Bacteria are single-celled organisms. They come in many shapes and sizes. Most bacteria are not harmful. Pathogenic bacteria cause infectious diseases.

 Colonising bacteria live and multiply harmlessly without causing disease. The microbiome refers to the trillions of bacteria colonising the human body, mostly in the gut. The bacteria in the microbiome play many important roles, such as protecting against pathogenic bacteria, synthesising vitamins and interacting with the nervous system.

Bacteria can be categorised into aerobic and anaerobic, gram-positive and gram-negative, and atypical bacteria. Learning where bacteria fall within these categories helps determine effective antibiotics.

Aerobic bacteria require oxygen, whereas anaerobic bacteria do not. Gram-positive bacteria have a thick peptidoglycan cell wall that stains with crystal violet stain. Gram-negative bacteria do not have a thick peptidoglycan cell wall or stain with crystal violet stain but will stain with other stains. Atypical bacteria cannot be stained or cultured in the normal way.

Bacteria can also be classified based on their shapes. Rod-shaped bacteria are called bacilli. Circle-shaped bacteria are called cocci.


Physiology and Antibiotics

The cell wall is a structure that surrounds the outer cell membrane in gram-positive bacteria. Antibiotics that work by inhibiting cell wall synthesis can be divided into those with a beta-lactam ring (e.g., penicillins, cephalosporins and carbapenems) and those without a beta-lactam ring (e.g., vancomycin and teicoplanin).

Nucleic acid is an essential component of bacterial DNA. Metronidazole works by inhibiting nucleic acid synthesis.

Ribosomes are responsible for synthesising proteins within the bacteria cell. Antibiotics that target the ribosome to interrupt protein synthesis include macrolides (e.g., clarithromycin), tetracyclines (e.g., doxycycline) and gentamicin.

Folic acid is essential for synthesising and regulating DNA within the bacteria. Folic acid cannot be directly imported into the bacteria cell, and entry requires a chain of intermediates. This chain starts with para-aminobenzoic acid (PABA), which is directly absorbed across the cell membrane into the cell. PABA is converted to dihydrofolic acid (DHFA), which is converted inside the cell to tetrahydrofolic acid (THFA), then folic acid. Antibiotics can be used to disrupt steps along this chain:

  • Sulfamethoxazole blocks the conversion of PABA to DHFA
  • Trimethoprim blocks the conversion of DHFA to THFA


Gram Stain

A gram stain is used as a quick way to look for bacteria in a sample under the microscope. There are two steps.

Firstly, a crystal violet stain is added, which binds to molecules in gram-positive bacteria’s thick peptidoglycan cell wall, turning them violet.

Then a counterstain (such as safranin) is added, which binds to the cell membrane in bacteria that do not have a cell wall (gram-negative bacteria), turning them red/pink.



Gram-positive cocci include:

  • Staphylococcus
  • Streptococcus
  • Enterococcus


Gram-positive rods can be remembered with the “corny Mike’s list of basic cars” mnemonic:

  • Corny – Corneybacteria
  • Mike’s – Mycobacteria
  • List of – Listeria
  • Basic – Bacillus
  • Cars – Nocardia


Gram-positive anaerobes can be remembered with the “CLAP” mnemonic:

  • C Clostridium
  • LLactobacillus
  • AActinomyces
  • PPropionibacterium


If a bacteria is not listed above, it is probably gram-negative. Common gram-negative bacteria are:

  • Neisseria meningitidis
  • Neisseria gonorrhoea
  • Haemophilia influenza
  • Escherichia coli (E. coli)
  • Klebsiella
  • Pseudomonas aeruginosa
  • Moraxella catarrhalis


Atypical Bacteria

Atypical bacteria cannot be cultured in the normal way or detected using a gram stain. Atypical pneumonia refers to pneumonia caused by atypical bacteria. 

The five causes of atypical pneumonia can be remembered with the “Legions of psittaci MCQs” mnemonic:

  • Legions – Legionella pneumophila
  • Psittaci – Chlamydia psittaci
  • M – Mycoplasma pneumoniae
  • C – Chlamydophila pneumoniae
  • Qs – Q fever (coxiella burneti)


Methicillin-Resistant Staphylococcus Aureus

Methicillin-resistant Staphylococcus aureus (MRSA) refers to Staphylococcus aureus bacteria that have become resistant to beta-lactam antibiotics (e.g., penicillins, cephalosporins and carbapenems).

MRSA arises where there is frequent use of antibiotics, such as in healthcare settings. Think about MRSA in nursing home residents and patients with frequent hospital admissions.

People are often colonised with MRSA bacteria and have them living harmlessly on their skin and respiratory tract. When infection develops, it can be hard to treat. Patients being admitted for surgery or inpatient treatment are screened for MRSA colonisation by taking nose and groin swabs. When identified, extra measures are taken to eradicate the MRSA and stop it from spreading. Eradication usually involves a combination of chlorhexidine body washes and antibacterial nasal creams.

Antibiotics used to treat MRSA include: 

  • Doxycycline
  • Clindamycin
  • Vancomycin
  • Teicoplanin
  • Linezolid


Extended-Spectrum Beta-Lactamase Bacteria

Extended-spectrum beta-lactamase (ESBL) bacteria have developed resistance to beta-lactam antibiotics (e.g., penicillins, cephalosporins and carbapenems). They produce beta-lactamase enzymes that destroy the beta-lactam ring on the antibiotic. They can be resistant to a very broad range of antibiotics. 

ESBLs tend to be E. coli or Klebsiella and typically cause urinary tract infections. They can cause other types of infection, such as pneumonia and septicaemia.

The usual treatment options are:

  • Nitrofurantoin
  • Fosfomycin
  • Carbapenems (e.g., meropenem or imipenem)


Last updated July 2023