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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: closed (31 January 2022) | Viewed by 29470

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Special Issue Editor

Dr. Kirill Sharshov

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Guest Editor

Research Institute of Experimental and Clinical Medicine FRC FTM, Novosibirsk, Russia
Interests: avian influenza virus; zoonotic diseases; virus ecology; influenza; avulavirus; molecular epidemiology
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Over the past ten years, humanity has faced new challenges in the fields of human and animal health, including emerging viral infections. The widespread occurrence of emerging and re-emerging pathogens (e.g., highly pathogenic avian influenza virus (HPAIV), the new COVID-2019 of zoonotic nature, coronaviruses that cause severe acute respiratory syndrome (SARS), and Middle East respiratory syndrome (MERS)) present a serious threat to humans. Avian pathogens cause devastating economic losses in poultry industries worldwide. Poultry is one of the main sources of protein in Asia. For instance, in China alone, with a population of more than 1.3 billion people, poultry meat consumption increased to 19.6 kg/year per person (FAO). According to official estimates, this is over 25 million tons per year, or more than 12.7 billion birds. Therefore, poultry farming in Southeast Asia is considered one of the main “vessels” where avian pathogens can evolve. With migrations of wild birds, spread to other regions is possible, as we have seen worldwide with the H5N8 influenza virus. In addition, avian pathogens can cause devastating epizootics among wild birds and threaten the planet’s bioresources. The importance of wild birds as potential vectors of disease has received recent renewed interest, especially in the frame of the global virome/microbiome concept. Understanding the spread of bacterial and viral pathogens in wild birds may serve as a useful model for examining the spread of other disease organisms, both amongst birds, and from birds to other taxa.

This Special Issue aims to summarize recent advances, and to attract new research articles that address actual pathogens of poultry and wild birds. It also aims to compare the epidemiological situation across avian pathogens or countries.

Dr. Kirill Sharshov
Guest Editor

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.

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 diseases
Bacterial and viral pathogens
Wild birds
Poultry
Molecular epidemiology
Avian virome
Avian microbiome

Published Papers (11 papers)

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Editorial

Jump to: Research, Review, Other

5 pages, 193 KiB

Open AccessEditorial

Avian Pathogens: Editorial and the Perspectives of Research

by Kirill Sharshov

Microorganisms 2022, 10(3), 543; https://doi.org/10.3390/microorganisms10030543 - 28 Feb 2022

Viewed by 1821

Abstract

In the last ten years, humanity has faced new challenges in the field of human and animal health, including emerging viral infections [...] Full article

(This article belongs to the Special Issue Avian Pathogens)

Research

Jump to: Editorial, Review, Other

11 pages, 1157 KiB

Open AccessArticle

Genomic Analysis of Escherichia coli Longitudinally Isolated from Broiler Breeder Flocks after the Application of an Autogenous Vaccine

by Liča Lozica, Kasper Rømer Villumsen, Ganwu Li, Xiao Hu, Maja Maurić Maljković and Željko Gottstein

Microorganisms 2022, 10(2), 377; https://doi.org/10.3390/microorganisms10020377 - 6 Feb 2022

Cited by 7 | Viewed by 1983

Abstract

Escherichia coli is the main bacterial cause of major economic losses and animal welfare issues in poultry production. In this study, we investigate the effect of an autogenous vaccine on E. coli strains longitudinally isolated from broiler breeder flocks on two farms. In total, 115 E. coli isolates were sequenced using Illumina technologies, and compared based on a single-nucleotide polymorphism (SNP) analysis of the core-genome and antimicrobial resistance (AMR) genes they carried. The results showed that SNP-based phylogeny corresponds to a previous multilocus-sequence typing (MLST)-based phylogeny. Highly virulent sequence types (STs), including ST117-F, ST95-B2, ST131-B2 and ST390-B2, showed a higher level of homogeneity. On the other hand, less frequent STs, such as ST1485, ST3232, ST7013 and ST8573, were phylogenetically more distant and carried a higher number of antimicrobial resistance genes in most cases. In total, 25 antimicrobial genes were detected, of which the most prevalent were mdf(A) (100%), sitABCD (71.3%) and tet(A) (13.91%). The frequency of AMR genes showed a decreasing trend over time in both farms. The highest prevalence was detected in strains belonging to the B1 phylogenetic group, confirming the previous notion that commensal strains act as reservoirs and carry more resistance genes than pathogenic strains that are mostly associated with virulence genes. Full article

(This article belongs to the Special Issue Avian Pathogens)

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15 pages, 1032 KiB

Open AccessArticle

Development and Validation of a New TaqMan Real-Time PCR for the Detection of Ornithobacterium rhinotracheale

by Amro Hashish, Avanti Sinha, Yuko Sato, Nubia R. Macedo and Mohamed El-Gazzar

Microorganisms 2022, 10(2), 341; https://doi.org/10.3390/microorganisms10020341 - 1 Feb 2022

Cited by 9 | Viewed by 2981 | Correction

Abstract

Ornithobacterium rhinotracheale (ORT) has been associated with poultry respiratory disease worldwide. The organism is fastidious and isolation is challenging. One TaqMan real-time PCR (qPCR) assay has been developed for the detection of ORT. However, during validating the ORT qPCR, the assay performance was suboptimal. During the in silico evaluation, deviations from the basic parameters for primers and probes designs (e.g., presence of stable undesirable primer-dimers) were observed. The suboptimal design led to low efficiency and low sensitivity of the assay. Initially, modification on the probe was carried out to improve the performance of the assay. However, the assay’s performance (efficiency and sensitivity) was still suboptimal. In this manuscript, we describe the development of a new qPCR assay and the comparison of its performance with the currently available assay. A highly efficient, sensitive, and specific qPCR assay was developed with approximately 1000-folds reduction in the limit of detection (from 3 × 10⁶ plasmid DNA copies/mL to 1 × 10³ plasmid DNA copies/mL). Additionally, the efficiency of the new assay (E = 98.70%) was significantly better than the current assay (E = 73.18%). The newly developed assay is an improved diagnostic tool for the sensitive and efficient diagnosis of ORT from clinical samples. Full article

(This article belongs to the Special Issue Avian Pathogens)

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15 pages, 1882 KiB

Open AccessArticle

Interferon Signaling in Chickens Plays a Crucial Role in Inhibiting Influenza Replication in DF1 Cells

by Daniel S. Layton, Kostlend Mara, Meiling Dai, Luis Fernando Malaver-Ortega, Tamara J. Gough, Kerri Bruce, Kristie A. Jenkins and Andrew G. D. Bean

Microorganisms 2022, 10(1), 133; https://doi.org/10.3390/microorganisms10010133 - 10 Jan 2022

Cited by 7 | Viewed by 2126

Abstract

Influenza A viruses (IAV) pose a constant threat to human and poultry health. Of particular interest are the infections caused by highly pathogenic avian influenza (HPAI) viruses, such as H5N1, which cause significant production issues. In response to influenza infection, cells activate immune mechanisms that lead to increased interferon (IFN) production. To investigate how alterations in the interferon signaling pathway affect the cellular response to infection in the chicken, we used CRISPR/Cas9 to generate a chicken cell line that lacks a functional the type I interferon receptor (IFNAR1). We then assessed viral infections with the WSN strain of influenza. Cells lacking a functional IFNAR1 receptor showed reduced expression of the interferon stimulated genes (ISG) such as Protein Kinase R (PKR) and Myxovirus resistance (Mx) and were more susceptible to viral infection with WSN. We further investigated the role or IFNAR1 on low pathogenicity avian influenza (LPAI) strains (H7N9) and a HPAI strain (H5N1). Intriguingly, Ifnar^−/− cells appeared more resistant than WT cells when infected with HPAI virus, potentially indicating a different interaction between H5N1 and the IFN signaling pathway. Our findings support that ChIFNAR1 is a key component of the chicken IFN signaling pathway and these data add contributions to the field of host-avian pathogen interaction and innate immunity in chickens. Full article

(This article belongs to the Special Issue Avian Pathogens)

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13 pages, 3910 KiB

Open AccessArticle

Survey on the Presence of Viruses of Economic and Zoonotic Importance in Avifauna in Northern Italy

by Tiziana Trogu, Sabrina Canziani, Sara Salvato, Clara Tolini, Guido Grilli, Mario Chiari, Marco Farioli, Loris Alborali, Alessandra Gaffuri, Giovanni Sala, Alessandro Bianchi, Carlo Rosignoli, Paola Prati, Matteo Gradassi, Enrica Sozzi, Davide Lelli, Antonio Lavazza and Ana Moreno

Microorganisms 2021, 9(9), 1957; https://doi.org/10.3390/microorganisms9091957 - 15 Sep 2021

Cited by 3 | Viewed by 2176

Abstract

Wild birds play an important role in the circulation and spread of pathogens that are potentially zoonotic or of high economic impact on zootechnical production. They include, for example, West Nile virus (WNV), Usutu virus (USUV), avian influenza virus (AIV), and Newcastle disease virus (NDV), which, despite having mostly an asymptomatic course in wild birds, have a strong impact on public health and zootechnical production. This study investigated the presence of these viruses in several wild bird species from North Italy during the biennium 2019–2020. Wild birds derived from 76 different species belonging to 20 orders. Out of 679 birds, 27 were positive for WNV (lineage 2) with a prevalence of 4%; all birds were negative for USUV; one gull was positive for H13N6 influenza virus, and 12 samples were positive for NDV with a prevalence of 2%. Despite the low prevalence observed, the analyses performed on these species provide further data, allowing a better understanding of the diffusion and evolution of diseases of both economic and zoonotic importance. Full article

(This article belongs to the Special Issue Avian Pathogens)

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12 pages, 1371 KiB

Open AccessArticle

Genome-Resolved Metagenomic Analyses Reveal the Presence of a Putative Bacterial Endosymbiont in an Avian Nasal Mite (Rhinonyssidae; Mesostigmata)

by Carolina Osuna-Mascaró, Jorge Doña, Kevin P. Johnson and Manuel de Rojas

Microorganisms 2021, 9(8), 1734; https://doi.org/10.3390/microorganisms9081734 - 14 Aug 2021

Cited by 1 | Viewed by 2456

Abstract

Rhinonyssidae (Mesostigmata) is a family of nasal mites only found in birds. All species are hematophagous endoparasites, which may damage the nasal cavities of birds, and also could be potential reservoirs or vectors of other infections. However, the role of members of Rhinonyssidae as disease vectors in wild bird populations remains uninvestigated, with studies of the microbiomes of Rhinonyssidae being almost non-existent. In the nasal mite (Tinaminyssus melloi) from rock doves (Columba livia), a previous study found evidence of a highly abundant putatively endosymbiotic bacteria from Class Alphaproteobacteria. Here, we expanded the sample size of this species (two different hosts- ten nasal mites from two independent samples per host), incorporated contamination controls, and increased sequencing depth in shotgun sequencing and genome-resolved metagenomic analyses. Our goal was to increase the information regarding this mite species and its putative endosymbiont. We obtained a metagenome assembled genome (MAG) that was estimated to be 98.1% complete and containing only 0.9% possible contamination. Moreover, the MAG has characteristics typical of endosymbionts (namely, small genome size an AT bias). Overall, our results support the presence of a potential endosymbiont, which is the first described for avian nasal mites to date, and improve the overall understanding of the microbiota inhabiting these mites. Full article

(This article belongs to the Special Issue Avian Pathogens)

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9 pages, 4142 KiB

Open AccessCommunication

A Genetically Engineered Commercial Chicken Line Is Resistant to Highly Pathogenic Avian Leukosis Virus Subgroup J

by Ahmed Kheimar, Romina Klinger, Luca D. Bertzbach, Hicham Sid, You Yu, Andelé M. Conradie, Benjamin Schade, Brigitte Böhm, Rudolf Preisinger, Venugopal Nair, Benedikt B. Kaufer and Benjamin Schusser

Microorganisms 2021, 9(5), 1066; https://doi.org/10.3390/microorganisms9051066 - 14 May 2021

Cited by 11 | Viewed by 4319

Abstract

Viral diseases remain a major concern for animal health and global food production in modern agriculture. In chickens, avian leukosis virus subgroup J (ALV-J) represents an important pathogen that causes severe economic loss. Until now, no vaccine or antiviral drugs are available against ALV-J and strategies to combat this pathogen in commercial flocks are desperately needed. CRISPR/Cas9 targeted genome editing recently facilitated the generation of genetically modified chickens with a mutation of the chicken ALV-J receptor Na⁺/H⁺ exchanger type 1 (chNHE1). In this study, we provide evidence that this mutation protects a commercial chicken line (NHE1ΔW38) against the virulent ALV-J prototype strain HPRS-103. We demonstrate that replication of HPRS-103 is severely impaired in NHE1ΔW38 birds and that ALV-J-specific antigen is not detected in cloacal swabs at later time points. Consistently, infected NHE1ΔW38 chickens gained more weight compared to their non-transgenic counterparts (NHE1W38). Histopathology revealed that NHE1W38 chickens developed ALV-J typical pathology in various organs, while no pathological lesions were detected in NHE1ΔW38 chickens. Taken together, our data revealed that this mutation can render a commercial chicken line resistant to highly pathogenic ALV-J infection, which could aid in fighting this pathogen and improve animal health in the field. Full article

(This article belongs to the Special Issue Avian Pathogens)

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10 pages, 1379 KiB

Open AccessArticle

Vector-Borne Blood Parasites of the Great-Tailed Grackle (Quiscalus mexicanus) in East-Central Texas, USA

by Andrew J. Golnar, Matthew C. I. Medeiros, Katlyn Rosenbaum, Justin Bejcek, Sarah A. Hamer and Gabriel L. Hamer

Microorganisms 2021, 9(3), 504; https://doi.org/10.3390/microorganisms9030504 - 27 Feb 2021

Cited by 4 | Viewed by 2496

Abstract

Great-tailed grackles (Quiscalus mexicanus) have dramatically expanded into North America over the past century. However, little is known about the blood that parasites they support. Here, for the first time, we document an assemblage of trypanosome, haemosporida, and filarial nematodes co-circulating in invasive great-tailed grackles. Between February and July, 2015, 61 individuals were captured in an urban environment of College Station, Texas. Field microscopy and molecular diagnostics indicate that 52% (24/46) were visually infected with filarioid nematodes, 24% (11/46) with avian trypanosomes, and 73% (n = 44/60) with haemosporida parasites, such as Haemoproteus (Parahaemoproteus) and Plasmodium cathemerium. Overall, 87% of great-tailed grackles were infected with blood parasites. Although 50% of individuals hosted parasites from multiple phylum, no patterns of parasite assembly were observed. Results indicate that great-tailed grackles can support a relatively high level of blood parasitism. However, the consequences for avian health remain to be determined. Full article

(This article belongs to the Special Issue Avian Pathogens)

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13 pages, 1970 KiB

Open AccessArticle

The Evolutionary Dynamics of Influenza A Viruses Circulating in Mallards in Duck Hunting Preserves in Maryland, USA

by Nídia S. Trovão, Jacqueline M. Nolting, Richard D. Slemons, Martha I. Nelson and Andrew S. Bowman

Microorganisms 2021, 9(1), 40; https://doi.org/10.3390/microorganisms9010040 - 25 Dec 2020

Cited by 3 | Viewed by 2815

Abstract

Duck hunting preserves (DHP) have resident populations of farm-raised mallard ducks, which create potential foci for the evolution of novel influenza A viruses (IAVs). Through an eleven-year (2003–2013) IAV surveillance project in seven DHPs in Maryland, USA, we frequently identified IAVs in the resident, free-flying mallard ducks (5.8% of cloacal samples were IAV-positive). The IAV population had high genetic diversity, including 12 HA subtypes and 9 NA subtypes. By sequencing the complete genomes of 290 viruses, we determined that genetically diverse IAVs were introduced annually into DHP ducks, predominantly from wild birds in the Anatidae family that inhabit the Atlantic and Mississippi flyways. The relatively low viral gene flow observed out of DHPs suggests that raised mallards do not sustain long-term viral persistence nor do they serve as important sources of new viruses in wild birds. Overall, our findings indicate that DHPs offer reliable samples of the diversity of IAV subtypes, and could serve as regional sentinel sites that mimic the viral diversity found in local wild duck populations, which would provide a cost-efficient strategy for long-term IAV monitoring. Such monitoring could allow for early identification and characterization of viruses that threaten bird species of high economic and environmental interest. Full article

(This article belongs to the Special Issue Avian Pathogens)

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Review

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12 pages, 14726 KiB

Open AccessReview

An Outbreak of Highly Pathogenic Avian Influenza (H7N7) in Australia and the Potential for Novel Influenza A Viruses to Emerge

by Andrew T. Bisset and Gerard F. Hoyne

Microorganisms 2021, 9(8), 1639; https://doi.org/10.3390/microorganisms9081639 - 31 Jul 2021

Cited by 5 | Viewed by 3151

Abstract

In 2020, several geographically isolated farms in Victoria, Australia, experienced an outbreak of highly pathogenic avian influenza (HPAI) virus H7N7 and low pathogenic avian influenza (LPAI) viruses H5N2 and H7N6. Effective containment and control measures ensured the eradication of these viruses but the event culminated in substantial loss of livestock and significant economic impact. The avian HPAI H7N7 virus generally does not infect humans; however, evidence shows the ocular pathway presents a favourable tissue tropism for human infection. Through antigenic drift, mutations in the H7N7 viral genome may increase virulence and pathogenicity in humans. The Victorian outbreak also detected LPAI H7N6 in emus at a commercial farm. Novel influenza A viruses can emerge by mixing different viral strains in a host susceptible to avian and human influenza strains. Studies show that emus are susceptible to infections from a wide range of influenza viral subtypes, including H5N1 and the pandemic H1N1. The emu’s internal organs and tissues express abundant cell surface sialic acid receptors that favour the attachment of avian and human influenza viruses, increasing the potential for internal genetic reassortment and the emergence of novel influenza A viruses. This review summarises the historical context of H7N7 in Australia, considers the potential for increased virulence and pathogenesis through mutations and draws attention to the emu as potentially an unrecognised viral mixing vessel. Full article

(This article belongs to the Special Issue Avian Pathogens)

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