Metatranscriptomic Analysis Reveals Active Bacterial Communities in Diabetic Foot Infections.

Honghua Hu,Matthew Malone,Martha Zakrzewski,Fatemah Sadeghpour Heravi,Karen Vickery

doi:10.3389/fmicb.2020.01688

Abstract

Despite the extended view of the composition of diabetic foot infections (DFIs), little is known about which transcriptionally active bacterial communities are pertinent to infection, and if any differences are associated with increased infection severity. We applied a RNA sequencing approach to analyze the composition, function, and pathogenicity of the active bacterial communities in DFIs. Taxonomic profiling of bacterial transcripts revealed the presence of 14 bacterial phyla in DFIs. The abundance of the Spiroplasma, Vibrio, and Mycoplasma were significantly different in different infection severities (P < 0.05). Mild and severe stages of infections were dominated by Staphylococcus aureus and Porphyromonas asaccharolytica, respectively. A total of 132 metabolic pathways were identified of which ribosome and thiamin being among the most highly transcribed pathways. Moreover, a total of 131 antibiotic resistance genes, primarily involved in the multidrug efflux pumps/exporters, were identified. Furthermore, iron acquisition systems (synthesize and regulation of siderophores) and pathways involved in the synthesis and regulation of cell-surface components associated with adhesion, colonization, and movement of bacterial cells were the most common virulence factors. These virulence factors may help bacteria compete for scares resources and survive the host wound proteases. Characterization of transcriptionally active bacterial communities can help to provide an understanding of the role of key pathogens in the development of DFIs. Such information can be clinically useful allowing replacement of DFIs empirical therapy with targeted treatment.

Highlights

Diabetic foot infections (DFIs) are a frequent cause of hospitalization and typically precede events such as lower extremity amputation (Lavery et al, 2003)
Traditional approaches to identify pathogens colonized in DFIs have relied on culture-based methods that are limited to detect bacterial species grown under standard laboratory conditions (Heravi et al, 2020)
Infection severity was determined using the International Working Group of the Diabetic Foot (IWGDF), Perfusion, Extent, Depth, Infection and Sensation (PEDIS) classification system, and patients were assigned (PEDIS 2 refers to mild infection, PEDIS 3 refers to moderate infection, PEDIS 4 refers to severe infection) (Lipsky et al, 2016)

Summary

Introduction

Diabetic foot infections (DFIs) are a frequent cause of hospitalization and typically precede events such as lower extremity amputation (Lavery et al, 2003). Traditional approaches to identify pathogens colonized in DFIs have relied on culture-based methods that are limited to detect bacterial species grown under standard laboratory conditions (Heravi et al, 2020). Several studies have identified that diabetic foot ulcers were composed of a complex bacterial community consisting of aerobes, anaerobes, fastidious, and unculturable microorganisms using 16S rRNA sequencing (Smith et al, 2016; Gardiner et al, 2017). The 16S rRNA approach is limited to genomically present but transcriptionally inactive bacterial communities. It does not provide insight into the potential or actual function of the bacterial community in DFIs. High-throughput RNA sequencing or metatranscriptomic analysis is a promising tool to obtain insights into the functionality of active bacterial communities. Metatranscriptomics has addressed the limitation of microarray assays such as unspecific hybridization signals (Zhao et al, 2016)

Methods

Results

Conclusion