Medical Microbiology

• Microbiology


  The study of microscopic organisms, such as bacteria, fungi, and protists. It also includes the study of viruses, which are not technically classified as living organisms but do contain genetic material. Microbiology research encompasses all aspects of these microorganisms such as their behaviour, evolution, ecology, biochemistry, and physiology, along with the pathology of diseases that they cause.
• Microbiology roles in routine NHS labs


  • Bacteriology - the study of bacteria
  • Mycology - the study of fungi
  • Parasitology - the study of parasites
  • Virology - the study of viruses
  • Serology - the diagnostic examination of blood serum (specifically for the diagnosis of microbial infection)
  • Molecular Microbiology - diagnosis of microbial infection using molecular techniques
• Microbiology roles in routine NHS labs - Specimen types


  • Urines
  • Faeces/faeces/enteric/poo bench
  • Wounds/pus/swab/ general bench
  • Genital /GUM bench
  • Screening bench
  • Tissues/Fluids
  • Blood Cultures
  • TB/Cat 3/CL3/ High Risk Lab/sputum/ spit bench
  • ID & Sens bench
  • Mycology
  • Virology/serology
  • Molecular bench
• Bacteriology - the holy trinity


  • Microscopy
  • Culture
  • Sensitivity
• Microscopy


  • Uses microscopes (light, inverted, phase contrast, mercury bulb, blue light LED)
  • Typically, to properly view bacteria you need a magnification of 400x to 1000x
• Gram Stain


  Most widely used stain in microbiology, discovered by the Danish scientist and physician Hans Christian Joachim Gram in 1884. Heat fix sample on microscope slide, primary stain (Crystal Violet), mordant (Iodine/Lugols Iodine), decolourisation (Ethanol/Acetone), counter-stain (Safranin/Carbol Fuchsin).
• Gram Stain - Results


  • Mixed Gram Stain
  • Bacterial Vaginosis
• Other applications of stains


  • Auramine Phenol stain for Mycobacteria
  • Ziehl Neelsen stain for Mycobacteria, Cryptosporidium
  • Acid/Base stain for white cell differentiation
  • Indian Ink for yeasts, especially Cryptococcus
  • Wet preparation for cell count, Trichomonas and Candida
• Culture


  1. Pathological samples received into the laboratory

  2. Specimens processed as per Standard Operating Procedure

  3. Samples cultured onto appropriate solid/liquid culture media

  4. After incubation, culture plates are interpreted to determine whether a pathogen is present
• Culture Media Types


  • Simple media - e.g. Nutrient Agar
  • Complex media - e.g. Blood Agar
  • Enriched media - e.g. Chocolate Agar
  • Selective media - e.g. XLD
  • Differential media - e.g. CLED
  • Transport medium - e.g. VTM
• Plate Streaking


  • Plate streaking method
• Mixed Cultures


  • Mixed culture picture
• Sensitivity (Antimicrobial susceptibility testing)


  It is important to undertake antimicrobial susceptibility testing on potential pathogens. Empirical treatment of infection before actual susceptibilities is known is important. However, as antimicrobial resistance is increasing, it is essential that the exact antibiogram for the pathogen being studied is known to ensure that any treatment being undertaken is effective.
• Susceptibility Testing Methods


  • Broth Dilution
  • Antibiotic Gradient
  • Disc Diffusion Test
  • Dilution method and MIC determination
• Susceptibility Testing Standards


  • BSAC - British Society for Antimicrobial Susceptibility
  • EUCAST - European Committee on Antimicrobial Susceptibility Testing
• Susceptibility Testing Methods


  • Clindamycin E test
  • Vancomycin E test
• Identification


  In addition to susceptibility testing, many organisms have to be identified. This can be done through a variety of manual or automated systems which look at the organisms biochemical profile – the way it metabolised and ferments sugars and the action of pre formed enzymes. MALDI-ToF can be used to identify organisms by their proteomic signature. Identification can be used to aid diagnosis and treatment or can be important for epidemiological study.
• Antigen/Antibody Tests


  • Urinary Legionella Antigen
  • Urinary Streptococcus pneumoniae Antigen
  • Helicobacter pylori Faecal Antigen
  • Clostridium dificille GDH
  • Clostridium dificille toxin
  • Faecal rotavirus antigen
  • Respiratory Syncytial Virus antigen
  • Salmonella, Shigella, Vibrio antigen agglutination
• Mycology


  Culture of pathological samples specifically for the isolation and identification of yeasts and fungi
• Fungal structures


  • Fungal structures picture
• Parasitology


  1. Usually performed in the enterics department

  2. Faecal samples are centrifuged and treated to remove vegetable matter and fats

  3. The sample is filtered

  4. This allows ova and cysts of parasites to pass through

  5. The deposit of these centrifuged and filtered faecal samples is observed using light microscopy
• Parasitology


  • Mixed helminths
  • Ascaris lumbricoides
• Virology/Serology


  Viral culture now largely superseded, especially in routine diagnostic labs. Serology looks for the presence of viral antibodies or antigens in serum samples using enzyme Immunoassay. Largely an automated process. Analysers can run 4 enzyme immunoassay tests at the same time, reducing time to result. As with bacteriology, relevant clinical details usually absent on the request.
• Virology/Serology Tests


  • HIV antibody/antigen
  • Hepatitis B Virus (antibody, antigen, core antibody)
  • Hepatitis C antibody
  • Hepatitis A antibody
  • Rubella antibody
  • Toxoplasma antibody
  • Mycoplasma antibody
  • Syphilis antibody
  • CMV antibody
  • VZ antibody
• Molecular Microbiology


  Often carried out in the Virology/Serology department. Utilises PCR. Looks for the presence of viral/bacterial target genetic material. Largely an automated process. Can determine the presence /absence of genetic material as well as quantifying the amount of virus present in the sample.
• Molecular Microbiology Tests


  • HIV confirmation
  • HIV genotyping
  • HIV viral load
  • HCV genotyping
  • HCV viral load
  • Chlamydia PCR
  • Neisseria gonorrhoeae PCR
• Additional Resources


  • Practice exam question, activities on culture media and microscopy (in the activity tab of the NOW room)
  • Further reading on related topics/journal articles (in the resources tab of the NOW room)
  • Blank PowerPoint presentation of the material covered (in the resources tab)