Diversity and host specificity of Borrelia burgdorferi's outer surface protein C (ospC) alleles in synanthropic mammals, with a notable ospC allele U absence from mixed infections

Interactions among pathogen genotypes that vary in host specificity may affect overall transmission dynamics in multi-host systems. Borrelia burgdorferi, a bacterium that causes Lyme disease, is typically transmitted among wildlife by Ixodes ticks. Despite the existence of many alleles of B. burgdorferi’s sensu stricto outer surface protein C (ospC) gene, most human infections are caused by a small number of ospC alleles [“human infectious alleles” (HIAs)], suggesting variation in host specificity associated with ospC. To characterize the wildlife host association of B. burgdorferi’s ospC alleles, we used metagenomics to sequence ospC alleles from 68 infected individuals belonging to eight mammalian species trapped at three sites in suburban New Brunswick, New Jersey (USA). We found that multiple allele (“mixed”) infections were common. HIAs were most common in mice (Peromyscus spp.) and only one HIA was detected at a site where mice were rarely captured. OspC allele U was exclusively f..., , , # Diversity and host specificity of Borrelia burgdorferi's outer surface protein C (ospC) alleles in synanthropic mammals, with a notable ospC allele U absence from mixed infections

This repository includes raw sequence reads, SAMtools coverage data, coverage data graphs, metadata, and R code that allow one to reproduce all of the analyses in our manuscript.

## Description of the data and file structure

Raw sequence reads (fastq format) are presented in a tarred/compressed file called \"221028_KLY7P_Ellis copy.tar\".

\"Shifflett et al. 2023_metadata.xlsx\" is the main data file. There are two sheets that are called separately in the R code. They describe the captured animals and provide additional information including whether they were infected and what species they belong to and where and when they were captured. The first sheet, “Data”, lists the date of capture, the site an individual was captured at, the common name for the species (under “animal”), the scientific name for the sp...