Using genetic data to identify transmission risk factors: statistical assessment and application to tuberculosis transmission
Authors: Goldstein Isaac H. , Bayer Damon , Barilar Ivan , Kizito Balladiah , Matsiri Ogopotse , Modongo Chawangwa , Zetola Nicola M. , Niemann Stefan , Minin Volodymyr M. , Shin Sanghyuk S. 
Published: December 2021

Identifying host factors that influence infectious disease transmission is an important step toward developing interventions to reduce disease incidence. Recent advances in methods for reconstructing infectious disease transmission events using pathogen genomic and epidemiological data open the door for investigation of host factors that affect onward transmission. While most transmission reconstruction methods are designed to work with densely sampled outbreaks, these methods are making their way into surveillance studies, where the fraction of sampled cases with sequenced pathogens could be relatively low. Surveillance studies that use transmission event reconstruction then use the reconstructed events as response variables (i.e., infection source status of each sampled case) and use host characteristics as predictors (e.g., presence of HIV infection) in regression models. We use simulations to study estimation of the effect of a host factor on probability of being an infection source via this multi-step inferential procedure. UsingTransPhylo— a widely-used method for Bayesian estimation of infectious disease transmission events — and logistic regression, we find that low sensitivity of identifying infection sources leads to dilution of the signal, biasing logistic regression coefficients toward zero. We show that increasing the proportion of sampled cases improves sensitivity and some, but not all properties of the logistic regression inference. Application of these approaches to real world data from a population-based TB study in Botswana fails to detect an association between HIV infection and probability of being a TB infection source. We conclude that application of a pipeline, where one first usesTransPhyloand sparsely sampled surveillance data to infer transmission events and then estimates effects of host characteristics on probabilities of these events, should be accompanied by a realistic simulation study to better understand biases stemming from imprecise transmission event inference.

Author summary

Factors that affect infectious disease transmission are poorly understood, which impede efforts to prevent the spread of infectious diseases. Recently, software packages have been developed to infer transmission histories of infectious disease outbreaks using data from infectious disease genetics and epidemiology. These software packages have been used as part of methods to identify individual characteristics that affect infectious disease transmission. We used computer simulation to explore whether a statistical pipeline using the software packageTransPhylocan successfully identify individual risk factors for being an infection source in a realistic public health setting where only a small proportion of pathogens are sequenced. We simulated tuberculosis (TB) outbreaks with different odds of being an infection source for TB transmission between people living with and without HIV. We found that theTransPhylo-based pipeline consistently underestimated the odds ratio for the association between HIV and being an infection source for TB transmission. We then applied this method to data from a TB study from Botswana and found no evidence of an association between HIV and being an infection source for TB transmission. Identification of transmission risk factors may be difficult in settings with low sampling proportion for genetic data.