{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,6,9]],"date-time":"2026-06-09T11:59:20Z","timestamp":1781006360712,"version":"3.54.1"},"reference-count":59,"publisher":"Frontiers Media SA","license":[{"start":{"date-parts":[[2023,8,28]],"date-time":"2023-08-28T00:00:00Z","timestamp":1693180800000},"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":"Background<\/jats:title>Aminoglycosides, as important clinical antimicrobials, are used as second-line drugs for treating multidrug-resistant tuberculosis or combined with \u03b2-lactam drugs for treating severe infections such as sepsis. Aminoglycoside-modifying enzyme (AME) is the most important mechanism of aminoglycoside resistance and deserves more attention.<\/jats:p><\/jats:sec>Methods<\/jats:title>The bacterium Kluyvera intermedia<\/jats:italic> DW18 was isolated from the sewage of an animal farm using the conventional method. The agar dilution method was used to determine the minimum inhibitory concentrations (MICs) of antimicrobials. A novel resistance gene was cloned, and the enzyme was expressed. The kinetic parameters were measured by a SpectraMax M5 multifunctional microplate reader. Bioinformatic analysis was performed to reveal the genetic context of the aph(3\u2032)-Id<\/jats:italic> gene and its phylogenetic relationship with other AMEs.<\/jats:p><\/jats:sec>Results<\/jats:title>A novel aminoglycoside 3\u2032-O<\/jats:italic>-phosphotransferase gene designated aph(3\u2032)-Id<\/jats:italic> was identified in K. intermedia<\/jats:italic> DW18 and shared the highest amino acid identity of 77.49% with the functionally characterized aminoglycoside 3\u2032-O<\/jats:italic>-phosphotransferase APH(3\u2032)-Ia. The recombinant plasmid carrying the novel resistance gene (pMD19-aph(3\u2032)-Id<\/jats:italic>\/E. coli<\/jats:italic> DH5\u03b1) showed 1,024-, 512-, 128- and 16-fold increased MIC levels for kanamycin, ribostamycin, paromomycin and neomycin, respectively, compared with the reference strain DH5\u03b1. APH(3\u2032)-Id showed the highest catalytic efficiency for ribostamycin [k<\/jats:italic>cat<\/jats:sub>\/K<\/jats:italic>m<\/jats:sub> of (4.96 \u00b1 1.63) \u00d7 105<\/jats:sup> M\u22121<\/jats:sup>\/s\u22121<\/jats:sup>], followed by paromomycin [k<\/jats:italic>cat<\/jats:sub>\/K<\/jats:italic>m<\/jats:sub> of (2.18 \u00b1 0.21) \u00d7 105<\/jats:sup> M\u22121<\/jats:sup>\/s\u22121<\/jats:sup>], neomycin [k<\/jats:italic>cat<\/jats:sub>\/K<\/jats:italic>m<\/jats:sub> of (1.73 \u00b1 0.20) \u00d7 105<\/jats:sup> M\u22121<\/jats:sup>\/s\u22121<\/jats:sup>], and kanamycin [k<\/jats:italic>cat<\/jats:sub>\/K<\/jats:italic>m<\/jats:sub> of (1.10 \u00b1 0.18) \u00d7 105<\/jats:sup> M\u22121<\/jats:sup>\/s\u22121<\/jats:sup>]. Three conserved functional domains of the aminoglycoside phosphotransferase family and ten amino acid residues responsible for the phosphorylation of kanamycin were found in the amino acid sequence of APH(3\u2032)-Id. No mobile genetic element (MGE) was discovered surrounding the aph(3\u2032)-Id<\/jats:italic> gene.<\/jats:p><\/jats:sec>Conclusion<\/jats:title>In this work, a novel aminoglycoside 3\u2019-O<\/jats:italic>-phosphotransferase gene designated aph(3\u2032)-Id<\/jats:italic> encoded in the chromosome of the environmental isolate Kluyvera intermedia<\/jats:italic> DW18 was identified and characterized. These findings will help clinicians select effective antimicrobials to treat infections caused by pathogens with this kind of resistance gene.<\/jats:p><\/jats:sec>","DOI":"10.3389\/fmicb.2023.1224464","type":"journal-article","created":{"date-parts":[[2023,8,28]],"date-time":"2023-08-28T12:28:45Z","timestamp":1693225725000},"update-policy":"https:\/\/doi.org\/10.3389\/crossmark-policy","source":"Crossref","is-referenced-by-count":5,"title":["Identification and characterization of a novel chromosomal aminoglycoside 3\u2019-O-phosphotransferase, APH(3\u2032)-Id, from Kluyvera intermedia DW18 isolated from the sewage of an animal farm"],"prefix":"10.3389","volume":"14","author":[{"given":"Yuning","family":"Sha","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Naru","family":"Lin","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Guozhi","family":"Zhang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yuan","family":"Zhang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jingxuan","family":"Zhao","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Junwan","family":"Lu","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Tingting","family":"Zhu","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Xueya","family":"Zhang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Qiaoling","family":"Li","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Hailin","family":"Zhang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Xi","family":"Lin","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Kewei","family":"Li","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Qiyu","family":"Bao","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Dong","family":"Li","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1965","published-online":{"date-parts":[[2023,8,28]]},"reference":[{"key":"ref1","doi-asserted-by":"publisher","first-page":"D690","DOI":"10.1093\/nar\/gkac920","article-title":"CARD 2023: expanded curation, support for machine learning, and resistome prediction at the comprehensive antibiotic resistance database","volume":"51","author":"Alcock","year":"2023","journal-title":"Nucleic Acids Res."},{"key":"ref2","doi-asserted-by":"publisher","first-page":"106","DOI":"10.1054\/drup.2001.0197","article-title":"Aminoglycoside-modifying enzymes: mechanisms of catalytic processes and inhibition","volume":"4","author":"Azucena","year":"2001","journal-title":"Drug Resist. Updat."},{"key":"ref3","doi-asserted-by":"publisher","first-page":"648","DOI":"10.3389\/fmicb.2014.00648","article-title":"Shotgun metagenomics reveals a wide array of antibiotic resistance genes and mobile elements in a polluted lake in India","volume":"5","author":"Bengtsson-Palme","year":"2014","journal-title":"Front. Microbiol."},{"key":"ref4","doi-asserted-by":"publisher","first-page":"366","DOI":"10.1038\/s41592-021-01101-x","article-title":"Sensitive protein alignments at tree-of-life scale using DIAMOND","volume":"18","author":"Buchfink","year":"2021","journal-title":"Nat. Methods"},{"key":"ref5","doi-asserted-by":"publisher","first-page":"887","DOI":"10.1183\/13993003.00432-2015","article-title":"Classification of antituberculosis drugs: a new proposal based on the most recent evidence","volume":"46","author":"Caminero","year":"2015","journal-title":"Eur. Respir. J."},{"key":"ref6","doi-asserted-by":"publisher","first-page":"334","DOI":"10.1309\/61xp-4ktl-jywm-5h35","article-title":"Clinically significant Kluyvera infections: a report of seven cases","volume":"123","author":"Carter","year":"2005","journal-title":"Am. J. Clin. Pathol."},{"key":"ref7","doi-asserted-by":"publisher","first-page":"1011","DOI":"10.2174\/1389203721666200915113630","article-title":"Development of peptides that inhibit aminoglycoside-modifying enzymes and \u03b2-lactamases for control of resistant Bacteria","volume":"21","author":"Costa","year":"2020","journal-title":"Curr. Protein Pept. Sci."},{"key":"ref8","doi-asserted-by":"publisher","first-page":"457","DOI":"10.1038\/nature10388","article-title":"Antibiotic resistance is ancient","volume":"477","author":"D\u2019Costa","year":"2011","journal-title":"Nature"},{"key":"ref9","doi-asserted-by":"publisher","first-page":"580","DOI":"10.1097\/CCM.0b013e31827e83af","article-title":"Surviving sepsis campaign: international guidelines for management of severe sepsis and septic shock: 2012","volume":"41","author":"Dellinger","year":"2013","journal-title":"Crit. Care Med."},{"key":"ref10","doi-asserted-by":"publisher","first-page":"270","DOI":"10.1016\/j.jhazmat.2011.05.018","article-title":"Enhanced tolerance and remediation of anthracene by transgenic tobacco plants expressing a fungal glutathione transferase gene","volume":"192","author":"Dixit","year":"2011","journal-title":"J. Hazard. Mater."},{"key":"ref11","doi-asserted-by":"publisher","first-page":"e00086","DOI":"10.3389\/fmicb.2013.00086","article-title":"Mobile elements, zoonotic pathogens and commensal bacteria: conduits for the delivery of resistance genes into humans, production animals and soil microbiota","volume":"4","author":"Djordjevic","year":"2013","journal-title":"Front. Microbiol."},{"key":"ref12","doi-asserted-by":"publisher","first-page":"88","DOI":"10.1086\/518605","article-title":"16S ribosomal RNA methylation: emerging resistance mechanism against aminoglycosides","volume":"45","author":"Doi","year":"2007","journal-title":"Clin. Infect. Dis."},{"key":"ref13","doi-asserted-by":"publisher","first-page":"919","DOI":"10.1128\/jcm.13.5.919-933.1981","article-title":"Kluyvera, a new (redefined) genus in the family Enterobacteriaceae: identification of Kluyvera ascorbata sp. nov. and Kluyvera cryocrescens sp. nov. in clinical specimens","volume":"13","author":"Farmer","year":"1981","journal-title":"J. Clin. Microbiol."},{"key":"ref14","doi-asserted-by":"publisher","first-page":"1107","DOI":"10.1126\/science.1220761","article-title":"The shared antibiotic resistome of soil bacteria and human pathogens","volume":"337","author":"Forsberg","year":"2012","journal-title":"Science"},{"key":"ref15","doi-asserted-by":"publisher","first-page":"3784","DOI":"10.1093\/nar\/gkg563","article-title":"ExPASy: the proteomics server for in-depth protein knowledge and analysis","volume":"31","author":"Gasteiger","year":"2003","journal-title":"Nucleic Acids Res."},{"key":"ref16","doi-asserted-by":"publisher","first-page":"2473","DOI":"10.1093\/bioinformatics\/btab007","article-title":"Clinker & clustermap.Js: automatic generation of gene cluster comparison figures","volume":"37","author":"Gilchrist","year":"2021","journal-title":"Bioinformatics"},{"key":"ref17","doi-asserted-by":"crossref","first-page":"197","DOI":"10.1007\/0-387-30746-X_9","article-title":"The genus Enterobacter","volume-title":"The prokaryotes: A handbook on the biology of Bacteria volume 6: Proteobacteria: Gamma subclass","author":"Grimont","year":"2006"},{"key":"ref18","doi-asserted-by":"publisher","first-page":"854","DOI":"10.1104\/pp.114.237180","article-title":"Arabidopsis glutathione transferases U24 and U25 exhibit a range of detoxification activities with the environmental pollutant and explosive, 2,4,6-trinitrotoluene","volume":"165","author":"Gunning","year":"2014","journal-title":"Plant Physiol."},{"key":"ref19","doi-asserted-by":"publisher","first-page":"887","DOI":"10.1016\/s0092-8674(00)80274-3","article-title":"Structure of an enzyme required for aminoglycoside antibiotic resistance reveals homology to eukaryotic protein kinases","volume":"89","author":"Hon","year":"1997","journal-title":"Cells"},{"key":"ref20","doi-asserted-by":"publisher","first-page":"5114","DOI":"10.1038\/s41467-018-07641-9","article-title":"High throughput ANI analysis of 90K prokaryotic genomes reveals clear species boundaries","volume":"9","author":"Jain","year":"2018","journal-title":"Nat. Commun."},{"key":"ref21","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":"ref22","doi-asserted-by":"publisher","first-page":"6964","DOI":"10.1074\/jbc.M513257200","article-title":"Hydrolysis of ATP by aminoglycoside 3\u2032-phosphotransferases: an unexpected cost to bacteria for harboring an antibiotic resistance enzyme","volume":"281","author":"Kim","year":"2006","journal-title":"J. Biol. Chem."},{"key":"ref23","doi-asserted-by":"publisher","first-page":"1141","DOI":"10.1107\/s1744309106042072","article-title":"Crystallization and initial crystallographic characterization of the Corynebacterium glutamicum nitrilotriacetate monooxygenase component a","volume":"62","author":"Kim","year":"2006","journal-title":"Acta Crystallogr. Sect. F Struct. Biol. Cryst. Commun."},{"key":"ref24","doi-asserted-by":"publisher","first-page":"2567","DOI":"10.1073\/pnas.0409727102","article-title":"Genomic insights that advance the species definition for prokaryotes","volume":"102","author":"Konstantinidis","year":"2005","journal-title":"Proc. Natl. Acad. Sci. U. S. A."},{"key":"ref25","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1101\/cshperspect.a027029","article-title":"Aminoglycosides: an overview","volume":"6","author":"Krause","year":"2016","journal-title":"Cold Spring Harb. Perspect. Med."},{"key":"ref26","doi-asserted-by":"publisher","first-page":"W293","DOI":"10.1093\/nar\/gkab301","article-title":"Interactive tree of life (iTOL) v5: an online tool for phylogenetic tree display and annotation","volume":"49","author":"Letunic","year":"2021","journal-title":"Nucleic Acids Res."},{"key":"ref27","doi-asserted-by":"publisher","first-page":"2787","DOI":"10.1093\/jac\/dkab272","article-title":"Identification and characteristics of a novel aminoglycoside phosphotransferase, APH(3\u2032)-IId, from an MDR clinical isolate of Brucella intermedia","volume":"76","author":"Lu","year":"2021","journal-title":"J. Antimicrob. Chemother."},{"key":"ref28","doi-asserted-by":"publisher","first-page":"3375","DOI":"10.1128\/aac.45.12.3375-3380.2001","article-title":"Resistance-nodulation-cell division-type efflux pump involved in aminoglycoside resistance in Acinetobacter baumannii strain BM4454","volume":"45","author":"Magnet","year":"2001","journal-title":"Antimicrob. Agents Chemother."},{"key":"ref29","doi-asserted-by":"publisher","first-page":"365","DOI":"10.1126\/science.1159483","article-title":"Antibiotics and antibiotic resistance genes in natural environments","volume":"321","author":"Mart\u00ednez","year":"2008","journal-title":"Science"},{"key":"ref30","doi-asserted-by":"publisher","first-page":"3348","DOI":"10.1128\/aac.00419-13","article-title":"The comprehensive antibiotic resistance database","volume":"57","author":"McArthur","year":"2013","journal-title":"Antimicrob. Agents Chemother."},{"key":"ref31","doi-asserted-by":"publisher","first-page":"611","DOI":"10.1002\/elsc.200720218","article-title":"Dechlorination of pesticides by a specific bacterial glutathione S-transferase, BphKLB400: potential for bioremediation","volume":"7","author":"Mcguinness","year":"2007","journal-title":"Eng. Life Sci."},{"key":"ref32","doi-asserted-by":"publisher","first-page":"268","DOI":"10.1093\/molbev\/msu300","article-title":"IQ-TREE: a fast and effective stochastic algorithm for estimating maximum-likelihood phylogenies","volume":"32","author":"Nguyen","year":"2015","journal-title":"Mol. Biol. Evol."},{"key":"ref33","first-page":"4","volume-title":"GeneDoc: Analysis and visualization of genetic variation","author":"Nicholas","year":"1997"},{"key":"ref34","doi-asserted-by":"publisher","first-page":"491","DOI":"10.1016\/s0022-2836(03)00121-9","article-title":"The crystal structure of aminoglycoside-3\u2032-phosphotransferase-IIa, an enzyme responsible for antibiotic resistance","volume":"327","author":"Nurizzo","year":"2003","journal-title":"J. Mol. Biol."},{"key":"ref35","doi-asserted-by":"publisher","first-page":"217","DOI":"10.1016\/0022-2836(81)90438-1","article-title":"Nucleotide sequence of the kanamycin resistance transposon Tn903","volume":"147","author":"Oka","year":"1981","journal-title":"J. Mol. Biol."},{"key":"ref36","doi-asserted-by":"publisher","first-page":"e01549","DOI":"10.3389\/fmicb.2018.01549","article-title":"Characterization of NDM-encoding plasmids from Enterobacteriaceae recovered from Czech hospitals","volume":"9","author":"Paskova","year":"2018","journal-title":"Front. Microbiol."},{"key":"ref37","doi-asserted-by":"publisher","first-page":"437","DOI":"10.1099\/ijs.0.63071-0","article-title":"Phylogenetic relationships of the genus Kluyvera: transfer of Enterobacter intermedius izard et al. 1980 to the genus Kluyvera as Kluyvera intermedia comb. nov. and reclassification of Kluyvera cochleae as a later synonym of K. intermedia","volume":"55","author":"Pavan","year":"2005","journal-title":"Int. J. Syst. Evol. Microbiol."},{"key":"ref38","doi-asserted-by":"publisher","first-page":"422","DOI":"10.1016\/s0176-6724(87)80222-5","article-title":"Human isolates of Enterobacter intermedium","volume":"266","author":"Prats","year":"1987","journal-title":"Zentralbl Bakteriol Mikrobiol Hyg A"},{"key":"ref39","doi-asserted-by":"publisher","first-page":"877","DOI":"10.1038\/nbt984","article-title":"Cold-shock induced high-yield protein production in Escherichia coli","volume":"22","author":"Qing","year":"2004","journal-title":"Nat. Biotechnol."},{"key":"ref40","doi-asserted-by":"publisher","first-page":"151","DOI":"10.1016\/j.drup.2010.08.003","article-title":"Aminoglycoside modifying enzymes","volume":"13","author":"Ramirez","year":"2010","journal-title":"Drug Resist. Updat."},{"key":"ref41","doi-asserted-by":"publisher","first-page":"622","DOI":"10.1128\/aac.02271-13","article-title":"Detection of BlaGES-5 in Carbapenem-resistant Kluyvera intermedia isolates recovered from the hospital environment","volume":"58","author":"Ribeiro","year":"2014","journal-title":"Antimicrob. Agents Chemother."},{"key":"ref42","doi-asserted-by":"publisher","first-page":"1249","DOI":"10.1128\/aac.45.4.1249-1253.2001","article-title":"In70 of plasmid pAX22, a Bla(VIM-1)-containing integron carrying a new aminoglycoside phosphotransferase gene cassette","volume":"45","author":"Riccio","year":"2001","journal-title":"Antimicrob. Agents Chemother."},{"key":"ref43","doi-asserted-by":"publisher","first-page":"19126","DOI":"10.1073\/pnas.0906412106","article-title":"Shifting the genomic gold standard for the prokaryotic species definition","volume":"106","author":"Richter","year":"2009","journal-title":"Proc. Natl. Acad. Sci. U. S. A."},{"key":"ref44","article-title":"PyMOL","author":"Schr\u00f6dinger","year":"2023"},{"key":"ref45","doi-asserted-by":"publisher","first-page":"140","DOI":"10.1186\/s40168-017-0360-9","article-title":"Towards a balanced view of the bacterial tree of life","volume":"5","author":"Schulz","year":"2017","journal-title":"Microbiome"},{"key":"ref46","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":"ref47","doi-asserted-by":"publisher","first-page":"138","DOI":"10.1128\/mr.57.1.138-163.1993","article-title":"Molecular genetics of aminoglycoside resistance genes and familial relationships of the aminoglycoside-modifying enzymes","volume":"57","author":"Shaw","year":"1993","journal-title":"Microbiol. Rev."},{"key":"ref48","doi-asserted-by":"publisher","first-page":"12681","DOI":"10.1021\/bi00039a026","article-title":"Purification, characterization, and investigation of the mechanism of aminoglycoside 3\u2032-phosphotransferase type Ia","volume":"34","author":"Siregar","year":"1995","journal-title":"Biochemistry"},{"key":"ref49","doi-asserted-by":"publisher","first-page":"1129","DOI":"10.1107\/s2059798319015079","article-title":"Structural basis for the diversity of the mechanism of nucleotide hydrolysis by the aminoglycoside-2-phosphotransferases","volume":"75","author":"Smith","year":"2019","journal-title":"Acta Crystallogr D Struct Biol"},{"key":"ref50","doi-asserted-by":"publisher","first-page":"153","DOI":"10.1186\/s13059-018-1540-z","article-title":"SKESA: strategic k-mer extension for scrupulous assemblies","volume":"19","author":"Souvorov","year":"2018","journal-title":"Genome Biol."},{"key":"ref51","doi-asserted-by":"publisher","first-page":"444","DOI":"10.1179\/joc.2002.14.5.444","article-title":"Natural antibiotic susceptibility of Enterobacter spp., with special reference to Enterobacter aerogenes and Enterobacter intermedius strains","volume":"14","author":"Stock","year":"2002","journal-title":"J. Chemother."},{"key":"ref52","doi-asserted-by":"publisher","first-page":"191","DOI":"10.1042\/bj20130317","article-title":"Structure-guided optimization of protein kinase inhibitors reverses aminoglycoside antibiotic resistance","volume":"454","author":"Stogios","year":"2013","journal-title":"Biochem. J."},{"key":"ref53","doi-asserted-by":"publisher","first-page":"67","DOI":"10.3389\/fmicb.2012.00067","article-title":"Distribution of quinolones, sulfonamides, tetracyclines in aquatic environment and antibiotic resistance in indochina","volume":"3","author":"Suzuki","year":"2012","journal-title":"Front. Microbiol."},{"key":"ref54","doi-asserted-by":"publisher","first-page":"452","DOI":"10.1128\/aac.02049-12","article-title":"Novel aminoglycoside 2-phosphotransferase identified in a gram-negative pathogen","volume":"57","author":"Toth","year":"2013","journal-title":"Antimicrob. Agents Chemother."},{"key":"ref55","doi-asserted-by":"publisher","first-page":"497","DOI":"10.1016\/j.celrep.2013.01.027","article-title":"The impact of aminoglycosides on the dynamics of translation elongation","volume":"3","author":"Tsai","year":"2013","journal-title":"Cell Rep."},{"key":"ref56","doi-asserted-by":"publisher","first-page":"430","DOI":"10.1128\/cmr.16.3.430-450.2003","article-title":"Versatility of aminoglycosides and prospects for their future","volume":"16","author":"Vakulenko","year":"2003","journal-title":"Clin. Microbiol. Rev."},{"key":"ref57","doi-asserted-by":"publisher","first-page":"e112963","DOI":"10.1371\/journal.pone.0112963","article-title":"Pilon: an integrated tool for comprehensive microbial variant detection and genome assembly improvement","volume":"9","author":"Walker","year":"2014","journal-title":"PLoS One"},{"key":"ref58","doi-asserted-by":"publisher","first-page":"W296","DOI":"10.1093\/nar\/gky427","article-title":"SWISS-MODEL: homology modelling of protein structures and complexes","volume":"46","author":"Waterhouse","year":"2018","journal-title":"Nucleic Acids Res."},{"key":"ref59","doi-asserted-by":"publisher","first-page":"e1005595","DOI":"10.1371\/journal.pcbi.1005595","article-title":"Unicycler: resolving bacterial genome assemblies from short and long sequencing reads","volume":"13","author":"Wick","year":"2017","journal-title":"PLoS Comput. Biol."}],"container-title":["Frontiers in Microbiology"],"original-title":[],"link":[{"URL":"https:\/\/www.frontiersin.org\/articles\/10.3389\/fmicb.2023.1224464\/full","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,8,28]],"date-time":"2023-08-28T12:28:48Z","timestamp":1693225728000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.frontiersin.org\/articles\/10.3389\/fmicb.2023.1224464\/full"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2023,8,28]]},"references-count":59,"alternative-id":["10.3389\/fmicb.2023.1224464"],"URL":"https:\/\/doi.org\/10.3389\/fmicb.2023.1224464","relation":{},"ISSN":["1664-302X"],"issn-type":[{"value":"1664-302X","type":"electronic"}],"subject":[],"published":{"date-parts":[[2023,8,28]]},"article-number":"1224464"}}