Cross-sectional study characterizing the porcine faecal microbiome in commercial farms

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

The organic horticultural farming system is a horticultural farming technique that relies on natural materials in its production and is a sustainable agriculture, in contrast to the conventional horticultural farming system which still relies on chemicals in its production process. The purpose of this research was to compare organic and conventional horticultural farming systems in Getasan district, Semarang. This study is a cross-sectional descriptive-analytical study that employed survey methodologies. This study was conducted from July to December 2019 using a sample of 314 respondents, 90 organic horticulture farmers and 224 conventional horticulture farmers as research subjects. Research results showed that the average total additional cost of restoring soil nutrients in 100 m2 / year for organic horticulture farming was IDR. 69,958.33 less than the cost for conventional farming systems, which was IDR. 79,550.00 per 100 m2 per year, with a p-value of 0.032*. The cost of purchasing fertilizer in year / 100m2 on a conventional horticultural farm was IDR. 90,575.78, greater than the cost of organic horticulture farming which was only IDR. 73,170.38 with a p-value< 0,001*. The average yield of organic horticulture farms was somewhat higher than that of conventional farms during each growing season. The average annual income from yields in 100 m2/year for organic horticulture production was IDR 2,449,246.32, while conventional IDR. 2,369,641.10 with p-value of 0.441 although not statistically significant. The average profit per 100 m2 / year for an organic horticultural farming system was IRD. 1,549,303.42, which is greater than the profit value for a conventional horticultural farming system, which was IDR. 1,450,109.82, 959,289.06, although statistically not significant, with p-value = 0.228. The total annual production cost for the organic horticulture farming system was less than the conventional system, which was IDR 901,346.78 for the organic horticulture farming system and IDR. 921,084.17 for conventional, for every 100 m2 / year with p-value = 0.383, even though not statistically significant. Statistically, there was no significant difference in labor costs between the two agricultural systems, p-value 0.702, but descriptive analysis shows that the average labor cost per 100 m2/year for organic horticulture farming was IDR. 588,859.57, which is less than IDR. 591,760.50 for conventional horticulture farming. Based on the parameters analyzed, the outcome of this study demonstrates that the organic horticulture farming system is superior to the conventional horticultural farming system. Key words: Environmental value Fertilization costs, Cultivation profits, Labor expenses, Production costs

Background and Aim:Classical swine fever (CSF) is one of the primary diseases in animals in Indonesia, particularly areas that supply pig meat to the country, such as Karanganyar district, Central Java. The government has tried to prevent and control the disease by vaccination, but it has not yet given effective results. Therefore, another attempt to prevent the recurrence of CSF cases is to apply biosecurity in pig farms by looking for risk factors associated with on-farm and off-farm contact. This study aims to determine the contact rate and investigate the risk factors associated with on-farm and off-farm contact in commercial and smallholder pig farms in Karanganyar, Central Java, Indonesia, in the context of controlling CSF disease.Materials and Methods:This study used a cross-sectional study design in which the pig farm was designed as the observed epidemiological unit. The contact structure data were conducted by sampling using a two-stage random method. We selected Karanganyar district because it is the center of a pig farm in the Central Java Province and has many CSF cases in several years before. The study was conducted for more or less 1 month from August to September 2019. The contact data were collected from 37 smallholder farms and 27 commercial farms within interviews. Risk factors for contact with pigs were analyzed using logistic regression using theStatistix Program version 8.0.(www.statistix.com)Results:In comparison to smallholder farms, commercial farms had 2.38 and 3.32 times higher contact rate in outside farms and inside farms, respectively. Two factors increased the risk for on-farm contacts including commercials type farm (p=0.0012; odds ratio [OR]=8.32) with contact rate of 1.24 times/day and the time interval of CSF vaccination for 1-3 months (p=0.0013; OR=8.43) with contact rate of 0.98 times/day, and three factors increased the risk for off-farm contacts including the commercial farm type (p=0.012; OR=4.88) with 1.50 contact/day, the time interval of CSF vaccination for 1-3 months (p=0.036; OR=3.83) with 1.30 contact/day, and farmers with experience in pig husbandry <5 years (p=0.075; OR=3.56) with 1.13 contact/day.Conclusion:This study shows that commercial farms and short CSF vaccination intervals increased the risk of either off-farm or on-farm contacts. The contact structure of pig farms in Karanganyar district is similar to that in other areas in Indonesia. Reducing the risk of contacts either outside or inside the pig farms is essential to prevent disease transmission. Enhancing communication and education to pig farmers and surveillance is also necessary to prevent such diseases in pigs.

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.

ABSTRACTOrganic farming has been promoted in Thailand by King Rama the ninth. In addition to being healthier for consumers, organic farming is healthier for agricultural workers. The cross-sectional study was conducted to investigate the frequency of chronic disease conditions, accidents, health symptoms, and ergonomic problems among 243 conventional (pesticide using) farmers and 235 organic farmers. Data were collected using questionnaires in face-to-face interviews. The results indicated symptoms that could be related to pesticide exposure (skin rashes, water blisters, headache, dizziness, and loss of appetite) were significantly higher among conventional farmers than organic farmers. The organic farmers reported significantly more health symptoms such as hives, chest pain, mild fever, flatulence, and frequent urination than the conventional farmers. The organic farmers reported significantly more pain, numbness, or weakness in the wrists/hands, fingers, upper back, hips, and ankles/feet than conventional farmers.

The silent pandemic of antimicrobial resistance (AR) has been on the rise for the past decades. It is essential to determine the burden of AR in animal farms that spreads leading to human exposure. A total of 100 samples including soil, litter, animal excreta, and wastewater were collected from seven conventional and one organic farm in Egypt. The prevalence of extended-spectrum β-lactamase-producing Escherichia coli (ESBL-producing E. coli), fluoroquinolone-resistant E. coli, fluoroquinolone-resistant Salmonella, and vancomycin-resistant enterococci (VRE) was determined in studied farms. Conventional farms had a higher prevalence of antimicrobial-resistant bacteria than the organic farm (73.81%vs. 18.75%, P<.001). In conventional farms 21.43% of samples yielded mixed isolates; however, in the organic farm, only single isolates of ESBL-producing E. coli were detected. The most prevalent ESBL-production gene was blaTEM (82.14%), followed by blaCTX-M (48.22%), and blaSHV (19.64%), either alone or in combination with another gene. The most prevalent fluoroquinolone-resistance genes were qnrS (82.69%) and qnrB (42.30%), either alone or in combination with another gene(s). A total of five VRE isolates harbored vanA gene (83.33%), none carried vanB gene, and one isolate was negative for both genes. The studied conventional livestock farms had significantly higher rates of serious AR threats than the organic farm.

Worldwide, farm animals, in particular poultry, are an important reservoir for Campylobacter spp. However, information on Campylobacter colonization in farm animals in Africa is scarce. Hence, this cross-sectional study determined antibiotic-resistant Campylobacter from both commercial and smallholder farm animals in the Asante Akim North Municipality of Ghana. Fecal samples from poultry and livestock kept by commercial and smallholder farms were collected and analyzed using standard microbiological methods. The overall Campylobacter frequency was 20.3% (n/N = 322/1,585), and frequencies detected were similarly high in isolates from commercial (21.0%, n/N = 169/805) and smallholder (19.6%, n/N = 153/780) farms. Species isolated were C. coli (67.7%, n/N = 218/322) and C. jejuni (32.3%, n/N = 104/322). However, the frequency of C. coli was 2.1 (95% CI: 1.8-2.5) times higher than what was found for C. jejuni. Campylobacter frequencies in the rainy season was 22.2% (n/N = 258/1,160) and 15.1% (n/N = 64/425) in the dry season (prevalence ratio = 1.48, 95% CI: 1.2-1.9). About 1.7% (n/N = 6/322) of the Campylobacter isolates, all from smallholder farms, were susceptible to all antibiotics tested. Multidrug resistance was observed for 4.7% (n/N = 15/322) of the Campylobacter isolates, of which 93.3% (n/N = 14/15) occurred in isolates from commercial farms. This study highlights the need for the implementation of control programs, in commercial farming but also at the smallholder farm level, to formulate clear guidelines aimed at decreasing Campylobacter contamination of meat products and reducing the use of antibiotics in the farming sector.

The objective of this cross-sectional study was to compare the prevalence of Salmonella and antimicrobial-resistant Salmonella, as well as investigate the distribution of this pathogen in organic and conventional broiler poultry farms. Fecal (n = 420), feed (n = 140), and drinking water (n = 140) samples were collected from birds at 3 and 8 weeks of age for 2-flock cycles. One house was sampled per farm at three organic and four conventional broiler farms from the same company in North Carolina. All samples were analyzed for the presence of Salmonella using selective enrichment techniques. Further phenotypic (antimicrobial susceptibility) and genotypic (pulsed-field gel electrophoresis [PFGE]) testing were performed. Salmonella prevalences in fecal samples were 5.6% (10/180) and 38.8% (93/240) from organic and conventional farms, respectively. From feed, 5.0% (3/60) and 27.5% (22/80) of the samples were positive for Salmonella from organic and conventional farms, respectively. None of the water samples were positive for Salmonella. Seventy isolates were characterized by antimicrobial susceptibility and PFGE types. The two most common resistance phenotypes were single resistance to streptomycin (36.2% [25/58]: conventional; 25% [3/12] organic), and multidrug resistance to six antimicrobial agents: ampicillin-streptomycin-amoxicillin/clavulanic acid-cephalothin-ceftiofur-cefoxitin (AmStAxChCfFx; 39.7%: conventional only). Genotypic analysis using PFGE showed clonality among isolates within and between the two types of farms. The results of our study suggest that within this poultry company, the prevalence of fecal Salmonella was lower in certified-organic birds than in conventionally raised birds, and the prevalence of antimicrobial-resistant Salmonella was also higher in conventionally raised birds than in certified-organic birds.

To determine and compare levels and patterns of antimicrobial resistance among Escherichia coli isolated from pigs on farms that did not use antimicrobial agents versus pigs produced under conventional methods. Cross-sectional study. Sample Population-35 antimicrobial-free and 60 conventional swine farms. Farms were visited once, and fecal samples were collected from 15 finisher pigs if available. One E coli isolate from each sample was tested for susceptibility pattern to 14 antimicrobial agents by use of microbroth dilution. E coli isolates were recovered from 1,381 (97.1%) of 1,422 fecal samples. Herd size was significantly larger for conventional swine farms. Resistance to ceftriaxone, ciprofloxacin, or nalidixic acid was not observed on any of the 95 farms. Three isolates from 2 conventional farms were resistant to ceftiofur. Conventional farms had significantly higher levels of resistance to ampicillin, sulfamethoxazole, tetracycline, and chloramphenicol, compared with antimicrobial-free farms. Fourteen percent of E coli isolates were susceptible or had intermediate resistance to all the tested antimicrobial agents. The 3 most frequent patterns of multiple resistance were streptomycin-tetracycline, sulfamethoxazole-tetracycline, and kanamycin-streptomycin-sulfamethoxazole-tetracycline. Cessation of antimicrobial use did not appear to result in an immediate reduction in antimicrobial resistance in swine farms. Prospective studies of long-term antimicrobial usage and cessation are needed to estimate the extent to which food animal production may be contributing to antimicrobial drug resistance and might provide a direct measure of the rates of reversibility of antimicrobial drug resistance that might be achieved by curtailing antimicrobial usage.

BackgroundArcobacter species are considered emerging foodborne pathogens that can potentially cause serious infections in animals and humans. This cross-sectional study determined the frequency of potentially pathogenic Arcobacter spp. in both commercial and smallholder farm animals in Ghana and Tanzania. A total of 1585 and 1047 (poultry and livestock) samples were collected in Ghana and Tanzania, respectively. Selective enrichment media, along with oxidase and Gram testing, were employed for isolation of suspected Arcobacter spp. and confirmation was done using MALDI-TOF MS. Antibiotic susceptibility was assessed through disk diffusion method and ECOFFs were generated, for interpretation, based on resulting inhibition zone diameters.ResultsThe overall Arcobacter frequency was higher in Ghana (7.0%, n = 111) than in Tanzania (2.0%, n = 21). The frequency of Arcobacter in commercial farms in Ghana was 10.3% (n/N = 83/805), while in Tanzania, it was 2.8% (n/N = 12/430). Arcobacter was detected in only 3.6% (n/N = 28/780) of the samples from smallholder farms in Ghana and 1.5% (n/N = 9/617) of the samples from Tanzania. For commercial farms, in Ghana, the presence of Arcobacter was more abundant in pigs (45.1%, n/N = 37/82), followed by ducks (38.5%, n/N = 10/26) and quails (35.7%, n/N = 10/28). According to MALDI-TOF-based species identification, Arcobacter butzleri (91.6%, n/N = 121/132), Arcobacter lanthieri (6.1%, n/N = 8/132), and Arcobacter cryaerophilus (2.3%, n/N = 3/132) were the only three Arcobacter species detected at both study sites. Almost all of the Arcobacter from Ghana (98.2%, n/N = 109/111) were isolated during the rainy season. The inhibition zone diameters recorded for penicillin, ampicillin, and chloramphenicol allowed no determination of an epidemiological cut-off value. However, the results indicated a general resistance to these three antimicrobials. Multidrug resistance was noted in 57.1% (n/N = 12/21) of the Arcobacter isolates from Tanzania and 45.0% (n/N = 50/111) of those from Ghana. The type of farm (commercial or smallholder) and source of the sample (poultry or livestock) were found to be associated with multi-drug resistance.ConclusionsThe high levels of MDR Arcobacter detected from farms in both countries call for urgent attention and comprehensive strategies to mitigate the spread of antimicrobial resistance in these pathogens.

Pesticides have a severe impact on environmental pollution and human health, causing significant self-poisoning deaths in low- and middle-income countries. This study examines inflammation in farmers due to pesticide exposure by measuring MCP-1, IL-1β, and levels of ACTH. Using a cross-sectional design, 312 participants from conventional and organic farmer groups in Dau District, Malang Regency, were randomly selected. Results showed IL-1β levels were 633.29 ± 33.20 pg/mL in conventional farmers and 308.52 ± 65.18 pg/L in organic farmers (p < 0.001), MCP-1 levels were 506.58 ± 75.24 and 141.19 ± 39.19 pg/L, and ACTH levels were 456.64 ± 118.34 pg/L and 61.09 ± 15.98 pg/L, respectively (p < 0.001). These findings suggest that pesticide exposure induces vascular inflammation, evidenced by increased inflammatory markers in conventional farmers.

BackgroundA thorough understanding of lameness prevalence is essential for evaluating the impact of this condition on the dairy industry and assessing the effectiveness of preventive strategies designed to minimize its occurrence. Therefore, this cross-sectional study aimed to ascertain the prevalence of lameness and identify potential risk factors associated with lameness in Holstein Friesian crossbred cows across both commercial and smallholder dairy production systems in Bengaluru Rural District of Karnataka, India.MethodsThe research encompassed six commercial dairy farms and 139 smallholder dairy farms, involving a total of 617 Holstein Friesian crossbred cattle. On-site surveys were conducted at the farms, employing a meticulously designed questionnaire. Lameness in dairy cattle was assessed subjectively using a locomotion scoring system. Both bivariate and binary logistic regression models were employed for risk assessment, while principal components analysis (PCA) was conducted to address the high dimensionality of the data and capture the underlying structure of the explanatory variables.ResultsThe overall lameness prevalence of 21.9% in commercial dairy farms and 4.6% in smallholder dairy farms. Various factors such as age, body weight, parity, body condition score (BCS), floor type, hock and knee injuries, animal hygiene, provision of hoof trimming, and the presence of hoof lesions were found to be significantly associated with lameness. Binary logistic regression analysis indicated that the odds of lameness in crossbred cows increased with higher parity, decreased BCS, presence of hard flooring, poor animal hygiene, and the existence of hoof lesions. These factors were identified as potential risk factors for lameness in dairy cows. Principal component analysis unveiled five components explaining 71.32% of the total variance in commercial farms and 61.21% in smallholder dairy farms. The extracted components demonstrated higher loadings of housing and management factors (such as hoof trimming and provision of footbath) and animal-level factors (including parity, age, and BCS) in relation to lameness in dairy cows.ConclusionsThe findings suggest that principal component analysis effectively reduces the dimensionality of risk factors. Addressing these identified risk factors for lameness is crucial for the strategic management of lameness in dairy cows. Future research in India should investigate the effectiveness of management interventions targeted at the identified risk factors in preventing lameness in dairy cattle across diverse environments.

Association between farm biosecurity practices and antimicrobial usage on commercial chicken farms in Chattogram, Bangladesh

The COVID-19 pandemic has had a substantial impact on various economic sectors, including poultry production and trading in Bangladesh. We aimed to estimate the total economic losses and determine the causes behind these losses in commercial chicken farms during the COVID-19 in Bangladesh. We conducted a cross-sectional study using both qualitative and quantitative approaches across six districts from September to December 2021. The data collection involved semi-structured questionnaire interviews with 220 commercial poultry farmers and conducting in-depth interviews (IDIs) with 20 farm owners. We employed stepwise regression analysis to determine the optimal model for forecasting the average losses per farm caused by COVID-19. This model was built using the average reduced egg price, reduced bird price, and increased feed price of each individual farm. These averages were then used to predict the average farm loss, which was subsequently extrapolated to determine the total national loss. We estimated that the national loss in the small and medium-scale poultry sector during the COVID-19 lockdown amounted to 98.5 million USD, with the model predicting an average economic loss of $1407.6 per commercial farm. The majority (90%) of farmers experienced losses during this period. Majority of broiler (83.54%) and layer (80.65%) farmers, and approximately half of the Sonali farmers (54.10%) had to change their trading patterns or supply chains. After the pandemic period, about 33.33% of broilers, 31.03% of layer, and 45.90% of Sonali farmers managed to recover their losses. The poultry farmers encountered numerous challenges that impeded their ability to sell birds. These challenges resulted from transportation restrictions, widespread rumors leading to a sharp decline in demand, and significant losses from reduced egg and live bird prices. Consequently, some farmers were forced to close their farms, while others adapted by changing their trading patterns. To cope with the financial strain, some farmers resorted to obtaining loans from financial organizations, or seeking help from relatives, and a fortunate few received incentives from the government. Farmers suggested price monitoring, trainings, low-interest loans, and government incentives. Additionally, the formation of farmer's associations, exempting poultry from restrictions and lockdown, raising mass awareness, and including farmers' representatives in pandemic preparedness teams are deemed essential measures to safeguard the economic interests in any future pandemic crises. The marginal and small-scale poultry sectors in Bangladesh were severely impacted by the COVID-19 pandemic and the subsequent lockdown, with many farmers still struggling in recuperating their financial losses. It is imperative for the government to aids these farmers to support their contributions to protein supply and poverty alleviation in the community.

Danish dairy farmers' acceptance of and willingness to use semen from bulls produced by means of in vitro embryo production and genomic selection