Campylobacter coli - an important foodborne pathogen

Broiler farming practices using new or re-used bedding, inclusive of free-range, have no impact on Campylobacter levels, species diversity, Campylobacter community profiles and Campylobacter bacteriophages

A multi-stage option to address food-safety can be produced by a clearer understanding of Campylobacter's persistence through the broiler production chain, its environmental niche and its interaction with bacteriophages. This study addressed Campylobacter levels, species, genotype, bacteriophage composition/ levels in caeca, litter, soil and carcasses across commercial broiler farming practices to inform on-farm management, including interventions. Broilers were sequentially collected as per company slaughter schedules over two-years from 17 farms, which represented four commercially adopted farming practices, prior to the final bird removal (days 39-53). The practices were conventional full clean-out, conventional litter re-use, free-range-full cleanout and free-range-litter re-use. Caeca, litter and soil collected on-farm, and representative carcases collected at the processing plant, were tested for Campylobacter levels, species dominance and Campylobacter bacteriophages. General community profiling via denaturing gradient gel electrophoresis of the flaA gene was used to establish the population relationships between various farming practices on representative Campylobacter isolates. The farming practice choices did not influence the high caeca Campylobacter levels (log 7.5 to log 8.5 CFU/g), the carcass levels (log 2.5 to log 3.2 CFU/carcass), the C. jejuni/C. coli dominance and the on-farm bacteriophage presence/levels. A principal coordinate analysis of the flaA distribution for farm and litter practices showed strong separation but no obvious farming practice related grouping of Campylobacter. Bacteriophages originated from select farms, were not practice-dependent, and were detected in the environment (litter) only if present in the birds (caeca). This multifaceted study showed no influence of farming practices on on-farm Campylobacter dynamics. The significance of this study means that a unified on-farm risk-management could be adopted irrespective of commercial practice choices to collectively address caeca Campylobacter levels, as well as the potential to include Campylobacter bacteriophage biocontrol. The impact of this study means that there are no constraints in re-using bedding or adopting free-range farming, thus contributing to environmentally sustainable (re-use) and emerging (free-range) broiler farming choices.

Fecal-related anthropogenic sources are key determinants of lake microbiomes through microbial source tracking

Lake microbiomes are essential indicators of lake health and are strongly influenced by allochthonous microbial communities from various sources within the watershed. However, quantifying the contributions of multiple inputs to lake microbiomes is challenging because of the complex nature of river‒lake systems and the presence of many untraceable sources. Here, Jianhu Lake‒‒a geographically simple and closed plateau lake in southwestern China, was surveyed to disentangle the contributions of five distinct sources (three input rivers that receive town sewage, stormwater runoff, and creek spring water, as well as two nonpoint sources, duck ponds and dry farmland) to the overall lake microbiomes. We found that feces-loading sources, namely town sewage and duck aquaculture, accounted for 48.7% of the total variations in lake microbiomes. In contrast, the combined contribution of the remaining three sources amounted to 13.21%, despite these less-influential sources (e.g., stormwater runoff) may introduce an even larger volume of allochthonous materials into the lake. In addition, approximately 38.1% of the variations in the lake microbiomes were attributed to unknown sources. Sewage effluents also caused a significant loss of lake microbial diversity, and there was a tendency for large-scale microbial homogeneity in lake sediments that resembled those from duck ponds. We then used a targeted approach to track host-specific fecal pollution, and found that human feces were the primary source, followed by ruminant and chicken/duck feces, all of which can be successfully traced back to the feces-loading sources. In our further modelling of sediment transport from three rivers into the whole lake, we observed a significant relationship between sediment accumulation and adsorbed microorganisms only for the sewage-receiving river. Together, lines of evidence indicate that both point and nonpoint fecal-related anthropogenic sources possess discriminatory power for shaping microbial geographic patterns of the lake, posing threats to the survival of local indigenous lake microbiomes.

UK-wide risk factor study of broiler carcases highly contaminated with Campylobacter

Campylobacter is a major cause of food poisoning and is typically the most common cause of gastroenteritis in the UK. Data collected at broiler farm and abattoir level, for slaughter batches that were sampled for UK-wide monitoring, were used to generate two epidemiological risk factor models. A total of 483 batches slaughtered between January 2016 and March 2017 were used in the analysis, coming from 19 abattoirs representing more than 85% of UK broiler production. For each selected slaughter batch, one carcase was sampled after primary chilling and 10 randomly sampled birds had caecal samples collected at the evisceration point. Samples were used for Campylobacter identification and quantification. Two multivariable mixed-effects models were designed, one with the binary outcome for the detection of a highly contaminated (>1000 colony forming units (CFU)/g) Campylobacter-positive carcase, whereas the other used the Campylobacter colony count (CFU/g) carcase outcome. The results suggest that caecal colonization within the batch was a key factor for the occurrence of Campylobacter on carcases, and many factors that were identified in the model were also likely to be related to colonization or related to the risk of introduction of Campylobacter from partial depopulation (referred to as thinning) of ~30% of the flock approximately 1 week before full flock depopulation events. The amount of neck skin in the sample was another key factor identified and was included in both models as a risk factor. The models have also identified other factors which may be related to the general health and husbandry on-farm (use of prebiotics or vaccines, and identification of the product used for drinking line cleaning), whereas the other factors may identify control points related to transmission within a farm. The identification of these variables could help focus control efforts on-farm, especially for relatively easy improvements, such as improving the provision of house-specific bird-weighing buckets/cages in houses.

Gold Nanoparticle and Polymerase Chain Reaction (PCR)-Based Colorimetric Assay for the Identification of Campylobacter spp. in Chicken Carcass

Campylobacteriosis is a common cause of gastrointestinal disease. In this study, we suggest a general strategy of applying gold nanoparticles (AuNPs) in colorimetric biosensors to detect Campylobacter in chicken carcass. Polymerase chain reaction (PCR) was utilized for the amplification of the target genes, and the thiolated PCR products were collected. Following the blending of colloid AuNPs with PCR products, the thiol bound to the surface of AuNPs, forming AuNP-PCR products. The PCR products had a sufficient negative charge, which enabled AuNPs to maintain a dispersed formation under electrostatic repulsion. This platform presented a color change as AuNPs aggregate. It did not need additional time and optimization of pH for PCR amplicons to adhere to the AuNPs. The specificity of AuNPs of modified primer pairs for mapA from Campylobacter jejuni and ceuE from Campylobacter coli was activated perfectly (C. jejuni, p-value: 0.0085; C. coli, p-value: 0.0239) when compared to Salmonella Enteritidis and Escherichia coli as non-Campylobacter species. Likewise, C. jejuni was successfully detected from artificially contaminated chicken carcass samples. According to the sensitivity test, at least 15 ng/μL of Campylobacter PCR products or 1×10³ CFU/mL of cells in the broth was needed for the detection using the optical method.

Campylobacter spp. isolated from poultry in Iran: Antibiotic resistance profiles, virulence genes, and molecular mechanisms

Campylobacter spp. genera is one of the most common causes of microbial enteritis worldwide. The objective of this work was to investigate the antimicrobial resistance (AMR) patterns, virulence genes, and genetic variation of thermophilic Campylobacter species collected from chicken meat samples in Iran. A total of 255 meat specimens were taken and transferred to the laboratory. Culture methods were utilized to identify the Campylobacter genus, and PCR and sequencing were performed to confirm the organisms. Antimicrobial susceptibility evaluation was performed using broth microdilution for six antimicrobials [ciprofloxacin (CIP), nalidixic acid (NAL), sitafloxacin (SIT), erythromycin (ERY), tetracycline (TET), and gentamicin (GEN)]. By using PCR, AMR and virulence genes were detected. The detection rate of Campylobacter spp. was 64 (25.09%) out of 255 meat samples, with C. jejuni and C. coli accounting for 41 (64.06%) and 14 (21.87%), respectively. Other Campylobacter isolates accounted for 14.06% of the total (nine samples). The antibiotic susceptibility of all Campylobacter isolates was tested using six antibiotics, and all (100%) were resistant to CIP and NAL. However, TET resistance was observed in 93.9% and 83.3% of C. jejuni and C. coli isolates, respectively. Four (8.2%) C. jejuni isolates were multidrug-resistant (MDR), while none of the C. coli isolates were MDR. Two of the four MDR isolates were resistant to CIP, NAL, TET, and ERY, whereas the other two isolates were resistant to CIP, NAL, TET, and GEN. The values of the Minimum Inhibitory Concentration (MIC) were as follows: CIP, 64-256 μg/ml; NAL, 128-512 μg/ml; TET, 2-1024 μg/ml; SIT, 0.25-1 μg/ml; ERY, 1-32 μg/ml; and GEN, 1-256 μg/ml. recR, dnaJ, cdtC, cdtB, cdtA, flaA, ciaB, cadF, and pidA were discovered in more than 50% of C. jejuni isolates, although wlaN, virbll, cgtB, and ceuE were found in <50%. flaA, cadF, pidA, and ciaB were discovered in more than 50% of the C. coli samples, whereas recR, cdtC, cdtB, cdtA, and cgtB were found in less than half. For C. coli, the percentages for wlaN, dnaJ, virbll, and ceuE were all zero. The results of this study show Campylobacter isolates obtained from poultry have higher resistance to quinolones and TET, pathogenicity potential, and varied genotypes.

Isolation Rate of Campylobacter Spp. and Detection of Virulence Genes of Campylobacter jejuni Across the Broiler Chain

The aim of the study was to identify the isolation rate of thermotolerant campylobacters in a small-scale broiler-meat production farm over a one-year period. The second deliverable of the study was to determine the potential virulence markers. The laboratory investigation was performed on 283 samples (cloacal swabs, caeca, carcass swabs) collected on three sampling points (farm, slaughter line, and cold storage). The isolates obtained with the conventional microbiological method were confirmed with multiplex PCR for identification of campylobacters. The presence of 10 virulence genes was analyzed in the C. jejuni isolates (flaA, racR, virB11, dnaJ, wlaN, cadF, ciaB, cdtA, cdtB, cdtC). Out of 283 samples, 169 (59.7%) were confirmed as Campylobacter spp., 111 (39.2%) C. jejuni, and 43 (15.2%) C. coli. C. jejuni was the most prevalent in all sampling points. Campylobacter spp. showed a characteristically seasonal prevalence with the highest isolation rate during the warmer period of the year. We detected the cadF and ciaB genes in all C. jejuni isolates. The flaA gene was present in 50% of the examined strains. The cdt genes (cdtA, cdtB, and cdtC) were confirmed in 52.8%, 52.8%, and 47.2% of the C. jejuni strains, respectively. C. jejuni showed 15 profiles of virulence patterns with four predominant profiles.

Estimating the Number of Illnesses Caused by Agents Transmitted Commonly Through Food: A Scoping Review

Estimates of the overall human health impact of agents transmitted commonly through food complement surveillance and help guide food safety interventions and regulatory initiatives. The purpose of this scoping review was to summarize the methods and reporting practices used in studies that estimate the total number of illnesses caused by these agents. We identified and included 43 studies published from January 1, 1995, to December 31, 2019, by searching PubMed and screening selected articles for other relevant publications. Selected articles presented original estimates of the number of illnesses caused by ≥1 agent transmitted commonly through food. The number of agents (species or subspecies for pathogens) included in each study ranged from 1 to 31 (median: 4.5; mean: 9.2). Of the 40 agents assessed across the 43 studies, the most common agent was Salmonella (36; 84% of studies), followed by Campylobacter (33; 77%), Shiga toxin-producing Escherichia coli (25; 58%), and norovirus (20; 47%). Investigators used a variety of data sources and methods that could be grouped into four distinct estimation approaches-direct, surveillance data scaled-up, syndrome or population scaled-down, and inferred. Based on our review, we propose four recommendations to improve the interpretability, comparability, and reproducibility of studies that estimate the number of illnesses caused by agents transmitted commonly through food. These include providing an assessment of statistical and nonstatistical uncertainty, providing a ranking of estimates by agent, including uncertainties; describing the rationale used to select agents and data sources; and publishing raw data and models, along with clear, detailed methods. These recommendations could lead to better decision-making about food safety policies. Although these recommendations have been made in the context of illness estimation for agents transmitted commonly through food, they also apply to estimates of other health outcomes and conditions.

Toll-Like Receptor-4 Is Involved in Mediating Intestinal and Extra-Intestinal Inflammation in Campylobacter coli-Infected Secondary Abiotic IL-10-/- Mice

Human Campylobacter infections are emerging worldwide and constitute significant health burdens. We recently showed that the immunopathological sequelae in Campylobacter jejuni-infected mice were due to Toll-like receptor (TLR)-4 dependent immune responses induced by bacterial lipooligosaccharide (LOS). Information regarding the molecular mechanisms underlying Campylobacter coli-host interactions are scarce, however. Therefore, we analyzed C. coli-induced campylobacteriosis in secondary abiotic IL-10^−/− mice with and without TLR4. Mice were infected perorally with a human C. coli isolate or with a murine commensal Escherichia coli as apathogenic, non-invasive control. Independent from TLR4, C. coli and E. coli stably colonized the gastrointestinal tract, but only C. coli induced clinical signs of campylobacteriosis. TLR4^−/− IL-10^−/− mice, however, displayed less frequently fecal blood and less distinct histopathological and apoptotic sequelae in the colon versus IL-10^−/− counterparts on day 28 following C. coli infection. Furthermore, C. coli-induced colonic immune cell responses were less pronounced in TLR4^−/− IL-10^−/− as compared to IL-10^−/− mice and accompanied by lower pro-inflammatory mediator concentrations in the intestines and the liver of the former versus the latter. In conclusion, our study provides evidence that TLR4 is involved in mediating C. coli-LOS-induced immune responses in intestinal and extra-intestinal compartments during murine campylobacteriosis.

Toll-Like Receptor-4 Dependent Intestinal and Systemic Sequelae Following Peroral Campylobacter coli Infection of IL10 Deficient Mice Harboring a Human Gut Microbiota

Zoonotic Campylobacter, including C. jejuni and C. coli, are among the most prevalent agents of food-borne enteritis worldwide. The immunopathological sequelae of campylobacteriosis are caused by Toll-like Receptor-4 (TLR4)-dependent host immune responses, induced by bacterial lipooligosaccharide (LOS). In order to investigate C. coli-host interactions, including the roles of the human gut microbiota and TLR4, upon infection, we applied a clinical acute campylobacteriosis model, and subjected secondary abiotic, TLR4-deficient IL10-/- mice and IL10-/- controls to fecal microbiota transplantation derived from human donors by gavage, before peroral C. coli challenge. Until day 21 post-infection, C. coli could stably colonize the gastrointestinal tract of human microbiota-associated (hma) mice of either genotype. TLR4-deficient IL10-/- mice, however, displayed less severe clinical signs of infection, that were accompanied by less distinct apoptotic epithelial cell and innate as well as adaptive immune cell responses in the colon, as compared to IL10-/- counterparts. Furthermore, C. coli infected IL10-/-, as opposed to TLR4-deficient IL10-/-, mice displayed increased pro-inflammatory cytokine concentrations in intestinal and, strikingly, systemic compartments. We conclude that pathogenic LOS might play an important role in inducing TLR4-dependent host immune responses upon C. coli infection, which needs to be further addressed in more detail.

Prevalence, Population Diversity and Antimicrobial Resistance of Campylobacter coli Isolated in Italian Swine at Slaughterhouse

Campylobacter spp. are among the microorganisms most commonly associated with foodborne disease. Swine are known to be the main reservoir of Campylobacter coli and a possible source infection of humans as a result of carcass contamination at slaughter. The aim of this study was to evaluate the prevalence of C. coli contamination in swine carcasses, the antimicrobial resistance (AMR) patterns of isolates and the genetic diversity between strains obtained from swine and those isolated from humans. The prevalence of contamination was higher on carcasses (50.4%) than in faeces (32.9%). The 162 C. coli isolated from swine were examined by pulsed-field gel electrophoresis (PFGE) and multi-locus sequence typing (MLST). The results of PFGE indicated a high genetic diversity among the isolates, with 25 different PFGE types. MLST assigned 51 sequence types (STs) to isolates. The most common genotype was ST-854 (16.04%), ST-9264 (10.49 %) and ST-1016 (6.08 %). Results of AMR showed a high resistance to quinolones and fluoroquinolones together with aminoglycosides and tetracycline. Many strains were multi-resistant with predominant R-type TeSCipNa (57%). Five resistance genes were detected along with mutation in the gyrA gene. A strong correlation between phenotypic and genotypic resistance was found for fluoroquinolone and tetracycline. Genetic profiles obtained in swine isolates were compared to those of 11 human strains. All human strains and 64.19% of animal strains (104/162) were assigned to the ST-828 clonal complex.

Antimicrobial resistance patterns and molecular resistance markers of Campylobacter jejuni isolates from human diarrheal cases

The aim of this study is to characterize the antimicrobial resistance of Campylobacter jejuni recovered from diarrheal patients in Belgium, focusing on the genetic diversity of resistant strains and underlying molecular mechanisms of resistance among Campylobacter jejuni resistant strains isolated from diarrheal patients in Belgium. Susceptibility profile of 199 clinical C. jejuni isolates was determined by minimum inhibitory concentrations against six commonly-used antibiotics (ciprofloxacin, nalidixic acid, tetracycline, streptomycin, gentamicin, and erythromycin). High rates of resistance were observed against nalidixic acid (56.3%), ciprofloxacin (55.8%) and tetracycline (49.7%); these rates were similar to those obtained from different national reports in broilers intended for human consumption. Alternatively, lower resistance rates to streptomycin (4.5%) and erythromycin (2%), and absolute sensitivity to gentamicin were observed. C. jejuni isolates resistant to tetracycline or quinolones (ciprofloxacin and/or nalidixic acid) were screened for the presence of the tetO gene and the C257T mutation in the quinolone resistance determining region (QRDR) of the gyrase gene gyrA, respectively. Interestingly, some of the isolates that displayed phenotypic resistance to these antimicrobials lacked the corresponding genetic determinants. Among erythromycin-resistant isolates, a diverse array of potential molecular resistance mechanisms was investigated, including the presence of ermB and mutations in the 23S rRNA gene, the rplD and rplV ribosomal genes, and the regulatory region of the cmeABC operon. Two of the four erythromycin-resistant isolates harboured the A2075G transition mutation in the 23S rRNA gene; one of these isolates exhibited further mutations in rplD, rplV and in the cmeABC regulatory region. This study expands the current understanding of how different genetic determinants and particular clones shape the epidemiology of antimicrobial resistance in C. jejuni in Belgium. It also reveals many questions in need of further investigation, such as the role of other undetermined molecular mechanisms that may potentially contribute to the antimicrobial resistance of Campylobacter.

Investigation of potential pathogenicity of Willaertia magna by investigating the transfer of bacteria pathogenicity genes into its genome

Willaertia magna c2c maky is a thermophilic amoeba closely related to the genus Naegleria. This free-living amoeba has the ability to eliminate Legionella pneumophila, which is an amoeba-resisting bacterium living in an aquatic environment. To prevent the proliferation of L. pneumophila in cooling towers, the use of W. magna as natural biocide has been proposed. To provide a better understanding of the W. magna genome, whole-genome sequencing was performed through the study of virulence factors and lateral gene transfers. This amoeba harbors a genome of 36.5 megabases with 18,519 predicted genes. BLASTp analyses reported protein homology between 136 W. magna sequences and amoeba-resistant microorganisms. Horizontal gene transfers were observed based on the basis of the phylogenetic reconstruction hypothesis. We detected 15 homologs of N. fowleri genes related to virulence, although these latter were also found in the genome of N. gruberi, which is a non-pathogenic amoeba. Furthermore, the cytotoxicity test performed on human cells supports the hypothesis that the strain c2c maky is a non-pathogenic amoeba. This work explores the genomic repertory for the first draft genome of genus Willaertia and provides genomic data for further comparative studies on virulence of related pathogenic amoeba, N. fowleri.

Viability Quantitative PCR Utilizing Propidium Monoazide, Spheroplast Formation, and Campylobacter coli as a Bacterial Model

A viability quantitative PCR (qPCR) utilizing propidium monoazide (PMA) is presented for rapid quantification of viable cells using the foodborne pathogen Campylobacter coli as a bacterial model. It includes optimized spheroplast formation via lysozyme and EDTA, induction of a mild osmotic shock for enhancing the selective penetration of PMA into dead cells, and exploitation of an internal sample process control (ISPC) involving cell inactivation to assess residual false-positive signals within each sample. Spheroplasting of bacteria in exponential phase did not permit PMA entrance into viable cells since a strong linear relationship was detected between simple qPCR and PMA-qPCR quantification, and no differences were observed regardless of whether spheroplasting was utilized. The PMA-qPCR signal suppression of dead cells was elevated using spheroplast formation. With regard to the ISPC, cell inactivation by hydrogen peroxide resulted in higher signal suppression during qPCR than heat inactivation did. Viability quantification of C. coli cells by optimized spheroplasting-PMA-qPCR with ISPC was successfully applied in an aging pure culture under aerobic conditions and artificially inoculated meat. The same method exhibited a high linear range of quantification (1.5 to 8.5 log10 viable cells ml-1), and results were highly correlated with culture-based enumeration. PMA-qPCR quantification of viable cells can be affected by their rigidity, age, culture media, and niches, but spheroplast formation along with osmotic shock and the use of a proper ISPC can address such variations. The developed methodology could detect cells in a viable-but-nonculturable state and might be utilized for the quantification of other Gram-negative bacteria.IMPORTANCE There is need for rapid and accurate methods to detect viable bacterial cells of foodborne pathogens. Conventional culture-based methods are time-consuming and unable to detect bacteria in a viable-but-nonculturable state. The high sensitivity and specificity of the quantitative PCR (qPCR) are negated by its inability to differentiate the DNAs from viable and dead cells. The combination of propidium monoazide (PMA), a DNA-intercalating dye, with qPCR assays is promising for detection of viable cells. Despite encouraging results, these assays still encounter various challenges, such as false-positive signals by dead cells and the lack of an internal control identifying these signals per sample. The significance of our research lies in enhancing the selective entrance of PMA into dead Campylobacter coli cells via spheroplasting and in developing an internal sample process control, thus delivering reliable results in pure cultures and meat samples, approaches that can be applicable to other Gram-negative pathogens.

Tongue coating microbiome as a potential biomarker for gastritis including precancerous cascade

The development of gastritis is associated with an increased risk of gastric cancer. Current invasive gastritis diagnostic methods are not suitable for monitoring progress. In this work based on 78 gastritis patients and 50 healthy individuals, we observed that the variation of tongue-coating microbiota was associated with the occurrence and development of gastritis. Twenty-one microbial species were identified for differentiating tongue-coating microbiomes of gastritis and healthy individuals. Pathways such as microbial metabolism in diverse environments, biosynthesis of antibiotics and bacterial chemotaxis were up-regulated in gastritis patients. The abundance of Campylobacter concisus was found associated with the gastric precancerous cascade. Furthermore, Campylobacter concisus could be detected in tongue coating and gastric fluid in a validation cohort containing 38 gastritis patients. These observations provided biological evidence of tongue diagnosis in traditional Chinese medicine, and indicated that tongue-coating microbiome could be a potential non-invasive biomarker, which might be suitable for long-term monitoring of gastritis.

Disinfectant and Antimicrobial Susceptibility Profiles of Campylobacter coli Isolated in 1998 to 1999 and 2015 from Swine and Commercial Pork Chops

Susceptibility profiles were determined for 111 Campylobacter coli strains obtained in 1998 to 1999 and 2015 from market age pigs and pork chops against 22 disinfectants and 9 antimicrobials. Resistance to tetracycline (TET) was observed in 44.4% of 1998 to 1999 strains, and the antibiotic resistance profile was TET. But strains obtained in 2015 from swine and retail pork chops had 75% TET resistance and the antibiotic resistance profile was TET, followed by azithromycin-erythromycin-TET-telithromycin-clindamycin. Antimicrobial resistance increased in 2015 strains. All strains were resistant to triclosan, and 84.1% and 95.8% of strains in 1998 to 1999 and 2015, respectively, were chlorhexidine resistant. All strains were susceptible to benzalkonium chloride. There was a shift toward higher susceptibility to chlorhexidine, triclosan, P-128, OdoBan, CPB, and CPC in 2015 swine and pork chop strains compared with 1998 to 1999 strains. The disinfectants Tek-Trol and providone-iodine, tris(hydroxylmethyl)nitromethane (THN) and formaldehyde demonstrated the highest susceptibilities. Didecyldimethylammonium chloride (C10AC) appeared to be about equally effective as benzyldimethyltetradecylammonium chloride (C14BAC) for inhibiting C. coli, and both were more effective than C8AC and C12BAC, but C16BAC was not efficient at inhibiting C. coli. The BACs, C12BAC and C14BAC, were the most effective ingredients in DC&R. Also, C12BAC and C14BAC, or these two in synergy with C10AC were responsible for inhibition of C. coli at high P-128 MICs. No cross-resistance was observed between antibiotics and disinfectants. The continued use of THN and formaldehyde in DC&R should be evaluated since these components are not effective, and their inclusion adds unwanted chemicals in the environment. PRACTICAL APPLICATION: Campylobacter species cause diarrheal disease throughout the world. Disinfectants are often used on the farm, in veterinary medicine, by the food processing industry, in restaurants, and in consumer's homes. Limited information is available in the literature showing how disinfectants or disinfectant components may affect the many different foodborne pathogens, and, specifically, Campylobacter coli studied here. The knowledge generated in this study concerning the interactions of a broad array of disinfectants against C. coli may well affect the types of disinfectants and disinfectant formulations allowable for use by medical personnel, producers, food processors, restaurants, and consumers.

PhasomeIt: an 'omics' approach to cataloguing the potential breadth of phase variation in the genus Campylobacter

Hypermutable simple sequence repeats (SSRs) are drivers of phase variation (PV) whose stochastic, high-frequency, reversible switches in gene expression are a common feature of several pathogenic bacterial species, including the human pathogen Campylobacter jejuni. Here we examine the distribution and conservation of known and putative SSR-driven phase variable genes – the phasome – in the genus Campylobacter. PhasomeIt, a new program, was specifically designed for rapid identification of SSR-mediated PV. This program detects the location, type and repeat number of every SSR. Each SSR is linked to a specific gene and its putative expression state. Other outputs include conservation of SSR-driven phase-variable genes and the ‘core phasome’ – the minimal set of PV genes in a phylogenetic grouping. Analysis of 77 complete Campylobacter genome sequences detected a ‘core phasome’ of conserved PV genes in each species and a large number of rare PV genes with few, or no, homologues in other genome sequences. Analysis of a set of partial genome sequences, with food-chain-associated metadata, detected evidence of a weak link between phasome and source host for disease-causing isolates of sequence type (ST)-828 but not the ST-21 or ST-45 complexes. Investigation of the phasomes in the genus Campylobacter provided evidence of overlapping but distinctive mechanisms of PV-mediated adaptation to specific niches. This suggests that the phasome could be involved in host adaptation and spread of campylobacters. Finally, this tool is malleable and will have utility for studying the distribution and genic effects of other repetitive elements in diverse bacterial species.

Interactions of organic acids with Campylobacter coli from swine

Campylobacter coli is a bacterial species that is a major cause of diarrheal disease worldwide, and Campylobacter spp. are among the top 5 foodborne pathogens in the United States. During food production organic acids (OAs) are often used to remove bacteria from animal carcasses. The interactions of six OAs with 111 C. coli strains obtained from swine and retail pork chops were studied by determining the molar minimum inhibitory concentrations (MICMs) of the C. coli strains, and the pH at the MICMs. The Henderson-Hasselbalch equation was used to calculate the concentrations of the undissociated and dissociated OAs at the MICMs of the C. coli strains. The results for the 111 different C. coli strains obtained from different locations were treated as a single group for each OA since many of the C. coli strains behaved similarly to each different OA. Inhibition of C. coli was not dependent on pH or on the undissociated OA species, but C. coli inhibition correlated with the dissociated OA species. Therefore, if the concentration of the dissociated OAs decreases from optimum, one may then expect that C. coli bacteria would escape disinfection. The concentration of the dissociated OA should be carefully controlled in a carcass wash. We suggest maintaining a concentration of the dissociated acetic, butyric, citric, formic, lactic and propionic acids at 29, 23, 11, 35, 22 and 25 mM, respectively, when using a carcass wash with these OAs to remove C. coli bacteria. However, due to C. coli utilization of acetate, formate, lactate and propionate, these four OAs may not be the best choice to use for a carcass wash to remove C. coli contamination. Of the six OAs, citric acid was the most efficient at inhibiting C. coli.

New colorimetric aptasensor for rapid on-site detection of Campylobacter jejuni and Campylobacter coli in chicken carcass samples

Campylobacter is the most common cause of infectious intestinal disease, with nearly all cases caused by two species: C. jejuni and C. coli. We recently reported a gold nanoparticle-based two-stage aptasensing platform, which was improved in the present study for the rapid and on-site detection of both C. jejuni and C. coli in food samples. Compared to the previous platform, the improved platform yielded a more obvious colour change from red to purple due to the aggregation of gold nanoparticles, and does not require additional time or a pH optimization step for the aptamers to be adsorbed onto the gold nanoparticles. Using a highly specific aptamer that binds to live C. jejuni and C. coli, the improved aptasensor was highly effective for testing pure culture samples. The accuracy of the newly developed platform was comparable (p = 0.688) to that of the gold-standard detection method of tazobactam-supplemented culture, whereas it was superior to the official agar-based detection method (p = 0.016) in a validation study with 50 naturally contaminated chicken carcass samples. This is the first study on a colorimetric sensor that targets both live C. coli and C. jejuni in naturally contaminated samples. In addition, we provide the first evidence that both morphological status and the amount of Campylobacter present play key roles in the effectiveness of colorimetric detection. Thus, suitable selection of an antibody or aptamer with consideration of the morphological status of pathogens in samples is essential for direct detection without enrichment. Our data suggest that the sensor developed in this study can provide an excellent screening method, with a reduction in the detection time from 48 h to 30 min after enrichment, thus saving time, labour, and cost.

Emerging mechanisms of antimicrobial resistance in bacteria and fungi: advances in the era of genomics

Bacteria and fungi continue to develop new ways to adapt and survive the lethal or biostatic effects of antimicrobials through myriad mechanisms. Novel antibiotic resistance genes such as lsa(C), erm(44), VCC-1, mcr-1, mcr-2, mcr-3, mcr-4, bla _KLUC-3 and bla _KLUC-4 were discovered through comparative genomics and further functional studies. As well, mutations in genes that hitherto were unknown to confer resistance to antimicrobials, such as trm, PP2C, rpsJ, HSC82, FKS2 and Rv2887, were shown by genomics and transcomplementation assays to mediate antimicrobial resistance in Acinetobacter baumannii, Staphylococcus aureus, Enterococcus faecium, Saccharomyces cerevisae, Candida glabrata and Mycobacterium tuberculosis, respectively. Thus, genomics, transcriptomics and metagenomics, coupled with functional studies are the future of antimicrobial resistance research and novel drug discovery or design.

Characterization of the Microbiome along the Gastrointestinal Tract of Growing Turkeys

The turkey microbiome is largely understudied, despite its relationship with bird health and growth, and the prevalence of human pathogens such as Campylobacter spp. In this study we investigated the microbiome within the small intestine (SI), caeca (C), large intestine (LI), and cloaca (CL) of turkeys at 6, 10, and 16 weeks of age. Eight turkeys were dissected within each age category and the contents of the SI, C, LI, and CL were harvested. 16S rDNA based QPCR was performed on all samples and samples for the four locations within three birds/age group were sequenced using ion torrent-based sequencing of the 16S rDNA. Sequencing data showed on a genus level, an abundance of Lactobacillus, Streptococcus, and Clostridium XI (38.2, 28.1, and 13.0% respectively) irrespective of location and age. The caeca exhibited the greatest microbiome diversity throughout the development of the turkey. PICRUSt data predicted an array of bacterial function, with most differences being apparent in the caeca of the turkeys as they matured. QPCR revealed that the caeca within 10 week old birds, contained the most Campylobacter spp. Understanding the microbial ecology of the turkey gastrointestinal tract is essential in terms of understanding production efficiency and in order to develop novel strategies for targeting Campylobacter spp.

Composition and diversity of mucosa-associated microbiota along the entire length of the pig gastrointestinal tract; dietary influences

Mucosa-associated microbial populations of the gastrointestinal tract are in intimate contact with the outer mucus layer. This proximity offers these populations a higher potential, than lumenal microbiota, in exerting effects on the host. Functional characteristics of the microbiota and influences of host-physiology shape the composition and activity of the mucosa-associated bacterial community. We have shown previously that inclusion of an artificial sweetener, SUCRAM, included in the diet of weaning piglets modulates the composition of lumenal-residing gut microbiota and reduces weaning-related gastrointestinal disorders. In this study, using Illumina sequencing we characterised the mucosa-associated microbiota along the length of the intestine of piglets, and determined the effect of SUCRAM supplementation on mucosa-associated populations. There were clear distinctions in the composition of mucosa-associated microbiota, between small and large intestine, concordant with differences in regional oxygen distribution and nutrient provision by the host. There were significant differences in the composition of mucosa-associated compared with lumenal microbiota in pig caecum. Dietary supplementation with SUCRAM affected mucosa-associated bacterial community structure along the length of the intestinal tract. Most notably, there was a substantial reduction in predominant Campylobacter populations proposing that SUCRAM supplementation of swine diet has potential for reducing meat contamination and promoting food safety.

Sensitivity of Direct Culture, Enrichment and PCR for Detection of Campylobacter jejuni and C. coli in Broiler Flocks at Slaughter

Broiler chicken flocks are a significant source of Campylobacter jejuni and Campylobacter coli that result in the major public health problem of campylobacteriosis. Accurate estimates of the prevalence of both C. coli and C. jejuni in flocks would enhance epidemiological understanding, risk assessment and control options. This study combined results from a panel of 10 detection tests (direct culture, enrichment and PCR) on caecal samples from flocks at slaughter. A parallel interpretation approach was used to determine the presence of Campylobacter spp. and for C. jejuni and C. coli individually. The sample was considered positive if at least one method detected the target and this interpretation was taken to represent a 'proxy gold standard' for detection in the absence of a gold standard reference test. The sensitivity of each individual method to detect Campylobacter spp., C. jejuni and C. coli was then estimated relative to the proxy gold standard. Enrichment in adapted Exeter broth (deficient in polymyxin B) with a resuscitation step was 100% sensitive, whilst direct culture on modified charcoal cefoperazone deoxycholate agar (mCCDA) was highly sensitive (97.9%). Enrichment methods using Preston broth and Bolton broth were significantly less sensitive. Enrichment in Exeter broth promoted the recovery of C. jejuni, whilst enrichment in Bolton broth favoured C. coli. A RT-PCR detection test could identify 80% of flocks that were co-colonised with both species. This study found that 76.3% (n = 127) of flocks were colonised with Campylobacter spp. The majority (95.9%) of Campylobacter-positive flocks were colonised with C. jejuni; however, approximately one-third of positive flocks were simultaneously colonised with both C. jejuni and C. coli. The findings highlight the impact of different detection methodologies on the accuracy of the estimated incidence of both C. jejuni and C. coli entering the abattoir within broiler flocks and the associated public health risks.

Sensitivity to Enterocins of Thermophilic Campylobacter spp. from Different Poultry Species

Campylobacter spp. have been isolated from various animals, including poultry. They are rapidly transmitted throughout broiler sheds by the fecal-oral route. A promising strategy to reduce Campylobacter spp. in poultry may be done due to the beneficial properties of probiotic bacteria and their bacteriocins. In this study, inhibition spectrum/activity of different enterocins was evaluated against Campylobacter spp. (isolated from different poultry) to indicate further practical use of enterocins. Enterocins are antimicrobial proteinaceous substances produced mostly by enterococci. Feces from broiler chickens (10), laying hens (47), ostriches (140), and ducks (40) were screened. Altogether, 23 strains were allotted to the species Campylobacter jejuni and Campylobacter coli using MALDI TOF mass spectrometry and confirmed by genotyping (PCR method). In the feces of ostriches, Campylobacter spp. were not confirmed. Campylobacter spp. isolated from different poultry showed resistance to nalidixic acid, ciprofloxacin, and ampicillin. Interestingly, strains demonstrating antibiotic resistance revealed sensitivity to at least one of the nine enterocins used (except C. coli Kc1, SZ3, and C. jejuni 1/D). Almost 52% strains were inhibited by Ent A (P). Enterocins can therefore be used to prevent or reduce Campylobacter spp.; it is a basis for practical use.

Genetic Diversity of Campylobacter jejuni and Campylobacter coli Isolates from Conventional Broiler Flocks and the Impacts of Sampling Strategy and Laboratory Method

The genetic diversity of Campylobacter jejuni and Campylobacter coli isolates from commercial broiler farms was examined by multilocus sequence typing (MLST), with an assessment of the impact of the sample type and laboratory method on the genotypes of Campylobacter isolated. A total of 645 C. jejuni and 106 C. coli isolates were obtained from 32 flocks and 17 farms, with 47 sequence types (STs) identified. The Campylobacter jejuni isolates obtained by different sampling approaches and laboratory methods were very similar, with the same STs identified at similar frequencies, and had no major effect on the genetic profile of Campylobacter population in broiler flocks at the farm level. For C. coli, the results were more equivocal. While some STs were widely distributed within and among farms and flocks, analysis of molecular variance (AMOVA) revealed a high degree of genetic diversity among farms for C. jejuni, where farm effects accounted for 70.5% of variance, and among flocks from the same farm (9.9% of variance for C. jejuni and 64.1% for C. coli). These results show the complexity of the population structure of Campylobacter in broiler production and that commercial broiler farms provide an ecological niche for a wide diversity of genotypes. The genetic diversity of C. jejuni isolates among broiler farms should be taken into account when designing studies to understand Campylobacter populations in broiler production and the impact of interventions. We provide evidence that supports synthesis of studies on C. jejuni populations even when laboratory and sampling methods are not identical.

Status of vaccine research and development for Campylobacter jejuni

Campylobacter jejuni is one of the leading causes of bacterial diarrhea worldwide and is associated with a number of sequelae, including Guillain-Barre Syndrome, reactive arthritis, irritable bowel syndrome and growth stunting/malnutrition. Vaccine development against C. jejuni is complicated by its antigenic diversity, a lack of small animal models, and a poor understanding of the bacterium's pathogenesis. Vaccine approaches have been limited to recombinant proteins, none of which have advanced beyond Phase I testing. Genomic analyses have revealed the presence of a polysaccharide capsule on C. jejuni. Given the success of capsule-conjugate vaccines for other mucosal pathogens of global importance, efforts to evaluate this established approach for C. jejuni are also being pursued. A prototypical capsule-conjugate vaccine has demonstrated efficacy against diarrheal disease in non-human primates and is currently in Phase I testing. In addition to proof of concept studies, more data on the global prevalence of capsular types, and a better understanding of the acute and chronic consequences of C. jejuni are needed to inform investments for a globally relevant vaccine.

A transferable plasticity region in Campylobacter coli allows isolates of an otherwise non-glycolytic food-borne pathogen to catabolize glucose

Thermophilic Campylobacter species colonize the intestine of agricultural and domestic animals commensally but cause severe gastroenteritis in humans. In contrast to other enteropathogenic bacteria, Campylobacter has been considered to be non-glycolytic, a metabolic property originally used for their taxonomic classification. Contrary to this dogma, we demonstrate that several Campylobacter coli strains are able to utilize glucose as a growth substrate. Isotopologue profiling experiments with (13) C-labeled glucose suggested that these strains catabolize glucose via the pentose phosphate and Entner-Doudoroff (ED) pathways and use glucose efficiently for de novo synthesis of amino acids and cell surface carbohydrates. Whole genome sequencing of glycolytic C. coli isolates identified a genomic island located within a ribosomal RNA gene cluster that encodes for all ED pathway enzymes and a glucose permease. We could show in vitro that a non-glycolytic C. coli strain could acquire glycolytic activity through natural transformation with chromosomal DNA of C. coli and C. jejuni subsp. doylei strains possessing the ED pathway encoding plasticity region. These results reveal for the first time the ability of a Campylobacter species to catabolize glucose and provide new insights into how genetic macrodiversity through intra- and interspecies gene transfer expand the metabolic capacity of this food-borne pathogen.

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.

Dynamic of Campylobacter Species Contamination Along a Poultry Slaughtering Chain

The prevalence of Campylobacters was studied in a poultry farm and along the slaughtering chain. Fifteen swabs from a farm and 75 samples (swabs and rinsates) from its slaughterhouse were collected. All the faecal and cloacal farm swabs were contaminated by Campylobacter jejuni and C. coli against 50% for breast swabs. C. jejuni had a concentration of 6.26, 6.34 and 5.38 Log10 CFU/mL in faecal, cloacal and breast swabs respectively. Rinsates showed an almost constant concentration of Campylobacters (6 Log10 CFU/mL) with a predominance of the presumptive C. jejuni. C. lari was found in 22% of eviscerated samples. Faecal coliforms and E. coli, used as indicators, were detected in all samples (5.46 and 5.15 Log10 CFU/mL, respectively). Final chilling and chlorine (50 ppm) treatments decreased them to acceptable levels, unlike for Campylobacters. Further investigation of the dynamics of Campylobacters and their response to prevention and treatment measures is required.

Prevalence, antibiogram and risk factors of thermophilic Campylobacter spp. in dressed porcine carcass of Chitwan, Nepal

BACKGROUND

Campylobacter is the primary cause of food borne gastroenteritis. Moreover, the emergence of multiple drug resistant campylobacters from poultry and pork has produced a potential threat to public health. Research addressing these issues is sparse in Nepal. So, this cross-sectional study aims at determining the prevalence, antibiogram and risk factors of campylobacters from dressed porcine carcass of Chitwan, Nepal.

RESULTS

We collected 139 samples of dressed porcine carcass from 10 different pork shops located in Chitwan district and processed according to OIE Terrestrial Manual, 2008, chapter 2.8.10. Antibiogram of identified Campylobacter spp. was evaluated against nine commonly used antibiotics by using disc diffusion method following CLSI guidelines. The prevalence of Campylobacter spp. was 38.84% (C. coli 76% and C. jejuni 24%). There was no significant difference (p > 0.05) between the prevalence rate of male (32.4%) and female (41%) carcass. Ampicillin and erythromycin showed the highest resistance (92.59% each) followed by colistin (72.2%), tetracycline (61.1%), nalidixic acid and cotrimoxazole (44.4% each), ciprofloxacin (31.5%) and gentamicin (5.56%). Moreover, 77.8% of the isolates were resistant to more than two antimicrobials. Nalidixic acid and tetracycline showed significant difference (p < 0.05) in the resistivity pattern among different species of Campylobacters. The association between prevalence rate and regular sanitization of slaughter slab equipments was significant (p < 0.05). Similarly, prevalence rate was significantly associated (p < 0.01) with chilling and contamination of intestinal content with carcass.

CONCLUSIONS

The pork meat of Chitwan is highly contaminated with antibiotic-resistant Campylobacters and slaughtering practices play significant role in contamination. It is necessary to train the butchers about hygienic slaughtering practice. The consumers as well as butchers should adopt safety measures to prevent themselves from antibiotic resistant campylobacters. The veterinary practitioners should adopt prudent use of antibiotics in pigs.

Bayesian analysis of culture and PCR methods for detection of Campylobacter spp. in broiler caecal samples

The objective of this study was to estimate the sensitivity and specificity of a culture method and a polymerase chain reaction (PCR) method for detection of two Campylobacter species: C. jejuni and C. coli. Data were collected during a 3-year survey of UK broiler flocks, and consisted of parallel sampling of caeca from 436 batches of birds by both PCR and culture. Batches were stratified by season (summer/non-summer) and whether they were the first depopulation of the flock, resulting in four sub-populations. A Bayesian approach in the absence of a gold standard was adopted, and the sensitivity and specificity of the PCR and culture for each Campylobacter subtype was estimated, along with the true C. jejuni and C. coli prevalence in each sub-population. Results indicated that the sensitivity of the culture method was higher than that of PCR in detecting both species when the samples were derived from populations infected with at most one species of Campylobacter. However, from a mixed population, the sensitivity of culture for detecting both C. jejuni or C. coli is reduced while PCR is potentially able to detect both species, although the total probability of correctly identifying at least one species by PCR is similar to that of the culture method.

Comparative genomics of unintrogressed Campylobacter coli clades 2 and 3

BACKGROUND

Campylobacter jejuni and C. coli share a multitude of risk factors associated with human gastrointestinal disease, yet their phylogeny differs significantly. C. jejuni is scattered into several lineages, with no apparent linkage, whereas C. coli clusters into three distinct phylogenetic groups (clades) of which clade 1 has shown extensive genome-wide introgression with C. jejuni, yet the other two clades (2 and 3) have less than 2% of C. jejuni ancestry. We characterized a C. coli strain (76339) with four novel multilocus sequence type alleles (ST-5088) and having the capability to express gamma-glutamyltranspeptidase (GGT); an accessory feature in C. jejuni. Our aim was to further characterize unintrogressed C. coli clades 2 and 3, using comparative genomics and with additional genome sequences available, to investigate the impact of horizontal gene transfer in shaping the accessory and core gene pools in unintrogressed C. coli.

RESULTS

Here, we present the first fully closed C. coli clade 3 genome (76339). The phylogenomic analysis of strain 76339, revealed that it belonged to clade 3 of unintrogressed C. coli. A more extensive respiratory metabolism among unintrogressed C. coli strains was found compared to introgressed C. coli (clade 1). We also identified other genes, such as serine proteases and an active sialyltransferase in the lipooligosaccharide locus, not present in C. coli clade 1 and we further propose a unique scenario for the evolution of Campylobacter ggt.

CONCLUSIONS

We propose new insights into the evolution of the accessory genome of C. coli clade 3 and C. jejuni. Also, in silico analysis of the gene content revealed that C. coli clades 2 and 3 have genes associated with infection, suggesting they are a potent human pathogen, and may currently be underreported in human infections due to niche separation.

Effects of fluoroquinolone treatment and group housing of pigs on the selection and spread of fluoroquinolone-resistant Campylobacter

There are concerns that the use of fluoroquinolones (FQs) and group housing of food animals may contribute to the development of bacterial FQ resistance. Here, we studied the effects of administering FQ to pigs on the selection of FQ-resistant Campylobacter. Fifteen pigs were randomly allocated to either a group treated with FQs (enrofloxacin or norfloxacin), or an untreated control group. The number of FQ-resistant Campylobacter in feces was determined using appropriate selective agar containing enrofloxacin. FQ-resistant Campylobacter from samples of both groups were observed on days 3 and 4. These bacteria persisted for up to 21 days after treatment was discontinued. To evaluate the effect of group housing on the transmission of FQ-resistant Campylobacter, five pigs infected with FQ-sensitive Campylobacter pigs and one pig infected with FQ-resistant Campylobacter were housed together. On day 3, FQ-resistant Campylobacter were isolated from all six pigs. Moreover, FQ-resistant Campylobacter were isolated from environmental samples from the pen. These results indicate that the treatment of pigs with FQs selects for and spreads FQ-resistant Campylobacter among the pen. Therefore, responsible and prudent use of FQs at pig farms is required to prevent the emergence and transmission of FQ-resistant Campylobacter.

Elucidating the aetiology of human Campylobacter coli infections

There has been little research on the determinants of Campylobacter coli infection, despite its contributing up to 10% of human Campylobacter infections. A case-control and two case-case study methods explored the aetiology of C. coli over a one year period across Scotland. The case-control multivariate model found an increased risk of C. coli infection in people older than 19 years (O.R. = 3.352), and during the summer months (O.R. = 2.596), while residing in an urban area decreased the risk (O.R. = 0.546). The first case-case study compared C. coli and C. jejuni cases and also showed a higher risk of C. coli during the summer (O.R. = 1.313) and in people older than 19 years (O.R. = 0.791). Living in an urban area was associated with a reduced risk of infection (O.R. = 0.769). Multi-locus sequence typing (MLST) indicated that sheep and chicken C. coli sequence types (STs) were most frequently found in humans whilst those from cattle and pigs were rarer. MLST diversity was high in isolates from pigs and chicken, intermediate in human isolates, and low in ruminant isolates. The second case-case study used MLST data to ascribe putative sources of infection to the cases. The putative source for 40% of cases was chicken, with 60% acquired from other sources (ruminants 54% and pigs 6%). The case-case analysis also showed that female gender was a risk factor (O.R. = 1.940), which may be explained by females being more likely to prepare poultry in the home. These findings indicate differences between the aetiology of C. coli and C. jejuni infections: this should be taken into account by public health professionals when developing strategies to reduce the burden of human campylobacteriosis.

Effects of feeding finisher pigs with chicory or lupine feed for one week or two weeks before slaughter with respect to levels of Bifidobacteria and Campylobacter

This study aimed to assess whether inclusion of chicory or lupine (prebiotics) in the diet of pre-slaughter pigs for just 1 or 2 weeks could change the composition of their intestinal microbiota, stimulate the growth of bifidobacteria and help to lower the amount of thermoplilic Campylobacter spp. (mainly Campylobacter jejuni and Campylobacter coli), which are a major cause of food-borne infections in humans. A total of 48 pigs that had an initial live weight of 90 kg were fed with either a lupine (organic concentrate with 25% blue lupine seeds), chicory (organic concentrate with 10% dried chicory roots) or control (100% organic concentrate) diet for 1 week (24 pigs) or 2 weeks (24 pigs) before slaughter. The Campylobacter spp. level in rectal faecal samples after 0, 1 and 2 weeks of feeding and in the luminal content from ileum, caecum and colon at slaughter was determined by direct plating on modified charcoal-cefoperazone-deoxycholate agar plates. DNA extracted from the luminal content of distal ileum and caecum was used for terminal restriction fragment length polymorphism (T-RFLP) analysis of the composition of intestinal microbiota and for measuring the amount of bifidobacterial and total bacterial DNA by quantitative real-time PCR (qPCR). Campylobacter spp. were excreted by all pigs and present in the luminal content from distal ileum to midway colon with particularly high numbers in the caecum, but the excretion was reduced by 10-fold in pigs fed lupines for 1 week as compared with control- and chicory-fed pigs (mean log(10) 2.9 v. 4.1 CFU/g; P < 0.05). The qPCR analysis showed that feeding with lupines resulted in higher levels of bifidobacteria in caecum as compared with the other diets (P < 0.05). T-RFLP analysis showed that four of the most abundant bacteria with terminal restriction fragment values >5% relative to the intensity of total abundance differed between the feed treatments (P < 0.05). Therefore, this study showed that even a short-term alternative feeding strategy with prebiotics in the diet of pre-slaughter pigs elicited changes in the composition of the intestinal microbiota, where lupine increased the level of bifidobacteria in caecum and reduced the Campylobacter spp. excretion level after 1 week.

Comparative characterization of the virulence gene clusters (lipooligosaccharide [LOS] and capsular polysaccharide [CPS]) for Campylobacter coli, Campylobacter jejuni subsp. jejuni and related Campylobacter species

Campylobacter jejuni subsp. jejuni and Campylobacter coli are leading causes of gastroenteritis, with virulence linked to cell surface carbohydrate diversity. Although the associated gene clusters are well studied for C. jejuni subsp. jejuni, C. coli has been largely neglected. Here we provide comparative analysis of the lipooligosaccharide (LOS) and capsular polysaccharide (CPS) gene clusters, using genome and cluster sequence data for 36 C. coli strains, 67 C. jejuni subsp. jejuni strains and ten additional Campylobacter species. Similar to C. jejuni subsp. jejuni, C. coli showed high LOS/CPS gene diversity, with each cluster delineated into eight gene content classes. This diversity was predominantly due to extensive gene gain/loss, with the lateral transfer of genes likely occurring both within and between species and also between the LOS and CPS. Additional mechanisms responsible for LOS/CPS diversity included phase-variable homopolymeric repeats, gene duplication/inactivation, and possibly host environment selection pressure. Analyses also showed that (i) strains of C. coli and Campylobacter upsaliensis possessed genes homologous to the sialic acid genes implicated in the neurological disorder Guillain-Barré syndrome (GBS), and (ii) C. coli LOS classes were differentiated between bovine and poultry hosts, potentially aiding post infection source tracking.

Prevalence and Antimicrobial Resistance of Thermophilic Campylobacter Isolated from Chicken in Côte d'Ivoire

Thermophilic Campylobacters are major causes of gastroenteritis in human. The main risk factor of infection is consumption of contaminated or by cross-contaminated poultry meat. In Côte d'Ivoire, gastroenteritis is usually observed but no case of human campylobacteriosis has been formally reported to date. The aims of this study were to determine prevalence and antimicrobial resistance of Campylobacter jejuni and Campylobacter coli isolated from chickens ceaca in commercial slaughter in Abidjan. Between May and November 2009, one hundred and nineteen (119) chicken caeca samples were collected and analyzed by passive filtration method followed by molecular identification (PCR). From these 119 samples, 76 (63.8%) were positive to Campylobacter tests. Among the positive colonies, 51.3% were C. jejuni and 48.7% were C. coli. Of the 39 C. jejuni isolates, 79.5%, 38.5%, 17.9%, 10.3%, and 7.7% were, respectively, resistant, to nalidixic acid, ciprofloxacin, amoxicillin, erythromycin, and gentamicin. Among the 37 isolates of C. coli, 78.4%, 43.2%, 13.5%, 8.1%, and 0% were resistant, respectively, to the same antibiotics. In conclusion, we reported in this study the presence of high Campylobacter contamination of the studied chickens. Molecular identification of the bacteria was performed and determination of high resistance to antimicrobials of the fluoroquinolone family was revealed.

Antimicrobial susceptibility, pulsed-field gel electrophoresis, and multi-locus sequence typing of Campylobacter coli in swine before, during, and after the slaughter process

The objective of this study was to determine persistence of clonal strains from farm to retail by assessing the clonal relatedness of Campylobacter coli isolated on farm, peri-harvest, and at processing from 11 individually identified pigs. Phenotypic (antimicrobial susceptibility) and genotypic (pulsed field gel electrophoresis [PFGE] and multi-locus sequence typing [MLST]) characterization of isolates was conducted. There was high genetic diversity of Campylobacter isolates from on-farm fecal samples. Campylobacter isolates from farm, post-evisceration, hide, and carcass samples showed similar phenotypes and belonged to the same genotypic clusters based on PFGE and sequence types (STs) based on MLST. Five STs that have not been previously reported were identified (ST-4083, ST-4084, ST-4085, ST-4086, ST-4087). Despite high genotypic diversity of C. coli on farm, retail meat products were consistently contaminated with isolates of the same STs, particularly ST854 and ST1056, as isolates collected from previous stages confirming persistence of strains from pre- to post-harvest.

Antibiotic susceptibility of Salmonella, Campylobacter coli, and Campylobacter jejuni isolated from Northern German fattening pigs

This study was conducted to assess the antimicrobial susceptibility rate of Salmonella and Campylobacter spp. isolated from Northern German fattening pigs. From 540 lymph node samples, 16 Salmonella Typhimurium, 1 Salmonella Brandenburg, 37 Campylobacter coli, and 11 Campylobacter jejuni strains were isolated. Antibiotic susceptibility testing was carried out by the broth dilution method. The 14 tested antibiotics for Salmonella were ampicillin, cefotaxime, ceftazidime, chloramphenicol, ciprofloxacin, colistin, florfenicol, gentamicin, kanamycin, nalidixic acid, streptomycin, sulfamethoxazole, tetracycline, and trimethoprim. The eight tested antibiotics for Campylobacter spp. were ampicillin, ampicillin-sulbactam (2:1), ciprofloxacin, erythromycin, gentamicin, nalidixic acid, sulfamethoxazole-trimethoprim (1:19), and tetracycline. In total, 93.7% (n = 16) of Salmonella Typhimurium, 75.7% (n = 37) of C. coli, and 54.5% (n = 11) of C. jejuni isolates were resistant to at least one of the tested antibiotics. Multiresistance to three antibiotics was observed in 75% of Salmonella Typhimurium, 16.2% of C. coli, and 0% of C. jejuni isolates. Pansusceptibility was detected in 6.3% of Salmonella Typhimurium, 24.3% of C. coli, and 45.5% of C. jejuni isolates. Multiresistance is defined as resistance to three or more antibiotics, and pansusceptibility is defined as not having resistance to any antibiotic. Regarding drugs of last resort--cefotaxime, ciprofloxacin, and nalidixic acid--resistance was not common among Salmonella (6.3%). The resistance rate of Campylobacter spp. to last-resort drugs--erythromycin, ciprofloxacin, and nalidixic acid--varied between species. The observed trend was not statistically significant. No C. coli isolates and few C. jejuni isolates (9.1%) were resistant to erythromycin. In contrast to C. jejuni, the C. coli isolates were more likely to be resistant to ciprofloxacin (9.1 and 18.9%, respectively) and nalidixic acid (0 and 13.5%, respectively). The same phenomenon was detected for tetracycline (27.3 and 62.2%, respectively), sulfamethoxazole (9.1 and 43.2%, respectively), and ampicillin (9.1 and 21.6%, respectively).

Campylobacter coli isolates from Finnish farrowing farms using aminopenicillins: high prevalence of bla(OXA-61) and β-lactamase production, but low MIC values

Antimicrobial treatment of animals may select resistance in Campylobacter to antimicrobial agents belonging to several classes of compounds. We investigated the effect of widely used aminopenicillin therapy on the minimum inhibitory concentration (MIC) levels in porcine Campylobacter coli isolates and investigated the presence of a β-lactamase gene and β-lactamase production. Epidemiological cut-off values (ECOFFs) were applied to detect decreased susceptibility. Fifty-three isolates were obtained from aminopenicillin-treated (ampicillin or amoxicillin) sows and piglets during and up to 3 weeks post-treatment. All isolates had ampicillin MICs below the ECOFF (≤ 8 μg/mL). An additional 63 isolates were sampled before treatment or from other untreated sows and piglets. Of these isolates, four had ampicillin MICs above the ECOFF. All ciprofloxacin MICs were below the ECOFF (≤ 1 μg/mL), except for three isolates from untreated sows and four isolates after aminopenicillin therapy. One isolate originating from an untreated sow had an erythromycin MIC above the ECOFF (> 16 μg/mL). None of the isolates had MICs above the ECOFFs for two or three studied antimicrobials simultaneously. Of the 116 C. coli isolates, 90 (77.6%) isolates carried the bla(OXA-61) β-lactamase gene, and 63 (70.0%) of those produced β-lactamase. The isolates producing β-lactamase had higher ampicillin MICs than those without the bla(OXA-61) gene and production of β-lactamase. Proportion of the bla(OXA-61)-positive C. coli isolates was similar among untreated animals or during and after the treatment. In conclusion, C. coli isolates did not acquire high ampicillin MICs even though aminopenicillins were administered at therapeutic levels for several days. The bla(OXA-61) gene and production of β-lactamase increased ampicillin MICs in C. coli, but the values remained mainly under the ECOFF. We also demonstrated that aminopenicillin therapy did not select simultaneously resistance to the major antimicrobials used in human therapy against campylobacteriosis (i.e., erythromycin and ciprofloxacin).

Effect of thymol or diphenyliodonium chloride on performance, gut fermentation characteristics, and campylobacter colonization in growing swine

Food producing animals can be reservoirs of Campylobacter, a leading bacterial cause of human foodborne illness. Campylobacter spp. utilize amino acids as major carbon and energy substrates, a process that can be inhibited by thymol and diphenyliodonium chloride (DIC). To determine the effect of these potential additives on feed intake, live weight gain, and gut Campylobacter levels, growing pigs were fed standard grower diets supplemented with or without 0.0067 or 0.0201% thymol or 0.00014 or 0.00042% DIC in a replicated study design. Diets were offered twice daily for 7 days, during which time daily feed intake (mean ± SEM, 2.39 ± 0.06 kg day(-1)) and daily gain (0.62 ± 0.04 kg day(-1)) were unaffected (P > 0.05) by treatment. Pigs treated with DIC but not thymol tended to have lower rectal Campylobacter levels (P ∼ 0.07) (5.2 versus 4.2 and 4.4 log CFU g(-1) rectal contents for controls and 0.00014% DIC and 0.00042% DIC, respectively; SEM ∼ 0.26). However, DIC or thymol treatments did not affect (P > 0.05) ileal or cecal Campylobacter (1.6 ± 0.17 and 4.5 ± 0.26 log CFU g(-1), respectively), cecal total culturable anaerobes (9.8 ± 0.10 log CFU g(-1)), or accumulations of major fermentation end products within collected gut contents. These results suggest that thymol and DIC were appreciably absorbed, degraded, or otherwise made unavailable in the proximal alimentary tract and that encapsulation technologies will likely be needed to deliver effective concentrations of these compounds to the lower gut to achieve in vivo reductions of Campylobacter.

Longitudinal study of the persistence of antimicrobial-resistant campylobacter strains in distinct Swine production systems on farms, at slaughter, and in the environment

The objectives of this study were to compare and characterize the prevalence of antimicrobial-resistant (AR) Campylobacter in conventional and antimicrobial-free (ABF) production systems on farms, at slaughter, and in the environment. Fecal and environmental samples were collected from ABF farms (pigs, 1,239; environment, 797) and conventional farms (pigs, 1,650; environment, 1,325). At slaughter, we collected samples from carcasses, including postevisceration swabs, postchill swabs, and mesenteric lymph nodes from ABF systems (postevisceration swabs, 182; postchill swabs, 199; mesenteric lymph nodes, 184) and conventional systems (postevisceration swabs, 272; postchill swabs, 271; mesenteric lymph nodes, 255) at separate processing facilities. We also sampled the processing plant environment, including truck and lairage floor swab samples (ABF, 115; conventional, 90). Overall, a total of 2,908 Campylobacter isolates, including Campylobacter coli (farm, 2,557, 99.8%; slaughter, 341, 98.3%) and Campylobacter jejuni (farm, 4, 0.2%; slaughter, 6, 1.7%), were isolated in the study. There was no significant difference in the prevalence of Campylobacter between ABF and conventionally raised pigs (farrowing, P = 0.20; nursery, P = 0.06; finishing, P = 0.24) and the environment (P = 0.37). At slaughter, Campylobacter was isolated from all of the stages, including postchill. The highest frequencies of resistance were exhibited against tetracycline (ABF, 48.2%; conventional, 88.3%). Ciprofloxacin-resistant C. coli isolates were observed in conventionally raised (17.1%) and ABF (1.2%) pigs (P = 0.11). Antimicrobial use data from conventional farms indicated significant associations between oxytetracycline use and tetracycline resistance in the nursery pigs (P = 0.01), between tiamulin exposure and azithromycin and erythromycin resistance in nursery (P < 0.01) and finishing (P < 0.01) pigs, and between enrofloxacin exposure and ciprofloxacin and nalidixic acid resistance in farrowing (P < 0.01) and nursery (P < 0.01) pigs. Identical antimicrobial resistance profiles were observed in the pigs and their environments on farms and at slaughter. In summary, our results highlight the persistence and dissemination of AR Campylobacter from farm to slaughter in ABF and conventionally raised pigs and their environments.

Campylobacter jejuni infection and virulence-associated genes in children with moderate to severe diarrhoea admitted to emergency rooms in northeastern Brazil

Campylobacter is an important cause of foodborne gastroenteritis. We determined the occurrence of Campylobacter jejuni and Campylobacter coli, using culture-based methods and PCRs targeting virulence-associated genes (VAGs) among children aged ≤14 years who were treated for diarrhoea at emergency rooms in northeastern Brazil. Genomic DNA was extracted directly from stool samples collected from 366 children. A questionnaire was also applied to qualify the clinical conditions presented by each child at the time of admission. C. jejuni and C. coli were detected in 16.4 % (60/366) and 1.4 % (5/366) of the diarrhoeal samples, respectively, by PCR, a much higher proportion than that detected by conventional methods. C. jejuni VAGs were detected in the following proportions of hipO-positive samples: ciaB, 95 % (57/60); dnaJ, 86.7 % (52/60); racR, 98.3 % (59/60); flaA, 80 % (48/60); pldA, 45 % (27/60); cdtABC, 95 % (57/60); and pVir 0 % (0/60). Particular symptoms, such as blood in faeces, vomiting, fever, and/or abdominal pain, were not associated with detection of C. jejuni nor were they associated with any particular VAG or combination of VAGs (P>0.05). C. jejuni and its VAGs were detected in a substantial proportion of the children admitted. Further efforts shall be directed towards elucidating whether these genetic factors or their expressed proteins play a role in Campylobacter pathogenesis.

Influence of production system on the rate of onset of Campylobacter colonization in chicken flocks reared extensively in the United Kingdom

1. Because thermophilic Campylobacter spp. are common in chicken flocks reared extensively, cross-sectional and longitudinal studies were carried out on organic and free-range farms to determine the onset of colonisation (lag phase) and likely sources of flock infection. 2. For 14 organic and 14 free range flocks, there was a difference in lag phases, with the former being colonized at a mean of 14·1 d in comparison with 31·6 d for the latter. Whereas most free-range flocks became colonized when released on to pasture, those reared organically were usually colonized at the housed brooding stage. 3. Further study of organic flocks on three farms over 7 successive crop cycles confirmed that colonisation was strongly influenced by the prevailing husbandry conditions and was not a consequence of the length of the rearing period. 4. Molecular epidemiological investigations on a farm showing the shortest lag phase, using PFGE typing with two different restriction enzymes (SmaI and KpnI) and flaA SVR sequence typing, revealed that potential sources of colonisation for organic chickens were already present on the farm at the time of chick placement. Such sources included the ante area of the brooding house, surrounding pasture and other livestock being kept on the farm. 5. Overall, the study demonstrated that, under UK conditions, the prevalence of colonisation was greater in extensive flocks (95-100%) than it was for conventional broilers (55%), similar to the situation in other countries, but all three management systems showed comparable levels of caecal carriage in positive birds (log(10)/g 6·2-6·7).

Evolution of an agriculture-associated disease causing Campylobacter coli clade: evidence from national surveillance data in Scotland

The common zoonotic pathogen Campylobacter coli is an important cause of bacterial gastroenteritis worldwide but its evolution is incompletely understood. Using multilocus sequence type (MLST) data of 7 housekeeping genes from a national survey of Campylobacter in Scotland (2005/6), and a combined population genetic-phylogenetics approach, we investigated the evolutionary history of C. coli. Genealogical reconstruction of isolates from clinical infection, farm animals and the environment, revealed a three-clade genetic structure. The majority of farm animal, and all disease causing genotypes belonged to a single clade (clade 1) which had comparatively low synonymous sequence diversity, little deep branching genetic structure, and a higher number of shared alleles providing evidence of recent clonal decent. Calibration of the rate of molecular evolution, based on within-species genetic variation, estimated a more rapid rate of evolution than in traditional estimates. This placed the divergence of the clades at less than 2500 years ago, consistent with the introduction of an agricultural niche having had an effect upon the evolution of the C. coli clades. Attribution of clinical isolate genotypes to source, using an asymmetric island model, confirmed that strains from chicken and ruminants, and not pigs or turkeys, are the principal source of human C. coli infection. Taken together these analyses are consistent with an evolutionary scenario describing the emergence of agriculture-associated C. coli lineage that is an important human pathogen.