Staphylococcus epidermidis clones express Staphylococcus aureus-type wall teichoic acid to shift from a commensal to pathogen lifestyle

Staphylococcus capitis: insights into epidemiology, virulence, and antimicrobial resistance of a clinically relevant bacterial species

SUMMARYStaphylococcus capitis is divided into two subspecies, S. capitis subsp. ureolyticus (renamed urealyticus in 1992; ATCC 49326) and S. capitis subsp. capitis (ATCC 27840), and fits with the archetype of clinically relevant coagulase-negative staphylococci (CoNS). S. capitis is a commensal bacterium of the skin in humans, which must be considered an opportunistic pathogen of interest particularly as soon as it is identified in a clinically relevant specimen from an immunocompromised patient. Several studies have highlighted the potential determinants underlying S. capitis pathogenicity, resistance profiles, and virulence factors. In addition, mobile genetic element acquisitions and mutations contribute to S. capitis genome adaptation to its environment. Over the past decades, antibiotic resistance has been identified for S. capitis in almost all the families of the currently available antibiotics and is related to the emergence of multidrug-resistant clones of high clinical significance. The present review summarizes the current knowledge concerning the taxonomic position of S. capitis among staphylococci, the involvement of this species in human colonization and diseases, the virulence factors supporting its pathogenicity, and the phenotypic and genomic antimicrobial resistance profiles of this species.

Wall teichoic acid substitution with glucose governs phage susceptibility of Staphylococcus epidermidis

The species- and clone-specific susceptibility of Staphylococcus cells for bacteriophages is governed by the structures and glycosylation patterns of wall teichoic acid (WTA) glycopolymers. The glycosylation-dependent phage-WTA interactions in the opportunistic pathogen Staphylococcus epidermidis and in other coagulase-negative staphylococci (CoNS) have remained unknown. We report a new S. epidermidis WTA glycosyltransferase TagE whose deletion confers resistance to siphoviruses such as ΦE72 but enables binding of otherwise unbound podoviruses. S. epidermidis glycerolphosphate WTA was found to be modified with glucose in a tagE-dependent manner. TagE is encoded together with the enzymes PgcA and GtaB providing uridine diphosphate-activated glucose. ΦE72 transduced several other CoNS species encoding TagE homologs, suggesting that WTA glycosylation via TagE is a frequent trait among CoNS that permits interspecies horizontal gene transfer. Our study unravels a crucial mechanism of phage-Staphylococcus interaction and horizontal gene transfer, and it will help in the design of anti-staphylococcal phage therapies.IMPORTANCEPhages are highly specific for certain bacterial hosts, and some can transduce DNA even across species boundaries. How phages recognize cognate host cells remains incompletely understood. Phages infecting members of the genus Staphylococcus bind to wall teichoic acid (WTA) glycopolymers with highly variable structures and glycosylation patterns. How WTA is glycosylated in the opportunistic pathogen Staphylococcus epidermidis and in other coagulase-negative staphylococci (CoNS) species has remained unknown. We describe that S. epidermidis glycosylates its WTA backbone with glucose, and we identify a cluster of three genes responsible for glucose activation and transfer to WTA. Their inactivation strongly alters phage susceptibility patterns, yielding resistance to siphoviruses but susceptibility to podoviruses. Many different CoNS species with related glycosylation genes can exchange DNA via siphovirus ΦE72, suggesting that glucose-modified WTA is crucial for interspecies horizontal gene transfer. Our finding will help to develop antibacterial phage therapies and unravel routes of genetic exchange.

Phage susceptibility determinants of the opportunistic pathogen Staphylococcus epidermidis

Staphylococcus epidermidis is a common member of the human skin and nose microbiomes and a frequent cause of invasive infections. Transducing phages accomplish the horizontal transfer of resistance and virulence genes by mispackaging of mobile-genetic elements, contributing to severe, therapy-refractory S. epidermidis infections. Lytic phages on the other hand can be interesting candidates for new anti-S. epidermidis phage therapies. Despite the importance of phages, we are only beginning to unravel S. epidermidis phage interactions. Recent studies shed new light on S. epidermidis phage diversity, host range, and receptor specificities. Modulation of cell wall teichoic acids, the major phage receptor structures, along with other phage defense mechanisms, are crucial determinants for S. epidermidis susceptibility to different phage groups.

Cryo-EM analysis of S. aureus TarL, a polymerase in wall teichoic acid biogenesis central to virulence and antibiotic resistance

Wall teichoic acid (WTA), a covalent adduct of Gram-positive bacterial cell wall peptidoglycan, contributes directly to virulence and antibiotic resistance in pathogenic species. Polymerization of the Staphylococcus aureus WTA ribitol-phosphate chain is catalyzed by TarL, a member of the largely uncharacterized TagF-like family of membrane-associated enzymes. We report the cryo-electron microscopy structure of TarL, showing a tetramer that forms an extensive membrane-binding platform of monotopic helices. TarL is composed of an amino-terminal immunoglobulin-like domain and a carboxyl-terminal glycosyltransferase-B domain for ribitol-phosphate polymerization. The active site of the latter is complexed to donor substrate cytidine diphosphate-ribitol, providing mechanistic insights into the catalyzed phosphotransfer reaction. Furthermore, the active site is surrounded by electropositive residues that serve to retain the lipid-linked acceptor for polymerization. Our data advance general insight into the architecture and membrane association of the still poorly characterized monotopic membrane protein class and present molecular details of ribitol-phosphate polymerization that may aid in the design of new antimicrobials.

Insights into the role of the respiratory tract microbiome in defense against bacterial pneumonia

The respiratory tract microbiome (RTM) is a microbial ecosystem inhabiting different niches throughout the airway. A critical role for the RTM in dictating lung infection outcomes is underlined by recent efforts to identify community members benefiting respiratory tract health. Obligate anaerobes common in the oropharynx and lung such as Prevotella and Veillonella are associated with improved pneumonia outcomes and activate several immune defense pathways in the lower airway. Colonizers of the nasal cavity, including Corynebacterium and Dolosigranulum, directly impact the growth and virulence of lung pathogens, aligning with robust clinical correlations between their upper airway abundance and reduced respiratory tract infection risk. Here, we highlight recent work identifying respiratory tract bacteria that promote airway health and resilience against disease, with a focus on lung infections and the underlying mechanisms driving RTM-protective benefits.

Commensal production of a broad-spectrum and short-lived antimicrobial peptide polyene eliminates nasal Staphylococcus aureus

Antagonistic bacterial interactions often rely on antimicrobial bacteriocins, which attack only a narrow range of target bacteria. However, antimicrobials with broader activity may be advantageous. Here we identify an antimicrobial called epifadin, which is produced by nasal Staphylococcus epidermidis IVK83. It has an unprecedented architecture consisting of a non-ribosomally synthesized peptide, a polyketide component and a terminal modified amino acid moiety. Epifadin combines a wide antimicrobial target spectrum with a short life span of only a few hours. It is highly unstable under in vivo-like conditions, potentially as a means to limit collateral damage of bacterial mutualists. However, Staphylococcus aureus is eliminated by epifadin-producing S. epidermidis during co-cultivation in vitro and in vivo, indicating that epifadin-producing commensals could help prevent nasal S. aureus carriage. These insights into a microbiome-derived, previously unknown antimicrobial compound class suggest that limiting the half-life of an antimicrobial may help to balance its beneficial and detrimental activities.

Insight into the structure, biosynthesis, isolation method and biological function of teichoic acid in different gram-positive microorganisms: A review

Teichoic acid (TA) is a weakly anionic polymer present in the cell walls of Gram-positive bacteria. It can be classified into wall teichoic acid (WTA) and lipoteichoic acid (LTA) based on its localization in the cell wall. The structure and biosynthetic pathway of TAs are strain-specific and have a significant role in maintaining cell wall stability. TAs have various beneficial functions, such as immunomodulatory, anticancer and antioxidant activities. However, the purity and yield of TAs are generally not high, and different isolation methods may even affect their structural integrity, which limits the research progress on the probiotic functions of TA. This paper reviews an overview of the structure and biosynthetic pathway of TAs in different strains, as well as the research progress of the isolation and purification methods of TAs. Furthermore, this review also highlights the current research status on the biological functions of TAs. Through a comprehensive understanding of this review, it is expected to pave the way for advancements in isolating and purifying high-quality TAs and, in turn, lay a foundation for contributing to the development of targeted probiotic therapies.

Molecular characteristics and clinical features of Staphylococcus epidermidis healthcare-associated late-onset bacteremia among infants hospitalized in neonatal intensive care units

BACKGROUND

Though Staphylococcus epidermidis was the most common pathogen of late-onset sepsis (LOS) in neonatal intensive care units (NICUs), there haves been scanty reports on molecular epidemiology of S. epidermidis isolates from infants stayed in NICU and on correlation of molecular characteristics with clinical features in these infants.

METHODS

We collected and characterized S. epidermidis bloodstream isolates from infants hospitalized in NICU of a medical center in Taiwan between 2018 and 2020. Medical records of these infants were retrospectively reviewed.

RESULTS

A total of 107 isolates identified from 78 episodes of bacteremia in 75 infants were included for analysis. Of the 78 isolates (episodes), 24 pulsotypes, 11 sequence types (STs), and 5 types of staphylococcal chromosomal cassette (type I-V) were identified. ST59 and its single locus variant ST1124 (37.2%) comprised the most common strain, followed by ST35 (14.1%), ST2 (11.5%), and ST89 (10.3%). All but 5 isolates (73/78, 93.6%) belonged to clonal complex (CC) 2. Comparing infants infected with genetically different strains, the patients with underlying immune disease were significantly associated with ST2 infection (P = 0.021), while no statistically significant differences were found in terms of clinical and laboratory characteristics. Only 3.8% of the isolates were susceptible to oxacillin.

CONCLUSIONS

More than 90% of S. epidermidis bloodstream isolates from infants in NICU in Taiwan were resistant to oxacillin. Though diverse, more than 90% of the isolates (episodes) belonged to CC2. No statistically significant differences were found in terms of clinical characteristics among the infants infected with genetically different strains.

Invasive Staphylococcus epidermidis uses a unique processive wall teichoic acid glycosyltransferase to evade immune recognition

Staphylococcus epidermidis expresses glycerol phosphate wall teichoic acid (WTA), but some health care-associated methicillin-resistant S. epidermidis (HA-MRSE) clones produce a second, ribitol phosphate (RboP) WTA, resembling that of the aggressive pathogen Staphylococcus aureus. RboP-WTA promotes HA-MRSE persistence and virulence in bloodstream infections. We report here that the TarM enzyme of HA-MRSE [TarM(Se)] glycosylates RboP-WTA with glucose, instead of N-acetylglucosamine (GlcNAc) by TarM(Sa) in S. aureus. Replacement of GlcNAc with glucose in RboP-WTA impairs HA-MRSE detection by human immunoglobulin G, which may contribute to the immune-evasion capacities of many invasive S. epidermidis. Crystal structures of complexes with uridine diphosphate glucose (UDP-glucose), and with UDP and glycosylated poly(RboP), reveal the binding mode and glycosylation mechanism of this enzyme and explain why TarM(Se) and TarM(Sa) link different sugars to poly(RboP). These structural data provide evidence that TarM(Se) is a processive WTA glycosyltransferase. Our study will support the targeted inhibition of TarM enzymes, and the development of RboP-WTA targeting vaccines and phage therapies.

Wall Teichoic Acid Mediates Staphylococcus aureus Binding to Endothelial Cells via the Scavenger Receptor LOX-1

The success of Staphylococcus aureus as a major cause for endovascular infections depends on effective interactions with blood-vessel walls. We have previously shown that S. aureus uses its wall teichoic acid (WTA), a surface glycopolymer, to attach to endothelial cells. However, the endothelial WTA receptor remained unknown. We show here that the endothelial oxidized low-density lipoprotein receptor 1 (LOX-1) interacts with S. aureus WTA and permits effective binding of S. aureus to human endothelial cells. Purified LOX-1 bound to isolated S. aureus WTA. Ectopic LOX-1 expression led to increased binding of S. aureus wild type but not of a WTA-deficient mutant to a cell line, and LOX-1 blockage prevented S. aureus binding to endothelial cells. Moreover, WTA and LOX-1 expression levels correlated with the efficacy of the S. aureus-endothelial interaction. Thus, LOX-1 is an endothelial ligand for S. aureus, whose blockage may help to prevent or treat severe endovascular infections.

Cryptic susceptibility to penicillin/β-lactamase inhibitor combinations in emerging multidrug-resistant, hospital-adapted Staphylococcus epidermidis lineages

Global spread of multidrug-resistant, hospital-adapted Staphylococcus epidermidis lineages underscores the need for new therapeutic strategies. Here we show that many S. epidermidis isolates belonging to these lineages display cryptic susceptibility to penicillin/β-lactamase inhibitor combinations under in vitro conditions, despite carrying the methicillin resistance gene mecA. Using a mouse thigh model of S. epidermidis infection, we demonstrate that single-dose treatment with amoxicillin/clavulanic acid significantly reduces methicillin-resistant S. epidermidis loads without leading to detectable resistance development. On the other hand, we also show that methicillin-resistant S. epidermidis is capable of developing increased resistance to amoxicillin/clavulanic acid during long-term in vitro exposure to these drugs. These findings suggest that penicillin/β-lactamase inhibitor combinations could be a promising therapeutic candidate for treatment of a high proportion of methicillin-resistant S. epidermidis infections, although the in vivo risk of resistance development needs to be further addressed before they can be incorporated into clinical trials.

Characterisation of neonatal Staphylococcus capitis NRCS-A isolates compared with non NRCS-A Staphylococcus capitis from neonates and adults

Staphylococcus capitis is a frequent cause of late-onset sepsis in neonates admitted to Neonatal Intensive Care Units (NICU). One clone of S. capitis, NRCS-A has been isolated from NICUs globally although the reasons for the global success of this clone are not well understood.We analysed a collection of S. capitis colonising babies admitted to two NICUs, one in the UK and one in Germany as well as corresponding pathological clinical isolates. Genome analysis identified a population structure of three groups; non-NRCS-A isolates, NRCS-A isolates, and a group of 'proto NRCS-A' - isolates closely related to NRCS-A but not associated with neonatal infection. All bloodstream isolates belonged to the NRCS-A group and were indistinguishable from strains carried on the skin or in the gut. NRCS-A isolates showed increased tolerance to chlorhexidine and antibiotics relative to the other S. capitis as well as enhanced ability to grow at higher pH values. Analysis of the pangenome of 138 isolates identified characteristic nsr and tarJ genes in both the NRCS-A and proto groups. A CRISPR-cas system was only seen in NRCS-A isolates which also showed enrichment of genes for metal acquisition and transport.We found evidence for transmission of S. capitis NRCS-A within NICU, with related isolates shared between babies and multiple acquisitions by some babies. Our data show NRCS-A strains commonly colonise uninfected babies in NICU representing a potential reservoir for potential infection. This work provides more evidence that adaptation to survive in the gut and on skin facilitates spread of NRCS-A, and that metal acquisition and tolerance may be important to the biology of NRCS-A. Understanding how NRCS-A survives in NICUs can help develop infection control procedures against this clone.

Cross-species communication via agr controls phage susceptibility in Staphylococcus aureus

Bacteria use quorum sensing (QS) to coordinate group behavior in response to cell density, and some bacterial viruses (phages) also respond to QS. In Staphylococcus aureus, the agr-encoded QS system relies on accumulation of auto-inducing cyclic peptides (AIPs). Other staphylococci also produce AIPs of which many inhibit S. aureus agr. We show that agr induction reduces expression of tarM, encoding a glycosyltransferase responsible for α-N-acetylglucosamine modification of the major S. aureus phage receptor, the wall teichoic acids. This allows lytic phage Stab20 and related phages to infect and kill S. aureus. However, in mixed communities, producers of inhibitory AIPs like S. haemolyticus, S. caprae, and S. pseudintermedius inhibit S. aureus agr, thereby impeding phage infection. Our results demonstrate that cross-species interactions dramatically impact phage susceptibility. These interactions likely influence microbial ecology and impact the efficacy of phages in medical and biotechnological applications such as phage therapy.

Improved Genomic Prediction of Staphylococcus epidermidis Isolation Sources with a Novel Polygenic Score

Staphylococcus epidermidis infections can be challenging to diagnose due to the species frequent contamination of clinical specimens and indolent course of infection. Nevertheless, S. epidermidis is the major cause of late-onset sepsis among premature infants and of intravascular infection in all age groups. Prior work has shown that bacterial virulence factors, antimicrobial resistances, and strains have up to 80% in-sample accuracy to distinguish hospital from community sources, but are unable to distinguish true bacteremia from blood culture contamination. Here, a phylogeny-informed genome-wide association study of 88 isolates was used to estimate effect sizes of particular genomic variants for isolation sources. A "polygenic score" was calculated for each isolate as the summed effect sizes of its repertoire of genomic variants. Predictive models of isolation sources based on polygenic scores were tested with in-samples and out-samples from prior studies of different patient populations. Polygenic scores from accessory genes (AGs) distinguished hospital from community sources with the highest accuracy to date, up to 98% for in-samples and 65% to 91% for various out-samples, whereas scores from single nucleotide polymorphisms (SNPs) had lower accuracy. Scores from AGs and SNPs achieved the highest in-sample accuracy to date, up to 76%, in distinguishing infection from contaminant sources within a hospital. Model training and testing data sets with more similar population structures resulted in more accurate predictions. This study reports the first use of a polygenic score for predicting a complex bacterial phenotype and shows the potential of this approach for enhancing S. epidermidis diagnosis.

Modulation of MRSA virulence gene expression by the wall teichoic acid enzyme TarO

Phenol-soluble modulins (PSMs) and Staphylococcal protein A (SpA) are key virulence determinants for community-associated methicillin-resistant Staphylococcus aureus (CA-MRSA), an important human pathogen that causes a wide range of diseases. Here, using chemical and genetic approaches, we show that inhibition of TarO, the first enzyme in the wall teichoic acid (WTA) biosynthetic pathway, decreases the expression of genes encoding PSMs and SpA in the prototypical CA-MRSA strain USA300 LAC. Mechanistically, these effects are linked to the activation of VraRS two-component system that directly represses the expression of accessory gene regulator (agr) locus and spa. The activation of VraRS was due in part to the loss of the functional integrity of penicillin-binding protein 2 (PBP2) in a PBP2a-dependent manner. TarO inhibition can also activate VraRS in a manner independent of PBP2a. We provide multiple lines of evidence that accumulation of lipid-linked peptidoglycan precursors is a trigger for the activation of VraRS. In sum, our results reveal that WTA biosynthesis plays an important role in the regulation of virulence gene expression in CA-MRSA, underlining TarO as an attractive target for anti-virulence therapy. Our data also suggest that acquisition of PBP2a-encoding mecA gene can impart an additional regulatory layer for the modulation of key signaling pathways in S. aureus.

Antibacterial and Antibiofilm Activities of Sertindole and Its Antibacterial Mechanism against Staphylococcus aureus

As methicillin-resistant Staphylococcus aureus has become the most prevalent antibiotic-resistant pathogen in many countries, there is an urgent demand to develop novel antibacterial agents. The purpose of this study is to investigate sertindole's antibacterial and antibiofilm properties, as well as its antibacterial mechanism against S. aureus. The MIC₅₀ and MIC₉₀ values for sertindole against S. aureus were both determined to be 50 μM, and sertindole significantly reduced S. aureus growth at a subinhibitory concentration of 1/2× MIC. Sertindole also showed remarkable potency in inhibiting the development of biofilms. Additionally, proteomic analysis revealed that sertindole could dramatically decrease the biosynthesis of amino acids and trigger the cell wall stress response and oxidative stress response. A series of tests, including membrane permeability assays, quantitative real-time reverse transcription-PCR, and electron microscope observations, revealed that sertindole disrupts cell integrity. The two-component system VraS/VraR knockout S. epidermis strain also showed enhanced sensitivity to sertindole. Overall, our data suggested that sertindole exhibited antibacterial and biofilm-inhibiting activities against S. aureus and that its antibacterial actions may involve the destruction of cell integrity.

Staphylococcus epidermidis and its dual lifestyle in skin health and infection

The coagulase-negative bacterium Staphylococcus epidermidis is a member of the human skin microbiota. S. epidermidis is not merely a passive resident on skin but actively primes the cutaneous immune response, maintains skin homeostasis and prevents opportunistic pathogens from causing disease via colonization resistance. However, it is now appreciated that S. epidermidis and its interactions with the host exist on a spectrum of potential pathogenicity derived from its high strain-level heterogeneity. S. epidermidis is the most common cause of implant-associated infections and is a canonical opportunistic biofilm former. Additional emerging evidence suggests that some strains of S. epidermidis may contribute to the pathogenesis of common skin diseases. Here, we highlight new developments in our understanding of S. epidermidis strain diversity, skin colonization dynamics and its multifaceted interactions with the host and other members of the skin microbiota.

Cec4-Derived Peptide Inhibits Planktonic and Biofilm-Associated Methicillin Resistant Staphylococcus epidermidis

Staphylococcus epidermidis is part of the normal microbiota that colonizes the skin and mucosal surfaces of human beings. Previous studies suggested that S. epidermidis possessed low virulence, but recent studies confirmed that it can acquire high virulence from Staphylococcus aureus and with the increasing detection of methicillin-resistant S. epidermidis. It has become a major pathogen of graft-associated and hospital-acquired infections. In previous studies, we modified the antimicrobial peptide Cec4 (41 amino acids) and obtained the derived peptide C9 (16 amino acids) showing better antimicrobial activity against S. epidermidis with an MIC value of 8 μg/mL. The peptide has rapid bactericidal activity without detectable high-level resistance, showing certain inhibition and eradication ability on S. epidermidis biofilms. The damage of cell membrane structures by C9 was observed by scanning emission microscopy (SEM) and transmission electron microscopy (TEM). In addition, C9 altered the S. epidermidis cell membrane permeability, depolarization levels, fluidity, and reactive oxygen species (ROS) accumulation and possessed the ability to bind genomic DNA. Analysis of the transcriptional profiles of C9-treated cells revealed changes in genes involved in cell wall and ribosome biosynthesis, membrane protein transport, oxidative stress, and DNA transcription regulation. At the same time, the median lethal dose of C9 in mice was more than 128 mg/kg, and the intraperitoneal administration of 64 mg/kg was less toxic to the liver and kidneys of mice. Furthermore, C9 also showed a certain therapeutic effect on the mouse bacteremia model. In conclusion, C9 may be a candidate drug against S. epidermidis, which has the potential to be further developed as an antibacterial therapeutic agent. IMPORTANCE S. epidermidis is one of the most important pathogens of graft-related infection and hospital-acquired infection. The growing problem of antibiotic resistance, as well as the emergence of bacterial pathogenicity, highlights the need for antimicrobials with new modes of action. Antimicrobial peptides have been extensively studied over the past 30 years as ideal alternatives to antibiotics, and we report here that the derived peptide C9 is characterized by rapid bactericidal and antibiofilm activity, avoiding the development of resistance by acting on multiple nonspecific targets of the cell membrane or cell components. In addition, it has therapeutic potential against S. epidermidis infection in vivo. This study provides a rationale for the further development and application of C9 as an effective candidate antibiotic.

Transcriptome Mining to Identify Molecular Markers for the Diagnosis of Staphylococcus epidermidis Bloodstream Infections

Bloodstream infections caused by Staphylococcus epidermidis are often misdiagnosed since no diagnostic marker found so far can unequivocally discriminate "true" infection from sample contamination. While attempts have been made to find genomic and/or phenotypic differences between invasive and commensal isolates, possible changes in the transcriptome of these isolates under in vivo-mimicking conditions have not been investigated. Herein, we characterized the transcriptome, by RNA sequencing, of three clinical and three commensal isolates after 2 h of exposure to whole human blood. Bioinformatics analysis was used to rank the genes with the highest potential to distinguish invasive from commensal isolates and among the ten genes identified as candidates, the gene SERP2441 showed the highest potential. A collection of 56 clinical and commensal isolates was then used to validate, by quantitative PCR, the discriminative power of the selected genes. A significant variation was observed among isolates, and the discriminative power of the selected genes was lost, undermining their potential use as markers. Nevertheless, future studies should include an RNA sequencing characterization of a larger collection of isolates, as well as a wider range of conditions to increase the chances of finding further candidate markers for the diagnosis of bloodstream infections caused by S. epidermidis.

Functional analysis of intergenic regulatory regions of genes encoding surface adhesins in Staphylococcus aureus isolates from periprosthetic joint infections

Staphylococcus aureus is a leading cause of prosthetic joint infections (PJI). Surface adhesins play an important role in the primary attachment to plasma proteins that coat the surface of prosthetic devices after implantation. Previous efforts to identify a genetic component of the bacterium that confers an enhanced capacity to cause PJI have focused on gene content, kmers, or single-nucleotide polymorphisms (SNPs) in coding sequences. Here, using a collection of S. aureus strains isolated from PJI and wounds, we investigated whether genetic variations in the regulatory region of genes encoding surface adhesins lead to differences in their expression levels and modulate the capacity of S. aureus to colonize implanted prosthetic devices. The data revealed that S. aureus isolates from the same clonal complex (CC) contain a specific pattern of SNPs in the regulatory region of genes encoding surface adhesins. As a consequence, each clonal lineage shows a specific profile of surface proteins expression. Co-infection experiments with representative isolates of the most prevalent CCs demonstrated that some lineages have a higher capacity to colonize implanted catheters in a murine infection model, which correlated with a greater ability to form a biofilm on coated surfaces with plasma proteins. Together, results indicate that differences in the expression level of surface adhesins may modulate the propensity of S. aureus strains to cause PJI. Given the high conservation of surface proteins among staphylococci, our work lays the framework for investigating how diversification at intergenic regulatory regions affects the capacity of S. aureus to colonize the surface of medical implants.

The In Vitro Antimicrobial and Antibiofilm Activities of Lysozyme against Gram-Positive Bacteria

Objective

To analyze the in vitro antibacterial and antibiofilm activities of lysozyme (LYS) and its combination with various drugs against Gram-positive bacteria (GPB, n = 9), thus to provide an exploration direction for drug development.

Methods

The minimum inhibitory concentrations (MICs) of linezolid (LZD), amikacin (AMK), ceftriaxone/sulbactam (CRO/SBT), cefotaxime/sulbactam (CTX/SBT), piperacillin/sulbactam (PIP/SBT), doxycycline (DOX), levofloxacin (LVX), amoxicillin/clavulanate potassium (7 : 1, AK71), imipenem (IPM), azithromycin (AZM), and their combinations with LYS were determined with tuber twice dilution. The antimicrobial and antibiofilm activities of LYS, AZM, LVX, and their combinations with others were evaluated through MTT and crystal violet assay.

Results

High-dose LYS (30 μg/mL) combined with PIP/SBT and AK71, respectively, showed synergistic antibacterial activities against methicillin-resistant Staphylococcus aureus (MRSA), while it showed no synergistic activities when combined with other drugs. LYS and AZM inhibited the biofilm formation of one MRSA strain, but they and LVX had no similar activities against methicillin-resistant Staphylococcus epidermidis (MRSE) or vancomycin-resistant Enterococcus faecium (VREF). Particularly, LYS increased the permeability of biofilms of MRSA 33 and exhibited antibiofilm activities against MRSA 31 (inhibition rate = 38.1%) and MRSE 61 (inhibition rate = 46.6%). The combinations of PIP/SBT+LYS, AMK+LYS, and LZD+LYS showed stronger antibiofilm activities against MRSA 62, MRSE 62, MRSE 63, and VREF 11.

Conclusion

The antimicrobial and antibiofilm activities of LYS against MRSA were better than AZM, while that of LYS against MRSE and VREF, respectively, was similar with AZM and LVX.

Development of an artificial synovial fluid useful for studying Staphylococcus epidermidis joint infections

Staphylococcus epidermidis is a major causative agent of prosthetic joint infections (PJI). The ability to form biofilms supports this highly selective pathogenic potential. In vitro studies essentially relying on phenotypic assays and genetic approaches have provided a detailed picture of the molecular events contributing to biofilm assembly. A major limitation in these studies is the use of synthetic growth media, which significantly differs from the environmental conditions S. epidermidis encounters during host invasion. Building on evidence showing that growth in serum substantially affects S. epidermidis gene expression profiles and phenotypes, the major aim of this study was to develop and characterize a growth medium mimicking synovial fluid, thereby facilitating research addressing specific aspects related to PJI. Using fresh human plasma, a protocol was established allowing for the large-scale production of a medium that by biochemical analysis matches key characteristics of synovial fluid and therefore is referred to as artificial synovial fluid (ASF). By analysis of biofilm-positive, polysaccharide intercellular adhesion (PIA)-producing S. epidermidis 1457 and its isogenic, PIA- and biofilm-negative mutant 1457-M10, evidence is provided that the presence of ASF induces cluster formation in S. epidermidis 1457 and mutant 1457-M10. Consistent with the aggregative properties, both strains formed multilayered biofilms when analyzed by confocal laser scanning microscopy. In parallel to the phenotypic findings, expression analysis after growth in ASF found upregulation of genes encoding for intercellular adhesins (icaA, aap, and embp) as well as atlE, encoding for the major cell wall autolysin being responsible for eDNA release. In contrast, growth in ASF was associated with reduced expression of the master regulator agr. Collectively, these results indicate that ASF induces expression profiles that are able to support intercellular adhesion in both PIA-positive and PIA-negative S. epidermidis. Given the observation that ASF overall induced biofilm formation in a collection of S. epidermidis isolates from PJI, the results strongly support the idea of using growth media mimicking host environments. ASF may play an important role in future studies related to the pathogenesis of S. epidermidis PJI.

The Staphylococcus epidermidis Transcriptional Profile During Carriage

The virulence factors of the opportunistic human pathogen Staphylococcus epidermidis have been a main subject of research. In contrast, limited information is available on the mechanisms that allow the bacterium to accommodate to the conditions during carriage, a prerequisite for pathogenicity. Here, we tested the hypothesis that the adaptation of S. epidermidis at different anatomical sites is reflected by differential gene regulation. We used qPCR to profile S. epidermidis gene expression in vivo in nose and skin swabs of 11 healthy individuals. Despite some heterogeneity between individuals, significant site-specific differences were detected. For example, expression of the S. epidermidis regulator sarA was found similarly in the nose and on the skin of all individuals. Also, genes encoding colonization and immune evasion factors (sdrG, capC, and dltA), as well as the sphingomyelinase encoding gene sph, were expressed at both anatomical sites. In contrast, expression of the global regulator agr was almost inactive in the nose but readily present on the skin. A similar site-specific expression profile was also identified for the putative chitinase-encoding SE0760. In contrast, expression of the autolysine-encoding gene sceD and the wall teichoic acid (WTA) biosynthesis gene tagB were more pronounced in the nose as compared to the skin. In summary, our analysis identifies site-specific gene expression patterns of S. epidermidis during colonization. In addition, the observed expression signature was significantly different from growth in vitro. Interestingly, the strong transcription of sphingomyelinase together with the low expression of genes encoding the tricarboxylic acid cycle (TCA) suggests very good nutrient supply in both anatomical niches, even on the skin where one might have suspected a rather lower nutrient supply compared to the nose.

Genetic Determinants of Surface Accessibility in Staphylococcus aureus

Bacterial cell walls represent one of the most prominent targets of antibacterial agents. These agents include natural products (e.g., vancomycin) and proteins stemming from the innate immune system (e.g., peptidoglycan-recognition proteins and lysostaphin). Among bacterial pathogens that infect humans, Staphylococcus aureus (S. aureus) continues to impose a tremendous healthcare burden across the globe. S. aureus has evolved countermeasures that can directly restrict the accessibility of innate immune proteins, effectively protecting itself from threats that target key cell well components. We recently described a novel assay that directly reports on the accessibility of molecules to the peptidoglycan layer within the bacterial cell wall of S. aureus. The assay relies on site-specific chemical remodeling of the peptidoglycan with a biorthogonal handle. Here, we disclose the application of our assay to a screen of a nonredundant transposon mutant library for susceptibility of the peptidoglycan layer with the goal of identifying genes that contribute to the control of cell surface accessibility. We discovered several genes that resulted in higher accessibility levels to the peptidoglycan layer and showed that these genes modulate sensitivity to lysostaphin. These results indicate that this assay platform can be leveraged to gain further insight into the biology of bacterial cell surfaces.

Bacterial microbiota of the contact lens surface and associated care behaviours

Introduction

Contact lens (CL) wear has been reported to cause changes to the microbiome of the ocular surface. More insight into the alteration of this microenvironment can help to understand the pathogenesis of CL-related eye infections. Knowledge of the relationship between the CL wearer's behaviours and pathogens would help health care providers focus on each step of proper CL care. This study aims to determine the behaviours that might be associated with the community of bacteria on CL.

Methods

A cross-sectional design was performed using anonymous questionnaires to obtain demographic data and assess hygiene practices among volunteering wearers. The CLs used were collected to evaluate the prevalence of pathogenic bacteria associated with ocular infections by PCR and microbiota analysis.

Results

The bacterial microbiota study revealed a total of 19 genera and 26 isolated strains from 20 eligible CLs. Enterobacter, Staphylococcus, and Achromobacter were the main genus in this subject population. Staphylococcus pasteuri and Achromobacter agilis were the most common pathogens at 65% and 35%, respectively. Enterobacter mori, a nonpathogenic organism, was found to be the most predominant strain, accounting for 27.51% of the total bacterial constituents. The risk behaviour of CL wear that was significantly associated with A. agilis contamination was cleaning the CL case with tap water (P value = 0.04).

Conclusions

This is the first study focusing on the association between the culture selected microbial community on the CL surface and compehensive behavioural characteristics. Environmental contamination was the main source of microbes found on CL surfaces. An emphasis in patient education should be placed on careful handling during the CL care routine and managing the hygiene of the surroundings.

Look Who's Talking: Host and Pathogen Drivers of Staphylococcus epidermidis Virulence in Neonatal Sepsis

Preterm infants are at increased risk for invasive neonatal bacterial infections. S. epidermidis, a ubiquitous skin commensal, is a major cause of late-onset neonatal sepsis, particularly in high-resource settings. The vulnerability of preterm infants to serious bacterial infections is commonly attributed to their distinct and developing immune system. While developmentally immature immune defences play a large role in facilitating bacterial invasion, this fails to explain why only a subset of infants develop infections with low-virulence organisms when exposed to similar risk factors in the neonatal ICU. Experimental research has explored potential virulence mechanisms contributing to the pathogenic shift of commensal S. epidermidis strains. Furthermore, comparative genomics studies have yielded insights into the emergence and spread of nosocomial S. epidermidis strains, and their genetic and functional characteristics implicated in invasive disease in neonates. These studies have highlighted the multifactorial nature of S. epidermidis traits relating to pathogenicity and commensalism. In this review, we discuss the known host and pathogen drivers of S. epidermidis virulence in neonatal sepsis and provide future perspectives to close the gap in our understanding of S. epidermidis as a cause of neonatal morbidity and mortality.

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

Coagulase-negative Staphylococcus (CoNS) is the most common pathogen causing traumatic endophthalmitis. Among which, Staphylococcus epidermidis is the most common species that colonizes human skin, eye surfaces, and nasal cavity. It is also the main cause of nosocomial infection, specially foreign body-related bloodstream infections (FBR-BSIs). Although some studies have reported the genome characteristics of S. epidermidis, the genome of ocular trauma-sourced S. epidermidis strain and a comprehensive understanding of its pathogenicity are still lacking. Our study sequenced, analyzed, and reported the whole genomes of 11 ocular trauma-sourced samples of S. epidermidis that caused traumatic endophthalmitis. By integrating publicly available genomes, we obtained a total of 187 S. epidermidis samples from healthy and diseased eyes, skin, respiratory tract, and blood. Combined with pan-genome, phylogenetic, and comparative genomic analyses, our study showed that S. epidermidis, regardless of niche source, exhibits two founder lineages with different pathogenicity. Moreover, we identified several potential biomarkers associated with the virulence of S. epidermidis, including essD, uhpt, sdrF, sdrG, fbe, and icaABCDR. EssD and uhpt have high homology with esaD and hpt in Staphylococcus aureus, showing that the genomes of S. epidermidis and S. aureus may have communicated during evolution. SdrF, sdrG, fbe, and icaABCDR are related to biofilm formation. Compared to S. epidermidis from blood sources, ocular-sourced strains causing intraocular infection had no direct relationship with biofilm formation. In conclusion, this study provided additional data resources for studies on S. epidermidis and improved our understanding of the evolution and pathogenicity among strains of different sources.

Multi-species host range of staphylococcal phages isolated from wastewater

The host range of bacteriophages defines their impact on bacterial communities and genome diversity. Here, we characterize 94 novel staphylococcal phages from wastewater and establish their host range on a diversified panel of 117 staphylococci from 29 species. Using this high-resolution phage-bacteria interaction matrix, we unveil a multi-species host range as a dominant trait of the isolated staphylococcal phages. Phage genome sequencing shows this pattern to prevail irrespective of taxonomy. Network analysis between phage-infected bacteria reveals that hosts from multiple species, ecosystems, and drug-resistance phenotypes share numerous phages. Lastly, we show that phages throughout this network can package foreign genetic material enclosing an antibiotic resistance marker at various frequencies. Our findings indicate a weak host specialism of the tested phages, and therefore their potential to promote horizontal gene transfer in this environment.

Staphylococcal trafficking and infection - from 'nose to gut' and back

Staphylococcus aureus is an opportunistic human pathogen, which is a leading cause of infections worldwide. The challenge in treating S. aureus infection is linked to the development of multidrug-resistant strains and the mechanisms employed by this pathogen to evade the human immune defenses. In addition, S. aureus can hide asymptomatically in particular ‘protective’ niches of the human body for prolonged periods of time. In the present review, we highlight recently gained insights in the role of the human gut as an endogenous S. aureus reservoir next to the nasopharynx and oral cavity. In addition, we address the contribution of these ecological niches to staphylococcal transmission, including the roles of particular triggers as modulators of the bacterial dissemination. In this context, we present recent advances concerning the interactions between S. aureus and immune cells to understand their possible roles as vehicles of dissemination from the gut to other body sites. Lastly, we discuss the factors that contribute to the switch from colonization to infection. Altogether, we conclude that an important key to uncovering the pathogenesis of S. aureus infection lies hidden in the endogenous staphylococcal reservoirs, the trafficking of this bacterium through the human body and the subsequent immune responses.

DNA glycosylases for 8-oxoguanine repair in Staphylococcus aureus

GO system is part of base excision DNA repair and is required for the correct repair of 8-oxoguanine (8-oxoG), one of the most abundant oxidative lesions. Due to the ability of 8-oxoG to mispair with A, this base is highly mutagenic, and its repair requires two enzymes: Fpg that removes 8-oxoG from 8-oxoG:C pairs, and MutY that excises the normal A from 8-oxoG:A mispairs. Here we characterize the properties of putative GO system DNA glycosylases from Staphylococcus aureus, an important human opportunistic pathogen that causes hospital infections and presents a serious health concern due to quick spread of antibiotic-resistant strains. In addition to Fpg and MutY from the reference NCTC 8325 strain (SauFpg1 and SauMutY), we have also studied an Fpg homolog from a multidrug-resistant C0673 isolate (SauFpg2), which is different from SauFpg1 in its sequence. Both SauFpg enzymes showed the highest activity at pH 7.0-9.0 and NaCl concentrations 25-75 mM (SauFpg1) or 50-100 mM (SauFpg2), whereas SauMutY was active at a broad pH range and had a salt optimum at ∼75 mM NaCl. Both SauFpg1 and SauFpg2 bound and cleaved duplexes containing 8-oxoG, 5-hydroxyuracil, 5,6-dihydrouracil or apurinic/apyrimidinic site paired with C, T, or G, but not with A. For SauFpg1 and SauFpg2, 8-oxoG was the best substrate tested, and 5,6-dihydrouracil was the worst one. SauMutY efficiently excised adenine from duplex substrates containing A:8-oxoG or A:G pairs. SauFpg enzymes were readily trapped on DNA by NaBH₄ treatment, indicating formation of a Schiff base reaction intermediate. Surprisingly, SauMutY was also trapped significantly better than its E. coli homolog. All three S. aureus GO glycosylases drastically reduced spontaneous mutagenesis when expressed in an fpg mutY E. coli double mutant. Overall, we conclude that S. aureus possesses an active GO system, which could possibly be targeted for sensitization of this pathogen to oxidative stress.