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Potential dissemination and persistence of Clostridium perfringens along the slaughtering process in French cattle, pig or poultry slaughterhouses.

Clostridium perfringens is a major foodborne pathogen associated with meat products, yet its dissemination routes and persistence within slaughterhouses remain poorly understood. In this study, whole-genome sequencing combined with multilocus sequence typing (MLST), core genome MLST (cgMLST), and core single nucleotide polymorphism (SNP) analysis was applied to 286 C. perfringens isolates collected from cattle, pig, and poultry slaughterhouses in France. MLST analysis revealed extensive genetic diversity, with most isolates assigned to novel allelic profiles rather than previously described sequence types. Phylogenetic analyses based on cgMLST and SNP data revealed frequent recovery of closely related isolates from feces, meat, surfaces, and air, highlighting widespread dissemination of strains within slaughterhouses during processing. Notably, close genetic related isolates recovered from air and other sample types are consistent with air-associated dissemination within slaughterhouse environments. In addition, the detection of closely related strains across different sampling campaigns suggests the potential persistence of C. perfringens within slaughterhouse environments over time. Most isolates were classified as toxinotype A (97.9%), with a few belonging to toxinotypes D (1.0%) and G (1.0%), and in silico analyses revealed a broad distribution of virulence-associated genes. Antimicrobial resistance genes (ARGs) were commonly detected, particularly those conferring resistance to tetracyclines, although isolates carrying multiple ARGs remained infrequent. Overall, this study provides new insights into the genomic diversity, dissemination pathways, and persistence of C. perfringens in multi-species slaughterhouses. These findings highlight the potential role of air-associated dissemination in contamination dynamics and underscore the importance of improved hygiene control strategies to mitigate food safety risks along the meat production chain.

Antimicrobial resistance gene (ARG)

Tigecycline-resistant Staphylococcus in waiting pens of a pig slaughterhouse: genomic insights into a food safety alert.

BACKGROUND: The waiting pens of slaughterhouses represent a critical control point in the 'farm-to-fork' continuum, yet their role in the emergence and dissemination of antimicrobial resistance remains understudied. This study investigated tigecycline-resistant Staphylococcus (TRS) in these high-risk zones to assess their prevalence, resistance mechanisms, and transmission dynamics. METHODS: 400 samples were collected from the waiting pens of a pig slaughterhouse in Guangzhou, China. Antimicrobial susceptibility testing, whole-genome sequencing, phylogenetic analysis, and molecular cloning were employed to characterize resistance mechanisms and transmission patterns. RESULTS: 78 TRS strains were isolated and classified into three species, including S. borealis, S. ureilyticus, and S. pasteuri. These isolates exhibited multidrug-resistant phenotypes and carried new mutations in rpsJ and tet(M), which were functionally confirmed to reduce tigecycline susceptibility. Phylogenetic evidence demonstrated clonal transmission between pig farms and the slaughterhouse. The tet(M) gene was located within Staphylococcal cassette chromosome mec elements mediated by IS257, while tet(L) was carried by plasmids formed through IS256/IS257-mediated recombination. CONCLUSIONS: Waiting pens serve as crucial reservoirs for the amplification and dissemination of antimicrobial resistance. Our findings underscore the urgent need for enhanced biosecurity measures, improved waste management, and routine molecular surveillance in these high-risk zones to mitigate the spread of resistance along the food production chain.

Animals

Some hygienic problems in the production of meat and bone meal from slaughterhouse offal and animal carcasses.

A study of uncut anthrax-infected slaughterhouse waste in the sterilizer of an animal destructor after the prescribed heating at 130 degrees C for 30 min showed that in 17 cases Bacillus anthracis was able to survive. The determination of z-values for B. anthracis and B. stearothermophilus showed that when slaughterhouse waste is cut up into pieces of no more that 50 g weight the temperature at the centre may lie between 120 degrees C for 20 min and 130 degrees C for 10 min for destruction of spore formers. The resulting animal meal is of improved protein quality by this treatment. These results and conclusions cannot be directly transferred to fat bath treatment of meat, because of the significant difference caused by the use of vapour pressure methods.

Abattoirs

Gut eczema in slaughterhouse workers.

In Danish bacon factories workers eviscerating and cleansing gut casings commonly develop a vesicular eczema starting in the finger webs, from where it spreads to the sides of the fingers. The eruption is called "gut eczema" or "fat eczema" by the workers. It is self-limiting, lasts for 1--2 weeks, and can recur at intervals of months or years. The etiology is unknown. Prick tests with extracts of ascaris and several organs of the pigs were negative.

Abattoirs

Salmonella dublin infection in adult cattle: a slaughter house and knackery survey in South West Wales.

A survey was carried out between June 1970 and December 1971 in which gall bladders from cattle either slaughtered for food consumption or disposed of through knackeries were cultured for salmonellas. Salmonella dublin was isolated from 28 of 1917 gall-bladders of adult cattle killed in the slaughterhouse at Carmarthen, and from 23 of 197 gall-bladders obtained from adult cattle sent to a knackery at Abergwili, near Carmarthen. The results are compared with a similar survey carried out in 1947 and 1948. Between June and November 1971 gall-bladders and uteri were also obtained from a slaughterhouse in Newcastle Emlyn, North Carmarthenshire, and a knackery in Tanygroes, South Cardiganshire. S. dublin was cultured from two gall-bladders but from none of the uteri of the 161 slaughterhouse cases. Seven of the 46 cows from the knackery yielded S. dublin on culture: 2 in the gall-bladder only, 3 in the uterus only and 2 in both gall bladder and uterus.

Abattoirs

Repeated Cross-Sectional Surveillance and ORF5-Based Molecular Epidemiology of Porcine Reproductive and Respiratory Syndrome Virus in Anhui Province, China, 2019-2024.

Porcine reproductive and respiratory syndrome virus (PRRSV) remains a major threat to swine production, and its circulation after the African swine fever outbreak requires continued surveillance. This study investigated the temporal, regional, and genetic characteristics of PRRSV in Anhui Province from September 2019 to November 2024. Ten rounds of repeated cross-sectional surveillance were conducted at 147 slaughterhouses and 21 rendering plants. Tissue samples were collected by random, cluster, or risk-based sampling, pooled in groups of five, and tested by RT-qPCR. Representative positive samples with Ct values < 25 underwent ORF5 amplification, Sanger sequencing, and phylogenetic analysis. A total of 994 site visits yielded 18,733 tissue samples. No positive samples were detected in autumn 2020 or spring 2021, whereas PRRSV was detected again from autumn 2021 and subsequently fluctuated. The highest site-level positivity was 41.18% in autumn 2023, and the highest estimated individual-level positivity was 4.66% in spring 2023. Regional differences were statistically significant, with the highest site-level positivity in northern Anhui, and pooled-sample positivity was higher in rendering plants than in slaughterhouses. All 24 ORF5 sequences belonged to PRRSV-2 and mainly clustered with NADC30-like, NADC34-like, or MLV/classical strains. These findings demonstrate temporal fluctuations and lineage coexistence, supporting continued multisource surveillance and broader genomic and antigenic evaluation.

NADC30-like

[Staphylococcus aureus in poultry--biochemical characteristics, antibiotic resistance and phage pattern (author's transl)].

In a poultry processing plant in northern Germany 1412 swabs were taken from poultry carcasses together with 608 swabs from the personnel. The broilers came from 22 different chicken farms. The swabs taken from the poultry and those taken from the personnel proved to be 35% and 48% Staph. aureus positive respectively. The swabs taken from the feathers and from the skin were staphylococcal positive at a higher level (47%) than the swabs taken from the cloaca (19%) and the throat (23%). Between 8% and 63% of the animals from the various chicken farms were Staph. aureus positive. The frequency of staphylococcal contamination increased during the course of slaughter. 57% of the swabs taken from the gloves and the hands and 42% from the aprons of the personnel were Staph. aureus positive. Some biochemical properties, the phage patterns, and the antibiotic resistance against oleandomycin, erythromycin, bacitracin, streptomycin, tetracyclin, penicillin, chloramphenicol, virginiamycin and flavomycin were determined from 445 poultry and 345 personnel Staph. aureus isolates. Only small differences could be established between both sources in this way. Only 20% of the personnel and 34% of the chicken strains were resistant to antibiotics. In the strains collected from personnel, penicillin-resistance predominated while the poultry isolates showed predominantly tetracyclin-resistance. Of all antibiotics applied nutritively in the chicken fattening, there was a higher resistance only against oleandomycin (11% of the poultry strains). Between the chicken farms there was a different frequency of resistance (0--68%). The source of the staphylococci could be determined for only some of the strains. Only 2.5% of the chicken isolates showed characteristics described in the literature to be "poultry-specific", whereas 37% of the personnel and 24% of the poultry isolates were shown to be "human-specific" strains. It seems that the vast majority of the staphylococci originated from the slaughterhouse personnel. The rest of the strains differed in varying combinations of their properties from the given species characteristics. Although Staph. aureus was brought into the slaughterhouse by the poultry, the contaminations of the final product seemed to originate mainly from human beings.

Abattoirs

Generation of germline-transmitting transgenic sheep by piggyBac-mediated transgenesis using pronuclear and cytoplasmic gene injection approaches.

Sheep represent an important large-animal model for biomedical research and biopharmaceutical production. Although the piggyBac transposon system offers efficient and stable genomic integration, the optimal gene delivery strategy for ovine embryos remains unclear. This study evaluated piggyBac-mediated transgenesis using pronuclear injection (PNI) in both in vivo- and in vitro-derived embryos and assessed cytoplasmic injection (CTI) as an alternative approach. In vivo-derived embryos were obtained from superovulated K&#x131;v&#x131;rc&#x131;k ewes approximately 40&#x2009;h after gonadotropin-releasing hormone administration, whereas in vitro-derived embryos were produced from slaughterhouse-derived oocytes. All embryos were injected with the hyperactive piggyBac transposase-based pmhyGENIE-3 construct (10&#x2009;ng/&#xb5;L). In vivo-derived embryos were transferred immediately after injection, whereas in vitro-derived embryos were cultured for 3&#x2009;days and screened for EGFP expression prior to transfer. Among 65 in vitro-derived embryos injected by PNI, no transgenic offspring was obtained. In contrast, PNI of 19 in vivo-derived embryos resulted in one transgenic lamb (5.3%). CTI of 12 in vivo-derived embryos similarly produced one transgenic lamb (8.3%). Whole-genome sequencing of the healthy founder male produced by CTI identified a single detectable genomic integration locus on chromosome 10 within a non-coding RNA locus (LOC121820439). Germline transmission was confirmed by in vitro fertilization using sperm from the founder male, with EGFP expression detected in 10.1% (10/99) resulting embryos. These findings provide proof-of-concept evidence for piggyBac-mediated transgenesis in sheep and support the feasibility of cytoplasmic injection as an alternative gene-delivery approach under the conditions tested.

Animals

Comparison of luteolytic effectiveness of several prostaglandin analogs in heifers and relative binding affinity for bovine luteal prostaglandin binding sites.

The relative binding affinities for both the prostaglandin (PG)E1 and PGF2alpha specific bovine luteal binding sites were determined for five PGE and fourteen PGF derivatives and analogs. Relative binding affinity was determined in vitro using membranes prepared from bovine corpora luteal (CL) obtained from the slaughterhouse. The parent structure of the analog was a dominant feature in determining the affinity for the respective PG binding site. Luteolysis was determined in cattle following intramuscular injection of various doses of prostaglandin once between days 6 and 14 after estrus and measuring CL regression by ovarian palpation per rectum, interval between injection and return to estrus and duration of the subsequent estrous cycle. A dose which was luteolytic was established for each of eight PGF-type compounds, and a dose which was not luteolytic was also established. There appeared to be limited association between the relative affinity for the PGF2alpha specific site in vitro and the estimated luteolytic dose range of these PGF analogs when tested in cattle. Differences in in vivo luteolytic potency for the compounds tested could not be explained by differences in binding affinity. Differences in metabolism and absorption may also be important in the determination of in vivo potency.

Animals

Genome-scale evolution and phylodynamics of swine influenza A viruses in China: a genomic epidemiology study.

BACKGROUND: Pigs are recognised as crucial intermediate hosts for the emergence of influenza viruses of pandemic potential. As the largest pork-producing nation, China hosts a complex ecosystem of swine influenza viruses (SIVs). We aimed to investigate the evolutionary processes, spatiotemporal dynamics, and biological characteristics of SIVs in China. METHODS: From Jan 15, 2016, to Dec 22, 2020, we collected nasal swabs from pigs at eight abattoirs and 16 swine farms in the Guangdong, Henan, and Shandong provinces of China, as part of SIV surveillance. SIVs were detected with RT-PCR. Positive samples underwent viral isolation and genome sequencing. We analysed evolution and spatiotemporal dynamics using the whole genomes of isolated SIVs, as well as genome sequences of SIV isolates from human infections worldwide retrieved from the Global Initiative on Sharing All Influenza Data and GenBank Flu databases up to April 28, 2024. Viral sequences without a sample collection area or date were excluded from the analysis. Viral receptor-binding properties and in-vitro replication of strains isolated in this study were evaluated with a solid-phase binding assay and various cell lines, including Madin-Darby canine kidney cells, porcine alveolar macrophages, primary porcine trachea epithelial cells, human bronchial epithelioid, and human lung adenocarcinoma epithelial (A549) cells. Viral replication and transmission studies were conducted in 33 guinea pigs and 13 pigs. Additionally, we collected serum samples from pig farm workers and members of the general public recruited by the Third Affiliated Hospital of Sun Yat-sen University between Feb 28 and May 11, 2023, to detect specific antibodies against Eurasian avian-like A(H1) and human-like A(H3N2) SIVs using the haemagglutination inhibition assay. FINDINGS: 23 (1&#xb7;3%) of 1818 nasal swabs collected in abattoirs had SIVs; 22 (0&#xb7;9%) of 2375 swabs from swine farms had SIVs. Further viral isolation yielded 39 strains of SIV. We identified 534 A(H1N1), 69 A(H1N2), and 92 A(H3N2) SIVs, representing 20 genotypes within the Eurasian avian-like lineage, 14 within the classical swine A(H1) lineage, and 16 within the human-like A(H3N2) lineage. The introduction of the A(H1N1)pdm/09 virus significantly influenced the internal gene pool of SIVs, enhancing genotypic diversity in China. Notably, the Eurasian avian-like A(H1), classical swine A(H1), and human-like A(H3N2) lineages showed human-mediated spread over long distances between provinces, with the Eurasian avian-like A(H1) lineage showing the most prevalent spread pathways. Eurasian avian-like A(H1) SIVs showed a preference for binding to sialic acid &#x3b1;-2,6 glycan receptors, predominantly found in humans, resulting in an increased production of progeny viruses in human airway epithelial cells, as well as effective transmission and infectivity among guinea pigs and pigs. Among 54 eligible serum samples collected from pig farm workers (24 from slaughterhouses and 30 from swine farms), 23 (43%) were seropositive for Eurasian avian-like A(H1) SIVs and 46 (85%) for human-like A(H3N2) SIVs. Among 100 eligible samples from members of the general public, 14 (14%) were seropositive for Eurasian avian-like A(H1) SIVs and 85 (85%) for human-like A(H3N2) SIVs. INTERPRETATION: This study elucidates the evolutionary processes and spatiotemporal patterns of SIVs, highlighting potential risks to public health. These findings are crucial for informing public health interventions that aim to prevent future SIV epidemics in China and other countries worldwide. FUNDING: Scientific Innovation Strategy-Construction of High-Level Academy of Agriculture Science-Distinguished Scholar (R2020PY-JC001).

Animals

Sleep-promoting factor S: purification and properties.

Sleep-promoting factor was purified from acid/acetone extracts of whole brains of rabbits and from brainstems of slaughterhouse cattle. Intraventricular infusion of extracts purified by means of ion exchange and gel filtration induced excess slow-wave sleep in rabbits for 5-10 hr. The procedure is simple and provides material suitable for physiological studies. Further treatment by partition chromatography and electrophoresis yielded an active product that was purified at least 1 million-fold. This product was inactivated by incubation with mixed carboxypeptidases A and B. Amino acid analysis of acid hydrolysates indicated that the effective dose was less than 150 pmol per rabbit and the original concentration in brain tissue was of the order of 30 pmol/g of brain.

Animals

Genomic characterisation and lytic potential of phage SF01 against multidrug-resistant Salmonella enterica subsp. enterica, a key agent of infection in poultry.

1. Salmonella enterica remains the key cause of salmonellosis in poultry, causing high morbidity and mortality. Due to the unprecedented resistance of S. enterica to antibiotics, bacteriophages have emerged as a powerful alternative to conventional antibiotics treatment for salmonellosis.2. In this study, a strain was isolated from infected broiler chickens and whole-genome sequencing (WGS) identified the strain SFD-01 as S. enterica subsp. enterica. Bioinformatics analyses revealed that the genome was 4.6 Mb in size with 4559 coding sequences (CDS), 77 tRNAs and 4 rRNAs. Additionally, 119 virulence genes, 125 antimicrobial resistance genes, 5 mobile genetic elements, 2 prophages and multiple copies of pathogenicity islands (SPI) were identified in the genome.3. To address this, bacteriophage SF01 was isolated from wastewater near a chicken slaughterhouse against host strain SFD-01. Transmission electron microscopy revealed that the phage had an 85-nm icosahedral head and a 130-nm long contractile tail. The Felixounavirus SF01 exhibited high stability across pH 3-9. Phage lytic activity at a multiplicity of infection of 0.01 restricted the bacterial growth.4. Whole genome analysis (WGS) identified phage SF01 as a Felixounavirus with 88-kb genome composed of 174 CDS, 20 tRNA genes and with no lysogenic markers, resistance genes or virulence factors. The strict lytic potential of phage SF01 makes it a highly viable option for use in the potential biocontrol of the novel strain S. enterica subsp. enterica serotype 42:z4,z23.

Felixounavirus

A rapid and simple clonality assay for bovine leukemia virus-infected cells by amplified fragment length polymorphism (AFLP) analysis.

UNLABELLED: Enzootic bovine leukosis (EBL), although eradicated in some European countries, is still the most common neoplastic disease of cattle, caused by the bovine leukemia virus (BLV). During the progression of EBL, BLV-infected cells clonally expand, and some of which result in tumor onset. The clonality of BLV-infected cells is generally evaluated with NGS or Sanger sequencing. Although these methods clearly distinguish EBL from non-EBL cases, the procedures are complex and not practical for routine veterinary diagnosis. In this study, we developed an amplified fragment length polymorphism (AFLP) analysis for BLV clonality assay (BLV-AFLP). This analysis uses restriction enzyme digestion to amplify the chimeric regions of BLV 3' linear transcribed region (LTR) and host genome through conventional polymerase chain reaction (PCR) and visualizes the results by gel-electrophoresis. The method was established using cattle samples representing different stages of the disease: BLV-uninfected, non-EBL, and EBL cattle. Non-EBL cattle showed smeared bands, indicating polyclonal proliferation, while EBL cattle showed distinct bands, indicating clonal expansion. The results of BLV-AFLP correlated well with those of previously reported methods, suggesting its efficacy in detecting clonal proliferation. The validation using blood samples of non-EBL cattle and tumor samples of EBL cattle confirmed that BLV-AFLP could effectively identify clonal proliferation in EBL samples. Moreover, the emergence of dominant clones in the tumor at later stages was successfully detected before EBL onset in some cattle, highlighting its sensitivity and potential for early detection. Overall, BLV-AFLP is suitable for practical use in the field, improving BLV management strategies and minimizing economic losses. IMPORTANCE: Enzootic bovine leukosis (EBL) is routinely diagnosed based on external manifestations at the farm, such as the presence of tumors and/or general lymph node enlargement. However, due to the nonspecific clinical manifestations of EBL, over half of EBL cases are unrecognized at the farm, with most cases being diagnosed during postmortem inspection at the slaughterhouse. Early detection and monitoring of clonal expansion are necessary for managing EBL and reducing economic losses. In this study, we developed BLV-AFLP that represents a significant advancement in the diagnosis of EBL in cattle. This method can rapidly assess the clonal proliferation of BLV-infected cells, crucial for distinguishing between asymptomatic and EBL cattle. Additionally, tracking clonal dynamics offers insights into the disease's progression, potentially providing strategies for avoiding economic losses. Overall, as BLV-AFLP is a simple and rapid test for detecting EBL, it is feasible and efficient for routine veterinary practice.

Leukemia Virus, Bovine

Microbiome and resistome successions in pig carcasses and fresh pork meat throughout slaughtering, processing and shelf-life.

BACKGROUND: Slaughterhouses and meat cutting plants represent potential hotspots for the spread and transfer of spoilage and pathogenic, including antimicrobial resistant, bacteria to meat and meat products. Here, we characterise the progression of the microbiome and resistome of two pork cuts (loin and sirloin) at different stages of processing, from the slaughter line to the end of shelf-life. To this end, we analysed samples from facility surfaces, carcasses, and meat cuts using whole metagenome sequencing. RESULTS: The taxonomic and antimicrobial resistance gene (ARG) profiles of carcasses and meat cuts were significantly influenced by the point of sampling and the processing room. The facility surfaces were found to be the main source of some abundant genera, such as Anoxybacillus, Acinetobacter, Pseudomonas, and Brochothrix, in carcasses and meat cuts. A total of 1,291 metagenome-assembled genomes were reconstructed, corresponding to the most prevalent species identified in the taxonomic analysis at the read level. A reduction in bacterial and ARGs richness and diversity was observed for carcasses and meat cuts along the production chain, which suggests that processing procedures are effective in reducing bacterial and ARGs loads. Nonetheless, an increase in the ARGs load was observed at two sampling points: the carcass after evisceration and the sirloin at the end of its shelf-life (in this case linked to the increase of a single gene, tet(L)). The ARGs most frequently detected were those associated with resistance to tetracyclines, aminoglycosides, and lincosamides. Acinetobacter (in processing environments and carcass/meat samples) and Staphylococcus (in carcasses and meat) were identified as the main genera associated with the ARGs found. CONCLUSIONS: Overall, our results provide the most detailed metagenomics-based perspective on the microbial successions of pig carcasses and fresh meat cuts during slaughtering, processing, and commercialisation. The observations made suggest that selection pressures imposed by processing steps and contact with facility surfaces contribute to shaping the microbiome and resistome of the two pork products throughout their production line and shelf-life. Video Abstract.

Animals

Molecular epidemiological characteristics of H9N2 subtype avian influenza virus in the external environment of western Zhejiang, China, 2014-2025.

OBJECTIVE: To elucidate the epidemiological distribution patterns of avian influenza virus (AIV) in the external environment of western Zhejiang from 2014 to 2025, analyze the molecular epidemiological characteristics of the H9N2 subtype, and assess its public health risks. METHODS: According to the Zhejiang Provincial Surveillance Program for Avian Influenza in Occupationally Exposed Populations and External Environments, real-time RT-PCR was used to detect AIV subtypes in environmental specimens. H9N2-positive samples with cycle threshold values <30 were inoculated into specific pathogen-free (SPF) embryonated chicken eggs for virus isolation, followed by whole-genome sequencing and bioinformatics analysis for phylogenetic and molecular characterization. RESULTS: A total of 7,762 specimens were tested from 2014 to 2025, with an overall positivity rate of 34.64% (2,689/7,762) for AIV. Significant differences in positivity rates were observed in seasons, regions, sampling sites, and specimen types (all p&#x202f;<&#x202f;0.001). AIV activity peaked in winter and spring, with the highest rates detected in live poultry markets and chopping board swabs. The H9 was the predominant subtype, with co-circulation of multiple subtypes. All 48 H9N2 subtype isolates belonged to the G57 genotype, with the hemagglutinin (HA) and neuraminidase (NA) genes falling into the Y280-like branch, while the internal genes exhibited a mosaic pattern combining G1-like and F/98-like lineages. Molecular characterization analysis revealed multiple mammalian adaptive mutations, involving alterations in receptor-binding sites (T163N, H191N, T197D, T198V, Q234L, Q235M), antigenic epitopes (D280G, N285S), and glycosylation sites (218NRTF, 313NCSK). NA stalk deletion (62-64 aa), along with multiple mutations in the hemadsorption site (E/K368N, D369S/G, D401G/V, N402D, W403L/R, Q432H). Additionally, multiple key amino acid substitutions were also identified in the internal proteins. CONCLUSION: The external environment in western Zhejiang exhibits a high prevalence of AIVs with pronounced spatiotemporal clustering. H9 was the dominant subtype and co-circulated with multiple subtypes, with live poultry markets and slaughterhouses identified as high-risk settings. The H9N2 subtype AIV has accumulated multiple mammalian adaptive mutations, and exhibits genetic linkages across eastern Chinese provinces. These findings collectively underscore the need for an integrated One Health surveillance and early-warning system to reduce the risk of human infections with avian influenza.

Influenza in Birds