Avian campylobacteriosis, prevalence, sources, hazards, antibiotic resistance, poultry meat contamination, and control measures: a comprehensive review

Avian campylobacteriosis is a vandal infection that poses human health hazards. Campylobacter is usually colonized in the avian gut revealing mild signs in the infected birds, but retail chicken carcasses have high contamination levels of Campylobacter spp. Consequently, the contaminated avian products constitute the main source of human infection with campylobacteriosis and result in severe clinical symptoms such as diarrhea, abdominal pain, spasm, and deaths in sensitive cases. Thus, the current review aims to shed light on the prevalence of Campylobacter in broiler chickens, Campylobacter colonization, bird immunity against Campylobacter, sources of poultry infection, antibiotic resistance, poultry meat contamination, human health hazard, and the use of standard antimicrobial technology during the chicken processing of possible control strategies to overcome such problems.

Isolation and Characterization of Group III Campylobacter jejuni-Specific Bacteriophages From Germany and Their Suitability for Use in Food Production

Campylobacter spp. are a major cause of bacterial foodborne diarrhea worldwide. While thermophilic Campylobacter species asymptomatically colonize the intestines of chickens, most human infections in industrial countries have been attributed to consumption of chicken meat or cross-contaminated products. Bacteriophages (phages) are natural predators of bacteria and their use at different stages of the food production chain has been shown to reduce the public health burden of human campylobacteriosis. However, regarding regulatory issues, the use of lytic phages in food is still under discussion and evaluation. This study aims to identify lytic phages suitable for reducing Campylobacter bacteria along the food production chain. Therefore, four of 19 recently recovered phages were further characterized in detail for their lytic efficacy against different Campylobacter field strains and their suitability under food production settings at different temperatures and pH values. Based on the results of this study, the phages vB_CjM-LmqsCP1-4 and vB_CjM-LmqsCP1-5 appear to be promising candidates for the reduction of Campylobacter jejuni in food production settings.

Mapping foodborne pathogen contamination throughout the conventional and alternative poultry supply chains

Recently, there has been a consumer push for natural and organic food products. This has caused alternative poultry production, such as organic, pasture, and free-range systems, to grow in popularity. Due to the stricter rearing practices of alternative poultry production systems, different types of levels of microbiological risks might be present for these systems when compared to conventional production systems. Both conventional and alternative production systems have complex supply chains that present many different opportunities for flocks of birds or poultry meat to be contaminated with foodborne pathogens. As such, it is important to understand the risks involved during each step of production. The purpose of this review is to detail the potential routes of foodborne pathogen transmission throughout the conventional and alternative supply chains, with a special emphasis on the differences in risk between the two management systems, and to identify gaps in knowledge that could assist, if addressed, in poultry risk-based decision making.

Antimicrobial Resistance, FlaA Sequencing, and Phylogenetic Analysis of Campylobacter Isolates from Broiler Chicken Flocks in Greece

Human campylobacteriosis caused by thermophilic Campylobacter species is the most commonly reported foodborne zoonosis. Consumption of contaminated poultry meat is regarded as the main source of human infection. This study was undertaken to determine the antimicrobial susceptibility and the molecular epidemiology of 205 Campylobacter isolates derived from Greek flocks slaughtered in three different slaughterhouses over a 14-month period. A total of 98.5% of the isolates were resistant to at least one antimicrobial agent. In terms of multidrug resistance, 11.7% of isolates were resistant to three or more groups of antimicrobials. Extremely high resistance to fluoroquinolones (89%), very high resistance to tetracycline (69%), and low resistance to macrolides (7%) were detected. FlaA sequencing was performed for the subtyping of 64 C. jejuni and 58 C. coli isolates. No prevalence of a specific flaA type was observed, indicating the genetic diversity of the isolates, while some flaA types were found to share similar antimicrobial resistance patterns. Phylogenetic trees were constructed using the neighbor-joining method. Seven clusters of the C. jejuni phylogenetic tree and three clusters of the C. coli tree were considered significant with bootstrap values >75%. Some isolates clustered together were originated from the same or adjacent farms, indicating transmission via personnel or shared equipment. These results are important and help further the understanding of the molecular epidemiology and antimicrobial resistance of Campylobacter spp. derived from poultry in Greece.

Using farm management practices to predict Campylobacter prevalence in pastured poultry farms

Contamination of poultry products by Campylobacter is often associated with farm management practices and processing plant practices. A longitudinal study was conducted on 11 pastured poultry farms in southeastern United States from 2014 to 2017. In this study, farm practices and processing variables were used as predictors for a random forest (RF) model to predict Campylobacter prevalence in pastured poultry farms and processing environments. Individual RF models were constructed for fecal, soil and whole carcass rinse after processing (WCR-P) samples. The performance of models was evaluated by the area under curve (AUC) from the receiver operating characteristics curve. The AUC values were 0.902, 0.894, and 0.864 for fecal, soil, and WCR-P models, respectively. Relative importance plots were generated to predict the most important variable in each RF model. Animal source of feces was identified as the most important variable in fecal model and the soy content of the brood feed was the most important variable for soil model. For WCR-P model, the average flock age showed the strongest impact on RF model. These RF models can help pastured poultry growers with food safety control strategies to reduce Campylobacter prevalence in pastured poultry farms.

A Mathematical Modeling Approach to Uncover Factors Influencing the Spread of Campylobacter in a Flock of Broiler-Breeder Chickens

Despite continued efforts to improve biosecurity protocols, Campylobacter continues to be detected in the majority of commercial chicken flocks across Europe. Using an extensive data set of Campylobacter prevalence within a chicken breeder flock for over a year, multiple Bayesian models are presented to explore the dynamics of the spread of Campylobacter in response to seasonal variation, species-specificity, bird health, and total colonization prevalence. These models indicated that birds within the flock varied greatly in their response to bacterial challenge, and that this phenomenon had a large impact on the overall prevalence of different species of Campylobacter. Campylobacter jejuni appeared more frequently in the summer, while Campylobacter coli persisted for a longer duration, amplified by the most susceptible birds in the flock. Our study suggests that strains of Campylobacter that appear most frequently likely possess no demographic advantage, but are instead amplified due to the health of the birds that ingest it.

Effect of Litter Treatment on Campylobacter jejuni in Broilers and on Cecal Microbiota

Since 2018, when a process hygiene criterion for Campylobacter in broilers at the slaughterhouse was implemented across Europe, efforts to reduce Campylobacter at farm level have increased. Despite numerous studies aiming to reduce Campylobacter colonization in broilers, no efficient control strategy has been identified so far. The present work assessed first the efficacy of a commercial litter treatment to reduce Campylobacter colonization in broilers during two in-vivo trials and second, its impact on cecal microbiota. The treatment does not affect broiler growth and no effect on Campylobacter counts was observed during the in-vivo trials. Nevertheless, cecal microbiota were affected by the treatment. Alpha and beta diversity were significantly different for the control and litter-treated groups on day 35. In addition, several taxa were identified as significantly associated with the different experimental groups. Further work is needed to find a suitable control measure combining different strategies in order to reduce Campylobacter.

Impact of Skip-a-Day and Every-Day Feeding Programs for Broiler Breeder Pullets on the Recovery of Salmonella and Campylobacter following challenge

The impact of restrictive feeding programs on Salmonella and Campylobacter colonization and persistence after challenge was investigated for broiler breeder pullets housed in an experimental rearing facility. Pullet-chicks were placed on litter in 3 feeding program rooms and each room contained 2 replicate pens. The feeding programs were: (1) Skip-a-day in trough feeders (SAD); (2) Every-day in trough feeders (EDT); (3) Every-day on the pen litter (EDL). On d 1, an additional group of hatchmate chicks were housed in a separate room and gavaged with Salmonella Typhimurium, to later serve as seeder chicks. After seeders were confirmed Salmonella-positive at wk 4, at wk 5 seeders were placed into each feeding program pen to commingle with 135 penmates. At 7, 9, 11, 17, 18, and 20 wk the litter surface in each pen was sampled using intermittently stepped-on drag-swabs. At 8, 12, 16, and 20 wk of age the ceca were sampled from 10 penmates/pen and 2 pooled spleen samples/pen were collected. SAD litter remained Salmonella-positive through 20 wk of age while EDL and EDT pens had no detectible litter Salmonella recovery by 18 and 20 wk. EDL fed pens had no direct (<102 cfu/mL) litter Salmonella recovery during the entirety of the experiment. Salmonella prevalence for ceca from SAD pullets was significantly (P < 0.05) higher at 8 wk (70%) compared to EDT (40%) and EDL (30%). At wk 12, SAD pullets for both on and off-feed sampling days had significantly higher Salmonella recovery (40%), compared to EDT and EDL (both at 5% recovery). By 16 and 20 wk, only the SAD pullets on the on-feed day (48 h without feed) had recovery of Salmonella at 20%. Salmonella recovery in pooled spleen samples did not appear associated with feeding treatments (22% positive). The remaining pullets challenged with Campylobacter at 21 wk produced similar trends as was seen for Salmonella. SAD program pullets had significantly higher Campylobacter from ceca (80 to 100%) compared to pullets on EDL (30 to 60%) or EDT (40 to 95%). These results suggest that using a Skip-a-Day feeding program for broiler breeder pullets contributes to persistently higher Salmonella and Campylobacter ceca colonization and litter prevalence.

Knowledge gaps in control of Campylobacter for prevention of campylobacteriosis

Campylobacteriosis is an important, worldwide public health problem with numerous socio-economic impacts. Since 2015, approximately 230,000 cases have been reported annually in Europe. In the United States, Australia and New Zealand, campylobacteriosis is the most commonly reported disease. Poultry and poultry products are considered important sources of human infections. Poultry meat can become contaminated with Campylobacter during slaughter if live chickens are intestinal carriers. Campylobacter spp. can be transferred from animals to humans through consumption and handling of contaminated food products, with fresh chicken meat being the most commonly implicated food type. Regarding food-borne disease, the most important Campylobacter species are Campylobacter jejuni and Campylobacter coli. In humans, clinical signs of campylobacteriosis include diarrhoea, abdominal pain, fever, headache, nausea and vomiting. Most cases of campylobacteriosis are sporadic and self-limiting, but there are post-infection complications, for example, Guillain-Barrés syndrome. This review summarizes an analysis undertaken by the DISCONTOOLS group of experts on campylobacteriosis. Gaps were identified in: (i) knowledge of true number of infected humans; (ii) mechanisms of pathogenicity to induce infection in humans; (iii) training to prevent transfer of Campylobacter from raw to ready-to-eat food; (iv) development of effective vaccines; (v) understanding transmission routes to broiler flocks; (vi) knowledge of bacteriocins, bacteriophages and antimicrobial peptides as preventive therapies; (vii) ration formulation as an effective preventive measure at a farm level; (viii) development of kits for rapid detection and quantification of Campylobacter in animals and food products; and (ix) development of more effective antimicrobials for treatment of humans infected with Campylobacter. Some of these gaps are relevant worldwide, whereas others are more related to problems encountered with Campylobacter in industrialized countries.

Nonculturability Might Underestimate the Occurrence of Campylobacter in Broiler Litter

We investigated the contribution of litter to the occurrence of Campylobacter on three broiler farms, which were known to have low (LO) and high (HI-A and HI-B) Campylobacter prevalence. For this purpose, we collected litter samples (n = 288) during and after two rearing cycles from each farm. We evaluated the occurrence of Campylobacter (using selective enrichment and quantitative real-time polymerase chain reaction [q-PCR] analysis) in the litter samples as well as the litter's pH and moisture content. Ceca from each flock (n = 144) were harvested at slaughter age and used to quantify Campylobacter colony-forming units (CFUs). Campylobacter was only retrieved from 7 litter samples that were collected from HI-A and HI-B during the growing period, but no Campylobacter was isolated from LO farms. The q-PCR analysis detected Campylobacter in pooled litter samples from all three farms. However, in litter collected during the same rotation, Campylobacter levels were significantly higher (p < 0.05) in HI-A and HI-B litter samples in comparison to those in LO. Cecal samples from HI-A and HI-B yielded relatively high numbers of Campylobacter CFUs, which were undetectable in LO samples. Litter's pH and moisture did not affect the overall occurrence of Campylobacter in litter and ceca on any of the farms. Our data suggest that Campylobacter was generally more abundant in litter that was collected from farms with highly colonized flocks. Therefore, better approaches for assessing the occurrence of Campylobacter in litter might be warranted in order to reduce the dissemination of these pathogens on and off poultry farms.

Occurrence and genotypes of Campylobacter species in broilers during the rearing period

Poultry are the main source of Campylobacter infection worldwide. To obtain information on Campylobacter-infected flocks and create a reference for preventing and controlling Campylobacter at farm level, Campylobacter isolates were recovered from broilers and the environments of nine chicken flocks in two farms during growth. The genetic relationship between the Campylobacter isolates was determined using multilocus sequence typing. Flocks were colonized as early as 3 weeks after introduction to the farm. The highest colonization rate was more than 90% and occurred 4-6 weeks after introduction to the farm. Quantitative data showed that the highest Campylobacter loads appeared at 1-2 weeks after initial colonization. Campylobacter loads in cloacal swabs in four flocks were significantly higher at 5 weeks than at 3 weeks (P < 0.05). Multilocus sequence typing of 171 selected isolates revealed 20 sequence types (STs), which consisted of 12 STs for Campylobacter jejuni and eight for Campylobacter coli isolates. The STs of the Campylobacter isolates recovered from farm 1 were more diversified than those from farm 2. The STs of environmental samples were highly consistent with those of the cloacal swab samples. The consistency between Campylobacter STs in the environmental and cloacal swab samples suggested that the environment might be one of the main sources of infection. Thus, our study highlights the prevalence and contamination load of Campylobacter in broilers during their rearing period and emphasizes the need for control and prevention measures for Campylobacter infection in broilers, which is also important for human health.

In vitro investigations into the use of antimicrobials in combination to maintain efficacy of fluoroquinolones in poultry

The aim of this study was to determine if apramycin, colistin or lincomycin-spectinomycin, in combination with enrofloxacin, was able prevent the emergence of mutants with reduced susceptibility to fluoroquinolone antibiotics in vitro. MICs were determined for enrofloxacin alone and in combination for panels of Campylobacter (n=37), Escherichia coli (n=52) and Salmonella (n=52) isolates. MIC results suggested that apramycin, colistin and lincomycin-spectinomycin worked in an additive/indifferent way when each was combined with enrofloxacin. Apramycin was considered the most promising antibiotic for combination-therapy in conjunction with enrofloxacin, and further evaluations (MBCs, MPCs and time-kill-curves) were performed for this combination for selected isolates. Results suggest combination-therapy of enrofloxacin with apramycin increases the efficacy, as well as decreasing the emergence and survival of bacteria with mutational resistance to fluoroquinolone antibiotics. Such combination-therapy, minimising the development of mutational resistance, may have relevance for Campylobacter, E. coli and Salmonella infections in poultry.

Prevalence and Distribution of Campylobacter jejuni in Small-Scale Broiler Operations

Campylobacter jejuni has been recognized as one of the most prevalent causes of foodborne bacterial illnesses in humans. Previous studies have focused on the transmission routes of C. jejuni from commercial flock farms to the final retail product. The objective of this study was to determine the prevalence of C. jejuni and Campylobacter spp. in eggshells, live birds, feed, drinking water, and the rearing environment in a small-scale broiler operation. Broilers were raised under two different production systems: (i) environmentally controlled housing and (ii) open-air housing with two replications. Each week, samples were collected from eggshells, bird feces, feed, drinking water, enclosures (vertical walls of bird housing), and feed troughs for enumeration and isolation testing. All samples were plated on modified charcoal-cefoperazone-deoxycholate agar to determine the log CFU per gram and percent prevalence of Campylobacter spp. Isolation of C. jejuni was verified with latex agglutination and hippurate hydrolysis tests. The results from this study suggest that vertical transmission of these bacteria from egg surfaces to newly hatched chicks is not a significant risk factor. The results also suggest that the prevalence of C. jejuni at time of harvest (week 6) was significantly higher (P < 0.05) in the open-air housing broilers than in those in the environmentally controlled housing. Elevated levels of cross-contaminants, especially water and feed, may have played a role in this outcome.

Campylobacter epidemiology from breeders to their progeny in Eastern Spain

While horizontal transmission is a route clearly linked to the spread of Campylobacter at the farm level, few studies support the transmission of Campylobacter spp. from breeder flocks to their offspring. Thus, the present study was carried out to investigate the possibility of vertical transmission. Breeders were monitored from the time of housing day-old chicks, then throughout the laying period (0 to 60 wk) and throughout their progeny (broiler fattening, 1 to 42 d) until slaughter. All samples were analyzed according with official method ISO 10272:2006. Results revealed that on breeder farms, Campylobacter isolation started from wk 16 and reached its peak at wk 26, with 57.0% and 93.2% of positive birds, respectively. After this point, the rate of positive birds decreased slightly to 86.0% at 60 wk. However, in broiler production all day-old chicks were found negative for Campylobacter spp, and the bacteria was first isolated at d 14 of age (5.0%), with a significant increase in detection during the fattening period with 62% of Campylobacter positive animals at the end of the production cycle. Moreover, non-positive sample was determined from environmental sources. These results could be explained because Campylobacter may be in a low concentration or in a non-culturable form, as there were several studies that successfully detected Campylobacter DNA, but failed to culture. This form can survive in the environment and infect successive flocks; consequently, further studies are needed to develop more modern, practical, cost-effective and suitable techniques for routine diagnosis.

Comparison of different sampling types across the rearing period in broiler flocks for isolation of Campylobacter spp

Campylobacter is the most common bacterial cause of human gastrointestinal disease in most developed countries. It is generally accepted that poultry products are a significant source of foodborne Campylobacter infections in humans. Assessing the effectiveness of any potential intervention at farm level requires monitoring of the Campylobacter status of broiler flocks, using appropriate sampling methods. The aim of this study was to assess the influence of the sample type across the rearing period for the detection of Campylobacter spp. at farm level. During this study, 21 commercial broiler farms were intensively sampled. Each farm was visited and sampled at different times during the rearing period (d 1, 7, 14, 21, 28, 35, and 42). On the first day of rearing, the status of the house and the day-old flock was evaluated, and environmental and cecal samples were collected. During rearing, 4 different sample types were collected: feces with sock swabs (sock swabs), feces directly from the litter (feces), cloacal swabs, and cecal content. All samples were analyzed according to ISO 10272-1:2006 (Annex E) and also by direct culture. The results of this study showed that Campylobacter spp. were detected in all of the sample types on d 14 of rearing. From this point on, the detection increased significantly, with a maximum detection rate by the end of rearing, regardless of the sample type. All samples that were negative upon direct culture were also negative after pre-enrichment. At the end of rearing, the percentage of samples positive for Campylobacter spp. was 71.4% for cecal samples, 61.9% for cloacal swabs, 45.2% for sock swabs, and 69.1% for fecal samples. C. jejuni was detected in all the sample types, with positive rates ranging from 67.1 to 76.0% for cecal samples and cloacal content, respectively. Cecal samples, cloacal swabs, and fecal samples cultured by direct plating onto modified charcoal cefoperazone deoxycholate agar (mCCDA) without pre-enrichment have the same sensitivity for detection of Campylobacter spp. in broiler flocks independent of the day of rearing.

Thermotolerant Campylobacter during Broiler Rearing: Risk Factors and Intervention

Thermotolerant Campylobacters are one of the most important bacterial causative agents of human gastrointestinal illness worldwide. In most European Union (EU) member states human campylobacteriosis is mainly caused by infection with Campylobacter jejuni or Campylobacter coli following consumption or inadequate handling of Campylobacter-contaminated poultry meat. To date, no effective strategy to control Campylobacter colonization of broilers during rearing is available. In this review, we describe the public health problem posed by Campylobacter presence in broilers and list and critically review all currently known measures that have been researched to lower the numbers of Campylobacter bacteria in broilers during rearing. We also discuss the most promising measures and which measures should be investigated further. We end this review by elaborating on readily usable measures to lower Campylobacter introduction and Campylobacter numbers in a broiler flock.

Intestinal carriage and excretion of Campylobacter jejuni in chickens exposed at different ages

Campylobacter jejuni is usually recovered from chickens in commercial broiler farms after 2 to 3 weeks of age. This study was conducted to clarify whether fecal excretion is associated with the age of exposure to this bacterium. Day-of-hatch broiler chickens were separated from a flock in a local commercial farm, kept in isolation rooms, and esophageally inoculated with C. jejuni (5.5 × 10(7) to 5.4 × 10(8) CFU) at 0, 7, 14, 21, 28, and 35 days of age. The remaining chicks were placed on the farm. Fecal samples obtained from the birds with the experimental infection and those reared on the farm were monitored for C. jejuni. Cecal contents obtained on necropsy were also cultured. In chickens inoculated with C. jejuni at 0 to 14 days of age, fecal excretion of C. jejuni was not observed until 42 days of age, although the organism was recovered from the cecal contents of these birds. When chickens were inoculated at 21 to 35 days of age, C. jejuni was isolated from fecal samples 2 or 3 days after inoculation, and the birds continually shed the organism until they reached 49 days of age, with the maximal numbers of the organism ranging from 1.7 × 10(8) to 1.0 × 10(10) CFU/g. In the commercial broiler farm, C. jejuni was first isolated from fecal samples obtained from two of five chickens at 28 days of age, and the organism was isolated from all five birds tested at 43 days of age. Restriction fragment length polymorphism analysis of the fla gene of C. jejuni isolates revealed that birds on the farm were colonized with C. jejuni after placement of the chickens on the farm. These observations indicate that chickens younger than 2 to 3 weeks old may carry C. jejuni in the ceca if they were exposed to this organism. Our results also suggest that fecal excretion of C. jejuni in commercial broiler chickens older than 3 to 4 weeks of age may be mainly caused by exposure of chickens at this age to this organism.

The long-term dynamics of Campylobacter colonizing a free-range broiler breeder flock: an observational study

A free-range broiler breeder flock was studied in order to determine the natural patterns of Campylobacter colonization over a period of 63 weeks. Campylobacter sequence types (STs) were not mutually exclusive and on average colonized only 17.7% of the birds tested at any time. Campylobacter STs typically reached a peak in prevalence upon initial detection in the flock before tailing off, although the ST and antigenic flaA short variable region in combination were stable over a number of months. There was evidence that, with a couple of exceptions, the ecology of C. jejuni and C. coli differed, with the latter forming a more stable population. Despite being free range, no newly colonizing STs were detected over a 6-week period in autumn and a 10-week period in winter, towards the end of the study. There was limited evidence that those STs identified among broiler chicken flocks on the same farm site were likely to colonize the breeder flock earlier (R(2) 0.16, P 0.01). These results suggest that there is natural control of Campylobacter dynamics within a flock which could potentially be exploited in designing new intervention strategies, and that the two different species should perhaps be considered separately.

Prevalence and pathogenic potential of campylobacter isolates from free-living, human-commensal american crows

Recent studies have suggested a potential role for wild birds in zoonotic transmission of Campylobacter jejuni, the leading cause of gastroenteritis in humans worldwide. In this study, we detected Campylobacter spp. in 66.9% (85/127) of free-ranging American crows (Corvus brachyrhyncos) sampled in the Sacramento Valley of California in 2012 and 2013. Biochemical testing and sequence analysis of 16S rRNA revealed that 93% of isolates (n = 70) were C. jejuni, with cytolethal distending toxin (CDT) and flagellin A genes detected by PCR in 20% and 46% of the C. jejuni isolates (n = 59), respectively. The high prevalence of C. jejuni, coupled with the occurrence of known virulence markers CDT and flagellin A, demonstrates that crows shed Campylobacter spp. in their feces that are potentially pathogenic to humans. Crows are abundant in urban, suburban, and agricultural settings, and thus further study to determine their role in zoonotic transmission of Campylobacter will inform public health.

Comparative analysis of Campylobacter populations within individual market-age broilers using Fla gene typing method

Campylobacter species is the most common human pathogen causing gastrointestinal infections in humans, and poultry is considered a major source of this pathogen. In this project, we aim to study the genetic diversity of Campylobacter populations within individual chickens using cecal samples to understand the nature of intestinal colonization in chickens by Campylobacter species. Genotyping was conducted based on the DNA sequence of short variable regions (SVR) in the flaA gene. Cecal samples were collected from 9 market-age broiler chickens and used for isolation of Campylobacter genomic DNA. The SVR fragments of 400 bp were amplified using SVR-specific primers, cloned, and sequenced. Sequencing results obtained from 86 clones (~10 clones/bird) showed that on an average 23.25% of clones had mutations within individuals. The mutations did not show any consistent pattern, suggesting a random nature of the mutations. When translated SVR sequences were analyzed, on average 20.57% of strains carried altered amino acid sequences in SVR within individuals. Four translated sequences had nonsense mutations to produce truncated proteins. These results suggest that there are multiple genotypes colonizing in a cecum and the occurrence of truncated FlaA protein may represent a novel mechanism for evasion of adaptive immune responses.

The poultry-associated microbiome: network analysis and farm-to-fork characterizations

Microbial communities associated with agricultural animals are important for animal health, food safety, and public health. Here we combine high-throughput sequencing (HTS), quantitative-PCR assays, and network analysis to profile the poultry-associated microbiome and important pathogens at various stages of commercial poultry production from the farm to the consumer. Analysis of longitudinal data following two flocks from the farm through processing showed a core microbiome containing multiple sequence types most closely related to genera known to be pathogenic for animals and/or humans, including Campylobacter, Clostridium, and Shigella. After the final stage of commercial poultry processing, taxonomic richness was ca. 2-4 times lower than the richness of fecal samples from the same flocks and Campylobacter abundance was significantly reduced. Interestingly, however, carcasses sampled at 48 hr after processing harboured the greatest proportion of unique taxa (those not encountered in other samples), significantly more than expected by chance. Among these were anaerobes such as Prevotella, Veillonella, Leptrotrichia, and multiple Campylobacter sequence types. Retail products were dominated by Pseudomonas, but also contained 27 other genera, most of which were potentially metabolically active and encountered in on-farm samples. Network analysis was focused on the foodborne pathogen Campylobacter and revealed a majority of sequence types with no significant interactions with other taxa, perhaps explaining the limited efficacy of previous attempts at competitive exclusion of Campylobacter. These data represent the first use of HTS to characterize the poultry microbiome across a series of farm-to-fork samples and demonstrate the utility of HTS in monitoring the food supply chain and identifying sources of potential zoonoses and interactions among taxa in complex communities.

Campylobacter jejuni is highly susceptible to killing by chicken host defense peptide cathelicidin-2 and suppresses intestinal cathelicidin-2 expression in young broilers

Little is known about the interactions of chicken host defense peptides (HDPs) with Campylobacter jejuni in young chicks. To examine the role of the chicken HDP, cathelicidin-2 (CATH-2) in host-pathogen interactions we challenged 4-day-old Ross 308 broilers with a chicken-derived C. jejuni isolate (WS356) and used the chicken pathogen Salmonella enterica Enteritidis phage type 4 (FGT1) as a reference. Immunohistochemical staining was used to localize CATH-2, C. jejuni and Salmonella enteritidis. Intestinal CATH-2 mRNA expression levels were determined by quantitative PCR. Antibacterial activities of CATH-2 peptide against C. jejuni and S. enteritidis isolates were assessed in colony count assays. In contrast to S. enteritidis, C. jejuni was not seen to attach to intestinal epithelium and C. jejuni challenge did not result in recruitment of CATH-2 containing heterophils to the small intestinal lamina propria. Minimal inhibitory concentrations found for CATH-2 peptide against human- and chicken-derived C. jejuni isolates were similar (0.6-2.5 μM) and much lower than for S. enteritidis (20 μM). Compared to wild-type C. jejuni 81116, the lipooligosaccharide (LOS)-deficient 81116ΔwaaF mutant was much more susceptible to CATH-2. Interestingly, CATH-2 mRNA expression levels in the small intestine were significantly lower 48 h p.i. in C. jejuni-challenged chicks. These findings indicate that human clinical and chicken-derived C. jejuni are equally highly susceptible to chicken CATH-2 peptide and that C. jejuni uses LOS to protect itself to some extent against HDPs. Moreover, suppression of intestinal CATH-2 expression levels may be part of the C. jejuni immune evasion strategy.

Biosecurity-based interventions and strategies to reduce Campylobacter spp. on poultry farms

The prevention and control of Campylobacter colonization of poultry flocks are important public health strategies for the control of human campylobacteriosis. A critical review of the literature on interventions to control Campylobacter in poultry on farms was undertaken using a systematic approach. Although the focus of the review was on aspects appropriate to the United Kingdom poultry industry, the research reviewed was gathered from worldwide literature. Multiple electronic databases were employed to search the literature, in any language, from 1980 to September 2008. A primary set of 4,316 references was identified and scanned, using specific agreed-upon criteria, to select relevant references related to biosecurity-based interventions. The final library comprised 173 references. Identification of the sources of Campylobacter in poultry flocks was required to inform the development of targeted interventions to disrupt transmission routes. The approach used generally involved risk factor-based surveys related to culture-positive or -negative flocks, usually combined with a structured questionnaire. In addition, some studies, either in combination or independently, undertook intervention trials. Many of these studies were compromised by poor design, sampling, and statistical analysis. The evidence for each potential source and route of transmission on the poultry farm was reviewed critically, and the options for intervention were considered. The review concluded that, in most instances, biosecurity on conventional broiler farms can be enhanced and this should contribute to the reduction of flock colonization. However, complementary, non-biosecurity-based approaches will also be required in the future to maximize the reduction of Campylobacter-positive flocks at the farm level.

Use of bioluminescence imaging to monitor Campylobacter survival in chicken litter

AIM

The aim of this study was to develop a novel approach for characterizing the growth and persistence of Campylobacter in different poultry-rearing environments. Specifically, we constructed bioluminescent Campylobacter strains and used them to monitor the survival of these pathogens in litter (bedding) material.

METHODS AND RESULTS

We inserted shuttle plasmids carrying the luminescence genes (luxCDABE) into C. jejuni and C. coli to construct bioluminescent strains of these pathogens. The strains were spiked into microcosms containing samples of litter-washings and dry litter collected from different enclosures that housed broiler chickens. Our results show that C. jejuni and C. coli survived for at least 20 days in reused (old) litter while the growth of these pathogens was inhibited in clean (new) litter. Furthermore, our results suggest that the availability of nutrients and the condition of the litter (reused vs new) are important factors in the persistence of these pathogens.

CONCLUSIONS

Reused litter can potentially predispose chickens to Campylobacter contamination and maintaining clean litter might reduce the incidences of colonization with these pathogens.

SIGNIFICANCE AND IMPACT OF THE STUDY

Bioluminescence provided a simple, sensitive, and rapid approach for analysing the growth dynamics of Campylobacter. Using this technology, we highlighted the potential role of litter material in maintaining these pathogens in the chicken environment.

Longitudinal molecular epidemiological study of thermophilic campylobacters on one conventional broiler chicken farm

Improved understanding of the ecology and epidemiology of Campylobacter in the poultry farm environment is key to developing appropriate farm-based strategies for preventing flock colonization. The sources of Campylobacter causing broiler flock colonization were investigated on one poultry farm and its environment, from which samples were obtained on three occasions during each of 15 crop cycles. The farm was adjacent to a dairy farm, with which there was a shared concreted area and secondary entrance. There was considerable variation in the Campylobacter status of flocks at the various sampling times, at median ages of 20, 26, and 35 days, with 3 of the 15 flocks remaining negative at slaughter. Campylobacters were recoverable from various locations around the farm, even while the flock was Campylobacter negative, but the degree of environmental contamination increased substantially once the flock was positive. Molecular typing showed that strains from house surroundings and the dairy farm were similar to those subsequently detected in the flock and that several strains intermittently persisted through multiple crop cycles. The longitudinal nature of the study suggested that bovine fecal Campylobacter strains, initially recovered from the dairy yard, may subsequently colonize poultry. One such strain, despite being repeatedly recovered from the dairy areas, failed to colonize the concomitant flock during later crop cycles. The possibility of host adaptation of this strain was investigated with 16-day-old chickens experimentally exposed to this strain naturally present in, or spiked into, bovine feces. Although the birds became colonized by this infection model, the strain may preferentially infect cattle. The presence of Campylobacter genotypes in the external environment of the poultry farm, prior to their detection in broiler chickens, confirms the horizontal transmission of these bacteria into the flock and highlights the risk from multispecies farms.

Growth phase-dependent activation of the DccRS regulon of Campylobacter jejuni

Two-component systems are widespread prokaryotic signal transduction devices which allow the regulation of cellular functions in response to changing environmental conditions. The two-component system DccRS (Cj1223c-Cj1222c) of Campylobacter jejuni is important for the colonization of chickens. Here, we dissect the DccRS system in more detail and provide evidence that the sensor DccS selectively phosphorylates the cognate effector, DccR. Microarray expression profiling, real-time reverse transcription-PCR (RT-PCR), electrophoretic mobility shift assay, and primer extension analyses revealed that the DccRS regulon of strain 81116 consists of five promoter elements, all containing the consensus direct repeat sequence WTTCAC-N6-TTCACW covering the putative -35 promoter regions. One of these promoters is located in front of an operon encoding a putative macrolide efflux pump while the others are in front of genes coding for putative periplasmic or membrane proteins. The DccRS-regulated genes in C. jejuni strain 81116 are needed to enhance early in vivo growth of C. jejuni in 7-day-old chickens. The DccRS system is activated in the late stationary bacterial growth phase, probably by released metabolic products. Whole-genome mRNA profiling and real-time RT-PCR analysis under these conditions demonstrated that the system has no influence on the transcription of genes outside the DccRS regulon.

Space–time patterns ofCampylobacterspp. colonization in broiler flocks, 2002–2006

This study was performed to investigate space–time patterns ofCampylobacterspp. colonization in broiler flocks in Norway. Data on theCampylobacterspp. status at the time of slaughter of 16 054 broiler flocks from 580 farms between 2002 and 2006 was included in the study. Spatial relative risk maps together with maps of space–time clustering were generated, the latter by using spatial scan statistics. These maps identified the same areas almost every year where there was a higher risk for a broiler flock to test positive forCampylobacterspp. during the summer months. A modifiedK-function analysis showed significant clustering at distances between 2·5 and 4 km within different years. The identification of geographical areas with higher risk forCampylobacterspp. colonization in broilers indicates that there are risk factors associated withCampylobacterspp. colonization in broiler flocks varying with region and time, e.g. climate, landscape or geography. These need to be further explored. The results also showed clustering at shorter distances indicating that there are risk factors forCampylobacterspp. acting in a more narrow scale as well.

Gnotobiotic IL-10; NF-kappaB mice develop rapid and severe colitis following Campylobacter jejuni infection

Limited information is available on the molecular mechanisms associated with Campylobacter jejuni (C. jejuni) induced food-borne diarrheal illnesses. In this study, we investigated the function of TLR/NF-kappaB signaling in C. jejuni induced pathogenesis using gnotobiotic IL-10(-/-); NF-kappaB(EGFP) mice. In vitro analysis showed that C. jejuni induced IkappaB phosphorylation, followed by enhanced NF-kappaB transcriptional activity and increased IL-6, MIP-2alpha and NOD2 mRNA accumulation in infected-mouse colonic epithelial cells CMT93. Importantly, these events were blocked by molecular delivery of an IkappaB inhibitor (Ad5IkappaBAA). NF-kappaB signalling was also important for C.jejuni-induced cytokine gene expression in bone marrow-derived dendritic cells. Importantly, C. jejuni associated IL-10(-/-); NF-kappaB(EGFP) mice developed mild (day 5) and severe (day 14) ulcerating colonic inflammation and bloody diarrhea as assessed by colonoscopy and histological analysis. Macroscopic analysis showed elevated EGFP expression indicating NF-kappaB activation throughout the colon of C. jejuni associated IL-10(-/-); NF-kappaB(EGFP) mice, while fluorescence microscopy revealed EGFP positive cells to be exclusively located in lamina propria mononuclear cells. Pharmacological NF-kappaB inhibition using Bay 11-7085 did not ameliorate C. jejuni induced colonic inflammation. Our findings indicate that C. jejuni induces rapid and severe intestinal inflammation in a susceptible host that correlates with enhanced NF-kappaB activity from lamina propria immune cells.

Reduction of thermotolerant Campylobacter species on broiler carcasses following physical decontamination at slaughter

To reduce the incidences of human Campylobacter infections, a number of countries are investigating methods for reducing human exposure to Campylobacter from broiler meat. In addition to implementing biosecurity measures at the farm, Campylobacter may be controlled by reducing Campylobacter counts through physical decontamination of the meat. The current study was conducted to compare the Campylobacter-reducing ability of three physical decontamination techniques, forced air chilling, crust freezing, and steam-ultrasound, performed in the plant with naturally contaminated broiler chickens. The effects of all three techniques were evaluated and compared with the effect of freezing. Mean reductions obtained were 0.44 log CFU per carcass, 0.42 log CFU per sample, and > or = 2.51 log CFU per carcass, respectively. All techniques resulted in significant reductions of the Campylobacter concentration on the carcasses (P < 0.05). However, none of the techniques were as effective as freezing based on reductions in Campylobacter counts and on adverse effects. The increase in Campylobacter counts on carcasses following visceral rupture during the evisceration operation also was examined. Visceral rupture resulted in an increase of 0.9 log CFU per carcass, suggesting that Campylobacter counts also may be reduced by optimizing the hygienic design of equipment or by physical removal of fecal contamination.

Identification of Campylobacter jejuni proteins recognized by maternal antibodies of chickens

Campylobacter jejuni is one of the leading bacterial causes of food-borne gastroenteritis. Infection with C. jejuni is frequently acquired through the consumption of undercooked poultry or foods cross-contaminated with raw poultry. Given the importance of poultry as a reservoir for Campylobacter organisms, investigators have performed studies to understand the protective role of maternal antibodies in the ecology of Campylobacter colonization of poultry. In a previous study, chicks with maternal antibodies generated against the S3B strain of C. jejuni provided protection against Campylobacter colonization (O. Sahin, N. Luo, S. Huang, and Q. Zhang, Appl. Environ. Microbiol. 69:5372-5379, 2003). We obtained serum samples, collectively referred to as the C. jejuni S3B-SPF sera, from the previous study. These sera were determined to contain maternal antibodies that reacted against C. jejuni whole-cell lysates as judged by enzyme-linked immunosorbent assay. The antigens recognized by the C. jejuni S3B-SPF antibodies were identified by immunoblot analysis, coupled with mass spectrometry, of C. jejuni outer membrane protein extracts. This approach led to the identification of C. jejuni proteins recognized by the maternal antibodies, including the flagellin proteins and CadF adhesin. In vitro assays revealed that the C. jejuni S3B-SPF sera retarded the motility of the C. jejuni S3B homologous strain but did not retard the motility of a heterologous strain of C. jejuni (81-176). This finding provides a possible mechanism explaining why maternal antibodies confer enhanced protection against challenge with a homologous strain compared to a heterologous strain. Collectively, this study provides a list of C. jejuni proteins against which protective antibodies are generated in hens and passed to chicks.

Comparative metagenomics reveals host specific metavirulomes and horizontal gene transfer elements in the chicken cecum microbiome

BACKGROUND

The complex microbiome of the ceca of chickens plays an important role in nutrient utilization, growth and well-being of these animals. Since we have a very limited understanding of the capabilities of most species present in the cecum, we investigated the role of the microbiome by comparative analyses of both the microbial community structure and functional gene content using random sample pyrosequencing. The overall goal of this study was to characterize the chicken cecal microbiome using a pathogen-free chicken and one that had been challenged with Campylobacter jejuni.

METHODOLOGY/PRINCIPAL FINDINGS

Comparative metagenomic pyrosequencing was used to generate 55,364,266 bases of random sampled pyrosequence data from two chicken cecal samples. SSU rDNA gene tags and environmental gene tags (EGTs) were identified using SEED subsystems-based annotations. The distribution of phylotypes and EGTs detected within each cecal sample were primarily from the Firmicutes, Bacteroidetes and Proteobacteria, consistent with previous SSU rDNA libraries of the chicken cecum. Carbohydrate metabolism and virulence genes are major components of the EGT content of both of these microbiomes. A comparison of the twelve major pathways in the SEED Virulence Subsystem (metavirulome) represented in the chicken cecum, mouse cecum and human fecal microbiomes showed that the metavirulomes differed between these microbiomes and the metavirulomes clustered by host environment. The chicken cecum microbiomes had the broadest range of EGTs within the SEED Conjugative Transposon Subsystem, however the mouse cecum microbiomes showed a greater abundance of EGTs in this subsystem. Gene assemblies (32 contigs) from one microbiome sample were predominately from the Bacteroidetes, and seven of these showed sequence similarity to transposases, whereas the remaining sequences were most similar to those from catabolic gene families.

CONCLUSION/SIGNIFICANCE

This analysis has demonstrated that mobile DNA elements are a major functional component of cecal microbiomes, thus contributing to horizontal gene transfer and functional microbiome evolution. Moreover, the metavirulomes of these microbiomes appear to associate by host environment. These data have implications for defining core and variable microbiome content in a host species. Furthermore, this suggests that the evolution of host specific metavirulomes is a contributing factor in disease resistance to zoonotic pathogens.

Real-time PCR approach for detection of environmental sources of Campylobacter strains colonizing broiler flocks

Reducing colonization of poultry flocks by Campylobacter spp. is a key strategy in the control and prevention human campylobacteriosis. Horizontal transmission of campylobacters, from in and around the farm, is the presumed route of flock colonization. However, the identification and prioritization of sources are confounded by the ubiquitous nature of these organisms in the environment, their poor rates of recovery by standard culture methods, and the need for cost-effective and timely methods for strain-specific comparison. A real-time PCR screening test for the strain-specific detection of campylobacters in environmental samples has been developed to address this issue. To enable this approach, fluorescently labeled PCR oligonucleotide probes suitable for a LightCycler-based assay were designed to match a highly variable DNA segment within the flaA short variable region (SVR) of Campylobacter jejuni or C. coli. The capacity of such probes to provide strain-specific tools was investigated by using bacterial cultures and spiked and naturally contaminated poultry fecal and environmental samples. The sensitivity of two representative probes was estimated, by using two different C. jejuni strains, to be 1.3 x 10(2) to 3.7 x 10(2) CFU/ml in bacterial cultures and 6.6 x 10(2) CFU/ml in spiked fecal samples. The specificity of the SVR for C. jejuni and C. coli was confirmed by using a panel of strains comprising other Campylobacter species and naturally contaminated samples. The approach was field tested by sampling the environment and feces of chickens of two adjacently located poultry houses on a conventional broiler farm throughout the life of one flock. All environmental samples were enriched for 2 days, and then DNA was prepared and stored. Where feasible, campylobacter isolates were also recovered and stored for subsequent testing. A strain-specific probe based on the SVR of the strain isolated from the first positive chicken fecal sample was developed. This probe was then used to screen the stored environmental samples by real-time PCR. Pulsed-field gel electrophoresis was used to compare recovered environmental and fecal isolates to assess the specificity of the method. The results established the proof of principle that strain-specific probes, based on the SVR of flaA, can identify a flock-colonizing strain in DNA preparations from enriched environmental cultures. Such a novel strategy provides the opportunity to investigate the epidemiology of campylobacters in poultry flocks and allows targeted biosecurity interventions to be developed. The strategy may also have wider applications for the tracking of specific campylobacter strains in heavily contaminated environments.

Campylobacter jejuni colonization and transmission in broiler chickens: a modelling perspective

Campylobacter jejuni is one of the most common causes of acute enteritis in the developed world. The consumption of contaminated poultry, where C. jejuni is believed to be a commensal organism, is a major risk factor. However, the dynamics of this colonization process in commercially reared chickens is still poorly understood. Quantification of these dynamics of infection at an individual level is vital to understand transmission within populations and formulate new control strategies. There are multiple potential routes of introduction of C. jejuni into a commercial flock. Introduction is followed by a rapid increase in environmental levels of C. jejuni and the level of colonization of individual broilers. Recent experimental and epidemiological evidence suggest that the celerity of this process could be masking a complex pattern of colonization and extinction of bacterial strains within individual hosts. Despite the rapidity of colonization, experimental transmission studies exhibit a highly variable and unexplained delay time in the initial stages of the process. We review past models of transmission of C. jejuni in broilers and consider simple modifications, motivated by the plausible biological mechanisms of clearance and latency, which could account for this delay. We show how simple mathematical models can be used to guide the focus of experimental studies by providing testable predictions based on our hypotheses. We conclude by suggesting that competition experiments could be used to further understand the dynamics and mechanisms underlying the colonization process. The population models for such competition processes have been extensively studied in other ecological and evolutionary contexts. However, C. jejuni can potentially adapt phenotypically through phase variation in gene expression, leading to unification of ecological and evolutionary time-scales. For a theoretician, the colonization dynamics of C. jejuni offer an experimental system to explore these 'phylodynamics', the synthesis of population dynamics and evolutionary biology.

Prevalence and risk factors for Salmonella spp. and Campylobacter spp. caecal colonization in broiler chicken and turkey flocks slaughtered in Quebec, Canada

We conducted an observational study to estimate prevalence and risk factors for Salmonella spp. and Campylobacter spp. caecal colonization in poultry. Eighty-one broiler chicken and 59 turkey flocks selected among flocks slaughtered in the province of Quebec, Canada, were included in the study. Flock status was evaluated by culturing pooled caecal contents from about 30 birds per flock. Exposure to potential risk factors was evaluated with a questionnaire. Odds ratios were computed using multivariable logistic regression. The prevalence of Salmonella-positive flocks was 50% (95% CI: 37, 64) for chickens and 54% (95% CI: 39, 70) for turkeys, respectively. Odds of Salmonella colonization were 2.6 times greater for chicken flocks which failed to lock the chicken house permanently. In turkeys, odds of Salmonella colonization were 4.8-7.7 times greater for flocks which failed to be raised by <or=2 producers with no other visitors allowed onto the premises, or origin from a hatchery. The prevalence of Campylobacter-positive flocks was 35% (95% CI: 22, 49) for chickens and 46% (95% CI: 30, 62) for turkeys. Odds of colonization were 4.1 times higher for chicken flocks raised on farms with professional rodent control and 5.2 times higher for flocks with manure heap >200m from the poultry house, and also increased with the number of birds raised per year on the farm and with the age at slaughter. For turkeys, odds of Campylobacter flock colonization were 3.2 times greater in flocks having a manure heap at </=200m from poultry house and 4.2 times greater in flocks drinking unchlorinated water.

Evaluation of different plate media for direct cultivation of Campylobacter species from live broilers

Accurate identification and optimal culturing procedures for Campylobacter spp. from live broilers are needed for epidemiological studies. Because there is no standardized protocol, we designed and conducted studies to evaluate different selective media for the culturing and isolation of Campylobacter spp. from cecal and fecal samples obtained from battery-reared and commercial broilers. Five media selective for Campylobacter were evaluated: Campylobacter agar base, Campylobacter, Campy-Line, modified Campy-Cefex, and modified charcoal cefoperazone deoxycholate agar. With contaminated broilers reared in battery cages, Campylobacter agar base, Campylobacter, modified Campy-Cefex, and modified charcoal cefoperazone deoxycholate agar revealed similar isolation rates (P > 0.05), whereas Campy-Line showed a lower efficacy (P < 0.05). With commercial live broilers, modified Campy-Cefex agar was more consistent for the isolation of Campylobacter from feces, whereas modified Campy-Cefex and modified charcoal cefoperazone deoxycholate agar showed similar isolation rates from cecal samples. Campy-Line agar showed a lower identification rate (P < 0.05) for both fecal and cecal samples. A multiplex PCR assay used for identification showed that Campylobacter jejuni and Campylobacter coli DNA was present in the samples. Pulsed field gel electrophoresis restriction profiles differed among samples collected from different commercial farms but were similar for isolates from the same farm, suggesting clonal differences. No variation was seen in pulsed field gel electrophoresis patterns among isolates cultured on different media. Our data suggest that the choice of plate medium may influence the efficiency of isolating Campylobacter spp. from broiler chickens by direct plating from fecal or cecal samples.