Development and validation of a comparative genomic fingerprinting method for high-resolution genotyping of Campylobacter jejuni

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.

Comparative prevalence and diversity of Campylobacter jejuni strains in water and human beings over a 1-year period in southwestern Alberta, Canada

Campylobacter jejuni was isolated from diarrheic people, river water (Oldman River watershed), wastewater, and drinking water over a 1-year period in southwestern Alberta (2008-2009). High rates of campylobacteriosis were observed during the study period (≥115 cases/100K). Infections occurred throughout the year, with a peak in late summer and early autumn. The majority of infections occurred in people living in Lethbridge. Campylobacter jejuni was not isolated from municipal drinking water. In contrast, the bacterium was isolated from untreated and treated wastewater, and river water (all sites). There were no correlations between C. jejuni recovery/detection from water and river flow rates, water turbidity, or fecal coliforms. Campylobacter jejuni recovery from water did not correspond with the peak periods of campylobacteriosis. The bacterium was most commonly isolated downstream of wastewater outfalls; waterfowl congregated at these sites, particularly during the winter months. A comparison of subtypes from people and water revealed that the vast majority of subtypes in water did not correspond to subtypes recovered from diarrheic people, and were linked to waterfowl and other non-human animal sources. We conclude that water-borne C. jejuni did not contribute significantly to the high rates of campylobacteriosis observed in people during the study period.

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.

Rates of fluoroquinolone resistance in domestically acquired Campylobacter jejuni are increasing in people living within a model study location in Canada

Antimicrobial resistance was evaluated in Campylobacter jejuni isolated from 1291 diarrheic people over a 15-year period (2004-2018) in southwestern Alberta, a model location in Canada with a high rate of campylobacteriosis. The prevalence of resistance to chloramphenicol, clindamycin, erythromycin, and gentamicin was low during the examination period (≤4.8%). Resistance to tetracycline remained consistently high (41.6%-65.1%), and resistance was primarily conferred by plasmid-borne tetO (96.2%). Resistance rates to ciprofloxacin and nalidixic acid increased substantially over the examination period, with a maximal fluoroquinolone resistance (FQR) prevalence of 28.9% in 2016. The majority of C. jejuni isolates resistant to ciprofloxacin (93.9%) contained a C257T single nucleotide polymorphism within the gyrA chromosomal gene. Follow up with infected people indicated that the observed increase in FQR was primarily due to domestically acquired infections. Moreover, the majority of FQ-resistant C. jejuni subtypes (82.6%) were endemic in Canada, primarily linked to cattle and chicken reservoirs; 18.4% of FQ-resistant isolates were assigned to three subtypes, predominantly associated with cattle. Study findings indicate the need to prioritize FQR monitoring in C. jejuni infections in Canada and to elucidate the dynamics of the emergence and transmission of resistant C. jejuni strains within and from cattle and chicken reservoirs.

Dogs and Cats: Reservoirs for Highly Diverse Campylobacter jejuni and a Potential Source of Human Exposure

Assessing the carriage of Campylobacter in animal reservoirs is essential to better understand Campylobacter epidemiology. Here, we evaluated the prevalence of thermophilic Campylobacter spp. in dogs and cats, hereafter defined as pets, and characterized Campylobacter jejuni (C. jejuni) isolates to assess their genetic diversity and their potential link with isolates from other animals or human cases. During a 6-month period, 304 feces samples were collected from pets. A significantly higher prevalence of thermophilic Campylobacter spp. was found in dogs compared with cats, as well as in dogs ≤ 1-year-old compared with older dogs. C. jejuni was the predominant species found in pets, and its genomic characterization revealed a high genetic diversity. Genotypes comparison with previously characterized isolates revealed a partial overlap between C. jejuni isolates from pets, chicken, cattle, and clinical cases. This overlap suggests the potential role of livestock and humans in pets' exposure to Campylobacter, or vice versa. The isolation of pets' specific profiles may suggest the existence of other sources of pet contamination or imply that pets may constitute a reservoir for Campylobacter. Because of the proximity between humans and pets, along with their frequent carriage of C. jejuni, human exposure to Campylobacter from pets can be more important than previously thought.

"These Aren't the Strains You're Looking for": Recovery Bias of Common Campylobacter jejuni Subtypes in Mixed Cultures

Microbiological surveillance of the food chain plays a critical role in improving our understanding of the distribution and circulation of food-borne pathogens along the farm to fork continuum toward the development of interventions to reduce the burden of illness. The application of molecular subtyping to bacterial isolates collected through surveillance has led to the identification of strains posing the greatest risk to public health. Past evidence suggests that enrichment methods for Campylobacter jejuni, a leading bacterial foodborne pathogen worldwide, may lead to the differential recovery of subtypes, obscuring our ability to infer the composition of a mixed-strain sample and potentially biasing prevalence estimates in surveillance data. To assess the extent of potential selection bias resulting from enrichment-based isolation methods, we compared enrichment and non-enrichment isolation of mixed subtype cultures of C. jejuni, followed by subtype-specific enumeration using both colony plate-counts and digital droplet PCR. Results differed from the null hypothesis that similar proportions of C. jejuni subtypes are recovered from both methods. Our results also indicated a significant effect of subtype prevalence on isolation frequency post-recovery, with the recovery of more common subtypes being consistently favored. This bias was exacerbated when an enrichment step was included in the isolation procedure. Taken together, our results emphasize the importance of selecting multiple colonies per sample, and where possible, the use of both enrichment and non-enrichment isolation procedures to maximize the likelihood of recovering multiple subtypes present in a sample. Moreover, the effects of subtype-specific recovery bias should be considered in the interpretation of strain prevalence data toward improved risk assessment from microbiological surveillance data.

Clinically Relevant Campylobacter jejuni Subtypes Are Readily Found and Transmitted within the Cattle Production Continuum but Present a Limited Foodborne Risk

Increasing evidence exists for the role that cattle play in the epidemiology of campylobacteriosis. In this study, the prevalence and distribution of Campylobacter jejuni were longitudinally examined at the subspecies level in the beef cattle production continuum. Animals were subdivided into two groups: those that were not administered antibiotics and those that were administered the antimicrobial growth promoter chlortetracycline and sulfamethazine (AS700). Samples were longitudinally collected throughout the confined feeding operation (CFO) period and during the slaughter process, and C. jejuni was isolated and genotyped to assess subtype richness and to elucidate transmission dynamics from farm to fork. The bacterium was frequently isolated from cattle, and the bacterial densities shed in feces increased over the CFO period. Campylobacter jejuni was also isolated from digesta, hides, the abattoir environment, and carcasses. The administration of AS700 did not conspicuously reduce the C. jejuni densities in feces or within the intestine but significantly reduced the bacterial densities and the diversity of subtypes on abattoir samples. All cattle carried multiple subtypes, including clinically relevant subtypes known to represent a risk to human health. Instances of intra-animal longitudinal transmission were observed. Although clinically relevant subtypes were transmitted to carcasses via direct contact and aerosols, the bacterium could not be isolated nor could its DNA be detected in ground beef regardless of treatment. Although the evidence indicated that beef cattle represent a significant reservoir for C. jejuni, including high-risk subtypes strongly associated with the bovine host, they do not appear to represent a significant risk for direct foodborne transmission. This implicates alternate routes of human transmission.IMPORTANCE Limited information is available on the transmission of Campylobacter jejuni subtypes in the beef production continuum and the foodborne risk posed to humans. Cattle were colonized by diverse subtypes of C. jejuni, and the densities of the bacterium shed in feces increased during the confined feeding period. Campylobacter jejuni was readily associated with the digesta, feces, and hides of cattle entering the abattoir, as well as the local environment. Moreover, C. jejuni cells were deposited on carcasses via direct contact and aerosols, but the bacterium was not detected in the ground beef generated from contaminated carcasses. We conclude that C. jejuni bacterial cells associated with beef cattle do not represent a significant risk through food consumption and suggest that clinically relevant subtypes are transmitted through alternate routes of exposure.

Campylobacter jejuni Strain Dynamics in a Raccoon (Procyon lotor) Population in Southern Ontario, Canada: High Prevalence and Rapid Subtype Turnover

Free-ranging wildlife are increasingly recognized as potential reservoirs of disease-causing Campylobacter species such as C. jejuni and C. coli. Raccoons (Procyon lotor), which live at the interface of rural, urban, and more natural environments, are ideal subjects for exploring the potential role that wildlife play in the epidemiology of campylobacteriosis. We studied the prevalence and genetic diversity of Campylobacter from live-captured raccoons on five swine farms and five conservation areas in southwest Ontario. From 2011 to 2013, we collected fecal swabs (n = 1,096) from raccoons, and (n = 50) manure pit samples from the swine farm environment. We subtyped the resulting Campylobacter isolates (n = 581) using Comparative Genomic Fingerprinting (CGF) and 114 distinct subtypes were observed, including 96 and 18 subtypes among raccoon and manure pit isolates, respectively. Campylobacter prevalence in raccoons was 46.3%, with 98.7% of isolates recovered identified as C. jejuni. Novel raccoon-specific CGF subtypes (n = 40/96) accounted for 24.6% (n = 143/581) of Campylobacter isolates collected in this study. Our results also show that C. jejuni is readily acquired and lost in this wild raccoon population and that a high Campylobacter prevalence is observed despite transient carriage typically lasting 30 days or fewer. Moreover, although raccoons appeared to be colonized by species-adapted subtypes, they also harbored agriculture-associated genotypes that accounted for the majority of isolates observed (66.4%) and that are strongly associated with human infections. This suggests that raccoons may act as vectors in the transmission of clinically-relevant C. jejuni subtypes at the interface of rural, urban, and more natural environments.

Prevalence and genetic diversity of Campylobacter spp. in the production chain of broiler chickens in Lebanon and its association with the intestinal protozoan Blastocystis sp

Campylobacter jejuni is recognized as the most common foodborne pathogen associated with human gastroenteritis worldwide. Broilers are frequently infected by the bacteria and are considered the main source of exposure to humans. However, despite its public health impact, no recent data are currently available in Lebanon about Campylobacter spp. in poultry and human population. Therefore, this study aimed to determine the prevalence and genetic diversity of Campylobacter spp. in 227 ceca and on 227 carcasses of broiler chickens collected in Lebanese slaughterhouses. Overall, the prevalence of Campylobacter was shown to reach 67.0% in ceca and 17.2% on carcasses of Lebanese poultry. The only 2 Campylobacter species identified were C. jejuni and C. coli, with a slightly higher prevalence of C. coli in ceca and of C. jejuni on carcasses. A high level of genetic diversity was reported among the 51 C. jejuni isolates selected, since 25 distinct profiles were identified according to the comparative genomic fingerprinting typing method based on a subset of 40 genes using the 90% similarity threshold. Predominant clusters observed in Lebanese poultry isolates were also frequently found among French human clinical cases, highlighting that broiler chickens represent a potential reservoir for human campylobacteriosis. In addition, a significantly higher prevalence of Campylobacter spp. was found in slaughterhouse workers than in a cohort of hospitalized patients with no contact with poultry, confirming that contaminated broiler chickens in slaughterhouse appeared to be a non-negligible source of Campylobacter spp. transmission. Interestingly, a significant association between Campylobacter spp. and Blastocystis sp. has been observed. This correlation suggested that the presence of Campylobacter spp. would be favored when Blastocystis sp. is present and, similarly, the absence of one would favor the absence of the other. This is the first large-scale investigation focusing on the impact of Campylobacter spp. in broiler chickens in Lebanon and confirmed the need to implement prevention and control measures in the poultry production to reduce the burden of campylobacteriosis in the human population.

Tetracycline Resistant Campylobacter jejuni Subtypes Emanating from Beef Cattle Administered Non-Therapeutic Chlortetracycline are Longitudinally Transmitted within the Production Continuum but are Not Detected in Ground Beef

The impacts of the antimicrobial growth promoter (AGP), chlortetracycline with sulfamethazine (AS700), on the development of antimicrobial resistance and longitudinal transmission of Campylobacter jejuni within the beef production continuum were empirically determined. Carriage of tetracycline resistance determinants in the enteric bacterial community increased at a greater rate for AS700-treatment cattle. The majority of the bacteria from animals administered AS700 carried tetW. Densities of C. jejuni shed in feces increased over the confined feeding period, and the administration of AS700 did not conspicuously reduce C. jejuni densities in feces or within the intestine. The majority of C. jejuni isolates recovered were resistant to tetracycline, but the resistance rates to other antibiotics was low (≤20.1%). The richness of C. jejuni subtypes recovered from AS700-treated animals that were either resistant or susceptible to tetracycline was reduced, indicating selection pressure due to AGP administration. Moreover, a degree of subtype-specific resistance to tetracycline was observed. tetO was the primary tetracycline resistance determinant conferring resistance in C. jejuni isolates recovered from cattle and people. Clinically-relevant C. jejuni subtypes (subtypes that represent a risk to human health) that were resistant to tetracycline were isolated from cattle feces, digesta, hides, the abattoir environment, and carcasses, but not from ground beef. Thus, study findings indicate that clinically-relevant C. jejuni subtypes associated with beef cattle, including those resistant to antibiotics, do not represent a significant foodborne risk.

Whole genome sequencing and metagenomics for outbreak investigation, source attribution and risk assessment of food-borne microorganisms

This Opinion considers the application of whole genome sequencing (WGS) and metagenomics for outbreak investigation, source attribution and risk assessment of food‐borne pathogens. WGS offers the highest level of bacterial strain discrimination for food‐borne outbreak investigation and source‐attribution as well as potential for more precise hazard identification, thereby facilitating more targeted risk assessment and risk management. WGS improves linking of sporadic cases associated with different food products and geographical regions to a point source outbreak and can facilitate epidemiological investigations, allowing also the use of previously sequenced genomes. Source attribution may be favoured by improved identification of transmission pathways, through the integration of spatial‐temporal factors and the detection of multidirectional transmission and pathogen–host interactions. Metagenomics has potential, especially in relation to the detection and characterisation of non‐culturable, difficult‐to‐culture or slow‐growing microorganisms, for tracking of hazard‐related genetic determinants and the dynamic evaluation of the composition and functionality of complex microbial communities. A SWOT analysis is provided on the use of WGS and metagenomics for Salmonella and Shigatoxin‐producing Escherichia coli (STEC) serotyping and the identification of antimicrobial resistance determinants in bacteria. Close agreement between phenotypic and WGS‐based genotyping data has been observed. WGS provides additional information on the nature and localisation of antimicrobial resistance determinants and on their dissemination potential by horizontal gene transfer, as well as on genes relating to virulence and biological fitness. Interoperable data will play a major role in the future use of WGS and metagenomic data. Capacity building based on harmonised, quality controlled operational systems within European laboratories and worldwide is essential for the investigation of cross‐border outbreaks and for the development of international standardised risk assessments of food‐borne microorganisms.

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.

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.

Carriage of Campylobacter, Salmonella, and Antimicrobial-Resistant, Nonspecific Escherichia coli by Waterfowl Species Collected from Three Sources in Southern Ontario, Canada

Wild birds are considered a potential source of zoonotic pathogens. We report on the occurrence of Campylobacter, Salmonella, and antimicrobial-resistant, nonspecific Escherichia coli in ducks, grebes, and swans obtained by convenience while conducting related research with Canada Geese (Branta canadensis). Samples were obtained in southern Ontario, Canada, between 2013 and 2015 from hunter-caught birds, birds submitted for postmortem diagnosis, and fresh feces from live birds in parks. A secondary objective was to characterize Campylobacter genotypes using comparative genomic fingerprinting. Salmonella and E. coli isolates were tested for susceptibility to 15 antimicrobials using the Canadian Integrated Program for Antimicrobial Resistance Surveillance test panel. A total of 71 samples were collected from 15 different waterfowl species. We detected Campylobacter, Salmonella, and E. coli in 17, 3, and 84% of samples, respectively. Ten unique Campylobacter subtypes were identified, some of which had been identified previously in water, poultry, waterfowl, and human clinical cases. Both Salmonella isolates were pansusceptible and 15% of E. coli isolates were resistant to at least one antimicrobial, including resistance to antimicrobials of highest importance to human health. Source attribution studies should examine the role of waterfowl in the dissemination of these pathogens.

Frequent Implication of Multistress-Tolerant Campylobacter jejuni in Human Infections

Campylobacter jejuni, a major cause of bacterial foodborne illnesses, is considered highly susceptible to environmental stresses. In this study, we extensively investigated the stress tolerance of 121 clinical strains of C. jejuni against 5 stress conditions (aerobic stress, disinfectant exposure, freeze-thaw, heat treatment, and osmotic stress) that this pathogenic bacterium might encounter during foodborne transmission to humans. In contrast to our current perception about high stress sensitivity of C. jejuni, a number of clinical strains of C. jejuni were highly tolerant to multiple stresses. We performed population genetics analysis by using comparative genomic fingerprinting and showed that multistress-tolerant strains of C. jejuni constituted distinct clades. The comparative genomic fingerprinting subtypes belonging to multistress-tolerant clades were more frequently implicated in human infections than those in stress-sensitive clades. We identified unique stress-tolerant C. jejuni clones and showed the role of stress tolerance in human campylobacteriosis.

A repeated cross-sectional study of the epidemiology of Campylobacter and antimicrobial resistant Enterobacteriaceae in free-living Canada geese in Guelph, Ontario, Canada

From May through October 2016, we conducted a repeated cross-sectional study examining the effects of temporal, spatial, flock and demographic factors (i.e. juvenile vs. adult) on the prevalence of Campylobacter and antimicrobial resistant Enterobacteriaceae among 344 fresh faecal samples collected from Canada geese (Branta canadensis) from four locations where birds nested in Guelph, Ontario, Canada. The overall prevalence of Campylobacter among all fresh faecal samples was 9.3% and was greatest in the fall when these birds became more mobile following the nesting season. Based on 40 gene comparative genomic fingerprinting (CGF40), the increase in prevalence noted in the fall was matched by an increase in the number of unique CGF40 subtypes identified. Resistance to colistin was detected most commonly, in 6% of Escherichia coli isolates, and was highest in the late summer months. All colistin-resistant isolates were negative for the mcr-1 to mcr-5 genes; a chromosomal resistance mechanism (PmrB) was identified in all of these isolates. The prevalence of samples with E. coli exhibiting multi-class resistance or extended spectrum beta-lactamase was low (i.e. <2% of samples). The intra-class correlation coefficients, estimated from the variance components of multilevel logistic regression models, indicated that the shedding of Campylobacter and antimicrobial resistant E. coli among geese within a flock (i.e. birds collected from the same site on the same day) was moderately correlated. Spatial, temporal, and spatiotemporal clusters identified using the spatial scan statistic, largely supported the findings from our multi-level models. Salmonella was not isolated from any of the fresh faecal samples collected suggesting that its prevalence in this population of birds was very low.

Therapeutic administration of enrofloxacin in mice does not select for fluoroquinolone resistance inCampylobacter jejuni

Enrofloxacin is registered for therapeutic use in beef cattle to treat bovine respiratory disease in Canada. A murine model was used to experimentally examine the impact of therapeutic administration of enrofloxacin on fluoroquinolone resistance development in Campylobacter jejuni. Administration of enrofloxacin to mice via subcutaneous injection or per os routes resulted in equivalent levels of bioactive enrofloxacin within the intestine, but bioactivity was short-lived (<48 h after cessation). Enrofloxacin administration did not affect densities of total bacteria, Firmicutes, or Bacteroidetes in digesta and had modest impacts on densities of Enterobacteriaceae. All mice inoculated with C. jejuni NCTC 11168 became persistently colonized by the bacterium. Enrofloxacin reduced C. jejuni cell densities within the cecal and colonic digesta for all treatments, and densities shed in feces as a function of antibiotic duration. None of the C. jejuni isolates recovered from mice after administration of enrofloxacin (n = 260) developed resistance to ciprofloxacin regardless of method or duration of administration. Furthermore, only modest shifts in the minimum inhibitory concentration of the isolates by treatment were noted. The study findings indicate that the risk posed by short-term subcutaneous administration of enrofloxacin for the development of fluoroquinolone resistance in mammals is low.

Epidemiology of Campylobacter, Salmonella and antimicrobial resistant Escherichia coli in free-living Canada geese (Branta canadensis) from three sources in southern Ontario

Antimicrobial resistant bacteria and zoonotic pathogens have previously been isolated from Canada geese. We examined the prevalence of three enteric bacteria (i.e. Campylobacter, Salmonella, Escherichia coli) among Canada geese from three sampling sources in southern Ontario from 2013 through 2015. Samples were obtained by convenience from hunting groups, diagnostic birds submitted for post-mortem, and fresh faeces from live birds in parks. Escherichia coli isolates were isolated and tested for susceptibility to 15 antimicrobials using the Canadian Integrated Program for Antimicrobial Resistance Surveillance test panel. The prevalences of Salmonella, Campylobacter and E. coli were 0%, 11.2% and 72.6%, respectively. Among E. coli isolates, 7.9% were resistant to ≥1 class of antimicrobials and 5.6% were resistant to ≥2 classes of antimicrobials, with some including resistance to antimicrobials of highest importance in human medicine. A significant association between season and E. coli resistance among samples from live birds was noted; summer samples had no resistant E. coli isolates, whereas spring samples demonstrated the highest prevalence of E. coli resistant to ≥1 class of antimicrobials (20.0%) among all sources. In addition, Campylobacter coli were only isolated from the spring faecal samples. Flock-level clustering was an important statistical consideration, as flock was a significant random effect in all but two of our models. Detection of Campylobacter and antimicrobial resistant E. coli from Canada geese suggests that these birds may play a role in disseminating these organisms within the environment.

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.

A representative overview of the genetic diversity and lipooligosaccharide sialylation in Campylobacter jejuni along the broiler production chain in France and its comparison with human isolates

Campylobacter jejuni is the most common cause of bacterial gastroenteritis worldwide and is associated with post-infectious neuropathies. Moreover, the chicken reservoir is described as the main source of human infection and C. jejuni sialylated lipooligosaccharides seem to play an important role in the pathogenesis of neuropathies. In this study, MultiLocus Sequence Typing (MLST) and Comparative Genomic Fingerprinting using 40 assay genes (CGF40) were used to describe C. jejuni populations within clinical isolates and a representative collection of isolates from French poultry production. In addition, the sialylation of C. jejuni LOS was assessed. Here, we report high levels of genetic diversity among both chicken and human disease C. jejuni populations. The predominance of the ST-21, ST-45, and ST-464 complexes in chicken isolates and of the ST-21, ST-206, and ST-48 complexes in the clinical isolates was observed as were correlations between some MLST and CGF40 genotypes. Furthermore, some C. jejuni genotypes were frequently isolated among clinical cases as well as all along the broiler production chain, suggesting a potentially high implication of chicken in human campylobacteriosis in France. Finally, the LOS classes A, B and C were predominant within clinical C. jejuni isolates supporting the hypothesis of a benefit in infectivity for C. jejuni isolates showing sialylated LOS.

Prevalence of Thermophilic Campylobacter in Cattle Production at Slaughterhouse Level in France and Link Between C. jejuni Bovine Strains and Campylobacteriosis

Campylobacter is the leading cause of bacterial gastroenteritis in industrialized countries, with poultry reservoir as the main source of infection. Nevertheless, a recent study on source attribution showed that cattle could be a source of human contamination in France (Thépault et al., 2017). However, few data are available on thermophilic Campylobacter epidemiology in cattle in France. The aim of this study is to collect new data of thermophilic Campylobacter prevalence in these animals and to subtype C. jejuni isolates to assess the potential implication of cattle in campylobacteriosis. A 6-month survey was carried out in one of the largest European slaughterhouse of cattle. Based on a statistical representative sampling plan, 959 intestinal content samples (483 adult cattle and 476 calves) were collected. An adapted version of the ISO 10272 standard and Maldi-Tof were used for detection and speciation of thermophilic Campylobacter isolates. Within more than 2000 thermophilic Campylobacter isolates collected, a selection of 649 C. jejuni isolates was typed with Comparative Genomic Fingerprinting (CGF40) and a subset of 77 isolates was typed using Multilocus Sequence Typing (MLST). Simultaneously, clinical isolates occurred in France were genotyped. Prevalence of thermophilic Campylobacter in the global cattle population was 69.1% (CI_95% = 66.1, 72.1) at slaughterhouse level. In adult cattle, the prevalence was 39.3%, while 99.4% of calves were contaminated, and C. jejuni was the most prevalent species with prevalence of 37.3 and 98.5%, respectively and a higher genetic diversity in adult cattle. The prevalence of C. coli was lower with 3% in adult cattle and 12.5% in calves. MLST and CGF40 genotyping did not showed a high number of clusters within cattle isolates but the predominance of few clusters accounted for a large part of the population (CC-21, CC-61, CC-48, and CC-257). By comparison with clinical genotypes, genetic diversity was significantly lower in cattle. Moreover, significant overlap was observed between genotypes from both origins, with 3 of the 4 main cattle clusters present in human isolates. This study provides new insights on the epidemiology of thermophilic Campylobacter and C. jejuni in cattle production in France and their potential implication in human infection.

Subtype-Specific Selection for Resistance to Fluoroquinolones but Not to Tetracyclines Is Evident in Campylobacter jejuni Isolates from Beef Cattle in Confined Feeding Operations in Southern Alberta, Canada

Campylobacter jejuni was longitudinally isolated from beef cattle housed in four confined feeding operations (CFOs) in Southern Alberta, Canada, over 18 months. All of the cattle were administered a variety of antimicrobial agents (AMAs) nontherapeutically and metaphylactically during their time in the CFOs. In total, 7,966 C. jejuni isolates were recovered from cattle. More animals were colonized by the bacterium after >60 days in the CFO (interim) than were individuals upon entry at the CFO (arrival). Subtyping and resistance to seven AMAs were determined for 1,832 (23.0%) and 1,648 (20.7%) isolates, respectively. Increases in the proportion of isolates resistant to tetracycline were observed at all four CFOs between sample times and to ciprofloxacin and nalidixic acid at one or more CFOs. The vast majority of isolates resistant to tetracycline carried tetO, whereas ciprofloxacin resistance was predominantly attributed to mutations in the gyrA gene. Although considerable diversity was observed, a majority of C. jejuni isolates belonged to one of five predominant subtype clusters. There was no difference in subtype diversity by CFO, but the population structure differed between sample times. Selection for resistance to ciprofloxacin and nalidixic acid was subtype dependent, whereas selection for resistance to tetracycline was not. The findings indicate that a proportion of cattle entering CFOs carry resistant C. jejuni subtypes, and the characteristics of beef cattle CFOs facilitate transmission/proliferation of diverse subtypes, including those resistant to AMAs, which coupled with the densities of CFOs likely contribute to the high rates of cattle-associated campylobacteriosis in Southern Alberta.IMPORTANCE A small proportion of cattle entering a CFO carry Campylobacter jejuni, including subtypes resistant to AMAs. The large numbers of cattle arriving from diverse locations at the CFOs and intermingling within the CFOs over time, coupled with the high-density housing of animals, the high rates of transmission of C. jejuni subtypes among animals, and the extensive use of AMAs merge to create an ideal situation where the proliferation of diverse antimicrobial-resistant C. jejuni subtypes is facilitated. Considering that Southern Alberta reports high rates of campylobacteriosis in the human population and that many of these clinical cases are due to C. jejuni subtypes associated with cattle, it is likely that the characteristics of beef cattle CFOs favor the propagation of clinically relevant C. jejuni subtypes, including those resistant to medically important AMAs, which constitute a risk to human health.

Do contamination of and exposure to chicken meat and water drive the temporal dynamics of Campylobacter cases?

Campylobacteriosis, the most frequent bacterial enteric disease, shows a clear yet unexplained seasonality. The study purpose was to explore the influence of seasonal fluctuation in the contamination of and in the behaviour exposures to two important sources of Campylobacter on the seasonality of campylobacteriosis. Time series analyses were applied to data collected through an integrated surveillance system in Canada in 2005-2010. Data included sporadic, domestically-acquired cases of Campylobacter jejuni infection, contamination of retail chicken meat and of surface water by C. jejuni, and exposure to each source through barbequing and swimming in natural waters. Seasonal patterns were evident for all variables with a peak in summer for human cases and for both exposures, in fall for chicken meat contamination, and in late fall for water contamination. Time series analyses showed that the observed campylobacteriosis summer peak could only be significantly linked to behaviour exposures rather than sources contamination (swimming rather than water contamination and barbequing rather than chicken meat contamination). The results indicate that the observed summer increase in human cases may be more the result of amplification through more frequent risky exposures rather than the result of an increase of the Campylobacter source contamination.

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

Human campylobacteriosis is a common zoonosis with a significant burden in many countries. Its prevention is difficult because humans can be exposed to Campylobacter through various exposures: foodborne, waterborne or by contact with animals. This study aimed at attributing campylobacteriosis to sources at the point of exposure. It combined comparative exposure assessment and microbial subtype comparison with subtypes defined by comparative genomic fingerprinting (CGF). It used isolates from clinical cases and from eight potential exposure sources (chicken, cattle and pig manure, retail chicken, beef, pork and turkey meat, and surface water) collected within a single sentinel site of an integrated surveillance system for enteric pathogens in Canada. Overall, 1518 non-human isolates and 250 isolates from domestically-acquired human cases were subtyped and their subtype profiles analyzed for source attribution using two attribution models modified to include exposure. Exposure values were obtained from a concurrent comparative exposure assessment study undertaken in the same area. Based on CGF profiles, attribution was possible for 198 (79%) human cases. Both models provide comparable figures: chicken meat was the most important source (65-69% of attributable cases) whereas exposure to cattle (manure) ranked second (14-19% of attributable cases), the other sources being minor (including beef meat). In comparison with other attributions conducted at the point of production, the study highlights the fact that Campylobacter transmission from cattle to humans is rarely meat borne, calling for a closer look at local transmission from cattle to prevent campylobacteriosis, in addition to increasing safety along the chicken supply chain.

A Genome-Wide Association Study to Identify Diagnostic Markers for Human Pathogenic Campylobacter jejuni Strains

Campylobacter jejuni is a leading human enteric pathogen worldwide and despite an improved understanding of its biology, ecology, and epidemiology, limited tools exist for identifying strains that are likely to cause disease. In the current study, we used subtyping data in a database representing over 24,000 isolates collected through various surveillance projects in Canada to identify 166 representative genomes from prevalent C. jejuni subtypes for whole genome sequencing. The sequence data was used in a genome-wide association study (GWAS) aimed at identifying accessory gene markers associated with clinically related C. jejuni subtypes. Prospective markers (n = 28) were then validated against a large number (n = 3,902) of clinically associated and non-clinically associated genomes from a variety of sources. A total of 25 genes, including six sets of genetically linked genes, were identified as robust putative diagnostic markers for clinically related C. jejuni subtypes. Although some of the genes identified in this study have been previously shown to play a role in important processes such as iron acquisition and vitamin B₅ biosynthesis, others have unknown function or are unique to the current study and warrant further investigation. As few as four of these markers could be used in combination to detect up to 90% of clinically associated isolates in the validation dataset, and such markers could form the basis for a screening assay to rapidly identify strains that pose an increased risk to public health. The results of the current study are consistent with the notion that specific groups of C. jejuni strains of interest are defined by the presence of specific accessory genes.

Epidemiology of antimicrobial resistant Campylobacter spp. isolated from retail meats in Canada

Campylobacter is an important zoonotic pathogen found in livestock and can cause illness in humans following consumption of raw and undercooked meat products. The objectives of this study were to determine the prevalence of Campylobacter spp. in retail meat (poultry, turkey, pork and beef) purchased in Alberta, Canada and to assess antimicrobial resistance and genetic relatedness of recovered Campylobacter strains with previously isolated strains from clinical and environmental sources. A Comparative Genomic Fingerprinting (CGF) method was used for assessing genetic relatedness of isolates. A total of 606 samples comprising 204, 110, 145 and 147 samples of retail chicken, turkey, ground beef and pork, respectively, were obtained. Campylobacter was isolated from 23.5% (48/204) of chicken samples and 14.2% (8/110) of turkey samples. Pork and beef samples were negative for Campylobacter. Campylobacter jejuni was the most common (94.6%) spp. found followed by C. coli (5.4%). Resistance to tetracycline was found in 48.1% of isolates, followed by resistance to ciprofloxacin (5.5%), nalidixic acid (5.5%), azithromycin (1.78%), and erythromycin (1.78%). All isolates were susceptible to clindamycin, florfenicol, gentamicin and telithromycin. Tetracycline resistance was attributable to the presence of the tetO gene. CGF analysis showed that Campylobacter isolated from poultry meat in this study were genetically related to clinical isolates recovered from human infections and to those isolated from animals and the environment.

A Comparative Exposure Assessment of Campylobacter in Ontario, Canada

To inform source attribution efforts, a comparative exposure assessment was developed to estimate the relative exposure to Campylobacter, the leading bacterial gastrointestinal disease in Canada, for 13 different transmission routes within Ontario, Canada, during the summer. Exposure was quantified with stochastic models at the population level, which incorporated measures of frequency, quantity ingested, prevalence, and concentration, using data from FoodNet Canada surveillance, the peer-reviewed and gray literature, other Ontario data, and data that were specifically collected for this study. Models were run with @Risk software using Monte Carlo simulations. The mean number of cells of Campylobacter ingested per Ontarian per day during the summer, ranked from highest to lowest is as follows: household pets, chicken, living on a farm, raw milk, visiting a farm, recreational water, beef, drinking water, pork, vegetables, seafood, petting zoos, and fruits. The study results identify knowledge gaps for some transmission routes, and indicate that some transmission routes for Campylobacter are underestimated in the current literature, such as household pets and raw milk. Many data gaps were identified for future data collection consideration, especially for the concentration of Campylobacter in all transmission routes.

The EpiQuant Framework for Computing Epidemiological Concordance of Microbial Subtyping Data

A fundamental assumption in the use and interpretation of microbial subtyping results for public health investigations is that isolates that appear to be related based on molecular subtyping data are expected to share commonalities with respect to their origin, history, and distribution. Critically, there is currently no approach for systematically assessing the underlying epidemiology of subtyping results. Our aim was to develop a method for directly quantifying the similarity between bacterial isolates using basic sampling metadata and to develop a framework for computing the epidemiological concordance of microbial typing results. We have developed an analytical model that summarizes the similarity of bacterial isolates using basic parameters typically provided in sampling records, using a novel framework (EpiQuant) developed in the R environment for statistical computing. We have applied the EpiQuant framework to a data set comprising 654 isolates of the enteric pathogen Campylobacter jejuni from Canadian surveillance data in order to examine the epidemiological concordance of clusters obtained by using two leading C. jejuni subtyping methods. The EpiQuant framework can be used to directly quantify the similarity of bacterial isolates based on basic sample metadata. These results can then be used to assess the concordance between microbial epidemiological and molecular data, facilitating the objective assessment of subtyping method performance and paving the way for the improved application of molecular subtyping data in investigations of infectious disease.

Genomic insights from whole genome sequencing of four clonal outbreak Campylobacter jejuni assessed within the global C. jejuni population

BACKGROUND

Whole genome sequencing (WGS) is useful for determining clusters of human cases, investigating outbreaks, and defining the population genetics of bacteria. It also provides information about other aspects of bacterial biology, including classical typing results, virulence, and adaptive strategies of the organism. Cell culture invasion and protein expression patterns of four related multilocus sequence type 21 (ST21) C. jejuni isolates from a significant Canadian water-borne outbreak were previously associated with the presence of a CJIE1 prophage. Whole genome sequencing was used to examine the genetic diversity among these isolates and confirm that previous observations could be attributed to differential prophage carriage. Moreover, we sought to determine the presence of genome sequences that could be used as surrogate markers to delineate outbreak-associated isolates.

RESULTS

Differential carriage of the CJIE1 prophage was identified as the major genetic difference among the four outbreak isolates. High quality single-nucleotide variant (hqSNV) and core genome multilocus sequence typing (cgMLST) clustered these isolates within expanded datasets consisting of additional C. jejuni strains. The number and location of homopolymeric tract regions was identical in all four outbreak isolates but differed from all other C. jejuni examined. Comparative genomics and PCR amplification enabled the identification of large chromosomal inversions of approximately 93 kb and 388 kb within the outbreak isolates associated with transducer-like proteins containing long nucleotide repeat sequences. The 93-kb inversion was characteristic of the outbreak-associated isolates, and the gene content of this inverted region displayed high synteny with the reference strain.

CONCLUSIONS

The four outbreak isolates were clonally derived and differed mainly in the presence of the CJIE1 prophage, validating earlier findings linking the prophage to phenotypic differences in virulence assays and protein expression. The identification of large, genetically syntenous chromosomal inversions in the genomes of outbreak-associated isolates provided a unique method for discriminating outbreak isolates from the background population. Transducer-like proteins appear to be associated with the chromosomal inversions. CgMLST and hqSNV analysis also effectively delineated the outbreak isolates within the larger C. jejuni population structure.

Comparative genomic fingerprinting of Campylobacter: application in routine public health surveillance and epidemiological investigations

A subtyping methodology for Campylobacter, Comparative Genomic Fingerprinting (CGF40), has been described recently. The objective of this study was to assess the utility of CGF40 as a tool to enhance routine public health surveillance of campylobacteriosis. Isolates of Campylobacter from across the province were requested and sent for CGF40 subtyping. Epidemiological data from cases reported to public health officials in Nova Scotia, Canada, from January 2012 to March 2015 were linked with blinded CGF40 subtyping results. CGF40 was epidemiologically valid; subtyping discerned known epidemiologically related isolates and augmented case-finding. Predominant sources and locations of subtype detection from the national reference database showed some study subtypes were rare and even novel to the database, while others were more commonly identified over multiple years and with exposures locally and internationally. A case-case study design was applied to examine risk factors for the most common CGF40 subtypes detected. Differences in the epidemiology of different CGF40 subtypes were observed. Statistically significant associations were noted for specific subtypes with rural residence, local exposure, contact with a pet dog or cat, contact with chickens, and drinking unpasteurized milk. With prospective use, CGF40 could potentially identify unrecognized outbreaks and contribute to epidemiological investigations of case clusters.

Prevalence and Characteristics of Salmonella and Campylobacter in Retail Poultry Meat in Japan

This study was performed to determine the prevalence, antimicrobial susceptibility, and genetic relatedness of Salmonella enterica subsp. enterica and Campylobacter spp. in poultry meat, and to analyze the association of genetic types of these bacteria with their geographical distribution and antimicrobial resistance profiles. Salmonella and Campylobacter isolates have been detected, respectively, in 54 and 71 samples out of 100 samples tested. Nine Salmonella serotypes were found, including S. enterica subsp. enterica serovar Infantis (33%), Schwarzengrund (12%), Manhattan (9%), and others. Campylobacter jejuni and C. coli were detected in 64 (64%) and 14 (14%) samples, respectively. S. enterica subsp. enterica isolates were very frequently resistant to tetracycline (78.3%) and streptomycin (68.3%). Many C. jejuni and C. coli isolates were resistant to sulfamethoxazole/trimethoprim (90.5%), nalidixic acid (47.3%), ampicillin (45.9%), and ciprofloxacin (40.5%). Cluster analysis was performed for the Salmonella isolates using pulsed-field gel electrophoresis (PFGE) data. For Campylobacter isolates, the cluster analysis was based on both PFGE and comparative genomic fingerprinting. The molecular typing results were compared with the information about antimicrobial resistance and geographical locations in which the poultry meat was produced. This analysis revealed that C. jejuni strains with a particular genotype and antimicrobial resistance profile are spreading in specific areas of Japan.

Cluster Analysis of Campylobacter jejuni Genotypes Isolated from Small and Medium-Sized Mammalian Wildlife and Bovine Livestock from Ontario Farms

Using data collected from a cross-sectional study of 25 farms (eight beef, eight swine and nine dairy) in 2010, we assessed clustering of molecular subtypes of C. jejuni based on a Campylobacter-specific 40 gene comparative genomic fingerprinting assay (CGF40) subtypes, using unweighted pair-group method with arithmetic mean (UPGMA) analysis, and multiple correspondence analysis. Exact logistic regression was used to determine which genes differentiate wildlife and livestock subtypes in our study population. A total of 33 bovine livestock (17 beef and 16 dairy), 26 wildlife (20 raccoon (Procyon lotor), five skunk (Mephitis mephitis) and one mouse (Peromyscus spp.) C. jejuni isolates were subtyped using CGF40. Dendrogram analysis, based on UPGMA, showed distinct branches separating bovine livestock and mammalian wildlife isolates. Furthermore, two-dimensional multiple correspondence analysis was highly concordant with dendrogram analysis showing clear differentiation between livestock and wildlife CGF40 subtypes. Based on multilevel logistic regression models with a random intercept for farm of origin, we found that isolates in general, and raccoons more specifically, were significantly more likely to be part of the wildlife branch. Exact logistic regression conducted gene by gene revealed 15 genes that were predictive of whether an isolate was of wildlife or bovine livestock isolate origin. Both multiple correspondence analysis and exact logistic regression revealed that in most cases, the presence of a particular gene (13 of 15) was associated with an isolate being of livestock rather than wildlife origin. In conclusion, the evidence gained from dendrogram analysis, multiple correspondence analysis and exact logistic regression indicates that mammalian wildlife carry CGF40 subtypes of C. jejuni distinct from those carried by bovine livestock. Future studies focused on source attribution of C. jejuni in human infections will help determine whether wildlife transmit Campylobacter jejuni directly to humans.

Molecular and Statistical Analysis of Campylobacter spp. and Antimicrobial-Resistant Campylobacter Carriage in Wildlife and Livestock from Ontario Farms

The objectives of this study were to (i) compare the carriage of Campylobacter and antimicrobial-resistant Campylobacter among livestock and mammalian wildlife on Ontario farms, and (ii) investigate the potential sharing of Campylobacter subtypes between livestock and wildlife. Using data collected from a cross-sectional study of 25 farms in 2010, we assessed associations, using mixed logistic regression models, between Campylobacter and antimicrobial-resistant Campylobacter carriage and the following explanatory variables: animal species (beef, dairy, swine, raccoon, other), farm type (swine, beef, dairy), type of sample (livestock or wildlife) and Campylobacter species (jejuni, coli, other). Models included a random effect to account for clustering by farm where samples were collected. Samples were subtyped using a Campylobacter-specific 40 gene comparative fingerprinting assay. A total of 92 livestock and 107 wildlife faecal samples were collected, and 72% and 27% tested positive for Campylobacter, respectively. Pooled faecal samples from livestock were significantly more likely to test positive for Campylobacter than wildlife samples. Relative to dairy cattle, pig samples were at significantly increased odds of testing positive for Campylobacter. The odds of isolating Campylobacter jejuni from beef cattle samples were significantly greater compared to dairy cattle and raccoon samples. Fifty unique subtypes of Campylobacter were identified, and only one subtype was found in both wildlife and livestock samples. Livestock Campylobacter isolates were significantly more likely to exhibit antimicrobial resistance (AMR) compared to wildlife Campylobacter isolates. Campylobacter jejuni was more likely to exhibit AMR when compared to C. coli. However, C. jejuni isolates were only resistant to tetracycline, and C.  coli isolates exhibited multidrug resistance patterns. Based on differences in prevalence of Campylobacter spp. and resistant Campylobacter between livestock and wildlife samples, and the lack of similarity in molecular subtypes and AMR patterns, we concluded that the sharing of Campylobacter species between livestock and mammalian wildlife was uncommon.

Discriminative power of Campylobacter phenotypic and genotypic typing methods

The aim of this study was to compare different typing methods, individually and combined, for use in the monitoring of Campylobacter in food. Campylobacter jejuni (n=94) and Campylobacter coli (n=52) isolated from different broiler meat carcasses were characterized using multilocus sequence typing (MLST), flagellin gene A restriction fragment length polymorphism typing (flaA-RFLP), antimicrobial resistance profiling (AMRp), the presence/absence of 5 putative virulence genes; and, exclusively for C. jejuni, the determination of lipooligosaccharide (LOS) class. Discriminatory power was calculated by the Simpson's index of diversity (SID) and the congruence was measured by the adjusted Rand index and adjusted Wallace coefficient. MLST was individually the most discriminative typing method for both C. jejuni (SID=0.981) and C. coli (SID=0.957). The most discriminative combination with a SID of 0.992 for both C. jejuni and C. coli was obtained by combining MLST with flaA-RFLP. The combination of MLST with flaA-RFLP is an easy and feasible typing method for short-term monitoring of Campylobacter in broiler meat carcass.

Campylobacter species in animal, food, and environmental sources, and relevant testing programs in Canada

Campylobacter species, particularly thermophilic campylobacters, have emerged as a leading cause of human foodborne gastroenteritis worldwide, with Campylobacter jejuni, Campylobacter coli, and Campylobacter lari responsible for the majority of human infections. Although most cases of campylobacteriosis are self-limiting, campylobacteriosis represents a significant public health burden. Human illness caused by infection with campylobacters has been reported across Canada since the early 1970s. Many studies have shown that dietary sources, including food, particularly raw poultry and other meat products, raw milk, and contaminated water, have contributed to outbreaks of campylobacteriosis in Canada. Campylobacter spp. have also been detected in a wide range of animal and environmental sources, including water, in Canada. The purpose of this article is to review (i) the prevalence of Campylobacter spp. in animals, food, and the environment, and (ii) the relevant testing programs in Canada with a focus on the potential links between campylobacters and human health in Canada.

Extensive characterization of Campylobacter jejuni chicken isolates to uncover genes involved in the ability to compete for gut colonization

BACKGROUND

Campylobacter jejuni is responsible for human foodborne enteritis. This bacterium is a remarkable colonizer of the chicken gut, with some strains outcompeting others for colonization. To better understand this phenomenon, the objective of this study was to extensively characterize the phenotypic performance of C. jejuni chicken strains and associate their gut colonizing ability with specific genes.

RESULTS

C. jejuni isolates (n = 45) previously analyzed for the presence of chicken colonization associated genes were further characterized for phenotypic properties influencing colonization: autoagglutination and chemotaxis as well as adhesion to and invasion of primary chicken caecal cells. This allowed strains to be ranked according to their in vitro performance. After their in vitro capacity to outcompete was demonstrated in vivo, strains were then typed by comparative genomic fingerprinting (CGF). In vitro phenotypical properties displayed a linear variability among the tested strains. Strains possessing higher scores for phenotypical properties were able to outcompete others during chicken colonization trials. When the gene content of strains was compared, some were associated with different phenotypical scores and thus with different outcompeting capacities. Use of CGF profiles showed an extensive genetic variability among the studied strains and suggested that the outcompeting capacity is not predictable by CGF profile.

CONCLUSION

This study revealed a wide array of phenotypes present in C. jejuni strains, even though they were all recovered from chicken caecum. Each strain was classified according to its in vitro competitive potential and its capacity to compete for chicken gut colonization was associated with specific genes. This study also exposed the disparity existing between genetic typing and phenotypical behavior of C. jejuni strains.

Development of a comparative genomic fingerprinting assay for rapid and high resolution genotyping of Arcobacter butzleri

Background

Molecular typing methods are critical for epidemiological investigations, facilitating disease outbreak detection and source identification. Study of the epidemiology of the emerging human pathogen Arcobacter butzleri is currently hampered by the lack of a subtyping method that is easily deployable in the context of routine epidemiological surveillance. In this study we describe a comparative genomic fingerprinting (CGF) method for high-resolution and high-throughput subtyping of A. butzleri. Comparative analysis of the genome sequences of eleven A. butzleri strains, including eight strains newly sequenced as part of this project, was employed to identify accessory genes suitable for generating unique genetic fingerprints for high-resolution subtyping based on gene presence or absence within a strain.

Results

A set of eighty-three accessory genes was used to examine the population structure of a dataset comprised of isolates from various sources, including human and non-human animals, sewage, and river water (n=156). A streamlined assay (CGF₄₀) based on a subset of 40 genes was subsequently developed through marker optimization. High levels of profile diversity (121 distinct profiles) were observed among the 156 isolates in the dataset, and a high Simpson’s Index of Diversity (ID) observed (ID > 0.969) indicate that the CGF₄₀ assay possesses high discriminatory power. At the same time, our observation that 115 isolates in this dataset could be assigned to 29 clades with a profile similarity of 90% or greater indicates that the method can be used to identify clades comprised of genetically similar isolates.

Conclusions

The CGF₄₀ assay described herein combines high resolution and repeatability with high throughput for the rapid characterization of A. butzleri strains. This assay will facilitate the study of the population structure and epidemiology of A. butzleri.

Electronic supplementary material

The online version of this article (doi:10.1186/s12866-015-0426-4) contains supplementary material, which is available to authorized users.

Characterization of the Campylobacter jejuni population in the barnacle geese reservoir

Campylobacter spp. are the most common cause of bacterial gastroenteritis worldwide and have been isolated from a wide number of different hosts and environmental sources. Waterfowl is considered a natural reservoir for this zoonotic bacterium and may act as a potential infection source for human campylobacteriosis. In this study, faecal samples from 924 barnacle geese were tested for the presence of C. jejuni and C. coli. The resulting C. jejuni and C. coli populations were characterized by multilocus sequence typing (MLST), structure analysis by BAPS and phylogenetic analysis based on full genome sequences. The prevalences of C. jejuni in barnacle geese faeces were 11.5% and 23.1% in 2011 and 2012, respectively, and only 0.2% of the samples were positive for C. coli in both years. Furthermore, a possible adaption of the clonal complexes (CCs) ST-702 and ST-1034 to the barnacle geese reservoir was found, as these two CCs represented the majority of the typed isolates and were repeatedly isolated from different flocks at several time-points. Further core genome phylogenetic analysis using ClonalFrame revealed a formation of a distinct monophyletic lineage by these two CCs, suggesting a certain degree of clonality of the C. jejuni population adapted to barnacle geese. Therefore, although STs also commonly found in humans patients (e.g. ST-45) were among the barnacle geese C. jejuni isolates, this reservoir is probably an infrequent source for human campylobacteriosis.

Comparative variation within the genome of Campylobacter jejuni NCTC 11168 in human and murine hosts

Campylobacteriosis incited by C. jejuni is a significant enteric disease of human beings. A person working with two reference strains of C. jejuni National Collection of Type Cultures (NCTC) 11168 developed symptoms of severe enteritis including bloody diarrhea. The worker was determined to be infected by C. jejuni. In excess of 50 isolates were recovered from the worker's stool. All of the recovered isolates and the two reference strains were indistinguishable from each other based on comparative genomic fingerprint subtyping. Whole genome sequence analysis indicated that the worker was infected with a C. jejuni NCTC 11168 obtained from the American Type Culture Collection; this strain (NCTC 11168-GSv) is the genome sequence reference. After passage through the human host, major genetic changes including indel mutations within twelve contingency loci conferring phase variations were detected in the genome of C. jejuni. Specific and robust single nucleotide polymorphism (SNP) changes in the human host were also observed in two loci (Cj0144c, Cj1564). In mice inoculated with an isolate of C. jejuni NCTC 11168-GSv from the infected person, the isolate underwent further genetic variation. At nine loci, mutations specific to inoculated mice including five SNP changes were observed. The two predominant SNPs observed in the human host reverted in mice. Genetic variations occurring in the genome of C. jejuni in mice corresponded to increased densities of C. jejuni cells associated with cecal mucosa. In conclusion, C. jejuni NCTC 11168-GSv was found to be highly virulent in a human being inciting severe enteritis. Host-specific mutations in the person with enteritis occurred/were selected for in the genome of C. jejuni, and many were not maintained in mice. Information obtained in the current study provides new information on host-specific genetic adaptation by C. jejuni.

Double-locus sequence typing using porA and peb1A for epidemiological studies of Campylobacter jejuni

Campylobacter jejuni is the leading cause of foodborne bacterial gastroenteritis worldwide. Bacterial typing schemes play an important role in epidemiological investigations to trace the source and route of transmission of the infectious agent by identifying outbreak and differentiating among sporadic infections. In this study, a double-locus sequence typing (DLST) scheme for C. jejuni based on concatenated partial sequences of porA and peb1A genes is proposed. The DLST scheme was validated using 50 clinical and environmental C. jejuni strains isolated from human (C5, H, H15-H19), chicken (CH1-CH15), water (W2-W17), and ovine samples (OV1-OV6). The scheme was found to be highly discriminatory (discrimination index [DI]=0.964) and epidemiologically concordant based on C. jejuni strains studied. The DLST showed discriminatory power above 0.95 and excellent congruence to multilocus sequence typing and can be recommended as a rapid and low-cost typing scheme for epidemiological investigation of C. jejuni. It is suggested that the DLST scheme is suitable for identification of outbreak strains and differentiation of the sporadic infection strains.

Molecular epidemiology of Campylobacter jejuni human and chicken isolates from two health units

A study was conducted over a 2-year period in the Perth District and Wellington-Dufferin-Guelph health units in Ontario, with an objective of using comparative genomic fingerprinting (CGF) with a 40-gene assay (CGF40) to investigate the association between human cases of campylobacteriosis and spatially and temporally related Campylobacter isolates from retail chicken. CGF results were available for isolates from 115 human cases and 718 retail chicken samples. These data were combined with CGF results from a large reference database of Campylobacter isolates. Isolates were categorized into types based on >90% CGF40 fingerprint similarity (CGF-90%). CGF-90% types were categorized as chicken associated (CA90) when the proportion of animal isolates in the given type that originated from chicken was at least 80% and was statistically significant. Risk factor data were collected from cases by questionnaire. Urban cases were significantly more likely than rural cases to be CA90 and there were significantly fewer CA90 cases in the second year of the study. Due to the population distribution in Canada and most industrialized countries, the majority of campylobacteriosis cases are urban dwellers. Therefore, the association between urban cases and chicken-associated types of Campylobacter emphasizes the importance of educational and food safety efforts to reduce the impact of Campylobacter from retail chicken on public health. Sources other than chicken may be more important for rural dwellers.

Campylobacter jejuni colonization is associated with a dysbiosis in the cecal microbiota of mice in the absence of prominent inflammation

Background

Campylobacter jejuni causes enterocolitis in humans, but does not incite disease in asymptomatic carrier animals. To survive in the intestine, C. jejuni must successfully compete with the microbiota and overcome the host immune defense. Campylobacter jejuni colonization success varies considerably amongst individual mice, and we examined the degree to which the intestinal microbiota was affected in mice (i.e. a model carrier animal) colonized by C. jejuni at high relative to low densities.

Methods

Mice were inoculated with C. jejuni or buffer, and pathogen shedding and intestinal colonization were measured. Histopathologic scoring and quantification of mRNA expression for α-defensins, toll-like receptors, and cytokine genes were conducted. Mucosa-associated bacterial communities were characterized by two approaches: multiplexed barcoded pyrosequencing and terminal restriction fragment length polymorphism analysis.

Results

Two C. jejuni treatments were established based on the degree of cecal and colonic colonization; C. jejuni Group A animals were colonized at high cell densities, and C. jejuni Group B animals were colonized at lower cell densities. Histological examination of cecal and colonic tissues indicated that C. jejuni did not incite visible pathologic changes. Although there was no significant difference among treatments in expression of mRNA for α-defensins, toll-like receptors, or cytokine genes, a trend for increased expression of toll-like receptors and cytokine genes was observed for C. jejuni Group A. The results of the two methods to characterize bacterial communities indicated that the composition of the cecal microbiota of C. jejuni Group A mice differed significantly from C. jejuni Group B and Control mice. This difference was due to a reduction in load, diversity and richness of bacteria associated with the cecal mucosa of C. jejuni Group A mice.

Conclusions

High density colonization by C. jejuni is associated with a dysbiosis in the cecal microbiota independent of prominent inflammation.

Current methods for molecular typing of Campylobacter species

Campylobacter remains one of the most common bacterial causes of gastroenteritis worldwide. Tracking sources of this organism is challenging due to the large numbers of human cases, and the prevalence of this organism throughout the environment due to growth in a wide range of animal species. Many molecular subtyping methods have been developed to characterize Campylobacter species, but only a few are commonly used in molecular epidemiology studies. This review examines the applicability of these methods, as well as the role that emerging whole genome sequencing technologies will play in tracking sources of Campylobacter spp. infection.