Uncovering changes in microbiome profiles across commercial and backyard poultry farming systems

This study identified characteristics of poultry farming with a focus on practices that affect the detection of HPAI; and estimated the system sensitivity of passive surveillance for HPAI H5N1 in commercial and backyard chicken farms in Bayelsa-State, Nigeria. Field studies were carried out in Yenegoa and Ogbia local government areas in Bayelsa state. Willingness to report HPAI was highest in commercial poultry farms (13/13) than in Backyard farms (8/13). Poor means of dead bird disposal was common to both commercial and backyard farms. Administering some form of treatment to sick birds without prior consultation with a professional was higher in backyard farms (8/13) than in commercial farms (4/13). Consumption of sick birds was reported in 4/13 backyard farms and sale of dead birds was recorded in one commercial farm. The sensitivity of passive surveillance for HPAI was assessed using scenario tree modelling. A scenario tree model was developed and applied to estimate the sensitivity, i.e. the probability of detecting one or more infected chicken farms in Bayelsa state at different levels of disease prevalence. The model showed a median sensitivity of 100%, 67% and 23% for detecting HPAI by passive surveillance at a disease prevalence of 0.1%, a minimum of 10 and 3 infected poultry farms respectively. Passive surveillance system sensitivity at a design prevalence of 10 infected farms is increasable up to 86% when the disease detection in backyard chicken farms is enhanced.

Aim. To conduct a virological, PCR, PCR-RFLP and sequencing study of infectious laryngotracheitis virus (ILTV) isolates obtained from sick and dead chickens at industrial and backyard poultry farms in the eastern region of Ukraine collected over the years 2010–2019 and to establish their pathotype and relationship with internationally occurring strains. Methods. Material for virological studies was collected in the framework of research program of the NSC IEСVM during 2010-2019 in the poultry farms in the North-Eastern region of Ukraine, where the birds with the respiratory clinical signs were found. In total, 28 poultry farms were observed. ILTV isolates were obtained with conventional methods, using 10–12-day-old chicken embryos. A 0,2 ml of 10–20 % suspension of pathological material in PBS was used for inoculation. For in-depth studies, we used 4 isolates of ILTV obtained from sick and dead chickens from industrial and backyard poultry farms in Kharkiv, Luhansk, Donetsk, and Sumy regions from 2010–2019. The identification of ILTV isolates was performed via conventional PCR. The pathotype of ILTV strains was determined using PCR-RFLP (polymerase chain reaction – restriction fragment length polymorphism) analysis. The PCR-RFLP was performed at Royal GD, the Netherlands. The (partial) sequencing of the US8 gene was performed using Sanger sequencing method. The phylogenetic analysis, using sequences of 2 Ukrainian strains (MZ323228, MZ333273) and 17 international gene sequences present in GenBank, was performed using the Maximum Likelihood method. For comparative analysis, sequences of vaccine ILT virus strains were used. Results. Over the years 2010-2019, 7 isolates of ILTV were obtained from sick and dead poultry with typical clinical signs and internal lesions at industrial and backyard farms of the Kharkiv, Donetsk, Luhansk and Sumy regions, and the Autonomous Republic of Crimea. Other avian respiratory viral and bacterial pathogens were not detected. Five isolates were obtained from poultry of industrial holdings where vaccination against ILT is carried out. Using PCR-RFLP analysis of 4 isolates, we found that three of them (Sumy 6-11/19, A 04-12, B 2-10) to belong to vaccine-type ILTV strains and only one, B 59-11strain, belongs to wild-type ILTV. Vaccine-type ILTV strains circulated and possibly still circulate in Ukraine in industrial and backyard poultry farms among both vaccinated and non- vaccinated poultry. An ILTV wild-type strain was obtained from non-vaccinated chickens from a backyard farm, which may indicate an important role of backyard farms in maintaining the circulation of the virus. After partial sequencing and phylogenetic analysis of the ILTV US8 gene the two Ukrainian strains studied were placed into two different clusters: The vaccine-type B 2-10 strain, obtained from sick vaccinated chickens from an industrial farm, was close to vaccine-type strains circulating in, China, Italy and the USA. The wild-type B 59-11strain, obtained from sick non-vaccinated backyard chickens, was located in another cluster and closest to a the wild-type B 59-11 ILTV strain from Brazil. Conclusions. In this article we describe for the first time the characterization of vaccine-type and wild-type isolates of ILTV in industrial and backyard poultry farms, proving their relevance for the poultry production in Ukraine. The results obtained show the need and prospects for further monitoring of ILTV circulation in small backyard poultry farms and in industrial poultry farms, especially following the frequent use for vaccination of live attenuated wild-type ILTV strains in Ukraine. Further molecular, phylogenetic and epidemiological characterization of the strains obtained should be performed in the near future to further precise their attributes, epidemiology and origin.

Cross-sectional study on Chlamydiaceae prevalence and associated risk factors on commercial and backyard poultry farms in Mexico

Poultry (Gallus domesticus) farming plays an important role as an income generating enterprise in a developing country like Nepal, contributing more than 4% to the national Gross Domestic Product (GDP). Newcastle Disease (ND) is a major poultry disease affecting both commercial and backyard poultry production worldwide. There were more than 90 reported ND outbreaks in Nepal in 2018 with over 74,986 birds being affected. ND is responsible for over 7% of total poultry mortality in the country. Recent outbreaks of ND in 2021 affected many farms throughout Nepal and caused massive loss in poultry production. ND is caused by a single-stranded ribonucleic acid (RNA) virus that presents very similar clinical symptoms as Influenza A (commonly known as bird flu) adding much complexity to clinical disease identification and intervention. We conducted a nationwide ND and Influenza A (IA) prevalence study, collecting samples from representative commercial and backyard poultry farms from across the major poultry production hubs of Nepal. We used both serological and molecular assessments to determine disease exposure history and identification of strains of ND Virus (NDV). Of the 40 commercial farms tested, both NDV (n = 28, 70%) and IAV (n = 11, 27.5%) antibodies were detected in majority of the samples. In the backyard farms (n = 36), sero-prevalence of NDV and IAV were 17.5% (n = 7) and 7.5% (n = 3) respectively. Genotype II NDV was present in most of the commercial farms, which was likely due to live vaccine usage. We detected never reported Genotype I NDV in two backyard farm samples. Our investigation into 2021 ND outbreak implicated Genotype VII.2 NDV strain as the causative pathogen. Additionally, we developed a Tablet formulation of the thermostable I2-NDV vaccine (Ranigoldunga™) and assessed its efficacy on various (mixed) breeds of chicken (Gallus domesticus). Ranigoldunga™ demonstrated an overall efficacy >85% with a stability of 30 days at room temperature (25°C). The intraocularly administered vaccine was highly effective in preventing ND, including Genotype VII.2 NDV strain.

Chicken and pork are the most frequently consumed meat products in the Philippines. Swine and poultry are reared in either commercial farms (CMf) or backyard farms (BYf); the latter production system is relatively common and essential to food security in low- and middle-income countries (LMICs) such as the Philippines. Similar to resource-limited LMICs, antimicrobial use (AMU) surveillance has not yet been established; thus, AMU in food animals is a knowledge gap in understanding the emergence of antimicrobial resistance (AMR) in zoonotic foodborne bacteria in the country. This qualitative AMU pilot study aims to describe the antimicrobial active ingredients (AAIs) used and associated AMU practices (e.g., source of AAIs and informed AMU decisions) by poultry and swine CMf and BYf in the Philippines. Ninety-three farms across four regions in the Philippines voluntarily provided AMU information as part of a larger biosecurity and good practices study. The percentage of farms using AAI over the total number of farms was the metric used to describe AMU. In total, there were 30 AAIs used (CMf: n =27 and BYf: n = 13); per farm, the number of AAIs used ranged from 1 to 7. The spectrum of AAIs was more diverse in swine (n = 24) compared to poultry (n = 18). Enrofloxacin was the most frequently reported AAI in poultry (33%) and swine (36%) farms. Respiratory diseases were the most frequently reported reason for AMU in both species. Between production systems, significant differences were observed in the percentage of farms using amoxicillin (27% CMf vs. 3% BYf), colistin (17% CMf vs. 3% BYf), and oxytetracycline (12% CMf vs. 39% BYf). In terms of AMU practices, of important concern was the over-the-counter access of AAIs at retail outlets and the limited veterinary oversight in BYf. Our data indicated that antimicrobials critically important for human medicine are frequently used in poultry and swine farms in the Philippines. This study can inform the development of guidelines for curbing AMR through prudent AMU and serves as a reference point for AMU surveillance capacity development in the Philippines.

Over the past decade, there has been a rise in U.S. backyard poultry ownership, raising concern for residential area antimicrobial-resistant (AMR) Salmonella contamination. This study aims to lay the groundwork to better understand the persistence of AMR Salmonella in residential broiler production systems and make comparisons with commercial systems. Ten backyard and 10 commercial farms were sampled at three time points across bird production. Both fecal (n = 10) and environmental (soil, n = 5, litter/compost, n = 5, feeder, and waterer swabs, n = 6) samples were collected at each visit on days 10, 31, and 52 of production for backyard farms and days 10, 24, and 38 of production for commercial farms. AMR Salmonella was characterized phenotypically by broth microdilution and genotypically by whole-genome sequencing. Overall, Salmonella was more prevalent in commercial farm samples (52.31%) over backyard farms (19.10%). Kentucky (sequence type (ST) 152) was the most common serotype found in both backyard and commercial farms. Multidrug-resistant (MDR, resistance to ≥3 or more antimicrobial classes) isolates were found in both production systems, while ciprofloxacin- and nalidixic acid-resistant and intermediate isolates were more prevalent in commercial (33%) than backyard samples (1%). Plasmids that have been associated with MDR were found in Kentucky and Infantis isolates, particularly IncFIB(K)_1_Kpn3 megaplasmid (Infantis). Our study emphasizes the need to understand the selection pressures in disseminating megaplasmids in MDR Salmonella in distinct broiler production systems.

In Myanmar, where backyard, semi-intensive, and intensive pig (Sus scrofa domesticus) farming coexist, there is limited understanding of the zoonotic risks and antimicrobial resistance (AMR) associated with these farming practices. This study was conducted to investigate the prevalence, AMR and genomic features of Salmonella in pig farms in the Yangon region and the impact of farm intensification to provide evidence to support risk-based future management approaches. Twenty-three farms with different production scales were sampled for two periods with three sampling-visit each. Antimicrobial susceptibility tests and whole-genome sequencing were performed on the isolates. The prevalence of Salmonella was 44.5% in samples collected from backyard farms, followed by intensive (39.5%) and semi-intensive farms (19.5%). The prevalence of multi-drug resistant isolates from intensive farms (45/84, 53.6%) was higher than those from backyard (32/171, 18.7%) and semi-intensive farms (25/161, 15.5%). Among 28 different serovars identified, S. Weltevreden (40; 14.5%), S. Kentucky (38; 13.8%), S. Stanley (35, 12.7%), S. Typhimurium (22; 8.0%) and S. Brancaster (20; 7.3%) were the most prevalent serovars and accounted for 56.3% of the genome sequenced strains. The diversity of Salmonella serovars was highest in semi-intensive and backyard farms (21 and 19 different serovars, respectively). The high prevalence of globally emerging S. Kentucky ST198 was detected on backyard farms. The invasive-infection linked typhoid-toxin gene (cdtB) was found in the backyard farm isolated S. Typhimurium, relatively enriched in virulence and AMR genes, presented an important target for future surveillance. While intensification, in terms of semi-intensive versus backyard production, maybe a mitigator for zoonotic risk through a lower prevalence of Salmonella, intensive production appears to enhance AMR-associated risks. Therefore, it remains crucial to closely monitor the AMR and virulence potential of this pathogen at all scales of production. The results underscored the complex relationship between intensification of animal production and the prevalence, diversity and AMR of Salmonella from pig farms in Myanmar.

Highly Pathogenic Avian Influenza (HPAI) virus H5N1 and Low Pathogenic Avian Influenza (LPAI) virus H9N2 are endemic in Bangladesh and pose a threat to both poultry and human health. For effective avian influenza (AI) prevention and control, good knowledge of the factors influencing the epidemiology of avian influenza virus (AIV) circulation is crucial, but no in-depth investigations have thus far been conducted on poultry farms in Bangladesh.The overall aim of this research was to improve the understanding of the extent of H5 and H9 virus circulation on backyard, and commercial broiler and commercial layer chicken farms in Bangladesh and to identify risk factors associated with the presence of H5 and H9 virus. Furthermore, the research aimed to investigate the perceptions of chicken farmers to implement HPAI prevention and control measures in Bangladesh.Two cross-sectional studies were conducted in the Chittagong and Cox’s Bazaar districts of Bangladesh: 1) between February and April 2016 involving 144 backyard chicken farms in 42 villages, and 2) between February and April 2017 involving 106 commercial broiler and 113 commercial layer chicken farms. Blood samples, oropharyngeal swabs and cloacal swabs were collected from 576 chickens and 204 in-contact ducks on backyard farms, and from 954 broilers and 904 layers on commercial chicken farms. Questionnaires were used to collect data on farm-level and village-level risk factors for H5 and H9 seroprevalence and on farmer’s perceptions towards implementation of HPAI prevention and control measures.Although all sampled birds tested negative for H5 by RT-PCR, H5 seropositive chickens were detected in all three farming systems. The highest H5 seroprevalence was observed in ducks raised with chickens on backyard farms, 14.2% (95% CI: 10.0-19.8), compared to in-contact backyard chickens, 4.2% (95% CI: 2.8-6.1). H5 seroprevalence was lower in unvaccinated broiler chickens, 1.5% (95% CI: 0.9-2.5), than in unvaccinated layer chickens, 7.8% (95% CI: 6.1-9.8). H9 viral infection was detected by RT-PCR in 0.5% (95% CI: 0.2-1.3) and 0.6% (95% CI: 0.3-1.5) of chickens raised in broiler and layer farms, respectively and in 0.2% (95% CI: 0.0-1.2) of chickens on backyard farms suggesting a similar level of exposure to H9 virus is all farming systems. Backyard chickens and ducks showed similar H9 seroprevalence, 16.0% (95% CI: 13.2-19.2) and 15.7% (95% CI: 11.3-21.4) respectively, while it was 5.8% (95% CI: 4.3-7.6) in layers and 1.5% (95% CI: 0.9-2.5) in broilers. Over the course of a production cycle, H5 and H9 seroprevalence increased with the age of backyard and layer chickens. Clustering of H5 seropositivity in ducks was identified, highlighting that multiple ducks within a flock were H5 seropositive. This was in contrast to backyard and broiler and layer chickens, where only individual birds within flocks developed H5 antibodies.Using multilevel mixed modelling, farm- and village-level risk factors for AIV exposure for backyard farms were identified. For example, garbage around poultry house or on the farms (a farm-level risk factor) (OR for H5: 9.1, 95% CI: 1.7-48.8; OR for H9: 28.6, 95% CI:3.4-239.8) and crow abundance around garbage dumping places within villages (a village-level risk factor) (OR for H5:3.4, 95% CI: 1.1-10.8; OR for H9:13.1, 95% CI: 2.3-76.8) increased the odds for H5 and H9 seropositivity on backyard farms. Binomial logistic regression was used to identify farm-level risk factors for AIV exposure on commercial farms. For example, visits by workers from other commercial chicken farms during the current production cycle (OR for H5: 15.1, 95% CI: 2.8-80.8; OR for H9: 50.1, 95% CI:4.5- 552.7) increased the odds for seropositivity on broiler farms, while access of stray dogs to the sampled farm (OR for H5: 3.1, 95% CI: 1.1-9.1; OR for H9: 4.0, 95% CI:1.1-15.3) increased the odds for seropositivity on layer farms.Structural Equation Modelling was used to explore direct and indirect effects of farmers’ perceptions to implement HPAI prevention and control actions on their farms. Results highlighted that farmers working in different chicken production systems follow different decision-making processes. Perceived barriers to implement prevention and control measures (e.g. wearing protective equipment when handling chickens) refrained both broiler (β=-0.41, p<0.001) and backyard farmers (β=-0.52, p<0.001) to adopt interventions. Meanwhile perceived benefits (e.g. maintaining high biosecurity to reduce the risk of birds becoming sick) strongly influenced commercial broiler (β=0.44, p<0.001) and layer farmers’ (β=0.68, p<0.001), but not backyard farmers’ decisions. Information provided on HPAI control through media, meetings or via information campaigns played an important role in farmers’ decision making across all production systems.Overall, this project provided a holistic picture of the factors influencing the epidemiology of AIV circulation across diverse chicken production systems in Bangladesh. The project described AIV infection patterns, risk factors of infection and farmers perceptions to implement HPAI prevention and control measures. Results from this research project have been used to inform policy makers to develop recommendations and improve current AI prevention and control policies in Bangladesh.

Highly Pathogenic Avian Influenza Virus, Midwestern United States.

Salmonellosis is a common, widely distributed foodborne disease. Consumption of raw or undercooked chicken eggs infected with Salmonella has been reported in association with salmonellosis cases; however, minimum attention has been paid to regulate the quality of eggs released for consumption. This study aimed to investigate the presence of Salmonella in eggs collected from selected farms from Kosgama area and to compare the egg quality of backyard and commercial farms. Randomly purchased eggs from selected chicken farms were analyzed for the presence of Salmonella. Egg content was mixed thoroughly, and 25.0mL was inoculated into 225.0mL of 1% Buffered Peptone Water (BPW) and incubated at 350C (24h). From the pre-enriched specimen, 0.1ml was added to 10.0ml of Rappaport Vassiliadis broth and incubated at 420C (24h). The same procedure was followed for shells. Isolated cultures were streaked on Brilliant Green Agar (BGA) and Xylose Lysine Deoxycholate Agar (XLD) and incubated at 350C for 24h. Colonies were investigated with Gram staining, biochemical tests and serotyping was carried out to identify the species. Of 78 eggs, 35 were from backyard and 43 from commercial farms. Six specimens (4 from shell and 2 from content) yielded Salmonella (7.69 %). Four of the positive specimens were from backyard farms (4/35, 8.91%) and remaining two (2/43, 3.62%) were from commercial farms. Isolates were identified as S. Typhimurium and S. Enteriditis. The prevalence of Salmonella was 7.69 % (n=6). The proportion of Salmonella showed no significant difference (p=0.782) between backyard and commercial farms.

Extended-spectrum beta-lactamase (ESBL) Escherichia coli (E. coli) is an emerging pathogen of high concern given its resistance to extended-spectrum cephalosporins. Broiler chicken, which is the number one consumed meat in the United States and worldwide, can be a reservoir of ESBL E. coli. Backyard poultry ownership is on the rise in the United States, yet there is little research investigating prevalence of ESBL E. coli in this setting. This study aims to identify the prevalence and antimicrobial resistance profiles (phenotypically and genotypically) of ESBL E. coli in some backyard and commercial broiler farms in the U.S. For this study ten backyard and ten commercial farms were visited at three time-points across flock production. Fecal (n = 10), litter/compost (n = 5), soil (n = 5), and swabs of feeders and waterers (n = 6) were collected at each visit and processed for E. coli. Assessment of ESBL phenotype was determined through using disk diffusion with 3rd generation cephalosporins, cefotaxime and ceftazidime, and that with clavulanic acid. Broth microdilution and whole genome sequencing were used to investigate both phenotypic and genotypic resistance profiles, respectively. ESBL E. coli was more prevalent in backyard farms with 12.95% of samples testing positive whereas 0.77% of commercial farm samples were positive. All isolates contained a blaCTX-M gene, the dominant variant being blaCTX-M-1, and its presence was entirely due to plasmids. Our study confirms concerns of growing resistance to fourth generation cephalosporin, cefepime, as roughly half (51.4%) of all isolates were found to be susceptible dose-dependent and few were resistant. Resistance to non-beta lactams, gentamicin and ciprofloxacin, was also detected in our samples. Our study identifies prevalence of blaCTX-M type ESBL E. coli in U.S. backyard broiler farms, emphasizing the need for interventions for food and production safety.

Exploring contacts facilitating transmission of influenza A(H5N1) virus between poultry farms in West Java, Indonesia: A major role for backyard farms?

This study investigates the influence of environmental temperatures on feed intake and water consumption in broilers and layers across commercial and backyard poultry farms in Maiduguri, Borno State. Data were collected over six months from multiple farms, accounting for seasonal variations and management practices. The findings revealed significant differences in feed and water intake between commercial and backyard farms influenced by temperature fluctuations. Specifically, broilers showed higher sensitivity to temperature changes compared to layers. At temperatures below 25°C, broilers in commercial farms consumed significantly more feed (120 ± 0.5g) and less water (250 ± 0.3ml) compared to higher temperatures above 40°C where feed consumption decreased (100 ± 0.3g) and water intake increased (380 ± 0.6ml) (p &lt; 0.05). Layers followed a similar trend with higher feed intake (110 ± 0.5g) at temperatures below 25°C and increased water consumption (350 ± 0.5ml) at temperatures above 40°C (p &lt; 0.05). Comparative analysis indicated that commercial broilers had a significantly higher average feed intake during the rainy season (180 ± 0.5 g/day) compared to backyard broilers (120 ± 0.3 g/day, p &lt; 0.05), with similar patterns observed during the hot dry season. In contrast, backyard broilers consumed more water (350 ± 0.6 ml/day) than commercial broilers (300 ± 0.4 ml/day) during the hot dry season (p &lt; 0.05). These findings suggest that temperature management is crucial for optimizing poultry performance, with implications for different farming systems.

Risk factors for highly pathogenic avian influenza (HPAI) H5N1 infection in backyard chicken farms, Thailand

African swine fever (ASF) entered Georgia in 2007 and the EU in 2014. In the EU, the virus primarily spread in wild boar (Sus scrofa) in the period from 2014–2018. However, from the summer 2018, numerous domestic pig farms in Romania were affected by ASF. In contrast to the existing knowledge on ASF transmission routes, the understanding of risk factors and the importance of different transmission routes is still limited. In the period from May to September 2019, 655 Romanian pig farms were included in a matched case-control study investigating possible risk factors for ASF incursion in commercial and backyard pig farms. The results showed that close proximity to outbreaks in domestic farms was a risk factor in commercial as well as backyard farms. Furthermore, in backyard farms, herd size, wild boar abundance around the farm, number of domestic outbreaks within 2 km around farms, short distance to wild boar cases and visits of professionals working on farms were statistically significant risk factors. Additionally, growing crops around the farm, which could potentially attract wild boar, and feeding forage from ASF affected areas to the pigs were risk factors for ASF incursion in backyard farms.