Where a value of 0 indicates homogenous STs and a value of 1indicates a heterogeneous population with maximum diversity. Confidence intervals were calculated using a bootstrap method from the PopTools add-in for Microsoft Excel (available from http://www.cse.csiro.au/poptools).Table 1. Results of the logistic regression for the case-control study.Factors (A) Univariate AgeUnitO.R.C.I. (95 )P-valuechild adult1 3.346 1 0.878 1 2.531 1 0.573 1 0.654 1 0.985 1 1.167 1 1.034 1 1.?2.234?.013 ?0.678?.137 ?1.935?.311 ?0.437?.751 ?0.502?.851 ?0.880?.103 ?1.050?.298 ?0.924?.157 ?0.911?.?0.000*{ ?0.323 ?0.000*{ ?0.000*{ ?0.002*{ ?0.796 ?0.004*{ ?0.557 ?0.Gendermale femaleCase-case Chicken Attributed Strains versus Non Chicken StrainsThe C. coli STs from cases were assigned to putative source (chicken or non-chicken – cattle, pigs and sheep) when the attribution score was greater than 0.6 (See Files S3 and S4). This analysis then compared 113 C. coli cases attributed to chicken with the 181 non chicken cases as controls. Scores from 13 cases were too ambiguous to determine source and were removed from this further analysis.Seasonrest of year summerLocationrural urbanCarstairs cattle densitya pig densitya Title Loaded From File poultry densitya sheep densityaaffluent deprived low density high density low density high density low density high density low density high densityEthics Statement`The Multi-Centre Research Ethics Committee (MREC) for Scotland granted an ethical approval (REC ref: 06/MRE00/85) for acquisition and use of the dataset; additionally, approval for the research was obtained from the Research and Development Committee in each of the NHS Health Boards.Results Case-control StudyIn univariate analysis C. coli cases were more common in adults than children, in rural rather than urban environments, in affluent as opposed to deprived areas, in postcode sectors with a high pig density and during the summer compared to the remainder of the year (Table 1). These were the only statistically significant factors used in the multivariate analysis as none of the rest had P values ,0.25. The multivariate analysis also found that human campylobacteriosis from C. coli was statistically significantly associated with being an adult, living in a rural area, and contracting the disease during the summer months.(B) Multivariate age child adult season rest of year summer location rural urban 1 3.352 1 2.596 1 0.546 ?2.221?.059 ?1.969?.423 ?0.411?.724 ?0.000* ?0.000* ?0.000*Case-case Studies and MLST AnalysisThe first case-case analysis comparing C. coli cases to those from C. jejuni found that C. coli cases were more frequent in adults and during the summer months (Table 2). Only one other factor ?residence in a rural area – had P,0.25, and was added to the multivariate model. The multivariate analysis showed the same pattern with an increased probability of C. coli infection in adults, living in a rural areas and during the summer. The ClonalFrame phylogeny of C. coli sequence types (Fig. 1A) shows that particular clades dominated particular hosts. It was observed that 31 of cattle, 100 of sheep, 17 of pig and 62 of chicken ST’s are also found in humans. Attribution by STRUCTURE (Fig. 1B) assigns 41 of human clinical cases to sheep, 40 to chicken and lower proportions to cattle (14 ) and pigs (66 ). Simpson’s index (Fig. 1C) shows that pigs and chickens have the greatest Title Loaded From File diversity of C. coli ST’s, whilst cattle and sheep the least with humans being intermediate. The uni.Where a value of 0 indicates homogenous STs and a value of 1indicates a heterogeneous population with maximum diversity. Confidence intervals were calculated using a bootstrap method from the PopTools add-in for Microsoft Excel (available from http://www.cse.csiro.au/poptools).Table 1. Results of the logistic regression for the case-control study.Factors (A) Univariate AgeUnitO.R.C.I. (95 )P-valuechild adult1 3.346 1 0.878 1 2.531 1 0.573 1 0.654 1 0.985 1 1.167 1 1.034 1 1.?2.234?.013 ?0.678?.137 ?1.935?.311 ?0.437?.751 ?0.502?.851 ?0.880?.103 ?1.050?.298 ?0.924?.157 ?0.911?.?0.000*{ ?0.323 ?0.000*{ ?0.000*{ ?0.002*{ ?0.796 ?0.004*{ ?0.557 ?0.Gendermale femaleCase-case Chicken Attributed Strains versus Non Chicken StrainsThe C. coli STs from cases were assigned to putative source (chicken or non-chicken – cattle, pigs and sheep) when the attribution score was greater than 0.6 (See Files S3 and S4). This analysis then compared 113 C. coli cases attributed to chicken with the 181 non chicken cases as controls. Scores from 13 cases were too ambiguous to determine source and were removed from this further analysis.Seasonrest of year summerLocationrural urbanCarstairs cattle densitya pig densitya poultry densitya sheep densityaaffluent deprived low density high density low density high density low density high density low density high densityEthics Statement`The Multi-Centre Research Ethics Committee (MREC) for Scotland granted an ethical approval (REC ref: 06/MRE00/85) for acquisition and use of the dataset; additionally, approval for the research was obtained from the Research and Development Committee in each of the NHS Health Boards.Results Case-control StudyIn univariate analysis C. coli cases were more common in adults than children, in rural rather than urban environments, in affluent as opposed to deprived areas, in postcode sectors with a high pig density and during the summer compared to the remainder of the year (Table 1). These were the only statistically significant factors used in the multivariate analysis as none of the rest had P values ,0.25. The multivariate analysis also found that human campylobacteriosis from C. coli was statistically significantly associated with being an adult, living in a rural area, and contracting the disease during the summer months.(B) Multivariate age child adult season rest of year summer location rural urban 1 3.352 1 2.596 1 0.546 ?2.221?.059 ?1.969?.423 ?0.411?.724 ?0.000* ?0.000* ?0.000*Case-case Studies and MLST AnalysisThe first case-case analysis comparing C. coli cases to those from C. jejuni found that C. coli cases were more frequent in adults and during the summer months (Table 2). Only one other factor ?residence in a rural area – had P,0.25, and was added to the multivariate model. The multivariate analysis showed the same pattern with an increased probability of C. coli infection in adults, living in a rural areas and during the summer. The ClonalFrame phylogeny of C. coli sequence types (Fig. 1A) shows that particular clades dominated particular hosts. It was observed that 31 of cattle, 100 of sheep, 17 of pig and 62 of chicken ST’s are also found in humans. Attribution by STRUCTURE (Fig. 1B) assigns 41 of human clinical cases to sheep, 40 to chicken and lower proportions to cattle (14 ) and pigs (66 ). Simpson’s index (Fig. 1C) shows that pigs and chickens have the greatest diversity of C. coli ST’s, whilst cattle and sheep the least with humans being intermediate. The uni.
