Microbiology and parasitology analysis

The discipline of Microbiological and Parasitological Analysis includes the minimum contents of training, acquisition of competencies and skills that students must know about making, transporting and processing of samples for the diagnosis of infectious diseases and detection and identification of microorganisms pathogenic to human beings and animals, or which pose a risk to environmental and food.

• THEME 1. The laboratory of clinical analysis. Organization and general procedures. Biosecurity: categories of biohazard and containment levels. Safety and hygiene standards. General concepts about the collection, transport, storage and handling of biological material. Disposal of infectious waste. Quality control: methods and control areas.
• THEME 2. Bacteriological diagnosis techniques. Examination of samples in fresh and stained. Isolation and cultivation of bacteria. Conventional microbiological methods for bacterial identification. Commercial identification systems. Automated systems.
• THEME 3. Mycological diagnosis techniques. Examination of samples in fresh and stained. Isolation and cultivation of fungi. Conventional microbiological methods for the identification of fungi. Commercial identification systems.
• THEME 4. Techniques of virological diagnosis. Direct detection. Cytology and histology. Electron microscopy. Viral isolation. Characterization of viruses. Cytopathic effect. Inclusion bodies. Viral hemagglutination. Determination of tissue culture infectious dose. Trials of plates and transformation.
• THEME 5. Immunological diagnosis of infectious diseases. Detection of antigen in clinical samples. Immunologic techniques for the identification of microorganisms. Serodiagnosis of infectious diseases. Objectives, methods and interpretation of serological tests.
• THEME 6. Molecular techniques applied to the microbiological diagnosis. Fatty acids chromatographic analysis. Electrophoresis of proteins. Sequencing of nucleic acids. Hybridization of nucleic acids. Nucleic acid amplification by the polymerase chain reaction.
• THEME 7. Obtaining and processing of samples of food and water for microbiological analysis. Samples of food. Total plate count. Indicators of a lack of hygiene. Research of pathogens. Analysis of manipulators. Water samples. Aerobic plate count. Indicators of faecal contamination. Rapid detection of pathogens and indicators systems.
• THEME 8. Obtaining and processing of environmental samples for microbiological analysis. Environmental sampling strategies. Analysis of air samples: sedimentation and filtration. Surface analysis by plates of contact, tabs and the swab method.
• THEME 9. Diagnosis of infections of skin and soft tissue wounds. Collection, transport and storage. Protocol of microbiological study and interpretation of the results.
• THEME 10. Diagnosis of eye and ear infections. Microbiological study of exudate conjunctival and otic. Collection of specimens. Direct examination of stained samples. Immunological techniques. Protocol of microbiological study and interpretation of the results.
• THEME 11. Diagnosis of urinary tract infections. Collection, transport and storage. Microscopic examination of samples of sediment in fresh and stained. Indirect evidence. Urine culture. Protocol of microbiological study and interpretation of the results. The detection of antigens in urine.
• THEME 12. Diagnosis of gastrointestinal infections. Collection, transport and storage. Examination of stool samples in fresh and stained. Stool culture. Protocol of microbiological study and interpretation of the results. Antigen detection techniques.
• THEME 13. Diagnosis of respiratory infections. Collection, transportation and processing of nasopharyngeal exudate and sputum samples. Microscopic examination of stained samples. Protocol of microbiological study and interpretation of the results. Detection of antigens and diagnostic serological. Nucleic acid amplification.
• THEME 14. Microbiological study of vaginal and urethral exudates. Obtaining the samples. Microscopic examination of stained samples. Protocol of microbiological study and interpretation of the results.
• THEME 15. Microbiological study of cerebrospinal fluid and blood. Obtaining the samples. Microscopic examination of stained samples. Protocol of microbiological study and interpretation of the results.
• THEME 16. Susceptibility to antimicrobial agents. Sensitivity to antibacterial and antifungal agents. Methods of diffusion and dilution. Commercial systems. Alternative methods for the detection of resistance. Sensitivity to antiviral agents: plaque reduction assay. Detection of antimicrobial agents in tissues and biological fluids.
• THEME 17. The diagnosis in parasitology. Importance of medical history in the parasitological analysis.
• THEME 18. Parasitic coprology and. parasitic forms present in feces. Procedures for obtaining and preservation of samples. Macroscopic examination. Microscopic examination. Concentration techniques. Quantitative techniques. Stains. Non-parasitic elements in stools. Interpretation of results.
• THEME 19. Parasitic coprology II. Methods of concentration of larvae in feces. Stool culture of helminth and protozoa. Specific methods for the diagnosis of the enterobiosis.
• THEME 20. Parasitic coprology III. Application of immunological and molecular methods.
• THEME 21. Review Parasitology of the Genitourinary tract specimens: urine, urethral or vaginal discharge, prostatic secretion. Diagnostic laboratory of the trichomonosis. Diagnostic laboratory of the bladder schistosomosis.
• THEME 22. Parasitic Hematology. Parasitic forms present in blood. Collection of specimens. Fresh examination. Examination of stained preparations: thin smear and thick drop. Blood and test alternative methods in the diagnosis of parasitic diseases hemotisulares: malaria, filariasis, trypanosomosis and leishmaniasis.
• THEME 23. Parasitic Hematology II. Application of immunological and molecular methods. Methodology in the diagnosis of hydatidosis, toxoplasmosis, cysticercosis and trichinellosis. Interpretation of results.
• THEME 24. Parasites present in other biological samples. Examination of sputum. Examination of aspirated: bronchial, duodenal and liver. Examination of cerebrospinal fluid, lymph node fluid, bone marrow, skin and other tissues.
• THEME 25. Parasites present in samples of water, food, and environmental. Concentration and identification methods.

Program of practical classes:

MICROBIOLOGY:
Laboratory 1. Microbiological analysis of urine. Sediment examination and GRAM staining. Quantitative and qualitative urine culture. Identification by conventional methods and commercial systems.
Laboratory 2. Microbiological analysis of otic and vaginal exudates. Identification of fungal forms: examination of fresh and stained samples. Identification by conventional methods.
Laboratory 3.- Microbiological analysis of air and surfaces. Assessment of the effectiveness of chemical agents for the disinfection of surfaces.
Laboratory 4.- Identification of microorganisms by means of nucleic acid amplification by the polymerase chain reaction (PCR).
Laboratory 5.- Study of sensitivity to antimicrobials. Dilution and diffusion methods. Determination of the minimum inhibitory and microbicidal concentration.

PARASITOLOGY:
Laboratory 1. Parasitic coprology: macroscopic examination. Direct examination techniques. Stool concentration techniques. Identification of parasitic forms under the microscope. Graham technique for the diagnosis of the enterobiosis. Baerman method for the isolation of larvae of nematodes.
Laboratory 2. Parasitic Hematology: microscopic identification of parasitic forms in preparations stained blood. Microscopic identification of tissue parasitic forms. Determination of parasitic forms in environmental samples.

Basic

• Forbes, B.A., Sahm, D. F., Weissfeld, A. S. Diagnóstico Microbiológico (Bailey & Scott), 12a Ed., Editorial Médica Panamericana, 2009.

• Gillespie, S.H. Hawkey, P.M. 1995. Medical Parasitology: a práctical aproach. Ed. Oxford University Press, USA, 1º Ed., 1995.

• Riedel S. Morse, S. A., Miettzner,T.A. Miller, S. Jawetz Microbiología médica. McGraw Hill Lange. (28th edition). 2020.

Complementary

• AAPF (American Academy of Family Physicians). Atlas de Microscopía Clínica. 4ª Ed. Editorial Médica Panamericana.2015.
• Alvarez, M.V., E. Boquet, I. De Fez. Manual de técnicas en Microbiología Clínica. 2ª Ed. AEFA, 1990.
• Gamazo, C., I. López-Goñi y R. Díaz. Manual práctico de Microbiología. 3ª Ed. Masson, 2005.
• García, S. Lynne. Diagnostic medical parasitology. ASM Press, Washington, D.C. 6ªEd. 2016
• http://dpd.cdc.gov/dpdx/Default.htm. DPDx Laboratory identification of parasites of public health concern.
• https://www.seimc.org/documentos-cientificos/procedimientos-microbiolog…
• Murray, Patrick R., Ellen Jo Baron, James H. Jorgensen, Marie Louise Landry, and Michael A. Pfaller. Manual of Clinical Microbiology, 9º Ed. Washington, DC: ASM Press, 2007.
• OMS. Métodos básicos en el laboratorio en Parasitología Médica, 1992.
• Prats, G. 2012. Microbiología y Parasitología Médicas. Madrid: Editorial Médica Panamericana..
• Prats, G. Microbiología Clínica y Parasitología Médicas. Ed. Panamericana, 2013.
• Shors, Teri . Virus. Estudio molecular con orientación clínica. Ed. Médica Panamericana, 2009.

Competences

Knowledge:

- Con 03. Know how to apply the scientific method and acquire skills in the handling of legislation, sources of information, bibliography, preparation of protocols and other aspects considered necessary for the design and critical evaluation of preclinical and clinical trials.

Biology Module

- Con 22. Know the nature and behaviour of infectious agents.
- Con 32. Know and understand the basic fundamentals of clinical analysis and the characteristics and contents of laboratory diagnostic reports.
- Con 39. Know the analytical techniques related to laboratory diagnosis, toxics, food and environment.

Skills or abilities:

H/D02. Design, apply and evaluate reagents, methods and clinical analytical techniques, knowing the basic fundamentals of clinical analysis and the characteristics and contents of laboratory diagnostic reports.
H/D 04. Carry out hygienic-sanitary analyses (biochemical, bromatological, microbiological and parasitological, among others), especially those related to health in general and to food and the environment in particular.


Competences:
- Comp 01. Capacity for analysis and synthesis.
- Comp 02. Ability to organise and plan.
- Comp 03. Oral and written communication in one's own language.
- Comp 10. Team work.
- Comp 17. Ability to apply knowledge in practice.
- Comp 27. Concern for quality.

Teaching will consist of the following training activities:

- Lectures: lectures given by the lecturer with the support of various computer materials. Students will have access to complementary material in the virtual classroom for the study and preparation of the subject.

- Practical laboratory classes: these include classes that take place in the practical laboratory. The completion of the practicals is compulsory and essential to pass the subject and once completed they will be valid in the two academic years following the one in which they were taken.

- Tutorials: These will be scheduled by the teacher at the request of the students. Activities such as clarification of doubts about theory, practices or readings are proposed.

The two parts of the subject, Microbiological Analysis, which will represent 60% of the final mark, and Parasitological Analysis, which will represent 40% of the final mark, will be assessed independently, according to the following criteria:

- Microbiological Analysis: Assessment will be based on continuous assessment and a specific final test. The student's mark for this part of the subject will result from the assessment of the following sections:

1) Compulsory final specific test (face-to-face) based on objective questions and practical cases. In this test, the knowledge acquired in the practical laboratory classes will also be assessed: 75%.

2) Continuous assessment: 3 questionnaires to be carried out throughout the course in the classroom or through the virtual classroom or the MS Teams platform: 25%.


- Parasitological Analysis: The evaluation of this part of the subject will be based on a specific final test (face-to-face) consisting of objective questions and practical cases. The knowledge acquired in the practical laboratory classes will also be assessed in this test: 100%.

The assessment of the competences and skills acquired will be carried out:

In the exam: Con 22, Con32, Con 39, Comp 03
In the laboratory. Con 03, Comp 01, Comp 02; Comp 10, Comp 17, Comp 27, H/D02, H/D04


In order to pass the course, it will be necessary to achieve a minimum score of 50% in each of the parts of the specific final exam. If this minimum is not reached in any of the parts, the grade that will appear in the report will be that of the part not passed. If only one part of the subject is passed, the mark obtained in that part will only be retained in the same academic year.

If the student does not take the final exam in either of the two opportunities, he/she will be graded as ‘No-show’.

The student will not be able to pass the course if he/she does not take the laboratory practicals. In this case, their final mark for the course will be ‘No Show’.

In the case of students who are excused from class attendance, the evaluation will be based solely on the final exam and the completion of the practical classes (100% of the final grade).

In the 2nd opportunity of the academic year, the same evaluation criteria will be followed.

- For cases of fraudulent completion of exercises or tests, the provisions of the Regulations for the evaluation of the academic performance of students and the review of grades will be applied.

• Individual or group independent study: 65 hours
• Taking tests as part of the continuous assessment: 1h
• Realization of practices: 24h
• Total hours of personal work of the student: 90h

It is recommended to keep up to date with the subject in order to get the most out of it, to attend lectures, to attend regularly, not to progress without understanding and knowing the previous subject, to use the virtual platform as a complement, to consult the bibliography, to use the tutorial hours to resolve any doubts and to read the practical syllabus before going to do them.