Current Insights and Future Directions in Staphylococcus aureus Infections: Advances and Perspectives

Abstract

Staphylococcus aureus infections are a global health concern, causing various illnesses. Recent research has provided insights into the epidemiology and pathogenesis of these infections, including the role of virulence factors and immune evasion strategies. Understanding the genetic mechanisms responsible for resistance is crucial in dealing with antibiotic-resistant strains like MRSA, which is the focus of this chapter. We also explore the advancements in diagnostics and detection methods, such as PCR and whole-genome sequencing and alternative treatments, viz. anti-virulence agents, monoclonal antibodies, and innovative antimicrobial peptides, which have improved patient outcomes. We end the chapter with a focus on the future research required for developing effective vaccines and alternative therapeutics to address the increasing concern of Staphylococcus aureus infections.

1. Introduction

Staphylococcus aureus (S. aureus) is a Gram-positive bacterium that is part of the Staphylococcaceae family and is spherical in shape usually arranged in clusters [1, 2]. S. aureus has the ability to thrive in environments with varying levels of oxygen and has a diverse range of virulence factors that allow it to cause infections in humans posing a significant global health challenge [3]. S. aureus infections lead to various illness that span from minor skin and soft tissue inflammations, boils, and cellulitis to severe bloodstream infections—septicemia [4], endocarditis (infection of the heart valves), and pulmonary infections (pneumonia) [5]. They are responsible for healthcare-associated infections (HAIs) or nosocomial infections that occur in healthcare settings, commonly affecting individuals with compromised immune systems, or those with recent surgical procedures, or patients with invasive medical devices like catheters and/or ventilators [6] as well as community-acquired infections (CAI) manifesting as skin and wound infections, such as abscesses, as well as pneumonia in individuals who are otherwise healthy [7]. A strain of S. aureus that is resistant to numerous antibiotics, methicillin-resistant S. aureus (MRSA), poses significant challenges HAIs [8].

This study presents a broad overview of the latest findings and potential areas of exploration in the context of S. aureus infections, emphasizing recent progress and future possibilities. We first focus on the virulence, epidemiology, and pathogenesis of S. aureus infections [5]—recent research has provided valuable insights into the mechanisms used by S. aureus to cause persistent and recurrent infections, including the role of certain virulence factors and immune evasion strategies. We briefly look at these and move on to the progress made in diagnostics and detection methods—conventional methods for analyzing cultures can be quite time-consuming and may not always provide accurate results, resulting in delays in diagnosing conditions and potentially ineffective treatment. Nevertheless, advancements in molecular techniques, like polymerase chain reaction (PCR) and whole-genome sequencing, provide a swift and precise means of identifying S. aureus and its resistance profiles. These advancements hold promise in enhancing patient outcomes by enabling timely and precise antibiotic treatment.

We will then discuss the management and treatment of S. aureus infections. There have been growing concerns about the rising resistance to antibiotics, which has led to the investigation of alternative treatments viz. anti-virulence agents, monoclonal antibodies, and innovative antimicrobial peptides. Exploring alternative drug applications and advancing innovative treatment approaches, like phage therapy and immunotherapies, demonstrate potential in addressing S. aureus infections.

2. Regulation of S. aureus virulence factor

The regulation of virulence factors in S. aureus entails an intricate network that comprises interactions among genetic, biochemical, and environmental components. The regulatory mechanisms of S. aureus have a crucial function in its survival, pathogenicity, and adaptability and are essential for its capacity to attach to and infiltrate host tissues, avoid immune detection, and cause harm by means of toxins and enzymes. Understanding these virulence characteristics is important for the development of efficacious therapies and prevention measures against S. aureus infections.

The two-component system (TCS), a transcription regulator, plays a critical role in detecting environmental changes and converting them into coordinated regulatory reactions. Significantly, TCS systems, including the accessory gene regulator (agr) a quorum-sensing system and the S. aureus exoprotein expression (Sae) locus, are accountable for sensing and reacting to environmental stimuli. These pathways enable the regulation of toxins, surface proteins, and stress responses [9, 10]. In a typical TCS, an external signal activates a membrane-associated histidine kinase, leading to its autophosphorylation and subsequent phosphorylation of a response regulator. Once phosphorylated, the response regulator binds to specific DNA sequence motifs, thereby altering the expression of target genes. Most strains of S. aureus encode 16 different TCSs [11, 12], with one being essential (WalKR), while the other 15 can be inactivated [13, 14]. Notably, TCSs such as AgrAC, SaeRS, and ArlRS are directly linked to S. aureus virulence and regulate a large number of host-impacting secreted proteins.

The agr system, first described in 1986, is the most extensively studied and functions as a master virulence regulator through a quorum-sensing mechanism [9] to detect population density and regulate the expression of virulence factors accordingly. The SaeRS and ArlRS systems are involved in responding to specific environmental stimuli, such as changes in temperature, pH, and the presence of antimicrobial agents, thus modulating the expression of genes necessary for survival and pathogenicity. In addition to TCSs, S. aureus employs several cytoplasmic regulators like the SarA protein family of transcriptional regulators to adapt and survive in the host environment by modulating the expression of virulence genes in response to environmental and intracellular signals [11]. Table 1 summarizes the critical features and interplay of each system, elucidating their roles in the regulation of S. aureus virulence.

Regulatory system	Components	Key functions and features
Two-Component Systems	AgrAC, SaeRS, ArlRS	Detect environmental signals Regulate expression of host-impacting proteins [15].
Accessory Gene Regulator (agr)	agrA, agrC, agrD, agrB	Quorum-sensing system Master regulator of virulence genes [9, 16, 17, 18, 19, 20, 21, 22, 23].
Essential TCS	WalKR	Essential for cell viability Regulates cell wall metabolism and division [24].
SarA Protein Family	SarA, Rot, MgrA	Transcriptional regulators Modulate expression of a wide range of virulence genes [25, 26, 27, 28].
Alternative Sigma Factors	SigB, SigH	Regulate stress response and virulence gene expression under different environmental conditions [29, 30].

Table 1.

Summary of key regulatory systems in S. aureus.

Although there are multiple regulators in the area, this chapter will not delve into discussing them. However, readers who are interested may refer to a comprehensive review [15] and other literatures for more detailed information [15, 31, 32, 33, 34, 35].

3. Epidemiology of S. aureus infections

The incidence and spread of S. aureus infections (both HAIs and CAIs) exhibit variabilities among several geographical areas and populations [5, 36]. MRSA is the cause of about 20–30% of S. aureus cases in HAIs [37]. They are linked to higher fatality rates in comparison to infections caused by methicillin-susceptible S. aureus (MSSA).

Some common risk factors for S. aureus HAI are:

1. Hospitalization: The act of being admitted to a hospital raises the likelihood of contracting S. aureus infections [38], which includes both MSSA and MRSA [39].

2. Invasive devices, such as central venous catheters, urinary catheters, and surgical implants, can serve as entrance routes for S. aureus to cause infections [40].

3. Surgical site infections caused by S. aureus: Surgical site infections (SSIs) resulting from S. aureus are a frequent and important complication that occurs after surgical procedures [41]. S. aureus is a bacteria that is often found on the skin and in the nasal passages, pharynx [42], and other areas of the body in individuals who are in good health. Nevertheless, it has the potential to induce infections once entering the body via surgical incisions or wounds causing both superficial and deep SSIs [43]. SSIs affect the skin and subcutaneous tissue, whereas deep SSIs affect tissues or organs that are located further under the surface. SSIs can manifest as erythema, edema, discomfort, and exudate at the surgical site [44]. Multiple variables contribute to the occurrence of S. aureus infections in surgical sites. Failure to adhere to appropriate infection control protocols, such as maintaining a sterile environment and using clean devices, heightens the likelihood of S. aureus contamination. Initially, the bacteria carries a multitude of virulence characteristics (sticky proteins, poisons, and enzymes) that enable it to attach to and infiltrate tissues, evade the immune response, and induce tissue harm [45].

4. Specific patient characteristics/Vulnerable populations: People who have certain underlying medical conditions as well as the elderly may be more vulnerable to S. aureus infections due to immune system dysfunction [46, 47]. For example:

   • Preexisting medical disorders, such as diabetes or obesity, can heighten the vulnerability to S. aureus infections.

   • Human Immunodeficiency Virus/Acquired Immunodeficiency Syndrome (HIV/AIDS) compromises immune function and raises susceptibility to several infections [48], including S. aureus.

   • Patients with cancer who are receiving chemotherapy or radiation therapy also have compromised immune systems [48], which increases their susceptibility to S. aureus infections [49].

   • Patients in intensive care units (ICUs), who may be exposed to elevated amounts of antibiotics and have weakened immune systems, are more susceptible to developing S. aureus infections [50].

   • Patients with chronic lung disorders like Chronic Obstructive Pulmonary Disease (COPD) or asthma are prone to S. aureus lung infections due to their compromises lung function [51] and weak immune system.

   • The immune system can be weakened by advanced kidney illness, making one more vulnerable to S. aureus infections, especially bloodstream infections [52].

   • Individuals with autoimmune illnesses [53] are more susceptible to S. aureus infections due to immune system malfunction.

   • Individuals who get organ transplants frequently use immunosuppressive drugs, which impair immune function and raise the risk of S. aureus infections [54].

   • Immune system deterioration resulting from underlying cardiac problems [5] may heighten the vulnerability to bloodstream infections caused by S. aureus.

These are but a few instances of the many additional variables that can compromise immunity and raise the possibility of S. aureus infections.

S. aureus infections can impact people of all age groups in the community [55], without the need for prior contact with healthcare facilities. Community-acquired MRSA (CA-MRSA) infections are influenced by certain risk factors, which include:

1. Skin integrity: Skin infections, such as lacerations, punctures, or abrasions, serve as portals of entry for S. aureus to initiate infections [5].

2. Close contact: S. aureus is transmitted via direct skin-to-skin contact or contact with infected surfaces, making densely populated venues like schools, daycares, and athletic facilities possible sources of transmission. Athletes engaged in contact sports and activities, such as wrestling or football, face an elevated risk of contracting S. aureus skin infections, commonly referred to as “athlete’s skin.”

3. Sharing: Injection drug use can result in S. aureus bloodstream infections when individuals share infected needles and drug equipment [56].

4. Insufficient hygiene: Inadequate adherence to hand hygiene practices and lack of cleanliness can facilitate the spread of S. aureus in the population [57].

It should be emphasized that although particular populations may have a greater susceptibility to S. aureus infections, anybody has the potential to contract an infection. Implementing effective preventative measures, such as maintaining proper personal hygiene, consistently practicing handwashing, and adhering to appropriate infection control protocols, is essential for minimizing the spread and morbidity of S. aureus infections.

4. Clinical manifestations and treatment of S. aureus infections

From a clinical perspective, infections caused by S. aureus can exhibit a range of variations. The diagnosis and treatment of these infections are contingent upon the specific kind of infection and the features of the patient. This information does not serve as a replacement for expert medical counsel, and it is crucial to seek guidance from a healthcare professional for individualized evaluation and treatment. S. aureus infections can be categorized into bloodstream/cardiac, skin/soft tissue, respiratory, and bone/joint infections.

4.1 Bacteremia

Bacteremia is a critical medical condition characterized by the presence of bacteria in the bloodstream. It can occur due to initial infections [55], invasive medical procedures, or infections associated with implanted medical devices. Severe complications may occur, potentially resulting in sepsis, a serious systemic infection [56] that can be life-threatening. Understanding the clinical presentation of bacteremia [57] is crucial in order to quickly identify and treat the responsible organism, as different infections can have varying symptoms.

Antibiotics that are directed at the pathogen are the most important part of treatment. They stop bacteremia from getting worse and lower the risk of problems. Extensive study in academic contexts is necessary to advance our understanding of bacteremia.

4.1.1 Endocarditis

Endocarditis resulting from the damage to the inner lining and valves of the heart, often occurs after bacteremia. Common symptoms of this condition may include fever, a cardiac murmur, fatigue, night sweats, and difficulty breathing. Diagnosis requires blood cultures and echocardiograms, while treatment generally involves the administration of long-term intravenous antibiotics. There are instances where surgical intervention becomes necessary to repair or replace heart valves that have been affected.

4.2 Cutaneous and subcutaneous infections

S. aureus is capable of causing a range of infections affecting the skin and underlying soft tissues, such as furuncles, clusters of furuncles, localized collections of pus, inflammation of the skin and subcutaneous tissues [58], and infections in wounds. The clinical manifestations encompass erythema, edema, discomfort, and increased temperature at the site of infection. The diagnosis is typically made by evaluating the patient’s clinical symptoms; however, in severe cases or when the infection does not improve with initial therapy, cultures and laboratory tests may be performed. The treatment typically includes the surgical opening and removal of abscesses, as well as the administration of antibiotics [59], which is determined by the seriousness and site of the infection [60].

4.2.1 Abscesses and boils

Abscesses and boils are localized formations of pus caused by infection. They appear as painful, swollen masses filled with pus, often accompanied by redness and swelling in the surrounding area. Diagnosis of these conditions is achieved through a clinical examination and the analysis of pus samples. Treatment involves the drainage of abscesses and the administration of antibiotics [61].

4.2.2 Cellulitis

Cellulitis is a bacterial illness that affects the skin and tissues underneath [62]. It causes the skin to become red, swollen, heated, and painful. Diagnosis is achieved by means of clinical examination and occasionally validated with blood tests or cultures obtained from the afflicted region. Treatment entails the administration of antibiotics either by the mouth or through a vein, depending on the seriousness of the condition [63].

4.2.3 Impetigo

Impetigo, a highly transmissible dermatological infection prevalent among youngsters, results in the formation of red sores or blisters that burst, discharge fluid, and develop a yellow-brown scab. The diagnosis is established by doing a clinical examination and culturing the lesion. Treatment options include the use of topical or oral antibiotics.

4.3 Infections of the bones and joints

4.3.1 Osteomyelitis

Osteomyelitis, a bone infection, manifests as localized discomfort, elevated body temperature, inflammation, and increased heat [64]. The diagnosis is established by doing blood tests, imaging examinations such as X-rays or MRIs, and performing a bone sample. The treatment for this condition typically entails the administration of extended courses of antibiotics, and in certain cases, surgical intervention may be necessary to excise the contaminated bone.

4.3.2 Septic arthritis

Septic arthritis, a condition characterized by infection within a joint leading to inflammation, manifests as intense joint pain, edema, redness, and fever [65]. Diagnosis of the condition is achieved by analyzing joint fluid and conducting blood tests. Treatment involves administering antibiotics and draining the infected joint fluid [66].

4.4 Pneumonia

S. aureus pneumonia [67] can occur as either a primary infection or a secondary infection subsequent to influenza or other respiratory illnesses. Common symptoms of this condition may encompass coughing, chest discomfort, elevated body temperature, respiratory distress, and a productive cough accompanied by thick, pus-filled mucus. The diagnosis is usually made by conducting a comprehensive clinical assessment, along with performing chest imaging (such as chest X-ray), analyzing sputum cultures, and examining blood cultures. The treatment for S. aureus pneumonia typically involves the administration of intravenous antibiotics that are effective against the infections [68].

4.5 Management and treatment of infections caused by S. aureus

4.5.1 Preventive measures

Preventive measures are essential in reducing the occurrence and transmission of S. aureus infections [5]. Strict adherence to infection control protocols is crucial in preventing HAIs. Thorough hand hygiene practices are essential, including washing hands with soap and water or using alcohol-based hand sanitizers. It is important for healthcare providers to wear the necessary personal protective equipment, including gloves, gowns, and masks, when required.

Screening individuals by using either nasopharyngeal and pharyngeal swabs who may be at risk for S. aureus infections, such as those with a history of previous infections or colonization, can be an effective way to identify carriers of the bacteria, in addition to implementing infection control measures. Separating individuals who test positive for MRSA can effectively halt the transmission of the bacteria to other patients.

4.5.2 Antibiotics

When it comes to treating S. aureus infections, the selection of antibiotics is customized based on the strain’s susceptibility and the severity of the illness. Typically, beta-lactam antibiotics such as penicillin or cephalosporins are effective against methicillin-sensitive strains. Alternatively, methicillin-resistant strains necessitate the use of different antibiotics like vancomycin, daptomycin, or linezolid. By conducting susceptibility testing, one can ascertain the most suitable antibiotic for specific cases.

4.5.3 Surgical intervention

In more serious instances or when the infection is not showing improvement with antibiotic treatment alone, surgical intervention may be required. One aspect of this work may include the removal of abscesses or infected implants to eradicate the infection and facilitate the healing process.

4.5.4 Vaccines

Continual research is also dedicated to the development of vaccines against S. aureus to proactively prevent infections. However, it is important to note that there is not yet an approved vaccine against S. aureus.

5. Antibiotic resistance in S. aureus

Antibiotics are frequently the only option for treating serious bacterial infections, particularly when alternative treatments have been unsuccessful or when the infection presents a substantial health hazard. Their capacity to specifically target and eradicate bacteria has rendered them indispensable in contemporary medicine [69]. Antibiotics are specifically engineered to target particular bacteria or impede their proliferation and can be categorized into the following [70]:

• Penicillins, amoxicillin, and ampicillin, which are commonly prescribed for respiratory, skin, and urinary tract infections [71];

• Cephalosporins, such as cephalexin and ceftriaxone, which have a broader spectrum of activity and are used for more severe infections or when resistance to penicillins is suspected;

• Macrolides, such as erythromycin, clarithromycin, and azithromycin, which are typically used for respiratory tract infections and some sexually transmitted diseases;

• Fluoroquinolones, such as ciprofloxacin and levofloxacin, which are effective against a wide range of infections, including urinary tract infections, respiratory infections, and certain gastrointestinal infections.

• Vancomycin and Linezolid are frequently prescribed medicines for the treatment of MRSA and are effective against numerous Gram-positive bacteria.

Antibiograms and minimum inhibitory concentration (MIC) testing are critical tools in combating antibiotic resistance in S. aureus. These tests allow healthcare professionals to determine the susceptibility or resistance of bacterial strains to specific antibiotics. Regularly conducting antibiograms helps healthcare facilities monitor resistance patterns and make informed decisions about appropriate antibiotic treatment. Determining MIC of oxacillin is essential in identifying MRSA strains. A higher MIC of oxacillin compared to methicillin-susceptible strains indicates the presence of MRSA. By utilizing antibiograms and MIC testing, healthcare providers can accurately diagnose MRSA infections and tailor treatment accordingly. This is crucial for effective treatment, preventing the spread of MRSA, and improving patient outcomes.

In clinical practice, the administration of certain antibiotics is usually determined by considering the type and severity of the infection, as well as the susceptibility of the bacteria [72]. In cases of severe bacterial infections, such as sepsis, initial treatment may involve the use of broad-spectrum antibiotics like cephalosporins or fluoroquinolones [73]. This is done to offer immediate coverage until specific culture findings are obtained.

Although antibiotics have a crucial role, their usage is filled with difficulties mainly due to the over prescription and improper use of antibiotics, which greatly contribute to the emergence of antibiotic or antimicrobial resistance (AMR). AMR arises when bacteria are exposed to antibiotics multiple times and evolve methods by spontaneous genetic mutations or horizontal gene transfer from other bacteria to avoid their effects, making the medications less potent [74] as well as leading to the survival and multiplication of resistant bacteria. The phenomenon of resistance can disseminate worldwide, thereby rendering the treatment of illnesses that were previously susceptible to antibiotics progressively more challenging.

AMR in S. aureus, including strains like MRSA and Vancomycin-resistant S. aureus (VRSA), mostly occurs due to the acquisition of resistance genes found on mobile genetic components like plasmids or through changes in the chromosomes (for example, the mecA gene found in MRSA) that modify the locations targeted by antibiotics [75]. The mecA gene produces penicillin-binding protein 2a (PBP2a), which decreases the effectiveness of beta-lactam antibiotics such as methicillin and penicillin by enabling the bacteria to persist in synthesizing their cell walls [76]. However, VRSA develops resistance by acquiring the vanA gene cluster, which is usually obtained through the transfer of genes from vancomycin-resistant Enterococcus via horizontal gene transfer. The vanA gene modifies the peptidoglycan structure of the bacterial cell wall, hence diminishing the binding affinity and efficacy of vancomycin, which is a crucial antibiotic used as a last option [77].

In addition, strains of S. aureus have the ability to deactivate beta-lactam antibiotics by producing beta-lactamases through enzymatic processes [78]. Increased production of efflux pumps, which are specialized transporter proteins used by bacteria to expel antibiotics from their cellular interior to the external environment, reduces the intracellular concentration of the drug and contributes to antibiotic resistance. In addition, S. aureus biofilms, which are complex bacterial communities enclosed by an extracellular matrix, serve as a protective barrier against antibiotics. This barrier prevents the effective penetration of drugs and provides a safe-haven for persister cells that have an increased tolerance to antibiotics.

The complex mechanisms involved highlight the challenges posed by antibiotic-resistant S. aureus infections, where in certain instances, combination therapy with multiple antibiotics may be necessary to effectively treat infections that are resistant to standard treatment. This also underscores the urgent requirement for inventive strategies to address AMR in clinical environments as well as requiring ongoing research into creative treatment techniques and strong surveillance measures to effectively address these changing threats [79]. With the aim of tackling the emergence of AMR, antimicrobial stewardship programs promote the prudent utilization of antibiotics. This involves ensuring that prescriptions are appropriate, with the correct dosage and duration of treatment, to minimize the likelihood of resistance. In addition, healthcare practitioners stress the significance of responsible antibiotic utilization, which encompasses the practice of prescription antibiotics only when they are medically required, ensuring that patients adhere to the entire prescribed antibiotic regimen and refraining from using antibiotics for viral illnesses. Furthermore, continuous investigation into novel medicines and alternative therapies is important to tackle the escalating menace of AMR.

To summarize, antibiotics are typically used as a final option for treating serious bacterial illnesses, with different varieties designed to specifically target pathogen. It is imperative to implement stringent infection control measures, adopt proper Ab prescribing practices, and advance the discovery of novel antibiotics and alternative treatment techniques to effectively combat the proliferation of AMR S. aureus, which poses a significant risk to public health. All these also highlight the importance of proper diagnostic strategies that are readily available at the healthcare settings for proper prescriptions, which is discussed in the following section.

6. Diagnosis and detection of S. aureus infections

The diagnosis of S. aureus infections is a critical aspect of clinical microbiology [80]; although there may be instances of mild cases, infections caused by S. aureus have the potential to become serious and even result in death if not accurately diagnosed and appropriately treated. Prompt medical intervention is essential to avert any negative consequences. The diagnosis of infection encompasses various laboratory techniques including culture-based methods [81], molecular technique such as PCR [82], and serological assays [83]. Each method has its own set of advantages and challenges, and recent advances have enhanced their accuracy and efficiency. This section provides a detailed overview of these diagnostic approaches, emphasizing their significance and application in the detection of S. aureus infections.

6.1 Culture-based techniques: gold standards

The diagnosis of S. aureus infections still relies on culture-based approaches, which include carefully isolating and identifying the bacteria from clinical samples [84]. This is done by allowing the organism to grow on selected media under controlled conditions. The method begins by collecting various clinical samples, such as blood, pus, or nasal swabs, which are then placed onto specialized media, such as blood agar or mannitol salt agar. After being inoculated, the plates are carefully placed in an incubator and kept at temperatures usually between 35 and 37°C for a duration of 18–24 hours.

The identification of S. aureus colonies relies mostly on their unique morphological traits, the observed hemolysis patterns on blood agar, and the distinctive color changes displayed by colonies on the medium. Confirming the identity of S. aureus requires the coagulase and catalase tests: coagulase test is essential for distinguishing between coagulase-positive S. aureus [85] and coagulase-negative staphylococci [86]. This distinction is significant for making clinical decisions since coagulase-positive strains are associated with virulence factors. Catalase testing is useful for differentiating between staphylococci, which produce catalase, and streptococci, which do not produce catalase. This helps in accurately identifying the species.

6.1.1 Advantages and challenges

Although culture-based techniques are widely regarded as the most reliable method for identifying and assessing the susceptibility of bacteria, they present notable difficulties. These tests are very time-consuming, usually taking up to 48 hours to receive definitive results, which can cause a delay in starting targeted medication. Moreover, these approaches require laboratory professionals who are highly skilled in microbiological methods to accurately carry out and analyze the tests. Ultimately, culture-based methods continue to be essential in clinical microbiology due to their reliability and ability to provide a thorough profile of bacteria [87].

6.2 Serological assays

Serological assays play a crucial role in diagnosing systemic S. aureus infections and establishing past exposure by detecting particular antibodies or antigens linked to the pathogen [83]. Enzyme immunoassays (EIAs) and latex agglutination tests are commonly used among these assays. EIAs detect the presence of antigens, such as protein A or clumping factor, by using antibodies tagged with enzymes. These antibodies can identify antigen-antibody complexes, providing a clear indication of the presence of S. aureus. The process entails applying antibodies onto a surface, introducing the sample, and utilizing enzyme-labeled antibodies to attach to any existing antigen-antibody complexes [88]. This leads to a detectable signal, usually in the form of a color alteration. In contrast, latex agglutination assays identify surface proteins such as coagulase and protein A by utilizing latex particles that are covered with antibodies. These antibodies clump together, or agglutinate, when they come into contact with certain antigens, thus indicating the presence of S. aureus visibly [89].

6.2.1 Advantages and challenges

These assays are highly regarded for their noninvasive characteristics, as they use serum or plasma samples and provide rapid responses within minutes to hours. Although they have benefits, problems like the possibility of reacting with comparable antigens from other organisms and the restricted ability to measure quantities, mostly in a qualitative or semiquantitative manner, emphasize the importance of cautious interpretation in clinical contexts. However, serological assays continue to be crucial for quick and noninvasive detection of S. aureus, aiding in prompt clinical decision-making.

6.3 Molecular techniques

Molecular techniques, particularly PCR, have revolutionized the diagnosis of S. aureus infections by enabling rapid and precise identification of the bacterium’s genetic material [90].

6.3.1 Conventional PCR

It targets specific genes essential for S. aureus identification, such as nuc (encoding thermonuclease) and mecA (associated with methicillin resistance) [91, 92]. The process involves isolating DNA from clinical samples, amplifying target sequences using specific primers that flank the target gene regions, and visualizing the resulting amplified products through gel electrophoresis. This method allows for the detection and confirmation of S. aureus presence based on the presence or absence of specific DNA bands of expected sizes.

6.3.2 Real-time PCR (qPCR) for quantitative analysis

It enhances this process by enabling quantification of DNA in real-time during amplification [93]. It employs fluorescent dyes or probes that bind specifically to the amplified DNA, allowing for continuous monitoring of DNA accumulation as the reaction progresses. Real-time PCR [94] offers several advantages over conventional PCR, including faster turnaround times, as results can be obtained within hours rather than days, and the ability to provide quantitative data, which is crucial for determining the amount of target DNA present.

With multiplex PCR techniques, it becomes possible to detect multiple pathogens and resistance genes [90] all at once in a single assay.

6.3.3 Loop-mediated isothermal amplification (LAMP) for rapid diagnostics

Loop-mediated isothermal amplification (LAMP) is another molecular technique gaining prominence for its simplicity and rapidity [95]. LAMP amplifies DNA under isothermal conditions, meaning it operates at a constant temperature, typically between 60 and 65°C, using a set of four to six primers that recognize multiple regions within the target gene. This method does not require thermal cycling, which simplifies the process and reduces the equipment needed, making it suitable for resource-limited settings or point-of-care diagnostics [96].

6.3.4 Advantages and challenges

Molecular techniques play a crucial role in the rapid and accurate diagnosis of S. aureus infections, guiding appropriate treatment decisions and infection control measures. Continuous advancements in technology and methodologies promise to further enhance the sensitivity, specificity, and accessibility of these diagnostic tools, ultimately improving patient outcomes and public health responses to S. aureus infections and antibiotic resistance. Despite their advantages, molecular techniques also pose challenges. The initial setup costs for equipment such as thermal cyclers and real-time PCR machines, as well as the ongoing expense of reagents and consumables, can be prohibitive for some laboratories. Furthermore, the complexity of interpreting results and the requirement for trained personnel proficient in molecular biology techniques necessitate ongoing investment in training and quality assurance.

6.4 Advances and challenges in lab diagnosis of S. aureus infections

The diagnosis of S. aureus infections employs a range of laboratory techniques, each with distinct advantages and challenges. Culture-based methods remain the gold standard, while molecular techniques offer rapid and precise detection. Serological assays provide valuable insights into systemic infections. Advances in diagnostic technologies continue to enhance the accuracy and efficiency of S. aureus detection, but challenges such as antibiotic resistance and cost remain significant. Understanding and optimizing these diagnostic approaches are crucial for effective clinical management of S. aureus infections.

Recent developments using automated systems have significantly enhanced efficiency and speed revolutionizing both culture-based and molecular methods, significantly minimizing errors and delivering swift results [97]. Performing diagnostic tests at the patient’s bedside provides rapid results [98]. Nevertheless, the absence of standardized protocols for certain assays presents a significant challenge, as it results in variability in outcomes and hampers the ability to interpret and compare data across different laboratories. Addressing these challenges is essential to ensure precise and prompt diagnostics for every patient.

7. Future perspectives and research directions

Successful treatment and preventative strategies depend on understanding the virulence, epidemiology, and pathophysiology of S. aureus infections. The survival and pathogenicity of S. aureus are significantly influenced by the control of its virulence components, such as the two-component system and cytoplasmic regulators. Targeted therapy development can be facilitated by an understanding of regulatory processes. Technological developments in diagnostics and detection, such molecular approaches, have the potential to improve patient outcomes by facilitating accurate and timely administration of antibiotics. Furthermore, the growing resistance to antibiotics emphasizes the need for substitute therapies including monoclonal antibodies, antivirulence medicines, and creative antimicrobial peptides. S. aureus infections necessitate a customized assessment and course of care, specifically for serious illnesses like bacteremia and endocarditis; additional research is required to increase diagnostic precision and create more potent treatment plans.

7.1 Conventional research for vaccines development

Conventionally research in tackling infections has been focused on the study and development of vaccines and antimicrobial medicines. Researchers work to find safe and efficient ways to fight different infections through comprehensive laboratory testing, clinical trials, and focused studies. The development of a potent vaccination against S. aureus is a viable strategy. The primary objective is to find antigens that can elicit effective immune responses and develop vaccine formulations that specifically target strains or virulence characteristics. Multiple vaccine candidates are presently undergoing preclinical or clinical studies.

7.2 Challenges and possibilities in preventing and controlling S. aureus infections amidst the rise of antibiotic resistance

AMR, or the emergence and spread of strains resistant to antibiotics, might compromise the efficacy of vaccinations and cause diseases that were previously eradicated. AMR diminishes the effectiveness of antibiotics in treating illnesses, potentially leading to extended illness, elevated healthcare expenses, and elevated death rates. AMR may potentially reverse the progress gained in the fight against disease eradication when it comes to vaccinations by making some bacterial diseases more challenging to treat and manage. This has necessitated the need for alternative antimicrobial drugs to provide alternative treatment choices. Research is being conducted to investigate innovative antimicrobial agents, including antimicrobial peptides, bacteriophages, and immune-based therapeutics. These techniques focus on distinct mechanisms of action, which could potentially make them effective against strains of drugs that have developed resistance. Anti-virulence techniques focus on impeding the development or function of virulence factors, which play a critical role in the pathogenicity of S. aureus, instead of directly killing the bacteria. By diminishing the bacteria’s capacity to induce illness, these approaches can potentially mitigate the intensity of infections and augment the efficacy of current medications.

Enhancements in surveillance systems and diagnostic tests play a crucial role in identifying and monitoring the appearance and transmission of multidrug-resistant S. aureus strains and for devising specific treatment approaches. Gaining insight into the mechanisms that contribute to the transmission and dissemination of S. aureus in community settings is crucial for successful prevention and control. Antimicrobial stewardship involves ongoing initiatives to encourage the responsible use of antibiotics, which includes prescribing them appropriately and using de-escalation procedures. Implementing additional measures for infection control, such as rigorous cleaning standards, increased compliance with hand hygiene practices, and the application of antimicrobial coatings on surfaces, can effectively decrease the spread and acquisition of S. aureus infections. The advancement and assessment of novel treatment methods, such as the use of multiple therapies, approaches that target biofilms, present promising ways to combat antibiotic resistance in S. aureus.

7.3 Current developments in the study and treatment of S. aureus infections

The influence of host factors, such as weakened immune systems, coexisting medical conditions, and genetic predispositions, on the vulnerability to and consequences of S. aureus infections is currently being actively studied. Gaining insight into the interactions between hosts and pathogens can provide valuable guidance for tailoring individualized treatment strategies and prevention measures. Advancements are being made in the development of more efficient and precise procedures for assessing the susceptibility of microorganisms to antimicrobial agents. These methods will assist in choosing suitable medicines and provide guidance for personalized treatment approaches for S. aureus infections.

7.4 Developments in diagnostics of S. aureus infections

Swift diagnostic methods capable of detecting antibiotic resistance genes and forecasting antimicrobial susceptibility will facilitate prompt, focused, effective treatment, and management, ultimately contributing to the prevention and control of these infections. Traditional methods, such as culture and identification from clinical samples, can be time-consuming and require skilled laboratory personnel. Rapid diagnostic methods like PCR assays and Nucleic acid amplification techniques (NAATs) have been developed to detect S. aureus DNA within hours, enabling quicker diagnosis and appropriate therapy. Point-of-care tests are being developed to provide rapid results, reducing transmission risk in community settings.

8. Conclusions

As concluding remarks, we would like to summarize those future directions in combating S. aureus infections, particularly amidst escalating antibiotic resistance, involving multifaceted strategies aimed at enhancing treatment and control measures. Primary efforts include advancing vaccine development targeting specific antigens to stimulate robust immune responses and potentially reduce transmission rates. Simultaneously, research into alternative antimicrobial agents like antimicrobial peptides, bacteriophages, and immune-based therapies seeks to broaden therapeutic options against resistant strains. Antivirulence strategies, which focus on neutralizing virulence factors rather than solely eradicating bacteria, show promise in mitigating infection severity and optimizing current treatment efficacy. Addressing challenges involves bolstering surveillance systems to monitor multidrug-resistant strains, advancing rapid diagnostic technologies for predicting antibiotic resistance, and promoting antimicrobial stewardship to foster responsible antibiotic use and combat resistance emergence. Implementation of stringent infection control measures and continued exploration of innovative treatment modalities are essential for effectively managing the evolving landscape of S. aureus infections and combating antibiotic resistance.

Acknowledgments

The authors would like to acknowledge the financial support from Prime Minister’s Research Fellowship (PMRF, ID: 2001303—granted to SA), Scheme for Transformational and Advanced Research in Sciences (STARS), Ministry of Education, Government of India (MoE-STARS/STARS-1/784—granted to SD).

Conflict of interest

The authors declare no conflict of interest.

Appendices and nomenclature

• Antibiotic resistance

• Community-acquired infections

• Culture-based methods

• Cytoplasmic regulators

• Diagnosis

• Endocarditis

• Epidemiology

• Molecular methods

• Pathogenesis

• Pulmonary infections

• Regulatory proteins

• Staphylococcus aureus

• Septicemia

• Serological assay

• Two-component systems

• Virulence factors

MRSA	methicillin resistant S. aureus
HAIs	Healthcare-Associated Infections
PCR	polymerase chain reaction
TCS	two-component system
Agr	accessory gene regulator
QS	quorum sensing
AIP	autoinducing peptide
PSM	phenol soluble modulin
hld	delta-hemolysin gene
MSSA	methicillin-susceptible S. aureus
SSIs	surgical site infections
HIV/AIDS	Human Immunodeficiency Virus/Acquired Immunodeficiency Syndrome
ICUs	intensive care units
HIV	human immunodeficiency virus
COPD	chronic obstructive pulmonary disease
VRSA	vancomycin-resistant S. aureus
AMR	antimicrobial resistance
PBP	penicillin-binding protein
SSCmec	Staphylococcal Cassette Chromosome mec
MIC	minimum inhibitory concentration
EIA	enzyme immunoassays
LAMP	loop-mediated isothermal amplification
NAATs	nucleic acid amplification techniques