Multilocus Sequence Types of EnvironmentalCampylobacter jejuniIsolates and their Similarities to those of Human, Poultry and BovineC. jejuniIsolates

Prevalence and genotype diversity of Campylobacter jejuni in hunted reared pheasants (Phasianus colchicus) in Finland

Campylobacter spp., especially C. jejuni, is the most common zoonotic pathogen in humans worldwide. In Nordic countries, the prevalence of C. jejuni in broilers, which is an important reservoir of human infections, is generally low. Thus, other sources of domestically acquired infections besides chicken meat need to be considered. Game birds are known to carry a variety of zoonotic agents, including Campylobacter. The aim of this study was to investigate Campylobacter spp. carriage in a flock of reared pheasants at hunting in two successive samplings to better understand the dynamics of Campylobacter infections in pheasants. Overall, 72% of the intestinal samples were positive for Campylobacter spp. by direct culture on mCCDA. C. jejuni was the only species identified. The isolates were genotyped using whole genome sequencing (WGS), multilocus sequence typing (MLST), and ad hoc whole genome MLST (wgMLST). Two distinct C. jejuni clones were identified among the 18 isolates studied, representing MLST sequence types (STs) ST-45 and ST-699. The ST-45 isolates were closely related to previous human clinical isolates using core genome MLST (cgMLST). In contrast, the ST-699 isolates forming the dominant clone in the latter sampling were quite distinct from previously described cgMLST profiles from different hosts and sources worldwide. In conclusion, the intestine of reared pheasants is commonly colonized by C. jejuni and may carry genotypes relevant to infections in livestock and humans. Hygienic measures are needed to limit the spread of infection in reared flocks. Especially farmers and hunters having direct contact with pheasant offal need to be aware of the associated zoonosis risk to protect themselves and their working dogs alike. Biosecurity measures to improve the safety and reduce the zoonosis risk associated with pheasant farming should be further investigated.

Genomic Diversity of Campylobacter lari Group Isolates from Europe and Australia in a One Health Context

Members of the Campylobacter lari group are causative agents of human gastroenteritis and are frequently found in shellfish, marine waters, shorebirds, and marine mammals. Within a One Health context, we used comparative genomics to characterize isolates from a diverse range of sources and geographical locations within Europe and Australia and assess possible transmission of food, animal, and environmental isolates to the human host. A total of 158 C. lari isolates from Australia, Denmark, France, and Germany, which included 82 isolates from human stool and blood, 12 from food, 14 from domestic animal, 19 from waterbirds, and 31 from the environment were analyzed. Genome-wide analysis of the genetic diversity, virulence, and antimicrobial resistance (AMR) traits was carried-out. Most of the isolates belonged to C. lari subsp. lari (Cll; 98, 62.0%), while C. lari subsp. concheus and C. lari urease-positive thermotolerant Campylobacter (UPTC) were represented by 12 (7.6%) and 15 (9.5%) isolates, respectively. Furthermore, 33 (20.9%) isolates were not assigned a subspecies and were thus attributed to distant Campylobacter spp. clades. Whole-genome sequence-derived multilocus sequence typing (MLST) and core-genome MLST (cgMLST) analyses revealed a high genetic diversity with 97 sequence types (STs), including 60 novel STs and 14 cgMLST clusters (≤10 allele differences), respectively. The most prevalent STs were ST-21, ST-70, ST-24, and ST-58 (accounting for 13.3%, 4.4%, 3.8%, and 3.2% of isolates, respectively). A high prevalence of the 125 examined virulence-related loci (from 76.8 to 98.4% per isolate) was observed, especially in Cll isolates, suggesting a probable human pathogenicity of these strains. IMPORTANCE Currently, relatedness between bacterial isolates impacting human health is easily monitored by molecular typing methods. These approaches rely on discrete loci or whole-genome sequence (WGS) analyses. Campylobacter lari is an emergent human pathogen isolated from diverse ecological niches, including fecal material from humans and animals, aquatic environments, and seafood. The presence of C. lari in such diverse sources underlines the importance of adopting an integrated One Health approach in studying C. lari population structure for conducting epidemiological risk assessment. This retrospective study presents a comparative genomics analysis of C. lari isolates retrieved from two different continents (Europe and Australia) and from different sources (human, domestic animals, waterbirds, food, and environment). It was designed to improve knowledge regarding C. lari ecology and pathogenicity, important for developing effective surveillance and disease prevention strategies.

Molecular epidemiology of Campylobacter jejuni infection in Israel-a nationwide study

The incidence of Campylobacter infection in Israel, particularly among children <2 years of age, has risen over the last decade and became one of the highest among industrialized countries. This study explored the molecular epidemiology of Campylobacter jejuni in Israel over a decade (2003-2012) using multilocus sequence typing (MLST) combined with demographic metadata. Representative clinical isolates (438) from a large national repository together with selected veterinary isolates (74) were subject to MLST. The distribution of age groups, ethnicity and clinical source across various genotypes was evaluated using Poisson modelling. The 512 studied isolates were assigned 126 distinct sequence types (STs) (18.8% novel STs) grouped into 21 clonal complexes (CCs). Most human, poultry and bovine STs clustered together in the leading CCs. Three dominant STs (ST21, ST6608, ST4766) were detected only since 2006. Patients infected with the leading CCs were similarly distributed along densely populated areas. The frequency of blood isolates was higher in patients infected with CC353 (relative rate (RR)=2.0, 95% CI 1.03-3.9, adjusted p value (adj.p) 0.047) and CC42 (RR=4.4, 95% CI 1.7-11.6, adj.p 0.018) and lower with CC257 (RR=0.3, 95% CI 0.1-0.9, adj. p 0.047). The distribution of age groups and ethnicity also varied across the leading CCs. In conclusion, C. jejuni isolates in a national sample appeared highly diverse with a high proportion of new STs. Phylogenic analysis was compatible with poultry and cattle as possible food sources of clinical infection. Demographic characteristics of the infected patients coupled with strain invasiveness across different genotypes revealed a complex epidemiology of C. jejuni transmission in Israel.

Epidemiology of Campylobacter jejuni infections in Sweden, November 2011-October 2012: is the severity of infection associated with C. jejuni sequence type?

BACKGROUND

Campylobacter jejuni is among the most frequent causes of bacterial gastroenteritis in Europe. Over 8,000 C. jejuni multilocus sequence typing sequence types (STs) have been described; ST-21 and ST-45 have been identified as the most frequent types in all human studies so far. In contrast to other STs, ST-22 has been associated with the Guillain-Barré syndrome and ST-677 was recently linked to severe systemic infections in Finland. We investigated risk factors associated with hospitalisation in individuals with C. jejuni infections acquired in Sweden.

METHODS

A total of 1,075 individuals with domestically acquired C. jejuni infection diagnosed between November 2011 and October 2012 in Sweden were included in this retrospective cohort study. Typing data for the isolates as well as clinical data including hospitalisation dates and diagnosis codes for individuals with C. jejuni infection were obtained. Factors associated with hospitalisation and length of hospitalisation were investigated by multivariable analysis.

RESULTS

A total of 289 individuals were hospitalised due to C. jejuni infection (26.8%); those with co-morbidities were over 14 times more likely to become hospitalised than those without (odds ratio [OR]: 14.39, 95% confidence interval [CI]: 6.84-30.26). Those with underlying co-morbidities were also hospitalised longer than those without (4.22 days vs. 2.86 days), although this was not statistically significant. C. jejuni ST-257 (OR: 2.38; CI: 1.08-5.23), but not ST-22 or ST-677, was significantly associated with hospitalisation.

CONCLUSION

ST-677 was not associated with increased hospitalisation or a longer hospital stay in our study whilst ST-257 was. However, individuals with C. jejuni infections were generally more frequently hospitalised than previously demonstrated; this requires further consideration including possible targeted interventions.

Tracing isolates from domestic human Campylobacter jejuni infections to chicken slaughter batches and swimming water using whole-genome multilocus sequence typing

Campylobacter jejuni is the leading cause of bacterial gastroenteritis and chicken is considered a major reservoir and source of human campylobacteriosis. In this study, we investigated temporally related Finnish human (n=95), chicken (n=83) and swimming water (n=20) C. jejuni isolates collected during the seasonal peak in 2012 using multilocus sequence typing (MLST) and whole-genome MLST (wgMLST). Our objective was to trace domestic human C. jejuni infections to C. jejuni isolates from chicken slaughter batches and swimming water. At MLST level, 79% of the sequence types (STs) of the human isolates overlapped with chicken STs suggesting chicken as an important reservoir. Four STs, the ST-45, ST-230, ST-267 and ST-677, covered 75% of the human and 64% of the chicken isolates. In addition, 50% of the swimming water isolates comprised ST-45, ST-230 and ST-677. Further wgMLST analysis of the isolates within STs, accounting their temporal relationship, revealed that 22 of the human isolates (24%) were traceable back to C. jejuni positive chicken slaughter batches. None of the human isolates were traced back to swimming water, which was rather sporadically sampled. The highly discriminatory wgMLST, together with the patient background information and temporal relationship data with possible sources, offers a new, accurate approach to trace back the origin of domestic campylobacteriosis. Our results suggest that potentially a substantial proportion of campylobacteriosis cases during the seasonal peak most probably are due to other sources than chicken meat consumption. These findings warrant further wgMLST-based studies to reassess the role of other reservoirs in the Campylobacter epidemiology both in Finland and elsewhere.

Campylobacter jejuni and Campylobacter coli in wild birds on Danish livestock farms

BACKGROUND

Reducing the occurrence of campylobacteriosis is a food safety issue of high priority, as in recent years it has been the most commonly reported zoonosis in the EU. Livestock farms are of particular interest, since cattle, swine and poultry are common reservoirs of Campylobacter spp. The farm environment provides attractive foraging and breeding habitats for some bird species reported to carry thermophilic Campylobacter spp. We investigated the Campylobacter spp. carriage rates in 52 wild bird species present on 12 Danish farms, sampled during a winter and a summer season, in order to study the factors influencing the prevalence in wild birds according to their ecological guild. In total, 1607 individual wild bird cloacal swab samples and 386 livestock manure samples were cultured for Campylobacter spp. according to the Nordic Committee on Food Analysis method NMKL 119.

RESULTS

The highest Campylobacter spp. prevalence was seen in 110 out of 178 thrushes (61.8 %), of which the majority were Common Blackbird (Turdus merula), and in 131 out of 616 sparrows (21.3 %), a guild made up of House Sparrow (Passer domesticus) and Eurasian Tree Sparrow (Passer montanus). In general, birds feeding on a diet of animal or mixed animal and vegetable origin, foraging on the ground and vegetation in close proximity to livestock stables were more likely to carry Campylobacter spp. in both summer (P < 0.001) and winter (P < 0.001) than birds foraging further away from the farm or in the air. Age, fat score, gender, and migration range were not found to be associated with Campylobacter spp. carriage. A correlation was found between the prevalence (%) of C. jejuni in wild birds and the proportions (%) of C. jejuni in both manure on cattle farms (R(2) = 0.92) and poultry farms (R(2) = 0.54), and between the prevalence (%) of C. coli in wild birds and the proportions (%) of C. coli in manure on pig farms (R(2) = 0.62).

CONCLUSIONS

The ecological guild of wild birds influences the prevalence of Campylobacter spp. through the behavioural patterns of the birds. More specifically, wild birds eating food of animal or mixed animal and vegetable origin and foraging on the ground close to livestock were more likely to carry Campylobacter spp. than those foraging further away or hunting in the air. These findings suggest that wild birds may play a role in sustaining the epidemiology of Campylobacter spp. on farms.

Zoonotic Public Health Hazards in Backyard Chickens

Backyard poultry has become increasingly popular in industrialized countries. In addition to keeping chickens for eggs and meat, owners often treat the birds as pets. However, several pathogenic enteric bacteria have the potential for zoonotic transmission from poultry to humans but very little is known about the occurrence of zoonotic pathogens in backyard flocks. The occurrence and the antimicrobial resistance of Salmonella enterica, Campylobacter spp., Listeria monocytogenes and enteropathogenic Yersinia spp. was studied in 51 voluntary backyard chicken farms in Finland during October 2012 and January 2013. Campylobacter isolates were further characterized by pulsed-field gel electrophoresis (PFGE), and the occurrence of ESBL/AmpC-producing E. coli was investigated. The findings from this study indicate that backyard chickens are a reservoir of Campylobacter jejuni strains and a potential source of C. jejuni infection for humans. Backyard chickens can also carry L. monocytogenes, although their role as a primary reservoir is questionable. Campylobacter coli, Yersinia pseudotuberculosis and Salmonella enterica were only found sporadically in the faecal and environmental samples of backyard poultry in Finland. No Yersinia enterocolitica carrying the virulence plasmid was isolated. All pathogens were highly susceptible to most of the antimicrobials studied. Only a few AmpC- and no ESBL-producing E. coli were found.

The evolution of Campylobacter jejuni and Campylobacter coli

The global significance of Campylobacter jejuni and Campylobacter coli as gastrointestinal human pathogens has motivated numerous studies to characterize their population biology and evolution. These bacteria are a common component of the intestinal microbiota of numerous bird and mammal species and cause disease in humans, typically via consumption of contaminated meat products, especially poultry meat. Sequence-based molecular typing methods, such as multilocus sequence typing (MLST) and whole genome sequencing (WGS), have been instructive for understanding the epidemiology and evolution of these bacteria and how phenotypic variation relates to the high degree of genetic structuring in C. coli and C. jejuni populations. Here, we describe aspects of the relatively short history of coevolution between humans and pathogenic Campylobacter, by reviewing research investigating how mutation and lateral or horizontal gene transfer (LGT or HGT, respectively) interact to create the observed population structure. These genetic changes occur in a complex fitness landscape with divergent ecologies, including multiple host species, which can lead to rapid adaptation, for example, through frame-shift mutations that alter gene expression or the acquisition of novel genetic elements by HGT. Recombination is a particularly strong evolutionary force in Campylobacter, leading to the emergence of new lineages and even large-scale genome-wide interspecies introgression between C. jejuni and C. coli. The increasing availability of large genome datasets is enhancing understanding of Campylobacter evolution through the application of methods, such as genome-wide association studies, but MLST-derived clonal complex designations remain a useful method for describing population structure.

Antimicrobial Resistance and Multilocus Sequence Types of Finnish Campylobacter jejuni Isolates from Multiple Sources

Antimicrobial susceptibility was determined for 805 domestic Campylobacter jejuni isolates obtained from broilers (n = 459), bovines (n = 120), human patients (n = 95), natural waters (n = 80), wild birds (n = 35) and zoo animals/enclosures (n = 16) with known multilocus sequence types (MLST) for 450 isolates. The minimum inhibitory concentration (MIC) values for erythromycin, tetracycline, streptomycin, gentamicin and the quinolones ciprofloxacin and nalidixic acid were determined with the VetMIC method. MICs were compared with MLST types to find possible associations between sequence type and resistance. The proportions of resistant isolates were 5% (broilers), 6.3% (natural waters), 11.4% (wild birds), 11.6% (human patients), 16.7% (bovines) and 31.3% (zoo). The most common resistance among the human and bovine isolates was quinolone resistance alone while resistance to streptomycin alone was most often detected among the broiler isolates and tetracycline resistance was most commonly observed in the wild bird, water and zoo isolates. No or negligible resistance to erythromycin or gentamicin was detected. In all data, 12/26 of the tetracycline-resistant isolates were also resistant to streptomycin (P < 0.001) and the clonal complex (CC) ST-1034 CC showed a high proportion of 75% (9/12) of tetracycline-resistant isolates, most originating from the zoo and broilers with closely associated MLST types from these sources. No association between quinolone resistance and MLST type was seen. The low percentage of resistant isolates among the domestic Campylobacter infections is most probably due to the long-term controlled use of antimicrobials. However, the higher percentage of tetracycline resistance observed among the zoo isolates could present a risk for zoo visitors of acquisition of resistant C. jejuni. The resistance pattern of tetracycline and streptomycin most often found in ST-1034 CC could indicate a common resistance acquisition mechanism commonly present in this CC. Overall, MLST typing was found to be a useful method in recognition of potential genetic lineages associated with resistance.

Antimicrobial susceptibility profiles and molecular typing of Campylobacter jejuni and Campylobacter coli isolates from ducks in South Korea

Campylobacter is a food-borne zoonotic pathogen that causes human gastroenteritis worldwide. Campylobacter bacteria are commensal in the intestines of many food production animals, including ducks and chickens. The objective of the study was to determine the prevalence of Campylobacter species in domestic ducks, and the agar dilution method was used to determine resistance of the isolates to eight antibiotics. In addition, multilocus sequence typing (MLST) was performed to determine the sequence types (STs) of selected Campylobacter isolates. Between May and September 2012, 58 duck farms were analyzed, and 56 (96.6%) were positive for Campylobacter. Among the isolates, 82.1% were Campylobacter jejuni, 16.1% were C. coli, and one was unidentified by PCR. Of the 46 C. jejuni isolates, 87.0%, 10.9%, and 21.7% were resistant to ciprofloxacin, erythromycin, and azithromycin, respectively. Among the C. coli isolates, all 9 strains were resistant to ampicillin, and 77.8% and 33.3% were resistant to ciprofloxacin and azithromycin, respectively. The majority of the Campylobacter isolates were classified as multidrug resistant. Twenty-eight STs were identified, including 20 STs for C. jejuni and 8 STs for C. coli. The most common clonal complexes in C. jejuni were the ST-21 complex and the ST-45 complex, while the ST-828 complex predominated in C. coli. The majority of isolates were of STs noted in ducks and humans from earlier studies, along with seven STs previously associated only with human disease. These STs overlapped between duck and human isolates, indicating that Campylobacter isolates from ducks should be considered potential sources of human infection.

Multilocus sequence typing (MLST) and whole-genome MLST of Campylobacter jejuni isolates from human infections in three districts during a seasonal peak in Finland

A total of 95 human Campylobacter jejuni isolates acquired from domestic infections and collected from three districts in Finland during the seasonal peak (June to September) in 2012 were analyzed by PCR-based multilocus sequence typing (MLST) and by whole-genome sequencing (WGS). Four predominant sequence types (STs) were detected among the isolates: ST-45 (21%) and ST-230 (14%, ST-45 clonal complex [CC]), ST-267 (21%, ST-283 CC), and ST-677 (19%, ST-677 CC). In districts 1 and 3, most of the infections occurred from early July to the middle of August, with a peak at weeks 29 to 31, but in district 2, the infections were dispersed more evenly throughout 3 months (June to August). WGS data were used for further whole-genome MLST (wgMLST) analyses of the isolates representing the four common STs. Shared loci of the isolates within each ST were analyzed as distance matrices of allelic profiles by the neighbor-net algorithm. The highest allelic variations (>400 different alleles) were detected between different clusters of ST-45 isolates (1,121 shared loci), while ST-230 (1,264 shared loci), ST-677 (1,169 shared loci), and ST-267 isolates (1,217 shared loci) were less diverse with the clusters differing by <40 alleles. Closely related isolates showing no allelic variation (subclusters) were detected among all four major STs. In some cases, they originated from different districts, suggesting that isolates can be epidemiologically connected and may have the same infection source despite being originally identified as sporadic infections.

Development of a loop-mediated isothermal amplification assay for rapid, sensitive detection of Campylobacter jejuni in cattle farm samples

Campylobacter jejuni is a leading cause of bacterial foodborne disease worldwide. The detection of this organism in cattle and their environment is important for the control of C. jejuni transmission and the prevention of campylobacteriosis. Here, we describe the development of a rapid and sensitive method for the detection of C. jejuni in naturally contaminated cattle farm samples, based on real-time loop-mediated isothermal amplification (LAMP) of the hipO gene. The LAMP assay was specific (100% inclusivity and exclusivity for 84 C. jejuni and 41 non-C. jejuni strains, respectively), sensitive (detection limit of 100 fg/μl), and quantifiable (R(2) = 0.9133). The sensitivity of the LAMP assay was then evaluated for its application to the naturally contaminated cattle farm samples. C. jejuni strains were isolated from 51 (20.7%) of 246 cattle farm samples, and the presence of the hipO gene was tested using the LAMP assay. Amplification of the hipO gene by LAMP within 30 min (mean ~10.8 min) in all C. jejuni isolates (n = 51) demonstrated its rapidity and accuracy. Next, template DNA was prepared from a total of 186 enrichment broth cultures of cattle farm samples either by boiling or using a commercial kit, and the sensitivity of detection of C. jejuni was compared between the LAMP and PCR assays. In DNA samples prepared by boiling, the higher sensitivity of the LAMP assay (84.4%) compared with the PCR assay (35.5%) indicates that it is less susceptible to the existence of inhibitors in sample material. In DNA samples prepared using a commercial kit, both the LAMP and PCR assays showed 100% sensitivity. We anticipate that the use of this rapid, sensitive, and simple LAMP assay, which is the first of its kind for the identification and screening of C. jejuni in cattle farm samples, may play an important role in the prevention of C. jejuni contamination in the food chain, thereby reducing the risk of human campylobacteriosis.

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.

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.

A combination of MLST and CRISPR typing reveals dominant Campylobacter jejuni types in organically farmed laying hens

AIM

To elucidate the Campylobacter jejuni population in organically farmed laying hens in Finland, multilocus sequence typing (MLST) was combined with characterization of clustered regularly interspaced short palindromic repeat (CRISPR) sequences.

METHODS AND RESULTS

A total of 147 Camp. jejuni isolates, collected from organically farmed laying hens from 18 farms in 2003-2004, were previously analysed by pulsed-field gel electrophoresis. In the present study, subsets of the isolates were further analysed by MLST and CRISPR sequences. Fourteen STs were found by MLST. ST-50 (27%, 7/18 farms), ST-3272 (20%, 8/18 farms), ST-45 (12%, 7/18 farms) and ST-356 (12%, 5/18 farms) were the most common STs. CRISPR types were identical among all isolates of ST-50 (ST-21 clonal complex (CC)) and the most variable among ST-45 (ST-45 CC).

CONCLUSIONS

ST-3272 (UA), a common ST in this study, has been infrequently detected in other hosts. Other major STs (ST-50 and ST-45) have been common in several hosts such as conventional poultry and bovines. CRISPR typing provided additional discrimination between isolates of certain dominant STs and could be useful in further epidemiological studies.

SIGNIFICANCE AND IMPACT OF THE STUDY

This study gives new information about MLST and CRISPR types of Camp. jejuni among organically farmed laying hens.

Comparative genomics of unintrogressed Campylobacter coli clades 2 and 3

BACKGROUND

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

RESULTS

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

CONCLUSIONS

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