Source attribution of human campylobacteriosis at the point of exposure by combining comparative exposure assessment and subtype comparison based on comparative genomic fingerprinting

A Review on Microbiological Source Attribution Methods of Human Salmonellosis: From Subtyping to Whole-Genome Sequencing

Salmonella is one of the main causes of human foodborne illness. It is endemic worldwide, with different animals and animal-based food products as reservoirs and vehicles of infection. Identifying animal reservoirs and potential transmission pathways of Salmonella is essential for prevention and control. There are many approaches for source attribution, each using different statistical models and data streams. Some aim to identify the animal reservoir, while others aim to determine the point at which exposure occurred. With the advance of whole-genome sequencing (WGS) technologies, new source attribution models will greatly benefit from the discriminating power gained with WGS. This review discusses some key source attribution methods and their mathematical and statistical tools. We also highlight recent studies utilizing WGS for source attribution and discuss open questions and challenges in developing new WGS methods. We aim to provide a better understanding of the current state of these methodologies with application to Salmonella and other foodborne pathogens that are common sources of illness in the poultry and human sectors.

Surveillance of antimicrobial resistance in Escherichia coli, Salmonella, and Campylobacter recovered from laying hens, their environment and products in Canada indicated a stable level of resistance to critically important antimicrobials, in varying time periods between 2007 and 2021

The study objective was to determine the occurrence and antimicrobial resistance (AMR) attributes of select foodborne bacteria recovered from egg-producing (layer) chickens between 2007 and 2021 using different sample matrices (Study 1: liquid whole eggs, Study 2: spent hen cecal samples, Study 3: environmental sponge swabs and fecal samples from layer chicken barns, and Study 4: fecal samples from layer chicken barns). Samples from each study were submitted for the culture of Escherichia coli and Salmonella. In addition, samples from layer chicken barns were submitted for the culture of Campylobacter. Isolates were tested by microbroth dilution and interpreted using both clinical breakpoints and epidemiological cut-offs (ECOFFs). The ECOFFs were applied to detect non-wild type (NWT) strains. The proportion of resistant, NWT, and distribution of minimum inhibitory concentrations (MIC) were assessed. Ceftriaxone resistance was detected at a low-level in E. coli (< 2 %, all studies) and Salmonella (4.3 %, Study 2). Very low-level ciprofloxacin resistance was detected in E. coli (<1 %, Study 1) but a slightly elevated ciprofloxacin NWT E. coli (1 % to 6 %) observed. Only the farm fecal samples in Studies 2 and 3 were tested for Campylobacter as part of its study design, and moderate level ciprofloxacin resistance (<15 %) was observed. The MIC distribution patterns were similar across the organisms tested/studies and no substantial shifts in the distributions were detected. This analysis demonstrated that resistance to very important antimicrobials in bacteria from layers in Canada remains low, however, the detection of ciprofloxacin-resistant Campylobacter and the implications of this observation to the safety of egg products, and the role of laying flocks (i.e., as reservoir for resistant organisms) needs to be investigated.

Comparison of Source Attribution Methodologies for Human Campylobacteriosis

Campylobacter spp. are the most common cause of bacterial gastrointestinal infection in humans both in Denmark and worldwide. Studies have found microbial subtyping to be a powerful tool for source attribution, but comparisons of different methodologies are limited. In this study, we compare three source attribution approaches (Machine Learning, Network Analysis, and Bayesian modeling) using three types of whole genome sequences (WGS) data inputs (cgMLST, 5-Mers and 7-Mers). We predicted and compared the sources of human campylobacteriosis cases in Denmark. Using 7mer as an input feature provided the best model performance. The network analysis algorithm had a CSC value of 78.99% and an F1-score value of 67%, while the machine-learning algorithm showed the highest accuracy (98%). The models attributed between 965 and all of the 1224 human cases to a source (network applying 5mer and machine learning applying 7mer, respectively). Chicken from Denmark was the primary source of human campylobacteriosis with an average percentage probability of attribution of 45.8% to 65.4%, representing Bayesian with 7mer and machine learning with cgMLST, respectively. Our results indicate that the different source attribution methodologies based on WGS have great potential for the surveillance and source tracking of Campylobacter. The results of such models may support decision makers to prioritize and target interventions.

Molecular Epidemiological Evidence Implicates Cattle as a Primary Reservoir of Campylobacter jejuni Infecting People via Contaminated Chickens

The study aimed to determine the relative contribution of cattle to the burden of illness in a model agroecosystem with high rates of human campylobacteriosis (≥ 115 cases/100 K), and high densities of cattle, including large numbers of cattle housed in confined feeding operations (i.e., in southwestern Alberta, Canada). To accomplish this, a large-scale molecular epidemiological analysis of Campylobacter jejuni circulating within the study location was completed. In excess of 8000 isolates of C. jejuni from people (n = 2548 isolates), chickens (n = 1849 isolates), cattle (n = 2921 isolates), and water (n = 771 isolates) were subtyped. In contrast to previous studies, the source attribution estimates of clinical cases attributable to cattle vastly exceeded those attributed to chicken (i.e., three- to six-fold). Moreover, cattle were often colonized by C. jejuni (51%) and shed the bacterium in their feces. A large proportion of study isolates were found in subtypes primarily associated with cattle (46%), including subtypes infecting people and those associated with chickens (19%). The implication of cattle as a primary amplifying reservoir of C. jejuni subtypes in circulation in the study location is supported by the strong cattle association with subtypes that were found in chickens and in people, a lack of evidence indicating the foodborne transmission of C. jejuni from beef and dairy, and the large number of cattle and the substantial quantities of untreated manure containing C. jejuni cells. Importantly, the evidence implicated cattle as a source of C. jejuni infecting people through a transmission pathway from cattle to people via the consumption of chicken. This has implications for reducing the burden of campylobacteriosis in the study location and elsewhere.

Campylobacter Gastroenteritis Among Under-Five Children in Southwest Ethiopia

Background

Under-five children are at an increased risk for foodborne illnesses because of the ingenuousness of their immune system. Although Campylobacter species are one of the bacterial etiologies of gastroenteritis, Campylobacter gastroenteritis among under-five children is not well considered in Ethiopia. Therefore, this study aimed at exploring the prevalence, associated risk factors, and antibiotic susceptibility patterns of Campylobacter species among under-five children with diarrhea.

Methods

The institution-based cross-sectional study was conducted among under-five children with diarrhea at Jimma Medical Center, southwestern Ethiopia from January 5 to April 21, 2020. Stool samples were collected and inoculated into Campylobacter agar medium. Isolation and identification were done using standard bacteriological techniques. Antibiotic susceptibility testing was conducted on Mueller-Hinton agar supplemented with 10% sheep blood using disk diffusion techniques. Bivariate and multivariate logistic regressions were used to assess the associated risk factors.

Results

A total of 214 under-five children were enrolled. The prevalence of Campylobacter infection was 8.9%. Absence of caretakers' handwashing before preparation of food [AOR = 3.7, 95% CI: (1.2-10.8)], direct contact with domestic animals [AOR = 3.6, 95% CI: (1.0-12.7)], and consumption of raw dairy products [AOR = 4.5, 95% CI: (1.4-13.9)] are the factors associated with Campylobacter infection. Some Campylobacter species were found to be resistant to most available antibiotics.

Conclusion

The magnitude of Campylobacter gastroenteritis indicates the need for routine isolation and identification of Campylobacter species from all under-five children clinically diagnosed with diarrhea. Species that are resistant to the drug of choice for Campylobacteriosis are also emerging. Health education on the importance of pasteurization of milk and caretakers' handwashing can mitigate the transmission. Mechanism of handling of domestic animals should be considered to reduce transmission of zoonotic diseases like Campylobacteriosis.

Source Attribution of Human Campylobacteriosis Using Whole-Genome Sequencing Data and Network Analysis

Campylobacter spp. are a leading and increasing cause of gastrointestinal infections worldwide. Source attribution, which apportions human infection cases to different animal species and food reservoirs, has been instrumental in control- and evidence-based intervention efforts. The rapid increase in whole-genome sequencing data provides an opportunity for higher-resolution source attribution models. Important challenges, including the high dimension and complex structure of WGS data, have inspired concerted research efforts to develop new models. We propose network analysis models as an accurate, high-resolution source attribution approach for the sources of human campylobacteriosis. A weighted network analysis approach was used in this study for source attribution comparing different WGS data inputs. The compared model inputs consisted of cgMLST and wgMLST distance matrices from 717 human and 717 animal isolates from cattle, chickens, dogs, ducks, pigs and turkeys. SNP distance matrices from 720 human and 720 animal isolates were also used. The data were collected from 2015 to 2017 in Denmark, with the animal sources consisting of domestic and imports from 7 European countries. Clusters consisted of network nodes representing respective genomes and links representing distances between genomes. Based on the results, animal sources were the main driving factor for cluster formation, followed by type of species and sampling year. The coherence source clustering (CSC) values based on animal sources were 78%, 81% and 78% for cgMLST, wgMLST and SNP, respectively. The CSC values based on Campylobacter species were 78%, 79% and 69% for cgMLST, wgMLST and SNP, respectively. Including human isolates in the network resulted in 88%, 77% and 88% of the total human isolates being clustered with the different animal sources for cgMLST, wgMLST and SNP, respectively. Between 12% and 23% of human isolates were not attributed to any animal source. Most of the human genomes were attributed to chickens from Denmark, with an average attribution percentage of 52.8%, 52.2% and 51.2% for cgMLST, wgMLST and SNP distance matrices respectively, while ducks from Denmark showed the least attribution of 0% for all three distance matrices. The best-performing model was the one using wgMLST distance matrix as input data, which had a CSC value of 81%. Results from our study show that the weighted network-based approach for source attribution is reliable and can be used as an alternative method for source attribution considering the high performance of the model. The model is also robust across the different Campylobacter species, animal sources and WGS data types used as input.

Phylogenetic Analysis Reveals Source Attribution Patterns for Campylobacter spp. in Tennessee and Pennsylvania

Campylobacteriosis is the most common bacterial foodborne illness in the United States and is frequently associated with foods of animal origin. The goals of this study were to compare clinical and non-clinical Campylobacter populations from Tennessee (TN) and Pennsylvania (PA), use phylogenetic relatedness to assess source attribution patterns, and identify potential outbreak clusters. Campylobacter isolates studied (n = 3080) included TN clinical isolates collected and sequenced for routine surveillance, PA clinical isolates collected from patients at the University of Pennsylvania Health System facilities, and non-clinical isolates from both states for which sequencing reads were available on NCBI. Phylogenetic analyses were conducted to categorize isolates into species groups and determine the population structure of each species. Most isolates were C. jejuni (n = 2132, 69.2%) and C. coli (n = 921, 29.9%), while the remaining were C. lari (0.4%), C. upsaliensis (0.3%), and C. fetus (0.1%). The C. jejuni group consisted of three clades; most non-clinical isolates were of poultry (62.7%) or cattle (35.8%) origin, and 59.7 and 16.5% of clinical isolates were in subclades associated with poultry or cattle, respectively. The C. coli isolates grouped into two clades; most non-clinical isolates were from poultry (61.2%) or swine (29.0%) sources, and 74.5, 9.2, and 6.1% of clinical isolates were in subclades associated with poultry, cattle, or swine, respectively. Based on genomic similarity, we identified 42 C. jejuni and one C. coli potential outbreak clusters. The C. jejuni clusters contained 188 clinical isolates, 19.6% of the total C. jejuni clinical isolates, suggesting that a larger proportion of campylobacteriosis may be associated with outbreaks than previously determined.

A systematic review and meta-analysis of the efficacy of processing stages and interventions for controlling Campylobacter contamination during broiler chicken processing

Systematic review and meta-analysis were conducted to quantify the effects of processing stages and interventions on the prevalence and concentration of Campylobacter on broiler carcasses. To comprehensively capture relevant evidence, six databases were searched using the keywords "Campylobacter" and "broiler chicken." The literature search yielded 10,450 unique citations, and after applying predetermined inclusion and exclusion criteria, 72 and 53 relevant citations were included in meta-analyses for processing stages and interventions, respectively. As the two primary outcomes, log reduction and prevalence changes were estimated for each stage or intervention using a random-effects meta-analysis approach whenever possible. The outcome-level quality assessment was conducted following the Grading of Recommendations Assessment, Development, and Evaluation (GRADE) approach. The analysis revealed that scalding and chilling majorly reduces the prevalence and concentration of Campylobacter. Immersion chilling reduces the concentration regardless of chemical additives, but its effect on prevalence is not conclusive. The effects of carcass washing applications remain uncertain due to the inconsistency and imprecision of both outcomes. Defeathering and evisceration were identified as stages that can increase both prevalence and concentration. Both chemical and physical processing interventions provide limited efficacy in concentration and prevalence reduction. Major limitations of the review were inconsistency and imprecision at the outcome level and reporting issues and data gaps at the study level. The results are expected to inform quantitative microbial risk assessment model development and support evidence-based decision-making.

Bacteriophage Therapy to Reduce Colonization of Campylobacter jejuni in Broiler Chickens before Slaughter

Campylobacteriosis is the most commonly reported gastrointestinal disease in humans. Campybacter jejuni is the main cause of the infection, and bacterial colonization in broiler chickens is widespread and difficult to prevent, leading to high risk of occurrence in broiler meat. Phage therapy represents an alternative strategy to control Campylobacter in poultry. The aim of this work was to assess the efficacy of two field-isolated bacteriophages against experimental infections with an anti-microbial resistant (AMR) Campylobacter jejuni strain. A two-step phage application was tested according to a specific combination between chickens’ rearing time and specific multiplicities of infections (MOIs), in order to reduce the Campylobacter load in the animals at slaughtering and to limit the development of phage-resistant mutants. In particular, 75 broilers were divided into three groups (A, B and C), and phages were administered to animals of groups B and C at day 38 (Φ 16-izsam) and 39 (Φ 7-izsam) at MOI 0.1 (group B) and 1 (group C). All broilers were euthanized at day 40, and Campylobacter jejuni was enumerated in cecal contents. Reductions in Campylobacter counts were statistically significant in both group B (1 log₁₀ colony forming units (cfu)/gram (gr)) and group C (2 log₁₀ cfu/gr), compared to the control group. Our findings provide evidence about the ability of phage therapy to reduce the Campylobacter load in poultry before slaughtering, also associated with anti-microbial resistance pattern.

Monitoring of Antimicrobial Resistance to Aminoglycosides and Macrolides in Campylobacter coli and Campylobacter jejuni From Healthy Livestock in Spain (2002-2018)

Antimicrobial resistance (AMR) in Campylobacter spp. (Campylobacter coli and Campylobacter jejuni) is a concern due to its importance in public health, particularly when it involves aminoglycosides and macrolides, drugs of choice for treatment of human cases. Co-resistance to these two antimicrobial classes involves transfer of genetic elements and/or acquisition of mutations in different genetic loci, which can in turn spread through vertical or horizontal gene transfer (HGT) phenomena, with each route having different potential implications. This study aimed at evaluating the association between the presence of phenotypic resistance to these two antimicrobial classes in C. coli and C. jejuni recovered from livestock at slaughterhouses in Spain (as part of the AMR surveillance program), and at assessing the genetic heterogeneity between resistant and susceptible isolates by analysing the "short variable region" (SVR) of the flaA gene. Over the 2002-2018 period, antimicrobial susceptibility test results from 10,965 Campylobacter isolates retrieved from fecal samples of broilers, turkeys, pigs and cattle were collected to compare the proportion of resistant isolates and the Minimum Inhibitory Concentrations (MICs) against six antimicrobials including gentamicin (GEN), streptomycin (STR), and erythromycin (ERY). AMR-associated genes were determined for a group of 51 isolates subjected to whole genome sequencing, and the flaA SVR of a subset of 168 isolates from all hosts with different resistotypes was used to build a Neighbor-Joining-based phylogenetic tree and assess the existence of groups by means of "relative synonymous codon usage" (RSCU) analysis. The proportion of antimicrobial resistant isolates to both, aminoglycosides and macrolides, varied widely for C. coli (7-91%) and less for C. jejuni (all hosts 0-11%). Across hosts, these proportions were 7-56% in poultry, 12-82% in cattle, and 22-91% in pigs for C. coli and 0-8% in poultry and 1-11% in cattle for C. jejuni. Comparison of the MIC distributions revealed significant host-specific differences only for ERY in C. jejuni (p = 0.032). A significant association in the simultaneous presentation of AMR to both antimicrobial classes was observed across hosts/bacterial species. The flaA gene analysis showed clustering of isolates sharing resistotype and to a lesser degree bacterial species and host. Several resistance markers associated with resistance to aminoglycosides and macrolides were found among the sequenced isolates. The consistent association between the simultaneous presentation of AMR to aminoglycosides and macrolides in all hosts could be due to the persistence of strains and/or resistance mechanisms in Campylobacter populations in livestock over time. Further studies based on whole genome sequencing are needed to assess the epidemiological links between hosts and bacterial strains.

A pilot study revealing host-associated genetic signatures for source attribution of sporadic Campylobacter jejuni infection in Egypt

Campylobacter jejuni (C. jejuni), is considered among the most common bacterial causes of human bacterial gastroenteritis worldwide. The epidemiology and the transmission dynamics of campylobacteriosis in Egypt remain poorly defined due to the limited use of high-resolution typing methods. In this pilot study, we evaluated the discriminatory power of multiple typing 'gene-by-gene based' techniques to characterize C. jejuni obtained from different sources and estimate the relative contribution of different potential sources of C. jejuni infection in Egypt. Whole genome sequencing (WGS) was performed on 90 C. jejuni isolates recovered from clinical samples, retail chicken, and dairy products in Egypt from 2017 to 2018. Comparative genomic analysis was performed using conventional seven-locus multilocus sequence typing (MLST), ribosomal MLST (rMLST), core genome MLST (cgMLST), allelic variation in 15 host-segregating (HS) markers, and comparative genomic fingerprinting (CGF40). The probabilistic source attribution was performed via STRUCTURE software using MLST, CGF40, cgMLST and allelic variation in HS markers. Comparison of the discriminatory power of the aforementioned genotyping methods revealed cgMLST to be the most discriminative method, followed by HS markers. The source attribution analysis showed the role of retail chicken as a source of infection among clinical cases in Egypt when HS and cgMLST were used (64.2% and 52.3% of clinical isolates were assigned to this source, respectively). Interestingly, the cattle reservoir was also identified as a contributor to C. jejuni infection in Egypt; 35.8% and 47.7% of clinical isolates were assigned to this source by HS and cgMLST, respectively. Here, we provided evidence of the importance of using WGS typing methods to facilitate source tracking of C. jejuni. Our findings suggest the importance of non-poultry sources, together with the previously reported role of retail chicken in human campylobacteriosis in Egypt that can provide insights to inform national control measures.

Analysis of Campylobacter jejuni Subtype Distribution in the Chicken Broiler Production Continuum: a Longitudinal Examination To Identify Primary Contamination Points

Significant knowledge gaps exist in our understanding of Campylobacter jejuni contamination of the poultry production continuum. Microbiological surveillance and genotypic characterization were undertaken on C. jejuni isolates longitudinally recovered from three poultry farms (weekly samples), the abattoir at which birds were processed, and at retail over a 542-day period in southwestern Alberta, Canada, as a model location. Subtypes were compared to concurrent isolates from diarrheic humans living in the study region. Barn outbreaks in broiler chickens occurred infrequently. Subtypes from colonized birds, including clinically relevant subtypes of C. jejuni, were recovered within barns and from subsequent production stages. When C. jejuni was detected in barns, most birds rapidly became colonized by a limited number of subtypes late in the cycle. However, the diversity of subtypes recovered from birds in the abattoir increased substantially. Moreover, birds deemed free of C. jejuni upon exit from the barn became contaminated within the abattoir environment, and a high prevalence of meat at retail was contaminated with C. jejuni, including subtypes that had not been previously observed in the barns. The observed increase in prevalence of contamination and diversity of C. jejuni subtypes along the chicken production continuum indicates that birds from a relatively small number of barns contaminate transport trucks and the abattoir with C. jejuni strains, which are collectively transferred to poultry within the abattoir and conveyed to and persist on retail products. We conclude that the abattoir was the primary contamination point of poultry by C. jejuni but only a subset of subtypes were a high risk to human beings.IMPORTANCE The longitudinal examination of Campylobacter jejuni subtypes throughout the broiler production continuum is required to determine transmission mechanisms and to identify potential reservoirs and the foodborne risk posed. We showed that a limited number of C. jejuni subtypes are responsible for infrequent outbreaks in broilers within production barns and that colonized birds from a small number of farms are introduced into the abattoir where a high prevalence of carcasses are subsequently contaminated with a diversity of subtypes, which are transferred onto poultry in retail settings. However, only a subset of strains on poultry was determined to be clinically relevant. The study findings showed that resolving C. jejuni at the subtype level is important to ascertain health risks, and the knowledge obtained in the study provides information to mitigate clinically relevant subtypes to reduce the burden of campylobacteriosis.

The Data Behind Risk Analysis of Campylobacter Jejuni and Campylobacter Coli Infections

Campylobacter jejuni and Campylobacter coli are major causes of food-borne enteritis in humans. Poultry meat is known to be responsible for a large proportion of cases of human campylobacteriosis. However, other food-borne, environmental and animal sources are frequently associated with the disease in humans as well. Human campylobacteriosis causes gastroenteritis that in most cases is self-limiting. Nevertheless, the burden of the disease is relatively large compared with other food-borne diseases, which is mostly due to rare but long-lasting symptoms related to immunological sequelae. In order to pave the way to improved surveillance and control of human campylobacteriosis, we review here the data that is typically used for risk analysis to quantify the risk and disease burden, identify specific surveillance strategies and assist in choosing the most effective control strategies. Such data are mostly collected from the literature, and their nature is discussed here, for each of the three processes that are essential for a complete risk analysis procedure: risk assessment, risk management and risk communication. Of these, the first, risk assessment, is most dependent on data, and this process is subdivided into the steps of hazard identification, hazard characterization, exposure assessment and risk characterization. For each of these steps of risk assessment, information from published material that is typically collected will be summarized here. In addition, surveillance data are highly valuable for risk assessments. Different surveillance systems are employed in different countries, which can make international comparison of data challenging. Risk analysis typically results in targeted control strategies, and these again differ between countries. The applied control strategies are as yet not sufficient to eradicate human campylobacteriosis. The surveillance tools of Campylobacter in humans and exposure sources in place in different countries are briefly reviewed to better understand the Campylobacter dynamics and guide control strategies. Finally, the available control measures on different risk factors and exposure sources are presented.

Antimicrobial Resistance of Campylobacter in Broiler Chicken Along the Food Chain in Canada

Antimicrobial resistance (AMR) is a major public health threat worldwide. The main objective of this study was to compare AMR in Campylobacter from broiler chickens raised on Canadian farms and their products in different geographical regions of Canada. To do this, antimicrobial susceptibility results from isolates of Campylobacter recovered from a national microbiological baseline study conducted in federally registered establishments and in the retail marketplace were analyzed. Among 1460 isolates tested, 774 (53%) were resistant to at least one antimicrobial, with a predominance of three profiles: tetracycline (39%), quinolone-tetracycline (6.6%), and quinolones only (3.5%). The results showed no significant difference in the frequency of resistant profiles (p ≥ 0.05) among the isolates originating from different points in the food processing chain at slaughterhouses and in retail establishments. This suggests that AMR observed in Campylobacter isolates from raw chicken at retail originated further upstream in the system. A difference in the frequency of certain resistance profiles was observed between the regions of Canada. For instance, in British Columbia, there was more resistance to quinolones, while in Ontario and Quebec, Campylobacter isolates were more resistant to tetracyclines, macrolides, ketolides, and lincosamides. Comparison of AMR data from this study with those from the Canadian Integrated Program for Antimicrobial Resistance Surveillance (CIPARS) did not show any significant difference and provides evidence that CIPARS produces nationally representative resistance results.

Core Genome Multilocus Sequence Typing for Food Animal Source Attribution of Human Campylobacter jejuni Infections

Campylobacter jejuni is a major foodborne pathogen and common cause of bacterial enteritis worldwide. A total of 622 C. jejuni isolates recovered from food animals and retail meats in the United States through the National Antimicrobial Resistance Monitoring System between 2013 and 2017 were sequenced using an Illumina MiSeq. Sequences were combined with WGS data of 222 human isolates downloaded from NCBI and analyzed by core genome multilocus sequence typing (cgMLST) and traditional MLST. cgMLST allelic difference (AD) thresholds of 0, 5, 10, 25, 50, 100 and 200 identified 828, 734, 652, 543, 422, 298 and 197 cgMLST types among the 844 isolates, respectively, and traditional MLST identified 174 ST. The cgMLST scheme allowing an AD of 200 (cgMLST₂₀₀) revealed strong correlation with MLST. cgMLST₂₀₀ showed 40.5% retail chicken isolates, 56.5% swine, 77.4% dairy cattle and 78.9% beef cattle isolates shared cgMLST sequence type with human isolates. All ST-8 had the same cgMLST₂₀₀ type (cgMLST₂₀₀-12) and 74.3% of ST-8 and 75% cgMLST₂₀₀-12 were confirmed as sheep abortion virulence clones by PorA analysis. Twenty-nine acquired resistance genes, including 21 alleles of bla_OXA, tetO, aph(3′)-IIIa, ant(6)-Ia, aadE, aad9, aph(2′)-Ig, aph(2′)-Ih, sat4 plus mutations in gyrA, 23SrRNA and L22 were identified. Resistance genotypes were strongly linked with cgMLST₂₀₀ type for certain groups including 12/12 cgMLST₂₀₀-510 with the A103V substitution in L22 and 10/11 cgMLST₂₀₀-608 with the T86I GyrA substitution associated with macrolide and quinolone resistance, respectively. In summary, the cgMLST₂₀₀ threshold scheme combined with resistance genotype information could provide an excellent subtyping scheme for source attribution of human C. jejuni infections.

Prevalence, antibiotic resistance and genotypes of Campylobacter jejuni and Campylobacter coli isolated from chickens in Irbid governorate, Jordan

Campylobacter is the world's leading cause of bacterial gastroenteritis, causing nearly 9 million cases of food poisoning in Europe every year. Poultry is considered the main source of Campylobacter infection to humans. The objectives of the study were to determine occurrence of C. jejuni and C. coli in chickens, the antimicrobial resistance, genotypes, and relatedness of the isolates. A total of 177 chicken samples obtained from informal butcher shops (fresh), formal poultry slaughterhouses (refrigerated) and retail market (frozen) were analyzed. Isolation of Campylobacter spp. was conducted according to the ISO 10272-2006 method. Multiplex PCR was used for confirmation and identification of the isolates. The disk diffusion method was used to determine the antimicrobial resistance of the isolates and multilocus sequence typing was used for genotyping. The proportion of samples with Campylobacter spp. was 31.6% among all chicken samples (fresh and refrigerated 47.5%, frozen 0%) C. coli was isolated from 42.4% of chicken samples obtained from butcher shops and from 18.6% of samples obtained in formal slaughterhouses. C. jejuni was isolated from 17.0% of samples obtained in butcher shops and formal slaughterhouses. Campylobacter spp. was not isolated in frozen chicken samples. All tested isolates showed resistance toward ciprofloxacin and susceptibility toward imipenem and all of the isolates were multidrug resistant toward 5 or more antimicrobials. Three sequence types were identified among 10 C. coli isolates and seven sequence types were identified among 10 C. jejuni isolates. Among sequence types, chicken isolates shared similarities of both phenotypic and genetic levels.

Bacteriophages to Control Campylobacter in Commercially Farmed Broiler Chickens, in Australia

This study describes the development and use of bacteriophage cocktails to control Campylobacter in broiler chickens, in a commercial setting, in Queensland Australia, following the birds from farm to the processing plant. The components of the bacteriophage cocktails were selected to be effective against the maximum number of Campylobacter jejuni and Campylobacter coli isolates encountered on SE Queensland farms. Farms were identified that had suitable Campylobacter target populations and phage were undetectable 1 week prior to the intended treatment. Cocktails of phages were administered at 47 days of age. Groups of study birds were slaughtered the following day, on-farm, at the end of flock transport to the plant, and at processing (approximately 28 h post-treatment). On Farm A, the phage treatment significantly reduced Campylobacter levels in the ceca at the farm in the range of 1-3 log10 CFU/g (p = 0.007), compared to mock treated controls. However, individual birds sampled on farm (1/10) or following transport (2/10) exhibited high cecal Campylobacter counts with low phage titers, suggesting that treatment periods > 24 h may be required to ensure phage replication for effective biocontrol in vivo. At the time of the trial the control birds in Farm B were phage positive despite having been negative one week earlier. There was no significant difference in the cecal Campylobacter counts between the treatment and control groups following treatment but a fall of 1.7 log10 CFU/g was observed from that determined from birds collected the previous week (p = 0.0004). Campylobacter isolates from both farms retained sensitivity to the treatment phages. These trials demonstrated bacteriophages sourced from Queensland farms have the potential to reduce intestinal Campylobacter levels in market ready broiler chickens.

Prevalence of Campylobacter and Salmonella in African food animals and meat: A systematic review and meta-analysis

BACKGROUND

Campylobacter and Salmonella, particularly non-typhoidal Salmonella, are important bacterial enteric pathogens of humans which are often carried asymptomatically in animal reservoirs. Bacterial foodborne infections, including those derived from meat, are associated with illness and death globally but the burden is disproportionately high in Africa. Commercial meat production is increasing and intensifying in many African countries, creating opportunities and threats for food safety.

METHODS

Following Preferred Reporting Items for Systematic Reviews and Meta-analyses (PRISMA) guidelines, we searched six databases for English language studies published through June 2016, that reported Campylobacter or Salmonella carriage or infection prevalence in food animals and contamination prevalence in food animal products from African countries. A random effects meta-analysis and multivariable logistic regression were used to estimate the species-specific prevalence of Salmonella and Campylobacter and assess relationships between sample type and region and the detection or isolation of either pathogen.

RESULTS

Seventy-three studies reporting Campylobacter and 187 studies reporting Salmonella across 27 African countries were represented. Adjusted prevalence calculations estimate Campylobacter detection in 37.7% (95% CI 31.6-44.3) of 11,828 poultry samples; 24.6% (95% CI 18.0-32.7) of 1975 pig samples; 17.8% (95% CI 12.6-24.5) of 2907 goat samples; 12.6% (95% CI 8.4-18.5) of 2382 sheep samples; and 12.3% (95% CI 9.5-15.8) of 6545 cattle samples. Salmonella were detected in 13.9% (95% CI 11.7-16.4) of 25,430 poultry samples; 13.1% (95% CI 9.3-18.3) of 5467 pig samples; 9.3% (95% CI 7.2-12.1) of 2988 camel samples; 5.3% (95% CI 4.0-6.8) of 72,292 cattle samples; 4.8% (95% CI 3.6-6.3) of 11,335 sheep samples; and 3.4% (95% CI 2.2-5.2) of 4904 goat samples. 'External' samples (e.g. hide, feathers) were significantly more likely to be contaminated by both pathogens than 'gut' (e.g. faeces, cloaca) while meat and organs were significantly less likely to be contaminated than gut samples.

CONCLUSIONS

This study demonstrated widespread prevalence of Campylobacter species and Salmonella serovars in African food animals and meat, particularly in samples of poultry and pig origin. Source attribution studies could help ascertain which food animals are contributing to human campylobacteriosis and salmonellosis and direct potential food safety interventions.

MLST-based genetic relatedness of Campylobacter jejuni isolated from chickens and humans in Poland

Campylobacter jejuni infection is one of the most frequently reported foodborne bacterial diseases worldwide. The main transmission route of these microorganisms to humans is consumption of contaminated food, especially of chicken origin. The aim of this study was to analyze the genetic relatedness of C. jejuni from chicken sources (feces, carcasses, and meat) and from humans with diarrhea as well as to subtype the isolates to gain better insight into their population structure present in Poland. C. jejuni were genotyped using multilocus sequence typing (MLST) and sequence types (STs) were assigned in the MLST database. Among 602 isolates tested, a total of 121 different STs, including 70 (57.9%) unique to the isolates' origin, and 32 STs that were not present in the MLST database were identified. The most prevalent STs were ST464 and ST257, with 58 (9.6%) and 52 (8.6%) C. jejuni isolates, respectively. Isolates with some STs (464, 6411, 257, 50) were shown to be common in chickens, whereas others (e.g. ST21 and ST572) were more often identified among human C. jejuni. It was shown that of 47 human sequence types, 26 STs (106 isolates), 23 STs (102 isolates), and 29 STs (100 isolates) were also identified in chicken feces, meat, and carcasses, respectively. These results, together with the high and similar proportional similarity indexes (PSI) calculated for C. jejuni isolated from patients and chickens, may suggest that human campylobacteriosis was associated with contaminated chicken meat or meat products or other kinds of food cross-contaminated with campylobacters of chicken origin. The frequency of various sequence types identified in the present study generally reflects of the prevalence of STs in other countries which may suggest that C. jejuni with some STs have a global distribution, while other genotypes may be more restricted to certain countries.

Prebiotic Driven Increases in IL-17A Do Not Prevent Campylobacter jejuni Colonization of Chickens

Worldwide Campylobacter jejuni is a leading cause of foodborne disease. Contamination of chicken meat with digesta from C. jejuni-positive birds during slaughter and processing is a key route of transmission to humans through the food chain. Colonization of chickens with C. jejuni elicits host innate immune responses that may be modulated by dietary additives to provide a reduction in the number of campylobacters colonizing the gastrointestinal tract and thereby reduce the likelihood of human exposure to an infectious dose. Here we report the effects of prebiotic galacto-oligosaccharide (GOS) on broiler chickens colonized with C. jejuni when challenged at either an early stage in development at 6 days of age or 20 days old when campylobacters are frequently detected in commercial flocks. GOS-fed birds had increased growth performance, but the levels of C. jejuni colonizing the cecal pouches were unchanged irrespective of the age of challenge. Dietary GOS modulated the immune response to C. jejuni by increasing cytokine IL-17A expression at colonization. Correspondingly, reduced diversity of the cecal microbiota was associated with Campylobacter colonization in GOS-fed birds. In birds challenged at 6 days-old the reduction in microbial diversity was accompanied by an increase in the relative abundance of Escherichia spp. Whilst immuno-modulation of the Th17 pro-inflammatory response did not prevent C. jejuni colonization of the intestinal tract of broiler chickens, the study highlights the potential for combinations of prebiotics, and specific competitors (synbiotics) to engage with the host innate immunity to reduce pathogen burdens.

Food-to-Humans Bacterial Transmission

Microorganisms vehiculated by food might benefit health, cause minimal change within the equilibrium of the host microbial community or be associated with foodborne diseases. In this chapter we will focus on human pathogenic bacteria for which food is conclusively demonstrated as their transmission mode to human. We will describe the impact of foodborne diseases in public health, the reservoirs of foodborne pathogens (the environment, human and animals), the main bacterial pathogens and food vehicles causing human diseases, and the drivers for the transmission of foodborne diseases related to the food-chain, host or bacteria features. The implication of food-chain (foodborne pathogens and commensals) in the transmission of resistance to antibiotics relevant to the treatment of human infections is also evidenced. The multiplicity and interplay of drivers related to intensification, diversification and globalization of food production, consumer health status, preferences, lifestyles or behaviors, and bacteria adaptation to different challenges (stress tolerance and antimicrobial resistance) from farm to human, make the prevention of bacteria-food-human transmission a modern and continuous challenge. A global One Health approach is mandatory to better understand and minimize the transmission pathways of human pathogens, including multidrug-resistant pathogens and commensals, through food-chain.

Critical Orientation in the Jungle of Currently Available Methods and Types of Data for Source Attribution of Foodborne Diseases

With increased interest in source attribution of foodborne pathogens, there is a need to sort and assess the applicability of currently available methods. Herewith we reviewed the most frequently applied methods for source attribution of foodborne diseases, discussing their main strengths and weaknesses to be considered when choosing the most appropriate methods based on the type, quality, and quantity of data available, the research questions to be addressed, and the (epidemiological and microbiological) characteristics of the pathogens in question. A variety of source attribution approaches have been applied in recent years. These methods can be defined as top–down, bottom–up, or combined. Top–down approaches assign the human cases back to their sources of infection based on epidemiological (e.g., outbreak data analysis, case-control/cohort studies, etc.), microbiological (i.e., microbial subtyping), or combined (e.g., the so-called ‘source-assigned case-control study’ design) methods. Methods based on microbial subtyping are further differentiable according to the modeling framework adopted as frequency-matching (e.g., the Dutch and Danish models) or population genetics (e.g., Asymmetric Island Models and STRUCTURE) models, relying on the modeling of either phenotyping or genotyping data of pathogen strains from human cases and putative sources. Conversely, bottom–up approaches like comparative exposure assessment start from the level of contamination (prevalence and concentration) of a given pathogen in each source, and then go upwards in the transmission chain incorporating factors related to human exposure to these sources and dose-response relationships. Other approaches are intervention studies, including ‘natural experiments,’ and expert elicitations. A number of methodological challenges concerning all these approaches are discussed. In absence of an universally agreed upon ‘gold’ standard, i.e., a single method that satisfies all situations and needs for all pathogens, combining different approaches or applying them in a comparative fashion seems to be a promising way forward.

The role of parameterization in comparing source attribution models based on microbial subtyping for salmonellosis

Source attribution methods attribute human cases of a zoonotic disease to a certain source putatively responsible for this disease. Identifying and quantifying the contribution of different sources to human infections is important for taking appropriate actions for reducing the exposure of the consumer to zoonotic pathogens. One widely used method is the microbial subtyping approach, whose principle is to compare the frequency of pathogen subtypes from different sources (e.g. animals or food) with the frequency of these subtypes in human cases. This paper studies the relationship between a Bayesian microbial subtyping approach described by Hald and coworkers subsequently modified by David and coworkers, here called the Hald model, and a frequentist approach known as the "Dutch model." The comparison between the Bayesian and frequentist model is done for two data sets on salmonellosis in Germany from different time periods (year 2004-2007 and 2010-2011). The results of both approaches are in good agreement with each other for the used data. It is shown here mathematically that a certain parameterization can be used to transform the probabilistic Hald model into a deterministic form, which is equivalent to the Dutch model. That certain parameterization secures independence of the model outcomes from the choice of so-called unique subtypes (which are unique in the sense that they are found exclusively in one of the sources). It is shown that deviating from that certain parameterization leads variations in the model outcome dependent on which unique subtypes are chosen in the process of modelling.

Source attribution of Campylobacter jejuni shows variable importance of chicken and ruminants reservoirs in non-invasive and invasive French clinical isolates

Campylobacter jejuni is the most common cause of bacterial gastroenteritis worldwide. Mainly isolated from stool samples, C. jejuni can also become invasive. C. jejuni belongs to the commensal microbiota of a number of hosts, and infection by this bacterium can sometimes be traced back to exposure to a specific source. Here we genome sequenced 200 clinical isolates (2010–2016) and analyzed them with 701 isolate genomes from human infection, chicken, ruminants and the environment to examine the relative contribution of different reservoirs to non-invasive and invasive infection in France. Host-segregating genetic markers that can discriminate C. jejuni source were used with STRUCTURE software to probabilistically attribute the source of clinical strains. A self-attribution correction step, based upon the accuracy of source apportionment within each potential reservoir, improved attribution accuracy of clinical strains and suggested an important role for ruminant reservoirs in non-invasive infection and a potentially increased contribution of chicken as a source of invasive isolates. Structured sampling of Campylobacter in the clinic and from potential reservoirs provided evidence for variation in the contribution of different infection sources over time and an important role for non-poultry reservoirs in France. This provides a basis for ongoing genomic epidemiology surveillance and targeted interventions.

A strain comparison of Campylobacter isolated from retail poultry and human clinical cases in Atlantic Canada

Campylobacter is the leading cause of food-borne bacterial disease in Canada and many developed countries. One of the most common sources of human campylobacteriosis is considered to be the consumption or handling of raw or undercooked poultry. To date, few Canadian studies have investigated both the prevalence of Campylobacter on retail poultry and its potential impact on human clinical cases. The objective of this study was to evaluate the prevalence of Campylobacter spp. at the retail level and the correlation between subtypes recovered from chicken and those recovered from human clinical cases within the province of Nova Scotia, Canada. From this study 354 human clinical isolates were obtained from provincial hospital laboratories and a total of 480 packages of raw poultry cuts were sampled from retail outlets, yielding 312 isolates (65%), of all which were subtyped using comparative genomic fingerprinting (CGF). Of the 312 chicken isolates, the majority of isolates were C. jejuni (91.7%), followed by C. coli (7.7%) and C. lari (0.6%). Using CGF to subtype C. jejuni and C. coli isolates, 99 and 152 subtypes were recovered from chicken and clinical cases, respectively. The most prevalent human and chicken subtypes found in NS are similar to those observed nationally; indicating that the Campylobacter from this study appear to reflect of the profile of Campylobacter subtypes circulating nationally. Of the subtypes observed, only 36 subtypes were common between the two groups, however, these subtypes represented 48.3% of the clinical isolates collected. The findings from this study provides evidence that in Nova Scotia, retail poultry can act as a reservoir for Campylobacter subtypes that have been implicated in human illness.

Enhanced microbiological surveillance reveals that temporal case clusters contribute to the high rates of campylobacteriosis in a model agroecosystem

Infections by pathogenic Campylobacter species were determined in diarrheic (n = 2,217) and non-diarrheic control (n = 104) people in Southwestern Alberta (SWA), Canada over a 1-year period using specialized and conventional isolation, and direct PCR. Overall, 9.9% of diarrheic individuals were positive for C. jejuni (9.1%), C. upsaliensis (0.6%), and C. coli (0.5%). No C. lari was detected. Four diarrheic individuals were co-infected with C. jejuni and C. coli, and four different individuals were co-infected with C. jejuni and C. upsaliensis. Two control individuals were positive for C. jejuni. Approximately 50% of stools containing C. jejuni and/or C. coli were deemed negative by conventional isolation. Direct PCR for C. jejuni was less effective than culture-based detection. Most C. jejuni infections occurred in people living in the urban centers, but the prevalence of the bacterium was lower in females than males living in urban locations, and both males and females living in rural locations. Although C. jejuni was detected throughout the year, a trend for higher infection rates was observed in the late spring to early fall with a peak in August. Forty-six C. jejuni subtype clusters were identified, including 44 temporal case clusters attributed to 28 subtype groupings. The majority of infections (70.3%) were linked to subtypes associated with beef cattle. We conclude that many occurrences of pathogenic Campylobacter species were not detected by the conventional laboratory methodology, and temporal case clusters of C. jejuni subtypes associated with cattle contribute to the high rates of campylobacteriosis in SWA.

Parallel sequencing of porA reveals a complex pattern of Campylobacter genotypes that differs between broiler and broiler breeder chickens

Chicken meat represents an important source of Campylobacter infections of humans world-wide. A better understanding of Campylobacter epidemiology in commercial chicken flocks will facilitate the development of more effective intervention strategies. We developed a gene-specific parallel sequencing approach that efficiently indicated genetic diversity in farm-derived samples and revealed Campylobacter genotypes that would not be detected using microbiological culture. Parallel sequencing of the porA nucleotide fragment identified a different pattern of diversity in broiler flocks compared with broiler-breeder flocks at both individual bird and flock levels. Amongst the flocks tested, broiler flocks and individual birds were dominated by one or two porA fragment types whereas co-dominance with up to six porA fragment types was evident in breeder birds. A high proportion (83.6-93.3%) of porA variants were shared between broiler and breeder flocks. The porA-based diversity profiling could be a useful addition to the repertoire of tools employed to attribute potential sources of contamination for broiler flocks, including the environment, wild animals or other chickens. This approach can be extended to include other loci within Campylobacter and developed for molecular epidemiology studies of other bacterial species.

Phage Biocontrol of Campylobacter jejuni in Chickens Does Not Produce Collateral Effects on the Gut Microbiota

Bacteriophage biocontrol to reduce Campylobacter jejuni levels in chickens can reduce human exposure and disease acquired through the consumption of contaminated poultry products. Investigating changes in the chicken microbiota during phage treatment has not previously been undertaken but is crucial to understanding the system-wide effects of such treatments to establish a sustainable application. A phage cocktail containing two virulent Campylobacter phages was used to treat broiler chickens colonized with C. jejuni HPC5. Campylobacter counts from cecal contents were significantly reduced throughout the experimental period but were most effective 2 days post-treatment showing a reduction of 2.4 log10 CFU g-1 relative to mock-treated Campylobacter colonized controls. The administered phages replicated in vivo to establish stable populations. Bacteriophage predation of C. jejuni was not found to affect the microbiota structure but selectively reduced the relative abundance of C. jejuni without affecting other bacteria.

Genetic Diversity of Campylobacter Jejuni Isolated from the Poultry Food Chain

INTRODUCTION

Campylobacter jejuni is one of the most frequently reported causes of foodborne bacterial enteric disease worldwide. The main source of these microorganisms is contaminated food, especially of poultry origin. There are several molecular methods for differentiation of Campylobacter isolates at the subgenus level, and one of these is porA-typing based on the sequencing of the major outer-membrane protein (MOMP) encoding gene. The aim of the study was to test the molecular relationship of C. jejuni strains isolated at different points along the poultry food chain and assess the population structure of the isolates.

MATERIAL AND METHODS

A total of 451 C. jejuni were used in the study, and a DNA fragment of 630 bp of the MOMP encoding gene was amplified and sequenced.

RESULTS

One hundred and ten sequence types were identified, with 69 (62.7%) unique to the isolates' origin and 30 not present in the database. The most prevalent nucleotide variant 1 was detected in 37 (8.2%) strains. These isolates were identified in all poultry sources tested, especially in faeces (15 isolates) but also in poultry carcasses and meat (11 isolates in each).

CONCLUSION

The porA typing method was highly discriminative for C. jejuni of poultry origin since the Simpson's diversity index (D) achieved a value of 0.876, indicating considerable diversity in the bacterial population tested. The method may be further used for epidemiological investigation purposes.

Modelling the transmission dynamics of Campylobacter in Ontario, Canada, assuming house flies, Musca domestica, are a mechanical vector of disease transmission

Campylobacter's complicated dynamics and multiple transmission routes have made it difficult to describe using a mathematical framework. Vector-borne disease transmission has been proposed as a potential transmission route of Campylobacter with house flies acting as a mechanical vector. This study aimed to (i) determine if a basic SIR compartment model that included flies as a mechanical vector and incorporated a seasonally forced environment compartment could be used to capture the observed disease dynamics in Ontario, Canada, and (ii) use this model to determine potential changes to campylobacteriosis incidence using predicted changes to fly population size and fly activity under multiple climate change scenarios. The model was fit to 1 year of data and validated against 8 and 12 years of data. It accurately captured the observed incidence. We then explored changes in human disease incidence under multiple climate change scenarios. When fly activity levels were at a 25% increase, our model predicted a 28.15% increase in incidence by 2050 using the medium-low emissions scenario and 30.20% increase using the high emissions scenario. This model demonstrates that the dynamics of Campylobacter transmission can be captured by a model that assumes that the primary transmission of the pathogen occurs via insect vectors.

Ruminant and chicken: important sources of campylobacteriosis in France despite a variation of source attribution in 2009 and 2015

Pathogen source attribution studies are a useful tool for identifying reservoirs of human infection. Based on Multilocus Sequence Typing (MLST) data, such studies have identified chicken as a major source of C. jejuni human infection. The use of whole genome sequence-based typing methods offers potential to improve the precision of attribution beyond that which is possible from 7 MLST loci. Using published data and 156 novel C. jejuni genomes sequenced in this study, we performed probabilistic host source attribution of clinical C. jejuni isolates from France using three types of genotype data: comparative genomic fingerprints; MLST genes; 15 host segregating genes previously identified by whole genome sequencing. Consistent with previous studies, chicken was an important source of campylobacteriosis in France (31-63% of clinical isolates assigned). There was also evidence that ruminants are a source (22-55% of clinical isolates assigned), suggesting that further investigation of potential transmission routes from ruminants to human would be useful. Additionally, we found evidence of environmental and pet sources. However, the relative importance as sources varied according to the year of isolation and the genotyping technique used. Annual variations in attribution emphasize the dynamic nature of zoonotic transmission and the need to perform source attribution regularly.

The role of meat in foodborne disease: Is there a coming revolution in risk assessment and management?

Meat has featured prominently as a source of foodborne disease and a public health concern. For about the past 20 years the risk management paradigm has dominated international thinking about food safety. Control through the supply chain is supported by risk management concepts, as the public health risk at the point of consumption becomes the accepted outcome based measure. Foodborne pathogens can be detected at several points in the supply chain and determining the source of where these pathogens arise and how they behave throughout meat production and processing are important parts of risk based approaches. Recent improvements in molecular and genetic based technologies and data analysis for investigating source attribution and pathogen behaviour have enabled greater insights into how foodborne outbreaks occur and where controls can be implemented. These new approaches will improve our understanding of the role of meat in foodborne disease and are expected to have a significant impact on our understanding in the coming years.

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.

Use of whole-genome sequencing for Campylobacter surveillance from NARMS retail poultry in the United States in 2015

Whole genome sequencing (WGS) has become a rapid and affordable tool for public health surveillance and outbreak detection. In this study, we used the Illuminia MiSeq^® to sequence 589 Campylobacter isolates obtained in 2015 from retail poultry meats as part of the National Antimicrobial Resistance Monitoring System (NARMS). WGS data were used to identify the Campylobacter species and to compare the concordance between resistance genotypes and phenotypes. WGS accurately identified 386 C. jejuni and 203 C. coli using gyrA sequence information. Ten resistance genes, including tetO, bla_OXA-61, aph(2″)-Ic, aph(2″)-If, aph(2″)-Ig, aph(3')-III, ant(6)-1a, aadE, aph(3")-VIIa, and Inu(C), plus mutations in housekeeping genes (gyrA at position 86, 23S rRNA at position 2074 and 2075), were identified by WGS analysis. Overall, there was a high concordance between phenotypic resistance to a given drug and the presence of known resistance genes. Concordance between both resistance and susceptible phenotypes and genotype was 100% for ciprofloxacin, nalidixic acid, gentamicin, azithromycin, and florfenicol. A few discrepancies were observed for tetracycline, clindamycin, and telithromycin. The concordance between resistance phenotype and genotype ranged from 67.9% to 100%; whereas, the concordance between susceptible phenotype and genotype ranged from 98.0% to 99.6%. Our study demonstrates that WGS can correctly identify Campylobacter species and predict antimicrobial resistance with a high degree of accuracy.