Concordance and discordance of sequence survey methods for molecular epidemiology

PeerJ
Eduardo Castro-NallarKeith A Crandall

Abstract

The post-genomic era is characterized by the direct acquisition and analysis of genomic data with many applications, including the enhancement of the understanding of microbial epidemiology and pathology. However, there are a number of molecular approaches to survey pathogen diversity, and the impact of these different approaches on parameter estimation and inference are not entirely clear. We sequenced whole genomes of bacterial pathogens, Burkholderia pseudomallei, Yersinia pestis, and Brucella spp. (60 new genomes), and combined them with 55 genomes from GenBank to address how different molecular survey approaches (whole genomes, SNPs, and MLST) impact downstream inferences on molecular evolutionary parameters, evolutionary relationships, and trait character associations. We selected isolates for sequencing to represent temporal, geographic origin, and host range variability. We found that substitution rate estimates vary widely among approaches, and that SNP and genomic datasets yielded different but strongly supported phylogenies. MLST yielded poorly supported phylogenies, especially in our low diversity dataset, i.e., Y. pestis. Trait associations showed that B. pseudomallei and Y. pestis phylogenies are significantly ass...Continue Reading

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Datasets Mentioned

BETA
SRP023117

Methods Mentioned

BETA
chips
genotyping

Software Mentioned

kSNP
RTA
SCS
CutAdapt
CLCBio
TeachingDemos
MLST
TreeAnnotator
ggplot2
MrBayes

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