Avian diseases最新文献

{"title":"Application of Enzyme-Linked Lectin Assay for Evaluation of Neuraminidase and Neuraminidase Inhibition Activity of Avian Orthoavulavirus 1 (AOAV-1) and AOAV-1 Antibody.","authors":"Chang-Won Lee, Jessica Gladney","doi":"10.1637/aviandiseases-D-25-00049","DOIUrl":"https://doi.org/10.1637/aviandiseases-D-25-00049","url":null,"abstract":"<p><p>Detection of antibody response to Newcastle disease virus (NDV) or other avian orthoavulaviruses 1 (AOAVs-1) can serve as a useful tool for monitoring infection and response to vaccination. Two commonly used serologic tests for AOAV-1 are the hemagglutinin inhibition (HI) test and ELISA. Enzyme-linked lectin assay (ELLA) is based on the ability of the neuraminidase (NA), which is also part of the hemagglutinin-neuraminidase (HN) protein of AOAV-1, to cleave sialic acid residues from a substrate coated on the solid surface, and the assay is performed similarly to ELISA. The same ELLA can be applied to detect and quantify the neuraminidase inhibition (NI) antibody present in the sample. In this study, we first evaluated ELLA for measuring NA activity of different AOAV-1 strains on fetuin substrate. In contrast to influenza A virus, which shows optimal NA activity in neutral pH, all AOAV-1 strains tested showed higher NA activity under lower pH and the preference of specific pH varied by the strain. We established assay parameters, including the pH and temperature conditions, for optimal NA activity of two AOAV-1 strains and conducted ELLA to evaluate NI antibody (NI-ELLA). NI-ELLA was highly specific with antigen dose of 95% effective concentrations (EC₉₅), and showed less than 10% background nonspecific NI reactivity with all AOAV-1-negative sera collected from different poultry species. NI-ELLA was conducted to determine the endpoint titer of sera collected from birds vaccinated with Newcastle disease vaccine. The NI antibody titer determined by NI-ELLA correlated well with the HI antibody titer against the same antigen used for both tests, while showing a detection limit more than 20 times higher. Our study shows great potential of NI-ELLA as a functional antibody assay like the HI test to evaluate vaccine-induced antibody response against challenge virus, with the added advantages of being more sensitive and having a higher-throughput screening capability than the HI test.</p>","PeriodicalId":516846,"journal":{"name":"Avian diseases","volume":"69 3","pages":"326-333"},"PeriodicalIF":1.3,"publicationDate":"2025-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145152456","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Molecular Characterization of Variant Egyptian Avian Reovirus Isolates with Nucleotide Insertions and Deletions at the σC Coding Gene.","authors":"Hamdi Mohamed Sallam, Mostafa Mohamed Saleh, Sahar Youssef Haggag, Mohamed Ibrahim Algaous","doi":"10.1637/aviandiseases-D-25-00004","DOIUrl":"https://doi.org/10.1637/aviandiseases-D-25-00004","url":null,"abstract":"<p><p>Avian reovirus (ARV) is considered an important pathogen affecting poultry and recently has gained more attention because of its genetic diversity, prevalence, and several disease conditions associated with its infection. In Egypt, ARV-associated diseases are frequently reported despite implementation of ARV vaccination programs. Therefore, continuous screening for new variants is essential to improve related control measures. During this study, samples were collected from three Egyptian governorates for determination of the circulating ARV strains. Phylogenetic analysis based on the amino acid sequences of the σC protein revealed the identification of two genotyping clusters (GCs) of ARV (GC 4.4 and 5.2). Amino acid identity within each cluster was more than 94.9%. Meanwhile, the amino acid identity between the two clusters was less than 37.8%. Low amino acid identity (less than 27.2%) was found among the identified isolates and vaccine strains. Cluster 4-related isolates ReoHS3 and ReoHS6 were clustered together within a distinct clade, sharing not more than 83.1% amino acid identity with the closest strains. In addition, unique nucleotide insertion and deletion were found at the heptad repeat region of the σC coding gene of these two isolates. Despite the nucleotide deletion and insertion and the hypervariability at the heptad repeat region, the same length and the hydrophobicity at position \"a\" (and to some extent position \"d\") were maintained among the identified isolates. These results can clarify the significance of both the length of the heptad repeat region and the hydrophobicity at position \"a\" in the maintenance of the function of this region.</p>","PeriodicalId":516846,"journal":{"name":"Avian diseases","volume":"69 3","pages":"295-300"},"PeriodicalIF":1.3,"publicationDate":"2025-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145152558","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Evaluation of In-Contact Transmission Potential of H5N1 Avian Influenza Virus in House Crows (<i>Corvus splendens</i>).","authors":"Asha Kumari Verma, Manoj Kumar, Harshad V Murugkar, Shanmugasundaram Nagarajan, Chakradhar Tosh, Pushpendra Namdeo, Rupal Singh, Suman Mishra, Senthilkumar Dhanapal, Anubha Pathak, Vijendra Pal Singh, Aniket Sanyal","doi":"10.1637/aviandiseases-D-24-00085","DOIUrl":"https://doi.org/10.1637/aviandiseases-D-24-00085","url":null,"abstract":"<p><p>We evaluated the infection and transmission potential of the highly pathogenic avian influenza (HPAI) H5N1 virus from infected crows (<i>Corvus splendens</i>) to healthy in-contact crows. Six crows were inoculated with 10⁶ EID₅₀ of H5N1 virus (A/crow/India/01CA249/2021), and 24 hr later six in-contact crows were introduced with them. All the birds were observed for signs of illness, and swabs were collected up to 14 days postinfection (dpi). One of the infected birds showed dullness, ruffled feathers, shivering, and reluctance to move at 7 dpi, while the other five infected crows showed no significant clinical signs except ruffled feathers and some signs of mental confusion. All the in-contact crows remained asymptomatic throughout the experiment. Virus could be isolated in swabs of infected birds from 1 to 7 dpi, and viral quantification revealed viral shedding up to 8 dpi. Although virus was not isolated from the swabs collected from in-contact birds, low numbers of viral RNA copies were detected in some samples. Virus was isolated from the brain and trachea of most of the infected birds along with other tissues. Virus was also isolated from different tissues collected from three of the in-contact birds, albeit with low numbers of viral copies. All six infected and five in-contact crows were found to be seroconverted against H5N1 virus when analyzed on 14 dpi. These findings suggest that the H5N1 virus was transmitted to in-contact birds, but the infectious doses were low, resulting in only a limited infection. Our study highlights that H5N1 viruses may be transmitted by direct contact within the house crow population, a feature that might play an important role in the epidemiology of avian influenza.</p>","PeriodicalId":516846,"journal":{"name":"Avian diseases","volume":"69 3","pages":"237-242"},"PeriodicalIF":1.3,"publicationDate":"2025-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145152467","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Pathogenesis of an Avian Reovirus Isolate Displaying Enteric and Arthritic Tropisms.","authors":"Kathryn McCullough, Erich Linnemann, Vanessa Gauthiersloan, Holly S Sellers","doi":"10.1637/aviandiseases-D-25-00007","DOIUrl":"https://doi.org/10.1637/aviandiseases-D-25-00007","url":null,"abstract":"<p><p>Avian reoviruses (ARVs) within genetic cluster (GC) 2 represent a large, heterogenous group of currently circulating ARVs that have been isolated from clinical cases of tenosynovitis and malabsorption. In this study, the pathogenesis of an ARV GC 2 isolate was investigated via quantitative reverse transcriptase PCR (RT-qPCR), <i>in situ</i> hybridization (ISH), and histopathology, following oral or footpad inoculation. RT-qPCR detected ARV within the digital flexor tendon, heart, lung, liver, spleen, kidney, duodenum, cecum, cloacal bursa, and thymus. The highest viral RNA load was observed within the intestinal tract between 36 and 72 hr postinoculation (hpi). ISH demonstrated ARV within villous enterocytes throughout the intestines, follicle-associated epithelial (FAE) cells of the bursa, and the synovial membrane of the tendon. Histopathology within the intestine consisted of rare syncytia with negligible inflammation, whereas marked inflammation was present within the synovial tissues. The identity of infected enterocytes as avian \"M cells\" or infected synovial lining cells as macrophage-like synoviocytes (MLS) could not be histologically determined. However, the susceptibility of these varied cell types to infection with an ARV GC 2 virus demonstrates simultaneous potential enteric and arthritic roles in the pathogenesis of these reoviruses.</p>","PeriodicalId":516846,"journal":{"name":"Avian diseases","volume":"69 3","pages":"275-280"},"PeriodicalIF":1.3,"publicationDate":"2025-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145152634","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Characteristics of <i>Salmonella</i> spp. from Chickens That Died Within One Week of Age in Commercial Farms of Integrated Broiler Operations in South Korea.","authors":"Hye-Ri Jung, Young Ju Lee","doi":"10.1637/aviandiseases-D-24-00038","DOIUrl":"10.1637/aviandiseases-D-24-00038","url":null,"abstract":"<p><p>Nontyphoidal <i>Salmonella</i> spp. potentially lead to economic loss, thereby threatening the poultry industry; moreover, they are major pathogens that can cause human illness. In this study, <i>Salmonella</i> were isolated from the internal organs of chickens that had died within one week of age in 132 commercial farms of five integrated broiler operations. <i>Salmonella</i> were isolated from 35 (26.5%) farms, and the most frequently detected serovar was <i>Salmonella enterica</i> serovar Enteritidis, detected in 19 (14.4%) farms, followed by <i>Salmonella enterica</i> serovars Typhimurium (4 farms, 3.0%), <i>S</i>. Senftenberg (3 farms, 2.3%), <i>S</i>. Agona (2 farms, 1.5%), <i>S</i>. Montevideo (2 farms, 1.5%), <i>S</i>. Infantis (2 farms, 1.5%), <i>S</i>. Thompson (2 farms, 1.5%), and <i>S</i>. Bareilly (1 farm, 0.8%) (<i>P</i> < 0.05). In particular, <i>S</i>. Enteritidis was identified on farms (4.5%-22.2%) of all five operations. The prevalence of resistance to nalidixic acid (97.7%-100%) was significantly higher than that of resistance to other antimicrobials (0.0%-44.4%) in all five operations (<i>P</i> < 0.05), and the prevalence of multidrug resistance showed significant differences among the five integrated operations (<i>P</i> < 0.05). <i>S</i>. Enteritidis was divided into 18 pulsed-field gel electrophoresis pattern types; however, confirming the epidemiological relationship proved challenging. Moreover, 9 (14.5%) among 62 <i>S</i>. Enteritidis isolates harbored 2 kinds of β-lactamase genes, <i>bla</i>_TEM-1 (2 isolates) and <i>bla</i>_CTX-M-55 (7 isolates), and 4 (6.5%) <i>S</i>. Enteritidis isolates harbored 2 kinds of integrase genes: class 1 integron (2 isolates) and class 2 integron (2 isolates). Most of the 20 virulence genes tested were detected in more than 93.5% of <i>S</i>. Enteritidis isolates, but the <i>cbtB</i> and <i>pefA</i> genes were only detected in 2 isolates (3.2%) and 1 isolate (1.6%), respectively. This study indicates that various <i>Salmonella</i> spp., including <i>S</i>. Enteritidis and <i>S</i>. Typhimurium, are persistent in commercial broiler farms via vertical or horizontal transmission.</p>","PeriodicalId":516846,"journal":{"name":"Avian diseases","volume":"69 2","pages":"144-151"},"PeriodicalIF":0.0,"publicationDate":"2025-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144610837","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Induction of Trained Immunity in Broiler Chickens by Combination of <i>in Ovo</i> Delivery of Oligodeoxynucleotides Containing CpG Motifs and Intrapulmonary Delivery of a Live <i>Clostridium perfringens</i> Vaccine at Hatch to Protect Against <i>Escherichia coli</i> Septicemia Later in the Grow-Out Period.","authors":"Iresha Subhasinghe, Hemlata Gautam, Shelly Popowich, Lisanework E Ayalew, Suresh K Tikoo, Susantha Gomis","doi":"10.1637/aviandiseases-D-24-00093","DOIUrl":"10.1637/aviandiseases-D-24-00093","url":null,"abstract":"<p><p>Bacterial infections such as <i>Escherichia coli</i> and necrotic enteritis (NE) caused by <i>Clostridium perfringens</i> (CP) are responsible for significant economic losses in the broiler chicken industry. Our previous studies have involved trying to develop alternatives to antimicrobials and immunoprotective agents to such pathogens. Previously, we demonstrated that delivery of a single dose of oligodeoxynucleotides containing unmethylated cytosine-phosphodiester-guanine motifs (CpG-ODN) can promote antimicrobial immunity against yolk sac infections caused by <i>E. coli</i> and <i>Salmonella</i> by enriching immune compartments and activating immune cells. Recently, we have demonstrated delivery of CpG-ODN twice by the intramuscular (IM) route in neonatal broiler chickens at Days 1 and 4 of age to induce trained immunity and protect against lethal <i>E. coli</i> septicemia later in the grow-out period. The objectives of this study were to explore the ability of CpG-ODN to induce trained immunity in broiler chickens (1) by administering CpG-ODN by the <i>in ovo</i> route and intrapulmonary (IPL) route at hatch and (2) by administering CpG-ODN by the <i>in ovo</i> route and IPL delivery of a CP vaccine at hatch to protect against <i>E. coli</i> infections. Intramuscular (IM) delivery of CpG-ODN twice at Days 1 and 4 of age in neonatal broiler chickens induced trained immunity to protect against NE. Induction of trained immunity in broiler chickens led to a switch in cellular energy metabolism of immune cells from glycolysis to mitochondrial oxidative phosphorylation (OXPHOS) following two administrations of CpG-ODN. We have also demonstrated that delivery of CpG-ODN by the <i>in ovo</i> route followed by delivery of a live CP vaccine by the IPL route at hatch induced trained immunity and significantly (<i>P</i> < 0.0001) protected birds against <i>E. coli</i> septicemia at 27 days of age. Trained immunity was induced in broiler chickens only with administrations of CpG-ODN by the <i>in ovo</i> route followed by the IPL route at hatch or <i>in ovo</i> delivery of CpG-ODN followed by IPL delivery of a live CP vaccine at hatch. These birds were significantly (<i>P</i> < 0.0001) protected against lethal <i>E. coli</i> septicemia and NE later in the production cycle, demonstrating the utility of CpG-ODN for induction of trained immunity and broad-spectrum protection of broiler chickens against common lethal bacterial infections.</p>","PeriodicalId":516846,"journal":{"name":"Avian diseases","volume":"69 2","pages":"183-199"},"PeriodicalIF":0.0,"publicationDate":"2025-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144610841","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Recurring Airsacculitis in Late-Stage Production Leading to High Slaughterhouse Condemnation in a Commercial Turkey Farm.","authors":"Amin Mirzazadeh, Dieter Liebhart, Peter Mitsch, Robert Brackmann, Jan Ontong, Ivana Bilic, Claudia Hess","doi":"10.1637/aviandiseases-D-24-00102","DOIUrl":"10.1637/aviandiseases-D-24-00102","url":null,"abstract":"<p><p>Between May 2021 and June 2024, a series of slaughterhouse condemnations was documented in the male population of a commercial turkey farm in Lower Austria, Austria. The primary reasons for condemnation were severe airsacculitis, often accompanied by ascites and pleural effusion. Across various production cycles, the flocks either remained asymptomatic with lesions only being detected during carcass inspection at the slaughterhouse or showed a slight increase in mortality accompanied by clinical signs such as dyspnea, open-mouth breathing, and head shaking in some birds during the final weeks of the fattening period, at 16-22 weeks of age. Gross examination prior to slaughter typically revealed thoracic air sacs filled with large, firm, yellowish-white plaques, occupying a significant proportion. During the last two occurrences, microbiological and pathological investigations were conducted to identify the causative pathogens of this recurrent condition. Various infectious agents, including <i>Mycoplasma synoviae</i>, <i>Ornithobacterium rhinotracheale</i>, and <i>Aspergillus fumigatus</i>, were identified. The findings revealed the multifactorial nature of the condition, raising concerns about the impact on the health and welfare of turkeys, as well as the economic implications of such condemnations for the turkey industry.</p>","PeriodicalId":516846,"journal":{"name":"Avian diseases","volume":"69 2","pages":"223-229"},"PeriodicalIF":0.0,"publicationDate":"2025-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144610844","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Diagnosis of Inclusion Body Hepatitis in Chickens by Impression Smear Cytopathology.","authors":"Kathryn McCullough, Subhan Ullah, Jenny Nicholds, Maurice Raccoursier, Reece Bowers, Cole Taylor, Jason Sousa, Tiffani Allen, Adrea Mueller Slay, Daniel A Sebastián Pineda, Silvia Carnaccini, Holly S Sellers","doi":"10.1637/aviandiseases-D-24-00080","DOIUrl":"https://doi.org/10.1637/aviandiseases-D-24-00080","url":null,"abstract":"<p><p>Numerous reports and epidemiologic investigations in recent years identify adenoviral infection as an ongoing to increasing, international disease in commercially raised chickens. Impression smear cytopathology was evaluated as a tool for the diagnosis of adenoviral inclusion body hepatitis (IBH). In this study, 92, paired, Romanowsky-stained cytopathologic preparations and hematoxylin-and-eosin-stained histopathologic liver sections were evaluated from 54 chickens with experimentally induced or naturally occurring IBH. Large intranuclear inclusion bodies typical of adenoviruses were visible within hepatocytes on both cytopathology and histopathology. Cytopathologic to histopathologic percent positive agreement and percent negative agreement were 94% and 90%, respectively, with Œ = 0.81 (0.61-1.01, 95% confidence, <i>P</i> < 0.001). A subset of 20 cytopathologic samples evaluated by eight veterinary professionals as consistent or inconsistent with IBH yielded an average of 66% positive agreement and 98% negative agreement to the histopathologic diagnosis, across all observers, with Œ = 0.61 (0.53-0.68, 95% confidence, <i>P</i> < 0.001), resulting in a positive predictive value of 99% and a negative predictive value of 67%. Interobserver agreement was slightly higher (76% positive agreement, 94% negative agreement, Œ = 0.68 [0.65-0.71], 95% confidence, <i>P</i> < 0.001) within the 12 of these samples that originated from natural disease, with stable positive and negative predictive values. A rapid, cost-effective, tentative diagnosis of IBH via impression smear cytopathology at the time of necropsy can streamline further confirmatory laboratory testing and facilitate timely communication in the interim to affected parties, especially in locations with delayed access to a diagnostic laboratory.</p>","PeriodicalId":516846,"journal":{"name":"Avian diseases","volume":"69 2","pages":"206-211"},"PeriodicalIF":0.0,"publicationDate":"2025-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144610839","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Isolation and Characterization of <i>Pasteurella multocida</i> A from an Outbreak in Turkeys in Morocco and Vaccine Preparation and Evaluation.","authors":"Noha Semmate, Zahra Bamouh, Zouhair Elkarhat, Dounia Bkiri, Soufiane Elmejdoub, Ismail Kerbal, Khalid Omari Tadlaoui, Mehdi Elharrak","doi":"10.1637/aviandiseases-D-24-00074","DOIUrl":"10.1637/aviandiseases-D-24-00074","url":null,"abstract":"<p><p><i>Pasteurella multocida</i> is an important pathogen that causes fowl cholera (FC) in turkeys (<i>Meleagris</i>). The aim of this study was to isolate and characterize <i>P. multocida</i> from outbreaks of FC in turkeys for the first time in Morocco, both molecularly and pathologically, and to develop and evaluate an inactivated vaccine based on the isolated strain. Two farms in central Morocco were suspected of having FC. From each of these farms, two <i>P. multocida</i> isolates were characterized. Molecular analysis showed that both strains were identified as genotype A and serovars 3*4. Three oil-based vaccines were prepared using the virulent isolate strain after evaluating its pathogenicity in target species to determine the protective dose. The vaccines were evaluated through challenge tests and serologic responses. According to the results, a dose of 10⁹ colony-forming units showed 100% protection after challenge, and all animals became seropositive. Additionally, two vaccination programs were proposed to evaluate the duration of immunity: a double vaccination schedule <i>vs.</i> a triple vaccination schedule. The results indicated that the triple vaccination induced good protection after challenge and a high level of antibodies.</p>","PeriodicalId":516846,"journal":{"name":"Avian diseases","volume":"69 2","pages":"200-205"},"PeriodicalIF":0.0,"publicationDate":"2025-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144610842","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Use of Deep Amplicon Sequencing Based on the Cytochrome Oxidase I Gene to Quantify the Relative Percentages of <i>Eimeria</i> spp. Oocysts in Poultry Litter.","authors":"Mark C Jenkins, Carolyn Parker, Philip Campos, Kenneth Grimm, Cary Davies, Matthew S Tucker, Carl Heeder, Michael Quist, Peter Thompson","doi":"10.1637/aviandiseases-D-25-00006","DOIUrl":"10.1637/aviandiseases-D-25-00006","url":null,"abstract":"<p><p>The purpose of this study was to evaluate a deep amplicon sequencing approach for estimating the relative abundances of different <i>Eimeria</i> spp. oocysts in litter from commercial broiler farms that may or may not be experiencing necrotic enteritis (NE) infections. Oligonucleotide primers directed to the mitochondrial cytochrome oxidase I (COI) gene, a sequence that is conserved among all chicken <i>Eimeria</i> spp., were first used to PCR amplify <i>Eimeria acervulina</i>, <i>Eimeria maxima</i>, and <i>Eimeria tenella</i> oocyst DNA. COI amplification was applied to samples containing either a single <i>Eimeria</i> species or an equal mixture of <i>E. acervulina</i>, <i>E. maxima</i>, and <i>E. tenella</i> oocysts. Amplicon sequencing and mapping to the relevant COI sequences in the GenBank database confirmed the expected ∼100% mapping to the appropriate <i>Eimeria</i> sp. and in approximately equal percentages (∼33%) for mixtures of equal numbers of <i>Eimeria</i> spp. oocysts. This approach was then applied to DNA derived from <i>Eimeria</i> oocysts obtained at 0, 2, and 4 wk after chick placement (growout) from a total of 20 individual houses on six different commercial broiler farms. Of the seven <i>Eimeria</i> spp. known to infect chickens, only five were consistently found in litter at each collection time point: <i>E. acervulina</i>, <i>E. maxima</i>, <i>Eimeria mitis</i>, <i>Eimeria praecox</i>, and <i>E. tenella</i>. The relative numbers of <i>E. maxima</i> and non-<i>E. maxima</i> (<i>Eamipt</i>) oocysts in all litter samples as estimated by COI deep amplicon sequencing showed a modest correlation with the respective <i>E. maxima</i> or <i>Eamipt</i> oocyst counts (<i>R</i> ∼ 0.30). The results revealed an interesting phenomenon that supports the role of <i>E. mitis</i> in predisposing chickens to NE. In this study, the percentage of <i>E. mitis</i> as estimated by deep amplicon sequencing at 0, 2, and 4 wk growout showed a strong positive correlation with NE incidence (0 wk, <i>R</i> = 0.57; 2 wk, <i>R</i> = 0.52; 4 wk, <i>R</i> = 0.61). This study provides evidence for the usefulness of a deep amplicon sequencing approach to estimating the relative abundances of different <i>Eimeria</i> oocysts infecting chickens because it allows reactions to take place in a single tube, thus avoiding the time-consuming, labor-intensive, species-specific internal transcribed spacer 1 (ITS1) PCR analyses. More importantly, it allows one to explore relationships between NE incidence and the abundance of minor <i>Eimeria</i> species, which would have been missed by oocyst counting or ITS1 PCR because most <i>Eimeria</i> species are not distinguishable by microscopy, and ITS1 PCR is not quantitative.</p>","PeriodicalId":516846,"journal":{"name":"Avian diseases","volume":"69 2","pages":"177-182"},"PeriodicalIF":0.0,"publicationDate":"2025-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144610777","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}