Biosurveillance of emerging biothreats using scalable genotype clustering

Journal of Biomedical Informatics
Blanca GallegoEnrico Coiera

Abstract

Developments in molecular fingerprinting of pathogens with epidemic potential have offered new opportunities for improving detection and monitoring of biothreats. However, the lack of scalable definitions for infectious disease clustering presents a barrier for effective use and evaluation of new data types for early warning systems. A novel working definition of an outbreak based on temporal and spatial clustering of molecular genotypes is introduced in this paper. It provides an unambiguous way of clustering of causative pathogens and is adjustable to local disease prevalence and availability of public health resources. The performance of this definition in prospective surveillance is assessed in the context of community outbreaks of food-borne salmonellosis. Molecular fingerprinting augmented with the scalable clustering allows the detection of more than 50% of the potential outbreaks before they reach the midpoint of the cluster duration. Clustering in time by imposing restrictions on intervals between collection dates results in a smaller number of outbreaks but does not significantly affect the timeliness of detection. Clustering in space and time by imposing restrictions on the spatial and temporal distance between cases...Continue Reading

References

Feb 8, 2003·Proceedings of the National Academy of Sciences of the United States of America·Ben Y ReisKenneth D Mandl
Mar 31, 2005·Journal of Biomedical Informatics·David L BuckeridgeAndrew W Moore
Apr 11, 2006·Foodborne Pathogens and Disease·Robert V Tauxe
Sep 8, 2006·Statistics in Medicine·Simon H HeisterkampJanneke C M Heijne
Nov 11, 2006·Journal of Biomedical Informatics·David L Buckeridge
Jun 8, 2007·Emerging Infectious Diseases·Mia TorpdahlEva Møller Nielsen
Jul 5, 2007·Journal of Clinical Microbiology·K L HopkinsE J Threlfall
Oct 27, 2007·The Lancet Infectious Diseases·Pierre-Edouard FournierDidier Raoult

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