{"id":"https://openalex.org/W135884612","doi":null,"title":"Using genomics to improve Bacillus anthracis diagnostics and outbreak investigations","display_name":"Using genomics to improve Bacillus anthracis diagnostics and outbreak investigations","publication_year":2014,"publication_date":"2014-01-01","ids":{"openalex":"https://openalex.org/W135884612","mag":"135884612"},"language":"en","primary_location":{"id":"pmh:oai:pub.epsilon.slu.se:11345","doi":null,"is_oa":true,"landing_page_url":"https://pub.epsilon.slu.se/11345/1/agren_j_140811.pdf","pdf_url":"https://pub.epsilon.slu.se/11345/1/agren_j_140811.pdf","source":{"id":"https://openalex.org/S4306402317","display_name":"Epsilon Open Archive (Sveriges lantbruksuniversitet biblioteket (Swedish University of Agricultural Sciences))","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I298625061","host_organization_name":"Swedish University of Agricultural Sciences","host_organization_lineage":["https://openalex.org/I298625061"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"info:eu-repo/semantics/doctoralThesis"},"volume":null,"type":"dissertation","is_traditional":true,"indexed_in":[],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"https://pub.epsilon.slu.se/11345/1/agren_j_140811.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5040078164","display_name":"Joakim \u00c5gren","orcid":null,"observed_orcids":[]},"institutions":[],"countries":[],"is_corresponding":true,"raw_author_name":"Joakim \u00c5gren","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]}],"institutions":[],"countries_distinct_count":0,"institutions_distinct_count":0,"corresponding_author_ids":["https://openalex.org/A5040078164"],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":null,"has_fulltext":true,"cited_by_count":1,"citation_normalized_percentile":null,"cited_by_percentile_year":null,"biblio":{"volume":null,"issue":null,"first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11515","display_name":"Bacillus and Francisella bacterial research","score":0.9994999766349792,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},"topics":[{"id":"https://openalex.org/T11515","display_name":"Bacillus and Francisella bacterial research","score":0.9994999766349792,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":9.999999747378752e-05,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T11288","display_name":"Clostridium difficile and Clostridium perfringens research","score":0.0,"subfield":{"id":"https://openalex.org/subfields/2725","display_name":"Infectious Diseases"},"field":{"id":"https://openalex.org/fields/27","display_name":"Medicine"},"domain":{"id":"https://openalex.org/domains/4","display_name":"Health Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/bacillus-anthracis","display_name":"Bacillus anthracis","score":0.9980000257492065},{"id":"https://openalex.org/keywords/anthrax","display_name":"anthrax","score":0.8769999742507935},{"id":"https://openalex.org/keywords/outbreak-investigation","display_name":"outbreak investigation","score":0.7630000114440918},{"id":"https://openalex.org/keywords/strain-characterization","display_name":"strain characterization","score":0.6370000243186951},{"id":"https://openalex.org/keywords/beta-lactam-resistance","display_name":"beta-lactam resistance","score":0.9549999833106995},{"id":"https://openalex.org/keywords/penicillin-resistance","display_name":"penicillin resistance","score":0.9409999847412109},{"id":"https://openalex.org/keywords/genomic-divergence","display_name":"genomic divergence","score":0.7860000133514404},{"id":"https://openalex.org/keywords/whole-genome-sequencing","display_name":"whole genome sequencing","score":0.4259999990463257},{"id":"https://openalex.org/keywords/molecular-diagnosis","display_name":"molecular diagnosis","score":0.5580000281333923},{"id":"https://openalex.org/keywords/cattle","display_name":"cattle","score":0.43700000643730164}],"concepts":[{"id":"https://openalex.org/C2780239966","wikidata":"https://www.wikidata.org/wiki/Q614156","display_name":"Bacillus anthracis","level":3,"score":0.9711621403694153},{"id":"https://openalex.org/C116675565","wikidata":"https://www.wikidata.org/wiki/Q3241045","display_name":"Outbreak","level":2,"score":0.7420787215232849},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.647000789642334},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.49583491683006287},{"id":"https://openalex.org/C89423630","wikidata":"https://www.wikidata.org/wiki/Q7193","display_name":"Microbiology","level":1,"score":0.48975372314453125},{"id":"https://openalex.org/C189206191","wikidata":"https://www.wikidata.org/wiki/Q222046","display_name":"Genomics","level":4,"score":0.47879132628440857},{"id":"https://openalex.org/C159047783","wikidata":"https://www.wikidata.org/wiki/Q7215","display_name":"Virology","level":1,"score":0.33319002389907837},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.3135607838630676},{"id":"https://openalex.org/C523546767","wikidata":"https://www.wikidata.org/wiki/Q10876","display_name":"Bacteria","level":2,"score":0.25031566619873047},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.188604474067688}],"mesh":[],"locations_count":2,"locations":[{"id":"pmh:oai:pub.epsilon.slu.se:11345","doi":null,"is_oa":true,"landing_page_url":"https://pub.epsilon.slu.se/11345/1/agren_j_140811.pdf","pdf_url":"https://pub.epsilon.slu.se/11345/1/agren_j_140811.pdf","source":{"id":"https://openalex.org/S4306402317","display_name":"Epsilon Open Archive (Sveriges lantbruksuniversitet biblioteket (Swedish University of Agricultural Sciences))","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I298625061","host_organization_name":"Swedish University of Agricultural Sciences","host_organization_lineage":["https://openalex.org/I298625061"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"info:eu-repo/semantics/doctoralThesis"},{"id":"mag:135884612","doi":null,"is_oa":false,"landing_page_url":"https://pub.epsilon.slu.se/11345/1/agren_j_140811.pdf","pdf_url":null,"source":null,"license":null,"license_id":null,"version":null,"is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":null}],"best_oa_location":{"id":"pmh:oai:pub.epsilon.slu.se:11345","doi":null,"is_oa":true,"landing_page_url":"https://pub.epsilon.slu.se/11345/1/agren_j_140811.pdf","pdf_url":"https://pub.epsilon.slu.se/11345/1/agren_j_140811.pdf","source":{"id":"https://openalex.org/S4306402317","display_name":"Epsilon Open Archive (Sveriges lantbruksuniversitet biblioteket (Swedish University of Agricultural Sciences))","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I298625061","host_organization_name":"Swedish University of Agricultural Sciences","host_organization_lineage":["https://openalex.org/I298625061"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"info:eu-repo/semantics/doctoralThesis"},"sustainable_development_goals":[{"display_name":"Good health and well-being","score":0.5683000087738037,"id":"https://metadata.un.org/sdg/3"}],"study_designs":[],"awards":[],"funders":[],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W135884612.pdf","grobid_xml":"https://content.openalex.org/works/W135884612.grobid-xml"},"referenced_works_count":139,"referenced_works":["https://openalex.org/W1500908508","https://openalex.org/W1526527675","https://openalex.org/W1542755735","https://openalex.org/W1548638618","https://openalex.org/W1571616236","https://openalex.org/W1582413449","https://openalex.org/W1589747844","https://openalex.org/W1591183067","https://openalex.org/W1605976270","https://openalex.org/W1617959995","https://openalex.org/W1661941015","https://openalex.org/W1673187150","https://openalex.org/W1709300913","https://openalex.org/W1740300251","https://openalex.org/W1785756912","https://openalex.org/W1835663266","https://openalex.org/W1867854914","https://openalex.org/W1947671943","https://openalex.org/W1963563104","https://openalex.org/W1964717752","https://openalex.org/W1964986784","https://openalex.org/W1967086726","https://openalex.org/W1971403296","https://openalex.org/W1972564765","https://openalex.org/W1975128609","https://openalex.org/W1977633672","https://openalex.org/W1981292743","https://openalex.org/W1981563187","https://openalex.org/W1989462201","https://openalex.org/W1989791342","https://openalex.org/W1992108973","https://openalex.org/W1997871317","https://openalex.org/W1998225673","https://openalex.org/W2000827081","https://openalex.org/W2002114667","https://openalex.org/W2007720209","https://openalex.org/W2012068153","https://openalex.org/W2017666284","https://openalex.org/W2019763194","https://openalex.org/W2020800548","https://openalex.org/W2027258552","https://openalex.org/W2027586024","https://openalex.org/W2028797719","https://openalex.org/W2030093389","https://openalex.org/W2032969806","https://openalex.org/W2033455699","https://openalex.org/W2036501670","https://openalex.org/W2039652718","https://openalex.org/W2041257508","https://openalex.org/W2045262755","https://openalex.org/W2047832887","https://openalex.org/W2050169817","https://openalex.org/W2051903478","https://openalex.org/W2055043387","https://openalex.org/W2055078055","https://openalex.org/W2056290002","https://openalex.org/W2057581703","https://openalex.org/W2070978208","https://openalex.org/W2073952570","https://openalex.org/W2079404920","https://openalex.org/W2081790467","https://openalex.org/W2083366270","https://openalex.org/W2083435927","https://openalex.org/W2084069113","https://openalex.org/W2089216231","https://openalex.org/W2090931544","https://openalex.org/W2094628840","https://openalex.org/W2096037074","https://openalex.org/W2096094352","https://openalex.org/W2096565388","https://openalex.org/W2097492854","https://openalex.org/W2098321619","https://openalex.org/W2099935661","https://openalex.org/W2100141960","https://openalex.org/W2100874076","https://openalex.org/W2101676626","https://openalex.org/W2102355366","https://openalex.org/W2104332925","https://openalex.org/W2104547142","https://openalex.org/W2105077075","https://openalex.org/W2106063758","https://openalex.org/W2106428264","https://openalex.org/W2108175721","https://openalex.org/W2110670930","https://openalex.org/W2112945902","https://openalex.org/W2113153814","https://openalex.org/W2115102869","https://openalex.org/W2116372830","https://openalex.org/W2116577752","https://openalex.org/W2117179319","https://openalex.org/W2118401640","https://openalex.org/W2120048439","https://openalex.org/W2120266240","https://openalex.org/W2121403559","https://openalex.org/W2122828763","https://openalex.org/W2123712017","https://openalex.org/W2124611161","https://openalex.org/W2124715997","https://openalex.org/W2127652519","https://openalex.org/W2127923758","https://openalex.org/W2130641564","https://openalex.org/W2132017276","https://openalex.org/W2135614314","https://openalex.org/W2137951360","https://openalex.org/W2138270253","https://openalex.org/W2139237710","https://openalex.org/W2140775467","https://openalex.org/W2142678478","https://openalex.org/W2142867516","https://openalex.org/W2144340783","https://openalex.org/W2145282362","https://openalex.org/W2146169462","https://openalex.org/W2146809348","https://openalex.org/W2147375303","https://openalex.org/W2150832852","https://openalex.org/W2151185280","https://openalex.org/W2151361725","https://openalex.org/W2153738223","https://openalex.org/W2153922590","https://openalex.org/W2153983434","https://openalex.org/W2154586372","https://openalex.org/W2157612734","https://openalex.org/W2157852868","https://openalex.org/W2161781955","https://openalex.org/W2161987668","https://openalex.org/W2162055898","https://openalex.org/W2166194088","https://openalex.org/W2167757567","https://openalex.org/W2167869693","https://openalex.org/W2168420558","https://openalex.org/W2168436581","https://openalex.org/W2168833336","https://openalex.org/W2169053394","https://openalex.org/W2170025681","https://openalex.org/W2170804017","https://openalex.org/W2263804876","https://openalex.org/W2405126931","https://openalex.org/W2499849376","https://openalex.org/W2568756898"],"related_works":["https://openalex.org/W4225725684","https://openalex.org/W7036942815","https://openalex.org/W2010291891","https://openalex.org/W2009746070","https://openalex.org/W4281812988","https://openalex.org/W7144985020","https://openalex.org/W3130633714","https://openalex.org/W2156650715","https://openalex.org/W1997871317","https://openalex.org/W4411436697"],"abstract_inverted_index":{"The":[0,307,375],"bacterium":[1,192],"Bacillus":[2,89,97,231],"anthracis":[3,70,90,249,256,340,358],"causes":[4],"the":[5,17,31,45,74,113,116,141,149,161,177,183,188,229,244,261,288,325,351,373,391,422],"disease":[6],"anthrax,":[7],"primarily":[8],"in":[9,30,36,47,73,112,128,163,197,250,270,275,313,356,364],"herbivores":[10],"but":[11,119],"many":[12],"mammals":[13],"are":[14,54,76,103,121,335],"susceptible":[15],"to":[16,62,211,215,227,239,312,319,371,387,428],"disease.":[18],"Its":[19],"infective":[20],"form":[21],"is":[22,180],"as":[23,95,273,336,341],"a":[24,58,191,199,251,281,299,365,379,430],"dormant":[25],"spore":[26],"that":[27,234,285,323,331,410],"can":[28,193,286],"lie":[29],"soil":[32],"for":[33,254,338,398],"decades.":[34],"Thus,":[35],"its":[37],"cycle":[38],"of":[39,44,66,143,190,291,294,302,353,378,390,395,424,433],"infection,":[40],"it":[41],"spends":[42],"most":[43,137,236],"time":[46],"an":[48,303,348,382],"inactive":[49],"state":[50],"and":[51,85,99,127,134,151,182,207,222,260,272,361,393,420],"replication-induced":[52],"DNA-mutations":[53],"therefore":[55,100],"kept":[56],"at":[57],"minimum.":[59],"Partly":[60],"due":[61],"these":[63,157],"long":[64],"periods":[65],"inactivity,":[67],"all":[68,187,315],"B.":[69,240,248,255,339,357],"isolates":[71,346],"found":[72,265,370],"world":[75,114],"genetically":[77],"very":[78],"similar.":[79],"This":[80,297,328],"makes":[81],"strain":[82,380],"characterization":[83,301],"difficult":[84],"requires":[86],"high-resolution":[87],"technologies.":[88],"also":[91,310,385],"has":[92,109,175],"similar":[93],"DNA-content":[94],"other":[96],"spp.":[98,232],"diagnostic":[101,413],"cross-reactions":[102],"not":[104],"uncommon.":[105],"\\n":[106,171,220,343,401],"\\nAnthrax":[107],"incidence":[108],"steadily":[110],"declined":[111],"during":[115,381],"last":[117],"century":[118],"there":[120],"still":[122],"endemic":[123],"areas.":[124],"In":[125,202],"2008":[126],"2011":[129],"Sweden":[130],"suffered":[131],"two":[132],"large":[133],"costly":[135],"outbreaks,":[136],"likely":[138],"caused":[139],"by":[140],"disturbance":[142],"old":[144],"anthrax":[145,218,317,349,435],"epizootic":[146],"graves":[147],"from":[148,156,347],"1940s":[150],"1950s.":[152],"Several":[153],"studies":[154,224],"emanated":[155],"outbreaks":[158],"including":[159],"how":[160],"bacteria":[162],"cows":[164],"treated":[165],"with":[166,217],"penicillin":[167,169],"developed":[168],"resistance.":[170],"\\nNext-generation":[172],"sequencing":[173],"(NGS)":[174],"revolutionized":[176],"way":[178],"DNA":[179],"sequenced":[181,196],"whole":[184],"genome":[185,279],"(i.e.,":[186],"DNA)":[189],"now":[194],"be":[195,372],"only":[198],"few":[200],"days.":[201],"this":[203,404],"doctoral":[204],"thesis,":[205],"NGS":[206,397],"genomics":[208],"were":[209,225,235,359,369],"used":[210,269,311],"improve":[212],"our":[213,332],"capability":[214],"deal":[216],"outbreaks.":[219,436],"\\nGenomic":[221],"genetic":[223,289],"applied":[226],"identify":[228],"non-anthrax":[230],"available":[233],"closely":[237],"related":[238],"anthracis.":[241],"How":[242],"well":[243],"strains":[245,264],"could":[246],"mimic":[247],"model":[252,263],"system":[253],"spores":[257],"was":[258,283,309,384],"evaluated":[259],"best":[262],"have":[266,411],"since":[267],"been":[268],"exercises":[271],"controls":[274],"real":[276],"samples.":[277],"For":[278],"comparisons,":[280],"software":[282,308],"created":[284],"compare":[287],"content":[290],"several":[292],"hundreds":[293],"bacterial":[295],"genomes.":[296],"ensures":[298,330],"rapid":[300],"outbreak":[304,383],"pathogen\u2019s":[305],"genome.":[306],"silico-compare":[314],"published":[316],"PCR-assays":[318],"determine":[320],"which":[321],"assays":[322],"had":[324],"highest":[326],"specificity.":[327],"workflow":[329],"molecular":[333],"diagnostics":[334],"specific":[337],"possible.":[342],"\\nBy":[344],"using":[345,396],"outbreak,":[350],"mechanisms":[352],"beta-lactam":[354],"resistance":[355,418],"studied":[360,386],"chromosomal":[362],"mutations":[363],"negative":[366],"sigma":[367],"factor":[368],"cause.":[374],"genomic":[376,408,425],"divergence":[377],"gain":[388],"knowledge":[389],"strengths":[392],"limitations":[394],"epidemiological":[399,426],"investigations.":[400],"\\nIn":[402],"summary,":[403],"thesis":[405],"describes":[406],"different":[407],"approaches":[409],"improved":[412],"methods,":[414],"explained":[415],"ambiguous":[416],"antimicrobial":[417],"findings":[419],"enhanced":[421],"resolution":[423],"investigation":[427],"ensure":[429],"robust":[431],"handling":[432],"future":[434]},"counts_by_year":[{"year":2015,"cited_by_count":1}],"updated_date":"2026-09-09T07:26:56.047234","created_date":"2016-06-24T00:00:00"}