{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,25]],"date-time":"2026-09-25T00:22:10Z","timestamp":1790295730553,"version":"4.1.0"},"reference-count":75,"publisher":"MDPI AG","issue":"3","license":[{"start":{"date-parts":[[2021,3,14]],"date-time":"2021-03-14T00:00:00Z","timestamp":1615680000000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100010661","name":"Horizon 2020 Framework Programme","doi-asserted-by":"publisher","award":["773830"],"award-info":[{"award-number":["773830"]}],"id":[{"id":"10.13039\/100010661","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Microorganisms"],"abstract":"<jats:p>Antimicrobial resistance (AMR) is a major threat to public health worldwide. Currently, AMR typing changes from phenotypic testing to whole-genome sequence (WGS)-based detection of resistance determinants for a better understanding of the isolate diversity and elements involved in gene transmission (e.g., plasmids, bacteriophages, transposons). However, the use of WGS data in monitoring purposes requires suitable techniques, standardized parameters and approved guidelines for reliable AMR gene detection and prediction of their association with mobile genetic elements (plasmids). In this study, different sequencing and assembly strategies were tested for their suitability in AMR monitoring in Escherichia coli in the routines of the German National Reference Laboratory for Antimicrobial Resistances. To assess the outcomes of the different approaches, results from in silico predictions were compared with conventional phenotypic- and genotypic-typing data. With the focus on (fluoro)quinolone-resistant E.coli, five qnrS-positive isolates with multiple extrachromosomal elements were subjected to WGS with NextSeq (Illumina), PacBio (Pacific BioSciences) and ONT (Oxford Nanopore) for in depth characterization of the qnrS1-carrying plasmids. Raw reads from short- and long-read sequencing were assembled individually by Unicycler or Flye or a combination of both (hybrid assembly). The generated contigs were subjected to bioinformatics analysis. Based on the generated data, assembly of long-read sequences are error prone and can yield in a loss of small plasmid genomes. In contrast, short-read sequencing was shown to be insufficient for the prediction of a linkage of AMR genes (e.g., qnrS1) to specific plasmid sequences. Furthermore, short-read sequencing failed to detect certain duplications and was unsuitable for genome finishing. Overall, the hybrid assembly led to the most comprehensive typing results, especially in predicting associations of AMR genes and mobile genetic elements. Thus, the use of different sequencing technologies and hybrid assemblies currently represents the best approach for reliable AMR typing and risk assessment.<\/jats:p>","DOI":"10.3390\/microorganisms9030598","type":"journal-article","created":{"date-parts":[[2021,3,14]],"date-time":"2021-03-14T23:52:06Z","timestamp":1615765926000},"page":"598","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":60,"title":["Outcome of Different Sequencing and Assembly Approaches on the Detection of Plasmids and Localization of Antimicrobial Resistance Genes in Commensal Escherichia coli"],"prefix":"10.3390","volume":"9","author":[{"given":"Katharina","family":"Juraschek","sequence":"first","affiliation":[{"name":"Epidemiology, Zoonoses and Antimicrobial Resistance, German Federal Institute for Risk Assessment (BfR), Max-Dohrn Str. 8-10, 10589 Berlin, Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Maria","family":"Borowiak","sequence":"additional","affiliation":[{"name":"Study Centre for Genome Sequencing and Analysis, German Federal Institute for Risk Assessment (BfR), Max-Dohrn Str. 8-10, 10589 Berlin, Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-6874-233X","authenticated-orcid":false,"given":"Simon H.","family":"Tausch","sequence":"additional","affiliation":[{"name":"Study Centre for Genome Sequencing and Analysis, German Federal Institute for Risk Assessment (BfR), Max-Dohrn Str. 8-10, 10589 Berlin, Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3363-8225","authenticated-orcid":false,"given":"Burkhard","family":"Malorny","sequence":"additional","affiliation":[{"name":"Study Centre for Genome Sequencing and Analysis, German Federal Institute for Risk Assessment (BfR), Max-Dohrn Str. 8-10, 10589 Berlin, Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2966-2713","authenticated-orcid":false,"given":"Annemarie","family":"K\u00e4sbohrer","sequence":"additional","affiliation":[{"name":"Epidemiology, Zoonoses and Antimicrobial Resistance, German Federal Institute for Risk Assessment (BfR), Max-Dohrn Str. 8-10, 10589 Berlin, Germany"},{"name":"Unit for Veterinary Public Health and Epidemiology, University of Veterinary Medicine, Veterinaerplatz 1, 1210 Vienna, Austria"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Saria","family":"Otani","sequence":"additional","affiliation":[{"name":"DTU Food, National Food Institute, Technical University of Denmark, Kemitorvet, Building 204, 2800 Kgs Lyngby, Denmark"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-6303-8212","authenticated-orcid":false,"given":"Stefan","family":"Schwarz","sequence":"additional","affiliation":[{"name":"Institute of Microbiology and Epizootics, Department of Veterinary Medicine, Freie Universit\u00e4t Berlin, 14163 Berlin, Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4824-048X","authenticated-orcid":false,"given":"Diana","family":"Meemken","sequence":"additional","affiliation":[{"name":"Institute of Food Safety and Food Hygiene, Working Group Meat Hygiene, Department of Veterinary Medicine, Freie Universit\u00e4t Berlin, 14163 Berlin, Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Carlus","family":"Deneke","sequence":"additional","affiliation":[{"name":"Study Centre for Genome Sequencing and Analysis, German Federal Institute for Risk Assessment (BfR), Max-Dohrn Str. 8-10, 10589 Berlin, Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-6930-4358","authenticated-orcid":false,"given":"Jens Andre","family":"Hammerl","sequence":"additional","affiliation":[{"name":"Epidemiology, Zoonoses and Antimicrobial Resistance, German Federal Institute for Risk Assessment (BfR), Max-Dohrn Str. 8-10, 10589 Berlin, Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1968","published-online":{"date-parts":[[2021,3,14]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"545","DOI":"10.1089\/fpd.2017.2283","article-title":"National Antimicrobial Resistance Monitoring System: Two Decades of Advancing Public Health Through Integrated Surveillance of Antimicrobial Resistance","volume":"14","author":"Karp","year":"2017","journal-title":"Foodborne Pathog. Dis."},{"key":"ref_2","doi-asserted-by":"crossref","first-page":"115","DOI":"10.1016\/bs.afnr.2018.04.004","article-title":"Antimicrobial Resistance in the Food Chain in the European Union","volume":"86","author":"Moreno","year":"2018","journal-title":"Adv. Food Nutr. Res."},{"key":"ref_3","doi-asserted-by":"crossref","first-page":"78","DOI":"10.1111\/nyas.13289","article-title":"Antimicrobial resistance surveillance in the genomic age","volume":"1388","author":"McArthur","year":"2017","journal-title":"Ann. N. Y. Acad. Sci."},{"key":"ref_4","doi-asserted-by":"crossref","first-page":"577","DOI":"10.1016\/j.cmi.2017.09.013","article-title":"Review of antimicrobial resistance surveillance programmes in livestock and meat in EU with focus on humans","volume":"24","author":"Schrijver","year":"2018","journal-title":"Clin. Microbiol. Infect."},{"key":"ref_5","doi-asserted-by":"crossref","first-page":"957","DOI":"10.2147\/IDR.S237038","article-title":"Monitoring Antimicrobial Resistance and Drug Usage in the Human and Livestock Sector and Foodborne Antimicrobial Resistance in Six European Countries","volume":"13","author":"Varona","year":"2020","journal-title":"Infect. Drug Resist."},{"key":"ref_6","doi-asserted-by":"crossref","unstructured":"Angers-Loustau, A., Petrillo, M., Bengtsson-Palme, J., Berendonk, T., Blais, B., Chan, K.-G., Coque, T.M., Hammer, P., He\u00df, S., and Kagkli, D.M. (2018). The challenges of designing a benchmark strategy for bioinformatics pipelines in the identification of antimicrobial resistance determinants using next generation sequencing technologies. F1000Research, 7.","DOI":"10.12688\/f1000research.14509.2"},{"key":"ref_7","doi-asserted-by":"crossref","unstructured":"EFSA (2018). The European Union summary report on antimicrobial resistance in zoonotic and indicator bacteria from humans, animals and food in 2016. EFSA J., 16, e05182.","DOI":"10.2903\/j.efsa.2018.5182"},{"key":"ref_8","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1016\/j.meegid.2018.01.014","article-title":"Evaluating the use of whole-genome sequencing for outbreak investigations in the lack of closely related reference genome","volume":"59","author":"Abdelbary","year":"2018","journal-title":"Infect. Genet. Evol."},{"key":"ref_9","doi-asserted-by":"crossref","first-page":"1829","DOI":"10.3389\/fmicb.2017.01829","article-title":"Review on the Applications of Next Generation Sequencing Technologies as Applied to Food-Related Microbiome Studies","volume":"8","author":"Cao","year":"2017","journal-title":"Front. Microbiol."},{"key":"ref_10","doi-asserted-by":"crossref","first-page":"110","DOI":"10.1016\/j.mib.2014.11.014","article-title":"One chromosome, one contig: Complete microbial genomes from long-read sequencing and assembly","volume":"23","author":"Koren","year":"2015","journal-title":"Curr. Opin. Microbiol."},{"key":"ref_11","doi-asserted-by":"crossref","first-page":"252","DOI":"10.1016\/j.jgar.2019.10.013","article-title":"Extended-spectrum \u03b2-lactamase-producing Proteus mirabilis with multidrug resistance isolated from raw chicken in Singapore: Genotypic and phenotypic analysis","volume":"19","author":"Guo","year":"2019","journal-title":"J. Glob. Antimicrob. Resist."},{"key":"ref_12","doi-asserted-by":"crossref","first-page":"a036798","DOI":"10.1101\/cshperspect.a036798","article-title":"Next-Generation Sequencing Technologies","volume":"9","author":"McCombie","year":"2019","journal-title":"Cold Spring Harb. Perspect. Med."},{"key":"ref_13","doi-asserted-by":"crossref","first-page":"335","DOI":"10.1016\/j.cmi.2017.10.013","article-title":"Next-generation sequencing technologies and their application to the study and control of bacterial infections","volume":"24","author":"Besser","year":"2018","journal-title":"Clin. Microbiol. Infect."},{"key":"ref_14","doi-asserted-by":"crossref","first-page":"278","DOI":"10.1016\/j.gpb.2015.08.002","article-title":"PacBio Sequencing and Its Applications","volume":"13","author":"Rhoads","year":"2015","journal-title":"Genom. Proteom. Bioinform."},{"key":"ref_15","doi-asserted-by":"crossref","first-page":"e00286","DOI":"10.1128\/genomeA.00286-14","article-title":"Complete Genome Sequences of Eight Helicobacter pylori Strains with Different Virulence Factor Genotypes and Methylation Profiles, Isolated from Patients with Diverse Gastrointestinal Diseases on Okinawa Island, Japan, Determined Using PacBio Single-Molecule Real-Time Technology","volume":"2","author":"Satou","year":"2014","journal-title":"Genome Announc."},{"key":"ref_16","doi-asserted-by":"crossref","first-page":"2","DOI":"10.1016\/j.cmi.2016.11.012","article-title":"The role of whole genome sequencing in antimicrobial susceptibility testing of bacteria: Report from the EUCAST Subcommittee","volume":"23","author":"Ellington","year":"2017","journal-title":"Clin. Microbiol. Infect."},{"key":"ref_17","first-page":"1083","article-title":"The long reads ahead: De novo genome assembly using the MinION","volume":"6","author":"Risse","year":"2017","journal-title":"F1000Research"},{"key":"ref_18","doi-asserted-by":"crossref","first-page":"353","DOI":"10.2165\/11536360-000000000-00000","article-title":"Safety profile of the fluoroquinolones: Focus on levofloxacin","volume":"33","author":"Liu","year":"2010","journal-title":"Drug Saf."},{"key":"ref_19","doi-asserted-by":"crossref","first-page":"e1800141","DOI":"10.1002\/ardp.201800141","article-title":"Recent updates of fluoroquinolones as antibacterial agents","volume":"351","author":"Ezelarab","year":"2018","journal-title":"Arch. Pharm."},{"key":"ref_20","doi-asserted-by":"crossref","first-page":"629","DOI":"10.1016\/S1473-3099(06)70599-0","article-title":"The worldwide emergence of plasmid-mediated quinolone resistance","volume":"6","author":"Robicsek","year":"2006","journal-title":"Lancet Infect. Dis."},{"key":"ref_21","doi-asserted-by":"crossref","first-page":"3332","DOI":"10.1128\/AAC.48.9.3332-3337.2004","article-title":"Plasmid-encoded multidrug efflux pump conferring resistance to olaquindox in Escherichia coli","volume":"48","author":"Hansen","year":"2004","journal-title":"Antimicrob. Agents Chemother."},{"key":"ref_22","doi-asserted-by":"crossref","first-page":"12","DOI":"10.1111\/nyas.12830","article-title":"Mechanisms of drug resistance: Quinolone resistance","volume":"1354","author":"Hooper","year":"2015","journal-title":"Ann. N. Y. Acad. Sci."},{"key":"ref_23","first-page":"1537","article-title":"Mutations That Enhance the Ciprofloxacin Resistance of Escherichia coli with qnrA1","volume":"60","author":"Corcoran","year":"2015","journal-title":"Antimicrob. Agents Chemother."},{"key":"ref_24","doi-asserted-by":"crossref","first-page":"551","DOI":"10.1099\/jmm.0.000475","article-title":"Mechanisms of quinolone action and resistance: Where do we stand?","volume":"66","author":"Correia","year":"2017","journal-title":"J. Med. Microbiol."},{"key":"ref_25","unstructured":"European Commission (2013). Commission implementing decision of 12 november 2013 on the monitoring and reporting of antimicrobial resistance in zoonotic and commensal bacteria. Off. J. Eur. Union, L 303, 26\u201339."},{"key":"ref_26","first-page":"3359","article-title":"Rapid detection and discrimination of chromosome- and MCR-plasmid-mediated resistance to polymyxins by MALDI-TOF MS in Escherichia coli: The MALDIxin test","volume":"73","author":"Dortet","year":"2018","journal-title":"J. Antimicrob. Chemother."},{"key":"ref_27","unstructured":"PulsNet (2018, June 26). Standard Operating Procedure for PulseNet PFGE of Escherichia coli O157:H7, Escherichia coli Non-O157 (STEC), Salmonella Serotypes, Shigella Sonnei and Shigella Flexneri, Available online: https:\/\/www.cdc.gov\/pulsenet\/pdf\/ecoli-shigella-salmonella-pfge-protocol-508c.pdf."},{"key":"ref_28","doi-asserted-by":"crossref","first-page":"1128","DOI":"10.1093\/jac\/dkp111","article-title":"Mutational analysis of quinolone resistance in the plasmid-encoded pentapeptide repeat proteins QnrA, QnrB and QnrS","volume":"63","author":"Briales","year":"2009","journal-title":"J. Antimicrob. Chemother."},{"key":"ref_29","doi-asserted-by":"crossref","first-page":"253","DOI":"10.1016\/j.diagmicrobio.2011.01.004","article-title":"Rapid detection of qnr and qepA plasmid-mediated quinolone resistance genes using real-time PCR","volume":"70","author":"Guillard","year":"2011","journal-title":"Diagn. Microbiol. Infect. Dis."},{"key":"ref_30","doi-asserted-by":"crossref","first-page":"1305","DOI":"10.1128\/AAC.45.4.1305-1308.2001","article-title":"Multidrug resistance is mediated by large plasmids carrying a class 1 integron in the emergent Salmonella enterica serotype [4,5,12:i:-]","volume":"45","author":"Guerra","year":"2001","journal-title":"Antimicrob. Agents Chemother."},{"key":"ref_31","unstructured":"Sambrook, J., and Russel, D.W. (2001). Molecular Cloning: A Laboratory Manual, Cold Spring Harbor Laboratory Press."},{"key":"ref_32","doi-asserted-by":"crossref","first-page":"3317","DOI":"10.1093\/jac\/dkx327","article-title":"Identification of a novel transposon-associated phosphoethanolamine transferase gene, mcr-5, conferring colistin resistance in d-tartrate fermenting Salmonella enterica subsp. enterica serovar Paratyphi B","volume":"72","author":"Borowiak","year":"2017","journal-title":"J. Antimicrob. Chemother."},{"key":"ref_33","doi-asserted-by":"crossref","unstructured":"Chen, L., Zhang, J., Wang, J., Butaye, P., Kelly, P., Li, M., Yang, F., Gong, J., Yassin, A.K., and Guo, W. (2018). Newly identified colistin resistance genes, mcr-4 and mcr-5, from upper and lower alimentary tract of pigs and poultry in China. PLoS ONE, 13.","DOI":"10.1371\/journal.pone.0193957"},{"key":"ref_34","doi-asserted-by":"crossref","unstructured":"Wick, R.R., Judd, L.M., Gorrie, C.L., and Holt, K.E. (2017). Unicycler: Resolving bacterial genome assemblies from short and long sequencing reads. PLoS Comput. Biol., 13.","DOI":"10.1371\/journal.pcbi.1005595"},{"key":"ref_35","doi-asserted-by":"crossref","first-page":"540","DOI":"10.1038\/s41587-019-0072-8","article-title":"Assembly of long, error-prone reads using repeat graphs","volume":"37","author":"Kolmogorov","year":"2019","journal-title":"Nat. Biotechnol."},{"key":"ref_36","unstructured":"Seemann, T. (2019, September 04). Abricate. Available online: https:\/\/github.com\/tseemann\/abricate."},{"key":"ref_37","doi-asserted-by":"crossref","unstructured":"Feldgarden, M., Brover, V., Haft, D.H., Prasad, A.B., Slotta, D.J., Tolstoy, I., Tyson, G.H., Zhao, S., Hsu, C.-H., and McDermott, P.F. (2019). Validating the AMRFinder Tool and Resistance Gene Database by Using Antimicrobial Resistance Genotype-Phenotype Correlations in a Collection of Isolates. Antimicrob. Agents Chemother., 63.","DOI":"10.1128\/AAC.00483-19"},{"key":"ref_38","doi-asserted-by":"crossref","first-page":"D566","DOI":"10.1093\/nar\/gkw1004","article-title":"CARD 2017: Expansion and model-centric curation of the comprehensive antibiotic resistance database","volume":"45","author":"Jia","year":"2017","journal-title":"Nucleic Acids Res."},{"key":"ref_39","doi-asserted-by":"crossref","first-page":"2640","DOI":"10.1093\/jac\/dks261","article-title":"Identification of acquired antimicrobial resistance genes","volume":"67","author":"Zankari","year":"2012","journal-title":"J. Antimicrob. Chemother."},{"key":"ref_40","doi-asserted-by":"crossref","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":"ref_41","doi-asserted-by":"crossref","first-page":"D694","DOI":"10.1093\/nar\/gkv1239","article-title":"VFDB 2016: Hierarchical and refined dataset for big data analysis--10 years on","volume":"44","author":"Chen","year":"2016","journal-title":"Nucleic Acids Res."},{"key":"ref_42","doi-asserted-by":"crossref","first-page":"3895","DOI":"10.1128\/AAC.02412-14","article-title":"In silico detection and typing of plasmids using PlasmidFinder and plasmid multilocus sequence typing","volume":"58","author":"Carattoli","year":"2014","journal-title":"Antimicrob. Agents Chemother."},{"key":"ref_43","first-page":"e000064","article-title":"In silico serotyping of E. coli from short read data identifies limited novel O-loci but extensive diversity of O:H serotype combinations within and between pathogenic lineages","volume":"2","author":"Ingle","year":"2016","journal-title":"Microb. Genom."},{"key":"ref_44","first-page":"e000398","article-title":"Platon: Identification and characterization of bacterial plasmid contigs in short-read draft assemblies exploiting protein sequence-based replicon distribution scores","volume":"6","author":"Schwengers","year":"2020","journal-title":"Microb. Genom."},{"key":"ref_45","doi-asserted-by":"crossref","first-page":"295","DOI":"10.1007\/978-1-4939-9877-7_21","article-title":"MOBscan: Automated Annotation of MOB Relaxases","volume":"2075","author":"Vielva","year":"2020","journal-title":"Methods Mol. Biol."},{"key":"ref_46","doi-asserted-by":"crossref","first-page":"8365","DOI":"10.1038\/srep08365","article-title":"RASTtk: A modular and extensible implementation of the RAST algorithm for building custom annotation pipelines and annotating batches of genomes","volume":"5","author":"Brettin","year":"2015","journal-title":"Sci. Rep."},{"key":"ref_47","doi-asserted-by":"crossref","unstructured":"Alikhan, N.-F., Petty, N.K., Ben Zakour, N.L., and Beatson, S.A. (2011). BLAST Ring Image Generator (BRIG): Simple prokaryote genome comparisons. BMC Genom., 12.","DOI":"10.1186\/1471-2164-12-402"},{"key":"ref_48","first-page":"e000206","article-title":"MOB-suite: Software tools for clustering, reconstruction and typing of plasmids from draft assemblies","volume":"4","author":"Robertson","year":"2018","journal-title":"Microb. Genom."},{"key":"ref_49","doi-asserted-by":"crossref","first-page":"D8","DOI":"10.1093\/nar\/gkx1095","article-title":"Database resources of the National Center for Biotechnology Information","volume":"46","author":"Coordinators","year":"2018","journal-title":"Nucleic Acids Res."},{"key":"ref_50","doi-asserted-by":"crossref","first-page":"14649","DOI":"10.1038\/s41598-020-71207-3","article-title":"Impact of DNA extraction on whole genome sequencing analysis for characterization and relatedness of Shiga toxin-producing Escherichia coli isolates","volume":"10","author":"Nouws","year":"2020","journal-title":"Sci. Rep."},{"key":"ref_51","doi-asserted-by":"crossref","first-page":"16350","DOI":"10.1038\/s41598-019-52424-x","article-title":"Rapid, multiplexed, whole genome and plasmid sequencing of foodborne pathogens using long-read nanopore technology","volume":"9","author":"Taylor","year":"2019","journal-title":"Sci. Rep."},{"key":"ref_52","doi-asserted-by":"crossref","unstructured":"Oakeson, K.F., Wagner, J.M., Rohrwasser, A., and Atkinson-Dunn, R. (2018). Whole-Genome Sequencing and Bioinformatic Analysis of Isolates from Foodborne Illness Outbreaks of Campylobacter jejuni and Salmonella enterica. J. Clin. Microbiol., 56.","DOI":"10.1128\/JCM.00161-18"},{"key":"ref_53","first-page":"e000294","article-title":"Comparison of long-read sequencing technologies in the hybrid assembly of complex bacterial genomes","volume":"5","author":"Shaw","year":"2019","journal-title":"Microb. Genom."},{"key":"ref_54","doi-asserted-by":"crossref","first-page":"666","DOI":"10.1016\/j.tig.2018.05.008","article-title":"The Third Revolution in Sequencing Technology","volume":"34","author":"Jaszczyszyn","year":"2018","journal-title":"Trends Genet."},{"key":"ref_55","doi-asserted-by":"crossref","first-page":"661","DOI":"10.1055\/s-0039-1688446","article-title":"Next-Generation Sequencing and Emerging Technologies","volume":"45","author":"Kumar","year":"2019","journal-title":"Semin. Thromb. Hemost."},{"key":"ref_56","first-page":"e000132","article-title":"Completing bacterial genome assemblies with multiplex MinION sequencing","volume":"3","author":"Wick","year":"2017","journal-title":"Microb. Genom."},{"key":"ref_57","doi-asserted-by":"crossref","first-page":"265","DOI":"10.1016\/j.gpb.2016.05.004","article-title":"Oxford Nanopore MinION Sequencing and Genome Assembly","volume":"14","author":"Lu","year":"2016","journal-title":"Genom. Proteom. Bioinform."},{"key":"ref_58","doi-asserted-by":"crossref","unstructured":"Gonz\u00e1lez-Escalona, N., Allard, M.A., Brown, E.W., Sharma, S., and Hoffmann, M. (2019). Nanopore sequencing for fast determination of plasmids, phages, virulence markers, and antimicrobial resistance genes in Shiga toxin-producing Escherichia coli. PLoS ONE, 14.","DOI":"10.1101\/571364"},{"key":"ref_59","doi-asserted-by":"crossref","unstructured":"Forde, B.M., Ben Zakour, N.L., Stanton-Cook, M., Phan, M.-D., Totsika, M., Peters, K.M., Chan, K.G., Schembri, M.A., Upton, M., and Beatson, S.A. (2014). The complete genome sequence of Escherichia coli EC958: A high quality reference sequence for the globally disseminated multidrug resistant E. coli O25b:H4-ST131 clone. PLoS ONE, 9.","DOI":"10.1371\/journal.pone.0104400"},{"key":"ref_60","doi-asserted-by":"crossref","first-page":"99","DOI":"10.1016\/j.plasmid.2018.09.010","article-title":"Plasmid-mediated resistance is going wild","volume":"99","author":"Dolejska","year":"2018","journal-title":"Plasmid"},{"key":"ref_61","doi-asserted-by":"crossref","first-page":"215","DOI":"10.1016\/j.jgar.2018.10.014","article-title":"IncFII plasmid carrying antimicrobial resistance genes in Shigella flexneri: Vehicle for dissemination","volume":"16","author":"Sethuvel","year":"2019","journal-title":"J. Glob. Antimicrob. Resist."},{"key":"ref_62","doi-asserted-by":"crossref","first-page":"72","DOI":"10.1016\/j.plasmid.2018.09.001","article-title":"Antimicrobial resistance plasmid reservoir in food and food-producing animals","volume":"99","author":"Madec","year":"2018","journal-title":"Plasmid"},{"key":"ref_63","doi-asserted-by":"crossref","first-page":"1121","DOI":"10.1093\/jac\/dkx488","article-title":"Plasmids carrying antimicrobial resistance genes in Enterobacteriaceae","volume":"73","author":"Rozwandowicz","year":"2018","journal-title":"J. Antimicrob. Chemother."},{"key":"ref_64","doi-asserted-by":"crossref","first-page":"34","DOI":"10.1139\/cjm-2018-0275","article-title":"Horizontal transfer of antibiotic resistance genes in clinical environments","volume":"65","author":"Lerminiaux","year":"2019","journal-title":"Can. J. Microbiol."},{"key":"ref_65","doi-asserted-by":"crossref","first-page":"857","DOI":"10.1093\/bib\/bbx162","article-title":"Assessing the heterogeneity of in silico plasmid predictions based on whole-genome-sequenced clinical isolates","volume":"20","author":"Laczny","year":"2019","journal-title":"Brief. Bioinform."},{"key":"ref_66","doi-asserted-by":"crossref","first-page":"2388","DOI":"10.1093\/jac\/dku172","article-title":"Complete sequences of IncHI1 plasmids carrying blaCTX-M-1 and qnrS1 in equine Escherichia coli provide new insights into plasmid evolution","volume":"69","author":"Dolejska","year":"2014","journal-title":"J. Antimicrob. Chemother."},{"key":"ref_67","doi-asserted-by":"crossref","first-page":"279","DOI":"10.3389\/fvets.2019.00279","article-title":"Prevalence of Beta-Lactam and Quinolone\/Fluoroquinolone Resistance in Enterobacteriaceae from Dogs in France and Spain-Characterization of ESBL\/pAmpC Isolates, Genes, and Conjugative Plasmids","volume":"6","author":"Dupouy","year":"2019","journal-title":"Front. Vet. Sci."},{"key":"ref_68","doi-asserted-by":"crossref","first-page":"7674","DOI":"10.1038\/s41598-018-26073-5","article-title":"Genomic and functional characterisation of IncX3 plasmids encoding blaSHV-12 in Escherichia coli from human and animal origin","volume":"8","author":"Liakopoulos","year":"2018","journal-title":"Sci. Rep."},{"key":"ref_69","doi-asserted-by":"crossref","first-page":"373","DOI":"10.1093\/jac\/dki482","article-title":"OXA-type carbapenemases","volume":"57","author":"Hoiby","year":"2006","journal-title":"J. Antimicrob. Chemother."},{"key":"ref_70","doi-asserted-by":"crossref","unstructured":"Nguyen, M., Long, S.W., McDermott, P.F., Olsen, R.J., Olson, R., Stevens, R.L., Tyson, G.H., Zhao, S., and Davis, J.J. (2019). Using Machine Learning To Predict Antimicrobial MICs and Associated Genomic Features for Nontyphoidal Salmonella. J. Clin. Microbiol., 57.","DOI":"10.1128\/JCM.01260-18"},{"key":"ref_71","doi-asserted-by":"crossref","first-page":"48","DOI":"10.3389\/fmicb.2020.00048","article-title":"Evaluation of Machine Learning Models for Predicting Antimicrobial Resistance of Actinobacillus pleuropneumoniae from Whole Genome Sequences","volume":"11","author":"Liu","year":"2020","journal-title":"Front. Microbiol."},{"key":"ref_72","doi-asserted-by":"crossref","first-page":"1107","DOI":"10.3389\/fmicb.2019.01107","article-title":"Integrating Whole-Genome Sequencing Data Into Quantitative Risk Assessment of Foodborne Antimicrobial Resistance: A Review of Opportunities and Challenges","volume":"10","author":"Collineau","year":"2019","journal-title":"Front. Microbiol."},{"key":"ref_73","doi-asserted-by":"crossref","unstructured":"Su, M., Satola, S.W., and Read, T.D. (2019). Genome-Based Prediction of Bacterial Antibiotic Resistance. J. Clin. Microbiol., 57.","DOI":"10.1128\/JCM.01405-18"},{"key":"ref_74","doi-asserted-by":"crossref","first-page":"42","DOI":"10.2174\/1568026618666180206095224","article-title":"Genetic Mechanisms of Antibiotic Resistance and the Role of Antibiotic Adjuvants","volume":"18","author":"Pontes","year":"2018","journal-title":"Curr. Top. Med. Chem."},{"key":"ref_75","doi-asserted-by":"crossref","first-page":"5792","DOI":"10.1038\/ncomms6792","article-title":"Prediction of antibiotic resistance by gene expression profiles","volume":"5","author":"Suzuki","year":"2014","journal-title":"Nat. Commun."}],"container-title":["Microorganisms"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.mdpi.com\/2076-2607\/9\/3\/598\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,10,11]],"date-time":"2025-10-11T05:35:37Z","timestamp":1760160937000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.mdpi.com\/2076-2607\/9\/3\/598"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2021,3,14]]},"references-count":75,"journal-issue":{"issue":"3","published-online":{"date-parts":[[2021,3]]}},"alternative-id":["microorganisms9030598"],"URL":"https:\/\/doi.org\/10.3390\/microorganisms9030598","relation":{},"ISSN":["2076-2607"],"issn-type":[{"value":"2076-2607","type":"electronic"}],"subject":[],"published":{"date-parts":[[2021,3,14]]}}}