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Microorganisms
Special Issues
Avian Pathogens: Importance in Animal Health and Zoonotic Risks
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Avian Pathogens: Importance in Animal Health and Zoonotic Risks

A special issue of Microorganisms (ISSN 2076-2607). This special issue belongs to the section "Veterinary Microbiology".

Deadline for manuscript submissions: closed (28 February 2026) | Viewed by 4000

Special Issue Editors

Prof. Dr. Victor M. Petrone-Garcia

E-Mail
Guest Editor
Faculty of Higher Studies Cuautitlan, National Autonomous University of Mexico, Cuautitlán Izcalli, Mexico
Interests: avian; poultry; animal pathology; virology; mycoplasma; Eimeria; avian immunology; coccidiosis
Dr. Inkar Castellanos-Huerta

E-Mail Website
Guest Editor Assistant
Department of Poultry Science, University of Arkansas, Fayetteville, AR, USA
Interests: poultry; evaluation; integrity

Special Issue Information

Dear Colleagues,

Diseases caused by avian pathogens currently pose a significant threat to animal health, food security, and public health, particularly concerning zoonotic diseases. Among the high-risk pathogens are Salmonella spp., Escherichia coli, Mycoplasma spp., Clostridium perfringens, and other emerging agents, such as Enterococcus cecorum, avian influenza, and Histomonas meleagridis, which impact both the poultry industry and wild populations. An understanding of concepts such as evolutionary dynamics, genetic variability, and antimicrobial resistance—along with the necessity to enhance diagnosis, surveillance, and control—underscores the importance of expanding research and promoting a multidisciplinary approach. This encompasses the development of novel diagnostic tools, vaccines, biosecurity strategies, and microbiome studies to achieve these objectives.

The purpose of this edition is to compile a collection of articles based on research that reflects the most recent scientific advancements concerning the topic of “avian pathogens.” As a guest editor, I am honored to invite you to submit original research articles, reviews, brief communications, and case reports which address the following topics: genetic and evolutionary variation of avian pathogens; field outbreaks and risk assessment; antimicrobial resistance; the microbiome and its influence on avian health; molecular diagnosis; vaccination strategies; therapeutic options; and epidemiological investigations and field-level control measures.

We look forward your contributions, with the aim of assembling a valuable resource that will serve as a reference to augment scientific understanding and enhance strategies for controlling pathogenic agents within poultry farming.

Prof. Dr. Victor M. Petrone-Garcia
Guest Editor

Dr. Inkar Castellanos-Huerta
Guest Editor Assistant

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 250 words) can be sent to the Editorial Office for assessment.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Microorganisms is an international peer-reviewed open access monthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2700 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • avian pathogens
  • zoonosis
  • antimicrobial resistance
  • microbiome
  • molecular diagnosis

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Published Papers (4 papers)

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Research

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17 pages, 810 KB  
Article
Phenotypic and Molecular Characterization of ESBL/pAmpC-Associated Resistance in Poultry- and Hatchery-Derived Escherichia coli in Bosnia and Herzegovina
by Amira Koro-Spahić, Adis Softić, Emina Rešidbegović, Šejla Goletić Imamović, Naida Kapo, Aida Kavazović, Ilma Terzić, Dinaida Tahirović, Aida Kustura and Teufik Goletić
Microorganisms 2026, 14(2), 507; https://doi.org/10.3390/microorganisms14020507 - 21 Feb 2026
Viewed by 243
Abstract
Antimicrobial resistance (AMR) in poultry-associated Escherichia coli (E. coli) is a persistent One Health concern, particularly when ESBL/pAmpC determinants co-occur with resistance to multiple antimicrobial classes. Between March and October 2024, we investigated commensal E. coli from three interconnected compartments of [...] Read more.
Antimicrobial resistance (AMR) in poultry-associated Escherichia coli (E. coli) is a persistent One Health concern, particularly when ESBL/pAmpC determinants co-occur with resistance to multiple antimicrobial classes. Between March and October 2024, we investigated commensal E. coli from three interconnected compartments of the poultry production chain in Bosnia and Herzegovina (parent-breeder flocks, commercial broiler farms, hatchery-associated material). A total of 333 samples were examined, and 99 E. coli isolates were recovered (29.7%). Phenotypic characterization included ESBL confirmation, disk diffusion susceptibility testing, and EUVSEC broth microdilution. Targeted real-time PCR assays were used to screen key ESBL/pAmpC-associated genes and selected carbapenemase and plasmid-mediated colistin resistance targets within the targeted panel. ESBL phenotypes were detected in 52/99 isolates (52.5%), and multidrug resistance was highly prevalent across compartments (93/99; 93.9%). ESBL/pAmpC-associated genes were detected in 91/99 isolates (91.9%), with blaTEM predominating. Gene pattern analysis indicated that blaTEM occurred most frequently as a single determinant and as part of the predominant multi-gene combinations, most notably blaTEM + blaCMY and blaTEM + blaCTX-M, while blaSHV was sporadic. Carbapenemase genes (blaKPC, blaNDM, blaGES, blaOXA-48) and mcr-1 to mcr-9 were not detected. Overall, our findings indicate a substantial ESBL/MDR burden throughout the poultry production chain, supporting the need for strengthening antimicrobial stewardship and biosecurity measures across both farms and hatcheries. Full article
(This article belongs to the Special Issue Avian Pathogens: Importance in Animal Health and Zoonotic Risks)
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22 pages, 2587 KB  
Article
Comparison of Gut Microbiome Profile of Chickens Infected with Three Eimeria Species Reveals New Insights on Pathogenicity of Avian Coccidia
by Nianyu Xue, Dandan Liu, Qianqian Feng, Yu Zhu, Cheng Cheng, Feiyan Wang, Shijie Su, Jinjun Xu and Jianping Tao
Microorganisms 2025, 13(12), 2752; https://doi.org/10.3390/microorganisms13122752 - 3 Dec 2025
Cited by 1 | Viewed by 1067
Abstract
Avian coccidiosis is an intestinal disease caused by Eimeria spp. infection. A deeper understanding of the interaction between host gut microbiota and the Eimeria parasite is crucial for developing alternative therapies to control avian coccidiosis. Here, we used full-length sequencing of 16S ribosomal [...] Read more.
Avian coccidiosis is an intestinal disease caused by Eimeria spp. infection. A deeper understanding of the interaction between host gut microbiota and the Eimeria parasite is crucial for developing alternative therapies to control avian coccidiosis. Here, we used full-length sequencing of 16S ribosomal RNA amplicons to compare changes in the gut microbiota of chickens infected with Eimeria tenella, Eimeria maxima, and Eimeria necatrix, aiming to identify both species-specific and common alterations in gut microbiota at 4 and 10 days post-infection. The result revealed that infection with all three Eimeria species led to a decrease in the abundance of the microbial genera Limosilactobacillus, Streptococcus, Alistipes, Lactobacillus and Phocaeicola, while the abundance of Bacteroides, Escherichia and Ligilactobacillus increased. Escherichia and Enterococcus were most abundant in the jejunum of the E. necatrix-infected group and in the cecum of the E. tenella-infected group, whereas Megamonas abundance was highest in the E. maxima-infected group. LEfSe analysis showed that infection with all three Eimeria species significantly reduced the abundance of 13 bacterial species, including Acetilactobacillus jinshanensis, Bacteroides ndongoniae, Barnesiella viscericola, Christensenella minuta, Enterocloster clostridioformis, Gemella haemolysans_A, Granulicatella adiacens, Lawsonibacter sp000177015, Limosilactobacillus reuteri, Limosilactobacillus reuteri_D, Limosilactobacillus vaginalis_A, Limosilactobacillus caviae, Limosilactobacillus vaginalis. Infection with E. tenella significantly increased the abundance of five bacterial species, including Bacteroides fragilis, Enterococcus cecorum, Helicobacter pylori, Methylovirgula ligni, and Phocaeicola sp900066445. Infection with E. maxima significantly increased the abundance of seven bacterial species, including Clostridioides difficile, Faecalibacterium prausnitzii, Mediterraneibacter torques, Muribaculum intestinale, Mediterraneibacter massiliensis, Phascolarctobacterium faecium, and Phocaeicola plebeius. Infection with E. necatrix significantly increased the abundance of seven bacterial species, including Alistipes sp900290115, Anaerotignum faecicola, Bacteroides fragilis_A, Escherichia coli, Harryflintia acetispora, Pseudoclostridium thermosuccinogenes, and Tidjanibacter inops_A. The results showed that Eimeria infection causes significant species- and time-dependent changes in the gut microbiota of chickens. These findings enhance our understanding of coccidiosis pathogenesis and offer potential targets for developing probiotics. Full article
(This article belongs to the Special Issue Avian Pathogens: Importance in Animal Health and Zoonotic Risks)
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Review

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19 pages, 1937 KB  
Review
Advances in Infectious Bursal Disease Virus Vaccines—A Review
by Weiwei Wang, Jiafeng Wu, Nansong Jiang, Qizhang Liang, Rongchang Liu, Qiuling Fu, Guanghua Fu, Tianchao Wei, Chunhe Wan, Longfei Cheng, Yu Huang, Xiumiao He, Ping Wei and Hongmei Chen
Microorganisms 2025, 13(12), 2801; https://doi.org/10.3390/microorganisms13122801 - 9 Dec 2025
Viewed by 1615
Abstract
Infectious Bursal Disease (IBD) is an immunosuppressive viral disease caused by the Infectious Bursal Disease Virus (IBDV). It primarily affects young chickens, targeting the bursa of Fabricius, and poses significant economic threats to the poultry industry. To date, in addition to strict biosecurity [...] Read more.
Infectious Bursal Disease (IBD) is an immunosuppressive viral disease caused by the Infectious Bursal Disease Virus (IBDV). It primarily affects young chickens, targeting the bursa of Fabricius, and poses significant economic threats to the poultry industry. To date, in addition to strict biosecurity measures, large-scale immunization is the optimal strategy and effective method to prevent and control IBDV infection. The emergence of new variant strains has made it more urgent to develop new vaccination strategies against IBD. Over the past few decades, many high-quality vaccines have been available on the market for the control of IBD, which can provide solid protection against the infections and diseases caused by classic IBDV to very virulent IBDV that had been continuously evolving and were endemic worldwide. However, viruses are not static. As they continue to circulate and evolve in the fields, novel antigenic variant viruses have been emerged in the last few years, and vaccines need to keep up with their pace. Collectively, this review summarizes the strategic evolution of IBDV vaccines from traditional methods to cutting-edge molecular platforms, providing promising strategies for developing the next-generation vaccines with higher safety, efficacy, and the ability to keep pace with the antigenic drift in IBDV. Full article
(This article belongs to the Special Issue Avian Pathogens: Importance in Animal Health and Zoonotic Risks)
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Other

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9 pages, 8844 KB  
Brief Report
Ducklings Were Susceptible to Swine Acute Diarrhea Syndrome Coronavirus Under Experimental Conditions
by Teng Zhang, Longfa Li, Jiayi Wang, Jiale Yao, Guoqing Xu, Chaoliang Leng, Yong Wang and Lunguang Yao
Microorganisms 2025, 13(9), 2122; https://doi.org/10.3390/microorganisms13092122 - 11 Sep 2025
Viewed by 719
Abstract
Swine acute diarrhea syndrome coronavirus (SADS-CoV), similar to other coronaviruses, exhibits extensive host tropism and has caused huge losses to the pig industry since its first outbreak in 2017. However, the susceptibility of SADS-CoV in waterfowl remains unclear. In the present study, 10-day-old [...] Read more.
Swine acute diarrhea syndrome coronavirus (SADS-CoV), similar to other coronaviruses, exhibits extensive host tropism and has caused huge losses to the pig industry since its first outbreak in 2017. However, the susceptibility of SADS-CoV in waterfowl remains unclear. In the present study, 10-day-old ducklings were orally administered 5.95 log10 TCID50 (the tissue culture infective dose 50%) of SADS-CoV, with a medium serving as a control treatment, to assess ducklings’ susceptibility. Results indicated that the ducklings exhibited mild diarrhea symptoms, experienced slow weight gain, and one duckling died seven days after inoculation. Histopathological examination revealed that the viral infection caused pathological damage to the spleen, intestine, and lungs. Tissue immunofluorescence demonstrated viral replication in the spleen, lungs, and intestine. This study provides the first evidence that SADS-CoV can infect ducklings under laboratory conditions. Given that waterfowl may serve as significant reservoirs for various viruses, this finding raises considerable concerns. Full article
(This article belongs to the Special Issue Avian Pathogens: Importance in Animal Health and Zoonotic Risks)
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