Infectious Diseases Residency Program

Laboratory Objectives for ID Fellows

Specific Standards of Accreditation for Residency Programs in Adult Infectious Diseases

a) Laboratory Component of the Program

Each resident must gain an adequate experience in diagnostic microbiology and spend a minimum of 6 months total in an accredited residency program in medical microbiology. This training must be undertaken under the direct supervision of a specialist certified in medical microbiology, or with acceptable qualifications. The following areas of laboratory training are considered essential:

  1. General Bacteriolog
    • routine techniques including use of different culture media, specimen collection and primary inoculation, and various staining techniques.
    • bench experience and familiarity with special isolation and identification techniques related to urine, respiratory secretions, blood, tissue and body fluids, and enteric and anaerobic bacteriology.
    • antibiotic susceptibility testing and assays for antibiotic levels.
  2. TB, Fungi and Routine parasitology
    • specimen collection, transport and media for fungi and mycobacteria.
    • rhodamine staining for AFB and antibiotic sensitivity testing for mycobacteria.
    • identification of common fungi including candida, aspergillus, cryptococcus; fungal serology and antigen detection.
    • stool examination for ova, trophozoites, and larvae; concentration techniques; string test; special stains and serology.
  3. Virology, Mycoplasma and Chlamydia
    • virus isolation for herpes viruses, respiratory viruses, and enteric viruses.
    • virus serology including EBV, hepatitis, HIV, measles and rubella
    • chlamydia and mycoplasma isolation and antigen detection systems.
  4. Special Techniques
    • quantitative bacteriology, rapid diagnostic techniques, ELISA, immunofluorescence, DNA probes, and electronmicroscopy.
  5. Quality Management
    • The resident should:
      1. Understand what is meant by quality management:
        • Process that enhances the outcomes of medical care trhough continuous quality improvement
        • The desired outcome of all patient care must be to maintain or return the individual to the best possible state of health
      2. Know what quality management requires
        • Understanding and analysis of all elements or proceudres of medical care and treatment that influence the health outcome for the patient
        • Establishment of performacne expectations and standards for each element of care
        • Creation of a system to measure and evaluate whether the elements of care are meeting the expectations and standards (quality indicator statement)
        • Quality improvement through continuous monitoring of performance against the expectations and standards with a view to imrpovign the performacne and raising the standards
  6. Infection Control and Nosocomial Pathogens
    • role of microbiology laboratory in infection control and surveillance.
    • infection control unit organization and function.
    • epidemiology and laboratory investigation for nosocomial outbreaks, including biotyping, phage typing, and plasmid analysis.

WHIMIS training is a requirement before working in the laboratory. If you have not previously completed this training, you should contact the microbiology safety officer before you begin your rotation and arrange for a training session.

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General Laboratory Objectives

Communicator
Collaborator
Manager
Health Advocate
Scholar
Professional
Medical Expert

Communicator

  1. Communicate effectively and clearly with physicians, nurses, pharmacists and other healthcare providers through direct communication and/or telephone consultation. This consists of eliciting and synthesizing information followed by conveying appropriate recommendations. Communication should occur after consultation with a microbiologist.
  2. Communicate effectively with laboratory staff by actively listening to their concerns, eliciting relevant patient information and appropriate follow-up. Residents are expected to follow up with clinicians where indicated and provide education back to laboratory staff. This process should take place through consultation with a microbiologist.
  3. Develop a common understanding on issues, problems and clinical concerns with healthcare providers from any discipline to allow for a shared plan of care to be developed and to ensure that clinical management needs are met.
  4. Develop skills in communicating with Public Health and other health care agencies.

Collaborator

  1. Participate effectively and appropriately in a multidisciplinaty health care team involving laboratory technologists, microbiologists, physicians, infection control, nursing, pharmacy or other healthcare professions. Residents should be able to clearly describe their roles within the team and understand the roles of others.
  2. Demonstrate respect for diversity and differences at all times.
  3. Effectively work with other health professionals to prevent, negotiate and resolve interpersonal conflict.

Manager

  1. Effectively manage their career as residents, and develop career management skills needed for independent practice. Residents of all levels are responsible for time management, and priority setting. Residents use time management skills to ensure that unknown specimens are identified during the rotation, while still gaining the required bench experience and organizing and presenting at weekly plate rounds.

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Health Advocate

  1. Learn to identify important determinants of health affecting patients and how the laboratory can impact these. Health determinants such as income and social status, employment, education, social and physical environment, health services, age, gender and culture will be discussed and applied through interaction with other healthcare professionals during routine work.
  2. Recognize and respond to issues where advocacy is appropriate.
    Example: advocating for the introduction of a new test to benefit a specific patient, a population or the community or advocating for improvement such as shorter turn around times which may benefit specific patients or populations.
  3. Understand the importance of Quality assurance within the laboratory. Residents will be exposed to the concepts of quality assurance and quality management during laboratory rotations, academic halfdays, structured teaching sessions. Residents are encouraged to attend Microbiology quality management committee meetings.

Scholar

  1. Demonstrate evidence of a questioning and inquisitive attitude towards medical information and an appreciation of the necessity of ongoing research. This may be done by bringing forward relevant articles and critically appraising them, or by planning and implementing a research project to answer a question.
  2. Facilitate the education of technologists, patients, students and other health care professionals and contribute to the development of new knowledge.
  3. Demonstrate the ability to utilize information technology to optimize patient care, for ongoing medical education and other activity.

Professional

  1. Develop a knowledge of legal and ethical codes of professional behaviour and the obligations of the physician that apply to microbiology, including issues relating to the notification of communicable diseases, storage requirements for specimens, and reporting requirements.
  2. Demonstrate trustworthiness (honesty, confidentiality) with respect to technologists, patients, and other health care providers while recognizing their own personal limitations and a willingness to call upon others for their expertise.
  3. Demonstrate a willingness to accept peer and supervisor review of professional competence.
  4. Appreciate the moral and ethical implications of decisions made in laboratory medicine and the impact that this can have for patient care and research.

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Medical Expert

Bacteriology
Urinary Tract
Genitals
Enterics
Blood Cultures
Cerebrospinal Fluid
Wounds
Anaerobes
Antibiotic resistant Organisms

 

Bacteriology: Respiratory Bench

Pre-analytic Issues:

  1. Know the proper specimen collection techniques for all respiratory specimens including: throat swab, eye swabs, sinus aspirates, sputums, BAL, Bronchial wash
  2. Become familiar with proper transportation conditions and transport media for each of these specimens
  3. Be capable of listing specimen rejection criteria.
  4. Understand the specific quantitative criteria used for sputum acceptability.
  5. Know the minimum quantity of specimen that is appropriate for processing

Analytic Issues:

  1. Identify the media used in culturing respiratory organisms (including media set up for immunocompromised patients, the reasons for using it and identify each as selective/differential or both
  2. Know the appropriate diagnostic algorithms for processing throat swabs, sputum, BAL, protected brush, bronchial wash, nasopharyngeal swabs
  3. Know the common respiratory pathogens, their main laboratory diagnostic characteristics and their virulence factors
  4. Be able to identify respiratory organisms on a gram stain of sputum
  5. Know how to identify Haemophilus influenzae and differentiate it from other Haemophilus species
  6. Understand the different methods used for susceptibility testing
  7. Be familiar with which agents are reported as first-line for susceptibility and reasons for this.
  8. Understand the methods used to determine penicillin susceptibility for Streptococcus pneumoniae and MIC values for susceptible, intermediate and resistant strains
  9. Know the laboratory safety issues that apply to the proper handling of respiratory pathogens (ie. SARS or avian influenza)

Post-analytic:

  1. Know the expected turn-around times for the reporting of respiratory specimens
  2. Know which respiratory organisms are reportable to Public Health
  3. Be familiar with respiratory pathogens which require specimens to be sent out for testing (Legionella, chlamydia, mycoplasma, SARS, diphtheria, pertussis) and know what types of tests are available

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Urinary Tract

Preanalytic:

  1. Know the proper specimen collection techniques for urine from many sources (routine, catheterized patient, pregnant patient, cystoscopic collection)
  2. Be familiar with proper transportation conditions for urine specimens
  3. Be capable of listing specimen rejection criteria and understand the reasons for these rejections.

Analytic:

  1. Know the screening techniques which may be used for bacteriuria or pyuria and be able to discuss the utility of screening urines prior to culture. Know which populations should be excluded from screening.
  2. Know which media may be used for culturing urine specimens
  3. Know the quantitation used to work up urine specimens at the bench
  4. Understand the diagnostic algorithm for work-up of urinary specimens
  5. Know the most common urinary pathogens, how they are identified in the laboratory and their virulence factors.
  6. Understand the different methods used for susceptibility testing, including screening for ESBLs and VRE.
  7. Know the laboratory safety issues that apply to the proper handling of urinary pathogens.

Post-analytical:

  1. Know the expected turn-around times for the reporting of urinary tract specimens
  2. Be familiar with the first line agents reported on urinary isolates and the reasons for this choice.
  3. Understand the reporting of ESBLs, VRE and their clinical significance in urinary isolates.

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Genitals

Pre-Analytical:

  1. Know the proper specimen collection techniques for all genital specimens including: vaginal swabs, cervical swabs, urine, urethral swabs, vulvar swabs
  2. Understand which specimens should be ordered on different patient populations (children, sexually active adults, sexual assault, post-hysterectomy specimens, pregnant women)
  3. Become familiar with proper transportation conditions and transport media for each of these specimens
  4. Be capable of listing specimen rejection criteria.

Analytical:

  1. Be familiar with the diagnostic algorithm for the work-up of genital specimens.
  2. Be able to read a vaginal swab for causes of vaginitis and understand which pathogens are being looked for and their virulence factors
  3. Know which organisms can be cultured for and how this is done (culture media, atmospheric conditions, duration of incubation)
  4. Be familiar with the common genital pathogens, the laboratory detection of these and their virulence factors.
  5. Know how culture of gonorrhea is performed and possible problems with identifying this organism.
  6. Be familiar with molecular detection of pathogens found in genital specimens and the pros and cons of molecular diagnostics.
  7. Know what media should be used to detect Group B streptococcus from a vaginal swab and the approaches used to screening in pregnancy. Identify the virulence factors of this organism.
  8. Know how susceptibility testing for Group B streptococcus is performed.

Post-analytical:

  1. Be familiar with reporting of pathogens causing vaginitis, urethritis, and cervicitis.
  2. Understand how reporting of organisms identified by molecular detection is performed.
  3. Know which pathogens are reportable to Public Health

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Enterics

Pre-analytic Issues:

  1. Know the proper specimen collection techniques for enteric specimen, including transport media
  2. Become familiar with proper transportation conditions.
  3. Be capable of listing specimen rejection criteria.

Analytical Issues:

  1. Identify the media used in routine culturing enteric organisms, the reasons for using it and identify each as selective/differential or both
  2. Know the appropriate diagnostic algorithms for processing enteric specimens
  3. Know the common enteric pathogens, their main laboratory diagnostic characteristics and their virulence factors
  4. Be familiar with organisms not routinely cultured for (ie vibrio, plesiomonas) and identify when it would be reasonable to culture for these and how this would be done
  5. Learn current identification methods for diagnosing Clostridium difficile. Be familiar with other options for identifying this organisms.
  6. Understand the different methods used for susceptibility testing
  7. Be familiar with which organisms have susceptibilies reported on them and which drugs are reported as first-line agents.
  8. Know the laboratory safety issues that apply to the proper handling of enteric specimens

Post-analytical:

  1. Know the expected turn-around times for the reporting of enteric organisms
  2. Know which respiratory organisms are reportable to Public Health
  3. Be familiar with typing methods used for enteric pathogens

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Blood Cultures

Pre-analytical Issues:

  1. Know the proper blood collection techniques, including skin antisepsis.
  2. Have knowledge of the appropriate number and timing of blood cultures.
  3. Understand the role that volume of blood collected per bottle plays in the sensitivity of blood cultures. Know the minimum volume which should be collected.
  4. Have an understanding of the controversy surrounding the use of anaerobic blood cultures.
  5. Be capable of listing specimen rejection criteria.
  6. Have a general knowledge of the composition of blood culture media.

Analytical Issues:

  1. Identify the media used in culturing organisms isolated from blood culture bottles. Know the reasons for using each and identify each as selective/differential or both
  2. Gain experience in reading direct gram stains from blood culture bottles
  3. Know the appropriate diagnostic algorithms for processing blood culture specimens
  4. Know the incubation times for routine processing, unusual pathogens and endocarditis
  5. Be able to classify blood culture systems (non-automated, semi-automated and automated) and understand the principles behind each and identify their advantages and disadvantages.
  6. For one automated system know the principles of how the system works, the limitations of the system and it’s advantages.
  7. Know the common pathogens, their main laboratory diagnostic characteristics and their virulence factors
  8. Understand the different methods used for susceptibility testing of blood culture isolates
  9. Know the laboratory safety issues that apply to the proper handling of blood

Post-analytical:

  1. Know the expected turn-around times for the reporting of organisms from blood cultures
  2. Know which organisms are reportable to Public Health
  3. Be familiar with typing methods used for blood borne pathogens and know when you would use these
  4. Understand the concept of pseudobacteremia and how this diagnosis can be made

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Cerebrospinal Fluid/ sterile tissues and fluids

Pre-analytical Issues:

  1. Know the proper collection techniques for sterile sites, including skin antisepsis.
  2. Learn appropriate specimen collection and transportation conditions.
  3. Be capable of listing specimen rejection criteria.

Analytical Issues:

  1. Learn to read and interpret gram stains from sterile sites, including cytospin preparations.
  2. Identify the media used in culturing organisms from sterile sites. Know the reasons for using each and identify each as selective/differential or both
  3. Know the appropriate diagnostic algorithms for processing sterile site tissues and fluids
  4. Know the incubation times for routine processing
  5. Know the common pathogens, their main laboratory diagnostic characteristics and their virulence factors
  6. Understand the different methods used for susceptibility testing
  7. Know the different susceptibility criteria for cefotaxime from CSF and other sites
  8. Know the laboratory safety issues that apply to the proper handling of CSF and other bodily fluids
  9. Which pathogens from sterile sites would require prophylaxis of laboratory workers and what would this prophylaxis consist of?

Post-analytical:

  1. Know the expected turn-around times for the reporting of organisms from CSF and other sterile sites
  2. Know which organisms are reportable to the Medical Officer of Health
  3. Know which CSF organisms require infection control interventions, antibiotic prophylaxis and the indications for each

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Wounds

Pre-analytical Issues:

  1. Know the proper specimen collection techniques and indications for collecting wound specimens
  2. Become familiar with proper transportation conditions and transport media for wound specimens
  3. Be capable of listing specimen rejection criteria
  4. Gain an appreciation for the importance of providing clinical information to the Microbiology laboratory, as this is used in the interpretation of wound specimens

Analytical Issues:

  1. Identify the media used in culturing wound specimens, the reasons for using these and identify each as selective/differential or both
  2. Know the appropriate diagnostic algorithms for processing wound specimens
  3. Know the common pathogens, their main laboratory diagnostic characteristics and their virulence factors
  4. Be able to identify organisms on a gram stain
  5. Learn to interpret culture results from wounds (ie work-up 3 or less organisms, distinguish pathogens from commensal flora)
  6. Understand the different methods used for susceptibility testing
  7. Be familiar with which agents are reported as first-line for susceptibility and reasons for this
  8. Understand the importance if identifying MRSA and resistant Pseudomonas from wounds
  9. Know the laboratory safety issues that apply to the proper handling of wound pathogens (Bioterrorist agents)

Post-analytical:

  1. Know the expected turn-around times for the reporting of wound specimens
  2. Know which wound organisms are reportable to Public Health
  3. Be familiar with the limitations of swabs for detecting wound pathogens

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Anaerobes

Pre-analytical Issues:

  1. Know the proper specimen collection techniques and indications for collecting specimens for anaerobic culture
  2. Become familiar with proper transportation conditions and transport media available for anaerobic culture
  3. Be capable of listing specimen rejection criteria

Analytical Issues:

  1. Identify the culture systems, media and atmosphere systems used in culturing anaerobes
  2. Know the appropriate diagnostic algorithms for processing clinically significant anaerobes (Gram negative, gram positive, rods and cocci)
  3. Know the common pathogens, their main laboratory diagnostic characteristics and their virulence factors
  4. Be able to identify anaerobic organisms on a gram stain
  5. Know how to establish the presence of anaerobes in culture
  6. Learn to make presumptive identifications on common anaerobic organisms
  7. Know the indications for susceptibility testing and understand the different methods used for susceptibility testing in anaerobes and the strengths and limitations of these
  8. Know the typically resistant anaerobes
  9. Know the laboratory safety issues that apply to the proper handling of anaerobes

Post-analytical:

  1. Know the expected turn-around times for the reporting of anaerobic organisms
  2. Know which anaerobes have infection control implications
  3. Be familiar with reporting and interpreting mixed cultures (aerobes and anaerobes)
  4. Know the epidemiology, clinical significance and treatment of anaerobes

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Antibiotic resistant (Nosocomial) Organisms (AROs)

Pre-analytical Issues:

  1. Know the proper specimen collection techniques and indications for collecting specimens for surveillance
  2. Understand the principles behind screening for AROs
  3. Be capable of listing specimen rejection criteria

Analytical Issues:

  1. Identify the culture media used for MRSA, VRE, MDR Pseudomonas, Serratia and ESBLs and reasons for using each
  2. Know the appropriate diagnostic algorithms for processing AROs
  3. Know the common pathogens, their main laboratory diagnostic characteristics and their virulence factors
  4. Understand the confirmatory tests done for each ARO
  5. Understand the different methods used for susceptibility testing in AROs
  6. Know the laboratory safety issues that apply to the proper handling of anaerobes

Post-analytical:

  1. Know the appropriate infection control isolation measures that should be implemented for each ARO diagnosed in the laboratory
  2. Be familiar with the reporting of AROs and their susceptibilities
  3. Know the epidemiology, clinical significance and treatment of AROs

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Susceptibility Testing:

Mycobacteriology
Serology
Virology and Chlamydiology
Molecular Microbiology

  1. Be familiar with the techniques used to determine susceptibilities; broth dilution, agar dilution, disc diffusion, E-test, molecular detection, automated systems (VITEK)
  2. Be aware of the role that NCCLS has in establishing guidelines for susceptibility testing
  3. Be familiar with NCCLS breakpoints for;
    Staphylococcus aureus – methicillin, vancomycin
    Streptococcus pneumoniae – penicillin, cefotaxime
  4. Know the 3 types of β-lactamase, the principles of testing for these and their applications. Be familiar with the Bush-Meideros-Jacoby classification of β-lactamases
  5. Know which bug/drug combinations give the VITEK problems and alternative testing which may be used to confirm VITEK results
  6. Know the mechanisms of antibiotic resistance for common bug/drug combination
Mycobacteriology

General:

  • Know the different laboratory service levels of mycobacteriology
  • Know the epidemiology, clinical presentation, and management of different mycobacterial infections. Be able to classify non-tuberculose mycobacteria species based on clinical syndromes: lymphadenitis, cutaneous diseases, pulmonary disease and disseminated disease.
  • Be familiar with the Runyon classification and know both how to differentiate the following and list the most important organisms from each class: photochromogens, scotochromogens, non-photochromogens, and rapid growers
  • Understand the pathogenesis of disease and the histological features

Safety:

  • Have a good understanding of biosafety requirements, laboratory design and protective equipment appropriate for the mycobacteriology lab and/or required by legislation
  • Have knowledge of disinfectants used and procedures for spillage

Specimen Collection, Preparation And Staining:

  • Specimen processing:
    • appropriate specimens, methods of collection and transport
    • set-up for sterile vs non-sterile specimens
    • methods of digestion-decontamination: e.g.NaCL-NaOH (different percentages of NaOH), oxalic acid for Pseudomonas
  • Know the principles and methods of acid-fast stains
  • Know both the carbolfuchsin and flurochrome procedures (be familiar with the controls used)

Culture and Identification:

  • have a diagnotic algorithm for identifying MTB and non-MTB
  • Know the composition and use of the following media:
    Middlebrook 7H9, 7H10, 7H11, LJ, BACTEC 12B, BACTEC 13A 7H11S MGIT media
  • know the recommended guidelines for selecting different media; understand the principles and use of selective vs non-selective media
  • Be able to differentiate Mycobacteria based on incubation times, temperature, colonial morphology and biochemical tests. Be familiar with the colonial morphology of MTB complex
  • Know the biochemical tests required to diagnose MTB and know the principles and uses of the following tests : arylsulphatase, Tween hydrolysis, pyrazinimidase, iron uptake, catalase, nitrate reduction, 5% NaCl, T2H sensitivity, niacin
  • Know the special growth and temperature requirements of the following organisms :M. malmonese, M. xenopi, M. hemophilum, M. genavense
  • know the BACTEC method of isolation including the principles and the exact methodology; be able to compare the BACTEC system with the MGIT system
  • Be familiar with the use of DNA probes, PCR and other amplification processes and HPLC/GLC in identifying mycobacteria. Be able to discuss the principles, advantages and disadvantages of these methods. Know how to evaluate and incorporate these new technologies into laboratory practises.

Susceptibility Testing:

  • Know the mechanisms of resistance of the front line antituberculous drugs
  • Know principles and different methods of susceptibility testing, including BACTEC, agar disc elution, broth microdilution, E-test. Understand which drugs to test and how to report.
  • Be familiar with the patterns of resistance amongst the non-MTB

Quality Control:

  • Know appropriate methods for quality control in the mycobacteriology laboratory, including smears, contamination rates, BACTEC, media, etc.

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Serology

General Virus:

  • Understand the principles of virus serology in the diagnosis of viral disease and the determination of immune status
  • Review specific reference test procedures, CF EIA, and latex agglutination
  • Differentiate the methods, involved and the suitability of each method for the specific purpose of testing ie. whether for diagnosis or immunity
  • Review interpretation and significance of serological results
  • Understand limitations of virus serology

Hepatitis:

  • Review testing methodologies for all hepatitis tests; ie. EIA, Immunoblot Neutralization, PCR (qualitative, quantitative) and Genotyping (HCV)
  • Understand the principles of programs available for Hepatitis A, B, C and D testing; ie. disease prevention, confirmation of infection, prenatal and vaccination programs as well as epidemiology

HIV:

  • Understand the principles and procedures of tests that make up the current laboratory testing algorithm (EIA, Western Blot, p24 Antigen, PCR, Virus Culture, viral load)
  • Understand rationale and decisions regarding interpretation of laboratory test results
  • Understand the importance of patient demographics and risk assessment from quality assurance and surveillance perspectives
  • Learn various aspects of the Ontario voluntary testing population (anonymous, non nominal, nominal testing)

Syphilis:

  • Understand the principles of various treponemal and non-treponemal tests
  • Understand the kinetics of the immune response during infection and treatment
  • Basic application of serological test results and interpretation of results
  • Limitations of serological tests for syphilis, i.e. high risk and reinfected patient

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Virology and Chlamydiology

Objectives: The overall objectives are to acquire a comprehensive understanding of t
he infections and diseases caused by viruses and chlamydiae, their epidemiology, treatment and prevention, and relevant infection control practices.

General Requirements: To understand viral and chlamydial taxonomy, epidemiology, clinical presentation, laboratory diagnosis, and treatment and prevention of viral and chlamydial infections.

Specific Requirements:

Specific viruses/Chlamydiae

To understand the natural history of infections caused by specific viruses and chlamydiae. To be able to identify the viral agents responsible for specific clinical presentations.

Respiratory viruses:

Influenza A and B
Para-influenza 1,2,3 and 4
Respiratory syncytial virus
Adenovirus
Rhinovirus
SARS-Coronavirus

Gastrointestinal:

Enteroviruses
Rotaviruses
Norwalk and Norwalk-like virus
Astroviruses
Adenoviruses
Coronavirus

Rash:

Measles, mumps, rubella
Parvovirus B-19
Human herpesvirus 6, 7

Hepatitis viruses:

A,B,C,D,E, F and G

Herpes viruses:

Herpes simplex (HSV-1 , 2)
Varicella zoster (VZV)
Epstein-Barr virus (EBV)
Cytomegalovirus (CMV)

Human herpesvirus 6, 7
HHV-8 / Kaposi's sarcoma associated virus

Arboviruses:

Western, Eastern Equine Encephalitis
Venezuelan Equine Encephalitis
St. Louis, California Encephalitis, Powassan
Japanese B Encephalitis
Dengue, Yellow fever
West Nile Virus

Retroviruses:

Human immunodeficiency virus, HTLV-I,-II

Chlamydiae:

C. trachomatis, C. pneumoniae, C. psittaci

Specimen Collection and Preparation:

To understand appropriate collection, transportation, storage, handling and processing of specimens for each specimen type related to disease and laboratory technology:

Blood for serology
Nasopharyngeal aspirate / swab
Urine
Stool
Lesion swab
Biopsy
Urethral, cervical swabs
CSF

Diagnostic Approaches:

Cell Cultures:

To know the types of cell lines available and those used by the laboratory, including advantages and disadvantages of various commercial or in-house cell lines. To know the methods for maintaining cell lines, conditions of growth, media, antibiotics used, and assessment of cell viability. To know what types of viruses will grow in the various cell lines, and which ones are routinely set up for various clinical specimens.

Cynmolgous monkey kidney cells
Foreskin fibroblast
Mink lung
McCoy
Primary

To know the principles, and be able to recognize typical CPE and the expected time course for changes. To know which viruses will hemadsorb, the principles behind this test. To recognize typical immunofluorescence from culture. To know the principles of shell vial cultures and how to interpret the results. To know the principles of viral typing via HAI and neutralization tests.

Herpes viruses (HSV, VZV, CMV)
Adenovirus; enterovirus; influenza; parainfluenza; RSV
Chlamydia

Antigen Detection:

To know the principles of antigen detection, to be able to perform a DFA, and to be able to recognize a positive specimen with typical immunofluorescence:

Respiratory specimens: Para-influenza, influenza, RSV, adenovirus
Herpesviruses: Cytomegalovirus, herpes simplex, varicella zoster
Chlamydial specimens: Chlamydia trachomatis

Understand the performance of antigen tests for chlamydia and all viruses where commercial tests are available (rotavirus, RSV, influenza, etc.)

Nucleic Acid Detection:

  • To understand the principles of nucleic acid by hybridization (NAH) and nucleic acid amplification tests (NAAT), including polymerase chain reaction (PCR), ligase chain reaction (LCR), strand displacement (SDA), transcription mediated amplification (TMA).
  • To recognize the application of these methods for diagnosing infections such as HSV, CMV, HPV, respiratory viruses, hepatitis viruses, chlamydia species.
  • To appreciate the advantages and disadvantages of detecting nucleic acids in clinical specimens, including specific needs for workload and decontamination procedures.
  • To gain an understanding of the roles of qualitative and quantitative NAAT and the contributions of sequencing in diagnosing viral infections.

Serology:

To know the types of serological tests available, the technique of performing them, and the advantages and disadvantages. To know the tests often done and those rarely done but available.

To distinguish tests done to determine immunity from those to determine recent infection and/or disease.

To understand different types of serologic tests including:

  • Immunofluorescent assay (IFA): slide with organism, add serum and conjugated antibody, eg HSV, VZV, measles, mumps, parvovirus
  • Enzyme immunoassay (EIA): particle coated with antigen, can be automated system (IMx), eg HIV, MEIA for rubella
  • Complement fixation (CF) with paired sera (historical)
    eg influenza, RSV, adeno, measles, rubella
  • Latex agglutination (LA): slide agglutination
    eg CMV, rubella

Diagnosis of Hepatitis:

To know when specific antigen and antibody tests are indicated for diagnosis or immunity and to know how soon after infection they are present:

To know when confirmatory tests are required:

To know at what time following exposure specific markers (antigen and antibodies) appear:

  • Hepatitis A: IgG, IgM
  • Hepatitis B: HBsAntigen, HBs Antibody, HBc IgM antibody
  • HBeAntigen, HBeAntibod
  • Hepatitis C: HCV antibody
  • Hepatitis D: antibody

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Molecular Microbiology

Objectives:

1. To introduce the principles and application of molecular techniques used in the area of clinical diagnostic microbiology.

To gain knowledge of the emerging field of diagnostic Molecular Microbiology in which principles of nucleic acid analysis by nucleic acid (a) restriction fragment length polymorphism (RFLP), (b) amplification, (c) hybridization, and (d) sequencing as applied in detection and characterization of pathogenic microorganisms associated with infectious diseases.

This requires knowledge of the following areas:

  1. Basic science of nucleic acids,
  2. Nucleic acid isolation,
  3. Preparation of specimens for analysis,
  4. Analysis of nucleic acids using restriction endonucleases and agarose gel electrophoresis,
  5. Nucleic acid hybridization methods,
  6. In vitro nucleic acid amplification and detection methods.
  7. Automation in nucleic acid isolation and analysis.
  8. Pros and cons of molecular methods.

2. Appreciation of the application of these techniques which are used in three main areas of diagnostic Molecular Microbiology (molecular subtyping, identification of microorganisms, and determination of antibiotic resistance determinants.)

3. A small research project can be designed that will provide the resident with the opportunity to learn various molecular techniques, and to give hands-on experience in the above mentioned areas.

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