{"id":"https://openalex.org/W7225335378","doi":"https://doi.org/10.21203/rs.3.rs-11614101/v1","title":"A systematic review of whole-genome sequencing studies of Mycobacterium bovis that determine the direction of transmission between badgers and cattle","display_name":"A systematic review of whole-genome sequencing studies of Mycobacterium bovis that determine the direction of transmission between badgers and cattle","publication_year":2026,"publication_date":"2026-11-05","ids":{"openalex":"https://openalex.org/W7225335378","doi":"https://doi.org/10.21203/rs.3.rs-11614101/v1"},"language":"en","primary_location":{"id":"doi:10.21203/rs.3.rs-11614101/v1","doi":"https://doi.org/10.21203/rs.3.rs-11614101/v1","is_oa":true,"landing_page_url":"https://doi.org/10.21203/rs.3.rs-11614101/v1","pdf_url":"https://www.researchsquare.com/article/rs-11614101/latest.pdf","source":{"id":"https://openalex.org/S4306525896","display_name":"Research Square","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Research Square","raw_type":"posted-content"},"volume":null,"type":"preprint","is_traditional":true,"indexed_in":["crossref"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"https://www.researchsquare.com/article/rs-11614101/latest.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5009409711","display_name":"Paul Robert Torgerson","orcid":"https://orcid.org/0000-0003-4277-9983","observed_orcids":["https://orcid.org/0000-0003-4277-9983"]},"institutions":[{"id":"https://openalex.org/I202697423","display_name":"University of Zurich","ror":"https://ror.org/02crff812","country_code":"CH","type":"education","lineage":["https://openalex.org/I202697423"]}],"countries":["CH"],"is_corresponding":false,"raw_author_name":"Paul Torgerson","raw_affiliation_strings":["University of Zurich"],"raw_orcid":"https://orcid.org/0000-0003-4277-9983","affiliations":[{"raw_affiliation_string":"University of Zurich","institution_ids":["https://openalex.org/I202697423"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5000767483","display_name":"Giovanni Ghielmetti","orcid":"https://orcid.org/0000-0002-3936-9687","observed_orcids":["https://orcid.org/0000-0002-3936-9687"]},"institutions":[{"id":"https://openalex.org/I202697423","display_name":"University of Zurich","ror":"https://ror.org/02crff812","country_code":"CH","type":"education","lineage":["https://openalex.org/I202697423"]}],"countries":["CH"],"is_corresponding":false,"raw_author_name":"Giovanni Ghielmetti","raw_affiliation_strings":["University of Zurich"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"University of Zurich","institution_ids":["https://openalex.org/I202697423"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5160955091","display_name":"Thoma Langton","orcid":null,"observed_orcids":[]},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Thoma Langton","raw_affiliation_strings":["Herpetofauna Consultants"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Herpetofauna Consultants","institution_ids":[]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":null,"has_fulltext":true,"cited_by_count":0,"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/T10038","display_name":"Tuberculosis Research and Epidemiology","score":0.9609000086784363,"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"}},"topics":[{"id":"https://openalex.org/T10038","display_name":"Tuberculosis Research and Epidemiology","score":0.9609000086784363,"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"}},{"id":"https://openalex.org/T11560","display_name":"Animal Disease Management and Epidemiology","score":0.022199999541044235,"subfield":{"id":"https://openalex.org/subfields/1103","display_name":"Animal Science and Zoology"},"field":{"id":"https://openalex.org/fields/11","display_name":"Agricultural and Biological Sciences"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T11316","display_name":"Mycobacterium research and diagnosis","score":0.0020000000949949026,"subfield":{"id":"https://openalex.org/subfields/2713","display_name":"Epidemiology"},"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/mycobacterium-bovis","display_name":"Mycobacterium bovis","score":0.9990000128746033},{"id":"https://openalex.org/keywords/bovine-tuberculosis","display_name":"bovine tuberculosis","score":0.9670000076293945},{"id":"https://openalex.org/keywords/european-badger","display_name":"Meles meles","score":0.8199999928474426},{"id":"https://openalex.org/keywords/transmission-direction","display_name":"transmission direction","score":0.8679999709129333},{"id":"https://openalex.org/keywords/whole-genome-sequencing","display_name":"whole genome sequencing","score":0.6949999928474426},{"id":"https://openalex.org/keywords/transmission-clusters","display_name":"transmission clusters","score":0.7009999752044678},{"id":"https://openalex.org/keywords/host-sharing","display_name":"host sharing","score":0.6370000243186951},{"id":"https://openalex.org/keywords/spillover-transmission","display_name":"spillover transmission","score":0.7300000190734863},{"id":"https://openalex.org/keywords/disease-control","display_name":"disease control","score":0.45899999141693115},{"id":"https://openalex.org/keywords/sampling-bias","display_name":"sampling bias","score":0.5899999737739563},{"id":"https://openalex.org/keywords/transmission-modeling","display_name":"transmission modelling","score":0.4690000116825104}],"concepts":[{"id":"https://openalex.org/C2780423500","wikidata":"https://www.wikidata.org/wiki/Q1345042","display_name":"Meles","level":3,"score":0.8805999755859375},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.7849000096321106},{"id":"https://openalex.org/C2777146433","wikidata":"https://www.wikidata.org/wiki/Q638105","display_name":"Badger","level":2,"score":0.7739999890327454},{"id":"https://openalex.org/C761482","wikidata":"https://www.wikidata.org/wiki/Q118093","display_name":"Transmission (telecommunications)","level":2,"score":0.7644000053405762},{"id":"https://openalex.org/C53889494","wikidata":"https://www.wikidata.org/wiki/Q1240247","display_name":"Sympatric speciation","level":2,"score":0.6259999871253967},{"id":"https://openalex.org/C81977670","wikidata":"https://www.wikidata.org/wiki/Q585259","display_name":"Genetic diversity","level":3,"score":0.5009999871253967},{"id":"https://openalex.org/C193252679","wikidata":"https://www.wikidata.org/wiki/Q242125","display_name":"Phylogenetic tree","level":3,"score":0.430400013923645},{"id":"https://openalex.org/C68873052","wikidata":"https://www.wikidata.org/wiki/Q349856","display_name":"Genetic variation","level":3,"score":0.4162999987602234},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.38659998774528503},{"id":"https://openalex.org/C78458016","wikidata":"https://www.wikidata.org/wiki/Q840400","display_name":"Evolutionary biology","level":1,"score":0.3625999987125397},{"id":"https://openalex.org/C189206191","wikidata":"https://www.wikidata.org/wiki/Q222046","display_name":"Genomics","level":4,"score":0.3549000024795532},{"id":"https://openalex.org/C15151743","wikidata":"https://www.wikidata.org/wiki/Q903778","display_name":"Metagenomics","level":3,"score":0.3481000065803528},{"id":"https://openalex.org/C22593422","wikidata":"https://www.wikidata.org/wiki/Q3242583","display_name":"Pedigree chart","level":3,"score":0.33660000562667847},{"id":"https://openalex.org/C2779134260","wikidata":"https://www.wikidata.org/wiki/Q12136","display_name":"Disease","level":2,"score":0.31869998574256897},{"id":"https://openalex.org/C97669555","wikidata":"https://www.wikidata.org/wiki/Q4118435","display_name":"Molecular epidemiology","level":4,"score":0.3142000138759613},{"id":"https://openalex.org/C140779682","wikidata":"https://www.wikidata.org/wiki/Q210868","display_name":"Sampling (signal processing)","level":3,"score":0.30230000615119934},{"id":"https://openalex.org/C2780597670","wikidata":"https://www.wikidata.org/wiki/Q8001345","display_name":"Wildlife disease","level":3,"score":0.29440000653266907},{"id":"https://openalex.org/C2778497218","wikidata":"https://www.wikidata.org/wiki/Q133447","display_name":"Mycobacterium bovis","level":4,"score":0.29260000586509705},{"id":"https://openalex.org/C18903297","wikidata":"https://www.wikidata.org/wiki/Q7150","display_name":"Ecology","level":1,"score":0.29089999198913574},{"id":"https://openalex.org/C135763542","wikidata":"https://www.wikidata.org/wiki/Q106016","display_name":"Genotype","level":3,"score":0.2816999852657318},{"id":"https://openalex.org/C116675565","wikidata":"https://www.wikidata.org/wiki/Q3241045","display_name":"Outbreak","level":2,"score":0.28110000491142273},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.2709999978542328},{"id":"https://openalex.org/C2780263730","wikidata":"https://www.wikidata.org/wiki/Q4254955","display_name":"Horizontal transmission","level":3,"score":0.2671999931335449},{"id":"https://openalex.org/C90132467","wikidata":"https://www.wikidata.org/wiki/Q171184","display_name":"Phylogenetics","level":3,"score":0.2662999927997589},{"id":"https://openalex.org/C42629822","wikidata":"https://www.wikidata.org/wiki/Q1346408","display_name":"Geocoding","level":2,"score":0.25450000166893005},{"id":"https://openalex.org/C2992243407","wikidata":"https://www.wikidata.org/wiki/Q525512","display_name":"Disease transmission","level":2,"score":0.25380000472068787}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.21203/rs.3.rs-11614101/v1","doi":"https://doi.org/10.21203/rs.3.rs-11614101/v1","is_oa":true,"landing_page_url":"https://doi.org/10.21203/rs.3.rs-11614101/v1","pdf_url":"https://www.researchsquare.com/article/rs-11614101/latest.pdf","source":{"id":"https://openalex.org/S4306525896","display_name":"Research Square","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Research Square","raw_type":"posted-content"}],"best_oa_location":{"id":"doi:10.21203/rs.3.rs-11614101/v1","doi":"https://doi.org/10.21203/rs.3.rs-11614101/v1","is_oa":true,"landing_page_url":"https://doi.org/10.21203/rs.3.rs-11614101/v1","pdf_url":"https://www.researchsquare.com/article/rs-11614101/latest.pdf","source":{"id":"https://openalex.org/S4306525896","display_name":"Research Square","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Research Square","raw_type":"posted-content"},"sustainable_development_goals":[{"score":0.4000000059604645,"display_name":"Good health and well-being","id":"https://metadata.un.org/sdg/3"}],"study_designs":[{"display_name":"Systematic Review","id":"https://openalex.org/study-designs/systematic-review"}],"awards":[],"funders":[],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W7225335378.pdf","grobid_xml":"https://content.openalex.org/works/W7225335378.grobid-xml"},"referenced_works_count":7,"referenced_works":["https://openalex.org/W2099130762","https://openalex.org/W2589011796","https://openalex.org/W2594794296","https://openalex.org/W3035831134","https://openalex.org/W3111707100","https://openalex.org/W3173916389","https://openalex.org/W4401851875"],"related_works":["https://openalex.org/W2091264144","https://openalex.org/W2099130762","https://openalex.org/W3214937045","https://openalex.org/W4416850329","https://openalex.org/W2103810356","https://openalex.org/W3163082221","https://openalex.org/W3187770401","https://openalex.org/W2995774433","https://openalex.org/W2626351895","https://openalex.org/W4378173309"],"abstract_inverted_index":{"Abstract":[0],"Background:":[1],"Tuberculosis,":[2],"caused":[3],"by":[4,322],"Mycobacterium":[5],"bovis,":[6,52],"is":[7,309,320],"a":[8,73,111],"bacterial":[9],"disease":[10,122,388],"affecting":[11],"cattle":[12,103,146,211,252],"and":[13,19,40,72,87,99,104,136,147,159,169,173,177,191,203,212,229,246,251,283,318,335,340,346,351,380],"other":[14],"domestic":[15],"species,":[16],"wild":[17],"mammals,":[18],"with":[20,53,223,237],"resilience":[21],"to":[22,81,88,113,119,154,259,315,349,370,383],"survive":[23],"in":[24,64,93,226,264,376,387],"the":[25,45,79,105,115,244,275,306],"wider":[26],"environment":[27],"for":[28,138,184,313],"many":[29],"months.":[30],"Whole-genome":[31],"sequencing":[32],"(WGS)":[33],"methods":[34],"can":[35],"distinguish":[36],"closely":[37],"related":[38],"isolates":[39,71],"local":[41,187,204,292,331],"transmission":[42,60,90,171,192,217,281,293,301,366,378],"clusters.":[43],"However,":[44,214],"relatively":[46],"slow":[47],"evolutionary":[48],"rate":[49],"of":[50,117,133,167,175,206,216,272,277,355,359,365],"M.":[51,207,332],"substitutions":[54],"accumulating":[55],"more":[56],"slowly":[57],"than":[58],"individual":[59],"events":[61],"occur,":[62],"results":[63],"limited":[65],"genetic":[66,201],"divergence":[67],"between":[68,102,210,221],"epidemiologically":[69],"linked":[70],"weak":[74,267],"temporal":[75,158,268],"signal,":[76,269],"greatly":[77],"limiting":[78],"ability":[80],"determine":[82],"precisely":[83],"\u2018who":[84],"infected":[85],"whom\u2019":[86],"estimate":[89],"rates.":[91],"Differences":[92],"surveillance,":[94],"sampling":[95,156,227,350],"intensity,":[96],"geographic":[97,160],"coverage,":[98,161],"detection":[100],"probability":[101],"European":[106,148],"badger":[107,385],"Meles":[108],"meles":[109],"warrants":[110],"review":[112],"examine":[114],"strength":[116],"evidence,":[118],"better":[120],"inform":[121,371],"control":[123,389],"considerations.":[124],"Methods:":[125],"Following":[126],"PRISMA":[127],"guidance,":[128],"we":[129],"searched":[130],"PubMed/MEDLINE,":[131],"Web":[132],"Science,":[134],"Scopus,":[135],"Embase":[137],"peer-reviewed":[139],"studies":[140,197,222,233,328],"using":[141],"WGS":[142,327],"data":[143],"from":[144],"sympatric":[145],"badgers.":[149,213],"Studies":[150],"were":[151,256],"assessed":[152],"according":[153],"their":[155,381],"design,":[157],"genomic":[162,176,288],"diversity,":[163],"analytical":[164,230],"framework,":[165],"treatment":[166,276],"unsampled":[168,280],"environmental":[170,278],"pathways,":[172,282],"integration":[174],"epidemiological":[178,336],"data.":[179],"Evidence":[180],"was":[181],"considered":[182,310],"separately":[183],"host":[185,261],"sharing,":[186],"persistence,":[188],"maintenance,":[189],"spillover,":[190],"direction.":[193,304],"Results:":[194],"The":[195],"reviewed":[196],"consistently":[198],"showed":[199],"close":[200],"relationships":[202],"sharing":[205],"bovis":[208,333],"strains":[209,334],"estimates":[215,255,364],"direction":[218],"varied":[219],"substantially":[220],"large":[224],"variation":[225,375],"quality":[228],"approaches.":[231],"Some":[232],"reported":[234],"patterns":[235],"compatible":[236],"greater":[238],"badger-to-cattle":[239],"transmission,":[240],"while":[241],"others":[242],"indicated":[243],"opposite,":[245],"some":[247,354],"emphasized":[248],"within-species":[249],"spread":[250],"movement.":[253],"Directional":[254],"potentially":[257],"sensitive":[258,348],"unequal":[260],"sampling,":[262],"differences":[263],"surveillance":[265],"processes,":[266],"incomplete":[270],"observation":[271],"infection":[273],"chains,":[274],"or":[279,302],"especially":[284],"model":[285],"assumptions.":[286],"Close":[287],"similarity":[289],"supported":[290],"shared":[291,330],"histories":[294],"but":[295,338],"generally":[296],"did":[297],"not":[298],"establish":[299],"direct":[300],"its":[303],"Collectively":[305],"evidence":[307],"base":[308],"insu\ufb00iciently":[311],"rigorous":[312],"findings":[314],"be":[316],"definitive":[317],"this":[319],"recognised":[321],"most":[323],"authors.":[324],"Conclusions:":[325],"Current":[326],"demonstrate":[329],"connections,":[337],"directionality":[339],"reservoir":[341],"status":[342],"remain":[343],"highly":[344],"uncertain":[345],"particularly":[347],"modelling":[352],"assumptions":[353],"which":[356],"show":[357],"signs":[358],"confirmation":[360],"bias.":[361],"Existing":[362],"caveated":[363],"are":[367],"presently":[368],"insu\ufb00icient":[369],"generalised":[372],"conclusions":[373],"about":[374],"interspecies":[377],"rates":[379],"use":[382],"validate":[384],"intervention":[386],"strategy.":[390]},"counts_by_year":[],"updated_date":"2026-11-09T13:22:03.289127","created_date":"2026-11-06T00:00:00"}