title: Inferring social network structure from bacterial sequence data.
abstract: Using DNA sequence data from pathogens to infer transmission networks has traditionally been done in the context of epidemics and outbreaks. Sequence data could analogously be applied to cases of ubiquitous commensal bacteria; however, instead of inferring chains of transmission to track the spread of a pathogen, sequence data for bacteria circulating in an endemic equilibrium could be used to infer information about host contact networks. Here, we show--using simulated data--that multilocus DNA sequence data, based on multilocus sequence typing schemes (MLST), from isolates of commensal bacteria can be used to infer both local and global properties of the contact networks of the populations being sampled. Specifically, for MLST data simulated from small-world networks, the small world parameter controlling the degree of structure in the contact network can robustly be estimated. Moreover, we show that pairwise distances in the network--degrees of separation--correlate with genetic distances between isolates, so that how far apart two individuals in the network are can be inferred from MLST analysis of their commensal bacteria. This result has important consequences, and we show an example from epidemiology: how this result could be used to test for infectious origins of diseases of unknown etiology.
authors.affiliation: Department of Environmental Science, Policy and Management, University of California, Berkeley, California, United States of America. mateusz@berkeley.edu
authors.forename: Mateusz M
authors.initials: MM
authors.lastname: Pluciński
authors.forename: Richard
authors.initials: R
authors.lastname: Starfield
authors.forename: Rodrigo P P
authors.initials: RP
authors.lastname: Almeida
mesh_terms: D001419:Bacteria / Q000235:genetics*; D004269:DNA, Bacterial / Q000235:genetics*; D016013:Likelihood Functions; D012944:Social Support
chemical_list: D004269:DNA, Bacterial