BMOL3401 Research Task Structure Answers Sample

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Introduction to Research Task Structure Answers Sample

Q1: Culture-Independent Assessment of Microbial Diversity

The culture method of microbial analysis does not enable total analysis of the compound because it only detects those microorganisms that can fully grow on the culture media. Such methods are useful for identification of slow-growing or fastidious microorganisms that are not easily cultured under normal culture conditions.

BMOL3401 Research Task Structure Answers Sample

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Michael Brown 7 Years | MSc

• Techniques Used: The work starts with the extraction of DNA from the swab samples taken from hospital doors or from a wound site if it is a clinical sample. Subsequently, the isolated DNA goes through 16S rRNA gene sequencing for bacteria or whole metagenomic sequencing for other microorganisms like virus or fungi.
• Specimens: Swabs are taken as aseptically as possible and the DNA extraction is done using kit methods. 16S rRNA gene profiling can be performed through V3–V4 region of gene encoding 16S ribosomal RNA using high-throughput sequencing platforms like Illumina. Shotgun sequencing avoids targeted PCR and targets all DNA fragments making it relatively more precise.
• Output: These methods present taxonomic report of the microbial genera or species and relative quantity report demonstrating the distribution of the microbes.

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Comparison with Culture-Dependent Methods:

• Advantages: Detects both culturable and non-culturable microbes, higher sensitivity, greater microbial resolution.
• Disadvantages: Expensive, technically complex, no information on microbial viability or antibiotic resistance phenotypes.

In addition to the taxonomical analysis, there are culture independent employing functional properties of the microbial communities. It can be said that, shotgun metagenomics enable identification of genes associated with antibiotic resistance, virulence, or specific metabolic functions, which allows evaluating clinical risks (Demko AM et al., 2021). Metatranscriptomics is more advanced in that it does not just analyse the entire community DNA but records the function of the microbial populace. Some of those tools include QIIME2 and MEGAN that enable the sequencing data analysis and generate figures that include alpha and beta diversity charts. These techniques are especially used in health care systems to detect changes in microbial status resulting from episodes such as sanitation. Furthermore, integration of sequencing with other data types (for instance, patient results or antibiotic consumption) allowed for risk of infections or treatment results forecasting.

Reference

• Demko AM, Patin NV, Jensen PR. Microbial diversity in tropical marine sediments assessed using culture‐dependent and culture‐independent techniques. Environmental microbiology. 2021 Nov;23(11):6859-75.

Q2: Scientific Use of Cultured Microbes beyond Antibiotic Testing

While culturing is not comprehensive in obtaining microbial diversity, it is an indispensable tool to grow microbes in the laboratory for numerous application.

Scientific Use 1: Host-Microbe Interaction Studies

Cultured microbes are employed in order to understand the role of microbes and their connexion to the host physiology, immune system, and disease. For instance in gnotobiotic mouse model, mice which are germ-free are introduced to controlled microbiota. This makes it possible for the analysts to look at the contribution of single species or a group in processes such as gut formation or inflammation.

Scientific Use 2: Genetic Manipulation and Functional Studies

Selected cultured microbes facilitate molecular analysis through tools such as CRISPR-Cas systems. This can be achieved by knocking out genes, knocking in genes or modifying genes so as to investigate microbial metabolic capabilities, pathogenicity, or resistance traits. Such manipulations also make it easier to determine how the gene works and possibly what can be done to disrupt or fix the process.

Cultured microbes are also applied in the preparation of vaccines in which the particular or specific pathogens are cultivated and their virulent properties are inactivated or reduced in virulence and subsequently used in testing diseases on animal models before field trials are conducted (Cook MA, Wright GD, 2022). Furthermore, synthetic biology greatly employs culturable strains, for example E. coli as heterologous expression systems for proteins, enzymes or therapeutic goods. For instance, synthetic microbes which have been designed are used in other applications such as in delivery of drugs or monitoring of concentrations of certain diseases biomarkers. Cultured microbes also find application in evolution experiments, whereby microbes are subjected to selective pressures for some generations to enforce mutation rates, adaptations and assessments of resistance in the former natural environment but now pored over culture plates.

Q3: Importance of Addressing Hospital-Acquired UTIs

Patients are considered to be at a high risk of contracting HAUTIs in Australia and worldwide among HIAs. Consequently, they undergo significant clinical challenges due to the following factors.

Why Hospital-Acquired UTIs are so dangerous

Catheter Use: This logic points towards the use of indwelling urinary catheters as one of the main contributing factors toward the development of hospital-acquired pressure ulcers. They distort urine stream and serve as an excellent port of entry and abode for bacterial growth and biofilm formation and are commonly known as catheter-associated urinary tract infections CAUTIs.

• Sepsis: A significant aspect that brings about infection and resultant sepsis is immunocompromised patients, who are mostly hospitalised patients especially the elderly or critically ill patients.
• Antibiotic resistance: Most of the Uropathogens admit multiresistance in the hospital due to which it becomes difficult to treat them, therefore increases the duration of hospitalisation and mortality level.

Virulence Factor Study Example:

Fimbrial adhesins are microbial surface components involved in the adherence process; in the study done by Lee PT et al., 2022, the researchers focused on the type 1 and P fimbriae of Escherichia coli which is one of the leading causes of HAUTIs (1). Knockout mutants were employed to establish the impact of such adhesins’ deficiency with respect to bacterial attachment and biofilm development on the catheter surface. It was established that both fimbrial types affect colonisation and biofilm formation, which are crucial in the production of a long-lasting infection.

Impact on Diagnosis and Treatment:

These findings open up a discussion on the mechanisms of the pathogen in maintaining infection and can give hints on the best approach to therapy. For example, interference in fimbrial expression or the administration of anti-adhesive agents could work to prevent colonisation. Furthermore, detection of these virulence genes in clinical isolates may help to differentiate between higher and lower risk stains, which will help locate sources to detect more sensitive, to improve outcomes of such resistant strains.

Q4: Rapid Diagnostic Alternatives for UTIs

Background: Chromogenic agar is commonly employed in diagnostic laboratories for UTI identification since it is simple to use as well as provides better visual results. However, it involves the sample incubation for 18–24 hours, which hampers early clinical intervention and antibiotic use.

One such rapid alternative is the Loop-mediated Isothermal Amplification (LAMP) which is a nucleic acid amplification technique that enables confirmation of the presence of bacterial DNA in a short period without any requirement of thermal cycling.

The study by Santos M et al., (2022) proposed a LAMP-based method for rapid diagnosis of Escherichia coli in urine sample which takes less than an hour. The method showed high sensitivity and specificity in one-step reaction even if there were other microorganisms present and no DNA extraction was needed which would make it suitable for use in near-patient diagnosis.

Pros and Cons Compared to Chromogenic Agar:

Pros:

• Speed: Results in <1 hour vs. 18–24 hours.
• Prominence and partiality: suitable for recognising very low levels of bacteria and therefore is able to differentiate between pathogens.
• Early intervention: Enables prompt antibiotic administration.

Cons:

Cost: Due to the specificity of the processes that are used during the analysis, it costs more than other methods since it requires specialised reagents and instruments.

Expertise: The staff should undergo training so that they can be able to analyse the results as well as being conversant with equipment required for the job.

Sample throughput: Generally, it is designed to identify only one organism at a time, except when multiplexing is performed.

Some implications to the patient care include that: Use of Rapid tests such as the LAMP can reduced the time of diagnosis by:

• Faster symptom relief.
• Lower risk of complications (e.g., pyelonephritis or sepsis).
• Reduced empirical antibiotic use and improved antimicrobial stewardship.

Reference List

Journals

• Cook MA, Wright GD. The past, present, and future of antibiotics. Science translational medicine. 2022 Aug 10;14(657):eabo7793.
• Demko AM, Patin NV, Jensen PR. Microbial diversity in tropical marine sediments assessed using culture‐dependent and culture‐independent techniques. Environmental microbiology. 2021 Nov;23(11):6859-75.
• Fasugba O, McInnes E, Baye J, Cheng H, Gordon R, Middleton S. Barriers and enablers to implementinghospital-acquired urinary tract infection prevention strategies: a qualitative study using the Theoretical Domains Framework. Journal of Hospital Infection. 2021 Jul 1;113:172-9.
• Harris M, Fasolino T. New and emerging technologies for the diagnosis of urinary tract infections. Journal of Laboratory Medicine. 2022 Feb 23;46(1):3-15.
• Lee PT, Krecko LK, Savage S, O’Rourke AP, Jung HS, Ingraham A, Zarzaur BL, Scarborough JE. Which hospital-acquired conditions matter the most in trauma? An evidence-based approach for prioritizing trauma program improvement. Journal of Trauma and Acute Care Surgery. 2022 Oct 1;93(4):446-52.
• Santos M, Mariz M, Tiago I, Martins J, Alarico S, Ferreira P. A review on urinary tract infections diagnostic methods: Laboratory-based and point-of-care approaches. Journal of Pharmaceutical and Biomedical Analysis. 2022 Sep 20;219:114889.
• Xu R, Deebel N, Casals R, Dutta R, Mirzazadeh M. A new gold rush: a review of current and developing diagnostic tools for urinary tract infections. Diagnostics. 2021 Mar 9;11(3):479.