Higher genome variability within metabolism genes associates with recurrent Clostridium difficile infection

Maria Kulecka,Łukasz Targoński,Edyta Waker,Jerzy Ostrowski,Filip Ambrozkiewicz,Agnieszka Paziewska,Michał Mikula,Jan Walewski,Patrycja Cybula,Karolina Skubisz

doi:10.1186/s12866-021-02090-9

Abstract

BackgroundClostridium difficile (C. difficile) is a major source of healthcare-associated infection with a high risk of recurrence, attributable to many factors such as usage of antibiotics, older age and immunocompromised status of the patients. C. difficile has also a highly diverse genome, which may contribute to its high virulence. Herein we examined whether the genome conservation, measured as non-synonymous to synonymous mutations ratio (dN/dS) in core genes, presence of single genes, plasmids and prophages increased the risk of reinfection in a subset of 134 C. difficile isolates from our previous study in a singly hemato-oncology ward.MethodsC. difficile isolates were subjected to whole-genome sequencing (WGS) on Ion Torrent PGM sequencer. Genomes were assembled with MIRA5 and annotated with prokka and VRprofile. Logistic regression was used to asses the relationship between single gene presence and the odds of infection recurrence. DN/dS ratios were computed with codeml. Functional annotation was conducted with eggNOG-Mapper.ResultsWe have found that the presence of certain genes, associated with carbon metabolism and oxidative phosphorylation, increased the odds of infection recurrence. More core genes were under positive selective pressure in recurrent disease isolates – they were mostly associated with the metabolism of aminoacids. Finally, prophage elements were more prevalent in single infection isolates and plasmids did not influence the odds of recurrence.ConclusionsOur findings suggest higher genetic plasticity in isolates causing recurrent infection, associated mainly with metabolism. On the other hand, the presence of prophages seems to reduce the isolates’ virulence.

Highlights

Clostridium difficile (C. difficile) is a major source of healthcare-associated infection with a high risk of recurrence, attributable to many factors such as usage of antibiotics, older age and immunocompromised status of the patients
Clostridium difficile core genome There were 965 core genes discovered shared between isolates from ST1 and ST42
Specific gene presence as a predictor of recurrence In the logistic regression model, there were 5264 genes tested; while 192 reached statistical significance at a nominal p-value of 0.05, none of them were significant after correction for multiple hypothesis testing with the FDR method (Supplementary Table 3). 7 pathways are enriched in gene set which gives higher odds of infection recurrence, in only one of them the enrichment score reaches the highest value at rank smaller than 192: Oxidative phosphorylation (Table 1, Supplementary Table 4)

Summary

Introduction

Clostridium difficile (C. difficile) is a major source of healthcare-associated infection with a high risk of recurrence, attributable to many factors such as usage of antibiotics, older age and immunocompromised status of the patients. In large European hospital surveys from 10% [7] to 16% [6] Clostridium difficile infection (CDI) cases are associated with major complications, requiring admission to the intensive care unit and resulting in the death rate of 7 and 4% respectively. Another major concern when dealing with CDI is its tendency of recurrence which, according to the European Society of Clinical Microbiology and Infectious Diseases, is defined as a relapse of CDI clinical symptoms within 2–8 weeks of successful treatment of the initial episode. Immunocompromised patients typically present a higher risk of infection recurrence [19, 20]

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