Microbiology | Master Of Medicine

Category Archives: Microbiology

The structure of a virus

A virus is an infectious particle which can replicate only inside a cell using the synthetic mechanism of the cell. A virus when outside a living cell is usually dormant, and shows no signs of life.Almost two centuries had passed after Antony van Leeuwenhoek had discovered bacteria when Dmitri Ivanovsky’s 1892 article describing a non-bacterial pathogen infecting tobacco plants, and the discovery of the tobacco mosaic virus by Martinus Beijerinck in 1898 took place.Since then thousands of viruses have been described and classified according to their structure and properties.

It is believed that viruses evolved from bacterial plasmids or from bacteria themselves. Viruses are very small compared to bacteria and cannot be usually seen with a compound microscope.An electron microscope which has higher resolution can help in elucidating the structure of a virus. The resolving power of a compound microscope is 200nm(nanometer) and magnification of 2000x, whereas the resolving power of an electron microscope is 50pm(picometer) and  magnification up to 10,000,000x.

Structure of a virus

Virus particles (known as virions) consist of two to three parts

1.The genetic material made from either DNA or RNA.

2.A protein coat that protects these genes called capsid,and in some cases an envelope of lipids that surrounds the protein coat when they are outside a cell.Most enveloped viruses are dependent on the envelope for their infectivity.

The shapes of viruses range from simple helical and icosahedral forms to more complex structures. The nucleic acid of a virus can be DNA or RNA, and it can be single stranded, double stranded,linear, circular or segmented, positive sense, negative sense or ambisense(+/-). When the viruses infect a cell,they  integrate into the host DNA and replicates using the host machinery and gets released by bursting the cell.The two types of cycle undergone by virus inside a cell lysogenic and lytic cycle.These two cycles can occur in a host but both cannot occur simultaneously.

Types of human herpes viruses and associated diseases.

Herpes simplex virus

HHV 1- Herpes simplex virus type 1

HHV 2 – Herpes simplex virus type 2

HHV 3- Varicella Zoster virus

HHV 4 -Epstein Barr virus

HHV 5 – Cytomegalo virus

HHV 6- Human B cell lymphotropic virus

HHV 7 -RK virus

HHV 8 -Kaposi virus

Diseases associated with Herpes virus family.

HSV 1 – Usually causes lesions in and around mouth,Most common cause of sporadic encephalitis

HSV 2- Cause lesions in genital area, cause meningitis

HHV 6 causes Exanthem subitum/Roseola infantum also known as sixth disease.

HHV 8 is associated with Kaposi sarcoma and multicentric Castleman disease.

Also see diseases named first disease to sixth disease under exanthematous diseases..

Bacterial diarrhea: Invasive vs Non Invasive diarrhea.

Bacterial diarrhea’s can be classified into invasive and non invasive, this classification has an important role in determining treatment modalities.

Non Invasive Diarrhea

  • Caused by release of toxins from bacteria resulting in disruption of secretory process.
  • Characterized by watery diarrhea.
  • Blood and fecal leucocytes are characteristically absent.

Bacteria associated are:

  1. Staphylococcus aureus.
  2. Bacillus cereus
  3. Clostridium perfingens
  4. Enterotoxigenic E.Coli(ETEC)
  5. Vibrio cholerae

Invasive diarrhea.

Caused by direct damage to gastrointestinal tissue due to direct invasion by bacteria.

Diarrhea is characterized  by:

  • Fever
  • Dysentry(Blood in stools)
  • Fecal leucocytes

Bacteria associated are:

  1. Shigella
  2. Salmonella
  3. Yersenia enterocolitica.
  4. Enteroinvasive Ecoli(EIEC)
  5. Aeromonas
  6. Plesiomonas
  7. Listeria monocytogenes

Important parasites

Parasites causing malabsorption in adults

  1. Giardia Lamblia
  2. E.Histolytica
  3. H.Nana
  4. Strongyloides
  5. Cyclospora

Malabsorption in children

  1. G.Lamblia
  2. Isospora belli
  3. Cryptosporidium
  4. Ancylostoma duodenaLE
  5. E.Histolytica
  6. Capillaria phillipinensis

Man is the defenitive host in most parasitic infections except in:

  1. Echinococcus granulosus
  2. Plasmodium
  3. Taenia Solium(man is both defenitive and intermediate host)
  4. Toxoplasma gondii
  5. Sarcocytis lindemanii

Parasites causing autoinfection

These organisms establish life cycle within the same host eliminating the need for other hosts

  1. Capillaria philippinensis
  2. Cryptosporidium parvum
  3. Enterobius vermicularis
  4. Hymenolepis Nana
  5. Strongyloides stercoralis
  6. Taenia solium

Worms which do not multiply in man

  1. A.duodenale
  2. E.vermicularis
  3. W.bancrofti

Clonorchis sinensis

  1. Man is the defenitive host and snail secondary host in clonorchis sinensis
  2. Infection caused by ingestion of metcercaria
  3. Mature in bile canaliculi
  4. c/c infection associated with cholangitis,cholangio hepatitis and biliary obstrucion.

Dimorphic fungi

Can grow either as yeast or as mould depending on env conditions and temperature

Usually yeast at body temperature(37C) and as filamentous forms at room temperature(27C)

  1. Blastomycetes
  2. Paracoccidiomyces
  3. Blastomyces
  4. Sporothrix
  5. Candida albicans(not other candida)
  6. Histoplasma capsulatum
  7. Penicillin marneffi

Nematodes,Cestodes and trematodes


Round worms

  1. Enterobius Vermicularis-Pin worm
  2. Ascaris Lumbricoids-Giant round worm
  3. Trichinella spiralis
  4. Trichiuris trichiura
  5. Dracunculus mediensis
  6. Onchocerca volvulus
  7. Loa loa
  8. Wuchereria bancrofti
  9. Toxocara canis

Hook worms

  1. Strongyloides stercoralis
  2. Ancylostoma duodenale
  3. Necator americanus

Routes of infection




Tinea solium

Ingestion of larvae encysted in undercooked pork leads to intestiinal tapeworms.

Ingestion of eggs causes cysticercosis and neurocysticercosis

Mass lesions in brain have “Swiss cheese appearance”

DOC:Praziquantel for intestinal worms and cysticercosis, Albendazole for neurocysticercosis.

Echinococcus granulosus

Eggs in dog faeces on ingestion cause cysts in liver.

Causes anaphylaxis if antigens released from cysts

Also causes lung cysts.




Schistosoma hematobium and schistosoma mansoni.

Snails are host

Cercariae penetrate skin of humans cause granuloma,fibrosis and inflammations of spleen and liver

Portal HTN-Schistosoma mansoni

Bladder cancer and hematuria-Schistosoma hematobium


Clonorchis sinensis/Asian liver fluke

Undercooked fish

Causes inflammation of the biliary tract,pigmented gall stones

Associated with cholangiocarcinoma.


Paragonimus westermani

Undercooked crab meat.

Causes infection and secondary bacterial infection of lung.


Hepatitis Viruses

Hepatitis A(Infectious hepatitis)

  1. RNA picorna virus
  2. Feco-oral route of infection
  3. Mild self limiting disease,active immunization available.

Hepatitis B(Serum hepatitis)

  1. DNA hepadnavirus
  2. Parenteral/sexual transmission
  3. 1-2% mortality,95% cases resolve
  4. Primary HCC,cirrhosis

Hepatitis C(Post transfusion hepatitis)

  1. RNA flavi virus
  2. Parenteral/Sexual transmission
  3. a/c disease usually subclinical with high rate of chronicity 4%mortality
  4. a/w Primary HCC,cirrhosis,no vaccine.

Hepatitis D(Delta hepatitis)

  1. Defective enveloped RNA virus requires hep B as helper virus to replicate.
  2. Co infection/superinfection
  3. Coinfection-Both hep B and D acquired at same time- severe
  4. Superinfection-Hep D infection in a patient already infected with hep B-High mortality.
  5. Cirrhosis,fulminant hepatitis

Hepatitis E(Enteric Hepatitis)

  1. RNA calcivirus
  2. Feco oral route
  3. Severe, high mortality rate-20%
  4. No c/c infection,not associated with cancer.

Tips to remember

  • Hep C- Chronic,Cirrhosis,Carcinoma,carriers
  • Hep D- Defective,Dependent on Hep B
  • Hep E- Expectant mothers,Epidemics.

Hepatitis B serology

  1. HBsAg- First virologic marker detectable in serum after HBV infection.Indicates ACTIVE infection, either acute/chronic.
  2. Anti HBs-HBsAg antibody,provides immunity, persists for years.
  3. HBcAg- Not detectable in blood
  4. Anti HBc- Positive during window period.IgM anti HBc indicator of recent disease and IgG anti HBc indicator of Chronic disease.
  5. HBeAg- Indicates active viral replication and high infectivity.
  6. Anti HBe- When present in HBs Ag carrier, blood is less infectious.

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