Transmission and dose-response experiments for social animals: a reappraisal of the colonization biology of Campylobacter jejuni in chickens

Capturing complex interactions in disease ecology with simplicial sets

Network approaches have revolutionized the study of ecological interactions. Social, movement and ecological networks have all been integral to studying infectious disease ecology. However, conventional (dyadic) network approaches are limited in their ability to capture higher-order interactions. We present simplicial sets as a tool that addresses this limitation. First, we explain what simplicial sets are. Second, we explain why their use would be beneficial in different subject areas. Third, we detail where these areas are: social, transmission, movement/spatial and ecological networks and when using them would help most in each context. To demonstrate their application, we develop a novel approach to identify how pathogens persist within a host population. Fourth, we provide an overview of how to use simplicial sets, highlighting specific metrics, generative models and software. Finally, we synthesize key research questions simplicial sets will help us answer and draw attention to methodological developments that will facilitate this.

Lactic Acid Bacteria - A Promising Tool for Controlling Chicken Campylobacter Infection

Since 2005, campylobacteriosis has been the most common zoonotic disease in Europe. The main reservoir of pathogenic Campylobacter strains is broilers, which makes raw and undercooked poultry meat two major sources of disease. Infection in chicken flocks is most often asymptomatic, despite a high level of colonization reaching 106-109cfu/g in animal ceca. It is widely believed that controlling the level of colonization of the birds' digestive tract by pathogenic strains is a good way to increase food safety. Many treatments have been proposed to combat or at least reduce the level of colonization in animals reservoirs: probiotics, bacteriophages, vaccines, and anti-Campylobacter bacteriocins. This review focuses on the effects of Campylobacter infection on the chicken microbiome and colonization control strategies using probiotics (mostly lactic acid bacteria, LAB), which are live microorganisms included in the diet of animals as feed additives or supplements. Probiotics are not only an alternative to antibiotics, which were used for years as animal growth promoters, but they also constitute an effective protective barrier against excessive colonization of the digestive system by pathogenic bacteria, including Campylobacter. Moreover, one of the many beneficial functions of probiotics is the ability to manipulate the host's microbiota. Recently, there have also been some promising attempts to use lactic acid bacteria as a delivery system of oral vaccine against Campylobacter. Recombinant LAB strains induce primarily a mucosal immune response against foreign antigens, accompanied by at most a low-level immune response against carrier strains. Since the main barrier against the invasion of pathogens in the gastrointestinal tract is the intestinal mucosal membrane, the development of effective oral vaccines to protect animals against enteric infection is very reasonable.

Evaluation of Glycosylated FlpA and SodB as Subunit Vaccines Against Campylobacter jejuni Colonisation in Chickens

Campylobacter jejuni is the leading bacterial cause of human gastroenteritis worldwide and the handling or consumption of contaminated poultry meat is the key source of infection. C. jejuni proteins FlpA and SodB and glycoconjugates containing the C. jejuni N-glycan have been separately reported to be partially protective vaccines in chickens. In this study, two novel glycoproteins generated by protein glycan coupling technology-G-FlpA and G-SodB (with two and three N-glycosylation sites, respectively)-were evaluated for efficacy against intestinal colonisation of chickens by C. jejuni strain M1 relative to their unglycosylated variants. Two independent trials of the same design were performed with either a high challenge dose of 10⁷ colony-forming units (CFU) or a minimum challenge dose of 10² CFU of C. jejuni M1. While antigen-specific serum IgY was detected in both trials, no reduction in caecal colonisation by C. jejuni M1 was observed and glycosylation of vaccine antigens had no effect on the outcome. Our data highlight inconsistencies in the outcome of C. jejuni vaccination trials that may reflect antigen-, challenge strain-, vaccine administration-, adjuvant- and chicken line-specific differences from previously published studies. Refinement of glycoconjugate vaccines by increasing glycosylation levels or using highly immunogenic protein carriers could improve their efficacy.

Strain-Specific Differences in Survival of Campylobacter spp. in Naturally Contaminated Turkey Feces and Water

Campylobacter jejuni and Campylobacter coli are leading causes of human foodborne illness, with poultry as a major vehicle. Turkeys are frequently colonized with Campylobacter, but little is known about Campylobacter survival in turkey feces, even though fecal droppings are major vehicles for Campylobacter within-flock transmission as well as for environmental dissemination. Our objective was to examine survival of Campylobacter, including different strains, in freshly excreted feces from naturally colonized commercial turkey flocks and in suspensions of turkey feces in water from the turkey house. Fecal and water suspensions were stored at 4°C, and Campylobacter populations were enumerated on selective media at 48-h intervals. C. jejuni and C. coli isolates were characterized for resistance to a panel of antibiotics, and a subset was subtyped using multilocus sequence typing. Campylobacter was recovered from feces and water for up to 16 days. Analysis of 548 isolates (218 C. jejuni and 330 C. coli) revealed that C. jejuni survived longer than C. coli in feces (P = 0.0005), while the reverse was observed in water (P < 0.0001). Strain-specific differences in survival were noted. Multidrug-resistant C. jejuni isolates of sequence type 1839 (ST-1839) and the related ST-2935 were among the longest-surviving isolates in feces, being recovered for up to 10 to 16 days, while multidrug-resistant C. coli isolates of ST-1101 were recovered from feces for only up to 4 days. Data on Campylobacter survival upon excretion from the birds can contribute to further understanding of the transmission dynamics of this pathogen in the poultry production ecosystem.IMPORTANCE Campylobacter jejuni and Campylobacter coli are leading foodborne pathogens, with poultry as a major reservoir. Due to their growth requirements, these Campylobacter spp. may be unable to replicate once excreted by their avian hosts, but their survival in feces and the environment is critical for transmission in the farm ecosystem. Reducing the prevalence of Campylobacter-positive flocks can have major impacts in controlling both contamination of poultry products and environmental dissemination of the pathogens. However, understanding the capacity of these pathogens to survive in transmission-relevant vehicles such as feces and farmhouse water remains poorly understood, and little information is available on species- and strain-associated differences in survival. Here, we employed model conditions to investigate the survival of C. jejuni and C. coli from naturally colonized turkey flocks, and with diverse genotypes and antimicrobial resistance profiles, in turkey feces and in farmhouse water.

Dose-response and transmission: the nexus between reservoir hosts, environment and recipient hosts

Dose is the nexus between exposure and all upstream processes that determine pathogen pressure, and is thereby an important element underlying disease dynamics. Understanding the relationship between dose and disease is particularly important in the context of spillover, where nonlinearities in the dose-response could determine the likelihood of transmission. There is a need to explore dose-response models for directly transmitted and zoonotic pathogens, and how these interactions integrate within-host factors to consider, for example, heterogeneity in host susceptibility and dose-dependent antagonism. Here, we review the dose-response literature and discuss the unique role dose-response models have to play in understanding and predicting spillover events. We present a re-analysis of dose-response experiments for two important zoonotic pathogens (Middle East respiratory syndrome coronavirus and Nipah virus), to exemplify potential difficulties in differentiating between appropriate models with small exposure experiment datasets. We also discuss the data requirements needed for robust selection between dose-response models. We then suggest how these processes could be modelled to gain more realistic predictions of zoonotic transmission outcomes and highlight the exciting opportunities that could arise with increased collaboration between the virology and epidemiology disciplines. This article is part of the theme issue 'Dynamic and integrative approaches to understanding pathogen spillover'.

Field Interventions Against Colonization of Broilers by Campylobacter

Poultry accounts for a high proportion of human campylobacteriosis cases, and the problem of Campylobacter colonization of broiler flocks has proven to be intractable. Owing to their broad host range and genetic instability, Campylobacter organisms are ubiquitous and adaptable in the broiler farm environment, colonizing birds heavily and spreading rapidly after introduction into a flock. This review examines strategies to prevent or suppress such colonization, with a heavy emphasis on field investigations. Attempts to exclude Campylobacter via enhanced biosecurity and hygiene measures have met with mixed success. Reasons for this are becoming better understood as investigations focus on houses, ventilation, biosecurity practices, external operators, and compliance, among other factors. It is evident that piecemeal approaches are likely to fail. Complementary measures include feed and drinking water treatments applied in either preventive or suppressive modes using agents including organic acids and their derivatives, also litter treatments, probiotics, prebiotics, and alterations to diet. Some treatments aim to reduce the number of Campylobacter organisms entering abattoirs by suppressing intestinal colonization just before slaughter; these include acid water treatment or administration of bacteriophages or bacteriocins. Experimental vaccines historically have had little success, but some recent subunit vaccines show promise. Overall, there is wide variation in the control achieved, and consistency and harmonization of trials is needed to enable robust evaluation. There is also some potential to breed for resistance to Campylobacter. Good and consistent control of flock colonization by Campylobacter may require an as-yet undetermined combination of excellent biosecurity plus complementary measures.

Using Integrated Environmental Modeling to Assess Sources of Microbial Contamination in Mixed-Use Watersheds

Microbial fate and transport in watersheds should include a microbial source apportionment analysis that estimates the importance of each source, relative to each other and in combination, by capturing their impacts spatially and temporally under various scenarios. A loosely configured software infrastructure was used in microbial source-to-receptor modeling by focusing on animal- and human-impacted mixed-use watersheds. Components include data collection software, a microbial source module that determines loading rates from different sources, a watershed model, an inverse model for calibrating flows and microbial densities, tabular and graphical viewers, software to convert output to different formats, and a model for calculating risk from pathogen exposure. The system automates, as much as possible, the manual process of accessing and retrieving data and completes input data files of the models. The workflow considers land-applied manure from domestic animals on undeveloped areas; direct shedding (excretion) on undeveloped lands by domestic animals and wildlife; pastureland, cropland, forest, and urban or engineered areas; sources that directly release to streams from leaking septic systems; and shedding by domestic animals directly to streams. The infrastructure also considers point sources from regulated discharges. An application is presented on a real-world watershed and helps answer questions such as: What are the major microbial sources? What practices contribute to contamination at the receptor location? What land-use types influence contamination at the receptor location? and Under what conditions do these sources manifest themselves? This research aims to improve our understanding of processes related to pathogen and indicator dynamics in mixed-use watershed systems.

Designing group dose-response studies in the presence of transmission

Dose-response studies are used throughout pharmacology, toxicology and in clinical research to determine safe, effective, or hazardous doses of a substance. When involving animals, the subjects are often housed in groups; this is in fact mandatory in many countries for social animals, on ethical grounds. An issue that may consequently arise is that of unregulated between-subject dosing (transmission), where a subject may transmit the substance to another subject. Transmission will obviously impact the assessment of the dose-response relationship, and will lead to biases if not properly modelled. Here we present a method for determining the optimal design - pertaining to the size of groups, the doses, and the killing times - for such group dose-response experiments, in a Bayesian framework. Our results are of importance to minimising the number of animals required in order to accurately determine dose-response relationships. Furthermore, we additionally consider scenarios in which the estimation of the amount of transmission is also of interest. A particular motivating example is that of Campylobacter jejuni in chickens. Code is provided so that practitioners may determine the optimal design for their own studies.

The effect of the timing of exposure to Campylobacter jejuni on the gut microbiome and inflammatory responses of broiler chickens

BACKGROUND

Campylobacters are an unwelcome member of the poultry gut microbiota in terms of food safety. The objective of this study was to compare the microbiota, inflammatory responses, and zootechnical parameters of broiler chickens not exposed to Campylobacter jejuni with those exposed either early at 6 days old or at the age commercial broiler chicken flocks are frequently observed to become colonized at 20 days old.

RESULTS

Birds infected with Campylobacter at 20 days became cecal colonized within 2 days of exposure, whereas birds infected at 6 days of age did not show complete colonization of the sample cohort until 9 days post-infection. All birds sampled thereafter were colonized until the end of the study at 35 days (mean 6.1 log₁₀ CFU per g of cecal contents). The cecal microbiota of birds infected with Campylobacter were significantly different to age-matched non-infected controls at 2 days post-infection, but generally, the composition of the cecal microbiota were more affected by bird age as the time post infection increased. The effects of Campylobacter colonization on the cecal microbiota were associated with reductions in the relative abundance of OTUs within the taxonomic family Lactobacillaceae and the Clostridium cluster XIVa. Specific members of the Lachnospiraceae and Ruminococcaceae families exhibit transient shifts in microbial community populations dependent upon the age at which the birds become colonized by C. jejuni. Analysis of ileal and cecal chemokine/cytokine gene expression revealed increases in IL-6, IL-17A, and Il-17F consistent with a Th17 response, but the persistence of the response was dependent on the stage/time of C. jejuni colonization that coincide with significant reductions in the abundance of Clostridium cluster XIVa.

CONCLUSIONS

This study combines microbiome data, cytokine/chemokine gene expression with intestinal villus, and crypt measurements to compare chickens colonized early or late in the rearing cycle to provide insights into the process and outcomes of Campylobacter colonization. Early colonization results in a transient growth rate reduction and pro-inflammatory response but persistent modification of the cecal microbiota. Late colonization produces pro-inflammatory responses with changes in the cecal microbiota that will endure in market-ready chickens.

Overwintering of West Nile virus in a bird community with a communal crow roost

In temperate climates, transmission of West Nile virus (WNV) is detectable rarely during the coldest months (late fall through early spring), yet the virus has reappeared consistently during the next warm season. Several mechanisms may contribute to WNV persistence through winter, including bird-to-bird transmission among highly viremic species. Here we consider whether, under realistic scenarios supported by field and laboratory evidence, a winter bird community could sustain WNV through the winter in the absence of mosquitoes. With this purpose we constructed a deterministic model for a community of susceptible birds consisting of communally roosting crows, raptors and other birds. We simulated WNV introduction and subsequent transmission dynamics during the winter under realistic initial conditions and model parameterizations, including plausible contact rates for roosting crows. Model results were used to determine whether the bird community could yield realistic outbreaks that would result in WNV infectious individuals at the end of the winter, which would set up the potential for onward horizontal transmission into summer. Our findings strongly suggest that winter crow roosts could allow for WNV persistence through the winter, and our model results provide synthesis to explain inconclusive results from field studies on WNV overwintering in crow roosts.

Administration of Lactobacillus johnsonii FI9785 to chickens affects colonisation by Campylobacter jejuni and the intestinal microbiota

1. Campylobacter jejuni is the most common bacterial cause of human food-borne gastroenteritis in the world. A major source of human infection is the consumption of contaminated meat, particularly poultry. New control measures to reduce or eliminate this pathogen from the animal gastrointestinal tract are urgently required, and the use of probiotics as competitive exclusion agents is a promising biocontrol measure to reduce C. jejuni in the food chain. 2. In this study, we assessed the potential of Lactobacillus johnsonii FI9785, which has shown efficacy against Clostridium perfringens, to combat C. jejuni. The effect of prophylactic administration of L. johnsonii on the ability of C. jejuni to colonise chickens was determined. 3. Two doses of L. johnsonii given a week apart led to a reduction in C. jejuni colonisation in the caecal contents, but this biocontrol seemed reliant upon a high level of initial colonisation by the probiotic. 4. The microbial composition in the chicken gut was significantly altered by the probiotic treatment, as shown by denaturing gradient gel electrophoresis of 16S rRNA gene amplicons. 5. Together these results demonstrate the potential of this probiotic strain to be tested further as a competitive exclusion agent in poultry against C. jejuni.

Characterisation of Aerotolerant Forms of a Robust Chicken Colonizing Campylobacter coli

Campylobacter contaminated poultry meat is a major source of human foodborne illness. Campylobacter coli strain OR12 is a robust colonizer of chickens that was previously shown to outcompete and displace other Campylobacter strains from the chicken's gastrointestinal tract. This strain is capable of aerobic growth on blood agar. Serial aerobic passage increased this aerotolerance as assessed by quantitative assays for growth and survival on solid media. Aerotolerance was also associated with increased peroxide stress resistance. Aerobic passage did not alter cellular morphology or motility or hinder the microaerobic growth rate. Colonization of broiler chickens by aerotolerant C. coli OR12 was significantly lower than the wild-type strain at 3 days after challenge but not by 7 days, suggesting adaptation had occurred. Bacteria recovered from chickens had retained their aerotolerance, indicating this trait is stable. Whole genome sequencing enabled comparison with the wild-type sequence. Twenty-three point mutations were present, none of which were in genes known to affect oxidative stress resistance. Insertions or deletions caused frame shifts in several genes including, phosphoglycerate kinase and the b subunit of pyruvate carboxylase that suggest modification of central and carbohydrate metabolism in response to aerobic growth. Other genes affected include those encoding putative carbonic anhydrase, motility accessory factor, filamentous haemagglutinin, and aminoacyl dipeptidase proteins. Aerotolerance has the potential to affect environmental success and survival. Increased environmental survival outside of the host intestinal tract may allow opportunities for transmission between hosts. Resistance to oxidative stress may equate to increased virulence by virtue of reduced susceptibility to oxidative free radicals produced by host immune responses. Finally, resistance to ambient atmospheric oxygen may allow increased survival on chicken skin, and therefore constitutes an increased risk to public health.

Reduction of Campylobacter jejuni in broiler chicken by successive application of group II and group III phages

BACKGROUND

Bacteriophage treatment is a promising tool to reduce Campylobacter in chickens. Several studies have been published where group II or group III phages were successfully applied. However, these two groups of phages are different regarding their host ranges and host cell receptors. Therefore, a concerted activity of group II and group III phages might enhance the efficacy of a treatment and decrease the number of resistant bacteria.

RESULTS

In this study we have compared the lytic properties of some group II and group III phages and analysed the suitability of various phages for a reduction of C. jejuni in broiler chickens. We show that group II and group III phages exhibit different kinetics of infection. Two group III and one group II phage were selected for animal experiments and administered in different combinations to three groups of chickens, each containing ten birds. While group III phage CP14 alone reduced Campylobacter counts by more than 1 log10 unit, the concomitant administration of a second group III phage (CP81) did not yield any reduction, probably due to the development of resistance induced by this phage. One group of chickens received phage CP14 and, 24 hours later, group II phage CP68. In this group of animals, Campylobacter counts were reduced by more than 3 log10 units.

CONCLUSION

The experiments illustrated that Campylobacter phage cocktails have to be carefully composed to achieve the best results.

Spread and transmission of bacterial pathogens in experimental populations of the nematode Caenorhabditis elegans

Caenorhabditis elegans is frequently used as a model species for the study of bacterial virulence and innate immunity. In recent years, diverse mechanisms contributing to the nematode's immune response to bacterial infection have been discovered. Yet despite growing interest in the biochemical and molecular basis of nematode-bacterium associations, many questions remain about their ecology. Although recent studies have demonstrated that free-living nematodes could act as vectors of opportunistic pathogens in soil, the extent to which worms may contribute to the persistence and spread of these bacteria has not been quantified. We conducted a series of experiments to test whether colonization of and transmission between C. elegans nematodes could enable two opportunistic pathogens (Salmonella enterica and Pseudomonas aeruginosa) to spread on agar plates occupied by Escherichia coli. We monitored the transmission of S. enterica and P. aeruginosa from single infected nematodes to their progeny and measured bacterial loads both within worms and on the plates. In particular, we analyzed three factors affecting the dynamics of bacteria: (i) initial source of the bacteria, (ii) bacterial species, and (iii) feeding behavior of the host. Results demonstrate that worms increased the spread of bacteria through shedding and transmission. Furthermore, we found that despite P. aeruginosa's relatively high transmission rate among worms, its pathogenic effects reduced the overall number of worms colonized. This study opens new avenues to understand the role of nematodes in the epidemiology and evolution of pathogenic bacteria in the environment.

Harnessing the theoretical foundations of the exponential and beta-Poisson dose-response models to quantify parameter uncertainty using Markov Chain Monte Carlo

Dose-response models are the essential link between exposure assessment and computed risk values in quantitative microbial risk assessment, yet the uncertainty that is inherent to computed risks because the dose-response model parameters are estimated using limited epidemiological data is rarely quantified. Second-order risk characterization approaches incorporating uncertainty in dose-response model parameters can provide more complete information to decisionmakers by separating variability and uncertainty to quantify the uncertainty in computed risks. Therefore, the objective of this work is to develop procedures to sample from posterior distributions describing uncertainty in the parameters of exponential and beta-Poisson dose-response models using Bayes's theorem and Markov Chain Monte Carlo (in OpenBUGS). The theoretical origins of the beta-Poisson dose-response model are used to identify a decomposed version of the model that enables Bayesian analysis without the need to evaluate Kummer confluent hypergeometric functions. Herein, it is also established that the beta distribution in the beta-Poisson dose-response model cannot address variation among individual pathogens, criteria to validate use of the conventional approximation to the beta-Poisson model are proposed, and simple algorithms to evaluate actual beta-Poisson probabilities of infection are investigated. The developed MCMC procedures are applied to analysis of a case study data set, and it is demonstrated that an important region of the posterior distribution of the beta-Poisson dose-response model parameters is attributable to the absence of low-dose data. This region includes beta-Poisson models for which the conventional approximation is especially invalid and in which many beta distributions have an extreme shape with questionable plausibility.

Quantifying transmission of highly pathogenic and low pathogenicity H7N1 avian influenza in turkeys

Outbreaks of avian influenza in poultry can be devastating, yet many of the basic epidemiological parameters have not been accurately characterised. In 1999-2000 in Northern Italy, outbreaks of H7N1 low pathogenicity avian influenza virus (LPAI) were followed by the emergence of H7N1 highly pathogenic avian influenza virus (HPAI). This study investigates the transmission dynamics in turkeys of representative HPAI and LPAI H7N1 virus strains from this outbreak in an experimental setting, allowing direct comparison of the two strains. The fitted transmission rates for the two strains are similar: 2.04 (1.5-2.7) per day for HPAI, 2.01 (1.6-2.5) per day for LPAI. However, the mean infectious period is far shorter for HPAI (1.47 (1.3-1.7) days) than for LPAI (7.65 (7.0-8.3) days), due to the rapid death of infected turkeys. Hence the basic reproductive ratio, [Formula: see text] is significantly lower for HPAI (3.01 (2.2-4.0)) than for LPAI (15.3 (11.8-19.7)). The comparison of transmission rates and [Formula: see text] are critically important in relation to understanding how HPAI might emerge from LPAI. Two competing hypotheses for how transmission rates vary with population size are tested by fitting competing models to experiments with differing numbers of turkeys. A model with frequency-dependent transmission gives a significantly better fit to experimental data than density-dependent transmission. This has important implications for extrapolating experimental results from relatively small numbers of birds to the commercial poultry flock size, and for how control, including vaccination, might scale with flock size.

Following an imaginary Campylobacter population from farm to fork and beyond: a bacterial perspective

It has been known for decades that poultry meat is the most common single source for campylobacteriosis, yet the problem has not been solved. This review identifies some of the reasons why our attempts to reduce the incidence of this pathogen have largely failed. Based on the literature, the events a virtual population of Campylobacter may encounter, from growing in the gut of a broiler to eventually infecting humans and causing disease, are reviewed. Most steps in the farm-to-fork process are well studied, though there are gaps in our knowledge about survival and spread of Campylobacter populations before they enter the farm. Key events in the farm-to-fork chain that are suitable targets for prevention and control, to reduce food-borne campylobacteriosis, are indicated. Novel insights into the pathogenic mechanism responsible for disease in humans are summarized, which hypothesize that an overactive immune response is the reason for the typical inflammatory diarrhoea. A role of genetic microheterogeneity within a clonal population in this chain of events is being proposed here. The human host is not necessary for the survival of the bacterial species, nor have these bacteria specifically evolved to cause disease in that host. More likely, the species evolved for a commensal life in birds, and human disease can be considered as collateral damage owing to an unfortunate host-microbe interaction. The indirect environmental burden that results from poultry production should not be ignored as it may pose a diffuse, but possibly significant risk factor for disease.