{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,11,18]],"date-time":"2025-11-18T09:30:44Z","timestamp":1763458244075,"version":"3.41.2"},"reference-count":76,"publisher":"Frontiers Media SA","license":[{"start":{"date-parts":[[2023,6,1]],"date-time":"2023-06-01T00:00:00Z","timestamp":1685577600000},"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. Vet. Sci."],"abstract":"<jats:p>Bacteria of the genus <jats:italic>Salmonella<\/jats:italic> pose a major risk to livestock, the food economy, and public health. <jats:italic>Salmonella<\/jats:italic> infections are one of the leading causes of food poisoning. The identification of serovars of <jats:italic>Salmonella<\/jats:italic> achieved by their diverse surface antigens is essential to gain information on their epidemiological context. Traditionally, slide agglutination has been used for serotyping. In recent years, whole-genome sequencing (WGS) followed by <jats:italic>in silico<\/jats:italic> serotyping has been established as an alternative method for serotyping and the detection of genetic markers for <jats:italic>Salmonella<\/jats:italic>. Until now, WGS data generated with Illumina sequencing are used to validate <jats:italic>in silico<\/jats:italic> serotyping methods. Oxford Nanopore Technologies (ONT) opens the possibility to sequence ultra-long reads and has frequently been used for bacterial sequencing. In this study, ONT sequencing data of 28 <jats:italic>Salmonella<\/jats:italic> strains of different serovars with epidemiological relevance in humans, food, and animals were taken to investigate the performance of the <jats:italic>in silico<\/jats:italic> serotyping tools SISTR and SeqSero2 compared to traditional slide agglutination tests. Moreover, the detection of genetic markers for resistance against antimicrobial agents, virulence, and plasmids was studied by comparing WGS data based on ONT with WGS data based on Illumina. Based on the ONT data from flow cell version R9.4.1, <jats:italic>in silico<\/jats:italic> serotyping achieved an accuracy of 96.4 and 92% for the tools SISTR and SeqSero2, respectively. Highly similar sets of genetic markers comparing both sequencing technologies were identified. Taking the ongoing improvement of basecalling and flow cells into account, ONT data can be used for <jats:italic>Salmonella in silico<\/jats:italic> serotyping and genetic marker detection.<\/jats:p>","DOI":"10.3389\/fvets.2023.1178922","type":"journal-article","created":{"date-parts":[[2023,6,1]],"date-time":"2023-06-01T04:48:56Z","timestamp":1685594936000},"update-policy":"https:\/\/doi.org\/10.3389\/crossmark-policy","source":"Crossref","is-referenced-by-count":3,"title":["Oxford nanopore technologies\u2014a valuable tool to generate whole-genome sequencing data for in silico serotyping and the detection of genetic markers in Salmonella"],"prefix":"10.3389","volume":"10","author":[{"given":"Christine","family":"Thomas","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Ulrich","family":"Methner","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Manja","family":"Marz","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"J\u00f6rg","family":"Linde","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"1965","published-online":{"date-parts":[[2023,6,1]]},"reference":[{"volume-title":"Antibiotic Resistance Threats in the United States, 2019","year":"2019","key":"ref1"},{"key":"ref2","doi-asserted-by":"publisher","first-page":"e07666","DOI":"10.2903\/j.efsa.2021.6971","article-title":"European food safety authority and European Centre for Disease Prevention and Control the European Union one health 2021 Zoonoses report","volume":"19","year":"2022","journal-title":"EFSA J"},{"key":"ref3","doi-asserted-by":"publisher","first-page":"775","DOI":"10.1172\/JCI12561","article-title":"Diverse virulence traits underlying different clinical outcomes of Salmonella infection","volume":"107","author":"Fierer","year":"2001","journal-title":"J Clin Invest"},{"key":"ref4","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1016\/j.fm.2012.04.016","article-title":"Factors influencing the microbial safety of fresh produce: a review","volume":"32","author":"Olaimat","year":"2012","journal-title":"Food Microbiol"},{"key":"ref5","doi-asserted-by":"publisher","first-page":"333","DOI":"10.1017\/S0022172400034677","article-title":"The genus salmonella lignieres, 1900","volume":"34","year":"1934","journal-title":"J Hyg"},{"key":"ref6","article-title":"Antigenic Formulae of the Salmonella Serovars","volume-title":"WHO Collaborating Centre for Reference and Research on","author":"Grimont","year":"2007"},{"key":"ref7","doi-asserted-by":"publisher","first-page":"2993","DOI":"10.3389\/fmicb.2018.02993","article-title":"Salmonella serotyping using whole genome sequencing","volume":"9","author":"Ibrahim","year":"2018","journal-title":"Front Microbiol"},{"key":"ref8","doi-asserted-by":"publisher","first-page":"25","DOI":"10.1099\/00221287-116-1-25","article-title":"Rough mutants of Salmonella typhimurium: immunochemical and structural analysis of lipopolysaccharides from rfaH mutants","volume":"116","author":"Lindberg","year":"1980","journal-title":"Microbiology"},{"key":"ref9","doi-asserted-by":"publisher","first-page":"8648","DOI":"10.1128\/AEM.06538-11","article-title":"A whole-genome single nucleotide polymorphism-based approach to trace and identify outbreaks linked to a common Salmonella enterica subsp. enterica serovar Montevideo pulsed-field gel electrophoresis type","volume":"77","author":"den Bakker","year":"2011","journal-title":"Appl Environ Microbiol"},{"key":"ref10","doi-asserted-by":"publisher","first-page":"e87991","DOI":"10.1371\/journal.pone.0087991","article-title":"Evaluation of whole genome sequencing for outbreak detection of Salmonella enterica","volume":"9","author":"Leekitcharoenphon","year":"2014","journal-title":"PLoS One"},{"key":"ref11","doi-asserted-by":"publisher","first-page":"1074","DOI":"10.1099\/jmm.0.000325","article-title":"Characterization of new Salmonella serovars by whole-genome sequencing and traditional typing techniques","volume":"65","author":"Bale","year":"2016","journal-title":"J Med Microbiol"},{"key":"ref12","doi-asserted-by":"publisher","first-page":"289","DOI":"10.1128\/JCM.02200-15","article-title":"Usefulness of high-quality core genome single-nucleotide variant analysis for subtyping the highly clonal and the most prevalent Salmonella enterica serovar Heidelberg clone in the context of outbreak investigations","volume":"54","author":"Bekal","year":"2016","journal-title":"J Clin Microbiol"},{"key":"ref13","doi-asserted-by":"publisher","first-page":"e02265","DOI":"10.1128\/AEM.02265-19","article-title":"Performance and accuracy of four open-source tools for in silico serotyping of Salmonella spp. based on whole-genome short-read sequencing data","volume":"86","author":"Uelze","year":"2020","journal-title":"Appl Environ Microbiol"},{"key":"ref14","doi-asserted-by":"publisher","first-page":"e0147101","DOI":"10.1371\/journal.pone.0147101","article-title":"Kruczkiewicz, Peter, Laing, CR, Lingohr, EJ, Gannon, VPJ, Nash, JHE, Taboada, EN the Salmonella in silico typing resource (SISTR): an open web-accessible tool for rapidly typing and subtyping draft Salmonella genome assemblies","volume":"11","author":"Yoshida","year":"2016","journal-title":"PLoS One"},{"key":"ref15","doi-asserted-by":"publisher","first-page":"e01746","DOI":"10.1128\/AEM.01746-19","article-title":"SeqSero2: rapid and improved Salmonella serotype determination using whole-genome sequencing data","volume":"85","author":"Zhang","year":"2019","journal-title":"Appl Environ Microbiol"},{"key":"ref16","doi-asserted-by":"publisher","first-page":"1431E","DOI":"10.2903\/sp.efsa.2018.EN-1431","article-title":"Final report of ENGAGE\u2014establishing next generation sequencing ability for genomic analysis in Europe","volume":"15","author":"Hendriksen","year":"2018","journal-title":"EFSA Support Publ"},{"key":"ref17","doi-asserted-by":"publisher","first-page":"2954","DOI":"10.1128\/JCM.02347-10","article-title":"Rapid genoserotyping tool for classification of Salmonella serovars","volume":"49","author":"Franklin","year":"2011","journal-title":"J Clin Microbiol"},{"key":"ref18","doi-asserted-by":"publisher","first-page":"185","DOI":"10.1016\/j.diagmicrobio.2014.08.006","article-title":"Multi-laboratory evaluation of the rapid genoserotyping array (SGSA) for the identification of Salmonella serovars","volume":"80","author":"Yoshida","year":"2014","journal-title":"Diagn Microbiol Infect Dis"},{"key":"ref19","doi-asserted-by":"publisher","DOI":"10.48550\/arXiv.1303.3997","article-title":"Aligning sequence reads, clone sequences and assembly contigs with BWA-MEM","author":"Li","year":"2013","journal-title":"arXiv"},{"key":"ref20","doi-asserted-by":"publisher","first-page":"801","DOI":"10.1016\/j.humimm.2021.02.012","article-title":"Next-generation sequencing technologies: An overview","volume":"82","author":"Hu","year":"2021","journal-title":"Hum Immunol"},{"key":"ref21","doi-asserted-by":"publisher","first-page":"823","DOI":"10.1038\/s41592-022-01539-7","article-title":"Oxford Nanopore R10.4 long-read sequencing enables the generation of near-finished bacterial genomes from pure cultures and metagenomes without short-read or reference polishing","volume":"19","author":"Sereika","year":"2022","journal-title":"Nat Methods"},{"volume-title":"microPIPE: A Pipeline for High-Quality Bacterial Genome Construction Using ONT and Illumina Sequencing","year":"2021","author":"Murigneux","key":"ref22"},{"key":"ref23","doi-asserted-by":"publisher","first-page":"474","DOI":"10.1186\/s12864-021-07767-z","article-title":"MicroPIPE: validating an end-to-end workflow for high-quality complete bacterial genome construction","volume":"22","author":"Murigneux","year":"2021","journal-title":"BMC Genomics"},{"key":"ref24","doi-asserted-by":"publisher","first-page":"2666","DOI":"10.1093\/bioinformatics\/bty149","article-title":"NanoPack: visualizing and processing long-read sequencing data","volume":"34","author":"de Coster","year":"2018","journal-title":"Bioinformatics"},{"volume-title":"Porechop","year":"2017","author":"Wick","key":"ref25"},{"volume-title":"Japsa - Just Another Java Paackage for Sequence Analysis","year":"2019","author":"Nguyen","key":"ref26"},{"key":"ref27","doi-asserted-by":"publisher","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"},{"volume-title":"Racon - Consensus Module for Raw de novo DNA Assembly of Long Uncorrected Reads","year":"2019","author":"Sovic","key":"ref28"},{"volume-title":"Medaka","year":"2019","key":"ref29"},{"key":"ref30","doi-asserted-by":"publisher","first-page":"2253","DOI":"10.1093\/bioinformatics\/btz891","article-title":"NextPolish: a fast and efficient genome polishing tool for long-read assembly","volume":"36","author":"Jiang Hu","year":"2019","journal-title":"Bioinformatics"},{"volume-title":"WGSBAC: Modules for Genotyping and Characterisation of Bacterial Isolates Utilizing Whole-Genome-Sequencing Data","year":"2019","author":"Linde","key":"ref31"},{"volume-title":"FastQC: A Quality Control Tool for High Throughput Sequence Data","year":"2010","author":"Andrews","key":"ref32"},{"volume-title":"Shovill\u2014Assemble Bacterial Isolate Genomes from Illumina Paired-End Reads","year":"2020","author":"Seemann","key":"ref33"},{"key":"ref34","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":"ref35","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":"ref36","doi-asserted-by":"publisher","first-page":"257","DOI":"10.1186\/s13059-019-1891-0","article-title":"Improved metagenomic analysis with kraken 2","volume":"20","author":"Wood","year":"2019","journal-title":"Genome Biol"},{"volume-title":"ABRicate","year":"2020","author":"Seemann","key":"ref37"},{"key":"ref38","doi-asserted-by":"publisher","first-page":"D694","DOI":"10.1093\/nar\/gkv1239","article-title":"VFDB 2016: hierarchical and refined dataset for big data analysis\u201410 years on","volume":"44","author":"Chen","year":"2016","journal-title":"Nucleic Acids Res"},{"key":"ref39","doi-asserted-by":"publisher","first-page":"e0048319","DOI":"10.1128\/AAC.00483-19","article-title":"Validating the AMRFinder tool and resistance gene database by using antimicrobial resistance genotype-phenotype correlations in a collection of isolates","volume":"63","author":"Michael Feldgarden","year":"2019","journal-title":"Antimicrob Agents Chemother"},{"key":"ref40","doi-asserted-by":"publisher","first-page":"1741","DOI":"10.3389\/fmicb.2020.01741","article-title":"Emergence of multidrug-resistant Salmonella enterica subspecies enterica serovar infantis of multilocus sequence type 2283 in German broiler farms","volume":"11","author":"Garc\u00eda-Soto","year":"2020","journal-title":"Front Microbiol"},{"key":"ref41","doi-asserted-by":"publisher","first-page":"mgen000398","DOI":"10.1099\/mgen.0.000398","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":"ref42","doi-asserted-by":"publisher","first-page":"D733","DOI":"10.1093\/nar\/gkv1189","article-title":"Reference sequence (RefSeq) database at NCBI: current status, taxonomic expansion, and functional annotation","volume":"44","author":"O'Leary","year":"2016","journal-title":"Nucleic Acids Res"},{"key":"ref43","doi-asserted-by":"publisher","first-page":"741","DOI":"10.1089\/fpd.2010.0776","article-title":"A rapid and sensitive method to identify and differentiate Salmonella enterica serotype Typhimurium and Salmonella enterica serotype 4,[5], 12: i:-by combining traditional serotyping and multiplex polymerase chain reaction","volume":"8","author":"Barco","year":"2011","journal-title":"Foodborne Pathog Dis"},{"key":"ref44","doi-asserted-by":"publisher","first-page":"1","DOI":"10.3390\/microorganisms11010122","article-title":"Epidemiological analysis on the occurrence of Salmonella enterica subspecies enterica Serovar Dublin in the German Federal State Schleswig-Holstein Using Whole-Genome Sequencing","volume":"11","author":"Garc\u00eda-Soto","year":"2023","journal-title":"Microorganisms"},{"key":"ref45","doi-asserted-by":"publisher","first-page":"10555","DOI":"10.1038\/s41598-022-14492-4","article-title":"Whole genome sequencing analyses revealed that Salmonella enterica serovar Dublin strains from Brazil belonged to two predominant clades","volume":"12","author":"Campioni","year":"2022","journal-title":"Sci Rep"},{"key":"ref46","doi-asserted-by":"publisher","first-page":"16502","DOI":"10.1073\/pnas.0604636103","article-title":"The pathogen-associated iroA gene cluster mediates bacterial evasion of lipocalin 2","volume":"103","author":"Fischbach","year":"2006","journal-title":"Proc Natl Acad Sci"},{"key":"ref47","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1186\/s12917-018-1741-4","article-title":"Occurrence and characterisation of Salmonella enterica subspecies diarizonae serovar 61: k: 1, 5, (7) in sheep in the federal state of Thuringia, Germany","volume":"14","author":"Methner","year":"2018","journal-title":"BMC Vet Res"},{"key":"ref48","doi-asserted-by":"publisher","first-page":"000604","DOI":"10.1099\/mgen.0.000604","article-title":"Comparative genomics of Salmonella enterica subsp. diarizonae serovar 61:k:1,5,(7) reveals lineage-specific host adaptation of ST432","volume":"7","author":"Uelze","year":"2021","journal-title":"Microb Genom"},{"key":"ref49","doi-asserted-by":"publisher","first-page":"1367","DOI":"10.1099\/mic.0.000319","article-title":"SPI-9 of Salmonella enterica serovar Typhi is constituted by an operon positively regulated by RpoS and contributes to adherence to epithelial cells in culture","volume":"162","author":"Vel\u00e1squez","year":"2016","journal-title":"Microbiology"},{"key":"ref50","doi-asserted-by":"publisher","first-page":"146","DOI":"10.1128\/IAI.73.1.146-154.2005","article-title":"SipA, SopA, SopB, SopD, and SopE2 contribute to Salmonella enterica serotype Typhimurium invasion of epithelial cells","volume":"73","author":"Raffatellu","year":"2005","journal-title":"Infect Immun"},{"key":"ref51","doi-asserted-by":"publisher","first-page":"199","DOI":"10.1016\/j.mib.2009.01.004","article-title":"Control of Salmonella pathogenicity island-2 gene expression","volume":"12","author":"Fass","year":"2009","journal-title":"Curr Opin Microbiol"},{"key":"ref52","doi-asserted-by":"publisher","first-page":"504","DOI":"10.14202\/vetworld.2019.504-521","article-title":"A review of Salmonella enterica with particular focus on the pathogenicity and virulence factors, host specificity and antimicrobial resistance including multidrug resistance","volume":"12","author":"Jajere","year":"2019","journal-title":"Vet World"},{"key":"ref53","doi-asserted-by":"publisher","first-page":"598","DOI":"10.3390\/microorganisms9030598","article-title":"Outcome of different sequencing and assembly approaches on the detection of plasmids and localization of antimicrobial resistance genes in commensal Escherichia coli","volume":"9","author":"Juraschek","year":"2021","journal-title":"Microorganisms"},{"key":"ref54","doi-asserted-by":"publisher","first-page":"1864","DOI":"10.3389\/fmicb.2020.01864","article-title":"Frequency of antimicrobial resistance genes in Salmonella from Brazil by in silico whole-genome sequencing analysis: an overview of the last four decades","volume":"11","author":"Rodrigues","year":"2020","journal-title":"Front Microbiol"},{"key":"ref55","doi-asserted-by":"publisher","first-page":"e0249617","DOI":"10.1371\/journal.pone.0249617","article-title":"Antimicrobial resistance and genomic characterization of Salmonella Dublin isolates in cattle from the United States","volume":"16","author":"Srednik","year":"2021","journal-title":"PLoS One"},{"key":"ref56","doi-asserted-by":"publisher","first-page":"e0179005","DOI":"10.1371\/journal.pone.0179005","article-title":"Strong influence of livestock environments on the emergence and dissemination of distinct multidrug-resistant phenotypes among the population of non-typhoidal Salmonella","volume":"12","author":"An","year":"2017","journal-title":"PLoS One"},{"key":"ref57","doi-asserted-by":"publisher","first-page":"436","DOI":"10.1099\/jmm.0.003657-0","article-title":"Development of triclosan and antibiotic resistance in Salmonella enterica serovar Typhimurium","volume":"58","author":"Biro\u0161ova","year":"2009","journal-title":"J Med Microbiol"},{"key":"ref58","doi-asserted-by":"publisher","first-page":"499","DOI":"10.1016\/j.bjm.2016.09.021","article-title":"Prevalence, serotyping and antimicrobials resistance mechanism of Salmonella enterica isolated from clinical and environmental samples in Saudi Arabia","volume":"48","author":"El-Tayeb","year":"2017","journal-title":"Braz J Microbiol"},{"key":"ref59","doi-asserted-by":"publisher","first-page":"129","DOI":"10.1016\/j.jgar.2019.09.001","article-title":"Draft genome of a macrolide resistant XDR Salmonella enterica serovar Paratyphi a strain using a shotgun sequencing approach","volume":"19","author":"Khatoon","year":"2019","journal-title":"J Glob Antimicrob Resist"},{"key":"ref60","doi-asserted-by":"publisher","first-page":"1381","DOI":"10.1128\/AAC.04750-14","article-title":"First detection of conjugative plasmid-borne fosfomycin resistance gene fosA3 in Salmonella isolates of food origin","volume":"59","author":"Lin","year":"2015","journal-title":"Antimicrob Agents Chemother"},{"key":"ref61","doi-asserted-by":"publisher","first-page":"592","DOI":"10.3389\/fmicb.2018.00592","article-title":"Prediction of phenotypic antimicrobial resistance profiles from whole genome sequences of non-typhoidal Salmonella enterica","volume":"9","author":"Neuert","year":"2018","journal-title":"Front Microbiol"},{"key":"ref62","doi-asserted-by":"publisher","first-page":"1282","DOI":"10.4269\/ajtmh.19-0403","article-title":"Rapid emergence of florfenicol-resistant invasive non-typhoidal salmonella in China: a potential threat to public health","volume":"101","author":"Zhan","year":"2019","journal-title":"Am J Trop Med Hyg"},{"key":"ref63","doi-asserted-by":"publisher","first-page":"541","DOI":"10.1128\/CMR.00075-13","article-title":"Whole-genome sequencing in outbreak analysis","volume":"28","author":"Gilchrist","year":"2015","journal-title":"Clin Microbiol Rev"},{"key":"ref64","doi-asserted-by":"publisher","first-page":"13","DOI":"10.1016\/j.vetmic.2011.06.014","article-title":"Everything at once: comparative analysis of the genomes of bacterial pathogens","volume":"153","author":"Laing","year":"2011","journal-title":"Vet Microbiol"},{"key":"ref65","doi-asserted-by":"publisher","first-page":"701","DOI":"10.1038\/s41587-020-0422-6","article-title":"Complete, closed bacterial genomes from microbiomes using nanopore sequencing","volume":"38","author":"Moss","year":"2020","journal-title":"Nat Biotechnol"},{"key":"ref66","doi-asserted-by":"publisher","first-page":"2817","DOI":"10.3389\/fmicb.2019.02817","article-title":"IS26-mediated transfer of Bla NDM-1 as the Main route of resistance transmission during a polyclonal, multispecies outbreak in a German hospital","volume":"10","author":"Weber","year":"2019","journal-title":"Front Microbiol"},{"key":"ref67","doi-asserted-by":"publisher","first-page":"298","DOI":"10.1016\/j.ijmm.2013.02.001","article-title":"Plasmids and the spread of resistance","volume":"303","author":"Carattoli","year":"2013","journal-title":"Int J Med Microbiol"},{"key":"ref68","doi-asserted-by":"publisher","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":"ref69","doi-asserted-by":"publisher","first-page":"e0163122","DOI":"10.1128\/jcm.01631-22","article-title":"Real-time Nanopore Q20+ sequencing enables extremely fast and accurate Core genome MLST typing and democratizes access to high-resolution bacterial pathogen surveillance","volume":"61","author":"Wagner","year":"2023","journal-title":"J Clin Microbiol"},{"key":"ref70","doi-asserted-by":"publisher","first-page":"e0257521","DOI":"10.1371\/journal.pone.0257521","article-title":"Sequencing DNA with nanopores: troubles and biases","volume":"16","author":"Delahaye","year":"2021","journal-title":"PLoS One"},{"key":"ref71","doi-asserted-by":"publisher","first-page":"mgen000910","DOI":"10.1099\/mgen.0.000910","article-title":"Comparison of R9.4.1\/Kit10 and R10\/Kit12 Oxford Nanopore flowcells and chemistries in bacterial genome reconstruction","volume":"9","author":"Sanderson","year":"2022","journal-title":"Microb Genom"},{"key":"ref72","doi-asserted-by":"publisher","first-page":"103534","DOI":"10.1016\/j.fm.2020.103534","article-title":"A genoserotyping system for a fast and objective identification of Salmonella serotypes commonly isolated from poultry and pork food sectors in Belgium","volume":"91","author":"Gand","year":"2020","journal-title":"Food Microbiol"},{"key":"ref73","doi-asserted-by":"publisher","first-page":"giz104","DOI":"10.1093\/gigascience\/giz104","article-title":"Comparison of single-nucleotide variants identified by Illumina and Oxford Nanopore technologies in the context of a potential outbreak of Shiga toxin-producing Escherichia coli","volume":"8","author":"Greig","year":"2019","journal-title":"Gigascience"},{"key":"ref74","doi-asserted-by":"publisher","first-page":"e84","DOI":"10.1016\/S2666-5247(22)00301-9","article-title":"Evaluation of Nanopore sequencing for Mycobacterium tuberculosis drug susceptibility testing and outbreak investigation: a genomic analysis. Lancet","volume":"4","author":"Hall","year":"2023","journal-title":"Microbe"},{"key":"ref75","doi-asserted-by":"publisher","first-page":"1405","DOI":"10.1038\/s41591-020-0997-y","article-title":"Rapid SARS-CoV-2 whole-genome sequencing and analysis for informed public health decision-making in the Netherlands","volume":"26","author":"Oude Munnink","year":"2020","journal-title":"Nat Med"},{"key":"ref76","doi-asserted-by":"publisher","first-page":"e00583","DOI":"10.1128\/JCM.00583-20","article-title":"Assessing nanopore sequencing for clinical diagnostics: a comparison of next-generation sequencing (NGS) methods for Mycobacterium tuberculosis","volume":"59","author":"Smith","year":"2020","journal-title":"J Clin Microbiol"}],"container-title":["Frontiers in Veterinary Science"],"original-title":[],"link":[{"URL":"https:\/\/www.frontiersin.org\/articles\/10.3389\/fvets.2023.1178922\/full","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,6,1]],"date-time":"2023-06-01T04:49:04Z","timestamp":1685594944000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.frontiersin.org\/articles\/10.3389\/fvets.2023.1178922\/full"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2023,6,1]]},"references-count":76,"alternative-id":["10.3389\/fvets.2023.1178922"],"URL":"https:\/\/doi.org\/10.3389\/fvets.2023.1178922","relation":{},"ISSN":["2297-1769"],"issn-type":[{"type":"electronic","value":"2297-1769"}],"subject":[],"published":{"date-parts":[[2023,6,1]]},"article-number":"1178922"}}