Molecular source attribution.
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ABSTRACT:
SUBMITTER: Chao E
PROVIDER: S-EPMC9671344 | biostudies-literature | 2022 Nov
REPOSITORIES: biostudies-literature
Publications
Molecular source attribution.
Chao Elisa E Chato Connor C Vender Reid R Olabode Abayomi S AS Ferreira Roux-Cil RC Poon Art F Y AFY
PLoS computational biology 20221117 11
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Project description:Campylobacter infection is the most commonly notified bacterial enteritis in Germany. We performed a large combined case-control and source attribution study (Nov 2011-Feb 2014) to identify risk factors for sporadic intestinal Campylobacter infections and to determine the relative importance of various animal sources for human infections in Germany. We conducted multivariable logistic regression analysis to identify risk factors. Source attribution analysis was performed using the asymmetric island model based on MLST data of human and animal/food isolates. As animal sources we considered chicken, pig, pet dog or cat, cattle, and poultry other than chicken. Consumption of chicken meat and eating out were the most important risk factors for Campylobacter infections. Additional risk factors were preparation of poultry meat in the household; preparation of uncooked food and raw meat at the same time; contact with poultry animals; and the use of gastric acid inhibitors. The mean probability of human C. jejuni isolates to originate from chickens was highest (74%), whereas pigs were a negligible source for C. jejuni infections. Human C. coli isolates were likely to originate from chickens (56%) or from pigs (32%). Efforts need to be intensified along the food chain to reduce Campylobacter load, especially on chicken meat.
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Project description:The partitioning of pathogenic strains isolated in environmental or human cases to their sources is challenging. The pathogens usually colonize multiple animal hosts, including livestock, which contaminate the food-production chain and the environment (e.g. soil and water), posing an additional public-health burden and major challenges in the identification of the source. Genomic data opens up new opportunities for the development of statistical models aiming to indicate the likely source of pathogen contamination. Here, we propose a computationally fast and efficient multinomial logistic regression source-attribution classifier to predict the animal source of bacterial isolates based on 'source-enriched' loci extracted from the accessory-genome profiles of a pangenomic dataset. Depending on the accuracy of the model's self-attribution step, the modeller selects the number of candidate accessory genes that best fit the model for calculating the likelihood of (source) category membership. The Accessory genes-Based Source Attribution (AB_SA) method was applied to a dataset of strains of Salmonella enterica Typhimurium and its monophasic variant (S. enterica 1,4,[5],12:i:-). The model was trained on 69 strains with known animal-source categories (i.e. poultry, ruminant and pig). The AB_SA method helped to identify 8 genes as predictors among the 2802 accessory genes. The self-attribution accuracy was 80 %. The AB_SA model was then able to classify 25 of the 29 S. enterica Typhimurium and S. enterica 1,4,[5],12:i:- isolates collected from the environment (considered to be of unknown source) into a specific category (i.e. animal source), with more than 85 % of probability. The AB_SA method herein described provides a user-friendly and valuable tool for performing source-attribution studies in only a few steps. AB_SA is written in R and freely available at https://github.com/lguillier/AB_SA.
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| S-EPMC8313984 | biostudies-literature
Project description:BackgroundA substantial proportion of echinococcosis transmission to humans via contamination of food has been assumed. However, the relative importance of food as a transmission vehicle has previously been estimated through expert opinion rather than empirical data.ObjectiveTo find and evaluate empirical data that could be used to estimate the source attribution of echinococcosis, in particular the proportion that is transmitted through contaminated food.MethodsA systematic review was undertaken to identify reports on the risk factors for human cystic (CE) and alveolar (AE) echinococcosis. Data bases searched included PubMed, Scopus, Web of Knowledge, Cab Direct, Science Direct, Google Scholar, eLIBRARY.RU, CyberLeninka, CNKI and VIP. Search terms included Echinococc*, hydatid, epidemiology, logistic regression, risk factors, odds ratio, relative risk, risk factors. Reports, including grey literature where available, that had suitable data were selected and data were extracted. The main pathways of transmission were hypothesised to be contact with the definitive host, contaminated water, contaminated food and contaminated environment (other than food). For each study the attributable fraction for these potential sources of infection was calculated from the data presented. A meta-analysis was then undertaken to obtain pooled estimates for the relative contribution of these transmission pathways.ResultsData from 28 cross-sectional studies and 14 case-control studies were extracted. There was strong evidence for transmission by direct contact with dogs for both CE and AE. The estimated attributable fractions were 26.1% (CI 13.8%-39.6%) and 34.4% (CI 20.7% -48.2%) respectively. Transmission through contaminated water was estimated to be responsible for approximately 29.4% (CI 12.1%-51.7%) for CE and 24.8% (CI 10.6% to 42.6%) for AE. Contaminated food may be responsible for approximately 23.4% of CE cases (CI 2.1%-47.3%). Globally, there was insufficient evidence to conclude AE can be transmitted by food, although case control studies from low human incidence areas suggested that possibly 32.5% (CI 10.0%-53.2%) could be transmitted by food. There was also insufficient evidence that direct contact with foxes was a significant source of human disease. There were no suitable studies with a risk of environmental contact reported, but the residual attributable fraction thatwould likely include this pathway was approximately 21.1% for CE and 11.1% for AE.ConclusionsThe results support the hypothesis that dog contact and drinking contaminated water are major pathways of transmission of both CE and AE. For contaminated food, the results are less consistent, but suggest that it is an important transmission pathway and provide better evidence than expert elicitations as previously used.
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