{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,12]],"date-time":"2026-10-12T12:06:59Z","timestamp":1791806819653,"version":"4.3.4"},"reference-count":105,"publisher":"Microbiology Society","issue":"3","license":[{"start":{"date-parts":[[2026,3,18]],"date-time":"2026-03-18T00:00:00Z","timestamp":1773792000000},"content-version":"unspecified","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"NZ Ministry of Business, Innovation and Employment","award":["subcontract 3000036330"],"award-info":[{"award-number":["subcontract 3000036330"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2026,3,18]]},"abstract":"<jats:p>\n                    <jats:italic>Salmonella enterica<\/jats:italic>\n                    subsp.\n                    <jats:italic>enterica<\/jats:italic>\n                    serovar Enteritidis (\n                    <jats:italic>S<\/jats:italic>\n                    . Enteritidis) is the second most common serovar causing human salmonellosis in Aotearoa New Zealand (NZ). Sequence type (ST)183, which includes phage types 9a and 11, was the second most frequently isolated\n                    <jats:italic>S<\/jats:italic>\n                    . Enteritidis strain from human cases between 2020 and 2023. This ST is considered endemic in NZ as well as in mainland Europe and Great Britain, where the European hedgehog (\n                    <jats:italic>Erinaceus europaeus<\/jats:italic>\n                    ) is a recognized wildlife reservoir. Hedgehogs were introduced to NZ in the late 19th century; however, their role in the ecology of ST183 in NZ has not been formally evaluated. The aim of this study was to investigate whether hedgehogs act as a reservoir for\n                    <jats:italic>S<\/jats:italic>\n                    . Enteritidis ST183 in NZ and to assess the evolutionary history and epidemiology of this strain across human, animal and environmental contexts. We analysed human, animal and environmental ST183 isolates, including hedgehog carcasses opportunistically sampled in NZ, using Bayesian phylogenetic methods integrated with national epidemiological data. Although\n                    <jats:italic>S<\/jats:italic>\n                    . Enteritidis ST183 was isolated from three of 45 hedgehog carcasses during our study, consistent with recent prior detections of ST183 in NZ hedgehogs, Bayesian phylogenetic analysis supports a most recent common ancestor for currently circulating ST183 strains in the late 20th century, ~100\u2009years after the introduction of hedgehogs into NZ, providing no evidence that the strain was introduced concomitantly with hedgehogs. Epidemiological analysis revealed that, unlike in Europe, ST183 infections in NZ are more common in people aged over 60\u2009years compared with non-ST183\n                    <jats:italic>S<\/jats:italic>\n                    . Enteritidis infections, with rural residence and contact with farm animals identified as key risk factors. Together, these findings suggest that\n                    <jats:italic>S<\/jats:italic>\n                    . Enteritidis ST183 is established within the NZ rural environment, with evidence of interspecies transmission. While hedgehogs may contribute to the maintenance of ST183, they are unlikely to represent the original source of introduction, indicating a complex, multi-host ecology.\n                  <\/jats:p>","DOI":"10.1099\/mgen.0.001677","type":"journal-article","created":{"date-parts":[[2026,3,18]],"date-time":"2026-03-18T17:15:35Z","timestamp":1773854135000},"source":"Crossref","is-referenced-by-count":1,"title":["Phylodynamic analysis of Salmonella Enteritidis ST183 in Aotearoa New Zealand finds no evidence for introduction via European hedgehogs (Erinaceus europaeus)"],"prefix":"10.1099","volume":"12","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-3886-9599","authenticated-orcid":false,"given":"Hugo","family":"Strydom","sequence":"first","affiliation":[{"name":"Health Security, New Zealand Institute for Public Health and Forensic Science, Wellington, New Zealand"},{"name":"T\u0101wharau Ora | School of Veterinary Science, Massey University, Palmerston North, New Zealand"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0961-0281","authenticated-orcid":false,"given":"Shevaun","family":"Paine","sequence":"additional","affiliation":[{"name":"Health Security, New Zealand Institute for Public Health and Forensic Science, Wellington, New Zealand"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7066-2830","authenticated-orcid":false,"given":"David","family":"Welch","sequence":"additional","affiliation":[{"name":"School of Computer Science, University of Auckland, Auckland, New Zealand"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-6462-4769","authenticated-orcid":false,"given":"Jackie","family":"Wright","sequence":"additional","affiliation":[{"name":"Health Security, New Zealand Institute for Public Health and Forensic Science, Wellington, New Zealand"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2890-2191","authenticated-orcid":false,"given":"Collette","family":"Bromhead","sequence":"additional","affiliation":[{"name":"School of Health Sciences, Massey University, Wellington, New Zealand"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8892-3605","authenticated-orcid":false,"given":"Chris N.","family":"Niebuhr","sequence":"additional","affiliation":[{"name":"Manaaki Whenua \u2013 Landcare Research Group, Bioeconomy Science Institute, Lincoln, New Zealand"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8727-4968","authenticated-orcid":false,"given":"Ernest","family":"Williams","sequence":"additional","affiliation":[{"name":"Health Security, New Zealand Institute for Public Health and Forensic Science, Wellington, New Zealand"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-9873-0420","authenticated-orcid":false,"given":"Jennie","family":"Fischer","sequence":"additional","affiliation":[{"name":"Food Microbiology, Host-Pathogen-Interaction\/German National Reference Laboratory for Salmonella, German Federal Institute for Risk Assessment, Berlin, Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-6020-3841","authenticated-orcid":false,"given":"Laura","family":"Uelze","sequence":"additional","affiliation":[{"name":"Food Microbiology, Host-Pathogen-Interaction\/German National Reference Laboratory for Salmonella, German Federal Institute for Risk Assessment, Berlin, Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1047-6283","authenticated-orcid":false,"given":"Sandra","family":"Simon","sequence":"additional","affiliation":[{"name":"Unit of Enteropathogenic Bacteria and Legionella\/National Reference Centre for Salmonella and Other Bacterial Enteric Pathogens, Robert Koch Institute, Wernigerode, Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Michael","family":"Pietsch","sequence":"additional","affiliation":[{"name":"Unit of Enteropathogenic Bacteria and Legionella\/National Reference Centre for Salmonella and Other Bacterial Enteric Pathogens, Robert Koch Institute, Wernigerode, Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1706-7140","authenticated-orcid":false,"given":"Becki","family":"Lawson","sequence":"additional","affiliation":[{"name":"Institute of Zoology, Zoological Society of London, Regent\u2019s Park, London, England, UK"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5288-9089","authenticated-orcid":false,"given":"Marie Anne","family":"Chattaway","sequence":"additional","affiliation":[{"name":"NIHR HPRU in Genomics and Data Enabling, University of Warwick, Coventry, England, UK"},{"name":"Gastrointestinal Bacteria Reference Unit, United Kingdom Health Security Agency, London, England, UK"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7660-4466","authenticated-orcid":false,"given":"Sarah","family":"Jefferies","sequence":"additional","affiliation":[{"name":"Health Security, New Zealand Institute for Public Health and Forensic Science, Wellington, New Zealand"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0348-419X","authenticated-orcid":false,"given":"Joep","family":"de Ligt","sequence":"additional","affiliation":[{"name":"Health Security, New Zealand Institute for Public Health and Forensic Science, Wellington, New Zealand"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-6334-0657","authenticated-orcid":false,"given":"Nigel","family":"French","sequence":"additional","affiliation":[{"name":"New Zealand Food Safety Science and Research Centre, Massey University, Palmerston North, New Zealand"},{"name":"T\u0101wharau Ora | School of Veterinary Science, Massey University, Palmerston North, New Zealand"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"345","reference":[{"key":"R1","article-title":"Salmonella (non-typhoidal)"},{"key":"R2","doi-asserted-by":"publisher","DOI":"10.1016\/j.cll.2015.02.002"},{"key":"R3","article-title":"Annual report concerning foodborne diseases in New Zealand 2023","author":"Armstrong","year":"2024"},{"key":"R4","doi-asserted-by":"publisher","DOI":"10.1017\/S0950268800067765"},{"key":"R5","doi-asserted-by":"publisher","DOI":"10.1128\/JCM.38.10.3631-3635.2000"},{"key":"R6","doi-asserted-by":"publisher","DOI":"10.1371\/journal.ppat.1002776"},{"key":"R7","doi-asserted-by":"publisher","DOI":"10.1038\/s41598-017-18667-2"},{"key":"R8","article-title":"Salmonellosis Communicable Disease Control Manual","year":"2024"},{"key":"R9","article-title":"Notifiable diseases in New Zealand: Annual Report 2021","year":"2021"},{"key":"R10","article-title":"2023 Census population counts (by ethnic group, age, and M\u0101ori descent) and dwelling counts","year":"2023"},{"key":"R11","article-title":"Annual report concerning foodborne diseases in New Zealand 2021","author":"Pattis","year":"2022"},{"key":"R12","doi-asserted-by":"publisher","DOI":"10.1099\/mgen.0.001525"},{"key":"R13","doi-asserted-by":"publisher","DOI":"10.1136\/vr.128.11.245"},{"key":"R14","doi-asserted-by":"publisher","DOI":"10.3201\/eid1101.040752"},{"key":"R15","doi-asserted-by":"publisher","DOI":"10.3390\/microorganisms9091911"},{"key":"R16","doi-asserted-by":"publisher","DOI":"10.1053\/rvsc.2000.0384"},{"key":"R17","article-title":"Salmonella infection in farm livestock","author":"Buxton","year":"1949"},{"key":"R18","article-title":"Britain\u2019s first National Hedgehog Conservation Strategy. 2024","year":"2024"},{"key":"R19","article-title":"The state of Britain\u2019s hedgehogs 2022","author":"Wembridge","year":"2022"},{"key":"R20","doi-asserted-by":"publisher","DOI":"10.1016\/j.biocon.2025.111033"},{"key":"R21","doi-asserted-by":"publisher","DOI":"10.1007\/s12595-021-00363-9"},{"key":"R22","article-title":"Non-human Salmonella isolates"},{"key":"R23","first-page":"9","article-title":"Carriage of Salmonellae and Yersiniae by New Zealand hedgehogs","volume":"24","author":"Gorton","year":"1997","journal-title":"Surveillance"},{"key":"R24","article-title":"Hedgehogs"},{"key":"R25","doi-asserted-by":"publisher","DOI":"10.1080\/03014223.1975.9517886"},{"key":"R26","article-title":"Press; 1868;XIII(1717):3"},{"key":"R27","doi-asserted-by":"crossref","DOI":"10.1071\/9781486306299","volume-title":"The Handbook of New Zealand Mammals;","author":"King","year":"2021"},{"key":"R28","doi-asserted-by":"publisher","DOI":"10.20417\/nzjecol.44.7"},{"key":"R29","doi-asserted-by":"publisher","DOI":"10.1111\/mec.12331"},{"key":"R30","doi-asserted-by":"publisher","DOI":"10.3390\/d16010045"},{"key":"R31","article-title":"Case report form - Enteric Disease"},{"key":"R32","article-title":"Estimated resident population (ERP), subnational population estimates (urban rural) by ethnic group. Aotearoa Data Explorer"},{"key":"R33","article-title":"Urban\u2013rural profile"},{"key":"R34","author":"Wickham","year":"2016"},{"key":"R35","article-title":"Quantitative microbial risk assessment pilot study","author":"Leonard","year":"2020"},{"key":"R36","article-title":"Quantitative microbial risk assessment phase 2.1 \u2013 initial data collection and recommendations","author":"Leonard","year":"2021"},{"key":"R37","first-page":"1","volume-title":"Antigenic Formulae of the Salmonella Serovars","author":"Grimont","year":"2007"},{"key":"R38","doi-asserted-by":"publisher","DOI":"10.3389\/fmicb.2021.626941"},{"key":"R39","doi-asserted-by":"publisher","DOI":"10.3389\/fpubh.2019.00317"},{"key":"R40","doi-asserted-by":"publisher","DOI":"10.3390\/genes12050644"},{"key":"R41","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/bty560"},{"key":"R42","article-title":"Shovill","author":"Seeman","year":"2017","journal-title":"GitHub"},{"key":"R43","doi-asserted-by":"publisher","DOI":"10.7717\/peerj.6995"},{"key":"R44","doi-asserted-by":"publisher","DOI":"10.1186\/s13059-019-1891-0"},{"key":"R45","article-title":"Bakcharak","author":"Deneke","year":"2018","journal-title":"GitHub"},{"key":"R46","article-title":"ABRicate","author":"Seemann","year":"2017","journal-title":"GitHub"},{"key":"R47","doi-asserted-by":"publisher","DOI":"10.1128\/AAC.00483-19"},{"key":"R48","doi-asserted-by":"publisher","DOI":"10.1038\/s41598-021-91456-0"},{"key":"R49","doi-asserted-by":"publisher","DOI":"10.1099\/mgen.0.000398"},{"key":"R50","doi-asserted-by":"publisher","DOI":"10.1128\/AAC.02412-14"},{"key":"R51","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gki008"},{"key":"R52","doi-asserted-by":"publisher","DOI":"10.1099\/mgen.0.000151"},{"key":"R53","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0147101"},{"key":"R54","article-title":"mlst","author":"Seeman","year":"2015","journal-title":"GitHub"},{"key":"R55","article-title":"Antimicrobial susceptibility testing. EUCAST disk diffusion method"},{"key":"R56","article-title":"Clinical breakpoints and dosing of antibiotics"},{"key":"R57","article-title":"Performance standards for antimicrobial susceptibility testing; 26th ed"},{"key":"R58","article-title":"Performance standards for antimicrobial susceptibility testing; 32nd ed. CLSI supplement M100S","year":"2022"},{"key":"R59","article-title":"snippySnake - variant calling pipeline with snippy","author":"Deneke"},{"key":"R60","article-title":"Snippy","author":"Seemann","year":"2015","journal-title":"GitHub"},{"key":"R61","article-title":"snp-dists","author":"Seemann","year":"2017","journal-title":"GitHub"},{"key":"R62","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gku1196"},{"key":"R63","doi-asserted-by":"publisher","DOI":"10.1099\/mgen.0.000056"},{"key":"R64","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btz305"},{"key":"R65","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btl529"},{"key":"R66","doi-asserted-by":"publisher","DOI":"10.1093\/molbev\/mst028"},{"key":"R67","doi-asserted-by":"publisher","DOI":"10.1093\/ve\/vew007"},{"key":"R68","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pcbi.1006650"},{"key":"R69","doi-asserted-by":"publisher","DOI":"10.1007\/BF02101694"},{"key":"R70","first-page":"57","article-title":"Some probabilistic and statistical problems in the analysis of DNA sequences. in: some mathematical questions in biology - DNA sequence analysis","author":"Tavar\u00e9","year":"1986","journal-title":"J Theor Biol"},{"key":"R71","doi-asserted-by":"publisher","DOI":"10.1186\/s12862-017-0890-6"},{"key":"R72","doi-asserted-by":"publisher","DOI":"10.1093\/sysbio\/syac015"},{"key":"R73","doi-asserted-by":"publisher","DOI":"10.1080\/10635150500433722"},{"key":"R74","doi-asserted-by":"publisher","DOI":"10.1214\/ss\/1028905934"},{"key":"R75","doi-asserted-by":"publisher","DOI":"10.1007\/BF01406511"},{"key":"R76","doi-asserted-by":"publisher","DOI":"10.3201\/eid2009.131095"},{"key":"R77","doi-asserted-by":"publisher","DOI":"10.1101\/012401"},{"key":"R78","doi-asserted-by":"publisher","DOI":"10.1186\/1471-2148-13-221"},{"key":"R79","article-title":"Risk profile update: Salmonella (nontyphoidal) in and on eggs","author":"Kingsbury","year":"2024"},{"key":"R80","doi-asserted-by":"publisher","DOI":"10.1080\/1177083X.2016.1187636"},{"key":"R81","doi-asserted-by":"publisher","DOI":"10.1080\/03014223.1988.10422629"},{"key":"R82","article-title":"Some aspects of the ecology of hedgehogs (Erinaceus europaeus l.) in the Manawatu region","author":"Parkes","year":"1972"},{"key":"R83","doi-asserted-by":"publisher","DOI":"10.1016\/j.tim.2014.02.011"},{"key":"R84","article-title":"A study of tuberculosis in hedgehogs so as to predict the location of tuberculous possums","author":"Gorton","year":"1998"},{"key":"R85","doi-asserted-by":"publisher","DOI":"10.1038\/s41598-022-24150-4"},{"key":"R86","article-title":"AST news update June 2023: new! CLSI M100-ed33: updated aminoglycoside breakpoints for Enterobacterales and Pseudomonas aeruginosa","author":"Humphries","year":"2023"},{"key":"R87","doi-asserted-by":"publisher","DOI":"10.1128\/AEM.69.7.3687-3694.2003"},{"key":"R88","doi-asserted-by":"publisher","DOI":"10.1007\/s10534-010-9393-2"},{"key":"R89","doi-asserted-by":"publisher","DOI":"10.1111\/1462-2920.13837"},{"key":"R90","doi-asserted-by":"publisher","DOI":"10.1111\/j.1365-2958.2007.05963.x"},{"key":"R91","doi-asserted-by":"publisher","DOI":"10.1016\/j.vetmic.2005.10.030"},{"key":"R92","doi-asserted-by":"publisher","DOI":"10.1086\/513985"},{"key":"R93","doi-asserted-by":"publisher","DOI":"10.1007\/s15010-025-02556-2"},{"key":"R94","doi-asserted-by":"publisher","DOI":"10.1128\/AEM.69.1.548-553.2003"},{"key":"R95","first-page":"30","article-title":"Salmonella Enteritidis","volume":"24","author":"Gardner","year":"1997","journal-title":"Surveillance"},{"key":"R96","doi-asserted-by":"publisher","DOI":"10.1093\/sysbio\/syy048"},{"key":"R97","doi-asserted-by":"publisher","DOI":"10.1099\/mgen.0.000605"},{"key":"R98","doi-asserted-by":"publisher","DOI":"10.3201\/eid2306.161934"},{"key":"R99","doi-asserted-by":"publisher","DOI":"10.1080\/00480169.2014.914861"},{"key":"R100","first-page":"450","article-title":"Meat industry review","volume":"44","year":"1981","journal-title":"Reserve Bank N Z Bull"},{"key":"R101","article-title":"The value of incentives and subsidies for increasing livestock production","author":"Taylor","year":"1978"},{"key":"R102","article-title":"The sheep and cattle industries in New Zealand","author":"Scott","year":"1977"},{"key":"R103","article-title":"1978\/1979 Meat industry review","year":"1980"},{"key":"R104","doi-asserted-by":"publisher","DOI":"10.1093\/cid\/ciy919"},{"key":"R105","doi-asserted-by":"publisher","DOI":"10.3201\/eid2503.180899"}],"container-title":["Microbial Genomics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.microbiologyresearch.org\/content\/journal\/mgen\/10.1099\/mgen.0.001677?crawler=true&mimetype=application\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,3,18]],"date-time":"2026-03-18T17:15:39Z","timestamp":1773854139000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.microbiologyresearch.org\/content\/journal\/mgen\/10.1099\/mgen.0.001677"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,3,18]]},"references-count":105,"journal-issue":{"issue":"3","published-print":{"date-parts":[[2026,3,18]]}},"URL":"https:\/\/doi.org\/10.1099\/mgen.0.001677","relation":{},"ISSN":["2057-5858"],"issn-type":[{"value":"2057-5858","type":"electronic"}],"subject":[],"published":{"date-parts":[[2026,3,18]]}}}