Genetic and Phenotypic Characteristics of Staphylococcus aureus Isolates from Cystic Fibrosis Patients in Austria

The role of Staphylococcus aureus in cystic fibrosis pathogenesis and clinico-microbiological interactions

Cystic fibrosis (CF) is a progressive and inherited disease that affects approximately 70000 individuals all over the world annually. A mutation in the cystic fibrosis transmembrane conductance regulator (CFTR) gene serves as its defining feature. Bacterial infections have a significant impact on the occurrence and development of CF. In this manuscript, we discuss the role and virulence factors of Staphylococcus aureus as an important human pathogen with the ability to induce respiratory tract infections. Recent studies have reported S. aureus as the first isolated bacteria in CF patients. Methicillin-resistant Staphylococcus aureus (MRSA) pathogens are approximately resistant to all β-lactams. CF patients are colonized by MRSA expressing various virulence factors including toxins, and Staphylococcal Cassette Chromosome mec (SCCmec) types, and have the potential for biofilm formation. Therefore, variations in clinical outcomes will be manifested. SCCmec type II has been reported in CF patients more than in other SCCmec types from different countries. The small-colony variants (SCVs) as specific morphologic subtypes of S. aureus with slow growth and unusual properties can also contribute to persistent and difficult-to-treat infections in CF patients. The pathophysiology of SCVs is complicated and not fully understood. Patients with cystic fibrosis should be aware of the intrinsic risk factors for complex S. aureus infections, including recurring infections, physiological issues, or coinfection with P. aeruginosa.

Limited evidence of patient-to-patient transmission of Staphylococcus aureus strains between children with cystic fibrosis, Queensland, Australia

OBJECTIVES

Here we used whole genome sequencing (WGS) to understand strain diversity and potential for patient-to-patient transmission of Staphylococcus aureus among children with cystic fibrosis (CF) in Queensland, Australia.

METHODS

S. aureus isolates (n = 401) collected between January 2018 and April 2019 from 184 patients with CF (n = 318 isolates) and 76 patients without CF (n = 83 isolates) were subjected to WGS and subsequent multilocus sequence typing (MLST), and a phylogeny was constructed from core genome single nucleotide polymorphism (SNP) analysis. The subsequent data was compared with available patient information.

RESULTS

WGS revealed that patients with CF were essentially colonised by the same genotypes as those seen in patients without CF. Sequence types (ST) for our patients with CF were predominantly ST5 (20.1%), ST30 (7.3%), ST15 (6.3%) and ST8 (5.3%). Two Australian clones, ST93 and ST239, typically seen in skin infections and health-care settings, respectively, were notably absent from our patients with CF. Based on a SNP distance threshold of 14 SNPs, 20 cluster types involving 50/260 patients were evident; of these, 6 clusters contained only patients found to be siblings or otherwise living in the same household. Epidemiological relationships could not be determined for a remaining 14 cluster types involving 38 patients, comprising 2-7 (median 2) patients each. Multiple S. aureus genotypes were observed in 19/73 CF patients who provided more than one sample.

CONCLUSION

These results show that WGS is a useful tool for surveillance of S. aureus strains in children with CF and that the strains in our CF cohort were largely consistent with those circulating in patients without CF. Overall, this confirms previous findings and indicates that S. aureus acquisition in children with CF is similar to that of other patient groups, with limited evidence of potential patient-to-patient transmission within this patient group.

spa Typing and Molecular Characterization of Antimicrobial Resistance in Staphylococcus aureus Strains from Patients with Cystic Fibrosis

We characterized Staphylococcus aureus strains isolated from cystic fibrosis (CF) patients during screening for multidrug-resistant strains to determine mechanisms of antibiotic resistance and conduct spa typing. We investigated 53 S. aureus isolates collected from different CF patients, excluding multiple isolates from the same patient. Genotypic characterization was based on spa type (protein A); staphylococcal cassette chromosome mec (SCCmec) type for S. aureus resistant to methicillin (methicillin-resistant S. aureus [MRSA]); and resistance to the most common macrolides, lincosamides, and streptogramins b and fluoroquinolones. Most strains (78.41%) were resistant to one or more antibiotics; 16.96% were MRSA, whereas 69.81% showed resistance to erythromycin. MRSA strains revealed the acquisition and insertion of SCCmec of class I (n = 1) (hospital-acquired), IV (n = 5), and V (n = 1) (community-acquired), along with two cases that were not typeable. We detected 34 different spa types, with t571 being the most frequent. The spa minimum spanning tree of the tested strains showed evidence of strain relatedness.

Emergence and spread of worldwide Staphylococcus aureus clones among cystic fibrosis patients

Background

The aim of this study was to assess the relatedness of molecular types of Staphylococcus aureus isolates colonizing cystic fibrosis (CF) patients with their antimicrobial resistance and prevalence of toxin genes.

Methods

A total of 215 isolates from the airways of 107 patients with CF were tested for spa and SCCmec type, antimicrobial resistance and carriage of toxin genes.

Results

t015, t084, t091, t700 and t002 were the largest group (approximately 25%) among all 69 identified spa types. Five new spa types, t14286, t14287, t14288, t14289 and t14290, were identified and registered. Isolates from CF patients were clustered into 11 multi-locus sequence typing clonal complexes, with CC30, CC22, CC97, CC45, CC15 and CC5 being the most frequent ones. Twelve (5.6%) methicillin-resistant S. aureus (MRSA) isolates and 102 (47.7%) multidrug-resistant isolates were identified, along with three SCCmec types (I, III and V). All isolates (both MRSA and methicillin-sensitive S. aureus) were Panton–Valentine leucocidin-negative, and 56.7% harbored egc genes. This was the first study documenting the presence of ST398-V-t571 livestock-associated MRSA in a European patient with CF.

Conclusion

These findings imply that individuals with CF can also be colonized with animal-related ST398 MRSA, and justify constant monitoring of staphylococcal colonization and identification of epidemic S. aureus clones in this group.

Omics Approaches for the Study of Adaptive Immunity to Staphylococcus aureus and the Selection of Vaccine Candidates

Staphylococcus aureus is a dangerous pathogen both in hospitals and in the community. Due to the crisis of antibiotic resistance, there is an urgent need for new strategies to combat S. aureus infections, such as vaccination. Increasing our knowledge about the mechanisms of protection will be key for the successful prevention or treatment of S. aureus invasion. Omics technologies generate a comprehensive picture of the physiological and pathophysiological processes within cells, tissues, organs, organisms and even populations. This review provides an overview of the contribution of genomics, transcriptomics, proteomics, metabolomics and immunoproteomics to the current understanding of S. aureus‑host interaction, with a focus on the adaptive immune response to the microorganism. While antibody responses during colonization and infection have been analyzed in detail using immunoproteomics, the full potential of omics technologies has not been tapped yet in terms of T-cells. Omics technologies promise to speed up vaccine development by enabling reverse vaccinology approaches. In consequence, omics technologies are powerful tools for deepening our understanding of the “superbug” S. aureus and for improving its control.

Analysis and Characterization of Staphylococcus aureus Small Colony Variants Isolated From Cystic Fibrosis Patients in Austria

Cystic fibrosis (CF) is the most common hereditary lung disease in the Caucasian population, characterized by viscous bronchial secretion, consecutive defective mucociliary clearance, and unavoidable colonization with microorganisms. Besides Pseudomonas aeruginosa, Staphylococcus aureus is the most common bacterial species colonizing the CF respiratory tract. Under antibiotic pressure S. aureus is able to switch to small colony variants (SCV). These small colony variants can invade epithelial cells, overcome antibiotic therapy inside the cells and can be the starting point for extracellular recolonization. The aim of the present study was the isolation and characterization of S. aureus small colony variants from Austrian cystic fibrosis patients. Samples collected from 147 patients were screened for the presence of S. aureus wild-type and small colony variants. Antibiotic susceptibility testing and determination of the small colony variants causing auxotrophism were performed. Wild-type isolates were assigned to corresponding small colony variants with spa typing. In total, 17 different small colony variant isolates and 12 corresponding wild-type isolates were obtained. 13 isolates were determined thymidine auxotroph, 2 isolates were auxotroph for hemin, and none of the tested isolates was auxotroph for both, respectively. The presence of SCVs is directly related to a poor clinical outcome, therefore a monitoring of SCV prevalence is recommended. This study revealed rather low SCV ratios in CF patients compared to other countries.