Transmission identification of Escherichia coli aerosol in chicken houses to their environments using ERIC-PCR

Distribution and environmental dissemination of antibiotic resistance genes in poultry farms and surrounding ecosystems

Antibiotic resistance poses a significant threat to human and animal health worldwide, with farms serving as crucial reservoirs of Antibiotic Resistance Genes (ARGs) and Antibiotic-resistant bacteria. However, the distribution of ARGs in poultry farms and their transmission patterns in the environment remain poorly understood. This study collected samples of aerosol microorganisms, cloacal matter, soil, and vegetables from poultry farms and surrounding environments at three different distances. We used 16S rRNA gene sequencing and HT-qPCR to analyze the characteristics of aerosol microbial communities and the abundance of ARGs. At the phylum level, Proteobacteria, Firmicutes, and Bacteroidetes were dominant in cloacal samples, aerosol samples, and vegetable samples, while Proteobacteria Actinobacteriota and Acidobacteria dominated soil. Pseudomonas was dominant in cloacal samples at the genus level, whereas Fusobacterium was prevalent in soil. The diversity and richness of bacterial communities were more similar between cloacal samples than those observed between either sample type compared with soil. Our results showed that tetracycline and aminoglycoside ARG relative abundance was high across all sample types but significantly increased within feces/air compared to soils/vegetables. Association analysis revealed five potential host genera for ARG/MGE presence among various microbiota populations studied here. Our findings confirm that farms are important sources for the environmental dissemination of pathogens and ARGs.

Bioaerosols downwind from animal feeding operations: A comprehensive review

Bioaerosols originating from animal feeding operations (AFOs) may carry pathogens, allergens, and other hazardous biocomponents, such as endotoxins, posing a potential risk to community health and the environment when dispersed downwind. This review summarizes and synthesizes existing literature data on bioaerosols downwind from three major types of AFOs (swine, poultry, and cattle), covering their composition, concentration, dispersion patterns, measurement methodologies, potential health effects, and mitigation strategies. While many of these bioaerosols are typically detected only near AFOs, evidence indicates that certain bioaerosols, particularly viruses, can travel up to tens of kilometers downwind and remain infectious. Despite the critical importance of these bioaerosols, a refined modeling framework to simulate their transport and fate in downwind air has not yet been developed, nor have source attribution methods been established to track their origins in complex agricultural environments where multiple bioaerosols could co-exist. Therefore, it is imperative to further research downwind bioaerosols from AFOs, including their assessment, modeling, source attribution, and mitigation, to address the public health and environmental challenges associated with animal agriculture.

Surveillance of Escherichia coli in different types of chicken and duck hatcheries: one health outlook

Escherichia coli is an important zoonotic bacterium that significantly impacts one health concept. E. coli is normally detected in the gut of warm-blooded animals, but some serotypes can cause diseases in humans and animals. Moreover, it can continue for a long time in different environments, replicate in water, and survive outside different hosts. In this study, 171 samples collected from 10 different types of poultry hatcheries (automatic, semiautomatic, and manual "traditional" types) were examined for the prevalence of E. coli. PCR was applied to verify the E. coli isolates via 16S rRNA gene-specific primers. From the gathered samples, 62 E. coli isolates were recovered (36.3%). The highest prevalence was met with the manual "traditional" hatcheries (57.1%) with no significance difference (P = 0.243) in the 3 types of hatcheries. The incidence of E. coli varied significantly in different tested avian types and breeds. The prevalence was 35.7% in duck hatcheries and 37% in chicken hatcheries, with significant differences between breeds of both species (P = 0.024 and 0.001, respectively). The identification of zoonotic E. coli serotypes in this study is concerning, highlighting the need for collaborative efforts across various sectors, including social, environmental, and governance, to promote the adoption of the one health principle in the chicken business. Periodical surveillance, biosecurity measures at the hatcheries and farm levels, and boosting the immunity of birds were recommended to limit the risk of E. coli spread from avian sources to humans.

Effect of Ultraviolet Radiation on Reducing Airborne Escherichia coli Carried by Poultry Litter Particles

Airborne Escherichia coli (E. coli) originating in poultry houses can be transmitted outside poultry farms through the air, posing risks of barn-to-barn infection through airborne transmission. The objective of this study is to examine the effect of ultraviolet (UV) light on the inactivation of airborne E. coli carried by poultry dust particles under laboratory conditions. A system containing two chambers that were connected by a UV scrubber was designed in the study. In the upstream chamber of the system, airborne E. coli attached to dust particles were aerosolized by a dry aerosolization-based system. Two sets of air samplers were placed in the two chambers to collect the viable airborne E. coli. By comparing the concentration of airborne E. coli in the two chambers, the inactivation rates were calculated. The airborne E. coli inactivation rates were tested at different contact times with the aid of a vacuum pump (from 5.62 to 0.23 s of contact time) and different UV irradiance levels (of 1707 µW cm^-2 and 3422 µW cm^-2). The inactivation rates varied from over 99.87% and 99.95% at 5.62 s of contact time with 1707 µW cm^-2 and 3422 µW cm^-2 of UV irradiance to 72.90% and 86.60% at 0.23 s of contact time with 1707 µW cm^-2 and 3422 µW cm^-2 of UV irradiance. The designed system was able to create the average UV irradiation of 1707 µW cm^-2 and 3422 µW cm^-2 for one UV lamp and two UV lamps, respectively. The findings of this study may provide an understanding of the effect of UV light on the inactivation of airborne E. coli carried by dust particles and help to design an affordable mitigation system for poultry houses.

Study of antimicrobial activity and mechanism of vapor-phase cinnamaldehyde for killing Escherichia coli based on fumigation method

The vapor-phase antibacterial activity of essential oils makes them suitable for applications in air disinfection and other fields. At present, vapor-phase antibacterial activity of plant-based essential oils has rarely been reported. Herein, we report a new approach to investigate the antimicrobial activity and mechanism of vapor-phase cinnamaldehyde using Escherichia coli (E. coli) and three other pathogenic bacteria (Pseudomonas aeruginosa, Salmonella, Staphylococcus aureus) as model bacteria. Plate fumigation and agar block transfer techniques were used to determine the antimicrobial activities of vapor-phase cinnamaldehyde fumigation on the four types of bacteria, and the mechanism of action was determined by electrical conductivity (EC), OD260nm measurement, transmission electron microscopy (TEM), Fourier transform infrared spectroscopy (FTIR), and fluorescence spectroscopy. Cinnamaldehyde had good vapor-phase antibacterial activity against the four types of bacteria. The TEM, EC, and OD260nm measurements showed that after fumigation with cinnamaldehyde, the ultrastructures of the cells were damaged, and plasmolysis, cell collapse, and leakage of intracellular substances were observed. The FTIR and fluorescence spectroscopy analyses showed that the secondary and tertiary structures of bacterial membrane proteins were altered. These findings indicate that the cell membrane is an important target for plant-based essential oils to exert their vapor-phase antimicrobial effects. The results showed that plant-based essential oils can be developed as volatile broad-spectrum disinfection products and vapor-phase antiseptics.

Prevalence and Genetic Relationship of Predominant Escherichia coli Serotypes Isolated from Poultry, Wild Animals, and Environment in the Mekong Delta, Vietnam

Avian pathogenic Escherichia coli (APEC) is the main causative agent of avian colibacillosis, which is an important systemic disease of profound economic and clinical consequences for the poultry industry worldwide. In this study, 975 E. coli strains were isolated from 2,169 samples collected from cloacal swabs of chickens, in-farm wild animals (ants, geckos, flies, and rats), and environment. The highest proportion of E. coli isolation was obtained from chicken cloacal swabs with 71.05% (95% confidence interval (CI) 66.69-75.05%) followed by the proportions of 38.15% (95% CI 35.41-40.97%) and 38.11% (95% CI 34.15-42.24%) from wild animals or environment, respectively. Distribution of O-antigen serotypes of the E. coli isolates, including O1, O2, O18, and O78, was determined by PCR. The most predominant serotype was O18 (10.56%) followed by O2 (9.44%), O1 (7.79%), and O78 (6.56%). Of note, serotype O18 was more likely distributed in the examined wild animals, especially in geckos. Polymorphic DNA fingerprints, generated by ERIC-PCR, of representative E. coli strains of each serotype revealed genetic heterogeneity of the examined E. coli, and O18 was more divergent with 63 clusters formed from 66 isolates. Furthermore, several E. coli strains from different sample sources shared high DNA fingerprint relatedness, suggesting that there exists complex transmission of E. coli from chickens to wild animals and environment and vice versa in poultry husbandry settings. Although pathotypes of the examined E. coli were not determined in this study, our results provided important findings of epidemiological and genetic characteristics of E. coli in the Mekong Delta and highlighted the prerequisite of stricter biocontainment to reduce the prevalence and consequences of APEC in poultry production.

Multi-Omics Characterization of Host-Derived Bacillus spp. Probiotics for Improved Growth Performance in Poultry

Microbial feed ingredients or probiotics have been used widely in the poultry industry to improve production efficiency. Spore-forming Bacillus spp. offer advantages over traditional probiotic strains as Bacillus spores are resilient to high temperature, acidic pH, and desiccation. This results in increased strain viability during manufacturing and feed-pelleting processes, extended product shelf-life, and increased stability within the animal’s gastrointestinal tract. Despite numerous reports on the use of Bacillus spores as feed additives, detailed characterizations of Bacillus probiotic strains are typically not published. Insufficient characterizations can lead to misidentification of probiotic strains in product labels, and the potential application of strains carrying virulence factors, toxins, antibiotic resistance, or toxic metabolites. Hence, it is critical to characterize in detail the genomic and phenotypic properties of these strains to screen out undesirable properties and to tie individual traits to clinical outcomes and possible mechanisms. Here, we report a screening workflow and comprehensive multi-omics characterization of Bacillus spp. for use in broiler chickens. Host-derived Bacillus strains were isolated and screened for desirable probiotic properties. The phenotypic, genomic and metabolomic analyses of three probiotic candidates, two Bacillus amyloliquefaciens (Ba ATCC PTA126784 and ATCC PTA126785), and a Bacillus subtilis (Bs ATCC PTA126786), showed that all three strains had promising probiotic traits and safety profiles. Inclusion of Ba ATCC PTA12684 (Ba-PTA84) in the feed of broiler chickens resulted in improved growth performance, as shown by a significantly improved feed conversion ratio (3.3%), increased of European Broiler Index (6.2%), and increased average daily gain (ADG) (3.5%). Comparison of the cecal microbiomes from Ba PTA84-treated and control animals suggested minimal differences in microbiome structure, indicating that the observed growth promotion presumably was not mediated by modulation of cecal microbiome.

Dominant Enterobacteriaceae in tempeh were primarily originated from soybean

During tempeh production, boiling was considered as heat treatment that could significantly reduce or eliminate bacterial population in soybean before fungal inoculation. The objective of this study was to enumerate and trace Enterobacteriaceae communities in pre-boiling soybean, post-boiling soybean, and fresh tempeh designated as RTI and EMP. Standard plate count and qRT-PCR were employed to determine the culturable and non-culturable bacteria, while Enterobacterial Repetitive Intragenic Consensus PCR was conducted to determine the intraspecies genomic variations. Fresh tempeh from both RTI and EMP contained approximately 10⁷ and 10⁸ CFU/g of Enterobacteriaceae respectively. The number of bacteria in pre-boiling soybean were 10,000 times lower than in fresh tempeh. Our study showed that most Enterobacteriaceae were severely injured or quiescent during boiling process and quickly recovered up to 10⁹ CFU/g in fresh tempeh. Some Klebsiella isolates found in tempeh were genetically identical to isolates in soybean, but different from those of medical isolates. This study suggested that soybean could be the main origin of Klebsiella in fresh tempeh.

Evaluation of Live Bacterial Prophylactics to Decrease IncF Plasmid Transfer and Association With Intestinal Small RNAs

Chicken intestinal Escherichia coli are a reservoir for virulence and antimicrobial resistance (AMR) genes that are often carried on incompatibility group F (IncF) plasmids. The rapid transfer of these plasmids between bacteria in the gut contributes to the emergence of new multidrug-resistant and virulent bacteria that threaten animal agriculture and human health. Thus, the aim of the present study was to determine whether live bacterial prophylactics could affect the distribution of large virulence plasmids and AMR in the intestinal tract and the potential role of smRNA in this process. In this study, we tested ∼100 randomly selected E. coli from pullet feces (n = 3 per group) given no treatment (CON), probiotics (PRO), a live Salmonella vaccine (VAX), or both (P + V). E. coli isolates were evaluated via plasmid profiles and several phenotypic (siderophore production and AMR), and genotypic (PCR for virulence genes and plasmid typing) screens. P + V isolates exhibited markedly attenuated siderophore production, lack of AMR and virulence genes, which are all related to the loss of IncF and ColV plasmids (P < 0.0001). To identify a causal mechanism, we evaluated smRNA levels in the ceca mucus and found a positive association between smRNA concentrations and plasmid content, with both being significantly reduced in P + V birds compared to other groups (P < 0.01). To test this positive association between IncF plasmid transfer and host smRNA concentration, we evenly pooled smRNA per group and treated E. coli mating pairs with serial concentrations of smRNA in vitro. Higher smRNA concentrations resulted in greater rates of IncF plasmid transfer between E. coli donors (APEC O2 or VAX isolate IA-EC-001) and recipient (HS-4) (all groups; P < 0.05). Finally, RNAHybrid predictive analyses detected several chicken miRNAs that hybridize with pilus assembly and plasmid transfer genes on the IncF plasmid pAPEC-O2-R. Overall, we demonstrated P + V treatment reduced smRNA levels in the chicken ceca, which was associated with a reduction in potentially virulent E. coli. Furthermore, we propose a novel mechanism in which intestinal smRNAs signal plasmid exchange between E. coli. Investigations to understand the changes in bacterial gene expression as well as smRNAs responsible for this phenomenon are currently underway.

Live Bacterial Prophylactics in Modern Poultry

Commercial poultry farms frequently use live bacterial prophylactics like vaccines and probiotics to prevent bacterial infections. Due to the emergence of antibiotic-resistant bacteria in poultry animals, a closer examination into the health benefits and limitations of commercial, live prophylactics as an alternative to antibiotics is urgently needed. In this review, we summarize the peer-reviewed literature of several commercial live bacterial vaccines and probiotics. Per our estimation, there is a paucity of peer-reviewed published research regarding these products, making repeatability, product-comparison, and understanding biological mechanisms difficult. Furthermore, we briefly-outline significant issues such as probiotic-label accuracy, lack of commercially available live bacterial vaccines for major poultry-related bacteria such as Campylobacter and Clostridium perfringens, as well research gaps (i.e., probiotic-mediated vaccine adjuvancy, gut-brain-microbiota axis). Increased emphasis on these areas would open several avenues for research, ranging from improving protection against bacterial pathogens to using these prophylactics to modulate animal behavior.

Molecular Detection of Avian Pathogenic Escherichia coli (APEC) for the First Time in Layer Farms in Bangladesh and Their Antibiotic Resistance Patterns

Avian pathogenic Escherichia coli (APEC) causes significant economic losses in poultry industries. Here, we determined for the first time in Bangladesh, the prevalence of APEC-associated virulence genes in E. coli isolated from layer farms and their antibiotic resistance patterns. A total of 99 samples comprising internal organs, feces, and air were collected from 32 layer farms. Isolation was performed by culturing samples on eosin–methylene blue agar plates, while the molecular detection of APEC was performed by PCR, and antibiograms were performed by disk diffusion. Among the samples, 36 were positive for the APEC-associated virulence genes fimC, iucD, and papC. Out of 36 isolates, 7, 18, and 11 were positive, respectively, for three virulence genes (papC, fimC, and iucD), two virulence genes, and a single virulence gene. Although the detection of virulence genes was significantly higher in the internal organs, the air and feces were also positive. The antibiograms revealed that all the isolates (100%) were resistant to ampicillin and tetracycline; 97.2%, to chloramphenicol and erythromycin; 55.5%, to enrofloxacin; 50.0%, to norfloxacin and ciprofloxacin; 19.4%, to streptomycin; 11.1%, to colistin; and 8.33%, to gentamicin. Interestingly, all the isolates were multidrug-resistant (MDR). Spearman’s rank correlation coefficient analysis revealed the strongest significant correlation between norfloxacin and ciprofloxacin resistance. This is the first study in Bangladesh describing the molecular detection of APEC in layer farms. Isolated APEC can now be used for detailed genetic characterization and assessing the impact on public health.

Risk Factors for Antimicrobial Resistance in Escherichia coli in Pigs Receiving Oral Antimicrobial Treatment: A Systematic Review

The aim of this literature review was to identify risk factors in addition to antimicrobial treatment for antimicrobial resistance (AMR) occurrence in commensal Escherichia coli in pigs. A variety of studies were searched in 2014 and 2015. Studies identified as potentially relevant were assessed against eligibility criteria such as observation or experiment (no review), presentation of risk factors in addition to (single dosage) antimicrobial use, risk factors for but not resulting from AMR, and the same antimicrobial used and tested. Thirteen articles (nine on observational, four on experimental studies) were finally selected as relevant. It was reported that space allowance, production size/stage, cleanliness, entry of animals and humans into herds, dosage/frequency/route of administration, time span between treatment and sampling date, herd size, distance to another farm, coldness, and season had an impact on AMR occurrence. Associations were shown by one to four studies per factor and differed in magnitude, direction, and level of significance. The risk of bias was unclear in nearly half of the information of observational studies and in most of the information from experimental studies. Further research on the effects of specific management practices is needed to develop well-founded management advice.

Rapid detection for rabbit-derived dermatophytes using microsatellite-primed polymerase chain reaction

A method exhibiting high sensitivity, specificity and rapidity to detect pathogenic dermatophytes was developed using microsatellite-primed polymerase chain reaction (PCR) in combination with a clustering method. The DNA fragments of Trichophyton mentagrophyton, Microsporum gypseum and Microsporum canis were amplified by using the primer (GACA)4 to detect the DNA polymorphism fingerprints. Twenty-one clinical strains identified as T. mentagrophyton, M. gypseum or M. canis by morphological methods were distinguished according to the differences of standard stains' bands combined with NTSYS-pc2.10 software. The results showed that there were obvious and direct differences in the bands of the three pathogenic dermatophytes, and the similarity of isolated strains and standard strains were above 90%, in line with the results of morphological identification. The method is more accurate, rapid and simple, which is meaningful for the clinical diagnosis and epidemic research of the dermatophytes.

Formation and transmission of Staphylococcus aureus (including MRSA) aerosols carrying antibiotic-resistant genes in a poultry farming environment

There is a rather limited understanding concerning the antibiotic-resistance of the airborne S. aureus and the transmission of the antibiotic-resistant genes it carries Therefore, we isolated 149 S. aureus strains from the samples collected from the feces, the indoor air and the outdoor air of 6 chicken farms, and performed the research on them with 15 types of antibiotics and the REP-PCR trace identification. The 100% homologous strains were selected to conduct the research on the carrying and transmission status of the antibiotic-resistant genes. The results revealed that 5.37% strains (8/149) were resistant to methicillins (MRSA), and 94% strains (140/149) were resistant to compound sulfamethoxazole, etc. In addition, these strains displayed a resistance to multiple antibiotics (4, 5 or 6 types) and there were also 3 strains resistant to 9 antibiotics. It should be noted that the antibiotic-resistance of some strains isolated from the feces, the indoor and outdoor air was basically the same, and the strains with the same REP-PCR trace identification result carried the same type of antibiotic-resistant genes. The results showed that airborne transmission not only causes the spread of epidemic diseases but also exerts threats to the public health of a community.

Concentrations and diversity of microbes from four local bioaerosol emission sources in Finland

Microbial particles can readily be released into the air from different types of man-made sources such as waste operations. Microbiological emissions from different biological sources and their dispersion may be an issue of concern for area planning and for nearby residents. This study was designed to determine the concentrations and diversity of microbiological emissions from four different man-made source environments: waste center with composting windrows, sewage treatment plant, farming environment, and cattle manure spreading. Samples of airborne particles were collected onto polyvinyl chloride filters at three distances along the prevailing downwind direction, from each source environment during a period of approximately 1 week. These samples were analyzed for 13 species or assay groups of fungi, bacterial genus Streptomyces, and Gram-positive and -negative bacteria using quantitative polymerase chain reaction (PCR). Samples for determining the concentrations of viable fungi and bacteria were collected from all environments using a six-stage impactor. The results show that there were variations in the microbial diversity between the source environments. Specifically, composting was a major source for the fungal genera Aspergillus and Penicillium, particularly for Aspergillus fumigatus, and for the bacterial genus Streptomyces. Although the microbial concentrations in the sewage treatment plant area were significantly higher than those at 50 or 200 m distance from the plant area, in the farming environment or cattle manure spreading area, no significant difference was observed between different distances from the source. In summary, elevated concentrations of microbes that differ from background can only be detected within a few hundred meters from the source. This finding, reported earlier for culturable bacteria and fungi, could thus be confirmed using molecular methods that cover both culturable and nonculturable microbial material.

ERIC-PCR identification of the spread of airborne Escherichia coli in pig houses

To understand the spread of microbial aerosols in pig houses, with Escherichia coli (E. coli) as indicator, the airborne E. coli in 4 pig houses and their surroundings at different points 10, 50m upwind and 10, 50, 100, 200 and 400m downwind respectively from the pig houses were collected, and the concentrations were calculated at each sampling point. Furthermore, the feces of pigs were collected to separate E. coli. The ERIC-PCR (Enterobacterial Repetitive Intergenic Consensus-Polymerase Chain Reaction) technology was used to amplify the isolated E. coli DNA samples, then the amplified results were analyzed by NTSYS-pc (Version 2.10) to identify the similarity of isolated E. coli. The results showed that the airborne E. coli concentrations in indoor air of the 4 pig houses (21-35CFUm(-)(3) air) were much higher than those in upwind and downwind air (P<0.05), but there were no significant differences (P>0.05) at downwind distances. The ERIC-PCR results also showed that 52.4% of the fecal E. coli (four houses being respectively 2/4, 50%; 2/4, 50%; 3/6, 50%; 4/7, 57.1%) were identical to the indoor airborne E. coli isolates, and there was more than 90% similarity between the majority of E. coli (50%, 21/42) isolated from downwind air at 10, 50, 100 and 200m and those from indoor air or feces. It could be concluded that the aerosols in pig houses can spread to the surroundings, and thus effective measures should be taken to control and minimize the spread of microbial aerosols.

Characterization and deposition of respirable large- and small-particle bioaerosols

The deposition patterns of large-particle microbiological aerosols within the respiratory tract are not well characterized. A novel system (the flow-focusing aerosol generator [FFAG]) which enables the generation of large (>10-microm) aerosol particles containing microorganisms under laboratory conditions was characterized to permit determination of deposition profiles within the murine respiratory tract. Unlike other systems for generating large aerosol particles, the FFAG is compatible with microbiological containment and the inhalational challenge of animals. By use of entrapped Escherichia coli cells, Bacillus atrophaeus spores, or FluoSphere beads, the properties of aerosols generated by the FFAG were compared with the properties of aerosols generated using the commonly available Collison nebulizer, which preferentially generates small (1- to 3-microm) aerosol particles. More entrapped particulates (15.9- to 19.2-fold) were incorporated into 9- to 17-microm particles generated by the FFAG than by the Collison nebulizer. The 1- to 3-microm particles generated by the Collison nebulizer were more likely to contain a particulate than those generated by the FFAG. E. coli cells aerosolized using the FFAG survived better than those aerosolized using the Collison nebulizer. Aerosols generated by the Collison nebulizer and the FFAG preferentially deposited in the lungs and nasal passages of the murine respiratory tract, respectively. However, significant deposition of material also occurred in the gastrointestinal tract after inhalation of both the small (89.7%)- and large (61.5%)-particle aerosols. The aerosols generated by the Collison nebulizer and the FFAG differ with respect to mass distribution, distribution of the entrapped particulates, bacterial survival, and deposition within the murine respiratory tract.