Chicken Feces Research Articles

Comparative study of extraction methods of silver species from faeces of animals fed with silver-based nanomaterials

Extractions methods based on ultrapure water, tetramethylammonium hydroxide (TMAH), and tetrasodium pyrophosphate (TSPP) were applied to faeces collected from two in vivo experiments of pigs and chickens fed with a silver-based nanomaterial to study the fate and speciation of silver. For TMAH extraction, cysteine and CaCl2 were used to evaluate their stabilization effect on the silver forms. The analytical techniques single-particle inductively coupled plasma mass spectrometry (SP-ICP-MS), hydrodynamic chromatography hyphenated to ICP-MS (HDC-ICP-MS) and asymmetric flow field flow fractionation coupled to ICP-MS (AF4-ICP-MS) were applied to the simultaneous detection of particulate and dissolved silver. Results have shown that water extraction was a suitable option to assess the environmental release of silver, with percentages of 3 and 9% for faeces of pigs and chickens, respectively. The use of TMAH extraction combined with SP-ICP-MS analysis was useful to characterize Ag-containing particles (less than 1%). Both stabilizers, cysteine and CaCl2, have a similar effect on silver nanoparticle preservation for chicken faeces, whereas cysteine-Triton was better for pig samples. In any case, silver extraction efficiency with TMAH was low (39–42%) for both types of faeces due to a matrix effect. TSPP followed by ICP-MS enabled the fractionation of the silver in the faeces, with silver sulphide (41%) and ionic silver (62%) being the most abundant fractions.Graphical

Feasibility of a DNA biosensor assay based on loop-mediated isothermal amplification combined with a lateral flow dipstick assay for the visual detection of Ascaridia galli eggs in faecal samples

ABSTRACT Ascaridia galli is an important nematode that causes ascaridiasis in free-range and indoor system chicken farms. Infection with A. galli may damage the intestinal mucosa and inhibit nutrient absorption, leading to a reduced growth rate, weight loss and a decreased egg production. Consequently, A. galli infection is a significant health problem in chickens. In this study, we developed a loop-mediated isothermal amplification coupled with a lateral flow dipstick (LAMP-LFD) assay for the visual detection of A. galli eggs in faecal samples. The LAMP-LFD assay consists of six primers and one DNA probe that recognize the internal transcribed spacer 2 (ITS2) region; it can be performed within 70 min and the results can be interpreted with the naked eye. Using the LAMP-LFD assay developed in this study, A. galli DNA was specifically amplified without any cross-reactions with other related parasites (Heterakis gallinarum, Raillietina echinobothrida, R. tetragona, R. cesticillus, Cotugnia sp., Echinostoma miyagawai) and definitive hosts (Gallus gallus domesticus, Anas platyrhynchos domesticus). The minimum detectable DNA concentration was 5 pg/μl, and the detectable egg count was 50 eggs per reaction. The assay can be performed in a water bath, without the need for post-mortem morphological investigations and laboratory instruments. It is therefore a viable alternative for the detection of A. galli in chicken faeces and can replace classical methods in field screening for epidemiological investigations, veterinary health and poultry farming management. RESEARCH HIGHLIGHTS This is the first study using the LAMP-LFD assay for Ascaridia galli detection. The results can be observed by the naked eye. The developed assay can be used to detect Ascaridia galli eggs in faecal samples.

Prevalence of <i>Escherichia coli</i> and <i>Salmonella spp</i> Strains Isolated from Chicken Feces and Their Resistance to Antibiotics by Cefotaximase (CTX-M) Enzyme Production

The Increase in antibiotic resistance is a threat to the world health. Some resistant bacteria have the ability to transfer from animals to humans either through their stool or through their flesh. The spread and emergence of antibiotic resistance is therefore a public health problem. For this study, a total of 101 chickens were randomly selected from the busiest recreation areas of Ouagadougou and fresh chicken droppings taken directly from the animal's intestines were collected. Of the samples analyzed, 78.21% and 9.90% respectively contained <i>Escherichia coli</i> and <i>Salmonella spp</i>. For the 10 isolates of <i>Salmonella spp</i>, a resistance to CTX-M of 10%, 10% to CAZ, 10% to CRO and finally 70% resistant to AMC was observed. For the 79 strains of <i>Escherichia coli</i>, it was observed an absence of resistance to CTX-M, 3.79% to CAS, 3.79% to CRO and 84.81% of strain resistant to AMC. Four (4) mutil-resistant strains were identified and resistance genes were observed in 2 of these strains. The study revealed the presence of extended spectrum beta-lactamase genes in Enterobacteriaceae contained in chicken feces. A high consumption of flambé chickens infected or contaminated by these germs is then likely to increase the risk of development and spread of bacteria resistant to antibiotics in humans.

A Novel Phytogenic Formulation, EUBIO-BPSG, as a Promising One Health Approach to Replace Antibiotics and Promote Reproduction Performance in Laying Hens

Gut microbiota play a key role in health maintenance and disease pathogenesis in animals. Dietary phytochemicals are crucial factors shaping gut bacteria. Here, we investigated the function and mechanism of a phytogenic formulation, EUBIO-BPSG (BP), in laying hens. We found that BP dose-dependently improved health and egg production in 54-week-old hens. Furthermore, BP was correlated with increased fecal Lactobacillus, decreased Escherichia coli and Salmonella enterica, and reduced antibiotic resistance (AR) and antibiotic resistance genes (ARG) in chicken stools. The 16S rDNA data showed that BP increased seven genera of probiotics and reduced 13 genera of pathogens in chicken feces. In vitro co-culture experiments showed that BP at 4 µg/mL and above promoted growth of L. reuteri while large 100- and 200-fold higher doses suppressed growth of E. coli and S. enterica, respectively. Mechanistic studies indicated that L. reuteri and its supernatants antagonized growth of E. coli and S. enterica but not vice-versa. Five short-chain fatty acids and derivatives (SCFA) produced from L. reuteri directly killed both pathogens via membrane destruction. Furthermore, BP inhibited conjugation and recombination of ARG via interference with conjugation machinery and integrase activity in E. coli. Collectively, this work suggests that BP promotes host health and reproductive performance in laying hens through regulation of gut microbiota through increasing probiotics and decreasing pathogens and spreading ARG.

Microplastics exacerbate co-occurrence and horizontal transfer of antibiotic resistance genes

Microplastic pollution is a rising environmental issue worldwide. Microplastics can provide a niche for the microbiome, especially for antibiotic-resistant bacteria, which could increase the transmission of antibiotic resistance genes (ARGs). However, the interactions between microplastics and ARGs are still indistinct in environmental settings. Microplastics were found to be significantly correlated with ARGs (p < 0.001), based on the analysis of samples taken from a chicken farm and its surrounding farmlands. Analysis of chicken feces revealed the highest abundance of microplastics (14.9 items/g) and ARGs (6.24 ×108 copies/g), suggesting that chicken farms could be the hotspot for the co-spread of microplastics and ARGs. Conjugative transfer experiments were performed to investigate the effects of microplastic exposure for different concentrations and sizes on the horizontal gene transfer (HGT) of ARGs between bacteria. Results showed that the microplastics significantly enhanced the bacterial conjugative transfer frequency by 1.4–1.7 folds indicating that microplastics could aggravate ARG dissemination in the environment. Potential mechanisms related to the up-regulation of rpoS, ompA, ompC, ompF, trbBp, traF, trfAp, traJ, and down-regulation of korA, korB, and trbA were induced by microplastics. These findings highlighted the co-occurrence of microplastics and ARGs in the agricultural environment and the exacerbation of ARGs' prevalence via rising the HGT derived from microplastics.

Effects of organic acid and garlic powder supplementations in the diet on growth and intestinal microflora of the exotic Tam Hoang chickens

A study was carried out to evaluate the effect of diet’s organic acid (OG) and garlic powder (GP) on the growth, carcass quality, and intestinal microflora of Tam Hoang chickens. The experiment consisted of three treatments and four replications in a completely randomized design; each replication was a pen (20 chickens/pen), and males and females were raised separately. The treatmentswere:1/Cont: Basal diet (BD) no supplementation; 2/OG: BD + 1g Poulacid /kg feed; 3/GP: BD + 1 g garlic powder/kg feed. Results showed that chickens fed Cont (1451 g /head) had lower final live weight than those having OG (1568 g/head) and GP (1521 g/head/day). So, the average daily gain (ADG) of chickens in Cont (16.8 g/head/day) and GP (17.7 g/head/day) were lower than in OG (18.2 g/head/day). Average daily feed intake (ADFI) was similar in all treatments. Therefore, the feed conversion ratio (FCR) of chickens fed OG (3.04 kg feed/kg gain) was better than that in Cont (3.32 kg feed/kg gain). The density of Salmonella bacteria was not detectable in chicken feces at the 4th week age but became positive in Cont and GP treatments at the 10th week age. Supplementation of OG and GP reduced E. coli and Clostridium perfringens in the feces compared to control chickens at the 4th and 10th week age. In conclusion, adding OG or GP at the same dose (1g/kg feed) in Tam Hoang chicken diets improved ADG, FCR, and reduced E. coli and Clostridium perfringens densities in the feces compared to control chickens

Detection of Drug Resistant Elements from Broiler Feces Based on PCR Technology

Objective: The aim of this study is to detect various drug resistance elements from chicken feces by PCR technology, so as to lay a foundation for the application of PCR technology in the survey of drug resistance of intestinal microbiota. Methods: Genomic DNA was extracted from chicken feces, and different drug resistance elements were amplified by conventional PCR. Results: In this study, different classes of the drug-resistant genes <i>tet</i>A, <i>tet</i>B, <i>bla</i><SUB>SHV</SUB>, <i>bla</i><SUB>TEM</SUB>, <i>bla</i><SUB>CTX-M1</SUB>, <i>qnr</i>A, <i>aad</i>A1, <i>dfr</i>A1 and <i>sul</i>1 were observed from collected chicken feces, and the detection rates of different drug-resistant genes varied based on time point at which the genes were amplified. Wherein, <i>tet</i>B progressively increased with the prolongation of feeding time, while <i>bla</i><SUB>TEM</SUB> and <i>aad</i>A1 decreased with the prolongation of feeding time. In addition, integrase genes <i>int</i>I1 and <i>int</i>I2 were also detected in this study. Among the types of plasmid replicons, IncB/O, IncFIC, IncFIA, IncFIB, IncI1, IncN and IncFrep were detected in this study, and the number of replicon types carried by different samples ranged from 1 to 6, and the detection rate of plasmid replicons also had a time point difference, while, obvious regularity was not observed. In terms of the correlations between plasmids, the detected plasmids presented varying degrees of correlations. Conclusion: PCR technology could detect different drug resistance elements in intestinal microbiota.

Quantitative PCR versus metagenomics for monitoring antibiotic resistance genes: balancing high sensitivity and broad coverage.

The widespread occurrence of clinically relevant antibiotic resistance within humans, animals, and environment motivates the development of sensitive and accurate detection and quantification methods. Metagenomics and quantitative PCR (qPCR) are amongst the most used approaches. In this study, we aimed to evaluate and compare the performance of these methods to screen antibiotic resistance genes in animal faecal, wastewater, and water samples. Water and wastewater samples were from hospital effluent, different treatment stages of two treatment plants, and of the receiving river at the discharge point. The animal samples were from pig and chicken faeces. Antibiotic resistance gene coverage, sensitivity, and usefulness of the quantitative information were analyzed and discussed. While both methods were able to distinguish the resistome profiles and detect gradient stepwise mixtures of pig and chicken faeces, qPCR presented higher sensitivity for the detection of a few antibiotic resistance genes in water/wastewater. In addition, the comparison of predicted and observed antibiotic resistance gene quantifications unveiled the higher accuracy of qPCR. Metagenomics analyses, while less sensitive, provided a markedly higher coverage of antibiotic resistance genes compared to qPCR. The complementarity of both methods and the importance of selecting the best method according to the study purpose are discussed.

Persistence and molecular epidemiology of blaNDM-positive Gram-negative bacteria in three broiler farms: A longitudinal study (2015–2021)

Although carbapenems have not been approved for animal use, blaNDM-positive bacteria (NPB) are increasingly being detected in farm animals. It is important to investigate the routes and underlying mechanisms of evolution and transmission of animal-borne NPB. In this study, NPB recovered from chicken feces and environmental samples in three adjacent broiler farms were investigated. We found that 13.0% of Escherichia coli strains recovered from chicken feces during the period 2015–2016 carried the blaNDM gene. In 2017–2021, however, as many as 55.8% chicken and environmental samples collected during the breeding period were found to harbor NPB. Importantly, such strains were detectable in samples from farmland (10.3%, 8/78), vegetable fields (7.3%, 3/41), and environment of chicken farms (25.6%, 41/160) which had been left vacant for a long period of time. Intriguingly, different sequence types of NPB became dominant in different years. Both clonal dissemination of NPB and horizontal transmission of blaNDM-bearing plasmids were observed among different farms and among the environment niches inside and outside the farm houses. Worryingly, transmission of NPB and blaNDM-bearing plasmids between these farms and other places was also observed. All in all, our results suggested the persistence of NPB in chickens and farm environments, presumably due to extensive contamination by exogenous materials and transmission of NPB within the farm system. These events were aggravated by the increase in antibiotic usage and poor sanitary conditions in the farm houses. Stringent control measures should be implemented to arrest transmission of animal-borne NPB to the environment and the community.

Enterococcus faecium from chicken feces improves chicken immune response and alleviates Salmonella infections: a pilot study.

Probiotics reduce the emergence of antibiotic resistance in the livestock industry. Chicken feces are reservoirs of beneficial microbiomes. The aim of this study was to isolate putative probiotics from the intestinal contents of broiler chickens. Five fecal samples were collected from two poultry farms in Al-Ahsa, Saudi Arabia. Of the 11 morphologically distinct isolates from chicken feces (CF) samples, five isolates displayed positive reactions to Gram staining, catalase, and oxidase tests, and reacted negatively to a hemolytic assay. The isolates CF1, CF2, CF3, CF8, and CF11 were selected for further analysis of probiotic characterization, gastric survival capacity, antibiotic susceptibility, and antimicrobial activity against poultry infected with Salmonella enterica. CF2 and CF11 showed the highest hydrophobic values (> 51% hydrophobic nature). CF1, CF2, and CF11 showed potent antimicrobial activities. The active isolate CF2 was identified as Enterococcus faecium by 16s rRNA sequencing and showed a genetic similarity of 99.1%. An in vivo study was conducted using a chicken model. Enterococcus faecium-fed chickens showed an improved body weight and a lower mortality rate (17-34%). Salmonella enterica colony-forming unit (CFU) invasion in the spleen and thymus was significantly reduced in the E. faecium-fed chickens. The fecal S. enterica load was reduced from CFU 6.8 to 3.9/g in oral-administered E. faecium-fed chickens. Enterococcus faecium-fed chickens showed increased levels (P < 0.01) of butyric acid and reduced levels (P < 0.01) of intestinal interleukin 1 beta, C-reactive protein, and interferon gamma levels compared to those in the S. enterica-infected chicken group. In addition, E. faecium showed significant binding to Caco-2 epithelial cells in vitro and inhibited S. enterica colonization, indicating co-aggregation of E. faecium in epithelial cells. These results revealed that an E. faecium formulation could prevent bacterial infection and improve the quality of broiler chickens.

Effects of Cashew Nut Shell Liquid on Hindgut Fermentation and Microbiota of Chickens

Cashew nut shell liquid (CNSL), a feed additive for chickens, was evaluated for its influence on the hindgut environment by determining fermentation and bacterial profiles using cecal contents, fecal slurry and pure cultures. A farm-scale study showed that CNSL feeding to broiler chickens from 0 to 42 days of age improved body weight gain and lowered mortality. Cecal levels of short chain fatty acids increased with CNSL feeding, while ammonia and indole levels decreased. Feeding CNSL decreased the relative abundance of cecal bacteria belonging to some clostridial groups and Ruminococcaceae. In particular, Clostridium perfringens was undetectable following CNSL feeding. A pure culture study showed that CNSL (≥ 6.25 μg/ml) inhibited C. perfringens growth, accompanied by cell surface disruption based on electron microscopic observation. Fermentation profiles of slurry cultures prepared from feces of chickens were altered by CNSL supplementation toward less ammonia production. The lowered ammonia was correlated positively with the abundance of unclassified Lachnospiraceae and unclassified Ruminococcaceae, and negatively with unclassified Enterobacteriaceae and Sutterella. These results suggest that CNSL could exert its beneficial influence on the hindgut health of chickens through impacting the microbiota.

Examining the Extent of Contamination, Antibiotic Resistance, and Genetic Diversity of Clostridioides (Clostridium) difficile Strains in Meat and Feces of Some Native Birds of Iran.

Clostridioides (Clostridium) difficile (C. difficile) is one of the essential enteropathogens in humans and livestock and is a severe health threat, according to the Centre for Disease Control and Prevention. Also, antimicrobials are one of the most critical risk factors for C. difficile infection (CDI). The present study examined the infection, antibiotic resistance, and genetic diversity of the C. difficile strains in the meat and feces of some native birds (chicken, duck, quail, and partridge) in the Shahrekord region, Iran, from July 2018 to July 2019. Samples were grown on CDMN agar after an enrichment step. To determine the toxin profile, the tcdA, tcdB, tcdC, cdtA, and cdtB genes were detected via multiplex PCR. The antibiotic susceptibility of these isolates was examined using the disk diffusion method and followed based on MIC and epsilometric test. 300 meat samples of chicken, duck, partridge, and quail and 1100 samples of bird feces were collected from six traditional farms in Shahrekord, Iran. Thirty-five meat samples (11.6%) and 191 fecal samples (17.36%) contained C. difficile. Moreover, five toxigenic samples isolated had 5, 1, and 3 tcdA/B, tcdC, and cdtA/B genes. Out of the studied strains isolated from the 226 samples, two isolates belonging to ribotype RT027 and one isolated RT078 profile related to native chicken feces were observed from chicken sample. The antimicrobial susceptibility testing showed that all the strains are resistant to ampicillin, 28.57% are resistant to metronidazole, and 100% were susceptible to vancomycin. Based on the results, it can be concluded that the raw meat of birds might be a source of resistant C. difficile that poses a hygienic threat to the consumption of native bird meat. Nevertheless, further studies are essential to understand additional epidemiological features of C. difficile in bird meat.

Evaluation of antibiotic sensitivity of potential probiotic Bacillus strains isolated from chicken and pig feces

Nowadays, the misuse and overuse of antibiotics in livestock production leads to the appearance of antibiotic resistant strains that promotes the use of probiotics in feed to minimise/replace antibiotic consumption. Among them, Bacilli are common supplements for feed effectiveness and livestock health benefits. However, there is a growing concern about the development of antibiotic resistance and transfer of antibiotic resistance genes among bacteria. Thus, the European Food Safety Authority (EFSA) has suggested that products containing Bacillus strains intended to use as feed additive must be examined for susceptibility to antimicrobials of human and veterinary importance. In this study, the antibiotic susceptibility of potential probiotic Bacillus strains was investigated. A total of 59 Bacillus species were isolated from 10 samples of chicken and pig feces. Then, the in vitro probiotic characteristics including low pH tolerance, catalase activity, protease, amylase and cellulase enzymes production were tested to select appropriate isolates for further studies. Thirty-three promising probiotic strains were assessed for their antibiotic susceptibility against 13 antibiotics by disc diffusion method. In most cases, isolated Bacillus strains were susceptible to tested antibiotics. The obtained results demonstrated the potential application of Bacillus spp. as feed supplements in animal production.

Growth Performance, Gut Health, Welfare and Qualitative Behavior Characteristics of Broilers Fed Diets Supplemented with Dried Common (Olea europaea) Olive Pulp

The present study investigated the dietary impact of dried olive pulp (OP) on growth performance, gut health and some welfare and behavior characteristics of broilers. It was conducted in a commercial poultry farm using 108 13 day-old Ross male broilers. Chickens were equally and randomly assigned to 3 dietary treatments, CON, OP3 and OP6, based on the incorporation rate of OP in the ration (0%, 3%, and 6%, respectively). A beneficial impact on foot pad dermatitis (FPD) and feather cleanliness of OP-fed broilers was recorded. No adverse effects on qualitative behavior characteristics evaluated and on the overall growth performance of chickens were observed. No significant differences in the fecal microbiota population were observed among the groups. Changes of β-diversity in an age-dependent way were only observed. The feces of chickens across all age and dietary groups were mainly dominated by the phylum Firmicutes (62.3 to 95.1%), mainly represented by the genus Lactobacillus (32.9 to 78.2%), Proteobacteria (2.0 to 35.6%), and Actinobacteria (1.5 to 11.4%). Supplementing broilers’ diets with 3% and 6% OP beneficially affected chickens’ health and welfare without compromising their growth performance and gut health.

Occurrence of ESBL-producing avian pathogenic Escherichia coli (APEC) isolates in spiced chicken meat in Goias, Brazil.

Some extraintestinal pathogenic Escherichia coli isolates (ExPEC), obtained from humans and chickens avian pathogenic E. coli (APEC), share similar virulence genes. Thus, products of avian origin can be a source of human infection. Moreover, these APEC isolates are resistant to antimicrobials and can spread in the environment through the chicken feces. Although the development of multidrug-resistant (MDR) microorganisms in poultry is on the rise, healthcare entities have raised concerns since MDRs can horizontally transfer resistance genes to other microorganisms and complicate the management of human infections by MDR APEC. The results of our study showed that of 80 investigated spiced chicken meat samples, 55% were contaminated with E. coli, of which 34% (15/44) contaminate with APEC. No diarrheagenic E. coli (DEC) pathotypes were found. Twenty-six isolates were MDR E. coli. Among the APEC isolates, 87% (13/15) produced extended-spectrum beta-lactamase (ESBL). The emergence of MDR/ESBL-producing APEC with zoonotic potential for humans is extremely worrying. Therefore, further studies are required to identify the prevalence of MDR/ESBL-producing APEC in the entire chicken production chain from creation, slaughter, processing, and butchery.

PENGARUH PEMBERIAN HASIL FERMENTASI EKSTRAK BUAH LONTAR DAN FESES AYAM DALAM KONSENTRAT TERHADAP PEMANFAATAN ENERGI PADA TERNAK KAMBING (Effect of fermented palm fruits extract and chicken manure in concentrate on energy utilisation in goats)

This study aimed to investigate the effect of feeding palm fruit extrack and chicken manure on energy utilisation in goats. This study used a Latin Square Design with four treatments and four periods of data collection as replications. The four treatments were: BP (Botriochloa pertusa hay 40% + Leucaena leucocephala 30% + concentrate 30%), BPS (Botriochloa pertusa hay 40% + Leucaena leucocephala 30% + concentrate 20% + palm fruit extract 10%), BPFA (Botriochloa pertusa hay 40% +Leucaena leucocephala 30% + concentrate 20% + chicken feces 10%), BPSFA (Botriochloa pertusa hay 40% + Leucaena leucocephala 30% + concentrate 20% + palm fruit extract 5% + chicken feces 5%). The parameters measured consisted of the intake and digestibility of crude fiber, VFA concentration, and blood glucose levels. The result showed that feeding fermented of palm fruits extract at different levels in the concentrate have no significant effect (P&gt;0.05) on the intake and digestation of crude fiber and the concentration of blood glucose. However, it had a significant effect (P&lt;0.01) on the total VFA concentration. In conclusion, feeding fermented concentrate containing palm fruit extract and chicken feces increases the total VFA concentration but it does not increase the intake and digestation of crude fiber and the concentation of blood glucose in male goats.

Development of a duplex qPCR for the differentiation of a live attenuatedEscherichia coliaroA mutant vaccine strain from field isolates in chickens.

Avian pathogenic Escherichia coli (APEC) can cause colibacillosis in poultry, characterised by localised or systemic infections. Colibacillosis is considered one of the leading causes of economic losses in the poultry industry due to reduced performance, increased mortality, treatment costs and carcass condemnations. A live attenuated Escherichia coli O78 aroA gene mutant is widely used to prevent disease. However, no effective strategies to differentiate the vaccine strain from field strains are available, hampering follow-up of vaccination campaigns. In the current study, we report a PCR-based method to simultaneously detect the vaccine strain by targeting the vaccine-specific mutation in the aroA gene, as well as the wild type E. coli strains by targeting the xanQ gene. The specificity of this PCR was evaluated using 123 E. coli isolates, form which 5 WT aroA auxotrophic strains (WT strains with a natural aroA deficiency), as well as 7 non-Escherichia isolates. The PCR showed 100% sensitivity of the xanQ primers for E. coli detection and 100% sensitivity of the ΔaroA primers for the vaccine strain. In order to allow quantification of the vaccine strain in complex samples containing many different E. coli strains and other related organisms, such as chicken faeces, a probe-based duplex qPCR was developed. The limit of detection (LOD) of this duplex qPCR method was 8.4*103 copies/g faeces. The specificity of the duplex qPCR was confirmed by determining both the vaccine strain levels, and the total E. coli load in intestinal digesta from both vaccinated and non-vaccinated birds. E. coli could be detected in both vaccinated and non-vaccinated birds. The duplex qPCR was specific for the vaccine strain as this strain was detected in all vaccinated birds, whereas no signal was detected in non-vaccinated birds. The duplex qPCR is helpful in monitoring colonization and shedding of the vaccine strain.

Exploring the Microbial Community and Functional Characteristics of the Livestock Feces Using the Whole Metagenome Shotgun Sequencing.

The foodborne illness is the important public health concerns, and the livestock feces are known to be one of the major reservoirs of foodborne pathogens. Also, it was reported that 45.5% of foodborne illness outbreaks have been associated with the animal products contaminated with the livestock feces. In addition, it has been known that the persistence of a pathogens depends on many potential virulent factors including the various virulent genes. Therefore, the first step to understanding the public health risk of livestock feces is to identify and describe microbial communities and potential virulent genes that contribute to bacterial pathogenicity. We used the whole metagenome shotgun sequencing to evaluate the prevalence of foodborne pathogens and to characterize the virulence associated genes in pig and chicken feces. Our data showed that the relative abundance of potential foodborne pathogens, such as Bacillus cereus was higher in chickens than pigs at the species level while the relative abundance of foodborne pathogens including Campylobacter coli was only detected in pigs. Also, the microbial functional characteristics of livestock feces revealed that the gene families related to "Biofilm formation and quorum sensing" were highly enriched in pigs than chicken. Moreover, the variety of gene families associated with "Resistance to antibiotics and toxic compounds" were detected in both animals. These results will help us to prepare the scientific action plans to improve awareness and understanding of the public health risks of livestock feces.

Virulence potential of antimicrobial-resistant extraintestinal pathogenic Escherichia coli from retail poultry meat in a Caenorhabditis elegans model

Healthy poultry can be a reservoir for extraintestinal pathogenic Escherichia coli (ExPEC), some of which could be multidrug resistant to antimicrobials. These ExPEC strains could contaminate the environment and/or food chain representing thus, food safety and human health risk. However, few studies have shown the virulence of poultry-source antimicrobial-resistant (AMR) ExPEC in humans. This study characterized AMR ExPEC and investigated the virulence potential of some of their isolates in a Caenorhabditis elegans infection model. A total of 46 E. coli isolates from poultry (chicken, n = 29; turkey, n = 12) retail meats and chicken feces (n = 4), or humans (n = 1) were sequenced and identified as ExPEC. Except eight, all remaining 38 ExPEC isolates were resistant to at least one antibiotic and carried corresponding antimicrobial resistance genes (ARGs). About 27 of the 46 ExPEC isolates were multidrug-resistant (≥3 antibiotic classes). Seven ExPEC isolates from chicken or turkey meats were of serotype O25:H4 and sequence type (ST) 131 which clustered with an isolate from a human urinary tract infection (UTI) case having the same serotype and ST. The C. elegans challenge model using eight of studied ExPEC isolates harboring various ARGs and virulence genes (VGs) showed that regardless of their ARG or VG numbers in tested poultry meat and feces, ExPEC significantly reduced the life span of the nematode (P < 0.05) similarly to a human UTI isolate. This study indicated the pathogenic potential of AMR ExPEC from retail poultry meat or feces, but more studies are warranted to establish their virulence in poultry and human. Furthermore, relationships between specific resistance profiles and/or VGs in these E. coli isolates for their pathogenicity deserve investigations.

Metagenomics analysis of the morphological aspects and bacterial composition of broiler feces

In this descriptive study, we used metagenomics to analyze the relationship between the morphological aspects of chicken feces and its respective bacterial compositions. The microbiota composition was determined by sequencing the V4 region of the 16S rRNA genes collected from fresh broiler feces at 19 d old. In total, 48 samples were collected and divided into 8 groups of 6 samples each. The morphological changes studied were feed passage (FP) and reddish mucus (RM). Each was classified into 3 levels of intensity: 1 (slight), 2 (moderate), or 3 (intense). Thus, the 8 groups studied were feed passage (FP-1; FP-2; FP-3), reddish mucus (RM-1; RM-2; RM-3), normal ileal feces (NIF), and cecal discharge (CD). The alpha diversity (Shannon's index) revealed that the CD group showed greater diversity, and was significantly different from FP-2, FP-3, and RM-1. The beta diversity showed that the CD group samples were more homogeneous than the ileal feces groups. The relative abundance analysis revealed that Firmicutes and Proteobacteria were the most abundant phyla in the ileal feces groups. In CD, Firmicutes and Bacteroidetes were the most abundant. The relative abundance at the genus level revealed 136 different bacterial genera. In the ileal feces groups, the two most abundant genera were Lactobacillus and Escherichia/Shigella, except in the FP-1 and RM-2 groups, which had the opposite order. Unlike the others, the CD group had a higher abundance of Bacteroides and Faecalibacterium. When comparing the NIF group with the others, significant changes were found in the fecal microbiota, with nine genera for the FP groups, 19 for the RM groups, and 61 when compared to CD. The results of the present study suggest that evaluation of fecal morphology is a fundamental task that makes it possible to act quickly and assertively, as the morphological aspects of the feces may be related to the composition and structure of fecal microbiota.