Comparative genomics analysis of two Helcococcus kunzii strains co-isolated with Staphylococcus aureus from diabetic foot ulcers

Benjamin A R N Durand; Alex Yahiaoui Martinez; Damien Baud; Patrice François; Jean-Philippe Lavigne; Catherine Dunyach-Remy

doi:10.1016/j.ygeno.2022.110365

Comparative genomics analysis of two Helcococcus kunzii strains co-isolated with Staphylococcus aureus from diabetic foot ulcers

Genomics. 2022 May;114(3):110365. doi: 10.1016/j.ygeno.2022.110365. Epub 2022 Apr 9.

Authors

Benjamin A R N Durand¹, Alex Yahiaoui Martinez², Damien Baud³, Patrice François³, Jean-Philippe Lavigne⁴, Catherine Dunyach-Remy¹

Affiliations

¹ Bacterial Virulence and Chronic Infections, INSERM U1047, University of Montpellier, Department of Microbiology and Hospital Hygiene, University Hospital Nîmes, 30908 Nîmes, France.
² Department of Microbiology and Hospital Hygiene, University Hospital Nîmes, University of Montpellier, 30029 Nîmes, France.
³ Department of Infectious Diseases, Genomic Research Laboratory, Geneva University Hospitals, 1205 Geneva, Switzerland.
⁴ Bacterial Virulence and Chronic Infections, INSERM U1047, University of Montpellier, Department of Microbiology and Hospital Hygiene, University Hospital Nîmes, 30908 Nîmes, France. Electronic address: jean.philippe.lavigne@chu-nimes.fr.

PMID: 35413435
DOI: 10.1016/j.ygeno.2022.110365

Abstract

Helcococcus kunzii is a commensal Gram-positive bacterial species recovered from the human skin microbiota and considered as an opportunistic pathogen. Although little is known about its clinical significance, its increased abundance has been reported in infected wounds, particularly in foot ulcers in persons with diabetes. This species is usually detected in mixed cultures from human specimens and frequently isolated with Staphylococcus aureus. Modulation of staphylococci virulence by H. kunzii has been shown in an infection model of Caenorhabditis elegans. The aim of this study was to compare the genomes of two H. kunzii strains isolated from foot ulcers -isolate H13 and H10 showing high or low impact on S. aureus virulence, respectively- and the H. kunzii ATCC51366 strain. Whole genome analyses revealed some differences between the two strains: length (2.06 Mb (H13) and 2.05 Mb (H10) bp), GC content (29.3% (H13) and 29.5% (H10)) and gene content (1,884 (H13) and 1,786 (H10) predicted genes). The core-proteome phylogenies within the genus characterised H. kunzii H13 and H10 as genetically similar to their ancestor. The main differences between the strains were mainly in sugar-associated transporters and various hypothetical proteins. Five targets were identified as potentially involved in S. aureus virulence modulation in both genomes: the two-component iron export system and three autoinducer-like proteins. Moreover, H13 strain harbours a prophage inserted in 1,261,110-1,295,549 (attL-attR), which is absent in H10 strain. The prophage PhiCD38_2 was previously reported for its ability to modulate secretion profile, reinforcing the autoinducer-like hypothesis. In the future, transcriptomics or metaproteomics approaches could be performed to better characterize the H13 strain and possibly identify the underlying mechanism for S. aureus virulence modulation.

Keywords: Autoinducer-like protein; Diabetic foot ulcer; Genomic characterization; Helcococcus kunzii; Iron export; Phage.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Diabetes Mellitus*
Diabetic Foot* / microbiology
Genomics
Humans
Staphylococcal Infections* / microbiology
Staphylococcus aureus / genetics

Supplementary concepts

Helcococcus kunzii