Using sequence data to identify alternative routes and risk of infection: a case-study of campylobacter in Scotland

Epidemiological risk factor analyses are used to identify factors that influence the risk of individuals acquiring a particular infection. Such risk factor analyses commonly assume that the risk factors associated with different sources of exposure to infection are homogeneous [1–3]. However, in many cases there are multiple sources of infection and different risk factors may be associated with the different sources. Backward-tracing data on the sources of infection could be used to ascribe different risks to different sources of exposure.

Infection with C. jejuni can be acquired from consumption of contaminated food as well as through direct and indirect contact with animal faeces and has multiple hosts including poultry, ruminants and wild birds [4, 5]. Recent developments in the typing of Campylobacter bacteria permits the tracing of sources of infection for human cases of Campylobacteriosis [6]. Campylobacter can be classified by their allelic profile using Multi-Locus-Sequence-Type (MLST) typing techniques [7], which places isolates into specific Sequence Type (ST) profiles. Using STRUCTURE software [8] it is possible to calculate a probability of the ST originating from a particular species [6, 9].

Previous studies have identified an association between human C. jejuni infection in Scotland and lower social deprivation score (indicating lower social deprivation) and being a child living in an area of lower population density [10]. A recent study in New Zealand [11] typed C. jejuni isolates using MLST and used the Asymmetric Island probabilistic genetic attribution model [12] to divide these types into ruminant and poultry origin types. Logistic regression analysis of the two types demonstrated that cases of ruminant origin were more likely to occur in rural areas relative to those of poultry origin [11]. A similar methodology will be used in this paper to build on the risk factor analysis of Bessell et al. [10] by differentiating between the risks associated with different sources of infection. For example, one potential explanation for the association found by Bessell et al. [10] with lower deprivation could be differences in access to outdoor leisure activities. If this were the case, it might result in the less deprived being more exposed to ruminant strains should there be greater exposure to ruminant types in the environment.

By using the MLST technique to attribute isolates from C. jejuni cases to host sources [6], this paper has demonstrated that risk factors for infection depend upon the source of the pathogen. Whilst there is a range of potential sources of C. jejuni infections, this paper has demonstrated that human infections of C. jejuni that are attributable to sources in ruminants are more seasonal and occur more in rural areas than those assigned to poultry sources. Those that were unassigned had very similar epidemiologies to the poultry attributable types.

The work of Sheppard et al. [6] on assigning source probabilities to individual STs has made this analysis possible and it demonstrates that the majority of human cases were attributable to sources in poultry and ruminants or were unassigned (Table 1). However, the majority of STs were not assigned to a source of infection with a probability of greater than 95%. This is in part reflects the large number of STs that represented a small proportion of human infections (Table 1 Figure 1), and suggests that there are either a large number of C. jejuni to which humans have low susceptibility or to which humans are rarely exposed. Consequently, changes in human behaviour or environmental exposures could result in exposure to a large additional pool of bacteria. Twenty-two C. jejuni STs were assigned to wild bird origins, but there were only in 67 reported human cases assigned to an origin in wild birds. This suggests that whilst wild birds are a reservoir there is little mechanism for human exposure, although exposure to preschool children in playgrounds has been suggested elsewhere [18].

The comparisons of poultry attributed cases, ruminant attributed cases and unassigned cases (Tables 2 and 3) showed that ruminant assigned types were more common in children in rural areas in summertime. This may reflect a tendency to play outdoors in the summertime coupled with poor hygiene after playing outdoors. Strachan et al. [19] find similar results and attribute the differences to the consumption of contaminated chicken in urban areas and playing outdoors in rural areas. These findings are similar to those from New Zealand [11], although our larger sample size has enabled us to show that younger age groups in rural areas are at greater risk of infection with a ruminant types in addition to the effect of season. Thus, the heterogeneities in exposure to infection of C. jejuni are consistent across different countries, with similar mechanisms of infection occurring in all, despite the fact that the most common ST in New Zealand that is associated with poultry (ST474) differs from that in Scotland (ST257).

Previous studies [1, 10] have identified an association with increased incidence in younger individuals that live in more rural settings. This paper suggests that this is likely to be the result of infection with ruminant types, thus underlining the importance of identifying different sources of infections. Here, the density of the human population rather than the density of cattle and sheep has been identified as the measure of risk for infection with ruminant strains. This suggests that either population density is a better measure of exposure to ruminant sources or that it is some property of rural areas that determines the risk. One such property has been demonstrated to be consumption of water from untreated sources [20]. It is likely that consumption of water from private water sources will be greater in rural areas with lower population densities. ST45 was identified as a type that was associated with surface water sources during a period in the summer [20], however, in this study ST45 was attributed to sources in poultry.

This study did not demonstrate any difference in the risk associated with deprivation for different sources of infection. The relationship between campylobacteriosis and deprivation has been noted in Scotland [10], Denmark [1] and New Zealand [21], but the non-significance of deprivation in this study suggests that deprivation does not influence exposure to environmental sources.

The unassigned types had similar epidemiologies to the poultry types with the consequence that the only significant risk factors for being infected with a poultry rather than an unassigned type was overseas travel. This suggests that the majority of these unassigned types had a similar epidemiology to the poultry types, but insufficient isolates were found in the source assignment to demonstrate their origin and the association with overseas travel suggests that these may be exotic types. Bessell et al. [10] describe a higher likelihood of reporting infection in areas of lower deprivation and lower population density. These analyses show that the effect of rurality may be the signature of the ruminant origin cases.

By using a case-case approach this study did not seek to estimate population level risk of exposure. Rather this study analysed the subgroup of the population that has already been infected, with the principal risk factor being social deprivation [10]. Case-case analysis is a means of comparing risk factors within this sub-group of the population that has acquired infection [22] and has been employed elsewhere for comparing risk factors for infection between sources of C. jejuni [23]. As such, social deprivation remains the principal population level determinant of infection with C. jejuni but these analyses demonstrate that this does not vary between sources of infection.

Our results have demonstrated that over and above the previously demonstrated risk factors for infection at the population level [10], there are different risk factors for infection depending upon the sources of exposure to infection. Therefore, it is important to account for the source of infection in public health planning. The individuals that report infection depend upon the source of C. jejuni, with ruminant exposures more common among the young males in rural areas. For common genetic types, this analysis could be expanded to examine transmission routes that are specific to individual strains. By enhancing our ability to identify at-risk groups and the likely times at which these groups are at risk, public health messages can be targeted more effectively. The rapidly increasing capacity to conduct genetic typing of pathogens makes such traced epidemiological analysis more accessible and has the potential to substantially enhance epidemiological risk factor studies.