Impact of compounding error on strategies for subtyping pathogenic bacteria.

Foodborne Pathogens and Disease
Douglas R CallMin-Su Kang

Abstract

Comparative-omics will identify a multitude of markers that can be used for intraspecific discrimination between strains of bacteria. It seems intuitive that with this plethora of markers we can construct higher resolution subtyping assays using discrete markers to define strain "barcodes." Unfortunately, with each new marker added to an assay, overall assay robustness declines because errors are compounded exponentially. For example, the difference in accuracy of strain classification for an assay with 60 markers will change from 99.9% to 54.7% when average probe accuracy declines from 99.999% to 99.0%. To illustrate this effect empirically, we constructed a 19 probe bead-array for subtyping Listeria monocytogenes and showed that despite seemingly reliable individual probe accuracy (>97%), our best classification results at the strain level were <75%. A more robust strategy would use as few markers as possible to achieve strain discrimination. Consequently, we developed two variable number of tandem repeat (VNTR) assays (Vibrio parahaemolyticus and L. monocytogenes) and demonstrate that these assays along with a published assay (Salmonella enterica) produce robust results when products were machine scored. The discriminatory a...Continue Reading

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Citations

Nov 24, 2011·Avian Pathology : Journal of the W.V.P.A·Min S KangGab S Chung
Jul 14, 2010·Applied and Environmental Microbiology·Mathias SchmelcherMartin J Loessner
Jun 25, 2010·Journal of Clinical Microbiology·Tansy PetersElizabeth de Pinna
Apr 24, 2009·Journal of Clinical Microbiology·Margaret A DavisThomas E Besser
Apr 9, 2013·International Journal of Food Microbiology·Lisa BarcoAntonia Ricci
Jul 12, 2014·IET Nanobiotechnology·Loganathan PalanikumarChandrasekaran Balachandran
Jul 30, 2019·Frontiers in Microbiology·Silin TangMartin Wiedmann

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