Persistence of low and highly pathogenic avian influenza virus in reused poultry litter, effects of litter amendment use, and composting temperatures

Seasonal changes in bird communities on poultry farms and house sparrow-wild bird contacts revealed by camera trapping

Introduction

Wild birds are considered reservoirs of poultry pathogens although transmission routes have not been conclusively established. Here we use camera trapping to study wild bird communities on commercial layer and red-legged partridge farms over a one-year timeframe. We also analyze direct and indirect interactions of other bird species with the house sparrow (Passer domesticus), a potential bridge host.

Methods

We conducted camera trapping events between January 2018 and October 2019, in two caged layer farms, one free-range layer farm, and two red-legged partridge farms in South-Central Spain.

Results and Discussion

We observed wild bird visits on all types of farms, with the significantly highest occurrence on red-legged partridge farms where food and water are more easily accessible, followed by commercial caged layer farms, and free-range chicken farms. The house sparrow (Passer domesticus) followed by spotless starlings (Sturnus unicolor) was the most encountered species on all farms, with the highest frequency in caged layer farms. On partridge farms, the house sparrow accounted for 58% of the wild bird detections, while on the free-range chicken farm, it made up 11% of the detections. Notably, the breeding season, when food and water are scarce in Mediterranean climates, saw the highest number of wild bird visits to the farms. Our findings confirm that the house sparrow, is in direct and indirect contact with layers and red-legged partridges and other wild birds independent of the type of farm. Contacts between house sparrows and other bird species were most frequent during the breeding season followed by the spring migration period. The species most frequently involved in interactions with the house sparrow belonged to the order Passeriformes. The study provides a comparative description of the composition and seasonal variations of bird communities in different types of layer/ poultry farms in Southern Spain i.e. a Mediterranean climate. It confirms the effectiveness of biosecurity measures that restrict access to feed and water. Additionally, it underscores the importance of synanthropic species, particularly the house sparrow, as potential bridge vector of avian pathogens.

Treatment with Toll-like Receptor (TLR) Ligands 3 and 21 Prevents Fecal Contact Transmission of Low Pathogenic H9N2 Avian Influenza Virus (AIV) in Chickens

Transmission of H9N2 avian influenza virus (AIV) can occur in poultry by direct or indirect contact with infected individuals, aerosols, large droplets and fomites. The current study investigated the potential of H9N2 AIV transmission in chickens via a fecal route. Transmission was monitored by exposing naïve chickens to fecal material from H9N2 AIV-infected chickens (model A) and experimentally spiked feces (model B). The control chickens received H9N2 AIV. Results revealed that H9N2 AIV could persist in feces for up to 60-84 h post-exposure (PE). The H9N2 AIV titers in feces were higher at a basic to neutral pH. A higher virus shedding was observed in the exposed chickens of model B compared to model A. We further addressed the efficacy of Toll-like receptor (TLR) ligands to limit transmission in the fecal model. Administration of CpG ODN 2007 or poly(I:C) alone or in combination led to an overall decrease in the virus shedding, with enhanced expression of type I and II interferons (IFNs) and interferon-stimulating genes (ISGs) in different segments of the small intestine. Overall, the study highlighted that the H9N2 AIV can survive in feces and transmit to healthy naïve chickens. Moreover, TLR ligands could be applied to transmission studies to enhance antiviral immunity and reduce H9N2 AIV shedding.

Assessment Impacts of Ozone on Salmonella Typhimurium and Escherichia coli O157:H7 in Liquid Dairy Waste

Liquid dairy manure, which is produced in enormous quantities in flush dairy manure management systems, is commonly used as an alternative to chemical fertilizers. It provides nutrient benefits to crops and soils. While dairy waste is a well-accepted and widely used fertilizer, the presence of indicator organisms and human pathogens in manure may lead to pathogen contamination in crops and soils. This study is focused on the examination of ozone gas-based sterilization. In the past, ozone (O3) has been used for sanitizing various foods and solid surfaces, but the potential of O3 for eliminating human pathogens in liquid dairy waste is not studied yet. Pathogens such as Salmonella Typhimurium and Escherichia coli O157:H7 are reported to be present in liquid dairy manure, and this research evaluated the effects of various levels of ozone on the survival of these two pathogens. We designed a continuous type O3 treatment system that has four major components: (1) ozone generator using oxygen; (2) ozone concentration control by mixing with pure air; (3) continuous monitoring of ozone concentrations; and (4) ozone experiment chambers. Various levels of ozone (43.26, 87.40, and 132.46 mg·L−1) were produced in the ozone system, and subsequently, ozone was diffused through liquid manure. Liquid manure was exposed to ozone for multiple durations (30, 60, and 120 min). To determine the effectiveness of O3 in eliminating pathogens, time-series samples were collected and analyzed for determining the levels of S. typhimurium and E. coli O157:H7. Preliminary results showed that ozone concentrations of 132.46 mg/L, and exposure time of 120 min resulted in the reduced levels of E. coli and Salmonella. Low levels of ozone and limited exposure time were found to be less effective in pathogen removal potentially due to high solid contents. Additional studies carrying out experiments to evaluate the impacts of solids in combination with ozone concentrations will provide further insights into developing full-scale ozone-based treatment systems.

Litter Commensal Bacteria Can Limit the Horizontal Gene Transfer of Antimicrobial Resistance to Salmonella in Chickens

Fostering a "balanced" gut microbiome through the administration of beneficial microbes that can competitively exclude pathogens has gained a lot of attention and use in human and animal medicine. However, little is known about how microbes affect the horizontal gene transfer of antimicrobial resistance (AMR). To shed more light on this question, we challenged neonatal broiler chicks raised on reused broiler chicken litter-a complex environment made up of decomposing pine shavings, feces, uric acid, feathers, and feed-with Salmonella enterica serovar Heidelberg (S. Heidelberg), a model pathogen. Neonatal chicks challenged with S. Heidelberg and raised on reused litter were more resistant to S. Heidelberg cecal colonization than chicks grown on fresh litter. Furthermore, chicks grown on reused litter were at a lower risk of colonization with S. Heidelberg strains that encoded AMR on IncI1 plasmids. We used 16S rRNA gene sequencing and shotgun metagenomics to show that the major difference between chicks grown on fresh litter and those grown on reused litter was the microbiome harbored in the litter and ceca. The microbiome of reused litter samples was more uniform and enriched in functional pathways related to the biosynthesis of organic and antimicrobial molecules than that in fresh litter samples. We found that Escherichia coli was the main reservoir of plasmids encoding AMR and that the IncI1 plasmid was maintained at a significantly lower copy per cell in reused litter compared to fresh litter. These findings support the notion that commensal bacteria play an integral role in the horizontal transfer of plasmids encoding AMR to pathogens like Salmonella. IMPORTANCE Antimicrobial resistance spread is a worldwide health challenge, stemming in large part from the ability of microorganisms to share their genetic material through horizontal gene transfer. To address this issue, many countries and international organizations have adopted a One Health approach to curtail the proliferation of antimicrobial-resistant bacteria. This includes the removal and reduction of antibiotics used in food animal production and the development of alternatives to antibiotics. However, there is still a significant knowledge gap in our understanding of how resistance spreads in the absence of antibiotic selection and the role commensal bacteria play in reducing antibiotic resistance transfer. In this study, we show that commensal bacteria play a key role in reducing the horizontal gene transfer of antibiotic resistance to Salmonella, provide the identity of the bacterial species that potentially perform this function in broiler chickens, and also postulate the mechanism involved.

Highly Pathogenic Avian Influenza Viruses at the Wild-Domestic Bird Interface in Europe: Future Directions for Research and Surveillance

Highly pathogenic avian influenza (HPAI) outbreaks in wild birds and poultry are no longer a rare phenomenon in Europe. In the past 15 years, HPAI outbreaks—in particular those caused by H5 viruses derived from the A/Goose/Guangdong/1/1996 lineage that emerged in southeast Asia in 1996—have been occuring with increasing frequency in Europe. Between 2005 and 2020, at least ten HPAI H5 incursions were identified in Europe resulting in mass mortalities among poultry and wild birds. Until 2009, the HPAI H5 virus outbreaks in Europe were caused by HPAI H5N1 clade 2.2 viruses, while from 2014 onwards HPAI H5 clade 2.3.4.4 viruses dominated outbreaks, with abundant genetic reassortments yielding subtypes H5N1, H5N2, H5N3, H5N4, H5N5, H5N6 and H5N8. The majority of HPAI H5 virus detections in wild and domestic birds within Europe coincide with southwest/westward fall migration and large local waterbird aggregations during wintering. In this review we provide an overview of HPAI H5 virus epidemiology, ecology and evolution at the interface between poultry and wild birds based on 15 years of avian influenza virus surveillance in Europe, and assess future directions for HPAI virus research and surveillance, including the integration of whole genome sequencing, host identification and avian ecology into risk-based surveillance and analyses.