Predicting Vibrio cholerae infection and disease severity using metagenomics in a prospective cohort study

Abstract

23 2 CORRESPONDING AUTHOR : jesse.shapiro@umontreal.ca 24 25 RUNNING TITLE: Stool metagenomics predicts cholera 26 ABSTRACT (word count: 196) 27 28Background: Susceptibility to Vibrio cholerae infection is impacted by blood group, age, and 29 pre-existing immunity, but these factors only partially explain who becomes infected. A recent 30 study used 16S rRNA amplicon sequencing to quantify the composition of the gut microbiome 31 and identify predictive biomarkers of infection with limited taxonomic resolution. 32 Methods:To achieve increased resolution of gut microbial factors associated with V. cholerae 33 susceptibility and identify predictors of symptomatic disease, we applied deep shotgun 34 metagenomic sequencing to a cohort of household contacts of patients with cholera. 35Results: Using machine learning, we resolved species, strains, gene families, and cellular 36 pathways in the microbiome at the time of exposure to V. cholerae to identify markers that 37 predict infection and symptoms. Use of metagenomic features improved the precision and 38 accuracy of prediction relative to 16S sequencing. We also predicted disease severity, although 39 with greater uncertainty than our infection prediction. Species within the genera Prevotella and 40Bifidobacterium predicted protection from infection, and genes involved in iron metabolism also 41 correlated with protection. 42 Conclusion:Our results highlight the power of metagenomics to predict disease outcomes and 43 suggest specific species and genes for experimental testing to investigate mechanisms of 44 microbiome-related protection from cholera. 45 46

Environmental parameters associated with incidence and transmission of pathogenic Vibrio spp.

“…The shortcoming of DNA metagenomics is that viability or infectious potential of the microorganisms comprising the community cannot be determined without additional analyses to determine gene function and activity. Nevertheless, profile composition of all microorganisms present in a sample, e.g., bacteria, archaea, fungi, viruses, and protozoa, is highly informative (Brumfield et al, 2020), and metagenomics can provided useful insight to disease outcome, as has been shown for the gut microbiome during V. cholerae infection (Levade et al, 2021) and for patients with skin and soft tissue infections caused by rare pathogens such as V. vulnificus (Wang et al, 2020). Most valuable is the ability of HTS to identify multiple pathogens comprising a poly-microbial infection (De et al, 2020), to estimate antimicrobial resistance (Zhelyazkova et al, 2021), and to establish the quantitative microbial risk of Vibrio spp.…”

The Interface of Vibrio cholerae and the Gut Microbiome

“…Another set of studies examined the gut microbiomes of household contacts of Bangladeshi cholera patients who subsequently did or did not develop symptomatic disease. 51,52 Using metagenomic and machine learning approaches, Blautia, Ruminococcus, Bifidobacterium, and Prevotella species were associated with household contacts that remained uninfected, while Streptococcus, Prevotella, and other Blautia species were higher in individuals that were subsequently infected. The presence of multiple species within the same genus in both outcome groups, and findings that modulation of V. cholerae susceptibility can be driven by specific enzymatic functions (see below) suggest the specificity of microbial species as major drivers of V. cholerae pathogenesis in human populations.…”

A combination of metagenomic and cultivation approaches reveals hypermutator phenotypes within Vibrio cholerae infected patients

“…Household contact infections are known to exhibit a range of clinical outcomes from asymptomatic to severe symptomatic disease. We enrolled patients from February 2013 to May 2014, and collected demographic information, obtained rectal swabs, immunologic measures, and symptom histories during 30 days of prospective follow-up, as previously described (11)(12)(13). We excluded household contacts who reported antibiotic use during the week prior to enrollment.…”

“…Yet, many questions remain regarding asymptomatic carriers of V. cholerae, including their role and importance in the transmission chain during an epidemic (King et al 2008;Phelps, Simonsen, et Jensen 2019). Numerous observational studies have identified host factors that could impact the severity of symptoms, including lack of pre-existing immunity, blood group O status, age, polymorphisms in genes of the innate immune system, or variation in the gut microbiome (Harris et al 2005;2008;Weil, Khan, et al 2009;Midani et al 2018;Levade et al 2020).…”