IntroductionGenetic exchange plays the key role of enhancing evolution amongst bacteria species. Precisely, accumulated data on nucleotide sequences from various bacterial genera have shown the impacts of recombinations on nucleotide sequences. In regards to the previously mentioned views, a detailed review of mutations and recombinations, and tools used in tracking changes within strains and countries will highlight various aspects of the processes.

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Mutations and Recombinations in Bacterial Evolution
Notably, bacterial pathogens require to adapt rapidly to survive a variety of clinical interventions and immune responses in their hosts body (Chaguza et al., 2015). As such, some of pathogens introduce genomic variations to adapt to the hosts environment, elude clinical interventions and avoid measures taken by the host’s immune system. More elaborately, Didelot and Maiden (2010) indicate that genomic variations in bacterial pathogens occur due to DNA mismatch repair, and errors by DNA polymerase in the course of DNA replication. The previously mentioned changes in the encoded nucleotide base sequences are due to random mutations. Further, Bryant and Bentley (2012) note that prokaryotic sex or recombination-a process in which genomic variations within pathogenic bacteria can arise from the lateral transfer of DNA fragments and the subsequent integration into the host-bacteria’s genome-can also cause random mutations.

Notably, mutations observed in S. pneumoniae strains are closely related to its ability to transport DNA fragments from the environment and into its cytoplasm and the subsequent recombination with its genome. Chaguza et al. (2015), indicates that transported fragments of DNA are easily incorporated in the S. pneumonia’s genome through recombination. Didelot and Maiden (2010) suggest that Pneumococcal recombination mainly occur during chronic polyclonal infection, nasopharyngeal carriage, and biofilm formation. More precisely, the nasopharynx serves as a major reservoir for pneumococcal transmission; hence, it plays a vital role in propagating recombinant bacterium within the human populace. Didelot and Maiden (2010) suggest that recombination in S. pneumonia mainly occurs in the nasopharynx since it has a large number microbe species, and because the bacteria has a relatively thin capsule during nasopharyngeal carriage. The thin capsule facilitates the microbe’s attachment to the epithelial surface and also facilitates the uptake of exogenous DNA fragments (Chaguza et al. 2015).

Effect of mutation and recombination in S. pneumonia
Notably, the random mutations is S. pneumonia, due to gene-recombination, makes the bacterial pathogen more virulent. This is because the introduction of an exogenous gene in the pathogen’s DNA: enhances its ability to evade clinical interventions-such as pneumococcal conjugate vaccines (PCVs and antibiotics (Chaguza et al., 2016); adapt to the environment in the human body; and avoid measures taken by the host’s immune system. As a consequence, the resultant pathogens cause highly resistant forms of invasive pneumococcal disease (IPD) (Chaguza et al., 2016).

Tools to Track Changes in Bacteria Strains
The polymerase chain reaction (PCR) provides a mechanism through which small DNA samples are amplified to facilitate analysis. Through this process each strand of DNA serves as a template for DNA synthesis for the development of new DNA. This is because the addition of nucleotides and DNA polymerase facilitates the synthesis of new DNA strands. To initiate the process of amplifying DNA polymerase, short pieces of nucleic acid, known as primers are added to the DNA strand and DNA polymerase mixture (Metzker and Caskey, 2009). Interestingly, the primers become complementary to the ends of the target DNA, then the polymerase synthesizes additional complementary strands. After heating the synthesizes DNA new strands of DNA are established and the process repeated. Noting that the PCR process continues exponentially (Metzker and Caskey, 2009), the amount of target DNA increases tremendously, thus facilitating its analysis.

However, Metzker and Caskey (2009) points out that the main weakness of the PCR procedure is that it only amplifies considerably small, and specific strands of DNA as influenced by the type of primer. Therefore, it cannot amplify a complete genome for analysis. In this regard, lateral gene transfer and recombination complicates the process of tracking mutations among pathogens; since, fragments of extraneous genes are difficult to trace.

    References
  • Bryant, J., Chewapreecha, C., & Bentley, S. D. (2012). Developing insights into the mechanisms of evolution of bacterial pathogens from whole-genome sequences. Future Microbiology, 7(11), 1283–1296. http://doi.org/10.2217/fmb.12.108
  • Chaguza, C., Andam, C. P., Harris, S. R., Cornick, J. E., Yang, M., Bricio-Moreno, L., … & Kadioglu, A. (2016). Recombination in Streptococcus pneumoniae Lineages Increase with Carriage Duration and Size of the Polysaccharide Capsule. mBio, 7(5), e01053-16.
  • Chaguza, C., Cornick, J. E., & Everett, D. B. (2015). Mechanisms and impact of genetic recombination in the evolution of Streptococcus pneumoniae. Computational and Structural Biotechnology Journal, 13, 241–247. http://doi.org/10.1016/j.csbj.2015.03.007
  • Didelot, X., & Maiden, M. C. J. (2010). Impact of recombination on bacterial evolution. Trends in Microbiology, 18(7), 315–322. http://doi.org/10.1016/j.tim.2010.04.002
  • Metzker, M. L., & Caskey, C. T. (2009). Polymerase chain reaction (PCR). eLS.