Conducting an Epidemiologic Study and Making It FAIR: Reusable Tools and Procedures from a Population-Based Cohort Study.

Conducting large-scale epidemiologic studies requires powerful software for electronic data capture, data management, data quality assessments, and participant management. There is also an increasing need to make studies and the data collected findable, accessible, interoperable, and reusable (FAIR). However, reusable software tools from major studies, underlying such needs, are not necessarily known to other researchers. Therefore, this work gives an overview on the main tools used to conduct the internationally highly networked population-based project Study of Health in Pomerania (SHIP), as well as approaches taken to improve its FAIRness. Deep phenotyping, formalizing processes from data capture to data transfer, with a strong emphasis on cooperation and data exchange have laid the foundation for a broad scientific impact with more than 1500 published papers to date.

Identification of early predictors for infected necrosis in acute pancreatitis.

BACKGROUND: In acute pancreatitis, secondary infection of pancreatic necrosis is a complication that mostly necessitates interventional therapy. A reliable prediction of infected necrotizing pancreatitis would enable an early identification of patients at risk, which however, is not possible yet. METHODS: This study aims to identify parameters that are useful for the prediction of infected necrosis and to develop a prediction model for early detection. We conducted a retrospective analysis from the hospital information and reimbursement data system and screened 705 patients hospitalized with diagnosis of acute pancreatitis who underwent contrast-enhanced computed tomography and additional diagnostic puncture or drainage of necrotic collections. Both clinical and laboratory parameters were analyzed for an association with a microbiologically confirmed infected pancreatic necrosis. A prediction model was developed using a logistic regression analysis with stepwise inclusion of significant variables. The model quality was tested by receiver operating characteristics analysis and compared to single parameters and APACHE II score. RESULTS: We identified a total of 89 patients with necrotizing pancreatitis, diagnosed by computed tomography, who additionally received biopsy or drainage. Out of these, 59 individuals had an infected necrosis. Eleven parameters showed a significant association with an infection including C-reactive protein, albumin, creatinine, and alcoholic etiology, which were independent variables in a predictive model. This model showed an area under the curve of 0.819, a sensitivity of 0.692 (95%-CI [0.547-0.809]), and a specificity of 0.840 (95%-CI [0.631-0.947]), outperforming single laboratory markers and APACHE II score. Even in cases of missing values predictability was reliable. CONCLUSION: A model consisting of a few single blood parameters and etiology of pancreatitis might help for differentiation between infected and non-infected pancreatic necrosis and assist medical therapy in acute necrotizing pancreatitis.

Quality of life and sleep in individuals with irritable bowel syndrome according to different diagnostic criteria and inflammatory bowel diseases: A comparison using data from a population-based survey.

BACKGROUND: A proportion of irritable bowel syndrome (IBS) affected patients does not fulfil Rome criteria despite considerable impairment similarly to that in patients with organic gastrointestinal diseases.This investigation aims to examine differences regarding Mental (MQoL), Physical Quality of Life (PQoL), and sleep between IBS according to Rome III (IBS Rome), clinically defined IBS, inflammatory bowel diseases (IBD), and non-IBS/non-IBD individuals. METHODS: Data from SHIP-Trend (Study of Health in Pomerania, 2008-2012), a population-based cohort study in Germany, were used. RESULTS: Response was 50.1% (N = 4420). Prevalence was 3.5% for IBS Rome (95% confidence interval (CI): 3.0 - 4.1%, n = 148), 0.6% for clinically defined IBS (CI: 0.4 - 0.9%, n = 27), and 0.8% for IBD (CI: 0.6 - 1.1%, n = 34). Individuals with IBS Rome (4.54 (CI: -5.92; -3.17)) and clinically defined IBS (4.69 (CI: -7.82; -1.56)) had lower scores for MQoL compared to the non-IBS/non-IBD group. PQoL scores were lowered in IBS Rome (6.39 (CI: -7.89; -4.88)) and IBD (5.37 (CI: -8.51; -2.22)), but not in clinically defined IBS compared to the non-IBS/non-IBD group. IBS Rome was the only gastroenterological condition with higher odds of sleeping problems (odds ratio (OR) "falling asleep": 1.74; CI: 1.29; 2.36; OR "remaining asleep": 1.73; CI: 1.26; 2.38). CONCLUSIONS: IBS Rome is associated with reduced MQoL, PQoL, and sleep problems. Clinically defined IBS is associated only with reduced MQoL. Heterogeneity within IBS affected patients should be considered in clinical routine and screening for daily life impairment should be performed.

Comparability of size measurements of the pancreas in magnetic resonance imaging and transabdominal ultrasound.

INTRODUCTION: Transabdominal ultrasound (US) and magnetic resonance imaging (MRI) are commonly used for the examination of the pancreas in clinical routine. We therefore were interested in the concordance of these two imaging methods for the size measurement of the pancreas and how age, gender, and body mass index (BMI) affect the organ size. METHODS: A total of 342 participants from the Study of Health in Pomerania underwent whole-body MRI and transabdominal US on the same day, and the diameter of the pancreatic head, body, and tail were measured. The agreement between US and MRI measurements was assessed by Bland and Altman plots. Intraclass correlation coefficients were used to compare observers. A multivariable regression model was applied using the independent variables age, gender, and body mass index. RESULTS: Compared to MRI, abdominal US returned smaller values for each segment of the pancreas, with a high level of inconsistency between these two methods. The mean difference was 0.39, 0.18, and 0.54 cm for the head, body, and tail, respectively. A high interobserver variability was detected for US. Multivariable analysis showed that pancreatic size in all three segments increased with BMI in both genders whereas pancreatic head and tail size decreased with age, an effect more marked in women. CONCLUSIONS: Agreement of pancreatic size measurements is poor between US and MRI. These limitations should be considered when evaluating morphologic features for pathologic conditions or setting limits of normal size. Adjustments for BMI, gender, and age may also be warranted.

Irritable bowel syndrome, mental health, and quality of life: Data from a population-based survey in Germany (SHIP-Trend-0).

BACKGROUND: Irritable bowel syndrome (IBS) is associated with reduced quality of life and high healthcare costs. This study aimed to assess the prevalence and risk factors for IBS in a general adult population. METHODS: The Study of Health in Pomerania (SHIP) is a population-based cohort study in northeastern Germany. SHIP-Trend-0 participants enrolled from 2008 to 2012 were grouped according to Rome III criteria (main criteria: abdominal discomfort or crampy or bloating pain for at least six months plus 2/3 additional criteria). Factors associated with IBS were assessed using survey-weighted backward stepwise logistic regression. KEY RESULTS: The final data set included 4194 records. IBS prevalence was 3.5% (3.0%-4.2%). Unemployment (OR: 2.02, 1.26-3.21), headaches (OR: 2.37, 1.59-3.52), mental quality of life (OR: 0.95 per unit increase, 0.93-0.97), and interactions between gender and physical quality of life (P = 0.004) and gender and alexithymia (P = 0.002) predicted IBS probability. The model resulted in a good discrimination (area under the curve = 75.4%) and model fit (F = 0.72, P = 0.69). History of depression (OR: 2.77, 1.94-3.95), back pain (OR: 2.38, 1.69-3.35), early trauma (OR: 1.03, 1.02-1.04), and duration of inpatient treatment within the last twelve months (OR: 1.02, 1.01-1.04) lost their significance in multivariable analysis. CONCLUSIONS & INFERENCES: IBS prevalence was relatively low compared to other studies. Factors predicting IBS were of biological, psychological, and social nature. The association between IBS and pain in different areas of the body indicates a potential underlying complex somatic symptom disorder.

Regional Influences on Nutritional Iodine Status of Pregnant Women in Pakistan.

BACKGROUND: Pregnant women are particularly vulnerable to iodine deficiency. Considering the rural-urban disparities in nutritional status in Pakistan, this study aimed to assess regional influences on nutritional iodine status of pregnant women in Pakistan. METHODS: Data were collected from 1246 pregnant women in all trimesters of pregnancy who visited antenatal clinics for routine checkups in five Khyber Pakhtunkhwa province districts. Information concerning iodized salt intake and knowledge of iodine deficiency disorders (IDD) was obtained through an interview questionnaire. Goiter and urinary iodine concentration (UIC) levels were assessed by the palpation method and Sandell-Kolthoff reaction, respectively. Logistic regression analysis was used to quantify associations between residence (rural-urban), pregnancy trimester, and previous pregnancy outcomes with knowledge about IDD, iodized salt intake, presence of goiter, and UIC <150 µg/L. RESULTS: Among study participants, 87.7% had no knowledge about IDD, and only 21.0% were consuming iodized salt. Goiter was present in 25.5% of the women. The median UIC level was 131 µg/L, and 41.3% of study participants had a UIC ≥150 µg/L. There were no significant differences between pregnant women from rural and urban settings in regions with a solid socioeconomic status with respect to knowledge about IDD, iodized salt intake, iodine deficiency, and goiter prevalence. Urban-rural differences were observed only in socioeconomically disadvantaged districts. Only pregnant women living in the Lakki Marwat district had higher odds of having knowledge of IDD and iodized salt intake than those from rural regions. Trimesters of pregnancy and previous pregnancy outcomes had no significant effect on the outcome measures. CONCLUSIONS: Relative to a national nutrition survey conducted in Pakistan in 2011, the results from this study indicate that UIC levels remained stable with mild iodine deficiency, whereas rates of goiter and iodized salt intake remained high and low, respectively, especially in rural areas. Rural-urban disparities were observed only in socioeconomically disadvantaged districts, and these disparities limit the effectiveness of the IDD prevention program in rural areas in Pakistan. Thus, implementation of mandatory salt iodization requires improvement, and program effectiveness should be continuously monitored to prevent adverse health effects of iodine deficiency during pregnancy.

Analysis of lifestyle factors in patients with concomitant chronic pancreatitis and liver cirrhosis.

BACKGROUND & OBJECTIVES: Chronic pancreatitis (CP) and liver cirrhosis (LC) are common gastroenterological disorders but their co-incidence is considered to be rare. This study was designed to identify lifestyle factors that are associated with the development of concomitant LC in patients with CP. METHODS: In a retrospective case-control study between 2000 and 2005 122 patients with both CP and LC and 223 matched control patients with CP and no known liver disease were identified in 11 European university medical centers. Another 24 patients and 48 CP controls were identified in the period between 2006 and 2012. RESULTS: Alcoholism was most commonly regarded as aetiology for both CP (82.2%; 95% confidence interval (CI): 75.0-88.0%) and LC (79.5%; 95% CI: 72.0-85.7%) as compared to controls with CP only (68.6%; 95% CI: 62.7-74.1%). The preferred type of alcoholic beverage and pattern of alcohol intake were the only significant lifestyle factors in multivariate analysis. Frequency of alcohol intake (p = 0.105) and smoking status (p = 0.099) were not significant in bivariate analysis and dropped out of the multivariate model. Recurrent and chronic pancreatic pain was observed more often in patients with only CP, whereas gallstones were more common in individuals with both chronic disorders. CONCLUSIONS: These findings indicate that certain lifestyle factors might be important for the development of concomitant CP and LC. More studies will be needed to identify additional genetic and environmental factors underlying this association.

Performance of Hepatitis E Virus (HEV)-antibody tests: a comparative analysis based on samples from individuals with direct contact to domestic pigs or wild boar in Germany.

In Europe, Hepatitis E virus (HEV) genotype 3 causes most human infections, and domestic pigs and wild boar represent the main reservoirs. Contact to these animals represents one source of human infection. However, interpretation of studies is challenged in the absence of a serological gold standard. Hence, this study compared results of different HEV immunoassays. Plasma samples from 139 individuals who had professional contact to pigs (veterinarians, meat inspectors, slaughterhouse workers; n = 114) or hunted regularly (n = 25) were tested with assays specific for HEV IgG, HEV IgM, HEV IgA, and total HEV immunoglobulin as well as for viral RNA. Furthermore, overall HEV IgG was defined (i.e., two of three IgG assays reveal the same result) to compare serological findings. Borderline results were always quoted as positive. For IgG, apparent prevalence was higher in Wantai (48.2%) compared to Euroimmun (11.5%) and Mikrogen assays (17.3%) (p = 0.0001). The overall IgG prevalence was estimated to be 18.7%. For total Ig, Wantai (40.3%) also yielded higher prevalence than Euroimmun (15.8%) (p = 0.0001). The HEV IgM prevalence ranged from 0% (Euroimmun) to 4.3% (Mikrogen). Four percent of individuals tested IgA positive, whilst none harboured HEV RNA. Our results support previous studies that the higher IgG prevalence estimated with the Wantai assay result from a higher sensitivity of this test. However, further studies are needed to verify specificity given the challenge of defining true negative samples. The high percentage of individuals with HEV IgG observed in this study underlines that direct contact to pigs represents a risk factor for HEV infection.

Distribution of ticks infesting ruminants and risk factors associated with high tick prevalence in livestock farms in the semi-arid and arid agro-ecological zones of Pakistan.

BACKGROUND: Tick infestation is the major problem for animal health that causes substantial economic losses, particularly in tropical and subtropical countries. To better understand the spatial distribution of tick species and risk factors associated with tick prevalence in livestock in Pakistan, ticks were counted and collected from 471 animals, including 179 cattle, 194 buffaloes, 80 goats and 18 sheep, on 108 livestock farms in nine districts, covering both semi-arid and arid agro-ecological zones. RESULTS: In total, 3,807 ticks representing four species were collected: Hyalomma anatolicum (n = 3,021), Rhipicephalus microplus (n = 715), Hyalomma dromedarii (n = 41) and Rhipicephalus turanicus (n = 30). The latter species is reported for the first time from the study area. Rhipicephalus microplus was the predominant species in the semi-arid zone, whereas H. anatolicum was the most abundant species in the arid zone. The overall proportion of tick-infested ruminants was 78.3% (369/471). It was highest in cattle (89.9%), followed by buffaloes (81.4%), goats (60.0%) and sheep (11.1%). The median tick burden significantly differed among animal species and was highest in cattle (median 58), followed by buffaloes (median 38), goats (median 19) and sheep (median 4.5). Female animals had significantly higher tick burdens than males and, in large ruminants, older animals carried more ticks than younger animals. The intensity of infestation was significantly lower in indigenous animals compared to exotic and crossbred cows. Analysis of questionnaire data revealed that the absence of rural poultry, not using any acaricides, traditional rural housing systems and grazing were potential risk factors associated with a higher tick prevalence in livestock farms. CONCLUSION: Absence of rural poultry, not performing acaricide treatments, traditional rural housing systems and grazing were important risk factors associated with higher tick prevalence in livestock farms. Age, gender, breed and animal species significantly affected the intensity of tick infestation. This report also describes the presence of R. turanicus in the Punjab Province of Pakistan for the first time. The outcomes of this study will be useful in the planning of integrated control strategies for ticks and tick-borne diseases in Pakistan.

Surveillance strategies for Classical Swine Fever in wild boar - a comprehensive evaluation study to ensure powerful surveillance.

Surveillance of Classical Swine Fever (CSF) should not only focus on livestock, but must also include wild boar. To prevent disease transmission into commercial pig herds, it is therefore vital to have knowledge about the disease status in wild boar. In the present study, we performed a comprehensive evaluation of alternative surveillance strategies for Classical Swine Fever (CSF) in wild boar and compared them with the currently implemented conventional approach. The evaluation protocol was designed using the EVA tool, a decision support tool to help in the development of an economic and epidemiological evaluation protocol for surveillance. To evaluate the effectiveness of the surveillance strategies, we investigated their sensitivity and timeliness. Acceptability was analysed and finally, the cost-effectiveness of the surveillance strategies was determined. We developed 69 surveillance strategies for comparative evaluation between the existing approach and the novel proposed strategies. Sampling only within sub-adults resulted in a better acceptability and timeliness than the currently implemented strategy. Strategies that were completely based on passive surveillance performance did not achieve the desired detection probability of 95%. In conclusion, the results of the study suggest that risk-based approaches can be an option to design more effective CSF surveillance strategies in wild boar.

Epidemiological performance and subsequent costs of different surveillance strategies to control bovine herpesvirus type 1 in dairy farms.

This study aimed at comparing the surveillance program of bovine herpesvirus type 1 (BHV1) as laid down by EU Decision 2004/558/EC and 2007/584/EC ('conventional design') with an alternative design. The alternative design was based on monthly bulk-milk testing, clinical surveillance and a risk-based component that involves testing of animals that are purchased from non-free cattle herds. Scenario-tree analyses were carried out to determine sensitivities of the surveillance system (and its components) and the monthly confidence of freedom on herd-level. Also, the expected costs per surveillance design and components thereof were calculated. Results showed that the conventional (EU) and alternative surveillance designs to obtain a BHV1-free status performed equally well in terms of sensitivity. However, total costs per cattle herd to obtain a free status were highest in the conventional design. In an endemic situation and with a within-herd design prevalence of 10%, the conventional design led to a varying probability of freedom ranging from 99.6% to 100% per month. With the alternative design, in this situation, a constant probability of freedom of >99.9% per month was found. In a disease-free situation, both designs performed equally well (probability of freedom >99.9% per month). The yearly costs per farm for monitoring the disease-free status decreased by approximately 25% in the alternative design. The alternative strategy based on monthly bulk-milk monitoring therefore was deemed most cost-effective. This study showed that the surveillance regime to attain and maintain a BHV1-free status as described by EU-legislation can be improved to reduce the monitoring costs without reduction of the system's sensitivity, given a within-herd design prevalence of 10%. The assessment of various surveillance designs could be highly useful to support decision-making towards a more risk-based approach of animal health surveillance.

Spatio-temporal analyses of highly pathogenic avian influenza H5N1 outbreaks in the Mekong River Delta, Vietnam, 2009.

This paper presents the results of spatio-temporal analyses and epidemic modelling of HPAI H5N1 outbreaks that occurred in four provinces of the Mekong River Delta, Vietnam between January and March 2009. Significant spatio-temporal interaction of disease risk was observed within a distance of 10 km and 12 days following the detected onset of clinical signs. We estimate that the household-to-household infection rate within a commune was approximately 50 times greater than the household-to-household infection rate between communes. Our findings show that the predominant mechanism of infection transfer was local spread. A comparison of disease control procedures and veterinary capacity in communes with relatively high and low infection rates should help to identify procedures essential for effective outbreak management in this area of Vietnam.

Spatio-temporal epidemiology of highly pathogenic avian influenza outbreaks in the two deltas of Vietnam during 2003-2007.

Outbreaks of highly pathogenic avian influenza A subtype H5N1 have occurred in Vietnam as a series of epidemic waves since December 2003. We describe the spatial and temporal patterns of the HPAI H5N1 epidemics in the Red River Delta in the north (785 outbreaks in 606 communes) and the Mekong River Delta in the south of Vietnam (1313 outbreaks in 837 communes), where the epidemics were concentrated. Throughout the study period the percentage of outbreaks affecting ducks increased steadily to a peak of 78% during the 2006/2007 epidemic in both deltas. Five of the seven epidemic waves occurred in the period of active poultry population buildup immediately prior to the Vietnamese New Year (Tet festival). Recorded outbreaks were clustered in space and time within both deltas, consistent with infection transmission occurring via a combination of local and long-distance spread. Our analyses demonstrate that the epidemiology of HPAI in Vietnam has changed over the 4-year study period, with outbreaks now occurring in the warmer months of the year and ducks featuring more prominently as affected species. To determine the relative importance of local and long-distance spread on infection transmission, precise details of outbreak location, date of onset of clinical signs, and size and composition of the poultry population at risk need to be recorded during future outbreak responses.