Spatial distribution of poultry farms using point pattern modelling: A method to address livestock environmental impacts and disease transmission risks.

The distribution of farm locations and sizes is paramount to characterize patterns of disease spread. With some regions undergoing rapid intensification of livestock production, resulting in increased clustering of farms in peri-urban areas, measuring changes in the spatial distribution of farms is crucial to design effective interventions. However, those data are not available in many countries, their generation being resource-intensive. Here, we develop a farm distribution model (FDM), which allows the prediction of locations and sizes of poultry farms in countries with scarce data. The model combines (i) a Log-Gaussian Cox process model to simulate the farm distribution as a spatial Poisson point process, and (ii) a random forest model to simulate farm sizes (i.e. the number of animals per farm). Spatial predictors were used to calibrate the FDM on intensive broiler and layer farm distributions in Bangladesh, Gujarat (Indian state) and Thailand. The FDM yielded realistic farm distributions in terms of spatial clustering, farm locations and sizes, while providing insights on the factors influencing these distributions. Finally, we illustrate the relevance of modelling realistic farm distributions in the context of epidemic spread by simulating pathogen transmission on an array of spatial distributions of farms. We found that farm distributions generated from the FDM yielded spreading patterns consistent with simulations using observed data, while random point patterns underestimated the probability of large outbreaks. Indeed, spatial clustering increases vulnerability to epidemics, highlighting the need to account for it in epidemiological modelling studies. As the FDM maintains a realistic distribution of farm location and sizes, its use to inform mathematical models of disease transmission is particularly relevant for regions where these data are not available.

Changes in mammary infection status in dairy cows during the dry period using dry cow therapy approaches on three farms.

This case study evaluated the mammary infection status of dairy cows during the dry periods and explored the associated problems in their quarters with dry cow therapy (DCT). This study assessed intramammary infections, antibiotic efficacy, and antimicrobial resistance of pathogens in 464-quarter milk samples from 59 dairy cows during the dry periods after applying blanket DCT, non-DCT, and selective DCT approaches on three farms. The recovery rates of intramammary infections were 95% (19/20 quarters) with blanket DCT on farm A, 70% (14/20) with non-DCT on farm B, and 19% (4/21) with selective DCT on farm C. Analysis of mammary infections in cows with DCT revealed that mammary infections were controlled by blanket DCT, well controlled by non-DCT, and substantial problems remained in selective DCT. Lower intramammary infection prevalence in the quarters at postpartum appeared to be associated with higher recovery of mammary infections, fewer new infections, and lower uncured mammary infections within the herds. Antibacterial resistance in 14 coagulase-negative staphylococci isolated to six antimicrobial drugs was suggested to be linked to antibiotic use on the farm. Follow-up studies on the quarter-based infection status with DCT will assist in improving mastitis control in cows during the dry period.

Enhancing infection control practices and biosecurity plans on Swedish pig farms: insights, challenges, and strategies.

BACKGROUND: African swine fever (ASF) poses a threat to the global pig industry, leading to significant economic losses and widespread disruptions in pig farming and associated sectors. In September 2023, the first case of ASF in Swedish wild boar triggered immediate responses from authorities, including the establishment of restricted zones and culling measures. A new ASF certification programme for pig herds was initiated to improve biosecurity and proactive disease management. This survey aimed to assess the sentiments and actions of Swedish pig farmers six months post-outbreak, particularly regarding biosecurity measures. Such information is important to improve preparedness for future disease threats. A questionnaire was distributed to members of the Swedish pig producers' organisation. RESULTS: A total of 113 farmers responded (response rate 27%), with the majority considering the risk of ASF reappearing in Sweden as high. The estimated cost for connecting the farms to the ASF certification programme varied greatly, with a majority identifying cost as a substantial hurdle. While many farmers sought biosecurity advice from veterinarians, 43% had not implemented suggested measures. Over one third had not received concrete measures that would fit their farms, and 14% had not received any biosecurity advice from veterinarians at all. Discussions among farmers emphasized concerns about ASF outbreaks, transmission mechanisms, and regulatory compliance, highlighting the importance of ongoing communication and knowledge exchange to address the challenges posed by ASF effectively. Additionally, participants also mentioned the role of dense wild boar populations and shortcomings in municipal food waste management as important risk factors. CONCLUSIONS: The responding farmers expressed widespread concern about new ASF outbreaks. A majority identified cost as a substantial hurdle for joining the ASF certification programme. While many farmers consulted veterinarians for advice on biosecurity, a significant number had yet to implement suggested measures and one third had not received specific guidance suitable for their farms. Stakeholder conversations highlighted concerns about ASF outbreaks, transmission, and compliance. They also discussed the role of dense wild boar populations and issues with municipal food waste management as significant risk factors for ASF.

Low-cost biosecurity measures are associated with reduced detection of non-Typhoidal Salmonella in Nigerian poultry while inappropriate antibiotic use is widespread.

Large-scale poultry production in low- and middle-income countries may be a source of adulterated products (e.g., Salmonella contamination, antibiotic residues) that can be disseminated over wide areas. We employed a cross-sectional survey of 199 randomly selected poultry farms in Lagos State, Nigeria, to estimate the prevalence of non-typhoidal Salmonella (NTS), and biosecurity and antibiotic use practices. Pooled fecal samples were collected from laying chickens and from poultry handlers. Selective culture, biochemical assays, and PCR (invA) were used to isolate and confirm NTS isolates. NTS was detected at 14% of farms (28/199) and from 10% of farm workers (6/60). Multivariate logistic regression analysis indicated that antiseptic foot dips reduced the odds ratio (OR) for detecting NTS in chicken feces [OR: 0.55; 95% confidence interval (CI) 0.07-0.58]. Most farms (94.5%, 188/199) used antibiotics for treatment and prophylaxis, but no farms (0/199) exercised withdrawal before sale of products. Most farms (86.4%, 172/199) reported using antibiotic cocktails that included medically important colistin, ciprofloxacin, chloramphenicol, and gentamicin. Egg production in Lagos State relies heavily on antibiotics and antibiotic residues are likely passed to consumers through poultry products, but there is evidence that low-cost biosecurity controls are effective for limiting the presence of NTS on farms.

Sod farms drive habitat selection of a migratory grassland shorebird during a critical stopover period.

Migratory shorebirds are one of the fastest declining groups of North American avifauna. Yet, relatively little is known about how these species select habitat during migration. We explored the habitat selection of Buff-breasted Sandpipers (Calidris subruficollis) during spring and fall migration through the Texas Coastal Plain, a major stopover region for this species. Using tracking data from 118 birds compiled over 4 years, we found Buff-breasted Sandpipers selected intensively managed crops such as sod and short-stature crop fields, but generally avoided rangeland and areas near trees and shrubs. This work supports prior studies that also indicate the importance of short-stature vegetation for this species. Use of sod and corn varied by season, with birds preferring sod in spring, and avoiding corn when it is tall, but selecting for corn in fall after harvest. This dependence on cropland in the Texas Coastal Plain is contrary to habitat use observed in other parts of their non-breeding range, where rangelands are used extensively. The species' almost complete reliance on a highly specialized crop, sod, at this critical stopover site raises concerns about potential exposure to contaminants as well as questions about whether current management practices are providing suitable conditions for migratory grassland birds.

Quantification of wildlife visits to pig farms via camera traps in Japan.

Infectious diseases in livestock not only cause significant economic losses but also affect food security. Although wildlife may be involved in these infectious diseases by serving as reservoirs, research has primarily focused on livestock and related species. Moreover, while these species represent a potential threat in wildlife-borne infectious diseases, comprehensive surveys of the presence of various species are limited. In this study, we aimed to quantitatively investigate the occurrence of various mammals and birds at three pig farms in Japan. We conducted camera trap surveys from October 15, 2020, to March 24, 2022, and determined the relative abundance index inside and outside the sanitary control zone. Wild boar (Sus scrofa), sika deer (Cervus nippon), and Japanese serow (Capricornis crispus) were photographed only outside the sanitary control zone. In contrast, small and medium-sized mammals, such as feral cats (Felis catus), raccoons (Procyon lotor), and rodent species (Muridae), and birds, such as the rufous oriental turtle dove (Streptopelia orientalis) and crows of the genus Corvus, were photographed both inside and outside the sanitary control zone. This comprehensive quantitative evidence suggests that various mammals and birds may be in indirect contact with livestock, highlighting the need to improve biosecurity at livestock farms. Moreover, while fences are effective against large mammals, they are inefficient against small to medium-sized mammals and birds. Therefore, the results of this study provide important insights into enhancing biosecurity on livestock farms by strengthening physical fencing, disinfecting clothing and equipment, and complying with standards of hygiene management.

Embedding Water-Energy-Food nexus and circularity assessment for organization benchmarking: A case study for dairy farms.

The Water-Energy-Food (WEF) nexus approach is increasingly being used for supporting a transition to sustainable development, with initiatives involving the concept of circular economy (CE). In the agricultural sector in particular, assessing this nexus is crucial to ensure food security, control the consumption of key resources such as water and energy, as well as measure atmospheric emissions linked to climate change. This manuscript aims to propose a novel approach by coupling the WEF nexus with a circularity indicator, seeking to capture in a single index (the WEF+CEi) both performances in a sample of companies. The novel approach is applied to 30 dairy farms located in Galicia (NW Spain) to benchmark them in a holistic manner. To do this, the WEF nexus of each farm was represented through the following indicators: carbon footprint, water footprint, energy footprint, and food productivity. In addition, the percentage of circularity for each farm, and for the agro-industrial cooperative was measured thanks to the application of a circularity tool in percentage terms. Finally, the WEF+CEi indicator was obtained using the multicriteria mathematical tool of Data Envelopment Analysis (DEA). The results show that without considering the agro-industrial cooperative, the system is 51 % circular. On the other hand, considering the farms and the cooperative, the system goes up to 80 % of circularity. Finally, the proposed approach can support decision-making and provide insights for producers and stakeholders in the area.

Prevalence, antimicrobial resistance and genomic comparison of non-typhoidal salmonella isolated from pig farms with different levels of intensification in Yangon Region, Myanmar.

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.

Lignite reduces odour from broiler farms without reducing production performance.

An unavoidable consequence of chicken meat production is the generation of substantial quantities of spent litter. This poses several environmental and social challenges, as broiler farms become hotspots for odour emissions. The main source of odour from broiler litter is the microbial decomposition of organic material. Thus, lignite's previously shown capacity to reduce microbial activity in broiler litter was expected to reduce odour emissions from broiler housing. The effect of lignite on odour emission rate (OER) (ou/s) was investigated using dynamic olfactometry over two consecutive summer broiler grow-out cycles in Victoria, Australia, with lignite applied at 3.5 kg/m2. The air quality dispersion model, AERMOD, was used to investigate how lignite's effect on OER influenced the predicted odour dispersion distances and concentrations in the context of various Australian regulatory requirements. Additionally, the effect of lignite on bird production performance was also determined. This study showed that lignite reduced the OER from commercial broiler housing by an average of 56% over both grow-outs. This effect was observed for the duration of the trial. The observed reduction in OER reduced the required separation distances by 44-53% according to the state odour criteria for Victoria, New South Wales, Queensland and South Australia. There were no observed differences in feed conversion ratio, bird live weight or mortality throughout either grow-out. This study demonstrated the capacity of lignite to reduce odour emissions from commercial broiler housing without reducing bird production performance.

An unconventional approach to evaluating the environmental role of a productive system: An environmental assessment of beef farms in North-West Italy.

The environmental impact of livestock is often evaluated separately from the other agricultural activities involved in an integrated system, such as that of the rearing of Piemontese cattle in the area of origin of the breed. The most frequently used assessment methods (e.g. Footprint approaches or a Life Cycle Assessment) are in fact often used, through a product-based approach, to analyse a single productive process, but such methods do not consider the production of agro-ecological services, and they neglect the interactions that characterise complex systems. Moreover, such methods often only consider the negative aspects of the environmental impact and misrepresent less intensive agriculture practices. However the current gaps in knowledge about the carbon sequestration of agricultural ecosystems, which are complex and integrated systems, require further investigation and other types of analysis tools. A carbon (C) balance of 1223 Piemontese breed beef farms, located in North-West Italy, has been calculated to evaluate whether such a method could be applied to overcome the aforementioned limitations, to evaluate whether it could be used to describe a complex and integrated system, to highlight the relationships that exist between rearing and agricultural activities and to characterise their environmental roles. Conducting a mass balance involves considering the input and output material flows and their accumulation within a system. Thus, the data necessary to quantify the C input, output and internal fluxes of a system at the farm gate, pertaining to the vegetable and animal production processes (productive factors, crop yields, animal performances, productions and sales, reuses), were collected from official documentation, and were then completed and verified through site visits. The mass balance of the system was transformed into C fluxes using stoichiometric coefficients. The fluxes evaluated for the balance were then used to estimate the changes in the C stocks to highlight not only the C emissions or losses from the system, but also their contributions towards reducing environmental hazards. A sensitivity analysis was carried out to evaluate the uncertainty and the robustness of the obtained results. The net C exchange from plants was the flux that contributed the most, amounting to 94.3 % of the inputs, and this was followed by soil losses and animal gases released through respiration and enteric fermentation, which amounted to 42.8 and 36.2 % of the outputs, respectively. The C stored and released by the considered system was calculated considering the C fluxes. Plant, animal and soil storage sites were included in the system, whereas the air site was left out. A constant C content was assumed for the soil. The productive activities of the selected group of beef farms in the Consortium were calculated to remove 96.1 103 t of C from the atmosphere (air site) over a period of one year, and that this amount of C was transferred to plant growth and agricultural products (plant site) and to an increase in live weight (LW) of the animals (animal site). The rates of the stored C to agricultural and wooded areas and to the LW of the animals slaughtered in one year were 1.18 t ha-1 and 2.24 t C t-1 LW, respectively. The sensitivity analysis demonstrated that the C balance was always positive, even for the worst scenario. This study has shown that the examined beef production system, when analysed as an integrated and complex system, can be considered an important C sink and that it is necessary to reconsider the role that livestock, and ruminants in particular, play in the global greenhouse effect.

The ISVsa3-ORF2-abh-tet(X4) circular intermediate-mediated transmission of tigecycline resistance in Escherichia coli isolates from duck farms.

Tigecycline is a last-resort drug used to treat serious infections caused by multidrug-resistant bacteria. tet(X4) is a recently discovered plasmid-mediated tigecycline resistance gene that confers high-level resistance to tigecycline and other tetracyclines. Since the first discovery of tet(X4) in 2019, it has spread rapidly worldwide, and as a consequence, tigecycline has become increasingly ineffective in the clinical treatment of multidrug-resistant infections. In this study, we identified and analyzed tet(X4)-positive Escherichia coli isolates from duck farms in Hunan Province, China. In total, 976 samples were collected from nine duck farms. Antimicrobial susceptibility testing and whole-genome sequencing (WGS) were performed to establish the phenotypes and genotypes of tet(X4)-positive isolates. In addition, the genomic characteristics and transferability of tet(X4) were determined based on bioinformatics analysis and conjugation. We accordingly detected an E. coli strain harboring tet(X4) and seven other resistance genes in duck feces. Multi-locus sequence typing analysis revealed that this isolate belonged to a new clone, and subsequent genetic analysis indicated that tet(X4) was carried in a 4608-bp circular intermediate, flanked by ISVsa3-ORF2-abh elements. Moreover, it exhibited transferability to E. coli C600 with a frequency of 10-5. The detection of tet(X4)-harboring E, coli strains on duck farms enhances our understanding of tigecycline resistance dynamics. The transferable nature of the circular intermediate of tet(X4) contributing to the spread of tigecycline resistance genes poses a substantial threat to healthcare. Consequently, vigilant monitoring and proactive measures are necessary to prevent their spread.

Evaluating food security and nutritional pathways of rural farm families: Empirical evidence from northeast India.

The study aimed to ascertain a relationship between agricultural status, socioeconomic factors, and nutrition of farm families. The study was conducted in selected villages in the West Garo Hills district of Meghalaya, using Stratified Random Sampling (St. RS). Using pretested interview schedules, we collected primary data from respondents in 2020 and 2021, focusing on socioeconomic variables, body mass index, and income from agriculture and related sectors. The data was analysed using correlation analyses and separate combined regression estimates for each year and month were obtained. Results from the study indicate that agricultural income significantly influenced nutritional status (p < 0.05) and household income growth was also found significant. The region's agricultural production of cereals, pulses, and vegetables was insufficient, as was the production of meat and meat products, milk, and milk products. Hence, expenditure towards purchasing the above food groups from the market was found to be significant (p < 0.05). Therefore, the markets near the mainland especially in the hilly region play a crucial role in the nutritional pathway of rural farm families.

Case study on the relationship between transmission of antibiotic resistance genes and microbial community under freeze-thaw cycle on cold-region dairy farm.

Freeze-thaw cycle (FTC) is a naturally occurring phenomenon in high-latitude terrestrial ecosystems, which may exert influence on distribution and evolution of microbial community in the soil. The relationship between transmission of antibiotic resistance genes (ARGs) and microbial community was investigated upon the case study on the soil of cold-region dairy farm under seasonal FTC. The results demonstrated that 37 ARGs underwent decrease in the abundance of blaTEM from 80.4 % for frozen soil to 71.7 % for thawed soil, and that sul2 from 8.8 % for frozen soil to 6.5 % for thawed soil, respectively. Antibiotic deactivation was identified to be closely related to the highest relative abundance of blaTEM, and the spread of sulfonamide resistance genes (SRGs) occurred mainly via target modification. Firmicutes in frozen soil were responsible for dominating the abundance of ARGs by suppressing the native bacteria under starvation effect in cold regions, and then underwent horizontal gene transfer (HGT) among native bacteria through mobile genetic elements (MGEs). The TRB-C (32.6-49.1 %) and tnpA-06 (0.27-7.5 %) were significantly increased in frozen soil, while Int3 (0.67-10.6 %) and tnpA-04 (11.1-19.4 %) were up-regulated in thawed soil. Moreover, the ARGs in frozen soil primarily underwent HGT through MGEs, i.e. TRB-C and tnpA-06, with increased number of Firmicutes serving as carrier. The case study not only demonstrated relationship between transmission of ARGs and microbial community in the soil under practically relevant FTC condition, but also emphasized the importance for formulating better strategies for preventing FTC-induced ARGs in dairy farm in cold regions.

Inversion model of soil salinity in alfalfa covered farmland based on sensitive variable selection and machine learning algorithms.

Purpose: Timely and accurate monitoring of soil salinity content (SSC) is essential for precise irrigation management of large-scale farmland. Uncrewed aerial vehicle (UAV) low-altitude remote sensing with high spatial and temporal resolution provides a scientific and effective technical means for SSC monitoring. Many existing soil salinity inversion models have only been tested by a single variable selection method or machine learning algorithm, and the influence of variable selection method combined with machine learning algorithm on the accuracy of soil salinity inversion remain further studied. Methods: Firstly, based on UAV multispectral remote sensing data, by extracting the spectral reflectance of each sampling point to construct 30 spectral indexes, and using the pearson correlation coefficient (PCC), gray relational analysis (GRA), variable projection importance (VIP), and support vector machine-recursive feature elimination (SVM-RFE) to screen spectral index and realize the selection of sensitive variables. Subsequently, screened and unscreened variables as model input independent variables, constructed 20 soil salinity inversion models based on the support vector machine regression (SVM), back propagation neural network (BPNN), extreme learning machine (ELM), and random forest (RF) machine learning algorithms, the aim is to explore the feasibility of different variable selection methods combined with machine learning algorithms in SSC inversion of crop-covered farmland. To evaluate the performance of the soil salinity inversion model, the determination coefficient (R2), root mean square error (RMSE) and performance deviation ratio (RPD) were used to evaluate the model performance, and determined the best variable selection method and soil salinity inversion model by taking alfalfa covered farmland in arid oasis irrigation areas of China as the research object. Results: The variable selection combined with machine learning algorithm can significantly improve the accuracy of remote sensing inversion of soil salinity. The performance of the models has been improved markedly using the four variable selection methods, and the applicability varied among the four methods, the GRA variable selection method is suitable for SVM, BPNN, and ELM modeling, while the PCC method is suitable for RF modeling. The GRA-SVM is the best soil salinity inversion model in alfalfa cover farmland, with Rv 2 of 0.8888, RMSEv of 0.1780, and RPD of 1.8115 based on the model verification dataset, and the spatial distribution map of soil salinity can truly reflect the degree of soil salinization in the study area. Conclusion: Based on our findings, the variable selection combined with machine learning algorithm is an effective method to improve the accuracy of soil salinity remote sensing inversion, which provides a new approach for timely and accurate acquisition of crops covered farmland soil salinity information.

Insights into the enhanced adsorption of glyphosate by dissolved organic matter in farmland Mollisol: effects and mechanisms of action.

Dissolved organic matter (DOM) is easy to combine with residual pesticides and affect their morphology and environmental behavior. Given that the binding mechanism between DOM and the typical herbicide glyphosate in soil is not yet clear, this study used adsorption experiments, multispectral techniques, density functional theory, and pot experiments to reveal the interaction mechanism between DOM and glyphosate on Mollisol in farmland and their impact on the environment. The results show that the adsorption of glyphosate by Mollisol is a multilayer heterogeneous chemical adsorption process. After adding DOM, due to the early formation of DOM and glyphosate complex, the adsorption process gradually became dominated by single-layer chemical adsorption, and the adsorption capacity increased by 1.06 times. Glyphosate can quench the endogenous fluorescence of humic substances through a static quenching process dominated by hydrogen bonds and van der Waals forces, and instead enhance the fluorescence intensity of protein substances by affecting the molecular environment of protein molecules. The binding of glyphosate to protein is earlier, of which affinity stronger than that of humic acid. In this process, two main functional groups (C-O in aromatic groups and C-O in alcohols, ethers and esters) exist at the binding sites of glyphosate and DOM. Moreover, the complexation of DOM and glyphosate can effectively alleviate the negative impact of glyphosate on the soil. This study has certain theoretical guidance significance for understanding the environmental behavior of glyphosate and improving the sustainable utilization of Mollisol.

Assessing antimicrobial resistance profiles of Salmonella enterica in the pork production system.

Introduction. Salmonella enterica is a significant enteric pathogen affecting human and livestock health. Pork production is a common source of Salmonella contamination, with emerging multidrug resistance (MDR) posing a global health threat.Gap statement. Salmonella contamination and antimicrobial resistance (AMR) profiles in the pig production chain are underreported.Aim. To investigate the prevalence of S. enterica in the pig production chain and characterise their AMR profiles.Methodology. We collected 485 samples from pig farms, a standard pig abattoir and retail markets in Patthalung and Songkhla provinces in southern Thailand. Antimicrobial susceptibility testing was performed on these samples, and AMR profiles were determined.Results. S. enterica was detected in 68.67% of farm samples, 45.95% of abattoir samples and 50.67% of retail market samples. Analysis of 264 isolates, representing 18 serotypes, identified S. enterica serotype Rissen as the most prevalent. The predominant resistance phenotypes included ampicillin (AMP, 91.29%), tetracycline (TET, 88.26%) and streptomycin (STR, 84.47%). Over 80% of isolates showed resistance to three or more antimicrobial classes, indicating MDR. The AMP-STR-TET resistance pattern was found in nearly 70% of all MDR isolates across the production chain.Conclusions. The high prevalence of MDR is consistent with extensive antimicrobial use in the livestock sector. The presence of extensively resistant S. enterica highlights the urgent need for antimicrobial stewardship. Strengthening preventive strategies and control measures is crucial to mitigate the risk of MDR Salmonella spreading from farm to fork.

Transmission of dominant strains of Campylobacter jejuni and Campylobacter coli between farms and retail stores in Ecuador: Genetic diversity and antimicrobial resistance.

Thermotolerant Campylobacter is an important zoonotic pathogen known for causing gastroenteritis in humans, with poultry as its primary reservoir. A total of 468 samples were collected, of which 335 were chicken carcass samples (representing the food component), and 133 were chicken caeca samples (representing the animal component). These samples underwent culture, with colonies examined under a microscope. Species identification was achieved through multiplex PCR. Additionally, antimicrobial susceptibility profiles were determined using the Kirby-Bauer method, testing for sensitivity to gentamicin, ciprofloxacin, tetracycline, and erythromycin. Additionally, 55 C. jejuni (62.5%) and 33 C. coli (37.5%) isolates were selected for whole genome sequencing (WGS). A High prevalence of Campylobacter was observed, with rates of 95.5% (n = 127, CI95%: 92.5% - 98.5%) in the animal component and 72.5% (n = 243, CI95%: 69.9% - 75.1%) in the food component. Specifically, C. jejuni was detected in 33.1% (n = 42) of poultry farms and 38.3% (n = 93) of chicken carcasses, while C. coli was found in 64.6% (n = 82) of poultry farms and 60.5% (n = 147) of chicken carcasses. Antimicrobials with the highest rates of resistance (67%-100%) were ciprofloxacin and tetracycline, in both animal and food component isolates. Erythromycin resistance was notable, ranging from 22% to 33%, with only two C. jejuni isolates from retail were resistant to gentamicin. Furthermore, multidrug resistance was identified in 23% (20 isolates) of the Campylobacter isolates. Genetic analysis revealed the presence of fourteen resistance genes in both C. jejuni and C. coli isolates, including tet(O), blaOXA-460, blaOXA-184, blaOXA-489, blaOXA-193, blaOXA-784, blaOXA-603, aph(3')-IIIa, aad9, aph(2'')-If, aadE-Cc, sat4, and ant(6)-Ia. Additionally, twenty-five plasmids were detected in the 88 Campylobacter isolates examined. Interestingly, most isolates also harbored genes encoding putative virulence factors associated with pathogenicity, invasion, adherence, and production of cytolethal distending toxin (cdt): cheV, cheA, cheW, cheY, flaA, flgR, flaC, flaD, flgB, flgC, ciaB, ciaC. The WGS analysis showed the presence of several cgSTs in both animal and food components, with nine of them widely disseminated between components. Moreover, C. coli and C. jejuni isolates from different sources presented less than 11 single nucleotide polymorphisms (SNPs), suggesting clonality (16 isolates). Further analysis using SNP tree demonstrated widespread distribution of certain C. jejuni and C. coli clones across multiple farms and retail stores. This study presents, for the first-time, insights into the clonality, plasmid diversity, virulence, and antimicrobial resistance (AMR) of thermotolerant Campylobacter strains originating from the Ecuadorian poultry industry. The identification of AMR genes associated with the main antibiotics used in the treatment of campylobacteriosis in humans, highlights the importance of the prudent use of antimicrobials in the poultry industry. Additionally, this research remarks the need for regional studies to understand the epidemiology of this pathogen.

Spatial patterns of influenza A virus spread across compartments in commercial swine farms in the United States.

Multiple genetic variants of H1 and H3 influenza A viruses (IAVs) circulate concurrently in US swine farms. Understanding the spatial transmission patterns of IAVs among these farms is crucial for developing effective control strategies and mitigating the emergence of novel IAVs. In this study, we analysed 1909 IAV genomic sequences from 785 US swine farms, representing 33 farming systems across 12 states, primarily in the Midwest from 2004 to 2023. Bayesian phylogeographic analyses were performed to identify the dispersal patterns of both H1 and H3 virus genetic lineages and to elucidate their spatial migration patterns within and between different systems. Our results showed that both intra-system and inter-system migrations occurred between the swine farms, with intra-system migrations being more frequent. However, migration rates for H1 and H3 IAVs were similar between intra-system and inter-system migration events. Spatial migration patterns aligned with expected pig movement across different compartments of swine farming systems. Sow-Farms were identified as key sources of viruses, with bi-directional migration observed between these farms and other parts of the system, including Wean-to-Finish and Gilt-Development-Units. High intra-system migration was detected across farms in the same region, while spread to geographically distant intra- and inter-system farms was less frequent. These findings suggest that prioritizing resources towards systems frequently confronting influenza problems and targeting pivotal source farms, such as sow farms, could be an effective strategy for controlling influenza in US commercial swine operations.

Wild sympatric rodents inhabiting pig farm environments may facilitate the spillover of Enterocytozoon bieneusi from pig farms.

Enterocytozoon bieneusi is a zoonotic pathogen prevalent in mammalian and avian hosts across the globe. Wild small mammals, being abundant worldwide, serve as important sources of zoonotic disease transmission to humans. Here, 227 fecal samples were collected from five rodent and shrew species on 34 pig farms in China to investigate the prevalence and molecular characterization of E. bieneusi. The overall prevalence of E. bieneusi was 17.18% (39/227), with a distribution of 23.53% (32/136) in Rattus tanezumi, 8.62% (5/58) in Rattus norvegicus, and 8.00% (2/25) in Mus musculus. Eight E. bieneusi genotypes were identified, comprising four known genotypes: D (n = 8), EbpC (n = 8), PigEBITS7 (n = 9), and EbpA (n = 2), and four novel genotypes: CHPR1 (n = 7), CHPR2 (n = 1), CHPR3 (n = 2), and CHPR4 (n = 2). This study is the first to report E. bieneusi in rodents from pig farms in Henan, Shaanxi, and Shanxi Provinces in China. The host range of genotype EbpC was expanded with its first detection in M. musculus and R. tanezumi. All identified E. bieneusi genotypes belong to group 1, raising concerns about these sympatric rodents being reservoirs of zoonotic transmission. Moreover, the widespread distribution of genotype EbpC suggests potential cross-species transmission between sympatric rodents and domestic pigs. Our findings highlight the potential role of sympatric rodents in facilitating the spillover of E. bieneusi from pig farms, which could pose a potential public health threat.

Title: Les rongeurs sympatriques sauvages vivant dans les élevages porcins peuvent faciliter la propagation d'Enterocytozoon bieneusi. Abstract: Enterocytozoon bieneusi est un pathogène zoonotique répandu mondialement chez les hôtes mammifères et aviaires. Les petits mammifères sauvages, abondants dans le monde entier, constituent d'importantes sources de transmission de maladies zoonotiques à l'homme. Ici, 227 échantillons fécaux ont été collectés auprès de cinq espèces de rongeurs et de musaraignes dans 34 élevages porcins en Chine pour étudier la prévalence et la caractérisation moléculaire d'E. bieneusi. La prévalence globale d'E. bieneusi était de 17,18 % (39/227), avec une distribution de 23,53 % (32/136) chez Rattus tanezumi, 8,62 % (5/58) chez Rattus norvegicus et 8,00 % (2/25) chez Mus musculus. Huit génotypes d'E. bieneusi ont été identifiés, dont quatre génotypes connus (D (n = 8), EbpC (n = 8), PigEBITS7 (n = 9) et EbpA (n = 2)) et quatre génotypes nouveaux (CHPR1 (n = 7), CHPR2 (n = 1), CHPR3 (n = 2) et CHPR4 (n = 2)). Cette étude est la première à signaler la présence d'E. bieneusi chez des rongeurs provenant d'élevages porcins des provinces du Henan, du Shaanxi et du Shanxi en Chine. La gamme d'hôtes du génotype EbpC a été élargie avec sa première détection chez M. musculus et R. tanezumi. Tous les génotypes d'E. bieneusi identifiés appartiennent au groupe 1, ce qui soulève des inquiétudes quant au fait que ces rongeurs sympatriques soient des réservoirs de transmission zoonotique. De plus, la large distribution du génotype EbpC suggère une transmission interspécifique potentielle entre les rongeurs sympatriques et les porcs domestiques. Nos résultats soulignent le rôle potentiel des rongeurs sympatriques dans la facilitation de la propagation d'E. bieneusi à partir des élevages porcins, ce qui pourrait constituer une menace potentielle pour la santé publique.

Dissipation of pesticides and responses of bacterial, fungal and protistan communities in a multi-contaminated vineyard soil.

The effect of pesticide residues on non-target microorganisms in multi-contaminated soils remains poorly understood. In this study, we examined the dissipation of commonly used pesticides in a multi-contaminated vineyard soil and its effect on bacterial, fungal, and protistan communities. We conducted laboratory soil microcosm experiments under varying temperature (20°C and 30°C) and water content (20 % and 40 %) conditions. Pesticide dissipation half-lives ranged from 27 to over 300 days, depending on the physicochemical properties of the pesticides and the soil conditions. In both autoclaved and non-autoclaved soil experiments, over 50 % of hydrophobic pesticides (dimethomorph > isoxaben > simazine = atrazine = carbendazim) dissipated within 200 days at 20°C and 30°C. However, the contribution of biodegradation to the overall dissipation of soluble pesticides (rac-metalaxyl > isoproturon = pyrimethanil > S-metolachlor) increased to over 75 % at 30°C and 40 % water content. This suggests that soluble pesticides became more bioavailable, with degradation activity increasing with higher temperature and soil water content. In contrast, the primary process contributing to the dissipation of hydrophobic pesticides was sequestration to soil. High-throughput amplicon sequencing analysis indicated that water content, temperature, and pesticides had domain-specific effects on the diversity and taxonomic composition of bacterial, fungal, and protistan communities. Soil physicochemical properties had a more significant effect than pesticides on the various microbial domains in the vineyard soil. However, pesticide exposure emerged as a secondary factor explaining the variations in microbial communities, with a more substantial effect on protists compared to bacterial and fungal communities. Overall, our results highlight the variability in the dissipation kinetics and processes of pesticides in a multi-contaminated vineyard soil, as well as their effects on bacterial, fungal, and protistan communities.