Whole-genome sequencing reveals clonal expansion of multiresistant Staphylococcus haemolyticus in European hospitals

Abstract

ObjectivesStaphylococcus haemolyticus is an emerging cause of nosocomial infections, primarily affecting immunocompromised patients. A comparative genomic analysis was performed on clinical S. haemolyticus isolates to investigate their genetic relationship and explore the coding sequences with respect to antimicrobial resistance determinants and putative hospital adaptation.MethodsWhole-genome sequencing was performed on 134 isolates of S. haemolyticus from geographically diverse origins (Belgium, 2; Germany, 10; Japan, 13; Norway, 54; Spain, 2; Switzerland, 43; UK, 9; USA, 1). Each genome was individually assembled. Protein coding sequences (CDSs) were predicted and homologous genes were categorized into three types: Type I, core genes, homologues present in all strains; Type II, unique core genes, homologues shared by only a subgroup of strains; and Type III, unique genes, strain-specific CDSs. The phylogenetic relationship between the isolates was built from variable sites in the form of single nucleotide polymorphisms (SNPs) in the core genome and used to construct a maximum likelihood phylogeny.ResultsSNPs in the genome core regions divided the isolates into one major group of 126 isolates and one minor group of isolates with highly diverse genomes. The major group was further subdivided into seven clades (A–G), of which four (A–D) encompassed isolates only from Europe. Antimicrobial multiresistance was observed in 77.7% of the collection. High levels of homologous recombination were detected in genes involved in adherence, staphylococcal host adaptation and bacterial cell communication.ConclusionsThe presence of several successful and highly resistant clones underlines the adaptive potential of this opportunistic pathogen.

Staphylococcus haemolyticus – an emerging threat in the twilight of the antibiotics age

“…S. aureus versus Staphylococcus epidermidis and Staphylococcus haemolyticus shows *75% average nucleotide identity values, which proves their close genetic relatedness (Konstantinidis et al, 2006;Lamers et al, 2012). That fact is also indicated in the topology of a dendrogram based on the 16S rRNA sequence in Bergey's Manual of Systematic Bacteriology (Vos et al, 2009) as well as in whole-genome sequencing projects comparing different staphylococci strains (Takeuchi et al, 2005) and 134 isolates of S. haemolyticus from geographically diverse origins (Cavanagh et al, 2014).…”

“…During the next decades, multiresistance of S. haemolyticus was reported with an increasing frequency. Most of the analysed strains were resistant to the commonly used antiseptic agents and antibiotics, notably more frequently than strains of any other species amongst CNS (Cavanagh et al, 2014;Hope et al, 2008). Many authors reported S. haemolyticus strains as resistant to one or more antibiotics amongst penicillins, cephalosporins, macrolides, tetracyclines, quinolones, aminoglycosides, glycopeptides and fosfomycines (Holden et al, 2013;Lebeaux et al, 2012;Shittu et al, 2004).…”

“…In 2008, strains resistant to the majority of available antimicrobial agents were described for the first time (Campanile et al, 2008). Multiresistant S. haemolyticus strains spread in the hospital environment (Cavanagh et al, 2014;Rodríguez-Aranda et al, 2009). Ternes et al (2013) showed that 55.9% of infants carried multiresistant CNS in their nasal cavity.…”

“…SNP is also suggested to be of significant importance in the process of multiresistant strains selection (Cavanagh et al, 2014 (Cavanagh et al, 2014). The majority of them (77%) were multiresistant, defined as resistant to at least three antibiotics.…”

“…In a recent study, Barros et al (2012) noted that 75% of analysed S. haemolyticus isolates displayed multiresistance. This species also plays an important role in the dissemination of resistance genes, contributing to the emergence of epidemic clones of a more virulent nosocomial pathogen, S. aureus (Cavanagh et al, 2014;Fluit et al, 2013).…”