Comparative Genomic and Pan-Genomic Characterization of Staphylococcus epidermidis From Different Sources Unveils the Molecular Basis and Potential Biomarkers of Pathogenic Strains

The impact of oxygen content on Staphylococcus epidermidis pathogenesis in ocular infection based on clinical characteristics, transcriptome and metabolome analysis

Introduction

This study aims to delineate the etiology and prevalence of isolated pathogens, along with the clinical characteristics of endophthalmitis patients over a 9-year period at hospital in Southwest of China. Additionally, we investigating the metabolic and cellular processes related to environmental factors may offer novel insights into endophthalmitis.

Methods

We analyzed data pertaining to endophthalmitis patients treated at the Affiliated Hospital of Yunnan University from 2015 to 2023. According to our clinical data, we conducted an experiment based on transcriptomics and metabolomics analysis to verify whether environmental factors affect behavior of S. epidermidis by culturating S. epidermidis under oxic and microoxic condition.

Results

In this study, 2,712 fungi or bacteria strains have been analyzed, gram-positive bacteria constituted 65.08%, with S. epidermidis being the most predominant species (25.55%). Ophthalmic trauma was the primary pathogenic factor for S. epidermidis ocular infections. Regarding fluoroquinolones, S. epidermidis exhibited the higher resistance rate to levofloxacin than moxifloxacin. Moreover, our investigation revealed that S. epidermidis in microoxic environment increase in energy metabolism, amino acid metabolism, and membrane transport.

Conclusion

Our findings underscore the significance of S. epidermidis as a crucial pathogen responsible for infectious endophthalmitis. It is crucial to exercise vigilance when considering Levofloxacin as the first-line drug for empiric endophthalmitis treatment. The metabolites alteration observed during the commensal-to-pathogen conversion under microoxic condition serve as a pivotal environmental signal contributing to S. epidermidis metabolism remodeling, toward more pathogenic state.

[Distribution and Antibiotic Resistance Analysis of Ocular Bacterial Pathogens at a Tertiary Hospital From 2012 to 2021]

Objective

To analyze the distribution of ocular bacterial pathogens and their antibiotic resistance status at a tertiary-care hospital and to provide a reference for the appropriate use of antibiotics.

Methods

Retrospective analysis was conducted with bacteria isolated from the ophthalmic samples sent for lab analysis at a tertiary-care hospital from 2012 to 2021. The suspected bacterial strains were identified with automated systems for microbial identification and susceptibility analysis and matrix-assisted laser desorption/ionization time-of-flight mass spectrometer. VITEK 2 Compact, an automated microbial identification and antibiotic susceptibility analysis system, was used for antimicrobial susceptibility testing.

Results

A total of 1556 ophthalmology bacteria culture samples were collected, 574 of which showed bacterial growth, presenting an overall positive rate of 36.89%. Of the isolated bacteria, Gram-positive cocci, Gram-positive bacilli, Gram-negative bacilli, and Gram-negative cocci accounted for 63.15% (377/597), 18.76% (112/597), 17.09% (102/597), and 1.00% (6/597), respectively. Among the bacteria isolated in different years over the course of a decade, Gram-positive cocci always turned out to be the main cause of eye infections. Of the Gram-positive cocci, 73.47% (277/377) were isolated from patients with endophthalmitis, with the most important species being Staphylococcus epidermidis, which was followed by Streptococcus viridans. The rest, or 26.53% (100/377), of the Gram-positive cocci were isolated from patients with external eye infections, with the main isolated strains being Staphylococcus epidermidis, Streptococcus viridans, and Staphylococcus aureus. More than 70% of Staphylococcus epidermidis isolated from both endophthalmitis and external eye infections were resistant to methicillin. No strains resistant to vancomycin, linezolid, or tigecycline were detected. Staphylococcus epidermidis isolated from patients with external eye infections had a low rate of resistance to levofloxacin (2/27 or 7.41%), whereas those isolated from patients with endophthalmitis had a higher resistance rate (43/127 or 33.86%). The difference in drug resistance rate between the two groups was statistically significant (P<0.05).

Conclusion

The chief ocular bacterial pathogens identified in a tertiary-care hospital were Gram-positive cocci, among which, Staphylococcus epidermidis was the most common species. The Staphylococcus epidermidis identified in the hospital had a high rate of resistance to oxacillin, but remained highly sensitive to vancomycin, linezolid, and tigecycline. The endophthalmitis caused by Staphylococcus epidermidis in the hospital can be treated empirically with vancomycin and then the treatment plan can be further adjusted according to the results of the drug susceptibility test. However, the establishment of the breakpoint of drug susceptibility test is mainly based on the model of bloodstream infection and has limited reference value for the treatment of eye infection. The required drug distribution concentration at the infection site can be achieved by dose increase or local administration.

Beyond the Wild MRSA: Genetic Features and Phylogenomic Review of mecC-Mediated Methicillin Resistance in Non-aureus Staphylococci and Mammaliicocci

Methicillin resistance, mediated by the mecA gene in staphylococci and mammaliicocci, has caused tremendous setbacks in the use of antibiotics in human and veterinary medicine due to its high potential of presenting the multidrug resistance (MDR) phenotype. Three other mec analogs exist, of which the mecC has evolutionary been associated with methicillin-resistant Staphylococcus aureus (MRSA) in wild animals, thus loosely referred to as the wild MRSA. In this study, we present an epidemiological review and genomic analysis of non-aureus staphylococci and mammaliicocci that carry the mecC-mediated methicillin resistance trait and determine whether this trait has any relevant link with the One Health niches. All previous studies (2007 till 2023) that described the mecC gene in non-aureus staphylococci and mammaliicocci were obtained from bibliometric databases, reviewed, and systematically analyzed to obtain the antimicrobial resistance (AMR) and virulence determinants, mobilome, and other genetic contents. Moreover, core genome single-nucleotide polymorphism analysis was used to assess the relatedness of these strains. Of the 533 articles analyzed, only 16 studies (on livestock, environmental samples, milk bulk tanks, and wild animals) were eligible for inclusion, of which 17 genomes from 6 studies were used for various in silico genetic analyses. Findings from this systematic review show that all mecC-carrying non-aureus staphylococci were resistant to only beta-lactam antibiotics and associated with the classical SCCmec XI of S. aureusLGA251. Similarly, two studies on wild animals reported mecC-carrying Mammaliicoccus stepanovicii associated with SCCmec XI. Nevertheless, most of the mecC-carrying Mammaliicoccus species presented an MDR phenotype (including linezolid) and carried the SCCmec-mecC hybrid associated with mecA. The phylogenetic analysis of the 17 genomes revealed close relatedness (<20 SNPs) and potential transmission of M. sciuri and M. lentus strains in livestock farms in Algeria, Tunisia, and Brazil. Furthermore, closely related M. sciuri strains from Austria, Brazil, and Tunisia (<40 SNPs) were identified. This systematic review enhances our comprehension of the epidemiology and genetic organization of mecC within the non-aureus staphylococci and mammaliicocci. It could be hypothesized that the mecC-carrying non-aureus staphylococci are evolutionarily related to the wild MRSA-mecC. The potential implications of clonal development of a lineage of mecA/mecC carrying strains across multiple dairy farms in a vast geographical region with the dissemination of MDR phenotype is envisaged. It was observed that most mecC-carrying non-aureus staphylococci and mammaliicocci were reported in mastitis cases. Therefore, veterinarians and veterinary microbiology laboratories must remain vigilant regarding the potential existence of mecA/mecC strains originating from mastitis as a potential niche for this resistance trait.

Difficult-to-Treat Pathogens: A Review on the Management of Multidrug-Resistant Staphylococcus epidermidis

Multidrug-resistant Staphylococcus epidermidis (MDRSE) is responsible for difficult-to-treat infections in humans and hospital-acquired-infections. This review discusses the epidemiology, microbiology, diagnosis, and treatment of MDRSE infection and identifies knowledge gaps. By using the search term "pan resistant Staphylococcus epidermidis" OR "multi-drug resistant Staphylococcus epidermidis" OR "multidrug-resistant lineages of Staphylococcus epidermidis", a total of 64 records have been identified from various previously published studies. The proportion of methicillin resistance in S. epidermidis has been reported to be as high as 92%. Several studies across the world have aimed to detect the main phylogenetic lineages and antibiotically resistant genes through culture, mass spectrometry, and genomic analysis. Molecular biology tools are now available for the identification of S. epidermidis and its drug resistance mechanisms, especially in blood cultures. However, understanding the distinction between a simple colonization and a bloodstream infection (BSI) caused by S. epidermidis is still a challenge for clinicians. Some important parameters to keep in mind are the number of positive samples, the symptoms and signs of the patient, the comorbidities of the patient, the presence of central venous catheter (CVC) or other medical device, and the resistance phenotype of the organism. The agent of choice for empiric parenteral therapy is vancomycin. Other treatment options, depending on different clinical settings, may include teicoplanin, daptomycin, oxazolidinones, long-acting lipoglycopeptides, and ceftaroline. For patients with S. epidermidis infections associated with the presence of an indwelling device, assessment regarding whether the device warrants removal is an important component of management. This study provides an overview of the MDRSE infection. Further studies are needed to explore and establish the most correct form of management of this infection.

JMM Profile: Staphylococcus epidermidis

Staphylococcus epidermidis is the most abundant commensal bacterium of human skin. Despite protecting us from foreign invaders, S. epidermidis itself exploits human vulnerability when given the opportunity. Such opportunities arise when patients are immunocompromised or when biomedical implants present an opportunity to colonize the surface and form biofilms. S. epidermidis is one of the most frequently isolated organisms from implanted devices and from bloodstream infections. However, S. epidermidis infections are often recalcitrant to antibiotics because of biofilm-associated antibiotic tolerance. Furthermore, the emergence and spread of nearly pan-resistant strains is a considerable health concern. Symptoms can be subclinical, making diagnosis challenging, and treatment with antibiotics is inefficient. For now, infection prevention remains the best strategy available.