{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,10]],"date-time":"2026-09-10T11:11:19Z","timestamp":1789038679952,"version":"build-2803163510"},"reference-count":11,"publisher":"MDPI AG","issue":"18","license":[{"start":{"date-parts":[[2026,9,10]],"date-time":"2026-09-10T00:00:00Z","timestamp":1788998400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"Hubei Province\u2019s Major Special Projects for the Development of the Agricultural Microbiology Industry","award":["NYWSWZX2025-2027-04"],"award-info":[{"award-number":["NYWSWZX2025-2027-04"]}]},{"name":"China Agriculture Research System","award":["CARS-41"],"award-info":[{"award-number":["CARS-41"]}]},{"award":["CARS-41"],"award-info":[{"award-number":["CARS-41"]}],"id":[{"id":"https:\/\/ror.org\/03p5eky76","id-type":"ROR","asserted-by":"publisher"}]},{"name":"Hubei Province Modern Agricultural Industry Technology System-Poultry Egg Industry Technology System","award":["2025HBSTX4-04"],"award-info":[{"award-number":["2025HBSTX4-04"]}]},{"name":"2024 Annual Science and Technology Instructors Program in Wuhan City","award":["2024111203060843"],"award-info":[{"award-number":["2024111203060843"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Animals"],"abstract":"<jats:p>The increasing detection of Riemerella anatipestifer in chickens poses severe challenges to the poultry industry. However, the genomic differences among R. anatipestifer isolates from different poultry hosts remain poorly understood. Here, we investigated host-associated genomic differences among 158 R. anatipestifer strains isolated from different hosts in China, using pan-genome, phylogenetic, virulence factor, and antimicrobial resistance analyses. The core-genome phylogeny showed no apparent separation according to host, sampling period, or geographic origin. Conserved genes including groEL, tufA, and katB were detected in all strains, whereas tviB and ureG displayed host-associated distribution patterns. More than 40 putative antimicrobial resistance (AMR) genes were detected across 158 R. anatipestifer strains, indicating the presence of multiple putative AMR determinants. Among these, blaRAD-1, blaRASA-1, and dfrA36 exhibited host-associated distribution patterns. Pan-genome analysis further identified host-associated genomic differences in R. anatipestifer. These included genes contributing to cell-surface modification pathways mediated by pglH, and genes involved in toxin\u2013antitoxin system-dependent stress regulation via parD1\/parE1 and yefM-yoeB. Overall, our comparative genomic characterization of R. anatipestifer characterizes host-associated genomic differences and provides a basis for further investigation of their biological significance.<\/jats:p>","DOI":"10.3390\/ani16182847","type":"journal-article","created":{"date-parts":[[2026,9,10]],"date-time":"2026-09-10T10:27:21Z","timestamp":1789036041000},"page":"2847","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["Comparative Genomic Characterization of Riemerella anatipestifer Isolates from Chickens, Ducks, and Geese in China"],"prefix":"10.3390","volume":"16","author":[{"given":"Yunqing","family":"Guo","sequence":"first","affiliation":[{"name":"Key Laboratory of Prevention and Control Agents for Animal Bacteriosis, Ministry of Agriculture and Rural Affairs, Institute of Animal Sciences and Veterinary Medicine, Hubei Academy of Agricultural Sciences, Wuhan 430064, China"},{"name":"Key Laboratory of Animal Pathogenic Microbiology of Hubei Province, Institute of Animal Sciences and Veterinary Medicine, Hubei Academy of Agricultural Sciences, Wuhan 430064, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Rongrong","family":"Zhang","sequence":"additional","affiliation":[{"name":"Key Laboratory of Prevention and Control Agents for Animal Bacteriosis, Ministry of Agriculture and Rural Affairs, Institute of Animal Sciences and Veterinary Medicine, Hubei Academy of Agricultural Sciences, Wuhan 430064, China"},{"name":"Key Laboratory of Animal Pathogenic Microbiology of Hubei Province, Institute of Animal Sciences and Veterinary Medicine, Hubei Academy of Agricultural Sciences, Wuhan 430064, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Tengfei","family":"Zhang","sequence":"additional","affiliation":[{"name":"Key Laboratory of Prevention and Control Agents for Animal Bacteriosis, Ministry of Agriculture and Rural Affairs, Institute of Animal Sciences and Veterinary Medicine, Hubei Academy of Agricultural Sciences, Wuhan 430064, China"},{"name":"Key Laboratory of Animal Pathogenic Microbiology of Hubei Province, Institute of Animal Sciences and Veterinary Medicine, Hubei Academy of Agricultural Sciences, Wuhan 430064, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Wenting","family":"Zhang","sequence":"additional","affiliation":[{"name":"Key Laboratory of Prevention and Control Agents for Animal Bacteriosis, Ministry of Agriculture and Rural Affairs, Institute of Animal Sciences and Veterinary Medicine, Hubei Academy of Agricultural Sciences, Wuhan 430064, China"},{"name":"Key Laboratory of Animal Pathogenic Microbiology of Hubei Province, Institute of Animal Sciences and Veterinary Medicine, Hubei Academy of Agricultural Sciences, Wuhan 430064, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Qin","family":"Lu","sequence":"additional","affiliation":[{"name":"Key Laboratory of Prevention and Control Agents for Animal Bacteriosis, Ministry of Agriculture and Rural Affairs, Institute of Animal Sciences and Veterinary Medicine, Hubei Academy of Agricultural Sciences, Wuhan 430064, China"},{"name":"Key Laboratory of Animal Pathogenic Microbiology of Hubei Province, Institute of Animal Sciences and Veterinary Medicine, Hubei Academy of Agricultural Sciences, Wuhan 430064, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Qiao","family":"Hu","sequence":"additional","affiliation":[{"name":"Key Laboratory of Prevention and Control Agents for Animal Bacteriosis, Ministry of Agriculture and Rural Affairs, Institute of Animal Sciences and Veterinary Medicine, Hubei Academy of Agricultural Sciences, Wuhan 430064, China"},{"name":"Key Laboratory of Animal Pathogenic Microbiology of Hubei Province, Institute of Animal Sciences and Veterinary Medicine, Hubei Academy of Agricultural Sciences, Wuhan 430064, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Qingping","family":"Luo","sequence":"additional","affiliation":[{"name":"Key Laboratory of Prevention and Control Agents for Animal Bacteriosis, Ministry of Agriculture and Rural Affairs, Institute of Animal Sciences and Veterinary Medicine, Hubei Academy of Agricultural Sciences, Wuhan 430064, China"},{"name":"Key Laboratory of Animal Pathogenic Microbiology of Hubei Province, Institute of Animal Sciences and Veterinary Medicine, Hubei Academy of Agricultural Sciences, Wuhan 430064, China"},{"name":"Hubei Hongshan Laboratory, Wuhan 430070, China"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1968","published-online":{"date-parts":[[2026,9,10]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","unstructured":"Nowaczek, A., Dec, M., St\u0119pie\u0144-Py\u015bniak, D., Wilczy\u0144ski, J., and Urban-Chmiel, R. (2023). Characterization of Riemerella anatipestifer Strains isolated from various poultry species in Poland. Antibiotics, 12.","DOI":"10.3390\/antibiotics12121648"},{"key":"ref_2","doi-asserted-by":"crossref","first-page":"105687","DOI":"10.1016\/j.psj.2025.105687","article-title":"Emerging Riemerella anatipestifer infection in chickens: Pathogenic characteristics and host immune response profiles","volume":"104","author":"Lv","year":"2025","journal-title":"Poult. Sci."},{"key":"ref_3","doi-asserted-by":"crossref","first-page":"79","DOI":"10.2478\/jvetres-2019-0003","article-title":"Epidemiology and Antibiogram of Riemerella anatipestifer Isolated from Waterfowl Slaughterhouses in Taiwan","volume":"63","author":"Chang","year":"2019","journal-title":"J. Vet. Res."},{"key":"ref_4","doi-asserted-by":"crossref","first-page":"103497","DOI":"10.1016\/j.psj.2024.103497","article-title":"Genomic analysis and experimental pathogenic characterization of Riemerella anatipestifer isolates from chickens in China","volume":"103","author":"Chen","year":"2024","journal-title":"Poult. Sci."},{"key":"ref_5","doi-asserted-by":"crossref","first-page":"2711521","DOI":"10.1080\/21505594.2026.2711521","article-title":"Cross-host transmission of Riemerella anatipestifer to chickens: Genomic evolution and identification of the novel vapX-like-vapD toxin-antitoxin system","volume":"17","author":"Meng","year":"2026","journal-title":"Virulence"},{"key":"ref_6","doi-asserted-by":"crossref","unstructured":"Zhang, Y., Wang, X., Wang, Y., Sun, J., Dong, W., Meng, K., Li, G., and Yuan, X. (2025). Biological and genomic characteristics of chicken-derived Riemerella anatipestifer in China. Front. Microbiol., 29.","DOI":"10.3389\/fmicb.2025.1652106"},{"key":"ref_7","doi-asserted-by":"crossref","first-page":"105467","DOI":"10.1016\/j.psj.2025.105467","article-title":"Epidemiological investigation of Riemerella anatipestifer in large-scale chicken farms in 29 provinces of China from 2021 to 2024","volume":"104","author":"Zhang","year":"2025","journal-title":"Poult. Sci."},{"key":"ref_8","doi-asserted-by":"crossref","first-page":"e23763","DOI":"10.1096\/fj.202302694RR","article-title":"The GE296_RS03820 and GE296_RS03830 genes are involved in capsular polysaccharide biosynthesis in Riemerella anatipestifer","volume":"38","author":"Wu","year":"2024","journal-title":"FASEB J."},{"key":"ref_9","doi-asserted-by":"crossref","first-page":"e0313223","DOI":"10.1128\/spectrum.03132-23","article-title":"Genome-based assessment of antimicrobial resistance reveals the lineage specificity of resistance and resistance gene profiles in Riemerella anatipestifer from China","volume":"12","author":"Yang","year":"2024","journal-title":"Microbiol. Spectr."},{"key":"ref_10","doi-asserted-by":"crossref","first-page":"1117","DOI":"10.1093\/jac\/dkad058","article-title":"Identification of a novel carbapenem-hydrolysing class D \u03b2-lactamase RAD-1 in Riemerella anatipestifer","volume":"78","author":"Li","year":"2023","journal-title":"J. Antimicrob. Chemother."},{"key":"ref_11","doi-asserted-by":"crossref","first-page":"109456","DOI":"10.1016\/j.vetmic.2022.109456","article-title":"Characterization of RASA-1, a novel class A extended-spectrum beta-lactamase from Riemerella anatipestifer","volume":"270","author":"Luo","year":"2022","journal-title":"Vet. Microbiol."}],"container-title":["Animals"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.mdpi.com\/2076-2615\/16\/18\/2847\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,9,10]],"date-time":"2026-09-10T10:44:46Z","timestamp":1789037086000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.mdpi.com\/2076-2615\/16\/18\/2847"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,9,10]]},"references-count":11,"journal-issue":{"issue":"18","published-online":{"date-parts":[[2026,9]]}},"alternative-id":["ani16182847"],"URL":"https:\/\/doi.org\/10.3390\/ani16182847","relation":{},"ISSN":["2076-2615"],"issn-type":[{"value":"2076-2615","type":"electronic"}],"subject":[],"published":{"date-parts":[[2026,9,10]]}}}