Progressive genome-wide introgression in agricultural Campylobacter coli.

Hybridization between distantly related organisms can facilitate rapid adaptation to novel environments, but is potentially constrained by epistatic fitness interactions among cell components. The zoonotic pathogens Campylobacter coli and C. jejuni differ from each other by around 15% at the nucleotide level, corresponding to an average of nearly 40 amino acids per protein-coding gene. Using whole genome sequencing, we show that a single C. coli lineage, which has successfully colonized an agricultural niche, has been progressively accumulating C. jejuni DNA. Members of this lineage belong to two groups, the ST-828 and ST-1150 clonal complexes. The ST-1150 complex is less frequently isolated and has undergone a substantially greater amount of introgression leading to replacement of up to 23% of the C. coli core genome as well as import of novel DNA. By contrast, the more commonly isolated ST-828 complex bacteria have 10-11% introgressed DNA, and C. jejuni and nonagricultural C. coli lineages each have <2%. Thus, the C. coli that colonize agriculture, and consequently cause most human disease, have hybrid origin, but this cross-species exchange has so far not had a substantial impact on the gene pools of either C. jejuni or nonagricultural C. coli. These findings also indicate remarkable interchangeability of basic cellular machinery after a prolonged period of independent evolution.

Effects of seasonality and a diet of brassicas on the shedding of Escherichia coli O157 in sheep.

Sheep flocks were tested for Escherichia coli O157 from pooled fecal samples while they grazed on pasture in winter, brassicas in spring, and on pasture during the summer. The winter pasture study reported an average individual prevalence of 3.1% (95% confidence interval [CI]: 0.6-5.6%) and an average farm-level prevalence of 10.4% (95% CI: 2.1-18.8%) over the 3-year study period. The spring brassica study reported a prevalence of 0% and the summer pasture study had an individual prevalence of 6.3% (95% CI: 2.1-12.1%) and a farm prevalence of 36.8% (95% CI: 15.8-57.8%). Analysis showed significant differences between the shedding of E. coli O157 in sheep grazing on brassicas in spring when compared to sheep grazing on pasture in the summer (p<0.01) and in winter (p=0.044; odds ratio [OR]=0.106). Furthermore, sheep excreted a lower prevalence of E. coli O157 in winter while grazing on pasture (p=0.017; OR=0.199). E. coli O157 isolates were characterized using polymerase chain reaction for the presence of known virulence factors; all carried the eae and stx2 gene and 10/11 positive flocks possessed the stx2c gene, suggesting that sheep are a potential source of human infection.

Temporal variation and host association in the Campylobacter population in a longitudinal ruminant farm study.

Campylobacter jejuni and C. coli were quantified and typed, using multilocus sequence typing (MLST), from fecal samples collected from a mixed cattle and sheep farm during summer. Cattle had a significantly higher prevalence than sheep (21.9% [74/338] and 14.0% [30/214], respectively), but both decreased over time. There were no differences in the average Campylobacter concentrations shed by cattle (600 CFU g(-1)) and sheep (820 CFU g(-1)), although sheep did show a significant temporal reduction in the number of Campylobacter organisms shed in their feces. A total of 21 different sequence types (STs) (97.7% C. jejuni, 2.3% C. coli) were isolated from cattle, and 9 different STs were isolated from sheep (40.6% C. jejuni, 59.4% C. coli). The Campylobacter population in cattle was relatively stable, and the frequencies of genotypes isolated showed little temporal variation. However, the composition of subtypes isolated from sheep did show significant temporal differences. The cattle and sheep consistently showed significant differences in their carriage of Campylobacter species, STs, and CCs despite the fact that both were exposed to the same farming environment. This work has highlighted the patterns of a Campylobacter population on a ruminant farm by identifying the existence of both temporal and between-host variations.

Niche segregation and genetic structure of Campylobacter jejuni populations from wild and agricultural host species.

Bacterial populations can display high levels of genetic structuring but the forces that influence this are incompletely understood. Here, by combining modelling approaches with multilocus sequence data for the zoonotic pathogen Campylobacter, we investigated how ecological factors such as niche (host) separation relate to population structure. We analysed seven housekeeping genes from published C. jejuni and C. coli isolate collections from a range of food and wild animal sources as well as abiotic environments. By reconstructing genetic structure and the patterns of ancestry, we quantified C. jejuni host association, inferred ancestral populations, investigated genetic admixture in different hosts and determined the host origin of recombinant C. jejuni alleles found in hybrid C. coli lineages. Phylogenetically distinct C. jejuni lineages were associated with phylogenetically distinct wild birds. However, in the farm environment, phylogenetically distant host animals shared several C. jejuni lineages that could not be segregated according to host origin using these analyses. Furthermore, of the introgressed C. jejuni alleles found in C. coli lineages, 73% were attributed to genotypes associated with food animals. Our results are consistent with an evolutionary scenario where distinct Campylobacter lineages are associated with different host species but the ecological factors that maintain this are different in domestic animals such that phylogenetically distant animals can harbour closely related strains.

Antimicrobial resistance profiles of Campylobacter from humans, retail chicken meat, and cattle feces.

We determined the antimicrobial resistance profiles of Campylobacter isolates from cases of sporadic human infection (n = 119), retail chicken meat (n = 105), and cattle feces (n = 105). Ampicillin and tetracycline resistance was highest in human isolates (32% and 29%, respectively) and retail chicken isolates (25% and 25%, respectively), whereas nalidixic acid resistance was highest in cattle fecal isolates (20%). We found that the antimicrobial resistance profiles were more similar in human and chicken meat isolates than those observed when comparing human and cattle fecal isolates. When we analyzed the distribution of minimum inhibitory concentrations for each antibiotic, in each host, the distribution was similar between human and chicken meat isolates, whereas cattle fecal isolates remained highly distinct from the other two hosts. This study suggests that chicken may be a major source of human Campylobacter infection and that the antimicrobial resistances found in the Campylobacter from this source will therefore also be prevalent in clinical isolates.

Campylobacter genotyping to determine the source of human infection.

BACKGROUND: Campylobacter species cause a high proportion of bacterial gastroenteritis cases and are a significant burden on health care systems and economies worldwide; however, the relative contributions of the various possible sources of infection in humans are unclear. METHODS: National-scale genotyping of Campylobacter species was used to quantify the relative importance of various possible sources of human infection. Multilocus sequence types were determined for 5674 isolates obtained from cases of human campylobacteriosis in Scotland from July 2005 through September 2006 and from 999 Campylobacter species isolates from 3417 contemporaneous samples from potential human infection sources. These data were supplemented with 2420 sequence types from other studies, representing isolates from a variety of sources. The clinical isolates were attributed to possible sources on the basis of their sequence types with use of 2 population genetic models, STRUCTURE and an asymmetric island model. RESULTS: The STRUCTURE and the asymmetric island models attributed most clinical isolates to chicken meat (58% and 78% of Campylobacter jejuni and 40% and 56% of Campylobacter coli isolates, respectively), identifying it as the principal source of Campylobacter infection in humans. Both models attributed the majority of the remaining isolates to ruminant sources, with relatively few isolates attributed to wild bird, environment, swine, and turkey sources. CONCLUSIONS: National-scale genotyping was a practical and efficient methodology for the quantification of the contributions of different sources to human Campylobacter infection. Combined with the knowledge that retail chicken is routinely contaminated with Campylobacter, these results are consistent with the view that the largest reductions in human campylobacteriosis in industrialized countries will come from interventions that focus on the poultry industry.

Spatiotemporal homogeneity of Campylobacter subtypes from cattle and sheep across northeastern and southwestern Scotland.

Source attribution using molecular subtypes has implicated cattle and sheep as sources of human Campylobacter infection. Whether the Campylobacter subtypes associated with cattle and sheep vary spatiotemporally remains poorly known, especially at national levels. Here we describe spatiotemporal patterns of prevalence, bacterial enumeration, and subtype composition in Campylobacter isolates from cattle and sheep feces from northeastern (63 farms, 414 samples) and southwestern (71 farms, 449 samples) Scotland during 2005 to 2006. Isolates (201) were categorized as sequence type (ST), as clonal complex (CC), and as Campylobacter jejuni or Campylobacter coli using multilocus sequence typing (MLST). No significant difference in average prevalence (cattle, 22%; sheep, 25%) or average enumeration (cattle, 2.7 x 10(4) CFU/g; sheep, 2.0 x 10(5) CFU/g) was found between hosts or regions. The four most common STs (C. jejuni ST-19, ST-42, and ST-61 and C. coli ST-827) occurred in both hosts, whereas STs of the C. coli ST-828 clonal complex were more common in sheep. Neither host yielded evidence for regional differences in ST, CC, or MLST allele composition. Isolates from the two hosts combined, categorized as ST or CC, were more similar within than between farms but showed no further spatiotemporal trends up to 330 km and 50 weeks between farm samples. In contrast, both regions yielded evidence for significant differences in ST, CC, and allele composition between hosts, such that 65% of isolates could be attributed to a known host. These results suggest that cattle and sheep within the spatiotemporal scales analyzed are each capable of contributing homogeneous Campylobacter strains to human infections.

Campylobacter excreted into the environment by animal sources: prevalence, concentration shed, and host association.

An intensive study of 443 isolates of Campylobacter jejuni and Campylobacter coli from 2031 fecal samples excreted by animal sources including cattle, sheep, and pigs, a range of wild and domesticated avian species and pets is described. The prevalence found in the majority of animal sources ranged from 22% to 28% with poultry being highest at 41% and cats and dogs lowest (<5%). The average count excreted for each animal source was found not to be significantly different ranging from approximately 10(2) to 10(5) cfu/g. Multilocus sequence typing (MLST) identified phylogenies that exhibited host specificity. A number of clonal complexes (CCs) and sequence types (STs) were characteristic of particular hosts (e.g., CC-179, ST-637, and ST-1341 found only in pigeons and gulls). Analysis of genetic distance demonstrated numerous significant differences in the distribution of MLST types (CC, ST, and allele) between animal sources. Host association was quantified using structure that correctly assigned the nine animal sources with accuracies of 28%, 24%, and 55% at the CC, ST, and allele levels, respectively. This is substantially higher than would be expected by random allocation (11%) but farmyard poultry had the lowest assignment accuracy (13%, 13%, and 21%) suggesting that isolates were shared with a wide range of other animals. This study demonstrates the link between MLST type and host and provides data that can be used in risk assessment and food attribution models. Further, it demonstrates the applicability of MLST to characterize Campylobacter strains from a broad range of environmental sources.

Has retail chicken played a role in the decline of human campylobacteriosis?

Between 2001 and 2006, the incidence of human Campylobacter infections decreased by 10 and 27% in Scotland and the Grampian region of Scotland, respectively. Contemporaneous collection and analyses of human and retail-chicken isolates from Grampian were carried out over a 10-week period in 2001 and again in 2006 in order to determine whether the fall in the incidence of human infections was related to the retail-chicken exposure route. Rates of carriage of Campylobacter on chicken carcasses from retail outlets in Grampian in 2001 and 2006 were estimated. Chicken-derived Campylobacter isolates from 2001 (n = 84) and 2006 (n = 105) and human-derived isolates from patients with clinical cases of infection in 2001 (n = 172) and 2006 (n = 119) were typed by multilocus sequence typing. We found no evidence for statistically significant changes in prevalence and counts per carcass. We found by rarefaction that although the degree of diversity in humans tended to be higher than that in chickens, these differences were not significant. The genetic distance between chicken and human isolates from 2001 according to sequence type, clonal complex (CC), or allele composition was not significant, whereas the distances between 2006 isolates at the CC and allele levels were significant. This difference was attributable to a lower proportion of CC-21's being found in retail-chicken isolates from 2006 than in chicken isolates from 2001. We conclude that human exposure to Campylobacter via retail chicken is important and that changes in the population structure of campylobacters in this reservoir need to be taken into account in investigating human infection.

Escherichia coli O157: burger bug or environmental pathogen?

The three main pathways of Escherichia coli O157 infection are foodborne, environmental (including direct contact with animals and their faeces and contaminated water supplies) or person to person contact. The disease is often nicknamed the 'burger bug' but it appears that environmental risk factors may be more important. In this study we use four techniques (outbreak analysis, case-control studies, disease mapping and quantitative microbial risk assessment (QMRA)) to determine whether burgers or environmental pathways present the greater risk in Scotland. Analysis of E. coli O157 outbreaks in Scotland from 1994 to 2003 associated with either meat or dairy foods, or with environmental transmission shows that approximately 40% [M1] of these outbreaks were foodborne, 54% were environmental and 6% involved both transmission routes. However, the largest outbreaks tend to be foodborne accounting for 83% of outbreak cases. Case-control studies indicate strong risk associations with environmental exposure in Scotland, the UK as a whole and the USA, but burgers appear to be more of a risk in the USA. Canadian, Scottish and Swedish disease mapping studies found positive association with indicators of cattle density. In Grampian (North-East Scotland) we found that there was a positive association with cattle and sheep density (divided by human population density) as well as percentage of population on private water supplies. We found 63% of cases in rural postcodes compared with 37% urban after correcting for population differences suggesting that at least 26% of cases may be classified as environmental. QMRA showed that on average, the risk was 100 times greater when visiting a pasture than eating a burger in Grampian. However, it is difficult to determine which pathway actually causes most illnesses as it is unknown how many burgers are consumed daily and what is the frequency of human visits to pasture. The implementation of hygienic food processing post-1996 Central Scotland outbreak and the preference for 'well done' burgers may account for this food being a relatively low risk thus making the 'burger bug' term less appropriate in the UK.

The detection of Cryptosporidium parvum and Escherichia coli O157 in UK bivalve shellfish.

Optimised immunomagnetic separation methods to detect Cryptosporidium parvum and Escherichia coli O157 in UK shellfish are described. Whole tissue homogenates gave the best recoveries for C. parvum oocysts compared with gill or haemolymph extracts. The sensitivity of recovery from spiked samples was comparable to that achieved when processing water and varied from 12-34% in mussels, 48-69.5% in oysters and 30-65% in scallops. Maximum recovery of E. coli O157 was achieved by enriching in buffered peptone water supplemented with vancomycin at 42 degrees C. Increasing enrichment temperatures from 37 to 42 degrees C gave a significant increase in target number recovery. Implementation of these methods into monitoring programmes and end-product testing will enable shellfish producers to better assess product safety.

Does age acquired immunity confer selective protection to common serotypes of Campylobacter jejuni?

BACKGROUND: Campylobacter infection is a major cause of bacterial gastrointestinal disease. Exposure to Campylobacter is known to produce an immune response in humans that can prevent future symptomatic infections. Further, studies of the general population have shown that seroprevalence to Campylobacter increases with age. METHODS: A large collection of serotyped Campylobacter isolates, obtained from human clinical faecal samples, were analysed by comparing the ratio of uncommon to common serotypes by different age groups, using chi2 tests. RESULTS: We have identified that older age groups, as well as having generally lower incidence, are significantly less likely to be infected by the more common serotypes. CONCLUSION: These results are indicative of acquired immunity, however, further studies are needed to rule out the confounding effects of the variations in exposure pathways experienced by different age groups.

Multiple sample flow through immunomagnetic separator for concentrating pathogenic bacteria.

The standard method of immunomagnetic separation for isolating pathogenic bacteria from food and environmental matrices processes 1 ml volumes. Pathogens present at low levels (<0.5 pathogenic bacteria/g) will not be consistently detected by this method. Here a multiple sample flow through immunomagnetic separator has been designed and tested to process large volume samples (50 to 250 ml). Preliminary results show >97% recovery of polydisperse magnetic particles (diameter range 1 to 8 microm) containing 29-33% w/w Fe3O4 content. Between 70 and 130 times more of the pathogenic bacteria Escherichia coli O157 is recovered from PBS compared with the standard 1 ml method. Also, the recovery of E. coli O157 from beef mince homogenates, after a 4 h incubation at 42 degrees C, is between 80 and 180 times higher than the standard 1 ml method.

Dose response modelling of Escherichia coli O157 incorporating data from foodborne and environmental outbreaks.

A human dose response model for Escherichia coli O157 would enable prediction of risk of infection to humans following exposure from either foodborne or environmental pathways. However, due to the severe nature of the disease, volunteer human dose response studies cannot be carried out. Surrogate models from Shigella fed to humans and E. coli O157 to rabbits have been utilised but are significantly different to one another. In addition data obtained by animal exposure may not be representative for human beings. An alternative approach to generating and validating a dose response model is to use quantitative data obtained from actual human outbreaks. This work collates outbreak data obtained from global sources and these are fitted using exponential and beta-Poisson models. The best fitting model was found to be the beta-Poisson model using a beta-binomial likelihood and the authors favour the exact version of this model. The confidence levels in this model encompass a previously published Shigella dose response model. The potential incorporation of this model into QMRAs is discussed together with applications of the model to help explain foodborne outbreaks.

Is the prevalence and shedding concentrations of E. coli O157 in beef cattle in Scotland seasonal?

The prevalence of Escherichia coli O157 in Scottish beef cattle at abattoir was found to be greater during the cooler months [11.2% (95% CI, 8.4-13.9%)] compared to the warmer months [7.5% (95% CI, 5.4-9.6%)]; the reverse of seasonality of human infections. However, high shedding beef cattle (excreting 10(-4) g(-1)) appear to shed greater concentrations of E. coli O157 in the warmer months which may partly explain increased human infection seasonality at this time.

Quantitative risk assessment of human infection from Escherichia coli O157 associated with recreational use of animal pasture.

A quantitative microbial risk assessment incorporating Monte Carlo simulations is described which estimates the probability of Escherichia coli O157 infection of humans by visiting pasture previously grazed by cattle. The risk assessment is performed for a number of scenarios including a variation in the grazing period prior to the human visit, the duration of visit (8-h day or 24-h camp) and the level of E. coli O157 shed by the cattle. Assuming the cattle have been on the field for 28 days, followed directly by a human visit, and the proportion of animals shedding the organism are as described in previous surveys 5 +/- 1% (Synge, B.A., Gunn, G.J., Ternent, H.E., Hopkins, G.F., Thomson-Carter, F., Foster, G., Chase-Topping, M., McKendrick, I., 2001). Prevalence and factors affecting the shedding of verocytotoxin producing Escherichia coli O157 in beef cattle in Scotland. In: Concerted Action CT98-3935 Veroctotoxigenic E. coli in Europe, 5. Epidemiology of Verocytotoxigenic E. coli, Dublin, pp. 98-103.), a probability of infection of 0.1% is attained for 8- and 24-h periods when the cattle are shedding approximately 10(3) and 10(4) CFU g(-1), respectively. Monte Carlo simulations demonstrated that risk mitigation strategies of removing cattle from the pasture 4 weeks prior to the human visit in addition to physical removal of faeces showed significant reductions in potential infection rates.

Multiplex T-RFLP allows for increased target number and specificity: detection of Salmonella enterica and six species of Listeria in a single test.

A multiplex T-RFLP test was developed to detect and identify Salmonella enterica and all six species of Listeria inoculated into milk at minimal levels. Extensive in silico analysis was used to design a fifteen-primer, six-amplimer methodology and in vitro application showed target organism DNA, when amplified individually, yielded the predicted terminal restriction fragments (TRFs) following digestion. Non-target organisms were either not-amplified or yielded TRFs which did not interfere with target identification. Multiple target DNA analysis gave over 86% detection of total TRFs predicted, and this was improved to over 90% detection of total TRFs predicted when only two target DNA extracts were combined analysed. Co-inoculation of milk with five strains each of the target species of S. enterica and L. monocytogenes, along with five strains of the non-target species E. coli was followed by enrichment in SEL medium for M-TRFLP analysis. This allowed for detection of both target species in all samples, with detection of one S. enterica and two Listeria TRFs in all cases, and detection of a second S. enterica TRF in 91% of cases. This was from an initial inoculum of <5 cfu per 25 ml milk with a background of competing E. coli present, and gave a result from sampling of under 20 hours. The ability to increase target species number without loss of sensitivity means that extensive screening can be performed at reduced cost due to a reduction in the number of tests required.

Dose-response modeling of Salmonella using outbreak data.

Salmonella is a key human pathogen worldwide, most often associated with food poisoning incidences. There is a small number of predominant serotypes found in human cases. The role of exposure in the epidemiology of Salmonella can be explained using dose-response assessment both for infection and acute enteric illness. Dose-response studies are traditionally based on human challenge experiments but an alternative is to use outbreak data. Such data were collected from the published literature which included estimates of the dose ingested and the attack rate. Separate dose-response models for infection and illness given infection were fitted using a multi-level statistical framework. These models incorporated serotype and susceptibility as categorical covariates, and adjusted for heterogeneity in exposure. The results indicate that both the risk of infection and the risk of illness given infection increase with dose. The dose-response model incorporating data from all outbreaks had an infection ID50 of 7 CFU's and illness ID50 of 36 CFUs. This is indicative of much higher infectivity and pathogenicity compared with feeding studies of healthy human volunteers with laboratory adapted strains. No differences were found in the outbreak models between serotypes and susceptibility categories. However, for serotypes other than S. Enteritidis or S. Typhimurium, results indicate that a minor proportion of individuals exposed will not fall ill even at high doses. The dose-response relations indicate that outbreaks are associated with higher doses making it more likely to have a higher attack rate. Applications of the dose-response model in outbreak situations where either dose or attack rate is missing were successfully used to clarify the epidemiology. Finally, the dose-response models described here can be readily used in quantitative microbiological risk assessment to predict human infection and illness rates. A simple Excel spreadsheet implementing the model has been prepared and is available from the authors.

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

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

Campylobacter genotypes from food animals, environmental sources and clinical disease in Scotland 2005/6.

A nationwide multi-locus sequence typing (MLST) survey was implemented to analyze patterns of host association among Campylobacter jejuni and Campylobacter coli isolates from clinical disease in Scotland (July 2005-September 2006), food animals (chickens, cattle, sheep, pigs and turkey), non-food animals (wild birds) and the environment. Sequence types (STs) were determined for 5247 clinical isolates and 999 from potential disease sources (augmented with 2420 published STs). Certain STs were over represented among particular sample sets/host groups. These host-associated STs were identified for all sample groups in both Campylobacter species and host associated clonal complexes (groups of related STs) were characterized for C. jejuni. Some genealogical lineages were present in both human disease and food animal samples. This provided evidence for the relative importance of different infection routes/food animal sources in human disease. These results show robust associations of particular genotypes with potential infection sources supporting the contention that contaminated poultry is a major source of human disease.