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Wikipedia Edit: Monday November 17th Assignment
Link: Staphylococcus_aureus

"When observing the evolvement of S. aureus and its ability to adapt to each modified antibiotic, in general, there are two basic methods known as “band-based” or “sequence-based” . Keeping these two methods in mind, other methods like multilocus sequence typing (MLST), pulsed-field gel electrophoresis (PFGE), bacteriophage typing, spa locus typing, and SCCmec typing are often conducted more than others . With these methods,not only are we able to determine where strains of MRSA originated from, but where they currently reside . 	With MLST, this technique of typing utilizes fragments of several housekeeping genes known as aroE, glpF, gmk, pta, tip, and yqiL. These sequences are then assigned a number which give to a strong of several numbers that serve as the allelic profile. Although this is a common method, a limitation about this method is the maintenance of the micro-array which detects newly allelic profiles, making it a costly and time consuming experiment.

With PFGE, a method which is still very much utilized dating back to its first success in 1980s remains capable of helping differentiate Methicillin-resistant S. aureus isolates. To accomplish this, the technique uses multiple gel electrophoresis, along with a voltage gradient to display clear resolutions of molecules. The S. aureus fragments then transition down the gel producing specific band patters that are later compare with other isolates in hopes of identifying related strains. Limitations of the method include, practical difficulties with uniform band patterns and PFGE sensitivity as a whole.

Spa locus typing is also considered a popular technique that uses a single locus zone in a polymorphic region of S. aureus to distinguish any form of mutations. Although this technique is often inexpensive and less time consuming, the chance of losing discriminatory power makes it hard to differentiate between MLST CC’s exemplifies a crucial limitation."

FINAL DRAFT PAPER
Abstract To analyze the emergence of Methicillin-resistant Staphylococcus aureus it is important to first identify its initial presence. During World War II, this gram-positive bacteria S. aureus pioneered its way through a process of selection, causing multiple casualties from mold of corn steep liquid. Soon after, as a defense, this infection was treated with an antibiotic called “penicillinase” which had made its appearance in 1944 where it was later replaced with the modified agent known as methicillin in order to combat the penicillin-resistant S. aureus in 1959 (Kim 2009). Currently, approximately 80% of all S. aureus strain remain resistant while a little more than half of the strain also remain resistant to the methicillin. Methicillin-resistant Staphylococcus aureus (MRSA) has continued to stand as an infamous infection all over the world, generating an ongoing public health concern. Park (2012) states how the lethal infection led to approximately 278,000 hospitalizations and over 18,000 deaths in 2005, according to just one study. Symptoms of this infection typically consist of small bumps that have similar characteristics of pimples, which make it hard to detect actual manifestations of the bacteria. Having high resistance to most antibiotics, if transmitted, this bacterial strain is often accountable for multiple diseases like pneumonia, skin infections, and severe bacteraemia (Basset 2010). With high accumulations like this, it is vital that we examine exactly how Staphylococcus aureus has evolved in such a way to become so non receptive to antibiotics. Gradual Evolvement Once penicillin became resistant to the strain, methicillin soon followed right behind it, but why? With the continual use of methicillin, the Methicillin-sensitive S. aureus (MSSA) strains became highly resistance to the antibiotic. This was caused by a mecA gene that holds a genetically modified penicillin-binding protein (PBP) which is carried on a mobile genetic element known as staphylococcal chromosome cassette mec, (SCCmec). It consist of genetically structured elements that are resistant particularly to non-β-lactam antibiotics (Hiramatsu 2001). Unlike MSSA, where the β-lactam affix to PBPs on the cell wall, MRSA is unable to bind, leaving the peptidoglycan layer arranged, admitting the growth of MRSA (Deurenberg 2008). Similar to how the MSSA strain evolved, the SCCmec gene too became resistant to antibiotic vancomycin after high exposure of the treatment (Kim 2009). From this, we can infer two general reasonings as to why S. aureus became resistant to the above treatments. One being, the clear overuse of an antibiotic where it successfully destroys any harmless strains of bacteria, but also allows the resistant bacteria to take its place and multiply rapidly. Or, simply the possibility of the bacteria mutating over a period of time causing a resistance to the given antibiotic. When considering adaptation in evolution, what essential selective traits contributed to natural selection process? In order to conclude this, we must consider the genomic background of an organism. Typing Methods for Components When observing the evolvement of S. aureus and its ability to adapt to each modified antibiotic, in general, there are two basic methods known as “band-based” or “sequence-based” (Deurenberg 2008). However, multilocus sequence typing (MLST), pulsed-field gel electrophoresis (PFGE), bacteriophage typing, spa locus typing, and SCCmec typing are often conducted (Aires de Sousa and de Lencastre 2004). With these methods,not only are we able to determine where strains of MRSA originated from, but where they currently reside (Kim 2009). Multilocus sequence typing This technique of typing utilizes fragments of several housekeeping genes known as aroE, glpF, gmk, pta, tip, and yqiL. These sequences are then assigned a number which give to a strong of several numbers that serve as the allelic profile. One disadvantage to note about this method is the maintenance of the micro-array which detects newly allelic profiles, making it a costly and time consuming experiment (Deurenberg 2008). Pulsed-field gel electrophoresis PFGE utilizes multiple gel electrophoresis, along with a voltage gradient to display clear resolutions of molecules. The S. aureus fragments transition down the gel producing specific band patters that are later compare with other isolates in hopes of identifying related strains. Some disadvantages of the method include, practical difficulties with uniform band patterns and PFGE sensitivity as a whole. Spa locus typing With spa locus typing, we use a single locus zone in a polymorphic region of S. aureus to distinguish any form of mutations. Although this technique is often inexpensive and less time consuming, there chance of losing discriminatory power making it hard to differentiate between MLST CC’s. Brief Typing Methods of Research Enright et al. (2002) utilized SCCmec, and MLST typing to successfully identify five divergent lineages between MSSA and MRSA. Gomes et. al (2006) proposed a study where they were able characterize the genetic backgrounds of various isolates of a complex to finally indicate the step by step evolutionary ancestry of MRSA. Crisotomo et al. (2001) employed a range of tests from PFGE profiling to spa typing where investigated the early nature of MRSA and MSSA blood isolates to conclude where the first mecA gene was observed. With these various methods of research, scientist are able to link possible lineages together in order to pinpoint similar molecular traits that will potentially provide strengthen evidence for distinguished types of resistant patterns. '''Discussion ''' Methicillin-resistant Staphylococcus aureus displays evidence of adaptations caused by evolvement through adaptions. Seeing how response strategies of S. aureus often included the modification of a stronger antibiotic, this can serve as a prime example of evolutionary arms race. From the gradual resistance shown with antibiotics penicillin, methicillin, and now even vancomycin, it is clear that S. aureus has selective traits that allow the strain to change in a given environment while sustaining the ability to survive and reproduce. Since the bacteria is capable of modifying new genes from possible point mutations and take in drug-resistant DNA from adjacent bacteria, it can assimilate it into their own DNA. These unlinked point mutations that are conducive to inhibiting antibiotic resistance, allow the mutated bacteria to then pass on this trait to their offspring, which leads to the evolution of a fully resistant colony. Thus, a supportive inference would be that MRSA has developed through the process of natural selection that constituted the adaptations of multiple point mutations which formed a resistance to the antibiotic via horizontal transfer of genes. With the use of horizontal transfer, this lets us know that the bacteria does not always rely on random mutation for production of a new gene, thus increasing the rate of antibiotic resistance. With genes being carried on plasmids, mobile genetic elements and transposon (jumping genes), we know that they act as vectors to transfer these selected genes to other members of the same bacterial species. These lateral transfers of DNA arise from the mechanism of transformation, transduction, and conjugation which most likely plays a role in aiding in the transfer of pathogenetic islands from other bacteria which then gives rise to new virulence factors. Dating back to 1929 when Alexander Fleming’s recognized that bacteria would not grow near colonies of Pencillium, in the decades that followed this discovery, antibiotic resistance has only increased. Scientist and researchers continue to use biology and evolution of these antibiotic resistant organisms like S. aureus to hopefully find a way to slow the mutation rate or decrease stress these colonized populations. With different methods of typing isolates and biotechnology researchers like Enright, Gomes, and Crisotomo and their peers were able to distinguish different lineages between MRSA and MSSA. Since antimicrobial resistance is genetically based, the identification between these two strains can correlate genomic background to resistance patterns in order to target the acquisition of the SCCmec gene. That being said, we also know that the environment at which an organism lives in also plays a major role on its rate of adaption evolved in response to mutation. These changes in an organism’s environment force the organism to adapt to fit the new setting, eventually evoloving into a new species like Penillin-resistant S. aureus to Methicillin-Resistant S. aureus. With this knowledge and continual research of genetic variation of Methicillin-resistant Staphylococcus aureus, we can hopefully determine a form of control or explain the variability in virulence with the strain to decrease the virulence of this infectious disease. ' References' Basset P, Feil EJ, Zanetti G, Blanc DS. The Evolution and Dynamics of Methicillin-Resistant 		Staphylococcus aureus. ScienceDirect [Internet]. 2010 Oct 17 [cited 2014 Oct 26]. Available from: http://ac.els-cdn.com/b978012384890100025x/3-s2.0-b978012384890100025x-main.pdf?_tid=6d004798-5f27-11e4-aee5-00000aacb35d&acdnat=1414558546_889988a21c2e6c79bf16f60a8d7f858e Crisostomo, MI, Westh, H, Chung, M, Oliveira, D, de Lencastre, H. Proceedings of the National     Academy of Sciences. The evolution of methicillin resistance in Staphylococcus aureus: Similarity of genetic backgrounds in historically early methicillin-susceptible and -resistant isolates and contemporary epidemic clones. 2001;98(17):9865-9870. doi:10.1073/pnas.161272898. Deurenberg RH, Stobberingh EE. The evolution of Staphylococcus aureus. Infection, Genetics and Evolution [Internet]. 2008 Dec 8;8(6): 747-763. Available from: http://www.ncbi.nlm.nih.gov/pubmed/18718557 Enright, MC. The evolutionary history of methicillin-resistant Staphylococcus aureus (MRSA). Proceedings of the National Academy of Sciences. 2002;99(11):7687-7692. doi:10.1073/pnas.122108599. Hiramatsu K, Cui L, Kuroda M, Ito T. The emergence and evolution of methicillin-resistant Staphylococcus aureus. Trends in Microbiology [Internet]. 2001 Oct 1 [cited 2014 Oct 28];9(10): 486-493. Available from: http://www.sciencedirect.com/science/article/pii/s0966842x01021758 Kim, J. Understanding the Evolution of Methicillin-Resistant Staphylococcus aureus. Clinical Microbiology Newsletter. 2009;31(3):17-23. doi:10.1016/j.clinmicnews.2009.01.002.

Kuroda M, Ohta T, Uchiyama I, Baba T, Yuzawa H, Kobayashi I, Cui L, Oguchi A, Aoki K, Nagai Y, et al. Whole genome sequencing of meticillin-resistant Staphylococcus aureus. The Lancet [Internet]. 2001 Apr 21 [cited 2014 Oct 25];357(9264): 1225-1240. Available from: http://ac.els-cdn.com/s0140673600044032/1-s2.0-s0140673600044032-main.pdf?_tid=121efe1e-5e50-11e4-af74-00000aab0f6c&acdnat=1414466052_009a0d1771f8d449a646e5c153a5c729

Park M. How a MRSA strain came to flourish. The Chart RSS [Internet]. 2012 Feb 21 [cited 2014 Sep 8]. Available from: http://thechart.blogs.cnn.com/2012/02/21/how-a-mrsa-strain-came-to-flourish/

Sousa MAD, Conceicao T, Simas C, Lencastre HD. Comparison of Genetic Backgrounds of Methicillin-Resistant and -Susceptible Staphylococcus aureus Isolates from Portuguese Hospitals and the Community. Journal of Clinical Microbiology [Internet]. 2005 Oct 5;43(10): 5150-5157. Available from: http://www.ncbi.nlm.nih.gov/pmc/articles/pmc1248511/

OCTOBER 1ST ASSIGNMENT LINK ADDRESS: https://en.wikipedia.org/wiki/Methicillin-resistant_Staphylococcus_aureus

SUGGESTIONS: 1.)	I believe that with the additional information regarding some new research of Methicillin-resistant Staphylococcus aureus (MRSA), would provide readers with updated strategies of how we as a population are trying to treat the problematic infection. For example, discussion on the research of phytochemical therapy and it’s use/importance of found flavanoids could be insightful. (Citation): Alcaráz L, Blanco S, Puig O, Thomás F, Ferretti F. Antibacterial activity of flavonoids against methicillin-	resistant Staphylococcus aureus strains. National Center for Biotechnology Information			[Internet]. 2000 Jul 21 [cited 2014 Sep 30]. Available from: http://www.ncbi.nlm.nih.gov/			pubmed/10873434

Day AW. Activity of Plant Extracts used in Northern Nigerian Traditional Medicine Against methicillin-		Resistant Staphylococcus Aureus (MRSA). Nigerian Journal of Pharmaceutical Sciences. 2008 Mar 1 [cited 2014 Sep 30];7(1): 1-8. 2.)	I also think that additional information for other natural remedies of oils should be made. For example: Critricidal, tea tree and geranium oil. After testing with agar plates, researchers were able to conclude that a certain combination of both Critricidal and geranium oil displayed favorable effects against MRSA, serving as a possible alternate natural treatment.  (Citation): Edwards-Jones V, Buck R, Shawcross S, Dawson M, Dunn K. The effect of essential oils on methicillin-resistant Staphylococcus aureus using a dressing model. National Center for Biotechnology  Information [Internet]. 2004 Dec 30 [cited 2014 Oct 1]. Available from: http:www.ncbi.nlm.nih.gov/pubmed/15555788 3.)	A last possible suggestion would be to give more information regarding the subcategory “Restricting antibiotic use”. With the provided antibiotic classes and light touch on the possible associated risk increase of colonization of MRSA, I think further information on the dangers of this possibility could be beneficial to the reader. Perhaps research and provide supplementary information of the possible outcome of misuse or overuse of these classes of antibiotics.

Suggestion Sentence: After testing with agar plates, researchers were able to conclude that a certain combination of both Critricidal and geranium oil displayed favorable effects against MRSA, serving as a possible alternate natural treatment.

''Edwards-Jones V, Buck R, Shawcross S, Dawson M, Dunn K. The effect of essential oils on methicillin-resistant Staphylococcus aureus using a dressing model. National Center for Biotechnology 		 Information [Internet]. 2004 Dec 30 [cited 2014 Oct 1]. Available from: 					 http:www.ncbi.nlm.nih.gov/pubmed/15555788''

Research Topic: Evolution of Methicillin-Resistant Staphylococcus aureus (MRSA) Research Question: How has Methicillin-Resistant Staphylococcus aureus evolved in a way that it has become so resistant to antibiotics allowing it to become a lethal bacteria.

Annotated Bibliography:

1.) Crisostomo, MI, Westh, H, Chung, M, Oliveira, D, de Lencastre, H. Proceedings of the National     Academy of Sciences. The evolution of methicillin resistance in Staphylococcus aureus: Similarity of genetic backgrounds in historically early methicillin-susceptible and -resistant isolates and contemporary epidemic clones. 2001;98(17):9865-9870. doi:10.1073/pnas.161272898. →The authors and researchers from Universidade Nova de Losboa, Rockefeller University, and Denmark compared the genetic backgrounds and phenotypes of a group methicillin-susceptible S. aureus to isolate resembling MRSA strains. With this testing, they were able to correlate the mec gene to a specific phage group. this article can be helpful by providing information concerning the pathogenic process of the bacteria.

2.) Enright, MC. The evolutionary history of methicillin-resistant Staphylococcus aureus (MRSA). Proceedings of the National Academy of Sciences. 2002;99(11):7687-7692. doi:10.1073/pnas.122108599. →The authors, researchers in this article identified 11 major MRSA clones within five groups of related genotypes. With certain testing like Multilocus sequence typing (MLST) they were able to determine characteristics of isolated bacteria by using sequencing of genes. This article will be useful to help better understand the evolution of MRSA through cloning.

3.) Fong, IW, Drlica, K. Reemergence Of Established Pathogens In the 21st Century. New York: Kluwer Academic/Plenum Publishers; 2003. →Authors Fong and Drlica describe and explain multiple infections that have reemerged in the United States . Their analysis of MRSA’s resistance through discussion of pathogenesis will contribute to my work for as additional supporting information.

4.) JA Weigelt. MRSA. 2th ed. (Weigelt JA, eds.). New York, NY: Informa Healthcare; 2007. →John Weigelt’s book includes chapters covering the epidemiology and genetics where him and other authors discuss Methicillin-Resistant Staphylococcus aureus in depth providing various possible treatments for the bacteria. This can be incorporated into the wikipedia project because the book will provide insight in regarding the transmission and history of the resistant bacteria.

5.) Kim, J. Understanding the Evolution of Methicillin-Resistant Staphylococcus aureus. Clinical Microbiology Newsletter. 2009;31(3):17-23. doi:10.1016/j.clinmicnews.2009.01.002. →Dr. JiYeon Kim’s article not only discusses the evolution of MRSA, but basic background on the infection. This can contribute to the Wikipedia project because it provides history and knowledge on specific testing and genes that contribute to the infection that can be compiled in the project.