Bacterial strain typing distinguishes epidemiologically related or clonal isolates from unrelated isolates. Epidemiologically related isolates are viewed as descendants from a common precursor cell; thus, their genomic “fingerprints” will be indistinguishable but recognizably different from unrelated or random isolates from the same species.[
34] In addition to tracking outbreaks, genotyping is used to distinguish between contaminating and infecting isolates and between separate episodes of infection and relapse of disease.[
35]
Numerous techniques are available to differentiate
S. aureus, and specifically MRSA, isolates. Historically, isolates were distinguished by phenotypic methods, including antibiotic susceptibility testing and bacteriophage typing. Both methods have limitations, as genetically unrelated isolates commonly have the same antibiogram, and many
S. aureus isolates are nontypable by phage typing.[
34]
With the advent of molecular biology, strain typing is focused on DNA-based methods. Initial techniques compared restriction endonuclease patterns of chromosomal or plasmidDNA. The second-generation of genotyping methods included s southern blot hybridization using gene-specific probes, ribotyping, polymerase chain reaction (PCR)–based approaches, and pulsed-field gel electrophoresis (PFGE).[
36] These methods require subjective interpretation and comparison of patterns and fingerprint images. However, they still remain difficult to standardize between laboratories, and the image-based information is difficult to organize for rapid search and retrieval by computer. In addition, image-based methods do not provide biological criteria to evaluate the relatedness between different strains.[
37] DNA sequence analysis is an objective genotyping method; the genetic code (A-T-C-G) is highly portable and easily stored and analyzed in a relational database. Recent advances in DNA-sequencing technology, including rapid, affordable, high-throughput systems, have made it possible for sequencing to be considered as a viable typing method. Two different strategies have been used to provide genotyping data: multilocus sequence typing (MLST), which compares sequence variation in numerous housekeeping gene targets; and single-locus sequence typing, which compares sequence variation of a single target among strains to be typed.
Two
S. aureus genes conserved within the species, protein A (
spa) and coagulase (
coa), have variable short-sequence repeat (SSR) regions constructed from closely related 24- and 81-bp tandem repeat units, respectively. In both genes, the in-frame SSR units are degenerative, variable in number and variable in the order in which repeat units are organized. The genetic alterations in SSR regions include both point mutations and intragenic recombination that arise by slipped-strand mispairing during chromosomal replication and that result in a high degree of polymorphism.[
38,
39] DNA sequence analysis of the protein A repeat region provides an unambiguous, portable dataset that simplifies information-sharing between laboratories and facilitates creating a large-scale database for studying global and local epidemiology.[
40]
Molecular epidemiology studies using different techniques indicate that the massive geographic spread of MRSA results from the dissemination of relatively few epidemic clones.[
37,
41,
42] However, the “epidemic potential” depends on a multifactorial spectrum of bacterial genetic determinants, and the role the environment (selective usage of antibiotics, hygiene measures in the hospital) plays in their expression is unclear.
In 1999, MRSA accounted for >50% of
S. aureus isolates from patients in ICUs in the NNIS system; in 2003, 59.5% of
S. aureus isolates in NNIS ICUs were MRSA.[
43] Prevalence of MRSA in hospitalized patients in south India has been shown to be 31.1%.[
44] In Europe, the highest prevalence of MRSA in the hospitals was seen in Portugal (54%), Italy (43%-58%) and Netherlands (2%).[
45]