Quantifying multiple strain infections for a tick-borne pathogen using next-generation sequencing

Caroline Millins, Roman Biek

Quantification of multiple strain co-infections is important in the epidemiological study of infection in hosts and ticks, and the ecology and evolution of these pathogens. Measuring the dominant strain in genus or strain specific PCR’s can result in partial or mixed strain types which masks transmission events and mechanisms driving the ecology and evolution of these pathogens. Multilocus sequence typing using Sanger sequencing is not able to quantify mixed species co-infections in a single sample and can lead to misidentification of mixed sequence types. Epidemiological and ecological analyses are restricted by missing and sometimes mixed sequence types. We believe based on published data and from my own work that within species co-infections are common. With a method to detect these mixed infections we can test to see if strains are randomly assorted, and if evidence of aggregation is found we can try to detect potential mechanisms. For example, a recently published paper found aggregation of antigenically diverse strains of Borrelia burgdorferi s.l. (tick-borne cause of Lyme disease) in hosts suggesting a host immune mediated mechanism driving co-infections. Next generation sequencing offers great potential to provide the resolution to quantify mixed strain infections.

This project will;

1) Develop two methods to quantify mixed strain infection in host and tick samples, using next generation sequencing and

2) Provide a supportive training environment to allow me to develop my own bioinformatic toolkit. This will enable me to join the Omics’ field, which is revolutionizing approaches to investigation of zoonotic diseases.

First published: 10 August 2014

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