffolding pre-assembled contigs using SSPACE","volume":"27","author":"Boetzer","year":"2011","journal-title":"Bioinformatics"},{"key":"ref19","doi-asserted-by":"publisher","first-page":"3491","DOI":"10.1093\/jac\/dkaa345","article-title":"Res finder 4.0 for predictions of phenotypes from genotypes","volume":"75","author":"Bortolaia","year":"2020","journal-title":"J. Antimicrob. Chemother."},{"key":"ref20","doi-asserted-by":"publisher","first-page":"iv38","DOI":"10.1093\/jac\/dkab353","article-title":"The role of new carbapenem combinations in the treatment of multidrug-resistant gram-negative infections","volume":"76","author":"Bouza","year":"2021","journal-title":"J. Antimicrob. Chemother."},{"key":"ref21","doi-asserted-by":"publisher","first-page":"30","DOI":"10.1186\/s13036-017-0071-6","article-title":"Modeling the architecture of the regulatory system controlling methylenomycin production in Streptomyces coelicolor","volume":"11","author":"Bowyer","year":"2017","journal-title":"J. Biol. Eng."},{"key":"ref22","doi-asserted-by":"publisher","first-page":"5825","DOI":"10.1093\/molbev\/msab293","article-title":"Egg NOG-mapper v2: functional annotation, Orthology assignments, and domain prediction at the metagenomic scale","volume":"38","author":"Cantalapiedra","year":"2021","journal-title":"Mol. Biol. Evol."},{"key":"ref23","doi-asserted-by":"publisher","first-page":"3895","DOI":"10.1128\/AAC.02412-14","article-title":"Detection and typing of plasmids using plasmid finder and plasmid multilocus sequence typing","volume":"58","author":"Carattoli","year":"2014","journal-title":"Antimicrob. Agents Chemother."},{"key":"ref24","doi-asserted-by":"publisher","first-page":"S166","DOI":"10.1093\/cid\/ciad109","article-title":"Global epidemiology and mechanisms of resistance of Acinetobacter baumannii-calcoaceticus complex","volume":"76","author":"Castanheira","year":"2023","journal-title":"Clin. Infect. Dis."},{"key":"ref25","doi-asserted-by":"publisher","DOI":"10.1093\/jacamr\/dlab092","article-title":"Extended-spectrum \u03b2-lactamases: an update on their characteristics, epidemiology and detection","volume":"3","author":"Castanheira","year":"2021","journal-title":"JAC Antimicrob Resist"},{"key":"ref26","doi-asserted-by":"publisher","first-page":"1164","DOI":"10.3201\/eid2606.191121","article-title":"Antimicrobial resistance in Salmonella enterica Serovar Paratyphi B variant Java in poultry from Europe and Latin America","volume":"26","author":"Castellanos","year":"2020","journal-title":"Emerg. Infect. Dis."},{"key":"ref27","doi-asserted-by":"publisher","first-page":"24373","DOI":"10.1038\/srep24373","article-title":"BPGA- an ultra-fast pan-genome analysis pipeline","volume":"6","author":"Chaudhari","year":"2016","journal-title":"Sci. Rep."},{"key":"ref28","doi-asserted-by":"publisher","first-page":"1542","DOI":"10.1128\/AAC.02332-12","article-title":"Complete sequence of a Bla KPC-2-harboring Inc FII K1 plasmid from a Klebsiella pneumoniae sequence type 258 strain","volume":"57","author":"Chen","year":"2013","journal-title":"Antimicrob. Agents Chemother."},{"key":"ref29","doi-asserted-by":"publisher","first-page":"294","DOI":"10.3389\/fmicb.2015.00294","article-title":"NDM-1 encoded by a pNDM-BJ01-like plasmid p3SP-NDM in clinical Enterobacter aerogenes","volume":"6","author":"Chen","year":"2015","journal-title":"Front. Microbiol."},{"key":"ref30","doi-asserted-by":"publisher","first-page":"107","DOI":"10.1016\/j.str.2021.08.008","article-title":"In situ structure of the Acr AB-Tol C efflux pump at subnanometer resolution","volume":"30","author":"Chen","year":"2022","journal-title":"Structure"},{"key":"ref31","doi-asserted-by":"publisher","first-page":"16","DOI":"10.1186\/s44280-023-00017-9","article-title":"Intercontinental spread and clonal expansion of col RNA1 plasmid-bearing Salmonella Corvallis ST1541 strains: a genomic epidemiological study","volume":"1","author":"Chen","year":"2023","journal-title":"One Health Advances"},{"key":"ref32","doi-asserted-by":"publisher","first-page":"e3203","DOI":"10.1371\/journal.pone.0003203","article-title":"Identification and evolution of drug efflux pump in clinical Enterobacter aerogenes strains isolated in 1995 and 2003","volume":"3","author":"Chevalier","year":"2008","journal-title":"PLoS One"},{"key":"ref33","doi-asserted-by":"publisher","first-page":"2518","DOI":"10.1128\/AAC.48.7.2518-2523.2004","article-title":"Ram a is an alternate activator of the multidrug resistance Cascade in Enterobacter aerogenes","volume":"48","author":"Chollet","year":"2004","journal-title":"Antimicrob. Agents Chemother."},{"key":"ref34","doi-asserted-by":"publisher","DOI":"10.1128\/ecosalplus.esp-0010-2022","article-title":"The mar, sox, and rob Systems","volume":"11","author":"Chubiz","year":"2023","journal-title":"Eco Sal Plus"},{"key":"ref500","article-title":"Performance Standards for Antimicrobial Susceptibility Testing","year":"2023"},{"key":"ref1000","year":"2012","journal-title":"Resolu\u00e7\u00e3o N\u00ba"},{"key":"ref35","doi-asserted-by":"publisher","first-page":"117793222093806","DOI":"10.1177\/1177932220938064","article-title":"First steps in the analysis of prokaryotic Pan-genomes","volume":"14","author":"Costa","year":"2020","journal-title":"Bioinform Biol Insights"},{"key":"ref36","doi-asserted-by":"publisher","first-page":"W246","DOI":"10.1093\/nar\/gky425","article-title":"CRISPRCasFinder, an update of CRISRFinder, includes a portable version, enhanced performance and integrates search for Cas proteins","volume":"46","author":"Couvin","year":"2018","journal-title":"Nucleic Acids Res."},{"key":"ref37","doi-asserted-by":"publisher","first-page":"619","DOI":"10.3389\/fgene.2018.00619","article-title":"Comparative analysis of Genomic Island prediction tools","volume":"9","author":"da Silva Filho","year":"2018","journal-title":"Front. Genet."},{"key":"ref38","doi-asserted-by":"publisher","first-page":"931379","DOI":"10.3389\/fmed.2022.931379","article-title":"Whole genome sequencing of the multidrug-resistant Chryseobacterium indologenes isolated from a patient in Brazil","volume":"9","author":"Damas","year":"2022","journal-title":"Front. Med (Lausanne)"},{"key":"ref39","doi-asserted-by":"publisher","DOI":"10.1128\/CMR.00002-19","article-title":"Enterobacter spp.: update on taxonomy, clinical aspects, and emerging antimicrobial resistance","volume":"32","author":"Davin-Regli","year":"2019","journal-title":"Clin. Microbiol. Rev."},{"key":"ref40","doi-asserted-by":"publisher","first-page":"392","DOI":"10.3389\/fmicb.2015.00392","article-title":"Enterobacter aerogenes and Enterobacter cloacae; versatile bacterial pathogens confronting antibiotic treatment","volume":"6","author":"Davin-Regli","year":"2015","journal-title":"Front. Microbiol."},{"key":"ref41","doi-asserted-by":"publisher","first-page":"99","DOI":"10.1016\/j.jgar.2018.08.021","article-title":"Draft genome sequence of KPC-2-producing Pseudomonas aeruginosa recovered from a bloodstream infection sample in Brazil","volume":"15","author":"de Oliveira Santos","year":"2018","journal-title":"J. Glob. Antimicrob. Resist."},{"key":"ref42","doi-asserted-by":"publisher","first-page":"114006","DOI":"10.1016\/j.ijheh.2022.114006","article-title":"Prevalence of ESKAPE pathogens in the environment: antibiotic resistance status, community-acquired infection and risk to human health","volume":"244","author":"Denissen","year":"2022","journal-title":"Int. J. Hyg. Environ. Health"},{"key":"ref9001","doi-asserted-by":"publisher","first-page":"653","DOI":"10.1128\/AAC.01773-15","article-title":"Complete Sequences of IncU Plasmids Harboring Quinolone Resistance Genes qnrS2 and aac(6\\u0027)-Ib-cr in Aeromonas spp. from Ornamental Fish","volume":"60","author":"Dobiasova","year":"2016","journal-title":"Antimicrob Agents Chemother"},{"key":"ref43","doi-asserted-by":"publisher","first-page":"140","DOI":"10.1016\/j.chom.2019.10.022","article-title":"A Bioinformatic analysis of integrative Mobile genetic elements highlights their role in bacterial adaptation","volume":"27","author":"Durrant","year":"2020","journal-title":"Cell Host Microbe"},{"key":"ref44","doi-asserted-by":"publisher","first-page":"3198","DOI":"10.3389\/fmicb.2018.03198","article-title":"High prevalence of multidrug-resistant Klebsiella pneumoniae harboring several virulence and \u03b2-lactamase encoding genes in a Brazilian intensive care unit","volume":"9","author":"Ferreira","year":"2019","journal-title":"Front. Microbiol."},{"key":"ref45","doi-asserted-by":"publisher","first-page":"956","DOI":"10.3389\/fmicb.2020.00956","article-title":"Characterization of KPC-producing Serratia marcescens in an intensive care unit of a Brazilian tertiary hospital","volume":"11","author":"Ferreira","year":"2020","journal-title":"Front. Microbiol."},{"key":"ref46","doi-asserted-by":"publisher","DOI":"10.1590\/0037-8682-0460-2018","article-title":"Emergence of aph(3\u2019)-VI and accumulation of aminoglycoside modifying enzyme genes in KPC-2-possessing Enterobacter aerogenes isolates from infections and colonization in patients from Recife-PE, Brazil","volume":"52","author":"Firmo","year":"2019","journal-title":"Rev. Soc. Bras. Med. Trop."},{"key":"ref47","doi-asserted-by":"publisher","first-page":"38","DOI":"10.1007\/s13730-018-0360-z","article-title":"NDM-1-producing Enterobacter aerogenes isolated from a patient with a JJ ureteric stent in situ","volume":"8","author":"Franoli\u0107","year":"2019","journal-title":"CEN Case Rep."},{"key":"ref48","doi-asserted-by":"publisher","first-page":"167","DOI":"10.1186\/s12879-019-3801-1","article-title":"Nationwide epidemiology of carbapenem resistant Klebsiella pneumoniae isolates from Greek hospitals, with regards to plazomicin and aminoglycoside resistance","volume":"19","author":"Galani","year":"2019","journal-title":"BMC Infect. Dis."},{"key":"ref49","doi-asserted-by":"publisher","first-page":"88","DOI":"10.1590\/0037-8682-0227-2017","article-title":"Clonal relation and antimicrobial resistance pattern of extended-spectrum \u03b2-lactamase- and amp C \u03b2-lactamase-producing Enterobacter spp. isolated from different clinical samples in Tehran, Iran","volume":"51","author":"Ghanavati","year":"2018","journal-title":"Rev. Soc. Bras. Med. Trop."},{"key":"ref50","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":"ref51","doi-asserted-by":"publisher","first-page":"1649","DOI":"10.3389\/fmicb.2016.01649","article-title":"Genome sequencing of four multidrug-resistant Enterobacter aerogenes isolates from hospitalized patients in Brazil","volume":"7","author":"Grazziotin","year":"2016","journal-title":"Front. Microbiol."},{"key":"ref52","doi-asserted-by":"publisher","first-page":"20","DOI":"10.1177\/0300060513475965","article-title":"Plasmid-mediated quinolone resistance \u2013 current knowledge and future perspectives","volume":"41","author":"Guan","year":"2013","journal-title":"J. Int. Med. Res."},{"key":"ref53","doi-asserted-by":"publisher","DOI":"10.1128\/aac.00358-23","article-title":"Temocillin resistance in the Enterobacter cloacae Complex is conferred by a single point mutation in bae S, leading to overexpression of the Acr D efflux pump","volume":"67","author":"Gu\u00e9rin","year":"2023","journal-title":"Antimicrob. Agents Chemother."},{"key":"ref54","first-page":"113","volume-title":"Estimating maximum likelihood phylogenies with Phy ML","author":"Guindon","year":"2009"},{"key":"ref55","doi-asserted-by":"publisher","first-page":"212","DOI":"10.1128\/AAC.01310-13","article-title":"ARG-ANNOT, a new Bioinformatic tool to discover antibiotic resistance genes in bacterial genomes","volume":"58","author":"Gupta","year":"2014","journal-title":"Antimicrob. Agents Chemother."},{"key":"ref56","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":"ref57","doi-asserted-by":"publisher","first-page":"230","DOI":"10.1007\/s00203-022-02853-6","article-title":"The effects of antidepressants fluoxetine, sertraline, and amitriptyline on the development of antibiotic resistance in Acinetobacter baumannii","volume":"204","author":"Gurpinar","year":"2022","journal-title":"Arch. Microbiol."},{"key":"ref58","doi-asserted-by":"publisher","first-page":"66","DOI":"10.1016\/j.diagmicrobio.2013.10.001","article-title":"Increased prevalence of aminoglycoside resistance in clinical isolates of Escherichia coli and Klebsiella spp. in Norway is associated with the acquisition of AAC (3)-II and AAC (6\u2032)-Ib","volume":"78","author":"Haldorsen","year":"2014","journal-title":"Diagn. Microbiol. Infect. Dis."},{"key":"ref59","first-page":"95","article-title":"Bio edit: a user-friendly biological sequence alignment editor and analysis program for windows 95\/98\/NT","volume":"41","author":"Hall","year":"1999","journal-title":"Nucleic Acids Symp. Ser."},{"key":"ref9002","doi-asserted-by":"publisher","first-page":"290","DOI":"10.1111\/j.1472-765X.2012.03293.x","article-title":"First description of ColE-type plasmid in Aeromonas spp. carrying quinolone resistance (qnrS2) gene","volume":"55","author":"Han","year":"2012","journal-title":"Lett Appl Microbiol"},{"key":"ref60","doi-asserted-by":"publisher","first-page":"12","DOI":"10.1111\/j.1574-6968.2009.01879.x","article-title":"Effect of multidrug-efflux transporter genes on dipeptide resistance and overproduction in Escherichia coli","volume":"304","author":"Hayashi","year":"2010","journal-title":"FEMS Microbiol. Lett."},{"key":"ref61","doi-asserted-by":"publisher","first-page":"29","DOI":"10.1016\/j.micpath.2017.02.033","article-title":"Functional role of omp F and omp C porins in pathogenesis of avian pathogenic Escherichia coli","volume":"107","author":"Hejair","year":"2017","journal-title":"Microb. Pathog."},{"key":"ref62","doi-asserted-by":"publisher","first-page":"4229","DOI":"10.1038\/s41598-022-08200-5","article-title":"Salmonella Salamae and S. Waycross isolated from Nile perch in Lake Victoria show limited human pathogenic potential","volume":"12","author":"Hounmanou","year":"2022","journal-title":"Sci. Rep."},{"key":"ref63","doi-asserted-by":"publisher","DOI":"10.3389\/fmicb.2017.00297","article-title":"Type B chloramphenicol acetyltransferases are responsible for chloramphenicol resistance in Riemerella anatipestifer, China","volume":"8","author":"Huang","year":"2017","journal-title":"Front. Microbiol."},{"key":"ref64","doi-asserted-by":"publisher","first-page":"e99209","DOI":"10.1371\/journal.pone.0099209","article-title":"Resistance determinants and Mobile genetic elements of an NDM-1-encoding Klebsiella pneumoniae strain","volume":"9","author":"Hudson","year":"2014","journal-title":"PLoS One"},{"key":"ref65","doi-asserted-by":"publisher","first-page":"8","DOI":"10.1128\/mBio.00749-17","article-title":"Widespread Fosfomycin resistance in gram-negative Bacteria attributable to the chromosomal fos a gene","author":"Ito","year":"2017","journal-title":"MBio"},{"key":"ref66","doi-asserted-by":"publisher","first-page":"7","DOI":"10.1016\/j.gdata.2017.07.012","article-title":"Whole genome of Klebsiella aerogenes PX01 isolated from San Jacinto River sediment west of Baytown, Texas reveals the presence of multiple antibiotic resistance determinants and mobile genetic elements","volume":"14","author":"Iyer","year":"2017","journal-title":"Genom Data"},{"key":"ref67","doi-asserted-by":"publisher","first-page":"161","DOI":"10.1128\/CMR.00036-08","article-title":"Amp C \u03b2-Lactamases","volume":"22","author":"Jacoby","year":"2009","journal-title":"Clin. Microbiol. Rev."},{"key":"ref68","doi-asserted-by":"publisher","first-page":"22859","DOI":"10.1038\/s41598-021-02251-w","article-title":"High prevalence of multiple antibiotic resistance in clinical E. coli isolates from Bangladesh and prediction of molecular resistance determinants using WGS of an XDR isolate","volume":"11","author":"Jain","year":"2021","journal-title":"Sci. Rep."},{"key":"ref69","doi-asserted-by":"publisher","first-page":"684","DOI":"10.1186\/s12864-017-4065-z","article-title":"Evolution of mobile genetic element composition in an epidemic methicillin-resistant Staphylococcus aureus: temporal changes correlated with frequent loss and gain events","volume":"18","author":"Jamrozy","year":"2017","journal-title":"BMC Genomics"},{"key":"ref70","doi-asserted-by":"publisher","first-page":"326","DOI":"10.5483\/BMBRep.2023-0070","article-title":"Acr AB-Tol C, a major efflux pump in gram negative bacteria: toward understanding its operation mechanism","volume":"56","author":"Jang","year":"2023","journal-title":"BMB Rep."},{"key":"ref71","doi-asserted-by":"publisher","first-page":"577","DOI":"10.1146\/annurev-genet-112414-055018","article-title":"Integrative and conjugative elements (ICEs): what they do and how they work","volume":"49","author":"Johnson","year":"2015","journal-title":"Annu. Rev. Genet."},{"key":"ref72","doi-asserted-by":"publisher","first-page":"376","DOI":"10.1111\/j.1574-6976.2008.00136.x","article-title":"Genomic islands: tools of bacterial horizontal gene transfer and evolution","volume":"33","author":"Juhas","year":"2009","journal-title":"FEMS Microbiol. Rev."},{"key":"ref73","doi-asserted-by":"publisher","first-page":"722","DOI":"10.3390\/pathogens11070722","article-title":"The predominance of Klebsiella aerogenes among Carbapenem-resistant Enterobacteriaceae infections in Japan","volume":"11","author":"Kamio","year":"2022","journal-title":"Pathogens"},{"key":"ref74","doi-asserted-by":"publisher","first-page":"726","DOI":"10.1016\/j.jmb.2015.11.006","article-title":"Blast KOALA and ghost KOALA: KEGG tools for functional characterization of genome and metagenome sequences","volume":"428","author":"Kanehisa","year":"2016","journal-title":"J. Mol. Biol."},{"key":"ref75","doi-asserted-by":"publisher","first-page":"772","DOI":"10.1093\/molbev\/mst010","article-title":"MAFFT multiple sequence alignment software version 7: improvements in performance and usability","volume":"30","author":"Katoh","year":"2013","journal-title":"Mol. Biol. Evol."},{"key":"ref76","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1089\/mdr.2006.9990","article-title":"Ram a, a transcriptional regulator, and Acr AB, an RND-type efflux pump, are associated with decreased susceptibility to Tigecycline in Enterobacter cloacae","volume":"13","author":"Keeney","year":"2007","journal-title":"Microb. Drug Resist."},{"key":"ref77","doi-asserted-by":"publisher","first-page":"6","DOI":"10.1128\/mSphere.00452-21","article-title":"Distribution of antimicrobial resistance and virulence genes within the prophage-associated regions in nosocomial pathogens","author":"Kondo","year":"2021","journal-title":"mSphere"},{"key":"ref78","doi-asserted-by":"publisher","DOI":"10.1590\/0001-3765202220200825","article-title":"Evaluation of partial 12S rRNA, 16S rRNA, COI and Cytb gene sequence datasets for potential single DNA barcode for hylids (Anura: Hylidae)","volume":"94","author":"Koroiva","year":"2022","journal-title":"An. Acad. Bras. Cienc."},{"key":"ref79","doi-asserted-by":"publisher","first-page":"539","DOI":"10.1111\/j.1469-0691.2011.03607.x","article-title":"Membrane permeability, a pivotal function involved in antibiotic resistance and virulence in Enterobacter aerogenes clinical isolates","volume":"18","author":"Lavigne","year":"2012","journal-title":"Clin. Microbiol. Infect."},{"key":"ref80","doi-asserted-by":"publisher","first-page":"D660","DOI":"10.1093\/nar\/gky1123","article-title":"ICEberg 2.0: an updated database of bacterial integrative and conjugative elements","volume":"47","author":"Liu","year":"2019","journal-title":"Nucleic Acids Res."},{"key":"ref81","doi-asserted-by":"publisher","first-page":"577","DOI":"10.2147\/IDR.S235975","article-title":"Carbapenem-resistant Klebsiella aerogenes clinical isolates from a teaching Hospital in Southwestern China: detailed molecular epidemiology, resistance determinants, risk factors and clinical outcomes","volume":"13","author":"Ma","year":"2020","journal-title":"Infect. Drug Resist."},{"key":"ref82","doi-asserted-by":"publisher","first-page":"3066","DOI":"10.1093\/jac\/dkw258","article-title":"Impact of AAC (6\u2032)-Ib-cr in combination with chromosomal-mediated mechanisms on clinical quinolone resistance in Escherichia coli","volume":"71","author":"Machuca","year":"2016","journal-title":"J. Antimicrob. Chemother."},{"key":"ref83","doi-asserted-by":"publisher","first-page":"268","DOI":"10.1111\/j.1469-0691.2011.03570.x","article-title":"Multidrug-resistant, extensively drug-resistant and pandrug-resistant bacteria: an international expert proposal for interim standard definitions for acquired resistance","volume":"18","author":"Magiorakos","year":"2012","journal-title":"Clin. Microbiol. Infect."},{"key":"ref84","doi-asserted-by":"publisher","first-page":"1695","DOI":"10.1128\/AAC.40.7.1695","article-title":"Identification for mar mutants among quinolone-resistant clinical isolates of Escherichia coli","volume":"40","author":"Maneewannakul","year":"1996","journal-title":"Antimicrob. Agents Chemother."},{"key":"ref85","doi-asserted-by":"publisher","first-page":"2559","DOI":"10.1016\/j.bbamem.2007.06.008","article-title":"The Enterobacter aerogenes outer membrane efflux proteins Tol C and Eef C have different channel properties","volume":"1768","author":"Masi","year":"2007","journal-title":"Biochim. Biophys. Acta Biomembr."},{"key":"ref86","doi-asserted-by":"publisher","first-page":"60","DOI":"10.1186\/1471-2105-14-60","article-title":"Genome sequence-based species delimitation with confidence intervals and improved distance functions","volume":"14","author":"Meier-Kolthoff","year":"2013","journal-title":"BMC Bioinformatics"},{"key":"ref87","doi-asserted-by":"publisher","first-page":"D801","DOI":"10.1093\/nar\/gkab902","article-title":"TYGS and LPSN: a database tandem for fast and reliable genome-based classification and nomenclature of prokaryotes","volume":"50","author":"Meier-Kolthoff","year":"2022","journal-title":"Nucleic Acids Res."},{"key":"ref88","doi-asserted-by":"publisher","DOI":"10.1128\/AAC.00806-18","article-title":"Genes and proteins involved in qnr S1 induction","volume":"62","author":"Mon\u00e1rrez","year":"2018","journal-title":"Antimicrob. Agents Chemother."},{"key":"ref89","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1155\/2021\/2145176","article-title":"Detection of Oqx AB efflux pumps, a multidrug-resistant agent in bacterial infection in patients referring to teaching hospitals in Ahvaz, southwest of Iran","volume":"2021","author":"Moosavian","year":"2021","journal-title":"Int. J. Microbiol."},{"key":"ref90","doi-asserted-by":"publisher","first-page":"539","DOI":"10.3389\/fmicb.2019.00539","article-title":"Emerging strategies to combat ESKAPE pathogens in the era of antimicrobial resistance: a review","volume":"10","author":"Mulani","year":"2019","journal-title":"Front. Microbiol."},{"key":"ref91","doi-asserted-by":"publisher","first-page":"4161","DOI":"10.1128\/JB.184.15.4161-4167.2002","article-title":"The putative response regulator bae R stimulates multidrug resistance of Escherichia coli via a novel multidrug exporter system, Mdt ABC","volume":"184","author":"Nagakubo","year":"2002","journal-title":"J. Bacteriol."},{"key":"ref92","doi-asserted-by":"publisher","first-page":"363","DOI":"10.1016\/j.resmic.2018.03.001","article-title":"RND transporters in the living world","volume":"169","author":"Nikaido","year":"2018","journal-title":"Res. Microbiol."},{"key":"ref93","doi-asserted-by":"publisher","first-page":"5803","DOI":"10.1128\/JB.183.20.5803-5812.2001","article-title":"Analysis of a complete library of putative drug transporter genes in Escherichia coli","volume":"183","author":"Nishino","year":"2001","journal-title":"J. Bacteriol."},{"key":"ref94","doi-asserted-by":"publisher","first-page":"1897","DOI":"10.3390\/w12071897","article-title":"Antibiotic resistance genes occurrence in wastewaters from selected pharmaceutical facilities in Nigeria","volume":"12","author":"Obayiuwana","year":"2020","journal-title":"Water (Basel)"},{"key":"ref95","doi-asserted-by":"publisher","first-page":"182","DOI":"10.3389\/fmicb.2017.00182","article-title":"Plasmid classification in an era of whole-genome sequencing: application in studies of antibiotic resistance epidemiology","volume":"8","author":"Orlek","year":"2017","journal-title":"Front. Microbiol."},{"key":"ref96","doi-asserted-by":"publisher","first-page":"73","DOI":"10.1186\/s12929-023-00960-0","article-title":"Various arrangements of mobile genetic elements among CC147 subpopulations of Klebsiella pneumoniae harboring Bla NDM-1: a comparative genomic analysis of carbapenem resistant strains","volume":"30","author":"Pajand","year":"2023","journal-title":"J. Biomed. Sci."},{"key":"ref97","doi-asserted-by":"publisher","first-page":"621527","DOI":"10.3389\/fpubh.2021.621527","article-title":"Emergence of NDM-5 producing Carbapenem-resistant Klebsiella aerogenes in a pediatric Hospital in Shanghai, China","volume":"9","author":"Pan","year":"2021","journal-title":"Front. Public Health"},{"key":"ref98","doi-asserted-by":"publisher","first-page":"1010","DOI":"10.3201\/eid2406.171648","article-title":"Genomic epidemiology of global Carbapenemase-producing Enterobacter spp., 2008\u20132014","volume":"24","author":"Peirano","year":"2018","journal-title":"Emerg. Infect. Dis."},{"key":"ref99","doi-asserted-by":"publisher","first-page":"948","DOI":"10.1093\/jac\/dkn341","article-title":"Plasmid-mediated quinolone resistance in Aeromonas allosaccharophila recovered from a Swiss lake","volume":"62","author":"Pic\u00e3o","year":"2008","journal-title":"J. Antimicrob. Chemother."},{"key":"ref100","doi-asserted-by":"publisher","first-page":"75","DOI":"10.1111\/j.1469-0691.2007.01865.x","article-title":"Genetic support of extended-spectrum \u03b2-lactamases","volume":"14","author":"Poirel","year":"2008","journal-title":"Clin. Microbiol. Infect."},{"key":"ref101","doi-asserted-by":"publisher","first-page":"1253","DOI":"10.1093\/molbev\/msn083","article-title":"jModelTest: Phylogenetic Model Averaging","volume":"25","author":"Posada","year":"2008","journal-title":"Mol. Biol. Evol."},{"key":"ref102","doi-asserted-by":"publisher","first-page":"2640","DOI":"10.1128\/AAC.46.8.2640-2643.2002","article-title":"The Acr AB-Tol C efflux pump contributes to multidrug resistance in the nosocomial pathogen Enterobacter aerogenes","volume":"46","author":"Pradel","year":"2002","journal-title":"Antimicrob. Agents Chemother."},{"key":"ref103","doi-asserted-by":"publisher","first-page":"516","DOI":"10.1111\/apm.12528","article-title":"Isolation of Enterobacter aerogenes carrying bla TEM-1 and Bla KPC-3 genes recovered from a hospital intensive care unit","volume":"124","author":"Pulcrano","year":"2016","journal-title":"APMIS"},{"key":"ref104","doi-asserted-by":"publisher","first-page":"39","DOI":"10.1016\/j.ijantimicag.2011.02.012","article-title":"Genetic regulation of the ram a locus and its expression in clinical isolates of Klebsiella pneumoniae","volume":"38","author":"Rosenblum","year":"2011","journal-title":"Int. J. Antimicrob. Agents"},{"key":"ref105","doi-asserted-by":"publisher","first-page":"12","DOI":"10.1128\/mBio.02060-21","article-title":"TnCentral: a prokaryotic transposable element database and web portal for transposon analysis","author":"Ross","year":"2021","journal-title":"mBio"},{"key":"ref106","doi-asserted-by":"publisher","first-page":"1929","DOI":"10.1099\/ijs.0.000161","article-title":"Cautionary tale of using 16S rRNA gene sequence similarity values in identification of human-associated bacterial species","volume":"65","author":"Rossi-Tamisier","year":"2015","journal-title":"Int. J. Syst. Evol. Microbiol."},{"key":"ref107","doi-asserted-by":"publisher","first-page":"3430","DOI":"10.1128\/AAC.00591-08","article-title":"Real-time PCR and statistical analyses of acr AB and ram a expression in clinical isolates of Klebsiella pneumoniae","volume":"52","author":"Ruzin","year":"2008","journal-title":"Antimicrob. Agents Chemother."},{"key":"ref108","doi-asserted-by":"publisher","first-page":"256","DOI":"10.1016\/j.jgar.2023.04.013","article-title":"Genomic analysis of fluoroquinolone-resistant Leclercia adecarboxylata carrying the ISKpn19-orf-qnr S1-\u0394IS3-Bla LAP-2 module in a synanthropic pigeon, Brazil","volume":"33","author":"Sano","year":"2023","journal-title":"J. Glob. Antimicrob. Resist."},{"key":"ref109","doi-asserted-by":"publisher","first-page":"2068","DOI":"10.1093\/bioinformatics\/btu153","article-title":"Prokka: rapid prokaryotic genome annotation","volume":"30","author":"Seemann","year":"2014","journal-title":"Bioinformatics"},{"key":"ref110","doi-asserted-by":"publisher","first-page":"79","DOI":"10.1186\/s13756-021-00941-8","article-title":"Novel chromosomal insertions of ISEcp1-Bla CTX-M-15 and diverse antimicrobial resistance genes in Zambian clinical isolates of Enterobacter cloacae and Escherichia coli","volume":"10","author":"Shawa","year":"2021","journal-title":"Antimicrob. Resist. Infect. Control"},{"key":"ref111","doi-asserted-by":"publisher","first-page":"3883","DOI":"10.2147\/IDR.S228130","article-title":"Coexistence of blaNDM-1 and rmt C on a transferrable plasmid of a novel ST192 Klebsiella aerogenes clinical isolate","volume":"12","author":"Shen","year":"2019","journal-title":"Infect. Drug Resist."},{"key":"ref112","doi-asserted-by":"publisher","first-page":"137","DOI":"10.4014\/jmb.1409.09041","article-title":"Characterization of trimethoprim-sulfamethoxazole resistance genes and their relatedness to class 1 Integron and insertion sequence common region in gram-negative Bacilli","volume":"25","author":"Shin","year":"2015","journal-title":"J. Microbiol. Biotechnol."},{"key":"ref113","doi-asserted-by":"publisher","first-page":"e80796","DOI":"10.1371\/journal.pone.0080796","article-title":"Immunoproteomic analysis of proteins expressed by two related pathogens, Burkholderia multivorans and Burkholderia cenocepacia, during human infection","volume":"8","author":"Shinoy","year":"2013","journal-title":"PLoS One"},{"key":"ref114","doi-asserted-by":"publisher","first-page":"D32","DOI":"10.1093\/nar\/gkj014","article-title":"ISfinder: the reference Centre for bacterial insertion sequences","volume":"34","author":"Siguier","year":"2006","journal-title":"Nucleic Acids Res."},{"key":"ref115","doi-asserted-by":"publisher","first-page":"865","DOI":"10.1111\/1574-6976.12067","article-title":"Bacterial insertion sequences: their genomic impact and diversity","volume":"38","author":"Siguier","year":"2014","journal-title":"FEMS Microbiol. Rev."},{"key":"ref116","doi-asserted-by":"publisher","first-page":"3210","DOI":"10.1093\/bioinformatics\/btv351","article-title":"BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs","volume":"31","author":"Sim\u00e3o","year":"2015","journal-title":"Bioinformatics"},{"key":"ref117","doi-asserted-by":"publisher","first-page":"1806","DOI":"10.1128\/AAC.02101-13","article-title":"Role of Omp a in the multidrug resistance phenotype of Acinetobacter baumannii","volume":"58","author":"Smani","year":"2014","journal-title":"Antimicrob. Agents Chemother."},{"key":"ref118","doi-asserted-by":"publisher","DOI":"10.1128\/spectrum.04415-22","article-title":"Brevundimonas brasiliensis sp. nov.: a new multidrug-resistant species isolated from a patient in Brazil","volume":"11","author":"Soares","year":"2023","journal-title":"Microbiol. Spectr."},{"key":"ref119","doi-asserted-by":"publisher","DOI":"10.1590\/0037-8682-0262-2020","article-title":"First report of a Bla NDM-resistant gene in a Klebsiella aerogenes clinical isolate from Brazil","volume":"54","author":"Soares","year":"2021","journal-title":"Rev. Soc. Bras. Med. Trop."},{"key":"ref120","doi-asserted-by":"publisher","first-page":"116624","DOI":"10.1016\/j.envpol.2021.116624","article-title":"\u03b2-Lactam antibiotics and antibiotic resistance in Asian lakes and rivers: an overview of contamination, sources and detection methods","volume":"275","author":"Sta Ana","year":"2021","journal-title":"Environ. Pollut."},{"key":"ref121","doi-asserted-by":"publisher","first-page":"3882","DOI":"10.1093\/bioinformatics\/btaa250","article-title":"Phigaro: high-throughput prophage sequence annotation","volume":"36","author":"Starikova","year":"2020","journal-title":"Bioinformatics"},{"key":"ref122","doi-asserted-by":"publisher","first-page":"270","DOI":"10.3389\/fcimb.2018.00270","article-title":"Local repressor Acr R regulates Acr AB efflux pump required for biofilm formation and virulence in Acinetobacter nosocomialis","volume":"8","author":"Subhadra","year":"2018","journal-title":"Front. Cell. Infect. Microbiol."},{"key":"ref123","doi-asserted-by":"publisher","DOI":"10.1128\/spectrum.00673-22","article-title":"Spread of Carbapenem-resistant Klebsiella pneumoniae clinical isolates producing NDM-type Metallo-\u03b2-lactamase in Myanmar","volume":"10","author":"Takei","year":"2022","journal-title":"Microbiol. Spectr."},{"key":"ref124","doi-asserted-by":"publisher","first-page":"1446","DOI":"10.1093\/cid\/ciz173","article-title":"A primer on amp C \u03b2-lactamases: necessary knowledge for an increasingly multidrug-resistant world","volume":"69","author":"Tamma","year":"2019","journal-title":"Clin. Infect. Dis."},{"key":"ref125","doi-asserted-by":"publisher","first-page":"52","DOI":"10.1186\/s13756-020-00711-y","article-title":"Emerging coexistence of three PMQR genes on a multiple resistance plasmid with a new surrounding genetic structure of qnr S2 in E. coli in China","volume":"9","author":"Tao","year":"2020","journal-title":"Antimicrob. Resist. Infect. Control"},{"key":"ref126","doi-asserted-by":"publisher","first-page":"039","DOI":"10.3855\/jidc.3380","article-title":"Antibiotic resistance and detection of the sul 2 gene in urinary isolates of Escherichia coli in patients from Brazil","volume":"8","author":"Teichmann","year":"2014","journal-title":"J. Infect. Develop. Countries"},{"key":"ref127","doi-asserted-by":"publisher","first-page":"451","DOI":"10.1186\/s12864-022-08678-3","article-title":"From a large-scale genomic analysis of insertion sequences to insights into their regulatory roles in prokaryotes","volume":"23","author":"Tempel","year":"2022","journal-title":"BMC Genomics"},{"key":"ref128","doi-asserted-by":"publisher","first-page":"1861","DOI":"10.3389\/fmicb.2019.01861","article-title":"Whole-genome sequencing redefines Shewanella taxonomy","volume":"10","author":"Thorell","year":"2019","journal-title":"Front. Microbiol."},{"key":"ref129","doi-asserted-by":"publisher","first-page":"105918","DOI":"10.1016\/j.ijantimicag.2020.105918","article-title":"Effects of different resistance mechanisms on antimicrobial resistance in Acinetobacter baumannii: a strategic system for screening and activity testing of new antibiotics","volume":"55","author":"Tsai","year":"2020","journal-title":"Int. J. Antimicrob. Agents"},{"key":"ref130","doi-asserted-by":"publisher","first-page":"1841","DOI":"10.1128\/JCM.06848-11","article-title":"Comparative evaluation of a prototype chromogenic medium (Chrom ID CARBA) for detecting carbapenemase-producing enterobacteriaceae in surveillance rectal swabs","volume":"50","author":"Vrioni","year":"2012","journal-title":"J. Clin. Microbiol."},{"key":"ref131","doi-asserted-by":"publisher","first-page":"2795","DOI":"10.3390\/microorganisms11112795","article-title":"Multidrug-resistant Escherichia coli isolate of Chinese bovine origin carrying the Bla CTX-M-55 gene located in IS26-mediated composite Translocatable units","volume":"11","author":"Wang","year":"2023","journal-title":"Microorganisms"},{"key":"ref9003","doi-asserted-by":"publisher","first-page":"e0159418","DOI":"10.1371\/journal.pone.0159418","article-title":"High Prevalence of Plasmid-Mediated Quinolone Resistance and IncQ Plasmids Carrying qnrS2 Gene in Bacteria from Rivers near Hospitals and Aquaculture in China","volume":"11","author":"Wen","year":"2016","journal-title":"PLoS One"},{"key":"ref132","doi-asserted-by":"publisher","first-page":"367","DOI":"10.1128\/JB.183.1.367-374.2001","article-title":"Evaluation of a structural model of Pseudomonas aeruginosa outer membrane protein Opr M, an efflux component involved in intrinsic antibiotic resistance","volume":"183","author":"Wong","year":"2001","journal-title":"J. Bacteriol."},{"key":"ref133","doi-asserted-by":"publisher","first-page":"3290","DOI":"10.1128\/AAC.00310-15","article-title":"Evolution and dissemination of Oqx AB-like efflux pumps, an emerging quinolone resistance determinant among members of Enterobacteriaceae","volume":"59","author":"Wong","year":"2015","journal-title":"Antimicrob. Agents Chemother."},{"key":"ref134","doi-asserted-by":"publisher","first-page":"W52","DOI":"10.1093\/nar\/gkz333","article-title":"Ortho Venn 2: a web server for whole-genome comparison and annotation of orthologous clusters across multiple species","volume":"47","author":"Xu","year":"2019","journal-title":"Nucleic Acids Res."},{"key":"ref135","doi-asserted-by":"publisher","first-page":"999","DOI":"10.2147\/IDR.S243197","article-title":"Molecular characterization of Carbapenem-resistant Serratia marcescens clinical isolates in a tertiary Hospital in Hangzhou, China","volume":"13","author":"Xu","year":"2020","journal-title":"Infect. Drug Resist."},{"key":"ref136","doi-asserted-by":"publisher","DOI":"10.1128\/spectrum.01032-23","article-title":"Identification and genetic characterization of conjugative plasmids encoding Coresistance to ciprofloxacin and cephalosporin in foodborne Vibrio spp","volume":"11","author":"Xu","year":"2023","journal-title":"Microbiol Spectr."},{"key":"ref137","doi-asserted-by":"publisher","first-page":"1613","DOI":"10.1099\/ijsem.0.001755","article-title":"Introducing EzBioCloud: a taxonomically united database of 16S rRNA gene sequences and whole-genome assemblies","volume":"67","author":"Yoon","year":"2017","journal-title":"Int. J. Syst. Evol. Microbiol."},{"key":"ref138","doi-asserted-by":"publisher","first-page":"3675","DOI":"10.1016\/j.psj.2020.03.064","article-title":"Role of Lsr R in the regulation of antibiotic sensitivity in avian pathogenic Escherichia coli","volume":"99","author":"Yu","year":"2020","journal-title":"Poult. Sci."},{"key":"ref139","doi-asserted-by":"publisher","first-page":"1153366","DOI":"10.3389\/fmicb.2023.1153366","article-title":"First report of coexistence of Bla KPC-2-, Bla NDM-1- and mcr-9-carrying plasmids in a clinical carbapenem-resistant Enterobacter hormaechei isolate","volume":"14","author":"Yuan","year":"2023","journal-title":"Front. Microbiol."},{"key":"ref140","doi-asserted-by":"publisher","first-page":"1008905","DOI":"10.3389\/fmicb.2022.1008905","article-title":"In silico characterization of Bla NDM-harboring plasmids in Klebsiella pneumoniae","volume":"13","author":"Zeng","year":"2022","journal-title":"Front. Microbiol."},{"key":"ref141","doi-asserted-by":"publisher","first-page":"98","DOI":"10.1016\/j.ebiom.2017.04.032","article-title":"Nationwide surveillance of clinical Carbapenem-resistant Enterobacteriaceae (CRE) strains in China","volume":"19","author":"Zhang","year":"2017","journal-title":"EBioMedicine"},{"key":"ref142","doi-asserted-by":"publisher","first-page":"729","DOI":"10.26599\/FSHW.2022.9250062","article-title":"Mobile genetic elements facilitate the transmission of antibiotic resistance genes in multidrug-resistant Enterobacteriaceae from duck farms","volume":"13","author":"Zheng","year":"2024","journal-title":"Food Sci. Human Wellness"}],"container-title":["Frontiers in Microbiology"],"original-title":[],"link":[{"URL":"https:\/\/www.frontiersin.org\/articles\/10.3389\/fmicb.2024.1352851\/full","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2024,2,15]],"date-time":"2024-02-15T14:26:01Z","timestamp":1708007161000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.frontiersin.org\/articles\/10.3389\/fmicb.2024.1352851\/full"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2024,2,14]]},"references-count":147,"alternative-id":["10.3389\/fmicb.2024.1352851"],"URL":"https:\/\/doi.org\/10.3389\/fmicb.2024.1352851","relation":{},"ISSN":["1664-302X"],"issn-type":[{"value":"1664-302X","type":"electronic"}],"subject":[],"published":{"date-parts":[[2024,2,14]]},"article-number":"1352851"}}