Impact of Eimeria tenella Coinfection on Campylobacter jejuni Colonization of the Chicken

Interplay of poultry-microbiome interactions - influencing factors and microbes in poultry infections and metabolic disorders

1. The poultry microbiome and its stability at every point in time, either free range or reared under different farming systems, is affected by several environmental and innate factors. The interaction of the poultry birds with their microbiome, as well as several inherent and extraneous factors contribute to the microbiome dynamics. A poor understanding of this could worsen poultry heath and result in disease/metabolic disorders.2. Many diseased states associated with poultry have been linked to dysbiosis state, where the microbiome experiences some perturbation. Dysbiosis itself is too often downplayed; however, it is considered a disease which could lead to more serious conditions in poultry. The management of interconnected factors by conventional and emerging technologies (sequencing, nanotechnology, robotics, 3D mini-guts) could prove to be indispensable in ensuring poultry health and welfare.3. Findings showed that high-throughput technological advancements enhanced scientific insights into emerging trends surrounding the poultry gut microbiome and ecosystem, the dysbiotic condition, and the dynamic roles of intrinsic and exogenous factors in determining poultry health. Yet, a combination of conventional, -omics based and other techniques further enhance characterisation of key poultry microbiome actors, their mechanisms of action, and roles in maintaining gut homoeostasis and health, in a bid to avert metabolic disorders and infections.4. In conclusion, there is an important interplay of innate, environmental, abiotic and biotic factors impacting on poultry gut microbiome homoeostasis, dysbiosis, and overall health. Associated infections and metabolic disorders can result from the interconnected nature of these factors. Emerging concepts (interkingdom or network signalling and neurotransmitter), and future technologies (mini-gut models, cobots) need to include these interactions to ensure accurate control and outcomes.

The financial cost of coccidiosis in Algerian chicken production: a major challenge for the poultry sector

Coccidiosis, caused by parasites of the genus Eimeria, is a significant economic burden to the poultry industry. In this study, we conducted a comprehensive analysis to evaluate the financial losses associated with Eimeria infection in chickens in Algeria, relying on data provided by key stakeholders in the Algerian poultry industry to assess sub-clinical as well as clinical impact. We employed the updated 2020 version of a model established to estimate the cost of coccidiosis in chickens, taking into consideration specific cultural and technical aspects of poultry farming in Algeria. The findings predict economic losses due to coccidiosis in chickens of approximately £86.7 million in Algeria for the year 2022, representing £0.30 per chicken raised. The majority of the cost was attributed to morbidity (74.9%), emphasizing the substantial economic impact of reduced productivity including decreased bodyweight gain and increased feed conversion ratio. Costs associated with control measures made up 20.5% of the total calculated cost, with 4.6% of the cost related to mortality. These figures provide a clear indication of the scope and economic impact of Eimeria infection of chickens in Algeria, illustrating the impact of practices common across North Africa. They underscore the ongoing requirement for effective preventive and control measures to reduce these financial losses while improving productivity and welfare, ensuring the economic sustainability of the Algerian poultry industry.

Defining optimal dietary starch, oil, and amino acid inclusion levels for broilers experiencing a coccidiosis challenge

Alternative methods to alleviate coccidiosis in broilers are of interest to producers, including dietary strategies to minimize disruptions in growth rate and efficiency when faced with health challenges. Our objective was to determine optimal combinations of dietary starch, amino acids (AA), and oil to benefit productivity of broilers experiencing Eimeria-induced immune activation. Two trials were conducted using 1,536 male Ross 308 broiler chicks in floor pens randomly assigned to 1 of 17 experimental treatments. All birds received common starter (d 0-10) and finisher (d 24-35) diets, and only differed based on their assigned experimental grower diet (d 10-24). Trial 1 experimental grower diets ranged from 2,700 to 3,300 kcal/kg AME. Trial 2 included 10 experimental grower diets following a simplex lattice design consisting of 3 basal lots formulated to have the highest starch (45.4%), oil (10.2%), or AA density (120, 1.33% digestible Lys) and mixed in 4 equally spaced levels for each component (0, 0.33, 0.67, 1). These mixtures enabled varying densities of AA (80-120% of recommendation), starch:oil (4:1-20:1), and AME (2,940-3,450 kcal/kg). Bird and feeder weights were collected on d 0, 10, 24, and 35, and birds were exposed to an Eimeria challenge on d 11 or 12. In trial 2, excreta samples were collected for AME determination and carcasses were processed on d 36. Data were analyzed using ANOVA, t test, or regression. In Trial 1, BW gain and feed conversion were improved (P < 0.05) by increasing dietary AME. In Trial 2, birds receiving diets containing AA at 93 to 107% of recommendations and higher oil exhibited improved (P < 0.05) performance, but increased starch at the expense of oil reduced performance (P < 0.05). Relative breast and fat pad weights were not influenced by diet in Trial 2. We determined that broilers mildly challenged with Eimeria would exhibit highest BW gain when receiving diets containing 35.8% starch, 8.9% oil, and 101.3% of AA recommendations, which can be utilized by producers to maintain productivity under health-challenged conditions.

The risk-benefit balance of resistance to ionophores in Enterococcus faecium and Enterococcus faecalis for ionophore coccidiostats in broiler chickens

In recent years, publications and debate have emerged in the scientific literature that have linked the use of ionophore coccidiostats, which are themselves not medically important and not related to any therapeutic antibiotics used in human and animal medicine, to resistance development to medically important antibiotics in Enterococcus faecium and Enterococcus faecalis, isolated from broilers and broiler meat. This has been based on the discovery of genes, now named NarAB, that appear to result in elevated MICs of the ionophores narasin, salinomycin and maduramycin and that these are linked to genes responsible for resistance to antibiotics that may be clinically relevant in human medicine. This article will seek to review the most significant publications in this regard and will also examine national antimicrobial resistance surveillance programmes in Norway, Sweden, Denmark and the Netherlands, in order to further evaluate this concern. The conclusion of the review is that the risk that enterococci may pass from broilers to humans and that antimicrobial resistance gene transfer may occur is negligible, remains unquantified and is highly unlikely to be of significance to human health. Indeed, to date no human nosocomial infections have been linked to poultry sources. Concurrently a review of the possible impact of a policy that limits access for poultry farmers and poultry veterinarians to ionophore coccidiostats in broilers indicates predictable negative consequences with regard to antibiotic resistance of significance to animal welfare and to human health.

In-vivo anticoccidial efficacy of green synthesized iron-oxide nanoparticles using Ficus racemosa Linn leaf extract. (Moraceae) against Emeria tenella infection in broiler chicks

Coccidiosis is an acute gastrointestinal parasitic disease and causes approximately $2.80 to $3.27 per m2 loss in a broiler farm of a 33-day-old flock. In this study, iron oxide nanoparticles (IONPs) were green synthesized using the aqueous leaf extract of Ficus racemosa as a reducing and capping agent to reduce the emerging resistance in coccidia spores against conventional treatments and boost the immune level in broilers. These IONPs were evaluated for their impacts on the growth performance, biochemistry, blood profile, and histology in the coccidiodized broiler chicken with Emeria tenella under in vivo conditions. The characteristics and stability of particles were obtained using UV-Vis spectroscopy, Fourier transforms infrared (FTIR), X-Ray diffraction (XRD), energy dispersive X-ray absorption (EDX), scanning electron microscopy (SEM), zeta potential and zeta size. The results indicated that IONPs at the moderate dose of 15 mg/kg (p = 0.001) reduced the coccidial impacts by eliminating oocyst shedding per gram feces (up to 91%) and reducing clinical symptoms (lesions (LS = 0), bloody diarrhea (No), and mortality (0%) in chicken at day 10 of treatment as compared to the negative control group-B (infected & non-treated). A dose-dependent and time-dependent trend were observed during treatments (10, 15, and 20 mg/kg) of 1-3 weeks using IONPs against the coccidial impacts on the growth parameters (body weight gain, mean feed consumption, feed conversion ratio) and biochemistry (plasma glucose, total protein, uric acid, ALT, AST, and ALP) in chickens. Additionally, F. racemosa IONPs at a dose of 15 and 20 mg/kg significantly recovered the parasitized and highly damaged hepatocytes, liver tissues, and ceca tissues after 1-3 weeks of treatment in broiler chickens. Overall, the 15 mg/kg concentration of IONPs exhibited fast recovery and growth enhancement in coccidiodized broilers. Therefore, the 15 mg/kg dose of green synthesized IONPs using leaf extract of F. racemosa could be a potential and safe anticoccidial agent with targeted implications in the poultry industry.

Interplay between Eimeria acervulina and Cryptosporidium parvum during In Vitro Infection of a Chicken Macrophage Cell Line (HD11)

BACKGROUND

Eimeria acervulina is a frequent intestinal pathogen of chickens, causing economic impact on the poultry industry. Cryptosporidium parvum is a neglected parasite in chickens. However, because of its zoonotic potential, poultry cryptosporidiosis may pose a risk to public health. Little is known about the parasite-host interactions during coinfection with both parasites. In this study, we investigated the possible interactions during in vitro coinfection of E. acervulina and C. parvum in a chicken macrophage cell line (HD11).

METHODS

HD11 cells were inoculated with E. acervulina and C. parvum sporozoites and incubated 2, 6, 12, 24, and 48 h post infection (hpi). Mono-infections for each parasite were also investigated. Real-time PCR was used to quantify parasite replication. Additionally, macrophage mRNA expression levels of IFN-γ, TNF-α, iNOS, and IL-10 were measured.

RESULTS

For both parasites, multiplication was, in most groups, lower in the coinfection group (COIG) compared with mono-infections. However, at 6 hpi, the number of C. parvum copies was higher in co-infections. Intracellular replication started to decrease from 12 hpi onward, and it was almost undetectable by 48 hpi in all groups. Infections resulted in low expression of all cytokines, except at 48 hpi.

CONCLUSIONS

Infection of avian macrophages with both E. acervulina and C. parvum seemed to hinder intracellular replication for both parasites in comparison to mono-infection. A clear reduction in intracellular parasites from 12 hpi onward details the important role potentially played by macrophages in host control of these parasites.

Effects of challenge with Clostridium perfringens, Eimeria and both on ileal microbiota of yellow feather broilers

In the poultry industry worldwide, Clostridium perfringens has been causing major economic loss as it can cause necrotic enteritis (NE). The coccidial infection has been considered as the most important predisposing factor of NE caused by C. perfringens. In this study, we aimed to advance our knowledge on ileal microbiota of yellow feather broilers under C. perfringens and/or Eimeria challenge. Total of 80 healthy day old yellow feather broilers were randomly assigned to four groups including: Control, C. perfringens challenge group (C. Per), Eimeria challenge group (Cocc), and C. perfringens plus Eimeria challenge group (Comb). On day 14, the Cocc and Comb group broilers were orally gavaged 1 ml PBS solution containing 25,000 oocysts of Eimeria brunetti and 25,000 oocysts of Eimeria maxima. Starting on day 17, the C. Per and Comb group broilers were orally gavaged 10 mL of C. perfringens per bird (4 × 107 CFU/mL, ATCC® 13124™ Strain) every day for 6 days. 16S rRNA gene sequencing was performed on extracted DNA of ileal digesta samples. The results showed that C. perfringens alone did not affect the alpha diversity of ileal microbiome in yellow feather broilers but co-infection with Eimeria significantly decreased the diversity of ileal microbiota. C. perfringens and Eimeria challenge also decreased the relative abundance of beneficial bacteria including Bacteroidetes at the phylum level and Faecalibacterium at the genus level. At the species level, the relative abundance of Candidatus Arthromitus was significantly decreased in the Eimeria challenged groups. This microbial shift information of ileal microbiota under C. Perfringens and Eimeria challenge provide important reference data for the development of therapeutic approaches to necrotic enteritis in yellow-feather broiler chickens.

Influence of Eimeria maxima coccidia infection on gut microbiome diversity and composition of the jejunum and cecum of indigenous chicken

Coccidiosis is an economically significant protozoan disease and an intracellular parasite that significantly impacts poultry production. The gastrointestinal tract microbiota plays a central role in host health and metabolism, and these microbes enhance chickens’ immune systems and nutrient absorption. In this study, we analyzed the abundance and diversity of microbiota of the jejunum and cecum of a dual-purpose indigenous Horro chicken following Eimeria maxima infection. We compared microbial abundance, composition, and diversity at the 4- and 7- days post-infection using 16S rRNA gene sequencing. We obtained, on average, 147,742 and 132,986 high-quality sequences per sample for jejunum and cecum content, respectively. Firmicutes, Proteobacteria, Campilobacterota and Bacteroidota were the major microbial phylum detected in the jejunum content. Firmicutes were the dominant phylum for 4- and 7-days jejunum control groups accounting for (>60% of the sequences). In the infected group Campilobacterota was the dominant phylum in the jejunum (> 24% of sequences) at 4-and 7-days post-infection groups, while Proteobacteria was predominant at 4- and 7-days post-infection of the cecum (> 40% of the sequences). The microbial genus Lactobacillus and Helicobacter were found in the jejunum, while Alistipes, Barnesiella and Faecalibacterium were detected in the cecum. In the jejunum, Helicobacter was dominant at 4 -and-7 days post-infection (≥24%), and Lactobacillus was dominant at 4 -and 7- days in the control group (> 50%). In 4- and 7-days post-infection, Alistipes genus was the more prevalent (> 38%) in the cecum. Thus, clear differences were observed in the bacterial microbiota distribution and abundance between the jejunum and cecum, as well as between infected and control groups for both tissues. The results indicate that chicken intestinal microbial imbalance (dysbiosis) is associated with Eimeria parasite infection and will likely affect the host-microbial non-pathogenic and pathogenic molecular interactions.

Case of necrotic enteritis associated with campylobacteriosis and coccidiosis in an adult Indian peacock (Pavo cristatus)

Background

To date, Campylobacter jejuni has not been found to be pathogenic to peafowl. The available publications show that out of a total of 44 samples tested from peafowl, this bacterium was isolated only in two cases. Eimeria pavonina infestations in the peafowl have been described, but no fatal cases have been reported yet.

Case presentation

The four-year-old peacock was presented with chronic diarrhea, emaciation and weakness. Post mortem examination revealed enlarged and pale kidneys, small intestinal mucosal necrosis and thickening of intestinal wall, and pericardial effusion. The histopathological examination revealed necrotic enteritis with marked mononuclear cells infiltration associated with the presence of coccidia, additionally there was histological evidence of septicemia in liver and kidneys. Bacteria identification was based on light microscopy of the small intestine sample, culture, and biochemical tests. Further identification was based on PCR. Antimicrobial susceptibility profile was created by determination of minimal inhibitory concentration (MIC) values for 6 antimicrobial agents from 5 different classes. PCR assays were performed to detect virulence factors genes responsible for motility, cytolethal distending toxin production, adhesion and internalization. Bacteriology of the small intestine sample showed abundant growth almost exclusively of Campylobacter jejuni, resistant to ciprofloxacin, gentamycin and ampicillin. Bacteria was sensitive to Amoxicillin + clavulanic acid, tetracycline, and erythromycin. All tested virulence factors genes have been detected. The parasitological examination was performed by microscopic examination of fresh faeces and intestinal content, and revealed the moderate number of Eimeria pavonina, Histomonas meleagridis, single Capillaria spp. eggs as well Heterakis spp. like parasites.

Conclusion

The above case shows that a virulent isolate of Campylobacter jejuni in combination with a parasitic invasion may cause chronic enteritis in peafowl, which most likely led to extreme exhaustion of the host organism and death.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12917-022-03260-1.

Coccidia-Microbiota Interactions and Their Effects on the Host

As a common parasitic disease in animals, coccidiosis substantially affects the health of the host, even in the absence of clinical symptoms and intestinal tract colonization. Gut microbiota is an important part of organisms and is closely related to the parasite and host. Parasitic infections often have adverse effects on the host, and their pathogenic effects are related to the parasite species, parasitic site and host-parasite interactions. Coccidia-microbiota-host interactions represent a complex network in which changes in one link may affect the other two factors. Furthermore, coccidia-microbiota interactions are not well understood and require further research. Here, we discuss the mechanisms by which coccidia interact directly or indirectly with the gut microbiota and the effects on the host. Understanding the mechanisms underlying coccidia-microbiota-host interactions is important to identify new probiotic strategies for the prevention and control of coccidiosis.

The in vitro and in vivo anti-virulent effect of organic acid mixtures against Eimeria tenella and Eimeria bovis

Eimeria tenella and Eimeria bovis are complex parasites responsible for the condition of coccidiosis, that invade the animal gastrointestinal intestinal mucosa causing severe diarrhoea, loss of appetite or abortions, with devastating impacts on the farming industry. The negative impacts of these parasitic infections are enhanced by their role in promoting the colonisation of the gut by common foodborne pathogens. The aim of this study was to test the anti-Eimeria efficacy of maltodextrin, sodium chloride, citric acid, sodium citrate, silica, malic acid, citrus extract, and olive extract individually, in vitro and in combination, in vivo. Firstly, in vitro infection models demonstrated that antimicrobials reduced (p < 0.05), both singly and in combination (AG), the ability of E. tenella and E. bovis to infect MDBK and CLEC-213 epithelial cells, and the virulence reduction was similar to that of the anti-coccidial drug Robenidine. Secondly, using an in vivo broiler infection model, we demonstrated that AG reduced (p = 0.001) E. tenella levels in the caeca and excreted faeces, reduced inflammatory oxidative stress, improved the immune response through reduced ROS, increased Mn-SOD and SCFA levels. Levels of IgA and IgM were significantly increased in caecal tissues of broilers that received 0.5% AG and were associated with improved (p < 0.0001) tissue lesion scores. A prophylactic approach increased the anti-parasitic effect in vivo, and results indicated that administration from day 0, 5 and 10 post-hatch reduced tissue lesion scores (p < 0.0001) and parasite excretion levels (p = 0.002). Conclusively, our in vitro and in vivo results demonstrate that the natural antimicrobial mixture (AG) reduced parasitic infections through mechanisms that reduced pathogen virulence and attenuated host inflammatory events.

Impact assessment of the reduction or removal of ionophores used for controlling coccidiosis in the UK broiler industry

Coccidiosis is a complex parasitic disease ubiquitous in all types of poultry production. It can have both a direct effect on bird health and welfare with significant negative impacts on the production parameters and indirect effect as it predisposes to other pathogens. Ionophore coccidiostats have been used safely for over 45 years by poultry producers. Concerns have been raised that their use in livestock production could promote the development of antibiotic resistance, but their unique mode of action makes it unlikely. Conversely their removal can result in increased use of therapeutic antibiotics to treat disease posing a greater risk of antibiotic resistance development. Economic and environmental models examining the impact of the removal of ionophore coccidiostats from UK production suggest the annual cost to the broiler sector would be between £68.02-£109.95 million and result in an additional 84,000 tonnes CO₂ e being produced per annum. Any cost increase would make this wholesome and affordable animal protein less affordable to poorer sectors of society. Increased greenhouse gas production, demand for water and land as a result of less efficient production will impact on climate change targets.

Understanding the interactions between Eimeria infection and gut microbiota, towards the control of chicken coccidiosis: a review

The gastrointestinal tract in poultry harbours a diverse microbial community that serves a crucial role in digestion and protection. Disruption of the gut environment due to Eimeria spp. parasite infection causes an imbalance in intestinal homeostasis, driving the increment of pathogens such as Clostridium species. Coccidiosis infection affects the composition and integrity of gut microbiota, resulting in elevated susceptibility to diseases that pose a serious threat to the overall health and productivity of chickens. Anticoccidial drugs have proven effective in curbing coccidiosis but with concerning drawbacks like drug resistance and drug residues in meat. The exploration of natural alternative strategies such as probiotics and phytochemicals is significant in controlling coccidiosis through modification and restoration of gut microbiota, without inducing drug resistance. Understanding the interaction between Eimeria parasites and gut microbiota is crucial for the control and prevention of coccidiosis, and the development of novel alternative treatments.

Determinants of Eimeria and Campylobacter infection dynamics in UK domestic sheep: the role of co-infection

Coccidiosis caused by Eimeria species is a well-recognized disease of livestock. Enteric Eimeria infections are common, but disease usually only manifests when infection intensity is abnormally high. Campylobacter species are important zoonotic enteric bacterial pathogens for which livestock are important reservoir hosts. The diversity and epidemiology of ovine Eimeria and Campylobacter infections on two farms in north-western England were explored through a 24-month survey of shedding in sheep feces. Most animals were infected with at least one of 10 different Eimeria species, among which E. bakuensis and E. ovinoidalis were most common. An animal's age and the season of sampling were associated with the probability and intensity of Eimeria infection. Season of sampling was also associated with the probability of Campylobacter infection. Interestingly, higher intensities of Eimeria infections were significantly more common in animals not co-infected with Campylobacter. We explored the determinants of E. bakuensis and E. ovinoidalis infections, observing that being infected with either significantly increased the likelihood of infection with the other. The prevalence of E. ovinoidalis infections was significantly lower in sheep infected with Campylobacter. Recognition that co-infectors shape the dynamics of parasite infection is relevant to the design of effective infection control programmes.

Quantitative trait loci and transcriptome signatures associated with avian heritable resistance to Campylobacter

Campylobacter is the leading cause of bacterial foodborne gastroenteritis worldwide. Handling or consumption of contaminated poultry meat is a key risk factor for human campylobacteriosis. One potential control strategy is to select poultry with increased resistance to Campylobacter. We associated high-density genome-wide genotypes (600K single nucleotide polymorphisms) of 3000 commercial broilers with Campylobacter load in their caeca. Trait heritability was modest but significant (h² = 0.11 ± 0.03). Results confirmed quantitative trait loci (QTL) on chromosomes 14 and 16 previously identified in inbred chicken lines, and detected two additional QTLs on chromosomes 19 and 26. RNA-Seq analysis of broilers at the extremes of colonisation phenotype identified differentially transcribed genes within the QTL on chromosome 16 and proximal to the major histocompatibility complex (MHC) locus. We identified strong cis-QTLs located within MHC suggesting the presence of cis-acting variation in MHC class I and II and BG genes. Pathway and network analyses implicated cooperative functional pathways and networks in colonisation, including those related to antigen presentation, innate and adaptive immune responses, calcium, and renin–angiotensin signalling. While co-selection for enhanced resistance and other breeding goals is feasible, the frequency of resistance-associated alleles was high in the population studied and non-genetic factors significantly influenced Campylobacter colonisation.

Re-calculating the cost of coccidiosis in chickens

Coccidiosis, caused by Eimeria species parasites, has long been recognised as an economically significant disease of chickens. As the global chicken population continues to grow, and its contribution to food security intensifies, it is increasingly important to assess the impact of diseases that compromise chicken productivity and welfare. In 1999, Williams published one of the most comprehensive estimates for the cost of coccidiosis in chickens, featuring a compartmentalised model for the costs of prophylaxis, treatment and losses, indicating a total cost in excess of £38 million in the United Kingdom (UK) in 1995. In the 25 years since this analysis the global chicken population has doubled and systems of chicken meat and egg production have advanced through improved nutrition, husbandry and selective breeding of chickens, and wider use of anticoccidial vaccines. Using data from industry representatives including veterinarians, farmers, production and health experts, we have updated the Williams model and estimate that coccidiosis in chickens cost the UK £99.2 million in 2016 (range £73.0-£125.5 million). Applying the model to data from Brazil, Egypt, Guatemala, India, New Zealand, Nigeria and the United States resulted in estimates that, when extrapolated by geographical region, indicate a global cost of ~ £10.4 billion at 2016 prices (£7.7-£13.0 billion), equivalent to £0.16/chicken produced. Understanding the economic costs of livestock diseases can be advantageous, providing baselines to evaluate the impact of different husbandry systems and interventions. The updated cost of coccidiosis in chickens will inform debates on the value of chemoprophylaxis and development of novel anticoccidial vaccines.

Dissection of the cecal microbial community in chickens after Eimeria tenella infection

Background

Eimeria spp. are responsible for chicken coccidiosis which is the most important enteric protozoan disease resulting in tremendous economic losses in the poultry industry. Understanding the interaction between the avian cecal microbiota and coccidia is of interest in the development of alternative treatments that do not rely on chemotherapeutics and do not lead to drug resistance.

Methods

We utilized 16S rRNA gene sequencing to detect the dynamics of the cecal microbial community in AA broilers challenged with Eimeria tenella. Histopathological analysis of the cecum was also conducted.

Results

We found that microbial shifts occur during the infection. Lactobacillus, Faecalibacterium, Ruminococcaceae UCG-013, Romboutsia and Shuttleworthia decreased in abundance. However, the opportunistic pathogens Enterococcus and Streptococcus increased in abundance over time in response to the infection.

Conclusions

Eimeria tenella disrupts the integrity of the cecal microbiota and could promote the establishment and growth of potentially pathogenic bacteria. Defining bacterial populations affected by coccidial infection might help identify bacterial markers for intestinal disease as well as populations or species that could be beneficial in maintaining and restoring gut homeostasis during and after infection with E. tenella.

Emerging threat of Eimeria operational taxonomic units (OTUs) on poultry production

Coccidiosis is an antagonistic poultry disease which negatively impacts animal welfare and productivity. The disease is caused by an obligate, intracellular protozoon known as Eimeria. Several Eimeria species known to infect chickens have been well documented. However, recent studies have elucidated the emergence of three novel genetic variants or operational taxonomic units (OTUs). The discovery of OTUx, OTUy and OTUz complicates the identification and diagnosis of coccidiosis. OTUs are clusters of unknown or uncultivated organisms that are grouped according to a similarity in DNA sequence to a set of specific gene markers. OTUs have been reported in the Earth's Southern Hemisphere, including Australia, Venezuela, India, Zambia, Uganda, Tanzania, China and Ghana. Elucidating their impact on the poultry industry is fundamental in preventing anticoccidial resistance and to access the potential of OTUs as vaccine candidates to provide cross-protection against similar Eimeria species. The identification of OTUs further decreases the risk of false negative coccidial diagnosis. Therefore, this article reviews the importance and risk imposed by OTUs, coupled with their prevalence and geographical distribution in chickens globally.