Microorganisms organised by Gram stain and metabolism

Frequently, the college will present the candidate with some of this information; eg. "this is a Gram-negative rod in the anaerobic bottle. What could it be?" Thus, the SAQ becomes a game of "Name That Microbe". The table below lists selected organisms which for whatever reason seemed to be of interest. Needless to say, the list is not definitive.

"Name That Microbe"

Gram-positive organisms

Gram-negative organisms





Obligate aerobes
  • Coagulase-negative Staph (Staphylococcus epidermitis)
  • Staphylococcus aureus
  • Streptococcus pneumoniae
  • Streptococcus pyogenes
  • Bacillus anthracis
  • Corynebacterium diphtheriae
  • Nocardia asteroides
  • Moraxella catarrhalis
  • Neisseria gonorrhoeae
  • Neisseria meningitidis
  • Pseudomonas aeruginosa
  • Haemophilus influenzae
  • Serratia marcescens
  • Bordetella pertussis
  • Burkholderia cepacia
  • Legionella pneumophila
  • Stenotrophomonas maltophilia
  • Acinetobacter baumanii
  • Vibrio vulnificus
  • Vibrio cholerae
Facultative anaerobes
  • Enterococcus faecalis
  • Enterococcus faecium
  • Listeria monocytogenes
  • Escherichia coli
  • Citrobacter kozeri
  • Enterobacter cloacae
  • Enterobacter aerogenes
  • Klebsiella oxytoca
  • Klebsiella pneumophila
  • Morganella morganii
  • Proteus mirabilis
  • Salmonella typhi
  • Shigella dysenteriae
  • Yersinia pestis
Obligate anaerobes


  • Clostridium difficile
  • Clostridium perfringens
  • Clostridium botulinum
  • Clostridium tetani
  • Veilonella
Strictly speaking, "microaerophilic"
  • Campylobacter jejuni
  • Helicobacter pylori


True anaerobe:
  • Bacteroides fragilis

Non-Gram-stained organisms: the Atypical Pneumonia Group

  • Mycobacterium avium complex (MAC)
  • Mycobacterium tuberculosis
  • Mycoplasma pneumoniae
  • Chlamydia pneumonia, trachomatis  and psittaci

Yeasts and fungi:

  • Candida albicans
  • Candida non-albicans (glabrata, tropicalis, what have you)
  • Cryptococcus neoformans
  • Histoplasma capsulatum
  • Pneumocystis jirovecii
  • Aspergillus fumigatus
  • Zygomycetes


  • Toxoplasma Gondii
  • Giardia lamblia
  • Cryptosporidium
  • Plasmodium sp. (mainly falciparum and vivax)


  • Cytomegalovirus
  • Herpes simplex virus
  • Varicella zoster virus
  • Enterovirus
  • Epstein-Barr Virus
  • Hepatitis A, B, C
  • HIV
  • The viral pneumonia: Human Metapneumovirus, Influenza virus, Parainfluenza, RSV, Rhinovirus.

Historical scenarios suggestive of a specific pathogen:

There are certain key words in the SAQ text which might alert one to a specific pathogen.

For instance, one immediately forms an opinion about the febrile traveller returning from Thailand with purulent urethral discharge. One doesn't even need to hear about their polyarthropathy.

To simplify revision, all such previously examined scenarios (as well as ones which have never been seen before) are collected together into one table. Where appropriate, links point to the specific SAQs.

Historical Associations of Specific Infectious Agents


Unique historical features

Vibrio vulnificus

Seafood poisoning; fishermen, "coastal slipways", wounds inflicted by angry sea organisms.

Coxiella burnetii

AKA "Q fever"; Abattoir workers, cattle farmers; haemoptysis, pneumonia, heart failure and infective endocarditis.

Rabies, Lyssavirus

Encephalitis following a flying fox bite

Burkholderia pseudomallei

Melioidosis: Gram negative sepsis in a patient recently returned from Papua New Guinea during the wet season

S.pneumoniae; N.meninitides

Meningitis in a post splenectomy patient
 Listeria monocytogenes Meningitis with a Gram-positive rod in the CSF

Brucella sp.

Cattle farmers with arthralgia, pneumonia and endocarditis


Febrile rat owner or rodent enthusiast

Ebola VHF

Returning African missionary

Arboviral encephalitis

Decreased level of consciousness (+/- seizures) in a febrile bushwalker


Black nasal discharge and cranial nerve palsy

A list of organisms intrinsically resistant to imipenem:

(this is found in Question 23.3 from the first paper of 2013, and Question 25.3 from the second paper of 2009. References are available.)

  • Stenotrophomonas maltophila (previously known as Bacterium bookeri and Pseudomonas maltophili, aaccording to Oh's Manual p.727 it has intrinsic carbapenemase)
  • Pseudomonas cepacia
  • Enterococcus faecium
  • MRSA

A list of organisms intrinsically resistant to glycopeptides (eg. vancomycin and tecoplanin):

  • Lactobacillus casei 
  • Pediococcus pentosaceus
  • Leuconostoc mesenteroides

A list of organisms potentially responsible for pneumonia in an AIDS patient:

A good free full-text article is available to discuss the origins of nonspecific pulmonary inflitrates on the chest Xray of the AIDS patient. Not surprisingly, in 97% of cases the pulmonary infiltrates are infectious in nature.

In order of frequency:

  • S.pneumoniae, H.influenzae, Legionella - 60%
  • Pneumocystis - 20%
  • Viruses - 5%
  • Fungal infections - 2%
  • Protozoal parasites - 0.5%.


Billot-Klein, D., et al. "Modification of peptidoglycan precursors is a common feature of the low-level vancomycin-resistant VANB-type Enterococcus D366 and of the naturally glycopeptide-resistant species Lactobacillus casei, Pediococcus pentosaceus, Leuconostoc mesenteroides, and Enterococcus gallinarum." Journal of bacteriology 176.8 (1994): 2398-2405.

Bax, H. I., et al. "Brucellosis, an uncommon and frequently delayed diagnosis."Neth J Med 65.9 (2007): 352-355.

Segal, Leopoldo N., et al. "HIV-1 and bacterial pneumonia in the era of antiretroviral therapy." Proceedings of the American Thoracic Society 8.3 (2011): 282-287.

Feldman, Charles. "Pneumonia associated with HIV infection." Current opinion in infectious diseases 18.2 (2005): 165-170.

Arora, V. K., and S. V. Kumar. "Pattern of opportunistic pulmonary infections in HIV sero-positive subjects: observations from Pondicherry, India." The Indian journal of chest diseases & allied sciences 41.3 (1998): 135-144.

Benito, Natividad, et al. "Pulmonary infections in HIV-infected patients: an update in the 21st century." European Respiratory Journal 39.3 (2012): 730-745.