Recurring Necrotic Enteritis Outbreaks in Commercial Broiler Chicken Flocks Strongly Influence Toxin Gene Carriage and Species Richness in the Resident Clostridium perfringens Population

Determination of the virulence status of Clostridium perfringens strains using a chicken intestinal ligated loop model is important for understanding the pathogenesis of necrotic

Necrotic enteritis (NE) is a poultry intestinal disease caused by virulent strains of the bacterium Clostridium perfringens (C. perfringens). This anaerobic bacterium produces a wide range of enzymes and toxins in the gut which leads to NE development. It is generally accepted by the poultry veterinarians that netB-positive C. perfringens strains are virulent and netB-negative strains do not cause NE. However, NE pathogenesis remains unclear as contradictory results have been reported. The use of experimental in vivo models is a valuable tool to understand the pathogenesis of a disease. In this study, a chicken ligated loop model was used to determine the virulence status of 79 C. perfringens strains from various geographical locations, sources, and genotype profiles. According to our model and based on histologic lesion scoring, 9 C. perfringens strains were classified as commensal, 35 as virulent, and 34 as highly virulent. The virulence of only 1 C. perfringens strain could not be classified as its lesion score was variable (from <10 to >15). In general, NE lesions were more severe in intestinal loops inoculated with netB-positive C. perfringens strains than those inoculated with netB-negative strains. The prevalence of netB among strains classified as commensal, virulent, and highly virulent was 56% (5/9), 54%, (19/35), and 59% (20/34). These results suggest that NetB is not required to cause NE lesions and that other factors are also involved. The classification of the virulence status of C. perfringens strains should not be based solely on the presence or absence of this toxin. Therefore, the use of an in vivo model is essential to distinguish commensal from virulent strains of C. perfringens.

Routes of dispersion of antibiotic resistance genes from the poultry farm system

Poultry farms are hotspots for the development and spread of antibiotic resistance genes (ARGs), due to high stocking densities and extensive use of antibiotics, posing a threat of spread and contagion to workers and the external environment. Here, we applied shotgun metagenome sequencing to characterize the gut microbiome and resistome of poultry, workers and their households - also including microbiomes from the internal and external farm environment - in three different farms in Italy during a complete rearing cycle. Our results highlighted a relevant overlap among the microbiomes of poultry, workers, and their families (gut and skin), with clinically relevant ARGs and associated mobile elements shared in both poultry and human samples. On a finer scale, the reconstruction of species-level genome bins (SGBs) allowed us to delineate the dynamics of microorganism and ARGs dispersion from farm systems. We found the associations with worker microbiomes representing the main route of ARGs dispersion from poultry to human populations. Collectively, our findings clearly demonstrate the urgent need to implement more effective procedures to counteract ARGs dispersion from poultry food systems and the relevance of metagenomics-based metacommunity approaches to monitor the ARGs dispersion process for the safety of the working environment on farms.

Magnolol Supplementation Alters Serum Parameters, Immune Homeostasis, Amino Acid Profiles, and Gene Expression of Amino Acid Transporters in Growing Pigs

This study investigated whether dietary supplementation with magnolol affects growth performance, anti-inflammatory abilities, serum and muscle amino acid profiles, and metabolisms in growing pigs. A total of 42 seventy-days-old growing barrows (Duroc × Landrace × Yorkshire) were randomly allocated into two dietary groups: Con, control group (basal diet); and Mag, magnolol group (basal diet supplemented with 400 mg/kg of magnolol). The results revealed that dietary supplementation with magnolol had no effect (p > 0.05) on growth performance. However, magnolol supplementation remarkably increased (p < 0.05) the serum content of albumin, total protein, immunoglobulin G, immunoglobulin M, and interleukin-22. In addition, dietary magnolol supplementation altered the amino acid (AA) profiles in serum and dorsal muscle and particularly increased (p < 0.05) the serum content of arginine and muscle glutamate. Simultaneously, the mRNA expression of genes associated with AA transport in jejunum (SLC38A2, SLC1A5, and SLC7A1) and ileum (SLC1A5 and SLC7A1) was higher (p < 0.05) in the Mag group than in the Con group. Additionally, the serum metabolomics analysis showed that the addition of magnolol significantly enhanced (p < 0.05) arginine biosynthesis, as well as D-glutamine and D-glutamate metabolism. Overall, these results suggested that dietary supplementation with magnolol has the potential to improve the accumulation of AAs, protein synthesis, immunity, and body health in growing pigs by increasing intestinal absorption and the transport of AAs.

Systematic profiling of the chicken gut microbiome reveals dietary supplementation with antibiotics alters expression of multiple microbial pathways with minimal impact on community structure

BACKGROUND

The emergence of antimicrobial resistance is a major threat to global health and has placed pressure on the livestock industry to eliminate the use of antibiotic growth promotants (AGPs) as feed additives. To mitigate their removal, efficacious alternatives are required. AGPs are thought to operate through modulating the gut microbiome to limit opportunities for colonization by pathogens, increase nutrient utilization, and reduce inflammation. However, little is known concerning the underlying mechanisms. Previous studies investigating the effects of AGPs on the poultry gut microbiome have largely focused on 16S rDNA surveys based on a single gastrointestinal (GI) site, diet, and/or timepoint, resulting in an inconsistent view of their impact on community composition.

METHODS

In this study, we perform a systematic investigation of both the composition and function of the chicken gut microbiome, in response to AGPs. Birds were raised under two different diets and AGP treatments, and 16S rDNA surveys applied to six GI sites sampled at three key timepoints of the poultry life cycle. Functional investigations were performed through metatranscriptomics analyses and metabolomics.

RESULTS

Our study reveals a more nuanced view of the impact of AGPs, dependent on age of bird, diet, and intestinal site sampled. Although AGPs have a limited impact on taxonomic abundances, they do appear to redefine influential taxa that may promote the exclusion of other taxa. Microbiome expression profiles further reveal a complex landscape in both the expression and taxonomic representation of multiple pathways including cell wall biogenesis, antimicrobial resistance, and several involved in energy, amino acid, and nucleotide metabolism. Many AGP-induced changes in metabolic enzyme expression likely serve to redirect metabolic flux with the potential to regulate bacterial growth or produce metabolites that impact the host.

CONCLUSIONS

As alternative feed additives are developed to mimic the action of AGPs, our study highlights the need to ensure such alternatives result in functional changes that are consistent with site-, age-, and diet-associated taxa. The genes and pathways identified in this study are therefore expected to drive future studies, applying tools such as community-based metabolic modeling, focusing on the mechanistic impact of different dietary regimes on the microbiome. Consequently, the data generated in this study will be crucial for the development of next-generation feed additives targeting gut health and poultry production. Video Abstract.

Role of Clostridium perfringens Necrotic Enteritis B-like Toxin in Disease Pathogenesis

Necrotic enteritis (NE) is a devastating enteric disease caused by Clostridium perfringens type A/G that impacts the global poultry industry by compromising the performance, health, and welfare of chickens. Coccidiosis is a major contributing factor to NE. Although NE pathogenesis was believed to be facilitated by α-toxin, a chromosome-encoded phospholipase C enzyme, recent studies have indicated that NE B-like (NetB) toxin, a plasmid-encoded pore-forming heptameric protein, is the primary virulence factor. Since the discovery of NetB toxin, the occurrence of NetB⁺ C. perfringens strains has been increasingly reported in NE-afflicted poultry flocks globally. It is generally accepted that NetB toxin is the primary virulent factor in NE pathogenesis although scientific evidence is emerging that suggests other toxins contribute to NE. Because of the complex nature of the host-pathogen interaction in NE pathogenesis, the interaction of NetB with other potential virulent factors of C. perfringens needs better characterization. This short review will summarize the primary virulence factors involved in NE pathogenesis with an emphasis on NetB toxin, and a new detection method for large-scale field screening of NetB toxin in biological samples from NE-afflicted commercial broiler flocks.

Putative antigenic proteins identified by comparative and subtractive reverse vaccinology in necrotic enteritis-causing Clostridium perfringens isolated from broiler chickens

BACKGROUND

Avian necrotic enteritis (NE) caused by Clostridium perfringens is a disease with a major economic impact, generating losses estimated to 6 billion of dollars annually for the poultry industry worldwide. The incidence of the disease is particularly on the rise in broiler chicken flocks eliminating the preventive use of antibiotics. To date, no alternative allows for the efficient prevention of NE and a control of the disease using a vaccinal strategy would be mostly prized. For this purpose, comparative and subtractive reverse vaccinology identifying putative immunogenic bacterial surface proteins is one of the most promising approaches.

RESULTS

A comparative genomic study was performed on 16 C. perfringens strains isolated from healthy broiler chickens and from broilers affected with necrotic enteritis. Results showed that the analyzed genomes were composed of 155,700 distinct proteins from which 13% were identified as extracellular, 65% as cytoplasmic and 22% as part of the bacterial membrane. The evaluation of the immunogenicity of these proteins was determined using the prediction software VaxiJen®.

CONCLUSIONS

For the most part, proteins with the highest scores were associated with an extracellular localisation. For all the proteins analyzed, the combination of both the immunogenicity score and the localisation prediction led to the selection of 12 candidate proteins that were mostly annotated as hypothetical proteins. We describe 6 potential candidates of higher interest due to their antigenic potential, their extracellular localisation, and their possible role in virulence of C. perfringens.

Research Note: Prevalence and molecular characteristics of Clostridium perfringens in "no antibiotics ever" broiler farms

Clostridium perfringens (C. perfringens) is the etiological agent of necrotic enteritis and gangrenous dermatitis; 2 diseases that cause significant economic and welfare concerns to the broiler industry. Previously, Clostridium-related diseases were managed with the use of antimicrobial growth promoters fed to broilers that improved gut health and performance. The recent shift to no antibiotics ever (NAE) production has increased the incidence of Clostridium-related diseases. The objective of this study was to identify C. perfringens prevalence and toxinotypes in NAE farms. Samples of litter, feces, and cloacal swabs were collected from 4 NAE broiler farms in the summer of 2019, on d 28 and d 56 of one flock cycle. A total of 734 presumptive isolates were obtained from 192 samples collected in the study. Irrespective of the age of flock and sample type, all 192 samples contained at least one colony presumptively identified as C. perfringens on Perfringens agar plate with morphology as a single, round colony with opaque ring and black center. All isolates were further screened using PCR for confirmation, toxinotyping, and identification of virulence-associated genes. Only 9 isolates among the 734 presumptive isolates were confirmed as C. perfringens and all confirmed isolates were toxinotype A with variation in presence of netB, cpb2, and tpeL. More extensive studies are required to assess the prevalence and virulence of C. perfringens in NAE farms.

Impacts of Short-Term Antibiotic Withdrawal and Long-Term Judicious Antibiotic Use on Resistance Gene Abundance and Cecal Microbiota Composition on Commercial Broiler Chicken Farms in Québec

The ever-increasing problem of antibiotic resistance makes routine use of antibiotics in animal production no longer considered as a reasonable and viable practice. The Chicken Farmers of Canada have developed and are implementing an Antimicrobial Use Reduction Strategy, which has the ultimate goal of eliminating the preventive use of medically important antibiotics in broiler chicken and turkey production. However, very little is known about the real overall impact of an antibiotic use reduction strategy in complex ecosystems, such as the bird intestine or the commercial broiler chicken farm. The main objectives of the present study were to compare the abundance of antibiotic resistance-encoding genes, characterize the intestinal microbiota composition, and evaluate the presence of Clostridium perfringens, in six commercial poultry farms adopting short-term antibiotic withdrawal and long-term judicious use strategy. Implementing an antibiotic-free program over a 15-months period did not reduce the abundance of many antibiotic resistance-encoding genes, whereas the judicious use of antibiotics over 6 years was found effective. The short-term antibiotic withdrawal and the long-term judicious use strategy altered the intestinal microbiota composition, with the Ruminococcaceae and Lachnospiraceae families being negatively impacted. These findings are in agreement with the lower production performance and with the increased C. perfringens populations observed for farms phasing out the use of antibiotics. Adopting a conventional rearing program on commercial broiler chicken farms selected for specific antibiotic resistance-encoding genes in many barns. This study highlights the potential impacts of different rearing programs in poultry production and will help guide future policies in order to reduce the use of antibiotics while maintaining production performance.

Impacts of antibiotic reduction strategies on zootechnical performances, health control, and Eimeria spp. excretion compared with conventional antibiotic programs in commercial broiler chicken flocks

Increasing efforts have been made in recent years to reduce antimicrobial use in animal production. The objective of this prospective study was to evaluate, in commercial broiler chicken farms, 2 antibiotic reduction strategies that eliminated the use of antibiotics important for human medicine, in comparison with the conventional use of antibiotics. On 7 broiler chicken farms, a house was allocated to the antibiotic reduction treatments for 6 consecutive flocks, whereas a similar house on the same premises was assigned to the conventional use of antibiotics (CONV) for 6 consecutive flocks. The antibiotic reduction strategies consisted of continuous in-feed use of ionophores (TX1) and continuous in-feed use of ionophores with butyric acid (TX2). In the 84 flocks, zootechnical performance was recorded, lesion scoring at 21 and 28 D of age was performed, and fecal samples were recovered during grow out for Eimeria spp. oocysts counts. There was no statistical difference between TX1, TX2, and CONV for weights at slaughter, feed conversion ratios, average daily gains, age at slaughter, total mortalities, and condemnations. The probability of identifying oocysts in the fecal samples significantly increased with the age of the flock, but there was no significant treatment effect between 7 and 16 D of age. At 19 D of age, the probability of a sample containing oocysts was higher in TX1 than in CONV, but TX2 was not statistically different from TX1 and CONV. Predicted oocysts per gram in CONV flocks were significantly lower between 22 and 34 D of age than in TX1 and TX2 flocks, whereas there were no significant differences between TX1 and TX2 for all ages. Lesion scoring of the gastrointestinal system showed no differences for coccidiosis scores between TX1, TX2, and CONV. No lesions of necrotic enteritis were observed. In conclusion, it was possible to adequately control intestinal diseases and maintain zootechnical performances by relying exclusively on ionophores, when compared with broiler chicken flocks using standard shuttle programs with antibiotic growth promoters.

Phylogenomic analysis of gastroenteritis-associated Clostridium perfringens in England and Wales over a 7-year period indicates distribution of clonal toxigenic strains in multiple outbreaks and extensive involvement of enterotoxin-encoding (CPE) plasmids

Clostridium perfringens is a major enteric pathogen known to cause gastroenteritis in human adults. Although major outbreak cases are frequently reported, only limited whole-genome sequencing (WGS) based studies have been performed to understand the genomic epidemiology and virulence gene content of outbreak-associated C. perfringens strains. We performed phylogenomic analysis on 109 C. perfringens isolates (human and food) obtained from disease cases in England and Wales between 2011 and 2017. Initial findings highlighted the enhanced discriminatory power of WGS in profiling outbreak C. perfringens strains, when compared to the current Public Health England referencing laboratory technique of fluorescent amplified fragment length polymorphism analysis. Further analysis identified that isogenic C. perfringens strains were associated with nine distinct care-home-associated outbreaks over the course of a 5-year interval, indicating a potential common source linked to these outbreaks or transmission over time and space. As expected, the enterotoxin cpe gene was encoded in all but 4 isolates (96.3 %; 105/109), with virulence plasmids encoding cpe (particularly pCPF5603 and pCPF4969 plasmids) extensively distributed (82.6 %; 90/109). Genes encoding accessory virulence factors, such as beta-2 toxin, were commonly detected (46.7 %; 51/109), and genes encoding phage proteins were also frequently identified. Overall, this large-scale genomic study of gastroenteritis-associated C. perfringens suggested that three major cpe-encoding (toxinotype F) genotypes underlie these outbreaks: strains carrying (1) pCPF5603 plasmid, (2) pCPF4969 plasmid and (3) chromosomal-cpe strains. Our findings substantially expanded our knowledge on type F C. perfringens involved in human-associated gastroenteritis, with further studies required to fully probe the dissemination and regional reservoirs of this enteric pathogen, which may help devise effective prevention strategies to reduce the food-poisoning disease burden in vulnerable patients, such as the elderly.

Molecular detection and characterization of Clostridium perfringens toxin genes causing necrotic enteritis in broiler chickens

A total of 464 samples comprising of cloacal swabs from necrotic enteritis suspected live birds (191), intestinal scrapings from dead birds with symptoms of necrotic enteritis (91), and apparently healthy birds (182) were collected from selected districts of AP. The samples were subjected to multiplex PCR for simultaneous detection of α, β, and β2 toxin genes and uniplex PCR for the detection of NetB gene. Multiplex PCR screening of samples reveled α toxin gene positives from (cpa) 248/282 (87.94%) necrotic enteritis suspected and 40/182 (21.97%) apparently healthy samples. Among cpa positives 142/248 (57.25%) and 3/40 (7.5%) were positive for β2 toxin gene in necrotic enteritis suspected and apparently healthy birds respectively, indicating the involvement of C. perfringens type A, with minor pore forming toxin gene cpb2 in causing necrotic enteritis in poultry. None of the sample was positive for β toxin gene. The present research indicates C. perfringens type A along with β2 toxin gene was responsible for causing necrotic enteritis in broiler chickens in some parts of Andhra Pradesh in India. Phylogenetic relationship of amplified cpa and cpb2 amino acids sequences from present C. perfringens isolates were studied. The analysis reveals the sequence identity of cpb2 gene of the present isolates and variations at both nucleotide and amino acid level with the published sequences of cpb2 gene of C. perfringens isolates from different animal species of the USA, Iran, Netherlands, and Japan.

Broiler chicken carcasses and their associated abattoirs as a source of enterotoxigenic Clostridium perfringens: Prevalence and critical steps for contamination

Clostridium perfringens ranks among the three most frequent bacterial pathogens causing human foodborne diseases in Canada, and poultry meat products are identified as a source of infection for humans. The objective of the current study was to estimate the proportion of broiler chicken flocks, carcasses and various environmental samples from critical locations of the slaughter plant positive for the presence of C. perfringens enterotoxin encoding gene (cpe). From the 16 visits conducted, 25% of the 79 flocks sampled, 10% of the 379 carcasses sampled and 5% of the 217 environmental samples collected were found positive for cpe. The proportion of cpe-positive carcasses was statistically different between surveyed plants, with 17.0% for one abattoir and 2.2% for the other. For the most contaminated plant, cpe-positive carcasses were identified at each step of the processing line, with prevalence varying between 10.0% and 25.0%, whereas this prevalence varied between 0% and 25.0% for the environmental surfaces sampled. Based on the results obtained, enterotoxigenic C. perfringens strains could potentially represent a risk for the consumer.