Determination of an Interaction Network between an Extracellular Bacterial Pathogen and the Human Host

Abstract

A major gap in understanding infectious diseases is the lack of information about molecular interaction networks between pathogens and the human host. Haemophilus ducreyi causes the genital ulcer disease chancroid in adults and is a leading cause of cutaneous ulcers in children in the tropics. We developed a model in which human volunteers are infected on the upper arm with H. ducreyi until they develop pustules. To define the H. ducreyi and human interactome, we determined bacterial and host transcriptomic and host metabolomic changes in pustules. We found that in vivo H. ducreyi transcripts were distinct from those in the inocula, as were host transcripts in pustule and wounded control sites. Many of the upregulated H. ducreyi genes were found to be involved in ascorbic acid and anaerobic metabolism and inorganic ion/nutrient transport. The top 20 significantly expressed human pathways showed that all were involved in immune responses. We generated a bipartite network for interactions between host and bacterial gene transcription; multiple positively correlated networks contained H. ducreyi genes involved in anaerobic metabolism and host genes involved with the immune response. Metabolomic studies showed that pustule and wounded samples had different metabolite compositions; the top ion pathway involved ascorbate and aldarate metabolism, which correlated with the H. ducreyi transcriptional response and upregulation of host genes involved in ascorbic acid recycling. These data show that an interactome exists between H. ducreyi and the human host and suggest that H. ducreyi exploits the metabolic niche created by the host immune response. IMPORTANCE Dual RNA sequencing (RNA-seq) offers the promise of determining an interactome at a transcriptional level between a bacterium and the host but has yet to be done on any bacterial infection in human tissue. We performed dual RNA-seq and metabolomics analyses on wounded and infected sites following experimental infection of the arm with H. ducreyi. Our results suggest that H. ducreyi survives in an abscess by utilizing l-ascorbate as an alternative carbon source, possibly taking advantage of host ascorbic acid recycling, and that H. ducreyi also adapts by upregulating genes involved in anaerobic metabolism and inorganic ion and nutrient transport. To our knowledge, this is the first description of an interaction network between a bacterium and the human host at a site of infection.

In vivo transcriptome analysis provides insights into host-dependent expression of virulence factors by Yersinia entomophaga MH96, during infection of Galleria mellonella

“…Knowledge of those genes activated specifically within host tissues allows insight into the genetic determinants of in vivo colonization and pathogenicity. An often used strategy involves transcriptional analysis of pathogen gene expression (transcriptomics) based on patterns of mRNA transcript abundance during infection ( Deng et al 2018 ; Valenzuela-Miranda and Gallardo-Escárate 2018 ; Nobori et al 2018 ; Arenas et al 2019 ; Griesenauer et al 2019 ; Haueisen et al 2019 ; Ibberson and Whiteley 2019 ; Sun et al 2019 ; Tang et al 2019 ; Fan et al 2020 ; Luo et al 2020 ).…”

Comprehensive host-pathogen protein-protein interaction network analysis

“…There are many real bipartite networks such as actor-movie network [35] which illustrates the movies and the actors playing in them, author-article network [36] which shows the articles and theirs authors, gene-disease network [37][38][39][40][41][42][43] which reveals diseases and their targeted genes, metabolite-enzyme network [44][45][46] which shows metabolites and their corresponding enzymes, and host-pathogen PPI network such as fungal pathogen scedosporium aurantiacum with human long epithelial cells [47], Leptospira interrogans and Homo sapiens [48], extracellular bacterial pathogen and human host [49], zika virus non-structural proteins and human host proteins [50], bacterial and fungal pathogens and maize stalks host [51].…”

Novel Approaches for Systems Biology of Metabolism-Oriented Pathogen-Human Interactions: A Mini-Review

“…The results provided evidence for a key role of host glucose homeostasis in vivo during animal infection, and it was proposed that a glucoserich diet improved host outcomes in Candida infection. In a recent study, ulcer-associated pathogen Haemophilus ducreyi was investigated in detail by collecting dual transcriptomic and host metabolomic data from infected human tissue (Griesenauer et al, 2019). The results suggest the consumption of ascorbic acid and adaptation of anaerobic metabolism as survival mechanisms by the pathogen in glucose-poor abscess environment.…”