M 1st September 2005 to 31st August 2006. This comprised 52 of the total

M 1st September 2005 to 31st August 2006. This comprised 52 of the total reported Scottish cases over this period. Case information was anonymous but included the postcode sector of main residence, age, gender, and the date of the laboratory report [13] (See File S1). Human Eledoisin population data stratified by age, postcode sector and gender was obtained from the 2001 Scottish census. The Carstairs index of deprivation was used to describe the socioeconomic status of the human population [27]. Cattle, pig, sheep and poultry numbers in 2 by 2 km tetrads were obtained from the 2004 Scottish agricultural census and these were Hypericin cost integrated into postcode sectors using ArcView 3.3 (ESRI, Redlands, California, USA).Risk Factors for Case-control and Case-case AnalysisSix parameters were available as putative risk factors; (1) age (young – 0219 yrs old and adult – .20 yrs old), (2) gender (male or female), (3) season (summer – June to August – or the rest of the year), (4) rural or urban human population density (rural – ,200 individuals/km2, urban – 200 individuals/km2), (5) deprived (Carstairs index 0) or affluent (Carstairs index ,0) and (6) animal population density. The animal population density (cattle, pigs, poultry and sheep) were subdivided into four groups: group 1 (null density), group 2 (low density), group 3 (medium density), 16985061 group 4 (high density) for each postcode sector (see File S1). All of the predictive variables were used in three observational analyses employing univariate and multivariate logistic regression employing the epidemiological modelling software package EGRET (EGRET, version 2.0.3, Cytel Software Corporation, Cambridge, MA, USA). Results for each risk factor were considered as statistically significant when P,0.05. Factors from the univariate analyses with a P value of ,0.25 were used in the multivariate analysis.Case-controlThis analysis compared the 307 C. coli clinical cases with 921 controls generated by randomly sampling the human population as described by the Scottish census (www.scrol.gov.uk).Case-case C. coli versus C. jejuni307 C. coli cases were compared with the 2,733 C. jejuni cases as controls.MLST AnalysisThe clonal genealogy of C. coli sequence types (STs) was estimated using a model-based approach for determining bacterial microevolution: ClonalFrame software (version 1.0; http://www2. warwick.ac.uk/fac/sci/statistics/staff/research/didelot/ clonalframe/[28]. This approach incorporates both point mutation and recombination events. The program was run with 50,000 “burn-in” iterations which are discarded to minimise the effects of initial values followed by 50,000 data collection iterations. The consensus trees represent combined data from three independent runs, with 75 consensus required for inference of relatedness. The probable reservoir origin of C. coli MLST sequence types (STs) was investigated by STRUCTURE genetic population software [29]. Using this method, STs can be probabilistically assigned to ancestral populations based on their frequency. A source dataset of C. coli strains with known origins was used as a source reference population and clinical isolates were attributed toAetiology of Human Campylobacter coli Infectionsthis based on ST similarities (See File S2). This source dataset comprised 85 cattle, 322 pigs, 459 chicken and 57 sheep isolates (see File S3) obtained from both the PubMLST database and the CaMPS study [13]. The diversity of cases was determined by Simpson’s index [30].M 1st September 2005 to 31st August 2006. This comprised 52 of the total reported Scottish cases over this period. Case information was anonymous but included the postcode sector of main residence, age, gender, and the date of the laboratory report [13] (See File S1). Human population data stratified by age, postcode sector and gender was obtained from the 2001 Scottish census. The Carstairs index of deprivation was used to describe the socioeconomic status of the human population [27]. Cattle, pig, sheep and poultry numbers in 2 by 2 km tetrads were obtained from the 2004 Scottish agricultural census and these were integrated into postcode sectors using ArcView 3.3 (ESRI, Redlands, California, USA).Risk Factors for Case-control and Case-case AnalysisSix parameters were available as putative risk factors; (1) age (young – 0219 yrs old and adult – .20 yrs old), (2) gender (male or female), (3) season (summer – June to August – or the rest of the year), (4) rural or urban human population density (rural – ,200 individuals/km2, urban – 200 individuals/km2), (5) deprived (Carstairs index 0) or affluent (Carstairs index ,0) and (6) animal population density. The animal population density (cattle, pigs, poultry and sheep) were subdivided into four groups: group 1 (null density), group 2 (low density), group 3 (medium density), 16985061 group 4 (high density) for each postcode sector (see File S1). All of the predictive variables were used in three observational analyses employing univariate and multivariate logistic regression employing the epidemiological modelling software package EGRET (EGRET, version 2.0.3, Cytel Software Corporation, Cambridge, MA, USA). Results for each risk factor were considered as statistically significant when P,0.05. Factors from the univariate analyses with a P value of ,0.25 were used in the multivariate analysis.Case-controlThis analysis compared the 307 C. coli clinical cases with 921 controls generated by randomly sampling the human population as described by the Scottish census (www.scrol.gov.uk).Case-case C. coli versus C. jejuni307 C. coli cases were compared with the 2,733 C. jejuni cases as controls.MLST AnalysisThe clonal genealogy of C. coli sequence types (STs) was estimated using a model-based approach for determining bacterial microevolution: ClonalFrame software (version 1.0; http://www2. warwick.ac.uk/fac/sci/statistics/staff/research/didelot/ clonalframe/[28]. This approach incorporates both point mutation and recombination events. The program was run with 50,000 “burn-in” iterations which are discarded to minimise the effects of initial values followed by 50,000 data collection iterations. The consensus trees represent combined data from three independent runs, with 75 consensus required for inference of relatedness. The probable reservoir origin of C. coli MLST sequence types (STs) was investigated by STRUCTURE genetic population software [29]. Using this method, STs can be probabilistically assigned to ancestral populations based on their frequency. A source dataset of C. coli strains with known origins was used as a source reference population and clinical isolates were attributed toAetiology of Human Campylobacter coli Infectionsthis based on ST similarities (See File S2). This source dataset comprised 85 cattle, 322 pigs, 459 chicken and 57 sheep isolates (see File S3) obtained from both the PubMLST database and the CaMPS study [13]. The diversity of cases was determined by Simpson’s index [30].