{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,10,9]],"date-time":"2025-10-09T01:06:04Z","timestamp":1759971964087,"version":"build-2065373602"},"reference-count":48,"publisher":"Elsevier BV","license":[{"start":{"date-parts":[[2019,9,1]],"date-time":"2019-09-01T00:00:00Z","timestamp":1567296000000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.elsevier.com\/tdm\/userlicense\/1.0\/"},{"start":{"date-parts":[[2019,9,1]],"date-time":"2019-09-01T00:00:00Z","timestamp":1567296000000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.elsevier.com\/legal\/tdmrep-license"},{"start":{"date-parts":[[2019,7,5]],"date-time":"2019-07-05T00:00:00Z","timestamp":1562284800000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc-nd\/4.0\/"}],"content-domain":{"domain":["clinicalkey.com","clinicalkey.com.au","clinicalkey.es","clinicalkey.fr","clinicalkey.jp","elsevier.com","sciencedirect.com"],"crossmark-restriction":true},"short-container-title":["Forensic Science International"],"published-print":{"date-parts":[[2019,9]]},"DOI":"10.1016\/j.forsciint.2019.06.027","type":"journal-article","created":{"date-parts":[[2019,7,1]],"date-time":"2019-07-01T22:51:04Z","timestamp":1562021464000},"page":"109869","update-policy":"https:\/\/doi.org\/10.1016\/elsevier_cm_policy","source":"Crossref","is-referenced-by-count":2,"special_numbering":"C","title":["A likelihood ratio-based approach for improved source attribution in microbiological forensic investigations"],"prefix":"10.1016","volume":"302","author":[{"given":"Petter","family":"Lindgren","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Kerstin","family":"Myrtenn\u00e4s","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Mats","family":"Forsman","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Anders","family":"Johansson","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Per","family":"Stenberg","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Anders","family":"Nordgaard","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8254-5842","authenticated-orcid":false,"given":"Jon","family":"Ahlinder","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"78","reference":[{"key":"10.1016\/j.forsciint.2019.06.027_bib0005","doi-asserted-by":"crossref","first-page":"1964","DOI":"10.1128\/JCM.00046-16","article-title":"Expansion of microbial forensics","volume":"54","author":"Schmedes","year":"2016","journal-title":"J. Clin. Microbiol."},{"key":"10.1016\/j.forsciint.2019.06.027_bib0010","doi-asserted-by":"crossref","first-page":"2209","DOI":"10.1128\/AEM.71.5.2209-2213.2005","article-title":"Toward a system of microbial forensics: from sample collection to interpretation of evidence","volume":"71","author":"Budowle","year":"2005","journal-title":"Appl. Environ. Microbiol."},{"key":"10.1016\/j.forsciint.2019.06.027_bib0015","doi-asserted-by":"crossref","first-page":"836","DOI":"10.1038\/444836a","article-title":"Benghazi study group, molecular epidemiology: HIV-1 and HCV sequences from libyan outbreak","volume":"444","author":"de Oliveira","year":"2006","journal-title":"Nature"},{"key":"10.1016\/j.forsciint.2019.06.027_bib0020","doi-asserted-by":"crossref","first-page":"9","DOI":"10.1186\/2041-2223-5-9","article-title":"Validation of high throughput sequencing and microbial forensics applications","volume":"5","author":"Budowle","year":"2014","journal-title":"Investig. Genet."},{"key":"10.1016\/j.forsciint.2019.06.027_bib0025","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pcbi.1003397","article-title":"Inferring the source of transmission with phylogenetic data","volume":"9","author":"Volz","year":"2013","journal-title":"PLoS Comput. Biol."},{"key":"10.1016\/j.forsciint.2019.06.027_bib0030","doi-asserted-by":"crossref","first-page":"344","DOI":"10.1111\/1556-4029.12065","article-title":"Legal, technical, and interpretational considerations in the forensic analysis of viruses","volume":"58","author":"Wilson","year":"2013","journal-title":"J. Forensic Sci."},{"key":"10.1016\/j.forsciint.2019.06.027_bib0035","doi-asserted-by":"crossref","first-page":"76","DOI":"10.1186\/1741-7007-11-76","article-title":"Molecular evolution in court: analysis of a large hepatitis C virus outbreak from an evolving source","volume":"11","author":"Gonz\u00e1lez-Candelas","year":"2013","journal-title":"BMC Biol."},{"key":"10.1016\/j.forsciint.2019.06.027_bib0040","first-page":"101","article-title":"DNA evidence: probability, population genetics, and the courts","volume":"7","author":"Kaye","year":"1993","journal-title":"Harv. J. Law Technol."},{"key":"10.1016\/j.forsciint.2019.06.027_bib0045","doi-asserted-by":"crossref","first-page":"155","DOI":"10.1111\/1467-985X.00264","article-title":"Inferences from DNA data: population histories, evolutionary processes and forensic match probabilities","volume":"166","author":"Wilson","year":"2003","journal-title":"J. R. Stat. Soc. Ser. A Stat. Soc."},{"year":"2010","series-title":"Data Analysis in Forensic Science: A Bayesian Decision Perspective","author":"Taroni","key":"10.1016\/j.forsciint.2019.06.027_bib0050"},{"key":"10.1016\/j.forsciint.2019.06.027_bib0055","doi-asserted-by":"crossref","first-page":"178","DOI":"10.1016\/j.fsigen.2017.02.007","article-title":"The factor of 10 in forensic DNA match probabilities","volume":"28","author":"Gittelson","year":"2017","journal-title":"Forensic Sci. Int. Genet."},{"key":"10.1016\/j.forsciint.2019.06.027_bib0060","doi-asserted-by":"crossref","first-page":"773","DOI":"10.1080\/01621459.1995.10476572","article-title":"Bayes factors","volume":"90","author":"Kass","year":"1995","journal-title":"J. Am. Stat. Assoc."},{"key":"10.1016\/j.forsciint.2019.06.027_bib0065","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1093\/lpr\/mgr020","article-title":"Scale of conclusions for the value of evidence","volume":"11","author":"Nordgaard","year":"2012","journal-title":"Law Probab. Risk"},{"year":"2010","series-title":"Bacterial Population Genetics in Infectious Disease","author":"Robinson","key":"10.1016\/j.forsciint.2019.06.027_bib0070"},{"key":"10.1016\/j.forsciint.2019.06.027_bib0075","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pgen.1001036","article-title":"Microevolution of Helicobacter pylori during prolonged infection of single hosts and within families","volume":"6","author":"Morelli","year":"2010","journal-title":"PLoS Genet."},{"key":"10.1016\/j.forsciint.2019.06.027_bib0080","doi-asserted-by":"crossref","first-page":"385","DOI":"10.1093\/molbev\/msn264","article-title":"Rapid evolution and the importance of recombination to the gastroenteric pathogen Campylobacter jejuni","volume":"26","author":"Wilson","year":"2009","journal-title":"Mol. Biol. Evol."},{"key":"10.1016\/j.forsciint.2019.06.027_bib0085","doi-asserted-by":"crossref","first-page":"268","DOI":"10.1186\/1471-2164-13-268","article-title":"Genome characterisation of the genus Francisella reveals insight into similar evolutionary paths in pathogens of mammals and fish","volume":"13","author":"Sj\u00f6din","year":"2012","journal-title":"BMC Genomics"},{"key":"10.1016\/j.forsciint.2019.06.027_bib0090","doi-asserted-by":"crossref","first-page":"860","DOI":"10.1098\/rstb.2011.0303","article-title":"Insights from genomic comparisons of genetically monomorphic bacterial pathogens","volume":"367","author":"Achtman","year":"2012","journal-title":"Philos. Trans. R. Soc. B Biol. Sci."},{"key":"10.1016\/j.forsciint.2019.06.027_bib0095","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.forsciint.2019.06.027_bib0100","doi-asserted-by":"crossref","first-page":"491","DOI":"10.1038\/ng.806","article-title":"A framework for variation discovery and genotyping using next-generation DNA sequencing data","volume":"43","author":"DePristo","year":"2011","journal-title":"Nat. Genet."},{"key":"10.1016\/j.forsciint.2019.06.027_bib0105","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1186\/1471-2164-14-96","article-title":"Ultra-deep mutant spectrum profiling: improving sequencing accuracy using overlapping read pairs","volume":"14","author":"Chen-Harris","year":"2013","journal-title":"BMC Genomics"},{"key":"10.1016\/j.forsciint.2019.06.027_bib0110","first-page":"1","article-title":"Density estimation for statistics and data analysis","author":"Silverman","year":"1986","journal-title":"Monogr. Stat. Appl. Probab."},{"key":"10.1016\/j.forsciint.2019.06.027_bib0115","doi-asserted-by":"crossref","first-page":"237","DOI":"10.1016\/S0015-7368(86)72490-0","article-title":"Statistical discriminant analysis in forensic science","volume":"26","author":"Aitken","year":"1986","journal-title":"J. Forensic Sci. Soc."},{"key":"10.1016\/j.forsciint.2019.06.027_bib0120","doi-asserted-by":"crossref","first-page":"499","DOI":"10.2307\/2348086","article-title":"Statistical inference in crime investigations using deoxyribonucleic acid profiling","volume":"41","author":"Berry","year":"1992","journal-title":"Appl. Stat."},{"key":"10.1016\/j.forsciint.2019.06.027_bib0125","doi-asserted-by":"crossref","first-page":"109","DOI":"10.1046\/j.0035-9254.2003.05271.x","article-title":"Evaluation of trace evidence in the form of multivariate data","volume":"53","author":"Aitken","year":"2004","journal-title":"J. R. Stat. Soc. Ser. C Appl. Stat."},{"key":"10.1016\/j.forsciint.2019.06.027_bib0130","doi-asserted-by":"crossref","first-page":"49","DOI":"10.1111\/j.1556-4029.2008.00905.x","article-title":"Classification of glass fragments based on elemental composition and refractive index","volume":"54","author":"Zadora","year":"2009","journal-title":"J. Forensic Sci."},{"key":"10.1016\/j.forsciint.2019.06.027_bib0135","doi-asserted-by":"crossref","first-page":"266","DOI":"10.1016\/j.aca.2008.12.013","article-title":"Likelihood ratio model for classification of forensic evidence","volume":"642","author":"Zadora","year":"2009","journal-title":"Anal. Chim. Acta"},{"key":"10.1016\/j.forsciint.2019.06.027_bib0140","doi-asserted-by":"crossref","first-page":"267","DOI":"10.1002\/cem.2699","article-title":"Chemometrics comes to court: evidence evaluation of chem-bio threat agent attacks","volume":"29","author":"Ahlinder","year":"2015","journal-title":"J. Chemom."},{"key":"10.1016\/j.forsciint.2019.06.027_bib0145","first-page":"1","article-title":"Assessing the genome level diversity of Listeria monocytogenes from contaminated ice cream and environmental samples linked to a listeriosis outbreak in the United States","volume":"12","author":"Chen","year":"2017","journal-title":"PLoS One"},{"key":"10.1016\/j.forsciint.2019.06.027_bib0150","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":"Bolger","year":"2014","journal-title":"Bioinformatics"},{"key":"10.1016\/j.forsciint.2019.06.027_bib0155","doi-asserted-by":"crossref","first-page":"1117","DOI":"10.1101\/gr.089532.108","article-title":"ABySS: a parallel assembler for short read sequence data","volume":"19","author":"Simpson","year":"2009","journal-title":"Genome Res."},{"key":"10.1016\/j.forsciint.2019.06.027_bib0160","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.forsciint.2019.06.027_bib0165","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pone.0011147","article-title":"progressiveMauve: multiple genome alignment with gene gain, loss and rearrangement","volume":"5","author":"Darling","year":"2010","journal-title":"PLoS One"},{"key":"10.1016\/j.forsciint.2019.06.027_bib0170","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1371\/journal.pone.0162624","article-title":"Towards a DNA barcode reference database for spiders and harvestmen of Germany","volume":"11","author":"Astrin","year":"2016","journal-title":"PLoS One"},{"key":"10.1016\/j.forsciint.2019.06.027_bib0175","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1371\/journal.pcbi.1003537","article-title":"BEAST 2: a software platform for bayesian evolutionary analysis","volume":"10","author":"Bouckaert","year":"2014","journal-title":"PLoS Comput. Biol."},{"key":"10.1016\/j.forsciint.2019.06.027_bib0180","doi-asserted-by":"crossref","first-page":"1069","DOI":"10.1093\/sysbio\/sys042","article-title":"Is the general time-reversible model bad for molecular phylogenetics?","volume":"61","author":"Sumner","year":"2012","journal-title":"Syst. Biol."},{"key":"10.1016\/j.forsciint.2019.06.027_bib0185","doi-asserted-by":"crossref","first-page":"28","DOI":"10.1111\/2041-210X.12628","article-title":"Ggtree: an r package for visualization and annotation of phylogenetic trees with their covariates and other associated data","volume":"8","author":"Yu","year":"2017","journal-title":"Methods Ecol. Evol."},{"key":"10.1016\/j.forsciint.2019.06.027_bib0190","doi-asserted-by":"crossref","first-page":"209","DOI":"10.1128\/jb.49.3.209-231.1945","article-title":"The morphology of bacterium tularense","volume":"49","author":"Hesselbrock","year":"1945","journal-title":"J. Bacteriol."},{"key":"10.1016\/j.forsciint.2019.06.027_bib0195","series-title":"Francisella tularensis: Persistence, Dissemination and Source Attribution : a Theoretical and Computational Approach [Dissertation]","article-title":"Biological amplification of low frequency mutations for bacterial source attribution","author":"Dwibedi","year":"2019"},{"year":"2013","series-title":"Vegan: Community Ecology Package. R Package Version 2.0-7","author":"Oksanen","key":"10.1016\/j.forsciint.2019.06.027_bib0200"},{"year":"2009","series-title":"ggplot2","author":"Wickham","key":"10.1016\/j.forsciint.2019.06.027_bib0205"},{"key":"10.1016\/j.forsciint.2019.06.027_bib0210","doi-asserted-by":"crossref","first-page":"349","DOI":"10.1038\/sj.hdy.6800946","article-title":"The effect of non-additive genetic interactions on selection in multi-locus genetic models","volume":"98","author":"Hallander","year":"2007","journal-title":"Heredity (Edinb)"},{"key":"10.1016\/j.forsciint.2019.06.027_bib0215","doi-asserted-by":"crossref","first-page":"357","DOI":"10.1038\/nmeth.1923","article-title":"Fast gapped-read alignment with Bowtie 2","volume":"9","author":"Langmead","year":"2012","journal-title":"Nat. Methods"},{"key":"10.1016\/j.forsciint.2019.06.027_bib0220","doi-asserted-by":"crossref","first-page":"568","DOI":"10.1101\/gr.129684.111","article-title":"VarScan 2: somatic mutation and copy number alteration discovery in cancer by exome sequencing","volume":"22","author":"Koboldt","year":"2012","journal-title":"Genome Res."},{"key":"10.1016\/j.forsciint.2019.06.027_bib0225","doi-asserted-by":"crossref","first-page":"2032","DOI":"10.1093\/bioinformatics\/btv098","article-title":"Sambamba: fast processing of NGS alignment formats","volume":"31","author":"Tarasov","year":"2015","journal-title":"Bioinformatics"},{"key":"10.1016\/j.forsciint.2019.06.027_bib0230","doi-asserted-by":"crossref","first-page":"578","DOI":"10.1038\/nrmicro2174","article-title":"Bacterial gene amplification: implications for the evolution of antibiotic resistance","volume":"7","author":"Sandegren","year":"2009","journal-title":"Nat. Rev. Microbiol."},{"key":"10.1016\/j.forsciint.2019.06.027_bib0235","doi-asserted-by":"crossref","first-page":"45","DOI":"10.1038\/nature24287","article-title":"The dynamics of molecular evolution over 60,000 generations","volume":"551","author":"Good","year":"2017","journal-title":"Nature"},{"key":"10.1016\/j.forsciint.2019.06.027_bib0240","doi-asserted-by":"crossref","first-page":"15803","DOI":"10.1038\/s41598-018-33622-5","article-title":"Whole genome sequencing for investigations of meningococcal outbreaks in the United States: a retrospective analysis","volume":"8","author":"Whaley","year":"2018","journal-title":"Sci. Rep."}],"container-title":["Forensic Science International"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/api.elsevier.com\/content\/article\/PII:S0379073819302841?httpAccept=text\/xml","content-type":"text\/xml","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/api.elsevier.com\/content\/article\/PII:S0379073819302841?httpAccept=text\/plain","content-type":"text\/plain","content-version":"vor","intended-application":"text-mining"}],"deposited":{"date-parts":[[2025,10,8]],"date-time":"2025-10-08T17:57:06Z","timestamp":1759946226000},"score":1,"resource":{"primary":{"URL":"https:\/\/linkinghub.elsevier.com\/retrieve\/pii\/S0379073819302841"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2019,9]]},"references-count":48,"alternative-id":["S0379073819302841"],"URL":"https:\/\/doi.org\/10.1016\/j.forsciint.2019.06.027","relation":{},"ISSN":["0379-0738"],"issn-type":[{"type":"print","value":"0379-0738"}],"subject":[],"published":{"date-parts":[[2019,9]]},"assertion":[{"value":"Elsevier","name":"publisher","label":"This article is maintained by"},{"value":"A likelihood ratio-based approach for improved source attribution in microbiological forensic investigations","name":"articletitle","label":"Article Title"},{"value":"Forensic Science International","name":"journaltitle","label":"Journal Title"},{"value":"https:\/\/doi.org\/10.1016\/j.forsciint.2019.06.027","name":"articlelink","label":"CrossRef DOI link to publisher maintained version"},{"value":"article","name":"content_type","label":"Content Type"},{"value":"\u00a9 2019 The Authors. Published by Elsevier B.V.","name":"copyright","label":"Copyright"}],"article-number":"109869"}}