{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,6,15]],"date-time":"2026-06-15T12:45:15Z","timestamp":1781527515584,"version":"3.54.1"},"update-to":[{"DOI":"10.1371\/journal.pcbi.1007134","type":"new_version","label":"New version","source":"publisher","updated":{"date-parts":[[2020,3,17]],"date-time":"2020-03-17T00:00:00Z","timestamp":1584403200000}}],"reference-count":49,"publisher":"Public Library of Science (PLoS)","issue":"3","license":[{"start":{"date-parts":[[2020,3,5]],"date-time":"2020-03-05T00:00:00Z","timestamp":1583366400000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100009139","name":"German Center for Infection Research","doi-asserted-by":"crossref","award":["8000 701\u20133 (HZI)"],"award-info":[{"award-number":["8000 701\u20133 (HZI)"]}],"id":[{"id":"10.13039\/100009139","id-type":"DOI","asserted-by":"crossref"}]},{"DOI":"10.13039\/100009139","name":"German Center for Infection Research","doi-asserted-by":"crossref","award":["TI06.001"],"award-info":[{"award-number":["TI06.001"]}],"id":[{"id":"10.13039\/100009139","id-type":"DOI","asserted-by":"crossref"}]},{"name":"German Center of Infection Research","award":["8032808811"],"award-info":[{"award-number":["8032808811"]}]},{"name":"German Network for Bioinformatics Infrastructure","award":["FKZ 031A533B"],"award-info":[{"award-number":["FKZ 031A533B"]}]},{"DOI":"10.13039\/501100001659","name":"German Research Foundation","doi-asserted-by":"crossref","award":["SFB-TR84 project A04 (TRR84\/3 2018)"],"award-info":[{"award-number":["SFB-TR84 project A04 (TRR84\/3 2018)"]}],"id":[{"id":"10.13039\/501100001659","id-type":"DOI","asserted-by":"crossref"}]},{"DOI":"10.13039\/501100001659","name":"German Research Foundation","doi-asserted-by":"crossref","award":["KFO309 Z1 (GO 2037\/5-1)"],"award-info":[{"award-number":["KFO309 Z1 (GO 2037\/5-1)"]}],"id":[{"id":"10.13039\/501100001659","id-type":"DOI","asserted-by":"crossref"}]},{"DOI":"10.13039\/501100001659","name":"German Research Foundation","doi-asserted-by":"crossref","award":["SFB-TR84 project B08 (TRR84\/3 2018)"],"award-info":[{"award-number":["SFB-TR84 project B08 (TRR84\/3 2018)"]}],"id":[{"id":"10.13039\/501100001659","id-type":"DOI","asserted-by":"crossref"}]},{"DOI":"10.13039\/501100001659","name":"German Research Foundation","doi-asserted-by":"crossref","award":["SFB1021 Z02 (SFB 1021\/2 2017)"],"award-info":[{"award-number":["SFB1021 Z02 (SFB 1021\/2 2017)"]}],"id":[{"id":"10.13039\/501100001659","id-type":"DOI","asserted-by":"crossref"}]},{"DOI":"10.13039\/501100001659","name":"German Research Foundation","doi-asserted-by":"crossref","award":["KFO309 Z1 (HA 5225\/1-1)"],"award-info":[{"award-number":["KFO309 Z1 (HA 5225\/1-1)"]}],"id":[{"id":"10.13039\/501100001659","id-type":"DOI","asserted-by":"crossref"}]}],"content-domain":{"domain":["www.ploscompbiol.org"],"crossmark-restriction":false},"short-container-title":["PLoS Comput Biol"],"DOI":"10.1371\/journal.pcbi.1007134","type":"journal-article","created":{"date-parts":[[2020,3,5]],"date-time":"2020-03-05T13:43:33Z","timestamp":1583415813000},"page":"e1007134","update-policy":"https:\/\/doi.org\/10.1371\/journal.pcbi.corrections_policy","source":"Crossref","is-referenced-by-count":78,"title":["ASA3P: An automatic and scalable pipeline for the assembly, annotation and higher-level analysis of closely related bacterial isolates"],"prefix":"10.1371","volume":"16","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-4216-2721","authenticated-orcid":true,"given":"Oliver","family":"Schwengers","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Andreas","family":"Hoek","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Moritz","family":"Fritzenwanker","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4706-8507","authenticated-orcid":true,"given":"Linda","family":"Falgenhauer","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Torsten","family":"Hain","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Trinad","family":"Chakraborty","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Alexander","family":"Goesmann","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"340","published-online":{"date-parts":[[2020,3,5]]},"reference":[{"key":"pcbi.1007134.ref001","doi-asserted-by":"crossref","first-page":"5463","DOI":"10.1073\/pnas.74.12.5463","article-title":"DNA sequencing with chain-terminating inhibitors","volume":"74","author":"F Sanger","year":"1977","journal-title":"Proc Natl Acad Sci U S A"},{"key":"pcbi.1007134.ref002","doi-asserted-by":"crossref","first-page":"418","DOI":"10.1016\/j.tig.2014.07.001","article-title":"Ten years of next-generation sequencing technology","volume":"30","author":"EL van Dijk","year":"2014","journal-title":"Trends Genet"},{"key":"pcbi.1007134.ref003","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":"S Goodwin","year":"2016","journal-title":"Nat Rev Genet"},{"key":"pcbi.1007134.ref004","doi-asserted-by":"crossref","first-page":"397","DOI":"10.1126\/science.270.5235.397","article-title":"The minimal gene complement of Mycoplasma genitalium","volume":"270","author":"CM Fraser","year":"1995","journal-title":"Science"},{"key":"pcbi.1007134.ref005","doi-asserted-by":"crossref","first-page":"496","DOI":"10.1126\/science.7542800","article-title":"Whole-genome random sequencing and assembly of Haemophilus influenzae Rd","volume":"269","author":"RD Fleischmann","year":"1995","journal-title":"Science"},{"key":"pcbi.1007134.ref006","doi-asserted-by":"crossref","first-page":"D851","DOI":"10.1093\/nar\/gkx1068","article-title":"RefSeq: an update on prokaryotic genome annotation and curation","volume":"46","author":"DH Haft","year":"2018","journal-title":"Nucleic Acids Res"},{"key":"pcbi.1007134.ref007","doi-asserted-by":"crossref","first-page":"1272","DOI":"10.1128\/JCM.03237-12","article-title":"A genomic day in the life of a clinical microbiology laboratory","volume":"51","author":"SW Long","year":"2013","journal-title":"J Clin Microbiol"},{"key":"pcbi.1007134.ref008","doi-asserted-by":"crossref","first-page":"601","DOI":"10.1038\/nrg3226","article-title":"Transforming clinical microbiology with bacterial genome sequencing","volume":"13","author":"X Didelot","year":"2012","journal-title":"Nat Rev Genet"},{"key":"pcbi.1007134.ref009","doi-asserted-by":"crossref","first-page":"13950","DOI":"10.1073\/pnas.0506758102","article-title":"Genome analysis of multiple pathogenic isolates of Streptococcus agalactiae: Implications for the microbial \u201cpan-genome","volume":"102","author":"H Tettelin","year":"2005","journal-title":"Proceedings of the National Academy of Sciences"},{"key":"pcbi.1007134.ref010","doi-asserted-by":"crossref","first-page":"16","DOI":"10.1016\/j.jbiotec.2016.12.022","article-title":"Application of next generation sequencing in clinical microbiology and infection prevention","volume":"243","author":"RH Deurenberg","year":"2017","journal-title":"J Biotechnol"},{"key":"pcbi.1007134.ref011","unstructured":"Review on Antimicrobial Resistance. Tackling Drug-Resistant Infections Globally: final report and recommendations [Internet]. Wellcome Trust; 2016 May. Available: https:\/\/amr-review.org\/sites\/default\/files\/160525_Final%20paper_with%20cover.pdf"},{"key":"pcbi.1007134.ref012","doi-asserted-by":"crossref","first-page":"347","DOI":"10.3389\/fpubh.2017.00347","article-title":"ECDC National Microbiology Focal Points and Experts Group ENMFPAE. Survey on the Use of Whole-Genome Sequencing for Infectious Diseases Surveillance: Rapid Expansion of European National Capacities, 2015\u20132016","volume":"5","author":"J Revez","year":"2017","journal-title":"Frontiers in public health"},{"key":"pcbi.1007134.ref013","doi-asserted-by":"crossref","first-page":"e02183","DOI":"10.1128\/mBio.02183-15","article-title":"Demography and Intercontinental Spread of the USA300 Community-Acquired Methicillin-Resistant Staphylococcus aureus Lineage","volume":"7","author":"P Glaser","year":"2016","journal-title":"MBio"},{"key":"pcbi.1007134.ref014","doi-asserted-by":"crossref","first-page":"653","DOI":"10.1101\/gr.147710.112","article-title":"A genomic portrait of the emergence, evolution, and global spread of a methicillin-resistant Staphylococcus aureus pandemic","volume":"23","author":"MTG Holden","year":"2013","journal-title":"Genome Res"},{"key":"pcbi.1007134.ref015","first-page":"35","article-title":"Emergence and Spread of Antimicrobial Resistance: Recent Insights from Bacterial Population Genomics","volume":"398","author":"U N\u00fcbel","journal-title":"Curr Top Microbiol Immunol"},{"key":"pcbi.1007134.ref016","doi-asserted-by":"crossref","first-page":"990","DOI":"10.1016\/S1473-3099(17)30325-0","article-title":"Effect of antibiotic stewardship on the incidence of infection and colonisation with antibiotic-resistant bacteria and Clostridium difficile infection: a systematic review and meta-analysis","volume":"17","author":"D Baur","year":"2017","journal-title":"Lancet Infect Dis"},{"key":"pcbi.1007134.ref017","doi-asserted-by":"crossref","first-page":"2247","DOI":"10.1021\/acs.jafc.7b00473","article-title":"Microbial Cell Factories for the Production of Terpenoid Flavor and Fragrance Compounds","volume":"66","author":"FM Schempp","year":"2018","journal-title":"J Agric Food Chem"},{"key":"pcbi.1007134.ref018","doi-asserted-by":"crossref","first-page":"140","DOI":"10.1016\/j.biotechadv.2012.09.001","article-title":"Unconventional microbial systems for the cost-efficient production of high-quality protein therapeutics","volume":"31","author":"JL Corchero","journal-title":"Biotechnol Adv"},{"key":"pcbi.1007134.ref019","doi-asserted-by":"crossref","first-page":"383","DOI":"10.1007\/s10295-011-1082-9","article-title":"Industrial production of recombinant therapeutics in Escherichia coli and its recent advancements","volume":"39","author":"C-J Huang","year":"2012","journal-title":"J Ind Microbiol Biotechnol"},{"key":"pcbi.1007134.ref020","doi-asserted-by":"crossref","first-page":"953","DOI":"10.4014\/jmb.1412.12079","article-title":"Production of Biopharmaceuticals in E. coli: Current Scenario and Future Perspectives","volume":"25","author":"MN Baeshen","year":"2015","journal-title":"J Microbiol Biotechnol"},{"key":"pcbi.1007134.ref021","doi-asserted-by":"crossref","first-page":"211","DOI":"10.1111\/j.1751-7915.2007.00020.x","article-title":"Microbial-based motor fuels: science and technology","volume":"1","author":"LP Wackett","year":"2008","journal-title":"Microb Biotechnol"},{"key":"pcbi.1007134.ref022","doi-asserted-by":"crossref","first-page":"5681","DOI":"10.1007\/s00253-013-4949-z","article-title":"Bacteria-mediated bisphenol A degradation","volume":"97","author":"W Zhang","year":"2013","journal-title":"Appl Microbiol Biotechnol"},{"key":"pcbi.1007134.ref023","doi-asserted-by":"crossref","first-page":"152","DOI":"10.3109\/1040841X.2011.640979","article-title":"Microbial remediation of explosive waste","volume":"38","author":"B Singh","year":"2012","journal-title":"Crit Rev Microbiol"},{"key":"pcbi.1007134.ref024","doi-asserted-by":"crossref","first-page":"542","DOI":"10.1038\/ismej.2014.169","article-title":"The dual role of microbes in corrosion","volume":"9","author":"N Kip","year":"2015","journal-title":"ISME J"},{"key":"pcbi.1007134.ref025","doi-asserted-by":"crossref","first-page":"e1002195","DOI":"10.1371\/journal.pbio.1002195","article-title":"Big Data: Astronomical or Genomical?","volume":"13","author":"ZD Stephens","year":"2015","journal-title":"PLoS Biol"},{"key":"pcbi.1007134.ref026","first-page":"1","article-title":"The real cost of sequencing: Scaling computation to keep pace with data generation. Genome Biol","volume":"17","author":"P Muir","year":"2016","journal-title":"Genome Biology"},{"key":"pcbi.1007134.ref027","doi-asserted-by":"crossref","first-page":"2857","DOI":"10.1128\/JCM.00949-16","article-title":"Assuring the Quality of Next-Generation Sequencing in Clinical Microbiology and Public Health Laboratories","volume":"54","author":"AS Gargis","year":"2016","journal-title":"J Clin Microbiol"},{"key":"pcbi.1007134.ref028","doi-asserted-by":"crossref","first-page":"75","DOI":"10.1186\/1471-2164-9-75","article-title":"The RAST Server: Rapid Annotations using Subsystems Technology","volume":"9","author":"RK Aziz","year":"2008","journal-title":"BMC Genomics"},{"key":"pcbi.1007134.ref029","doi-asserted-by":"crossref","first-page":"D535","DOI":"10.1093\/nar\/gkw1017","article-title":"Improvements to PATRIC, the all-bacterial Bioinformatics Database and Analysis Resource Center","volume":"45","author":"AR Wattam","year":"2017","journal-title":"Nucleic Acids Res"},{"key":"pcbi.1007134.ref030","doi-asserted-by":"crossref","first-page":"2068","DOI":"10.1093\/bioinformatics\/btu153","article-title":"Prokka: Rapid prokaryotic genome annotation","volume":"30","author":"T Seemann","year":"2014","journal-title":"Bioinformatics"},{"key":"pcbi.1007134.ref031","doi-asserted-by":"crossref","first-page":"2114","DOI":"10.1093\/bioinformatics\/btu170","article-title":"Trimmomatic: A flexible trimmer for Illumina sequence data","volume":"30","author":"AM Bolger","year":"2014","journal-title":"Bioinformatics"},{"key":"pcbi.1007134.ref032","doi-asserted-by":"crossref","first-page":"455","DOI":"10.1089\/cmb.2012.0021","article-title":"SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing","volume":"19","author":"A Bankevich","year":"2012","journal-title":"J Comput Biol"},{"key":"pcbi.1007134.ref033","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":"C-S Chin","year":"2013","journal-title":"Nat Methods"},{"key":"pcbi.1007134.ref034","doi-asserted-by":"crossref","first-page":"e1005595","DOI":"10.1371\/journal.pcbi.1005595","article-title":"Unicycler: Resolving bacterial genome assemblies from short and long sequencing reads. Phillippy AM, editor","volume":"13","author":"RR Wick","year":"2017","journal-title":"PLoS Comput Biol"},{"key":"pcbi.1007134.ref035","doi-asserted-by":"crossref","first-page":"2443","DOI":"10.1093\/bioinformatics\/btv171","article-title":"MeDuSa: A multi-draft based scaffolder","volume":"31","author":"E Bosi","year":"2015","journal-title":"Bioinformatics"},{"key":"pcbi.1007134.ref036","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":"B Jia","year":"2017","journal-title":"Nucleic Acids Res"},{"key":"pcbi.1007134.ref037","doi-asserted-by":"crossref","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":"L Chen","year":"2016","journal-title":"Nucleic Acids Res"},{"key":"pcbi.1007134.ref038","doi-asserted-by":"crossref","first-page":"81","DOI":"10.1099\/ijs.0.64483-0","article-title":"DNA-DNA hybridization values and their relationship to whole-genome sequence similarities","volume":"57","author":"J Goris","year":"2007","journal-title":"Int J Syst Evol Microbiol"},{"key":"pcbi.1007134.ref039","doi-asserted-by":"crossref","first-page":"R46","DOI":"10.1186\/gb-2014-15-3-r46","article-title":"Kraken: ultrafast metagenomic sequence classification using exact alignments","volume":"15","author":"DE Wood","year":"2014","journal-title":"Genome Biol"},{"key":"pcbi.1007134.ref040","doi-asserted-by":"crossref","first-page":"421","DOI":"10.1186\/1471-2105-10-421","article-title":"BLAST+: architecture and applications","volume":"10","author":"C Camacho","year":"2009","journal-title":"BMC Bioinformatics"},{"key":"pcbi.1007134.ref041","doi-asserted-by":"crossref","first-page":"D590","DOI":"10.1093\/nar\/gks1219","article-title":"The SILVA ribosomal RNA gene database project: improved data processing and web-based tools","volume":"41","author":"C Quast","year":"2013","journal-title":"Nucleic Acids Res"},{"key":"pcbi.1007134.ref042","doi-asserted-by":"crossref","first-page":"R12","DOI":"10.1186\/gb-2004-5-2-r12","article-title":"Versatile and open software for comparing large genomes","volume":"5","author":"S Kurtz","year":"2004","journal-title":"Genome Biol"},{"key":"pcbi.1007134.ref043","first-page":"2017","article-title":"A RESTful application programming interface for the PubMLST molecular typing and genome databases","author":"KA Jolley","year":"2017","journal-title":"Database"},{"key":"pcbi.1007134.ref044","doi-asserted-by":"crossref","first-page":"357","DOI":"10.1038\/nmeth.1923","article-title":"Fast gapped-read alignment with Bowtie 2","volume":"9","author":"B Langmead","year":"2012","journal-title":"Nat Methods"},{"key":"pcbi.1007134.ref045","doi-asserted-by":"crossref","first-page":"3094","DOI":"10.1093\/bioinformatics\/bty191","article-title":"Minimap2: pairwise alignment for nucleotide sequences","volume":"34","author":"H Li","year":"2018","journal-title":"Bioinformatics"},{"key":"pcbi.1007134.ref046","doi-asserted-by":"crossref","first-page":"2078","DOI":"10.1093\/bioinformatics\/btp352","article-title":"The Sequence Alignment\/Map format and SAMtools","volume":"25","author":"H Li","year":"2009","journal-title":"Bioinformatics"},{"key":"pcbi.1007134.ref047","doi-asserted-by":"crossref","first-page":"80","DOI":"10.4161\/fly.19695","article-title":"A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff","volume":"6","author":"P Cingolani","year":"2012","journal-title":"Fly"},{"key":"pcbi.1007134.ref048","doi-asserted-by":"crossref","first-page":"e9490","DOI":"10.1371\/journal.pone.0009490","article-title":"FastTree 2\u2014approximately maximum-likelihood trees for large alignments","volume":"5","author":"MN Price","year":"2010","journal-title":"PLoS One"},{"key":"pcbi.1007134.ref049","doi-asserted-by":"crossref","first-page":"3691","DOI":"10.1093\/bioinformatics\/btv421","article-title":"Roary: Rapid large-scale prokaryote pan genome analysis","volume":"31","author":"AJ Page","year":"2015","journal-title":"Bioinformatics"}],"updated-by":[{"DOI":"10.1371\/journal.pcbi.1007134","type":"new_version","label":"New version","source":"publisher","updated":{"date-parts":[[2020,3,17]],"date-time":"2020-03-17T00:00:00Z","timestamp":1584403200000}}],"container-title":["PLOS Computational Biology"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pcbi.1007134","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2020,3,17]],"date-time":"2020-03-17T13:44:13Z","timestamp":1584452653000},"score":1,"resource":{"primary":{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pcbi.1007134"}},"subtitle":[],"editor":[{"given":"Mihaela","family":"Pertea","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"editor"}]}],"short-title":[],"issued":{"date-parts":[[2020,3,5]]},"references-count":49,"journal-issue":{"issue":"3","published-online":{"date-parts":[[2020,3,5]]}},"URL":"https:\/\/doi.org\/10.1371\/journal.pcbi.1007134","relation":{"has-preprint":[{"id-type":"doi","id":"10.1101\/654319","asserted-by":"object"}]},"ISSN":["1553-7358"],"issn-type":[{"value":"1553-7358","type":"electronic"}],"subject":[],"published":{"date-parts":[[2020,3,5]]}}}