Impact of feed supplementation with antimicrobial agents on growth performance of broiler chickens, Clostridium perfringens and enterococcus counts, and antibiotic resistance phenotypes and distribution of antimicrobial resistance determinants in Escherichia coli isolates

Expression of chicken epidermal growth factor (cEGF) in Escherichia coli regulates the microflora structure of the duodenum to improve growth performance and intestinal morphogenesis in broilers

1. A study used gene synthesis to obtain the functional domains of chicken epidermal growth factor (cEGF) and examined their impact on broiler growth performance, small intestinal morphology, digestive enzyme activities in the intestinal contents and the structure of duodenal microflora.2. The pET-32a-cEGF recombinant expression vector was constructed. The specific band at 26 KDa was shown by SDS-PAGE analysis and WB results. The purified protein content was shown to be 1687 μg/ml by assay.3. A total of 180 healthy, one-day-old Arbor Acres male, white-feathered broilers were randomly divided into three dietary treatment groups (six replicate pens, 10 birds per replicate): A control diet (ND); cEGF diet (cEGF), control supplemented with 250 mg/kg cEGF and the control diet (CD) supplemented with 250 mg/kg chlortetracycline.4. The results showed that feeding the cEGF and CD diet reduced FCR of broilers aged 1-21 d, average daily feed intake (ADFI) at 22-42 d, and the FCR in the whole period (1-42 d; p < 0.05). Compared with the ND group, the cEGF diet increased duodenal α-amylase and alkaline phosphatase activities in the 1-21 d, duodenal lipase, alkaline phosphatase, and ileal alkaline phosphatase activities in the post-period and increased villus height in the duodenum and ileum (p < 0.05). In addition, the ACE and Chao1 index for the birds fed cEGF were higher than the ND group (p < 0.05). At the phyla level, Firmicutes and Proteobacteria were dominant in all groups. At the genus level, the dominant genus was Lactobacillus. The LEfSe analysis showed that the cEGF group was enriched by 11 species including Brevibacillus, Eisenbergiella, Cloacibacterium, Butyricoccus spp.5. The addition of 250 mg/kg cEGF to the diet can increase growth performance by improving intestinal development and digestive enzyme activity, which may be related to the duodenal intestinal microflora. Therefore, cEGF is an effective alternative to antibiotics in broiler farming.

Quantifying health risks from ESBL-producing Escherichia coli in Dutch broiler production chains and potential interventions using compartmental models

Extended-spectrum beta-lactamase (ESBL)-producing Escherichia coli (E. coli) in animals are considered a human health threat, because this type of bacteria can serve as a reservoir of antibiotic resistant genes and act as a continuous threat of the emergence of new resistant bacteria, in addition to the direct effect of making infection untreatable. Although the prevalence of ESBL producing bacteria in broilers was drastically reduced in the Netherlands, chicken meat still has the highest prevalence among meat products. Therefore, further control of the ESBL-producing E. coli in the broiler production chain is important to reduce public health risks. The main objectives of this study were to evaluate the effectiveness of intervention scenarios to reduce the transmission of ESBL-producing E. coli in the broiler production chain and to quantitatively estimate the risk to public health. In this study, we developed two different types of transmission models that described the observed time-related decline in prevalence during a production round: one with time-dependent decline in susceptibility and one with partial immunity to phylogenetic groups. Both models incorporated the environmental contamination effect between production rounds and within flocks. The parameter values, including transmission rate and recovery rate, were estimated by Approximate Bayesian computation (ABC) method using data from a longitudinal study in a Dutch organic broiler farm. We applied the models to the three production stages in the broiler production chain, beginning from the Parent Stock (PS) farms, the hatcheries, and to the broiler farms. In our models, eggs were collected from different parent stock farms and transported to the hatchery and from there to a broiler farm.The size of a flock and the number of farms were adjusted to the Dutch situation. Both models were able to describe the observed dynamics within and between the production stages equally well, with estimated ESBL-producing E. coli prevalence of 8.98% and 11.47% in broilers at slaughter and 0.12% and 0.15% in humans due to chicken consumption. Both models indicated that improving farm management to eliminate the bacteria from the environment was the most effective intervention, making this outcome robust. Although chicken meat consumption is not a major risk factor for human carriage of the bacteria according to our models, reducing the bacteria in the PS and broiler farm environment to at least one percent can further decrease the prevalence in humans.

Efficacy of Bacillus subtilis to replace in-feed antibiotics of broiler chickens under necrotic enteritis-challenged experiments: a systematic review and meta-analysis

Necrotic enteritis (NE) and coccidiosis are among the most prevalent infectious diseases in broiler chickens, contributing to large profitability losses. Bacillus subtilis is a promising direct-fed probiotic to counter various pathogens infection in broiler chickens. Here, we performed a meta-analysis to investigate the effects of B. subtilis on broiler chickens performance. A total of 28 studies were selected according to a PRISMA checklist. Random-effect model and mixed-effect model of meta-analysis were fitted to estimate the overall effects of B. subtilis (BS) treatment compared to either the control group (CON) or NE-infected group (NEinf) as a baseline. Hedges' g effect size and its variance were used as estimators of standardized mean difference (SMD) calculation where the results were presented at a 95% confidence interval (95% CI) of the SMD. Overall, NEinf broiler chickens depressed (P < 0.01) body weight (BW), average daily gain (ADG), and feed intake, and elevated (P < 0.01) feed conversion ratio (FCR). Treatment with BS improved ADG and final BW of NEinf with no difference (P = 0.15) between BS and antibiotics (AB), indicating that they had comparable efficacy to treat NE in broiler chickens. BS supplemented to uninfected CON (BSS) improved (P < 0.01) final BW, ADG, and FCR. Compared to CON, BS, and AB failed to recover the FCR but these treatments decreased (P < 0.01) FCR when compared to the NEinf group with similar efficacy (P = 0.97). As expected, NEinf birds had a higher mortality rate (P < 0.01) and higher lesion score (P < 0.01) compared to CON, and treatment using AB and BS successfully decreased (P < 0.01) the mortality rate and lesion score. Compared to BS, AB was more effective to lower (P = 0.01) mortality rate, but comparable (P = 0.65) to minimize lesion score. To conclude, B. subtilis could be an effective natural additive to replace in-feed antibiotics in broiler chickens challenged with C. perfringens. However, the efficacy to reduce mortality rate was better with antibiotics treatment.

Co-occurrence of genes for antibiotic resistance and arsenic biotransformation in paddy soils

Paddy soils are potential hotspots of combined contamination with arsenic (As) and antibiotics, which may induce co-selection of antibiotic resistance genes (ARGs) and As biotransformation genes (ABGs), resulting in dissemination of antimicrobial resistance and modification in As biogeochemical cycling. So far, little information is available for these co-selection processes and specific patterns between ABGs and ARGs in paddy soils. Here, the 16S rRNA amplicon sequencing and high-throughput quantitative PCR and network analysis were employed to investigate the dynamic response of ABGs and ARGs to As stress and manure application. The results showed that As stress increased the abundance of ARGs and mobile genetic elements (MGEs), resulting in dissemination risk of antimicrobial resistance. Manure amendment increased the abundance of ABGs, enhanced As mobilization and methylation in paddy soil, posing risk to food safety. The frequency of the co-occurrence between ABGs and ARGs, the host bacteria carrying both ARGs and ABGs were increased by As or manure treatment, and remarkably boosted in soils amended with both As and manure. Multidrug resistance genes were found to have the preference to be co-selected with ABGs, which was one of the dominant co-occurring ARGs in all treatments, and manure amendment increased the frequency of Macrolide-Lincosamide-Streptogramin B resistance (MLSB) to co-occur with ABGs. Bacillus and Clostridium of Firmicutes are the dominant host bacteria carrying both ABGs and ARGs in paddy soils. This study would extend our understanding on the co-selection between genes for antibiotics and metals, also unveil the hidden environmental effects of combined pollution.

Antibiotic profiling of multidrug resistant pathogens in one-day-old chicks imported from Belgium to benin

BACKGROUND

Little data exist on the presence of resistant pathogens in day-old chicks imported into Benin. The occurrence of pathogenic bacteria was assessed in 180 one-day-old chicks imported from Belgium and received at the Cardinal Bernardin Gantin International Airport in Cotonou (Benin). The samples included swabbing the blisters of 180 chicks, followed by 18 pools of 10 swabs for bacterial isolation. Classic bacteriological methods based on Gram staining, culture on specific media and biochemical characterization were used. Antibacterial susceptibility screening to antibiotics was conducted using the Kirby-Bauer disc diffusion method, and the results were interpreted according to guidelines from the European Committee on Antimicrobial Susceptibility Testing (EUCAST). DNA extraction was performed by the heat treatment method. Resistance genes were screened by real-time PCR.

RESULTS

We isolated 32 bacteria, including Escherichia coli (50%), Enterococcus spp. (28%), and coagulase-negative staphylococci (10%). The isolates were investigated for antibiotic resistance against antibiotics using the disk diffusion method and showed that in the Escherichia coli strains isolated, the highest rate of resistance was obtained against ciprofloxacin (81%), followed by trimethoprim + sulfamethoxazole (62%). Enterobacter cloacae was sensitive to all the antibiotics tested. Pseudomonas spp. resistant to amoxicillin and trimethoprim + sulfamethoxazole was noted. The SulII gene was found in all cloacal samples, while the SulI and bla_TEM genes were present at 44.44% and 16.67%, respectively.

CONCLUSION

This study confirms that imported day-old chicks can be a potential source of dissemination of resistant bacteria in poultry production. A system for immediate detection of resistant bacteria in chicks upon arrival in the country is thus needed.

Growth studies in commercial broiler birds offered citric acid in formulated feed with low mineral density

Study of 35 days was conducted to evaluate citric acid (CA) as an additive in poultry broiler feed with lower mineral content of calcium (Ca) and total phosphorus (TP) in commercial broiler poultry birds for its effect on growth, nutrient utilization, carcass characteristics, and economics. Vancobb-400 strain day old broiler chicks were divided into four main treatment groups T_0, T₁, T₂, and T_3. Treatment groups were further divided into eight replicates with ten chicks in each. T₀ served as control, given standard corn-soy flakes-based ration (Pre-starter %: Crude protein (CP)-23, Ca-1.00, TP-0.70; Starter %: CP-22, Ca-1.10, TP-0.72, and Finisher %: CP-20, Ca-0.99, TP-0.70). Treatment T₁ served as positive control with added 0.5% CA (Pre-starter %: CP-23, Ca-1.00, TP-0.70; Starter %: CP-22, Ca-1.10, TP-0.72 and Finisher %: CP-20, Ca-0.99, TP-0.70). Treatment T₂ was given feed containing 0.5% CA with low Ca and TP content (Pre-starter %: CP-23, Ca-0.90, TP-0.66; Starter %: CP-22, Ca-0.99, TP-0.71 and Finisher %: CP-20, Ca-0.90, TP-0.69), whereas treatment T₃ was given feed containing 0.5% CA with moderately low Ca and TP content (Pre-starter %: CP-23, Ca-0.80, TP-0.65; Starter %: CP-22, Ca-0.88, TP-0.70 and Finisher %: CP-20, Ca-0.79, TP-0.68). Birds offered moderately low Ca and TP with 0.5% CA addition, exhibited higher growth rate (P < 0.05), better nutrient utilization with positive influence on dressing percentage and forequarters weight. Economics of broiler feeding revealed that 0.5% CA supplementation fetched highest gross return above feed cost in broiler birds offered feed with moderately low Ca and TP content whereas lowest profit was recorded in feed with low content of Ca and TP. In conclusion, supplementation of 0.5% CA in feed with low and moderately low Ca and TP content positively influenced overall growth, and carcass characteristics. Economics of broiler feeding with moderately low Ca and TP content revealed highest profit with CA (0.5%) supplementation.

Effects of paraprobiotic as replacements for antibiotic on performance, immunity, gut health and carcass characteristics in broiler chickens

This study sought to determine the effects of dietary paraprobiotic (PPB) on broiler chicken performance, immunity, gut health, and carcass traits. A total of 240 day-old CARIBRO Vishal commercial broiler chicks of identical body weight randomly divided into six treatment groups, each with five replicates and eight chicks in each replicate. Six dietary treatments were preapared: T₁ = (control diet), T₂ = T₁ + 0.02% (w/v) chlortetracycline (CTC), T₃ = T₁ + 0.2% (w/v) PPB, T₄ = T₁ + 0.4% (w/v) PPB, T₅ = T₁ + 0.6% (w/v) PPB and T₆ = T₁ + 0.8% (w/v) PPB, respectively. Body weight gain (BWG) significantly (P ≤ 0.05) increased in the T₅ (0.6% PPB) and T₆ (0.8% PPB) group. At the same time the feed intake significantly (P ≤ 0.05) decreased and the feed conversion ratio (FCR) significantly (P ≤ 0.05) improved in T₅ and T₆ group. There was a significant (P ≤ 0.05) increase in cell-mediated immunity and haem-agglutination titre (HA titre) in the 0.6% and 0.8% PPB supplemented groups compare to the control group (T₁). The percentage of carcass traits and organ weights did not significantly differ between the PPB-supplemented and control groups, but the percentage of live weight in cut up parts showed a significant improvement (P ≤ 0.05) in the PPB-supplemented group. At 42 days, villus height, width, and crypt depth all significantly (P ≤ 0.05) increased in the groups supplemented with 0.6 and 0.8% para-probiotics (T₅ and T₆). The results show that para-probiotics can be added to broiler diets at a rate of 0.6% (w/v) to enhance performance, immunity, gut health, and breast yield. The para-probiotic may therefore be a useful substitution for antibiotic growth promoters in the diet of chickens.

Production systems and important antimicrobial resistant-pathogenic bacteria in poultry: a review

Economic losses and market constraints caused by bacterial diseases such as colibacillosis due to avian pathogenic Escherichia coli and necrotic enteritis due to Clostridium perfringens remain major problems for poultry producers, despite substantial efforts in prevention and control. Antibiotics have been used not only for the treatment and prevention of such diseases, but also for growth promotion. Consequently, these practices have been linked to the selection and spread of antimicrobial resistant bacteria which constitute a significant global threat to humans, animals, and the environment. To break down the antimicrobial resistance (AMR), poultry producers are restricting the antimicrobial use (AMU) while adopting the antibiotic-free (ABF) and organic production practices to satisfy consumers' demands. However, it is not well understood how ABF and organic poultry production practices influence AMR profiles in the poultry gut microbiome. Various Gram-negative (Salmonella enterica serovars, Campylobacter jejuni/coli, E. coli) and Gram-positive (Enterococcus spp., Staphylococcus spp. and C. perfringens) bacteria harboring multiple AMR determinants have been reported in poultry including organically- and ABF-raised chickens. In this review, we discussed major poultry production systems (conventional, ABF and organic) and their impacts on AMR in some potential pathogenic Gram-negative and Gram-positive bacteria which could allow identifying issues and opportunities to develop efficient and safe production practices in controlling pathogens.

Amoxicillin and thiamphenicol treatments may influence the co-selection of resistance genes in the chicken gut microbiota

The aim of this study was to assess the dynamics of microbial communities and antimicrobial resistance genes (ARGs) in the chicken gut following amoxicillin and thiamphenicol treatments and potential co-selection of ARGs. To this purpose, the microbial community composition, using 16S rRNA NGS, and the abundance of ARGs conferring resistance to β-lactams and phenicols, using qPCRs, were determined. Results revealed that the administered antimicrobials did not significantly reduce the gut microbiota diversity, but changed its composition, with taxa (e.g. Gallibacterium and Megamonas) being enriched after treatment and replacing other bacteria (e.g. Streptococcus and Bifidobacterium). Positive correlations were found between ARGs (e.g. cmlA, bla_CMY-2, and bla_SHV) and the relative abundance of specific taxa (e.g. Lactobacillus and Subdoligranulum). The selective pressure exerted by both amoxicillin and thiamphenicol resulted in an increased abundance of ARGs conferring resistance to β-lactams (e.g. bla_TEM-1, bla_SHV, and bla_CTX-M1-like) and phenicols (e.g. floR and cmlA). These findings, together with the co-occurrence of genes conferring resistance to the two antimicrobial classes (e.g. bla_TEM-1 and cmlA), suggest a possible interaction among antimicrobials on resistance emergence, possibly due to the presence of mobile genetic elements (MGEs) carrying multiple resistance determinants.

Oral Administration of a Phage Cocktail to Reduce Salmonella Colonization in Broiler Gastrointestinal Tract-A Pilot Study

Salmonella contamination in poultry meat products can lead to serious foodborne illness and economic loss from product recalls. It is crucial to control Salmonella contamination in poultry from farm to fork. Bacteriophages (phages) are viruses of bacteria that offer several advantages, especially their specificity to target bacteria. In our study, three Salmonella phages (vB_SenS_KP001, vB_SenS_KP005, and vB_SenS_WP110) recovered from a broiler farm and wastewater treatment stations showed high lysis ability ranging from 85.7 to 96.4% on over 56 serovars of Salmonella derived from several sources, including livestock and a broiler farm environment. A three-phage cocktail reduced S. Enteritidis and S. Typhimurium, in vitro by 3.9 ± 0.0 and 3.9 ± 0.2 log units at a multiplicity of infection (MOI) of 10³ and 3.8 ± 0.4 and 4.1 ± 0.2 log units at MOI of 10⁴ after 6 h post-phage treatment. A developed phage cocktail did not cause phage resistance in Salmonella during phage treatments for three passages. Phages could survive under simulated chicken gastrointestinal conditions in the presence of gastric acid for 2 h (100.0 ± 0.0% survivability), bile salt for 1 h (98.1 ± 1.0% survivability), and intestinal fluid for 4 h (100 ± 0.0% survivability). Each phage was in the phage cocktail at a concentration of up to 9.0 log PFU/mL. These did not cause any cytotoxicity to human fibroblast cells or Caco-2 cells as indicated by the percent of cell viability, which remained nearly 100% as compared with the control during 72 h of co-culture. The phage cocktail was given to broilers raised in commercial conditions at a 9 log PFU/dose for five doses, while naturally occurring Salmonella cells colonized in the gastrointestinal tract of broilers were significantly reduced as suggested by a considerably lower Salmonella prevalence from over 70 to 0% prevalence after four days of phage treatment. Our findings suggest that a phage cocktail is an effective biocontrol agent to reduce Salmonella present in the guts of broilers, which can be applied to improve food safety in broiler production.

Metagenomic assembly reveals hosts and mobility of common antibiotic resistome in animal manure and commercial compost

BACKGROUND

Antibiotics and antibiotic resistance genes (ARGs) used in intensive animal farming threaten human health worldwide; however, the common resistome, ARG mobility, and ARG host composition in different animal manures and mixed manure composts remain unclear. In the present study, metagenomic assembly and cross-sample mapping were used to comprehensively decipher the common resistome and its potential mobility and hosts in animal manure and composts.

RESULTS

In total, 201 ARGs were shared among different animal (layer, broiler, swine, beef cow, and dairy cow) manures and accounted for 86-99% of total relative abundance of ARGs. Except for multidrug, sulfonamide, and trimethoprim resistance genes, the relative abundance of most ARGs in composts was significantly lower than that in animal manure. Procrustes analysis indicated that antibiotic residues positively correlated with ARG composition in manure but not in composts. More than 75% ARG subtypes were shared between plasmids and chromosomes in our samples. Transposases could play a pivotal role in mediating the transfer of ARGs between different phyla in animal manure and composting. Cross-sample mapping to contigs carrying ARGs showed that the hosts of common resistome in manure had preference on animal species, and the dominant genus of ARG host shifted from Enterococcus in manure to Pseudomonas in composts. The broad host range and linking with diverse mobile genetic elements (MGEs) were two key factors for ARGs, such as sul1 and aadA, which could survive during composting. The multidrug resistance genes represented the dominant ARGs in pathogenic antibiotic-resistant bacteria in manure but could be effectively controlled by composting.

CONCLUSIONS

Our experiments revealed the common resistome in animal manure, classified and relative quantified the ARG hosts, and assessed the mobility of ARGs. Composting can mitigate ARGs in animal manure by altering the bacterial hosts; however, persistent ARGs can escape from the removal because of diverse host range and MGEs. Our findings provide an overall background for source tracking, risk assessment, and control of livestock ARGs.

Effects of litter from antimicrobial-fed broiler chickens on soil bacterial community structure and diversity

This study examined changes in soil bacterial community composition and diversity in response to fertilization with litter from chickens fed diet with no antibiotics, bambermycin, penicillin, bacitracin, salinomycin, and mix of salinomycin and bacitracin. Litter was applied to 24 agricultural-plots. Non-fertilized plots were used as a negative control. Soil samples collected from the studied plots were used to quantify Escherichia coli by plate counts, and Clostridium perfringens by qPCR. The 16S-rRNA gene sequencing was performed for microbiota analysis. Following litter application in December, the population size of E.coli was 5.4 log CFU/g, however, regardless of treatments the result revealed 5.2 and 1.4 log CFU/g of E.coli in soil sampled in January and March, respectively. Fertilization with antibiotic treated litter increased (P < 0.05) the relative abundance of Proteobacteria, Actinobacteria and Firmicutes in soil, but decreased Acidobacteria and Verrucomicrobia groups. The alpha-diversity parameters were higher (P < 0.05) in non-fertilized soil compared to the fertilized ones, suggesting that litter application was a major factor in shaping the soil bacterial communities. These results may help develop efficient litter management strategies like composting, autoclaving, or anaerobic digestion of poultry litter before application to land for preservation of soil health and crop productivity.

Village-Indigenous Chicken Bacterial Carriage after the Heavy Rains of 2018, Kenya: Indicator on Environmental Contamination with Pathogenic/Zoonotic Bacteria

Food borne diseases are one of the major human disease conditions worldwide. Most of them are of bacterial origin and chickens are a major source of such bacteria; they are consumed at high rate worldwide and tend to harbor the zoonotic bacteria without showing signs of illness. Running rain water tends to increase environmental contamination, since it carries various substances from one area to another; this results in village-indigenous chickens picking more bacteria from the environment as they roam/scavenge around for food. Thus, after the rain, the chickens' intestinal contents may contain more bacteria quantity-wise and type-wise. This study was carried-out to determine whether that was the case after heavy rains of 2018.120 intestine samples were collected from indigenous chickens from three slaughterhouses in Nairobi for bacterial quantification using the Miles and Misra technique; bacterial isolation and identification were carried out using standard bacteriological procedures. Intestines from the slaughterhouses had different mean bacterial counts: Kangemi had the highest (1.3 × 10¹² colony-forming units per ml), followed by Burma (5.6 × 10¹¹), then Kariokor (4.7 × 10¹¹). E. coli was the most isolated at 85.8%, followed by genera Staphylococcus (55%), Streptococcus (43.3%), Bacillus (41.66%), Listeria (38.3%), Proteus (24.16%), Klebsiella (7.5%), Campylobacter (2.5%), Pseudomonas (6%), and Streptobacillus (0.83%). The study showed that the indigenous chickens carry a variety of bacteria in types and numbers, some of them being zoonotic. Apart from picking more bacteria as a result of environmental contamination during rainy season, the weather and bird-handling further stress the birds, thus contributing to higher bacterial multiplication and higher bacterial carriage. If slaughter is not done right, these intestinal bacteria can easily cause contamination of respective chicken meat; thus, if pathogenic, it can cause food poisoning to consumers of the meat. Therefore, it is recommended that precaution be taken while slaughtering chickens for consumption. In addition, where possible, free-range indigenous chickens be confined during rainy seasons to reduce their exposure to contaminated environment.

Genomic Characterization of Two Escherichia fergusonii Isolates Harboring mcr-1 Gene From Farm Environment

The prevalence and transmission of mobile colistin resistance (mcr) genes have led to a severe threat to humans and animals. Escherichia fergusonii is an emerging pathogen which is closely related to a variety of diseases. However, the report of mcr genes harboring E. fergusonii is still rare. One study in Brazil reported the E. fergusonii isolates with IncHI2-type plasmids harboring mcr-1. A Chinese study reported two strains carrying mcr-1 gene with the same plasmid type IncI2. Here, we identified two strains of E. fergusonii carrying mcr-1 gene from farm environments with IncX4-type and IncI2-type plasmids, respectively. To our best knowledge, this is the first report about mcr-1 gene located on IncX4-type plasmid in E. fergusonii. We investigate the resistance mechanism of colistin-resistant Escherichia fergusonii strains 6S41-1 and 5ZF15-2-1 and elucidate the genetic context of plasmids carrying mcr-1 genes. In addition, we also investigated chromosomal mutations mediated colistin resistance in these two strains. Species identification was performed using MALDI-TOF MS and 16S rRNA gene sequencing. The detection of mcr-1 gene was determined by PCR and Sanger sequencing. S1-pulsed-field gel electrophoresis (PFGE), Southern blotting, antimicrobial susceptibility testing, conjugation experiments, complete genome sequencing, and core genome analysis were conducted to investigate the characteristics of isolates harboring mcr-1. The mcr-1 genes on two strains were both plasmids encoded and the typical IS26-parA-mcr-1-pap2 cassette was identified in p6S41-1 while a nikA-nikB-mcr-1 locus sites on the conjugative plasmid p5ZF15-2-1. In addition, Core genome analysis reveals that E. fergusonii 6S41-1 and 5ZF15-2-1 have close genetic relationships. The mcr-1 gene is located on conjugative IncI2-type plasmid p5ZF15-2-1, which provides support for its further transmission. In addition, there’s the possibility of mcr-1 spreading to humans through farm environments and thereby threatening public health. Therefore, continuous monitoring and investigations of mcr-1 among Enterobacteriaceae in farm environments are necessary to control the spread.

Riboflavin and Bacillus subtilis effects on growth performance and woody-breast of Ross 708 broilers with or without Eimeria spp. challenge

This study was conducted to assess the effects of the dietary supplementation of riboflavin (as a bile salt hydrolase [BSH] inhibitor) and Bacillus subtilis on growth performance and woody breast of male broilers challenged with Eimeria spp. Intestinal bacteria, including supplemented probiotics, can produce BSH enzymes that deconjugate conjugated bile salts and reduce fat digestion. A 3 × 2 × 2 (riboflavin × Bacillus subtilis × Eimeria spp. challenge) factorial arrangement of treatments in randomized complete block design was used. On d 14, birds were gavaged with 20× doses of commercial cocci vaccine (Coccivac^R-B52, Merck Animal Health, Omaha, NE). Dietary treatment of riboflavin and B. subtilis did not affect body weight (BW), body weight gain (BWG), and feed conversion (FCR) d 0 to 14 and overall d 0 to 41. Eimeria spp challenge reduced BWG, feed intake (FI), and increased FCR between d 14 to 28, but increased BWG and lowered FCR between d 28 to 35. There were no effects of the Eimeria spp. challenge on the overall d 0 to 41 FCR and FI, but BWG was reduced. Eimeria spp. challenge increased the abdominal fat pad weight and slight woody breast incidences on processed birds on d 42. Dietary inclusion of B. subtilis and riboflavin at tested levels did not help birds to mitigate the negative impact of Eimeria spp. challenge to enhance the growth performance.

Effects of Postbiotics and Paraprobiotics as Replacements for Antibiotics on Growth Performance, Carcass Characteristics, Small Intestine Histomorphology, Immune Status and Hepatic Growth Gene Expression in Broiler Chickens

Background: This experiment was designed to investigate how replacing antibiotics with postbiotics and paraprobiotics could affect growth performance, small intestine morphology, immune status, and hepatic growth gene expression in broiler chickens. Methods: The experiment followed a completely randomized design (CRD) in which eight treatments were replicated six times with seven birds per replicate. A total of 336, one-day-old (COBB 500) chicks were fed with the eight treatment diets, which include T1 = negative control (Basal diet), T2 = positive control (Basal diet + 0.01% (w/w) Oxytetracycline), T3 = Basal diet + 0.2% (v/w) postbiotic TL1, T4 = Basal diet + 0.2% (v/w) postbiotic RS5, T5 = Basal diet + 0.2% (v/w) paraprobiotic RG11, T6 = Basal diet + 0.2% (v/w) postbiotic RI11, T7 = Basal diet + 0.2% (v/w) paraprobiotic RG14, T8 = Basal diet + 0.2% (v/w) paraprobiotic RI11, for 35 days in a closed house system. Results: The growth performance indicators (final body weight, cumulative weight gain, and feed conversion ratio) were not significantly (p > 0.05) affected by the dietary treatments. However, feed intake recorded a significant (p < 0.05) change in the starter and finisher phases across the dietary treatments. Paraprobiotic RG14 had significantly (p < 0.05) lower abdominal fat and intestines. Villi heights were significantly (p < 0.05) increased, while the crypt depth decreased significantly due to dietary treatments. The dietary treatments significantly influenced colon mucosa sIgA (p < 0.05). Similarly, plasma immunoglobulin IgM level recorded significant (p < 0.05) changes at the finisher phase. In this current study, the hepatic GHR and IGF-1 expressions were significantly (p < 0.05) increased by postbiotics and paraprobiotics supplementation. Conclusions: Therefore, it was concluded that postbiotics and paraprobiotics differ in their effect on broiler chickens. However, they can replace antibiotics without compromising the growth performance, carcass yield, and immune status of broiler chickens.

Virulence Genotype and Phenotype of Multiple Antimicrobial-Resistant Escherichia coli Isolates from Broilers Assessed from a "One-Health" Perspective

ABSTRACT

Extraintestinal pathogenic Escherichia coli (ExPEC) include several serotypes that have been associated with colibacillosis in poultry and with urinary tract infections (UTIs) and newborn meningitis in humans. In this study, 57 antimicrobial-resistant E. coli from apparently healthy broiler chickens were characterized for their health and safety risks. These isolates belonged to 12 serotypes, and isolates of the same serotype were clonal based on single nucleotide variant analysis. Most of the isolates harbored plasmids; IncC and IncFIA were frequently detected. The majority of the resistant isolates harbored plasmid-mediated resistance genes, including aph(3″)-Ib, aph(6)-Id, blaCMY-2, floR, sul1, sul2, tet(A), and tet(B), in agreement with their resistant phenotypes. The class 1 integron was detected in all E. coli serotypes except O124:H25 and O7:H6. Of the 57 broiler E. coli isolates, 27 were avian pathogenic, among which 18 were also uropathogenic E. coli and the remainder were other ExPEC. The two isolates of serotype O161:H4 (ST117) were genetically related to the control avian pathogenic strains and a clinical isolate associated with UTIs. A strain of serotype O159:H45 (ST101) also was closely related to a UTI isolate. The detected virulence factors included adhesins, invasins, siderophores, type III secretion systems, and toxins in combination with other virulence determinants. A broiler isolate of serotype O7:H18 (ST38) carried the ibeA gene encoding a protein involved in invasion of brain endothelium on a 102-kbp genetic island. This isolate moderately adhered and invaded Caco-2 cells and induced mortality (42.5%) in a day-old-chick infection model. The results of this study suggest that multiple antimicrobial-resistant E. coli isolates recovered from apparent healthy broilers can be pathogenic and act as reservoirs for antimicrobial resistance genes, highlighting the necessity of their assessment in a "One-Heath" context.

HIGHLIGHTS

Antimicrobial Resistance Phenotypes and Genotypes of Escherichia coli Isolates from Broiler Chickens Fed Encapsulated Cinnamaldehyde and Citral

ABSTRACT

This study was conducted to investigate the effects of in-feed encapsulated cinnamaldehyde (CIN) and citral (CIT) alone or in combination on antimicrobial resistance (AMR) phenotypes and genotypes of Escherichia coli isolates recovered from feces of 6-, 16-, 23-, and 27-day-old broiler chickens. The five dietary treatments including the basal diet (negative control [NC]) and the basal diet supplemented with 55 ppm of bacitracin (BAC), 100 ppm of encapsulated CIN, 100 ppm of encapsulated CIT, or 100 ppm each of encapsulated CIN and encapsulated CIT (CIN+CIT). Antimicrobial susceptibility testing of 240 E. coli isolates revealed that the most common resistance was to β-lactams, aminoglycosides, sulfonamides, and tetracycline; however, the prevalence of AMR decreased (P < 0.05) as birds aged. The prevalence of resistance to amoxicillin-clavulanic acid, ceftiofur, ceftriaxone, cefoxitin, gentamicin, and sulfonamide was lower (P < 0.05) in isolates from the CIN or CIN+CIT groups than in isolates from the NC or BAC groups. Whole genome sequencing of 227 of the 240 isolates revealed 26 AMR genes and 19 plasmids, but the prevalence of some AMR genes and the number of plasmids were lower (P < 0.05) in E. coli isolated from CIN or CIN+CIT birds than in isolates from NC or BAC birds. The most prevalent resistance genes were tet(A) (108 isolates), aac(3)-VIa (91 isolates), aadA1 (86 isolates), blaCMY-2 (78 isolates), sul1 (77 isolates), aph(3)-Ib (58 isolates), aph(6)-Id (58 isolates), and sul2 (24 isolates). The numbers of most virulence genes carried by isolates increased (P < 0.05) in chickens from 6 to 27 days of age. The prevalence of E. coli O21:H16 isolates was lower (P < 0.05) in CIN and CIN+CIT, and the colibacillosis-associated multilocus sequence type (ST117) was most prevalent in isolates from 23-day-old chickens. A phylogenetic tree of whole genome sequences revealed a close relationship between 25 of the 227 isolates and human or broiler extraintestinal pathogenic E. coli strains. These findings indicate that AMR and virulence genotypes of E. coli could be modulated by providing encapsulated CIN or CIN+CIT feed supplements, but further investigation is needed to determine the mechanisms of the effects of these supplements.

HIGHLIGHTS

The effect of Candida famata and Lactobacillus plantarum on the number of coliforms and the antibiotic resistance and virulence of Escherichia coli in the gut of broilers

This study was undertaken to determine the effect of a yeast (Candida famata) and a bacterium (Lactobacillus plantarum), administered alone or in combination in the drinking water, on the population of yeast, Lactobacillus sp. and coliforms, and the prevalence of antimicrobial resistance (AMR) and virulence genes in Escherichia coli (E. coli) isolated from digesta samples taken throughout the life of broiler chickens. Male (Ross 308) day-old chicks (220) were used. C. famata (isolated from a chicken) and L. plantarum (isolated from a pig) were administered via the drinking water. Water was provided either untreated or with C. famata (CF; 10⁸/ml), L. plantarum (LP; 10⁵-10⁸/ml), or a combination of CF and LP (10⁶-10⁸/ml) in water hoppers on 2 days each week for 35 days. Administering probiotics did not affect the growth performance in broiler chickens. No significant interactions were observed between main effects, and neither CF nor LP had any effect on the population size of Lactobacillus sp. or coliforms. The administration of C. famata increased the population density of yeasts in the small intestine at these ages. The population density of coliforms, Lactobacillus sp. and yeast decreased with age (P < 0.001). There was no significant effect of probiotics on the prevalence of phenotypic AMR and virulence genes in these studies. The prevalence of E. coli that was resistant to ampicillin and tetracycline, as well as carrying ≥3 virulence-associated genes, was greatest at the end of the starter phase (around 8 days old), before declining through the grower and finisher phases. There was only limited evidence that administering either CF or LP affected either the AMR or the virulence of E. coli in the bird. However, tetracycline resistance in E. coli was associated (P < 0.001, P < 0.01, P < 0.05, and P < 0.05) with the carriage of the iron uptake systems of E. coli D, iron-repressible protein, increased serum survival and temperature-sensitive haemagglutinin genes respectively, suggesting that the accumulation of iron and the genetic element conferring tetracycline resistance may be intertwined.

Extended-spectrum cephalosporin resistance in Escherichia coli from broiler chickens raised with or without antibiotics in Ontario, Canada

Extended-spectrum cephalosporin (ESC)-resistant Escherichia coli were isolated from fecal samples enriched in ESC-containing broth over two years from broiler chickens raised with and without therapeutic antimicrobials. Pooled samples were obtained from 13 different farms in Canada over two rearing cycles each. Resistant isolates were screened for bla_CMY, bla_CTX-M, and bla_SHV by PCR, and several isolates were sequenced and assembled using Oxford Nanopore MinION technology. Flocks raised with or without antimicrobials contained similar ESC-resistant E. coli. Some plasmids were found in isolates from both farm types and many shared replicon types (IncI1, F, C, and B/O/K/Z) and resistance determinants. Although the use of cephalosporins has stopped in poultry production in Canada, the prevalence of ESC-resistant E. coli found in this study remained high; therefore, further studies are required to determine routes of transmission and persistence.

Rethinking Manure Application: Increase in Multidrug-Resistant Enterococcus spp. in Agricultural Soil Following Chicken Litter Application

The current study investigated the impact of chicken litter application on the abundance of multidrug-resistant Enterococcus spp. in agricultural soil. Soil samples were collected from five different strategic places on a sugarcane farm before and after manure application for four months. Chicken litter samples were also collected. Enterococci were enumerated using the Enterolert^®/Quanti-Tray 2000^® system and confirm and differentiated into species using real-time PCR. The antibiotic susceptibility profile of the isolates was determined using the disk diffusion method following the European Committee on Antimicrobial Susceptibility Testing (EUCAST) guidelines. The overall mean bacterial count was significantly higher (p < 0.05) in manure-amended soil (3.87 × 10⁷ MPN/g) than unamended soil (2.89 × 10⁷ MPN/g). Eight hundred and thirty-five enterococci (680 from soil and 155 from litter) were isolated, with E. casseliflavus being the most prevalent species (469; 56.2%) and E. gallinarum being the least (16; 1.2%). Approximately 56% of all the isolates were resistant to at least one antibiotic tested, with the highest resistance observed against tetracycline (33%) and the lowest against chloramphenicol (0.1%); 17% of E. faecium were resistant to quinupristin-dalfopristin. Additionally, 27.9% (130/466) of the isolates were multidrug-resistant, with litter-amended soil harbouring more multidrug-resistant (MDR) isolates (67.7%; 88/130) than unamended soil (10.0%; 13/130). All isolates were susceptible to tigecycline, linezolid and gentamicin. About 7% of the isolates had a multiple antimicrobial resistance index > 0.2, indicative of high antibiotic exposure. Although organic fertilizers are regarded as eco-friendly compared to chemical fertilizers for improving soil fertility, the application of untreated animal manure could promote the accumulation of antibiotics and their residues and antibiotic-resistant bacteria in the soil, creating an environmental reservoir of antimicrobial resistance, with potential human and environmental health risks.

Effects of hulless barley and exogenous beta-glucanase levels on ileal digesta soluble beta-glucan molecular weight, digestive tract characteristics, and performance of broiler chickens

The reduced use of antibiotics in poultry feed has led to the investigation of alternatives to antibiotics, and one such substitution is fermentable carbohydrates. Exogenous β-glucanase (BGase) is commonly used in poultry fed barley-based diets to reduce digesta viscosity. The effects of hulless barley (HB) and BGase levels on ileal digesta soluble β-glucan molecular weight, digestive tract characteristics, and performance of broiler chickens were determined. A total of 360 day-old broilers were housed in battery cages (4 birds per cage) and fed graded levels of high β-glucan HB (CDC Fibar; 0, 30, and 60% replacing wheat) and BGase (Econase GT 200 P; 0, 0.01, and 0.1%) in a 3 × 3 factorial arrangement. Beta-glucan peak molecular weight in the ileal digesta was lower with 30 and 60 than 0% HB, whereas the peak decreased with increasing BGase. The weight average molecular weight was lower at 0.1 than 0% BGase in wheat diets, whereas in HB diets, it was lower at 0.01 and 0.1 than 0% BGase. The maximum molecular weight was lower with 0.01 and 0.1 than 0% BGase regardless of the HB level. The maximum molecular weight was lower with HB than wheat at 0 or 0.01% BGase. Overall, empty weights and lengths of digestive tract sections increased with increasing HB, but there was no BGase effect. Hulless barley decreased the duodenum and jejunum contents, whereas increasing the gizzard (diets with BGase), ileum, and colon contents. The jejunum and small intestine contents decreased with increasing BGase. Ileal and colon pH increased with increasing HB, but there was no BGase effect. Treatment effects were minor on short-chain fatty acids levels and performance. In conclusion, exogenous BGase depolymerized the ileal digesta soluble β-glucan in broiler chickens in a dose-dependent manner. Overall, feed efficiency was impaired by increasing HB levels. However, HB and BGase did not affect carbohydrate fermentation in the ileum and ceca, although BGase decreased ileal viscosity and improved feed efficiency at the 0.1% dietary level.

Poultry and Wild Birds as a Reservoir of CMY-2 Producing Escherichia coli: The First Large-Scale Study in Greece

Resistance mediated by β-lactamases is a globally spread menace. The aim of the present study was to determine the occurrence of Escherichia coli producing plasmid-encoded AmpC β-lactamases (pAmpC) in animals. Fecal samples from chickens (n = 159), cattle (n = 104), pigs (n = 214), and various wild bird species (n = 168), collected from different Greek regions during 2018-2020, were screened for the presence of pAmpC-encoding genes. Thirteen E. coli displaying resistance to third-generation cephalosporins and a positive AmpC confirmation test were detected. bla_CMY-2 was the sole pAmpC gene identified in 12 chickens' and 1 wild bird (Eurasian magpie) isolates and was in all cases linked to an upstream ISEcp1-like element. The isolates were classified into five different sequence types: ST131, ST117, ST155, ST429, and ST1415. Four chickens' stains were assigned to ST131, while five chickens' strains and the one from the Eurasian magpie belonged to ST117. Seven pAmpC isolates co-harbored genes conferring resistance to tetracyclines (tetM, tetB, tetC, tetD), 3 carried sulfonamide resistance genes (sulI and sulII), and 10 displayed mutations in the quinolone resistance-determining regions of gyrA (S83L+D87N) and parC (S80I+E84V). This report provides evidence of pAmpC dissemination, describing for the first time the presence of CMY-2 in chickens and wild birds from Greece.

Old problems and new solutions: antibiotic alternatives in food animal production

The antimicrobial resistance crisis is a Global Health challenge that impacts humans, animals, and the environment alike. In response to increased demands for animal protein and by-products, there has been a substantial increase in the use of antimicrobial agents in the animal industry. Indeed, they are extensively used to prevent, control, and (or) treat disease in animals. In addition to infection control, in-feed supplementation with antimicrobials became common practice for growth promotion of livestock. Unfortunately, the global overuse of antimicrobials has contributed to the emergence and spread of resistance. As such, many countries have implemented policies and approaches to eliminate the use of antimicrobials as growth promoters in food animals, which necessitates the need for alternate and One Health strategies to maintain animal health and welfare. This review summarizes the antimicrobial resistance crisis from Global Health and One Health perspectives. In addition, we outline examples of potential alternate strategies to circumvent antimicrobial use in animal husbandry practices, including antivirulence agents, bacteriophages, and nutritional measures to control bacterial pathogens. Overall, these alternate strategies require further research and development efforts, including assessment of efficacy and the associated development, manufacturing, and labor costs.

Characterization of β-lactamase and quinolone resistant Clostridium perfringens recovered from broiler chickens with necrotic enteritis in Bangladesh

BACKGROUND

Clostridium perfringens causes necrotic enteritis (NE) and is considered a major economic burden in the broiler industry and a significant foodborne pathogen, worldwide.

AIMS

Clostridium perfringens isolated from NE affected broiler chickens was aimed to characterize and the presence of β-lactamase and quinolone resistant genes were also investigated in the isolates.

METHODS

A total of 224 intestinal and caecal specimens were collected from NE affected broiler chickens and cultured to isolate C. perfringens. The toxicogenic characterization of C. perfringens was appraised using polymerase chain reaction (PCR) and antibiotic susceptibility testing (disc diffusion method). The selected C. perfringens isolates were characterized for β-lactamase and quinolone encoding genes by PCR analysis.

RESULTS

All isolates were cultured positive for C. perfringens and the toxin-encoding genes of C. perfringens (α-, β-, β2-, ε-, ι-, and enterotoxin) were also identified. About 65.6% of isolates had a multi-drug resistant (MDR) profile but none of these isolates were resistant or susceptible to all screened antibiotics. A subset of isolates, 160 and 98 were analyzed for β-lactamase and quinolone genes, respectively, and recognized bla TEM, bla SHV, and bla OXA in 64 (40%; CI: 32.35-48.03%; P<0.001) isolates, and qnrB and qnrS in 28 (28.57%; CI: 19.90-38.58%; P<0.001) isolates except qnrA.

CONCLUSION

Therefore, the isolates of C. perfringens were toxicogenic and carried β-lactamase, and quinolone resistance genes. Nowadays, the rational use of antibiotics and safe production of broiler chickens are the major concern to save public health.

Molecular Epidemiology of Antibiotic-Resistant Escherichia coli from Farm-To-Fork in Intensive Poultry Production in KwaZulu-Natal, South Africa

The increased use of antibiotics in food animals has resulted in the selection of drug-resistant bacteria across the farm-to-fork continuum. This study aimed to investigate the molecular epidemiology of antibiotic-resistant Escherichia coli from intensively produced poultry in the uMgungundlovu District, KwaZulu-Natal, South Africa. Samples were collected weekly between August and September 2017 from hatching to final retail products. E. coli was isolated on eosin methylene blue agar, identified biochemically, and confirmed using polymerase chain reaction (PCR). Susceptibility to 19 antibiotics was ascertained by the Kirby–Bauer disc diffusion method. PCR was used to test for resistance genes. The clonal similarity was investigated using enterobacterial repetitive intergenic consensus polymerase chain reaction (ERIC-PCR). In total, 266 E. coli isolates were obtained from all the samples, with 67.3% being non-susceptible to at least one antibiotic tested and 6.7% multidrug resistant. The highest non-susceptibility was to ampicillin (48.1%) and the lowest non-susceptibility to ceftriaxone and azithromycin (0.8%). Significant non-susceptibility was observed to tetracycline (27.4%), nalidixic acid (20.3%), trimethoprim-sulfamethoxazole (13.9%), and chloramphenicol (11.7%) which have homologues used in the poultry industry. The most frequently observed resistance genes were bla_CTX-M (100%), sul1 (80%), tetA (77%), and tetB (71%). ERIC-PCR grouped isolates into 27 clusters suggesting the spread of diverse clones across the farm-to-fork continuum. This reiterates the role of intensive poultry farming as a reservoir and a potential vehicle for the transmission of antibiotic resistance, with potentially severe public health implications, thus, requiring prompt and careful mitigation measures to protect human and environmental health.

Development of an endolysin enzyme and its cell wall-binding domain protein and their applications for biocontrol and rapid detection of Clostridium perfringens in food

Clostridium perfringens is a well-known pathogen that causes food-borne illnesses. Although bacteriophages can be effective natural food preservatives, phage endolysin and cell wall-binding domain (CBD) provide useful materials for lysis of C. perfringens and rapid detection. The genome of phage CPAS-15 consists of 51.8-kb double-stranded circular DNA with 78 open reading frames, including an endolysin gene. The apparent absence of a virulence factor or toxin gene suggests its safety in food applications. C. perfringens endolysin (LysCPAS15) inhibits host cells by up to a 3-log reduction in 2 h, and enhanced green fluorescent protein (EGFP)-fused CBD protein (EGFP-LysCPAS15_CBD1) detects C. perfringens within 5 min. Both exhibit broader host range spectra and higher stabilities than a bacteriophage. Tests in milk show the same host lysis and specific detection activities, with no hindrance effect from food matrices, indicating that endolysin and its CBD can provide food extended protection from C. perfringens contamination.

Effect of Bacillus velezensis to substitute in-feed antibiotics on the production, blood biochemistry and egg quality indices of laying hens

BACKGROUND

The excessive use of antibiotics in the livestock feed industry caused inevitable side effects of microbial resistance. Besides this residual antibiotics in animal-derived foodstuff imposed serious health problems for humans. So this study aimed to investigate the potential use of Bacillus velezensis to substitute antibiotics for poultry production. A total of 468, 49-week-old Hy-Line Brown chickens, were randomly divided into four groups the control group (regular diet), experiment group I (0.1% B. veleznesis), experiment group II (0.2% B. veleznesis), and antibiotic group (50 mg/kg flavomycin), with three replicates per group and trial period consisted on 42 days.

RESULTS

The results showed that, compared with the control group, the average egg production rate and daily feed intake of experimental groups I and II increased significantly (P < 0.05), while the average egg weight was increased in experimental group II as compared to (I) (P < 0.01). The feed conversion ratio was decreased (P > 0.05) in group (II) Egg quality parameters such as yolk weight of the experimental group II was increased, but that of the antibiotic group and experiment group I was decreased, neither significant (P > 0.05). Moreover, the eggshell strength, yolk color, albumen height, and Haugh unit were significantly increased (P < 0.05). Compared with the control group, probiotic groups can increase the progesterone and motilin (P > 0.05) but decrease the secretin and cholecystokinin in the blood plasma (P > 0.05).

CONCLUSIONS

This study suggested that B. velezensis can substitute in-feed-antibiotics and improved most of the study parameters significantly. Which suggested that B. velezensis has potential future application value to replace the feed antibiotics.

Variations of the Escherichia coli population in the digestive tract of broilers

We explored the between-group and temporal variations in the intestinal Escherichia coli populations of broilers under experimental conditions, taking both antimicrobial resistance and virulence into consideration. Four replicates of 45 commercial chicks were reared in four animal facilities. On their first day of life (Day 0), they were orally inoculated with two extended-spectrum-cephalosporin-resistant (ESCR) E. coli (2.72 log₁₀ CFU of a bla _CMY-2- and 2.55 log₁₀ CFU of a bla _CTX-M-carrying E. coli). Faecal samples were then collected weekly and caecal samples were obtained from birds sacrificed on Days 21 or 42. The total, ESC-, ciprofloxacin- and gentamicin-resistant E. coli populations were enumerated on MacConkey (MC) and MC-supplemented media, and eight virulence-associated genes (VAGs) (iroN, iutA, iss, ompT, hlyF, vat, frz_orf4 , and fyuA) were sought by PCR on isolates obtained on MC agar. The results showed significant between-group differences in the size of the resistant sub-populations and the presence of VAGs. Contrary to bla _CTX-M-positive strains, bla _CMY-positive strains persisted up to Day 42, but represented only a minor fraction of the total E. coli population. The ESC-, gentamicin- and ciprofloxacin-resistant populations decreased over time. Isolates obtained during the first week contained a mean of 5.1 VAGs. The percentages of some VAG profiles differed between faecal isolates on Day 41 and caecal isolates on Day 42. The fluctuations or differences between E. coli isolates according to group, age, and faecal or caecal origin need to be considered when designing experimental protocols and seeking to improve colibacillosis control. RESEARCH HIGHLIGHTS Temporal variations in the intestinal E. coli populations of broilers was studied. The antibiotic-resistant populations decreased over time. Virulence profiles differed between faecal isolates on Day 41 and caecal isolates on Day 42. Strains with the highest numbers of virulence genes were present during the first days.

Antimicrobial Susceptibility of Escherichia coli and ESBL-Producing Escherichia coli Diffusion in Conventional, Organic and Antibiotic-Free Meat Chickens at Slaughter

Simple Summary

Following the spread of antibiotic resistance and the high consumption of chicken meat, conventional poultry-producing companies have turned to antibiotic-free and organic lines of products. Our work investigated E. coli susceptibility to different antimicrobials and extended-spectrum β-lactamase (ESBL) E. coli diffusion from samples collected in slaughterhouse from conventional (C), organic (O) and reared without antibiotics (ABF) chickens. Conventional samples showed the highest number of E. coli strains resistant to ampicillin (89.6%), trimethoprim/sulfamethoxazole (62.2%), nalidixic acid (57.8%), ciprofloxacin (44.4%), and cefotaxime (43.7%), with prevalent patterns of multi-resistance to three (35.1%) and to four antimicrobials (31.3%). The highest numbers of ESBL E. coli were observed in conventional and the lowest in organic. Our results are relevant with an influence of farming typology regarding the susceptibility of E. coli and the presence of ESBL E. coli. Conventional farms, in which the use of antibiotics is allowed, showed samples with the highest number of strains resistant to antimicrobials commonly used in poultry as well as the highest amounts of ESBL E. coli. Organic samples exhibited the lowest value for ESBL due to a lack of antimicrobial treatment in chickens and the possibility to have access to the outdoors, limiting contact with litter as a potential source of resistant bacteria.

Abstract

As a result of public health concerns regarding antimicrobial resistance in animal-based food products, conventional poultry companies have turned to ‘raised without antibiotics’ (ABF) and organic farming systems. In this work, we evaluated the influence of rearing systems on antimicrobial susceptibility in E. coli and extended-spectrum β-lactamase (ESLB) E. coli diffusion in conventional (C), organic (O) and antibiotic free (ABF) chicken samples collected from cloacal swabs and skin samples in slaughterhouse. The E. coli isolates from conventional (135), antibiotic-free (131) and organic (140) samples were submitted to the Kirby–Bauer method and ESBL E. coli were analyzed by the microdilution test. Conventional samples showed the highest number of strains resistant to ampicillin (89.6%; p < 0.01), cefotaxime (43.7%; p < 0.01), nalidixic acid (57.8%; p < 0.01), ciprofloxacin (44.4%; p < 0.001), and trimethoprim/sulfamethoxazole (62.2%; p < 0.01), with patterns of multi-resistance to three (35.1%) and to four antimicrobials (31.3%), whereas most of the E. coli isolated from antibiotic-free and organic chicken samples revealed a co-resistance pattern (29.2% and 39%, respectively). The highest number of ESBL E. coli was observed in conventional, in both cloacal and skin samples and the lowest in organic (p < 0.001). Our results are consistent with the effect of conventional farming practices on E. coli antimicrobial resistance and ESBL E. coli number, due to the use of antimicrobials and close contact with litter for most of the production cycle.

Tectorigenin reduces type IV pilus-dependent cell adherence in Clostridium perfringens

Clostridium perfringens is an anaerobic, Gram-positive bacterium that causes a range of diseases in humans and animals around the globe. The type IV pilus (TFP) system plays a key role in the colonization and invasion of host cells, biofilm formation and gliding motility, which is vital for C. perfringens infection. Therefore, targeting TFP function may be a promising strategy for the treatment of C. perfringens infection. Here, we investigated the potential inhibitory effects of tectorigenin (TE), an isoflavone extracted from the rhizome of the Chinese herb Belamcanda chinensis (L.) DC, on gliding motility, biofilm formation, adherence to cells and antibacterial activity of C. perfringens. Tectorigenin significantly inhibited gliding motility, biofilm formation and adherence to Caco-2 cells without observable antibacterial activity against C. perfringens. In addition, we also demonstrated that the inhibitory effect of TE on TFP function appears to be partially achieved by the suppression of TFP-associated genes. These findings demonstrate that TE may have the potential to be developed as a new anti-virulence drug for C. perfringens infection, particularly for the targeting of TFP.

Combination of Bacillus licheniformis and Salinomycin: Effect on the Growth Performance and GIT Microbial Populations of Broiler Chickens

Simple Summary

The beneficial effects of Bacillus spp. probiotic preparations used for poultry are well-documented and characterized by growth performance improvement and positive modulation of gastrointestinal tract (GIT) microbiota. Moreover, the favorable influence of salinomycin has been frequently studied as an ionophore coccidiostat, as well as an antimicrobial agent. However, limited data are available in terms of the parallel usage of both Bacillus licheniformis DSM 28710 and salinomycin in poultry diets. From a practical point of view, evaluating the potential interactions between this species and agent is crucial to assess their parallel usage, and the current study confirmed the positive effect of their mixture on the modulation of pH value in the crop and ceca, as well as the GIT microbiota, especially in the jejunum and ceca. Additionally, the results obtained in this study show positive effects of B. licheniformis on the growth performance, as well as the influence of both experimental factors used separately in the case of GIT microbiota modulations.

Abstract

The aim of the study was to investigate the effect of Bacillus licheniformis and salinomycin supplementation in broiler diets as individual factors or in combination on the growth performance, GIT morphometry, and microbiota populations. Four hundred one-day-old Ross 308 chicks were randomly distributed to four dietary treatments (10 replicates, 10 birds each). The following treatments were applied: NC—no additives; NC + SAL—salinomycin addition (60 mg/kg diet), NC + PRO—B. licheniformis DSM 28710 preparation (1.6 × 10⁹ CFU/kg; 500 mg/kg diet), and NC + SAL + PRO—combination of salinomycin and B. licheniformis. Probiotic administration resulted in improvement (p < 0.05) of the performance parameters, including body weight gain (1–10 d, and 11–22 d) and feed conversion ratio (11–22 d, 1–36 d). An interaction (p < 0.05) between experimental factors was observed in terms of lower pH values in the crop (tendency, p = 0.053) and ceca. Both factors lowered the alpha diversity and Enterobacteriaceae and promoted Bacillaceae communities in the jejunum (p < 0.05). Interactions were also observed in terms of reducing Clostridiaceae in the ceca. In conclusion, the combined use of B. licheniformis and salinomycin in broilers’ diets had beneficial effects.

Non-viable chicken embryos: an overlooked niche harbouring a significant source of multidrug resistant bacteria in the poultry production

Antimicrobial resistance (AMR) is a global issue, posing a grave threat to the public, animal, and environmental health. The AMR surveillance at the level of the hatchery is crucial to develop an AMR control strategy in the poultry industry. The objective of this study was to investigate the AMR profiles of bacteria isolated from yolk material of non-viable broiler chicken embryos at hatch from commercial hatcheries in western Canada. Antimicrobial susceptibility testing was done using the Kirby–Bauer disk diffusion method focusing on Escherichia coli (n = 170) and Enterococcus (n = 256) species, which are commonly used as indicators of AMR evolution. E. coli isolates were resistant to tetracycline, ampicillin, amoxycillin-clavulanic acid, triple sulpha, ceftiofur, gentamycin, and spectinomycin at the rate of 52.9%, 50.6%, 40.0% 31.8%, 29.4%, 29.4%, 21.8% respectively. Among those, 37.1% of E. coli were multidrug resistant. The descending order of antimicrobial resistance of E. faecalis was; tetracycline (61.9%), ceftiofur (46.2%), bacitracin (43.9%), erythromycin (31.4%) and tylosin (27.4%). Multidrug resistance was detected in 40.4% of E. faecalis isolates, and 85.7% of E. faecium isolates. To the best of our knowledge, this is the first report on AMR surveillance of non-viable chicken embryos. Overall, the present study revealed that non-viable chicken embryos, an overlooked niche for AMR surveillance, harbour multidrug-resistant E. coli, and enterococci that can be a substantial source of superbugs in the environment. Our data also highlight the urgency of including non-viable chicken embryos in AMR surveillance programme to understand AMR dissemination and its control.

Effects of encapsulated cinnamaldehyde and citral on the performance and cecal microbiota of broilers vaccinated or not vaccinated against coccidiosis

This study investigated the effects of encapsulated cinnamaldehyde (CIN) and citral (CIT) alone or in combination (CIN + CIT) on the growth performance and cecal microbiota of nonvaccinated broilers and broilers vaccinated against coccidiosis. Vaccinated (1,600) and nonvaccinated (1,600) 0-day-old male Cobb500 broilers were randomly allocated to 5 treatments: basal diet (control) and basal diet supplemented with bacitracin (BAC, 55 ppm), CIN (100 ppm), CIT (100 ppm), and CIN (100 ppm) + CIT (100 ppm). In general, body weight (BW) and feed conversion ratio were significantly improved in birds treated with BAC, CIN, CIT, and CIN + CIT (P < 0.05) but were all decreased in vaccinated birds compared with nonvaccinated birds (P < 0.05). Significant interactions (P < 0.05) between vaccination and treatments for average daily gain during the periods of starter (day 0–9) and BW on day 10 were noted. Broilers receiving vaccines (P < 0.01) or feed supplemented with BAC, CIN, CIT, or CIN + CIT (P < 0.01) showed reductions in mortality rate from day 0 to 28. The incidences of minor coccidiosis were higher (P < 0.05) in vaccinated birds than in nonvaccinated birds. Diet supplementation with BAC or tested encapsulated essential oils showed comparable effects on the coccidiosis incidences. Similar to BAC, CIN and its combination with CIT reduced both incidence and severity of necrotic enteritis (P < 0.05). No treatment effects were observed on the cecal microbiota at the phyla level. At the genus level, significant differences between vaccination and treatment groups were observed for 5 (Lactobacillus, Ruminococcus, Faecalibacterium, Enterococcus, and Clostridium) of 40 detected genera (P < 0.05). The genus Lactobacillus was more abundant in broilers fed with CIT, while Clostridium and Enterococcus were less abundant in broilers fed with CIN, CIT, or CIN + CIT in both the vaccinated and nonvaccinated groups. Results from this study suggested that CIN alone or in combination with CIT in feed could improve chicken growth performance to the level comparable with BAC and alter cecal microbiota composition.

Antimicrobial resistance, diarrheagenic and avian pathogenic virulence genes in Escherichia coli from poultry feed and the ingredients

ABSTRACT Diarrheagenic (DEC) and avian pathogenic Escherichia coli (APEC) are associated with intestinal and extra-intestinal infections (ExPEC), respectively. We aimed to analyze the antimicrobial susceptibility, gene encoding virulence factors associated to DEC and APEC, and phylogenetic classification in E. coli isolated from 320 samples of feed and ingredients. Antimicrobial susceptibility was performed using the disk diffusion method and Multiple Antibiotic Resistance (MAR) Index and Multi-Drug Resistance (MDR) were calculated. Phylogenetic classification was performed on samples harboring DEC and/or APEC virulence-associated genes. A total of 110 E. coli strains were isolated in 15% (49/320) of the evaluated inputs (n=13 vegetable meal; n=33 animal meal, n=3 feed). In general, the isolates showed the highest rates of antimicrobial resistance to sulfonamide and cefazolin and 18% (20/110) were multi-drug resistant. MAR index of feed samples was the highest (0.467). Six and five strains had APEC and DEC virulence-associated genes, respectively, and belonging to phylogenetic groups A and B1. These findings point to the need for strict microbiological control during the production process of these foods.

Resistance Reservoirs and Multi-Drug Resistance of Commensal Escherichia coli From Excreta and Manure Isolated in Broiler Houses With Different Flooring Designs

Carriage of resistant bacteria and spread of antimicrobial resistance (AMR) in the environment through animal manure pose a potential risk for transferring AMR from poultry and poultry products to the human population. Managing this risk is becoming one of the most important challenges in livestock farming. This study focused on monitoring the prevalence of multi-drug resistance (MDR) bacteria and development of AMR depending on flooring. In two experiments (2 × 15,000 birds), broilers were always divided in two different stables. In the control group, the entire floor pen was covered with litter material and in the experimental group, the flooring system was partly modified by installing elevated slat platforms equipped with water lines and feed pans. Over the whole fattening period, excreta and manure samples were taken (days 2, 22, and 32). In total, 828 commensal E. coli isolates were collected. The development and prevalence of resistance against four different antibiotic classes (quinolones, β-lactams, tetracyclines, and sulfonamides) were examined by using broth microdilution. At the end of the trials, the amount of manure per square metre was twice as high below the elevated platforms compared to the control group. Approximately 58% of E. coli isolates from excreta showed resistance against at least one antibacterial agent at day 2. During and at the end of the fattening period, resistant E. coli isolates at least against one of the four antibacterial agents were observed in excreta (46 and 46%, respectively), and manure samples (14 and 42%, respectively), despite the absence of antibacterial agent usage. In spite of less contact to manure in the experimental group, the prevalence of resistant E. coli isolates was significantly higher. Birds preferred the elevated areas which inevitably led to a local high population density. Animal-to-animal contact seems to be more important for spreading antimicrobial resistant bacteria than contact to the litter-excreta mixture. Therefore, attractive areas in poultry housing inducing crowding of animals might foster transmission of AMR. In poultry farming, enrichment is one of the most important aims for future systems. Consequently, there is a need for keeping birds not carrying resistant bacteria at the start of life.

Unknown Risk on the Farm: Does Agricultural Use of Ionophores Contribute to the Burden of Antimicrobial Resistance?

Ionophores are the second most widely used class of antibiotic in agriculture, with over 4 million kilograms sold in the United States in 2016. Because ionophores are not used in humans, it is widely assumed that their agricultural use will not impact human health. Consequently, these drugs have not been subject to the same regulations as medically important antibiotics.

Ionophores are the second most widely used class of antibiotic in agriculture, with over 4 million kilograms sold in the United States in 2016. Because ionophores are not used in humans, it is widely assumed that their agricultural use will not impact human health. Consequently, these drugs have not been subject to the same regulations as medically important antibiotics. Here, I argue that the current evidence base is insufficient to conclude that ionophores do not contribute to human relevant antimicrobial resistance. It is unclear whether ionophore resistance can result in cross-resistance to medically important antibiotics. Moreover, recent evidence suggests that ionophore use may coselect for resistance to vancomycin in some cases. Systematic investigation of the consequences of agricultural ionophore use for human health is therefore imperative.

Resistance to antimicrobials used at hatchery level among clinical Escherichia coli isolates from Ontario broilers

Antimicrobials are used for prophylactic purposes in some flocks because chicks are susceptible to pathogenic bacterial infection at the hatchery stage. The objectives of this study were to assess temporal changes in resistance to ceftiofur, gentamicin, and spectinomycin in Escherichia coli clinical isolates from Ontario broiler chickens between 2008 and 2015, to determine whether stage of production, year and season are predictors of resistance, and whether published data on antimicrobial use help to interpret the temporal patterns in resistance. Logistic regression revealed that stage of production, year, and season were significant predictors of resistance to all 3 antimicrobials. Resistance to ceftiofur fluctuated over time, with a trend towards decreasing resistance between 2013 to 2015; resistance to gentamicin and spectinomycin increased over the study period, with significantly high resistance clusters identified from 2013 to 2015. Comparisons with published hatchery-level antimicrobial use data suggest that these trends may reflect changes in use of ceftiofur and spectinomycin in Ontario.

Biofilm research within irrigation water distribution systems: Trends, knowledge gaps, and future perspectives

Biofilms in irrigation water distribution systems (IWDSs) play an essential role in spreading pathogens, chemical pollutants, and environmental pollutants into downstream irrigated crops and thus should be considered a potential threat to food safety. Although the role of biofilms in drinking water distribution systems has been extensively studied in the last decade, the research on IWDS biofilms in this period has been limited. This review identifies research gaps in the field of IWDS biofilms, provides perspectives on experimental designs for investigating IWDS biofilms, and suggests potential strategies worth pursuing in IWDS management. The current state of the art of IWDS biofilms is discussed, and an analysis of the challenges in IWDS biofilm research is presented. Furthermore, this review proposes useful advanced technologies that allow a practical, in-depth fundamental understanding of IWDS biofilms. In a nutshell, this article provides future directions and insights into detailed experimental designs on a relatively under-reported research topic: "IWDS biofilms."

Prevalence of antibiotic-resistant E. coli in broilers challenged with a multi-resistant E. coli strain and received ampicillin, an organic acid-based feed additive or a synbiotic preparation

The aim of this study was to evaluate the effect of ampicillin, an organic acid-based feed additive and a synbiotic preparation on the prevalence of antibiotic-resistant E. coli in the ceca of broilers. A total of 2000 broiler chickens (Ross 708) were randomly assigned to 5 groups with 8 replicates. The negative control group was the only group that was not subjected to avian pathogenic E. coli challenge, while all the other 4 groups received a multi-resistant E. coli strain that was resistant to ampicillin, cephalexin, and nalidixic acid as an oral challenge. The second group served as a challenge control, and the third group received the antibiotic ampicillin via water for 5 d. The fourth group received a feed additive based on organic acids and cinnamaldehyde, and the fifth group received a synbiotic preparation via feed and water. On day 17 and 38 of the trial, cecal samples from 3 birds from each of the 40 pens were obtained, and the E. coli counts and abundances of antibiotic-resistant E. coli were determined. Oral challenge with an avian pathogenic E. coli strain did not influence the performance, and there was no significant difference in growth performance between groups. The total E. coli count was lower (P < 0.05) in the group supplemented with the synbiotic than in the challenge control group on day 38 of the trial. Administration of an antibiotic for 5 d led to a significant increase in the abundance of E. coli strains resistant to ampicillin, amoxicillin-clavulanic acid, cefoxitin, and ceftriaxone. There was no increase in the abundance of antibiotic-resistant E. coli observed in the groups that received feed supplemented with an organic acid/cinnamaldehyde-based feed additive or a synbiotic. Moreover, the effects of the tested feed additives on the prevalence of resistant E. coli are demonstrated by the lower ceftriaxone minimal inhibitory concentration values for this group than for the antibiotic group. Additionally, the synbiotic group exhibited lower ceftriaxone minimal inhibitory concentration values than the antibiotic group.

Egg Production in Poultry Farming Is Improved by Probiotic Bacteria

Antimicrobial resistance (AMR) is one of the most serious threats for human health in the near future. Livestock has played an important role in the appearance of antibiotic-resistant bacteria, intestinal dysbiosis in farming animals, or the spread of AMR among pathogenic bacteria of human concern. The development of alternatives like probiotics is focused on maintaining or improving production levels while diminishing these negative effects of antibiotics. To this end, we supplied the potential probiotic Enterococcus faecalis UGRA10 in the diet of laying hens at a final concentration of 10⁸ Colony Forming Units per gram (CFU/g) of fodder. Its effects have been analyzed by: (i) investigating the response of the ileum and caecum microbiome; and (ii) analyzing the outcome on eggs production. During the second half of the experimental period (40 to 76 days), hens fed E. faecalis UGRA10 maintained egg production, while control animals dropped egg production. Supplementation diet with E. faecalis UGRA10 significantly increased ileum and caecum bacterial diversity (higher bacterial operational taxonomic unit richness and Faith’s diversity index) of laying hens, with animals fed the same diet showing a higher similarity in microbial composition. These results point out to the beneficial effects of E. faecalis UGRA10 in egg production. Future experiments are necessary to unveil the underlying mechanisms that mediate the positive response of animals to this treatment.