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

Deadline for manuscript submissions: 30 June 2025 | Viewed by 6799

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Prof. Dr. Renfu Yin

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Key Laboratory of Zoonosis Research, Ministry of Education, College of Veterinary Medicine, Jilin University, Xi’an Road 5333, Changchun 130062, China
Interests: poultry diseases; avian viruses; Newcastle disease virus; avian influenza virus; emerging avian pathogens
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Prof. Dr. Aleksandar Dodovski

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Faculty of Veterinary Medicine–Skopje, Ss. Cyril and Methodius University in Skopje, Lazar Pop Trajkov 5-7, 1000 Skopje, Macedonia
Interests: avian viruses and diseases; molecular epidemiology; host-pathogen interaction
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Special Issue Information

Dear Colleagues,

This Special Issue is the continuation of our previous Special Issue, titled "Poultry Pathogens and Poultry Diseases".

Based on the number of animals, poultry represents the largest domestic animal stock in the world, and poultry eggs and meat supply affordable, high-quality protein. Poultry husbandry, especially on a small scale, is efficient and renewable and can provide a ready source of nutrition and income. However, poultry diseases caused by various strains of pathogens, such as avian influenza, Newcastle disease, Salmonellosis, and parasitic and fungal pathogens, can cause significant economic losses and even lead to life-threatening diseases in animals and humans. Therefore, understanding poultry pathogens and effective strategies for preventing and controlling avian diseases are critical to protecting animals and people.

Poultry diseases, being very complex in nature, are a constant threat to poultry health and production. They can have transboundary characteristics, i.e., they can easily spread across borders via different routes (wild birds, trade, fomites) and have a high socio-economic impact, affecting livelihoods in both developing and developed countries. Some pathogens are zoonotic and, therefore, have pandemic-causing potential. Because of their importance, major poultry diseases are listed by the World Organization for Animal Health. The detection of these diseases in a country, region, or continent will require the implementation of compulsory control measures, which highly affect the poultry industry. Due to high mortality and decreases in production (eggs and meat), they cause huge economic losses for poultry producers, thus impeding the trade of and market for foods of animal origin. To alleviate the detrimental effects, highly focused research is needed.

Prof. Dr. Renfu Yin
Prof. Dr. Aleksandar Dodovski
Guest Editors

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 100 words) can be sent to the Editorial Office for announcement on this website.

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Keywords

poultry pathogens
poultry diseases
avian viruses and diseases

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Related Special Issue

Poultry Pathogens and Poultry Diseases in Microorganisms (11 articles)

Published Papers (7 papers)

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Research

20 pages, 3689 KiB

Open AccessArticle

Molecular Characterization, Antibiotic Resistance, and Biofilm Formation of Escherichia coli Isolated from Commercial Broilers from Four Chinese Provinces

by Saqib Nawaz, Muhammad Shoaib, Cuiqin Huang, Wei Jiang, Yinli Bao, Xiuyi Wu, Lianhua Nie, Wenyan Fan, Zhihao Wang, Zhaoguo Chen, Huifang Yin and Xiangan Han

Microorganisms 2025, 13(5), 1017; https://doi.org/10.3390/microorganisms13051017 - 28 Apr 2025

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Abstract

Escherichia coli (E. coli) represents a significant etiological agent of colibacillosis in poultry, resulting in considerable economic losses for the global poultry sector. The present study aimed to determine molecular characterization, antibiotic resistance, and biofilm formation of E. coli strains isolated from diseased broilers from four provinces of China. A total of 200 tissue samples were collected from the intestine, liver, crop, heart, and spleen and processed for microbiological examination. Molecular detection of E. coli strains, virulence genes, and serotypes was performed using polymerase chain reaction (PCR). Antibiotic susceptibility testing and biofilm formation were assessed using disk diffusion and 96-well microtiter plate assays. The study retrieved 68% (136/200) of E. coli strains from collected samples. Most of the E. coli strains were resistant to enrofloxacin (56%), followed by cefepime (54%), amoxicillin/clavulanate (52%), streptomycin (50%), ampicillin (48%), clindamycin (47%), kanamycin (41%), polymyxin B (37%), tetracycline (35%), sulfamethoxazole/trimethoprim (33%), ceftazidime (31%), meropenem (4.7%), and florfenicol (2.9%). Similarly, the E. coli strains tested positive for at least one virulence gene and specific serotypes. Among these, O145 was the most prevalent serotype, identified in 22 isolates (16.2%), followed by O8 (12.5%), O102 (11.8%), and O9 (11.0%). The tsh gene (10.2%) was the most prevalent virulence gene. This study found that 47.1% of E. coli strains were biofilm-producing, with 62.5% exhibiting weak biofilm production, 29.7% mild biofilm production, and 7.8% strong biofilm production. Similarly, 24.2% of the E. coli strains were avian pathogenic E. coli strains due to the presence of five or more virulence genes, specifically tsh, ompA, fimC, iss, fyuA, and astA, in a single strain by multiplex PCR. The present study recommends continuous surveillance and effective control measures to reduce the burden of avian pathogenic E. coli-related infections in poultry. Full article

(This article belongs to the Special Issue Poultry Pathogens and Poultry Diseases, 2nd Edition)

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17 pages, 4462 KiB

Open AccessArticle

Molecular Epidemiology and Antibiotic Resistance Associated with Avian Pathogenic Escherichia coli in Shanxi Province, China, from 2021 to 2023

by Fangfang Li, Mengya Li, Lianhua Nie, Jiakun Zuo, Wenyan Fan, Liyan Lian, Jiangang Hu, Shuming Chen, Wei Jiang, Xiangan Han and Haidong Wang

Microorganisms 2025, 13(3), 541; https://doi.org/10.3390/microorganisms13030541 - 27 Feb 2025

Viewed by 398

Abstract

Avian Pathogenic Escherichia coli (APEC) constitutes a major etiological agent of avian colibacillosis, which significantly hinders the development of the poultry industry. Conducting molecular epidemiological studies of APEC plays a crucial role in its prevention and control. This study aims to elucidate the molecular epidemiological characteristics of Avian Pathogenic Escherichia coli in Shanxi Province. In this study, 135 APEC strains were isolated and identified from 150 liver samples of diseased and deceased chickens exhibiting clinical symptoms, which were collected from farms in Shanxi Province between 2021 and 2023. The isolates were then analyzed for phylogenetic clustering, drug resistance, resistance genes, virulence genes, and biofilm formation capabilities. The results revealed that the proportions of the A, B1, B2, and D evolutionary subgroups were 26.67%, 32.59%, 17.78%, and 15.56%, respectively. The drug resistance testing results indicated that 92% of the isolates exhibited resistance to cotrimoxazole, kanamycin, chloramphenicol, amoxicillin, tetracycline, and other antibiotics. In contrast, 95% of the strains were sensitive to ofloxacin, amikacin, and ceftazidime. The most prevalent resistance genes included tetracycline-related (tetA) at 88.15%, followed by beta-lactam-related (bla-TEM) at 85.19%, and peptide-related (mcr1) at 12.59%. The virulence gene analysis revealed that ibeB, ompA, iucD, and mat were present in more than 90% of the isolates. The results revealed that 110 strains were biofilm-positive, corresponding to a detection rate of 81.48%. No significant correlation was found between the drug resistance genes, virulence genes, and the drug resistance phenotype. A moderate negative correlation was observed between the adhesion-related gene tsh and biofilm formation ability (r = −0.38). This study provides valuable insights into the prevention and control of avian colibacillosis in Shanxi Province. Full article

(This article belongs to the Special Issue Poultry Pathogens and Poultry Diseases, 2nd Edition)

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14 pages, 758 KiB

Open AccessArticle

Infectious Bronchitis Virus (IBV) in Vaccinated and Non-Vaccinated Broilers in Brazil: Surveillance and Persistence of Vaccine Viruses

by Gleidson Biasi Carvalho Salles, Giulia Von Tönnemann Pilati, Beatriz Pereira Savi, Mariane Dahmer, Eduardo Correa Muniz, Josias Rodrigo Vogt, Antonio José de Lima Neto and Gislaine Fongaro

Microorganisms 2025, 13(3), 521; https://doi.org/10.3390/microorganisms13030521 - 27 Feb 2025

Viewed by 705

Abstract

Infectious bronchitis virus (IBV) poses a significant threat to poultry worldwide, necessitating robust surveillance and vaccination strategies. This study aimed to conduct IBV surveillance in Brazil, assess potential vaccine viral escapes, and evaluate vaccine persistence in vaccinated broilers. A total of 1000 tracheal swabs from 100 flocks across six states were analyzed using RT-PCR. The results showed that 91% of the flocks tested positive for IBV. The detected strains included GI-1, GI-11, and GI-23. Notably, 90% of batches received vaccines containing either GI-1 or GI-11 lineages. The study revealed vaccine persistence in 67 samples between days 16 and 32 post-vaccination. In contrast, unvaccinated batches had a high prevalence of IBV GI-11 strains (70%). These findings highlight widespread IBV circulation in Brazil with persistent viral presence in vaccinated birds and wild viruses in unvaccinated ones. Collectively, the data reveal a widespread presence of IBV in Brazil, characterized by prolonged viral persistence in vaccinated animals and the occurrence of wild viruses in both unvaccinated birds and those vaccinated against specific strains. It can be concluded from this study that there was a widespread occurrence of IBV in Brazil, providing long viral persistence in vaccinated animals, as well as the occurrence of wild virus in unvaccinated birds or birds vaccinated against individual strains. Full article

(This article belongs to the Special Issue Poultry Pathogens and Poultry Diseases, 2nd Edition)

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16 pages, 2259 KiB

Open AccessArticle

Comparative Genomic Analysis of Campylobacter Plasmids Identified in Food Isolates

by Yiping He, Gretchen Elizabeth Dykes, Siddhartha Kanrar, Yanhong Liu, Nereus W. Gunther IV, Katrina L. Counihan, Joe Lee and Joseph A. Capobianco

Microorganisms 2025, 13(1), 206; https://doi.org/10.3390/microorganisms13010206 - 18 Jan 2025

Cited by 1 | Viewed by 1114

Abstract

Campylobacter is one of the leading bacterial causes of gastroenteritis worldwide. It frequently contaminates poultry and other raw meat products, which are the primary sources of Campylobacter infections in humans. Plasmids, known as important mobile genetic elements, often carry genes for antibiotic resistance, virulence, and self-mobilization. They serve as the main vectors for transferring genetic material and spreading resistance and virulence among bacteria. In this study, we identified 34 new plasmids from 43 C. jejuni and C. coli strains isolated from retail meat using long-read and short-read genome sequencing. Pangenomic analysis of the plasmid assemblies and reference plasmids from GenBank revealed five distinct groups, namely, pTet, pVir, mega plasmids (>80 kb), mid plasmids (~30 kb), and small plasmids (<6 kb). Pangenomic analysis identified the core and accessory genes in each group, indicating a high degree of genetic similarity within groups and substantial diversity between the groups. The pTet plasmids were linked to tetracycline resistance phenotypes in host strains. The mega plasmids carry multiple genes (e.g., aph(3’)-III, type IV and VI secretion systems, and type II toxin–antitoxin systems) important for plasmid mobilization, virulence, antibiotic resistance, and the persistence of Campylobacter. Together, the identification and comprehensive genetic characterization of new plasmids from Campylobacter food isolates contributes to understanding the mechanisms of gene transfer, particularly the spread of genetic determinants of virulence and antibiotic resistance in this important pathogen. Full article

(This article belongs to the Special Issue Poultry Pathogens and Poultry Diseases, 2nd Edition)

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13 pages, 2098 KiB

Open AccessArticle

Immunogenicity of Type IV Pilin Proteins from Clostridium perfringens in Chickens

by Audrey Charlebois, Nicolas Deslauriers, Lila Maduro and Martine Boulianne

Microorganisms 2025, 13(1), 120; https://doi.org/10.3390/microorganisms13010120 - 9 Jan 2025

Viewed by 930

Abstract

Clostridium perfringens, the causative agent of necrotic enteritis in chickens, is controlled by in-feed antibiotics. With increasing pressure to reduce antimicrobial use, the development of alternative preventive tools is needed. Type IV pili proteins have been shown to be immunogenic in many Gram-positive bacteria. The aims of this study were to evaluate the immunogenic potential of pilins (PilA1, PilA2 and PilA3) from C. perfringens in chickens and to verify their ability to protect against necrotic enteritis. Chickens were immunized twice with 50 µg of recombinant proteins and adjuvant, resulting in a good and specific serum antibody response. Next, one-day-old chicks were injected three times with the same vaccines, and then infected with C. perfringens. Mean OD₄₅₀ values ten times higher than the controls were obtained for IgY (p < 0.05) and a significantly lower cecal count of C. perfringens was observed in the birds injected with PilA3. However, no reduction in the severity of intestinal lesions was observed. All three pilin proteins were shown to be highly immunogenic in the chickens. Although immunization with the pilins did not protect the birds against necrotic enteritis in this study, it was interesting to observe that vaccination with the recombinant PilA3 protein reduced C. perfringens cecal colonization. Full article

(This article belongs to the Special Issue Poultry Pathogens and Poultry Diseases, 2nd Edition)

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13 pages, 3744 KiB

Open AccessArticle

Invasion of Chicken Intestinal Cells Is Higher for Enterococcus cecorum Lesion Strains Compared to Cloacal Strains in an Organoid Model

by Lonneke Vervelde, Thijs T. M. Manders, Samira Kammourieh and Jeanine Wiegel

Microorganisms 2025, 13(1), 50; https://doi.org/10.3390/microorganisms13010050 - 31 Dec 2024

Cited by 1 | Viewed by 1562

Abstract

Some strains of Enterococcus cecorum can cause spondylitis and bacterial osteomyelitis. Translocation and bacteremia are pivotal to the pathogenesis and clinical disease. Virulence typing to distinguish extra-intestinal disease of lesion from cloacal strains remains difficult. We investigated if organoids can be applied to differentiate between E. cecorum strains that are more or less virulent. Floating chicken intestinal organoids combine the complex cell system of the gut with an easily accessible apical-out orientation. The organoids were treated with four E. cecorum strains that differ in original isolation, lesion, or cloacal, and bacterial load was determined after 3 and 6 h by quantitative PCR and bacterial plating. Independent of the inoculum dose or time post inoculation, DNA levels of E. cecorum marginally differed between the strains. To determine if this was caused by adherence of bacteria to the epithelial cells, an invasion assay was developed. The organoids were inoculated with the different E. cecorum strains and after 3 or 6 h treated with an antimicrobial mixture, lysed, and quantified by bacterial plate counting. Significantly higher (p < 0.0001) numbers of bacteria isolated from lesions invaded the organoids compared to cloacal strains in a dose-dependent manner. Higher numbers of bacteria isolated from lesions invaded the organoids compared to cloacal strains in a dose-dependent manner. This study is a major step in the development of a model to study the interaction between E. cecorum and the chicken host and a model to test novel intervention strategies to prevent translocation of bacteria. Full article

(This article belongs to the Special Issue Poultry Pathogens and Poultry Diseases, 2nd Edition)

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10 pages, 677 KiB

Open AccessArticle

Antimicrobial Resistance of Enterococcus Isolates from Poultry Farms in the Republic of Serbia (Autonomous Province of Vojvodina)

by Maja Velhner, Bojana Prunić, Nevenka Aleksić, Dalibor Todorović, Slobodan Knežević and Dragana Ljubojević Pelić

Microorganisms 2024, 12(7), 1483; https://doi.org/10.3390/microorganisms12071483 - 20 Jul 2024

Cited by 2 | Viewed by 1633

Abstract

Enterococcus species are significant intestinal commensals of animals, including poultry. However, they have emerged as important opportunistic infective agents in both veterinary and human medicine as well as major nosocomial pathogens, owing to their increasing antimicrobial resistance. This research aimed to investigate the prevalence and antimicrobial resistance patterns of Enterococcus spp. isolated from poultry farms in the north of Serbia. A total of 40 samples of overshoes or feces were collected from 40 poultry farms and analyzed for the presence of Enterococcus spp. using PCR or MALDI-TOF mass spectrometry for their identification. The number of isolates was 40 and included 11 isolates from laying hens, 2 isolates from turkeys, 3 from broiler breeders, and 24 from broilers. The Kirby–Bauer disk diffusion method was used to test for antibiotic susceptibility in accordance with the Clinical and Laboratory Standards Institute and EUCAST guidelines. The results showed that Enterococcus faecalis was isolated from 37.5% farms, and E. faecium from 42.5%. E. hirae was identified in 15% of poultry establishments, and E. durans and E. thialandicus on 2.5%. Notably, resistance to erythromycin, streptomycin, fluoroquinolones, and tetracyclines among the frequently used antibiotics was found. Furthermore, 35% of the isolates had multidrug resistance (MDR). In order to prevent the spread of antibiotic resistance in chicken farming and protect the health of the public and animals alike, our findings highlight the critical need for improved surveillance and control measures. To effectively establish a containment strategy for Enterococcus spp. isolated from poultry farms, more research into the processes behind their antibiotic resistance is required. Full article

(This article belongs to the Special Issue Poultry Pathogens and Poultry Diseases, 2nd Edition)

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