Infectious Disease Epidemiology How do we use statistics? Laura MacDougall BC Centre for Disease Control SFU, Stat 305, April 5, 2012
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1 Infectious Disease Epidemiology How do we use statistics? Laura MacDougall BC Centre for Disease Control SFU, Stat 305, April 5, 2012
2 Epidemiology The study of the distribution and determinants of disease in (human) populations; its application to control health problems Last, 2001 Components of ID epidemiology Surveillance Outbreak investigation Research
3 Surveillance
4 Surveillance framework Collection, analysis, interpretation and dissemination of data that leads to action to prevent and control disease Collection Action Analysis Dissemination Interpretation
5 Data sources Reportable diseases Laboratories Administrative data Physician billings Hospitalisations Clinical data Clinics or emergency dpt Vital statistics Births Deaths Hospitals, health facilities Schools, daycares, workplace Surveys Immunization registries Vaccine-associated adverse reaction data
6 Data collected Person Demographics (age, sex, ethnicity) Clinical (symptoms, lab data) Place Residence Exposure Time Onset specimen collection diagnosis reported Exposures/risk factors Travel, food history, sexual practices, immunization history
7 Automatic aberration detection Automatic detection of statistically significant change in distribution of disease (i.e. outbreak) Methods Identify electronic retrospective data to forecast expected numbers Select a method (e.g. time series, regression, CUSUM) to adjust for trends, seasons, past outbreaks and develop model Determine alert threshold Apply model to prospective data Identify and interpret signals detected
8 Automatic aberration detection example BCCDC 2007
9 Outbreak Response
10 A family cluster is detected Onset February 20/03 5/6 symptomatic 2 hospitalized 3 lab confirmed Food history: Frozen chicken nuggets French toast
11 An outbreak? 6 Incidence of S. Heidelberg in 2003 vs. 5 year average ( ) 5 4 No. cases YR AVE 2003 Week
12 Methods Case-control study Cases Lab confirmed January 1 April 1, cases only ; 1 case per household Recall period 7 days prior to onset Controls 1:1 age matched: 0-6, 7-17, 18+ Forward digit dialing Recall period 7 days prior to interview
13 Risk Factors Exposure MOR 95% CI # cases exposed* # controls exposed Nuggets alone < OR < /20 4/18 Strips alone undefined 6/19 0/18 Nuggets + strips < OR < /19 4/18 Nuggets + strips (excl. restaurant i.e. McDonalds) < OR < /19 1/18 *For one case, no information on strip exposure was provided. No other risk factor significant L. MacDougall, M. Fyfe et al. J Food Prot Jun;67(6):1111-5
14 Consumer attitudes + beliefs Considered product pre-cooked 1/3 cases, 1/3 controls 27% always or sometimes used microwave 35% washed hands less frequently after handling nuggets vs. raw chicken 37% re-packaged their strips Of these, only 26% kept cooking instructions L. MacDougall, M. Fyfe et al. J Food Prot Jun;67(6):1111-5
15 Conclusion Frozen chicken nuggets/strips are a risk factor for S. Heidelberg infection Contributes significantly to the baseline (non-outbreak) rate of infection in BC Labels must be changed to clearly identify nuggets/strips as a raw product Consumer education required
16 Actions taken Local press release to consumers CFIA and BCCDC Labelling changes! Before After
17 Research
18 A Cryptic Story An increase in the number of animal and human cryptococcosis noted in 2001 Clinical symptoms: prolonged cough, sharp chest pain, unexplained shortness of breath, severe headache, fever, night sweats, weight loss; skin lesions (animals) Profiles of human cases did not fit the traditional understanding of cryptococcosis All cases resided on or had visited Vancouver Island prior to the onset of illness 5
19 Emergence of C. gattii on VI Hospitalizations for cryptococcal infection in HIV-negative patients by location of treatment, BC (N=158) Mainland Island Fyfe CCDR 2008
20 Emergence of C. gattii on VI Number of isolates Cryptococcus isolates by serotype, BC, (N=36) B D A Fyfe CCDR 2008
21 Risk factors? Case control study 30 cases from Matched to 2 controls by sex Controls required recent normal CXR Standard questionnaire administered Population control study 218 cases from Compared to population data Age and sex distribution (BC Statistics) Smoking prevalence (Canadian Community Health Survey) Cancer prevalence (BC Cancer Agency) HIV, COPD prevalence (published data) MacDougall EID, 2011 Feb;17(2):193-9
22 Risk factors (results) Risk factor Case control study mor (95%CI) Case vs. population control prevalence (p-value) Age > 50y Not significant 72.4% vs. 31.3% (p<0.001) Male sex Not evaluated 55.8% vs. 49.6% (p=0.198) Smoking 1.18 ( ) 41.9% vs. 17.8% (p<0.001) Systemic steroid use 8.1 ( ) Not evaluated Chronic lung disease 3.2 ( ) 4.1% vs. 8.0% (p=0.090) Cancer 2.0 ( ) 24.7% vs. 3.6% (p<0.001) HIV infection Not evaluated 3.7% vs 0.2% (p<0.001) MacDougall EID, 2011 Feb;17(2):193-9
23
24 Study Objective To delineate the geographic areas where Cryptococcus gattii is currently established and forecast areas that could support Cryptococcus gattii in the future for targeted public health messaging of Cryptococcus gattii risk and prioritization of environmental sampling S. Mak, MSc thesis, 2009
25 Elevation Methodology and Data Aspect Slope Biogeoclimatic January Temp (x3) July Temp (x3) Precipitation (x3) Soil (x2) GARP Determine significant variables Human Animal Environmental Resulting models S. Mak, MSc thesis, 2009
26 S. Mak, MSc thesis, 2009
27 S. Mak, MSc thesis, 2009
28 S. Mak, MSc thesis, 2009
29 Conclusion (1) Suitable ecological niche for Cryptococcus gattii is available on the BC mainland Cryptococcus gattii distribution in BC associated with areas having >1 o C January average temperature and <770m elevation (mean = 100m) Animal distribution of cryptococcosis corresponds directly with human distribution S. Mak, MSc thesis, 2009
30 Conclusion (2) Ecological niche modeling of Cryptococcus gattii produced very accurate predictions (>98% accuracy) The ecological niche model based on environmental sampling data produced the most conservative forecast Environmental sampling for Cryptococcus gattii in geographic locations identified as optimal ecological niche areas are currently underway S. Mak, MSc thesis, 2009
31 Summary Both simple and complex statistics are useful in communicable disease epidemiology Are important for surveillance, outbreak response and research Used to: Identify outbreaks Examine risk factors Persuade policy makers and the public
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