**1. Introduction**

The first isolation of Staphylococci was carried out by Alexander Ogston during the investigation of the septicemia and wound infection bacteria in 1880, the microscopical examination of 88 pus specimens revealed the presence of Grampositive cocci (*S. aureus*) [1]. In clinical observations, the most important species of Staphylococcus genus are *Staphylococcus aureus* and *Staphylococcus epidermids*, further falling into categories based on their coagulase activity. *S. aureus* is coagulase positive, expressing several virulence factors supporting host immune response evasion. *S. epidermidis* being coagulase negative, usually less virulent, able to avoid the host immune system by forming and resulting in its hiding in a biofilm [2]. *Staphylococcus aureus* (SA) represents one of the most important microorganisms that are part of the normal micro flora in humans, with ability to cause very serious infections in certain conditions. Approximately 20–30% of the general human population is persistently colonized with SA. Primary and natural reservoir of *S. aureus* is the asymptomatic carriage by humans, using the anterior nasal mucosa as the main ecological niche. The risk of subsequent infection increases as the colonization provides a reservoir open to bacteria introduction as host defences are breached [3]. Adding to humans and domestic animals, livestock and fomites can also serve as joint reservoirs, providing this bacterial pathogen with dramatic relevance in human and veterinary medicine. *Staphylococcus aureus* can cause a wide variety of infections in range from common, mild skin and soft tissue infections to hematogenous infections with multi organ injuries. *Staphylococcus aureus* is infamous for its ability to become resistant to antibiotics, resulting in issues with treatment of these infections due to the resistance development, especially with methicillin-resistant SA [4]. The virulence of *S. aureus* is multifactorial due to the combined actions of a variety of virulence factors that facilitate tissue adhesion, immune evasion, and host cell injury [5]. These virulence factors involve both structural, such as surface adhesins which provide adherence to host tissues, and secreted factors, such as enzymes, that convert host tissue into nutrients. Anyway, a lot more significant is the secretion of a variety of pyrogenic toxins also known as superantigens; the Panton–Valentine leukocidin (PVL) and toxic shock syndrome toxin-1 (TSST-1) as most remarkable [6].

### **1.1 Methicillin-resistant** *Staphylococcus aureus*

Methicillin-Resistant *Staphylococcus aureus* (MRSA) should be taken into accounted for great concern. It is the cause of bacterium infections in various parts of body. As it develops resistance to usually prescribed antibiotics, its treatments becomes more difficult than with most strains of *Staphylococcus aureus*. MRSA is sometimes called a super bug. Methicillin-resistant *Staphylococcus aureus* (MRSA), or multidrug-resistant *S. aureus*, first described in the United Kingdom in the early 1960s, are *S. aureus* strains which developed resistance through natural selection process to all available penicillins and other β-lactam antimicrobial drugs. Methicillin resistant *Staphylococcus aureus* (MRSA) being one of the most important hospital pathogens, becomes responsible for community infection in patients without previous health-care contact at the end of the last century. Worldwide, it is mainly responsible for a broad spectrum of nosocomial and community associated infections and cause of endemic and epidemic infections in many parts of the world. Methicillin resistance in S.aureus developed through the acquisition of the mecA gene located on mobile genomic island designated staphylococcal chromosome cassette mec (SCCmec) by methicillin-susceptible S.aureus [7]. The mecA gene is primary cause for the synthesis of a novel penicillin-binding protein known as penicillin-binding protein 2a, that decreased binding affinity for penicillin and cephalosporins. It follows that MRSA strains are resistant to all ß-lactam antibiotics. In the beginning, MRSA was susceptible to nonbeta lactam antibiotics. Later, namely, from the late 1979s to this day, new strains of MRSA resistant to multi-non- ß-lactam agents including aminoglycosides, with only vancomycin left as an antibiotic of last resort for treating MRSA infections, appeared. These strains, also described as epidemic MRSA (EMRSA or HA-MRSA), have had the capacity to spread extensively causing serious infections worldwide and mostly among in-hospital patients [8].

*Distribution and Molecular Detection of Methicilin-Resistant* Staphylococcus aureus *DOI: http://dx.doi.org/10.5772/intechopen.98655*

#### **1.2 What is community-associated MRSA?**

During 1990s, in Western Australia, a new MRSA type appeared and it was causing infections in the community of younger and healthy people without previously reported history of hospital admission or medical treatment [9]. These types of MRSA strains were described as community-acquired, communityoriginated, community-associated, or community-onset MRSA (CA-MRSA). HA-MRSA and CA-MRSA belong to different genetic lineages. While CA-MRSA strains are usually sensitive to antibiotics other than beta-lactams and contain staphylococcal cassette chromosome SCCmec type IV, V or VII, HAMRSA are generally multidrug-resistant and harbour larger SCCmec type I, II or III [10]. MRSA pathogenicity is related to extensive arsenal of virulence factors and toxins. The most common and probably important is the Panton-Valentine leukocidin (PVL) toxin being lethal to neutrophils and associated with skin and soft tissue infections as well as severe necrotizing pneumonia. Huge number of CA-MRSA clones have developed on every continent [11]. Notably, these CA-MRSA strains, initially, were associated with community-onset (CO) infections, have been entering hospitals and may be replacing the conventional HA-MRSA strains with significant clinical and public health implications [12]. However, CA-MRSA penetration is still mostly undefined due to lack of thorough exploration of in large number of hospitals as well as knowledge of the risk factors involved in nosocomial transmission of CA-MRSA compared with HA-MRSA [13]. The prevalence of in vitro resistance to non-β-lactam antimicrobial agents could be increasing among MRSA strains related to community transmission. MRSA typing is an essential component of an overall follow up system of describing epidemiological trends and control strategies for infections. Contemporary challenges for MRSA typing are focused on choosing the most appropriate technique in terms of efficiency, reliability, ease of performance and cost included. The phenotypic methods in general are prone easier performance, interpretation, cost efficiency and wide availability, and less discrimination. The genotypic methods are rather expensive and technically demanding, however more discriminatory. Latest technologies that involve sequencing of various genes are emerging as highly applicable with wide throughput typing systems. Still there is no consensus regarding the single best method for typing of MRSA strains [14]. Pulsed-field gel electrophoresis (PFGE) has become the 'gold standard' for genotyping method of MRSA for over a decade, and it has been used widely for local outbreak investigation, long-term surveillance of MRSA infections at regional and national levels and for international comparisons [7]. Recently, in Europe, harmonization efforts to standardize the PFGE typing protocol of MRSA as well as to enable multicentric comparison of PFGE data have been made. The macro restriction analysis of chromosomal DNA using PFGE is a reference method for *Staphylococcus aureus* typing and can be combined with other methods [15].

#### **1.3 Detection and diagnosis of MRSA strains**

Identifying the causative organism can be challenging in treatment *Staphylococcus aureus* infection, especially for resistant strains. Traditional culture and susceptibility testing for MRSA lasts between 48 and 72 h, taking a 16- to 24-h incubation and 16 to 24 h more in completing the susceptibility tests. Latest progress in molecular and nonmolecular testing methods greatly reduced the time needed to detect MRSA [16]. These rapid and sensitive screening assays could contribute to infection control and reducing overall costs. With a rapid test,

Bauer et al. [17] observed bacteremia patients diagnosed with MRSA had a shorter length of stay and lower hospital costs, and for patients with MSSA, the switch from empiric to targeted therapy was 1.6 days shorter. Use of rapid molecular diagnostic tests rather than conventional methods is also related to a significantly lower mortality risk for patients with bloodstream infections (odds ratio (OR) [95% CI] 0.66 [0.54–0.80]), including those caused by Gram-positive organisms (OR [95% CI] 0.73 [0.55–0.97]). Combining rapid molecular testing with an antibiotic stewardship program will be able to lower the mortality risk [18]. Individual hospitals in decision making about the tests used should consider the specificity, sensitivity, price, turnaround time, and expertise, necessary for each test [16, 19]. Modification to the traditional culture method is the use of chromogenic agar, producing a colour reaction in the bacterial cultures. These media also contain antibiotics where only resistant bacteria is able to grow. According to this, MRSA can be detected in 20 to 26 h [16]. In clinical practice, the use of chromogenic media has been seen to shorten the time to aimed MRSA treatment by 12 h [20]. Another innovation in MRSA detection is the development of real-time polymerase chain reaction (PCR) tests with the ability to detect genes specific to *S. aureus*. In making difference in MRSA strains from MSSA or methicillin resistant coagulase-negative staphylococci, PCR methods are aimed at a part of DNA where the MRSA-specific SCCmec gene meets the *S. aureus* orfX gene. The PCR tests are usually performed directly on samples taken from blood or a nasal or wound swab, and results can be available within 1 to 3 h [16]. In clinical practice, generally, the turnaround times from taking samples to complete results are generally longer due to the length of time needed to transport samples, conduct the test, and send the results. As a rule, the overall time is usually much shorter with PCR-based assays than with chromogenic media culture [21]. Moreover, PCR tests showed pooled estimates for sensitivity and specificity of 92.5 and 97.0%, respectively, in the meta-analysis described earlier. In addition, the sensitivity of PCR has been notably higher than the one on chromogenic media, and the specificity was significantly higher than the one on traditional culture [19]. In relation to MRSA detection by chromogenic agar, PCR shortened the overall time of patient isolation as well as number of days patients were inadequately isolated during their hospital stay [21].
