{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,11,4]],"date-time":"2026-11-04T07:07:05Z","timestamp":1793776025584,"version":"4.6.1"},"reference-count":94,"publisher":"Elsevier BV","license":[{"start":{"date-parts":[[2019,4,1]],"date-time":"2019-04-01T00:00:00Z","timestamp":1554076800000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.elsevier.com\/tdm\/userlicense\/1.0\/"},{"start":{"date-parts":[[2019,4,1]],"date-time":"2019-04-01T00:00:00Z","timestamp":1554076800000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.elsevier.com\/legal\/tdmrep-license"},{"start":{"date-parts":[[2020,3,11]],"date-time":"2020-03-11T00:00:00Z","timestamp":1583884800000},"content-version":"am","delay-in-days":345,"URL":"http:\/\/www.elsevier.com\/open-access\/userlicense\/1.0\/"}],"funder":[{"DOI":"10.13039\/100000001","name":"National Science Foundation","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100000001","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["elsevier.com","sciencedirect.com"],"crossmark-restriction":true},"short-container-title":["Journal of Microbiological Methods"],"published-print":{"date-parts":[[2019,4]]},"DOI":"10.1016\/j.mimet.2019.03.001","type":"journal-article","created":{"date-parts":[[2019,3,5]],"date-time":"2019-03-05T11:37:14Z","timestamp":1551785834000},"page":"138-147","update-policy":"https:\/\/doi.org\/10.1016\/elsevier_cm_policy","source":"Crossref","is-referenced-by-count":21,"special_numbering":"C","title":["Nanopore ultra-long read sequencing technology for antimicrobial resistance detection in Mannheimia haemolytica"],"prefix":"10.1016","volume":"159","author":[{"given":"Alexander","family":"Lim","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3264-2652","authenticated-orcid":false,"given":"Bryan","family":"Naidenov","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Haley","family":"Bates","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Karyn","family":"Willyerd","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2659-835X","authenticated-orcid":false,"given":"Timothy","family":"Snider","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Matthew Brian","family":"Couger","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2203-0433","authenticated-orcid":false,"given":"Charles","family":"Chen","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Akhilesh","family":"Ramachandran","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"78","reference":[{"key":"10.1016\/j.mimet.2019.03.001_bb0005","doi-asserted-by":"crossref","first-page":"28","DOI":"10.3390\/antibiotics7020028","article-title":"Isolation, characterization, and antibacterial activity of hard-to-culture actinobacteria from cave moonmilk deposits","volume":"7","author":"Adam","year":"2018","journal-title":"Antibiotics."},{"key":"10.1016\/j.mimet.2019.03.001_bb0010","doi-asserted-by":"crossref","first-page":"40","DOI":"10.7171\/jbt.17-2801-007","article-title":"Precision metagenomics: rapid metagenomic analyses for infectious disease diagnostics and public health surveillance","volume":"28","author":"Afshinnekoo","year":"2017","journal-title":"J. Biomol. Tech."},{"key":"10.1016\/j.mimet.2019.03.001_bb0015","doi-asserted-by":"crossref","first-page":"1174","DOI":"10.1093\/gbe\/evu092","article-title":"Dissecting Vancomycin-intermediate resistance in Staphylococcus aureus using genome-wide association","volume":"6","author":"Alam","year":"2014","journal-title":"Genome Biol. Evol."},{"issue":"Suppl. 1","key":"10.1016\/j.mimet.2019.03.001_bb0020","doi-asserted-by":"crossref","first-page":"29","DOI":"10.1093\/jac\/48.suppl_1.29","article-title":"The development of the BSAC standardized method of disc diffusion testing","volume":"48","author":"Andrews","year":"2001","journal-title":"J. Antimicrob. Chemother."},{"key":"10.1016\/j.mimet.2019.03.001_bb0025","doi-asserted-by":"crossref","first-page":"296","DOI":"10.1038\/nbt.3103","article-title":"MinION nanopore sequencing identifies the position and structure of a bacterial antibiotic resistance island","volume":"33","author":"Ashton","year":"2015","journal-title":"Nat. Biotechnol."},{"key":"10.1016\/j.mimet.2019.03.001_bb0030","doi-asserted-by":"crossref","first-page":"D621","DOI":"10.1093\/nar\/gkr846","article-title":"ICEberg: a web-based resource for integrative and conjugative elements found in Bacteria","volume":"40","author":"Bi","year":"2012","journal-title":"Nucleic Acids Res."},{"key":"10.1016\/j.mimet.2019.03.001_bb0035","doi-asserted-by":"crossref","first-page":"674","DOI":"10.1128\/AAC.01086-12","article-title":"Comparative genomics of IncL\/M-type plasmids: evolution by acquisition of resistance genes and insertion sequences","volume":"57","author":"Bonnin","year":"2013","journal-title":"Antimicrob. Agents Chemother."},{"key":"10.1016\/j.mimet.2019.03.001_bb0040","doi-asserted-by":"crossref","DOI":"10.1093\/gigascience\/gix007","article-title":"MinION\u2122 nanopore sequencing of environmental metagenomes: a synthetic approach","volume":"6","author":"Brown","year":"2017","journal-title":"GigaScience"},{"key":"10.1016\/j.mimet.2019.03.001_bb0045","doi-asserted-by":"crossref","first-page":"1932","DOI":"10.1016\/j.bbadis.2014.06.015","article-title":"Next generation sequencing technology: advances and applications","volume":"1842","author":"Buermans","year":"2014","journal-title":"Biochim. Biophys. Acta Mol. basis Dis."},{"key":"10.1016\/j.mimet.2019.03.001_bb0050","doi-asserted-by":"crossref","first-page":"2402","DOI":"10.1128\/JCM.00267-10","article-title":"Comparison of meropenem MICs and susceptibilities for carbapenemase-producing Klebsiella pneumoniae isolates by various testing methods","volume":"48","author":"Bulik","year":"2010","journal-title":"J. Clin. Microbiol."},{"key":"10.1016\/j.mimet.2019.03.001_bb0055","doi-asserted-by":"crossref","first-page":"421","DOI":"10.1186\/1471-2105-10-421","article-title":"BLAST+: architecture and applications","volume":"10","author":"Camacho","year":"2009","journal-title":"BMC Bioinf."},{"key":"10.1016\/j.mimet.2019.03.001_bb0060","doi-asserted-by":"crossref","first-page":"9","DOI":"10.1111\/j.1365-2958.2004.04113.x","article-title":"The impact of prophages on bacterial chromosomes","volume":"53","author":"Canchaya","year":"2004","journal-title":"Mol. Microbiol."},{"key":"10.1016\/j.mimet.2019.03.001_bb0065","doi-asserted-by":"crossref","first-page":"18022","DOI":"10.1038\/s41598-017-18364-0","article-title":"Nanopore DNA sequencing and genome assembly on the international Space Station","volume":"7","author":"Castro-Wallace","year":"2017","journal-title":"Sci. Rep."},{"key":"10.1016\/j.mimet.2019.03.001_bb0070","doi-asserted-by":"crossref","first-page":"563","DOI":"10.1038\/nmeth.2474","article-title":"Nonhybrid, finished microbial genome assemblies from long-read SMRT sequencing data","volume":"10","author":"Chin","year":"2013","journal-title":"Nat. Methods"},{"key":"10.1016\/j.mimet.2019.03.001_bb0075","doi-asserted-by":"crossref","first-page":"915","DOI":"10.1038\/nbt.1966","article-title":"Efficient de novo assembly of single-cell bacterial genomes from short-read data sets","volume":"29","author":"Chitsaz","year":"2011","journal-title":"Nat. Biotechnol."},{"key":"10.1016\/j.mimet.2019.03.001_bb0080","doi-asserted-by":"crossref","first-page":"169","DOI":"10.1017\/S1466252314000188","article-title":"Pathogen variation across time and space: sequencing to characterize Mannheimia haemolytica diversity","volume":"15","author":"Clawson","year":"2014","journal-title":"Anim. Health Res. Rev."},{"key":"10.1016\/j.mimet.2019.03.001_bb0085","doi-asserted-by":"crossref","first-page":"982","DOI":"10.1186\/s12864-016-3316-8","article-title":"Genomic signatures of Mannheimia haemolytica that associate with the lungs of cattle with respiratory disease, an integrative conjugative element, and antibiotic resistance genes","volume":"17","author":"Clawson","year":"2016","journal-title":"BMC Genomics"},{"key":"10.1016\/j.mimet.2019.03.001_bb0090","series-title":"Performance Standards for Antimicrobial Disk and Dilution Susceptibility Tests for Bacteria Isolated from Animals. CLSI supplement VET08","author":"CLSI","year":"2018"},{"key":"10.1016\/j.mimet.2019.03.001_bb2555","doi-asserted-by":"crossref","first-page":"1394","DOI":"10.1101\/gr.2289704","article-title":"Mauve: multiple alignment of conserved genomic sequence with rearrangements","volume":"14","author":"Darling","year":"2004","journal-title":"Genome Res."},{"key":"10.1016\/j.mimet.2019.03.001_bb0095","doi-asserted-by":"crossref","first-page":"601","DOI":"10.1038\/nrg3226","article-title":"Transforming clinical microbiology with bacterial genome sequencing","volume":"13","author":"Didelot","year":"2012","journal-title":"Nat. Rev. Genet."},{"key":"10.1016\/j.mimet.2019.03.001_bb0100","doi-asserted-by":"crossref","DOI":"10.1128\/genomeA.00318-13","article-title":"Complete genome sequence of Mannheimia haemolytica strain 42548 from a case of bovine respiratory disease","volume":"1","author":"Eidam","year":"2013","journal-title":"Genome Announc."},{"key":"10.1016\/j.mimet.2019.03.001_bb0105","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pone.0047768","article-title":"Mind the gap: upgrading genomes with Pacific biosciences RS long-read sequencing technology","volume":"7","author":"English","year":"2012","journal-title":"PLoS One"},{"key":"10.1016\/j.mimet.2019.03.001_bb0110","doi-asserted-by":"crossref","first-page":"1232","DOI":"10.1038\/nbt.2432","article-title":"Genome-wide mapping of methylated adenine residues in pathogenic Escherichia coli using single-molecule real-time sequencing","volume":"30","author":"Fang","year":"2012","journal-title":"Nat. Biotechnol."},{"key":"10.1016\/j.mimet.2019.03.001_bb0115","series-title":"Tthe FAO Action Plan on Antimicrobial Resistance 2016\u20132020","author":"FAO","year":"2016"},{"key":"10.1016\/j.mimet.2019.03.001_bb0120","series-title":"Antimicrobial resistance in food and agriculture","author":"FAO","year":"2017"},{"key":"10.1016\/j.mimet.2019.03.001_bb0125","doi-asserted-by":"crossref","first-page":"W30","DOI":"10.1093\/nar\/gkv397","article-title":"HMMER web server: 2015 update","volume":"43","author":"Finn","year":"2015","journal-title":"Nucleic Acids Res."},{"key":"10.1016\/j.mimet.2019.03.001_bb0130","doi-asserted-by":"crossref","first-page":"D279","DOI":"10.1093\/nar\/gkv1344","article-title":"The Pfam protein families database: towards a more sustainable future","volume":"44","author":"Finn","year":"2016","journal-title":"Nucleic Acids Res."},{"key":"10.1016\/j.mimet.2019.03.001_bb0135","doi-asserted-by":"crossref","first-page":"1069","DOI":"10.3389\/fmicb.2017.01069","article-title":"Metagenomics: the next culture-independent game changer","volume":"8","author":"Forbes","year":"2017","journal-title":"Front. Microbiol."},{"key":"10.1016\/j.mimet.2019.03.001_bb0140","doi-asserted-by":"crossref","first-page":"49","DOI":"10.1038\/nrg3624","article-title":"Bacterial genome sequencing in the clinic: bioinformatic challenges and solutions","volume":"15","author":"Fricke","year":"2014","journal-title":"Nat. Revi. Genet."},{"key":"10.1016\/j.mimet.2019.03.001_bb0145","first-page":"1","article-title":"Review of bacterial and viral zoonotic infections transmitted by dogs","volume":"8","author":"Ghasemzadeh","year":"2015","journal-title":"J. Med. Life"},{"key":"10.1016\/j.mimet.2019.03.001_bb0150","doi-asserted-by":"crossref","first-page":"7257","DOI":"10.1128\/JB.00675-06","article-title":"The genome sequence of Mannheimia haemolytica A1: insights into virulence, natural competence, and Pasteurellaceae phylogeny","volume":"188","author":"Gioia","year":"2006","journal-title":"J. Bacteriol."},{"key":"10.1016\/j.mimet.2019.03.001_bb0155","doi-asserted-by":"crossref","first-page":"333","DOI":"10.1038\/nrg.2016.49","article-title":"Coming of age: ten years of next-generation sequencing technologies","volume":"17","author":"Goodwin","year":"2016","journal-title":"Nat. Rev. Genet."},{"key":"10.1016\/j.mimet.2019.03.001_bb0160","doi-asserted-by":"crossref","first-page":"1182","DOI":"10.1128\/JCM.03117-13","article-title":"Prediction of Staphylococcus aureus antimicrobial resistance by whole-genome sequencing","volume":"52","author":"Gordon","year":"2014","journal-title":"J. Clin. Microbiol."},{"key":"10.1016\/j.mimet.2019.03.001_bb0165","doi-asserted-by":"crossref","first-page":"99","DOI":"10.1186\/s13073-015-0220-9","article-title":"Rapid metagenomic identification of viral pathogens in clinical samples by real-time nanopore sequencing analysis","volume":"7","author":"Greninger","year":"2015","journal-title":"Genome Med."},{"key":"10.1016\/j.mimet.2019.03.001_bb0170","doi-asserted-by":"crossref","first-page":"63","DOI":"10.1186\/s13073-018-0572-z","article-title":"Comprehensive antibiotic-linked mutation assessment by resistance mutation sequencing (RM-seq)","volume":"10","author":"Gu\u00e9rillot","year":"2018","journal-title":"Genome Med."},{"key":"10.1016\/j.mimet.2019.03.001_bb0175","doi-asserted-by":"crossref","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":"10.1016\/j.mimet.2019.03.001_bb0180","doi-asserted-by":"crossref","DOI":"10.1128\/genomeA.00188-13","article-title":"Complete closed genome sequences of Mannheimia haemolytica serotypes A1 and A6 isolated from cattle","volume":"1","author":"Harhay","year":"2013","journal-title":"Genome Announc."},{"key":"10.1016\/j.mimet.2019.03.001_bb0185","doi-asserted-by":"crossref","first-page":"139","DOI":"10.1128\/JCM.02452-13","article-title":"Rapid whole-genome sequencing for detection and characterization of microorganisms directly from clinical samples","volume":"52","author":"Hasman","year":"2014","journal-title":"J. Clin. Microbiol."},{"key":"10.1016\/j.mimet.2019.03.001_bb0190","doi-asserted-by":"crossref","DOI":"10.1128\/genomeA.00417-15","article-title":"Complete closed genome sequences of a Mannheimia haemolytica serotype A1 leukotoxin deletion mutant and its wild-type parent strain","volume":"3","author":"Heaton","year":"2015","journal-title":"Genome Announc."},{"key":"10.1016\/j.mimet.2019.03.001_bb0195","doi-asserted-by":"crossref","first-page":"459","DOI":"10.1038\/nrg3922","article-title":"Evolutionary consequences of drug resistance: shared principles across diverse targets and organisms","volume":"16","author":"Hughes","year":"2015","journal-title":"Nat. Rev. Genet."},{"key":"10.1016\/j.mimet.2019.03.001_bb0200","doi-asserted-by":"crossref","first-page":"2223","DOI":"10.1093\/bioinformatics\/bts429","article-title":"Gene and translation initiation site prediction in metagenomic sequences","volume":"28","author":"Hyatt","year":"2012","journal-title":"Bioinformatics."},{"key":"10.1016\/j.mimet.2019.03.001_bb0205","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pgen.1007758","article-title":"A fast and agnostic method for bacterial genome-wide association studies: bridging the gap between k-mers and genetic events","volume":"14","author":"Jaillard","year":"2018","journal-title":"PLoS Genet."},{"key":"10.1016\/j.mimet.2019.03.001_bb0210","doi-asserted-by":"crossref","first-page":"239","DOI":"10.1186\/s13059-016-1103-0","article-title":"The Oxford Nanopore MinION: delivery of nanopore sequencing to the genomics community","volume":"17","author":"Jain","year":"2016","journal-title":"Genome Biol."},{"key":"10.1016\/j.mimet.2019.03.001_bb0215","doi-asserted-by":"crossref","first-page":"338","DOI":"10.1038\/nbt.4060","article-title":"Nanopore sequencing and assembly of a human genome with ultra-long reads","volume":"36","author":"Jain","year":"2018","journal-title":"Nat. Biotechnol."},{"key":"10.1016\/j.mimet.2019.03.001_bb0220","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":"10.1016\/j.mimet.2019.03.001_bb0225","doi-asserted-by":"crossref","first-page":"1501","DOI":"10.1128\/JCM.03617-13","article-title":"Real-time whole-genome sequencing for routine typing, surveillance, and outbreak detection of verotoxigenic Escherichia coli","volume":"52","author":"Joensen","year":"2014","journal-title":"J. Clin. Microbiol."},{"key":"10.1016\/j.mimet.2019.03.001_bb0230","doi-asserted-by":"crossref","first-page":"1749","DOI":"10.1086\/647952","article-title":"Antimicrobial susceptibility testing: a review of general principles and contemporary practices","volume":"49","author":"Jorgensen","year":"2009","journal-title":"Clin. Infect. Dis."},{"key":"10.1016\/j.mimet.2019.03.001_bb0235","doi-asserted-by":"crossref","first-page":"415","DOI":"10.1038\/nrg3493","article-title":"Molecular genetic testing and the future of clinical genomics","volume":"14","author":"Katsanis","year":"2013","journal-title":"Nat. Rev. Genet."},{"key":"10.1016\/j.mimet.2019.03.001_bb0240","doi-asserted-by":"crossref","first-page":"403","DOI":"10.1093\/jac\/dki210","article-title":"Tet(L)-mediated tetracycline resistance in bovine Mannheimia and Pasteurella isolates","volume":"56","author":"Kehrenberg","year":"2005","journal-title":"J. Antimicrob. Chemother."},{"key":"10.1016\/j.mimet.2019.03.001_bb0245","doi-asserted-by":"crossref","DOI":"10.1128\/genomeA.00129-15","article-title":"Complete genome sequence of Mannheimia haemolytica strain Mh10517 isolated from sheep in South Africa","volume":"3","author":"Kidanemariam Gelaw","year":"2015","journal-title":"Genome Announc."},{"key":"10.1016\/j.mimet.2019.03.001_bb0250","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pone.0149520","article-title":"Comparative genomic analysis of Mannheimia haemolytica from bovine sources","volume":"11","author":"Klima","year":"2016","journal-title":"PLoS One"},{"key":"10.1016\/j.mimet.2019.03.001_bb0255","doi-asserted-by":"crossref","first-page":"722","DOI":"10.1101\/gr.215087.116","article-title":"Canu: scalable and accurate long-read assembly via adaptive k-mer weighting and repeat separation","volume":"27","author":"Koren","year":"2017","journal-title":"Genome Res."},{"key":"10.1016\/j.mimet.2019.03.001_bb0260","doi-asserted-by":"crossref","first-page":"401","DOI":"10.1016\/j.tig.2014.07.003","article-title":"Whole-genome sequencing to control antimicrobial resistance","volume":"30","author":"K\u00f6ser","year":"2014","journal-title":"Trends Genet."},{"key":"10.1016\/j.mimet.2019.03.001_bb3555","doi-asserted-by":"crossref","first-page":"1639","DOI":"10.1101\/gr.092759.109","article-title":"Circos: an information aesthetic for comparative genomics","volume":"19","author":"Krzywinski","year":"2009","journal-title":"Genome Res."},{"key":"10.1016\/j.mimet.2019.03.001_bb0265","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pgen.1004941","article-title":"GC-content evolution in bacterial genomes: the biased gene conversion hypothesis expands","volume":"11","author":"Lassalle","year":"2015","journal-title":"PLoS Genet."},{"key":"10.1016\/j.mimet.2019.03.001_bb0270","doi-asserted-by":"crossref","first-page":"3530","DOI":"10.1128\/JCM.01069-17","article-title":"Rapid Nanopore sequencing of plasmids and resistance gene detection in clinical isolates","volume":"55","author":"Lemon","year":"2017","journal-title":"J. Clin. Microbiol."},{"key":"10.1016\/j.mimet.2019.03.001_bb0275","doi-asserted-by":"crossref","first-page":"3125","DOI":"10.1093\/nar\/gki631","article-title":"Recognizing the pseudogenes in bacterial genomes","volume":"33","author":"Lerat","year":"2005","journal-title":"Nucleic Acids Res."},{"key":"10.1016\/j.mimet.2019.03.001_bb0280","series-title":"Aligning sequence reads, clone sequences and assembly contigs with BWA-MEM","author":"Li","year":"2013"},{"key":"10.1016\/j.mimet.2019.03.001_bb0285","doi-asserted-by":"crossref","first-page":"2078","DOI":"10.1093\/bioinformatics\/btp352","article-title":"The sequence alignment\/map format and SAMtools","volume":"25","author":"Li","year":"2009","journal-title":"Bioinformatics."},{"key":"10.1016\/j.mimet.2019.03.001_bb0290","first-page":"566","article-title":"VRprofile: gene-cluster-detection-based profiling of virulence and antibiotic resistance traits encoded within genome sequences of pathogenic bacteria","volume":"19","author":"Li","year":"2018","journal-title":"Brief Bioinform."},{"key":"10.1016\/j.mimet.2019.03.001_bb0295","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1093\/gigascience\/gix132","article-title":"Efficient generation of complete sequences of MDR-encoding plasmids by rapid assembly of MinION barcoding sequencing data","volume":"7","author":"Li","year":"2018","journal-title":"GigaScience."},{"key":"10.1016\/j.mimet.2019.03.001_bb0300","doi-asserted-by":"crossref","first-page":"121","DOI":"10.1101\/gr.141705.112","article-title":"Sequencing the unsequenceable: expanded CGG-repeat alleles of the fragile X gene","volume":"23","author":"Loomis","year":"2013","journal-title":"Genome Res."},{"key":"10.1016\/j.mimet.2019.03.001_bb0305","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":"Genomics Proteomics Bioinformatics."},{"key":"10.1016\/j.mimet.2019.03.001_bb0310","doi-asserted-by":"crossref","first-page":"413","DOI":"10.1177\/1040638713485227","article-title":"Antimicrobial multidrug resistance and coresistance patterns of Mannheimia haemolytica isolated from bovine respiratory disease cases--a three-year (2009-2011) retrospective analysis","volume":"25","author":"Lubbers","year":"2013","journal-title":"J. Vet. Diagn. Investig."},{"key":"10.1016\/j.mimet.2019.03.001_bb0315","doi-asserted-by":"crossref","first-page":"7","DOI":"10.1016\/j.ygeno.2009.09.002","article-title":"Bacterial genomic G+C composition-eliciting environmental adaptation","volume":"95","author":"Mann","year":"2010","journal-title":"Genomics."},{"key":"10.1016\/j.mimet.2019.03.001_bb0320","doi-asserted-by":"crossref","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":"10.1016\/j.mimet.2019.03.001_bb0325","doi-asserted-by":"crossref","DOI":"10.1128\/microbiolspec.VMBF-0016-2015","article-title":"Mechanisms of antibiotic resistance","volume":"4","author":"Munita","year":"2016","journal-title":"Microbiol. Spect."},{"key":"10.1016\/j.mimet.2019.03.001_bb0330","doi-asserted-by":"crossref","first-page":"705","DOI":"10.1111\/jvim.12547","article-title":"Mannheimia haemolytica in feedlot cattle: prevalence of recovery and associations with antimicrobial use, resistance, and health outcomes","volume":"29","author":"Noyes","year":"2015","journal-title":"J. Vet. Intern. Med."},{"key":"10.1016\/j.mimet.2019.03.001_bb0340","doi-asserted-by":"crossref","first-page":"D206","DOI":"10.1093\/nar\/gkt1226","article-title":"The SEED and the Rapid Annotation of microbial genomes using Subsystems Technology (RAST)","volume":"42","author":"Overbeek","year":"2014","journal-title":"Nucleic Acids Res."},{"key":"10.1016\/j.mimet.2019.03.001_bb0345","doi-asserted-by":"crossref","first-page":"114","DOI":"10.1186\/s13059-015-0677-2","article-title":"Rapid draft sequencing and real-time nanopore sequencing in a hospital outbreak of Salmonella","volume":"16","author":"Quick","year":"2015","journal-title":"Genome Biol."},{"key":"10.1016\/j.mimet.2019.03.001_bb0350","doi-asserted-by":"crossref","first-page":"228","DOI":"10.1038\/nature16996","article-title":"Real-time, portable genome sequencing for Ebola surveillance","volume":"530","author":"Quick","year":"2016","journal-title":"Nature."},{"key":"10.1016\/j.mimet.2019.03.001_bb0355","doi-asserted-by":"crossref","first-page":"709","DOI":"10.1056\/NEJMoa1106920","article-title":"Origins of the E. coli strain causing an outbreak of hemolytic-uremic syndrome in Germany","volume":"365","author":"Rasko","year":"2011","journal-title":"N. Engl. J. Med."},{"key":"10.1016\/j.mimet.2019.03.001_bb0360","doi-asserted-by":"crossref","first-page":"1749","DOI":"10.1086\/647952","article-title":"Antimicrobial susceptibility testing: a review of general principles and contemporary practices","volume":"49","author":"Reller","year":"2009","journal-title":"Clin. Infect. Dis."},{"key":"10.1016\/j.mimet.2019.03.001_bb0365","doi-asserted-by":"crossref","first-page":"231","DOI":"10.3311\/PPee.10015","article-title":"Beyond homopolymer errors: a systematic investigation of nanopore-based DNA sequencing characteristics using HLA-DQA2","volume":"61","author":"S\u00e1rk\u00f6zy","year":"2017","journal-title":"Periodica Polytechnica Electr. Eng. Comput. Sci."},{"key":"10.1016\/j.mimet.2019.03.001_bb0370","doi-asserted-by":"crossref","first-page":"104","DOI":"10.1093\/jac\/dkw397","article-title":"Identification of bacterial pathogens and antimicrobial resistance directly from clinical urines by nanopore-based metagenomic sequencing","volume":"72","author":"Schmidt","year":"2017","journal-title":"J. Antimicrob. Chemother."},{"key":"10.1016\/j.mimet.2019.03.001_bb0375","doi-asserted-by":"crossref","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":"10.1016\/j.mimet.2019.03.001_bb0380","doi-asserted-by":"crossref","first-page":"791","DOI":"10.3389\/fmicb.2015.00791","article-title":"MALDI-TOF mass spectrometry: an emerging technology for microbial identification and diagnosis","volume":"6","author":"Singhal","year":"2015","journal-title":"Front. Microbiol."},{"key":"10.1016\/j.mimet.2019.03.001_bb0385","doi-asserted-by":"crossref","first-page":"321","DOI":"10.1146\/annurev.mi.39.100185.001541","article-title":"Measurement of in situ activities of nonphotosynthetic microorganisms in aquatic and terrestrial habitats","volume":"39","author":"Staley","year":"1985","journal-title":"Annu. Rev. Microbiol."},{"key":"10.1016\/j.mimet.2019.03.001_bb0390","doi-asserted-by":"crossref","first-page":"2234","DOI":"10.1093\/jac\/dkt180","article-title":"Predicting antimicrobial susceptibilities for Escherichia coli and Klebsiella pneumoniae isolates using whole genomic sequence data","volume":"68","author":"Stoesser","year":"2013","journal-title":"J. Antimicrob. Chemother."},{"key":"10.1016\/j.mimet.2019.03.001_bb0395","doi-asserted-by":"crossref","first-page":"2007","DOI":"10.1007\/s10096-017-3024-6","article-title":"Bacterial genome sequencing in clinical microbiology: a pathogen-oriented review","volume":"36","author":"Tagini","year":"2017","journal-title":"Eur. J. Clin. Microbiol. Infect. Dis."},{"key":"10.1016\/j.mimet.2019.03.001_bb0400","first-page":"7","article-title":"Antimicrobial Resistance in Agriculture","author":"Thanner","year":"2016","journal-title":"mBio."},{"key":"10.1016\/j.mimet.2019.03.001_bb0405","doi-asserted-by":"crossref","first-page":"2763","DOI":"10.1093\/jac\/dkv186","article-title":"WGS accurately predicts antimicrobial resistance in Escherichia coli","volume":"70","author":"Tyson","year":"2015","journal-title":"J. Antimicrobial Chemother."},{"key":"10.1016\/j.mimet.2019.03.001_bb0410","doi-asserted-by":"crossref","first-page":"266","DOI":"10.1101\/gr.221184.117","article-title":"MinION-based long-read sequencing and assembly extends the Caenorhabditis elegans reference genome","volume":"28","author":"Tyson","year":"2018","journal-title":"Genome Res."},{"key":"10.1016\/j.mimet.2019.03.001_bb0415","doi-asserted-by":"crossref","first-page":"1272","DOI":"10.3389\/fmicb.2017.01272","article-title":"A case study into microbial genome assembly gap sequences and finishing strategies","volume":"8","author":"Utturkar","year":"2017","journal-title":"Front. Microbiol."},{"key":"10.1016\/j.mimet.2019.03.001_bb0420","doi-asserted-by":"crossref","first-page":"1142","DOI":"10.1038\/ejhg.2014.279","article-title":"Next-generation sequencing-based genome diagnostics across clinical genetics centers: implementation choices and their effects","volume":"23","author":"Vrijenhoek","year":"2015","journal-title":"Eur. J. Hum. Genet."},{"key":"10.1016\/j.mimet.2019.03.001_bb0425","doi-asserted-by":"crossref","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":"10.1016\/j.mimet.2019.03.001_bb0430","series-title":"Antimicrobial Resistance Arising from Food-Animal Productions and its Mitigation","author":"Wang","year":"2012"},{"key":"10.1016\/j.mimet.2019.03.001_bb0435","series-title":"Antimicrobial resistance","author":"WHO","year":"2018"},{"key":"10.1016\/j.mimet.2019.03.001_bb0440","doi-asserted-by":"crossref","DOI":"10.1099\/mgen.0.000132","article-title":"Completing bacterial genome assemblies with multiplex MinION sequencing","volume":"3","author":"Wick","year":"2017","journal-title":"Microbial. Genomics."},{"key":"10.1016\/j.mimet.2019.03.001_bb0445","doi-asserted-by":"crossref","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."},{"key":"10.1016\/j.mimet.2019.03.001_bb0450","doi-asserted-by":"crossref","first-page":"143","DOI":"10.1016\/j.vetmic.2018.06.005","article-title":"Multidrug resistant Mannheimia haemolytica isolated from high-risk beef stocker cattle after antimicrobial metaphylaxis and treatment for bovine respiratory disease","volume":"221","author":"Woolums","year":"2018","journal-title":"Vet. Microbiol."},{"key":"10.1016\/j.mimet.2019.03.001_bb0455","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":"10.1016\/j.mimet.2019.03.001_bb0460","doi-asserted-by":"crossref","first-page":"771","DOI":"10.1093\/jac\/dks496","article-title":"Genotyping using whole-genome sequencing is a realistic alternative to surveillance based on phenotypic antimicrobial susceptibility testing","volume":"68","author":"Zankari","year":"2013","journal-title":"J. Antimicrob. Chemother."},{"key":"10.1016\/j.mimet.2019.03.001_bb0465","doi-asserted-by":"crossref","first-page":"4115","DOI":"10.1128\/AAC.00366-08","article-title":"A plasmid-borne blaOXA-58 gene confers imipenem resistance to Acinetobacter baumannii isolates from a Lebanese hospital","volume":"52","author":"Zarrilli","year":"2008","journal-title":"Antimicrob. Agents Chemother."}],"container-title":["Journal of Microbiological Methods"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/api.elsevier.com\/content\/article\/PII:S0167701218306961?httpAccept=text\/xml","content-type":"text\/xml","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/api.elsevier.com\/content\/article\/PII:S0167701218306961?httpAccept=text\/plain","content-type":"text\/plain","content-version":"vor","intended-application":"text-mining"}],"deposited":{"date-parts":[[2025,9,28]],"date-time":"2025-09-28T23:59:24Z","timestamp":1759103964000},"score":1,"resource":{"primary":{"URL":"https:\/\/linkinghub.elsevier.com\/retrieve\/pii\/S0167701218306961"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2019,4]]},"references-count":94,"alternative-id":["S0167701218306961"],"URL":"https:\/\/doi.org\/10.1016\/j.mimet.2019.03.001","relation":{},"ISSN":["0167-7012"],"issn-type":[{"value":"0167-7012","type":"print"}],"subject":[],"published":{"date-parts":[[2019,4]]},"assertion":[{"value":"Elsevier","name":"publisher","label":"This article is maintained by"},{"value":"Nanopore ultra-long read sequencing technology for antimicrobial resistance detection in Mannheimia haemolytica","name":"articletitle","label":"Article Title"},{"value":"Journal of Microbiological Methods","name":"journaltitle","label":"Journal Title"},{"value":"https:\/\/doi.org\/10.1016\/j.mimet.2019.03.001","name":"articlelink","label":"CrossRef DOI link to publisher maintained version"},{"value":"article","name":"content_type","label":"Content Type"},{"value":"\u00a9 2019 Elsevier B.V. All rights reserved.","name":"copyright","label":"Copyright"}]}}