Genetic diversity of Campylobacter jejuni isolates from farm animals and the farm environment

Meta-analyses of the global multilocus genotypes of the human pathogen Campylobacter jejuni

Campylobacter infections are a leading cause of bacterial diarrheal illness worldwide, with increasing reports of outbreaks in both developing and developed countries. Most studies investigating strain genotypes and epidemiology of Campylobacter jejuni examined on a local scale. Using the archived multilocus sequence typing data at seven loci, and associated strain metadata from the PubMLST database, here we investigated the spatial and temporal genetic structure of the global population of C. jejuni. Our analyses revealed evidence for clonal dispersals of multiple sequence types (STs) among countries and continents. However, despite the observed clonal dispersal and that most genetic variations were found within individual geographic subpopulations, both the non-clone-corrected and clone-corrected samples showed evidence of significant genetic differentiation among national and continental subpopulations, with non-clone-corrected samples showing greater differentiation than clone-corrected samples. Phylogenetic incompatibility analyses provided evidence for recombination within each continental subpopulation. However, linkage disequilibrium analyses rejected the hypothesis of random recombination across the samples. Temporally, multiple STs were found to persist across four decades and the five globally most common STs showed relatively stable frequencies over the last two decades. We discussed the implications of our results to food security, disease transmission, and public health management.

Prevalence and Subtype Characterization of Campylobacter in Ceca of Commercial Broiler Chickens at Processing - A 452 Flock, Seven-year Survey

Human Campylobacter infections have been associated with chicken and other poultry meat products. Environmental conditions such as temperature and season can affect Campylobacter recoverability from chicken meat products. In the presented study, we sought to investigate the relationship between ambient weather conditions and the isolation of Campylobacter from chicken flocks, as well as the subtype of these isolates. Campylobacter was isolated from the ceca of broilers collected in a commercial processing facility over 7 years, representing 452 flocks. Isolates were subjected to whole-genome sequencing and subtyping by multilocus sequence typing (MLST). Approximately 60% (269/452) of flocks sampled were positive for Campylobacter. There was no significant effect on the presence of detectable Campylobacter by month, season, temperature, or rainfall during grow-out or transportation. Sixty-eight different STs were detected; 45 C. jejuni and 23 C. coli. Diversity as measured by Shannon's diversity index was higher in the spring and fall than in mid-winter and summer. We concluded that in the warm temperate climate of the Southeastern U.S., seasonality does not affect the rate of Campylobacter isolation from broilers, but the diversity of isolates was higher in the milder spring and fall seasons.

Aerotolerance and Multi-Locus Sequence Typing of Campylobacter jejuni Isolated from Commercial Broiler Processing Plants

Campylobacter jejuni is one of the leading causes of acute diarrhea in the United States. Despite being a microaerophilic pathogen, C. jejuni continues to endure within the domain of food production, especially in poultry processing. Recent research on aerotolerance indicates that close monitoring of this pathogen is necessary. A total of 40 C. jejuni isolates previously obtained from commercial broiler processing plants were analyzed for aerotolerance and genetic diversity. In addition, the effect of aerotolerance and storage time (days) on the survival of C. jejuni on broiler drumsticks at refrigeration (4 °C) and freezing conditions (-20 °C) was also evaluated. Out of 40 isolates, 25 (62.5%) were aero-sensitive (AS), 10 (25%) were intermediately aerotolerant (IAT), and 5 (12.5%) were hyper aerotolerant (HAT). The isolates belonged to four clonal complexes (CCs) and six sequence types, with the majority of isolates assigned to the CC-353 clonal complex. C. jejuni counts were reduced by 0.40 log CFU/g after 7 days at 4 °C and by 1.50 log CFU/g after 14 days at -20 °C, respectively, irrespective of aerotolerance (p < 0.001). At both refrigeration (p < 0.013) and freezing (p < 0.001), HAT showed greater reductions as compared to AS and IAT. These findings suggest that both refrigeration and freezing reduce C. jejuni counts.

Outbreaks of Campylobacteriosis Caused by Drinking Raw Milk in Japan: Evidence of Relationship Between Milk and Patients by Using Whole Genome Sequencing

Raw milk may contain some infectious bacteria and usually requires pasteurization before drinking. In this study, we report rare outbreaks of campylobacteriosis associated with raw milk in Japan, and the application of whole genome sequencing (WGS) to studies on foodborne diseases. In August 2018, there were three outbreaks of campylobacteriosis, presumably caused by the consumption of unpasteurized raw milk, derived from the same farm; thus, these three outbreaks seemed to be associated with a single contaminant at the farm. Therefore, we analyzed Campylobacter jejuni isolates obtained at the three locations using several genetic methods. The sequence type of each isolate, revealed by multilocus sequence typing, was ST-61, and the profile determined using pulsed-field gel electrophoresis was the same; however, neither method could distinguish these from previously obtained strains. Subsequently, we performed WGS and single nucleotide variant (SNV) analysis that provided evidence of clonality, indicating that C. jejuni contamination was attributed to the farm. As in this study, evidence suggests that SNV analysis provides molecular biological support in cases with sufficient epidemiological information. Hence, similar analytical methods may be used in other sporadic cases to elucidate the relevance of the cases.

Comparative genomics and phylogenomics of Campylobacter unveil potential novel species and provide insights into niche segregation

Campylobacter is a bacterial genus associated with community outbreaks and gastrointestinal symptoms. Studies on Campylobacter generally focus on specific pathogenic species such as C. coli and C. jejuni. Currently, there are thousands of publicly available Campylobacter genomes, allowing a more complete assessment of the genus diversity. In this work, we report a network-based analysis of all available Campylobacter genomes to explore the genus structure and diversity, revealing potentially new species and elucidating genus features. We also hypothesize that the previously established Clade III of C. coli is in fact a novel species (referred here as Campylobacter spp12). Finally, we found a negative correlation between pangenome fluidity and saturation coefficient, with potential implications to the lifestyles of distinct Campylobacter species. Since pangenome analysis depends on the number of available genomes, this correlation could help estimate pangenome metrics of Campylobacter species with less sequenced genomes, helping understand their lifestyle and niche adaptation. Together, our results indicate that the Campylobacter genus should be re-evaluated, with particular attention to the interplay between genome structure and niche segregation.

Investigation on the colonisation of Campylobacter strains in the pig intestine depending on available metabolites

Campylobacter (C.) spp. represent one of the most important causes for food-borne bacterial pathogen in humans worldwide. The aim of this study was to investigate metabolic requirements of two Campylobacter strains of different species based on substrate utilisation (in vitro). Based on these results, a correlation between the colonisation and the available substrates in different intestinal sections was recorded using an animal model. Campylobacter coli (ST-5777) and C. jejuni (ST-122) were used to inoculate 16 pigs, respectively, and one group of 16 pigs was used as control. The strains differed significantly in substrate utilisation - C. coli was able to metabolise various substrates (acetate, asparagine, serine, fucose, and propionate), while C. jejuni only utilised serine. Metabolomic analysis of intestinal content from different gut sections showed the presence of all previously tested metabolites, except for fucose. A significantly larger amount of glucose was found in the jejunum of those pigs infected with C. coli, while neither strain utilised it in vitro. The analysis of the intestinal contents revealed a very low proportion of Campylobacterales in the total microbiome, suggesting that the small percentage of the inoculated Campylobacter strains in the gut microflora of the animals is too low to cause differences between the control and infected groups in the composition of the metabolome. Nevertheless, knowledge of specific nutritional requirements of the pathogens combined with proof of different metabolites in the intestinal segments may provide clues about the site of colonisation in the host and improve our understanding of this zoonotic germ.

European Starlings (Sturnus vulgaris) as Vectors and Reservoirs of Pathogens Affecting Humans and Domestic Livestock

European starlings are an abundant, widespread avian species frequently found in close association with human development and agriculture. The ability of starlings to carry and disperse pathogens of humans and domesticated livestock has received considerable attention, including studies of enteric bacteria, viruses, and some fungi. To investigate the importance of European starlings as disease vectors, I reviewed and assessed the available literature, comprising several hundred published papers. Although a wide variety of potential pathogens have been reported in starlings, the strongest evidence suggests that they may be responsible for harboring and dispersing some species of enteric bacteria, with Escherichia coli and Campylobacter jejuni of perhaps greatest interest, and primarily in the context of dairies, concentrated animal feeding operations, and other intensive livestock agriculture.

Population Biology and Comparative Genomics of Campylobacter Species

The zoonotic pathogen Campylobacter is the leading cause for bacterial foodborne infections in humans. Campylobacters are most commonly transmitted via the consumption of undercooked poultry meat or raw milk products. The decreasing costs of whole genome sequencing enabled large genome-based analyses of the evolution and population structure of this pathogen, as well as the development of novel high-throughput molecular typing methods. Here, we review the evolutionary development and the population diversity of the two most clinically relevant Campylobacter species; C. jejuni and C. coli. The state-of-the-art phylogenetic studies showed clustering of C. jejuni lineages into host specialists and generalists with coexisting lifestyles in chicken and livestock-associated hosts, as well as the separation of C. coli isolates of riparian origin (waterfowl, water) from C. coli isolated from clinical and farm-related samples. We will give an overview of recombination between both species and the potential impact of horizontal gene transfer on host adaptation in Campylobacter. Additionally, this review briefly places the current knowledge of the population structure of other Campylobacter species such as C. lari, C. concisus and C. upsaliensis into perspective. We also provide an overview of how molecular typing methods such as multilocus sequence typing (MLST) and whole genome MLST have been used to detect and trace Campylobacter outbreaks along the food chain.

Prevalence and antimicrobial susceptibility of Campylobacter isolated from retail chickens in Thailand

Campylobacter is an important foodborne pathogen causing bacterial gastroenteritis worldwide; however, there has been a lack of information over the past decade on its occurrence, antibiotic susceptibility and genetic diversity in Thailand. Poultry meat is considered as a reservoir for transmission of Campylobacter to humans. This study determines the prevalence and antimicrobial resistance patterns of Campylobacter spp. on chicken samples purchased from 50 local wet markets and supermarkets in central Thailand. Of the 296 samples, 99 (33.5%) were contaminated with C. jejuni, 54 (18.2%) were C. coli and 15 (5.1%) were contaminated with both species. Antibiotic resistance rate is higher among C. coli isolates; 100%, 76.8%, 37.7%, 36.2% and 13.0% were resistant to quinolones, cyclines, macrolides, clindamycin and gentamicin, respectively. Most of the C. jejuni isolates were resistant to quinolones (79.8%) and cyclines (38.6%) whereas resistance to macrolides, clindamycin and gentamicin was found to be 1.8%. Multi-drug resistance (i.e. to three or more unrelated antimicrobials) was detected in 37.7% of C. coli and 1.8% of C. jejuni isolates. This study has revealed high contamination rates and alarming levels of antimicrobial resistance in Campylobacter spp. isolated from retail chicken samples in Thailand, suggesting the necessity of implementing interventions to reduce its prevalence from farm to table in the country.

Quantitative approach to assess the compliance to a performance objective (PO) of Campylobacter jejuni in poultry meat in France

Predictive modelling is used in microbiological risk assessment to quantify the growth and inactivation of microorganisms through the use of mathematical models. Campylobacter jejuni is one of the main foodborne pathogens and broiler meat is considered as the most important source of human campylobacteriosis. The purpose of this study was to assess the effects of heating and chilling during the poultry slaughter process on inactivation kinetics of Campylobacter jejuni during chilled storage in order to predict its contamination level prior to preparation and consumption in the consumer's home, and then to assess the compliance to a Performance Objective (PO). Three strains of C. jejuni were submitted to consecutive heat (54 °C for 3 min) and cold (3 °C for 2 h) stresses, mimicking the two main slaughtering steps, i.e. scalding and chilling, by inoculating chicken fillets with three different concentrations (4, 6 and 8 log₁₀ CFU/g). Fillets were then stored at 6 °C during 17 days under the modified atmosphere currently used by food processors (70% O₂/30% CO₂). For all strains, bacterial log reduction was the lowest when inoculated at 8 log₁₀ CFU/g. One strain showed an enhanced resistance during cold storage after application of stressing steps, suggesting an impact of the cell history on further bacterial resistance. Taking strain variability into account, after six days of storage, predictions showed compliance of ready-to-be-cooked chicken meat with a hypothetical PO of 2.55 log₁₀ CFU/g, value set before the meat enters the consumer's home by the ICMSF (International Commission on Microbiological Specifications for Foods). This study opens the path to assess the compliance to a PO of Campylobacter jejuni in poultry meat and more generally provides inputs to refine microbiological risk assessment by taking into account the cell history and more particularly the impact of stressful steps on the subsequent inactivation at consumer's home.

Prevalence and Genetic Diversity of C. Jejuni Isolated from Broilers and their Environment Using flaA-RFLP Typing and MLST Analysis

Campylobacter is highly diverse genetically and also undergoes frequent intraspecific recombination. A major source of campylobacteriosis, which is transmitted to humans is found in poultry. The assessment of the genetic diversity among Campylobacter population is critical to our understanding of the epidemiology. The genetic diversity of Campylobacter jejuni isolates in broilers and their environment were investigated by flaA-restriction fragment length polymorphism (RFLP) and multilocus sequence typing (MLST). The study revealed that 92.3% of the examined broiler flocks were contaminated with Campylobacter spp. A total number of 35 different flaA types defined by flaA-RFLP were found in 448 C. jejuni isolates originated from broilers, litter, puddles, zones, anteroom and wild birds. The most dominant flaA type was XXV. MLST defined 20 sequence types (STs) belonging to 10 clonal complexes (CCs). Among all the STs 9 isolates (15%) were consigned to 2 different STs (ST-7413 and ST-4800), which could not be assigned. The most common CCs were ST-21 and ST-179. The ST-21 CC was common in broilers and environment (puddle water and concentric zones) and the ST-179 CC was specific to wild birds, but also was found in puddle water and concentric zones.

Gene pool transmission of multidrug resistance among Campylobacter from livestock, sewage and human disease

The use of antimicrobials in human and veterinary medicine has coincided with a rise in antimicrobial resistance (AMR) in the food-borne pathogens Campylobacter jejuni and Campylobacter coli. Faecal contamination from the main reservoir hosts (livestock, especially poultry) is the principal route of human infection but little is known about the spread of AMR among source and sink populations. In particular, questions remain about how Campylobacter resistomes interact between species and hosts, and the potential role of sewage as a conduit for the spread of AMR. Here, we investigate the genomic variation associated with AMR in 168 C. jejuni and 92 C. coli strains isolated from humans, livestock and urban effluents in Spain. AMR was tested in vitro and isolate genomes were sequenced and screened for putative AMR genes and alleles. Genes associated with resistance to multiple drug classes were observed in both species and were commonly present in multidrug-resistant genomic islands (GIs), often located on plasmids or mobile elements. In many cases, these loci had alleles that were shared among C. jejuni and C. coli consistent with horizontal transfer. Our results suggest that specific antibiotic resistance genes have spread among Campylobacter isolated from humans, animals and the environment.

Aerotolerance and multilocus sequence typing among Campylobacter jejuni strains isolated from humans, broiler chickens, and cattle in Miyazaki Prefecture, Japan

Campylobacter jejuni is one of the leading causes of human gastroenteritis in Japan. As chickens and cattle are common reservoirs for C. jejuni, this microaerophilic, stress-sensitive bacterium can overcome and survive various stress conditions during zoonotic transmission, particularly foodborne, to humans. How C. jejuni overcomes stress conditions is, however, unclear. In the present study, 70 C. jejuni strains isolated from various sources (26 human, 20 broilers, and 24 cattle isolates) in Miyazaki, Japan, from 2010 to 2012, were subjected to multilocus sequence typing (MLST) and aerotolerance testing (aerobic shaking at 200 rpm). The results demonstrated that C. jejuni strains from Miyazaki belonged to 12 clonal complexes (CCs) and 43 sequence types (STs). CC-21 and CC-460 were mainly detected in human clinical strains. Most tested strains were aerotolerant, and only one (1.4%) was deemed sensitive to aerobic stress. Approximately 40% strains survived the 24-hr vigorous aerobic shaking at 200 rpm, and these hyper-aerotolerant strains were more prevalent in broiler and cattle isolates than in human isolates. Phylogenetic analysis divided the strains into five clusters, each showing a different pattern of host association. Thus, we have demonstrated for the first time that C. jejuni strains with increased tolerance to aerobic stress are highly prevalent in broilers and cattle in Miyazaki, Japan, and that certain clonal populations are frequently implicated in human infection in this area.

High Prevalence of Fluoroquinolone-Resistant Campylobacter Bacteria in Sheep and Increased Campylobacter Counts in the Bile and Gallbladders of Sheep Medicated with Tetracycline in Feed

Campylobacter is a major foodborne pathogen in humans and a significant cause of abortion in sheep. Although ruminants are increasingly recognized as important reservoirs for Campylobacter species, limited information is available about the molecular epidemiology and antimicrobial resistance (AMR) profiles of sheep Campylobacter Here, we describe a two-trial study that examined Campylobacter profiles in sheep and determined whether in-feed tetracycline (TET) influenced the distribution and AMR profiles of Campylobacter Each trial involved 80 commercial sheep naturally infected with Campylobacter: 40 of these sheep were medicated with tetracycline in feed, while the other 40 received feed without antibiotics. Fecal and bile samples were collected for the isolation of Campylobacter The bacterial isolates were analyzed for antimicrobial susceptibility and genotypes. The results revealed that 87.0% and 61.3% of the fecal and bile samples were positive for Campylobacter (Campylobacter jejuni and Campylobacter coli), with no significant differences between the medicated and nonmedicated groups. All but one of the tested Campylobacter isolates were resistant to tetracycline. Although fluoroquinolone (FQ) resistance remained low in C. jejuni (1.7%), 95.0% of the C. coli isolates were resistant to FQ. Genotyping revealed that C. jejuni sequence type 2862 (ST2862) and C. coli ST902 were the predominant genotypes in the sheep. Feed medication with tetracycline did not affect the overall prevalence, species distribution, and AMR profiles of Campylobacter, but it did increase the total Campylobacter counts in bile and gallbladder. These findings identify predominant Campylobacter clones, reveal the high prevalence of FQ-resistant C. coli, and provide new insights into the epidemiology of Campylobacter in sheep.IMPORTANCE Campylobacter is a major cause of foodborne illness in humans, and antibiotic-resistant Campylobacter is considered a serious threat to public health in the United States and worldwide. As a foodborne pathogen, Campylobacter commonly exists in the intestinal tract of ruminant animals, such as sheep and cattle. Results from this study reveal the predominant genotypes and high prevalence of tetracycline (TET) and fluoroquinolone (FQ) resistance in sheep Campylobacter The finding on fluoroquinolone resistance in sheep Campylobacter is unexpected, as this class of antibiotics is not used for sheep in the United States, and it may suggest the transmission of fluoroquinolone-resistant Campylobacter from cattle to sheep. Additionally, the results demonstrate that in-feed medication with tetracycline increases Campylobacter counts in gallbladders, suggesting that the antibiotic promotes Campylobacter colonization of the gallbladder. These findings provide new information on Campylobacter epidemiology in sheep, which may be useful for curbing the spread of antibiotic-resistant Campylobacter in animal reservoirs.

Extending statistical models for source attribution of zoonotic diseases: a study of campylobacteriosis

Preventing and controlling zoonoses through the design and implementation of public health policies requires a thorough understanding of transmission pathways. Modelling jointly the epidemiological data and genetic information of microbial isolates derived from cases provides a methodology for tracing back the source of infection. In this paper, the attribution probability for human cases of campylobacteriosis for each source, conditional on the extent to which each case resides in a rural compared to urban environment, is estimated. A model that incorporates genetic data and evolutionary processes is applied alongside a newly developed genetic-free model. We show that inference from each model is comparable except for rare microbial genotypes. Further, the effect of 'rurality' may be modelled linearly on the logit scale, with increasing rurality leading to the increasing likelihood of ruminant-sourced campylobacteriosis.

Characterization of Campylobacter spp. isolated from wild birds in the Antarctic and Sub-Antarctic

A lack of knowledge of naturally occurring pathogens is limiting our ability to use the Antarctic to study the impact human-mediated introduction of infectious microorganisms have on this relatively uncontaminated environment. As no large-scale coordinated effort to remedy this lack of knowledge has taken place, we rely on smaller targeted efforts to both study present microorganisms and monitor the environment for introductions. In one such effort, we isolated Campylobacter species from fecal samples collected from wild birds in the Antarctic Peninsula and the sub-Antarctic island of South Georgia. Indeed, in South Georgia, we found Campylobacter lari and the closely related Campylobacter peloridis, but also distantly related human-associated multilocus sequence types of Campylobacter jejuni. In contrast, in the Antarctic Peninsula, we found C. lari and two closely related species, Campylobacter subantarcticus and Campylobacter volucris, but no signs of human introduction. In fact, our finding of human-associated sequence types of C. jejuni in South Georgia, but not in the Antarctic Peninsula, suggests that efforts to limit the spread of infectious microorganisms to the Antarctic have so far been successful in preventing the introduction of C. jejuni. However, we do not know how it came to South Georgia and whether the same mode of introduction could spread it from there to the Antarctic Peninsula.

Multilocus sequence typing of Campylobacter jejuni and Campylobacter coli to identify potential sources of colonization in commercial turkey farms

Poultry are the main reservoir for thermophilic Campylobacter spp., which is the most common causative agent of human bacterial gastroenteritis. The epidemiology of Campylobacter in poultry, particularly in turkeys, is not completely understood. This study aimed at identifying potential sources and transmission routes of thermophilic Campylobacter spp. in commercial turkey farms. C. jejuni and C. coli isolates from breeders (n = 29, 20 C. jejuni and 9 C. coli) and their progeny (n = 51, 18 C. jejuni and 33 C. coli) reared in two different farms for three sequential production cycles were analysed by multilocus sequence typing (MLST). Strains (n = 88, 42 C. jejuni and 46 C. coli) isolated from environmental (i.e. anteroom and in-house overshoes), water (i.e. drinkers and water line), and pest (i.e. flies, Alphitobius diaperinus, and mice) sources were also examined. MLST of C. jejuni and C. coli isolates resulted in 13 and 12 different sequence types (STs) belonging to six and one previously-described clonal complexes (CCs), respectively. Three novel STs were identified. Genetic similarities were detected between isolates from fattening turkeys and the considered environmental, water, and pest sources, and with the breeders to a lesser extent. Source attribution analysis estimated that environmental and water sources accounted for most (∼75%) of fattening turkey isolates and were therefore identified as the most likely sources of flock colonization, followed by pests (∼20%) and breeders (∼5%). These sources may thus be targeted by control measures to mitigate the risk of Campylobacter colonization in commercial turkeys. RESEARCH HIGHLIGHTS High occurrence of C. jejuni and C. coli in commercial turkey flocks. High genetic diversity of C. jejuni and C. coli in commercial turkey flocks. Horizontal transmission responsible for Campylobacter colonization of commercial turkey flocks. Environmental and water sources involved in Campylobacter colonization of commercial turkey flocks. Strategies for prevention and control of Campylobacter colonization of commercial turkey flocks are needed.

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.

Campylobacter jejuni transcriptome changes during loss of culturability in water

Background

Water serves as a potential reservoir for Campylobacter, the leading cause of bacterial gastroenteritis in humans. However, little is understood about the mechanisms underlying variations in survival characteristics between different strains of C. jejuni in natural environments, including water.

Results

We identified three Campylobacter jejuni strains that exhibited variability in their ability to retain culturability after suspension in tap water at two different temperatures (4°C and 25°C). Of the three, strains C. jejuni M1 exhibited the most rapid loss of culturability whilst retaining viability. Using RNAseq transcriptomics, we characterised C. jejuni M1 gene expression in response to suspension in water by analyzing bacterial suspensions recovered immediately after introduction into water (Time 0), and from two sampling time/temperature combinations where considerable loss of culturability was evident, namely (i) after 24 h at 25°C, and (ii) after 72 h at 4°C. Transcript data were compared with a culture-grown control. Some gene expression characteristics were shared amongst the three populations recovered from water, with more genes being up-regulated than down. Many of the up-regulated genes were identified in the Time 0 sample, whereas the majority of down-regulated genes occurred in the 25°C (24 h) sample.

Conclusions

Variations in expression were found amongst genes associated with oxygen tolerance, starvation and osmotic stress. However, we also found upregulation of flagellar assembly genes, accompanied by down-regulation of genes involved in chemotaxis. Our data also suggested a switch from secretion via the sec system to via the tat system, and that the quorum sensing gene luxS may be implicated in the survival of strain M1 in water. Variations in gene expression also occurred in accessory genome regions. Our data suggest that despite the loss of culturability, C. jejuni M1 remains viable and adapts via specific changes in gene expression.

Will the emergence of core genome MLST end the role of in silico MLST?

The technological advancement of molecular epidemiological analysis using next-generation sequencing (NGS) for foodborne pathogens has a groundbreaking impact over the past three years. In particular, the emergence of cg (core genome) multilocus sequence typing(MLST) has a significant impact. This is because this technology made it possible for many researchers to carry out molecular epidemiological analysis on foodborne pathogens in a common language, using common definitions. The resolution of core genome MLST (cgMLST) far surpasses that of MLST, which only uses seven (usually, in some cases five) housekeeping genes. Therefore, cgMLST would in no doubt terminate the role of conventional MLST as the molecular epidemiological tool. However, the role of MLST would probably not end all together. Rather, the sequence type (ST) of the conventional MLST is expected to be used as in silico MLST by a wider range of researchers than ever in the next 10 years. This is because, with the arrival of the NGS era, we have come to be able to obtain ST of conventional MLST by simply entering the NGS text file into one's own PC. In other words, acquisition of ST data is no longer limited to researchers aiming to conduct MLST for the first place. The impact of such a change is large. In silico MLST will continue to be used as a tool for understanding the broad characteristics of bacterial strains. This review aimed to summarize the main information on STs that have been accumulated for representative foodborne pathogens, in particular for potential NGS users in this new era who have been not familiar with MLST until now.

MLST genotypes of Campylobacter jejuni isolated from broiler products, dairy cattle and human campylobacteriosis cases in Lithuania

Background

Campylobacter (C.) jejuni is the leading cause of human campylobacteriosis worldwide. We performed a molecular epidemiological study to investigate the genetic relationship among C. jejuni strains isolated from human diarrhoeal patients, broiler products and dairy cattle in Lithuania.

Methods

The C. jejuni isolates from human clinical cases, dairy cattle and broiler products were genotyped using multilocus sequence typing (MLST). Allele numbers for each housekeeping gene, sequence type (ST), and clonal complex (CC) were assigned by submitting the DNA sequences to the C. jejuni MLST database (http://pubmlst.org/campylobacter). Based on the obtained sequence data of the housekeeping genes a phylogenetic analysis of the strains was performed and a minimum spanning tree (MST) was calculated.

Results

Among the 262 C. jejuni strains (consisting of 43 strains isolated from dairy cattle, 102 strains isolated from broiler products and 117 clinical human C. jejuni strains), 82 different MLST sequence types and 22 clonal complexes were identified. Clonal complexes CC21 and CC353 predominated among the C. jejuni strains. On ST-level, five sequence types (ST-5, ST-21, ST-50, ST-464 and ST-6410) were dominating and these five STs accounted for 35.9% (n = 94) of our isolates. In addition, 51 (19.5%) C. jejuni strains representing 27 (32.9%) STs were reported for the first time in the PubMLST database (http://pubmlst.org/campylobacter). The highest Czekanowski index or proportional similarity index (PSI) was calculated for C. jejuni strains isolated from human campylobacteriosis cases and broiler products (PSI = 0.32) suggesting a strong link between broiler strains and human cases. The PSI of dairy cattle and human samples was lower (PSI = 0.11), suggesting a weaker link between bovine strains and human cases. The calculated Simpson’s index of all C. jejuni isolates showed a high genetic diversity (D = 0.96).

Conclusion

Our results suggest that broiler products are the most important source of human campylobacteriosis in Lithuania. The study provides information on MLST type distribution and genetic relatedness of C. jejuni strains from humans, broiler products and dairy cattle in Lithuania for the first time, enabling a better understanding of the transmission pathways of C. jejuni in this country.

Multilocus sequence typing of Campylobacter jejuni and Campylobacter coli isolates from poultry, cattle and humans in Nigeria

AIMS

To determine the genetic diversity of Campylobacter jejuni and Campylobacter coli isolates from Nigeria and to identify the association between multilocus sequence types and hosts (poultry, cattle and humans).

METHODS AND RESULTS

Isolates were identified using multiplex PCR assays. Multilocus sequence typing (MLST) was used to determine the genetic diversity of 36 Camp. jejuni and 24 Camp. coli strains isolated from poultry, cattle and humans. Of the 36 Camp. jejuni genotyped, 21 sequence types (ST) were found, 9 (43%) were new while of the 24 Camp. coli isolates genotyped, 22 STs were identified with 14 (64%) being new. The most prevalent sequence type was ST1932 followed by ST1036 and ST607 while the prevalent clonal complexes were CC-828, CC-460 and CC-353.

CONCLUSIONS

Campylobacter isolates from Nigeria were found to be diverse with novel genotypes. There was overlap of CC-828, CC-460 and CC-353 between the poultry, cattle and human isolates. Genetic exchange was also detected in two of the Camp. coli isolates.

SIGNIFICANCE AND IMPACT OF THE STUDY

This study highlights the genetic diversity of Campylobacter strains in Nigeria, demonstrating that Camp. jejuni and Camp. coli isolates are diverse and have both local and global strains. The predominant sequence types and clonal complexes found in this study differ from other countries; this exemplifies that different predominant Campylobacter populations exist between countries.

Variation in Campylobacter Multilocus Sequence Typing Subtypes from Chickens as Detected on Three Plating Media

The objective of this study was to compare subtypes of Campylobacter jejuni and Campylobacter coli detected on three selective Campylobacter plating media to determine whether each medium selected for different subtypes. Fifty ceca and 50 carcasses (representing 50 flocks) were collected from the evisceration line in a commercial broiler processing plant. Campylobacter was cultured and isolated from cecal contents and carcass rinses on Campy-Cefex, Campy Line, and RF Campylobacter jejuni/coli agars. When a positive result was obtained with all three media, one colony of the most prevalent morphology on each medium was selected for further analysis by full genome sequencing and multilocus sequence typing. Sequence types were assigned according to PubMLST. A total of 49 samples were positive for Campylobacter on all three media. Forty samples contained only C. jejuni , three had only C. coli , and both species were detected in six samples. From 71% of samples, Campylobacter isolates of the same sequence type were recovered on all three media. From 81.6% of samples, isolates were all from the same clonal complex. From significantly fewer samples (26%, P < 0.01), one medium recovered an isolate with a sequence type different from the type recovered on the other two media. When multiple sequence types were detected, six times the medium with the odd sequence type was Campy-Cefex, four times it was Campy-Line, and six times it was RF Campylobacter jejuni/coli . From one sample, three sequence types were detected. In most cases, all three plating media allowed detection of the same type of Campylobacter from complex naturally contaminated chicken samples.

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.

High Prevalence and Genetic Diversity of Campylobacter jejuni in Wild Crows and Pigeons

The occurrence, seasonal variation and genetic diversity of Campylobacter spp. in pigeons and crows over a 1-year period were evaluated. Campylobacter spp. were isolated from 166 (34.6 %) out of 480 wild bird faecal samples. The occurrence of Campylobacter spp. in faecal samples was higher among crows (39.2 %) than pigeons (30.0 %), (P < 0.05). Campylobacter jejuni was the most common species detected among wild bird faecal samples (98.2 %). Meanwhile, Campylobacter coli prevalence in wild bird faecal samples was low-6 %. The Simpson's diversity index of C. jejuni flaA RFLP types was lower in pigeons (D = 0.88) compared with C. jejuni isolates detected in crows (D = 0.97). Obtained results revealed that C. jejuni are widely prevalent among crows and pigeons, indicating these wild birds as potential infection sources to humans. Further studies are required to determine crows and pigeons role in zoonotic transmission of Campylobacter.

Multilocus Sequence Types of Campylobacter jejuni Isolates from Different Sources in Eastern China

Campylobacter jejuni is a major food-borne pathogen that causes human gastroenteritis in many developed countries. In our study, we applied multilocus sequence typing (MLST) technology to 167 C. jejuni isolates from diverse sources in Eastern China to examine their genetic diversity. MLST defined 94 sequence types (STs) belonging to 18 clonal complexes (CCs). Forty-five STs from 60 isolates (36%) and 22 alleles have not been previously documented in an international database. One hundred and two isolates, accounting for 61.1% of all isolates, belonged to eight clonal complexes. The eight major CCs were also the most common complexes from different sources. The most common ST type of isolates from human and food was ST-353. The dominant ST type in chicken and foods was ST-354. Among 21 STs that contained two or more different sources isolates, 15 STs contained human isolates and isolates from other sources, suggesting that potentially pathogenic strains are not restricted to specific lineages.

Insights into potential pathogenesis mechanisms associated with Campylobacter jejuni-induced abortion in ewes

Background

Campylobacter jejuni is commonly found in the gastrointestinal tract of many food-animals including sheep without causing visible clinical symptoms of disease. However, C. jejuni has been implicated in ovine abortion cases worldwide. Specifically, in the USA, the C. jejuni sheep abortion (SA) clone has been increasingly associated with sheep abortion. In vivo studies in sheep (the natural host) are needed to better characterize the virulence potential and pathogenesis of this clone.

Results

Pregnant ewes intravenously (IV) or orally inoculated with ovine or bovine abortion-associated C. jejuni SA clones exhibited partial or complete uterine prolapse with retained placenta, and abortion or stillbirth, whereas delivery of healthy lambs occurred in pregnant ewes inoculated with C. jejuni 81–176 or in the uninfected group. In sheep inoculated with the SA clone, histopathological lesions including suppurative necrotizing placentitis and/or endometritis coincided with: 1) increased apoptotic death of trophoblasts, 2) increased expression of the host genes (e.g. genes encoding interleukin IL-6 and IL-15) related to cellular necrosis and pro-inflammatory responses in uterus, and 3) decreased expression of the genes encoding GATA binding protein 6, chordin, and insulin-like 3 (INSL3) that account for embryonic development in uterus. Immunohistochemistry revealed localization of bacterial antigens in trophoblasts lining the chorioallantoic membrane of ewes inoculated with the C. jejuni SA clone.

Conclusions

The results showed that C. jejuni SA clones are capable of causing abortion or stillbirth in experimentally infected sheep. Furthermore, down- or up-regulation of specific genes in the uterus of infected pregnant ewes might implicate host genes in facilitating the disease progression. Since the C. jejuni SA strains share genotypic similarities with clones that have been isolated from human clinical cases of gastroenteritis, these strains might represent a potential public health risk.

Electronic supplementary material

The online version of this article (doi:10.1186/s12917-014-0274-8) contains supplementary material, which is available to authorized users.

Multilocus sequence typing confirms wild birds as the source of a Campylobacter outbreak associated with the consumption of raw peas

From August to September 2008, the Centers for Disease Control and Prevention (CDC) assisted the Alaska Division of Public Health with an outbreak investigation of campylobacteriosis occurring among the residents of Southcentral Alaska. During the investigation, pulsed-field gel electrophoresis (PFGE) of Campylobacter jejuni isolates from human, raw pea, and wild bird fecal samples confirmed the epidemiologic link between illness and the consumption of raw peas contaminated by sandhill cranes for 15 of 43 epidemiologically linked human isolates. However, an association between the remaining epidemiologically linked human infections and the pea and wild bird isolates was not established. To better understand the molecular epidemiology of the outbreak, C. jejuni isolates (n=130; 59 from humans, 40 from peas, and 31 from wild birds) were further characterized by multilocus sequence typing (MLST). Here we present the molecular evidence to demonstrate the association of many more human C.jejuni infections associated with the outbreak with raw peas and wild bird feces. Among all sequence types (STs) identified, 26 of 39 (67%) were novel and exclusive to the outbreak. Five clusters of overlapping STs (n=32 isolates; 17 from humans, 2 from peas, and 13 from wild birds) were identified. In particular, cluster E (n=7 isolates; ST-5049) consisted of isolates from humans,peas, and wild birds. Novel STs clustered closely with isolates typically associated with wild birds and the environment but distinct from lineages commonly seen in human infections. Novel STs and alleles recovered from human outbreak isolates allowed additional infections caused by these rare genotypes to be attributed to the contaminated raw peas.

Prevalence and genotypes of Campylobacter jejuni from urban environmental sources in comparison with clinical isolates from children

This study aimed to investigate the prevalence of Campylobacter jejuni in potential contamination sources that are not regularly monitored such as free-living urban pigeons and crows, dogs, cats and urban environmental water and to assess the possible impact on the epidemiology of campylobacteriosis in children using multilocus sequence typing (MLST). Campylobacter spp. were detected in 36.2 % of faecal samples of free-living urban birds and in 40.4 % of environmental water samples. A low prevalence of Campylobacter spp. was detected in dogs and cats, with 7.9 and 9.1 %, respectively. Further identification of isolates revealed that environmental water and pet samples were mostly contaminated by other Campylobacter spp. than C. jejuni, whereas C. jejuni was the most prevalent species in faecal samples of free-living birds (35.4 %). This species was the dominant cause of campylobacteriosis in children (91.5 %). In addition, the diversity of C. jejuni MLST types in free-living birds and children was investigated. Clonal complex (CC) 179 was predominant among free-living urban birds; however, only two isolates from children were assigned to this CC. One dog and one child isolate were assigned to the same clonal complex (CC48) and sequence type (ST) 918. The dominant two clonal complexes among the child clinical isolates (CC353 and CC21) were not detected among C. jejuni strains isolated from environmental sources examined in this study. As only two CCs were shared by environmental and child C. jejuni isolates and a high number of novel alleles and STs were found in C. jejuni isolated from free-living urban birds and environmental water, there is probably only a limited link between urban environmental sources and campylobacteriosis in children, particularly in rather cold climatic conditions.

Comparative population structure analysis of Campylobacter jejuni from human and poultry origin in Bangladesh

Campylobacter jejuni is the most important cause of antecedent infections leading to Guillain-Barré syndrome (GBS) and Miller Fisher syndrome (MFS). The objective of the present study was to define the genetic diversity, population structure, and potential role of poultry in the transmission of Campylobacter to humans in Bangladesh. We determined the population structure of C. jejuni isolated from poultry (n = 66) and patients with enteritis (n = 39) or GBS (n = 10). Lipooligosaccharide (LOS) typing showed that 50/66 (76 %) C. jejuni strains isolated from poultry could be assigned to one of five LOS locus classes (A-E). The distribution of neuropathy-associated LOS locus classes A, B, and C were 30/50 (60 %) among the typable strains isolated from poultry. The LOS locus classes A, B, and C were significantly associated with GBS and enteritis-related C. jejuni strains more than for the poultry strains [(31/38 (82 %) vs. 30/50 (60 %), p < 0.05]. Multilocus sequence typing (MLST) defined 15 sequence types (STs) and six clonal complexes (CCs) among poultry isolates, including one ST-3740 not previously documented. The most commonly identified type, ST-5 (13/66), in chicken was seen only once among human isolates (1/49) (p < 0.001). Amplified fragment length polymorphism (AFLP) revealed three major clusters (A, B, and C) among C. jejuni isolated from humans and poultry. There seems to be a lack of overlap between the major human and chicken clones, which suggests that there may be additional sources for campylobacteriosis other than poultry in Bangladesh.

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.

Role of environmental survival in transmission of Campylobacter jejuni

Campylobacter species are the most common cause of bacterial gastroenteritis, with C. jejuni responsible for the majority of these cases. Although it is clear that livestock, and particularly poultry, are the most common source, it is likely that the natural environment (soil and water) plays a key role in transmission, either directly to humans or indirectly via farm animals. It has been shown using multilocus sequence typing that some clonal complexes (such as ST-45) are more frequently isolated from environmental sources such as water, suggesting that strains vary in their ability to survive in the environment. Although C. jejuni are fastidious microaerophiles generally unable to grow in atmospheric levels of oxygen, C. jejuni can adapt to survival in the environment, exhibiting aerotolerance and starvation survival. Biofilm formation, the viable but nonculturable state, and interactions with other microorganisms can all contribute to survival outside the host. By exploiting high-throughput technologies such as genome sequencing and RNA Seq, we are well placed to decipher the mechanisms underlying the variations in survival between strains in environments such as soil and water and to better understand the role of environmental persistence in the transmission of C. jejuni directly or indirectly to humans.

Prevalence in bulk tank milk and epidemiology of Campylobacter jejuni in dairy herds in Northern Italy

Thermotolerant Campylobacter spp. are frequently the cause of human gastroenteritis and have assumed more importance in Italy following the increased consumption of raw milk. Our objectives were to determine the prevalence and genotypes of Campylobacter spp. in dairy herds and to investigate the possible sources of bulk milk contamination. Bulk milk from dairy herds (n = 282) was cultured for Campylobacter spp. and Enterobacteriaceae. At three Campylobacter jejuni-positive farms, bovine feces, pigeon intestines, milk, and water points were also investigated. Isolates were identified by PCR and genotyped using multilocus sequence typing (MLST). C. jejuni was detected in 34 (12%) bulk milk samples. The strains belonged to 14 sequence types, and the most common clonal complexes were CC-21, CC-48, and CC-403. No association was demonstrated between the presence of C. jejuni and high levels of Enterobacteriaceae in bulk milk. At the three farms examined, C. jejuni was isolated from bovine feces (25/82 [30.5%]), pigeon intestines (13/60 [21.7%]), bulk milk (10/24 [41.7%]), and water points (4/16 [25%]). MLST revealed lineages that were common between milk and bovine feces but distinct between cattle and pigeons. In one herd, C. jejuni with the same genotype was isolated repeatedly from bulk milk and a cow with an udder infection. Our results showed a high prevalence of C. jejuni in bulk milk and suggested that udder excretion, in addition to fecal matter, may be a route of bulk milk contamination. MLST analysis indicated that pigeons are probably not relevant for the transmission of C. jejuni to cattle and for milk contamination.

Molecular Typing of Campylobacter jejuni and Campylobacter coli Isolated from Various Retail Meats by MLST and PFGE

Campylobacter species are one of the leading causes of foodborne disease in the United States. Campylobacter jejuni and Campylobacter coli are the two main species of concern to human health and cause approximately 95% of human infections. Molecular typing methods, such as pulsed-field gel electrophoresis (PFGE) and multilocus sequence typing (MLST) are often used to source track foodborne bacterial pathogens. The aim of the present study was to compare PFGE and MLST in typing strains of C. jejuni and C. coli that were isolated from different Oklahoma retail meat sources. A total of 47 Campylobacter isolates (28 C. jejuni and 19 C. coli) isolated from various retail meat samples (beef, beef livers, pork, chicken, turkey, chicken livers, and chicken gizzards) were subjected to pulsed-field gel electrophoresis (PFGE) and multilocus sequence typing (MLST). PFGE was able to group the 47 Campylobacter isolates into two major clusters (one for C. jejuni and one for C. coli) but failed to differentiate the isolates according to their source. MLST revealed 21 different sequence types (STs) that belonged to eight different clonal complexes. Twelve of the screened Campylobacter isolates (8 C. jejuni and 4 C. coli) did not show any defined STs. All the defined STs of C. coli isolates belonged to ST-828 complex. The majority of C. jejuni isolates belonged to ST-353, ST-607, ST-52, ST-61, and ST-21 complexes. It is worthy to mention that, while the majority of Campylobacter isolates in this study showed STs that are commonly associated with human infections along with other sources, most of the STs from chicken livers were solely reported in human cases. In conclusion, retail meat Campylobacter isolates tested in this study particularly those from chicken livers showed relatedness to STs commonly associated with humans. Molecular typing, particularly MLST, proved to be a helpful tool in suggesting this relatedness to Campylobacter human isolates.

Campylobacteriosis in urban versus rural areas: a case-case study integrated with molecular typing to validate risk factors and to attribute sources of infection

Campylobacter infection is a leading cause of bacterial gastroenteritis worldwide, and most clinical cases appear as isolated, sporadic infections for which the source is rarely apparent. From July 2005 to December 2007 we conducted a prospective case-case study of sporadic, domestically-acquired Campylobacter enteritis in rural versus urban areas and a prevalence study of Campylobacter in animal and environmental sources in the Eastern Townships, Quebec. Isolates were typed using Multilocus Sequence Typing (MLST) to reinforce the case-case findings and to assign a source probability estimate for each human isolate. The risk of human campylobacteriosis was 1.89-fold higher in rural than urban areas. Unconditional multivariate logistic regression analysis identified two independent risk factors associated with human Campylobacter infections acquired in rural area: occupational exposure to animals (OR = 10.6, 95% CI: 1.2–91, p = 0.032), and household water coming from a private well (OR = 8.3, 95% CI: 3.4–20.4, p<0.0001). A total of 851 C. jejuni isolates (178 human, 257 chicken, 87 bovine, 266 water, 63 wild bird) were typed using MLST. Among human isolates, the incidence rates of clonal complexes (CC) CC-21, CC-45, and CC-61 were higher in rural than urban areas. MLST-based source attribution analysis indicated that 64.5% of human C. jejuni isolates were attributable to chicken, followed by cattle (25.8%), water (7.4%), and wild birds (2.3%). Chicken was the attributable source for the majority of cases, independent of residential area, sex and age. The increased incidence in rural compared to urban areas was associated with occupational exposure to animals, particularly cattle among those aged 15–34 years, and with consumption of private well water. Both bovine and water exposure appeared to contribute to the seasonal variation in campylobacteriosis. These results provide a basis for developing public education and preventive programs targeting the risk factors identified.

Multilocus sequence typing of Campylobacter jejuni and Campylobacter coli strains isolated from environmental waters in the Mediterranean area

Campylobacter jejuni and Campylobacter coli are important animal-related waterborne pathogens that are distributed worldwide. To further understand Campylobacter populations in water from the Mediterranean area, the genetic diversity of environmental strains was analyzed using multilocus sequence typing (MLST). MLST was also used to determine the potential geographical differences between these bacterial strains and other campylobacters isolated worldwide. The typing study was conducted using 58 strains isolated from the Llobregat river and other water sources, such as urban sewage, animal wastewater and clinical samples. Thirty-nine different sequence types were obtained; eight of these sequences were described for the first time in this study, suggesting the presence of local strains. The identified C. jejuni strains were the most diverse population, whereas the identified C. coli strains showed a high clonal structure, which clustered most of the sequence types into a few clonal complexes. The strains were not exclusively related to specific water sources. However, comparing the identified strains with an international database showed that most of the Mediterranean strains that were exclusively isolated from environmental waters have previously been isolated from similar sources, particularly those obtained from river water. Additional studies, including those in different geographical areas using a wide range of Campylobacter sources, are required to improve the global knowledge concerning Campylobacter dissemination in the environment.

Genotypes and antibiotic resistance of canine Campylobacter jejuni isolates

Campylobacter jejuni is the most important cause of bacterial gastroenteritis in humans. It is a commensal in many wild and domestic animals, including dogs. Whereas genotypes of human and chicken C. jejuni isolates have been described in some detail, only little information on canine C. jejuni genotypes is available. To gain more information on genotypes of canine C. jejuni and their zoonotic potential, isolates from routine diagnostics of diarrheic dogs as well as isolates of a prevalence study in non-diarrheic dogs were analyzed. Prevalence of thermophilic Campylobacter among non-diarrheic dogs was 6.3% for C. jejuni, 5.9% for Campylobacter upsaliensis and 0.7% for Campylobacter coli. The C. jejuni isolates were genotyped by multi locus sequence typing (MLST) and flaB typing. Resistance to macrolides and quinolones was genetically determined in parallel. Within the 134 genotyped C. jejuni isolates 57 different sequence types (ST) were found. Five STs were previously unrecognized. The most common STs were ST-48 (11.2%), ST-45 (10.5%) and ST-21 (6.0%). Whereas no macrolide resistance was found, 28 isolates (20.9%) were resistant to quinolones. ST-45 was significantly more prevalent in diarrheic than in non-diarrheic dogs. Within the common time frame of isolation 94% of the canine isolates had a ST that was also found in human clinical isolates. In conclusion, prevalence of C. jejuni in Swiss dogs is low but there is a large genetic overlap between dog and human isolates. Given the close contact between human and dogs, the latter should not be ignored as a potential source of human campylobacteriosis.

Marginal zone lymphomas and infectious agents

A link with infectious agents, bacteria and viruses in particular, has been reported for many lymphoma entities. Marginal zone lymphomas (extranodal, nodal and splenic forms) are frequently associated with chronic infections, with important clinical, molecular, biological, and therapeutic implications. The well-known correlation between Helicobacter pylori and gastric MALT-lymphoma, the recently reported links between Chlamydophila psittaci and ocular adnexal MALT-lymphoma and Borrelia burgdorferi and cutaneous MALT lymphoma constitute the best studied examples of lymphomagenic activity of bacteria, while the hepatitis C virus represents the most extensively investigated virus associated with marginal zone lymphomas. Biological and clinical features, therapeutic implications and future perspectives of these lymphoma-microbial associations are discussed in this review.

Campylobacter jejuni colonization and population structure in urban populations of ducks and starlings in New Zealand

A repeated cross-sectional study was conducted to determine the prevalence of Campylobacter spp. and the population structure of C. jejuni in European starlings and ducks cohabiting multiple public access sites in an urban area of New Zealand. The country's geographical isolation and relatively recent history of introduction of wild bird species, including the European starling and mallard duck, create an ideal setting to explore the impact of geographical separation on the population biology of C. jejuni, as well as potential public health implications. A total of 716 starling and 720 duck fecal samples were collected and screened for C. jejuni over a 12 month period. This study combined molecular genotyping, population genetics and epidemiological modeling and revealed: (i) higher Campylobacter spp. isolation in starlings (46%) compared with ducks (30%), but similar isolation of C. jejuni in ducks (23%) and starlings (21%), (ii) significant associations between the isolation of Campylobacter spp. and host species, sampling location and time of year using logistic regression, (iii) evidence of population differentiation, as indicated by F_ST, and host-genotype association with clonal complexes CC ST-177 and CC ST-682 associated with starlings, and clonal complexes CC ST-1034, CC ST-692, and CC ST-1332 associated with ducks, and (iv) greater genetic diversity and genotype richness in ducks compared with starlings. These findings provide evidence that host-associated genotypes, such as the starling-associated ST-177 and ST-682, represent lineages that were introduced with the host species in the 19th century. The isolation of sequence types associated with human disease in New Zealand indicate that wild ducks and starlings need to be considered as a potential public health risk, particularly in urban areas.

We applied molecular epidemiology and population genetics to obtain insights in to the population structure, host-species relationships, gene flow and evolution of Campylobacter jejuni in urban ducks and starlings.

Short communication: Survey of animal-borne pathogens in the farm environment of 13 dairy operations

A survey was conducted on 13 dairies to determine the occurrence of 5 animal-borne pathogens (Salmonella enterica, Escherichia coli O157:H7, Campylobacter jejuni, Mycobacterium avium ssp. paratuberculosis, and Cryptosporidium parvum) and their distributions across farm elements (feces, bedding, milk filters, stored manure, field soil, and stream water). Presence of C. parvum was measured only in feces and stored manure. All but one farm were positive for at least one pathogen species, and 5 farms were positive for 3 species. Escherichia coli O157:H7 was detected on 6 farms and in all farm elements, including milk filters. Mycobacterium avium ssp. paratuberculosis was detected on 10 of 13 farms and in all farm elements except for milk filters. Salmonella enterica and C. jejuni were detected at lower frequencies and were not identified in soil, stream water, or milk filters on any of the 13 farms. Cryptosporidium parvum was detected in feces but not in stored manure. Stored manure had the highest occurrence of pathogens (73%), followed by feces (50%), milk filters, bedding, soil, and water (range from 23 to 31%). Association of pathogen presence with farm management factors was examined by t-test; however, the small number of study farms and samples may limit the scope of inference of the associations. Pathogens had a higher prevalence in maternity pen bedding than in calf bedding, but total pathogen occurrence did not differ in calf compared with lactating cow feces or in soils with or without manure incorporation. Herd size and animal density did not appear to have a consistent effect on pathogen occurrence. The extent of pathogen prevalence and distribution on the farms indicates considerable public health risks associated with not only milk and meat consumption and direct animal contact, but also potential dissemination of the pathogens into the agroecosystem.

Detection of genetic diversity in Campylobacter jejuni isolated from a commercial turkey flock using flaA typing, MLST analysis and microarray assay

Campylobacter is genetically highly diverse and undergoes frequent intraspecific recombination. Turkeys have been identified as an important reservoir for Campylobacter jejuni which is of public health significance. The assessment of the genetic diversity among Campylobacter population is critical for our understanding of the epidemiology of this bacterium. The genetic profiles were different according to the molecular typing methods used. The performance of established flaA genotyping, multilocus sequencing typing (MLST) and DNA microarray assay based on the ArrayTube™ technology was evaluated using 14 Campylobacter jejuni isolated from a commercial turkey flock. The flaA typing was performed using PCR-RFLP with restriction enzymes Sau3AI, AluI, a ‘composite’ flaA analysis of AluI and Sau3AI and DdeI. The 14 isolates were differentiated into 3, 5, 7 and 9 genotypes, respectively. Entire flaA gene and short variable region (SVR) sequences were analysed. Sequencing of the entire flaA provided 11 different genotypes. flaA-SVR sequence analysis detected 8 flaA alleles and 4 flaA peptides. One new flaA allele type (528) was identified. MLST analysis represented 10 different sequence types (STs) and 5 clonal complexes (CCs). The microarray assay recognised 14 different genotypes. The discriminatory indices were 0.560, 0.802, 0.857, and 0.912 for flaA-RFLP depending on the used enzymes, 0.890 for flaA-SVR, 0.967 for entire flaA sequencing, 0.945 for MLST and 1.00 for the DNA microarray assay. The flaA gene was genetically stable over 20 passages on blood agar. In conclusion, the different typing tools demonstrated a high level of genetic heterogeneity of Campylobacter jejuni in a turkey flock, indicating that a single flock can be infected by multiple genotypes within one rearing cycle. DNA microarray-based assays had the highest discriminatory power when compared with other genotyping tools.

Marked host specificity and lack of phylogeographic population structure of Campylobacter jejuni in wild birds

Zoonotic pathogens often infect several animal species, and gene flow among populations infecting different host species may affect the biological traits of the pathogen including host specificity, transmissibility and virulence. The bacterium Campylobacter jejuni is a widespread zoonotic multihost pathogen, which frequently causes gastroenteritis in humans. Poultry products are important transmission vehicles to humans, but the bacterium is common in other domestic and wild animals, particularly birds, which are a potential infection source. Population genetic studies of C. jejuni have mainly investigated isolates from humans and domestic animals, so to assess C. jejuni population structure more broadly and investigate host adaptation, 928 wild bird isolates from Europe and Australia were genotyped by multilocus sequencing and compared to the genotypes recovered from 1366 domestic animal and human isolates. Campylobacter jejuni populations from different wild bird species were distinct from each other and from those from domestic animals and humans, and the host species of wild bird was the major determinant of C. jejuni genotype, while geographic origin was of little importance. By comparison, C. jejuni differentiation was restricted between more phylogenetically diverse farm animals, indicating that domesticated animals may represent a novel niche for C. jejuni and thereby driving the evolution of those bacteria as they exploit this niche. Human disease is dominated by isolates from this novel domesticated animal niche.

Differences in the fecal concentrations and genetic diversities of Campylobacter jejuni populations among individual cows in two dairy herds

Dairy cows have been identified as common carriers of Campylobacter jejuni, which causes many of the human gastroenteritis cases reported worldwide. To design on-farm management practices that control the human infection sourced from dairy cows, the first step is to acquire an understanding of the excretion patterns of the cow reservoir. We monitored the same 35 cows from two dairy farms for C. jejuni excretion fortnightly for up to 12 months. The objective was to examine the concentration of C. jejuni and assess the genetic relationship of the C. jejuni populations excreted by individual cows. Significant differences (P < 0.01) in C. jejuni fecal concentration were observed among the 35 cows, with median concentrations that varied by up to 3.6 log(10) · g(-1) feces. A total of 36 different genotypes were identified from the 514 positive samples by using enterobacterial repetitive intergenic consensus (ERIC)-PCR. Although 22 of these genotypes were excreted by more than one cow, the analysis of frequencies and distribution of the genotypes by model-based statistics revealed a high degree of individuality in the C. jejuni population in each cow. The observed variation in the frequency of excretion of a genotype among cows and the analysis by multilocus sequence typing (MLST) of these genotypes suggest that excretion of C. jejuni in high numbers is due to a successful adaptation of a particular genotype to a particular cow's gut environment, but that animal-related factors render some individual cows resistant to colonization by particular genotypes. The reasons for differences in C. jejuni colonization of animals warrant further investigation.